Multiple sequence alignment - TraesCS2B01G312500

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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 TraesCS2B01G312500 chr2B 100.000 3769 0 0 1 3769 447821462 447825230 0.000000e+00 6961.0
1 TraesCS2B01G312500 chr2B 95.378 238 11 0 3513 3750 233079187 233078950 2.750000e-101 379.0
2 TraesCS2B01G312500 chr2D 93.375 1932 66 28 1866 3769 376354145 376356042 0.000000e+00 2802.0
3 TraesCS2B01G312500 chr2D 89.954 1314 77 25 547 1828 376352853 376354143 0.000000e+00 1644.0
4 TraesCS2B01G312500 chr2D 88.037 535 24 12 1 509 376352150 376352670 6.970000e-167 597.0
5 TraesCS2B01G312500 chr2A 88.695 1203 77 28 641 1828 509577291 509578449 0.000000e+00 1413.0
6 TraesCS2B01G312500 chr2A 92.582 728 46 6 1865 2592 509578450 509579169 0.000000e+00 1038.0
7 TraesCS2B01G312500 chr2A 90.418 814 28 21 2591 3379 509579292 509580080 0.000000e+00 1026.0
8 TraesCS2B01G312500 chr2A 89.362 752 30 27 2650 3376 509990722 509991448 0.000000e+00 900.0
9 TraesCS2B01G312500 chr2A 94.335 406 19 1 3364 3769 509580097 509580498 1.490000e-173 619.0
10 TraesCS2B01G312500 chr2A 91.443 409 19 3 3364 3769 509991468 509991863 7.120000e-152 547.0
11 TraesCS2B01G312500 chr2A 91.185 329 12 5 1 329 509548665 509548976 7.480000e-117 431.0
12 TraesCS2B01G312500 chr2A 94.545 110 4 2 425 534 509548982 509549089 6.470000e-38 169.0
13 TraesCS2B01G312500 chr1A 93.852 244 15 0 3513 3756 36266033 36265790 5.950000e-98 368.0
14 TraesCS2B01G312500 chr5B 84.946 93 14 0 3536 3628 661863401 661863309 1.110000e-15 95.3


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 TraesCS2B01G312500 chr2B 447821462 447825230 3768 False 6961.0 6961 100.000000 1 3769 1 chr2B.!!$F1 3768
1 TraesCS2B01G312500 chr2D 376352150 376356042 3892 False 1681.0 2802 90.455333 1 3769 3 chr2D.!!$F1 3768
2 TraesCS2B01G312500 chr2A 509577291 509580498 3207 False 1024.0 1413 91.507500 641 3769 4 chr2A.!!$F2 3128
3 TraesCS2B01G312500 chr2A 509990722 509991863 1141 False 723.5 900 90.402500 2650 3769 2 chr2A.!!$F3 1119

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
444 471 0.179034 GGCATTAGTCCAGAGGGCTG 60.179 60.000 0.0 0.0 41.93 4.85 F
1233 1430 0.250338 AGTTCAACCCGCTGTTCTCC 60.250 55.000 0.0 0.0 34.00 3.71 F
1596 1795 1.003118 ACTCGTAAAATGCCTGCTCCA 59.997 47.619 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2522 0.329596 GTTCTGGCAAGGGATGAGGT 59.670 55.000 0.00 0.0 0.0 3.85 R
2470 2685 1.004277 TCTTCCCGTGCTTTATTGGCT 59.996 47.619 0.00 0.0 0.0 4.75 R
3384 3786 0.966179 TCTGCGCTCCAAGTAAGACA 59.034 50.000 9.73 0.0 0.0 3.41 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
46 47 3.582998 ATATGCACATTGTACCTGCCT 57.417 42.857 0.00 0.00 0.00 4.75
74 75 3.788227 TTGAGTACCATGCTGGAGTTT 57.212 42.857 8.91 0.00 40.96 2.66
80 81 2.893424 ACCATGCTGGAGTTTTGGATT 58.107 42.857 8.91 0.00 40.96 3.01
105 106 5.680619 TCTTACATTATACAAGGTGCTGGG 58.319 41.667 0.00 0.00 30.00 4.45
118 119 1.336755 GTGCTGGGATTTTGACGTTGT 59.663 47.619 0.00 0.00 0.00 3.32
261 262 4.130857 TGTTGAAACATGCCTCTCGTTTA 58.869 39.130 0.00 0.00 33.18 2.01
272 273 5.168569 TGCCTCTCGTTTAAACTGTAGATG 58.831 41.667 16.01 12.59 0.00 2.90
275 276 5.805994 CCTCTCGTTTAAACTGTAGATGTCC 59.194 44.000 16.01 0.00 0.00 4.02
277 278 5.048504 TCTCGTTTAAACTGTAGATGTCCGT 60.049 40.000 16.01 0.00 0.00 4.69
302 303 6.765989 TCACTAGTTGACTATTGCACAGTTTT 59.234 34.615 0.00 0.00 31.54 2.43
331 332 3.636764 GGTTGGGATCATTGGGTGTAATC 59.363 47.826 0.00 0.00 0.00 1.75
332 333 3.207265 TGGGATCATTGGGTGTAATCG 57.793 47.619 0.00 0.00 0.00 3.34
333 334 1.880027 GGGATCATTGGGTGTAATCGC 59.120 52.381 0.00 0.00 0.00 4.58
335 336 2.549754 GGATCATTGGGTGTAATCGCAG 59.450 50.000 0.00 0.00 0.00 5.18
338 339 4.209307 TCATTGGGTGTAATCGCAGTTA 57.791 40.909 0.00 0.00 0.00 2.24
339 340 3.936453 TCATTGGGTGTAATCGCAGTTAC 59.064 43.478 2.20 2.20 35.60 2.50
341 342 2.967362 TGGGTGTAATCGCAGTTACAG 58.033 47.619 10.25 0.00 43.16 2.74
344 345 2.618053 GTGTAATCGCAGTTACAGCCT 58.382 47.619 10.25 0.00 43.16 4.58
345 346 3.000727 GTGTAATCGCAGTTACAGCCTT 58.999 45.455 10.25 0.00 43.16 4.35
346 347 4.178540 GTGTAATCGCAGTTACAGCCTTA 58.821 43.478 10.25 0.00 43.16 2.69
347 348 4.032558 GTGTAATCGCAGTTACAGCCTTAC 59.967 45.833 10.25 10.63 43.16 2.34
385 412 1.146263 CCCCTGCGGTGATAGAACC 59.854 63.158 0.00 0.00 36.82 3.62
434 461 2.544480 GCCTTGAAACGGCATTAGTC 57.456 50.000 0.00 0.00 46.77 2.59
437 464 2.420022 CCTTGAAACGGCATTAGTCCAG 59.580 50.000 0.00 0.00 0.00 3.86
443 470 1.690219 CGGCATTAGTCCAGAGGGCT 61.690 60.000 0.00 0.00 0.00 5.19
444 471 0.179034 GGCATTAGTCCAGAGGGCTG 60.179 60.000 0.00 0.00 41.93 4.85
445 472 0.833287 GCATTAGTCCAGAGGGCTGA 59.167 55.000 0.00 0.00 45.17 4.26
446 473 1.419387 GCATTAGTCCAGAGGGCTGAT 59.581 52.381 0.00 0.00 45.17 2.90
447 474 2.158696 GCATTAGTCCAGAGGGCTGATT 60.159 50.000 0.00 0.00 45.17 2.57
448 475 3.686691 GCATTAGTCCAGAGGGCTGATTT 60.687 47.826 0.00 0.00 45.17 2.17
449 476 4.530875 CATTAGTCCAGAGGGCTGATTTT 58.469 43.478 0.00 0.00 45.17 1.82
450 477 4.657814 TTAGTCCAGAGGGCTGATTTTT 57.342 40.909 0.00 0.00 45.17 1.94
451 478 5.772393 TTAGTCCAGAGGGCTGATTTTTA 57.228 39.130 0.00 0.00 45.17 1.52
452 479 4.227864 AGTCCAGAGGGCTGATTTTTAG 57.772 45.455 0.00 0.00 45.17 1.85
453 480 3.054065 AGTCCAGAGGGCTGATTTTTAGG 60.054 47.826 0.00 0.00 45.17 2.69
454 481 2.242196 TCCAGAGGGCTGATTTTTAGGG 59.758 50.000 0.00 0.00 45.17 3.53
455 482 2.027385 CAGAGGGCTGATTTTTAGGGC 58.973 52.381 0.00 0.00 45.17 5.19
456 483 1.925959 AGAGGGCTGATTTTTAGGGCT 59.074 47.619 0.00 0.00 0.00 5.19
457 484 3.117888 CAGAGGGCTGATTTTTAGGGCTA 60.118 47.826 0.00 0.00 45.17 3.93
462 489 4.098044 GGGCTGATTTTTAGGGCTAAAGAC 59.902 45.833 0.00 0.00 36.52 3.01
502 529 2.228914 GCGGACACGGCGTTATCTC 61.229 63.158 11.19 2.26 41.36 2.75
509 536 1.138036 CGGCGTTATCTCACGTCCA 59.862 57.895 0.00 0.00 41.90 4.02
510 537 1.138047 CGGCGTTATCTCACGTCCAC 61.138 60.000 0.00 0.00 41.90 4.02
512 539 1.670674 GGCGTTATCTCACGTCCACAA 60.671 52.381 0.00 0.00 42.43 3.33
513 540 2.268298 GCGTTATCTCACGTCCACAAT 58.732 47.619 0.00 0.00 42.43 2.71
514 541 3.441163 GCGTTATCTCACGTCCACAATA 58.559 45.455 0.00 0.00 42.43 1.90
516 543 4.085055 GCGTTATCTCACGTCCACAATATG 60.085 45.833 0.00 0.00 42.43 1.78
517 544 5.278604 CGTTATCTCACGTCCACAATATGA 58.721 41.667 0.00 0.00 35.34 2.15
518 545 5.746721 CGTTATCTCACGTCCACAATATGAA 59.253 40.000 0.00 0.00 35.34 2.57
519 546 6.254804 CGTTATCTCACGTCCACAATATGAAA 59.745 38.462 0.00 0.00 35.34 2.69
520 547 7.201487 CGTTATCTCACGTCCACAATATGAAAA 60.201 37.037 0.00 0.00 35.34 2.29
521 548 8.612619 GTTATCTCACGTCCACAATATGAAAAT 58.387 33.333 0.00 0.00 0.00 1.82
523 550 8.731275 ATCTCACGTCCACAATATGAAAATTA 57.269 30.769 0.00 0.00 0.00 1.40
524 551 8.554835 TCTCACGTCCACAATATGAAAATTAA 57.445 30.769 0.00 0.00 0.00 1.40
525 552 8.664798 TCTCACGTCCACAATATGAAAATTAAG 58.335 33.333 0.00 0.00 0.00 1.85
526 553 7.247728 TCACGTCCACAATATGAAAATTAAGC 58.752 34.615 0.00 0.00 0.00 3.09
527 554 6.472163 CACGTCCACAATATGAAAATTAAGCC 59.528 38.462 0.00 0.00 0.00 4.35
528 555 6.377146 ACGTCCACAATATGAAAATTAAGCCT 59.623 34.615 0.00 0.00 0.00 4.58
529 556 7.554835 ACGTCCACAATATGAAAATTAAGCCTA 59.445 33.333 0.00 0.00 0.00 3.93
530 557 8.070171 CGTCCACAATATGAAAATTAAGCCTAG 58.930 37.037 0.00 0.00 0.00 3.02
531 558 7.862873 GTCCACAATATGAAAATTAAGCCTAGC 59.137 37.037 0.00 0.00 0.00 3.42
533 560 8.362639 CCACAATATGAAAATTAAGCCTAGCAT 58.637 33.333 0.00 0.00 0.00 3.79
566 737 9.752961 AAGTAACAAAGTTTAGTGTGTTTTTGT 57.247 25.926 0.00 0.00 39.59 2.83
570 741 8.113173 ACAAAGTTTAGTGTGTTTTTGTCCTA 57.887 30.769 0.00 0.00 34.68 2.94
571 742 8.745590 ACAAAGTTTAGTGTGTTTTTGTCCTAT 58.254 29.630 0.00 0.00 34.68 2.57
596 767 2.872388 CGTCCGCCTGCATCCCTAT 61.872 63.158 0.00 0.00 0.00 2.57
606 777 2.621998 CTGCATCCCTATTGAGCAAAGG 59.378 50.000 0.00 0.00 34.45 3.11
828 1016 5.462405 AGTGCGAATTAGAGTATTCCGATC 58.538 41.667 0.00 0.00 32.12 3.69
831 1019 4.082136 GCGAATTAGAGTATTCCGATCCCT 60.082 45.833 0.00 0.00 32.12 4.20
845 1033 4.284490 TCCGATCCCTATTTCCATGAGAAG 59.716 45.833 0.00 0.00 35.40 2.85
906 1103 2.231478 CGACAGCTCCCAGTTCTCTTAA 59.769 50.000 0.00 0.00 0.00 1.85
1054 1251 4.329545 TGGCCTTCACCTCCACGC 62.330 66.667 3.32 0.00 0.00 5.34
1057 1254 4.760047 CCTTCACCTCCACGCGGG 62.760 72.222 12.47 6.05 38.37 6.13
1058 1255 4.003788 CTTCACCTCCACGCGGGT 62.004 66.667 12.47 4.70 38.11 5.28
1149 1346 2.614734 CGGAGGTTAAAGTCTTCACCCC 60.615 54.545 9.40 9.37 30.15 4.95
1164 1361 2.669240 CCCTCCACTCCCGTTTCC 59.331 66.667 0.00 0.00 0.00 3.13
1165 1362 1.918800 CCCTCCACTCCCGTTTCCT 60.919 63.158 0.00 0.00 0.00 3.36
1166 1363 1.296715 CCTCCACTCCCGTTTCCTG 59.703 63.158 0.00 0.00 0.00 3.86
1167 1364 1.192146 CCTCCACTCCCGTTTCCTGA 61.192 60.000 0.00 0.00 0.00 3.86
1169 1366 1.374252 CCACTCCCGTTTCCTGACG 60.374 63.158 0.00 0.00 42.43 4.35
1171 1368 2.809601 CTCCCGTTTCCTGACGCG 60.810 66.667 3.53 3.53 41.50 6.01
1174 1371 4.072088 CCGTTTCCTGACGCGCAC 62.072 66.667 5.73 0.41 41.50 5.34
1176 1373 4.072088 GTTTCCTGACGCGCACCG 62.072 66.667 5.73 0.00 44.21 4.94
1196 1393 1.486211 CACATCCTCCCCTTACGTCT 58.514 55.000 0.00 0.00 0.00 4.18
1201 1398 1.569548 TCCTCCCCTTACGTCTCATCT 59.430 52.381 0.00 0.00 0.00 2.90
1216 1413 1.000993 ATCTCCGGCCAGTCTCAGT 59.999 57.895 2.24 0.00 0.00 3.41
1231 1428 0.468226 TCAGTTCAACCCGCTGTTCT 59.532 50.000 0.00 0.00 34.00 3.01
1233 1430 0.250338 AGTTCAACCCGCTGTTCTCC 60.250 55.000 0.00 0.00 34.00 3.71
1234 1431 1.301401 TTCAACCCGCTGTTCTCCG 60.301 57.895 0.00 0.00 34.00 4.63
1237 1434 3.569049 AACCCGCTGTTCTCCGTCG 62.569 63.158 0.00 0.00 28.45 5.12
1261 1458 2.107343 ACGCGTGCAGTGGTTACA 59.893 55.556 12.93 0.00 33.90 2.41
1335 1532 1.631072 CGAAATGCTCGTGTAGGCG 59.369 57.895 0.00 0.00 42.89 5.52
1348 1545 1.026718 GTAGGCGGCAGTTTCATGCT 61.027 55.000 13.08 0.00 45.75 3.79
1363 1560 7.167302 CAGTTTCATGCTTTGTTCGACAAATTA 59.833 33.333 11.71 6.50 45.79 1.40
1364 1561 7.704472 AGTTTCATGCTTTGTTCGACAAATTAA 59.296 29.630 11.71 4.18 45.79 1.40
1386 1583 2.787473 TAGTGCTATTTGCCAGTGCT 57.213 45.000 0.00 0.00 42.00 4.40
1403 1600 1.066908 TGCTGCTGCTTGTGTTTTACC 59.933 47.619 17.00 0.00 40.48 2.85
1428 1625 4.095483 GTGGTGGTCTTCAATAGATGCTTG 59.905 45.833 0.00 0.00 34.79 4.01
1467 1666 8.298030 ACTCATTTTGTTTTGCTATTAAGTGC 57.702 30.769 0.00 0.00 0.00 4.40
1474 1673 6.908825 TGTTTTGCTATTAAGTGCCAACTAG 58.091 36.000 11.97 0.00 34.77 2.57
1521 1720 2.293170 GGAGCCCATCTTTTAGCAGAC 58.707 52.381 0.00 0.00 0.00 3.51
1551 1750 9.747898 TTGTTTATCAAGTCAATATGGGTAACT 57.252 29.630 0.00 0.00 0.00 2.24
1552 1751 9.391006 TGTTTATCAAGTCAATATGGGTAACTC 57.609 33.333 0.00 0.00 0.00 3.01
1559 1758 7.865706 AGTCAATATGGGTAACTCAATGTTC 57.134 36.000 0.00 0.00 39.89 3.18
1561 1760 7.554118 AGTCAATATGGGTAACTCAATGTTCTG 59.446 37.037 0.00 0.00 39.89 3.02
1593 1792 5.699097 TTTTTACTCGTAAAATGCCTGCT 57.301 34.783 13.81 0.00 42.48 4.24
1594 1793 4.939509 TTTACTCGTAAAATGCCTGCTC 57.060 40.909 0.04 0.00 32.64 4.26
1596 1795 1.003118 ACTCGTAAAATGCCTGCTCCA 59.997 47.619 0.00 0.00 0.00 3.86
1606 1813 1.335145 GCCTGCTCCAATATGCCAAT 58.665 50.000 0.00 0.00 0.00 3.16
1651 1858 1.338389 GGGCTTACGCTCTTGTGGTTA 60.338 52.381 0.00 0.00 32.44 2.85
1655 1862 4.240096 GCTTACGCTCTTGTGGTTACTTA 58.760 43.478 0.00 0.00 0.00 2.24
1658 1865 3.000727 ACGCTCTTGTGGTTACTTATGC 58.999 45.455 0.00 0.00 0.00 3.14
1769 1981 8.405418 AGGAGGTTTACTATCTTTCCAAAAAC 57.595 34.615 0.00 0.00 0.00 2.43
1784 1996 9.100554 CTTTCCAAAAACGGGTAAATTTAACTT 57.899 29.630 12.85 0.00 0.00 2.66
1847 2059 9.968743 CATTACTTAACTTAACTAAAAGAGCCG 57.031 33.333 0.00 0.00 0.00 5.52
1848 2060 9.933723 ATTACTTAACTTAACTAAAAGAGCCGA 57.066 29.630 0.00 0.00 0.00 5.54
1849 2061 9.762933 TTACTTAACTTAACTAAAAGAGCCGAA 57.237 29.630 0.00 0.00 0.00 4.30
1850 2062 8.307921 ACTTAACTTAACTAAAAGAGCCGAAG 57.692 34.615 0.00 0.00 0.00 3.79
1851 2063 7.930325 ACTTAACTTAACTAAAAGAGCCGAAGT 59.070 33.333 0.00 0.00 0.00 3.01
1852 2064 9.415544 CTTAACTTAACTAAAAGAGCCGAAGTA 57.584 33.333 0.00 0.00 29.17 2.24
1853 2065 9.762933 TTAACTTAACTAAAAGAGCCGAAGTAA 57.237 29.630 0.00 0.00 29.17 2.24
1854 2066 8.667076 AACTTAACTAAAAGAGCCGAAGTAAA 57.333 30.769 0.00 0.00 29.17 2.01
1855 2067 8.843885 ACTTAACTAAAAGAGCCGAAGTAAAT 57.156 30.769 0.00 0.00 0.00 1.40
1856 2068 9.281371 ACTTAACTAAAAGAGCCGAAGTAAATT 57.719 29.630 0.00 0.00 0.00 1.82
1860 2072 9.888878 AACTAAAAGAGCCGAAGTAAATTTAAC 57.111 29.630 0.00 0.00 0.00 2.01
1861 2073 9.281371 ACTAAAAGAGCCGAAGTAAATTTAACT 57.719 29.630 0.00 0.00 0.00 2.24
1967 2182 7.516198 AGTTGCTTCTGATTTACAATGAACT 57.484 32.000 0.00 0.00 0.00 3.01
2157 2372 1.347707 AGAATCGTTGGGCTCTGTTCA 59.652 47.619 0.00 0.00 0.00 3.18
2307 2522 9.181061 GTTATGGCCAAGTATTAGAAGGTTTAA 57.819 33.333 10.96 0.00 0.00 1.52
2470 2685 2.879103 AATTTGCCTCCGAGGAAGAA 57.121 45.000 19.33 9.04 37.67 2.52
2522 2737 5.123820 GGCAAGGCAAGTTTTTCTTTTCTTT 59.876 36.000 0.00 0.00 33.63 2.52
2549 2764 4.040952 TCTTTTGAAGAACTAGCAGGAGCT 59.959 41.667 0.00 0.00 44.10 4.09
2562 2777 2.715046 CAGGAGCTGTGCCTTTATCAA 58.285 47.619 0.00 0.00 32.12 2.57
2574 2789 6.483307 TGTGCCTTTATCAATATAGTGCTGTC 59.517 38.462 0.00 0.00 0.00 3.51
2584 2799 2.921634 TAGTGCTGTCGCTAGTTCAG 57.078 50.000 0.00 0.00 36.97 3.02
2783 3129 1.748493 ACCTGAAAATGCGTGTTGTGT 59.252 42.857 0.00 0.00 0.00 3.72
2832 3193 2.689646 GACGCTGTTAGAGAAAAGCCT 58.310 47.619 0.00 0.00 31.84 4.58
2833 3194 2.413453 GACGCTGTTAGAGAAAAGCCTG 59.587 50.000 0.00 0.00 31.84 4.85
2919 3280 7.149144 CGCGTAATATTGTGCTGAATTTTATGG 60.149 37.037 0.00 3.20 0.00 2.74
2961 3322 7.880059 TCGAAGAGCATATCAGATAATGTTG 57.120 36.000 0.00 0.00 0.00 3.33
3155 3519 0.955428 CGTACTGTGGCTGCCAATGT 60.955 55.000 25.23 24.68 34.18 2.71
3169 3533 5.172687 TGCCAATGTACTCAATGGTAGAA 57.827 39.130 4.59 0.00 44.15 2.10
3175 3539 8.023128 CCAATGTACTCAATGGTAGAAACTTTG 58.977 37.037 0.00 0.00 39.17 2.77
3220 3589 5.456548 TGTCATTTGAATGTCACATTGCT 57.543 34.783 8.05 0.00 37.65 3.91
3221 3590 5.845103 TGTCATTTGAATGTCACATTGCTT 58.155 33.333 8.05 0.00 37.65 3.91
3222 3591 5.692654 TGTCATTTGAATGTCACATTGCTTG 59.307 36.000 8.05 0.69 37.65 4.01
3223 3592 5.921976 GTCATTTGAATGTCACATTGCTTGA 59.078 36.000 8.05 3.11 37.65 3.02
3224 3593 6.588756 GTCATTTGAATGTCACATTGCTTGAT 59.411 34.615 8.05 0.00 37.65 2.57
3225 3594 6.588373 TCATTTGAATGTCACATTGCTTGATG 59.412 34.615 8.05 5.38 37.65 3.07
3226 3595 4.443913 TGAATGTCACATTGCTTGATGG 57.556 40.909 8.05 0.00 0.00 3.51
3227 3596 3.827876 TGAATGTCACATTGCTTGATGGT 59.172 39.130 8.05 0.00 0.00 3.55
3228 3597 5.008980 TGAATGTCACATTGCTTGATGGTA 58.991 37.500 8.05 0.00 0.00 3.25
3229 3598 4.970662 ATGTCACATTGCTTGATGGTAC 57.029 40.909 0.00 0.00 0.00 3.34
3230 3599 2.741517 TGTCACATTGCTTGATGGTACG 59.258 45.455 0.00 0.00 0.00 3.67
3231 3600 3.000041 GTCACATTGCTTGATGGTACGA 59.000 45.455 0.00 0.00 0.00 3.43
3232 3601 3.435327 GTCACATTGCTTGATGGTACGAA 59.565 43.478 0.00 0.00 0.00 3.85
3233 3602 4.094887 GTCACATTGCTTGATGGTACGAAT 59.905 41.667 0.00 0.00 0.00 3.34
3234 3603 4.699735 TCACATTGCTTGATGGTACGAATT 59.300 37.500 0.00 0.00 0.00 2.17
3235 3604 5.182950 TCACATTGCTTGATGGTACGAATTT 59.817 36.000 0.00 0.00 0.00 1.82
3236 3605 5.286797 CACATTGCTTGATGGTACGAATTTG 59.713 40.000 0.00 0.00 0.00 2.32
3237 3606 5.048083 ACATTGCTTGATGGTACGAATTTGT 60.048 36.000 3.29 3.29 0.00 2.83
3238 3607 4.418013 TGCTTGATGGTACGAATTTGTG 57.582 40.909 8.70 0.00 0.00 3.33
3239 3608 4.068599 TGCTTGATGGTACGAATTTGTGA 58.931 39.130 8.70 0.00 0.00 3.58
3240 3609 4.517075 TGCTTGATGGTACGAATTTGTGAA 59.483 37.500 8.70 0.00 0.00 3.18
3241 3610 4.851558 GCTTGATGGTACGAATTTGTGAAC 59.148 41.667 8.70 0.00 0.00 3.18
3242 3611 4.655440 TGATGGTACGAATTTGTGAACG 57.345 40.909 8.70 0.00 0.00 3.95
3243 3612 2.953640 TGGTACGAATTTGTGAACGC 57.046 45.000 8.70 0.00 0.00 4.84
3244 3613 2.210961 TGGTACGAATTTGTGAACGCA 58.789 42.857 8.70 0.00 0.00 5.24
3245 3614 2.809119 TGGTACGAATTTGTGAACGCAT 59.191 40.909 8.70 0.00 0.00 4.73
3384 3786 3.187227 CACGTTAGTTCTTGCTTGATGCT 59.813 43.478 0.00 0.00 43.37 3.79
3391 3793 4.453819 AGTTCTTGCTTGATGCTGTCTTAC 59.546 41.667 0.00 0.00 43.37 2.34
3494 3899 2.858344 GCATGAATGAACTCATTGCTGC 59.142 45.455 9.63 12.89 45.72 5.25
3495 3900 3.444916 CATGAATGAACTCATTGCTGCC 58.555 45.455 9.63 0.00 45.72 4.85
3496 3901 2.799017 TGAATGAACTCATTGCTGCCT 58.201 42.857 9.63 0.00 45.72 4.75
3497 3902 2.490509 TGAATGAACTCATTGCTGCCTG 59.509 45.455 9.63 0.00 45.72 4.85
3522 3927 2.642700 CCGTCGGTGGCAAAAAGG 59.357 61.111 2.08 0.00 0.00 3.11
3525 3930 1.658114 GTCGGTGGCAAAAAGGACC 59.342 57.895 0.00 0.00 0.00 4.46
3643 4048 1.152271 TCTCCTTCCTCCCCTTCTTGT 59.848 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.124560 TGTCTCTCTCGCGATACTACTG 58.875 50.000 10.36 0.00 0.00 2.74
80 81 7.291416 TCCCAGCACCTTGTATAATGTAAGATA 59.709 37.037 0.00 0.00 0.00 1.98
105 106 6.526674 ACAAACTCTGAAACAACGTCAAAATC 59.473 34.615 0.00 0.00 0.00 2.17
118 119 6.537355 AGATCCAGATCAACAAACTCTGAAA 58.463 36.000 10.17 0.00 38.96 2.69
261 262 4.765856 ACTAGTGACGGACATCTACAGTTT 59.234 41.667 0.00 0.00 0.00 2.66
277 278 5.468540 ACTGTGCAATAGTCAACTAGTGA 57.531 39.130 18.79 4.39 44.59 3.41
295 296 0.951558 CCAACCGCAGCTAAAACTGT 59.048 50.000 0.00 0.00 39.96 3.55
302 303 0.546122 AATGATCCCAACCGCAGCTA 59.454 50.000 0.00 0.00 0.00 3.32
408 435 3.532896 CCGTTTCAAGGCAGCTAGA 57.467 52.632 0.00 0.00 0.00 2.43
434 461 2.659428 CCCTAAAAATCAGCCCTCTGG 58.341 52.381 0.00 0.00 40.69 3.86
437 464 2.443958 AGCCCTAAAAATCAGCCCTC 57.556 50.000 0.00 0.00 0.00 4.30
443 470 5.714806 CCTTGGTCTTTAGCCCTAAAAATCA 59.285 40.000 2.50 0.00 34.95 2.57
444 471 5.949952 TCCTTGGTCTTTAGCCCTAAAAATC 59.050 40.000 2.50 0.00 34.95 2.17
445 472 5.899278 TCCTTGGTCTTTAGCCCTAAAAAT 58.101 37.500 2.50 0.00 34.95 1.82
446 473 5.321927 CTCCTTGGTCTTTAGCCCTAAAAA 58.678 41.667 2.50 0.00 34.95 1.94
447 474 4.809691 GCTCCTTGGTCTTTAGCCCTAAAA 60.810 45.833 2.50 0.00 34.95 1.52
448 475 3.308188 GCTCCTTGGTCTTTAGCCCTAAA 60.308 47.826 1.03 1.03 34.28 1.85
449 476 2.238898 GCTCCTTGGTCTTTAGCCCTAA 59.761 50.000 0.00 0.00 0.00 2.69
450 477 1.838077 GCTCCTTGGTCTTTAGCCCTA 59.162 52.381 0.00 0.00 0.00 3.53
451 478 0.621082 GCTCCTTGGTCTTTAGCCCT 59.379 55.000 0.00 0.00 0.00 5.19
452 479 0.328258 TGCTCCTTGGTCTTTAGCCC 59.672 55.000 0.00 0.00 32.14 5.19
453 480 2.200373 TTGCTCCTTGGTCTTTAGCC 57.800 50.000 0.00 0.00 32.14 3.93
454 481 3.057245 CCTTTTGCTCCTTGGTCTTTAGC 60.057 47.826 0.00 0.00 0.00 3.09
455 482 3.057245 GCCTTTTGCTCCTTGGTCTTTAG 60.057 47.826 0.00 0.00 36.87 1.85
456 483 2.890945 GCCTTTTGCTCCTTGGTCTTTA 59.109 45.455 0.00 0.00 36.87 1.85
457 484 1.688735 GCCTTTTGCTCCTTGGTCTTT 59.311 47.619 0.00 0.00 36.87 2.52
462 489 0.390735 GCATGCCTTTTGCTCCTTGG 60.391 55.000 6.36 0.00 42.00 3.61
496 523 8.731275 ATTTTCATATTGTGGACGTGAGATAA 57.269 30.769 0.00 0.00 0.00 1.75
498 525 7.630242 AATTTTCATATTGTGGACGTGAGAT 57.370 32.000 0.00 0.00 0.00 2.75
499 526 8.554835 TTAATTTTCATATTGTGGACGTGAGA 57.445 30.769 0.00 0.00 0.00 3.27
502 529 6.472163 GGCTTAATTTTCATATTGTGGACGTG 59.528 38.462 0.00 0.00 0.00 4.49
541 568 9.401873 GACAAAAACACACTAAACTTTGTTACT 57.598 29.630 0.00 0.00 37.18 2.24
543 570 8.578151 AGGACAAAAACACACTAAACTTTGTTA 58.422 29.630 0.00 0.00 37.18 2.41
544 571 7.438564 AGGACAAAAACACACTAAACTTTGTT 58.561 30.769 0.00 0.00 37.18 2.83
546 573 9.019764 CATAGGACAAAAACACACTAAACTTTG 57.980 33.333 0.00 0.00 0.00 2.77
548 575 7.558444 TCCATAGGACAAAAACACACTAAACTT 59.442 33.333 0.00 0.00 0.00 2.66
549 576 7.057894 TCCATAGGACAAAAACACACTAAACT 58.942 34.615 0.00 0.00 0.00 2.66
550 577 7.266922 TCCATAGGACAAAAACACACTAAAC 57.733 36.000 0.00 0.00 0.00 2.01
587 758 2.936202 TCCTTTGCTCAATAGGGATGC 58.064 47.619 9.38 0.00 0.00 3.91
593 764 7.844482 CAAAGTTTTGTTCCTTTGCTCAATAG 58.156 34.615 0.00 0.00 40.56 1.73
632 803 9.813080 GACTTAACTTGCTGAAGTATTACTTTG 57.187 33.333 10.32 7.98 41.87 2.77
637 808 8.946085 CCATTGACTTAACTTGCTGAAGTATTA 58.054 33.333 0.00 0.00 41.87 0.98
731 903 8.082242 CCTCTTCGGTTCAAAAAGTTTTCATAT 58.918 33.333 0.32 0.00 0.00 1.78
732 904 7.422399 CCTCTTCGGTTCAAAAAGTTTTCATA 58.578 34.615 0.32 0.00 0.00 2.15
815 1003 5.403512 TGGAAATAGGGATCGGAATACTCT 58.596 41.667 0.00 0.00 0.00 3.24
828 1016 4.428294 TCAGCTTCTCATGGAAATAGGG 57.572 45.455 0.00 0.00 33.07 3.53
831 1019 7.707624 AAAACATCAGCTTCTCATGGAAATA 57.292 32.000 0.00 0.00 33.07 1.40
867 1058 2.745884 CGGGGCAGAAATCGCACA 60.746 61.111 0.00 0.00 33.14 4.57
906 1103 1.935327 GCCAGTTCGTCGCTAGGTCT 61.935 60.000 0.00 0.00 0.00 3.85
1107 1304 3.181523 CGATGAAGAGCTTGTGTGTGATG 60.182 47.826 0.00 0.00 0.00 3.07
1149 1346 0.037232 GTCAGGAAACGGGAGTGGAG 60.037 60.000 0.00 0.00 46.69 3.86
1174 1371 1.146263 GTAAGGGGAGGATGTGCGG 59.854 63.158 0.00 0.00 0.00 5.69
1176 1373 0.179081 GACGTAAGGGGAGGATGTGC 60.179 60.000 0.00 0.00 46.39 4.57
1177 1374 1.409427 GAGACGTAAGGGGAGGATGTG 59.591 57.143 0.00 0.00 46.39 3.21
1178 1375 1.006758 TGAGACGTAAGGGGAGGATGT 59.993 52.381 0.00 0.00 46.39 3.06
1179 1376 1.776662 TGAGACGTAAGGGGAGGATG 58.223 55.000 0.00 0.00 46.39 3.51
1180 1377 2.178106 AGATGAGACGTAAGGGGAGGAT 59.822 50.000 0.00 0.00 46.39 3.24
1181 1378 1.569548 AGATGAGACGTAAGGGGAGGA 59.430 52.381 0.00 0.00 46.39 3.71
1182 1379 1.957877 GAGATGAGACGTAAGGGGAGG 59.042 57.143 0.00 0.00 46.39 4.30
1183 1380 1.957877 GGAGATGAGACGTAAGGGGAG 59.042 57.143 0.00 0.00 46.39 4.30
1184 1381 1.749635 CGGAGATGAGACGTAAGGGGA 60.750 57.143 0.00 0.00 46.39 4.81
1196 1393 1.000359 TGAGACTGGCCGGAGATGA 60.000 57.895 21.41 0.00 0.00 2.92
1201 1398 1.118965 TTGAACTGAGACTGGCCGGA 61.119 55.000 21.41 0.00 0.00 5.14
1216 1413 1.301401 CGGAGAACAGCGGGTTGAA 60.301 57.895 1.39 0.00 40.63 2.69
1231 1428 3.785499 CGCGTGAGAGTCGACGGA 61.785 66.667 10.46 0.00 36.09 4.69
1233 1430 2.865603 CACGCGTGAGAGTCGACG 60.866 66.667 34.93 11.98 44.22 5.12
1234 1431 3.166630 GCACGCGTGAGAGTCGAC 61.167 66.667 41.19 17.94 44.22 4.20
1237 1434 2.049985 ACTGCACGCGTGAGAGTC 60.050 61.111 41.19 23.53 44.22 3.36
1331 1528 1.181098 AAAGCATGAAACTGCCGCCT 61.181 50.000 0.00 0.00 43.33 5.52
1335 1532 2.053627 CGAACAAAGCATGAAACTGCC 58.946 47.619 0.00 0.00 43.33 4.85
1386 1583 2.098934 CACAGGTAAAACACAAGCAGCA 59.901 45.455 0.00 0.00 0.00 4.41
1403 1600 3.624861 GCATCTATTGAAGACCACCACAG 59.375 47.826 0.00 0.00 36.93 3.66
1467 1666 0.895530 TTCCCGAGAGCACTAGTTGG 59.104 55.000 0.00 0.00 0.00 3.77
1474 1673 4.120589 CCTAAACTTATTCCCGAGAGCAC 58.879 47.826 0.00 0.00 0.00 4.40
1521 1720 9.874205 ACCCATATTGACTTGATAAACAAAATG 57.126 29.630 0.00 0.00 38.08 2.32
1535 1734 7.554118 CAGAACATTGAGTTACCCATATTGACT 59.446 37.037 0.00 0.00 41.51 3.41
1580 1779 4.301628 GCATATTGGAGCAGGCATTTTAC 58.698 43.478 0.00 0.00 0.00 2.01
1581 1780 3.321682 GGCATATTGGAGCAGGCATTTTA 59.678 43.478 0.00 0.00 0.00 1.52
1593 1792 5.843969 TCCTACTCACTATTGGCATATTGGA 59.156 40.000 0.00 0.00 0.00 3.53
1594 1793 5.934625 GTCCTACTCACTATTGGCATATTGG 59.065 44.000 0.00 0.00 0.00 3.16
1596 1795 5.846714 AGGTCCTACTCACTATTGGCATATT 59.153 40.000 0.00 0.00 0.00 1.28
1606 1813 2.292257 ACATGGCAGGTCCTACTCACTA 60.292 50.000 0.00 0.00 35.26 2.74
1743 1953 9.511272 GTTTTTGGAAAGATAGTAAACCTCCTA 57.489 33.333 0.00 0.00 0.00 2.94
1746 1956 7.303261 CCGTTTTTGGAAAGATAGTAAACCTC 58.697 38.462 0.00 0.00 0.00 3.85
1747 1957 6.208007 CCCGTTTTTGGAAAGATAGTAAACCT 59.792 38.462 0.00 0.00 0.00 3.50
1765 1977 9.467258 GCTCTTTAAGTTAAATTTACCCGTTTT 57.533 29.630 8.48 0.00 0.00 2.43
1769 1981 8.036273 TCAGCTCTTTAAGTTAAATTTACCCG 57.964 34.615 8.48 0.00 0.00 5.28
1784 1996 8.936864 GCTAGTTTGAATTACTTCAGCTCTTTA 58.063 33.333 5.63 0.00 42.19 1.85
1828 2040 9.762933 TTTACTTCGGCTCTTTTAGTTAAGTTA 57.237 29.630 0.00 0.00 30.90 2.24
1829 2041 8.667076 TTTACTTCGGCTCTTTTAGTTAAGTT 57.333 30.769 0.00 0.00 30.90 2.66
1830 2042 8.843885 ATTTACTTCGGCTCTTTTAGTTAAGT 57.156 30.769 0.00 0.00 32.20 2.24
1834 2046 9.888878 GTTAAATTTACTTCGGCTCTTTTAGTT 57.111 29.630 0.00 0.00 0.00 2.24
1835 2047 9.281371 AGTTAAATTTACTTCGGCTCTTTTAGT 57.719 29.630 0.00 0.00 0.00 2.24
1841 2053 8.727910 CCTTTTAGTTAAATTTACTTCGGCTCT 58.272 33.333 0.00 0.00 0.00 4.09
1842 2054 8.509690 ACCTTTTAGTTAAATTTACTTCGGCTC 58.490 33.333 0.00 0.00 0.00 4.70
1843 2055 8.400184 ACCTTTTAGTTAAATTTACTTCGGCT 57.600 30.769 0.00 0.00 0.00 5.52
1844 2056 8.291740 TGACCTTTTAGTTAAATTTACTTCGGC 58.708 33.333 0.00 0.00 0.00 5.54
1950 2165 8.274322 ACCCATGATAGTTCATTGTAAATCAGA 58.726 33.333 0.00 0.00 40.70 3.27
2077 2292 4.074970 GCTTGGATGGAGTGAGAGAAAAA 58.925 43.478 0.00 0.00 0.00 1.94
2157 2372 8.574251 TTGCATATAACAACTGTATCCAACTT 57.426 30.769 0.00 0.00 0.00 2.66
2307 2522 0.329596 GTTCTGGCAAGGGATGAGGT 59.670 55.000 0.00 0.00 0.00 3.85
2470 2685 1.004277 TCTTCCCGTGCTTTATTGGCT 59.996 47.619 0.00 0.00 0.00 4.75
2522 2737 8.645498 GCTCCTGCTAGTTCTTCAAAAGAAGAA 61.645 40.741 14.66 14.66 41.02 2.52
2547 2762 5.471456 AGCACTATATTGATAAAGGCACAGC 59.529 40.000 0.00 0.00 0.00 4.40
2549 2764 6.356556 ACAGCACTATATTGATAAAGGCACA 58.643 36.000 0.00 0.00 0.00 4.57
2625 2969 2.867624 TGCATTGCTCAGGTCTTCTTT 58.132 42.857 10.49 0.00 0.00 2.52
2633 2977 3.418675 CAAGCTTGCATTGCTCAGG 57.581 52.632 14.65 5.11 40.22 3.86
2663 3007 5.515626 GTCGACATATATAACTCGCCCATTC 59.484 44.000 11.55 0.00 0.00 2.67
2879 3240 7.804600 ACAATATTACGCGTCGATTACATTAGA 59.195 33.333 18.63 0.00 0.00 2.10
2919 3280 2.543848 TCGATGTGTTGTTCTTGCAGAC 59.456 45.455 0.00 0.00 0.00 3.51
2939 3300 7.172875 ACAGCAACATTATCTGATATGCTCTTC 59.827 37.037 16.58 0.00 39.21 2.87
2961 3322 2.407696 GTCGACGAGGTTAAAGAACAGC 59.592 50.000 0.00 0.00 37.29 4.40
3155 3519 5.007682 GGGCAAAGTTTCTACCATTGAGTA 58.992 41.667 0.00 0.00 0.00 2.59
3169 3533 2.024369 CCTTAGGTATGGGGGCAAAGTT 60.024 50.000 0.00 0.00 0.00 2.66
3175 3539 1.420514 GTTCTCCTTAGGTATGGGGGC 59.579 57.143 0.00 0.00 0.00 5.80
3216 3585 4.517075 TCACAAATTCGTACCATCAAGCAA 59.483 37.500 0.00 0.00 0.00 3.91
3217 3586 4.068599 TCACAAATTCGTACCATCAAGCA 58.931 39.130 0.00 0.00 0.00 3.91
3218 3587 4.678509 TCACAAATTCGTACCATCAAGC 57.321 40.909 0.00 0.00 0.00 4.01
3219 3588 5.079406 CGTTCACAAATTCGTACCATCAAG 58.921 41.667 0.00 0.00 0.00 3.02
3220 3589 4.611807 GCGTTCACAAATTCGTACCATCAA 60.612 41.667 0.00 0.00 0.00 2.57
3221 3590 3.120477 GCGTTCACAAATTCGTACCATCA 60.120 43.478 0.00 0.00 0.00 3.07
3222 3591 3.120477 TGCGTTCACAAATTCGTACCATC 60.120 43.478 0.00 0.00 0.00 3.51
3223 3592 2.809119 TGCGTTCACAAATTCGTACCAT 59.191 40.909 0.00 0.00 0.00 3.55
3224 3593 2.210961 TGCGTTCACAAATTCGTACCA 58.789 42.857 0.00 0.00 0.00 3.25
3225 3594 2.953640 TGCGTTCACAAATTCGTACC 57.046 45.000 0.00 0.00 0.00 3.34
3226 3595 3.602062 CCAATGCGTTCACAAATTCGTAC 59.398 43.478 0.00 0.00 0.00 3.67
3227 3596 3.816091 CCAATGCGTTCACAAATTCGTA 58.184 40.909 0.00 0.00 0.00 3.43
3228 3597 2.660490 CCAATGCGTTCACAAATTCGT 58.340 42.857 0.00 0.00 0.00 3.85
3229 3598 1.386412 GCCAATGCGTTCACAAATTCG 59.614 47.619 0.00 0.00 0.00 3.34
3230 3599 2.402305 TGCCAATGCGTTCACAAATTC 58.598 42.857 0.00 0.00 41.78 2.17
3231 3600 2.035704 TCTGCCAATGCGTTCACAAATT 59.964 40.909 0.00 0.00 41.78 1.82
3232 3601 1.612950 TCTGCCAATGCGTTCACAAAT 59.387 42.857 0.00 0.00 41.78 2.32
3233 3602 1.028130 TCTGCCAATGCGTTCACAAA 58.972 45.000 0.00 0.00 41.78 2.83
3234 3603 1.246649 ATCTGCCAATGCGTTCACAA 58.753 45.000 0.00 0.00 41.78 3.33
3235 3604 1.246649 AATCTGCCAATGCGTTCACA 58.753 45.000 0.00 0.00 41.78 3.58
3236 3605 2.352503 AAATCTGCCAATGCGTTCAC 57.647 45.000 0.00 0.00 41.78 3.18
3237 3606 3.005684 AGAAAAATCTGCCAATGCGTTCA 59.994 39.130 0.00 0.00 41.78 3.18
3238 3607 3.365820 CAGAAAAATCTGCCAATGCGTTC 59.634 43.478 0.00 0.00 41.78 3.95
3239 3608 3.243839 ACAGAAAAATCTGCCAATGCGTT 60.244 39.130 5.78 0.00 41.19 4.84
3240 3609 2.297033 ACAGAAAAATCTGCCAATGCGT 59.703 40.909 5.78 0.00 41.19 5.24
3241 3610 2.919229 GACAGAAAAATCTGCCAATGCG 59.081 45.455 5.78 0.00 41.19 4.73
3242 3611 4.082354 AGAGACAGAAAAATCTGCCAATGC 60.082 41.667 5.78 0.00 41.19 3.56
3243 3612 5.392811 GGAGAGACAGAAAAATCTGCCAATG 60.393 44.000 5.78 0.00 41.19 2.82
3244 3613 4.704057 GGAGAGACAGAAAAATCTGCCAAT 59.296 41.667 5.78 0.00 41.19 3.16
3245 3614 4.074970 GGAGAGACAGAAAAATCTGCCAA 58.925 43.478 5.78 0.00 41.19 4.52
3384 3786 0.966179 TCTGCGCTCCAAGTAAGACA 59.034 50.000 9.73 0.00 0.00 3.41
3391 3793 1.737838 TGGTATTTCTGCGCTCCAAG 58.262 50.000 9.73 0.00 0.00 3.61
3522 3927 2.048127 GTGCTCCGGTGACAGGTC 60.048 66.667 7.92 0.00 0.00 3.85
3525 3930 2.430921 GTCGTGCTCCGGTGACAG 60.431 66.667 7.92 0.00 37.11 3.51


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

AutoCloner maintained by Alex Coulton.