Multiple sequence alignment - TraesCS6A01G371500

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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 TraesCS6A01G371500 chr6A 100.000 2228 0 0 1 2228 595658078 595660305 0.000000e+00 4115.0
1 TraesCS6A01G371500 chr6A 89.415 1247 65 45 65 1273 595647494 595648711 0.000000e+00 1509.0
2 TraesCS6A01G371500 chr6D 88.526 1072 52 28 283 1312 450164337 450165379 0.000000e+00 1232.0
3 TraesCS6A01G371500 chr6D 91.095 685 23 17 1562 2228 450165474 450166138 0.000000e+00 893.0
4 TraesCS6A01G371500 chr6D 82.108 1034 78 49 281 1274 450136212 450137178 0.000000e+00 785.0
5 TraesCS6A01G371500 chr6D 90.667 75 2 2 1483 1556 450165373 450165443 6.550000e-16 95.3
6 TraesCS6A01G371500 chr6B 86.691 1082 53 40 306 1312 682655528 682656593 0.000000e+00 1116.0
7 TraesCS6A01G371500 chr6B 80.568 1091 89 52 280 1312 682587876 682588901 0.000000e+00 726.0
8 TraesCS6A01G371500 chr6B 88.613 483 35 13 1755 2228 682656868 682657339 8.930000e-159 569.0
9 TraesCS6A01G371500 chr6B 89.516 124 9 3 1645 1766 682656727 682656848 1.070000e-33 154.0
10 TraesCS6A01G371500 chr6B 89.157 83 5 4 1480 1561 682656577 682656656 1.410000e-17 100.0
11 TraesCS6A01G371500 chr1A 95.364 151 7 0 1324 1474 60910958 60911108 7.950000e-60 241.0
12 TraesCS6A01G371500 chr1A 94.118 153 9 0 1322 1474 378253096 378253248 1.330000e-57 233.0
13 TraesCS6A01G371500 chr1A 94.040 151 9 0 1324 1474 104918856 104919006 1.720000e-56 230.0
14 TraesCS6A01G371500 chr7B 93.377 151 10 0 1324 1474 750579098 750578948 8.010000e-55 224.0
15 TraesCS6A01G371500 chr5D 91.304 161 13 1 1315 1474 76972635 76972475 3.730000e-53 219.0
16 TraesCS6A01G371500 chr5D 92.715 151 10 1 1324 1474 380078775 380078924 1.340000e-52 217.0
17 TraesCS6A01G371500 chr4D 88.462 182 17 3 1295 1474 351463617 351463796 1.340000e-52 217.0
18 TraesCS6A01G371500 chr3A 92.667 150 11 0 1325 1474 694963555 694963406 1.340000e-52 217.0
19 TraesCS6A01G371500 chr2A 92.715 151 8 2 1324 1474 39159111 39159258 4.820000e-52 215.0


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 TraesCS6A01G371500 chr6A 595658078 595660305 2227 False 4115.00 4115 100.00000 1 2228 1 chr6A.!!$F2 2227
1 TraesCS6A01G371500 chr6A 595647494 595648711 1217 False 1509.00 1509 89.41500 65 1273 1 chr6A.!!$F1 1208
2 TraesCS6A01G371500 chr6D 450136212 450137178 966 False 785.00 785 82.10800 281 1274 1 chr6D.!!$F1 993
3 TraesCS6A01G371500 chr6D 450164337 450166138 1801 False 740.10 1232 90.09600 283 2228 3 chr6D.!!$F2 1945
4 TraesCS6A01G371500 chr6B 682587876 682588901 1025 False 726.00 726 80.56800 280 1312 1 chr6B.!!$F1 1032
5 TraesCS6A01G371500 chr6B 682655528 682657339 1811 False 484.75 1116 88.49425 306 2228 4 chr6B.!!$F2 1922

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
27 28 0.299300 CTGACGACGTTTGCGAACAA 59.701 50.0 16.98 0.00 42.0 2.83 F
29 30 0.382636 GACGACGTTTGCGAACAAGG 60.383 55.0 16.98 6.99 42.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1200 0.036022 GAGCTGCTTGTTCTCCTGGT 59.964 55.0 2.53 0.0 0.00 4.00 R
1443 1582 0.178944 ACCAACCCAAAGGCTAACCC 60.179 55.0 0.00 0.0 36.11 4.11 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
23 24 3.033764 GCCTGACGACGTTTGCGA 61.034 61.111 0.13 0.00 42.00 5.10
24 25 2.591311 GCCTGACGACGTTTGCGAA 61.591 57.895 0.13 0.00 42.00 4.70
25 26 1.200839 CCTGACGACGTTTGCGAAC 59.799 57.895 6.77 6.77 42.00 3.95
26 27 1.484227 CCTGACGACGTTTGCGAACA 61.484 55.000 16.98 0.00 42.00 3.18
27 28 0.299300 CTGACGACGTTTGCGAACAA 59.701 50.000 16.98 0.00 42.00 2.83
28 29 0.299300 TGACGACGTTTGCGAACAAG 59.701 50.000 16.98 9.20 42.00 3.16
29 30 0.382636 GACGACGTTTGCGAACAAGG 60.383 55.000 16.98 6.99 42.00 3.61
30 31 0.806884 ACGACGTTTGCGAACAAGGA 60.807 50.000 16.98 0.00 42.00 3.36
31 32 0.382636 CGACGTTTGCGAACAAGGAC 60.383 55.000 16.98 0.83 42.00 3.85
32 33 0.382636 GACGTTTGCGAACAAGGACG 60.383 55.000 16.98 4.89 42.78 4.79
33 34 1.085501 ACGTTTGCGAACAAGGACGT 61.086 50.000 16.98 5.55 44.31 4.34
34 35 0.382636 CGTTTGCGAACAAGGACGTC 60.383 55.000 16.98 7.13 41.33 4.34
35 36 0.653636 GTTTGCGAACAAGGACGTCA 59.346 50.000 18.91 0.00 37.04 4.35
36 37 0.653636 TTTGCGAACAAGGACGTCAC 59.346 50.000 18.91 6.91 37.04 3.67
37 38 1.484227 TTGCGAACAAGGACGTCACG 61.484 55.000 18.91 12.78 0.00 4.35
38 39 2.844146 CGAACAAGGACGTCACGC 59.156 61.111 18.91 0.00 0.00 5.34
39 40 2.654912 CGAACAAGGACGTCACGCC 61.655 63.158 18.91 0.00 0.00 5.68
40 41 2.654912 GAACAAGGACGTCACGCCG 61.655 63.158 18.91 3.07 0.00 6.46
41 42 4.657824 ACAAGGACGTCACGCCGG 62.658 66.667 18.91 0.00 0.00 6.13
57 58 4.201122 GGCCTGGCCCTGGATCAG 62.201 72.222 27.77 2.18 44.06 2.90
58 59 3.415087 GCCTGGCCCTGGATCAGT 61.415 66.667 11.43 0.00 0.00 3.41
59 60 2.914289 CCTGGCCCTGGATCAGTC 59.086 66.667 0.00 0.00 0.00 3.51
60 61 2.750657 CCTGGCCCTGGATCAGTCC 61.751 68.421 0.00 0.00 45.31 3.85
748 817 3.031013 AGCTAGCCTTCTTCTTCCTCTC 58.969 50.000 12.13 0.00 0.00 3.20
749 818 3.031013 GCTAGCCTTCTTCTTCCTCTCT 58.969 50.000 2.29 0.00 0.00 3.10
811 900 1.750193 ACTGCCATTTCACGGTATGG 58.250 50.000 4.38 4.38 43.40 2.74
821 916 2.658593 CGGTATGGAGAAGCGGCG 60.659 66.667 0.51 0.51 34.37 6.46
920 1016 6.673106 TGTTCTTAAATCAAGCGCAAACATA 58.327 32.000 11.47 0.00 33.94 2.29
923 1019 9.450807 GTTCTTAAATCAAGCGCAAACATATAT 57.549 29.630 11.47 0.00 33.94 0.86
950 1046 7.925993 TGGAGTATGTTTTAGTTTGAACACTG 58.074 34.615 0.00 0.00 38.46 3.66
956 1063 6.559810 TGTTTTAGTTTGAACACTGACCATG 58.440 36.000 0.00 0.00 31.30 3.66
981 1088 1.542915 GATGTGAATGTGCTGCAGGTT 59.457 47.619 17.12 0.07 0.00 3.50
988 1100 1.673665 GTGCTGCAGGTTGCTAGCT 60.674 57.895 17.12 0.00 45.31 3.32
992 1104 1.760527 TGCAGGTTGCTAGCTGGAA 59.239 52.632 24.90 0.00 45.45 3.53
1039 1151 0.391793 GCTGTACCTGGAGAACCTGC 60.392 60.000 0.00 0.09 37.04 4.85
1099 1211 4.311700 TGCTGGACCAGGAGAACA 57.688 55.556 23.09 9.03 31.21 3.18
1117 1229 3.729965 AAGCAGCTCCTCGCCGATG 62.730 63.158 0.00 0.00 40.39 3.84
1290 1429 3.202097 GGAAGCTCTAGTCATCTTTGCC 58.798 50.000 0.00 0.00 0.00 4.52
1312 1451 7.542025 TGCCAAAAACTAGCTAGTAGTAGTAC 58.458 38.462 26.29 13.67 41.50 2.73
1313 1452 6.977502 GCCAAAAACTAGCTAGTAGTAGTACC 59.022 42.308 26.29 7.96 41.50 3.34
1314 1453 7.363268 GCCAAAAACTAGCTAGTAGTAGTACCA 60.363 40.741 26.29 0.00 41.50 3.25
1315 1454 8.189460 CCAAAAACTAGCTAGTAGTAGTACCAG 58.811 40.741 26.29 8.44 41.50 4.00
1316 1455 8.738106 CAAAAACTAGCTAGTAGTAGTACCAGT 58.262 37.037 26.29 3.67 41.50 4.00
1317 1456 9.965902 AAAAACTAGCTAGTAGTAGTACCAGTA 57.034 33.333 26.29 0.00 41.50 2.74
1318 1457 9.612066 AAAACTAGCTAGTAGTAGTACCAGTAG 57.388 37.037 26.29 6.30 41.50 2.57
1319 1458 7.912778 ACTAGCTAGTAGTAGTACCAGTAGT 57.087 40.000 24.97 7.89 40.47 2.73
1320 1459 9.427821 AACTAGCTAGTAGTAGTACCAGTAGTA 57.572 37.037 26.29 3.94 41.50 1.82
1321 1460 9.600432 ACTAGCTAGTAGTAGTACCAGTAGTAT 57.400 37.037 24.97 0.00 40.47 2.12
1322 1461 9.859427 CTAGCTAGTAGTAGTACCAGTAGTATG 57.141 40.741 12.92 0.95 32.28 2.39
1323 1462 7.678837 AGCTAGTAGTAGTACCAGTAGTATGG 58.321 42.308 10.94 0.00 46.47 2.74
1324 1463 7.512058 AGCTAGTAGTAGTACCAGTAGTATGGA 59.488 40.741 10.94 0.00 43.57 3.41
1325 1464 7.818930 GCTAGTAGTAGTACCAGTAGTATGGAG 59.181 44.444 10.94 0.00 43.57 3.86
1326 1465 7.077050 AGTAGTAGTACCAGTAGTATGGAGG 57.923 44.000 4.02 0.00 43.57 4.30
1327 1466 6.848631 AGTAGTAGTACCAGTAGTATGGAGGA 59.151 42.308 4.02 0.00 43.57 3.71
1328 1467 5.939447 AGTAGTACCAGTAGTATGGAGGAC 58.061 45.833 0.00 0.00 43.57 3.85
1329 1468 4.875578 AGTACCAGTAGTATGGAGGACA 57.124 45.455 0.00 0.00 43.57 4.02
1330 1469 4.794334 AGTACCAGTAGTATGGAGGACAG 58.206 47.826 0.00 0.00 43.57 3.51
1331 1470 3.033659 ACCAGTAGTATGGAGGACAGG 57.966 52.381 0.00 0.00 43.57 4.00
1332 1471 2.320781 CCAGTAGTATGGAGGACAGGG 58.679 57.143 0.00 0.00 43.57 4.45
1333 1472 1.689273 CAGTAGTATGGAGGACAGGGC 59.311 57.143 0.00 0.00 0.00 5.19
1334 1473 0.674534 GTAGTATGGAGGACAGGGCG 59.325 60.000 0.00 0.00 0.00 6.13
1335 1474 0.260816 TAGTATGGAGGACAGGGCGT 59.739 55.000 0.00 0.00 0.00 5.68
1336 1475 1.043673 AGTATGGAGGACAGGGCGTC 61.044 60.000 0.00 0.00 44.57 5.19
1337 1476 2.125326 TATGGAGGACAGGGCGTCG 61.125 63.158 0.00 0.00 46.42 5.12
1338 1477 2.561467 TATGGAGGACAGGGCGTCGA 62.561 60.000 0.00 0.00 46.42 4.20
1339 1478 4.131088 GGAGGACAGGGCGTCGAC 62.131 72.222 5.18 5.18 46.42 4.20
1340 1479 4.131088 GAGGACAGGGCGTCGACC 62.131 72.222 9.89 9.89 46.42 4.79
1341 1480 4.988716 AGGACAGGGCGTCGACCA 62.989 66.667 21.82 0.00 46.42 4.02
1342 1481 4.436998 GGACAGGGCGTCGACCAG 62.437 72.222 21.82 15.01 46.42 4.00
1343 1482 3.681835 GACAGGGCGTCGACCAGT 61.682 66.667 21.82 18.93 34.19 4.00
1344 1483 3.222354 GACAGGGCGTCGACCAGTT 62.222 63.158 21.82 1.64 34.19 3.16
1345 1484 2.738521 CAGGGCGTCGACCAGTTG 60.739 66.667 21.82 4.97 29.21 3.16
1346 1485 4.003788 AGGGCGTCGACCAGTTGG 62.004 66.667 21.82 0.00 42.17 3.77
1348 1487 4.681978 GGCGTCGACCAGTTGGCT 62.682 66.667 10.58 0.00 39.32 4.75
1349 1488 3.414700 GCGTCGACCAGTTGGCTG 61.415 66.667 10.58 0.00 42.22 4.85
1364 1503 3.993535 CTGGGCAGCTGAGGTTTC 58.006 61.111 20.43 0.00 0.00 2.78
1365 1504 1.377994 CTGGGCAGCTGAGGTTTCT 59.622 57.895 20.43 0.00 0.00 2.52
1366 1505 0.959372 CTGGGCAGCTGAGGTTTCTG 60.959 60.000 20.43 0.00 0.00 3.02
1368 1507 3.272031 GCAGCTGAGGTTTCTGCC 58.728 61.111 20.43 0.00 46.13 4.85
1369 1508 1.601759 GCAGCTGAGGTTTCTGCCA 60.602 57.895 20.43 0.00 46.13 4.92
1370 1509 1.584380 GCAGCTGAGGTTTCTGCCAG 61.584 60.000 20.43 0.00 46.13 4.85
1371 1510 3.272031 GCTGAGGTTTCTGCCAGC 58.728 61.111 0.00 0.00 44.00 4.85
1372 1511 2.338785 GCTGAGGTTTCTGCCAGCC 61.339 63.158 0.00 0.00 44.39 4.85
1373 1512 1.676967 CTGAGGTTTCTGCCAGCCC 60.677 63.158 0.00 0.00 0.00 5.19
1374 1513 2.747855 GAGGTTTCTGCCAGCCCG 60.748 66.667 0.00 0.00 0.00 6.13
1385 1524 4.697756 CAGCCCGCCCAAGTTCGA 62.698 66.667 0.00 0.00 0.00 3.71
1386 1525 4.394712 AGCCCGCCCAAGTTCGAG 62.395 66.667 0.00 0.00 0.00 4.04
1387 1526 4.699522 GCCCGCCCAAGTTCGAGT 62.700 66.667 0.00 0.00 0.00 4.18
1388 1527 2.434359 CCCGCCCAAGTTCGAGTC 60.434 66.667 0.00 0.00 0.00 3.36
1389 1528 2.657237 CCGCCCAAGTTCGAGTCT 59.343 61.111 0.00 0.00 0.00 3.24
1390 1529 1.446272 CCGCCCAAGTTCGAGTCTC 60.446 63.158 0.00 0.00 0.00 3.36
1391 1530 1.801913 CGCCCAAGTTCGAGTCTCG 60.802 63.158 16.33 16.33 42.10 4.04
1392 1531 1.446272 GCCCAAGTTCGAGTCTCGG 60.446 63.158 21.63 5.51 40.88 4.63
1393 1532 1.446272 CCCAAGTTCGAGTCTCGGC 60.446 63.158 21.63 14.54 40.88 5.54
1394 1533 1.289066 CCAAGTTCGAGTCTCGGCA 59.711 57.895 21.63 6.68 40.88 5.69
1395 1534 1.009389 CCAAGTTCGAGTCTCGGCAC 61.009 60.000 21.63 17.49 40.88 5.01
1410 1549 4.059459 CACGAACACGCGGTGCTC 62.059 66.667 12.47 6.54 36.98 4.26
1411 1550 4.578898 ACGAACACGCGGTGCTCA 62.579 61.111 12.47 0.00 36.98 4.26
1412 1551 4.059459 CGAACACGCGGTGCTCAC 62.059 66.667 12.47 0.00 36.98 3.51
1413 1552 4.059459 GAACACGCGGTGCTCACG 62.059 66.667 12.47 0.00 36.98 4.35
1419 1558 2.665185 GCGGTGCTCACGGAGTTT 60.665 61.111 11.07 0.00 41.61 2.66
1420 1559 2.668280 GCGGTGCTCACGGAGTTTC 61.668 63.158 11.07 0.00 41.61 2.78
1421 1560 1.006102 CGGTGCTCACGGAGTTTCT 60.006 57.895 1.90 0.00 41.61 2.52
1422 1561 1.009389 CGGTGCTCACGGAGTTTCTC 61.009 60.000 1.90 0.00 41.61 2.87
1423 1562 0.670854 GGTGCTCACGGAGTTTCTCC 60.671 60.000 5.79 5.79 46.44 3.71
1437 1576 7.323049 GGAGTTTCTCCTATAAAGAAAAGCC 57.677 40.000 8.38 10.42 46.41 4.35
1438 1577 6.884836 GGAGTTTCTCCTATAAAGAAAAGCCA 59.115 38.462 8.38 0.00 46.41 4.75
1439 1578 7.393515 GGAGTTTCTCCTATAAAGAAAAGCCAA 59.606 37.037 8.38 0.00 46.41 4.52
1440 1579 8.112016 AGTTTCTCCTATAAAGAAAAGCCAAC 57.888 34.615 10.15 1.39 42.63 3.77
1441 1580 7.724061 AGTTTCTCCTATAAAGAAAAGCCAACA 59.276 33.333 10.15 0.00 42.63 3.33
1442 1581 8.357402 GTTTCTCCTATAAAGAAAAGCCAACAA 58.643 33.333 10.15 0.00 42.63 2.83
1443 1582 7.687941 TCTCCTATAAAGAAAAGCCAACAAG 57.312 36.000 0.00 0.00 0.00 3.16
1444 1583 6.659242 TCTCCTATAAAGAAAAGCCAACAAGG 59.341 38.462 0.00 0.00 41.84 3.61
1445 1584 5.714806 TCCTATAAAGAAAAGCCAACAAGGG 59.285 40.000 0.00 0.00 38.09 3.95
1452 1591 4.843624 GCCAACAAGGGTTAGCCT 57.156 55.556 0.00 0.00 35.90 4.58
1453 1592 3.051617 GCCAACAAGGGTTAGCCTT 57.948 52.632 10.22 10.22 35.90 4.35
1454 1593 1.338107 GCCAACAAGGGTTAGCCTTT 58.662 50.000 13.55 2.76 35.90 3.11
1458 1597 3.765968 CAAGGGTTAGCCTTTGGGT 57.234 52.632 13.55 0.00 45.03 4.51
1459 1598 2.009681 CAAGGGTTAGCCTTTGGGTT 57.990 50.000 13.55 0.00 45.03 4.11
1460 1599 1.618343 CAAGGGTTAGCCTTTGGGTTG 59.382 52.381 13.55 0.00 45.03 3.77
1461 1600 0.114364 AGGGTTAGCCTTTGGGTTGG 59.886 55.000 0.00 0.00 34.28 3.77
1462 1601 0.178944 GGGTTAGCCTTTGGGTTGGT 60.179 55.000 0.00 0.00 34.28 3.67
1463 1602 1.254026 GGTTAGCCTTTGGGTTGGTC 58.746 55.000 0.00 0.00 34.28 4.02
1464 1603 1.203013 GGTTAGCCTTTGGGTTGGTCT 60.203 52.381 0.00 0.00 34.28 3.85
1465 1604 2.160205 GTTAGCCTTTGGGTTGGTCTC 58.840 52.381 0.00 0.00 34.28 3.36
1466 1605 1.440618 TAGCCTTTGGGTTGGTCTCA 58.559 50.000 0.00 0.00 34.28 3.27
1467 1606 0.779997 AGCCTTTGGGTTGGTCTCAT 59.220 50.000 0.00 0.00 34.45 2.90
1468 1607 1.147817 AGCCTTTGGGTTGGTCTCATT 59.852 47.619 0.00 0.00 34.45 2.57
1469 1608 1.970640 GCCTTTGGGTTGGTCTCATTT 59.029 47.619 0.00 0.00 34.45 2.32
1470 1609 2.368548 GCCTTTGGGTTGGTCTCATTTT 59.631 45.455 0.00 0.00 34.45 1.82
1471 1610 3.181455 GCCTTTGGGTTGGTCTCATTTTT 60.181 43.478 0.00 0.00 34.45 1.94
1500 1639 6.644347 AGTACCAGTAGTATGTAGTGTACGT 58.356 40.000 0.00 0.00 32.28 3.57
1501 1640 7.782049 AGTACCAGTAGTATGTAGTGTACGTA 58.218 38.462 0.00 0.00 32.28 3.57
1642 1832 9.530633 GAAAGATAGTTCACGTTATTCCAGTAT 57.469 33.333 0.00 0.00 0.00 2.12
1728 1919 2.853594 CGTCATGTTTATGCAATGCCAC 59.146 45.455 1.53 0.00 34.21 5.01
1783 2004 9.242477 CTCCTTGACTGATTTTCTTTTCTTTTC 57.758 33.333 0.00 0.00 0.00 2.29
1805 2027 1.142688 AAAGGGGTGCCTCACAGGAT 61.143 55.000 0.00 0.00 37.67 3.24
1806 2028 1.856539 AAGGGGTGCCTCACAGGATG 61.857 60.000 0.00 0.00 37.67 3.51
1807 2029 2.439156 GGGTGCCTCACAGGATGC 60.439 66.667 0.00 0.00 42.53 3.91
1808 2030 2.352422 GGTGCCTCACAGGATGCA 59.648 61.111 0.00 0.00 42.53 3.96
2021 2249 3.559171 GGCATATATTCCTGGCTTTCCGA 60.559 47.826 0.00 0.00 35.25 4.55
2025 2253 2.044123 ATTCCTGGCTTTCCGATGAC 57.956 50.000 0.00 0.00 34.14 3.06
2043 2271 5.220548 CGATGACAGTAAAGCAGGAAATGAG 60.221 44.000 0.00 0.00 0.00 2.90
2046 2277 4.583871 ACAGTAAAGCAGGAAATGAGGAG 58.416 43.478 0.00 0.00 0.00 3.69
2089 2320 0.836400 ATCTCTTGGGTGGACGTGGT 60.836 55.000 0.00 0.00 0.00 4.16
2131 2362 5.105635 ACTCGTGAATTGAATTGCAATGGAT 60.106 36.000 13.82 4.73 46.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.591311 TTCGCAAACGTCGTCAGGC 61.591 57.895 0.00 1.94 41.18 4.85
7 8 1.200839 GTTCGCAAACGTCGTCAGG 59.799 57.895 0.00 0.00 41.18 3.86
8 9 0.299300 TTGTTCGCAAACGTCGTCAG 59.701 50.000 0.00 0.00 41.18 3.51
9 10 0.299300 CTTGTTCGCAAACGTCGTCA 59.701 50.000 0.00 0.00 41.18 4.35
10 11 0.382636 CCTTGTTCGCAAACGTCGTC 60.383 55.000 0.00 0.00 41.18 4.20
11 12 0.806884 TCCTTGTTCGCAAACGTCGT 60.807 50.000 0.00 0.00 41.18 4.34
12 13 0.382636 GTCCTTGTTCGCAAACGTCG 60.383 55.000 0.00 0.00 41.18 5.12
13 14 0.382636 CGTCCTTGTTCGCAAACGTC 60.383 55.000 0.00 0.00 36.88 4.34
14 15 1.085501 ACGTCCTTGTTCGCAAACGT 61.086 50.000 4.91 4.91 44.63 3.99
15 16 0.382636 GACGTCCTTGTTCGCAAACG 60.383 55.000 3.51 0.00 43.19 3.60
16 17 0.653636 TGACGTCCTTGTTCGCAAAC 59.346 50.000 14.12 0.00 36.56 2.93
17 18 0.653636 GTGACGTCCTTGTTCGCAAA 59.346 50.000 14.12 0.00 36.56 3.68
18 19 1.484227 CGTGACGTCCTTGTTCGCAA 61.484 55.000 14.12 0.00 35.53 4.85
19 20 1.947146 CGTGACGTCCTTGTTCGCA 60.947 57.895 14.12 0.00 0.00 5.10
20 21 2.844146 CGTGACGTCCTTGTTCGC 59.156 61.111 14.12 0.00 0.00 4.70
21 22 2.654912 GGCGTGACGTCCTTGTTCG 61.655 63.158 14.12 9.14 0.00 3.95
22 23 2.654912 CGGCGTGACGTCCTTGTTC 61.655 63.158 14.12 0.00 0.00 3.18
23 24 2.660552 CGGCGTGACGTCCTTGTT 60.661 61.111 14.12 0.00 0.00 2.83
24 25 4.657824 CCGGCGTGACGTCCTTGT 62.658 66.667 14.12 0.00 0.00 3.16
41 42 3.412624 GACTGATCCAGGGCCAGGC 62.413 68.421 10.69 1.26 35.51 4.85
42 43 2.750657 GGACTGATCCAGGGCCAGG 61.751 68.421 9.04 9.04 45.47 4.45
43 44 2.914289 GGACTGATCCAGGGCCAG 59.086 66.667 6.18 0.00 45.47 4.85
51 52 3.244561 TGAAAGTGGTCTTGGACTGATCC 60.245 47.826 0.00 0.00 46.48 3.36
52 53 4.008074 TGAAAGTGGTCTTGGACTGATC 57.992 45.455 0.00 0.00 33.79 2.92
53 54 4.288105 AGATGAAAGTGGTCTTGGACTGAT 59.712 41.667 0.00 0.00 33.79 2.90
54 55 3.648067 AGATGAAAGTGGTCTTGGACTGA 59.352 43.478 0.00 0.00 33.79 3.41
55 56 3.750130 CAGATGAAAGTGGTCTTGGACTG 59.250 47.826 0.00 0.00 33.79 3.51
56 57 3.392616 ACAGATGAAAGTGGTCTTGGACT 59.607 43.478 0.00 0.00 33.79 3.85
57 58 3.744660 ACAGATGAAAGTGGTCTTGGAC 58.255 45.455 0.00 0.00 33.79 4.02
58 59 4.437682 AACAGATGAAAGTGGTCTTGGA 57.562 40.909 0.00 0.00 33.79 3.53
59 60 5.997746 TCTAAACAGATGAAAGTGGTCTTGG 59.002 40.000 0.00 0.00 33.79 3.61
60 61 6.708054 AGTCTAAACAGATGAAAGTGGTCTTG 59.292 38.462 0.00 0.00 33.79 3.02
61 62 6.831976 AGTCTAAACAGATGAAAGTGGTCTT 58.168 36.000 0.00 0.00 35.14 3.01
62 63 6.426646 AGTCTAAACAGATGAAAGTGGTCT 57.573 37.500 0.00 0.00 0.00 3.85
63 64 8.603242 TTTAGTCTAAACAGATGAAAGTGGTC 57.397 34.615 0.65 0.00 0.00 4.02
64 65 9.574516 AATTTAGTCTAAACAGATGAAAGTGGT 57.425 29.630 7.20 0.00 0.00 4.16
693 756 1.604278 GTGAGGAAGAACTTGTGGTGC 59.396 52.381 0.00 0.00 0.00 5.01
748 817 1.089920 GACAATGGCACTGGTAGCAG 58.910 55.000 20.16 20.16 0.00 4.24
749 818 0.692476 AGACAATGGCACTGGTAGCA 59.308 50.000 0.00 0.00 0.00 3.49
811 900 2.909762 GAAATGCAGCGCCGCTTCTC 62.910 60.000 17.80 2.86 36.40 2.87
821 916 3.446516 AGGAAAGGATTGAGAAATGCAGC 59.553 43.478 0.00 0.00 0.00 5.25
923 1019 8.962679 AGTGTTCAAACTAAAACATACTCCAAA 58.037 29.630 0.00 0.00 37.67 3.28
956 1063 1.066605 GCAGCACATTCACATCCATCC 59.933 52.381 0.00 0.00 0.00 3.51
981 1088 0.252239 TCCTCCACTTCCAGCTAGCA 60.252 55.000 18.83 0.00 0.00 3.49
988 1100 1.617018 CGCTCCATCCTCCACTTCCA 61.617 60.000 0.00 0.00 0.00 3.53
991 1103 2.370445 CCCGCTCCATCCTCCACTT 61.370 63.158 0.00 0.00 0.00 3.16
992 1104 2.765807 CCCGCTCCATCCTCCACT 60.766 66.667 0.00 0.00 0.00 4.00
1077 1189 3.972971 CTCCTGGTCCAGCAGCTGC 62.973 68.421 31.53 31.53 42.49 5.25
1088 1200 0.036022 GAGCTGCTTGTTCTCCTGGT 59.964 55.000 2.53 0.00 0.00 4.00
1117 1229 2.126965 CTGCTGCTTGCGCTTGAC 60.127 61.111 9.73 0.00 46.63 3.18
1290 1429 8.738106 ACTGGTACTACTACTAGCTAGTTTTTG 58.262 37.037 30.40 19.34 35.37 2.44
1312 1451 2.320781 CCCTGTCCTCCATACTACTGG 58.679 57.143 0.00 0.00 37.66 4.00
1313 1452 1.689273 GCCCTGTCCTCCATACTACTG 59.311 57.143 0.00 0.00 0.00 2.74
1314 1453 1.754555 CGCCCTGTCCTCCATACTACT 60.755 57.143 0.00 0.00 0.00 2.57
1315 1454 0.674534 CGCCCTGTCCTCCATACTAC 59.325 60.000 0.00 0.00 0.00 2.73
1316 1455 0.260816 ACGCCCTGTCCTCCATACTA 59.739 55.000 0.00 0.00 0.00 1.82
1317 1456 1.001760 ACGCCCTGTCCTCCATACT 59.998 57.895 0.00 0.00 0.00 2.12
1318 1457 1.442148 GACGCCCTGTCCTCCATAC 59.558 63.158 0.00 0.00 42.04 2.39
1319 1458 2.125326 CGACGCCCTGTCCTCCATA 61.125 63.158 0.00 0.00 45.23 2.74
1320 1459 3.461773 CGACGCCCTGTCCTCCAT 61.462 66.667 0.00 0.00 45.23 3.41
1321 1460 4.671590 TCGACGCCCTGTCCTCCA 62.672 66.667 0.00 0.00 45.23 3.86
1322 1461 4.131088 GTCGACGCCCTGTCCTCC 62.131 72.222 0.00 0.00 45.23 4.30
1323 1462 4.131088 GGTCGACGCCCTGTCCTC 62.131 72.222 9.92 0.00 45.23 3.71
1324 1463 4.988716 TGGTCGACGCCCTGTCCT 62.989 66.667 9.92 0.00 45.23 3.85
1325 1464 4.436998 CTGGTCGACGCCCTGTCC 62.437 72.222 9.92 0.00 45.23 4.02
1326 1465 3.222354 AACTGGTCGACGCCCTGTC 62.222 63.158 9.92 0.00 44.53 3.51
1327 1466 3.231736 AACTGGTCGACGCCCTGT 61.232 61.111 9.92 1.25 35.88 4.00
1328 1467 2.738521 CAACTGGTCGACGCCCTG 60.739 66.667 9.92 0.00 0.00 4.45
1329 1468 4.003788 CCAACTGGTCGACGCCCT 62.004 66.667 9.92 0.00 0.00 5.19
1331 1470 4.681978 AGCCAACTGGTCGACGCC 62.682 66.667 9.92 0.00 37.57 5.68
1332 1471 3.414700 CAGCCAACTGGTCGACGC 61.415 66.667 9.92 6.10 40.48 5.19
1347 1486 0.959372 CAGAAACCTCAGCTGCCCAG 60.959 60.000 9.47 0.70 0.00 4.45
1348 1487 1.073722 CAGAAACCTCAGCTGCCCA 59.926 57.895 9.47 0.00 0.00 5.36
1349 1488 2.338785 GCAGAAACCTCAGCTGCCC 61.339 63.158 9.47 0.00 46.94 5.36
1350 1489 3.272031 GCAGAAACCTCAGCTGCC 58.728 61.111 9.47 0.00 46.94 4.85
1352 1491 1.584380 GCTGGCAGAAACCTCAGCTG 61.584 60.000 20.86 7.63 46.29 4.24
1353 1492 1.303155 GCTGGCAGAAACCTCAGCT 60.303 57.895 20.86 0.00 46.29 4.24
1354 1493 3.272031 GCTGGCAGAAACCTCAGC 58.728 61.111 20.86 0.00 44.34 4.26
1355 1494 1.676967 GGGCTGGCAGAAACCTCAG 60.677 63.158 20.86 0.00 0.00 3.35
1356 1495 2.436109 GGGCTGGCAGAAACCTCA 59.564 61.111 20.86 0.00 0.00 3.86
1357 1496 2.747855 CGGGCTGGCAGAAACCTC 60.748 66.667 20.86 0.00 0.00 3.85
1368 1507 4.697756 TCGAACTTGGGCGGGCTG 62.698 66.667 0.26 0.00 0.00 4.85
1369 1508 4.394712 CTCGAACTTGGGCGGGCT 62.395 66.667 0.26 0.00 0.00 5.19
1370 1509 4.699522 ACTCGAACTTGGGCGGGC 62.700 66.667 0.00 0.00 0.00 6.13
1371 1510 2.434359 GACTCGAACTTGGGCGGG 60.434 66.667 0.00 0.00 0.00 6.13
1372 1511 1.446272 GAGACTCGAACTTGGGCGG 60.446 63.158 0.00 0.00 0.00 6.13
1373 1512 1.801913 CGAGACTCGAACTTGGGCG 60.802 63.158 20.25 0.00 43.74 6.13
1374 1513 1.446272 CCGAGACTCGAACTTGGGC 60.446 63.158 26.11 0.00 43.74 5.36
1375 1514 1.446272 GCCGAGACTCGAACTTGGG 60.446 63.158 26.11 8.44 43.74 4.12
1376 1515 1.009389 GTGCCGAGACTCGAACTTGG 61.009 60.000 26.11 16.73 43.74 3.61
1377 1516 1.337817 CGTGCCGAGACTCGAACTTG 61.338 60.000 26.11 9.89 43.74 3.16
1378 1517 1.081376 CGTGCCGAGACTCGAACTT 60.081 57.895 26.11 0.00 43.74 2.66
1379 1518 1.512996 TTCGTGCCGAGACTCGAACT 61.513 55.000 26.11 0.00 43.74 3.01
1380 1519 1.081641 TTCGTGCCGAGACTCGAAC 60.082 57.895 26.11 20.37 43.74 3.95
1381 1520 1.081641 GTTCGTGCCGAGACTCGAA 60.082 57.895 26.11 11.05 43.74 3.71
1382 1521 2.255881 TGTTCGTGCCGAGACTCGA 61.256 57.895 26.11 4.13 43.74 4.04
1383 1522 2.081212 GTGTTCGTGCCGAGACTCG 61.081 63.158 18.08 18.08 37.14 4.18
1384 1523 2.081212 CGTGTTCGTGCCGAGACTC 61.081 63.158 0.00 0.00 37.14 3.36
1385 1524 2.050351 CGTGTTCGTGCCGAGACT 60.050 61.111 0.00 0.00 37.14 3.24
1386 1525 3.764049 GCGTGTTCGTGCCGAGAC 61.764 66.667 0.00 1.78 37.14 3.36
1393 1532 4.059459 GAGCACCGCGTGTTCGTG 62.059 66.667 4.92 6.73 45.59 4.35
1394 1533 4.578898 TGAGCACCGCGTGTTCGT 62.579 61.111 4.92 0.00 44.63 3.85
1395 1534 4.059459 GTGAGCACCGCGTGTTCG 62.059 66.667 4.92 0.00 44.63 3.95
1396 1535 4.059459 CGTGAGCACCGCGTGTTC 62.059 66.667 4.92 11.55 42.61 3.18
1402 1541 2.665185 AAACTCCGTGAGCACCGC 60.665 61.111 1.36 0.00 32.04 5.68
1403 1542 1.006102 AGAAACTCCGTGAGCACCG 60.006 57.895 1.36 0.00 32.04 4.94
1404 1543 0.670854 GGAGAAACTCCGTGAGCACC 60.671 60.000 1.97 0.00 41.08 5.01
1405 1544 2.828933 GGAGAAACTCCGTGAGCAC 58.171 57.895 1.97 0.00 41.08 4.40
1414 1553 7.923414 TGGCTTTTCTTTATAGGAGAAACTC 57.077 36.000 10.98 0.00 41.42 3.01
1415 1554 7.724061 TGTTGGCTTTTCTTTATAGGAGAAACT 59.276 33.333 10.98 0.00 41.42 2.66
1416 1555 7.882179 TGTTGGCTTTTCTTTATAGGAGAAAC 58.118 34.615 10.98 4.09 41.42 2.78
1417 1556 8.472007 TTGTTGGCTTTTCTTTATAGGAGAAA 57.528 30.769 8.49 8.49 40.36 2.52
1418 1557 7.176690 CCTTGTTGGCTTTTCTTTATAGGAGAA 59.823 37.037 0.00 0.00 0.00 2.87
1419 1558 6.659242 CCTTGTTGGCTTTTCTTTATAGGAGA 59.341 38.462 0.00 0.00 0.00 3.71
1420 1559 6.127619 CCCTTGTTGGCTTTTCTTTATAGGAG 60.128 42.308 0.00 0.00 0.00 3.69
1421 1560 5.714806 CCCTTGTTGGCTTTTCTTTATAGGA 59.285 40.000 0.00 0.00 0.00 2.94
1422 1561 5.480422 ACCCTTGTTGGCTTTTCTTTATAGG 59.520 40.000 0.00 0.00 0.00 2.57
1423 1562 6.590234 ACCCTTGTTGGCTTTTCTTTATAG 57.410 37.500 0.00 0.00 0.00 1.31
1424 1563 6.987403 AACCCTTGTTGGCTTTTCTTTATA 57.013 33.333 0.00 0.00 32.13 0.98
1425 1564 5.887214 AACCCTTGTTGGCTTTTCTTTAT 57.113 34.783 0.00 0.00 32.13 1.40
1426 1565 6.399639 CTAACCCTTGTTGGCTTTTCTTTA 57.600 37.500 0.00 0.00 35.87 1.85
1427 1566 5.276461 CTAACCCTTGTTGGCTTTTCTTT 57.724 39.130 0.00 0.00 35.87 2.52
1428 1567 4.937201 CTAACCCTTGTTGGCTTTTCTT 57.063 40.909 0.00 0.00 35.87 2.52
1443 1582 0.178944 ACCAACCCAAAGGCTAACCC 60.179 55.000 0.00 0.00 36.11 4.11
1444 1583 1.203013 AGACCAACCCAAAGGCTAACC 60.203 52.381 0.00 0.00 36.11 2.85
1445 1584 2.160205 GAGACCAACCCAAAGGCTAAC 58.840 52.381 0.00 0.00 36.11 2.34
1446 1585 1.777878 TGAGACCAACCCAAAGGCTAA 59.222 47.619 0.00 0.00 36.11 3.09
1447 1586 1.440618 TGAGACCAACCCAAAGGCTA 58.559 50.000 0.00 0.00 36.11 3.93
1448 1587 0.779997 ATGAGACCAACCCAAAGGCT 59.220 50.000 0.00 0.00 36.11 4.58
1449 1588 1.632589 AATGAGACCAACCCAAAGGC 58.367 50.000 0.00 0.00 36.11 4.35
1450 1589 4.687901 AAAAATGAGACCAACCCAAAGG 57.312 40.909 0.00 0.00 40.04 3.11
1470 1609 9.300681 ACACTACATACTACTGGTACTACAAAA 57.699 33.333 0.00 0.00 32.72 2.44
1471 1610 8.868522 ACACTACATACTACTGGTACTACAAA 57.131 34.615 0.00 0.00 32.72 2.83
1472 1611 9.383519 GTACACTACATACTACTGGTACTACAA 57.616 37.037 0.00 0.00 32.72 2.41
1473 1612 7.706607 CGTACACTACATACTACTGGTACTACA 59.293 40.741 0.00 0.00 32.72 2.74
1474 1613 7.707035 ACGTACACTACATACTACTGGTACTAC 59.293 40.741 0.00 0.00 32.72 2.73
1475 1614 7.782049 ACGTACACTACATACTACTGGTACTA 58.218 38.462 0.00 0.00 32.72 1.82
1476 1615 6.644347 ACGTACACTACATACTACTGGTACT 58.356 40.000 0.00 0.00 32.72 2.73
1477 1616 6.910536 ACGTACACTACATACTACTGGTAC 57.089 41.667 0.00 0.00 32.72 3.34
1478 1617 7.782049 AGTACGTACACTACATACTACTGGTA 58.218 38.462 26.55 0.00 36.09 3.25
1479 1618 6.644347 AGTACGTACACTACATACTACTGGT 58.356 40.000 26.55 0.00 36.09 4.00
1480 1619 8.138074 TCTAGTACGTACACTACATACTACTGG 58.862 40.741 26.55 5.94 38.47 4.00
1481 1620 9.689976 ATCTAGTACGTACACTACATACTACTG 57.310 37.037 26.55 0.00 38.47 2.74
1500 1639 6.486056 CCAGCTCTAATGGACCTATCTAGTA 58.514 44.000 0.00 0.00 40.51 1.82
1501 1640 5.329399 CCAGCTCTAATGGACCTATCTAGT 58.671 45.833 0.00 0.00 40.51 2.57
1607 1780 4.503007 CGTGAACTATCTTTCGTACCCATG 59.497 45.833 0.00 0.00 0.00 3.66
1617 1790 9.886132 AATACTGGAATAACGTGAACTATCTTT 57.114 29.630 0.00 0.00 0.00 2.52
1619 1792 8.475639 ACAATACTGGAATAACGTGAACTATCT 58.524 33.333 0.00 0.00 0.00 1.98
1642 1832 3.138304 ACTGCAGATTTCGCAAGTACAA 58.862 40.909 23.35 0.00 39.30 2.41
1783 2004 0.675633 CTGTGAGGCACCCCTTTTTG 59.324 55.000 0.00 0.00 43.12 2.44
1805 2027 1.330234 AGAATGGTTGTGTGCATGCA 58.670 45.000 18.46 18.46 0.00 3.96
1806 2028 2.443887 AAGAATGGTTGTGTGCATGC 57.556 45.000 11.82 11.82 0.00 4.06
1807 2029 3.737266 GTCAAAGAATGGTTGTGTGCATG 59.263 43.478 0.00 0.00 0.00 4.06
1808 2030 3.638160 AGTCAAAGAATGGTTGTGTGCAT 59.362 39.130 0.00 0.00 0.00 3.96
1953 2180 8.286800 GCAAGAAAAACAAACAATATAAACCCC 58.713 33.333 0.00 0.00 0.00 4.95
2001 2228 5.352569 GTCATCGGAAAGCCAGGAATATATG 59.647 44.000 0.00 0.00 0.00 1.78
2021 2249 4.946157 CCTCATTTCCTGCTTTACTGTCAT 59.054 41.667 0.00 0.00 0.00 3.06
2025 2253 4.583871 ACTCCTCATTTCCTGCTTTACTG 58.416 43.478 0.00 0.00 0.00 2.74
2043 2271 9.853555 CATGATCAGAATACTGTTCTATACTCC 57.146 37.037 0.09 0.00 43.81 3.85
2089 2320 3.311106 GAGTTCAACCGATCGTGTTGTA 58.689 45.455 30.75 24.67 42.82 2.41
2131 2362 1.241990 ACCTCGAGTCAAGCGCTACA 61.242 55.000 12.05 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.