Multiple sequence alignment - TraesCS1B01G293200

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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 TraesCS1B01G293200 chr1B 100.000 2318 0 0 1 2318 510814669 510812352 0.000000e+00 4281
1 TraesCS1B01G293200 chr1B 91.085 1346 115 3 1 1345 533811581 533812922 0.000000e+00 1816
2 TraesCS1B01G293200 chr1B 84.861 469 66 2 1850 2318 673724284 673723821 3.490000e-128 468
3 TraesCS1B01G293200 chr1B 82.957 487 67 12 1844 2318 44373168 44373650 2.130000e-115 425
4 TraesCS1B01G293200 chr1B 92.771 83 6 0 1344 1426 7601737 7601655 1.120000e-23 121
5 TraesCS1B01G293200 chr2B 96.208 1345 46 3 1 1345 751294000 751292661 0.000000e+00 2196
6 TraesCS1B01G293200 chr2B 86.840 1345 171 5 1 1344 115905323 115903984 0.000000e+00 1498
7 TraesCS1B01G293200 chr2B 90.976 410 33 4 1432 1838 657718148 657718556 1.210000e-152 549
8 TraesCS1B01G293200 chr2B 84.282 439 57 8 1844 2272 88852202 88852638 3.560000e-113 418
9 TraesCS1B01G293200 chr2B 83.982 437 61 5 1845 2272 88907250 88907686 5.960000e-111 411
10 TraesCS1B01G293200 chr7B 95.985 1345 50 2 1 1344 74304274 74302933 0.000000e+00 2182
11 TraesCS1B01G293200 chr7B 81.481 459 74 6 1845 2293 5192372 5192829 1.310000e-97 366
12 TraesCS1B01G293200 chr5B 90.970 1351 112 5 1 1345 281242805 281244151 0.000000e+00 1810
13 TraesCS1B01G293200 chr5B 82.446 507 57 14 1844 2318 639096286 639095780 4.610000e-112 414
14 TraesCS1B01G293200 chr5B 91.765 85 6 1 1344 1428 377146084 377146167 1.460000e-22 117
15 TraesCS1B01G293200 chr6A 89.211 1344 139 3 1 1344 511536379 511537716 0.000000e+00 1674
16 TraesCS1B01G293200 chr6A 88.914 1344 143 3 1 1344 97342666 97341329 0.000000e+00 1652
17 TraesCS1B01G293200 chr6A 81.042 480 69 8 1844 2303 435311271 435311748 1.690000e-96 363
18 TraesCS1B01G293200 chr6B 88.856 1346 141 6 1 1345 478884224 478882887 0.000000e+00 1646
19 TraesCS1B01G293200 chr6B 89.947 378 26 7 1432 1805 554025466 554025097 5.790000e-131 477
20 TraesCS1B01G293200 chr6B 92.941 85 6 0 1344 1428 18484103 18484019 8.700000e-25 124
21 TraesCS1B01G293200 chr4A 88.559 1346 145 5 1 1343 494000391 494001730 0.000000e+00 1624
22 TraesCS1B01G293200 chr4A 95.294 85 4 0 1344 1428 614007604 614007688 4.020000e-28 135
23 TraesCS1B01G293200 chr7A 91.768 413 31 3 1432 1842 712973847 712974258 2.580000e-159 571
24 TraesCS1B01G293200 chr7A 87.055 309 40 0 1844 2152 473013309 473013001 1.320000e-92 350
25 TraesCS1B01G293200 chr2D 86.105 475 66 0 1844 2318 56115677 56116151 1.590000e-141 512
26 TraesCS1B01G293200 chr6D 87.327 434 46 4 1894 2318 400551945 400551512 2.680000e-134 488
27 TraesCS1B01G293200 chr3D 82.609 506 55 17 1844 2318 354265471 354265974 1.280000e-112 416
28 TraesCS1B01G293200 chr5D 86.427 361 22 8 1503 1842 473048060 473047706 1.010000e-98 370
29 TraesCS1B01G293200 chr5D 86.196 326 17 10 1503 1807 510490192 510490510 6.180000e-86 327
30 TraesCS1B01G293200 chr5D 90.058 171 17 0 2148 2318 329621263 329621433 3.000000e-54 222
31 TraesCS1B01G293200 chr5D 91.463 82 7 0 1347 1428 473048218 473048137 1.880000e-21 113
32 TraesCS1B01G293200 chr7D 85.873 361 23 9 1503 1842 602284053 602283700 2.190000e-95 359
33 TraesCS1B01G293200 chr7D 85.596 361 24 9 1503 1842 602279782 602279429 1.020000e-93 353
34 TraesCS1B01G293200 chr4D 85.873 361 23 9 1503 1842 468417067 468417420 2.190000e-95 359
35 TraesCS1B01G293200 chr2A 87.031 293 22 7 1503 1792 109602018 109602297 1.340000e-82 316
36 TraesCS1B01G293200 chr2A 95.294 85 4 0 1344 1428 705761286 705761202 4.020000e-28 135
37 TraesCS1B01G293200 chrUn 91.765 85 7 0 1344 1428 425671146 425671062 4.050000e-23 119
38 TraesCS1B01G293200 chrUn 90.588 85 7 1 1344 1428 344692110 344692193 6.770000e-21 111
39 TraesCS1B01G293200 chr5A 91.860 86 6 1 1344 1428 688289119 688289204 4.050000e-23 119


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 TraesCS1B01G293200 chr1B 510812352 510814669 2317 True 4281.0 4281 100.0000 1 2318 1 chr1B.!!$R2 2317
1 TraesCS1B01G293200 chr1B 533811581 533812922 1341 False 1816.0 1816 91.0850 1 1345 1 chr1B.!!$F2 1344
2 TraesCS1B01G293200 chr2B 751292661 751294000 1339 True 2196.0 2196 96.2080 1 1345 1 chr2B.!!$R2 1344
3 TraesCS1B01G293200 chr2B 115903984 115905323 1339 True 1498.0 1498 86.8400 1 1344 1 chr2B.!!$R1 1343
4 TraesCS1B01G293200 chr7B 74302933 74304274 1341 True 2182.0 2182 95.9850 1 1344 1 chr7B.!!$R1 1343
5 TraesCS1B01G293200 chr5B 281242805 281244151 1346 False 1810.0 1810 90.9700 1 1345 1 chr5B.!!$F1 1344
6 TraesCS1B01G293200 chr5B 639095780 639096286 506 True 414.0 414 82.4460 1844 2318 1 chr5B.!!$R1 474
7 TraesCS1B01G293200 chr6A 511536379 511537716 1337 False 1674.0 1674 89.2110 1 1344 1 chr6A.!!$F2 1343
8 TraesCS1B01G293200 chr6A 97341329 97342666 1337 True 1652.0 1652 88.9140 1 1344 1 chr6A.!!$R1 1343
9 TraesCS1B01G293200 chr6B 478882887 478884224 1337 True 1646.0 1646 88.8560 1 1345 1 chr6B.!!$R2 1344
10 TraesCS1B01G293200 chr4A 494000391 494001730 1339 False 1624.0 1624 88.5590 1 1343 1 chr4A.!!$F1 1342
11 TraesCS1B01G293200 chr3D 354265471 354265974 503 False 416.0 416 82.6090 1844 2318 1 chr3D.!!$F1 474
12 TraesCS1B01G293200 chr5D 473047706 473048218 512 True 241.5 370 88.9450 1347 1842 2 chr5D.!!$R1 495
13 TraesCS1B01G293200 chr7D 602279429 602284053 4624 True 356.0 359 85.7345 1503 1842 2 chr7D.!!$R1 339

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
495 498 0.179062 ATGCACGAAGCCTCTGGATC 60.179 55.0 0.0 0.0 44.83 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1495 0.031857 AGCGATGCTTCATCTCTCGG 59.968 55.0 5.42 0.0 38.59 4.63 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
73 74 0.243365 TTTGGATGACAATGGCGCAC 59.757 50.000 10.83 0.00 39.21 5.34
195 196 0.768997 TTCCGGAAAAGAGTGGGGGA 60.769 55.000 16.28 0.00 0.00 4.81
211 212 1.003233 GGGGATTCACGGTGAGAAGTT 59.997 52.381 11.14 0.00 0.00 2.66
234 235 7.495934 AGTTCATACAAACTGGCTACATATGAC 59.504 37.037 10.38 0.00 38.06 3.06
253 254 8.892723 CATATGACCATAATGTTATTACGGCAT 58.107 33.333 0.00 0.00 0.00 4.40
255 256 7.899178 TGACCATAATGTTATTACGGCATAG 57.101 36.000 0.00 0.00 0.00 2.23
351 352 1.753930 TGAAGATCAATGCATGGCGT 58.246 45.000 0.00 0.00 0.00 5.68
424 425 2.356313 CGCGCTCAACCTGTCAGT 60.356 61.111 5.56 0.00 0.00 3.41
447 448 0.621862 GTGGGTTGGAGGAGGAGGAT 60.622 60.000 0.00 0.00 0.00 3.24
495 498 0.179062 ATGCACGAAGCCTCTGGATC 60.179 55.000 0.00 0.00 44.83 3.36
726 732 4.678509 TTACAAGTCCATAAAGCTTGCG 57.321 40.909 0.00 0.00 42.20 4.85
974 986 0.960364 TTCTTCTGCAATGACCCGCC 60.960 55.000 0.00 0.00 0.00 6.13
975 987 2.745884 TTCTGCAATGACCCGCCG 60.746 61.111 0.00 0.00 0.00 6.46
976 988 4.776322 TCTGCAATGACCCGCCGG 62.776 66.667 0.00 0.00 0.00 6.13
1071 1084 2.890847 AATCGGACTCGGCTGAAGCG 62.891 60.000 0.00 0.00 43.26 4.68
1239 1252 2.049526 CGTACTGAGCGTGCCACA 60.050 61.111 0.00 0.00 0.00 4.17
1261 1274 3.249189 TCTGGCTGGGCTCGGTTT 61.249 61.111 0.00 0.00 0.00 3.27
1330 1343 6.779860 ACTCTTCAATAAAGCTCCCTTTACA 58.220 36.000 0.00 0.00 44.02 2.41
1361 1374 5.491323 AAAAAGGAGACTAGGAACCTCAG 57.509 43.478 0.00 0.00 42.68 3.35
1362 1375 3.837399 AAGGAGACTAGGAACCTCAGT 57.163 47.619 0.00 0.20 42.68 3.41
1363 1376 4.949966 AAGGAGACTAGGAACCTCAGTA 57.050 45.455 0.00 0.00 42.68 2.74
1364 1377 5.475398 AAGGAGACTAGGAACCTCAGTAT 57.525 43.478 0.00 0.00 42.68 2.12
1366 1379 4.479056 AGGAGACTAGGAACCTCAGTATGA 59.521 45.833 0.00 0.00 41.65 2.15
1368 1381 6.355271 AGGAGACTAGGAACCTCAGTATGAAT 60.355 42.308 0.00 0.00 43.16 2.57
1369 1382 7.147105 AGGAGACTAGGAACCTCAGTATGAATA 60.147 40.741 0.00 0.00 43.16 1.75
1384 1397 9.397280 TCAGTATGAATAGAAGATATACCTCGG 57.603 37.037 0.00 0.00 45.97 4.63
1385 1398 9.397280 CAGTATGAATAGAAGATATACCTCGGA 57.603 37.037 0.00 0.00 39.69 4.55
1388 1401 7.646548 TGAATAGAAGATATACCTCGGATGG 57.353 40.000 0.00 0.00 0.00 3.51
1389 1402 7.182760 TGAATAGAAGATATACCTCGGATGGT 58.817 38.462 4.86 4.86 43.66 3.55
1390 1403 7.339721 TGAATAGAAGATATACCTCGGATGGTC 59.660 40.741 2.96 0.00 41.22 4.02
1391 1404 4.011023 AGAAGATATACCTCGGATGGTCG 58.989 47.826 2.96 0.00 41.22 4.79
1392 1405 3.715638 AGATATACCTCGGATGGTCGA 57.284 47.619 2.96 0.00 41.22 4.20
1393 1406 4.030314 AGATATACCTCGGATGGTCGAA 57.970 45.455 2.96 0.00 41.22 3.71
1394 1407 3.757493 AGATATACCTCGGATGGTCGAAC 59.243 47.826 0.00 0.00 41.22 3.95
1396 1409 1.378882 TACCTCGGATGGTCGAACGG 61.379 60.000 0.00 0.00 41.22 4.44
1397 1410 2.707849 CCTCGGATGGTCGAACGGT 61.708 63.158 0.00 0.00 38.77 4.83
1398 1411 1.214589 CTCGGATGGTCGAACGGTT 59.785 57.895 0.00 0.00 38.77 4.44
1400 1413 1.080366 CGGATGGTCGAACGGTTGA 60.080 57.895 0.00 0.00 0.00 3.18
1401 1414 0.459585 CGGATGGTCGAACGGTTGAT 60.460 55.000 0.00 0.00 0.00 2.57
1402 1415 1.006832 GGATGGTCGAACGGTTGATG 58.993 55.000 0.00 0.00 0.00 3.07
1404 1417 0.611200 ATGGTCGAACGGTTGATGGA 59.389 50.000 0.00 0.00 0.00 3.41
1407 1420 1.080366 TCGAACGGTTGATGGACGG 60.080 57.895 0.00 0.00 0.00 4.79
1408 1421 1.080366 CGAACGGTTGATGGACGGA 60.080 57.895 0.00 0.00 0.00 4.69
1409 1422 1.076533 CGAACGGTTGATGGACGGAG 61.077 60.000 0.00 0.00 0.00 4.63
1410 1423 0.245539 GAACGGTTGATGGACGGAGA 59.754 55.000 0.00 0.00 0.00 3.71
1413 1426 1.596934 GGTTGATGGACGGAGAGCA 59.403 57.895 0.00 0.00 0.00 4.26
1414 1427 0.036388 GGTTGATGGACGGAGAGCAA 60.036 55.000 0.00 0.00 0.00 3.91
1416 1429 1.734465 GTTGATGGACGGAGAGCAAAG 59.266 52.381 0.00 0.00 0.00 2.77
1417 1430 0.391661 TGATGGACGGAGAGCAAAGC 60.392 55.000 0.00 0.00 0.00 3.51
1418 1431 0.391661 GATGGACGGAGAGCAAAGCA 60.392 55.000 0.00 0.00 0.00 3.91
1419 1432 0.392193 ATGGACGGAGAGCAAAGCAG 60.392 55.000 0.00 0.00 0.00 4.24
1422 1435 2.348998 CGGAGAGCAAAGCAGGGT 59.651 61.111 0.00 0.00 0.00 4.34
1423 1436 1.302832 CGGAGAGCAAAGCAGGGTT 60.303 57.895 0.00 0.00 0.00 4.11
1424 1437 1.301677 CGGAGAGCAAAGCAGGGTTC 61.302 60.000 0.00 0.00 0.00 3.62
1425 1438 0.962855 GGAGAGCAAAGCAGGGTTCC 60.963 60.000 0.00 0.00 0.00 3.62
1426 1439 1.301677 GAGAGCAAAGCAGGGTTCCG 61.302 60.000 0.00 0.00 0.00 4.30
1429 1442 2.335712 GCAAAGCAGGGTTCCGAGG 61.336 63.158 0.00 0.00 0.00 4.63
1430 1443 1.374947 CAAAGCAGGGTTCCGAGGA 59.625 57.895 0.00 0.00 0.00 3.71
1432 1445 0.036875 AAAGCAGGGTTCCGAGGAAG 59.963 55.000 4.57 0.00 34.49 3.46
1434 1447 2.291043 GCAGGGTTCCGAGGAAGGA 61.291 63.158 4.57 0.00 38.79 3.36
1444 1457 5.862678 TTCCGAGGAAGGAAAATTTGTTT 57.137 34.783 0.00 0.00 46.36 2.83
1445 1458 5.862678 TCCGAGGAAGGAAAATTTGTTTT 57.137 34.783 0.00 0.00 37.36 2.43
1446 1459 6.963083 TCCGAGGAAGGAAAATTTGTTTTA 57.037 33.333 0.00 0.00 37.36 1.52
1447 1460 6.977213 TCCGAGGAAGGAAAATTTGTTTTAG 58.023 36.000 0.00 0.00 37.36 1.85
1448 1461 6.773685 TCCGAGGAAGGAAAATTTGTTTTAGA 59.226 34.615 0.00 0.00 37.36 2.10
1452 1465 8.547481 AGGAAGGAAAATTTGTTTTAGAAGGA 57.453 30.769 0.00 0.00 0.00 3.36
1453 1466 8.988060 AGGAAGGAAAATTTGTTTTAGAAGGAA 58.012 29.630 0.00 0.00 0.00 3.36
1454 1467 9.607988 GGAAGGAAAATTTGTTTTAGAAGGAAA 57.392 29.630 0.00 0.00 0.00 3.13
1458 1471 8.208224 GGAAAATTTGTTTTAGAAGGAAAGGGA 58.792 33.333 0.00 0.00 0.00 4.20
1459 1472 9.607988 GAAAATTTGTTTTAGAAGGAAAGGGAA 57.392 29.630 0.00 0.00 0.00 3.97
1460 1473 9.967451 AAAATTTGTTTTAGAAGGAAAGGGAAA 57.033 25.926 0.00 0.00 0.00 3.13
1461 1474 9.613428 AAATTTGTTTTAGAAGGAAAGGGAAAG 57.387 29.630 0.00 0.00 0.00 2.62
1462 1475 7.964666 TTTGTTTTAGAAGGAAAGGGAAAGA 57.035 32.000 0.00 0.00 0.00 2.52
1465 1478 6.040504 TGTTTTAGAAGGAAAGGGAAAGAAGC 59.959 38.462 0.00 0.00 0.00 3.86
1466 1479 2.784347 AGAAGGAAAGGGAAAGAAGCG 58.216 47.619 0.00 0.00 0.00 4.68
1467 1480 1.200252 GAAGGAAAGGGAAAGAAGCGC 59.800 52.381 0.00 0.00 0.00 5.92
1468 1481 0.609406 AGGAAAGGGAAAGAAGCGCC 60.609 55.000 2.29 0.00 0.00 6.53
1469 1482 1.502190 GAAAGGGAAAGAAGCGCCG 59.498 57.895 2.29 0.00 0.00 6.46
1470 1483 0.953960 GAAAGGGAAAGAAGCGCCGA 60.954 55.000 2.29 0.00 0.00 5.54
1471 1484 0.536460 AAAGGGAAAGAAGCGCCGAA 60.536 50.000 2.29 0.00 0.00 4.30
1473 1486 1.671379 GGGAAAGAAGCGCCGAACT 60.671 57.895 2.29 0.00 0.00 3.01
1474 1487 1.636570 GGGAAAGAAGCGCCGAACTC 61.637 60.000 2.29 0.00 0.00 3.01
1475 1488 1.416434 GAAAGAAGCGCCGAACTCG 59.584 57.895 2.29 0.00 39.44 4.18
1485 1498 4.753877 CGAACTCGCAGTCGCCGA 62.754 66.667 0.00 0.00 35.26 5.54
1490 1503 2.824489 TCGCAGTCGCCGAGAGAT 60.824 61.111 0.00 0.00 35.26 2.75
1491 1504 2.653448 CGCAGTCGCCGAGAGATG 60.653 66.667 0.00 0.00 33.11 2.90
1492 1505 2.801421 GCAGTCGCCGAGAGATGA 59.199 61.111 0.00 0.00 0.00 2.92
1493 1506 1.139734 GCAGTCGCCGAGAGATGAA 59.860 57.895 0.00 0.00 0.00 2.57
1495 1508 0.869454 CAGTCGCCGAGAGATGAAGC 60.869 60.000 0.00 0.00 0.00 3.86
1496 1509 1.139734 GTCGCCGAGAGATGAAGCA 59.860 57.895 0.00 0.00 0.00 3.91
1497 1510 0.249238 GTCGCCGAGAGATGAAGCAT 60.249 55.000 0.00 0.00 0.00 3.79
1498 1511 0.031314 TCGCCGAGAGATGAAGCATC 59.969 55.000 0.00 0.00 40.80 3.91
1503 1516 3.682766 AGAGATGAAGCATCGCTGG 57.317 52.632 11.89 0.00 46.15 4.85
1504 1517 0.532417 AGAGATGAAGCATCGCTGGC 60.532 55.000 11.89 0.00 46.15 4.85
1506 1519 2.890109 GATGAAGCATCGCTGGCCG 61.890 63.158 0.00 0.00 39.62 6.13
1517 4288 1.089481 CGCTGGCCGCTGAGAAATTA 61.089 55.000 15.78 0.00 36.13 1.40
1538 4309 1.900585 GAATCGCTGCGTGAACTGCA 61.901 55.000 22.48 0.00 40.70 4.41
1550 4321 0.654683 GAACTGCATGCGAGATGGAC 59.345 55.000 19.64 1.63 0.00 4.02
1554 4325 0.390998 TGCATGCGAGATGGACGAAA 60.391 50.000 14.09 0.00 0.00 3.46
1595 4366 5.937165 TTTATCGACATGCACGTACTAAC 57.063 39.130 11.53 0.00 0.00 2.34
1597 4368 1.814394 TCGACATGCACGTACTAACCT 59.186 47.619 11.53 0.00 0.00 3.50
1604 4375 5.105064 ACATGCACGTACTAACCTAGGAAAT 60.105 40.000 17.98 3.64 0.00 2.17
1654 4425 3.738830 TTTGACCTGCACGTAGTAACT 57.261 42.857 0.00 0.00 41.61 2.24
1655 4426 4.852134 TTTGACCTGCACGTAGTAACTA 57.148 40.909 0.00 0.00 41.61 2.24
1656 4427 3.837213 TGACCTGCACGTAGTAACTAC 57.163 47.619 0.00 0.00 41.61 2.73
1657 4428 3.148412 TGACCTGCACGTAGTAACTACA 58.852 45.455 0.00 0.00 41.61 2.74
1658 4429 3.189910 TGACCTGCACGTAGTAACTACAG 59.810 47.826 0.00 0.00 41.61 2.74
1668 4439 5.932303 ACGTAGTAACTACAGTAGGAACGAA 59.068 40.000 20.07 8.13 41.94 3.85
1698 4469 1.758514 CTGGCTCCCTTCCTAGCGA 60.759 63.158 0.00 0.00 39.71 4.93
1699 4470 1.743321 CTGGCTCCCTTCCTAGCGAG 61.743 65.000 0.00 0.00 39.71 5.03
1720 4508 2.795389 GCGTACGTTCCATCGTGCC 61.795 63.158 17.90 0.00 43.93 5.01
1785 4573 4.165372 ACCGGAAATATGTTGGACCATAGT 59.835 41.667 9.46 0.00 31.19 2.12
1786 4574 4.755123 CCGGAAATATGTTGGACCATAGTC 59.245 45.833 0.00 0.00 42.73 2.59
1787 4575 5.454755 CCGGAAATATGTTGGACCATAGTCT 60.455 44.000 0.00 0.00 43.05 3.24
1863 4654 1.001376 GGGTAAGGGAGAGGGACGT 59.999 63.158 0.00 0.00 0.00 4.34
1864 4655 0.259938 GGGTAAGGGAGAGGGACGTA 59.740 60.000 0.00 0.00 0.00 3.57
1871 4662 2.124236 AGAGGGACGTAGCGGAGG 60.124 66.667 0.00 0.00 0.00 4.30
1890 4681 4.147449 CTCTGTCCGCCGCCATCA 62.147 66.667 0.00 0.00 0.00 3.07
1930 4723 3.453679 GAGGACGAGCGGCTCCTT 61.454 66.667 23.36 11.26 37.00 3.36
1944 4737 1.229082 TCCTTGCGTGGGTCTACCT 60.229 57.895 0.00 0.00 41.11 3.08
1947 4740 1.534476 TTGCGTGGGTCTACCTCCA 60.534 57.895 0.00 0.00 41.11 3.86
2003 4796 1.071605 CCTCTGAAAGAACGCGAAGG 58.928 55.000 15.93 1.07 46.34 3.46
2009 4802 0.318762 AAAGAACGCGAAGGCTCTCT 59.681 50.000 15.93 0.00 36.88 3.10
2010 4803 0.109039 AAGAACGCGAAGGCTCTCTC 60.109 55.000 15.93 0.00 36.88 3.20
2081 4874 3.121030 CTCGGCTGGCCAAACTCG 61.121 66.667 7.01 8.61 35.37 4.18
2095 4888 4.473520 CTCGGGCGCCAACAGGAT 62.474 66.667 30.85 0.00 0.00 3.24
2108 4901 4.779733 AGGATCGGGCCGTCCAGT 62.780 66.667 33.57 20.20 36.96 4.00
2144 4937 1.527380 ATCGTCTCCTCCTCCTCGC 60.527 63.158 0.00 0.00 0.00 5.03
2163 4986 2.786495 CCGACGATCCTCCACCAGG 61.786 68.421 0.00 0.00 45.15 4.45
2183 5006 4.693532 CCGAAGGCTACAGTTGCA 57.306 55.556 9.30 0.00 46.14 4.08
2245 5068 8.690884 TGGTGAAGTTCAATTTCATTTCAAGTA 58.309 29.630 7.25 0.00 36.96 2.24
2253 5076 9.638239 TTCAATTTCATTTCAAGTATTAGGTGC 57.362 29.630 0.00 0.00 0.00 5.01
2287 5110 5.288015 TGTCCGTCGTTTATGTGAACTTTA 58.712 37.500 0.00 0.00 0.00 1.85
2296 5119 6.347402 CGTTTATGTGAACTTTAGTGGACCTG 60.347 42.308 0.00 0.00 0.00 4.00
2303 5126 4.497291 ACTTTAGTGGACCTGTGAACAA 57.503 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.150567 CTCAGCCGAGCTTGATTCCG 61.151 60.000 1.22 0.00 36.40 4.30
195 196 5.147330 TGTATGAACTTCTCACCGTGAAT 57.853 39.130 2.19 0.00 36.69 2.57
211 212 6.126911 TGGTCATATGTAGCCAGTTTGTATGA 60.127 38.462 1.90 0.00 0.00 2.15
234 235 6.093495 CACCCTATGCCGTAATAACATTATGG 59.907 42.308 11.31 11.31 34.85 2.74
253 254 2.356741 GGGCATTACTTGAAGCACCCTA 60.357 50.000 0.00 0.00 33.11 3.53
255 256 0.817654 GGGCATTACTTGAAGCACCC 59.182 55.000 0.00 0.00 0.00 4.61
351 352 0.322098 CCATAGTCCCCGTTGCACAA 60.322 55.000 0.00 0.00 0.00 3.33
424 425 2.196595 CTCCTCCTCCAACCCACATAA 58.803 52.381 0.00 0.00 0.00 1.90
726 732 0.460284 CCTCCGTAGTGTGACATGCC 60.460 60.000 0.00 0.00 0.00 4.40
954 966 0.881118 GCGGGTCATTGCAGAAGAAA 59.119 50.000 0.00 0.00 0.00 2.52
959 971 4.776322 CCGGCGGGTCATTGCAGA 62.776 66.667 20.56 0.00 0.00 4.26
974 986 2.002586 CATGTAGTTCTGCTTCCACCG 58.997 52.381 0.00 0.00 0.00 4.94
975 987 1.740025 GCATGTAGTTCTGCTTCCACC 59.260 52.381 0.00 0.00 35.49 4.61
976 988 1.394917 CGCATGTAGTTCTGCTTCCAC 59.605 52.381 0.00 0.00 36.23 4.02
1071 1084 6.909357 GTGCATCATTTGTCAAGCTAGATAAC 59.091 38.462 0.00 0.00 0.00 1.89
1227 1240 4.240103 ACAGCTGTGGCACGCTCA 62.240 61.111 26.16 4.85 40.97 4.26
1239 1252 3.715097 GAGCCCAGCCAGACAGCT 61.715 66.667 0.00 0.00 46.45 4.24
1261 1274 4.504864 CCACAAGTCCTCAATACAAGGTGA 60.505 45.833 0.00 0.00 35.29 4.02
1345 1358 6.969993 ATTCATACTGAGGTTCCTAGTCTC 57.030 41.667 0.00 0.00 0.00 3.36
1346 1359 7.817440 TCTATTCATACTGAGGTTCCTAGTCT 58.183 38.462 0.00 0.00 0.00 3.24
1347 1360 8.466617 TTCTATTCATACTGAGGTTCCTAGTC 57.533 38.462 0.00 0.00 0.00 2.59
1349 1362 8.698973 TCTTCTATTCATACTGAGGTTCCTAG 57.301 38.462 0.00 0.00 0.00 3.02
1351 1364 9.836179 ATATCTTCTATTCATACTGAGGTTCCT 57.164 33.333 0.00 0.00 0.00 3.36
1358 1371 9.397280 CCGAGGTATATCTTCTATTCATACTGA 57.603 37.037 0.00 0.00 0.00 3.41
1359 1372 9.397280 TCCGAGGTATATCTTCTATTCATACTG 57.603 37.037 0.00 0.00 0.00 2.74
1362 1375 9.355916 CCATCCGAGGTATATCTTCTATTCATA 57.644 37.037 0.00 0.00 0.00 2.15
1363 1376 7.841729 ACCATCCGAGGTATATCTTCTATTCAT 59.158 37.037 0.00 0.00 40.98 2.57
1364 1377 7.182760 ACCATCCGAGGTATATCTTCTATTCA 58.817 38.462 0.00 0.00 40.98 2.57
1366 1379 6.319152 CGACCATCCGAGGTATATCTTCTATT 59.681 42.308 0.00 0.00 43.38 1.73
1368 1381 5.046087 TCGACCATCCGAGGTATATCTTCTA 60.046 44.000 0.00 0.00 43.38 2.10
1369 1382 4.011023 CGACCATCCGAGGTATATCTTCT 58.989 47.826 0.00 0.00 43.38 2.85
1371 1384 4.030314 TCGACCATCCGAGGTATATCTT 57.970 45.455 0.00 0.00 43.38 2.40
1373 1386 3.425892 CGTTCGACCATCCGAGGTATATC 60.426 52.174 0.00 0.00 43.38 1.63
1375 1388 1.875514 CGTTCGACCATCCGAGGTATA 59.124 52.381 0.00 0.00 43.38 1.47
1376 1389 0.666913 CGTTCGACCATCCGAGGTAT 59.333 55.000 0.00 0.00 43.38 2.73
1377 1390 1.378882 CCGTTCGACCATCCGAGGTA 61.379 60.000 0.00 0.00 43.38 3.08
1378 1391 2.707849 CCGTTCGACCATCCGAGGT 61.708 63.158 0.00 0.00 46.82 3.85
1380 1393 1.076533 CAACCGTTCGACCATCCGAG 61.077 60.000 0.00 0.00 39.90 4.63
1381 1394 1.080366 CAACCGTTCGACCATCCGA 60.080 57.895 0.00 0.00 36.70 4.55
1382 1395 0.459585 ATCAACCGTTCGACCATCCG 60.460 55.000 0.00 0.00 0.00 4.18
1383 1396 1.006832 CATCAACCGTTCGACCATCC 58.993 55.000 0.00 0.00 0.00 3.51
1384 1397 1.006832 CCATCAACCGTTCGACCATC 58.993 55.000 0.00 0.00 0.00 3.51
1385 1398 0.611200 TCCATCAACCGTTCGACCAT 59.389 50.000 0.00 0.00 0.00 3.55
1386 1399 0.320073 GTCCATCAACCGTTCGACCA 60.320 55.000 0.00 0.00 0.00 4.02
1387 1400 1.349259 CGTCCATCAACCGTTCGACC 61.349 60.000 0.00 0.00 0.00 4.79
1388 1401 1.349259 CCGTCCATCAACCGTTCGAC 61.349 60.000 0.00 0.00 0.00 4.20
1389 1402 1.080366 CCGTCCATCAACCGTTCGA 60.080 57.895 0.00 0.00 0.00 3.71
1390 1403 1.076533 CTCCGTCCATCAACCGTTCG 61.077 60.000 0.00 0.00 0.00 3.95
1391 1404 0.245539 TCTCCGTCCATCAACCGTTC 59.754 55.000 0.00 0.00 0.00 3.95
1392 1405 0.246635 CTCTCCGTCCATCAACCGTT 59.753 55.000 0.00 0.00 0.00 4.44
1393 1406 1.890894 CTCTCCGTCCATCAACCGT 59.109 57.895 0.00 0.00 0.00 4.83
1394 1407 1.519455 GCTCTCCGTCCATCAACCG 60.519 63.158 0.00 0.00 0.00 4.44
1396 1409 1.734465 CTTTGCTCTCCGTCCATCAAC 59.266 52.381 0.00 0.00 0.00 3.18
1397 1410 1.945819 GCTTTGCTCTCCGTCCATCAA 60.946 52.381 0.00 0.00 0.00 2.57
1398 1411 0.391661 GCTTTGCTCTCCGTCCATCA 60.392 55.000 0.00 0.00 0.00 3.07
1400 1413 0.392193 CTGCTTTGCTCTCCGTCCAT 60.392 55.000 0.00 0.00 0.00 3.41
1401 1414 1.004560 CTGCTTTGCTCTCCGTCCA 60.005 57.895 0.00 0.00 0.00 4.02
1402 1415 1.743252 CCTGCTTTGCTCTCCGTCC 60.743 63.158 0.00 0.00 0.00 4.79
1404 1417 2.056906 AACCCTGCTTTGCTCTCCGT 62.057 55.000 0.00 0.00 0.00 4.69
1407 1420 1.301677 CGGAACCCTGCTTTGCTCTC 61.302 60.000 0.00 0.00 0.00 3.20
1408 1421 1.302832 CGGAACCCTGCTTTGCTCT 60.303 57.895 0.00 0.00 0.00 4.09
1409 1422 1.301677 CTCGGAACCCTGCTTTGCTC 61.302 60.000 0.00 0.00 0.00 4.26
1410 1423 1.302832 CTCGGAACCCTGCTTTGCT 60.303 57.895 0.00 0.00 0.00 3.91
1413 1426 0.036875 CTTCCTCGGAACCCTGCTTT 59.963 55.000 0.00 0.00 0.00 3.51
1414 1427 1.679898 CTTCCTCGGAACCCTGCTT 59.320 57.895 0.00 0.00 0.00 3.91
1416 1429 1.838073 TTCCTTCCTCGGAACCCTGC 61.838 60.000 0.00 0.00 38.12 4.85
1417 1430 0.690762 TTTCCTTCCTCGGAACCCTG 59.309 55.000 0.00 0.00 42.50 4.45
1418 1431 1.441695 TTTTCCTTCCTCGGAACCCT 58.558 50.000 0.00 0.00 42.50 4.34
1419 1432 2.509166 ATTTTCCTTCCTCGGAACCC 57.491 50.000 0.00 0.00 42.50 4.11
1422 1435 5.862678 AAACAAATTTTCCTTCCTCGGAA 57.137 34.783 0.00 0.00 41.16 4.30
1423 1436 5.862678 AAAACAAATTTTCCTTCCTCGGA 57.137 34.783 0.00 0.00 32.29 4.55
1424 1437 6.977213 TCTAAAACAAATTTTCCTTCCTCGG 58.023 36.000 0.00 0.00 38.91 4.63
1425 1438 7.595130 CCTTCTAAAACAAATTTTCCTTCCTCG 59.405 37.037 0.00 0.00 38.91 4.63
1426 1439 8.638873 TCCTTCTAAAACAAATTTTCCTTCCTC 58.361 33.333 0.00 0.00 38.91 3.71
1430 1443 9.613428 CCTTTCCTTCTAAAACAAATTTTCCTT 57.387 29.630 0.00 0.00 38.91 3.36
1432 1445 8.208224 TCCCTTTCCTTCTAAAACAAATTTTCC 58.792 33.333 0.00 0.00 38.91 3.13
1434 1447 9.967451 TTTCCCTTTCCTTCTAAAACAAATTTT 57.033 25.926 0.00 0.00 41.07 1.82
1435 1448 9.613428 CTTTCCCTTTCCTTCTAAAACAAATTT 57.387 29.630 0.00 0.00 34.92 1.82
1436 1449 8.988060 TCTTTCCCTTTCCTTCTAAAACAAATT 58.012 29.630 0.00 0.00 0.00 1.82
1437 1450 8.547481 TCTTTCCCTTTCCTTCTAAAACAAAT 57.453 30.769 0.00 0.00 0.00 2.32
1438 1451 7.964666 TCTTTCCCTTTCCTTCTAAAACAAA 57.035 32.000 0.00 0.00 0.00 2.83
1439 1452 7.417456 GCTTCTTTCCCTTTCCTTCTAAAACAA 60.417 37.037 0.00 0.00 0.00 2.83
1440 1453 6.040504 GCTTCTTTCCCTTTCCTTCTAAAACA 59.959 38.462 0.00 0.00 0.00 2.83
1441 1454 6.448006 GCTTCTTTCCCTTTCCTTCTAAAAC 58.552 40.000 0.00 0.00 0.00 2.43
1442 1455 5.240844 CGCTTCTTTCCCTTTCCTTCTAAAA 59.759 40.000 0.00 0.00 0.00 1.52
1444 1457 4.324267 CGCTTCTTTCCCTTTCCTTCTAA 58.676 43.478 0.00 0.00 0.00 2.10
1445 1458 3.868754 GCGCTTCTTTCCCTTTCCTTCTA 60.869 47.826 0.00 0.00 0.00 2.10
1446 1459 2.784347 CGCTTCTTTCCCTTTCCTTCT 58.216 47.619 0.00 0.00 0.00 2.85
1447 1460 1.200252 GCGCTTCTTTCCCTTTCCTTC 59.800 52.381 0.00 0.00 0.00 3.46
1448 1461 1.248486 GCGCTTCTTTCCCTTTCCTT 58.752 50.000 0.00 0.00 0.00 3.36
1452 1465 0.536460 TTCGGCGCTTCTTTCCCTTT 60.536 50.000 7.64 0.00 0.00 3.11
1453 1466 1.072505 TTCGGCGCTTCTTTCCCTT 59.927 52.632 7.64 0.00 0.00 3.95
1454 1467 1.671379 GTTCGGCGCTTCTTTCCCT 60.671 57.895 7.64 0.00 0.00 4.20
1455 1468 1.636570 GAGTTCGGCGCTTCTTTCCC 61.637 60.000 7.64 0.00 0.00 3.97
1458 1471 3.550656 CGAGTTCGGCGCTTCTTT 58.449 55.556 7.64 0.00 35.37 2.52
1468 1481 4.753877 TCGGCGACTGCGAGTTCG 62.754 66.667 4.99 0.00 44.10 3.95
1469 1482 2.876645 CTCGGCGACTGCGAGTTC 60.877 66.667 4.99 0.00 44.10 3.01
1470 1483 3.329688 CTCTCGGCGACTGCGAGTT 62.330 63.158 4.99 0.00 44.10 3.01
1471 1484 3.805307 CTCTCGGCGACTGCGAGT 61.805 66.667 4.99 0.00 44.10 4.18
1473 1486 2.824489 ATCTCTCGGCGACTGCGA 60.824 61.111 4.99 0.00 44.10 5.10
1474 1487 2.598619 TTCATCTCTCGGCGACTGCG 62.599 60.000 4.99 0.00 44.10 5.18
1475 1488 0.869454 CTTCATCTCTCGGCGACTGC 60.869 60.000 4.99 0.00 41.71 4.40
1476 1489 0.869454 GCTTCATCTCTCGGCGACTG 60.869 60.000 4.99 1.16 0.00 3.51
1478 1491 0.249238 ATGCTTCATCTCTCGGCGAC 60.249 55.000 4.99 0.00 0.00 5.19
1480 1493 1.274126 CGATGCTTCATCTCTCGGCG 61.274 60.000 0.00 0.00 38.59 6.46
1481 1494 1.555741 GCGATGCTTCATCTCTCGGC 61.556 60.000 5.42 0.00 38.59 5.54
1482 1495 0.031857 AGCGATGCTTCATCTCTCGG 59.968 55.000 5.42 0.00 38.59 4.63
1483 1496 1.130140 CAGCGATGCTTCATCTCTCG 58.870 55.000 5.42 0.00 34.26 4.04
1484 1497 1.500108 CCAGCGATGCTTCATCTCTC 58.500 55.000 0.00 0.00 34.26 3.20
1485 1498 0.532417 GCCAGCGATGCTTCATCTCT 60.532 55.000 0.00 0.06 36.52 3.10
1487 1500 1.525535 GGCCAGCGATGCTTCATCT 60.526 57.895 0.00 0.00 38.59 2.90
1488 1501 2.890109 CGGCCAGCGATGCTTCATC 61.890 63.158 2.24 0.00 36.40 2.92
1489 1502 2.898840 CGGCCAGCGATGCTTCAT 60.899 61.111 2.24 0.00 36.40 2.57
1501 1514 0.908910 TCCTAATTTCTCAGCGGCCA 59.091 50.000 2.24 0.00 0.00 5.36
1502 1515 2.038387 TTCCTAATTTCTCAGCGGCC 57.962 50.000 0.00 0.00 0.00 6.13
1503 1516 2.221981 CGATTCCTAATTTCTCAGCGGC 59.778 50.000 0.00 0.00 0.00 6.53
1504 1517 2.221981 GCGATTCCTAATTTCTCAGCGG 59.778 50.000 0.00 0.00 0.00 5.52
1506 1519 3.303659 GCAGCGATTCCTAATTTCTCAGC 60.304 47.826 0.00 0.00 0.00 4.26
1517 4288 1.016130 CAGTTCACGCAGCGATTCCT 61.016 55.000 24.65 8.87 0.00 3.36
1538 4309 0.824109 TCCTTTCGTCCATCTCGCAT 59.176 50.000 0.00 0.00 0.00 4.73
1589 4360 8.645110 CCTTTCCGATTATTTCCTAGGTTAGTA 58.355 37.037 9.08 0.00 0.00 1.82
1595 4366 6.769512 TGATCCTTTCCGATTATTTCCTAGG 58.230 40.000 0.82 0.82 0.00 3.02
1597 4368 8.436778 TGATTGATCCTTTCCGATTATTTCCTA 58.563 33.333 0.00 0.00 0.00 2.94
1604 4375 6.055588 GGAACTGATTGATCCTTTCCGATTA 58.944 40.000 0.00 0.00 35.07 1.75
1637 4408 3.190118 ACTGTAGTTACTACGTGCAGGTC 59.810 47.826 16.53 0.89 39.58 3.85
1640 4411 4.633126 TCCTACTGTAGTTACTACGTGCAG 59.367 45.833 21.08 14.48 39.58 4.41
1654 4425 4.007282 CGATTCGTTCGTTCCTACTGTA 57.993 45.455 0.00 0.00 43.01 2.74
1655 4426 2.860062 CGATTCGTTCGTTCCTACTGT 58.140 47.619 0.00 0.00 43.01 3.55
1698 4469 0.454600 ACGATGGAACGTACGCATCT 59.545 50.000 23.07 12.91 44.72 2.90
1699 4470 0.570734 CACGATGGAACGTACGCATC 59.429 55.000 16.72 17.97 44.76 3.91
1785 4573 2.628559 CCCTCCCCAGGTAACATGTAGA 60.629 54.545 0.00 0.00 38.30 2.59
1786 4574 1.768870 CCCTCCCCAGGTAACATGTAG 59.231 57.143 0.00 0.00 38.30 2.74
1787 4575 1.626913 CCCCTCCCCAGGTAACATGTA 60.627 57.143 0.00 0.00 38.30 2.29
1812 4603 3.861797 CCGGGTCCCCAAGATCGG 61.862 72.222 1.00 0.00 37.66 4.18
1841 4632 2.435693 CCCTCTCCCTTACCCGCAG 61.436 68.421 0.00 0.00 0.00 5.18
1842 4633 2.365105 CCCTCTCCCTTACCCGCA 60.365 66.667 0.00 0.00 0.00 5.69
1848 4639 0.465097 CGCTACGTCCCTCTCCCTTA 60.465 60.000 0.00 0.00 0.00 2.69
1930 4723 1.982395 CTGGAGGTAGACCCACGCA 60.982 63.158 0.00 0.00 36.42 5.24
1986 4779 0.033504 AGCCTTCGCGTTCTTTCAGA 59.966 50.000 5.77 0.00 41.18 3.27
1988 4781 0.033504 AGAGCCTTCGCGTTCTTTCA 59.966 50.000 5.77 0.00 41.18 2.69
1990 4783 0.318762 AGAGAGCCTTCGCGTTCTTT 59.681 50.000 5.77 0.00 41.18 2.52
2003 4796 2.236382 CGATGGCAAGCGAGAGAGC 61.236 63.158 0.00 0.00 37.39 4.09
2009 4802 2.510012 CTGCTCGATGGCAAGCGA 60.510 61.111 0.00 0.00 42.99 4.93
2010 4803 2.806856 GACTGCTCGATGGCAAGCG 61.807 63.158 0.00 0.00 41.94 4.68
2038 4831 2.261671 GTCGCCTTCTCCTTCGCA 59.738 61.111 0.00 0.00 0.00 5.10
2113 4906 0.755686 AGACGATGATGAGGCCCTTC 59.244 55.000 0.00 0.00 0.00 3.46
2123 4916 1.544537 CGAGGAGGAGGAGACGATGAT 60.545 57.143 0.00 0.00 0.00 2.45
2144 4937 2.758327 TGGTGGAGGATCGTCGGG 60.758 66.667 9.20 0.00 34.37 5.14
2170 4993 2.347490 CCGGTGCAACTGTAGCCT 59.653 61.111 0.00 0.00 43.33 4.58
2193 5016 4.442454 CCGGCCCTTTCCCCTTCC 62.442 72.222 0.00 0.00 0.00 3.46
2245 5068 6.826741 ACGGACAATTTTATACTGCACCTAAT 59.173 34.615 0.00 0.00 0.00 1.73
2250 5073 4.092383 ACGACGGACAATTTTATACTGCAC 59.908 41.667 0.00 0.00 0.00 4.57
2253 5076 8.385111 ACATAAACGACGGACAATTTTATACTG 58.615 33.333 0.00 0.00 0.00 2.74
2262 5085 4.312443 AGTTCACATAAACGACGGACAAT 58.688 39.130 0.00 0.00 34.27 2.71
2287 5110 0.179056 CGGTTGTTCACAGGTCCACT 60.179 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.