Multiple sequence alignment - TraesCS3B01G287400

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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 TraesCS3B01G287400 chr3B 100.000 2705 0 0 1 2705 460164146 460161442 0.000000e+00 4922
1 TraesCS3B01G287400 chr3B 96.483 1052 29 5 1656 2704 10274649 10275695 0.000000e+00 1731
2 TraesCS3B01G287400 chr3B 96.201 1053 29 7 1656 2704 201502476 201503521 0.000000e+00 1712
3 TraesCS3B01G287400 chr3B 99.461 928 2 3 720 1645 10274273 10275199 0.000000e+00 1683
4 TraesCS3B01G287400 chr3B 99.353 927 2 2 720 1645 201502103 201503026 0.000000e+00 1676
5 TraesCS3B01G287400 chr3B 89.566 738 41 9 1 709 10273806 10274536 0.000000e+00 904
6 TraesCS3B01G287400 chr3B 89.566 738 38 11 1 709 201501637 201502364 0.000000e+00 900
7 TraesCS3B01G287400 chr6D 96.008 1052 33 6 1656 2704 431395233 431394188 0.000000e+00 1701
8 TraesCS3B01G287400 chr6D 98.920 926 9 1 720 1645 431395608 431394684 0.000000e+00 1653
9 TraesCS3B01G287400 chr6D 88.451 736 49 12 3 709 431396073 431395345 0.000000e+00 856
10 TraesCS3B01G287400 chr1B 95.913 1052 35 5 1656 2704 633724968 633726014 0.000000e+00 1698
11 TraesCS3B01G287400 chr1B 97.354 189 3 1 723 911 29508102 29508288 1.210000e-83 320
12 TraesCS3B01G287400 chr2D 95.913 1052 33 6 1656 2704 628281652 628282696 0.000000e+00 1696
13 TraesCS3B01G287400 chr2D 99.136 926 6 2 720 1645 628281277 628282200 0.000000e+00 1664
14 TraesCS3B01G287400 chr1A 95.913 1052 34 6 1656 2704 554469127 554468082 0.000000e+00 1696
15 TraesCS3B01G287400 chr1A 99.676 926 3 0 720 1645 554469503 554468578 0.000000e+00 1694
16 TraesCS3B01G287400 chr1A 89.730 740 38 12 1 709 554469971 554469239 0.000000e+00 911
17 TraesCS3B01G287400 chr5D 95.817 1052 35 6 1656 2704 6211745 6210700 0.000000e+00 1690
18 TraesCS3B01G287400 chr5D 95.817 1052 35 5 1656 2704 483799655 483798610 0.000000e+00 1690
19 TraesCS3B01G287400 chr5D 99.780 911 2 0 720 1630 6215900 6214990 0.000000e+00 1672
20 TraesCS3B01G287400 chr5D 98.158 923 14 2 723 1645 6212115 6211196 0.000000e+00 1607
21 TraesCS3B01G287400 chr5D 91.148 723 42 13 1 709 483800481 483799767 0.000000e+00 961
22 TraesCS3B01G287400 chr5D 90.055 724 40 11 1 709 6214037 6214743 0.000000e+00 909
23 TraesCS3B01G287400 chr5D 89.324 740 41 12 1 709 6216368 6215636 0.000000e+00 894
24 TraesCS3B01G287400 chr5D 88.889 738 45 13 1 709 6212585 6211856 0.000000e+00 874
25 TraesCS3B01G287400 chr3D 95.636 1054 34 8 1656 2704 21893209 21894255 0.000000e+00 1681
26 TraesCS3B01G287400 chr3D 98.060 928 14 3 720 1645 21892835 21893760 0.000000e+00 1611
27 TraesCS3B01G287400 chr1D 95.632 1053 35 8 1656 2704 254485624 254486669 0.000000e+00 1679
28 TraesCS3B01G287400 chr1D 90.456 723 47 12 1 709 254484801 254485515 0.000000e+00 933
29 TraesCS3B01G287400 chr1D 88.413 397 24 11 324 709 244419598 244419983 2.450000e-125 459
30 TraesCS3B01G287400 chr1D 87.406 397 28 11 324 709 244404066 244404451 1.150000e-118 436
31 TraesCS3B01G287400 chr1D 86.902 397 31 11 324 709 244397627 244398013 2.490000e-115 425
32 TraesCS3B01G287400 chr1D 89.691 194 9 4 527 709 426758560 426758753 1.250000e-58 237
33 TraesCS3B01G287400 chrUn 93.649 929 39 11 720 1644 379084613 379085525 0.000000e+00 1371
34 TraesCS3B01G287400 chrUn 89.702 738 39 10 1 709 414887149 414887878 0.000000e+00 907
35 TraesCS3B01G287400 chrUn 89.160 738 44 13 1 709 406374378 406375108 0.000000e+00 887
36 TraesCS3B01G287400 chrUn 95.946 74 1 1 638 709 398476833 398476760 4.730000e-23 119


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 TraesCS3B01G287400 chr3B 460161442 460164146 2704 True 4922.000000 4922 100.000000 1 2705 1 chr3B.!!$R1 2704
1 TraesCS3B01G287400 chr3B 10273806 10275695 1889 False 1439.333333 1731 95.170000 1 2704 3 chr3B.!!$F1 2703
2 TraesCS3B01G287400 chr3B 201501637 201503521 1884 False 1429.333333 1712 95.040000 1 2704 3 chr3B.!!$F2 2703
3 TraesCS3B01G287400 chr6D 431394188 431396073 1885 True 1403.333333 1701 94.459667 3 2704 3 chr6D.!!$R1 2701
4 TraesCS3B01G287400 chr1B 633724968 633726014 1046 False 1698.000000 1698 95.913000 1656 2704 1 chr1B.!!$F2 1048
5 TraesCS3B01G287400 chr2D 628281277 628282696 1419 False 1680.000000 1696 97.524500 720 2704 2 chr2D.!!$F1 1984
6 TraesCS3B01G287400 chr1A 554468082 554469971 1889 True 1433.666667 1696 95.106333 1 2704 3 chr1A.!!$R1 2703
7 TraesCS3B01G287400 chr5D 6210700 6216368 5668 True 1347.400000 1690 94.393600 1 2704 5 chr5D.!!$R1 2703
8 TraesCS3B01G287400 chr5D 483798610 483800481 1871 True 1325.500000 1690 93.482500 1 2704 2 chr5D.!!$R2 2703
9 TraesCS3B01G287400 chr5D 6214037 6214743 706 False 909.000000 909 90.055000 1 709 1 chr5D.!!$F1 708
10 TraesCS3B01G287400 chr3D 21892835 21894255 1420 False 1646.000000 1681 96.848000 720 2704 2 chr3D.!!$F1 1984
11 TraesCS3B01G287400 chr1D 254484801 254486669 1868 False 1306.000000 1679 93.044000 1 2704 2 chr1D.!!$F5 2703
12 TraesCS3B01G287400 chrUn 379084613 379085525 912 False 1371.000000 1371 93.649000 720 1644 1 chrUn.!!$F1 924
13 TraesCS3B01G287400 chrUn 414887149 414887878 729 False 907.000000 907 89.702000 1 709 1 chrUn.!!$F3 708
14 TraesCS3B01G287400 chrUn 406374378 406375108 730 False 887.000000 887 89.160000 1 709 1 chrUn.!!$F2 708

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
71 72 1.021968 AAAACGCTGCGTCTTCCTTT 58.978 45.0 29.07 20.5 39.99 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 1963 1.494721 ACAAGTTCCTCTTTGCCCAGA 59.505 47.619 0.0 0.0 33.63 3.86 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
58 59 2.361119 GGGATTCCCTGGAATAAAACGC 59.639 50.000 14.98 4.41 43.98 4.84
59 60 3.288092 GGATTCCCTGGAATAAAACGCT 58.712 45.455 11.31 0.00 43.98 5.07
71 72 1.021968 AAAACGCTGCGTCTTCCTTT 58.978 45.000 29.07 20.50 39.99 3.11
83 84 4.876107 GCGTCTTCCTTTGATTCCTTATGA 59.124 41.667 0.00 0.00 0.00 2.15
84 85 5.354234 GCGTCTTCCTTTGATTCCTTATGAA 59.646 40.000 0.00 0.00 37.38 2.57
166 168 4.522975 GAAATCCGGGCCAGGGGG 62.523 72.222 22.79 8.58 37.18 5.40
174 176 3.023735 GGCCAGGGGGTCATTCCT 61.024 66.667 0.00 0.00 39.19 3.36
182 184 1.354368 GGGGGTCATTCCTTTGACTCA 59.646 52.381 6.78 0.00 46.88 3.41
195 197 9.775854 ATTCCTTTGACTCATACTGATGATAAG 57.224 33.333 0.00 0.00 41.33 1.73
259 261 2.030091 GCCTATTTCTTTCGCGTACCAC 59.970 50.000 5.77 0.00 0.00 4.16
322 335 9.971922 GAATGAAGAAAAGAAGATTGGAAGAAA 57.028 29.630 0.00 0.00 0.00 2.52
352 365 3.653344 TCTCAACACATGAAGGAAGTCG 58.347 45.455 0.00 0.00 37.67 4.18
356 369 2.851195 ACACATGAAGGAAGTCGCTTT 58.149 42.857 0.00 0.00 0.00 3.51
357 370 2.549754 ACACATGAAGGAAGTCGCTTTG 59.450 45.455 0.00 0.00 0.00 2.77
438 451 6.531021 AGGAACAAACGAGGATAAGAGAAAA 58.469 36.000 0.00 0.00 0.00 2.29
475 491 8.196802 TGTTTTTGTCCAAGTGAGATATATCG 57.803 34.615 7.08 0.00 0.00 2.92
476 492 6.844696 TTTTGTCCAAGTGAGATATATCGC 57.155 37.500 9.33 9.33 0.00 4.58
477 493 5.529581 TTGTCCAAGTGAGATATATCGCA 57.470 39.130 14.36 14.36 34.20 5.10
478 494 5.728637 TGTCCAAGTGAGATATATCGCAT 57.271 39.130 20.13 4.80 38.80 4.73
479 495 6.834168 TGTCCAAGTGAGATATATCGCATA 57.166 37.500 20.13 0.00 38.80 3.14
480 496 6.621613 TGTCCAAGTGAGATATATCGCATAC 58.378 40.000 20.13 9.97 38.80 2.39
481 497 6.037098 GTCCAAGTGAGATATATCGCATACC 58.963 44.000 20.13 9.34 38.80 2.73
482 498 5.714806 TCCAAGTGAGATATATCGCATACCA 59.285 40.000 20.13 3.89 38.80 3.25
483 499 6.381133 TCCAAGTGAGATATATCGCATACCAT 59.619 38.462 20.13 0.87 38.80 3.55
484 500 7.044181 CCAAGTGAGATATATCGCATACCATT 58.956 38.462 20.13 9.24 38.80 3.16
485 501 7.223582 CCAAGTGAGATATATCGCATACCATTC 59.776 40.741 20.13 7.46 38.80 2.67
486 502 7.652524 AGTGAGATATATCGCATACCATTCT 57.347 36.000 20.13 9.37 38.80 2.40
487 503 8.072321 AGTGAGATATATCGCATACCATTCTT 57.928 34.615 20.13 0.00 38.80 2.52
488 504 8.194104 AGTGAGATATATCGCATACCATTCTTC 58.806 37.037 20.13 5.59 38.80 2.87
489 505 7.436673 GTGAGATATATCGCATACCATTCTTCC 59.563 40.741 20.13 1.90 38.80 3.46
490 506 7.343057 TGAGATATATCGCATACCATTCTTCCT 59.657 37.037 14.36 0.00 31.62 3.36
491 507 8.083828 AGATATATCGCATACCATTCTTCCTT 57.916 34.615 7.08 0.00 0.00 3.36
492 508 8.543774 AGATATATCGCATACCATTCTTCCTTT 58.456 33.333 7.08 0.00 0.00 3.11
493 509 9.167311 GATATATCGCATACCATTCTTCCTTTT 57.833 33.333 0.00 0.00 0.00 2.27
494 510 7.823745 ATATCGCATACCATTCTTCCTTTTT 57.176 32.000 0.00 0.00 0.00 1.94
495 511 5.560966 TCGCATACCATTCTTCCTTTTTC 57.439 39.130 0.00 0.00 0.00 2.29
496 512 5.007034 TCGCATACCATTCTTCCTTTTTCA 58.993 37.500 0.00 0.00 0.00 2.69
497 513 5.652014 TCGCATACCATTCTTCCTTTTTCAT 59.348 36.000 0.00 0.00 0.00 2.57
498 514 5.973565 CGCATACCATTCTTCCTTTTTCATC 59.026 40.000 0.00 0.00 0.00 2.92
499 515 6.276091 GCATACCATTCTTCCTTTTTCATCC 58.724 40.000 0.00 0.00 0.00 3.51
500 516 6.498304 CATACCATTCTTCCTTTTTCATCCG 58.502 40.000 0.00 0.00 0.00 4.18
501 517 4.662278 ACCATTCTTCCTTTTTCATCCGA 58.338 39.130 0.00 0.00 0.00 4.55
502 518 5.076873 ACCATTCTTCCTTTTTCATCCGAA 58.923 37.500 0.00 0.00 0.00 4.30
503 519 5.538433 ACCATTCTTCCTTTTTCATCCGAAA 59.462 36.000 0.00 0.00 39.38 3.46
504 520 6.095377 CCATTCTTCCTTTTTCATCCGAAAG 58.905 40.000 0.00 0.00 42.00 2.62
542 558 9.838339 ATTCTATTTCACTATTTCATTCCGTCT 57.162 29.630 0.00 0.00 0.00 4.18
544 560 9.967346 TCTATTTCACTATTTCATTCCGTCTAG 57.033 33.333 0.00 0.00 0.00 2.43
545 561 9.967346 CTATTTCACTATTTCATTCCGTCTAGA 57.033 33.333 0.00 0.00 0.00 2.43
547 563 8.873215 TTTCACTATTTCATTCCGTCTAGATC 57.127 34.615 0.00 0.00 0.00 2.75
548 564 7.825331 TCACTATTTCATTCCGTCTAGATCT 57.175 36.000 0.00 0.00 0.00 2.75
549 565 8.919777 TCACTATTTCATTCCGTCTAGATCTA 57.080 34.615 1.69 1.69 0.00 1.98
550 566 9.350951 TCACTATTTCATTCCGTCTAGATCTAA 57.649 33.333 3.57 0.00 0.00 2.10
551 567 9.619316 CACTATTTCATTCCGTCTAGATCTAAG 57.381 37.037 3.57 0.00 0.00 2.18
552 568 8.798402 ACTATTTCATTCCGTCTAGATCTAAGG 58.202 37.037 3.57 7.89 0.00 2.69
553 569 7.841282 ATTTCATTCCGTCTAGATCTAAGGA 57.159 36.000 14.02 14.02 0.00 3.36
554 570 7.655521 TTTCATTCCGTCTAGATCTAAGGAA 57.344 36.000 24.35 24.35 41.29 3.36
555 571 7.655521 TTCATTCCGTCTAGATCTAAGGAAA 57.344 36.000 25.21 14.68 40.56 3.13
556 572 7.655521 TCATTCCGTCTAGATCTAAGGAAAA 57.344 36.000 25.21 18.07 40.56 2.29
557 573 8.074613 TCATTCCGTCTAGATCTAAGGAAAAA 57.925 34.615 25.21 17.84 40.56 1.94
558 574 7.980099 TCATTCCGTCTAGATCTAAGGAAAAAC 59.020 37.037 25.21 8.56 40.56 2.43
559 575 6.218108 TCCGTCTAGATCTAAGGAAAAACC 57.782 41.667 15.11 0.00 39.35 3.27
575 591 7.351414 GGAAAAACCTAATGCACTGAAATTC 57.649 36.000 0.00 0.00 35.41 2.17
576 592 6.368791 GGAAAAACCTAATGCACTGAAATTCC 59.631 38.462 0.00 0.00 35.41 3.01
577 593 6.418057 AAAACCTAATGCACTGAAATTCCA 57.582 33.333 0.00 0.00 0.00 3.53
578 594 5.391312 AACCTAATGCACTGAAATTCCAC 57.609 39.130 0.00 0.00 0.00 4.02
579 595 4.666512 ACCTAATGCACTGAAATTCCACT 58.333 39.130 0.00 0.00 0.00 4.00
580 596 5.815581 ACCTAATGCACTGAAATTCCACTA 58.184 37.500 0.00 0.00 0.00 2.74
581 597 6.245408 ACCTAATGCACTGAAATTCCACTAA 58.755 36.000 0.00 0.00 0.00 2.24
582 598 6.891908 ACCTAATGCACTGAAATTCCACTAAT 59.108 34.615 0.00 0.00 0.00 1.73
583 599 8.052748 ACCTAATGCACTGAAATTCCACTAATA 58.947 33.333 0.00 0.00 0.00 0.98
584 600 9.071276 CCTAATGCACTGAAATTCCACTAATAT 57.929 33.333 0.00 0.00 0.00 1.28
587 603 8.978874 ATGCACTGAAATTCCACTAATATACA 57.021 30.769 0.00 0.00 0.00 2.29
588 604 8.800370 TGCACTGAAATTCCACTAATATACAA 57.200 30.769 0.00 0.00 0.00 2.41
589 605 9.237187 TGCACTGAAATTCCACTAATATACAAA 57.763 29.630 0.00 0.00 0.00 2.83
631 647 8.507524 GGTATCAAACCTATAGAGTTTTTGCT 57.492 34.615 13.48 6.96 45.75 3.91
632 648 8.957466 GGTATCAAACCTATAGAGTTTTTGCTT 58.043 33.333 13.48 6.61 45.75 3.91
633 649 9.989869 GTATCAAACCTATAGAGTTTTTGCTTC 57.010 33.333 13.48 1.42 35.28 3.86
634 650 8.635765 ATCAAACCTATAGAGTTTTTGCTTCA 57.364 30.769 13.48 0.27 35.28 3.02
635 651 8.458573 TCAAACCTATAGAGTTTTTGCTTCAA 57.541 30.769 13.48 0.00 35.28 2.69
636 652 8.908903 TCAAACCTATAGAGTTTTTGCTTCAAA 58.091 29.630 13.48 0.00 35.28 2.69
637 653 9.185192 CAAACCTATAGAGTTTTTGCTTCAAAG 57.815 33.333 13.48 0.00 35.28 2.77
638 654 8.691661 AACCTATAGAGTTTTTGCTTCAAAGA 57.308 30.769 0.00 0.00 34.72 2.52
639 655 8.691661 ACCTATAGAGTTTTTGCTTCAAAGAA 57.308 30.769 0.00 0.00 34.72 2.52
640 656 9.131791 ACCTATAGAGTTTTTGCTTCAAAGAAA 57.868 29.630 0.00 0.00 34.72 2.52
667 683 8.733092 AGAAATATCATCATAGAGTCAGGGAA 57.267 34.615 0.00 0.00 0.00 3.97
668 684 9.336462 AGAAATATCATCATAGAGTCAGGGAAT 57.664 33.333 0.00 0.00 0.00 3.01
669 685 9.381033 GAAATATCATCATAGAGTCAGGGAATG 57.619 37.037 0.00 0.00 0.00 2.67
670 686 5.758790 ATCATCATAGAGTCAGGGAATGG 57.241 43.478 0.00 0.00 0.00 3.16
671 687 4.819610 TCATCATAGAGTCAGGGAATGGA 58.180 43.478 0.00 0.00 0.00 3.41
672 688 5.218959 TCATCATAGAGTCAGGGAATGGAA 58.781 41.667 0.00 0.00 0.00 3.53
673 689 5.848369 TCATCATAGAGTCAGGGAATGGAAT 59.152 40.000 0.00 0.00 0.00 3.01
674 690 7.018769 TCATCATAGAGTCAGGGAATGGAATA 58.981 38.462 0.00 0.00 0.00 1.75
675 691 6.924913 TCATAGAGTCAGGGAATGGAATAG 57.075 41.667 0.00 0.00 0.00 1.73
676 692 6.624297 TCATAGAGTCAGGGAATGGAATAGA 58.376 40.000 0.00 0.00 0.00 1.98
677 693 6.723515 TCATAGAGTCAGGGAATGGAATAGAG 59.276 42.308 0.00 0.00 0.00 2.43
678 694 4.889780 AGAGTCAGGGAATGGAATAGAGT 58.110 43.478 0.00 0.00 0.00 3.24
679 695 4.898861 AGAGTCAGGGAATGGAATAGAGTC 59.101 45.833 0.00 0.00 0.00 3.36
680 696 4.624913 AGTCAGGGAATGGAATAGAGTCA 58.375 43.478 0.00 0.00 0.00 3.41
681 697 4.653341 AGTCAGGGAATGGAATAGAGTCAG 59.347 45.833 0.00 0.00 0.00 3.51
682 698 3.389329 TCAGGGAATGGAATAGAGTCAGC 59.611 47.826 0.00 0.00 0.00 4.26
683 699 2.366916 AGGGAATGGAATAGAGTCAGCG 59.633 50.000 0.00 0.00 0.00 5.18
684 700 2.365617 GGGAATGGAATAGAGTCAGCGA 59.634 50.000 0.00 0.00 0.00 4.93
685 701 3.181465 GGGAATGGAATAGAGTCAGCGAA 60.181 47.826 0.00 0.00 0.00 4.70
686 702 4.503991 GGGAATGGAATAGAGTCAGCGAAT 60.504 45.833 0.00 0.00 0.00 3.34
687 703 4.450419 GGAATGGAATAGAGTCAGCGAATG 59.550 45.833 0.00 0.00 0.00 2.67
688 704 4.944619 ATGGAATAGAGTCAGCGAATGA 57.055 40.909 0.00 0.00 34.79 2.57
689 705 4.736126 TGGAATAGAGTCAGCGAATGAA 57.264 40.909 0.00 0.00 40.43 2.57
690 706 5.084818 TGGAATAGAGTCAGCGAATGAAA 57.915 39.130 0.00 0.00 40.43 2.69
691 707 4.870426 TGGAATAGAGTCAGCGAATGAAAC 59.130 41.667 0.00 0.00 40.43 2.78
692 708 4.870426 GGAATAGAGTCAGCGAATGAAACA 59.130 41.667 0.00 0.00 40.43 2.83
693 709 5.525378 GGAATAGAGTCAGCGAATGAAACAT 59.475 40.000 0.00 0.00 40.43 2.71
694 710 6.701841 GGAATAGAGTCAGCGAATGAAACATA 59.298 38.462 0.00 0.00 40.43 2.29
695 711 7.386299 GGAATAGAGTCAGCGAATGAAACATAT 59.614 37.037 0.00 0.00 40.43 1.78
696 712 8.668510 AATAGAGTCAGCGAATGAAACATATT 57.331 30.769 0.00 0.00 40.43 1.28
697 713 6.595772 AGAGTCAGCGAATGAAACATATTC 57.404 37.500 0.00 0.00 40.43 1.75
698 714 6.108687 AGAGTCAGCGAATGAAACATATTCA 58.891 36.000 0.00 0.00 40.43 2.57
699 715 6.765036 AGAGTCAGCGAATGAAACATATTCAT 59.235 34.615 0.00 0.00 40.43 2.57
701 717 8.437360 AGTCAGCGAATGAAACATATTCATTA 57.563 30.769 14.43 0.00 45.88 1.90
702 718 8.892723 AGTCAGCGAATGAAACATATTCATTAA 58.107 29.630 14.43 0.00 45.88 1.40
703 719 8.947940 GTCAGCGAATGAAACATATTCATTAAC 58.052 33.333 14.43 10.42 45.88 2.01
704 720 8.672815 TCAGCGAATGAAACATATTCATTAACA 58.327 29.630 14.43 0.00 45.88 2.41
705 721 9.288124 CAGCGAATGAAACATATTCATTAACAA 57.712 29.630 14.43 0.00 45.88 2.83
706 722 9.289303 AGCGAATGAAACATATTCATTAACAAC 57.711 29.630 14.43 3.85 45.88 3.32
707 723 9.289303 GCGAATGAAACATATTCATTAACAACT 57.711 29.630 14.43 0.00 45.88 3.16
1170 1192 9.393512 ACTGATATTCAAGAGAAAAGGATTCTG 57.606 33.333 0.00 0.00 37.29 3.02
1730 1754 9.393512 ACTGATATTCAAGAGAAAAGGATTCTG 57.606 33.333 0.00 0.00 37.29 3.02
1846 1872 6.220726 ACACAAGGAAATAATACAATGGGC 57.779 37.500 0.00 0.00 0.00 5.36
1962 1989 4.550422 GGCAAAGAGGAACTTGTCATTTC 58.450 43.478 0.00 0.00 41.55 2.17
1967 1994 6.487689 AAGAGGAACTTGTCATTTCGAATC 57.512 37.500 0.00 0.00 41.55 2.52
1976 2003 4.148838 TGTCATTTCGAATCCTTGGGTTT 58.851 39.130 0.00 0.00 0.00 3.27
2270 6080 5.006386 AGCATAAATTCATTCGATCTCCCC 58.994 41.667 0.00 0.00 0.00 4.81
2278 6088 8.567285 AATTCATTCGATCTCCCCATATTAAC 57.433 34.615 0.00 0.00 0.00 2.01
2318 6129 9.793252 GCATGCATCTTTCTTTAGAAATAAAGA 57.207 29.630 14.21 14.33 41.89 2.52
2414 6225 6.920817 TGTAGTAGAATGACAACAGATTCGT 58.079 36.000 0.00 0.00 0.00 3.85
2415 6226 6.806739 TGTAGTAGAATGACAACAGATTCGTG 59.193 38.462 0.00 0.00 0.00 4.35
2484 6295 4.706476 AGAAATTCTGGGATTTGCGATTGA 59.294 37.500 0.00 0.00 29.75 2.57
2544 6355 7.228906 AGGAACAGATAACTCGATCGATTTCTA 59.771 37.037 22.05 8.35 0.00 2.10
2704 6515 4.700213 CGTTGATATTGAAGTTCCCCAAGT 59.300 41.667 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.704572 AGGAATCAAAGGAAGACGCAG 58.295 47.619 0.00 0.00 0.00 5.18
59 60 2.859165 AGGAATCAAAGGAAGACGCA 57.141 45.000 0.00 0.00 0.00 5.24
84 85 9.750783 CCTGAATTCTAATTGATTGGATATCCT 57.249 33.333 22.35 3.01 36.82 3.24
134 135 6.657541 GCCCGGATTTCCATATAAAGAATACA 59.342 38.462 0.73 0.00 35.14 2.29
226 228 7.682021 GCGAAAGAAATAGGCCAATTCAATAGT 60.682 37.037 5.01 0.00 0.00 2.12
231 233 3.181501 CGCGAAAGAAATAGGCCAATTCA 60.182 43.478 5.01 0.00 0.00 2.57
322 335 7.555087 TCCTTCATGTGTTGAGAAAACATTTT 58.445 30.769 0.00 0.00 35.27 1.82
326 339 5.652014 ACTTCCTTCATGTGTTGAGAAAACA 59.348 36.000 0.00 0.00 35.27 2.83
341 354 4.261572 CCAATTTCAAAGCGACTTCCTTCA 60.262 41.667 0.00 0.00 0.00 3.02
343 356 3.888930 TCCAATTTCAAAGCGACTTCCTT 59.111 39.130 0.00 0.00 0.00 3.36
406 419 4.383173 TCCTCGTTTGTTCCTTCCTTTAC 58.617 43.478 0.00 0.00 0.00 2.01
407 420 4.693042 TCCTCGTTTGTTCCTTCCTTTA 57.307 40.909 0.00 0.00 0.00 1.85
408 421 3.570912 TCCTCGTTTGTTCCTTCCTTT 57.429 42.857 0.00 0.00 0.00 3.11
409 422 3.790089 ATCCTCGTTTGTTCCTTCCTT 57.210 42.857 0.00 0.00 0.00 3.36
410 423 4.530946 TCTTATCCTCGTTTGTTCCTTCCT 59.469 41.667 0.00 0.00 0.00 3.36
438 451 8.955388 ACTTGGACAAAAACAATTAAAAGCAAT 58.045 25.926 0.00 0.00 0.00 3.56
451 465 7.126398 GCGATATATCTCACTTGGACAAAAAC 58.874 38.462 10.93 0.00 0.00 2.43
457 473 6.037098 GGTATGCGATATATCTCACTTGGAC 58.963 44.000 7.54 2.44 0.00 4.02
472 488 5.652014 TGAAAAAGGAAGAATGGTATGCGAT 59.348 36.000 0.00 0.00 0.00 4.58
473 489 5.007034 TGAAAAAGGAAGAATGGTATGCGA 58.993 37.500 0.00 0.00 0.00 5.10
474 490 5.309323 TGAAAAAGGAAGAATGGTATGCG 57.691 39.130 0.00 0.00 0.00 4.73
475 491 6.276091 GGATGAAAAAGGAAGAATGGTATGC 58.724 40.000 0.00 0.00 0.00 3.14
476 492 6.318648 TCGGATGAAAAAGGAAGAATGGTATG 59.681 38.462 0.00 0.00 0.00 2.39
477 493 6.423182 TCGGATGAAAAAGGAAGAATGGTAT 58.577 36.000 0.00 0.00 0.00 2.73
478 494 5.811190 TCGGATGAAAAAGGAAGAATGGTA 58.189 37.500 0.00 0.00 0.00 3.25
479 495 4.662278 TCGGATGAAAAAGGAAGAATGGT 58.338 39.130 0.00 0.00 0.00 3.55
480 496 5.643379 TTCGGATGAAAAAGGAAGAATGG 57.357 39.130 0.00 0.00 0.00 3.16
489 505 3.942130 AAGCCCTTTCGGATGAAAAAG 57.058 42.857 0.00 0.00 43.21 2.27
490 506 4.681074 AAAAGCCCTTTCGGATGAAAAA 57.319 36.364 0.00 0.00 43.21 1.94
491 507 4.681074 AAAAAGCCCTTTCGGATGAAAA 57.319 36.364 0.00 0.00 43.21 2.29
516 532 9.838339 AGACGGAATGAAATAGTGAAATAGAAT 57.162 29.630 0.00 0.00 0.00 2.40
518 534 9.967346 CTAGACGGAATGAAATAGTGAAATAGA 57.033 33.333 0.00 0.00 0.00 1.98
519 535 9.967346 TCTAGACGGAATGAAATAGTGAAATAG 57.033 33.333 0.00 0.00 0.00 1.73
521 537 9.482627 GATCTAGACGGAATGAAATAGTGAAAT 57.517 33.333 0.00 0.00 0.00 2.17
522 538 8.696374 AGATCTAGACGGAATGAAATAGTGAAA 58.304 33.333 0.00 0.00 0.00 2.69
523 539 8.239038 AGATCTAGACGGAATGAAATAGTGAA 57.761 34.615 0.00 0.00 0.00 3.18
524 540 7.825331 AGATCTAGACGGAATGAAATAGTGA 57.175 36.000 0.00 0.00 0.00 3.41
525 541 9.619316 CTTAGATCTAGACGGAATGAAATAGTG 57.381 37.037 2.02 0.00 0.00 2.74
526 542 8.798402 CCTTAGATCTAGACGGAATGAAATAGT 58.202 37.037 2.02 0.00 0.00 2.12
527 543 9.015367 TCCTTAGATCTAGACGGAATGAAATAG 57.985 37.037 12.49 0.05 0.00 1.73
528 544 8.935614 TCCTTAGATCTAGACGGAATGAAATA 57.064 34.615 12.49 0.00 0.00 1.40
529 545 7.841282 TCCTTAGATCTAGACGGAATGAAAT 57.159 36.000 12.49 0.00 0.00 2.17
530 546 7.655521 TTCCTTAGATCTAGACGGAATGAAA 57.344 36.000 18.69 4.94 0.00 2.69
531 547 7.655521 TTTCCTTAGATCTAGACGGAATGAA 57.344 36.000 21.24 10.95 31.33 2.57
532 548 7.655521 TTTTCCTTAGATCTAGACGGAATGA 57.344 36.000 21.24 14.51 31.33 2.57
533 549 7.224949 GGTTTTTCCTTAGATCTAGACGGAATG 59.775 40.741 21.24 1.93 31.33 2.67
534 550 7.125963 AGGTTTTTCCTTAGATCTAGACGGAAT 59.874 37.037 21.24 10.47 45.67 3.01
535 551 6.439692 AGGTTTTTCCTTAGATCTAGACGGAA 59.560 38.462 18.69 18.69 45.67 4.30
536 552 5.956563 AGGTTTTTCCTTAGATCTAGACGGA 59.043 40.000 2.02 7.79 45.67 4.69
537 553 6.223351 AGGTTTTTCCTTAGATCTAGACGG 57.777 41.667 2.02 5.64 45.67 4.79
538 554 9.250624 CATTAGGTTTTTCCTTAGATCTAGACG 57.749 37.037 2.02 0.00 45.67 4.18
539 555 9.047371 GCATTAGGTTTTTCCTTAGATCTAGAC 57.953 37.037 2.02 0.00 45.67 2.59
540 556 8.768397 TGCATTAGGTTTTTCCTTAGATCTAGA 58.232 33.333 2.02 0.00 45.67 2.43
541 557 8.831550 GTGCATTAGGTTTTTCCTTAGATCTAG 58.168 37.037 2.02 0.00 45.67 2.43
542 558 8.548877 AGTGCATTAGGTTTTTCCTTAGATCTA 58.451 33.333 0.00 0.00 45.67 1.98
543 559 7.337942 CAGTGCATTAGGTTTTTCCTTAGATCT 59.662 37.037 0.00 0.00 45.67 2.75
544 560 7.336931 TCAGTGCATTAGGTTTTTCCTTAGATC 59.663 37.037 0.00 0.00 45.67 2.75
545 561 7.175104 TCAGTGCATTAGGTTTTTCCTTAGAT 58.825 34.615 0.00 0.00 45.67 1.98
546 562 6.539173 TCAGTGCATTAGGTTTTTCCTTAGA 58.461 36.000 0.00 0.00 45.67 2.10
547 563 6.817765 TCAGTGCATTAGGTTTTTCCTTAG 57.182 37.500 0.00 0.00 45.67 2.18
548 564 7.589958 TTTCAGTGCATTAGGTTTTTCCTTA 57.410 32.000 0.00 0.00 45.67 2.69
549 565 6.478512 TTTCAGTGCATTAGGTTTTTCCTT 57.521 33.333 0.00 0.00 45.67 3.36
551 567 6.368791 GGAATTTCAGTGCATTAGGTTTTTCC 59.631 38.462 0.00 0.00 0.00 3.13
552 568 6.928492 TGGAATTTCAGTGCATTAGGTTTTTC 59.072 34.615 0.00 0.00 0.00 2.29
553 569 6.705825 GTGGAATTTCAGTGCATTAGGTTTTT 59.294 34.615 0.00 0.00 0.00 1.94
554 570 6.041979 AGTGGAATTTCAGTGCATTAGGTTTT 59.958 34.615 0.00 0.00 0.00 2.43
555 571 5.539955 AGTGGAATTTCAGTGCATTAGGTTT 59.460 36.000 0.00 0.00 0.00 3.27
556 572 5.079643 AGTGGAATTTCAGTGCATTAGGTT 58.920 37.500 0.00 0.00 0.00 3.50
557 573 4.666512 AGTGGAATTTCAGTGCATTAGGT 58.333 39.130 0.00 0.00 0.00 3.08
558 574 6.757897 TTAGTGGAATTTCAGTGCATTAGG 57.242 37.500 4.16 0.00 0.00 2.69
561 577 9.407380 TGTATATTAGTGGAATTTCAGTGCATT 57.593 29.630 4.16 0.00 0.00 3.56
562 578 8.978874 TGTATATTAGTGGAATTTCAGTGCAT 57.021 30.769 4.16 0.00 0.00 3.96
563 579 8.800370 TTGTATATTAGTGGAATTTCAGTGCA 57.200 30.769 4.16 0.00 0.00 4.57
606 622 8.507524 AGCAAAAACTCTATAGGTTTGATACC 57.492 34.615 15.65 0.00 41.90 2.73
607 623 9.989869 GAAGCAAAAACTCTATAGGTTTGATAC 57.010 33.333 15.65 9.07 41.90 2.24
608 624 9.733556 TGAAGCAAAAACTCTATAGGTTTGATA 57.266 29.630 15.65 0.76 41.90 2.15
609 625 8.635765 TGAAGCAAAAACTCTATAGGTTTGAT 57.364 30.769 15.65 10.26 41.90 2.57
610 626 8.458573 TTGAAGCAAAAACTCTATAGGTTTGA 57.541 30.769 15.65 0.00 41.90 2.69
611 627 9.185192 CTTTGAAGCAAAAACTCTATAGGTTTG 57.815 33.333 15.65 13.49 41.90 2.93
612 628 9.131791 TCTTTGAAGCAAAAACTCTATAGGTTT 57.868 29.630 11.39 11.39 44.70 3.27
613 629 8.691661 TCTTTGAAGCAAAAACTCTATAGGTT 57.308 30.769 0.00 0.57 32.75 3.50
614 630 8.691661 TTCTTTGAAGCAAAAACTCTATAGGT 57.308 30.769 0.00 0.00 32.75 3.08
641 657 9.828691 TTCCCTGACTCTATGATGATATTTCTA 57.171 33.333 0.00 0.00 0.00 2.10
642 658 8.733092 TTCCCTGACTCTATGATGATATTTCT 57.267 34.615 0.00 0.00 0.00 2.52
643 659 9.381033 CATTCCCTGACTCTATGATGATATTTC 57.619 37.037 0.00 0.00 0.00 2.17
644 660 8.327271 CCATTCCCTGACTCTATGATGATATTT 58.673 37.037 0.00 0.00 0.00 1.40
645 661 7.681598 TCCATTCCCTGACTCTATGATGATATT 59.318 37.037 0.00 0.00 0.00 1.28
646 662 7.194761 TCCATTCCCTGACTCTATGATGATAT 58.805 38.462 0.00 0.00 0.00 1.63
647 663 6.565036 TCCATTCCCTGACTCTATGATGATA 58.435 40.000 0.00 0.00 0.00 2.15
648 664 5.409712 TCCATTCCCTGACTCTATGATGAT 58.590 41.667 0.00 0.00 0.00 2.45
649 665 4.819610 TCCATTCCCTGACTCTATGATGA 58.180 43.478 0.00 0.00 0.00 2.92
650 666 5.557576 TTCCATTCCCTGACTCTATGATG 57.442 43.478 0.00 0.00 0.00 3.07
651 667 7.251936 TCTATTCCATTCCCTGACTCTATGAT 58.748 38.462 0.00 0.00 0.00 2.45
652 668 6.624297 TCTATTCCATTCCCTGACTCTATGA 58.376 40.000 0.00 0.00 0.00 2.15
653 669 6.496565 ACTCTATTCCATTCCCTGACTCTATG 59.503 42.308 0.00 0.00 0.00 2.23
654 670 6.629156 ACTCTATTCCATTCCCTGACTCTAT 58.371 40.000 0.00 0.00 0.00 1.98
655 671 6.031964 ACTCTATTCCATTCCCTGACTCTA 57.968 41.667 0.00 0.00 0.00 2.43
656 672 4.889780 ACTCTATTCCATTCCCTGACTCT 58.110 43.478 0.00 0.00 0.00 3.24
657 673 4.651503 TGACTCTATTCCATTCCCTGACTC 59.348 45.833 0.00 0.00 0.00 3.36
658 674 4.624913 TGACTCTATTCCATTCCCTGACT 58.375 43.478 0.00 0.00 0.00 3.41
659 675 4.742138 GCTGACTCTATTCCATTCCCTGAC 60.742 50.000 0.00 0.00 0.00 3.51
660 676 3.389329 GCTGACTCTATTCCATTCCCTGA 59.611 47.826 0.00 0.00 0.00 3.86
661 677 3.737850 GCTGACTCTATTCCATTCCCTG 58.262 50.000 0.00 0.00 0.00 4.45
662 678 2.366916 CGCTGACTCTATTCCATTCCCT 59.633 50.000 0.00 0.00 0.00 4.20
663 679 2.365617 TCGCTGACTCTATTCCATTCCC 59.634 50.000 0.00 0.00 0.00 3.97
664 680 3.735237 TCGCTGACTCTATTCCATTCC 57.265 47.619 0.00 0.00 0.00 3.01
665 681 5.292765 TCATTCGCTGACTCTATTCCATTC 58.707 41.667 0.00 0.00 0.00 2.67
666 682 5.282055 TCATTCGCTGACTCTATTCCATT 57.718 39.130 0.00 0.00 0.00 3.16
667 683 4.944619 TCATTCGCTGACTCTATTCCAT 57.055 40.909 0.00 0.00 0.00 3.41
668 684 4.736126 TTCATTCGCTGACTCTATTCCA 57.264 40.909 0.00 0.00 32.17 3.53
669 685 4.870426 TGTTTCATTCGCTGACTCTATTCC 59.130 41.667 0.00 0.00 32.17 3.01
670 686 6.595772 ATGTTTCATTCGCTGACTCTATTC 57.404 37.500 0.00 0.00 32.17 1.75
671 687 8.668510 AATATGTTTCATTCGCTGACTCTATT 57.331 30.769 0.00 0.00 32.17 1.73
672 688 7.928167 TGAATATGTTTCATTCGCTGACTCTAT 59.072 33.333 0.00 0.00 35.55 1.98
673 689 7.264947 TGAATATGTTTCATTCGCTGACTCTA 58.735 34.615 0.00 0.00 35.55 2.43
674 690 6.108687 TGAATATGTTTCATTCGCTGACTCT 58.891 36.000 0.00 0.00 35.55 3.24
675 691 6.349973 TGAATATGTTTCATTCGCTGACTC 57.650 37.500 0.00 0.00 35.55 3.36
676 692 6.932356 ATGAATATGTTTCATTCGCTGACT 57.068 33.333 1.09 0.00 35.79 3.41
677 693 8.947940 GTTAATGAATATGTTTCATTCGCTGAC 58.052 33.333 17.00 9.27 43.40 3.51
678 694 8.672815 TGTTAATGAATATGTTTCATTCGCTGA 58.327 29.630 17.00 3.01 43.40 4.26
679 695 8.839947 TGTTAATGAATATGTTTCATTCGCTG 57.160 30.769 17.00 0.00 43.40 5.18
680 696 9.289303 GTTGTTAATGAATATGTTTCATTCGCT 57.711 29.630 17.00 2.66 43.40 4.93
681 697 9.289303 AGTTGTTAATGAATATGTTTCATTCGC 57.711 29.630 17.00 12.97 43.40 4.70
1904 1930 6.067217 AGAACCACTTAGAATAGCCAACAT 57.933 37.500 0.00 0.00 0.00 2.71
1934 1961 2.958355 CAAGTTCCTCTTTGCCCAGAAA 59.042 45.455 0.00 0.00 33.63 2.52
1935 1962 2.091885 ACAAGTTCCTCTTTGCCCAGAA 60.092 45.455 0.00 0.00 33.63 3.02
1936 1963 1.494721 ACAAGTTCCTCTTTGCCCAGA 59.505 47.619 0.00 0.00 33.63 3.86
1942 1969 5.673337 TCGAAATGACAAGTTCCTCTTTG 57.327 39.130 0.00 0.00 33.63 2.77
1962 1989 5.193679 AGAATTCCTAAACCCAAGGATTCG 58.806 41.667 0.65 0.00 42.69 3.34
2204 6014 5.133941 TGACTACAAGCGAAGGAGATAGAT 58.866 41.667 0.00 0.00 0.00 1.98
2357 6168 6.799512 ACTGCAATGATGAATACCTTAAAGC 58.200 36.000 0.00 0.00 0.00 3.51
2392 6203 6.806739 CACACGAATCTGTTGTCATTCTACTA 59.193 38.462 0.00 0.00 0.00 1.82
2414 6225 9.298250 CTAAGCTAATCTAGTTCCCTATACACA 57.702 37.037 0.00 0.00 0.00 3.72
2415 6226 8.245491 GCTAAGCTAATCTAGTTCCCTATACAC 58.755 40.741 0.00 0.00 0.00 2.90
2475 6286 6.507958 TCTATTTTCCATGTTCAATCGCAA 57.492 33.333 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.