Polymorphism
| Type | Scaffold ID | Polymorphism position on scaffold11170 | Related gene model ID | Gene model direction | Gene model description |
|---|---|---|---|---|---|
| SNP | scaffold11170 | 109272 | cassava4.1_011965m | + | PFAM:PF00069,PF07714 Panther:PTHR22986 KOG:KOG0581 KEGG ec: KEGG Orthology: best arabidopsis TAIR10 hit name: AT1G73500.1 best arabidopsis TAIR10 hit symbol:ATMKK9,MKK9 best arabidopsis TAIR10 hit defline:MAP kinase kinase 9 |
| Synonymous / Nonsynonymous substitution |
|---|
| SNP in UTR |
Cyan: synonymous substitution Red: nonsynonymous substitution
Triangle: transversion substitution Dot: transition substitution Diamond: insertion/deletion
Triangle: transversion substitution Dot: transition substitution Diamond: insertion/deletion
| Allele | G/T ( Transversion substitution ) | |
| AM560-2 (Predicted CDS from genome sequence) | G | |
| CAS36.01 | - | |
| CAS36.04 | - | |
| CM21772 | - | |
| CM523-7 | - | |
| MCol22 | - | |
| IAC 12.829 | - | |
| KU50 | T | |
| MBra685 | - | |
| MCol1522 | - | |
| MNga2 | - | |
| MPer183 | - | |
| Mirassol | - | |
| SG107-35 | - | |
| Sauti, Gomani, Mbundumali, TME 1 and Mkondezi | T | |
| TMS30572 and CM2177-2 | - | |
| Unknown | G |
' ∗ ' : gap (insertion/deletion) ' − ' : No data
Polymorphism position Sauti, Gomani, Mbundumali, TME 1 and Mkondezi Unknown Unknown MCol22 MCol22 KU50 (MTAI16) KU50 (MTAI16) KU50 (MTAI16) KU50 (MTAI16) KU50 (MTAI16) AM560-2 Contig |
FF536383 DV445996 FG806521 DR085213 DR088321 DB924062 DB928763 DB938129 DB942402 DB946560 cassava4.1_011965m | .........10........20........30........40........50........60........70........80........90........100.......110.......120.......130.......140.......150.......160.......170.......180.......190.......200.......210.......220.......230.......240.......250.......260.......270.......280.......290.......300.......310.......320.......330.......340.......350.......360.......370.......380.......390.......400.......410.......420.......430.......440.......450.......460.......470.......480.......490.......500.......510.......520.......530.......540.......550.......560.......570.......580.......590.......600.......610.......620.......630.......640.......650.......660.......670.......680.......690.......700.......710.......720.......730.......740.......750.......760.......770.......780.......790.......800.......810.......820.......830.......840.......850.......860.......870.......880.......890.......900.......910.......920.......930.......940.......950.......960.......970.......980.......990.......1000......1010......1020......1030......1040......1050......1060......1070......1080......1090......1100......1110......1120......1130......1140......1150......1160......1170......1180......1190......1200......1210......1220......1230......1240......1250......1260......1270......1280......1290......1300......1310......1320......1330......1340......1350......1360......1370 ....................................................................................................................................................................P..............................................x.xxxxx.xxxxxx..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................P.......................................................................................................................................................................................................................................................P.......Px...................P................................................................................................................................................................................................................................. _____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________GAACCATAAAATCATCCATAGAGACATTAAACCTTCAAATTTGTTGGTGAAAAATGGGATGGAAGTGAAGATTGCTGATTTTGGTGTGAGCAAAATCATGTATCGAACTCTAGATGCTTGTAATTCATATGTGGGTACTTGTGCTTATATGAGCCCTGGACGCTTTGATCCTGATACTTATGGAGGAAACTATAATGGCTACGCTGCTGATATTTGGAGCTTGGGTCTTACCTTGTTGGAGCTTTATTTGGGTTATTTTCCATTTCTAACTCCTGGTCAAAGACCCGATTGGGCAACCTTGATGTGCGCTATATGCTTTGGTGACCCACCTAGCTTGCCAGAGAATGCGTCGGAGAAATTTCAGAGCTTTATCGAGTGTTGCTTACAGAAGGAATCTAGTAAGAGGTGGACAGCAGAACAACTATTGTCACACCCGTTTCTTTGTAAAGATCCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATTTTTTTTTTTTT**TCTTTTGTATATTCCGTTATAATCCTTATCTCTCTCAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTTTAATGTGATTCTG_________________________________________________________________________________________________________________________________________________ _________________________________________________________________________________________________________________________________________________________________________________________________________CAACTCCGTNATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCACGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACATCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGCTCATGTGGCTCGTCAAGTTCTTAATGGGCTAAACTACTTGCACAACCATAAAATCATCCATAGAGACATTAAACCTTCAAATTTGTTGGTGAAAAATGGGATGGAAGTGAAGATTGCTGATTTTGGTGTGAGCAAAATCATGTATCGAACTCTAGATGCTTGTAATTCATATGTGGGTACTTGTGCTTATATGAGCCCTGAACGCTTTGATCCTGATACTTATGGAGGAAACTATAATGGCTACGCTGCTGATATTTGGAGCTTGGGTCTTACCTTGTTGGAGCTTTATTTGGGTTATTTTCCATTTCTAACTCCTGGTCAAAGACCCGATTGGGCAACCTTGATGTGCGCTATATGCTTTGGTGACCCACCTAGCTTGCCA_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ _________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________CACTATTGTGACACACGTTCTTTGTAAAGATCCGAGATCCGAAAGATGAACCGGT*CATCGTAGT*CCAGTAACCAATCATATTTGTGGTTGAGTTTTGAATATAAGCGGCGGAATTCGGATGTTTTTTTCCTT**TCTTTTGTATATTCCCTTATAATCCTTATCTCTCACAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTT*AATGTGATTCTGAAAAAGCATGGTTGTGTATAACGTTTCATGCATGTGTTGTGCACAATATCAAATCCAAATCAAATGATTTGATTATTATAATTAATGAAAGGGTGGTTGGTTCTTGGTAGATTCTACAACCAACTTGCAA_______________ GTCCCGGTTCGGGAATTTTAACCCGATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCCCGAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTGGTCACTGCTTCTACAAACAACAACAACAACTCTGCGTTGATACCACTGCT_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ___________________________________TCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGTTGATACCACTGCT_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ___________________GAGATCATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCATGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACATCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGCTCATGTGGCTCGTCAAGTTCTTAATGGGCTAAACTACTTGCACAACCATAAAATCATCCATAGAGACATTAAACCTTCAAATTTGTTGGTGAAAAATGGGATGGAAGTGA_________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ________________TGGAAGATCATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCATGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACATCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGC_______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ _________________GGATGATCATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCATGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACTTCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGCTCATGTGGCTCGTCAAGTTCTTAATGGGCTAAACTACTTGCACAACCA_______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________GTCAAAGACCCGATTGGGCAACCTTGATGTGCGCTATATGCTTTGGTGACCCACCTAGCTTGCCAGAGAATGCGTCGGAGAAATTTCAGAGCTTTATCGAGTGTTGCTTACAGAAGGAATCTAGTAAGAGGTGGACAGCAGAACAACTATTGTCACACCCGTTTCTTTGTAAAGATCCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATTTTTTTTTTTTT**TCTTTTATATATTCCGTTATAATCCTTATCTCTCACAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTTTAATGTGATTCTGAAAAAGCATGGTTGTGTATAACGTTTCATGCATGTGTTGTGCACAATATCAAATCAAAATCAAATGATTTGATTATTATAATTAATGAAAGGGTGGTTGGTTCTTGGTAGATTCCACAACCAACTTGCAAAACTTGAAAATTGAT _________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________TGCTGATATTTGGAGCTTGGGTCTTTTGATGTTGGAGCTTTATTTGGGTTATTTTCCATTTCTAACTCCTGGTCAAAGACCCGATTGGGCAACCTTGATGTGCGCTATATGCTTTGGTGATCCGCCTAGCTTGCCAGAGAATGCGTCGGAGAAATTTCAGAGCTTTATCGAGTGTTGCTTACAGAAGGAATCTAGTAAGAGGTGGACAGCAGAACAACTATTGTCACACCCGTTTCTTTGTAAAGATCCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATTTTTTTTTTTTTTTTCTTTTGTATATTCCGTTATAATCCTTATCTCTCACAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTTTAATGTGATTCTGAAAAAGCATGGTTGTGTATAACGTTTC______________________________________________________________________________________________________________________ __________________GAAGATCATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTACCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCATGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACATCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGCTCATGTGGCTCGTCAAGTTCTTAATGGGCTAAACTACTTGCACAACCATAAAATCATCCATAGAGACATTAAACCTTCAAATTTGTTGGTGAAAAATGGGATGGAAGTGAAGATTGCTGATTTTGGTGTGAGCAAAATCATGTATCGAACTCTAGATGCTTGTAATTCATATGTGGGTACTTGTGCTTATATGAGCCCTGAACGCTTTGATCCTGATACTTATGGAGGAAACTATAATGGCTACGCTGCTGATATTTGGAGCTTGGGTCTTACCTTGTTGGAGCTTTATTTGGGTTATTTTCCATTTCTAACTCCAGGTCAAAGACCCGATTGGGCGACCTTGATGTGCGCTATATGCTTTGGTGACCCACCTAGCTTGCCAGAGAATGCGTCGGAGAAATTTCAGAGCTTTATCGAGTGTTGCTTACAGAAGGAATCTAGTAAGAGGTGGACAGCAGAACAACTATTGTCACACCCGTTTCTTTGTAAAGATCCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATGTTTTTTTCCTT**TCTTTTGTATATTCCCTTATAATCCTTATCTCTCACAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTTTAATGTGATTCTGAAAAAGCATGGTTGTGTATAACGTTTCATGCATGTGTTGTGCACAATATCAAATCCAAATCAAATGATTTGATTATTATAATTAATGAAAGGGTGGTTGGTTCTTGGTAGATTCCACAACCAACTTGCAAAACTTGAAAATTGAT GTCCCGGTTCGGGAATTTTAAGATCATTCCCTTTCTCTCTCCTCCTCCTTCTCTTCCTCCTCATCCTCTTGCCTATGGCCGTAGTACGTGAGCGCCGCCAACTCAACCTCCGCCTTCCTCTTCCTGAACTATCC*GAGCGCCGACCTCGCTTTCCTTTGCCACTCCCTCCTAGTG*TCACTGCTTCTACAAACAACAACAACAACTCTGCGATCTCTTCTAGTGATATTGAAAAGCTTCAAGTTCTGGGTCATGGTAATGGTGGTACCGTCTATAAAGTACGTCATAAGAAGACTTCCCAAGTTTATGCCCTTAAAGTTGTCCATGCCGATACCGATGACTCCCTCGTTCGCCGTCAAGTCTTCCGTGAAATGGACATCCTTCGACGTACTGATTCTCCATATATAGTTAAGTGCCATGGGATCTATGAGAAAGCCTCTGGTGATATAGCAATTTTAATGGAGTATATGGATTTGGGTACGCTTGATACGCTTCTACAAAAACAAGGTACTTTCTCTGAAGCTAAACTTGCTCATGTGGCTCGTCAAGTTCTTAATGGGCTAAACTACTTGCACAACCATAAAATCATCCATAGAGACATTAAACCTTCAAATTTGTTGGTGAAAAATGGGATGGAAGTGAAGATTGCTGATTTTGGTGTGAGCAAAATCATGTATCGAACTCTAGATGCTTGTAATTCATATGTGGGTACTTGTGCTTATATGAGCCCTGAACGCTTTGATCCTGATACTTATGGAGGAAACTATAATGGCTACGCTGCTGATATTTGGAGCTTGGGTCTTACCTTGTTGGAGCTTTATTTGGGTTATTTTCCATTTCTAACTCCTGGTCAAAGACCCGATTGGGCAACCTTGATGTGCGCTATATGCTTTGGTGACCCACCTAGCTTGCCAGAGAATGCGTCGGAGAAATTTCAGAGCTTTATCGAGTGTTGCTTACAGAAGGAATCTAGTAAGAGGTGGACAGCAGAACAACTATTGTCACACCCGTTTCTTTGTAAAGATCCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATTTTTTTTTTTTT**TCTTTTGTATATTCCGTTATAATCCTTATCTCTCACAGCGGTGAATCTCTGCTGATAAAGAAGAGAGAATCAAAATTTGTTTTTAATGTGATTCTGAAAAAGCATGGTTGTGTATAACGTTTCATGCATGTGTTGTGCACAATATCAAATCCAAATCAAATGATTTGATTATTATAATTAATGAAAGGGTGGTTGGTTCTTGGTAGATTCCACAACCAACTTGCAAAACTTGAAAATTGAT |
Primer
| Left Primer sequence | CCGAGATCCGAAAAATGAACC | |
| Left Primer start position | 109181 | |
| Left Primer sequence length | 21 | |
| Left Primer TM (DegC) | 62.869 | |
| Left Primer %GC | 47.619 | |
| Right Primer sequence | GAGATTCACCGCTGTGAGAGA | |
| Right Primer start position | 109332 | |
| Right Primer sequence length | 21 | |
| Right Primer TM (DegC) | 60.549 | |
| Right Primer %GC | 52.381 | |
| Amplicon | CCGAGATCCGAAAAATGAACCGGTTCATCGTAGTTCCAGAACCCAATCATATTTGTGGTTGAGTTTTGTATATAAGCGGCGGAATTCGGATGTTTTTTTC | |
| Amplicon length | 152 |
