Multiple sequence alignment - TraesCS2B01G220200

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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 TraesCS2B01G220200 chr2B 100.000 4634 0 0 1 4634 210666837 210662204 0.000000e+00 8558
1 TraesCS2B01G220200 chr2D 94.496 1508 56 13 2142 3647 152659903 152658421 0.000000e+00 2300
2 TraesCS2B01G220200 chr2D 96.906 1002 26 4 3638 4634 152656796 152655795 0.000000e+00 1674
3 TraesCS2B01G220200 chr2D 94.080 777 35 7 603 1371 152661282 152660509 0.000000e+00 1170
4 TraesCS2B01G220200 chr2D 90.970 598 27 10 1485 2082 152660498 152659928 0.000000e+00 780
5 TraesCS2B01G220200 chr2D 87.500 512 39 13 11 501 503913688 503913181 6.730000e-158 568
6 TraesCS2B01G220200 chr2D 97.143 105 3 0 512 616 152661419 152661315 1.320000e-40 178
7 TraesCS2B01G220200 chr2A 95.180 1224 45 7 1475 2696 148855056 148856267 0.000000e+00 1921
8 TraesCS2B01G220200 chr2A 87.527 1379 94 29 1 1371 148853628 148854936 0.000000e+00 1522
9 TraesCS2B01G220200 chr2A 94.421 950 37 8 2895 3840 148856825 148857762 0.000000e+00 1447
10 TraesCS2B01G220200 chr2A 94.358 709 31 7 3929 4634 148857769 148858471 0.000000e+00 1079
11 TraesCS2B01G220200 chr2A 99.412 170 1 0 2733 2902 148856265 148856434 4.500000e-80 309
12 TraesCS2B01G220200 chr3B 88.235 527 41 11 1 507 489694020 489694545 1.100000e-170 610
13 TraesCS2B01G220200 chr7D 88.039 510 40 12 11 501 414101884 414102391 6.680000e-163 584
14 TraesCS2B01G220200 chr7D 84.038 520 57 13 11 507 488690556 488691072 1.170000e-130 477
15 TraesCS2B01G220200 chr1D 87.280 511 45 9 11 502 211805624 211806133 2.420000e-157 566
16 TraesCS2B01G220200 chr1D 87.016 516 46 15 11 507 486752909 486752396 3.130000e-156 562
17 TraesCS2B01G220200 chr6D 86.220 508 51 12 11 501 101207576 101208081 2.450000e-147 532
18 TraesCS2B01G220200 chr5B 84.872 509 56 11 1 494 684060394 684060896 1.160000e-135 494
19 TraesCS2B01G220200 chr5B 81.471 340 46 10 1 326 611515872 611516208 3.560000e-66 263
20 TraesCS2B01G220200 chr5B 88.235 102 10 1 1387 1486 603453803 603453702 2.260000e-23 121
21 TraesCS2B01G220200 chr1A 82.937 504 60 12 11 507 584349842 584349358 9.210000e-117 431
22 TraesCS2B01G220200 chr4A 84.932 438 44 14 98 516 741029567 741030001 1.540000e-114 424
23 TraesCS2B01G220200 chr3A 88.304 342 30 9 172 507 538843097 538843434 7.220000e-108 401
24 TraesCS2B01G220200 chr3A 87.379 103 10 1 1387 1486 726119890 726119788 1.050000e-21 115
25 TraesCS2B01G220200 chr3D 88.270 341 28 11 172 507 411623685 411623352 9.340000e-107 398
26 TraesCS2B01G220200 chr3D 81.423 506 72 17 11 502 41801449 41801946 1.210000e-105 394
27 TraesCS2B01G220200 chrUn 89.286 112 10 2 1387 1496 86621765 86621876 6.250000e-29 139
28 TraesCS2B01G220200 chr7B 89.216 102 9 1 1387 1486 327855883 327855984 4.870000e-25 126
29 TraesCS2B01G220200 chr7B 85.981 107 13 1 1387 1491 16662299 16662193 3.790000e-21 113
30 TraesCS2B01G220200 chr4B 89.216 102 9 1 1387 1486 45409158 45409057 4.870000e-25 126
31 TraesCS2B01G220200 chr4B 87.379 103 10 1 1387 1486 315697358 315697256 1.050000e-21 115
32 TraesCS2B01G220200 chr6A 88.235 102 10 1 1387 1486 22197462 22197563 2.260000e-23 121
33 TraesCS2B01G220200 chr7A 87.379 103 10 1 1387 1486 189010207 189010309 1.050000e-21 115


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 TraesCS2B01G220200 chr2B 210662204 210666837 4633 True 8558.0 8558 100.0000 1 4634 1 chr2B.!!$R1 4633
1 TraesCS2B01G220200 chr2D 152655795 152661419 5624 True 1220.4 2300 94.7190 512 4634 5 chr2D.!!$R2 4122
2 TraesCS2B01G220200 chr2D 503913181 503913688 507 True 568.0 568 87.5000 11 501 1 chr2D.!!$R1 490
3 TraesCS2B01G220200 chr2A 148853628 148858471 4843 False 1255.6 1921 94.1796 1 4634 5 chr2A.!!$F1 4633
4 TraesCS2B01G220200 chr3B 489694020 489694545 525 False 610.0 610 88.2350 1 507 1 chr3B.!!$F1 506
5 TraesCS2B01G220200 chr7D 414101884 414102391 507 False 584.0 584 88.0390 11 501 1 chr7D.!!$F1 490
6 TraesCS2B01G220200 chr7D 488690556 488691072 516 False 477.0 477 84.0380 11 507 1 chr7D.!!$F2 496
7 TraesCS2B01G220200 chr1D 211805624 211806133 509 False 566.0 566 87.2800 11 502 1 chr1D.!!$F1 491
8 TraesCS2B01G220200 chr1D 486752396 486752909 513 True 562.0 562 87.0160 11 507 1 chr1D.!!$R1 496
9 TraesCS2B01G220200 chr6D 101207576 101208081 505 False 532.0 532 86.2200 11 501 1 chr6D.!!$F1 490
10 TraesCS2B01G220200 chr5B 684060394 684060896 502 False 494.0 494 84.8720 1 494 1 chr5B.!!$F2 493

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
704 814 0.254747 CATTCTTCCCCGGCAACCTA 59.745 55.0 0.0 0.0 0.00 3.08 F
1306 1422 0.532573 CCTCTTCGCCACTAGCTCAA 59.467 55.0 0.0 0.0 40.39 3.02 F
2046 2183 0.467290 TGTCCCCAAACTTCCACAGC 60.467 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2147 4.446371 GGGACAACAGACTTCTATGATGG 58.554 47.826 0.00 0.00 0.00 3.51 R
3284 3823 0.251297 CTGCCCCAGTGGAATCAACA 60.251 55.000 11.95 0.00 35.39 3.33 R
3900 6076 3.498774 GGTCTAATGGCATGACCTGAT 57.501 47.619 23.04 0.85 44.84 2.90 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
57 58 1.423541 AGTAAGACAATGTGGGTGGCA 59.576 47.619 0.00 0.00 0.00 4.92
129 130 3.822035 TTGGGCGGTGGGGTTTGA 61.822 61.111 0.00 0.00 0.00 2.69
169 199 2.750815 GGTTCGTCCGACTCCAATG 58.249 57.895 0.00 0.00 0.00 2.82
170 200 1.359459 GGTTCGTCCGACTCCAATGC 61.359 60.000 0.00 0.00 0.00 3.56
171 201 1.445410 TTCGTCCGACTCCAATGCG 60.445 57.895 0.00 0.00 0.00 4.73
172 202 2.829043 TTCGTCCGACTCCAATGCGG 62.829 60.000 0.00 0.00 46.08 5.69
173 203 2.264794 GTCCGACTCCAATGCGGT 59.735 61.111 0.00 0.00 45.02 5.68
174 204 2.100631 GTCCGACTCCAATGCGGTG 61.101 63.158 0.00 0.00 45.02 4.94
175 205 3.499737 CCGACTCCAATGCGGTGC 61.500 66.667 0.00 0.00 40.17 5.01
176 206 3.499737 CGACTCCAATGCGGTGCC 61.500 66.667 0.00 0.00 35.57 5.01
177 207 2.359850 GACTCCAATGCGGTGCCA 60.360 61.111 0.00 0.00 35.57 4.92
178 208 2.672996 ACTCCAATGCGGTGCCAC 60.673 61.111 0.00 0.00 35.57 5.01
211 241 2.745037 GGTGTCGGTGGTAGCCAA 59.255 61.111 0.00 0.00 34.18 4.52
230 260 1.001248 CCCCCACTTCCCTCTACGA 59.999 63.158 0.00 0.00 0.00 3.43
299 330 2.356125 GCATCCCTTCTTGAAGGTGCTA 60.356 50.000 25.13 12.48 38.31 3.49
340 374 1.302832 CCTCAGGCTGTGGTGGTTC 60.303 63.158 24.09 0.00 0.00 3.62
348 382 1.802337 CTGTGGTGGTTCGTCTCCGA 61.802 60.000 0.00 0.00 42.41 4.55
385 419 1.573829 GGTCATCCGCGCTTTTGTCA 61.574 55.000 5.56 0.00 0.00 3.58
394 428 1.654220 GCTTTTGTCAAGCTGCCGA 59.346 52.632 0.00 0.00 40.01 5.54
435 472 6.455360 TCTTTTTCTTTGAGCTTGATGTGT 57.545 33.333 0.00 0.00 0.00 3.72
514 557 2.148768 CCTTTTTCCGGTATATCGCCC 58.851 52.381 0.00 0.00 0.00 6.13
531 574 4.394712 CGACAGAAAGCCGGGCCT 62.395 66.667 17.02 0.00 0.00 5.19
599 705 2.755103 GTCCTTTTCCACAATGGGCTAG 59.245 50.000 0.00 0.00 38.32 3.42
600 706 1.478105 CCTTTTCCACAATGGGCTAGC 59.522 52.381 6.04 6.04 38.32 3.42
601 707 2.450476 CTTTTCCACAATGGGCTAGCT 58.550 47.619 15.72 0.00 38.32 3.32
602 708 3.620488 CTTTTCCACAATGGGCTAGCTA 58.380 45.455 15.72 4.59 38.32 3.32
603 709 3.281727 TTTCCACAATGGGCTAGCTAG 57.718 47.619 16.84 16.84 38.32 3.42
623 729 1.601412 GCTGAGCCACAAAGAAAGCAC 60.601 52.381 0.00 0.00 0.00 4.40
654 760 3.070576 GCCAGCCGCCAAAGGAAT 61.071 61.111 0.00 0.00 0.00 3.01
704 814 0.254747 CATTCTTCCCCGGCAACCTA 59.745 55.000 0.00 0.00 0.00 3.08
760 870 1.804326 CACCGTCGAGGCGTTAAGG 60.804 63.158 0.00 0.00 46.52 2.69
879 989 4.501071 GTCCGAACAGCACTAGGATTAAA 58.499 43.478 0.00 0.00 33.15 1.52
896 1006 6.374613 AGGATTAAAGGTCTGTTCCGAATTTC 59.625 38.462 0.00 0.00 0.00 2.17
911 1021 4.082571 CCGAATTTCCAGAGCTTGTGATTT 60.083 41.667 0.00 0.00 0.00 2.17
1022 1132 3.165875 TGTCCTCTTCGTCATCTTTCCT 58.834 45.455 0.00 0.00 0.00 3.36
1185 1301 0.913451 AGGAGCTGCTGGACCTCAAT 60.913 55.000 7.07 0.00 0.00 2.57
1303 1419 0.820871 CTTCCTCTTCGCCACTAGCT 59.179 55.000 0.00 0.00 40.39 3.32
1306 1422 0.532573 CCTCTTCGCCACTAGCTCAA 59.467 55.000 0.00 0.00 40.39 3.02
1342 1458 7.662258 GGAGAAGCTCTTAGGAACTTTAGTTTT 59.338 37.037 0.00 0.00 41.75 2.43
1343 1459 9.708092 GAGAAGCTCTTAGGAACTTTAGTTTTA 57.292 33.333 0.00 0.00 41.75 1.52
1371 1493 6.165577 ACTTGTTTAAATTGTGCCATCCATC 58.834 36.000 0.00 0.00 0.00 3.51
1372 1494 5.083533 TGTTTAAATTGTGCCATCCATCC 57.916 39.130 0.00 0.00 0.00 3.51
1373 1495 4.529769 TGTTTAAATTGTGCCATCCATCCA 59.470 37.500 0.00 0.00 0.00 3.41
1374 1496 5.189342 TGTTTAAATTGTGCCATCCATCCAT 59.811 36.000 0.00 0.00 0.00 3.41
1375 1497 3.830744 AAATTGTGCCATCCATCCATG 57.169 42.857 0.00 0.00 0.00 3.66
1376 1498 2.464796 ATTGTGCCATCCATCCATGT 57.535 45.000 0.00 0.00 0.00 3.21
1378 1500 2.234896 TGTGCCATCCATCCATGTTT 57.765 45.000 0.00 0.00 0.00 2.83
1381 1503 4.092279 TGTGCCATCCATCCATGTTTAAA 58.908 39.130 0.00 0.00 0.00 1.52
1382 1504 4.715792 TGTGCCATCCATCCATGTTTAAAT 59.284 37.500 0.00 0.00 0.00 1.40
1383 1505 5.189342 TGTGCCATCCATCCATGTTTAAATT 59.811 36.000 0.00 0.00 0.00 1.82
1384 1506 6.382282 TGTGCCATCCATCCATGTTTAAATTA 59.618 34.615 0.00 0.00 0.00 1.40
1385 1507 6.925165 GTGCCATCCATCCATGTTTAAATTAG 59.075 38.462 0.00 0.00 0.00 1.73
1390 1512 5.530915 TCCATCCATGTTTAAATTAGCTCCG 59.469 40.000 0.00 0.00 0.00 4.63
1392 1514 6.183360 CCATCCATGTTTAAATTAGCTCCGTT 60.183 38.462 0.00 0.00 0.00 4.44
1394 1516 5.941058 TCCATGTTTAAATTAGCTCCGTTCA 59.059 36.000 0.00 0.00 0.00 3.18
1395 1517 6.027749 CCATGTTTAAATTAGCTCCGTTCAC 58.972 40.000 0.00 0.00 0.00 3.18
1396 1518 6.128007 CCATGTTTAAATTAGCTCCGTTCACT 60.128 38.462 0.00 0.00 0.00 3.41
1397 1519 6.870971 TGTTTAAATTAGCTCCGTTCACTT 57.129 33.333 0.00 0.00 0.00 3.16
1398 1520 7.266922 TGTTTAAATTAGCTCCGTTCACTTT 57.733 32.000 0.00 0.00 0.00 2.66
1399 1521 7.708998 TGTTTAAATTAGCTCCGTTCACTTTT 58.291 30.769 0.00 0.00 0.00 2.27
1401 1523 9.836076 GTTTAAATTAGCTCCGTTCACTTTTAT 57.164 29.630 0.00 0.00 0.00 1.40
1405 1527 9.444600 AAATTAGCTCCGTTCACTTTTATAAGA 57.555 29.630 0.00 0.00 35.30 2.10
1406 1528 7.823149 TTAGCTCCGTTCACTTTTATAAGAC 57.177 36.000 0.00 0.00 35.30 3.01
1407 1529 4.863131 AGCTCCGTTCACTTTTATAAGACG 59.137 41.667 0.00 0.15 35.30 4.18
1408 1530 4.624452 GCTCCGTTCACTTTTATAAGACGT 59.376 41.667 0.00 0.00 35.30 4.34
1410 1532 6.347160 GCTCCGTTCACTTTTATAAGACGTTT 60.347 38.462 0.00 0.00 35.30 3.60
1412 1534 6.700960 TCCGTTCACTTTTATAAGACGTTTCA 59.299 34.615 0.00 0.00 35.30 2.69
1413 1535 7.007697 CCGTTCACTTTTATAAGACGTTTCAG 58.992 38.462 0.00 0.00 35.30 3.02
1414 1536 7.095940 CCGTTCACTTTTATAAGACGTTTCAGA 60.096 37.037 0.00 0.00 35.30 3.27
1415 1537 7.734726 CGTTCACTTTTATAAGACGTTTCAGAC 59.265 37.037 0.00 0.00 35.30 3.51
1417 1539 8.294341 TCACTTTTATAAGACGTTTCAGACAG 57.706 34.615 0.00 0.00 35.30 3.51
1419 1541 8.548721 CACTTTTATAAGACGTTTCAGACAGTT 58.451 33.333 0.00 0.00 35.30 3.16
1420 1542 8.762426 ACTTTTATAAGACGTTTCAGACAGTTC 58.238 33.333 0.00 0.00 35.30 3.01
1423 1545 8.827177 TTATAAGACGTTTCAGACAGTTCATT 57.173 30.769 0.00 0.00 0.00 2.57
1424 1546 5.409643 AAGACGTTTCAGACAGTTCATTG 57.590 39.130 0.00 0.00 0.00 2.82
1426 1548 5.116180 AGACGTTTCAGACAGTTCATTGAA 58.884 37.500 0.00 0.00 0.00 2.69
1443 1565 7.156876 TCATTGAACTATTTTGGGTGATGTC 57.843 36.000 0.00 0.00 0.00 3.06
1445 1567 4.006989 TGAACTATTTTGGGTGATGTCCG 58.993 43.478 0.00 0.00 0.00 4.79
1447 1569 4.295141 ACTATTTTGGGTGATGTCCGAA 57.705 40.909 0.00 0.00 0.00 4.30
1448 1570 4.855340 ACTATTTTGGGTGATGTCCGAAT 58.145 39.130 0.00 0.00 0.00 3.34
1450 1572 3.932545 TTTTGGGTGATGTCCGAATTG 57.067 42.857 0.00 0.00 0.00 2.32
1451 1573 2.577606 TTGGGTGATGTCCGAATTGT 57.422 45.000 0.00 0.00 0.00 2.71
1452 1574 2.107950 TGGGTGATGTCCGAATTGTC 57.892 50.000 0.00 0.00 0.00 3.18
1457 1579 3.334691 GTGATGTCCGAATTGTCTCCAA 58.665 45.455 0.00 0.00 34.45 3.53
1458 1580 3.125316 GTGATGTCCGAATTGTCTCCAAC 59.875 47.826 0.00 0.00 32.26 3.77
1459 1581 1.790755 TGTCCGAATTGTCTCCAACG 58.209 50.000 0.00 0.00 32.26 4.10
1460 1582 1.069513 TGTCCGAATTGTCTCCAACGT 59.930 47.619 0.00 0.00 32.26 3.99
1461 1583 1.725164 GTCCGAATTGTCTCCAACGTC 59.275 52.381 0.00 0.00 32.26 4.34
1462 1584 1.616865 TCCGAATTGTCTCCAACGTCT 59.383 47.619 0.00 0.00 32.26 4.18
1463 1585 2.036733 TCCGAATTGTCTCCAACGTCTT 59.963 45.455 0.00 0.00 32.26 3.01
1464 1586 3.256383 TCCGAATTGTCTCCAACGTCTTA 59.744 43.478 0.00 0.00 32.26 2.10
1465 1587 3.367025 CCGAATTGTCTCCAACGTCTTAC 59.633 47.826 0.00 0.00 32.26 2.34
1466 1588 3.985279 CGAATTGTCTCCAACGTCTTACA 59.015 43.478 0.00 0.00 32.26 2.41
1469 1591 6.510478 CGAATTGTCTCCAACGTCTTACAAAA 60.510 38.462 0.00 0.00 32.26 2.44
1470 1592 5.728351 TTGTCTCCAACGTCTTACAAAAG 57.272 39.130 0.00 0.00 0.00 2.27
1472 1594 4.569162 TGTCTCCAACGTCTTACAAAAGTG 59.431 41.667 0.00 0.00 34.13 3.16
1473 1595 4.807304 GTCTCCAACGTCTTACAAAAGTGA 59.193 41.667 0.00 0.00 34.13 3.41
1475 1597 5.292589 TCTCCAACGTCTTACAAAAGTGAAC 59.707 40.000 0.00 0.00 34.13 3.18
1477 1599 5.064198 TCCAACGTCTTACAAAAGTGAACAG 59.936 40.000 0.00 0.00 34.13 3.16
1479 1601 5.968387 ACGTCTTACAAAAGTGAACAGAG 57.032 39.130 0.00 0.00 34.13 3.35
1481 1603 4.211374 CGTCTTACAAAAGTGAACAGAGGG 59.789 45.833 0.00 0.00 34.13 4.30
1482 1604 5.365619 GTCTTACAAAAGTGAACAGAGGGA 58.634 41.667 0.00 0.00 34.13 4.20
1483 1605 5.467063 GTCTTACAAAAGTGAACAGAGGGAG 59.533 44.000 0.00 0.00 34.13 4.30
1500 1637 6.926272 CAGAGGGAGTAATAAAGTATGCACTC 59.074 42.308 0.00 0.00 32.29 3.51
1583 1720 6.575244 TTTCTTGTAGGGTCACCATATGAT 57.425 37.500 3.65 0.00 40.28 2.45
1605 1742 8.056088 TGATGGAGGGATATTTTTCCTTGATA 57.944 34.615 0.00 0.00 35.97 2.15
1677 1814 7.826690 TGATAAGTAACCTTCTTTCATTTGCC 58.173 34.615 0.00 0.00 31.89 4.52
1681 1818 6.303839 AGTAACCTTCTTTCATTTGCCACTA 58.696 36.000 0.00 0.00 0.00 2.74
1682 1819 5.453567 AACCTTCTTTCATTTGCCACTAC 57.546 39.130 0.00 0.00 0.00 2.73
1683 1820 4.469657 ACCTTCTTTCATTTGCCACTACA 58.530 39.130 0.00 0.00 0.00 2.74
1684 1821 4.520492 ACCTTCTTTCATTTGCCACTACAG 59.480 41.667 0.00 0.00 0.00 2.74
1685 1822 4.520492 CCTTCTTTCATTTGCCACTACAGT 59.480 41.667 0.00 0.00 0.00 3.55
1870 2007 6.925165 ACGACCTCAAAATAGTTCGTAAAGAA 59.075 34.615 0.00 0.00 36.31 2.52
1920 2057 9.912634 TGGAATCTGATTTGTTTTCATTAAGAC 57.087 29.630 4.11 0.00 0.00 3.01
1922 2059 8.970691 AATCTGATTTGTTTTCATTAAGACCG 57.029 30.769 0.00 0.00 0.00 4.79
1973 2110 2.092212 AGTGTATGGCCAAAGGGATGAG 60.092 50.000 10.96 0.00 35.59 2.90
2046 2183 0.467290 TGTCCCCAAACTTCCACAGC 60.467 55.000 0.00 0.00 0.00 4.40
2057 2194 1.549170 CTTCCACAGCCTACTACCGTT 59.451 52.381 0.00 0.00 0.00 4.44
2136 2273 6.317789 TCAAGATTCATCCAGAAACAACAC 57.682 37.500 0.00 0.00 40.22 3.32
2137 2274 5.241506 TCAAGATTCATCCAGAAACAACACC 59.758 40.000 0.00 0.00 40.22 4.16
2200 2337 7.430760 AGGATTAGAACACTCTAAAGAGCAT 57.569 36.000 6.91 0.00 45.20 3.79
2273 2410 1.202428 TGTTGCTTTTGTTTACCCGCC 60.202 47.619 0.00 0.00 0.00 6.13
2635 2774 2.634940 TCTTGGCTTAGAGCACAAGTCT 59.365 45.455 20.33 0.00 44.75 3.24
2636 2775 2.462456 TGGCTTAGAGCACAAGTCTG 57.538 50.000 2.04 0.00 44.75 3.51
2702 2843 5.449107 TCTGTCTATTTACTGGCCGTATC 57.551 43.478 0.00 0.00 0.00 2.24
3180 3719 5.124776 TGTTAGATTTAATTGCTGGAACCCG 59.875 40.000 0.00 0.00 0.00 5.28
3198 3737 5.219343 ACCCGGTAGTATAATTTAGCACC 57.781 43.478 0.00 0.00 0.00 5.01
3278 3817 7.926018 GTGACTTTCAAAACAAGGATTTACCAT 59.074 33.333 0.00 0.00 42.04 3.55
3284 3823 7.222872 TCAAAACAAGGATTTACCATTGCAAT 58.777 30.769 5.99 5.99 42.04 3.56
3423 3962 8.902806 CATGTATGTTCCAACATTACCAGTATT 58.097 33.333 10.15 0.00 46.95 1.89
3425 3964 9.961264 TGTATGTTCCAACATTACCAGTATTAA 57.039 29.630 10.15 0.00 46.95 1.40
3647 4186 3.307762 GCAAGATAGGGAGTCCTTTGTGT 60.308 47.826 9.58 0.00 41.56 3.72
3761 5937 7.885297 AGTTGTGACATAAACATGTGCTTTAT 58.115 30.769 0.00 0.00 34.45 1.40
3857 6033 0.895530 TTCAGGGTCGCTTCTTCGAT 59.104 50.000 0.00 0.00 40.84 3.59
3874 6050 3.961182 TCGATTACGTGAGCAAGATACC 58.039 45.455 0.00 0.00 40.69 2.73
3900 6076 4.919774 TCCTACTTATTGGAACTTGGCA 57.080 40.909 0.00 0.00 0.00 4.92
3919 6095 2.551459 GCATCAGGTCATGCCATTAGAC 59.449 50.000 8.58 0.00 43.03 2.59
3963 6139 8.510505 CACTTGATTTGTTTTTGAAGGGAAAAA 58.489 29.630 0.00 0.00 33.42 1.94
3993 6169 7.544915 GTGATAGTACTTAAGTTTCAGTGACCC 59.455 40.741 14.49 0.00 0.00 4.46
4070 6247 5.040635 TCACTTGAAACCAAATTTTCGCTC 58.959 37.500 0.00 0.00 38.17 5.03
4173 6350 1.053424 TCCCCTGTACAGTGGTTCAC 58.947 55.000 21.91 0.00 34.10 3.18
4244 6421 8.309163 TGGACAAATATTTCAAATGTTTGAGC 57.691 30.769 29.01 21.36 46.68 4.26
4364 6541 7.610865 ACAAATCAGACAAAACCTTTGAAAGA 58.389 30.769 6.49 1.63 0.00 2.52
4435 6612 5.183331 GCATATCAGTCGACCTATAACTCCA 59.817 44.000 13.01 0.00 0.00 3.86
4475 6655 4.070716 CAAGCACTCTTTCTGGTGATCTT 58.929 43.478 0.00 0.00 35.69 2.40
4479 6659 4.502962 CACTCTTTCTGGTGATCTTCTCC 58.497 47.826 0.00 0.00 35.69 3.71
4480 6660 4.222588 CACTCTTTCTGGTGATCTTCTCCT 59.777 45.833 0.00 0.00 35.69 3.69
4481 6661 4.466015 ACTCTTTCTGGTGATCTTCTCCTC 59.534 45.833 0.00 0.00 31.62 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.593196 CAACACGAGGCCAAGAAGAA 58.407 50.000 5.01 0.00 0.00 2.52
66 67 2.046411 AACACCATGCGCCATCGA 60.046 55.556 4.18 0.00 38.10 3.59
129 130 1.826385 CAAGGATTTCTCCCGCACTT 58.174 50.000 0.00 0.00 43.21 3.16
163 193 3.582242 ATGGTGGCACCGCATTGGA 62.582 57.895 30.14 12.56 42.58 3.53
164 194 2.561549 GAATGGTGGCACCGCATTGG 62.562 60.000 30.14 0.00 42.58 3.16
165 195 1.153784 GAATGGTGGCACCGCATTG 60.154 57.895 30.14 0.00 42.58 2.82
166 196 2.350458 GGAATGGTGGCACCGCATT 61.350 57.895 30.14 24.22 42.58 3.56
167 197 2.755469 GGAATGGTGGCACCGCAT 60.755 61.111 30.14 19.10 42.58 4.73
168 198 3.505790 AAGGAATGGTGGCACCGCA 62.506 57.895 30.14 15.66 42.58 5.69
169 199 2.676471 AAGGAATGGTGGCACCGC 60.676 61.111 30.14 21.24 42.58 5.68
170 200 0.609131 AAGAAGGAATGGTGGCACCG 60.609 55.000 30.14 0.00 42.58 4.94
171 201 0.890683 CAAGAAGGAATGGTGGCACC 59.109 55.000 29.75 29.75 39.22 5.01
172 202 1.909700 TCAAGAAGGAATGGTGGCAC 58.090 50.000 9.70 9.70 0.00 5.01
173 203 2.517959 CTTCAAGAAGGAATGGTGGCA 58.482 47.619 1.86 0.00 34.87 4.92
211 241 1.305887 CGTAGAGGGAAGTGGGGGT 60.306 63.158 0.00 0.00 0.00 4.95
299 330 1.153628 GATCTGCCGCGTACCAAGT 60.154 57.895 4.92 0.00 0.00 3.16
394 428 7.553760 AGAAAAAGAAGAAACAAATGCCAACAT 59.446 29.630 0.00 0.00 38.49 2.71
441 478 2.741553 CGTACACATAGCATTGCTGGGA 60.742 50.000 21.31 1.35 40.10 4.37
514 557 2.515996 TTAGGCCCGGCTTTCTGTCG 62.516 60.000 9.86 0.00 44.42 4.35
600 706 2.161211 GCTTTCTTTGTGGCTCAGCTAG 59.839 50.000 0.00 0.00 0.00 3.42
601 707 2.154462 GCTTTCTTTGTGGCTCAGCTA 58.846 47.619 0.00 0.00 0.00 3.32
602 708 0.957362 GCTTTCTTTGTGGCTCAGCT 59.043 50.000 0.00 0.00 0.00 4.24
603 709 0.670162 TGCTTTCTTTGTGGCTCAGC 59.330 50.000 0.00 0.00 0.00 4.26
604 710 1.952296 AGTGCTTTCTTTGTGGCTCAG 59.048 47.619 0.00 0.00 0.00 3.35
605 711 1.677576 CAGTGCTTTCTTTGTGGCTCA 59.322 47.619 0.00 0.00 0.00 4.26
606 712 1.949525 TCAGTGCTTTCTTTGTGGCTC 59.050 47.619 0.00 0.00 0.00 4.70
607 713 2.057137 TCAGTGCTTTCTTTGTGGCT 57.943 45.000 0.00 0.00 0.00 4.75
608 714 2.735823 CTTCAGTGCTTTCTTTGTGGC 58.264 47.619 0.00 0.00 0.00 5.01
609 715 2.544486 GGCTTCAGTGCTTTCTTTGTGG 60.544 50.000 0.00 0.00 0.00 4.17
610 716 2.544486 GGGCTTCAGTGCTTTCTTTGTG 60.544 50.000 0.00 0.00 0.00 3.33
611 717 1.683385 GGGCTTCAGTGCTTTCTTTGT 59.317 47.619 0.00 0.00 0.00 2.83
612 718 1.682854 TGGGCTTCAGTGCTTTCTTTG 59.317 47.619 0.00 0.00 0.00 2.77
613 719 1.683385 GTGGGCTTCAGTGCTTTCTTT 59.317 47.619 0.00 0.00 0.00 2.52
614 720 1.133668 AGTGGGCTTCAGTGCTTTCTT 60.134 47.619 0.00 0.00 0.00 2.52
623 729 1.448540 CTGGCGTAGTGGGCTTCAG 60.449 63.158 0.00 0.00 0.00 3.02
654 760 3.309848 GGGAATTGGGGATTTTCTCCTGA 60.310 47.826 0.00 0.00 44.28 3.86
744 854 1.515736 GACCTTAACGCCTCGACGG 60.516 63.158 0.00 0.00 37.37 4.79
750 860 0.389948 CTCGCTTGACCTTAACGCCT 60.390 55.000 0.00 0.00 0.00 5.52
760 870 4.436448 GCACGCTGCTCGCTTGAC 62.436 66.667 8.74 0.00 40.06 3.18
846 956 2.160205 CTGTTCGGACCTCAGTCTACA 58.840 52.381 0.00 0.00 43.05 2.74
879 989 2.637872 TCTGGAAATTCGGAACAGACCT 59.362 45.455 5.07 0.00 33.62 3.85
896 1006 2.095364 GCTCACAAATCACAAGCTCTGG 60.095 50.000 0.00 0.00 0.00 3.86
911 1021 4.124970 GCATCATCAGTTCATAGCTCACA 58.875 43.478 0.00 0.00 0.00 3.58
938 1048 2.623416 TCTGAAGAACTGTCGCTGAGAA 59.377 45.455 0.00 0.00 0.00 2.87
1113 1229 3.917760 CCTCCGCTCGATCCCCAC 61.918 72.222 0.00 0.00 0.00 4.61
1303 1419 2.909006 AGCTTCTCCCTGTCTTGATTGA 59.091 45.455 0.00 0.00 0.00 2.57
1306 1422 2.831565 AGAGCTTCTCCCTGTCTTGAT 58.168 47.619 0.00 0.00 0.00 2.57
1371 1493 6.027749 GTGAACGGAGCTAATTTAAACATGG 58.972 40.000 0.00 0.00 0.00 3.66
1372 1494 6.842163 AGTGAACGGAGCTAATTTAAACATG 58.158 36.000 0.00 0.00 0.00 3.21
1373 1495 7.448748 AAGTGAACGGAGCTAATTTAAACAT 57.551 32.000 0.00 0.00 0.00 2.71
1374 1496 6.870971 AAGTGAACGGAGCTAATTTAAACA 57.129 33.333 0.00 0.00 0.00 2.83
1375 1497 9.836076 ATAAAAGTGAACGGAGCTAATTTAAAC 57.164 29.630 0.00 0.00 0.00 2.01
1381 1503 7.222224 CGTCTTATAAAAGTGAACGGAGCTAAT 59.778 37.037 0.00 0.00 34.13 1.73
1382 1504 6.529125 CGTCTTATAAAAGTGAACGGAGCTAA 59.471 38.462 0.00 0.00 34.13 3.09
1383 1505 6.032094 CGTCTTATAAAAGTGAACGGAGCTA 58.968 40.000 0.00 0.00 34.13 3.32
1384 1506 4.863131 CGTCTTATAAAAGTGAACGGAGCT 59.137 41.667 0.00 0.00 34.13 4.09
1385 1507 4.624452 ACGTCTTATAAAAGTGAACGGAGC 59.376 41.667 0.00 0.00 35.75 4.70
1390 1512 8.545420 TGTCTGAAACGTCTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 34.13 3.18
1392 1514 7.924412 ACTGTCTGAAACGTCTTATAAAAGTGA 59.076 33.333 0.00 0.00 34.13 3.41
1394 1516 8.658499 AACTGTCTGAAACGTCTTATAAAAGT 57.342 30.769 0.00 0.00 34.13 2.66
1395 1517 8.761497 TGAACTGTCTGAAACGTCTTATAAAAG 58.239 33.333 0.00 0.00 0.00 2.27
1396 1518 8.651391 TGAACTGTCTGAAACGTCTTATAAAA 57.349 30.769 0.00 0.00 0.00 1.52
1397 1519 8.827177 ATGAACTGTCTGAAACGTCTTATAAA 57.173 30.769 0.00 0.00 0.00 1.40
1398 1520 8.708742 CAATGAACTGTCTGAAACGTCTTATAA 58.291 33.333 0.00 0.00 0.00 0.98
1399 1521 8.085909 TCAATGAACTGTCTGAAACGTCTTATA 58.914 33.333 0.00 0.00 0.00 0.98
1401 1523 6.277605 TCAATGAACTGTCTGAAACGTCTTA 58.722 36.000 0.00 0.00 0.00 2.10
1405 1527 5.156804 GTTCAATGAACTGTCTGAAACGT 57.843 39.130 18.03 0.00 39.23 3.99
1417 1539 7.378181 ACATCACCCAAAATAGTTCAATGAAC 58.622 34.615 17.67 17.67 42.25 3.18
1419 1541 6.152661 GGACATCACCCAAAATAGTTCAATGA 59.847 38.462 0.00 0.00 0.00 2.57
1420 1542 6.332630 GGACATCACCCAAAATAGTTCAATG 58.667 40.000 0.00 0.00 0.00 2.82
1423 1545 4.006989 CGGACATCACCCAAAATAGTTCA 58.993 43.478 0.00 0.00 0.00 3.18
1424 1546 4.258543 TCGGACATCACCCAAAATAGTTC 58.741 43.478 0.00 0.00 0.00 3.01
1426 1548 3.992943 TCGGACATCACCCAAAATAGT 57.007 42.857 0.00 0.00 0.00 2.12
1430 1552 3.226777 ACAATTCGGACATCACCCAAAA 58.773 40.909 0.00 0.00 0.00 2.44
1431 1553 2.817258 GACAATTCGGACATCACCCAAA 59.183 45.455 0.00 0.00 0.00 3.28
1432 1554 2.039746 AGACAATTCGGACATCACCCAA 59.960 45.455 0.00 0.00 0.00 4.12
1434 1556 2.280628 GAGACAATTCGGACATCACCC 58.719 52.381 0.00 0.00 0.00 4.61
1435 1557 2.280628 GGAGACAATTCGGACATCACC 58.719 52.381 0.00 0.00 0.00 4.02
1436 1558 2.972625 TGGAGACAATTCGGACATCAC 58.027 47.619 0.00 0.00 37.44 3.06
1445 1567 6.851330 CTTTTGTAAGACGTTGGAGACAATTC 59.149 38.462 0.00 0.00 42.44 2.17
1447 1569 5.820947 ACTTTTGTAAGACGTTGGAGACAAT 59.179 36.000 0.00 0.00 42.63 2.71
1448 1570 5.064198 CACTTTTGTAAGACGTTGGAGACAA 59.936 40.000 0.00 0.00 40.48 3.18
1450 1572 4.807304 TCACTTTTGTAAGACGTTGGAGAC 59.193 41.667 0.00 0.00 35.30 3.36
1451 1573 5.013568 TCACTTTTGTAAGACGTTGGAGA 57.986 39.130 0.00 0.00 35.30 3.71
1452 1574 5.064198 TGTTCACTTTTGTAAGACGTTGGAG 59.936 40.000 0.00 0.00 35.30 3.86
1457 1579 4.809426 CCTCTGTTCACTTTTGTAAGACGT 59.191 41.667 0.00 0.00 35.30 4.34
1458 1580 4.211374 CCCTCTGTTCACTTTTGTAAGACG 59.789 45.833 0.00 0.00 35.30 4.18
1459 1581 5.365619 TCCCTCTGTTCACTTTTGTAAGAC 58.634 41.667 0.00 0.00 35.30 3.01
1460 1582 5.130477 ACTCCCTCTGTTCACTTTTGTAAGA 59.870 40.000 0.00 0.00 35.30 2.10
1461 1583 5.368989 ACTCCCTCTGTTCACTTTTGTAAG 58.631 41.667 0.00 0.00 37.40 2.34
1462 1584 5.367945 ACTCCCTCTGTTCACTTTTGTAA 57.632 39.130 0.00 0.00 0.00 2.41
1463 1585 6.488769 TTACTCCCTCTGTTCACTTTTGTA 57.511 37.500 0.00 0.00 0.00 2.41
1464 1586 3.933861 ACTCCCTCTGTTCACTTTTGT 57.066 42.857 0.00 0.00 0.00 2.83
1465 1587 7.979444 TTATTACTCCCTCTGTTCACTTTTG 57.021 36.000 0.00 0.00 0.00 2.44
1466 1588 8.218488 ACTTTATTACTCCCTCTGTTCACTTTT 58.782 33.333 0.00 0.00 0.00 2.27
1469 1591 6.936968 ACTTTATTACTCCCTCTGTTCACT 57.063 37.500 0.00 0.00 0.00 3.41
1470 1592 7.224949 GCATACTTTATTACTCCCTCTGTTCAC 59.775 40.741 0.00 0.00 0.00 3.18
1472 1594 7.224949 GTGCATACTTTATTACTCCCTCTGTTC 59.775 40.741 0.00 0.00 0.00 3.18
1473 1595 7.048512 GTGCATACTTTATTACTCCCTCTGTT 58.951 38.462 0.00 0.00 0.00 3.16
1475 1597 6.821388 AGTGCATACTTTATTACTCCCTCTG 58.179 40.000 0.00 0.00 31.66 3.35
1477 1599 5.921408 CGAGTGCATACTTTATTACTCCCTC 59.079 44.000 0.00 0.00 37.25 4.30
1479 1601 5.598769 ACGAGTGCATACTTTATTACTCCC 58.401 41.667 0.00 0.00 37.25 4.30
1483 1605 9.646336 CCAAATTACGAGTGCATACTTTATTAC 57.354 33.333 0.00 0.00 37.25 1.89
1583 1720 7.168219 CGATATCAAGGAAAAATATCCCTCCA 58.832 38.462 3.12 0.00 40.59 3.86
1605 1742 5.755849 AGGATAATCAAGTGGGAAAACGAT 58.244 37.500 0.00 0.00 0.00 3.73
1671 1808 9.243105 ACATAAGAAAATACTGTAGTGGCAAAT 57.757 29.630 0.00 0.00 0.00 2.32
1681 1818 9.383519 CCTACACATCACATAAGAAAATACTGT 57.616 33.333 0.00 0.00 0.00 3.55
1682 1819 9.383519 ACCTACACATCACATAAGAAAATACTG 57.616 33.333 0.00 0.00 0.00 2.74
1683 1820 9.959721 AACCTACACATCACATAAGAAAATACT 57.040 29.630 0.00 0.00 0.00 2.12
1836 1973 7.458409 ACTATTTTGAGGTCGTACTTGAGTA 57.542 36.000 0.00 0.00 0.00 2.59
1838 1975 7.279470 GAACTATTTTGAGGTCGTACTTGAG 57.721 40.000 0.00 0.00 0.00 3.02
1920 2057 5.872617 TCTGTTTACATGTTATGAAGACCGG 59.127 40.000 2.30 0.00 0.00 5.28
1922 2059 7.907214 AGTCTGTTTACATGTTATGAAGACC 57.093 36.000 2.30 0.00 0.00 3.85
1960 2097 6.015180 TGCATATTAAATCTCATCCCTTTGGC 60.015 38.462 0.00 0.00 0.00 4.52
1994 2131 9.843704 TTCTATGATGGATCTCCTTCCTAATAA 57.156 33.333 9.04 1.24 38.89 1.40
1995 2132 9.486123 CTTCTATGATGGATCTCCTTCCTAATA 57.514 37.037 9.04 1.90 38.89 0.98
2010 2147 4.446371 GGGACAACAGACTTCTATGATGG 58.554 47.826 0.00 0.00 0.00 3.51
2103 2240 7.170277 TCTGGATGAATCTTGATTCTTTGACA 58.830 34.615 19.91 13.83 0.00 3.58
2133 2270 6.074648 TCCACAAAATTTCCTATTGAGGTGT 58.925 36.000 0.00 0.00 44.19 4.16
2136 2273 6.101997 GCTTCCACAAAATTTCCTATTGAGG 58.898 40.000 0.00 0.00 45.35 3.86
2137 2274 6.690530 TGCTTCCACAAAATTTCCTATTGAG 58.309 36.000 0.00 0.00 0.00 3.02
2278 2415 7.524294 TCAGAAGAAACAAAAGCAACATTTC 57.476 32.000 0.00 0.00 0.00 2.17
2410 2549 9.079833 CACACAATTATTTTTCCTGAATAGCAG 57.920 33.333 0.00 0.00 44.49 4.24
2702 2843 4.564372 CAGCGGATGGATACTGATAAATCG 59.436 45.833 0.00 0.00 37.61 3.34
3180 3719 4.564199 CCCCCGGTGCTAAATTATACTACC 60.564 50.000 0.00 0.00 0.00 3.18
3198 3737 1.743995 CGCAAGTTAAGGTCCCCCG 60.744 63.158 0.00 0.00 35.12 5.73
3278 3817 2.299582 CCCAGTGGAATCAACATTGCAA 59.700 45.455 11.95 0.00 41.56 4.08
3284 3823 0.251297 CTGCCCCAGTGGAATCAACA 60.251 55.000 11.95 0.00 35.39 3.33
3471 4010 6.874134 AGAAACGAAGCAACAACTATGTAGAT 59.126 34.615 0.00 0.00 39.40 1.98
3857 6033 3.853831 TTCGGTATCTTGCTCACGTAA 57.146 42.857 0.00 0.00 0.00 3.18
3874 6050 6.458342 GCCAAGTTCCAATAAGTAGGATTTCG 60.458 42.308 0.00 0.00 33.10 3.46
3900 6076 3.498774 GGTCTAATGGCATGACCTGAT 57.501 47.619 23.04 0.85 44.84 2.90
3919 6095 7.053316 TCAAGTGGGCAAAATTCATATATGG 57.947 36.000 12.78 0.00 0.00 2.74
3963 6139 9.355215 CACTGAAACTTAAGTACTATCACGATT 57.645 33.333 8.92 0.00 0.00 3.34
3964 6140 8.737175 TCACTGAAACTTAAGTACTATCACGAT 58.263 33.333 8.92 0.00 0.00 3.73
3978 6154 5.712917 ACAGTTTTTGGGTCACTGAAACTTA 59.287 36.000 5.57 0.00 40.43 2.24
4070 6247 3.809832 CCAACAACCTAGGAATGATAGCG 59.190 47.826 17.98 4.12 0.00 4.26
4173 6350 6.085555 ACTATGTTGGATGACAGTATACCG 57.914 41.667 0.00 0.00 32.19 4.02
4244 6421 1.043022 GCAAGGGGCCAATATTCTGG 58.957 55.000 4.39 0.00 39.71 3.86
4350 6527 6.406961 GGTGGAATGTCTCTTTCAAAGGTTTT 60.407 38.462 0.00 0.00 0.00 2.43
4364 6541 2.057922 AGGTGAACTGGTGGAATGTCT 58.942 47.619 0.00 0.00 0.00 3.41
4435 6612 0.842030 TGCTCCTTCTGTGGGATGGT 60.842 55.000 0.00 0.00 39.46 3.55
4475 6655 3.496692 CCATTGTTTGTGGTCTGAGGAGA 60.497 47.826 0.00 0.00 31.96 3.71
4479 6659 1.270550 GGCCATTGTTTGTGGTCTGAG 59.729 52.381 0.00 0.00 38.32 3.35
4480 6660 1.327303 GGCCATTGTTTGTGGTCTGA 58.673 50.000 0.00 0.00 38.32 3.27
4481 6661 1.039068 TGGCCATTGTTTGTGGTCTG 58.961 50.000 0.00 0.00 41.89 3.51


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

AutoCloner maintained by Alex Coulton.