Multiple sequence alignment - TraesCS2B01G260000

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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 TraesCS2B01G260000 chr2B 100.000 2339 0 0 1 2339 325636805 325639143 0.000000e+00 4320.0
1 TraesCS2B01G260000 chr2B 87.143 840 88 10 1512 2339 494378864 494378033 0.000000e+00 935.0
2 TraesCS2B01G260000 chr2B 81.584 543 68 20 1512 2044 105899788 105900308 1.000000e-113 420.0
3 TraesCS2B01G260000 chr2B 85.417 96 7 4 1511 1602 36792628 36792536 2.470000e-15 93.5
4 TraesCS2B01G260000 chr2A 96.850 1365 42 1 1 1364 382856647 382855283 0.000000e+00 2281.0
5 TraesCS2B01G260000 chr2A 96.337 1365 48 2 1 1363 77801819 77803183 0.000000e+00 2242.0
6 TraesCS2B01G260000 chr4B 96.426 1371 42 2 1 1364 364053869 364052499 0.000000e+00 2254.0
7 TraesCS2B01G260000 chr4B 94.805 154 8 0 1362 1515 38549777 38549624 8.350000e-60 241.0
8 TraesCS2B01G260000 chr6D 96.056 1369 51 3 1 1366 462399750 462398382 0.000000e+00 2226.0
9 TraesCS2B01G260000 chr6D 95.617 1369 54 6 1 1366 452072049 452070684 0.000000e+00 2191.0
10 TraesCS2B01G260000 chr6D 95.455 154 7 0 1362 1515 365722772 365722619 1.800000e-61 246.0
11 TraesCS2B01G260000 chr5A 96.117 1365 51 2 1 1363 472509195 472510559 0.000000e+00 2226.0
12 TraesCS2B01G260000 chr1D 96.117 1365 50 3 1 1362 176360146 176361510 0.000000e+00 2224.0
13 TraesCS2B01G260000 chr1D 95.022 1366 64 4 1 1363 356880592 356881956 0.000000e+00 2143.0
14 TraesCS2B01G260000 chr1D 82.953 833 86 32 1514 2337 270286905 270286120 0.000000e+00 701.0
15 TraesCS2B01G260000 chr7D 94.879 1367 66 4 1 1364 219850274 219848909 0.000000e+00 2134.0
16 TraesCS2B01G260000 chr1B 88.503 835 74 8 1514 2339 157942606 157941785 0.000000e+00 990.0
17 TraesCS2B01G260000 chr1B 85.919 838 90 10 1511 2338 188935023 188935842 0.000000e+00 869.0
18 TraesCS2B01G260000 chr1B 95.455 154 7 0 1362 1515 230032681 230032528 1.800000e-61 246.0
19 TraesCS2B01G260000 chr7B 88.053 837 72 9 1510 2334 68224426 68225246 0.000000e+00 966.0
20 TraesCS2B01G260000 chr7B 87.308 780 77 8 1569 2337 664960573 664959805 0.000000e+00 872.0
21 TraesCS2B01G260000 chr7B 85.629 835 103 7 1514 2339 84187776 84188602 0.000000e+00 861.0
22 TraesCS2B01G260000 chr6B 88.917 803 64 11 1547 2339 710637722 710638509 0.000000e+00 966.0
23 TraesCS2B01G260000 chr6B 88.020 793 76 8 1556 2339 120653010 120652228 0.000000e+00 920.0
24 TraesCS2B01G260000 chr6B 81.422 619 71 26 1514 2116 262271717 262271127 1.270000e-127 466.0
25 TraesCS2B01G260000 chr5B 87.563 796 81 13 1556 2339 619057036 619056247 0.000000e+00 905.0
26 TraesCS2B01G260000 chr5B 86.358 843 89 9 1511 2339 540355713 540356543 0.000000e+00 896.0
27 TraesCS2B01G260000 chr5B 83.838 396 43 13 1509 1894 443276930 443277314 7.950000e-95 357.0
28 TraesCS2B01G260000 chr5B 96.104 154 6 0 1362 1515 514315277 514315430 3.860000e-63 252.0
29 TraesCS2B01G260000 chr5D 83.690 840 87 20 1509 2337 302168931 302168131 0.000000e+00 747.0
30 TraesCS2B01G260000 chr5D 94.805 154 8 0 1362 1515 554400673 554400520 8.350000e-60 241.0
31 TraesCS2B01G260000 chr2D 78.667 750 120 26 1511 2235 16365553 16364819 1.640000e-126 462.0
32 TraesCS2B01G260000 chr2D 95.455 154 7 0 1362 1515 598631678 598631831 1.800000e-61 246.0
33 TraesCS2B01G260000 chr6A 95.455 154 7 0 1362 1515 47682287 47682134 1.800000e-61 246.0
34 TraesCS2B01G260000 chr6A 94.805 154 8 0 1362 1515 575539993 575540146 8.350000e-60 241.0
35 TraesCS2B01G260000 chr1A 95.455 154 7 0 1362 1515 306584954 306585107 1.800000e-61 246.0
36 TraesCS2B01G260000 chr1A 83.178 107 10 7 1497 1599 12780171 12780273 8.900000e-15 91.6


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 TraesCS2B01G260000 chr2B 325636805 325639143 2338 False 4320 4320 100.000 1 2339 1 chr2B.!!$F2 2338
1 TraesCS2B01G260000 chr2B 494378033 494378864 831 True 935 935 87.143 1512 2339 1 chr2B.!!$R2 827
2 TraesCS2B01G260000 chr2B 105899788 105900308 520 False 420 420 81.584 1512 2044 1 chr2B.!!$F1 532
3 TraesCS2B01G260000 chr2A 382855283 382856647 1364 True 2281 2281 96.850 1 1364 1 chr2A.!!$R1 1363
4 TraesCS2B01G260000 chr2A 77801819 77803183 1364 False 2242 2242 96.337 1 1363 1 chr2A.!!$F1 1362
5 TraesCS2B01G260000 chr4B 364052499 364053869 1370 True 2254 2254 96.426 1 1364 1 chr4B.!!$R2 1363
6 TraesCS2B01G260000 chr6D 462398382 462399750 1368 True 2226 2226 96.056 1 1366 1 chr6D.!!$R3 1365
7 TraesCS2B01G260000 chr6D 452070684 452072049 1365 True 2191 2191 95.617 1 1366 1 chr6D.!!$R2 1365
8 TraesCS2B01G260000 chr5A 472509195 472510559 1364 False 2226 2226 96.117 1 1363 1 chr5A.!!$F1 1362
9 TraesCS2B01G260000 chr1D 176360146 176361510 1364 False 2224 2224 96.117 1 1362 1 chr1D.!!$F1 1361
10 TraesCS2B01G260000 chr1D 356880592 356881956 1364 False 2143 2143 95.022 1 1363 1 chr1D.!!$F2 1362
11 TraesCS2B01G260000 chr1D 270286120 270286905 785 True 701 701 82.953 1514 2337 1 chr1D.!!$R1 823
12 TraesCS2B01G260000 chr7D 219848909 219850274 1365 True 2134 2134 94.879 1 1364 1 chr7D.!!$R1 1363
13 TraesCS2B01G260000 chr1B 157941785 157942606 821 True 990 990 88.503 1514 2339 1 chr1B.!!$R1 825
14 TraesCS2B01G260000 chr1B 188935023 188935842 819 False 869 869 85.919 1511 2338 1 chr1B.!!$F1 827
15 TraesCS2B01G260000 chr7B 68224426 68225246 820 False 966 966 88.053 1510 2334 1 chr7B.!!$F1 824
16 TraesCS2B01G260000 chr7B 664959805 664960573 768 True 872 872 87.308 1569 2337 1 chr7B.!!$R1 768
17 TraesCS2B01G260000 chr7B 84187776 84188602 826 False 861 861 85.629 1514 2339 1 chr7B.!!$F2 825
18 TraesCS2B01G260000 chr6B 710637722 710638509 787 False 966 966 88.917 1547 2339 1 chr6B.!!$F1 792
19 TraesCS2B01G260000 chr6B 120652228 120653010 782 True 920 920 88.020 1556 2339 1 chr6B.!!$R1 783
20 TraesCS2B01G260000 chr6B 262271127 262271717 590 True 466 466 81.422 1514 2116 1 chr6B.!!$R2 602
21 TraesCS2B01G260000 chr5B 619056247 619057036 789 True 905 905 87.563 1556 2339 1 chr5B.!!$R1 783
22 TraesCS2B01G260000 chr5B 540355713 540356543 830 False 896 896 86.358 1511 2339 1 chr5B.!!$F3 828
23 TraesCS2B01G260000 chr5D 302168131 302168931 800 True 747 747 83.690 1509 2337 1 chr5D.!!$R1 828
24 TraesCS2B01G260000 chr2D 16364819 16365553 734 True 462 462 78.667 1511 2235 1 chr2D.!!$R1 724

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
548 553 0.03601 TGCAGTAGAGCAAAGGAGGC 60.036 55.0 0.0 0.0 42.46 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1449 0.106669 GTATTGGTGGGCCTCCTTCC 60.107 60.0 24.13 10.1 35.27 3.46 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
272 275 2.684881 GGTATGTTCTCGGTTCGGTCTA 59.315 50.000 0.00 0.00 0.00 2.59
336 340 0.182537 CATTCTAACGGGATGGGGCA 59.817 55.000 0.00 0.00 0.00 5.36
548 553 0.036010 TGCAGTAGAGCAAAGGAGGC 60.036 55.000 0.00 0.00 42.46 4.70
692 697 4.023365 TCACAATGTGCGTGAAATGATTGA 60.023 37.500 8.78 0.00 40.34 2.57
724 729 5.612688 ACATGGTATCTATGGTGGGAAAGAT 59.387 40.000 0.00 0.00 33.42 2.40
791 802 4.251169 TCAATGGGGATTCTAGCCCTTAT 58.749 43.478 0.00 0.00 45.30 1.73
885 897 6.037726 GGGTTTTGTGAAACTTAACGTTGAT 58.962 36.000 11.99 0.00 43.68 2.57
890 902 6.606234 TGTGAAACTTAACGTTGATGCTTA 57.394 33.333 11.99 0.00 38.04 3.09
978 990 4.657952 GGGGGAAACGGGAAGATG 57.342 61.111 0.00 0.00 0.00 2.90
1009 1021 2.198827 AGATGTGTTGATGGCGGAAA 57.801 45.000 0.00 0.00 0.00 3.13
1033 1045 6.289064 ACCTCGGCTCTTAAATTTGGTATAG 58.711 40.000 0.00 0.00 0.00 1.31
1194 1206 4.911053 ACTTCGTTGCTACTAGATTCGAG 58.089 43.478 0.00 0.00 0.00 4.04
1381 1394 5.404466 AAAAGAGGAGAGAGATGAGTGTG 57.596 43.478 0.00 0.00 0.00 3.82
1382 1395 3.017048 AGAGGAGAGAGATGAGTGTGG 57.983 52.381 0.00 0.00 0.00 4.17
1383 1396 1.408702 GAGGAGAGAGATGAGTGTGGC 59.591 57.143 0.00 0.00 0.00 5.01
1384 1397 0.102120 GGAGAGAGATGAGTGTGGCG 59.898 60.000 0.00 0.00 0.00 5.69
1385 1398 1.098869 GAGAGAGATGAGTGTGGCGA 58.901 55.000 0.00 0.00 0.00 5.54
1386 1399 1.680735 GAGAGAGATGAGTGTGGCGAT 59.319 52.381 0.00 0.00 0.00 4.58
1387 1400 1.680735 AGAGAGATGAGTGTGGCGATC 59.319 52.381 0.00 0.00 0.00 3.69
1388 1401 0.749649 AGAGATGAGTGTGGCGATCC 59.250 55.000 0.00 0.00 0.00 3.36
1389 1402 0.461548 GAGATGAGTGTGGCGATCCA 59.538 55.000 0.00 0.00 40.85 3.41
1390 1403 0.904649 AGATGAGTGTGGCGATCCAA 59.095 50.000 0.00 0.00 45.53 3.53
1391 1404 1.278985 AGATGAGTGTGGCGATCCAAA 59.721 47.619 0.00 0.00 45.53 3.28
1392 1405 2.083774 GATGAGTGTGGCGATCCAAAA 58.916 47.619 0.00 0.00 45.53 2.44
1393 1406 1.974265 TGAGTGTGGCGATCCAAAAA 58.026 45.000 0.00 0.00 45.53 1.94
1413 1426 2.415697 AAAAACAATGCTAAGCGCGT 57.584 40.000 8.43 0.00 43.27 6.01
1414 1427 1.685302 AAAACAATGCTAAGCGCGTG 58.315 45.000 8.43 0.00 43.27 5.34
1415 1428 0.871722 AAACAATGCTAAGCGCGTGA 59.128 45.000 8.43 0.00 43.27 4.35
1416 1429 0.871722 AACAATGCTAAGCGCGTGAA 59.128 45.000 8.43 0.00 43.27 3.18
1417 1430 0.165944 ACAATGCTAAGCGCGTGAAC 59.834 50.000 8.43 0.00 43.27 3.18
1418 1431 0.521242 CAATGCTAAGCGCGTGAACC 60.521 55.000 8.43 0.00 43.27 3.62
1419 1432 0.673644 AATGCTAAGCGCGTGAACCT 60.674 50.000 8.43 0.00 43.27 3.50
1420 1433 0.174845 ATGCTAAGCGCGTGAACCTA 59.825 50.000 8.43 0.00 43.27 3.08
1421 1434 0.457853 TGCTAAGCGCGTGAACCTAG 60.458 55.000 8.43 0.00 43.27 3.02
1422 1435 1.146358 GCTAAGCGCGTGAACCTAGG 61.146 60.000 7.41 7.41 0.00 3.02
1423 1436 1.146358 CTAAGCGCGTGAACCTAGGC 61.146 60.000 9.30 0.00 0.00 3.93
1424 1437 1.879737 TAAGCGCGTGAACCTAGGCA 61.880 55.000 9.30 0.00 0.00 4.75
1425 1438 2.725203 AAGCGCGTGAACCTAGGCAA 62.725 55.000 9.30 0.00 0.00 4.52
1426 1439 2.322081 GCGCGTGAACCTAGGCAAA 61.322 57.895 9.30 0.00 0.00 3.68
1427 1440 1.847890 GCGCGTGAACCTAGGCAAAA 61.848 55.000 9.30 0.00 0.00 2.44
1428 1441 0.110373 CGCGTGAACCTAGGCAAAAC 60.110 55.000 9.30 1.41 0.00 2.43
1429 1442 0.948678 GCGTGAACCTAGGCAAAACA 59.051 50.000 9.30 0.00 0.00 2.83
1430 1443 1.539827 GCGTGAACCTAGGCAAAACAT 59.460 47.619 9.30 0.00 0.00 2.71
1431 1444 2.030274 GCGTGAACCTAGGCAAAACATT 60.030 45.455 9.30 0.00 0.00 2.71
1432 1445 3.552068 GCGTGAACCTAGGCAAAACATTT 60.552 43.478 9.30 0.00 0.00 2.32
1433 1446 4.320641 GCGTGAACCTAGGCAAAACATTTA 60.321 41.667 9.30 0.00 0.00 1.40
1434 1447 5.764131 CGTGAACCTAGGCAAAACATTTAA 58.236 37.500 9.30 0.00 0.00 1.52
1435 1448 6.210078 CGTGAACCTAGGCAAAACATTTAAA 58.790 36.000 9.30 0.00 0.00 1.52
1436 1449 6.362283 CGTGAACCTAGGCAAAACATTTAAAG 59.638 38.462 9.30 0.00 0.00 1.85
1437 1450 6.645003 GTGAACCTAGGCAAAACATTTAAAGG 59.355 38.462 9.30 0.00 0.00 3.11
1438 1451 6.551601 TGAACCTAGGCAAAACATTTAAAGGA 59.448 34.615 9.30 0.00 0.00 3.36
1439 1452 6.987403 ACCTAGGCAAAACATTTAAAGGAA 57.013 33.333 9.30 0.00 0.00 3.36
1440 1453 6.993079 ACCTAGGCAAAACATTTAAAGGAAG 58.007 36.000 9.30 0.00 0.00 3.46
1441 1454 6.014584 ACCTAGGCAAAACATTTAAAGGAAGG 60.015 38.462 9.30 3.19 0.00 3.46
1442 1455 6.210584 CCTAGGCAAAACATTTAAAGGAAGGA 59.789 38.462 6.90 0.00 0.00 3.36
1443 1456 6.101650 AGGCAAAACATTTAAAGGAAGGAG 57.898 37.500 6.90 0.00 0.00 3.69
1444 1457 5.012046 AGGCAAAACATTTAAAGGAAGGAGG 59.988 40.000 6.90 0.00 0.00 4.30
1445 1458 4.690748 GCAAAACATTTAAAGGAAGGAGGC 59.309 41.667 6.90 0.00 0.00 4.70
1446 1459 5.237815 CAAAACATTTAAAGGAAGGAGGCC 58.762 41.667 6.90 0.00 0.00 5.19
1447 1460 3.101643 ACATTTAAAGGAAGGAGGCCC 57.898 47.619 6.90 0.00 0.00 5.80
1448 1461 2.381961 ACATTTAAAGGAAGGAGGCCCA 59.618 45.455 6.90 0.00 33.88 5.36
1449 1462 2.597578 TTTAAAGGAAGGAGGCCCAC 57.402 50.000 0.00 0.00 33.88 4.61
1450 1463 0.702316 TTAAAGGAAGGAGGCCCACC 59.298 55.000 0.00 3.23 33.88 4.61
1451 1464 0.476808 TAAAGGAAGGAGGCCCACCA 60.477 55.000 17.23 0.00 39.06 4.17
1452 1465 1.368268 AAAGGAAGGAGGCCCACCAA 61.368 55.000 17.23 0.00 39.06 3.67
1453 1466 1.149133 AAGGAAGGAGGCCCACCAAT 61.149 55.000 17.23 6.92 39.06 3.16
1454 1467 0.253630 AGGAAGGAGGCCCACCAATA 60.254 55.000 17.23 0.00 39.06 1.90
1455 1468 0.106669 GGAAGGAGGCCCACCAATAC 60.107 60.000 17.23 4.53 39.06 1.89
1456 1469 0.623723 GAAGGAGGCCCACCAATACA 59.376 55.000 17.23 0.00 39.06 2.29
1457 1470 1.215423 GAAGGAGGCCCACCAATACAT 59.785 52.381 17.23 0.00 39.06 2.29
1458 1471 0.552848 AGGAGGCCCACCAATACATG 59.447 55.000 17.23 0.00 39.06 3.21
1459 1472 0.550914 GGAGGCCCACCAATACATGA 59.449 55.000 11.18 0.00 39.06 3.07
1460 1473 1.064017 GGAGGCCCACCAATACATGAA 60.064 52.381 11.18 0.00 39.06 2.57
1461 1474 2.301346 GAGGCCCACCAATACATGAAG 58.699 52.381 0.00 0.00 39.06 3.02
1462 1475 1.922447 AGGCCCACCAATACATGAAGA 59.078 47.619 0.00 0.00 39.06 2.87
1463 1476 2.092212 AGGCCCACCAATACATGAAGAG 60.092 50.000 0.00 0.00 39.06 2.85
1464 1477 1.678101 GCCCACCAATACATGAAGAGC 59.322 52.381 0.00 0.00 0.00 4.09
1465 1478 2.684927 GCCCACCAATACATGAAGAGCT 60.685 50.000 0.00 0.00 0.00 4.09
1466 1479 3.624777 CCCACCAATACATGAAGAGCTT 58.375 45.455 0.00 0.00 0.00 3.74
1467 1480 4.019174 CCCACCAATACATGAAGAGCTTT 58.981 43.478 0.00 0.00 0.00 3.51
1468 1481 5.192927 CCCACCAATACATGAAGAGCTTTA 58.807 41.667 0.00 0.00 0.00 1.85
1469 1482 5.297776 CCCACCAATACATGAAGAGCTTTAG 59.702 44.000 0.00 0.00 0.00 1.85
1470 1483 5.882557 CCACCAATACATGAAGAGCTTTAGT 59.117 40.000 0.00 0.00 0.00 2.24
1471 1484 6.375455 CCACCAATACATGAAGAGCTTTAGTT 59.625 38.462 0.00 0.00 0.00 2.24
1472 1485 7.246311 CACCAATACATGAAGAGCTTTAGTTG 58.754 38.462 0.00 0.00 0.00 3.16
1473 1486 6.127897 ACCAATACATGAAGAGCTTTAGTTGC 60.128 38.462 0.00 0.00 0.00 4.17
1474 1487 6.094603 CCAATACATGAAGAGCTTTAGTTGCT 59.905 38.462 0.00 0.00 44.24 3.91
1475 1488 7.280876 CCAATACATGAAGAGCTTTAGTTGCTA 59.719 37.037 0.00 0.00 41.30 3.49
1476 1489 8.668353 CAATACATGAAGAGCTTTAGTTGCTAA 58.332 33.333 0.00 0.00 41.30 3.09
1477 1490 8.792830 ATACATGAAGAGCTTTAGTTGCTAAA 57.207 30.769 0.00 2.01 41.30 1.85
1478 1491 7.693969 ACATGAAGAGCTTTAGTTGCTAAAT 57.306 32.000 0.00 0.00 41.30 1.40
1479 1492 7.756558 ACATGAAGAGCTTTAGTTGCTAAATC 58.243 34.615 0.00 0.00 41.30 2.17
1480 1493 7.391554 ACATGAAGAGCTTTAGTTGCTAAATCA 59.608 33.333 0.00 3.92 41.30 2.57
1481 1494 7.928307 TGAAGAGCTTTAGTTGCTAAATCAT 57.072 32.000 2.34 0.00 41.30 2.45
1482 1495 8.340618 TGAAGAGCTTTAGTTGCTAAATCATT 57.659 30.769 2.34 0.00 41.30 2.57
1483 1496 9.448438 TGAAGAGCTTTAGTTGCTAAATCATTA 57.552 29.630 2.34 0.00 41.30 1.90
1495 1508 7.760131 TGCTAAATCATTAAATGAAGCAAGC 57.240 32.000 0.00 0.00 43.66 4.01
1496 1509 7.549839 TGCTAAATCATTAAATGAAGCAAGCT 58.450 30.769 0.00 0.00 43.66 3.74
1497 1510 8.036575 TGCTAAATCATTAAATGAAGCAAGCTT 58.963 29.630 7.07 7.07 43.66 3.74
1498 1511 9.520204 GCTAAATCATTAAATGAAGCAAGCTTA 57.480 29.630 7.37 0.00 43.50 3.09
1500 1513 7.998753 AATCATTAAATGAAGCAAGCTTAGC 57.001 32.000 7.37 5.67 43.50 3.09
1501 1514 6.513806 TCATTAAATGAAGCAAGCTTAGCA 57.486 33.333 18.74 3.03 36.11 3.49
1502 1515 6.923012 TCATTAAATGAAGCAAGCTTAGCAA 58.077 32.000 18.74 7.95 36.11 3.91
1503 1516 6.808212 TCATTAAATGAAGCAAGCTTAGCAAC 59.192 34.615 18.74 13.35 36.11 4.17
1504 1517 3.582714 AATGAAGCAAGCTTAGCAACC 57.417 42.857 18.74 10.13 36.26 3.77
1505 1518 1.979855 TGAAGCAAGCTTAGCAACCA 58.020 45.000 18.74 11.91 36.26 3.67
1506 1519 2.517959 TGAAGCAAGCTTAGCAACCAT 58.482 42.857 18.74 0.00 36.26 3.55
1507 1520 3.684908 TGAAGCAAGCTTAGCAACCATA 58.315 40.909 18.74 1.95 36.26 2.74
1508 1521 4.078537 TGAAGCAAGCTTAGCAACCATAA 58.921 39.130 18.74 0.00 36.26 1.90
1621 1654 2.729491 GACCTTGTTTTGCGCCGC 60.729 61.111 4.18 0.00 0.00 6.53
1640 1673 1.892329 GCTTTGGGCCAAATCCAGAGA 60.892 52.381 30.51 7.50 38.38 3.10
1747 1785 1.151587 AGAGGAGGCCCTTTTCCCA 60.152 57.895 0.00 0.00 44.53 4.37
1978 2034 1.228398 TGGAAGGCGGATGTGCAAA 60.228 52.632 0.00 0.00 36.28 3.68
2128 2220 1.293963 CGCGGCGATGATGAATCCAT 61.294 55.000 19.16 0.00 35.29 3.41
2134 2226 2.353704 GCGATGATGAATCCATCCGGTA 60.354 50.000 0.00 0.00 46.64 4.02
2244 2339 0.179048 CGGGCTATGCTGATGGTGAA 60.179 55.000 0.00 0.00 0.00 3.18
2299 2394 2.043248 ATGGACGCCCGGTCTAGT 60.043 61.111 0.00 0.00 45.35 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 275 4.798882 TGGTTCCACTCCACAAAATAAGT 58.201 39.130 0.00 0.00 0.00 2.24
548 553 0.682209 CATCCCCAGCCTTGTCCAAG 60.682 60.000 0.00 0.00 38.14 3.61
724 729 2.703536 TCTCCTTGTGCACTAACTTCCA 59.296 45.455 19.41 0.00 0.00 3.53
791 802 5.681337 TGATGCATTTACGAAGTTTGACA 57.319 34.783 0.00 0.00 37.78 3.58
885 897 5.815581 AGTAGGTCATGGTCAAAATAAGCA 58.184 37.500 0.00 0.00 0.00 3.91
890 902 5.340027 CCCCTAAGTAGGTCATGGTCAAAAT 60.340 44.000 3.71 0.00 42.03 1.82
978 990 3.932710 TCAACACATCTTCGCAATAGTCC 59.067 43.478 0.00 0.00 0.00 3.85
1009 1021 3.434940 ACCAAATTTAAGAGCCGAGGT 57.565 42.857 0.00 0.00 0.00 3.85
1194 1206 0.664761 TTGCTTCTCTGTTGCAGTGC 59.335 50.000 8.58 8.58 38.01 4.40
1366 1379 1.098869 TCGCCACACTCATCTCTCTC 58.901 55.000 0.00 0.00 0.00 3.20
1367 1380 1.680735 GATCGCCACACTCATCTCTCT 59.319 52.381 0.00 0.00 0.00 3.10
1368 1381 1.269517 GGATCGCCACACTCATCTCTC 60.270 57.143 0.00 0.00 0.00 3.20
1369 1382 0.749649 GGATCGCCACACTCATCTCT 59.250 55.000 0.00 0.00 0.00 3.10
1370 1383 0.461548 TGGATCGCCACACTCATCTC 59.538 55.000 0.00 0.00 39.92 2.75
1371 1384 0.904649 TTGGATCGCCACACTCATCT 59.095 50.000 0.00 0.00 45.94 2.90
1372 1385 1.737838 TTTGGATCGCCACACTCATC 58.262 50.000 0.00 0.00 45.94 2.92
1373 1386 2.198827 TTTTGGATCGCCACACTCAT 57.801 45.000 0.00 0.00 45.94 2.90
1374 1387 1.974265 TTTTTGGATCGCCACACTCA 58.026 45.000 0.00 0.00 45.94 3.41
1403 1416 1.146358 CCTAGGTTCACGCGCTTAGC 61.146 60.000 5.73 0.23 43.95 3.09
1404 1417 1.146358 GCCTAGGTTCACGCGCTTAG 61.146 60.000 11.31 0.00 0.00 2.18
1405 1418 1.153706 GCCTAGGTTCACGCGCTTA 60.154 57.895 11.31 0.00 0.00 3.09
1406 1419 2.434359 GCCTAGGTTCACGCGCTT 60.434 61.111 11.31 0.00 0.00 4.68
1407 1420 2.725203 TTTGCCTAGGTTCACGCGCT 62.725 55.000 11.31 0.00 0.00 5.92
1408 1421 1.847890 TTTTGCCTAGGTTCACGCGC 61.848 55.000 11.31 0.00 0.00 6.86
1409 1422 0.110373 GTTTTGCCTAGGTTCACGCG 60.110 55.000 11.31 3.53 0.00 6.01
1410 1423 0.948678 TGTTTTGCCTAGGTTCACGC 59.051 50.000 11.31 0.00 0.00 5.34
1411 1424 3.915437 AATGTTTTGCCTAGGTTCACG 57.085 42.857 11.31 0.00 0.00 4.35
1412 1425 6.645003 CCTTTAAATGTTTTGCCTAGGTTCAC 59.355 38.462 11.31 3.25 0.00 3.18
1413 1426 6.551601 TCCTTTAAATGTTTTGCCTAGGTTCA 59.448 34.615 11.31 0.00 0.00 3.18
1414 1427 6.988522 TCCTTTAAATGTTTTGCCTAGGTTC 58.011 36.000 11.31 0.00 0.00 3.62
1415 1428 6.987403 TCCTTTAAATGTTTTGCCTAGGTT 57.013 33.333 11.31 0.00 0.00 3.50
1416 1429 6.014584 CCTTCCTTTAAATGTTTTGCCTAGGT 60.015 38.462 11.31 0.00 0.00 3.08
1417 1430 6.210584 TCCTTCCTTTAAATGTTTTGCCTAGG 59.789 38.462 3.67 3.67 0.00 3.02
1418 1431 7.227049 TCCTTCCTTTAAATGTTTTGCCTAG 57.773 36.000 0.00 0.00 0.00 3.02
1419 1432 6.210584 CCTCCTTCCTTTAAATGTTTTGCCTA 59.789 38.462 0.00 0.00 0.00 3.93
1420 1433 5.012046 CCTCCTTCCTTTAAATGTTTTGCCT 59.988 40.000 0.00 0.00 0.00 4.75
1421 1434 5.237815 CCTCCTTCCTTTAAATGTTTTGCC 58.762 41.667 0.00 0.00 0.00 4.52
1422 1435 4.690748 GCCTCCTTCCTTTAAATGTTTTGC 59.309 41.667 0.00 0.00 0.00 3.68
1423 1436 5.237815 GGCCTCCTTCCTTTAAATGTTTTG 58.762 41.667 0.00 0.00 0.00 2.44
1424 1437 4.286032 GGGCCTCCTTCCTTTAAATGTTTT 59.714 41.667 0.84 0.00 0.00 2.43
1425 1438 3.838317 GGGCCTCCTTCCTTTAAATGTTT 59.162 43.478 0.84 0.00 0.00 2.83
1426 1439 3.181412 TGGGCCTCCTTCCTTTAAATGTT 60.181 43.478 4.53 0.00 0.00 2.71
1427 1440 2.381961 TGGGCCTCCTTCCTTTAAATGT 59.618 45.455 4.53 0.00 0.00 2.71
1428 1441 2.760650 GTGGGCCTCCTTCCTTTAAATG 59.239 50.000 4.53 0.00 0.00 2.32
1429 1442 2.292257 GGTGGGCCTCCTTCCTTTAAAT 60.292 50.000 17.38 0.00 0.00 1.40
1430 1443 1.076513 GGTGGGCCTCCTTCCTTTAAA 59.923 52.381 17.38 0.00 0.00 1.52
1431 1444 0.702316 GGTGGGCCTCCTTCCTTTAA 59.298 55.000 17.38 0.00 0.00 1.52
1432 1445 0.476808 TGGTGGGCCTCCTTCCTTTA 60.477 55.000 24.13 0.27 35.27 1.85
1433 1446 1.368268 TTGGTGGGCCTCCTTCCTTT 61.368 55.000 24.13 0.00 35.27 3.11
1434 1447 1.149133 ATTGGTGGGCCTCCTTCCTT 61.149 55.000 24.13 3.33 35.27 3.36
1435 1448 0.253630 TATTGGTGGGCCTCCTTCCT 60.254 55.000 24.13 9.49 35.27 3.36
1436 1449 0.106669 GTATTGGTGGGCCTCCTTCC 60.107 60.000 24.13 10.10 35.27 3.46
1437 1450 0.623723 TGTATTGGTGGGCCTCCTTC 59.376 55.000 24.13 12.42 35.27 3.46
1438 1451 1.063717 CATGTATTGGTGGGCCTCCTT 60.064 52.381 24.13 14.47 35.27 3.36
1439 1452 0.552848 CATGTATTGGTGGGCCTCCT 59.447 55.000 24.13 8.77 35.27 3.69
1440 1453 0.550914 TCATGTATTGGTGGGCCTCC 59.449 55.000 17.79 17.79 35.27 4.30
1441 1454 2.092429 TCTTCATGTATTGGTGGGCCTC 60.092 50.000 4.53 0.00 35.27 4.70
1442 1455 1.922447 TCTTCATGTATTGGTGGGCCT 59.078 47.619 4.53 0.00 35.27 5.19
1443 1456 2.301346 CTCTTCATGTATTGGTGGGCC 58.699 52.381 0.00 0.00 0.00 5.80
1444 1457 1.678101 GCTCTTCATGTATTGGTGGGC 59.322 52.381 0.00 0.00 0.00 5.36
1445 1458 3.287867 AGCTCTTCATGTATTGGTGGG 57.712 47.619 0.00 0.00 0.00 4.61
1446 1459 5.882557 ACTAAAGCTCTTCATGTATTGGTGG 59.117 40.000 0.00 0.00 0.00 4.61
1447 1460 6.992063 ACTAAAGCTCTTCATGTATTGGTG 57.008 37.500 0.00 0.00 0.00 4.17
1448 1461 6.127897 GCAACTAAAGCTCTTCATGTATTGGT 60.128 38.462 0.00 0.00 0.00 3.67
1449 1462 6.094603 AGCAACTAAAGCTCTTCATGTATTGG 59.905 38.462 0.00 0.00 38.01 3.16
1450 1463 7.081526 AGCAACTAAAGCTCTTCATGTATTG 57.918 36.000 0.00 0.00 38.01 1.90
1451 1464 8.792830 TTAGCAACTAAAGCTCTTCATGTATT 57.207 30.769 0.00 0.00 42.32 1.89
1452 1465 8.792830 TTTAGCAACTAAAGCTCTTCATGTAT 57.207 30.769 0.00 0.00 42.32 2.29
1453 1466 8.792830 ATTTAGCAACTAAAGCTCTTCATGTA 57.207 30.769 6.04 0.00 42.32 2.29
1454 1467 7.391554 TGATTTAGCAACTAAAGCTCTTCATGT 59.608 33.333 14.32 0.00 41.23 3.21
1455 1468 7.755591 TGATTTAGCAACTAAAGCTCTTCATG 58.244 34.615 14.32 0.00 41.23 3.07
1456 1469 7.928307 TGATTTAGCAACTAAAGCTCTTCAT 57.072 32.000 14.32 0.00 41.23 2.57
1457 1470 7.928307 ATGATTTAGCAACTAAAGCTCTTCA 57.072 32.000 14.32 8.95 41.23 3.02
1468 1481 9.362539 CTTGCTTCATTTAATGATTTAGCAACT 57.637 29.630 27.60 0.00 46.95 3.16
1469 1482 8.112449 GCTTGCTTCATTTAATGATTTAGCAAC 58.888 33.333 27.60 22.33 46.95 4.17
1471 1484 7.549839 AGCTTGCTTCATTTAATGATTTAGCA 58.450 30.769 21.68 21.68 44.44 3.49
1472 1485 7.998753 AGCTTGCTTCATTTAATGATTTAGC 57.001 32.000 18.08 18.08 39.76 3.09
1474 1487 9.520204 GCTAAGCTTGCTTCATTTAATGATTTA 57.480 29.630 9.86 0.00 39.39 1.40
1475 1488 8.036575 TGCTAAGCTTGCTTCATTTAATGATTT 58.963 29.630 9.86 0.00 39.39 2.17
1476 1489 7.549839 TGCTAAGCTTGCTTCATTTAATGATT 58.450 30.769 9.86 1.25 39.39 2.57
1477 1490 7.104043 TGCTAAGCTTGCTTCATTTAATGAT 57.896 32.000 9.86 0.00 39.39 2.45
1478 1491 6.513806 TGCTAAGCTTGCTTCATTTAATGA 57.486 33.333 9.86 3.20 37.55 2.57
1479 1492 6.035327 GGTTGCTAAGCTTGCTTCATTTAATG 59.965 38.462 9.86 0.00 0.00 1.90
1480 1493 6.101997 GGTTGCTAAGCTTGCTTCATTTAAT 58.898 36.000 9.86 0.00 0.00 1.40
1481 1494 5.010516 TGGTTGCTAAGCTTGCTTCATTTAA 59.989 36.000 9.86 0.00 0.00 1.52
1482 1495 4.522405 TGGTTGCTAAGCTTGCTTCATTTA 59.478 37.500 9.86 0.00 0.00 1.40
1483 1496 3.321682 TGGTTGCTAAGCTTGCTTCATTT 59.678 39.130 9.86 0.00 0.00 2.32
1484 1497 2.892852 TGGTTGCTAAGCTTGCTTCATT 59.107 40.909 9.86 0.00 0.00 2.57
1485 1498 2.517959 TGGTTGCTAAGCTTGCTTCAT 58.482 42.857 9.86 0.00 0.00 2.57
1486 1499 1.979855 TGGTTGCTAAGCTTGCTTCA 58.020 45.000 9.86 2.06 0.00 3.02
1487 1500 4.666237 CTTATGGTTGCTAAGCTTGCTTC 58.334 43.478 9.86 7.94 0.00 3.86
1488 1501 3.119352 GCTTATGGTTGCTAAGCTTGCTT 60.119 43.478 9.86 12.65 44.88 3.91
1489 1502 2.424956 GCTTATGGTTGCTAAGCTTGCT 59.575 45.455 9.86 0.00 44.88 3.91
1490 1503 2.802256 GCTTATGGTTGCTAAGCTTGC 58.198 47.619 9.86 11.34 44.88 4.01
1496 1509 5.097742 TGCTCTTAGCTTATGGTTGCTAA 57.902 39.130 0.00 7.14 45.78 3.09
1497 1510 4.753516 TGCTCTTAGCTTATGGTTGCTA 57.246 40.909 0.00 0.00 42.97 3.49
1498 1511 3.634397 TGCTCTTAGCTTATGGTTGCT 57.366 42.857 0.00 0.00 42.97 3.91
1499 1512 4.133078 AGATGCTCTTAGCTTATGGTTGC 58.867 43.478 0.00 0.00 42.97 4.17
1500 1513 4.754114 GGAGATGCTCTTAGCTTATGGTTG 59.246 45.833 0.00 0.00 42.97 3.77
1501 1514 4.410228 TGGAGATGCTCTTAGCTTATGGTT 59.590 41.667 0.00 0.00 42.97 3.67
1502 1515 3.969976 TGGAGATGCTCTTAGCTTATGGT 59.030 43.478 0.00 0.00 42.97 3.55
1503 1516 4.567971 CTGGAGATGCTCTTAGCTTATGG 58.432 47.826 0.00 0.00 42.97 2.74
1504 1517 3.995705 GCTGGAGATGCTCTTAGCTTATG 59.004 47.826 0.00 0.00 42.97 1.90
1505 1518 3.007831 GGCTGGAGATGCTCTTAGCTTAT 59.992 47.826 17.10 0.00 42.97 1.73
1506 1519 2.366916 GGCTGGAGATGCTCTTAGCTTA 59.633 50.000 17.10 0.00 42.97 3.09
1507 1520 1.140652 GGCTGGAGATGCTCTTAGCTT 59.859 52.381 17.10 0.00 42.97 3.74
1508 1521 0.758123 GGCTGGAGATGCTCTTAGCT 59.242 55.000 17.10 0.00 42.97 3.32
1554 1567 1.847328 CTAAAAATTCGCCTGGGGGT 58.153 50.000 11.17 0.00 34.45 4.95
1621 1654 1.821136 GTCTCTGGATTTGGCCCAAAG 59.179 52.381 15.21 0.51 36.76 2.77
1696 1729 3.283684 CCCACGCCACTTTTCGCA 61.284 61.111 0.00 0.00 0.00 5.10
1747 1785 2.346365 GAAGCGGGAGGAAACGGT 59.654 61.111 0.00 0.00 43.21 4.83
1955 2011 1.982395 ACATCCGCCTTCCAGTCGA 60.982 57.895 0.00 0.00 0.00 4.20
1998 2054 1.220749 GGTCCTGTTGCGCCTATCA 59.779 57.895 4.18 0.00 0.00 2.15
2154 2246 3.446570 GCGCTTTGCTGGCTCCAT 61.447 61.111 0.00 0.00 41.73 3.41
2235 2330 1.612991 CCACCGTGGATTTCACCATCA 60.613 52.381 12.68 0.00 40.96 3.07


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

AutoCloner maintained by Alex Coulton.