Multiple sequence alignment - TraesCS6A01G257400

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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 TraesCS6A01G257400 chr6A 100.000 4068 0 0 1 4068 479634574 479638641 0.000000e+00 7513
1 TraesCS6A01G257400 chr6A 93.559 590 15 3 1 569 49498849 49499436 0.000000e+00 857
2 TraesCS6A01G257400 chr6D 95.866 2661 72 19 707 3342 338932557 338935204 0.000000e+00 4270
3 TraesCS6A01G257400 chr6D 87.775 728 74 12 3347 4068 441918454 441919172 0.000000e+00 837
4 TraesCS6A01G257400 chr6B 95.579 2669 75 19 698 3343 481398227 481395579 0.000000e+00 4235
5 TraesCS6A01G257400 chr2D 88.721 727 66 11 3347 4065 489573081 489573799 0.000000e+00 874
6 TraesCS6A01G257400 chr2D 88.243 723 73 10 3348 4068 576460176 576459464 0.000000e+00 854
7 TraesCS6A01G257400 chr2D 82.764 644 107 4 1143 1784 507827405 507826764 4.560000e-159 571
8 TraesCS6A01G257400 chr2D 82.842 577 92 5 2338 2912 507826125 507825554 1.010000e-140 510
9 TraesCS6A01G257400 chr2D 80.732 410 63 14 1939 2340 507826618 507826217 5.110000e-79 305
10 TraesCS6A01G257400 chr3D 88.276 725 74 8 3347 4066 475867310 475866592 0.000000e+00 857
11 TraesCS6A01G257400 chr7A 87.705 732 74 14 3340 4065 37287206 37286485 0.000000e+00 839
12 TraesCS6A01G257400 chr7A 87.312 733 80 12 3343 4068 628356930 628357656 0.000000e+00 826
13 TraesCS6A01G257400 chr7D 87.775 728 73 13 3347 4068 14555700 14554983 0.000000e+00 837
14 TraesCS6A01G257400 chr7D 87.466 726 76 14 3347 4066 65761568 65760852 0.000000e+00 822
15 TraesCS6A01G257400 chr2A 87.671 730 77 12 3347 4068 699983780 699984504 0.000000e+00 837
16 TraesCS6A01G257400 chr2A 82.636 645 108 4 1142 1784 652332112 652331470 5.900000e-158 568
17 TraesCS6A01G257400 chr2A 82.444 581 95 5 2337 2915 652330830 652330255 6.070000e-138 501
18 TraesCS6A01G257400 chr2A 80.964 415 61 16 1935 2340 652331328 652330923 3.050000e-81 313
19 TraesCS6A01G257400 chr2B 92.164 587 26 3 1 569 272462306 272461722 0.000000e+00 811
20 TraesCS6A01G257400 chr2B 82.198 646 109 6 1142 1784 596651745 596651103 5.940000e-153 551
21 TraesCS6A01G257400 chr2B 82.272 581 96 5 2337 2915 596650467 596649892 2.820000e-136 496
22 TraesCS6A01G257400 chr2B 81.159 414 62 14 1935 2340 596650961 596650556 6.560000e-83 318
23 TraesCS6A01G257400 chr5A 92.683 574 16 4 1 554 43222622 43222055 0.000000e+00 804
24 TraesCS6A01G257400 chr5A 82.000 200 34 2 2713 2911 683231929 683231731 6.990000e-38 169
25 TraesCS6A01G257400 chr5B 85.154 586 57 13 4 569 599228058 599228633 1.270000e-159 573
26 TraesCS6A01G257400 chr5B 85.128 585 59 11 4 569 613387579 613388154 1.270000e-159 573
27 TraesCS6A01G257400 chr1D 74.533 911 199 28 2011 2912 261735188 261736074 2.310000e-97 366
28 TraesCS6A01G257400 chr1B 74.286 910 203 26 2011 2912 350398409 350397523 5.000000e-94 355
29 TraesCS6A01G257400 chr4D 77.861 533 112 6 1185 1714 500851781 500851252 3.920000e-85 326
30 TraesCS6A01G257400 chr4B 76.896 567 120 11 1154 1714 644828293 644827732 1.100000e-80 311
31 TraesCS6A01G257400 chr4B 73.096 591 128 28 2338 2911 644827051 644826475 8.980000e-42 182
32 TraesCS6A01G257400 chr3B 94.118 136 4 1 569 700 768079391 768079526 1.920000e-48 204
33 TraesCS6A01G257400 chr3B 94.118 136 4 1 569 700 768174056 768174191 1.920000e-48 204
34 TraesCS6A01G257400 chr3B 92.647 136 6 1 569 700 767860554 767860689 4.150000e-45 193
35 TraesCS6A01G257400 chr3B 92.647 136 6 1 569 700 767975044 767975179 4.150000e-45 193
36 TraesCS6A01G257400 chr7B 79.897 194 31 8 382 569 208143545 208143354 7.090000e-28 135


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 TraesCS6A01G257400 chr6A 479634574 479638641 4067 False 7513.000000 7513 100.000000 1 4068 1 chr6A.!!$F2 4067
1 TraesCS6A01G257400 chr6A 49498849 49499436 587 False 857.000000 857 93.559000 1 569 1 chr6A.!!$F1 568
2 TraesCS6A01G257400 chr6D 338932557 338935204 2647 False 4270.000000 4270 95.866000 707 3342 1 chr6D.!!$F1 2635
3 TraesCS6A01G257400 chr6D 441918454 441919172 718 False 837.000000 837 87.775000 3347 4068 1 chr6D.!!$F2 721
4 TraesCS6A01G257400 chr6B 481395579 481398227 2648 True 4235.000000 4235 95.579000 698 3343 1 chr6B.!!$R1 2645
5 TraesCS6A01G257400 chr2D 489573081 489573799 718 False 874.000000 874 88.721000 3347 4065 1 chr2D.!!$F1 718
6 TraesCS6A01G257400 chr2D 576459464 576460176 712 True 854.000000 854 88.243000 3348 4068 1 chr2D.!!$R1 720
7 TraesCS6A01G257400 chr2D 507825554 507827405 1851 True 462.000000 571 82.112667 1143 2912 3 chr2D.!!$R2 1769
8 TraesCS6A01G257400 chr3D 475866592 475867310 718 True 857.000000 857 88.276000 3347 4066 1 chr3D.!!$R1 719
9 TraesCS6A01G257400 chr7A 37286485 37287206 721 True 839.000000 839 87.705000 3340 4065 1 chr7A.!!$R1 725
10 TraesCS6A01G257400 chr7A 628356930 628357656 726 False 826.000000 826 87.312000 3343 4068 1 chr7A.!!$F1 725
11 TraesCS6A01G257400 chr7D 14554983 14555700 717 True 837.000000 837 87.775000 3347 4068 1 chr7D.!!$R1 721
12 TraesCS6A01G257400 chr7D 65760852 65761568 716 True 822.000000 822 87.466000 3347 4066 1 chr7D.!!$R2 719
13 TraesCS6A01G257400 chr2A 699983780 699984504 724 False 837.000000 837 87.671000 3347 4068 1 chr2A.!!$F1 721
14 TraesCS6A01G257400 chr2A 652330255 652332112 1857 True 460.666667 568 82.014667 1142 2915 3 chr2A.!!$R1 1773
15 TraesCS6A01G257400 chr2B 272461722 272462306 584 True 811.000000 811 92.164000 1 569 1 chr2B.!!$R1 568
16 TraesCS6A01G257400 chr2B 596649892 596651745 1853 True 455.000000 551 81.876333 1142 2915 3 chr2B.!!$R2 1773
17 TraesCS6A01G257400 chr5A 43222055 43222622 567 True 804.000000 804 92.683000 1 554 1 chr5A.!!$R1 553
18 TraesCS6A01G257400 chr5B 599228058 599228633 575 False 573.000000 573 85.154000 4 569 1 chr5B.!!$F1 565
19 TraesCS6A01G257400 chr5B 613387579 613388154 575 False 573.000000 573 85.128000 4 569 1 chr5B.!!$F2 565
20 TraesCS6A01G257400 chr1D 261735188 261736074 886 False 366.000000 366 74.533000 2011 2912 1 chr1D.!!$F1 901
21 TraesCS6A01G257400 chr1B 350397523 350398409 886 True 355.000000 355 74.286000 2011 2912 1 chr1B.!!$R1 901
22 TraesCS6A01G257400 chr4D 500851252 500851781 529 True 326.000000 326 77.861000 1185 1714 1 chr4D.!!$R1 529
23 TraesCS6A01G257400 chr4B 644826475 644828293 1818 True 246.500000 311 74.996000 1154 2911 2 chr4B.!!$R1 1757

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
669 693 0.038343 GCATGGTGGCGAATGTGTTT 60.038 50.000 0.0 0.0 0.00 2.83 F
671 695 0.038343 ATGGTGGCGAATGTGTTTGC 60.038 50.000 0.0 0.0 42.88 3.68 F
759 783 0.108756 GACAAGTACGGGACAGAGCC 60.109 60.000 0.0 0.0 0.00 4.70 F
1058 1118 0.178973 TCCGTCTCTCAACCAGGTGA 60.179 55.000 0.0 0.0 0.00 4.02 F
2932 3144 1.070776 GTGTTTCCTCTCGTTTCACGC 60.071 52.381 0.0 0.0 42.21 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1582 2.038329 ACCCACCTGTAGGCGCTA 59.962 61.111 7.64 0.0 39.32 4.26 R
1812 1873 2.591715 GGTCAGTTGGCAGTGCGT 60.592 61.111 9.45 0.0 0.00 5.24 R
1917 1982 2.919494 GCTTGGTCCCTGCAAACCG 61.919 63.158 7.78 0.0 38.45 4.44 R
2956 3168 1.003116 GCACATCAGTTGATCCATCGC 60.003 52.381 0.00 0.0 31.21 4.58 R
3884 4122 1.006571 TTTGAGAGTCACGGGCGTC 60.007 57.895 0.00 0.0 0.00 5.19 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
133 134 4.778534 TCGAGAAGAGACGGTAAACAAT 57.221 40.909 0.00 0.00 0.00 2.71
526 550 2.738480 TCGGGACCGACAAACAGG 59.262 61.111 9.76 0.00 44.01 4.00
541 565 4.522789 ACAAACAGGCAATTCCGAATACTT 59.477 37.500 0.00 0.00 40.77 2.24
569 593 3.719268 ATGTCTACATCCAAACAGGCA 57.281 42.857 0.00 0.00 37.29 4.75
570 594 3.500448 TGTCTACATCCAAACAGGCAA 57.500 42.857 0.00 0.00 37.29 4.52
571 595 3.826524 TGTCTACATCCAAACAGGCAAA 58.173 40.909 0.00 0.00 37.29 3.68
572 596 3.820467 TGTCTACATCCAAACAGGCAAAG 59.180 43.478 0.00 0.00 37.29 2.77
573 597 4.072131 GTCTACATCCAAACAGGCAAAGA 58.928 43.478 0.00 0.00 37.29 2.52
574 598 4.518970 GTCTACATCCAAACAGGCAAAGAA 59.481 41.667 0.00 0.00 37.29 2.52
575 599 4.761739 TCTACATCCAAACAGGCAAAGAAG 59.238 41.667 0.00 0.00 37.29 2.85
576 600 3.565307 ACATCCAAACAGGCAAAGAAGA 58.435 40.909 0.00 0.00 37.29 2.87
577 601 4.154942 ACATCCAAACAGGCAAAGAAGAT 58.845 39.130 0.00 0.00 37.29 2.40
578 602 4.590222 ACATCCAAACAGGCAAAGAAGATT 59.410 37.500 0.00 0.00 37.29 2.40
579 603 5.070847 ACATCCAAACAGGCAAAGAAGATTT 59.929 36.000 0.00 0.00 37.29 2.17
580 604 4.947645 TCCAAACAGGCAAAGAAGATTTG 58.052 39.130 0.00 0.00 37.29 2.32
581 605 4.405358 TCCAAACAGGCAAAGAAGATTTGT 59.595 37.500 2.65 0.00 37.29 2.83
582 606 5.596361 TCCAAACAGGCAAAGAAGATTTGTA 59.404 36.000 2.65 0.00 37.29 2.41
583 607 6.097554 TCCAAACAGGCAAAGAAGATTTGTAA 59.902 34.615 2.65 0.00 37.29 2.41
584 608 6.760770 CCAAACAGGCAAAGAAGATTTGTAAA 59.239 34.615 2.65 0.00 0.00 2.01
585 609 7.042523 CCAAACAGGCAAAGAAGATTTGTAAAG 60.043 37.037 2.65 0.00 0.00 1.85
586 610 5.532557 ACAGGCAAAGAAGATTTGTAAAGC 58.467 37.500 2.65 0.00 0.00 3.51
587 611 5.068987 ACAGGCAAAGAAGATTTGTAAAGCA 59.931 36.000 2.65 0.00 0.00 3.91
588 612 5.403466 CAGGCAAAGAAGATTTGTAAAGCAC 59.597 40.000 2.65 0.00 0.00 4.40
589 613 5.068987 AGGCAAAGAAGATTTGTAAAGCACA 59.931 36.000 2.65 0.00 34.51 4.57
590 614 5.403466 GGCAAAGAAGATTTGTAAAGCACAG 59.597 40.000 2.65 0.00 38.72 3.66
591 615 6.208644 GCAAAGAAGATTTGTAAAGCACAGA 58.791 36.000 2.65 0.00 38.72 3.41
592 616 6.865205 GCAAAGAAGATTTGTAAAGCACAGAT 59.135 34.615 2.65 0.00 38.72 2.90
593 617 7.148853 GCAAAGAAGATTTGTAAAGCACAGATG 60.149 37.037 2.65 0.00 38.72 2.90
602 626 4.565360 GCACAGATGCCATGGCTA 57.435 55.556 35.53 22.71 46.97 3.93
603 627 2.328235 GCACAGATGCCATGGCTAG 58.672 57.895 35.53 23.55 46.97 3.42
604 628 0.465097 GCACAGATGCCATGGCTAGT 60.465 55.000 35.53 24.16 46.97 2.57
605 629 2.020694 GCACAGATGCCATGGCTAGTT 61.021 52.381 35.53 18.59 46.97 2.24
606 630 2.372264 CACAGATGCCATGGCTAGTTT 58.628 47.619 35.53 15.75 42.51 2.66
607 631 2.357009 CACAGATGCCATGGCTAGTTTC 59.643 50.000 35.53 22.55 42.51 2.78
608 632 2.240667 ACAGATGCCATGGCTAGTTTCT 59.759 45.455 35.53 24.13 42.51 2.52
609 633 2.617308 CAGATGCCATGGCTAGTTTCTG 59.383 50.000 35.53 29.15 42.51 3.02
610 634 2.507058 AGATGCCATGGCTAGTTTCTGA 59.493 45.455 35.53 14.13 42.51 3.27
611 635 3.137913 AGATGCCATGGCTAGTTTCTGAT 59.862 43.478 35.53 18.38 42.51 2.90
612 636 2.646930 TGCCATGGCTAGTTTCTGATG 58.353 47.619 35.53 0.00 42.51 3.07
613 637 1.952296 GCCATGGCTAGTTTCTGATGG 59.048 52.381 29.98 0.00 38.26 3.51
614 638 2.579873 CCATGGCTAGTTTCTGATGGG 58.420 52.381 0.00 0.00 0.00 4.00
615 639 2.579873 CATGGCTAGTTTCTGATGGGG 58.420 52.381 0.00 0.00 0.00 4.96
616 640 0.918983 TGGCTAGTTTCTGATGGGGG 59.081 55.000 0.00 0.00 0.00 5.40
630 654 4.136978 GGGGGACAGAGAAGAGCA 57.863 61.111 0.00 0.00 0.00 4.26
631 655 2.614001 GGGGGACAGAGAAGAGCAT 58.386 57.895 0.00 0.00 0.00 3.79
632 656 1.794714 GGGGGACAGAGAAGAGCATA 58.205 55.000 0.00 0.00 0.00 3.14
633 657 1.691434 GGGGGACAGAGAAGAGCATAG 59.309 57.143 0.00 0.00 0.00 2.23
634 658 1.691434 GGGGACAGAGAAGAGCATAGG 59.309 57.143 0.00 0.00 0.00 2.57
635 659 2.672098 GGGACAGAGAAGAGCATAGGA 58.328 52.381 0.00 0.00 0.00 2.94
636 660 2.627699 GGGACAGAGAAGAGCATAGGAG 59.372 54.545 0.00 0.00 0.00 3.69
637 661 3.561143 GGACAGAGAAGAGCATAGGAGA 58.439 50.000 0.00 0.00 0.00 3.71
638 662 3.957497 GGACAGAGAAGAGCATAGGAGAA 59.043 47.826 0.00 0.00 0.00 2.87
639 663 4.588528 GGACAGAGAAGAGCATAGGAGAAT 59.411 45.833 0.00 0.00 0.00 2.40
640 664 5.509501 GGACAGAGAAGAGCATAGGAGAATG 60.510 48.000 0.00 0.00 0.00 2.67
651 675 1.760192 AGGAGAATGCATTGGTCTGC 58.240 50.000 18.59 13.32 42.62 4.26
656 680 4.848000 TGCATTGGTCTGCATGGT 57.152 50.000 0.00 0.00 46.76 3.55
657 681 2.268999 TGCATTGGTCTGCATGGTG 58.731 52.632 0.00 0.00 46.76 4.17
658 682 1.252215 TGCATTGGTCTGCATGGTGG 61.252 55.000 0.00 0.00 46.76 4.61
659 683 1.514087 CATTGGTCTGCATGGTGGC 59.486 57.895 0.00 0.00 0.00 5.01
660 684 2.048023 ATTGGTCTGCATGGTGGCG 61.048 57.895 0.00 0.00 36.28 5.69
661 685 2.482796 ATTGGTCTGCATGGTGGCGA 62.483 55.000 0.00 0.00 36.28 5.54
662 686 2.359850 GGTCTGCATGGTGGCGAA 60.360 61.111 0.00 0.00 36.28 4.70
663 687 1.750399 GGTCTGCATGGTGGCGAAT 60.750 57.895 0.00 0.00 36.28 3.34
664 688 1.430632 GTCTGCATGGTGGCGAATG 59.569 57.895 0.00 0.00 36.28 2.67
665 689 1.002257 TCTGCATGGTGGCGAATGT 60.002 52.632 0.00 0.00 36.28 2.71
666 690 1.138036 CTGCATGGTGGCGAATGTG 59.862 57.895 0.00 0.00 36.28 3.21
667 691 1.588824 CTGCATGGTGGCGAATGTGT 61.589 55.000 0.00 0.00 36.28 3.72
668 692 1.177895 TGCATGGTGGCGAATGTGTT 61.178 50.000 0.00 0.00 36.28 3.32
669 693 0.038343 GCATGGTGGCGAATGTGTTT 60.038 50.000 0.00 0.00 0.00 2.83
670 694 1.700523 CATGGTGGCGAATGTGTTTG 58.299 50.000 0.00 0.00 0.00 2.93
671 695 0.038343 ATGGTGGCGAATGTGTTTGC 60.038 50.000 0.00 0.00 42.88 3.68
676 700 3.280920 GCGAATGTGTTTGCCCAAA 57.719 47.368 0.00 0.00 38.56 3.28
677 701 1.794512 GCGAATGTGTTTGCCCAAAT 58.205 45.000 0.00 0.00 38.56 2.32
678 702 1.460359 GCGAATGTGTTTGCCCAAATG 59.540 47.619 0.00 0.00 38.56 2.32
679 703 1.460359 CGAATGTGTTTGCCCAAATGC 59.540 47.619 0.00 0.00 32.36 3.56
680 704 2.492012 GAATGTGTTTGCCCAAATGCA 58.508 42.857 0.00 0.00 40.07 3.96
687 711 1.753470 TGCCCAAATGCAAAGGTGG 59.247 52.632 0.00 0.00 38.56 4.61
688 712 1.053264 TGCCCAAATGCAAAGGTGGT 61.053 50.000 0.00 0.00 38.56 4.16
689 713 0.603439 GCCCAAATGCAAAGGTGGTG 60.603 55.000 0.00 0.00 0.00 4.17
690 714 0.758123 CCCAAATGCAAAGGTGGTGT 59.242 50.000 0.00 0.00 0.00 4.16
691 715 1.540797 CCCAAATGCAAAGGTGGTGTG 60.541 52.381 0.00 0.00 0.00 3.82
692 716 1.540797 CCAAATGCAAAGGTGGTGTGG 60.541 52.381 0.00 0.00 0.00 4.17
693 717 0.758123 AAATGCAAAGGTGGTGTGGG 59.242 50.000 0.00 0.00 0.00 4.61
694 718 0.398381 AATGCAAAGGTGGTGTGGGT 60.398 50.000 0.00 0.00 0.00 4.51
695 719 0.398381 ATGCAAAGGTGGTGTGGGTT 60.398 50.000 0.00 0.00 0.00 4.11
696 720 0.616111 TGCAAAGGTGGTGTGGGTTT 60.616 50.000 0.00 0.00 0.00 3.27
759 783 0.108756 GACAAGTACGGGACAGAGCC 60.109 60.000 0.00 0.00 0.00 4.70
760 784 0.830444 ACAAGTACGGGACAGAGCCA 60.830 55.000 0.00 0.00 0.00 4.75
925 985 4.531854 TGCTGCTTGGCCAGTATATAAAA 58.468 39.130 5.11 0.00 35.28 1.52
946 1006 2.358615 CACCCGCTGCTGCAAGTA 60.359 61.111 16.29 0.00 39.64 2.24
983 1043 2.047844 GTTCTCAGCGCAGGCAGA 60.048 61.111 11.47 1.32 43.41 4.26
1018 1078 2.156504 GCTATGGCATTCTTCATCGTCG 59.843 50.000 4.78 0.00 38.54 5.12
1058 1118 0.178973 TCCGTCTCTCAACCAGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
1073 1133 3.369892 CCAGGTGATCAATCTTCTTCCGT 60.370 47.826 0.00 0.00 0.00 4.69
1075 1135 4.093998 CAGGTGATCAATCTTCTTCCGTTG 59.906 45.833 0.00 0.00 0.00 4.10
1108 1168 3.593795 CGCATTCTTGAGCATTTGCGTC 61.594 50.000 6.92 0.00 45.55 5.19
1132 1193 1.089920 GGTGTTGCTGATCTTGCGAT 58.910 50.000 0.00 0.00 0.00 4.58
1795 1856 6.934645 CAGGATCTTGTTCAGTTACAAAGGTA 59.065 38.462 0.00 0.00 37.55 3.08
2932 3144 1.070776 GTGTTTCCTCTCGTTTCACGC 60.071 52.381 0.00 0.00 42.21 5.34
2939 3151 3.924686 TCCTCTCGTTTCACGCTAATTTC 59.075 43.478 0.00 0.00 42.21 2.17
3166 3378 3.106827 TCTCCATACAGAGTGGAATGCA 58.893 45.455 0.00 0.00 44.69 3.96
3167 3379 3.713248 TCTCCATACAGAGTGGAATGCAT 59.287 43.478 0.00 0.00 44.69 3.96
3168 3380 3.812262 TCCATACAGAGTGGAATGCATG 58.188 45.455 0.00 0.00 42.56 4.06
3169 3381 2.292569 CCATACAGAGTGGAATGCATGC 59.707 50.000 11.82 11.82 39.12 4.06
3235 3447 4.082787 CCGCACCTTATTGTGAGATTTGTT 60.083 41.667 0.00 0.00 38.16 2.83
3247 3459 5.238432 TGTGAGATTTGTTGATGCGTTAACT 59.762 36.000 13.97 0.00 0.00 2.24
3275 3487 2.510613 TGTACTAAACCTGCTTTGGCC 58.489 47.619 0.00 0.00 37.74 5.36
3321 3536 0.411848 TAGGCCTTCCCCCTTTTTGG 59.588 55.000 12.58 0.00 33.88 3.28
3343 3558 9.871175 TTTGGGAAGAAAAAGGTATACTAAACT 57.129 29.630 2.25 0.00 0.00 2.66
3344 3559 9.871175 TTGGGAAGAAAAAGGTATACTAAACTT 57.129 29.630 2.25 2.32 0.00 2.66
3393 3608 4.618489 CGTTGCAAAGATCACTTCAATTCC 59.382 41.667 6.52 0.00 35.05 3.01
3423 3638 2.203972 GACAAGTGGCGCACATGCAT 62.204 55.000 10.83 0.00 36.67 3.96
3445 3661 1.831389 CGTCACTTGTCGCAACCTGG 61.831 60.000 0.00 0.00 0.00 4.45
3504 3725 6.715344 ACGTTTTATCTCTTAAATCGTGCA 57.285 33.333 11.31 0.00 46.54 4.57
3526 3747 4.829064 TCCAAATCTTGAACCACTTTCG 57.171 40.909 0.00 0.00 36.97 3.46
3544 3765 1.226128 GCTGTTGGATTCTTCGCGC 60.226 57.895 0.00 0.00 0.00 6.86
3708 3934 4.421479 CGTGCCTCTCGCGGAAGT 62.421 66.667 6.13 0.00 44.36 3.01
3723 3949 3.387397 CGGAAGTAAAACCGTGACTCTT 58.613 45.455 0.00 0.00 43.53 2.85
3778 4013 2.762535 TTCATTTCCGAGGAGACACC 57.237 50.000 0.00 0.00 39.35 4.16
3794 4029 4.778415 CCGCCGTGACTCTCGTGG 62.778 72.222 0.24 0.00 0.00 4.94
3797 4032 1.006571 GCCGTGACTCTCGTGGAAA 60.007 57.895 0.24 0.00 0.00 3.13
3888 4128 4.187056 CCTTTTCGAGAGGGACGC 57.813 61.111 0.00 0.00 0.00 5.19
3901 4141 2.649034 GACGCCCGTGACTCTCAA 59.351 61.111 0.00 0.00 0.00 3.02
3902 4142 1.006571 GACGCCCGTGACTCTCAAA 60.007 57.895 0.00 0.00 0.00 2.69
3913 4153 4.024556 CGTGACTCTCAAAGAAAGCACAAT 60.025 41.667 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.378767 CCATGTGTGGCAATGGCA 58.621 55.556 5.05 5.05 43.71 4.92
133 134 2.125552 CTCCGCTGAATGTCGCCA 60.126 61.111 0.00 0.00 0.00 5.69
304 324 4.424711 GGTCAATCCGCCCTGCCA 62.425 66.667 0.00 0.00 0.00 4.92
522 546 2.423538 GCAAGTATTCGGAATTGCCTGT 59.576 45.455 8.76 0.00 41.65 4.00
523 547 3.070429 GCAAGTATTCGGAATTGCCTG 57.930 47.619 8.76 4.31 41.65 4.85
526 550 2.286418 CGGAGCAAGTATTCGGAATTGC 60.286 50.000 16.04 16.04 46.50 3.56
541 565 2.107366 TGGATGTAGACATTCGGAGCA 58.893 47.619 0.00 0.00 36.57 4.26
586 610 2.048444 AACTAGCCATGGCATCTGTG 57.952 50.000 37.18 20.90 44.88 3.66
587 611 2.240667 AGAAACTAGCCATGGCATCTGT 59.759 45.455 37.18 24.80 44.88 3.41
588 612 2.617308 CAGAAACTAGCCATGGCATCTG 59.383 50.000 37.18 30.88 44.88 2.90
589 613 2.507058 TCAGAAACTAGCCATGGCATCT 59.493 45.455 37.18 25.92 44.88 2.90
590 614 2.923121 TCAGAAACTAGCCATGGCATC 58.077 47.619 37.18 24.33 44.88 3.91
591 615 3.220110 CATCAGAAACTAGCCATGGCAT 58.780 45.455 37.18 23.86 44.88 4.40
592 616 2.646930 CATCAGAAACTAGCCATGGCA 58.353 47.619 37.18 21.91 44.88 4.92
593 617 1.952296 CCATCAGAAACTAGCCATGGC 59.048 52.381 30.12 30.12 42.33 4.40
594 618 2.579873 CCCATCAGAAACTAGCCATGG 58.420 52.381 7.63 7.63 0.00 3.66
595 619 2.579873 CCCCATCAGAAACTAGCCATG 58.420 52.381 0.00 0.00 0.00 3.66
596 620 1.496429 CCCCCATCAGAAACTAGCCAT 59.504 52.381 0.00 0.00 0.00 4.40
597 621 0.918983 CCCCCATCAGAAACTAGCCA 59.081 55.000 0.00 0.00 0.00 4.75
598 622 3.808984 CCCCCATCAGAAACTAGCC 57.191 57.895 0.00 0.00 0.00 3.93
613 637 1.691434 CTATGCTCTTCTCTGTCCCCC 59.309 57.143 0.00 0.00 0.00 5.40
614 638 1.691434 CCTATGCTCTTCTCTGTCCCC 59.309 57.143 0.00 0.00 0.00 4.81
615 639 2.627699 CTCCTATGCTCTTCTCTGTCCC 59.372 54.545 0.00 0.00 0.00 4.46
616 640 3.561143 TCTCCTATGCTCTTCTCTGTCC 58.439 50.000 0.00 0.00 0.00 4.02
617 641 5.531634 CATTCTCCTATGCTCTTCTCTGTC 58.468 45.833 0.00 0.00 0.00 3.51
618 642 4.202243 GCATTCTCCTATGCTCTTCTCTGT 60.202 45.833 0.00 0.00 45.80 3.41
619 643 4.309099 GCATTCTCCTATGCTCTTCTCTG 58.691 47.826 0.00 0.00 45.80 3.35
620 644 4.605640 GCATTCTCCTATGCTCTTCTCT 57.394 45.455 0.00 0.00 45.80 3.10
629 653 3.252701 GCAGACCAATGCATTCTCCTATG 59.747 47.826 9.53 5.36 45.77 2.23
630 654 3.484407 GCAGACCAATGCATTCTCCTAT 58.516 45.455 9.53 0.00 45.77 2.57
631 655 2.923121 GCAGACCAATGCATTCTCCTA 58.077 47.619 9.53 0.00 45.77 2.94
632 656 1.760192 GCAGACCAATGCATTCTCCT 58.240 50.000 9.53 3.62 45.77 3.69
640 664 1.514087 CCACCATGCAGACCAATGC 59.486 57.895 0.00 0.00 46.68 3.56
641 665 1.514087 GCCACCATGCAGACCAATG 59.486 57.895 0.00 0.00 0.00 2.82
642 666 2.048023 CGCCACCATGCAGACCAAT 61.048 57.895 0.00 0.00 0.00 3.16
643 667 2.672651 CGCCACCATGCAGACCAA 60.673 61.111 0.00 0.00 0.00 3.67
644 668 2.482796 ATTCGCCACCATGCAGACCA 62.483 55.000 0.00 0.00 0.00 4.02
645 669 1.750399 ATTCGCCACCATGCAGACC 60.750 57.895 0.00 0.00 0.00 3.85
646 670 1.308069 ACATTCGCCACCATGCAGAC 61.308 55.000 0.00 0.00 0.00 3.51
647 671 1.002257 ACATTCGCCACCATGCAGA 60.002 52.632 0.00 0.00 0.00 4.26
648 672 1.138036 CACATTCGCCACCATGCAG 59.862 57.895 0.00 0.00 0.00 4.41
649 673 1.177895 AACACATTCGCCACCATGCA 61.178 50.000 0.00 0.00 0.00 3.96
650 674 0.038343 AAACACATTCGCCACCATGC 60.038 50.000 0.00 0.00 0.00 4.06
651 675 1.700523 CAAACACATTCGCCACCATG 58.299 50.000 0.00 0.00 0.00 3.66
652 676 0.038343 GCAAACACATTCGCCACCAT 60.038 50.000 0.00 0.00 0.00 3.55
653 677 1.361993 GCAAACACATTCGCCACCA 59.638 52.632 0.00 0.00 0.00 4.17
654 678 1.372872 GGCAAACACATTCGCCACC 60.373 57.895 0.00 0.00 44.25 4.61
655 679 1.372872 GGGCAAACACATTCGCCAC 60.373 57.895 0.00 0.00 46.75 5.01
656 680 1.395045 TTGGGCAAACACATTCGCCA 61.395 50.000 0.00 0.00 46.75 5.69
657 681 0.249657 TTTGGGCAAACACATTCGCC 60.250 50.000 0.00 0.00 44.10 5.54
658 682 1.460359 CATTTGGGCAAACACATTCGC 59.540 47.619 0.00 0.00 32.51 4.70
659 683 1.460359 GCATTTGGGCAAACACATTCG 59.540 47.619 0.00 0.00 32.51 3.34
660 684 2.492012 TGCATTTGGGCAAACACATTC 58.508 42.857 0.00 0.00 41.65 2.67
661 685 2.634815 TGCATTTGGGCAAACACATT 57.365 40.000 0.00 0.00 41.65 2.71
669 693 1.053264 ACCACCTTTGCATTTGGGCA 61.053 50.000 7.94 0.00 43.19 5.36
670 694 0.603439 CACCACCTTTGCATTTGGGC 60.603 55.000 7.94 0.00 33.00 5.36
671 695 0.758123 ACACCACCTTTGCATTTGGG 59.242 50.000 7.94 1.88 33.00 4.12
672 696 1.540797 CCACACCACCTTTGCATTTGG 60.541 52.381 0.00 0.00 35.06 3.28
673 697 1.540797 CCCACACCACCTTTGCATTTG 60.541 52.381 0.00 0.00 0.00 2.32
674 698 0.758123 CCCACACCACCTTTGCATTT 59.242 50.000 0.00 0.00 0.00 2.32
675 699 0.398381 ACCCACACCACCTTTGCATT 60.398 50.000 0.00 0.00 0.00 3.56
676 700 0.398381 AACCCACACCACCTTTGCAT 60.398 50.000 0.00 0.00 0.00 3.96
677 701 0.616111 AAACCCACACCACCTTTGCA 60.616 50.000 0.00 0.00 0.00 4.08
678 702 0.539518 AAAACCCACACCACCTTTGC 59.460 50.000 0.00 0.00 0.00 3.68
679 703 1.202359 CGAAAACCCACACCACCTTTG 60.202 52.381 0.00 0.00 0.00 2.77
680 704 1.107945 CGAAAACCCACACCACCTTT 58.892 50.000 0.00 0.00 0.00 3.11
681 705 0.256464 TCGAAAACCCACACCACCTT 59.744 50.000 0.00 0.00 0.00 3.50
682 706 0.464916 GTCGAAAACCCACACCACCT 60.465 55.000 0.00 0.00 0.00 4.00
683 707 1.778027 CGTCGAAAACCCACACCACC 61.778 60.000 0.00 0.00 0.00 4.61
684 708 0.810823 TCGTCGAAAACCCACACCAC 60.811 55.000 0.00 0.00 0.00 4.16
685 709 0.810823 GTCGTCGAAAACCCACACCA 60.811 55.000 0.00 0.00 0.00 4.17
686 710 1.501337 GGTCGTCGAAAACCCACACC 61.501 60.000 0.00 0.00 0.00 4.16
687 711 1.936658 GGTCGTCGAAAACCCACAC 59.063 57.895 0.00 0.00 0.00 3.82
688 712 4.442018 GGTCGTCGAAAACCCACA 57.558 55.556 0.00 0.00 0.00 4.17
692 716 1.670083 CAGGGGGTCGTCGAAAACC 60.670 63.158 8.62 8.62 34.64 3.27
693 717 1.670083 CCAGGGGGTCGTCGAAAAC 60.670 63.158 0.00 0.00 0.00 2.43
694 718 2.745037 CCAGGGGGTCGTCGAAAA 59.255 61.111 0.00 0.00 0.00 2.29
695 719 4.011517 GCCAGGGGGTCGTCGAAA 62.012 66.667 0.00 0.00 36.17 3.46
759 783 1.330521 CGGGTTCGGCAATGATAACTG 59.669 52.381 0.00 0.00 0.00 3.16
760 784 1.065709 ACGGGTTCGGCAATGATAACT 60.066 47.619 0.00 0.00 41.39 2.24
946 1006 2.105477 ACTTCTGTGTCTGATGTGGCTT 59.895 45.455 0.00 0.00 0.00 4.35
983 1043 1.003580 CCATAGCCTGTGACCTTGTGT 59.996 52.381 0.00 0.00 0.00 3.72
996 1056 2.481952 GACGATGAAGAATGCCATAGCC 59.518 50.000 0.00 0.00 38.69 3.93
999 1059 2.135139 GCGACGATGAAGAATGCCATA 58.865 47.619 0.00 0.00 0.00 2.74
1018 1078 0.034670 AGGAGTCCAAGCAAGATGGC 60.035 55.000 12.86 0.00 37.88 4.40
1058 1118 2.290896 TGGGCAACGGAAGAAGATTGAT 60.291 45.455 0.00 0.00 37.60 2.57
1073 1133 1.202114 GAATGCGACTGAAATGGGCAA 59.798 47.619 0.00 0.00 37.15 4.52
1075 1135 1.098050 AGAATGCGACTGAAATGGGC 58.902 50.000 0.00 0.00 0.00 5.36
1108 1168 1.568612 AAGATCAGCAACACCGCACG 61.569 55.000 0.00 0.00 0.00 5.34
1521 1582 2.038329 ACCCACCTGTAGGCGCTA 59.962 61.111 7.64 0.00 39.32 4.26
1795 1856 6.565999 GCAGTGCGTTCTTTAAACAAGACTAT 60.566 38.462 0.00 0.00 0.00 2.12
1812 1873 2.591715 GGTCAGTTGGCAGTGCGT 60.592 61.111 9.45 0.00 0.00 5.24
1813 1874 3.716006 CGGTCAGTTGGCAGTGCG 61.716 66.667 9.45 0.00 0.00 5.34
1917 1982 2.919494 GCTTGGTCCCTGCAAACCG 61.919 63.158 7.78 0.00 38.45 4.44
2932 3144 3.667960 GCACGAACACTGCCAGAAATTAG 60.668 47.826 0.00 0.00 0.00 1.73
2956 3168 1.003116 GCACATCAGTTGATCCATCGC 60.003 52.381 0.00 0.00 31.21 4.58
3198 3410 2.339556 TGCGGCATTGGCTTACACC 61.340 57.895 8.71 0.00 40.87 4.16
3235 3447 7.489160 AGTACATAGATTCAGTTAACGCATCA 58.511 34.615 13.76 4.56 0.00 3.07
3247 3459 7.552687 CCAAAGCAGGTTTAGTACATAGATTCA 59.447 37.037 0.00 0.00 0.00 2.57
3343 3558 9.362539 GGTACTTCTCAATTAGTGATTTCGTAA 57.637 33.333 0.00 0.00 35.07 3.18
3344 3559 7.977853 GGGTACTTCTCAATTAGTGATTTCGTA 59.022 37.037 0.00 0.00 35.07 3.43
3345 3560 6.817140 GGGTACTTCTCAATTAGTGATTTCGT 59.183 38.462 0.00 0.00 35.07 3.85
3393 3608 1.597742 CCACTTGTCACAACCAGAGG 58.402 55.000 0.00 0.00 0.00 3.69
3504 3725 4.321230 GCGAAAGTGGTTCAAGATTTGGAT 60.321 41.667 0.00 0.00 35.83 3.41
3526 3747 1.226128 GCGCGAAGAATCCAACAGC 60.226 57.895 12.10 0.00 0.00 4.40
3544 3765 8.828644 CATGGAATCTAGTTTTGAAGATCTCAG 58.171 37.037 0.00 0.00 34.81 3.35
3610 3834 0.160182 CGGTTCGGTTCTTTCGTTCG 59.840 55.000 0.00 0.00 0.00 3.95
3619 3843 2.741211 GTGCTCCCGGTTCGGTTC 60.741 66.667 0.00 0.00 46.80 3.62
3708 3934 1.068895 TCCGCAAGAGTCACGGTTTTA 59.931 47.619 15.98 0.00 46.92 1.52
3774 4009 4.039357 CGAGAGTCACGGCGGTGT 62.039 66.667 22.05 5.79 44.68 4.16
3794 4029 3.423907 CGCAATAGGTACGGTTGTGTTTC 60.424 47.826 8.17 0.00 34.91 2.78
3797 4032 1.673626 CCGCAATAGGTACGGTTGTGT 60.674 52.381 12.80 0.00 42.01 3.72
3884 4122 1.006571 TTTGAGAGTCACGGGCGTC 60.007 57.895 0.00 0.00 0.00 5.19
3888 4128 1.801178 GCTTTCTTTGAGAGTCACGGG 59.199 52.381 0.00 0.00 0.00 5.28
3901 4141 3.428532 AGAGGCATGATTGTGCTTTCTT 58.571 40.909 0.00 0.00 44.45 2.52
3902 4142 3.015327 GAGAGGCATGATTGTGCTTTCT 58.985 45.455 0.00 3.13 44.45 2.52
3913 4153 2.496341 CTTCCGCGAGAGGCATGA 59.504 61.111 8.23 0.00 43.84 3.07
3976 4230 3.056328 GCCGTGCCTCTTGGGAAC 61.056 66.667 0.00 0.00 40.34 3.62
4001 4255 3.342627 CGGGTGTGCTTTCGCGAA 61.343 61.111 19.38 19.38 41.28 4.70


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

AutoCloner maintained by Alex Coulton.