Multiple sequence alignment - TraesCS6B01G106900

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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 TraesCS6B01G106900 chr6B 100.000 2228 0 0 1 2228 87506683 87508910 0.000000e+00 4115
1 TraesCS6B01G106900 chr6B 98.712 699 7 1 1530 2228 537323020 537322324 0.000000e+00 1240
2 TraesCS6B01G106900 chr6B 88.133 573 65 3 2 572 151413310 151413881 0.000000e+00 678
3 TraesCS6B01G106900 chr6D 96.064 813 27 4 604 1411 37414838 37415650 0.000000e+00 1319
4 TraesCS6B01G106900 chr6D 95.041 121 6 0 1409 1529 293324397 293324517 8.120000e-45 191
5 TraesCS6B01G106900 chr1B 98.862 703 4 1 1530 2228 60199350 60198648 0.000000e+00 1251
6 TraesCS6B01G106900 chr5A 98.440 705 11 0 1524 2228 58378978 58379682 0.000000e+00 1242
7 TraesCS6B01G106900 chr5A 98.712 699 7 1 1530 2228 454682430 454683126 0.000000e+00 1240
8 TraesCS6B01G106900 chr5A 85.657 502 66 6 75 572 71127581 71127082 7.050000e-145 523
9 TraesCS6B01G106900 chr3B 98.712 699 9 0 1530 2228 675633496 675634194 0.000000e+00 1242
10 TraesCS6B01G106900 chr5B 98.712 699 7 2 1530 2228 337174314 337173618 0.000000e+00 1240
11 TraesCS6B01G106900 chr5B 86.285 576 74 4 1 572 348579657 348580231 2.430000e-174 621
12 TraesCS6B01G106900 chr5B 94.262 122 6 1 1409 1529 696647315 696647194 3.780000e-43 185
13 TraesCS6B01G106900 chr6A 98.711 698 7 1 1531 2228 574530110 574530805 0.000000e+00 1238
14 TraesCS6B01G106900 chr6A 93.727 813 40 10 604 1411 48651684 48652490 0.000000e+00 1208
15 TraesCS6B01G106900 chr6A 78.103 580 111 15 1 572 511532643 511532072 9.790000e-94 353
16 TraesCS6B01G106900 chr3A 98.295 704 12 0 1525 2228 52582814 52583517 0.000000e+00 1234
17 TraesCS6B01G106900 chr3A 97.902 715 12 2 1515 2228 658750443 658749731 0.000000e+00 1234
18 TraesCS6B01G106900 chr7B 87.805 574 66 3 1 572 552705599 552706170 0.000000e+00 669
19 TraesCS6B01G106900 chr7B 87.631 574 65 4 1 572 552752589 552753158 0.000000e+00 662
20 TraesCS6B01G106900 chr7B 86.934 574 72 3 1 572 192802039 192802611 1.870000e-180 641
21 TraesCS6B01G106900 chr4B 81.498 454 82 2 4 455 38777455 38777002 2.700000e-99 372
22 TraesCS6B01G106900 chr2B 78.207 569 115 9 1 565 751297533 751298096 2.720000e-94 355
23 TraesCS6B01G106900 chr2B 99.153 118 1 0 1412 1529 412658360 412658243 1.730000e-51 213
24 TraesCS6B01G106900 chr2B 98.305 118 2 0 1412 1529 412643263 412643146 8.060000e-50 207
25 TraesCS6B01G106900 chr2B 98.305 118 2 0 1412 1529 412705757 412705640 8.060000e-50 207
26 TraesCS6B01G106900 chr2B 95.763 118 1 1 1412 1529 412712110 412711997 1.050000e-43 187
27 TraesCS6B01G106900 chr2B 93.966 116 7 0 1412 1527 799711464 799711349 2.270000e-40 176
28 TraesCS6B01G106900 chr7D 94.828 116 6 0 1414 1529 633809862 633809977 4.890000e-42 182
29 TraesCS6B01G106900 chr2A 94.068 118 7 0 1412 1529 532080903 532080786 1.760000e-41 180


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 TraesCS6B01G106900 chr6B 87506683 87508910 2227 False 4115 4115 100.000 1 2228 1 chr6B.!!$F1 2227
1 TraesCS6B01G106900 chr6B 537322324 537323020 696 True 1240 1240 98.712 1530 2228 1 chr6B.!!$R1 698
2 TraesCS6B01G106900 chr6B 151413310 151413881 571 False 678 678 88.133 2 572 1 chr6B.!!$F2 570
3 TraesCS6B01G106900 chr6D 37414838 37415650 812 False 1319 1319 96.064 604 1411 1 chr6D.!!$F1 807
4 TraesCS6B01G106900 chr1B 60198648 60199350 702 True 1251 1251 98.862 1530 2228 1 chr1B.!!$R1 698
5 TraesCS6B01G106900 chr5A 58378978 58379682 704 False 1242 1242 98.440 1524 2228 1 chr5A.!!$F1 704
6 TraesCS6B01G106900 chr5A 454682430 454683126 696 False 1240 1240 98.712 1530 2228 1 chr5A.!!$F2 698
7 TraesCS6B01G106900 chr3B 675633496 675634194 698 False 1242 1242 98.712 1530 2228 1 chr3B.!!$F1 698
8 TraesCS6B01G106900 chr5B 337173618 337174314 696 True 1240 1240 98.712 1530 2228 1 chr5B.!!$R1 698
9 TraesCS6B01G106900 chr5B 348579657 348580231 574 False 621 621 86.285 1 572 1 chr5B.!!$F1 571
10 TraesCS6B01G106900 chr6A 574530110 574530805 695 False 1238 1238 98.711 1531 2228 1 chr6A.!!$F2 697
11 TraesCS6B01G106900 chr6A 48651684 48652490 806 False 1208 1208 93.727 604 1411 1 chr6A.!!$F1 807
12 TraesCS6B01G106900 chr6A 511532072 511532643 571 True 353 353 78.103 1 572 1 chr6A.!!$R1 571
13 TraesCS6B01G106900 chr3A 52582814 52583517 703 False 1234 1234 98.295 1525 2228 1 chr3A.!!$F1 703
14 TraesCS6B01G106900 chr3A 658749731 658750443 712 True 1234 1234 97.902 1515 2228 1 chr3A.!!$R1 713
15 TraesCS6B01G106900 chr7B 552705599 552706170 571 False 669 669 87.805 1 572 1 chr7B.!!$F2 571
16 TraesCS6B01G106900 chr7B 552752589 552753158 569 False 662 662 87.631 1 572 1 chr7B.!!$F3 571
17 TraesCS6B01G106900 chr7B 192802039 192802611 572 False 641 641 86.934 1 572 1 chr7B.!!$F1 571
18 TraesCS6B01G106900 chr2B 751297533 751298096 563 False 355 355 78.207 1 565 1 chr2B.!!$F1 564

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
589 595 0.037419 GGGGAAAATTGCGTGCATGT 60.037 50.0 7.93 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1476 0.105224 TTTGCTGGTTTCGGAGTCGA 59.895 50.0 0.0 0.0 44.44 4.2 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
28 29 5.044328 AGGGATCCGGTAGCTTATGTATCTA 60.044 44.000 5.45 0.00 0.00 1.98
62 63 4.025396 GGCATGTGATCAAAGACTACATCG 60.025 45.833 0.00 0.00 30.15 3.84
77 78 2.073816 ACATCGTCCGCTTTGGTAAAG 58.926 47.619 0.00 0.00 41.46 1.85
92 93 3.181455 TGGTAAAGCCATCATACTCGCAT 60.181 43.478 0.00 0.00 43.61 4.73
102 103 5.105351 CCATCATACTCGCATATAAGGACCA 60.105 44.000 0.00 0.00 0.00 4.02
110 111 4.345547 TCGCATATAAGGACCACCATGTTA 59.654 41.667 0.00 0.00 38.94 2.41
125 126 0.834687 TGTTACGGAAGAGCCAGGGT 60.835 55.000 0.00 0.00 35.94 4.34
127 128 0.252103 TTACGGAAGAGCCAGGGTCT 60.252 55.000 16.01 16.01 42.52 3.85
143 144 2.359900 GGTCTTTGCTTCATCATCCGT 58.640 47.619 0.00 0.00 0.00 4.69
179 180 1.862201 CACGAAGCCTGTACAACGAAA 59.138 47.619 0.00 0.00 0.00 3.46
203 204 1.368579 GGGACCGACTGGACGAAAA 59.631 57.895 0.00 0.00 39.21 2.29
251 254 3.071023 CCGCCCTCATATCCTTGTAGAAA 59.929 47.826 0.00 0.00 0.00 2.52
255 258 4.103153 CCCTCATATCCTTGTAGAAAGCCA 59.897 45.833 0.00 0.00 0.00 4.75
256 259 5.397899 CCCTCATATCCTTGTAGAAAGCCAA 60.398 44.000 0.00 0.00 0.00 4.52
293 296 3.451402 TCAGTGTGAACCCTAGCTAGA 57.549 47.619 22.70 0.00 0.00 2.43
314 317 1.302033 CAGCCACCTCACGCTTTCT 60.302 57.895 0.00 0.00 31.40 2.52
316 319 0.886490 AGCCACCTCACGCTTTCTTG 60.886 55.000 0.00 0.00 28.56 3.02
342 346 2.028294 CGGGATCCTCCTCATCAATCTG 60.028 54.545 12.58 0.00 36.57 2.90
349 353 2.801111 CTCCTCATCAATCTGCACATCG 59.199 50.000 0.00 0.00 0.00 3.84
372 377 4.920640 TGAACTCCTCATCGTTAGATCC 57.079 45.455 0.00 0.00 34.23 3.36
376 381 2.625314 CTCCTCATCGTTAGATCCAGCA 59.375 50.000 0.00 0.00 34.23 4.41
384 389 2.416836 CGTTAGATCCAGCAGGTCGAAA 60.417 50.000 0.00 0.00 35.89 3.46
502 507 3.910490 GCGGCCAGAGAGATCGCT 61.910 66.667 2.24 0.00 42.62 4.93
572 578 1.641577 CGAGGAAGAAAAGCGTAGGG 58.358 55.000 0.00 0.00 0.00 3.53
573 579 1.739371 CGAGGAAGAAAAGCGTAGGGG 60.739 57.143 0.00 0.00 0.00 4.79
574 580 1.553704 GAGGAAGAAAAGCGTAGGGGA 59.446 52.381 0.00 0.00 0.00 4.81
575 581 1.982958 AGGAAGAAAAGCGTAGGGGAA 59.017 47.619 0.00 0.00 0.00 3.97
576 582 2.374170 AGGAAGAAAAGCGTAGGGGAAA 59.626 45.455 0.00 0.00 0.00 3.13
577 583 3.151554 GGAAGAAAAGCGTAGGGGAAAA 58.848 45.455 0.00 0.00 0.00 2.29
578 584 3.762288 GGAAGAAAAGCGTAGGGGAAAAT 59.238 43.478 0.00 0.00 0.00 1.82
579 585 4.219944 GGAAGAAAAGCGTAGGGGAAAATT 59.780 41.667 0.00 0.00 0.00 1.82
580 586 4.783764 AGAAAAGCGTAGGGGAAAATTG 57.216 40.909 0.00 0.00 0.00 2.32
581 587 3.056821 AGAAAAGCGTAGGGGAAAATTGC 60.057 43.478 0.00 0.00 0.00 3.56
582 588 0.808755 AAGCGTAGGGGAAAATTGCG 59.191 50.000 0.00 0.00 0.00 4.85
583 589 0.322187 AGCGTAGGGGAAAATTGCGT 60.322 50.000 0.00 0.00 0.00 5.24
584 590 0.179174 GCGTAGGGGAAAATTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
585 591 0.179174 CGTAGGGGAAAATTGCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
586 592 0.885196 GTAGGGGAAAATTGCGTGCA 59.115 50.000 0.00 0.00 0.00 4.57
587 593 1.476488 GTAGGGGAAAATTGCGTGCAT 59.524 47.619 0.00 0.00 0.00 3.96
588 594 0.247185 AGGGGAAAATTGCGTGCATG 59.753 50.000 0.09 0.09 0.00 4.06
589 595 0.037419 GGGGAAAATTGCGTGCATGT 60.037 50.000 7.93 0.00 0.00 3.21
590 596 1.349234 GGGAAAATTGCGTGCATGTC 58.651 50.000 7.93 0.53 0.00 3.06
591 597 1.336702 GGGAAAATTGCGTGCATGTCA 60.337 47.619 7.93 3.37 0.00 3.58
592 598 2.609350 GGAAAATTGCGTGCATGTCAT 58.391 42.857 7.93 0.00 0.00 3.06
593 599 2.346244 GGAAAATTGCGTGCATGTCATG 59.654 45.455 8.56 8.56 34.80 3.07
594 600 2.728690 AAATTGCGTGCATGTCATGT 57.271 40.000 14.26 0.00 34.19 3.21
595 601 1.985334 AATTGCGTGCATGTCATGTG 58.015 45.000 14.26 6.16 34.19 3.21
596 602 1.166989 ATTGCGTGCATGTCATGTGA 58.833 45.000 14.26 0.00 34.19 3.58
597 603 0.950116 TTGCGTGCATGTCATGTGAA 59.050 45.000 14.26 0.00 34.19 3.18
598 604 0.518195 TGCGTGCATGTCATGTGAAG 59.482 50.000 14.26 5.36 34.19 3.02
599 605 0.518636 GCGTGCATGTCATGTGAAGT 59.481 50.000 14.26 0.00 34.19 3.01
600 606 1.069022 GCGTGCATGTCATGTGAAGTT 60.069 47.619 14.26 0.00 34.19 2.66
601 607 2.605338 GCGTGCATGTCATGTGAAGTTT 60.605 45.455 14.26 0.00 34.19 2.66
602 608 3.228749 CGTGCATGTCATGTGAAGTTTC 58.771 45.455 14.26 0.00 0.00 2.78
709 716 5.670792 TGACGGACAGTACCAAGATAATT 57.329 39.130 0.00 0.00 0.00 1.40
923 931 4.036734 CGTTGCCTGCAATCCATAAATACT 59.963 41.667 7.94 0.00 38.28 2.12
1131 1139 2.671963 GTGCTCCCGGACCAAACC 60.672 66.667 0.73 0.00 0.00 3.27
1164 1172 1.567537 GTTCAACAGCAAGCGCGTA 59.432 52.632 8.43 0.00 45.49 4.42
1191 1199 0.800683 TCTACGATTCGCAACAGCCG 60.801 55.000 5.86 0.00 0.00 5.52
1292 1300 5.117287 GGTCGATCGACAGCTGAATAATAAC 59.883 44.000 39.98 19.62 46.20 1.89
1338 1347 3.377253 TGGATACGTTCCCTGTACTCT 57.623 47.619 12.35 0.00 44.77 3.24
1373 1382 6.634436 GCTCGGTTTATGCTTATTTCAATCAG 59.366 38.462 0.00 0.00 0.00 2.90
1392 1404 7.856145 AATCAGTAGAAGGTGATTGCTTAAG 57.144 36.000 0.00 0.00 40.98 1.85
1400 1412 5.041191 AGGTGATTGCTTAAGTCCTATGG 57.959 43.478 4.02 0.00 0.00 2.74
1402 1414 5.665812 AGGTGATTGCTTAAGTCCTATGGTA 59.334 40.000 4.02 0.00 0.00 3.25
1411 1423 9.832445 TGCTTAAGTCCTATGGTAAGAAATAAG 57.168 33.333 4.02 0.00 0.00 1.73
1412 1424 9.274206 GCTTAAGTCCTATGGTAAGAAATAAGG 57.726 37.037 4.02 0.00 0.00 2.69
1441 1453 9.503399 AAGTATATTTTTCGTCCTTCAACTCTT 57.497 29.630 0.00 0.00 0.00 2.85
1442 1454 9.503399 AGTATATTTTTCGTCCTTCAACTCTTT 57.497 29.630 0.00 0.00 0.00 2.52
1443 1455 9.756461 GTATATTTTTCGTCCTTCAACTCTTTC 57.244 33.333 0.00 0.00 0.00 2.62
1444 1456 4.789095 TTTTCGTCCTTCAACTCTTTCG 57.211 40.909 0.00 0.00 0.00 3.46
1445 1457 3.720949 TTCGTCCTTCAACTCTTTCGA 57.279 42.857 0.00 0.00 0.00 3.71
1446 1458 3.720949 TCGTCCTTCAACTCTTTCGAA 57.279 42.857 0.00 0.00 0.00 3.71
1447 1459 4.049546 TCGTCCTTCAACTCTTTCGAAA 57.950 40.909 10.71 10.71 0.00 3.46
1448 1460 4.049186 TCGTCCTTCAACTCTTTCGAAAG 58.951 43.478 28.26 28.26 37.36 2.62
1449 1461 3.802685 CGTCCTTCAACTCTTTCGAAAGT 59.197 43.478 31.29 16.12 37.31 2.66
1450 1462 4.980434 CGTCCTTCAACTCTTTCGAAAGTA 59.020 41.667 31.29 19.47 37.31 2.24
1451 1463 5.634020 CGTCCTTCAACTCTTTCGAAAGTAT 59.366 40.000 31.29 20.33 37.31 2.12
1452 1464 6.805271 CGTCCTTCAACTCTTTCGAAAGTATA 59.195 38.462 31.29 15.82 37.31 1.47
1453 1465 7.008447 CGTCCTTCAACTCTTTCGAAAGTATAG 59.992 40.741 31.29 24.54 37.31 1.31
1454 1466 6.812160 TCCTTCAACTCTTTCGAAAGTATAGC 59.188 38.462 31.29 0.00 37.31 2.97
1455 1467 6.590292 CCTTCAACTCTTTCGAAAGTATAGCA 59.410 38.462 31.29 14.52 37.31 3.49
1456 1468 7.117812 CCTTCAACTCTTTCGAAAGTATAGCAA 59.882 37.037 31.29 18.75 37.31 3.91
1457 1469 8.547967 TTCAACTCTTTCGAAAGTATAGCAAT 57.452 30.769 31.29 12.99 37.31 3.56
1458 1470 7.963981 TCAACTCTTTCGAAAGTATAGCAATG 58.036 34.615 31.29 21.03 37.31 2.82
1459 1471 6.910536 ACTCTTTCGAAAGTATAGCAATGG 57.089 37.500 31.29 14.62 37.31 3.16
1460 1472 6.407202 ACTCTTTCGAAAGTATAGCAATGGT 58.593 36.000 31.29 15.09 37.31 3.55
1461 1473 6.535508 ACTCTTTCGAAAGTATAGCAATGGTC 59.464 38.462 31.29 0.00 37.31 4.02
1462 1474 5.815740 TCTTTCGAAAGTATAGCAATGGTCC 59.184 40.000 31.29 0.00 37.31 4.46
1463 1475 4.067972 TCGAAAGTATAGCAATGGTCCC 57.932 45.455 0.00 0.00 0.00 4.46
1464 1476 3.709653 TCGAAAGTATAGCAATGGTCCCT 59.290 43.478 0.00 0.00 0.00 4.20
1465 1477 4.058817 CGAAAGTATAGCAATGGTCCCTC 58.941 47.826 0.00 0.00 0.00 4.30
1466 1478 3.753294 AAGTATAGCAATGGTCCCTCG 57.247 47.619 0.00 0.00 0.00 4.63
1467 1479 2.958818 AGTATAGCAATGGTCCCTCGA 58.041 47.619 0.00 0.00 0.00 4.04
1468 1480 2.628657 AGTATAGCAATGGTCCCTCGAC 59.371 50.000 0.00 0.00 38.38 4.20
1469 1481 1.794714 ATAGCAATGGTCCCTCGACT 58.205 50.000 0.00 0.00 39.15 4.18
1470 1482 1.112113 TAGCAATGGTCCCTCGACTC 58.888 55.000 0.00 0.00 39.15 3.36
1471 1483 1.153349 GCAATGGTCCCTCGACTCC 60.153 63.158 0.00 0.00 39.15 3.85
1472 1484 1.141881 CAATGGTCCCTCGACTCCG 59.858 63.158 0.00 0.00 39.15 4.63
1473 1485 1.000019 AATGGTCCCTCGACTCCGA 60.000 57.895 0.00 0.00 43.35 4.55
1474 1486 0.613853 AATGGTCCCTCGACTCCGAA 60.614 55.000 0.00 0.00 45.04 4.30
1475 1487 0.613853 ATGGTCCCTCGACTCCGAAA 60.614 55.000 0.00 0.00 45.04 3.46
1476 1488 1.214853 GGTCCCTCGACTCCGAAAC 59.785 63.158 0.00 0.00 45.04 2.78
1477 1489 1.214853 GTCCCTCGACTCCGAAACC 59.785 63.158 0.00 0.00 45.04 3.27
1478 1490 1.228644 TCCCTCGACTCCGAAACCA 60.229 57.895 0.00 0.00 45.04 3.67
1479 1491 1.215647 CCCTCGACTCCGAAACCAG 59.784 63.158 0.00 0.00 45.04 4.00
1480 1492 1.446272 CCTCGACTCCGAAACCAGC 60.446 63.158 0.00 0.00 45.04 4.85
1481 1493 1.289066 CTCGACTCCGAAACCAGCA 59.711 57.895 0.00 0.00 45.04 4.41
1482 1494 0.319555 CTCGACTCCGAAACCAGCAA 60.320 55.000 0.00 0.00 45.04 3.91
1483 1495 0.105224 TCGACTCCGAAACCAGCAAA 59.895 50.000 0.00 0.00 42.51 3.68
1484 1496 1.156736 CGACTCCGAAACCAGCAAAT 58.843 50.000 0.00 0.00 38.22 2.32
1485 1497 1.128692 CGACTCCGAAACCAGCAAATC 59.871 52.381 0.00 0.00 38.22 2.17
1486 1498 2.427506 GACTCCGAAACCAGCAAATCT 58.572 47.619 0.00 0.00 0.00 2.40
1487 1499 2.814336 GACTCCGAAACCAGCAAATCTT 59.186 45.455 0.00 0.00 0.00 2.40
1488 1500 4.000988 GACTCCGAAACCAGCAAATCTTA 58.999 43.478 0.00 0.00 0.00 2.10
1489 1501 4.003648 ACTCCGAAACCAGCAAATCTTAG 58.996 43.478 0.00 0.00 0.00 2.18
1490 1502 4.003648 CTCCGAAACCAGCAAATCTTAGT 58.996 43.478 0.00 0.00 0.00 2.24
1491 1503 4.000988 TCCGAAACCAGCAAATCTTAGTC 58.999 43.478 0.00 0.00 0.00 2.59
1492 1504 3.127030 CCGAAACCAGCAAATCTTAGTCC 59.873 47.826 0.00 0.00 0.00 3.85
1493 1505 3.127030 CGAAACCAGCAAATCTTAGTCCC 59.873 47.826 0.00 0.00 0.00 4.46
1494 1506 4.336280 GAAACCAGCAAATCTTAGTCCCT 58.664 43.478 0.00 0.00 0.00 4.20
1495 1507 3.636153 ACCAGCAAATCTTAGTCCCTC 57.364 47.619 0.00 0.00 0.00 4.30
1496 1508 2.912956 ACCAGCAAATCTTAGTCCCTCA 59.087 45.455 0.00 0.00 0.00 3.86
1497 1509 3.330701 ACCAGCAAATCTTAGTCCCTCAA 59.669 43.478 0.00 0.00 0.00 3.02
1498 1510 3.691609 CCAGCAAATCTTAGTCCCTCAAC 59.308 47.826 0.00 0.00 0.00 3.18
1499 1511 4.566488 CCAGCAAATCTTAGTCCCTCAACT 60.566 45.833 0.00 0.00 0.00 3.16
1500 1512 5.006386 CAGCAAATCTTAGTCCCTCAACTT 58.994 41.667 0.00 0.00 0.00 2.66
1501 1513 5.474876 CAGCAAATCTTAGTCCCTCAACTTT 59.525 40.000 0.00 0.00 0.00 2.66
1502 1514 5.707764 AGCAAATCTTAGTCCCTCAACTTTC 59.292 40.000 0.00 0.00 0.00 2.62
1503 1515 5.473504 GCAAATCTTAGTCCCTCAACTTTCA 59.526 40.000 0.00 0.00 0.00 2.69
1504 1516 6.016276 GCAAATCTTAGTCCCTCAACTTTCAA 60.016 38.462 0.00 0.00 0.00 2.69
1505 1517 7.470009 GCAAATCTTAGTCCCTCAACTTTCAAA 60.470 37.037 0.00 0.00 0.00 2.69
1506 1518 8.413229 CAAATCTTAGTCCCTCAACTTTCAAAA 58.587 33.333 0.00 0.00 0.00 2.44
1507 1519 6.937436 TCTTAGTCCCTCAACTTTCAAAAC 57.063 37.500 0.00 0.00 0.00 2.43
1508 1520 5.826208 TCTTAGTCCCTCAACTTTCAAAACC 59.174 40.000 0.00 0.00 0.00 3.27
1509 1521 3.976015 AGTCCCTCAACTTTCAAAACCA 58.024 40.909 0.00 0.00 0.00 3.67
1510 1522 3.954258 AGTCCCTCAACTTTCAAAACCAG 59.046 43.478 0.00 0.00 0.00 4.00
1511 1523 3.951680 GTCCCTCAACTTTCAAAACCAGA 59.048 43.478 0.00 0.00 0.00 3.86
1512 1524 4.584743 GTCCCTCAACTTTCAAAACCAGAT 59.415 41.667 0.00 0.00 0.00 2.90
1513 1525 5.768164 GTCCCTCAACTTTCAAAACCAGATA 59.232 40.000 0.00 0.00 0.00 1.98
1514 1526 6.264518 GTCCCTCAACTTTCAAAACCAGATAA 59.735 38.462 0.00 0.00 0.00 1.75
1515 1527 6.490040 TCCCTCAACTTTCAAAACCAGATAAG 59.510 38.462 0.00 0.00 0.00 1.73
1516 1528 6.265422 CCCTCAACTTTCAAAACCAGATAAGT 59.735 38.462 0.00 0.00 0.00 2.24
1517 1529 7.201911 CCCTCAACTTTCAAAACCAGATAAGTT 60.202 37.037 0.00 0.00 36.55 2.66
1518 1530 8.197439 CCTCAACTTTCAAAACCAGATAAGTTT 58.803 33.333 0.00 0.00 39.07 2.66
1526 1538 7.166167 TCAAAACCAGATAAGTTTAGTCCCTC 58.834 38.462 0.00 0.00 36.44 4.30
1573 1585 1.008403 ACTGGCACTACCCTCTAGGA 58.992 55.000 0.00 0.00 39.89 2.94
2113 2131 0.179009 CCTGTCATCCGGATTGCCAT 60.179 55.000 16.19 0.00 0.00 4.40
2191 2209 0.038166 ACCATGAGCCACCGTGAAAT 59.962 50.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.806247 GTCCTTATATGCGAGTATGATGGC 59.194 45.833 0.00 0.00 0.00 4.40
87 88 2.703536 ACATGGTGGTCCTTATATGCGA 59.296 45.455 0.00 0.00 34.23 5.10
88 89 3.126001 ACATGGTGGTCCTTATATGCG 57.874 47.619 0.00 0.00 34.23 4.73
92 93 4.288398 TCCGTAACATGGTGGTCCTTATA 58.712 43.478 0.00 0.00 34.23 0.98
102 103 0.981183 TGGCTCTTCCGTAACATGGT 59.019 50.000 0.00 0.00 37.80 3.55
110 111 1.128188 AAAGACCCTGGCTCTTCCGT 61.128 55.000 4.77 0.00 37.80 4.69
125 126 3.009723 GGAACGGATGATGAAGCAAAGA 58.990 45.455 0.00 0.00 0.00 2.52
127 128 2.091541 GGGAACGGATGATGAAGCAAA 58.908 47.619 0.00 0.00 0.00 3.68
143 144 1.078347 GTGCCTTGGGGATTGGGAA 59.922 57.895 0.00 0.00 33.58 3.97
170 171 2.563702 GGTCCCAACAGTTTCGTTGTA 58.436 47.619 3.39 0.00 43.89 2.41
179 180 1.458777 TCCAGTCGGTCCCAACAGT 60.459 57.895 0.00 0.00 0.00 3.55
188 189 1.952635 GCGTTTTCGTCCAGTCGGT 60.953 57.895 0.00 0.00 46.03 4.69
221 224 2.056906 ATATGAGGGCGGCCTGGAAC 62.057 60.000 38.01 21.45 0.00 3.62
251 254 1.716028 AAACCTTCTCCCCGTTGGCT 61.716 55.000 0.00 0.00 0.00 4.75
255 258 3.329814 ACTGATAAAACCTTCTCCCCGTT 59.670 43.478 0.00 0.00 0.00 4.44
256 259 2.910977 ACTGATAAAACCTTCTCCCCGT 59.089 45.455 0.00 0.00 0.00 5.28
342 346 1.795768 TGAGGAGTTCAACGATGTGC 58.204 50.000 0.00 0.00 31.34 4.57
349 353 5.044558 GGATCTAACGATGAGGAGTTCAAC 58.955 45.833 0.00 0.00 39.77 3.18
384 389 3.897505 CCAACCCTGTTCTTGAGGATTTT 59.102 43.478 0.00 0.00 31.48 1.82
393 398 2.597510 GCCGCCAACCCTGTTCTT 60.598 61.111 0.00 0.00 0.00 2.52
502 507 1.119684 CCCATACCACGACCTGATCA 58.880 55.000 0.00 0.00 0.00 2.92
565 571 0.179174 CACGCAATTTTCCCCTACGC 60.179 55.000 0.00 0.00 0.00 4.42
567 573 0.885196 TGCACGCAATTTTCCCCTAC 59.115 50.000 0.00 0.00 0.00 3.18
572 578 2.063156 TGACATGCACGCAATTTTCC 57.937 45.000 0.00 0.00 0.00 3.13
573 579 2.988493 ACATGACATGCACGCAATTTTC 59.012 40.909 15.49 0.00 0.00 2.29
574 580 2.732500 CACATGACATGCACGCAATTTT 59.267 40.909 15.49 0.00 0.00 1.82
575 581 2.030096 TCACATGACATGCACGCAATTT 60.030 40.909 15.49 0.00 0.00 1.82
576 582 1.540707 TCACATGACATGCACGCAATT 59.459 42.857 15.49 0.00 0.00 2.32
577 583 1.166989 TCACATGACATGCACGCAAT 58.833 45.000 15.49 0.00 0.00 3.56
578 584 0.950116 TTCACATGACATGCACGCAA 59.050 45.000 15.49 0.00 0.00 4.85
579 585 0.518195 CTTCACATGACATGCACGCA 59.482 50.000 15.49 0.00 0.00 5.24
580 586 0.518636 ACTTCACATGACATGCACGC 59.481 50.000 15.49 0.00 0.00 5.34
581 587 2.975410 AACTTCACATGACATGCACG 57.025 45.000 15.49 4.69 0.00 5.34
582 588 3.058983 TCGAAACTTCACATGACATGCAC 60.059 43.478 15.49 0.00 0.00 4.57
583 589 3.137533 TCGAAACTTCACATGACATGCA 58.862 40.909 15.49 0.00 0.00 3.96
584 590 3.811722 TCGAAACTTCACATGACATGC 57.188 42.857 15.49 0.00 0.00 4.06
585 591 6.857451 TGAATTTCGAAACTTCACATGACATG 59.143 34.615 21.42 14.02 0.00 3.21
586 592 6.969366 TGAATTTCGAAACTTCACATGACAT 58.031 32.000 21.42 0.43 0.00 3.06
587 593 6.370433 TGAATTTCGAAACTTCACATGACA 57.630 33.333 21.42 1.79 0.00 3.58
588 594 5.340667 GCTGAATTTCGAAACTTCACATGAC 59.659 40.000 21.42 11.51 0.00 3.06
589 595 5.239306 AGCTGAATTTCGAAACTTCACATGA 59.761 36.000 21.42 9.10 0.00 3.07
590 596 5.455392 AGCTGAATTTCGAAACTTCACATG 58.545 37.500 21.42 16.32 0.00 3.21
591 597 5.695851 AGCTGAATTTCGAAACTTCACAT 57.304 34.783 21.42 14.48 0.00 3.21
592 598 6.612247 TTAGCTGAATTTCGAAACTTCACA 57.388 33.333 21.42 13.67 0.00 3.58
593 599 8.507470 AAATTAGCTGAATTTCGAAACTTCAC 57.493 30.769 21.42 18.61 42.95 3.18
709 716 4.390264 TCCGTTTTCATGTATTCACACCA 58.610 39.130 0.00 0.00 37.54 4.17
738 746 7.658261 AGTAAAGGTATGGCTTCTTTTGTTTC 58.342 34.615 0.00 0.00 33.44 2.78
923 931 6.764379 TCACAATGACTCTTTACACATACCA 58.236 36.000 0.00 0.00 0.00 3.25
1338 1347 2.772077 TAAACCGAGCCAGTGCAATA 57.228 45.000 0.00 0.00 41.13 1.90
1373 1382 5.735766 AGGACTTAAGCAATCACCTTCTAC 58.264 41.667 1.29 0.00 0.00 2.59
1415 1427 9.503399 AAGAGTTGAAGGACGAAAAATATACTT 57.497 29.630 0.00 0.00 0.00 2.24
1416 1428 9.503399 AAAGAGTTGAAGGACGAAAAATATACT 57.497 29.630 0.00 0.00 0.00 2.12
1417 1429 9.756461 GAAAGAGTTGAAGGACGAAAAATATAC 57.244 33.333 0.00 0.00 0.00 1.47
1418 1430 8.653338 CGAAAGAGTTGAAGGACGAAAAATATA 58.347 33.333 0.00 0.00 0.00 0.86
1419 1431 7.386848 TCGAAAGAGTTGAAGGACGAAAAATAT 59.613 33.333 0.00 0.00 34.84 1.28
1420 1432 6.702723 TCGAAAGAGTTGAAGGACGAAAAATA 59.297 34.615 0.00 0.00 34.84 1.40
1421 1433 5.526111 TCGAAAGAGTTGAAGGACGAAAAAT 59.474 36.000 0.00 0.00 34.84 1.82
1422 1434 4.871557 TCGAAAGAGTTGAAGGACGAAAAA 59.128 37.500 0.00 0.00 34.84 1.94
1423 1435 4.435425 TCGAAAGAGTTGAAGGACGAAAA 58.565 39.130 0.00 0.00 34.84 2.29
1424 1436 4.049546 TCGAAAGAGTTGAAGGACGAAA 57.950 40.909 0.00 0.00 34.84 3.46
1425 1437 3.720949 TCGAAAGAGTTGAAGGACGAA 57.279 42.857 0.00 0.00 34.84 3.85
1426 1438 3.720949 TTCGAAAGAGTTGAAGGACGA 57.279 42.857 0.00 0.00 43.69 4.20
1427 1439 3.802685 ACTTTCGAAAGAGTTGAAGGACG 59.197 43.478 37.54 13.08 43.69 4.79
1428 1440 7.201453 GCTATACTTTCGAAAGAGTTGAAGGAC 60.201 40.741 37.54 15.65 43.69 3.85
1429 1441 6.812160 GCTATACTTTCGAAAGAGTTGAAGGA 59.188 38.462 37.54 10.60 43.69 3.36
1430 1442 6.590292 TGCTATACTTTCGAAAGAGTTGAAGG 59.410 38.462 37.54 20.45 43.69 3.46
1431 1443 7.582435 TGCTATACTTTCGAAAGAGTTGAAG 57.418 36.000 37.54 24.81 43.69 3.02
1432 1444 7.956420 TTGCTATACTTTCGAAAGAGTTGAA 57.044 32.000 37.54 20.22 43.69 2.69
1433 1445 7.064609 CCATTGCTATACTTTCGAAAGAGTTGA 59.935 37.037 37.54 19.74 43.69 3.18
1434 1446 7.148407 ACCATTGCTATACTTTCGAAAGAGTTG 60.148 37.037 37.54 25.65 43.69 3.16
1435 1447 6.879458 ACCATTGCTATACTTTCGAAAGAGTT 59.121 34.615 37.54 24.22 43.69 3.01
1436 1448 6.407202 ACCATTGCTATACTTTCGAAAGAGT 58.593 36.000 37.54 26.99 43.69 3.24
1437 1449 6.018669 GGACCATTGCTATACTTTCGAAAGAG 60.019 42.308 37.54 26.52 43.69 2.85
1438 1450 5.815740 GGACCATTGCTATACTTTCGAAAGA 59.184 40.000 37.54 23.56 39.31 2.52
1439 1451 5.007724 GGGACCATTGCTATACTTTCGAAAG 59.992 44.000 31.29 31.29 41.73 2.62
1440 1452 4.879545 GGGACCATTGCTATACTTTCGAAA 59.120 41.667 10.71 10.71 0.00 3.46
1441 1453 4.163458 AGGGACCATTGCTATACTTTCGAA 59.837 41.667 0.00 0.00 0.00 3.71
1442 1454 3.709653 AGGGACCATTGCTATACTTTCGA 59.290 43.478 0.00 0.00 0.00 3.71
1443 1455 4.058817 GAGGGACCATTGCTATACTTTCG 58.941 47.826 0.00 0.00 0.00 3.46
1444 1456 4.058817 CGAGGGACCATTGCTATACTTTC 58.941 47.826 0.00 0.00 0.00 2.62
1445 1457 3.709653 TCGAGGGACCATTGCTATACTTT 59.290 43.478 0.00 0.00 0.00 2.66
1446 1458 3.069729 GTCGAGGGACCATTGCTATACTT 59.930 47.826 0.00 0.00 37.19 2.24
1447 1459 2.628657 GTCGAGGGACCATTGCTATACT 59.371 50.000 0.00 0.00 37.19 2.12
1448 1460 2.628657 AGTCGAGGGACCATTGCTATAC 59.371 50.000 0.00 0.00 44.54 1.47
1449 1461 2.891580 GAGTCGAGGGACCATTGCTATA 59.108 50.000 0.00 0.00 44.54 1.31
1450 1462 1.689273 GAGTCGAGGGACCATTGCTAT 59.311 52.381 0.00 0.00 44.54 2.97
1451 1463 1.112113 GAGTCGAGGGACCATTGCTA 58.888 55.000 0.00 0.00 44.54 3.49
1452 1464 1.617947 GGAGTCGAGGGACCATTGCT 61.618 60.000 0.00 0.00 44.54 3.91
1453 1465 1.153349 GGAGTCGAGGGACCATTGC 60.153 63.158 0.00 0.00 44.54 3.56
1454 1466 1.141881 CGGAGTCGAGGGACCATTG 59.858 63.158 0.00 0.00 44.54 2.82
1455 1467 0.613853 TTCGGAGTCGAGGGACCATT 60.614 55.000 0.00 0.00 46.75 3.16
1456 1468 0.613853 TTTCGGAGTCGAGGGACCAT 60.614 55.000 0.00 0.00 46.75 3.55
1457 1469 1.228644 TTTCGGAGTCGAGGGACCA 60.229 57.895 0.00 0.00 46.75 4.02
1458 1470 1.214853 GTTTCGGAGTCGAGGGACC 59.785 63.158 0.00 0.00 46.75 4.46
1459 1471 1.214853 GGTTTCGGAGTCGAGGGAC 59.785 63.158 0.00 0.00 46.75 4.46
1460 1472 1.228644 TGGTTTCGGAGTCGAGGGA 60.229 57.895 0.00 0.00 46.75 4.20
1461 1473 1.215647 CTGGTTTCGGAGTCGAGGG 59.784 63.158 0.00 0.00 46.75 4.30
1462 1474 1.446272 GCTGGTTTCGGAGTCGAGG 60.446 63.158 0.00 0.00 46.75 4.63
1463 1475 0.319555 TTGCTGGTTTCGGAGTCGAG 60.320 55.000 0.00 0.00 46.75 4.04
1464 1476 0.105224 TTTGCTGGTTTCGGAGTCGA 59.895 50.000 0.00 0.00 44.44 4.20
1465 1477 1.128692 GATTTGCTGGTTTCGGAGTCG 59.871 52.381 0.00 0.00 37.82 4.18
1466 1478 2.427506 AGATTTGCTGGTTTCGGAGTC 58.572 47.619 0.00 0.00 0.00 3.36
1467 1479 2.568623 AGATTTGCTGGTTTCGGAGT 57.431 45.000 0.00 0.00 0.00 3.85
1468 1480 4.003648 ACTAAGATTTGCTGGTTTCGGAG 58.996 43.478 0.00 0.00 0.00 4.63
1469 1481 4.000988 GACTAAGATTTGCTGGTTTCGGA 58.999 43.478 0.00 0.00 0.00 4.55
1470 1482 3.127030 GGACTAAGATTTGCTGGTTTCGG 59.873 47.826 0.00 0.00 0.00 4.30
1471 1483 3.127030 GGGACTAAGATTTGCTGGTTTCG 59.873 47.826 0.00 0.00 0.00 3.46
1472 1484 4.336280 AGGGACTAAGATTTGCTGGTTTC 58.664 43.478 0.00 0.00 36.02 2.78
1473 1485 4.202567 TGAGGGACTAAGATTTGCTGGTTT 60.203 41.667 0.00 0.00 41.55 3.27
1474 1486 3.330701 TGAGGGACTAAGATTTGCTGGTT 59.669 43.478 0.00 0.00 41.55 3.67
1475 1487 2.912956 TGAGGGACTAAGATTTGCTGGT 59.087 45.455 0.00 0.00 41.55 4.00
1476 1488 3.634397 TGAGGGACTAAGATTTGCTGG 57.366 47.619 0.00 0.00 41.55 4.85
1477 1489 4.583871 AGTTGAGGGACTAAGATTTGCTG 58.416 43.478 0.00 0.00 41.55 4.41
1478 1490 4.917906 AGTTGAGGGACTAAGATTTGCT 57.082 40.909 0.00 0.00 41.55 3.91
1479 1491 5.473504 TGAAAGTTGAGGGACTAAGATTTGC 59.526 40.000 0.00 0.00 41.55 3.68
1480 1492 7.510549 TTGAAAGTTGAGGGACTAAGATTTG 57.489 36.000 0.00 0.00 41.55 2.32
1481 1493 8.414003 GTTTTGAAAGTTGAGGGACTAAGATTT 58.586 33.333 0.00 0.00 41.55 2.17
1482 1494 7.014326 GGTTTTGAAAGTTGAGGGACTAAGATT 59.986 37.037 0.00 0.00 41.55 2.40
1483 1495 6.490381 GGTTTTGAAAGTTGAGGGACTAAGAT 59.510 38.462 0.00 0.00 41.55 2.40
1484 1496 5.826208 GGTTTTGAAAGTTGAGGGACTAAGA 59.174 40.000 0.00 0.00 41.55 2.10
1485 1497 5.592688 TGGTTTTGAAAGTTGAGGGACTAAG 59.407 40.000 0.00 0.00 41.55 2.18
1486 1498 5.511363 TGGTTTTGAAAGTTGAGGGACTAA 58.489 37.500 0.00 0.00 41.55 2.24
1487 1499 5.104277 TCTGGTTTTGAAAGTTGAGGGACTA 60.104 40.000 0.00 0.00 41.55 2.59
1489 1501 3.951680 TCTGGTTTTGAAAGTTGAGGGAC 59.048 43.478 0.00 0.00 0.00 4.46
1490 1502 4.243793 TCTGGTTTTGAAAGTTGAGGGA 57.756 40.909 0.00 0.00 0.00 4.20
1491 1503 6.265422 ACTTATCTGGTTTTGAAAGTTGAGGG 59.735 38.462 0.00 0.00 0.00 4.30
1492 1504 7.277174 ACTTATCTGGTTTTGAAAGTTGAGG 57.723 36.000 0.00 0.00 0.00 3.86
1497 1509 8.847196 GGACTAAACTTATCTGGTTTTGAAAGT 58.153 33.333 0.00 0.00 37.88 2.66
1498 1510 8.297426 GGGACTAAACTTATCTGGTTTTGAAAG 58.703 37.037 0.00 0.00 37.88 2.62
1499 1511 8.002459 AGGGACTAAACTTATCTGGTTTTGAAA 58.998 33.333 0.00 0.00 36.02 2.69
1500 1512 7.523415 AGGGACTAAACTTATCTGGTTTTGAA 58.477 34.615 0.00 0.00 36.02 2.69
1501 1513 7.086685 AGGGACTAAACTTATCTGGTTTTGA 57.913 36.000 0.00 0.00 36.02 2.69
1502 1514 6.940298 TGAGGGACTAAACTTATCTGGTTTTG 59.060 38.462 0.00 0.00 41.55 2.44
1503 1515 7.086685 TGAGGGACTAAACTTATCTGGTTTT 57.913 36.000 0.00 0.00 41.55 2.43
1504 1516 6.697641 TGAGGGACTAAACTTATCTGGTTT 57.302 37.500 0.00 0.00 41.55 3.27
1505 1517 6.697641 TTGAGGGACTAAACTTATCTGGTT 57.302 37.500 0.00 0.00 41.55 3.67
1506 1518 6.215636 ACATTGAGGGACTAAACTTATCTGGT 59.784 38.462 0.00 0.00 41.55 4.00
1507 1519 6.653989 ACATTGAGGGACTAAACTTATCTGG 58.346 40.000 0.00 0.00 41.55 3.86
1508 1520 9.319143 CTTACATTGAGGGACTAAACTTATCTG 57.681 37.037 0.00 0.00 41.55 2.90
1509 1521 9.268282 TCTTACATTGAGGGACTAAACTTATCT 57.732 33.333 0.00 0.00 41.55 1.98
1510 1522 9.315525 GTCTTACATTGAGGGACTAAACTTATC 57.684 37.037 0.00 0.00 41.55 1.75
1511 1523 8.822805 TGTCTTACATTGAGGGACTAAACTTAT 58.177 33.333 0.00 0.00 41.55 1.73
1512 1524 8.197592 TGTCTTACATTGAGGGACTAAACTTA 57.802 34.615 0.00 0.00 41.55 2.24
1513 1525 7.074653 TGTCTTACATTGAGGGACTAAACTT 57.925 36.000 0.00 0.00 41.55 2.66
1514 1526 6.681729 TGTCTTACATTGAGGGACTAAACT 57.318 37.500 0.00 0.00 41.55 2.66
1515 1527 7.923414 ATTGTCTTACATTGAGGGACTAAAC 57.077 36.000 0.00 0.00 41.55 2.01
1516 1528 8.265055 CCTATTGTCTTACATTGAGGGACTAAA 58.735 37.037 0.00 0.00 41.55 1.85
1517 1529 7.635089 GCCTATTGTCTTACATTGAGGGACTAA 60.635 40.741 0.00 0.00 41.55 2.24
1518 1530 6.183360 GCCTATTGTCTTACATTGAGGGACTA 60.183 42.308 0.00 0.00 41.55 2.59
1522 1534 5.041191 AGCCTATTGTCTTACATTGAGGG 57.959 43.478 0.00 0.00 0.00 4.30
1526 1538 5.163519 CCCCAAAGCCTATTGTCTTACATTG 60.164 44.000 0.00 0.00 0.00 2.82
1562 1574 1.917099 TAGGCCACTCCTAGAGGGTA 58.083 55.000 5.01 0.00 45.41 3.69
2113 2131 4.347360 CATATTCTGATGCAGACTGGGA 57.653 45.455 4.26 0.00 40.46 4.37


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

AutoCloner maintained by Alex Coulton.