Multiple sequence alignment - TraesCS6B01G426700

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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 TraesCS6B01G426700 chr6B 100.000 2360 0 0 1 2360 695056653 695059012 0.000000e+00 4359
1 TraesCS6B01G426700 chr3D 96.245 1385 52 0 1 1385 69660429 69661813 0.000000e+00 2270
2 TraesCS6B01G426700 chr6A 96.026 1384 52 1 1 1384 502339292 502340672 0.000000e+00 2248
3 TraesCS6B01G426700 chr6A 95.579 1312 58 0 73 1384 532870195 532871506 0.000000e+00 2102
4 TraesCS6B01G426700 chr7B 95.445 1383 62 1 1 1383 84527265 84528646 0.000000e+00 2204
5 TraesCS6B01G426700 chr3A 95.366 1381 63 1 4 1384 681100864 681099485 0.000000e+00 2194
6 TraesCS6B01G426700 chr2B 95.843 1347 54 1 40 1384 717931261 717929915 0.000000e+00 2176
7 TraesCS6B01G426700 chr5B 94.725 1384 72 1 1 1384 633276927 633278309 0.000000e+00 2150
8 TraesCS6B01G426700 chr5B 80.508 826 137 14 1550 2356 703066921 703067741 1.550000e-171 612
9 TraesCS6B01G426700 chr4A 94.497 1381 76 0 4 1384 107232281 107230901 0.000000e+00 2130
10 TraesCS6B01G426700 chr2A 94.296 1385 70 6 1 1384 148651647 148653023 0.000000e+00 2111
11 TraesCS6B01G426700 chr3B 94.921 827 21 6 1551 2360 810962334 810961512 0.000000e+00 1275
12 TraesCS6B01G426700 chr3B 95.745 94 3 1 4 96 21802302 21802209 1.460000e-32 150
13 TraesCS6B01G426700 chr3B 80.128 156 22 8 1551 1703 45192764 45192913 8.920000e-20 108
14 TraesCS6B01G426700 chr1B 89.467 826 67 5 1550 2358 623538071 623537249 0.000000e+00 1026
15 TraesCS6B01G426700 chr7A 80.288 832 136 18 1550 2360 705364003 705363179 9.330000e-169 603


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 TraesCS6B01G426700 chr6B 695056653 695059012 2359 False 4359 4359 100.000 1 2360 1 chr6B.!!$F1 2359
1 TraesCS6B01G426700 chr3D 69660429 69661813 1384 False 2270 2270 96.245 1 1385 1 chr3D.!!$F1 1384
2 TraesCS6B01G426700 chr6A 502339292 502340672 1380 False 2248 2248 96.026 1 1384 1 chr6A.!!$F1 1383
3 TraesCS6B01G426700 chr6A 532870195 532871506 1311 False 2102 2102 95.579 73 1384 1 chr6A.!!$F2 1311
4 TraesCS6B01G426700 chr7B 84527265 84528646 1381 False 2204 2204 95.445 1 1383 1 chr7B.!!$F1 1382
5 TraesCS6B01G426700 chr3A 681099485 681100864 1379 True 2194 2194 95.366 4 1384 1 chr3A.!!$R1 1380
6 TraesCS6B01G426700 chr2B 717929915 717931261 1346 True 2176 2176 95.843 40 1384 1 chr2B.!!$R1 1344
7 TraesCS6B01G426700 chr5B 633276927 633278309 1382 False 2150 2150 94.725 1 1384 1 chr5B.!!$F1 1383
8 TraesCS6B01G426700 chr5B 703066921 703067741 820 False 612 612 80.508 1550 2356 1 chr5B.!!$F2 806
9 TraesCS6B01G426700 chr4A 107230901 107232281 1380 True 2130 2130 94.497 4 1384 1 chr4A.!!$R1 1380
10 TraesCS6B01G426700 chr2A 148651647 148653023 1376 False 2111 2111 94.296 1 1384 1 chr2A.!!$F1 1383
11 TraesCS6B01G426700 chr3B 810961512 810962334 822 True 1275 1275 94.921 1551 2360 1 chr3B.!!$R2 809
12 TraesCS6B01G426700 chr1B 623537249 623538071 822 True 1026 1026 89.467 1550 2358 1 chr1B.!!$R1 808
13 TraesCS6B01G426700 chr7A 705363179 705364003 824 True 603 603 80.288 1550 2360 1 chr7A.!!$R1 810

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
93 94 0.883833 CGCAGAGCCCAACAAGAAAT 59.116 50.0 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1455 0.034059 GCCCATGTCACGCTAGCTAT 59.966 55.0 13.93 0.0 0.0 2.97 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
93 94 0.883833 CGCAGAGCCCAACAAGAAAT 59.116 50.000 0.00 0.00 0.00 2.17
166 167 2.214216 CCGGTGACAGGGAGTTGGA 61.214 63.158 0.00 0.00 0.00 3.53
222 223 2.491693 GGATGTTCGAAGGATTTTGGCA 59.508 45.455 0.00 0.00 0.00 4.92
247 248 5.551305 TCCACTACCATTACATGAGATGG 57.449 43.478 22.18 22.18 46.57 3.51
256 257 5.768662 CCATTACATGAGATGGCAGATTTCT 59.231 40.000 15.62 0.00 36.68 2.52
295 296 2.119495 AGTCAGGGACTTTCACAGTGT 58.881 47.619 0.00 0.00 40.28 3.55
305 306 3.750130 ACTTTCACAGTGTGATCTGCATC 59.250 43.478 25.97 0.00 42.40 3.91
464 465 2.501723 ACAGTGCTATTCCCTGTCGATT 59.498 45.455 0.00 0.00 34.44 3.34
506 507 5.242838 ACTTGAAAATAAATCCGAGTTGCCA 59.757 36.000 0.00 0.00 0.00 4.92
510 511 2.489938 TAAATCCGAGTTGCCAAGCT 57.510 45.000 0.00 0.00 0.00 3.74
520 521 4.315803 GAGTTGCCAAGCTTGTAACTAGA 58.684 43.478 30.40 9.80 35.34 2.43
533 534 3.447586 TGTAACTAGAGGCCTGATGACAC 59.552 47.826 12.00 1.57 0.00 3.67
775 778 4.794248 TTGACACATGACGAAGAAACTG 57.206 40.909 0.00 0.00 0.00 3.16
903 906 9.120422 CCAAAGTATGGTTACGTGAAATTAAAC 57.880 33.333 0.00 0.00 44.85 2.01
1003 1007 2.098117 GCGGCTGCTAATCAAAAGATGT 59.902 45.455 11.21 0.00 38.39 3.06
1073 1077 4.095782 TGGTTTGAATCTTGCTAATACCGC 59.904 41.667 0.00 0.00 0.00 5.68
1088 1092 1.153449 CCGCCGGATGCAGTAAGAA 60.153 57.895 5.05 0.00 41.33 2.52
1169 1176 6.265422 TCTTCAGTCGCTTCATCCATTATAGA 59.735 38.462 0.00 0.00 0.00 1.98
1170 1177 6.596309 TCAGTCGCTTCATCCATTATAGAT 57.404 37.500 0.00 0.00 0.00 1.98
1171 1178 6.393171 TCAGTCGCTTCATCCATTATAGATG 58.607 40.000 0.00 0.00 42.08 2.90
1281 1288 4.844655 AGGTTAGCTAGGTTTTCTTCTCCA 59.155 41.667 0.00 0.00 0.00 3.86
1405 1412 5.796350 ATATCTAACGTGGAACTTTGTGC 57.204 39.130 0.00 0.00 28.38 4.57
1406 1413 2.907634 TCTAACGTGGAACTTTGTGCA 58.092 42.857 0.00 0.00 28.38 4.57
1407 1414 2.610374 TCTAACGTGGAACTTTGTGCAC 59.390 45.455 10.75 10.75 36.57 4.57
1408 1415 1.169577 AACGTGGAACTTTGTGCACA 58.830 45.000 17.42 17.42 39.63 4.57
1409 1416 1.169577 ACGTGGAACTTTGTGCACAA 58.830 45.000 27.96 27.96 39.63 3.33
1410 1417 1.542030 ACGTGGAACTTTGTGCACAAA 59.458 42.857 35.70 35.70 42.90 2.83
1443 1450 8.974060 AAATAGTGTCAGACTTTCCTAAAACA 57.026 30.769 1.31 0.00 35.96 2.83
1444 1451 8.974060 AATAGTGTCAGACTTTCCTAAAACAA 57.026 30.769 1.31 0.00 35.96 2.83
1445 1452 8.974060 ATAGTGTCAGACTTTCCTAAAACAAA 57.026 30.769 1.31 0.00 35.96 2.83
1446 1453 7.085052 AGTGTCAGACTTTCCTAAAACAAAC 57.915 36.000 1.31 0.00 0.00 2.93
1447 1454 6.095021 AGTGTCAGACTTTCCTAAAACAAACC 59.905 38.462 1.31 0.00 0.00 3.27
1448 1455 5.946972 TGTCAGACTTTCCTAAAACAAACCA 59.053 36.000 1.31 0.00 0.00 3.67
1449 1456 6.605594 TGTCAGACTTTCCTAAAACAAACCAT 59.394 34.615 1.31 0.00 0.00 3.55
1450 1457 7.776030 TGTCAGACTTTCCTAAAACAAACCATA 59.224 33.333 1.31 0.00 0.00 2.74
1451 1458 8.290325 GTCAGACTTTCCTAAAACAAACCATAG 58.710 37.037 0.00 0.00 0.00 2.23
1452 1459 7.040686 TCAGACTTTCCTAAAACAAACCATAGC 60.041 37.037 0.00 0.00 0.00 2.97
1453 1460 7.004691 AGACTTTCCTAAAACAAACCATAGCT 58.995 34.615 0.00 0.00 0.00 3.32
1454 1461 8.161425 AGACTTTCCTAAAACAAACCATAGCTA 58.839 33.333 0.00 0.00 0.00 3.32
1455 1462 8.336801 ACTTTCCTAAAACAAACCATAGCTAG 57.663 34.615 0.00 0.00 0.00 3.42
1456 1463 6.753107 TTCCTAAAACAAACCATAGCTAGC 57.247 37.500 6.62 6.62 0.00 3.42
1457 1464 4.873827 TCCTAAAACAAACCATAGCTAGCG 59.126 41.667 9.55 0.00 0.00 4.26
1458 1465 4.634443 CCTAAAACAAACCATAGCTAGCGT 59.366 41.667 9.55 0.00 0.00 5.07
1459 1466 4.419522 AAAACAAACCATAGCTAGCGTG 57.580 40.909 9.55 12.28 0.00 5.34
1460 1467 3.328382 AACAAACCATAGCTAGCGTGA 57.672 42.857 20.37 7.04 0.00 4.35
1461 1468 2.618053 ACAAACCATAGCTAGCGTGAC 58.382 47.619 20.37 0.00 0.00 3.67
1462 1469 2.028476 ACAAACCATAGCTAGCGTGACA 60.028 45.455 20.37 2.31 0.00 3.58
1463 1470 3.198068 CAAACCATAGCTAGCGTGACAT 58.802 45.455 20.37 1.30 0.00 3.06
1464 1471 2.515926 ACCATAGCTAGCGTGACATG 57.484 50.000 20.37 14.04 0.00 3.21
1465 1472 1.069204 ACCATAGCTAGCGTGACATGG 59.931 52.381 22.58 22.58 39.07 3.66
1466 1473 1.606480 CCATAGCTAGCGTGACATGGG 60.606 57.143 20.37 7.52 31.28 4.00
1467 1474 0.034059 ATAGCTAGCGTGACATGGGC 59.966 55.000 9.55 0.00 0.00 5.36
1468 1475 1.043116 TAGCTAGCGTGACATGGGCT 61.043 55.000 9.55 2.85 40.68 5.19
1469 1476 2.176273 GCTAGCGTGACATGGGCTG 61.176 63.158 0.00 4.99 37.62 4.85
1470 1477 1.517361 CTAGCGTGACATGGGCTGA 59.483 57.895 11.52 0.00 37.62 4.26
1471 1478 0.105593 CTAGCGTGACATGGGCTGAT 59.894 55.000 11.52 0.00 37.62 2.90
1472 1479 1.341209 CTAGCGTGACATGGGCTGATA 59.659 52.381 11.52 0.00 37.62 2.15
1473 1480 0.179073 AGCGTGACATGGGCTGATAC 60.179 55.000 0.00 0.00 35.31 2.24
1474 1481 1.160329 GCGTGACATGGGCTGATACC 61.160 60.000 0.00 0.00 0.00 2.73
1475 1482 0.465705 CGTGACATGGGCTGATACCT 59.534 55.000 0.00 0.00 0.00 3.08
1476 1483 1.134401 CGTGACATGGGCTGATACCTT 60.134 52.381 0.00 0.00 0.00 3.50
1477 1484 2.680805 CGTGACATGGGCTGATACCTTT 60.681 50.000 0.00 0.00 0.00 3.11
1478 1485 2.945668 GTGACATGGGCTGATACCTTTC 59.054 50.000 0.00 0.00 0.00 2.62
1479 1486 2.846206 TGACATGGGCTGATACCTTTCT 59.154 45.455 0.00 0.00 0.00 2.52
1480 1487 4.037222 TGACATGGGCTGATACCTTTCTA 58.963 43.478 0.00 0.00 0.00 2.10
1481 1488 4.660303 TGACATGGGCTGATACCTTTCTAT 59.340 41.667 0.00 0.00 0.00 1.98
1482 1489 5.843969 TGACATGGGCTGATACCTTTCTATA 59.156 40.000 0.00 0.00 0.00 1.31
1483 1490 6.501805 TGACATGGGCTGATACCTTTCTATAT 59.498 38.462 0.00 0.00 0.00 0.86
1484 1491 7.678171 TGACATGGGCTGATACCTTTCTATATA 59.322 37.037 0.00 0.00 0.00 0.86
1485 1492 7.852263 ACATGGGCTGATACCTTTCTATATAC 58.148 38.462 0.00 0.00 0.00 1.47
1486 1493 7.680310 ACATGGGCTGATACCTTTCTATATACT 59.320 37.037 0.00 0.00 0.00 2.12
1487 1494 9.201989 CATGGGCTGATACCTTTCTATATACTA 57.798 37.037 0.00 0.00 0.00 1.82
1488 1495 8.591114 TGGGCTGATACCTTTCTATATACTAC 57.409 38.462 0.00 0.00 0.00 2.73
1489 1496 8.174757 TGGGCTGATACCTTTCTATATACTACA 58.825 37.037 0.00 0.00 0.00 2.74
1490 1497 9.203163 GGGCTGATACCTTTCTATATACTACAT 57.797 37.037 0.00 0.00 0.00 2.29
1509 1516 6.992715 ACTACATACATGTATTCCTCCTTTGC 59.007 38.462 15.85 0.00 41.92 3.68
1510 1517 6.006275 ACATACATGTATTCCTCCTTTGCT 57.994 37.500 15.85 0.00 39.68 3.91
1511 1518 7.136822 ACATACATGTATTCCTCCTTTGCTA 57.863 36.000 15.85 0.00 39.68 3.49
1512 1519 7.220030 ACATACATGTATTCCTCCTTTGCTAG 58.780 38.462 15.85 2.52 39.68 3.42
1513 1520 4.455606 ACATGTATTCCTCCTTTGCTAGC 58.544 43.478 8.10 8.10 0.00 3.42
1514 1521 3.179443 TGTATTCCTCCTTTGCTAGCG 57.821 47.619 10.77 0.00 0.00 4.26
1515 1522 2.500098 TGTATTCCTCCTTTGCTAGCGT 59.500 45.455 10.77 0.00 0.00 5.07
1516 1523 3.702548 TGTATTCCTCCTTTGCTAGCGTA 59.297 43.478 10.77 0.00 0.00 4.42
1517 1524 2.961526 TTCCTCCTTTGCTAGCGTAG 57.038 50.000 10.77 9.46 0.00 3.51
1518 1525 1.112113 TCCTCCTTTGCTAGCGTAGG 58.888 55.000 22.63 22.63 0.00 3.18
1519 1526 1.112113 CCTCCTTTGCTAGCGTAGGA 58.888 55.000 26.84 26.84 35.57 2.94
1520 1527 1.202428 CCTCCTTTGCTAGCGTAGGAC 60.202 57.143 25.64 0.00 33.40 3.85
1521 1528 1.751924 CTCCTTTGCTAGCGTAGGACT 59.248 52.381 25.64 0.00 33.40 3.85
1522 1529 1.749634 TCCTTTGCTAGCGTAGGACTC 59.250 52.381 25.64 0.00 32.00 3.36
1523 1530 1.751924 CCTTTGCTAGCGTAGGACTCT 59.248 52.381 23.73 0.00 0.00 3.24
1524 1531 2.166664 CCTTTGCTAGCGTAGGACTCTT 59.833 50.000 23.73 0.00 0.00 2.85
1525 1532 3.440228 CTTTGCTAGCGTAGGACTCTTC 58.560 50.000 10.77 0.00 0.00 2.87
1526 1533 2.124277 TGCTAGCGTAGGACTCTTCA 57.876 50.000 10.77 0.00 0.00 3.02
1527 1534 2.443416 TGCTAGCGTAGGACTCTTCAA 58.557 47.619 10.77 0.00 0.00 2.69
1528 1535 2.823747 TGCTAGCGTAGGACTCTTCAAA 59.176 45.455 10.77 0.00 0.00 2.69
1529 1536 3.257375 TGCTAGCGTAGGACTCTTCAAAA 59.743 43.478 10.77 0.00 0.00 2.44
1530 1537 4.243270 GCTAGCGTAGGACTCTTCAAAAA 58.757 43.478 0.00 0.00 0.00 1.94
1736 1743 0.738389 CGTGAACCACCTGTTTGCTT 59.262 50.000 0.00 0.00 37.29 3.91
1815 1822 2.046217 GGCCGTCCCTTTGGAGAC 60.046 66.667 0.00 0.00 42.85 3.36
1858 1865 2.232452 CAGTCTCGACCAGGATGTTTCT 59.768 50.000 0.00 0.00 0.00 2.52
2032 2056 1.524355 CATCGGTATTCAGCTTCGCAG 59.476 52.381 0.00 0.00 0.00 5.18
2072 2096 6.183360 GCAGTCCATTGCCTTATTTGATTTTG 60.183 38.462 0.00 0.00 38.13 2.44
2262 2286 1.476085 CACCTCCACAGCAACAACAAA 59.524 47.619 0.00 0.00 0.00 2.83
2284 2308 0.034198 TTTCACGCGGACATCCTTCA 59.966 50.000 12.47 0.00 0.00 3.02
2335 2359 6.288294 CAATCTTCACCAGTATTCCGGAATA 58.712 40.000 29.13 29.13 32.50 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.411869 TCCAAATATACCCATGTCTGAGCA 59.588 41.667 0.00 0.00 0.00 4.26
166 167 2.584835 TGGTTAACCAGCTGCTCATT 57.415 45.000 23.69 0.00 42.01 2.57
222 223 7.000472 CCATCTCATGTAATGGTAGTGGAATT 59.000 38.462 16.37 0.00 46.73 2.17
247 248 2.231964 TGTTCCATGCCAAGAAATCTGC 59.768 45.455 0.00 0.00 0.00 4.26
256 257 2.964464 ACTTTGTCATGTTCCATGCCAA 59.036 40.909 0.00 0.00 0.00 4.52
305 306 8.875803 CAAATTGAAATTCACATTCTGTATGGG 58.124 33.333 0.00 0.00 39.13 4.00
318 319 5.033589 ACTTGTGCCCAAATTGAAATTCA 57.966 34.783 0.00 0.00 0.00 2.57
506 507 3.173965 TCAGGCCTCTAGTTACAAGCTT 58.826 45.455 0.00 0.00 0.00 3.74
510 511 4.081642 GTGTCATCAGGCCTCTAGTTACAA 60.082 45.833 0.00 0.00 0.00 2.41
520 521 1.059098 TGTCTTGTGTCATCAGGCCT 58.941 50.000 0.00 0.00 0.00 5.19
533 534 5.630061 TGCATTCGAACAACATATGTCTTG 58.370 37.500 9.23 7.41 42.99 3.02
567 568 0.109086 CGAGCATCTTCCACACGTCT 60.109 55.000 0.00 0.00 0.00 4.18
630 631 1.827789 TGCCAACACAAGCTCACCC 60.828 57.895 0.00 0.00 0.00 4.61
652 655 3.186909 GTTGTTCTGGAAGGCACAAAAC 58.813 45.455 0.00 0.00 38.62 2.43
775 778 5.745294 ACATATTGATTTGACATGCGCTTTC 59.255 36.000 9.73 2.43 0.00 2.62
903 906 1.257936 CTATCAAATCCCGCGTCAACG 59.742 52.381 4.92 0.00 43.27 4.10
994 998 5.049405 AGTCGAAGCAAAGGTACATCTTTTG 60.049 40.000 0.00 1.52 43.15 2.44
1003 1007 2.034939 TGAACGAGTCGAAGCAAAGGTA 59.965 45.455 21.50 0.00 0.00 3.08
1073 1077 3.310774 CACTTCATTCTTACTGCATCCGG 59.689 47.826 0.00 0.00 0.00 5.14
1088 1092 4.758674 CCATGCTATCCGAATTCACTTCAT 59.241 41.667 6.22 0.00 33.10 2.57
1170 1177 8.862325 AACCTAATGACATGAAATAACAGTCA 57.138 30.769 0.00 0.00 42.62 3.41
1281 1288 2.752903 GGCGTTATCCATCCAAACACTT 59.247 45.455 0.00 0.00 0.00 3.16
1385 1392 3.250040 GTGCACAAAGTTCCACGTTAGAT 59.750 43.478 13.17 0.00 0.00 1.98
1386 1393 2.610374 GTGCACAAAGTTCCACGTTAGA 59.390 45.455 13.17 0.00 0.00 2.10
1387 1394 2.353269 TGTGCACAAAGTTCCACGTTAG 59.647 45.455 19.28 0.00 0.00 2.34
1388 1395 2.357075 TGTGCACAAAGTTCCACGTTA 58.643 42.857 19.28 0.00 0.00 3.18
1389 1396 1.169577 TGTGCACAAAGTTCCACGTT 58.830 45.000 19.28 0.00 0.00 3.99
1390 1397 1.169577 TTGTGCACAAAGTTCCACGT 58.830 45.000 29.36 0.00 32.11 4.49
1391 1398 2.270275 TTTGTGCACAAAGTTCCACG 57.730 45.000 35.10 0.00 40.55 4.94
1417 1424 9.403583 TGTTTTAGGAAAGTCTGACACTATTTT 57.596 29.630 10.88 1.15 32.30 1.82
1418 1425 8.974060 TGTTTTAGGAAAGTCTGACACTATTT 57.026 30.769 10.88 1.54 32.30 1.40
1419 1426 8.974060 TTGTTTTAGGAAAGTCTGACACTATT 57.026 30.769 10.88 0.00 32.30 1.73
1420 1427 8.837389 GTTTGTTTTAGGAAAGTCTGACACTAT 58.163 33.333 10.88 0.00 32.30 2.12
1421 1428 7.281549 GGTTTGTTTTAGGAAAGTCTGACACTA 59.718 37.037 10.88 4.32 32.30 2.74
1422 1429 6.095021 GGTTTGTTTTAGGAAAGTCTGACACT 59.905 38.462 10.88 5.24 36.64 3.55
1423 1430 6.127842 TGGTTTGTTTTAGGAAAGTCTGACAC 60.128 38.462 10.88 1.18 0.00 3.67
1424 1431 5.946972 TGGTTTGTTTTAGGAAAGTCTGACA 59.053 36.000 10.88 0.00 0.00 3.58
1425 1432 6.445357 TGGTTTGTTTTAGGAAAGTCTGAC 57.555 37.500 0.00 0.00 0.00 3.51
1426 1433 7.040686 GCTATGGTTTGTTTTAGGAAAGTCTGA 60.041 37.037 0.00 0.00 0.00 3.27
1427 1434 7.040409 AGCTATGGTTTGTTTTAGGAAAGTCTG 60.040 37.037 0.00 0.00 0.00 3.51
1428 1435 7.004691 AGCTATGGTTTGTTTTAGGAAAGTCT 58.995 34.615 0.00 0.00 0.00 3.24
1429 1436 7.215719 AGCTATGGTTTGTTTTAGGAAAGTC 57.784 36.000 0.00 0.00 0.00 3.01
1430 1437 7.094334 GCTAGCTATGGTTTGTTTTAGGAAAGT 60.094 37.037 7.70 0.00 0.00 2.66
1431 1438 7.251281 GCTAGCTATGGTTTGTTTTAGGAAAG 58.749 38.462 7.70 0.00 0.00 2.62
1432 1439 6.128117 CGCTAGCTATGGTTTGTTTTAGGAAA 60.128 38.462 13.93 0.00 0.00 3.13
1433 1440 5.353123 CGCTAGCTATGGTTTGTTTTAGGAA 59.647 40.000 13.93 0.00 0.00 3.36
1434 1441 4.873827 CGCTAGCTATGGTTTGTTTTAGGA 59.126 41.667 13.93 0.00 0.00 2.94
1435 1442 4.634443 ACGCTAGCTATGGTTTGTTTTAGG 59.366 41.667 13.93 0.00 0.00 2.69
1436 1443 5.350365 TCACGCTAGCTATGGTTTGTTTTAG 59.650 40.000 13.93 0.00 0.00 1.85
1437 1444 5.121142 GTCACGCTAGCTATGGTTTGTTTTA 59.879 40.000 13.93 0.00 0.00 1.52
1438 1445 4.069304 TCACGCTAGCTATGGTTTGTTTT 58.931 39.130 13.93 0.00 0.00 2.43
1439 1446 3.435671 GTCACGCTAGCTATGGTTTGTTT 59.564 43.478 13.93 0.00 0.00 2.83
1440 1447 3.000727 GTCACGCTAGCTATGGTTTGTT 58.999 45.455 13.93 0.00 0.00 2.83
1441 1448 2.028476 TGTCACGCTAGCTATGGTTTGT 60.028 45.455 13.93 0.00 0.00 2.83
1442 1449 2.616960 TGTCACGCTAGCTATGGTTTG 58.383 47.619 13.93 0.00 0.00 2.93
1443 1450 3.198068 CATGTCACGCTAGCTATGGTTT 58.802 45.455 13.93 0.00 0.00 3.27
1444 1451 2.483714 CCATGTCACGCTAGCTATGGTT 60.484 50.000 13.93 0.00 32.44 3.67
1445 1452 1.069204 CCATGTCACGCTAGCTATGGT 59.931 52.381 13.93 0.00 32.44 3.55
1446 1453 1.606480 CCCATGTCACGCTAGCTATGG 60.606 57.143 13.93 16.30 35.88 2.74
1447 1454 1.788258 CCCATGTCACGCTAGCTATG 58.212 55.000 13.93 11.16 0.00 2.23
1448 1455 0.034059 GCCCATGTCACGCTAGCTAT 59.966 55.000 13.93 0.00 0.00 2.97
1449 1456 1.043116 AGCCCATGTCACGCTAGCTA 61.043 55.000 13.93 0.00 0.00 3.32
1450 1457 2.187946 GCCCATGTCACGCTAGCT 59.812 61.111 13.93 0.00 0.00 3.32
1451 1458 2.176273 CAGCCCATGTCACGCTAGC 61.176 63.158 4.06 4.06 0.00 3.42
1452 1459 0.105593 ATCAGCCCATGTCACGCTAG 59.894 55.000 0.00 0.00 0.00 3.42
1453 1460 1.068588 GTATCAGCCCATGTCACGCTA 59.931 52.381 0.00 0.00 0.00 4.26
1454 1461 0.179073 GTATCAGCCCATGTCACGCT 60.179 55.000 0.00 0.00 0.00 5.07
1455 1462 1.160329 GGTATCAGCCCATGTCACGC 61.160 60.000 0.00 0.00 0.00 5.34
1456 1463 0.465705 AGGTATCAGCCCATGTCACG 59.534 55.000 0.00 0.00 0.00 4.35
1457 1464 2.717639 AAGGTATCAGCCCATGTCAC 57.282 50.000 0.00 0.00 0.00 3.67
1458 1465 2.846206 AGAAAGGTATCAGCCCATGTCA 59.154 45.455 0.00 0.00 0.00 3.58
1459 1466 3.567478 AGAAAGGTATCAGCCCATGTC 57.433 47.619 0.00 0.00 0.00 3.06
1460 1467 6.959606 ATATAGAAAGGTATCAGCCCATGT 57.040 37.500 0.00 0.00 0.00 3.21
1461 1468 8.083828 AGTATATAGAAAGGTATCAGCCCATG 57.916 38.462 0.00 0.00 0.00 3.66
1462 1469 9.203163 GTAGTATATAGAAAGGTATCAGCCCAT 57.797 37.037 0.00 0.00 0.00 4.00
1463 1470 8.174757 TGTAGTATATAGAAAGGTATCAGCCCA 58.825 37.037 0.00 0.00 0.00 5.36
1464 1471 8.591114 TGTAGTATATAGAAAGGTATCAGCCC 57.409 38.462 0.00 0.00 0.00 5.19
1483 1490 8.148351 GCAAAGGAGGAATACATGTATGTAGTA 58.852 37.037 18.94 0.00 45.46 1.82
1484 1491 6.992715 GCAAAGGAGGAATACATGTATGTAGT 59.007 38.462 18.94 3.26 45.46 2.73
1485 1492 7.220030 AGCAAAGGAGGAATACATGTATGTAG 58.780 38.462 18.94 3.95 45.46 2.74
1486 1493 7.136822 AGCAAAGGAGGAATACATGTATGTA 57.863 36.000 18.94 7.14 46.21 2.29
1487 1494 6.006275 AGCAAAGGAGGAATACATGTATGT 57.994 37.500 18.94 9.29 44.48 2.29
1488 1495 6.148480 GCTAGCAAAGGAGGAATACATGTATG 59.852 42.308 18.94 6.09 0.00 2.39
1489 1496 6.234177 GCTAGCAAAGGAGGAATACATGTAT 58.766 40.000 12.75 12.75 0.00 2.29
1490 1497 5.611374 GCTAGCAAAGGAGGAATACATGTA 58.389 41.667 10.63 8.27 0.00 2.29
1491 1498 4.455606 GCTAGCAAAGGAGGAATACATGT 58.544 43.478 10.63 2.69 0.00 3.21
1492 1499 3.496130 CGCTAGCAAAGGAGGAATACATG 59.504 47.826 16.45 0.00 0.00 3.21
1493 1500 3.134804 ACGCTAGCAAAGGAGGAATACAT 59.865 43.478 16.45 0.00 0.00 2.29
1494 1501 2.500098 ACGCTAGCAAAGGAGGAATACA 59.500 45.455 16.45 0.00 0.00 2.29
1495 1502 3.180891 ACGCTAGCAAAGGAGGAATAC 57.819 47.619 16.45 0.00 0.00 1.89
1496 1503 3.321111 CCTACGCTAGCAAAGGAGGAATA 59.679 47.826 22.34 0.00 0.00 1.75
1497 1504 2.103263 CCTACGCTAGCAAAGGAGGAAT 59.897 50.000 22.34 0.00 0.00 3.01
1498 1505 1.480954 CCTACGCTAGCAAAGGAGGAA 59.519 52.381 22.34 0.00 0.00 3.36
1499 1506 1.112113 CCTACGCTAGCAAAGGAGGA 58.888 55.000 22.34 0.00 0.00 3.71
1500 1507 1.112113 TCCTACGCTAGCAAAGGAGG 58.888 55.000 24.42 18.69 33.18 4.30
1501 1508 1.751924 AGTCCTACGCTAGCAAAGGAG 59.248 52.381 27.33 13.03 38.79 3.69
1502 1509 1.749634 GAGTCCTACGCTAGCAAAGGA 59.250 52.381 24.42 24.42 35.77 3.36
1503 1510 1.751924 AGAGTCCTACGCTAGCAAAGG 59.248 52.381 21.26 21.26 0.00 3.11
1504 1511 3.119459 TGAAGAGTCCTACGCTAGCAAAG 60.119 47.826 16.45 10.79 0.00 2.77
1505 1512 2.823747 TGAAGAGTCCTACGCTAGCAAA 59.176 45.455 16.45 0.14 0.00 3.68
1506 1513 2.443416 TGAAGAGTCCTACGCTAGCAA 58.557 47.619 16.45 0.55 0.00 3.91
1507 1514 2.124277 TGAAGAGTCCTACGCTAGCA 57.876 50.000 16.45 0.00 0.00 3.49
1508 1515 3.505464 TTTGAAGAGTCCTACGCTAGC 57.495 47.619 4.06 4.06 0.00 3.42
1529 1536 3.223674 AGACATCAACCCGGAGTTTTT 57.776 42.857 0.73 0.00 36.18 1.94
1530 1537 2.951229 AGACATCAACCCGGAGTTTT 57.049 45.000 0.73 0.00 36.18 2.43
1531 1538 2.951229 AAGACATCAACCCGGAGTTT 57.049 45.000 0.73 0.00 36.18 2.66
1532 1539 2.951229 AAAGACATCAACCCGGAGTT 57.049 45.000 0.73 2.06 40.16 3.01
1533 1540 2.951229 AAAAGACATCAACCCGGAGT 57.049 45.000 0.73 0.00 0.00 3.85
1655 1662 2.180973 TGAAGCTAGGAGATCTGGGGAT 59.819 50.000 0.00 0.00 34.45 3.85
1736 1743 2.098614 TCACTGCTTGAAGGTTTTGCA 58.901 42.857 0.00 0.00 0.00 4.08
1815 1822 0.885879 TGCAAATCTCTTGCTGCTGG 59.114 50.000 10.51 0.00 45.13 4.85
1858 1865 0.460635 GTTGTCGCCCCGCTATAACA 60.461 55.000 0.00 0.00 28.99 2.41
2072 2096 4.820894 AACTCCTACCCAAGTACACATC 57.179 45.455 0.00 0.00 0.00 3.06
2262 2286 1.821216 AGGATGTCCGCGTGAAAATT 58.179 45.000 4.92 0.00 42.08 1.82
2284 2308 4.142182 GCAGATCTTACTGAGCTCTGTCTT 60.142 45.833 27.17 12.19 45.89 3.01
2335 2359 5.103771 AGTGGAATATCCCATCTGAAAAGCT 60.104 40.000 0.00 0.00 38.66 3.74


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

AutoCloner maintained by Alex Coulton.