Multiple sequence alignment - TraesCS2B01G326800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G326800 chr2B 100.000 3982 0 0 1 3982 467873969 467869988 0.000000e+00 7354
1 TraesCS2B01G326800 chr2D 91.048 3742 157 64 340 3982 394801219 394797557 0.000000e+00 4891
2 TraesCS2B01G326800 chr2D 95.114 307 11 2 2 307 394801513 394801210 7.740000e-132 481
3 TraesCS2B01G326800 chr2A 89.468 3760 167 94 340 3982 532868437 532864790 0.000000e+00 4538
4 TraesCS2B01G326800 chr2A 85.928 334 16 12 1 307 532868757 532868428 1.070000e-85 327


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G326800 chr2B 467869988 467873969 3981 True 7354.0 7354 100.000 1 3982 1 chr2B.!!$R1 3981
1 TraesCS2B01G326800 chr2D 394797557 394801513 3956 True 2686.0 4891 93.081 2 3982 2 chr2D.!!$R1 3980
2 TraesCS2B01G326800 chr2A 532864790 532868757 3967 True 2432.5 4538 87.698 1 3982 2 chr2A.!!$R1 3981

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
340 367 0.103208 CTCCCAGAAAGGATCGGACG 59.897 60.0 0.00 0.00 41.22 4.79 F
806 869 0.171007 GTGCACCGGGTCATCAAATG 59.829 55.0 5.22 0.00 0.00 2.32 F
1511 1669 0.179137 TCGCCTCGCATTCAGTACTG 60.179 55.0 17.17 17.17 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1621 0.394352 GACAGGGCGGATGGAATTGT 60.394 55.0 0.0 0.0 0.00 2.71 R
2638 2833 0.699577 TGGAGGGTCCTTGGGTTTCA 60.700 55.0 0.0 0.0 37.46 2.69 R
3158 3374 0.977395 AGGGGTTCTTCCTCAACTCG 59.023 55.0 0.0 0.0 39.70 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 69 6.128007 GGTTATGCATATATTACCACTGGCAC 60.128 42.308 16.99 4.22 32.29 5.01
66 70 4.429854 TGCATATATTACCACTGGCACA 57.570 40.909 0.00 0.00 0.00 4.57
90 97 3.126073 CGCACCATATCATCATATCCGG 58.874 50.000 0.00 0.00 0.00 5.14
91 98 3.181476 CGCACCATATCATCATATCCGGA 60.181 47.826 6.61 6.61 0.00 5.14
205 232 1.228063 CTCCAGCCAGCGCCATAAT 60.228 57.895 2.29 0.00 34.57 1.28
320 347 2.439701 CGGAGACCGGTAGGAGCA 60.440 66.667 7.34 0.00 44.15 4.26
321 348 2.772691 CGGAGACCGGTAGGAGCAC 61.773 68.421 7.34 0.00 44.15 4.40
322 349 1.380112 GGAGACCGGTAGGAGCACT 60.380 63.158 7.34 0.00 41.02 4.40
323 350 1.385756 GGAGACCGGTAGGAGCACTC 61.386 65.000 7.34 7.99 41.02 3.51
333 360 2.377136 GGAGCACTCCCAGAAAGGA 58.623 57.895 5.30 0.00 43.94 3.36
334 361 0.915364 GGAGCACTCCCAGAAAGGAT 59.085 55.000 5.30 0.00 43.94 3.24
335 362 1.134250 GGAGCACTCCCAGAAAGGATC 60.134 57.143 5.30 0.00 43.94 3.36
336 363 0.539051 AGCACTCCCAGAAAGGATCG 59.461 55.000 0.00 0.00 41.22 3.69
337 364 0.462759 GCACTCCCAGAAAGGATCGG 60.463 60.000 0.00 0.00 41.22 4.18
338 365 1.195115 CACTCCCAGAAAGGATCGGA 58.805 55.000 0.00 0.00 41.22 4.55
339 366 1.134670 CACTCCCAGAAAGGATCGGAC 60.135 57.143 0.00 0.00 41.22 4.79
340 367 0.103208 CTCCCAGAAAGGATCGGACG 59.897 60.000 0.00 0.00 41.22 4.79
341 368 1.521681 CCCAGAAAGGATCGGACGC 60.522 63.158 0.00 0.00 41.22 5.19
342 369 1.878522 CCAGAAAGGATCGGACGCG 60.879 63.158 3.53 3.53 41.22 6.01
343 370 1.138883 CAGAAAGGATCGGACGCGA 59.861 57.895 15.93 0.00 0.00 5.87
404 434 7.367159 ACGAACGAACATAATAATCACCAAA 57.633 32.000 0.14 0.00 0.00 3.28
441 471 4.900635 ATTGTTTTACTGGCCGATGATC 57.099 40.909 0.00 0.00 0.00 2.92
509 548 2.892425 CCGGTGGCGATTCTCTGC 60.892 66.667 0.00 0.00 0.00 4.26
511 550 1.880340 CGGTGGCGATTCTCTGCTC 60.880 63.158 0.00 0.00 0.00 4.26
512 551 1.522580 GGTGGCGATTCTCTGCTCC 60.523 63.158 0.00 0.00 0.00 4.70
514 553 0.809241 GTGGCGATTCTCTGCTCCTG 60.809 60.000 0.00 0.00 0.00 3.86
515 554 1.886777 GGCGATTCTCTGCTCCTGC 60.887 63.158 0.00 0.00 40.20 4.85
520 559 2.290122 ATTCTCTGCTCCTGCGTCGG 62.290 60.000 0.00 0.00 43.34 4.79
536 575 2.046604 GGACGGACCGGGGAAAAG 60.047 66.667 20.00 0.00 0.00 2.27
537 576 2.046604 GACGGACCGGGGAAAAGG 60.047 66.667 20.00 0.00 0.00 3.11
538 577 3.617143 GACGGACCGGGGAAAAGGG 62.617 68.421 20.00 0.00 0.00 3.95
539 578 3.324108 CGGACCGGGGAAAAGGGA 61.324 66.667 6.32 0.00 0.00 4.20
540 579 2.897762 CGGACCGGGGAAAAGGGAA 61.898 63.158 6.32 0.00 0.00 3.97
547 586 2.536066 CGGGGAAAAGGGAAGGAAAAT 58.464 47.619 0.00 0.00 0.00 1.82
568 619 0.253207 GAGAAAAGGGGAGGGGAGGA 60.253 60.000 0.00 0.00 0.00 3.71
600 651 1.209504 TCCCCGACAGCAAAATCTAGG 59.790 52.381 0.00 0.00 0.00 3.02
623 678 0.252696 GGGGGAGGGGAAAGCATTTT 60.253 55.000 0.00 0.00 39.27 1.82
697 752 1.783071 CCCACTACCCCTCTTCTCTC 58.217 60.000 0.00 0.00 0.00 3.20
698 753 1.289530 CCCACTACCCCTCTTCTCTCT 59.710 57.143 0.00 0.00 0.00 3.10
699 754 2.661718 CCACTACCCCTCTTCTCTCTC 58.338 57.143 0.00 0.00 0.00 3.20
700 755 2.243736 CCACTACCCCTCTTCTCTCTCT 59.756 54.545 0.00 0.00 0.00 3.10
701 756 3.551846 CACTACCCCTCTTCTCTCTCTC 58.448 54.545 0.00 0.00 0.00 3.20
702 757 3.202151 CACTACCCCTCTTCTCTCTCTCT 59.798 52.174 0.00 0.00 0.00 3.10
703 758 3.458487 ACTACCCCTCTTCTCTCTCTCTC 59.542 52.174 0.00 0.00 0.00 3.20
704 759 2.573463 ACCCCTCTTCTCTCTCTCTCT 58.427 52.381 0.00 0.00 0.00 3.10
705 760 2.509964 ACCCCTCTTCTCTCTCTCTCTC 59.490 54.545 0.00 0.00 0.00 3.20
706 761 2.780010 CCCCTCTTCTCTCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
707 762 3.181450 CCCCTCTTCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
708 763 3.181450 CCCTCTTCTCTCTCTCTCTCTCC 60.181 56.522 0.00 0.00 0.00 3.71
709 764 3.181450 CCTCTTCTCTCTCTCTCTCTCCC 60.181 56.522 0.00 0.00 0.00 4.30
710 765 3.713764 CTCTTCTCTCTCTCTCTCTCCCT 59.286 52.174 0.00 0.00 0.00 4.20
711 766 3.711704 TCTTCTCTCTCTCTCTCTCCCTC 59.288 52.174 0.00 0.00 0.00 4.30
712 767 2.408565 TCTCTCTCTCTCTCTCCCTCC 58.591 57.143 0.00 0.00 0.00 4.30
723 778 1.852965 CTCTCCCTCCCTCTCTCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
757 812 0.793617 ACCCCCTGAAGAAGAGGAGA 59.206 55.000 0.00 0.00 31.48 3.71
778 841 1.412343 GGAGAGGAGCCTTCATCACTC 59.588 57.143 0.00 0.00 36.61 3.51
806 869 0.171007 GTGCACCGGGTCATCAAATG 59.829 55.000 5.22 0.00 0.00 2.32
807 870 1.139520 GCACCGGGTCATCAAATGC 59.860 57.895 6.32 0.00 0.00 3.56
808 871 1.315257 GCACCGGGTCATCAAATGCT 61.315 55.000 6.32 0.00 0.00 3.79
809 872 0.734889 CACCGGGTCATCAAATGCTC 59.265 55.000 6.32 0.00 0.00 4.26
810 873 0.744414 ACCGGGTCATCAAATGCTCG 60.744 55.000 6.32 0.00 32.61 5.03
811 874 0.744414 CCGGGTCATCAAATGCTCGT 60.744 55.000 0.00 0.00 31.47 4.18
812 875 1.472552 CCGGGTCATCAAATGCTCGTA 60.473 52.381 0.00 0.00 31.47 3.43
813 876 1.593006 CGGGTCATCAAATGCTCGTAC 59.407 52.381 0.00 0.00 0.00 3.67
814 877 2.738643 CGGGTCATCAAATGCTCGTACT 60.739 50.000 0.00 0.00 0.00 2.73
825 891 1.213182 TGCTCGTACTCTCTCTCCCAT 59.787 52.381 0.00 0.00 0.00 4.00
859 925 3.013276 GCTTAAAAGCCCATTATCGGC 57.987 47.619 3.22 0.00 46.20 5.54
882 948 1.476007 GCCTGTGACCTCACCTCACT 61.476 60.000 2.98 0.00 45.88 3.41
883 949 0.605589 CCTGTGACCTCACCTCACTC 59.394 60.000 2.98 0.00 45.88 3.51
885 951 1.179174 TGTGACCTCACCTCACTCCG 61.179 60.000 2.98 0.00 45.88 4.63
903 998 1.539065 CCGCCTCGCAGTCATAATTCT 60.539 52.381 0.00 0.00 0.00 2.40
905 1000 2.139118 GCCTCGCAGTCATAATTCTCC 58.861 52.381 0.00 0.00 0.00 3.71
910 1005 3.005897 TCGCAGTCATAATTCTCCCTAGC 59.994 47.826 0.00 0.00 0.00 3.42
930 1025 7.233757 CCCTAGCATCTTTCTTACCACTAGTAT 59.766 40.741 0.00 0.00 0.00 2.12
931 1026 8.643324 CCTAGCATCTTTCTTACCACTAGTATT 58.357 37.037 0.00 0.00 0.00 1.89
934 1029 9.203163 AGCATCTTTCTTACCACTAGTATTAGT 57.797 33.333 0.00 0.00 40.79 2.24
941 1036 8.572884 TCTTACCACTAGTATTAGTAGGAGGA 57.427 38.462 18.66 3.30 38.05 3.71
942 1037 8.435982 TCTTACCACTAGTATTAGTAGGAGGAC 58.564 40.741 18.66 0.00 38.05 3.85
945 1040 6.183361 ACCACTAGTATTAGTAGGAGGACCTC 60.183 46.154 13.60 13.60 46.43 3.85
946 1041 6.240145 CACTAGTATTAGTAGGAGGACCTCC 58.760 48.000 30.65 30.65 46.43 4.30
970 1065 2.195567 TTGCTGCTGGAGTGGTTGC 61.196 57.895 0.00 0.00 0.00 4.17
975 1070 1.102809 TGCTGGAGTGGTTGCTTGTG 61.103 55.000 0.00 0.00 0.00 3.33
1020 1130 4.516195 GAAGGAGGAGGCGCGGAC 62.516 72.222 8.83 0.00 0.00 4.79
1059 1169 4.065281 GTGGACGACTCCCCGGTG 62.065 72.222 0.00 0.00 35.34 4.94
1077 1187 0.696143 TGGACAGGAAGGTGGTGGAA 60.696 55.000 0.00 0.00 0.00 3.53
1148 1273 1.228510 CCCTTCCCTTCCATGGCTC 59.771 63.158 6.96 0.00 0.00 4.70
1165 1292 2.545952 GGCTCGAATTCTCTAATGGCGA 60.546 50.000 3.52 0.00 33.98 5.54
1276 1409 5.327091 CAAACTGCACATAGACAGCATAAC 58.673 41.667 0.00 0.00 37.68 1.89
1305 1438 5.578776 GTCATCGTCCCATGTTTTTAATCC 58.421 41.667 0.00 0.00 0.00 3.01
1317 1450 7.039082 CCATGTTTTTAATCCTCCTTTCCTTCA 60.039 37.037 0.00 0.00 0.00 3.02
1328 1484 0.597568 TTTCCTTCACCATTGCTGCG 59.402 50.000 0.00 0.00 0.00 5.18
1329 1485 1.865788 TTCCTTCACCATTGCTGCGC 61.866 55.000 0.00 0.00 0.00 6.09
1330 1486 2.180017 CTTCACCATTGCTGCGCC 59.820 61.111 4.18 0.00 0.00 6.53
1331 1487 3.672255 CTTCACCATTGCTGCGCCG 62.672 63.158 4.18 0.00 0.00 6.46
1333 1489 4.041917 CACCATTGCTGCGCCGTT 62.042 61.111 4.18 0.00 0.00 4.44
1334 1490 3.294493 ACCATTGCTGCGCCGTTT 61.294 55.556 4.18 0.00 0.00 3.60
1335 1491 2.504681 CCATTGCTGCGCCGTTTC 60.505 61.111 4.18 0.00 0.00 2.78
1336 1492 2.562912 CATTGCTGCGCCGTTTCT 59.437 55.556 4.18 0.00 0.00 2.52
1337 1493 1.798725 CATTGCTGCGCCGTTTCTG 60.799 57.895 4.18 0.00 0.00 3.02
1338 1494 1.965930 ATTGCTGCGCCGTTTCTGA 60.966 52.632 4.18 0.00 0.00 3.27
1339 1495 1.915614 ATTGCTGCGCCGTTTCTGAG 61.916 55.000 4.18 0.00 0.00 3.35
1340 1496 4.451652 GCTGCGCCGTTTCTGAGC 62.452 66.667 4.18 0.00 0.00 4.26
1341 1497 2.740055 CTGCGCCGTTTCTGAGCT 60.740 61.111 4.18 0.00 0.00 4.09
1342 1498 2.280797 TGCGCCGTTTCTGAGCTT 60.281 55.556 4.18 0.00 0.00 3.74
1343 1499 1.845809 CTGCGCCGTTTCTGAGCTTT 61.846 55.000 4.18 0.00 0.00 3.51
1344 1500 1.282875 GCGCCGTTTCTGAGCTTTT 59.717 52.632 0.00 0.00 0.00 2.27
1345 1501 0.317854 GCGCCGTTTCTGAGCTTTTT 60.318 50.000 0.00 0.00 0.00 1.94
1378 1534 6.145696 ACACGTTTGCTCTGTACTAAAATCTC 59.854 38.462 0.00 0.00 0.00 2.75
1385 1543 7.217200 TGCTCTGTACTAAAATCTCAACAACT 58.783 34.615 0.00 0.00 0.00 3.16
1396 1554 6.712241 AATCTCAACAACTTCATACAGTCG 57.288 37.500 0.00 0.00 0.00 4.18
1511 1669 0.179137 TCGCCTCGCATTCAGTACTG 60.179 55.000 17.17 17.17 0.00 2.74
1523 1681 3.683365 TCAGTACTGCAGAGCAATCAA 57.317 42.857 23.35 0.00 38.41 2.57
1537 1695 2.033492 GCAATCAACAACTGCAAAGCAC 60.033 45.455 0.00 0.00 36.09 4.40
1559 1717 5.622856 CACGACTTGCTTCTCATTTTCTTTC 59.377 40.000 0.00 0.00 0.00 2.62
1565 1723 9.387257 ACTTGCTTCTCATTTTCTTTCATTTTT 57.613 25.926 0.00 0.00 0.00 1.94
1588 1746 1.066002 CACTTTGGCTATCCATTGGCG 59.934 52.381 0.00 0.00 43.05 5.69
1812 1976 4.158579 CACAGGACATGAGAGCACTAGTTA 59.841 45.833 0.00 0.00 0.00 2.24
1848 2012 4.729868 AGAAAGGTGTTGCTTGGATTAGT 58.270 39.130 0.00 0.00 0.00 2.24
1895 2063 4.681744 TGATTGTTTTCTTTCACCTGTGC 58.318 39.130 0.00 0.00 0.00 4.57
1977 2145 1.601419 CCGGCTACGACCTCCTCAAA 61.601 60.000 0.00 0.00 44.60 2.69
1992 2160 1.614903 CTCAAAGCCATCAAGGTGCAA 59.385 47.619 0.00 0.00 40.61 4.08
2021 2193 1.203523 GCATACGTGCCCATTTTTCCA 59.796 47.619 0.00 0.00 45.76 3.53
2066 2257 2.425143 TGTCCAATGCTCCCAGAATC 57.575 50.000 0.00 0.00 0.00 2.52
2088 2279 9.342308 GAATCTCATTACTAATTTCCATGGACA 57.658 33.333 15.91 8.93 0.00 4.02
2098 2289 1.462616 TCCATGGACATTTTCAGGCG 58.537 50.000 11.44 0.00 0.00 5.52
2183 2374 0.449388 CAGGTGAGCCTCGATTTTGC 59.551 55.000 0.00 0.00 44.97 3.68
2198 2389 3.726291 TTTTGCTTCCCCTTTTCTTCG 57.274 42.857 0.00 0.00 0.00 3.79
2242 2433 0.603975 GTCGATGAAGCTATGGGGGC 60.604 60.000 0.00 0.00 0.00 5.80
2386 2580 3.455910 AGTTCATTATGCTGCCTGTCCTA 59.544 43.478 0.00 0.00 0.00 2.94
2388 2582 3.041211 TCATTATGCTGCCTGTCCTAGT 58.959 45.455 0.00 0.00 0.00 2.57
2394 2588 1.552792 GCTGCCTGTCCTAGTTCTTCT 59.447 52.381 0.00 0.00 0.00 2.85
2430 2625 6.963242 CAGTATCAGTGAATTTTGAACATCCG 59.037 38.462 0.00 0.00 0.00 4.18
2479 2674 7.596248 GTGCATTCATTGTGTCTTTGTAATCTT 59.404 33.333 0.00 0.00 0.00 2.40
2532 2727 4.278669 CAGCTGATACCTGATAGTAACCGT 59.721 45.833 8.42 0.00 32.03 4.83
2618 2813 4.704833 AGCAAGGATGTGCCGCGT 62.705 61.111 4.92 0.00 46.14 6.01
2638 2833 2.206515 CTGAGGAGCTGCTCGAACGT 62.207 60.000 27.45 2.28 0.00 3.99
3029 3243 0.527385 GCTCTGCAAGGAGTAGCTCG 60.527 60.000 5.02 0.00 35.89 5.03
3122 3336 6.175712 AGATTCGTTTGCTTTGAGATTCTC 57.824 37.500 6.73 6.73 0.00 2.87
3123 3337 5.936956 AGATTCGTTTGCTTTGAGATTCTCT 59.063 36.000 14.54 0.00 0.00 3.10
3124 3338 4.997905 TCGTTTGCTTTGAGATTCTCTG 57.002 40.909 14.54 6.43 0.00 3.35
3125 3339 4.631131 TCGTTTGCTTTGAGATTCTCTGA 58.369 39.130 14.54 1.26 0.00 3.27
3126 3340 4.449068 TCGTTTGCTTTGAGATTCTCTGAC 59.551 41.667 14.54 3.11 0.00 3.51
3216 3432 4.170062 CGCACAATGAGGCAGGCG 62.170 66.667 0.00 0.00 38.45 5.52
3261 3477 3.386078 TGGATCTTGGCTGATCTACTGAC 59.614 47.826 16.30 4.46 41.72 3.51
3269 3485 3.429547 GGCTGATCTACTGACGTGACATT 60.430 47.826 0.00 0.00 0.00 2.71
3282 3498 3.951680 ACGTGACATTCAGGGAACTTTTT 59.048 39.130 0.00 0.00 40.21 1.94
3419 3639 4.401022 AGAAAAAGATGATGCAGACACCA 58.599 39.130 0.00 0.00 0.00 4.17
3467 3687 6.999871 TCTATACCGTCCATGTATTGTACTCA 59.000 38.462 0.00 0.00 31.60 3.41
3516 3736 1.069906 GTTCAGACAGCGAAATTGCGT 60.070 47.619 7.84 0.00 40.67 5.24
3534 3754 5.871465 TGCGTGATAGAATGTTTGCTTTA 57.129 34.783 0.00 0.00 0.00 1.85
3622 3843 0.768622 TGTACAAAGGTGGGTGAGGG 59.231 55.000 0.00 0.00 0.00 4.30
3671 3892 2.412323 CCTGCGGCATGTGATTGCT 61.412 57.895 1.75 0.00 42.38 3.91
3699 3920 4.074259 TCCTACTGCTACGTCTGTTGTAA 58.926 43.478 0.00 0.00 0.00 2.41
3708 3929 6.252015 TGCTACGTCTGTTGTAATTATCGTTC 59.748 38.462 0.00 0.00 0.00 3.95
3733 3954 2.996631 CATAGCTGCAAGTTCCTTCCT 58.003 47.619 1.02 0.00 35.30 3.36
3879 4100 4.481930 TTAGTTGGAATTGTCAGCAACG 57.518 40.909 0.00 0.00 37.44 4.10
3896 4117 3.618019 GCAACGGTACTTGGTGGATAAGA 60.618 47.826 5.96 0.00 0.00 2.10
3940 4162 7.227512 AGGATTCTAATAAAATGAAGGACAGCG 59.772 37.037 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 69 4.024302 GGATATGATGATATGGTGCGCATG 60.024 45.833 15.91 0.00 0.00 4.06
66 70 4.132336 GGATATGATGATATGGTGCGCAT 58.868 43.478 15.91 0.00 0.00 4.73
90 97 2.688794 GCTGCTTGAGTGCTGGCTC 61.689 63.158 0.00 0.00 36.12 4.70
91 98 2.672307 GCTGCTTGAGTGCTGGCT 60.672 61.111 0.00 0.00 33.41 4.75
205 232 1.600023 CAACCGTTTCCTGGCTTGTA 58.400 50.000 0.00 0.00 0.00 2.41
304 331 1.380112 AGTGCTCCTACCGGTCTCC 60.380 63.158 12.40 0.00 0.00 3.71
305 332 1.385756 GGAGTGCTCCTACCGGTCTC 61.386 65.000 12.40 9.78 46.16 3.36
306 333 1.380112 GGAGTGCTCCTACCGGTCT 60.380 63.158 12.40 0.00 46.16 3.85
307 334 3.208335 GGAGTGCTCCTACCGGTC 58.792 66.667 12.40 0.00 46.16 4.79
316 343 1.472376 CGATCCTTTCTGGGAGTGCTC 60.472 57.143 0.00 0.00 38.92 4.26
317 344 0.539051 CGATCCTTTCTGGGAGTGCT 59.461 55.000 0.00 0.00 38.92 4.40
318 345 0.462759 CCGATCCTTTCTGGGAGTGC 60.463 60.000 0.00 0.00 38.92 4.40
319 346 1.134670 GTCCGATCCTTTCTGGGAGTG 60.135 57.143 0.00 0.00 38.92 3.51
320 347 1.196012 GTCCGATCCTTTCTGGGAGT 58.804 55.000 0.00 0.00 38.92 3.85
321 348 0.103208 CGTCCGATCCTTTCTGGGAG 59.897 60.000 0.00 0.00 38.92 4.30
322 349 1.956629 GCGTCCGATCCTTTCTGGGA 61.957 60.000 0.00 0.00 39.95 4.37
323 350 1.521681 GCGTCCGATCCTTTCTGGG 60.522 63.158 0.00 0.00 36.20 4.45
324 351 1.878522 CGCGTCCGATCCTTTCTGG 60.879 63.158 0.00 0.00 36.29 3.86
325 352 1.138883 TCGCGTCCGATCCTTTCTG 59.861 57.895 5.77 0.00 38.82 3.02
326 353 3.599584 TCGCGTCCGATCCTTTCT 58.400 55.556 5.77 0.00 38.82 2.52
354 381 4.686191 ATTGAAAACCATTTGACCTGCA 57.314 36.364 0.00 0.00 0.00 4.41
357 384 7.446013 TCGTACTAATTGAAAACCATTTGACCT 59.554 33.333 0.00 0.00 0.00 3.85
441 471 1.070376 CCACGCGTTGCATCATATCAG 60.070 52.381 10.22 0.00 0.00 2.90
509 548 4.477975 GTCCGTCCGACGCAGGAG 62.478 72.222 15.64 1.67 41.68 3.69
520 559 2.046604 CCTTTTCCCCGGTCCGTC 60.047 66.667 11.06 0.00 0.00 4.79
530 569 4.416516 TCTCCATTTTCCTTCCCTTTTCC 58.583 43.478 0.00 0.00 0.00 3.13
531 570 6.419484 TTTCTCCATTTTCCTTCCCTTTTC 57.581 37.500 0.00 0.00 0.00 2.29
532 571 6.183361 CCTTTTCTCCATTTTCCTTCCCTTTT 60.183 38.462 0.00 0.00 0.00 2.27
533 572 5.307976 CCTTTTCTCCATTTTCCTTCCCTTT 59.692 40.000 0.00 0.00 0.00 3.11
534 573 4.840680 CCTTTTCTCCATTTTCCTTCCCTT 59.159 41.667 0.00 0.00 0.00 3.95
535 574 4.420206 CCTTTTCTCCATTTTCCTTCCCT 58.580 43.478 0.00 0.00 0.00 4.20
536 575 3.515502 CCCTTTTCTCCATTTTCCTTCCC 59.484 47.826 0.00 0.00 0.00 3.97
537 576 3.515502 CCCCTTTTCTCCATTTTCCTTCC 59.484 47.826 0.00 0.00 0.00 3.46
538 577 4.416516 TCCCCTTTTCTCCATTTTCCTTC 58.583 43.478 0.00 0.00 0.00 3.46
539 578 4.420206 CTCCCCTTTTCTCCATTTTCCTT 58.580 43.478 0.00 0.00 0.00 3.36
540 579 3.245766 CCTCCCCTTTTCTCCATTTTCCT 60.246 47.826 0.00 0.00 0.00 3.36
547 586 0.550147 CTCCCCTCCCCTTTTCTCCA 60.550 60.000 0.00 0.00 0.00 3.86
568 619 0.688087 GTCGGGGAATCTCTCCACCT 60.688 60.000 0.00 0.00 46.22 4.00
600 651 2.696504 CTTTCCCCTCCCCCTCCC 60.697 72.222 0.00 0.00 0.00 4.30
686 741 3.181450 GGAGAGAGAGAGAGAGAAGAGGG 60.181 56.522 0.00 0.00 0.00 4.30
697 752 1.421646 GAGAGGGAGGGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
698 753 1.010793 AGAGAGGGAGGGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
699 754 1.421646 GAGAGAGGGAGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
700 755 1.010793 AGAGAGAGGGAGGGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
701 756 1.421646 GAGAGAGAGGGAGGGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
702 757 1.010793 AGAGAGAGAGGGAGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
703 758 1.522900 AGAGAGAGAGGGAGGGAGAG 58.477 60.000 0.00 0.00 0.00 3.20
704 759 1.850345 GAAGAGAGAGAGGGAGGGAGA 59.150 57.143 0.00 0.00 0.00 3.71
705 760 1.133482 GGAAGAGAGAGAGGGAGGGAG 60.133 61.905 0.00 0.00 0.00 4.30
706 761 0.930726 GGAAGAGAGAGAGGGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
707 762 0.633921 TGGAAGAGAGAGAGGGAGGG 59.366 60.000 0.00 0.00 0.00 4.30
708 763 1.775385 GTGGAAGAGAGAGAGGGAGG 58.225 60.000 0.00 0.00 0.00 4.30
709 764 1.388547 CGTGGAAGAGAGAGAGGGAG 58.611 60.000 0.00 0.00 0.00 4.30
710 765 0.681564 GCGTGGAAGAGAGAGAGGGA 60.682 60.000 0.00 0.00 0.00 4.20
711 766 0.682855 AGCGTGGAAGAGAGAGAGGG 60.683 60.000 0.00 0.00 0.00 4.30
712 767 0.738389 GAGCGTGGAAGAGAGAGAGG 59.262 60.000 0.00 0.00 0.00 3.69
757 812 1.008206 AGTGATGAAGGCTCCTCTCCT 59.992 52.381 0.00 0.00 34.90 3.69
791 854 0.744414 CGAGCATTTGATGACCCGGT 60.744 55.000 0.00 0.00 0.00 5.28
806 869 1.877443 GATGGGAGAGAGAGTACGAGC 59.123 57.143 0.00 0.00 0.00 5.03
807 870 3.399330 GAGATGGGAGAGAGAGTACGAG 58.601 54.545 0.00 0.00 0.00 4.18
808 871 2.105134 GGAGATGGGAGAGAGAGTACGA 59.895 54.545 0.00 0.00 0.00 3.43
809 872 2.500229 GGAGATGGGAGAGAGAGTACG 58.500 57.143 0.00 0.00 0.00 3.67
810 873 2.812613 CGGGAGATGGGAGAGAGAGTAC 60.813 59.091 0.00 0.00 0.00 2.73
811 874 1.422024 CGGGAGATGGGAGAGAGAGTA 59.578 57.143 0.00 0.00 0.00 2.59
812 875 0.184933 CGGGAGATGGGAGAGAGAGT 59.815 60.000 0.00 0.00 0.00 3.24
813 876 1.178534 GCGGGAGATGGGAGAGAGAG 61.179 65.000 0.00 0.00 0.00 3.20
814 877 1.152652 GCGGGAGATGGGAGAGAGA 60.153 63.158 0.00 0.00 0.00 3.10
867 933 1.587054 CGGAGTGAGGTGAGGTCAC 59.413 63.158 1.17 1.17 44.02 3.67
882 948 0.464036 AATTATGACTGCGAGGCGGA 59.536 50.000 3.02 0.00 38.46 5.54
883 949 0.861837 GAATTATGACTGCGAGGCGG 59.138 55.000 0.00 0.00 41.29 6.13
885 951 2.139118 GGAGAATTATGACTGCGAGGC 58.861 52.381 0.00 0.00 0.00 4.70
903 998 4.362677 AGTGGTAAGAAAGATGCTAGGGA 58.637 43.478 0.00 0.00 0.00 4.20
905 1000 6.472686 ACTAGTGGTAAGAAAGATGCTAGG 57.527 41.667 0.00 0.00 31.69 3.02
941 1036 1.845205 AGCAGCAACAGGAGGAGGT 60.845 57.895 0.00 0.00 0.00 3.85
942 1037 1.376942 CAGCAGCAACAGGAGGAGG 60.377 63.158 0.00 0.00 0.00 4.30
944 1039 1.834856 CTCCAGCAGCAACAGGAGGA 61.835 60.000 12.85 0.00 43.07 3.71
945 1040 1.376942 CTCCAGCAGCAACAGGAGG 60.377 63.158 12.85 0.00 43.07 4.30
946 1041 4.298009 CTCCAGCAGCAACAGGAG 57.702 61.111 8.31 8.31 41.43 3.69
947 1042 1.071987 CACTCCAGCAGCAACAGGA 59.928 57.895 0.00 0.00 0.00 3.86
948 1043 1.970114 CCACTCCAGCAGCAACAGG 60.970 63.158 0.00 0.00 0.00 4.00
949 1044 0.820891 AACCACTCCAGCAGCAACAG 60.821 55.000 0.00 0.00 0.00 3.16
950 1045 1.102809 CAACCACTCCAGCAGCAACA 61.103 55.000 0.00 0.00 0.00 3.33
951 1046 1.656441 CAACCACTCCAGCAGCAAC 59.344 57.895 0.00 0.00 0.00 4.17
952 1047 2.195567 GCAACCACTCCAGCAGCAA 61.196 57.895 0.00 0.00 0.00 3.91
970 1065 2.757868 CCTCTCCTCTCTACCACACAAG 59.242 54.545 0.00 0.00 0.00 3.16
975 1070 2.158667 CCTCTCCTCTCCTCTCTACCAC 60.159 59.091 0.00 0.00 0.00 4.16
1059 1169 0.250770 GTTCCACCACCTTCCTGTCC 60.251 60.000 0.00 0.00 0.00 4.02
1148 1273 1.795286 GCCTCGCCATTAGAGAATTCG 59.205 52.381 0.00 0.00 37.93 3.34
1165 1292 2.560105 GCAGAGGAAAATTGAACAGCCT 59.440 45.455 0.00 0.00 0.00 4.58
1262 1395 3.902150 ACGATCGGTTATGCTGTCTATG 58.098 45.455 20.98 0.00 0.00 2.23
1268 1401 1.716050 CGATGACGATCGGTTATGCTG 59.284 52.381 20.98 0.00 46.51 4.41
1305 1438 2.490903 CAGCAATGGTGAAGGAAAGGAG 59.509 50.000 6.59 0.00 32.22 3.69
1344 1500 4.082679 ACAGAGCAAACGTGTTGGTAAAAA 60.083 37.500 12.77 0.00 0.00 1.94
1345 1501 3.440872 ACAGAGCAAACGTGTTGGTAAAA 59.559 39.130 12.77 0.00 0.00 1.52
1346 1502 3.011119 ACAGAGCAAACGTGTTGGTAAA 58.989 40.909 12.77 0.00 0.00 2.01
1347 1503 2.634600 ACAGAGCAAACGTGTTGGTAA 58.365 42.857 12.77 0.00 0.00 2.85
1348 1504 2.319136 ACAGAGCAAACGTGTTGGTA 57.681 45.000 12.77 0.00 0.00 3.25
1349 1505 1.937899 GTACAGAGCAAACGTGTTGGT 59.062 47.619 12.68 12.68 0.00 3.67
1350 1506 2.210116 AGTACAGAGCAAACGTGTTGG 58.790 47.619 10.89 0.00 0.00 3.77
1351 1507 5.398176 TTTAGTACAGAGCAAACGTGTTG 57.602 39.130 0.00 0.00 0.00 3.33
1352 1508 6.482308 AGATTTTAGTACAGAGCAAACGTGTT 59.518 34.615 0.00 0.00 0.00 3.32
1353 1509 5.989777 AGATTTTAGTACAGAGCAAACGTGT 59.010 36.000 0.00 0.00 0.00 4.49
1378 1534 3.421826 GCGACGACTGTATGAAGTTGTTG 60.422 47.826 0.00 10.78 43.48 3.33
1460 1618 1.949525 CAGGGCGGATGGAATTGTTAG 59.050 52.381 0.00 0.00 0.00 2.34
1461 1619 1.283613 ACAGGGCGGATGGAATTGTTA 59.716 47.619 0.00 0.00 0.00 2.41
1463 1621 0.394352 GACAGGGCGGATGGAATTGT 60.394 55.000 0.00 0.00 0.00 2.71
1464 1622 1.103398 GGACAGGGCGGATGGAATTG 61.103 60.000 0.00 0.00 0.00 2.32
1490 1648 1.132588 GTACTGAATGCGAGGCGATC 58.867 55.000 0.00 0.00 0.00 3.69
1511 1669 1.001048 TGCAGTTGTTGATTGCTCTGC 60.001 47.619 7.83 7.83 45.39 4.26
1523 1681 1.094785 AAGTCGTGCTTTGCAGTTGT 58.905 45.000 0.00 0.00 40.08 3.32
1537 1695 5.751680 TGAAAGAAAATGAGAAGCAAGTCG 58.248 37.500 0.00 0.00 0.00 4.18
1559 1717 4.222588 TGGATAGCCAAAGTGGGAAAAATG 59.777 41.667 0.00 0.00 42.49 2.32
1812 1976 1.318576 CTTTCTCCAACCGTGCCTTT 58.681 50.000 0.00 0.00 0.00 3.11
1895 2063 3.011085 TGCTCCTGCAGACAAACAG 57.989 52.632 17.39 2.01 45.31 3.16
1977 2145 2.097825 GAGATTTGCACCTTGATGGCT 58.902 47.619 0.00 0.00 40.22 4.75
2088 2279 2.503356 AGAGGACTCATCGCCTGAAAAT 59.497 45.455 1.75 0.00 33.84 1.82
2183 2374 1.079503 CGAGCGAAGAAAAGGGGAAG 58.920 55.000 0.00 0.00 0.00 3.46
2198 2389 2.927553 ACAAAAATGGATGCTCGAGC 57.072 45.000 30.42 30.42 42.50 5.03
2267 2459 1.251527 ACTGTCTGCCTACTGTCCCG 61.252 60.000 0.00 0.00 0.00 5.14
2269 2461 2.168496 TGTACTGTCTGCCTACTGTCC 58.832 52.381 0.00 0.00 34.02 4.02
2430 2625 5.021033 TGAGAAAAGCAGAGATCTCCATC 57.979 43.478 19.30 8.55 37.99 3.51
2490 2685 4.895889 AGCTGCAGGATTCTGTATAGTACA 59.104 41.667 17.12 0.00 42.78 2.90
2491 2686 5.010112 TCAGCTGCAGGATTCTGTATAGTAC 59.990 44.000 17.12 0.00 42.78 2.73
2532 2727 3.888930 CTGTCCCCAGCAAAAAGTTAAGA 59.111 43.478 0.00 0.00 0.00 2.10
2618 2813 1.886585 GTTCGAGCAGCTCCTCAGA 59.113 57.895 17.16 5.24 0.00 3.27
2638 2833 0.699577 TGGAGGGTCCTTGGGTTTCA 60.700 55.000 0.00 0.00 37.46 2.69
2679 2874 1.613925 GACAGCAGCTATATGGTCCGA 59.386 52.381 0.00 0.00 0.00 4.55
3029 3243 4.092771 TCACTCATAAGCTACGACACAC 57.907 45.455 0.00 0.00 0.00 3.82
3124 3338 2.027625 CAAGAACTGACGCCCGGTC 61.028 63.158 0.00 0.00 46.27 4.79
3125 3339 2.030562 CAAGAACTGACGCCCGGT 59.969 61.111 0.00 0.00 35.44 5.28
3126 3340 2.742372 CCAAGAACTGACGCCCGG 60.742 66.667 0.00 0.00 0.00 5.73
3135 3351 3.131850 CCCAACAAGGCCAAGAACT 57.868 52.632 5.01 0.00 35.39 3.01
3158 3374 0.977395 AGGGGTTCTTCCTCAACTCG 59.023 55.000 0.00 0.00 39.70 4.18
3216 3432 2.952310 GCCAAAAGGGACATCAGATACC 59.048 50.000 0.00 0.00 40.01 2.73
3261 3477 4.568152 AAAAAGTTCCCTGAATGTCACG 57.432 40.909 0.00 0.00 0.00 4.35
3282 3498 2.357637 CTCAACCAAGTGAAAGGCGAAA 59.642 45.455 0.00 0.00 0.00 3.46
3419 3639 5.281314 ACCTGACCTTTGAGACCATACTAT 58.719 41.667 0.00 0.00 0.00 2.12
3467 3687 4.937696 TGAATGCAATTACACGATTCGT 57.062 36.364 5.75 5.75 37.30 3.85
3516 3736 7.833682 TCCCATCTTAAAGCAAACATTCTATCA 59.166 33.333 0.00 0.00 0.00 2.15
3534 3754 5.433051 TCATCCAATAGAAAGGTCCCATCTT 59.567 40.000 0.00 0.00 0.00 2.40
3600 3820 3.009695 CCCTCACCCACCTTTGTACATTA 59.990 47.826 0.00 0.00 0.00 1.90
3622 3843 2.945008 TGTGATTTCAATGGCTCGGATC 59.055 45.455 0.00 0.00 0.00 3.36
3664 3885 2.417379 GCAGTAGGAAGACGAGCAATCA 60.417 50.000 0.00 0.00 0.00 2.57
3671 3892 2.005451 GACGTAGCAGTAGGAAGACGA 58.995 52.381 0.00 0.00 34.54 4.20
3733 3954 4.556233 CAGACGGTGAAATGTAGAACAGA 58.444 43.478 0.00 0.00 0.00 3.41
3879 4100 4.838904 AGGTTCTTATCCACCAAGTACC 57.161 45.455 3.48 3.48 41.35 3.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.