Multiple sequence alignment - TraesCS5A01G453400

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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 TraesCS5A01G453400 chr5A 100.000 2339 0 0 1 2339 634633874 634631536 0 4320
1 TraesCS5A01G453400 chr5A 94.749 1333 69 1 35 1367 343043994 343042663 0 2073
2 TraesCS5A01G453400 chr5A 96.051 785 28 2 1555 2339 552236072 552236853 0 1275
3 TraesCS5A01G453400 chr5A 89.100 789 66 7 1551 2339 113804984 113805752 0 963
4 TraesCS5A01G453400 chr1A 97.295 1331 35 1 32 1362 260841597 260842926 0 2257
5 TraesCS5A01G453400 chr1A 94.674 1333 71 0 35 1367 277626926 277625594 0 2069
6 TraesCS5A01G453400 chr1A 96.306 785 27 2 1555 2339 571993487 571994269 0 1288
7 TraesCS5A01G453400 chr4A 96.699 1333 43 1 32 1363 438390341 438391673 0 2217
8 TraesCS5A01G453400 chr4D 95.943 1331 52 2 32 1362 126638043 126639371 0 2158
9 TraesCS5A01G453400 chr4D 94.970 1332 64 3 32 1363 463910360 463911688 0 2085
10 TraesCS5A01G453400 chr4D 88.973 789 62 7 1554 2339 488872708 488871942 0 952
11 TraesCS5A01G453400 chr3B 95.561 1329 59 0 35 1363 541062947 541061619 0 2128
12 TraesCS5A01G453400 chr5D 94.461 1336 69 4 32 1364 63606652 63607985 0 2052
13 TraesCS5A01G453400 chr5D 88.854 628 40 9 1555 2181 406945365 406944767 0 745
14 TraesCS5A01G453400 chr7A 94.175 1339 75 2 35 1371 50184248 50182911 0 2037
15 TraesCS5A01G453400 chr7A 96.178 785 28 2 1555 2339 689944316 689943534 0 1282
16 TraesCS5A01G453400 chr6A 96.433 785 26 2 1555 2339 116697826 116697044 0 1293
17 TraesCS5A01G453400 chr2A 92.611 785 28 5 1555 2339 773311615 773312369 0 1101
18 TraesCS5A01G453400 chr7D 89.327 787 61 10 1555 2339 525763821 525763056 0 966
19 TraesCS5A01G453400 chr1B 89.086 788 62 13 1552 2339 548682303 548683066 0 957
20 TraesCS5A01G453400 chr2B 87.247 792 62 12 1555 2339 80544140 80544899 0 867


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 TraesCS5A01G453400 chr5A 634631536 634633874 2338 True 4320 4320 100.000 1 2339 1 chr5A.!!$R2 2338
1 TraesCS5A01G453400 chr5A 343042663 343043994 1331 True 2073 2073 94.749 35 1367 1 chr5A.!!$R1 1332
2 TraesCS5A01G453400 chr5A 552236072 552236853 781 False 1275 1275 96.051 1555 2339 1 chr5A.!!$F2 784
3 TraesCS5A01G453400 chr5A 113804984 113805752 768 False 963 963 89.100 1551 2339 1 chr5A.!!$F1 788
4 TraesCS5A01G453400 chr1A 260841597 260842926 1329 False 2257 2257 97.295 32 1362 1 chr1A.!!$F1 1330
5 TraesCS5A01G453400 chr1A 277625594 277626926 1332 True 2069 2069 94.674 35 1367 1 chr1A.!!$R1 1332
6 TraesCS5A01G453400 chr1A 571993487 571994269 782 False 1288 1288 96.306 1555 2339 1 chr1A.!!$F2 784
7 TraesCS5A01G453400 chr4A 438390341 438391673 1332 False 2217 2217 96.699 32 1363 1 chr4A.!!$F1 1331
8 TraesCS5A01G453400 chr4D 126638043 126639371 1328 False 2158 2158 95.943 32 1362 1 chr4D.!!$F1 1330
9 TraesCS5A01G453400 chr4D 463910360 463911688 1328 False 2085 2085 94.970 32 1363 1 chr4D.!!$F2 1331
10 TraesCS5A01G453400 chr4D 488871942 488872708 766 True 952 952 88.973 1554 2339 1 chr4D.!!$R1 785
11 TraesCS5A01G453400 chr3B 541061619 541062947 1328 True 2128 2128 95.561 35 1363 1 chr3B.!!$R1 1328
12 TraesCS5A01G453400 chr5D 63606652 63607985 1333 False 2052 2052 94.461 32 1364 1 chr5D.!!$F1 1332
13 TraesCS5A01G453400 chr5D 406944767 406945365 598 True 745 745 88.854 1555 2181 1 chr5D.!!$R1 626
14 TraesCS5A01G453400 chr7A 50182911 50184248 1337 True 2037 2037 94.175 35 1371 1 chr7A.!!$R1 1336
15 TraesCS5A01G453400 chr7A 689943534 689944316 782 True 1282 1282 96.178 1555 2339 1 chr7A.!!$R2 784
16 TraesCS5A01G453400 chr6A 116697044 116697826 782 True 1293 1293 96.433 1555 2339 1 chr6A.!!$R1 784
17 TraesCS5A01G453400 chr2A 773311615 773312369 754 False 1101 1101 92.611 1555 2339 1 chr2A.!!$F1 784
18 TraesCS5A01G453400 chr7D 525763056 525763821 765 True 966 966 89.327 1555 2339 1 chr7D.!!$R1 784
19 TraesCS5A01G453400 chr1B 548682303 548683066 763 False 957 957 89.086 1552 2339 1 chr1B.!!$F1 787
20 TraesCS5A01G453400 chr2B 80544140 80544899 759 False 867 867 87.247 1555 2339 1 chr2B.!!$F1 784

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
939 942 2.750237 GGGGCGGTTTTGCGAGAT 60.75 61.111 0.0 0.0 35.06 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2098 1.41271 ACACGCCTCTTCTCTTCAACA 59.587 47.619 0.0 0.0 0.0 3.33 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
165 166 6.213600 AGGACCTGATTAGACAAACTATGTGT 59.786 38.462 0.00 0.00 44.12 3.72
330 331 9.449719 AGTAAACTAAAACACTCTAATGGGATG 57.550 33.333 0.00 0.00 0.00 3.51
520 522 2.820059 AGAAGACACGAAGCACATGA 57.180 45.000 0.00 0.00 0.00 3.07
642 644 5.093849 TGGAATACCTTTTAGTTCTCCCG 57.906 43.478 0.00 0.00 37.04 5.14
764 766 4.540824 GAAACAACTCAGAATGCAACTCC 58.459 43.478 0.00 0.00 34.76 3.85
890 893 4.508461 TGAAACTCAATGTTGATGCCTG 57.492 40.909 0.00 0.00 39.13 4.85
895 898 6.403866 AACTCAATGTTGATGCCTGTTTTA 57.596 33.333 0.00 0.00 37.52 1.52
939 942 2.750237 GGGGCGGTTTTGCGAGAT 60.750 61.111 0.00 0.00 35.06 2.75
1010 1013 2.874701 CGGATGTTCTAATGGCAGAAGG 59.125 50.000 0.00 0.00 35.25 3.46
1272 1278 8.267183 AGATTTTCTTCAACTTTGGATTGGTTT 58.733 29.630 0.00 0.00 0.00 3.27
1315 1321 2.550830 ACTCAGCCTCACAAACGATT 57.449 45.000 0.00 0.00 0.00 3.34
1389 1395 9.529325 GTAATGAAGGGGAAAACTAAATTATGC 57.471 33.333 0.00 0.00 0.00 3.14
1390 1396 7.732222 ATGAAGGGGAAAACTAAATTATGCA 57.268 32.000 0.00 0.00 0.00 3.96
1391 1397 7.169158 TGAAGGGGAAAACTAAATTATGCAG 57.831 36.000 0.00 0.00 0.00 4.41
1392 1398 6.154363 TGAAGGGGAAAACTAAATTATGCAGG 59.846 38.462 0.00 0.00 0.00 4.85
1393 1399 4.962362 AGGGGAAAACTAAATTATGCAGGG 59.038 41.667 0.00 0.00 0.00 4.45
1394 1400 4.959839 GGGGAAAACTAAATTATGCAGGGA 59.040 41.667 0.00 0.00 0.00 4.20
1395 1401 5.423931 GGGGAAAACTAAATTATGCAGGGAA 59.576 40.000 0.00 0.00 0.00 3.97
1396 1402 6.070481 GGGGAAAACTAAATTATGCAGGGAAA 60.070 38.462 0.00 0.00 0.00 3.13
1397 1403 7.390823 GGGAAAACTAAATTATGCAGGGAAAA 58.609 34.615 0.00 0.00 0.00 2.29
1398 1404 7.880713 GGGAAAACTAAATTATGCAGGGAAAAA 59.119 33.333 0.00 0.00 0.00 1.94
1399 1405 8.717821 GGAAAACTAAATTATGCAGGGAAAAAC 58.282 33.333 0.00 0.00 0.00 2.43
1400 1406 9.267084 GAAAACTAAATTATGCAGGGAAAAACA 57.733 29.630 0.00 0.00 0.00 2.83
1401 1407 9.620259 AAAACTAAATTATGCAGGGAAAAACAA 57.380 25.926 0.00 0.00 0.00 2.83
1402 1408 8.831715 AACTAAATTATGCAGGGAAAAACAAG 57.168 30.769 0.00 0.00 0.00 3.16
1403 1409 8.189119 ACTAAATTATGCAGGGAAAAACAAGA 57.811 30.769 0.00 0.00 0.00 3.02
1404 1410 8.646900 ACTAAATTATGCAGGGAAAAACAAGAA 58.353 29.630 0.00 0.00 0.00 2.52
1405 1411 9.487790 CTAAATTATGCAGGGAAAAACAAGAAA 57.512 29.630 0.00 0.00 0.00 2.52
1406 1412 8.922931 AAATTATGCAGGGAAAAACAAGAAAT 57.077 26.923 0.00 0.00 0.00 2.17
1407 1413 7.910441 ATTATGCAGGGAAAAACAAGAAATG 57.090 32.000 0.00 0.00 0.00 2.32
1408 1414 4.751767 TGCAGGGAAAAACAAGAAATGT 57.248 36.364 0.00 0.00 46.82 2.71
1422 1428 7.042797 ACAAGAAATGTTTCATTACAGCAGT 57.957 32.000 8.09 0.00 40.06 4.40
1423 1429 8.165239 ACAAGAAATGTTTCATTACAGCAGTA 57.835 30.769 8.09 0.00 40.06 2.74
1424 1430 8.796475 ACAAGAAATGTTTCATTACAGCAGTAT 58.204 29.630 8.09 0.00 40.06 2.12
1425 1431 9.069078 CAAGAAATGTTTCATTACAGCAGTATG 57.931 33.333 8.09 0.00 39.61 2.39
1426 1432 8.340618 AGAAATGTTTCATTACAGCAGTATGT 57.659 30.769 8.09 0.00 39.61 2.29
1427 1433 8.796475 AGAAATGTTTCATTACAGCAGTATGTT 58.204 29.630 8.09 0.00 39.61 2.71
1428 1434 8.970691 AAATGTTTCATTACAGCAGTATGTTC 57.029 30.769 0.00 0.00 39.31 3.18
1429 1435 7.686438 ATGTTTCATTACAGCAGTATGTTCA 57.314 32.000 0.00 0.00 39.31 3.18
1430 1436 7.686438 TGTTTCATTACAGCAGTATGTTCAT 57.314 32.000 0.00 0.00 39.31 2.57
1431 1437 7.529158 TGTTTCATTACAGCAGTATGTTCATG 58.471 34.615 0.00 0.00 39.31 3.07
1432 1438 7.174772 TGTTTCATTACAGCAGTATGTTCATGT 59.825 33.333 0.00 0.00 39.31 3.21
1433 1439 7.686438 TTCATTACAGCAGTATGTTCATGTT 57.314 32.000 0.00 0.00 39.31 2.71
1434 1440 7.075674 TCATTACAGCAGTATGTTCATGTTG 57.924 36.000 0.00 0.00 39.31 3.33
1435 1441 6.654582 TCATTACAGCAGTATGTTCATGTTGT 59.345 34.615 0.00 0.00 40.72 3.32
1436 1442 7.821846 TCATTACAGCAGTATGTTCATGTTGTA 59.178 33.333 0.00 0.00 38.91 2.41
1437 1443 7.971183 TTACAGCAGTATGTTCATGTTGTAA 57.029 32.000 8.99 8.99 43.63 2.41
1438 1444 6.875948 ACAGCAGTATGTTCATGTTGTAAA 57.124 33.333 0.00 0.00 36.74 2.01
1439 1445 6.668323 ACAGCAGTATGTTCATGTTGTAAAC 58.332 36.000 0.00 0.00 43.64 2.01
1483 1489 9.685828 TTGTAAACGAATCAGGAAATAAAAAGG 57.314 29.630 0.00 0.00 0.00 3.11
1484 1490 8.301002 TGTAAACGAATCAGGAAATAAAAAGGG 58.699 33.333 0.00 0.00 0.00 3.95
1485 1491 7.533289 AAACGAATCAGGAAATAAAAAGGGA 57.467 32.000 0.00 0.00 0.00 4.20
1486 1492 7.533289 AACGAATCAGGAAATAAAAAGGGAA 57.467 32.000 0.00 0.00 0.00 3.97
1487 1493 7.158099 ACGAATCAGGAAATAAAAAGGGAAG 57.842 36.000 0.00 0.00 0.00 3.46
1488 1494 6.946009 ACGAATCAGGAAATAAAAAGGGAAGA 59.054 34.615 0.00 0.00 0.00 2.87
1489 1495 7.450323 ACGAATCAGGAAATAAAAAGGGAAGAA 59.550 33.333 0.00 0.00 0.00 2.52
1490 1496 8.470002 CGAATCAGGAAATAAAAAGGGAAGAAT 58.530 33.333 0.00 0.00 0.00 2.40
1491 1497 9.809096 GAATCAGGAAATAAAAAGGGAAGAATC 57.191 33.333 0.00 0.00 0.00 2.52
1492 1498 8.899887 ATCAGGAAATAAAAAGGGAAGAATCA 57.100 30.769 0.00 0.00 0.00 2.57
1493 1499 8.899887 TCAGGAAATAAAAAGGGAAGAATCAT 57.100 30.769 0.00 0.00 0.00 2.45
1494 1500 8.752187 TCAGGAAATAAAAAGGGAAGAATCATG 58.248 33.333 0.00 0.00 0.00 3.07
1495 1501 8.534496 CAGGAAATAAAAAGGGAAGAATCATGT 58.466 33.333 0.00 0.00 0.00 3.21
1496 1502 8.534496 AGGAAATAAAAAGGGAAGAATCATGTG 58.466 33.333 0.00 0.00 0.00 3.21
1497 1503 8.314021 GGAAATAAAAAGGGAAGAATCATGTGT 58.686 33.333 0.00 0.00 0.00 3.72
1500 1506 9.533831 AATAAAAAGGGAAGAATCATGTGTACT 57.466 29.630 0.00 0.00 0.00 2.73
1501 1507 7.454260 AAAAAGGGAAGAATCATGTGTACTC 57.546 36.000 0.00 0.00 0.00 2.59
1502 1508 5.762179 AAGGGAAGAATCATGTGTACTCA 57.238 39.130 0.00 0.00 0.00 3.41
1503 1509 5.762179 AGGGAAGAATCATGTGTACTCAA 57.238 39.130 1.11 0.00 0.00 3.02
1504 1510 6.126863 AGGGAAGAATCATGTGTACTCAAA 57.873 37.500 1.11 0.00 0.00 2.69
1505 1511 6.725364 AGGGAAGAATCATGTGTACTCAAAT 58.275 36.000 1.11 0.00 0.00 2.32
1506 1512 7.177878 AGGGAAGAATCATGTGTACTCAAATT 58.822 34.615 1.11 5.36 0.00 1.82
1507 1513 7.671398 AGGGAAGAATCATGTGTACTCAAATTT 59.329 33.333 1.11 0.00 0.00 1.82
1508 1514 7.970614 GGGAAGAATCATGTGTACTCAAATTTC 59.029 37.037 1.11 5.60 0.00 2.17
1509 1515 8.734386 GGAAGAATCATGTGTACTCAAATTTCT 58.266 33.333 1.11 7.51 0.00 2.52
1510 1516 9.766277 GAAGAATCATGTGTACTCAAATTTCTC 57.234 33.333 14.56 9.34 0.00 2.87
1511 1517 8.273780 AGAATCATGTGTACTCAAATTTCTCC 57.726 34.615 1.11 0.00 0.00 3.71
1512 1518 7.884877 AGAATCATGTGTACTCAAATTTCTCCA 59.115 33.333 1.11 0.00 0.00 3.86
1513 1519 8.408043 AATCATGTGTACTCAAATTTCTCCAA 57.592 30.769 1.11 0.00 0.00 3.53
1514 1520 7.202016 TCATGTGTACTCAAATTTCTCCAAC 57.798 36.000 1.11 0.00 0.00 3.77
1515 1521 6.770303 TCATGTGTACTCAAATTTCTCCAACA 59.230 34.615 1.11 0.00 0.00 3.33
1516 1522 6.371809 TGTGTACTCAAATTTCTCCAACAC 57.628 37.500 10.92 10.92 36.21 3.32
1517 1523 5.883115 TGTGTACTCAAATTTCTCCAACACA 59.117 36.000 14.34 14.34 41.52 3.72
1518 1524 6.545666 TGTGTACTCAAATTTCTCCAACACAT 59.454 34.615 14.34 0.00 39.60 3.21
1519 1525 6.857964 GTGTACTCAAATTTCTCCAACACATG 59.142 38.462 12.16 0.00 35.83 3.21
1530 1536 2.679450 CCAACACATGGCATCAAAGTG 58.321 47.619 12.56 12.56 43.80 3.16
1531 1537 2.063266 CAACACATGGCATCAAAGTGC 58.937 47.619 13.71 0.00 44.31 4.40
1538 1544 3.389741 GCATCAAAGTGCCTCGTTG 57.610 52.632 0.00 0.00 39.18 4.10
1539 1545 0.874390 GCATCAAAGTGCCTCGTTGA 59.126 50.000 8.97 8.97 45.28 3.18
1540 1546 1.135859 GCATCAAAGTGCCTCGTTGAG 60.136 52.381 11.30 6.62 44.67 3.02
1887 1902 3.438183 GACCTCACTGTCCTAACCCTAA 58.562 50.000 0.00 0.00 0.00 2.69
1905 1920 2.198827 AACCGTCTTCATTCATGGCA 57.801 45.000 0.00 0.00 0.00 4.92
1912 1927 3.204119 CATTCATGGCAGCGGCGA 61.204 61.111 12.98 0.00 42.47 5.54
2048 2064 0.779997 AACCAATCCCAGCCTCAACT 59.220 50.000 0.00 0.00 0.00 3.16
2081 2097 0.602638 ACGATTGTGAAGAGGCGCAA 60.603 50.000 10.83 0.00 41.85 4.85
2195 2214 7.749666 AGGTATGGCAACTGATCTATAATTGT 58.250 34.615 0.00 0.00 37.61 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.208903 GCTTCCCCTTCATTACTTATTAGTACA 58.791 37.037 0.00 0.00 36.61 2.90
10 11 8.208903 TGCTTCCCCTTCATTACTTATTAGTAC 58.791 37.037 0.00 0.00 36.61 2.73
11 12 8.326765 TGCTTCCCCTTCATTACTTATTAGTA 57.673 34.615 0.00 0.00 35.78 1.82
12 13 7.208064 TGCTTCCCCTTCATTACTTATTAGT 57.792 36.000 0.00 0.00 38.44 2.24
13 14 7.175641 CCATGCTTCCCCTTCATTACTTATTAG 59.824 40.741 0.00 0.00 0.00 1.73
14 15 7.004086 CCATGCTTCCCCTTCATTACTTATTA 58.996 38.462 0.00 0.00 0.00 0.98
15 16 5.835280 CCATGCTTCCCCTTCATTACTTATT 59.165 40.000 0.00 0.00 0.00 1.40
16 17 5.134339 TCCATGCTTCCCCTTCATTACTTAT 59.866 40.000 0.00 0.00 0.00 1.73
17 18 4.476846 TCCATGCTTCCCCTTCATTACTTA 59.523 41.667 0.00 0.00 0.00 2.24
18 19 3.269381 TCCATGCTTCCCCTTCATTACTT 59.731 43.478 0.00 0.00 0.00 2.24
19 20 2.852449 TCCATGCTTCCCCTTCATTACT 59.148 45.455 0.00 0.00 0.00 2.24
20 21 3.297134 TCCATGCTTCCCCTTCATTAC 57.703 47.619 0.00 0.00 0.00 1.89
21 22 3.181429 GGATCCATGCTTCCCCTTCATTA 60.181 47.826 6.95 0.00 0.00 1.90
22 23 2.425392 GGATCCATGCTTCCCCTTCATT 60.425 50.000 6.95 0.00 0.00 2.57
23 24 1.146566 GGATCCATGCTTCCCCTTCAT 59.853 52.381 6.95 0.00 0.00 2.57
24 25 0.552848 GGATCCATGCTTCCCCTTCA 59.447 55.000 6.95 0.00 0.00 3.02
25 26 0.178978 GGGATCCATGCTTCCCCTTC 60.179 60.000 15.23 0.00 45.08 3.46
26 27 1.933629 GGGATCCATGCTTCCCCTT 59.066 57.895 15.23 0.00 45.08 3.95
27 28 3.679755 GGGATCCATGCTTCCCCT 58.320 61.111 15.23 0.00 45.08 4.79
30 31 2.767960 ACAATTTGGGATCCATGCTTCC 59.232 45.455 15.23 4.05 31.53 3.46
31 32 3.788937 CACAATTTGGGATCCATGCTTC 58.211 45.455 15.23 0.00 31.53 3.86
32 33 2.093341 GCACAATTTGGGATCCATGCTT 60.093 45.455 15.23 0.00 33.35 3.91
33 34 1.483415 GCACAATTTGGGATCCATGCT 59.517 47.619 15.23 0.00 33.35 3.79
165 166 4.277239 CGTTGAGCGTCAATGGGA 57.723 55.556 10.35 0.00 39.16 4.37
330 331 0.327259 GGTTAGGTGTGGTTCTCCCC 59.673 60.000 0.00 0.00 0.00 4.81
520 522 9.178758 CTCCTTTGCTTTAGTACATAGGAAAAT 57.821 33.333 0.00 0.00 41.53 1.82
642 644 5.106157 CCCCATAATACGCAAATCTTGATCC 60.106 44.000 0.00 0.00 0.00 3.36
764 766 4.384056 GGCTATGATCCCCATTGATATCG 58.616 47.826 0.00 0.00 36.71 2.92
890 893 5.508994 CCCTTCAACATGTCCTGGTTAAAAC 60.509 44.000 0.00 0.00 0.00 2.43
895 898 1.499007 ACCCTTCAACATGTCCTGGTT 59.501 47.619 0.00 0.00 0.00 3.67
939 942 4.764823 CCTGCAATAAACCTACCTTTGTCA 59.235 41.667 0.00 0.00 0.00 3.58
1010 1013 7.328493 GTGTTAGTCCAAATTTGATGGCTAAAC 59.672 37.037 19.86 14.88 37.81 2.01
1018 1021 6.714810 TGTGCTAGTGTTAGTCCAAATTTGAT 59.285 34.615 19.86 7.63 0.00 2.57
1140 1146 4.832248 AGTGGAAGCAGTCATCGAAAATA 58.168 39.130 0.00 0.00 0.00 1.40
1272 1278 8.328758 AGTACAATTTCATTGATAGGTTCCTCA 58.671 33.333 3.47 0.00 42.83 3.86
1367 1373 6.154363 CCTGCATAATTTAGTTTTCCCCTTCA 59.846 38.462 0.00 0.00 0.00 3.02
1368 1374 6.406961 CCCTGCATAATTTAGTTTTCCCCTTC 60.407 42.308 0.00 0.00 0.00 3.46
1369 1375 5.425217 CCCTGCATAATTTAGTTTTCCCCTT 59.575 40.000 0.00 0.00 0.00 3.95
1370 1376 4.962362 CCCTGCATAATTTAGTTTTCCCCT 59.038 41.667 0.00 0.00 0.00 4.79
1371 1377 4.959839 TCCCTGCATAATTTAGTTTTCCCC 59.040 41.667 0.00 0.00 0.00 4.81
1372 1378 6.538945 TTCCCTGCATAATTTAGTTTTCCC 57.461 37.500 0.00 0.00 0.00 3.97
1373 1379 8.717821 GTTTTTCCCTGCATAATTTAGTTTTCC 58.282 33.333 0.00 0.00 0.00 3.13
1374 1380 9.267084 TGTTTTTCCCTGCATAATTTAGTTTTC 57.733 29.630 0.00 0.00 0.00 2.29
1375 1381 9.620259 TTGTTTTTCCCTGCATAATTTAGTTTT 57.380 25.926 0.00 0.00 0.00 2.43
1376 1382 9.271828 CTTGTTTTTCCCTGCATAATTTAGTTT 57.728 29.630 0.00 0.00 0.00 2.66
1377 1383 8.646900 TCTTGTTTTTCCCTGCATAATTTAGTT 58.353 29.630 0.00 0.00 0.00 2.24
1378 1384 8.189119 TCTTGTTTTTCCCTGCATAATTTAGT 57.811 30.769 0.00 0.00 0.00 2.24
1379 1385 9.487790 TTTCTTGTTTTTCCCTGCATAATTTAG 57.512 29.630 0.00 0.00 0.00 1.85
1381 1387 8.785946 CATTTCTTGTTTTTCCCTGCATAATTT 58.214 29.630 0.00 0.00 0.00 1.82
1382 1388 7.938490 ACATTTCTTGTTTTTCCCTGCATAATT 59.062 29.630 0.00 0.00 33.74 1.40
1383 1389 7.452562 ACATTTCTTGTTTTTCCCTGCATAAT 58.547 30.769 0.00 0.00 33.74 1.28
1384 1390 6.825610 ACATTTCTTGTTTTTCCCTGCATAA 58.174 32.000 0.00 0.00 33.74 1.90
1385 1391 6.418057 ACATTTCTTGTTTTTCCCTGCATA 57.582 33.333 0.00 0.00 33.74 3.14
1386 1392 5.294734 ACATTTCTTGTTTTTCCCTGCAT 57.705 34.783 0.00 0.00 33.74 3.96
1387 1393 4.751767 ACATTTCTTGTTTTTCCCTGCA 57.248 36.364 0.00 0.00 33.74 4.41
1398 1404 7.042797 ACTGCTGTAATGAAACATTTCTTGT 57.957 32.000 5.97 0.00 41.53 3.16
1399 1405 9.069078 CATACTGCTGTAATGAAACATTTCTTG 57.931 33.333 7.59 0.00 33.90 3.02
1400 1406 8.796475 ACATACTGCTGTAATGAAACATTTCTT 58.204 29.630 7.59 0.00 33.90 2.52
1401 1407 8.340618 ACATACTGCTGTAATGAAACATTTCT 57.659 30.769 7.59 0.00 33.90 2.52
1402 1408 8.970691 AACATACTGCTGTAATGAAACATTTC 57.029 30.769 7.59 0.00 33.62 2.17
1403 1409 8.575589 TGAACATACTGCTGTAATGAAACATTT 58.424 29.630 7.59 0.00 31.80 2.32
1404 1410 8.109705 TGAACATACTGCTGTAATGAAACATT 57.890 30.769 7.59 0.00 31.80 2.71
1405 1411 7.686438 TGAACATACTGCTGTAATGAAACAT 57.314 32.000 7.59 0.00 31.80 2.71
1406 1412 7.174772 ACATGAACATACTGCTGTAATGAAACA 59.825 33.333 15.28 9.03 32.09 2.83
1407 1413 7.530010 ACATGAACATACTGCTGTAATGAAAC 58.470 34.615 15.28 4.99 32.09 2.78
1408 1414 7.686438 ACATGAACATACTGCTGTAATGAAA 57.314 32.000 15.28 1.90 32.09 2.69
1409 1415 7.174772 ACAACATGAACATACTGCTGTAATGAA 59.825 33.333 15.28 1.06 32.09 2.57
1410 1416 6.654582 ACAACATGAACATACTGCTGTAATGA 59.345 34.615 15.28 0.00 32.09 2.57
1411 1417 6.845302 ACAACATGAACATACTGCTGTAATG 58.155 36.000 7.59 8.76 33.10 1.90
1412 1418 8.560355 TTACAACATGAACATACTGCTGTAAT 57.440 30.769 7.59 0.00 31.80 1.89
1413 1419 7.971183 TTACAACATGAACATACTGCTGTAA 57.029 32.000 7.59 0.00 31.80 2.41
1414 1420 7.442666 TGTTTACAACATGAACATACTGCTGTA 59.557 33.333 5.87 5.87 36.25 2.74
1415 1421 6.262049 TGTTTACAACATGAACATACTGCTGT 59.738 34.615 0.00 0.66 36.25 4.40
1416 1422 6.667370 TGTTTACAACATGAACATACTGCTG 58.333 36.000 0.00 0.00 36.25 4.41
1417 1423 6.875948 TGTTTACAACATGAACATACTGCT 57.124 33.333 0.00 0.00 36.25 4.24
1418 1424 7.922505 TTTGTTTACAACATGAACATACTGC 57.077 32.000 0.00 0.00 41.79 4.40
1423 1429 8.865090 TCCCTAATTTGTTTACAACATGAACAT 58.135 29.630 0.00 0.00 41.79 2.71
1424 1430 8.239038 TCCCTAATTTGTTTACAACATGAACA 57.761 30.769 0.00 0.00 41.79 3.18
1425 1431 9.535878 TTTCCCTAATTTGTTTACAACATGAAC 57.464 29.630 0.00 0.00 41.79 3.18
1450 1456 6.702716 TCCTGATTCGTTTACAACCTTTTT 57.297 33.333 0.00 0.00 0.00 1.94
1451 1457 6.702716 TTCCTGATTCGTTTACAACCTTTT 57.297 33.333 0.00 0.00 0.00 2.27
1452 1458 6.702716 TTTCCTGATTCGTTTACAACCTTT 57.297 33.333 0.00 0.00 0.00 3.11
1453 1459 6.894339 ATTTCCTGATTCGTTTACAACCTT 57.106 33.333 0.00 0.00 0.00 3.50
1454 1460 7.989416 TTATTTCCTGATTCGTTTACAACCT 57.011 32.000 0.00 0.00 0.00 3.50
1455 1461 9.465985 TTTTTATTTCCTGATTCGTTTACAACC 57.534 29.630 0.00 0.00 0.00 3.77
1457 1463 9.685828 CCTTTTTATTTCCTGATTCGTTTACAA 57.314 29.630 0.00 0.00 0.00 2.41
1458 1464 8.301002 CCCTTTTTATTTCCTGATTCGTTTACA 58.699 33.333 0.00 0.00 0.00 2.41
1459 1465 8.517056 TCCCTTTTTATTTCCTGATTCGTTTAC 58.483 33.333 0.00 0.00 0.00 2.01
1460 1466 8.638629 TCCCTTTTTATTTCCTGATTCGTTTA 57.361 30.769 0.00 0.00 0.00 2.01
1461 1467 7.533289 TCCCTTTTTATTTCCTGATTCGTTT 57.467 32.000 0.00 0.00 0.00 3.60
1462 1468 7.450323 TCTTCCCTTTTTATTTCCTGATTCGTT 59.550 33.333 0.00 0.00 0.00 3.85
1463 1469 6.946009 TCTTCCCTTTTTATTTCCTGATTCGT 59.054 34.615 0.00 0.00 0.00 3.85
1464 1470 7.391148 TCTTCCCTTTTTATTTCCTGATTCG 57.609 36.000 0.00 0.00 0.00 3.34
1465 1471 9.809096 GATTCTTCCCTTTTTATTTCCTGATTC 57.191 33.333 0.00 0.00 0.00 2.52
1466 1472 9.325248 TGATTCTTCCCTTTTTATTTCCTGATT 57.675 29.630 0.00 0.00 0.00 2.57
1467 1473 8.899887 TGATTCTTCCCTTTTTATTTCCTGAT 57.100 30.769 0.00 0.00 0.00 2.90
1468 1474 8.752187 CATGATTCTTCCCTTTTTATTTCCTGA 58.248 33.333 0.00 0.00 0.00 3.86
1469 1475 8.534496 ACATGATTCTTCCCTTTTTATTTCCTG 58.466 33.333 0.00 0.00 0.00 3.86
1470 1476 8.534496 CACATGATTCTTCCCTTTTTATTTCCT 58.466 33.333 0.00 0.00 0.00 3.36
1471 1477 8.314021 ACACATGATTCTTCCCTTTTTATTTCC 58.686 33.333 0.00 0.00 0.00 3.13
1474 1480 9.533831 AGTACACATGATTCTTCCCTTTTTATT 57.466 29.630 0.00 0.00 0.00 1.40
1475 1481 9.178758 GAGTACACATGATTCTTCCCTTTTTAT 57.821 33.333 0.00 0.00 0.00 1.40
1476 1482 8.160765 TGAGTACACATGATTCTTCCCTTTTTA 58.839 33.333 0.00 0.00 0.00 1.52
1477 1483 7.004086 TGAGTACACATGATTCTTCCCTTTTT 58.996 34.615 0.00 0.00 0.00 1.94
1478 1484 6.542821 TGAGTACACATGATTCTTCCCTTTT 58.457 36.000 0.00 0.00 0.00 2.27
1479 1485 6.126863 TGAGTACACATGATTCTTCCCTTT 57.873 37.500 0.00 0.00 0.00 3.11
1480 1486 5.762179 TGAGTACACATGATTCTTCCCTT 57.238 39.130 0.00 0.00 0.00 3.95
1481 1487 5.762179 TTGAGTACACATGATTCTTCCCT 57.238 39.130 0.00 0.00 0.00 4.20
1482 1488 7.396540 AATTTGAGTACACATGATTCTTCCC 57.603 36.000 0.00 0.00 0.00 3.97
1483 1489 8.734386 AGAAATTTGAGTACACATGATTCTTCC 58.266 33.333 0.00 0.00 0.00 3.46
1484 1490 9.766277 GAGAAATTTGAGTACACATGATTCTTC 57.234 33.333 0.00 5.60 0.00 2.87
1485 1491 8.734386 GGAGAAATTTGAGTACACATGATTCTT 58.266 33.333 0.00 3.21 0.00 2.52
1486 1492 7.884877 TGGAGAAATTTGAGTACACATGATTCT 59.115 33.333 0.00 11.78 0.00 2.40
1487 1493 8.044060 TGGAGAAATTTGAGTACACATGATTC 57.956 34.615 0.00 0.59 0.00 2.52
1488 1494 8.299570 GTTGGAGAAATTTGAGTACACATGATT 58.700 33.333 0.00 0.00 0.00 2.57
1489 1495 7.448161 TGTTGGAGAAATTTGAGTACACATGAT 59.552 33.333 0.00 0.00 0.00 2.45
1490 1496 6.770303 TGTTGGAGAAATTTGAGTACACATGA 59.230 34.615 0.00 0.00 0.00 3.07
1491 1497 6.857964 GTGTTGGAGAAATTTGAGTACACATG 59.142 38.462 0.00 0.00 34.91 3.21
1492 1498 6.545666 TGTGTTGGAGAAATTTGAGTACACAT 59.454 34.615 14.08 0.00 38.59 3.21
1493 1499 5.883115 TGTGTTGGAGAAATTTGAGTACACA 59.117 36.000 14.08 14.08 40.46 3.72
1494 1500 6.371809 TGTGTTGGAGAAATTTGAGTACAC 57.628 37.500 0.00 4.58 35.25 2.90
1495 1501 6.969366 CATGTGTTGGAGAAATTTGAGTACA 58.031 36.000 0.00 0.00 0.00 2.90
1511 1517 2.063266 GCACTTTGATGCCATGTGTTG 58.937 47.619 0.00 0.00 39.86 3.33
1512 1518 2.443887 GCACTTTGATGCCATGTGTT 57.556 45.000 0.00 0.00 39.86 3.32
1520 1526 0.874390 TCAACGAGGCACTTTGATGC 59.126 50.000 0.00 0.00 41.55 3.91
1521 1527 1.466167 CCTCAACGAGGCACTTTGATG 59.534 52.381 4.47 0.00 43.29 3.07
1522 1528 1.813513 CCTCAACGAGGCACTTTGAT 58.186 50.000 4.47 0.00 43.29 2.57
1523 1529 3.305709 CCTCAACGAGGCACTTTGA 57.694 52.632 4.02 4.02 43.29 2.69
1535 1541 3.246619 CTCGTCTAGAAGTTGCCTCAAC 58.753 50.000 5.55 1.71 43.83 3.18
1536 1542 2.891580 ACTCGTCTAGAAGTTGCCTCAA 59.108 45.455 5.55 0.00 0.00 3.02
1537 1543 2.515854 ACTCGTCTAGAAGTTGCCTCA 58.484 47.619 5.55 0.00 0.00 3.86
1538 1544 4.698583 TTACTCGTCTAGAAGTTGCCTC 57.301 45.455 5.55 0.00 0.00 4.70
1539 1545 5.185249 TCAATTACTCGTCTAGAAGTTGCCT 59.815 40.000 5.55 0.00 0.00 4.75
1540 1546 5.288952 GTCAATTACTCGTCTAGAAGTTGCC 59.711 44.000 5.55 0.00 0.00 4.52
1541 1547 5.862323 TGTCAATTACTCGTCTAGAAGTTGC 59.138 40.000 5.55 1.23 0.00 4.17
1542 1548 7.869016 TTGTCAATTACTCGTCTAGAAGTTG 57.131 36.000 5.55 3.11 0.00 3.16
1543 1549 8.882415 TTTTGTCAATTACTCGTCTAGAAGTT 57.118 30.769 5.55 0.00 0.00 2.66
1544 1550 8.882415 TTTTTGTCAATTACTCGTCTAGAAGT 57.118 30.769 5.55 4.06 0.00 3.01
1591 1598 4.657814 AAATGTGGTAGTTCTGTGGGAT 57.342 40.909 0.00 0.00 0.00 3.85
1887 1902 1.742761 CTGCCATGAATGAAGACGGT 58.257 50.000 0.00 0.00 0.00 4.83
1905 1920 1.745489 GGAGTTTGGATTCGCCGCT 60.745 57.895 0.00 0.00 40.66 5.52
1912 1927 2.750237 GGCGCCGGAGTTTGGATT 60.750 61.111 12.58 0.00 0.00 3.01
2081 2097 2.037772 ACACGCCTCTTCTCTTCAACAT 59.962 45.455 0.00 0.00 0.00 2.71
2082 2098 1.412710 ACACGCCTCTTCTCTTCAACA 59.587 47.619 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.