Multiple sequence alignment - TraesCS1A01G228600

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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 TraesCS1A01G228600 chr1A 100.000 3014 0 0 1 3014 399894448 399891435 0.000000e+00 5566
1 TraesCS1A01G228600 chr1A 92.369 1769 110 16 635 2385 433525763 433527524 0.000000e+00 2495
2 TraesCS1A01G228600 chr1A 95.036 1531 63 4 961 2488 106533183 106534703 0.000000e+00 2394
3 TraesCS1A01G228600 chr1A 92.139 1463 85 15 635 2073 433736710 433738166 0.000000e+00 2037
4 TraesCS1A01G228600 chr1A 88.396 1284 89 19 1138 2385 496853445 496852186 0.000000e+00 1491
5 TraesCS1A01G228600 chr1A 92.647 952 46 3 1437 2385 481217261 481218191 0.000000e+00 1349
6 TraesCS1A01G228600 chr1A 89.586 797 54 15 635 1408 481216477 481217267 0.000000e+00 985
7 TraesCS1A01G228600 chr1A 93.659 615 37 2 2385 2999 481218762 481219374 0.000000e+00 918
8 TraesCS1A01G228600 chr1A 97.264 329 9 0 635 963 106532811 106533139 2.620000e-155 558
9 TraesCS1A01G228600 chr1A 95.495 333 13 2 2385 2716 433528088 433528419 5.720000e-147 531
10 TraesCS1A01G228600 chr1A 92.015 263 17 3 2126 2385 433738523 433738784 1.710000e-97 366
11 TraesCS1A01G228600 chr1B 91.346 1768 100 18 635 2385 510207934 510209665 0.000000e+00 2368
12 TraesCS1A01G228600 chr1B 90.139 649 41 4 2385 3013 510210254 510210899 0.000000e+00 822
13 TraesCS1A01G228600 chr5D 93.282 1429 75 8 961 2385 88143325 88144736 0.000000e+00 2087
14 TraesCS1A01G228600 chr5D 92.713 645 30 9 4 634 436270134 436269493 0.000000e+00 915
15 TraesCS1A01G228600 chr5D 93.199 397 26 1 2617 3013 88145206 88145601 1.560000e-162 582
16 TraesCS1A01G228600 chr5D 96.061 330 12 1 635 963 88142952 88143281 1.230000e-148 536
17 TraesCS1A01G228600 chr1D 92.502 1347 63 14 1044 2382 83127368 83128684 0.000000e+00 1893
18 TraesCS1A01G228600 chr1D 86.660 1042 78 21 1376 2385 400411456 400410444 0.000000e+00 1098
19 TraesCS1A01G228600 chr1D 93.541 449 28 1 961 1408 82304375 82304823 0.000000e+00 667
20 TraesCS1A01G228600 chr1D 94.415 376 17 2 2639 3014 380586295 380586666 2.610000e-160 575
21 TraesCS1A01G228600 chr1D 96.667 330 10 1 635 963 83126585 83126914 5.680000e-152 547
22 TraesCS1A01G228600 chr1D 96.364 330 11 1 635 963 82304002 82304331 2.640000e-150 542
23 TraesCS1A01G228600 chr1D 90.323 248 21 2 1138 1384 400412099 400411854 3.750000e-84 322
24 TraesCS1A01G228600 chr1D 94.505 91 5 0 961 1051 83126958 83127048 1.130000e-29 141
25 TraesCS1A01G228600 chr6A 95.525 1095 49 0 961 2055 161156747 161155653 0.000000e+00 1751
26 TraesCS1A01G228600 chr6A 95.669 785 30 3 1740 2521 161397125 161396342 0.000000e+00 1258
27 TraesCS1A01G228600 chr6A 94.987 798 38 1 961 1756 161411986 161411189 0.000000e+00 1251
28 TraesCS1A01G228600 chr6A 96.371 496 16 2 2519 3013 161148093 161147599 0.000000e+00 815
29 TraesCS1A01G228600 chr6A 96.066 483 15 3 2043 2522 161148696 161148215 0.000000e+00 784
30 TraesCS1A01G228600 chr6A 95.152 495 23 1 2519 3013 161396219 161395726 0.000000e+00 780
31 TraesCS1A01G228600 chr6A 96.687 332 11 0 635 966 161157119 161156788 1.220000e-153 553
32 TraesCS1A01G228600 chr6A 95.495 333 14 1 635 966 161412359 161412027 5.720000e-147 531
33 TraesCS1A01G228600 chr5B 82.846 1778 218 53 639 2385 99742931 99744652 0.000000e+00 1513
34 TraesCS1A01G228600 chr5B 82.574 1779 219 58 635 2380 99391004 99392724 0.000000e+00 1483
35 TraesCS1A01G228600 chr4B 91.985 1098 43 11 1292 2385 451335689 451334633 0.000000e+00 1498
36 TraesCS1A01G228600 chr4B 91.803 1098 45 8 1292 2385 451311090 451310034 0.000000e+00 1487
37 TraesCS1A01G228600 chr4B 91.712 1098 45 9 1292 2385 451242309 451241254 0.000000e+00 1482
38 TraesCS1A01G228600 chr4B 94.118 629 35 2 2385 3013 451240686 451240060 0.000000e+00 955
39 TraesCS1A01G228600 chr4B 94.118 629 35 2 2385 3013 451334065 451333439 0.000000e+00 955
40 TraesCS1A01G228600 chr4B 93.959 629 36 2 2385 3013 451309466 451308840 0.000000e+00 950
41 TraesCS1A01G228600 chr4B 93.641 629 38 2 2385 3013 451260137 451259511 0.000000e+00 939
42 TraesCS1A01G228600 chr3B 82.565 1801 199 67 635 2384 633537337 633535601 0.000000e+00 1480
43 TraesCS1A01G228600 chr3D 83.702 1448 165 43 964 2385 549203053 549204455 0.000000e+00 1301
44 TraesCS1A01G228600 chr3D 92.438 648 33 11 4 636 189081337 189080691 0.000000e+00 911
45 TraesCS1A01G228600 chr2A 94.281 647 20 10 4 636 179798444 179797801 0.000000e+00 974
46 TraesCS1A01G228600 chr3A 94.210 639 26 5 4 634 577259844 577259209 0.000000e+00 965
47 TraesCS1A01G228600 chr3A 91.446 643 35 15 1 638 536903023 536903650 0.000000e+00 865
48 TraesCS1A01G228600 chr5A 91.049 648 40 15 1 634 118417365 118418008 0.000000e+00 859
49 TraesCS1A01G228600 chr7A 90.952 641 45 5 4 636 625749767 625749132 0.000000e+00 850
50 TraesCS1A01G228600 chr7D 90.881 647 35 17 4 638 599729589 599728955 0.000000e+00 846
51 TraesCS1A01G228600 chr4A 90.895 637 43 11 7 636 482516081 482515453 0.000000e+00 841


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 TraesCS1A01G228600 chr1A 399891435 399894448 3013 True 5566.000000 5566 100.000000 1 3014 1 chr1A.!!$R1 3013
1 TraesCS1A01G228600 chr1A 433525763 433528419 2656 False 1513.000000 2495 93.932000 635 2716 2 chr1A.!!$F2 2081
2 TraesCS1A01G228600 chr1A 496852186 496853445 1259 True 1491.000000 1491 88.396000 1138 2385 1 chr1A.!!$R2 1247
3 TraesCS1A01G228600 chr1A 106532811 106534703 1892 False 1476.000000 2394 96.150000 635 2488 2 chr1A.!!$F1 1853
4 TraesCS1A01G228600 chr1A 433736710 433738784 2074 False 1201.500000 2037 92.077000 635 2385 2 chr1A.!!$F3 1750
5 TraesCS1A01G228600 chr1A 481216477 481219374 2897 False 1084.000000 1349 91.964000 635 2999 3 chr1A.!!$F4 2364
6 TraesCS1A01G228600 chr1B 510207934 510210899 2965 False 1595.000000 2368 90.742500 635 3013 2 chr1B.!!$F1 2378
7 TraesCS1A01G228600 chr5D 88142952 88145601 2649 False 1068.333333 2087 94.180667 635 3013 3 chr5D.!!$F1 2378
8 TraesCS1A01G228600 chr5D 436269493 436270134 641 True 915.000000 915 92.713000 4 634 1 chr5D.!!$R1 630
9 TraesCS1A01G228600 chr1D 83126585 83128684 2099 False 860.333333 1893 94.558000 635 2382 3 chr1D.!!$F3 1747
10 TraesCS1A01G228600 chr1D 400410444 400412099 1655 True 710.000000 1098 88.491500 1138 2385 2 chr1D.!!$R1 1247
11 TraesCS1A01G228600 chr1D 82304002 82304823 821 False 604.500000 667 94.952500 635 1408 2 chr1D.!!$F2 773
12 TraesCS1A01G228600 chr6A 161155653 161157119 1466 True 1152.000000 1751 96.106000 635 2055 2 chr6A.!!$R2 1420
13 TraesCS1A01G228600 chr6A 161395726 161397125 1399 True 1019.000000 1258 95.410500 1740 3013 2 chr6A.!!$R3 1273
14 TraesCS1A01G228600 chr6A 161411189 161412359 1170 True 891.000000 1251 95.241000 635 1756 2 chr6A.!!$R4 1121
15 TraesCS1A01G228600 chr6A 161147599 161148696 1097 True 799.500000 815 96.218500 2043 3013 2 chr6A.!!$R1 970
16 TraesCS1A01G228600 chr5B 99742931 99744652 1721 False 1513.000000 1513 82.846000 639 2385 1 chr5B.!!$F2 1746
17 TraesCS1A01G228600 chr5B 99391004 99392724 1720 False 1483.000000 1483 82.574000 635 2380 1 chr5B.!!$F1 1745
18 TraesCS1A01G228600 chr4B 451333439 451335689 2250 True 1226.500000 1498 93.051500 1292 3013 2 chr4B.!!$R4 1721
19 TraesCS1A01G228600 chr4B 451240060 451242309 2249 True 1218.500000 1482 92.915000 1292 3013 2 chr4B.!!$R2 1721
20 TraesCS1A01G228600 chr4B 451308840 451311090 2250 True 1218.500000 1487 92.881000 1292 3013 2 chr4B.!!$R3 1721
21 TraesCS1A01G228600 chr4B 451259511 451260137 626 True 939.000000 939 93.641000 2385 3013 1 chr4B.!!$R1 628
22 TraesCS1A01G228600 chr3B 633535601 633537337 1736 True 1480.000000 1480 82.565000 635 2384 1 chr3B.!!$R1 1749
23 TraesCS1A01G228600 chr3D 549203053 549204455 1402 False 1301.000000 1301 83.702000 964 2385 1 chr3D.!!$F1 1421
24 TraesCS1A01G228600 chr3D 189080691 189081337 646 True 911.000000 911 92.438000 4 636 1 chr3D.!!$R1 632
25 TraesCS1A01G228600 chr2A 179797801 179798444 643 True 974.000000 974 94.281000 4 636 1 chr2A.!!$R1 632
26 TraesCS1A01G228600 chr3A 577259209 577259844 635 True 965.000000 965 94.210000 4 634 1 chr3A.!!$R1 630
27 TraesCS1A01G228600 chr3A 536903023 536903650 627 False 865.000000 865 91.446000 1 638 1 chr3A.!!$F1 637
28 TraesCS1A01G228600 chr5A 118417365 118418008 643 False 859.000000 859 91.049000 1 634 1 chr5A.!!$F1 633
29 TraesCS1A01G228600 chr7A 625749132 625749767 635 True 850.000000 850 90.952000 4 636 1 chr7A.!!$R1 632
30 TraesCS1A01G228600 chr7D 599728955 599729589 634 True 846.000000 846 90.881000 4 638 1 chr7D.!!$R1 634
31 TraesCS1A01G228600 chr4A 482515453 482516081 628 True 841.000000 841 90.895000 7 636 1 chr4A.!!$R1 629

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
292 331 0.098552 CACGCAACACACACACACAT 59.901 50.0 0.0 0.0 0.0 3.21 F
537 593 0.174845 CGGAAGTGTCGCATAGGGAA 59.825 55.0 0.0 0.0 0.0 3.97 F
1686 2715 0.613012 GGTGCAAGGCTCAAGGGAAT 60.613 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 2451 1.129998 CCTTCGCTTGTTGATGAGCTG 59.870 52.381 0.0 0.0 36.76 4.24 R
1840 2872 1.627329 TCAGCAGCTTCCTCAACTGAT 59.373 47.619 0.0 0.0 33.10 2.90 R
2851 5166 2.619849 CCTCTCAAGTGGCATGAATGGT 60.620 50.000 0.0 0.0 0.00 3.55 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
207 216 1.133664 CACACACGCAACAACACGT 59.866 52.632 0.00 0.00 44.75 4.49
233 271 2.277247 GTGCACACACACACACGC 60.277 61.111 13.17 0.00 46.61 5.34
289 328 2.482831 GCACGCAACACACACACA 59.517 55.556 0.00 0.00 0.00 3.72
292 331 0.098552 CACGCAACACACACACACAT 59.901 50.000 0.00 0.00 0.00 3.21
293 332 1.328986 CACGCAACACACACACACATA 59.671 47.619 0.00 0.00 0.00 2.29
535 591 1.515954 ACGGAAGTGTCGCATAGGG 59.484 57.895 0.00 0.00 46.97 3.53
536 592 0.968901 ACGGAAGTGTCGCATAGGGA 60.969 55.000 0.00 0.00 46.97 4.20
537 593 0.174845 CGGAAGTGTCGCATAGGGAA 59.825 55.000 0.00 0.00 0.00 3.97
538 594 1.202533 CGGAAGTGTCGCATAGGGAAT 60.203 52.381 0.00 0.00 0.00 3.01
539 595 2.035449 CGGAAGTGTCGCATAGGGAATA 59.965 50.000 0.00 0.00 0.00 1.75
540 596 3.491964 CGGAAGTGTCGCATAGGGAATAA 60.492 47.826 0.00 0.00 0.00 1.40
541 597 4.448210 GGAAGTGTCGCATAGGGAATAAA 58.552 43.478 0.00 0.00 0.00 1.40
542 598 4.879545 GGAAGTGTCGCATAGGGAATAAAA 59.120 41.667 0.00 0.00 0.00 1.52
543 599 5.531287 GGAAGTGTCGCATAGGGAATAAAAT 59.469 40.000 0.00 0.00 0.00 1.82
544 600 6.039382 GGAAGTGTCGCATAGGGAATAAAATT 59.961 38.462 0.00 0.00 0.00 1.82
545 601 7.404671 AAGTGTCGCATAGGGAATAAAATTT 57.595 32.000 0.00 0.00 0.00 1.82
546 602 8.514330 AAGTGTCGCATAGGGAATAAAATTTA 57.486 30.769 0.00 0.00 0.00 1.40
547 603 8.154649 AGTGTCGCATAGGGAATAAAATTTAG 57.845 34.615 0.00 0.00 0.00 1.85
548 604 7.228706 AGTGTCGCATAGGGAATAAAATTTAGG 59.771 37.037 0.00 0.00 0.00 2.69
549 605 7.227910 GTGTCGCATAGGGAATAAAATTTAGGA 59.772 37.037 0.00 0.00 0.00 2.94
550 606 7.227910 TGTCGCATAGGGAATAAAATTTAGGAC 59.772 37.037 0.00 0.00 0.00 3.85
551 607 7.444487 GTCGCATAGGGAATAAAATTTAGGACT 59.556 37.037 0.00 0.00 0.00 3.85
552 608 8.653191 TCGCATAGGGAATAAAATTTAGGACTA 58.347 33.333 0.00 0.00 0.00 2.59
553 609 8.936864 CGCATAGGGAATAAAATTTAGGACTAG 58.063 37.037 0.00 0.00 0.00 2.57
554 610 9.794719 GCATAGGGAATAAAATTTAGGACTAGT 57.205 33.333 0.00 0.00 0.00 2.57
558 614 8.832735 AGGGAATAAAATTTAGGACTAGTGTCA 58.167 33.333 0.00 0.00 44.61 3.58
559 615 9.457436 GGGAATAAAATTTAGGACTAGTGTCAA 57.543 33.333 0.00 0.00 44.61 3.18
564 620 7.611213 AAATTTAGGACTAGTGTCAAATCGG 57.389 36.000 0.00 0.00 44.61 4.18
565 621 4.730949 TTAGGACTAGTGTCAAATCGGG 57.269 45.455 0.00 0.00 44.61 5.14
566 622 2.816411 AGGACTAGTGTCAAATCGGGA 58.184 47.619 0.00 0.00 44.61 5.14
567 623 3.170717 AGGACTAGTGTCAAATCGGGAA 58.829 45.455 0.00 0.00 44.61 3.97
568 624 3.195825 AGGACTAGTGTCAAATCGGGAAG 59.804 47.826 0.00 0.00 44.61 3.46
569 625 3.194968 GGACTAGTGTCAAATCGGGAAGA 59.805 47.826 0.00 0.00 44.61 2.87
570 626 4.322499 GGACTAGTGTCAAATCGGGAAGAA 60.322 45.833 0.00 0.00 44.61 2.52
571 627 5.223449 ACTAGTGTCAAATCGGGAAGAAA 57.777 39.130 0.00 0.00 0.00 2.52
572 628 5.617252 ACTAGTGTCAAATCGGGAAGAAAA 58.383 37.500 0.00 0.00 0.00 2.29
573 629 6.059484 ACTAGTGTCAAATCGGGAAGAAAAA 58.941 36.000 0.00 0.00 0.00 1.94
574 630 5.183014 AGTGTCAAATCGGGAAGAAAAAC 57.817 39.130 0.00 0.00 0.00 2.43
575 631 4.887655 AGTGTCAAATCGGGAAGAAAAACT 59.112 37.500 0.00 0.00 0.00 2.66
576 632 5.359860 AGTGTCAAATCGGGAAGAAAAACTT 59.640 36.000 0.00 0.00 42.03 2.66
577 633 6.040247 GTGTCAAATCGGGAAGAAAAACTTT 58.960 36.000 0.00 0.00 39.13 2.66
578 634 6.533723 GTGTCAAATCGGGAAGAAAAACTTTT 59.466 34.615 0.00 0.00 39.13 2.27
579 635 6.754675 TGTCAAATCGGGAAGAAAAACTTTTC 59.245 34.615 6.79 6.79 45.22 2.29
580 636 6.200286 GTCAAATCGGGAAGAAAAACTTTTCC 59.800 38.462 10.57 0.00 45.84 3.13
581 637 5.862678 AATCGGGAAGAAAAACTTTTCCA 57.137 34.783 10.57 0.00 45.84 3.53
582 638 4.911514 TCGGGAAGAAAAACTTTTCCAG 57.088 40.909 10.57 1.23 45.84 3.86
583 639 4.274978 TCGGGAAGAAAAACTTTTCCAGT 58.725 39.130 10.57 0.00 45.84 4.00
584 640 4.097286 TCGGGAAGAAAAACTTTTCCAGTG 59.903 41.667 10.57 0.00 45.84 3.66
585 641 4.142249 CGGGAAGAAAAACTTTTCCAGTGT 60.142 41.667 10.57 0.00 45.84 3.55
586 642 5.348986 GGGAAGAAAAACTTTTCCAGTGTC 58.651 41.667 10.57 2.87 45.84 3.67
587 643 5.105513 GGGAAGAAAAACTTTTCCAGTGTCA 60.106 40.000 10.57 0.00 45.84 3.58
588 644 6.394809 GGAAGAAAAACTTTTCCAGTGTCAA 58.605 36.000 10.57 0.00 45.84 3.18
589 645 6.871492 GGAAGAAAAACTTTTCCAGTGTCAAA 59.129 34.615 10.57 0.00 45.84 2.69
590 646 7.549134 GGAAGAAAAACTTTTCCAGTGTCAAAT 59.451 33.333 10.57 0.00 45.84 2.32
591 647 9.581099 GAAGAAAAACTTTTCCAGTGTCAAATA 57.419 29.630 10.57 0.00 45.84 1.40
592 648 9.936759 AAGAAAAACTTTTCCAGTGTCAAATAA 57.063 25.926 10.57 0.00 45.84 1.40
593 649 9.586435 AGAAAAACTTTTCCAGTGTCAAATAAG 57.414 29.630 10.57 0.00 45.84 1.73
594 650 8.716646 AAAAACTTTTCCAGTGTCAAATAAGG 57.283 30.769 0.00 0.00 35.12 2.69
595 651 7.654022 AAACTTTTCCAGTGTCAAATAAGGA 57.346 32.000 0.00 0.00 35.12 3.36
596 652 7.654022 AACTTTTCCAGTGTCAAATAAGGAA 57.346 32.000 0.00 0.00 35.12 3.36
597 653 7.039313 ACTTTTCCAGTGTCAAATAAGGAAC 57.961 36.000 0.00 0.00 35.10 3.62
598 654 6.040504 ACTTTTCCAGTGTCAAATAAGGAACC 59.959 38.462 0.00 0.00 35.10 3.62
599 655 4.715534 TCCAGTGTCAAATAAGGAACCA 57.284 40.909 0.00 0.00 0.00 3.67
600 656 5.255397 TCCAGTGTCAAATAAGGAACCAT 57.745 39.130 0.00 0.00 0.00 3.55
601 657 6.381498 TCCAGTGTCAAATAAGGAACCATA 57.619 37.500 0.00 0.00 0.00 2.74
602 658 6.969043 TCCAGTGTCAAATAAGGAACCATAT 58.031 36.000 0.00 0.00 0.00 1.78
603 659 7.410174 TCCAGTGTCAAATAAGGAACCATATT 58.590 34.615 0.00 0.00 0.00 1.28
604 660 7.893302 TCCAGTGTCAAATAAGGAACCATATTT 59.107 33.333 7.85 7.85 33.15 1.40
605 661 8.531146 CCAGTGTCAAATAAGGAACCATATTTT 58.469 33.333 10.17 0.00 31.39 1.82
615 671 9.975218 ATAAGGAACCATATTTTAAGACAGTGT 57.025 29.630 0.00 0.00 0.00 3.55
616 672 7.923414 AGGAACCATATTTTAAGACAGTGTC 57.077 36.000 15.78 15.78 0.00 3.67
617 673 7.458397 AGGAACCATATTTTAAGACAGTGTCA 58.542 34.615 24.73 4.33 34.60 3.58
618 674 7.942341 AGGAACCATATTTTAAGACAGTGTCAA 59.058 33.333 24.73 10.81 34.60 3.18
619 675 8.573035 GGAACCATATTTTAAGACAGTGTCAAA 58.427 33.333 24.73 16.22 34.60 2.69
632 688 8.697507 AGACAGTGTCAAATAAGGAATTTTCT 57.302 30.769 24.73 0.00 35.54 2.52
633 689 8.787852 AGACAGTGTCAAATAAGGAATTTTCTC 58.212 33.333 24.73 0.00 35.54 2.87
975 1083 3.178540 AACCCACGGTGCCTCTGTC 62.179 63.158 1.68 0.00 35.34 3.51
977 1085 3.625897 CCACGGTGCCTCTGTCCA 61.626 66.667 1.68 0.00 32.67 4.02
987 1095 1.681793 GCCTCTGTCCAATACGCTAGA 59.318 52.381 0.00 0.00 0.00 2.43
1115 1551 1.977854 TGGTGTGTCAGATAGCAACCT 59.022 47.619 0.00 0.00 0.00 3.50
1230 1666 1.371145 GGCTAGCGAGTCGATGAGC 60.371 63.158 18.61 19.21 0.00 4.26
1245 1681 1.822615 GAGCCAGGGAAGAGAGCTC 59.177 63.158 5.27 5.27 42.74 4.09
1366 1919 5.522824 CGCACTCCCCTTTAATAGTAAAGAC 59.477 44.000 21.17 4.04 46.28 3.01
1403 2398 3.996480 AGTTTCTTCCTTCAGAGGTTCG 58.004 45.455 0.00 0.00 43.97 3.95
1540 2568 6.317893 GGTACTTCCAATCGGTACAATGATTT 59.682 38.462 0.00 0.00 37.95 2.17
1553 2581 7.545265 CGGTACAATGATTTTTGGATTTGATGT 59.455 33.333 0.00 0.00 0.00 3.06
1576 2604 2.158871 ACTACGAGTGGCCTTTTGACAA 60.159 45.455 3.32 0.00 0.00 3.18
1686 2715 0.613012 GGTGCAAGGCTCAAGGGAAT 60.613 55.000 0.00 0.00 0.00 3.01
1745 2777 5.261216 TCTTGGATGAGGGGTATGTTTTTC 58.739 41.667 0.00 0.00 0.00 2.29
1772 2804 6.615264 ACATCTATATGTTGCTTTGCTCAG 57.385 37.500 0.00 0.00 44.07 3.35
1833 2865 8.795786 TGTGCTTTACATTTCAGTTACAAATC 57.204 30.769 0.00 0.00 33.42 2.17
2005 3056 1.672363 ACGATACAACATGCATGCAGG 59.328 47.619 29.33 29.33 0.00 4.85
2040 3091 8.470002 ACACCTTGCCATTTATATCTTTCTTTC 58.530 33.333 0.00 0.00 0.00 2.62
2175 3559 8.006564 AGATGATGGTGATAAATTAACCCACAT 58.993 33.333 0.00 0.00 34.09 3.21
2256 3667 7.057894 AGACATCTAGACAAACCTACCTAGAG 58.942 42.308 0.00 0.00 40.34 2.43
2267 3678 7.654923 ACAAACCTACCTAGAGTTTCTAAAACG 59.345 37.037 0.00 0.00 31.54 3.60
2268 3679 6.278172 ACCTACCTAGAGTTTCTAAAACGG 57.722 41.667 0.00 0.00 0.00 4.44
2393 4560 3.394674 TGGTCAACGCTACATTTCTGA 57.605 42.857 0.00 0.00 0.00 3.27
2410 4577 8.468399 ACATTTCTGAAATTGGCAAACATTTTT 58.532 25.926 12.74 0.00 33.97 1.94
2777 5072 5.693769 TCATCTCCTTTCCCGTATTTCTT 57.306 39.130 0.00 0.00 0.00 2.52
2851 5166 0.679640 GGTGGCATTGTCCCATTCGA 60.680 55.000 0.00 0.00 34.34 3.71
2854 5169 0.679640 GGCATTGTCCCATTCGACCA 60.680 55.000 0.00 0.00 31.35 4.02
2922 5237 1.258982 GGCATCGACGCTAGTGATTTG 59.741 52.381 10.99 3.43 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.288294 TGAACGGAAATGTCATATAGGGAAG 58.712 40.000 0.00 0.00 0.00 3.46
257 296 3.130160 TGCGTGTGTGTTGCTGCA 61.130 55.556 0.00 0.00 0.00 4.41
289 328 1.227999 GCCTGCGTGTGTGTGTATGT 61.228 55.000 0.00 0.00 0.00 2.29
292 331 1.594021 CTGCCTGCGTGTGTGTGTA 60.594 57.895 0.00 0.00 0.00 2.90
293 332 2.896854 CTGCCTGCGTGTGTGTGT 60.897 61.111 0.00 0.00 0.00 3.72
533 589 9.457436 TTGACACTAGTCCTAAATTTTATTCCC 57.543 33.333 0.00 0.00 44.33 3.97
538 594 9.158233 CCGATTTGACACTAGTCCTAAATTTTA 57.842 33.333 0.00 0.00 44.33 1.52
539 595 7.120726 CCCGATTTGACACTAGTCCTAAATTTT 59.879 37.037 0.00 0.00 44.33 1.82
540 596 6.598064 CCCGATTTGACACTAGTCCTAAATTT 59.402 38.462 0.00 0.00 44.33 1.82
541 597 6.070424 TCCCGATTTGACACTAGTCCTAAATT 60.070 38.462 0.00 0.00 44.33 1.82
542 598 5.424252 TCCCGATTTGACACTAGTCCTAAAT 59.576 40.000 0.00 0.00 44.33 1.40
543 599 4.773674 TCCCGATTTGACACTAGTCCTAAA 59.226 41.667 0.00 0.00 44.33 1.85
544 600 4.346730 TCCCGATTTGACACTAGTCCTAA 58.653 43.478 0.00 0.00 44.33 2.69
545 601 3.972133 TCCCGATTTGACACTAGTCCTA 58.028 45.455 0.00 0.00 44.33 2.94
546 602 2.816411 TCCCGATTTGACACTAGTCCT 58.184 47.619 0.00 0.00 44.33 3.85
547 603 3.194968 TCTTCCCGATTTGACACTAGTCC 59.805 47.826 0.00 0.00 44.33 3.85
548 604 4.451629 TCTTCCCGATTTGACACTAGTC 57.548 45.455 0.00 0.00 45.19 2.59
549 605 4.884668 TTCTTCCCGATTTGACACTAGT 57.115 40.909 0.00 0.00 0.00 2.57
550 606 6.204882 AGTTTTTCTTCCCGATTTGACACTAG 59.795 38.462 0.00 0.00 0.00 2.57
551 607 6.059484 AGTTTTTCTTCCCGATTTGACACTA 58.941 36.000 0.00 0.00 0.00 2.74
552 608 4.887655 AGTTTTTCTTCCCGATTTGACACT 59.112 37.500 0.00 0.00 0.00 3.55
553 609 5.183014 AGTTTTTCTTCCCGATTTGACAC 57.817 39.130 0.00 0.00 0.00 3.67
554 610 5.845391 AAGTTTTTCTTCCCGATTTGACA 57.155 34.783 0.00 0.00 0.00 3.58
555 611 6.200286 GGAAAAGTTTTTCTTCCCGATTTGAC 59.800 38.462 14.85 0.00 44.49 3.18
556 612 6.127310 TGGAAAAGTTTTTCTTCCCGATTTGA 60.127 34.615 14.85 0.00 44.49 2.69
557 613 6.045955 TGGAAAAGTTTTTCTTCCCGATTTG 58.954 36.000 14.85 0.00 44.49 2.32
558 614 6.127168 ACTGGAAAAGTTTTTCTTCCCGATTT 60.127 34.615 14.85 0.00 44.49 2.17
559 615 5.362717 ACTGGAAAAGTTTTTCTTCCCGATT 59.637 36.000 14.85 0.00 44.49 3.34
560 616 4.893524 ACTGGAAAAGTTTTTCTTCCCGAT 59.106 37.500 14.85 0.00 44.49 4.18
561 617 4.097286 CACTGGAAAAGTTTTTCTTCCCGA 59.903 41.667 14.85 0.00 44.49 5.14
562 618 4.142249 ACACTGGAAAAGTTTTTCTTCCCG 60.142 41.667 14.85 1.74 44.49 5.14
563 619 5.105513 TGACACTGGAAAAGTTTTTCTTCCC 60.106 40.000 14.85 2.57 44.49 3.97
564 620 5.961272 TGACACTGGAAAAGTTTTTCTTCC 58.039 37.500 14.85 2.94 44.49 3.46
565 621 7.883229 TTTGACACTGGAAAAGTTTTTCTTC 57.117 32.000 14.85 0.98 44.49 2.87
566 622 9.936759 TTATTTGACACTGGAAAAGTTTTTCTT 57.063 25.926 14.85 0.00 44.49 2.52
567 623 9.586435 CTTATTTGACACTGGAAAAGTTTTTCT 57.414 29.630 14.85 0.00 44.49 2.52
568 624 8.817100 CCTTATTTGACACTGGAAAAGTTTTTC 58.183 33.333 1.64 8.48 44.38 2.29
569 625 8.536175 TCCTTATTTGACACTGGAAAAGTTTTT 58.464 29.630 1.64 0.00 36.83 1.94
570 626 8.073467 TCCTTATTTGACACTGGAAAAGTTTT 57.927 30.769 0.00 0.00 36.83 2.43
571 627 7.654022 TCCTTATTTGACACTGGAAAAGTTT 57.346 32.000 0.00 0.00 36.83 2.66
572 628 7.417456 GGTTCCTTATTTGACACTGGAAAAGTT 60.417 37.037 0.00 0.00 36.83 2.66
573 629 6.040504 GGTTCCTTATTTGACACTGGAAAAGT 59.959 38.462 0.00 0.00 40.93 2.66
574 630 6.040391 TGGTTCCTTATTTGACACTGGAAAAG 59.960 38.462 0.00 0.00 35.68 2.27
575 631 5.894393 TGGTTCCTTATTTGACACTGGAAAA 59.106 36.000 0.00 0.00 35.68 2.29
576 632 5.450453 TGGTTCCTTATTTGACACTGGAAA 58.550 37.500 0.00 0.00 35.68 3.13
577 633 5.055265 TGGTTCCTTATTTGACACTGGAA 57.945 39.130 0.00 0.00 0.00 3.53
578 634 4.715534 TGGTTCCTTATTTGACACTGGA 57.284 40.909 0.00 0.00 0.00 3.86
579 635 7.645058 AATATGGTTCCTTATTTGACACTGG 57.355 36.000 4.75 0.00 0.00 4.00
589 645 9.975218 ACACTGTCTTAAAATATGGTTCCTTAT 57.025 29.630 0.00 0.00 0.00 1.73
590 646 9.444600 GACACTGTCTTAAAATATGGTTCCTTA 57.555 33.333 1.58 0.00 0.00 2.69
591 647 7.942341 TGACACTGTCTTAAAATATGGTTCCTT 59.058 33.333 10.54 0.00 33.15 3.36
592 648 7.458397 TGACACTGTCTTAAAATATGGTTCCT 58.542 34.615 10.54 0.00 33.15 3.36
593 649 7.681939 TGACACTGTCTTAAAATATGGTTCC 57.318 36.000 10.54 0.00 33.15 3.62
606 662 9.136323 AGAAAATTCCTTATTTGACACTGTCTT 57.864 29.630 10.54 0.00 36.57 3.01
607 663 8.697507 AGAAAATTCCTTATTTGACACTGTCT 57.302 30.769 10.54 0.00 36.57 3.41
608 664 8.787852 AGAGAAAATTCCTTATTTGACACTGTC 58.212 33.333 1.86 1.86 36.57 3.51
609 665 8.697507 AGAGAAAATTCCTTATTTGACACTGT 57.302 30.769 0.00 0.00 36.57 3.55
618 674 9.692325 AGCAAGACATAGAGAAAATTCCTTATT 57.308 29.630 0.00 0.00 0.00 1.40
619 675 9.118300 CAGCAAGACATAGAGAAAATTCCTTAT 57.882 33.333 0.00 0.00 0.00 1.73
620 676 7.066284 GCAGCAAGACATAGAGAAAATTCCTTA 59.934 37.037 0.00 0.00 0.00 2.69
621 677 6.127786 GCAGCAAGACATAGAGAAAATTCCTT 60.128 38.462 0.00 0.00 0.00 3.36
622 678 5.356470 GCAGCAAGACATAGAGAAAATTCCT 59.644 40.000 0.00 0.00 0.00 3.36
623 679 5.449725 GGCAGCAAGACATAGAGAAAATTCC 60.450 44.000 0.00 0.00 0.00 3.01
624 680 5.576895 GGCAGCAAGACATAGAGAAAATTC 58.423 41.667 0.00 0.00 0.00 2.17
625 681 4.095483 CGGCAGCAAGACATAGAGAAAATT 59.905 41.667 0.00 0.00 0.00 1.82
626 682 3.624861 CGGCAGCAAGACATAGAGAAAAT 59.375 43.478 0.00 0.00 0.00 1.82
627 683 3.002791 CGGCAGCAAGACATAGAGAAAA 58.997 45.455 0.00 0.00 0.00 2.29
628 684 2.621338 CGGCAGCAAGACATAGAGAAA 58.379 47.619 0.00 0.00 0.00 2.52
629 685 1.134699 CCGGCAGCAAGACATAGAGAA 60.135 52.381 0.00 0.00 0.00 2.87
630 686 0.461548 CCGGCAGCAAGACATAGAGA 59.538 55.000 0.00 0.00 0.00 3.10
631 687 0.176680 ACCGGCAGCAAGACATAGAG 59.823 55.000 0.00 0.00 0.00 2.43
632 688 0.613260 AACCGGCAGCAAGACATAGA 59.387 50.000 0.00 0.00 0.00 1.98
633 689 1.009829 GAACCGGCAGCAAGACATAG 58.990 55.000 0.00 0.00 0.00 2.23
637 693 1.009829 CATAGAACCGGCAGCAAGAC 58.990 55.000 0.00 0.00 0.00 3.01
987 1095 3.118956 CGACCTTCATCTCTACCTGCTTT 60.119 47.826 0.00 0.00 0.00 3.51
1194 1630 3.629087 AGCCCCAATCTGATTTCTTCTG 58.371 45.455 0.00 0.00 0.00 3.02
1230 1666 2.498726 GCGAGCTCTCTTCCCTGG 59.501 66.667 12.85 0.00 0.00 4.45
1245 1681 2.100631 GTTGATGAGTGGACCCGCG 61.101 63.158 0.00 0.00 0.00 6.46
1403 2398 3.603532 TCATCAAGCTCATGAACCTCAC 58.396 45.455 5.95 0.00 32.06 3.51
1432 2451 1.129998 CCTTCGCTTGTTGATGAGCTG 59.870 52.381 0.00 0.00 36.76 4.24
1540 2568 6.370442 CCACTCGTAGTTACATCAAATCCAAA 59.630 38.462 0.00 0.00 0.00 3.28
1553 2581 3.069872 TGTCAAAAGGCCACTCGTAGTTA 59.930 43.478 5.01 0.00 0.00 2.24
1558 2586 1.757682 TTTGTCAAAAGGCCACTCGT 58.242 45.000 5.01 0.00 0.00 4.18
1686 2715 1.629043 AGAACTACAGAACCGGCTGA 58.371 50.000 15.11 0.00 39.20 4.26
1745 2777 9.428097 TGAGCAAAGCAACATATAGATGTATAG 57.572 33.333 2.88 0.00 45.93 1.31
1772 2804 9.875675 GATGCAACTTCAAGATAATATGAACTC 57.124 33.333 0.00 0.00 32.46 3.01
1833 2865 4.334759 CAGCTTCCTCAACTGATATGTTGG 59.665 45.833 7.40 0.00 45.15 3.77
1840 2872 1.627329 TCAGCAGCTTCCTCAACTGAT 59.373 47.619 0.00 0.00 33.10 2.90
2005 3056 7.722795 ATAAATGGCAAGGTGTTTAACAAAC 57.277 32.000 0.00 0.00 41.73 2.93
2175 3559 9.563898 CTATACTCTACAACAATGTACGTTTGA 57.436 33.333 13.51 0.01 41.05 2.69
2777 5072 5.104693 TGAAGTGTTTGGGAGTGAGACTAAA 60.105 40.000 0.00 0.00 0.00 1.85
2851 5166 2.619849 CCTCTCAAGTGGCATGAATGGT 60.620 50.000 0.00 0.00 0.00 3.55
2854 5169 3.201487 TCATCCTCTCAAGTGGCATGAAT 59.799 43.478 0.00 0.00 30.27 2.57


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

AutoCloner maintained by Alex Coulton.