Multiple sequence alignment - TraesCS1A01G184900

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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 TraesCS1A01G184900 chr1A 100.000 2999 0 0 1 2999 335547567 335544569 0.000000e+00 5539
1 TraesCS1A01G184900 chr1D 93.959 2003 74 18 752 2718 267590315 267592306 0.000000e+00 2985
2 TraesCS1A01G184900 chr1D 83.978 724 84 18 1 695 267589598 267590318 0.000000e+00 665
3 TraesCS1A01G184900 chr1D 83.030 165 14 10 2848 2999 267592891 267593054 1.450000e-28 137
4 TraesCS1A01G184900 chr1B 96.125 1574 56 4 932 2505 345418056 345416488 0.000000e+00 2564
5 TraesCS1A01G184900 chr1B 87.571 354 33 8 2493 2838 345411876 345411526 1.670000e-107 399
6 TraesCS1A01G184900 chr1B 93.333 75 5 0 2853 2927 345411474 345411400 8.790000e-21 111
7 TraesCS1A01G184900 chr3D 85.290 673 80 8 1 669 433434186 433433529 0.000000e+00 676
8 TraesCS1A01G184900 chr3D 87.097 589 55 17 1 569 602282130 602282717 0.000000e+00 647
9 TraesCS1A01G184900 chr2B 84.921 630 75 12 58 669 17832120 17831493 1.180000e-173 619
10 TraesCS1A01G184900 chr2B 87.500 424 38 4 1 409 423338958 423338535 2.710000e-130 475
11 TraesCS1A01G184900 chr2B 81.990 583 78 12 1 562 542556553 542555977 1.260000e-128 470
12 TraesCS1A01G184900 chr5B 83.038 678 102 10 1 667 548468372 548469047 1.190000e-168 603
13 TraesCS1A01G184900 chr5B 78.665 689 115 20 1 670 348443935 348444610 2.140000e-116 429
14 TraesCS1A01G184900 chr6B 82.794 680 97 11 2 669 579989727 579989056 9.260000e-165 590
15 TraesCS1A01G184900 chr4A 83.175 630 76 11 1 600 121158750 121159379 1.570000e-152 549
16 TraesCS1A01G184900 chr5D 84.055 577 77 4 1 563 437759920 437760495 2.630000e-150 542
17 TraesCS1A01G184900 chr5A 82.955 616 77 11 1 600 44367826 44368429 5.690000e-147 531
18 TraesCS1A01G184900 chr5A 79.483 619 109 14 65 670 394176615 394177228 9.940000e-115 424
19 TraesCS1A01G184900 chr2D 81.630 675 85 14 10 669 183037182 183036532 9.530000e-145 523
20 TraesCS1A01G184900 chr3B 81.260 635 77 17 1 598 244657846 244658475 2.710000e-130 475
21 TraesCS1A01G184900 chr7A 77.964 717 108 24 1 669 486870010 486870724 1.290000e-108 403
22 TraesCS1A01G184900 chrUn 83.077 325 54 1 348 672 331068953 331068630 8.130000e-76 294
23 TraesCS1A01G184900 chr2A 81.139 281 39 3 1 267 535122657 535122377 2.340000e-51 213


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 TraesCS1A01G184900 chr1A 335544569 335547567 2998 True 5539.000000 5539 100.000 1 2999 1 chr1A.!!$R1 2998
1 TraesCS1A01G184900 chr1D 267589598 267593054 3456 False 1262.333333 2985 86.989 1 2999 3 chr1D.!!$F1 2998
2 TraesCS1A01G184900 chr1B 345416488 345418056 1568 True 2564.000000 2564 96.125 932 2505 1 chr1B.!!$R1 1573
3 TraesCS1A01G184900 chr3D 433433529 433434186 657 True 676.000000 676 85.290 1 669 1 chr3D.!!$R1 668
4 TraesCS1A01G184900 chr3D 602282130 602282717 587 False 647.000000 647 87.097 1 569 1 chr3D.!!$F1 568
5 TraesCS1A01G184900 chr2B 17831493 17832120 627 True 619.000000 619 84.921 58 669 1 chr2B.!!$R1 611
6 TraesCS1A01G184900 chr2B 542555977 542556553 576 True 470.000000 470 81.990 1 562 1 chr2B.!!$R3 561
7 TraesCS1A01G184900 chr5B 548468372 548469047 675 False 603.000000 603 83.038 1 667 1 chr5B.!!$F2 666
8 TraesCS1A01G184900 chr5B 348443935 348444610 675 False 429.000000 429 78.665 1 670 1 chr5B.!!$F1 669
9 TraesCS1A01G184900 chr6B 579989056 579989727 671 True 590.000000 590 82.794 2 669 1 chr6B.!!$R1 667
10 TraesCS1A01G184900 chr4A 121158750 121159379 629 False 549.000000 549 83.175 1 600 1 chr4A.!!$F1 599
11 TraesCS1A01G184900 chr5D 437759920 437760495 575 False 542.000000 542 84.055 1 563 1 chr5D.!!$F1 562
12 TraesCS1A01G184900 chr5A 44367826 44368429 603 False 531.000000 531 82.955 1 600 1 chr5A.!!$F1 599
13 TraesCS1A01G184900 chr5A 394176615 394177228 613 False 424.000000 424 79.483 65 670 1 chr5A.!!$F2 605
14 TraesCS1A01G184900 chr2D 183036532 183037182 650 True 523.000000 523 81.630 10 669 1 chr2D.!!$R1 659
15 TraesCS1A01G184900 chr3B 244657846 244658475 629 False 475.000000 475 81.260 1 598 1 chr3B.!!$F1 597
16 TraesCS1A01G184900 chr7A 486870010 486870724 714 False 403.000000 403 77.964 1 669 1 chr7A.!!$F1 668

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
887 997 0.321122 GCAGGGGCGGAGAGAATATG 60.321 60.0 0.0 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2700 2845 0.666577 GAGCTGTTACGCTCGGTGTT 60.667 55.0 11.77 0.0 45.91 3.32 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
50 51 3.704566 TGAGAATATACTCCACTTGCCGT 59.295 43.478 0.00 0.00 36.22 5.68
142 167 2.037121 TCATTTGGTCAAGCTCTGTCGA 59.963 45.455 0.00 0.00 0.00 4.20
325 363 2.997897 AGGACGGGAGCGCTCTTT 60.998 61.111 34.46 19.92 0.00 2.52
427 517 3.094572 CAAATGGATCCTGCTGGTCTTT 58.905 45.455 14.23 3.37 34.23 2.52
433 524 0.474854 TCCTGCTGGTCTTTGGGGTA 60.475 55.000 9.73 0.00 34.23 3.69
434 525 0.404040 CCTGCTGGTCTTTGGGGTAA 59.596 55.000 0.51 0.00 0.00 2.85
507 613 1.806461 GCTCGGGCGTCCTCATATCA 61.806 60.000 3.66 0.00 0.00 2.15
517 623 4.507710 CGTCCTCATATCAACCCCATATG 58.492 47.826 0.00 0.00 36.08 1.78
522 628 5.726308 CCTCATATCAACCCCATATGTAGGA 59.274 44.000 14.35 0.01 35.77 2.94
540 646 1.388654 ATGGGTATGGGGGATGCCA 60.389 57.895 5.30 0.00 38.57 4.92
610 717 0.681733 ATCGTGACCAAGCAGTGACT 59.318 50.000 0.00 0.00 0.00 3.41
649 756 4.098654 ACATATGAGACGAGTTTGAGAGGG 59.901 45.833 10.38 0.00 0.00 4.30
681 791 6.701145 AGATGCTCTTATACAACTCGAAGA 57.299 37.500 0.00 0.00 0.00 2.87
696 806 9.796120 ACAACTCGAAGAAATATCTAGAAAGAG 57.204 33.333 0.00 0.00 33.77 2.85
699 809 8.349983 ACTCGAAGAAATATCTAGAAAGAGAGC 58.650 37.037 0.00 0.00 33.77 4.09
700 810 7.653647 TCGAAGAAATATCTAGAAAGAGAGCC 58.346 38.462 0.00 0.00 33.77 4.70
701 811 7.504238 TCGAAGAAATATCTAGAAAGAGAGCCT 59.496 37.037 0.00 0.00 33.77 4.58
702 812 7.807907 CGAAGAAATATCTAGAAAGAGAGCCTC 59.192 40.741 0.00 0.00 33.77 4.70
703 813 7.539034 AGAAATATCTAGAAAGAGAGCCTCC 57.461 40.000 0.00 0.00 34.49 4.30
704 814 7.305246 AGAAATATCTAGAAAGAGAGCCTCCT 58.695 38.462 0.00 0.00 34.49 3.69
705 815 8.452868 AGAAATATCTAGAAAGAGAGCCTCCTA 58.547 37.037 0.00 0.00 34.49 2.94
706 816 8.417273 AAATATCTAGAAAGAGAGCCTCCTAC 57.583 38.462 0.00 0.00 34.49 3.18
707 817 4.173290 TCTAGAAAGAGAGCCTCCTACC 57.827 50.000 0.00 0.00 0.00 3.18
708 818 1.770294 AGAAAGAGAGCCTCCTACCG 58.230 55.000 0.00 0.00 0.00 4.02
709 819 1.006162 AGAAAGAGAGCCTCCTACCGT 59.994 52.381 0.00 0.00 0.00 4.83
710 820 1.406180 GAAAGAGAGCCTCCTACCGTC 59.594 57.143 0.00 0.00 0.00 4.79
711 821 0.331954 AAGAGAGCCTCCTACCGTCA 59.668 55.000 0.00 0.00 0.00 4.35
712 822 0.553819 AGAGAGCCTCCTACCGTCAT 59.446 55.000 0.00 0.00 0.00 3.06
713 823 1.063567 AGAGAGCCTCCTACCGTCATT 60.064 52.381 0.00 0.00 0.00 2.57
714 824 1.757699 GAGAGCCTCCTACCGTCATTT 59.242 52.381 0.00 0.00 0.00 2.32
715 825 1.482593 AGAGCCTCCTACCGTCATTTG 59.517 52.381 0.00 0.00 0.00 2.32
716 826 1.480954 GAGCCTCCTACCGTCATTTGA 59.519 52.381 0.00 0.00 0.00 2.69
717 827 1.906574 AGCCTCCTACCGTCATTTGAA 59.093 47.619 0.00 0.00 0.00 2.69
718 828 2.093447 AGCCTCCTACCGTCATTTGAAG 60.093 50.000 0.00 0.00 0.00 3.02
719 829 2.093658 GCCTCCTACCGTCATTTGAAGA 60.094 50.000 0.00 0.00 0.00 2.87
720 830 3.432326 GCCTCCTACCGTCATTTGAAGAT 60.432 47.826 0.00 0.00 0.00 2.40
721 831 4.122776 CCTCCTACCGTCATTTGAAGATG 58.877 47.826 0.00 0.00 0.00 2.90
722 832 3.531538 TCCTACCGTCATTTGAAGATGC 58.468 45.455 0.00 0.00 0.00 3.91
723 833 3.055458 TCCTACCGTCATTTGAAGATGCA 60.055 43.478 0.00 0.00 0.00 3.96
724 834 3.879295 CCTACCGTCATTTGAAGATGCAT 59.121 43.478 0.00 0.00 0.00 3.96
725 835 4.336433 CCTACCGTCATTTGAAGATGCATT 59.664 41.667 0.00 0.00 0.00 3.56
726 836 5.527214 CCTACCGTCATTTGAAGATGCATTA 59.473 40.000 0.00 0.00 0.00 1.90
727 837 6.205464 CCTACCGTCATTTGAAGATGCATTAT 59.795 38.462 0.00 0.00 0.00 1.28
728 838 6.064846 ACCGTCATTTGAAGATGCATTATC 57.935 37.500 0.00 3.02 35.97 1.75
730 840 6.140786 CCGTCATTTGAAGATGCATTATCTG 58.859 40.000 0.00 0.00 45.41 2.90
758 868 4.222145 AGCACATTTTCAGATCAAATGCCT 59.778 37.500 13.95 9.45 42.91 4.75
772 882 8.815912 AGATCAAATGCCTTAAACCATAGTTTT 58.184 29.630 0.00 0.00 43.82 2.43
863 973 2.146342 CTCTAACAAGTGTGTGGCTGG 58.854 52.381 0.00 0.00 38.27 4.85
885 995 3.550974 GCAGGGGCGGAGAGAATA 58.449 61.111 0.00 0.00 0.00 1.75
886 996 2.062070 GCAGGGGCGGAGAGAATAT 58.938 57.895 0.00 0.00 0.00 1.28
887 997 0.321122 GCAGGGGCGGAGAGAATATG 60.321 60.000 0.00 0.00 0.00 1.78
888 998 1.342074 CAGGGGCGGAGAGAATATGA 58.658 55.000 0.00 0.00 0.00 2.15
889 999 1.694150 CAGGGGCGGAGAGAATATGAA 59.306 52.381 0.00 0.00 0.00 2.57
890 1000 2.104792 CAGGGGCGGAGAGAATATGAAA 59.895 50.000 0.00 0.00 0.00 2.69
891 1001 2.982488 AGGGGCGGAGAGAATATGAAAT 59.018 45.455 0.00 0.00 0.00 2.17
892 1002 4.020218 CAGGGGCGGAGAGAATATGAAATA 60.020 45.833 0.00 0.00 0.00 1.40
1296 1406 2.943978 CGCCACCGTCTCCCTCTTT 61.944 63.158 0.00 0.00 0.00 2.52
1984 2094 2.732597 GCCTACGAGAACTACACTGCAG 60.733 54.545 13.48 13.48 0.00 4.41
2056 2174 1.451067 CTCTTCTTCTTGCAGGCAGG 58.549 55.000 0.00 0.00 0.00 4.85
2078 2196 1.239968 GCACAGGCTGTTCCTTCCAG 61.240 60.000 19.43 5.12 44.75 3.86
2091 2209 2.954989 TCCTTCCAGAGAGTCATCATCG 59.045 50.000 0.00 0.00 0.00 3.84
2109 2227 8.994170 TCATCATCGGCGAAATACAAATAAATA 58.006 29.630 15.93 0.00 0.00 1.40
2164 2282 2.042686 TCAGCTGTGGCATATTCACC 57.957 50.000 14.67 0.00 41.70 4.02
2191 2309 5.047847 TGTTAGGCCGATTCGAATAAGAAG 58.952 41.667 11.38 0.00 33.19 2.85
2208 2326 3.947868 AGAAGGTGTTGTCATCTCATGG 58.052 45.455 0.00 0.00 33.38 3.66
2329 2447 2.805277 GCATTGTTGCTGAGTGTGC 58.195 52.632 0.00 0.00 45.77 4.57
2404 2522 0.972471 TCTGAATGCTCTCTCGGGCA 60.972 55.000 0.00 0.00 42.80 5.36
2517 2636 5.815581 TGGTTGTAGTTGAGCCATCTTTAT 58.184 37.500 0.00 0.00 0.00 1.40
2525 2644 7.765695 AGTTGAGCCATCTTTATCTTCAAAA 57.234 32.000 0.00 0.00 0.00 2.44
2526 2645 7.824672 AGTTGAGCCATCTTTATCTTCAAAAG 58.175 34.615 0.00 0.00 35.66 2.27
2527 2646 6.199937 TGAGCCATCTTTATCTTCAAAAGC 57.800 37.500 0.00 0.00 34.58 3.51
2529 2648 6.209192 TGAGCCATCTTTATCTTCAAAAGCAA 59.791 34.615 0.00 0.00 34.58 3.91
2530 2649 6.393171 AGCCATCTTTATCTTCAAAAGCAAC 58.607 36.000 0.00 0.00 34.58 4.17
2545 2664 1.632409 AGCAACTGATCCCACATCACT 59.368 47.619 0.00 0.00 0.00 3.41
2550 2669 4.104383 ACTGATCCCACATCACTTGTTT 57.896 40.909 0.00 0.00 36.00 2.83
2583 2702 7.459394 TCAATATTATTAGCTTATACCGCGC 57.541 36.000 0.00 0.00 0.00 6.86
2584 2703 7.036829 TCAATATTATTAGCTTATACCGCGCA 58.963 34.615 8.75 0.00 0.00 6.09
2585 2704 7.546316 TCAATATTATTAGCTTATACCGCGCAA 59.454 33.333 8.75 0.00 0.00 4.85
2589 2708 1.663695 AGCTTATACCGCGCAATTGT 58.336 45.000 8.75 0.62 0.00 2.71
2590 2709 2.828877 AGCTTATACCGCGCAATTGTA 58.171 42.857 8.75 3.21 0.00 2.41
2591 2710 3.199677 AGCTTATACCGCGCAATTGTAA 58.800 40.909 8.75 0.00 0.00 2.41
2592 2711 3.813166 AGCTTATACCGCGCAATTGTAAT 59.187 39.130 8.75 0.00 0.00 1.89
2597 2742 7.528481 TTATACCGCGCAATTGTAATATAGG 57.472 36.000 8.75 0.00 0.00 2.57
2598 2743 2.482721 ACCGCGCAATTGTAATATAGGC 59.517 45.455 8.75 0.00 0.00 3.93
2601 2746 4.334443 CGCGCAATTGTAATATAGGCATC 58.666 43.478 8.75 0.00 0.00 3.91
2603 2748 4.155826 GCGCAATTGTAATATAGGCATCCA 59.844 41.667 0.30 0.00 0.00 3.41
2623 2768 3.007940 CCATCTGGAACTGTGACAACCTA 59.992 47.826 0.00 0.00 37.39 3.08
2625 2770 2.037251 TCTGGAACTGTGACAACCTAGC 59.963 50.000 5.13 0.00 0.00 3.42
2632 2777 1.472878 TGTGACAACCTAGCTAGCTCG 59.527 52.381 23.26 15.60 0.00 5.03
2700 2845 4.803452 AGGACCTGAATTTTGTTGAAGGA 58.197 39.130 0.00 0.00 0.00 3.36
2702 2847 5.069119 AGGACCTGAATTTTGTTGAAGGAAC 59.931 40.000 0.00 0.00 34.84 3.62
2728 3293 1.673033 GCGTAACAGCTCCATGAGTGT 60.673 52.381 0.00 0.00 31.39 3.55
2734 3299 3.866651 ACAGCTCCATGAGTGTCATAAC 58.133 45.455 0.00 0.00 34.28 1.89
2747 3312 6.127730 TGAGTGTCATAACGAGCTTAGAATGA 60.128 38.462 0.00 0.00 0.00 2.57
2748 3313 6.810911 AGTGTCATAACGAGCTTAGAATGAT 58.189 36.000 0.00 0.00 0.00 2.45
2758 3324 8.136057 ACGAGCTTAGAATGATTTTGTCTATG 57.864 34.615 0.00 0.00 0.00 2.23
2775 3343 0.541764 ATGTTGAACGGCATTGGGGT 60.542 50.000 0.00 0.00 0.00 4.95
2785 3353 3.951680 ACGGCATTGGGGTTAAGATAAAG 59.048 43.478 0.00 0.00 0.00 1.85
2791 3359 6.406849 GCATTGGGGTTAAGATAAAGCATGAA 60.407 38.462 0.00 0.00 0.00 2.57
2821 3389 7.575414 TCATGGTATGCCGTAATACAAAATT 57.425 32.000 0.00 0.00 35.16 1.82
2822 3390 7.421599 TCATGGTATGCCGTAATACAAAATTG 58.578 34.615 0.00 0.00 35.16 2.32
2827 3395 5.440234 TGCCGTAATACAAAATTGTGTGT 57.560 34.783 11.74 1.34 42.31 3.72
2838 3406 6.866480 ACAAAATTGTGTGTTCTGACAGATT 58.134 32.000 5.87 0.00 40.49 2.40
2839 3407 6.753279 ACAAAATTGTGTGTTCTGACAGATTG 59.247 34.615 5.87 6.31 40.49 2.67
2840 3408 6.698008 AAATTGTGTGTTCTGACAGATTGA 57.302 33.333 5.87 0.00 36.20 2.57
2841 3409 5.679734 ATTGTGTGTTCTGACAGATTGAC 57.320 39.130 5.87 2.32 36.20 3.18
2843 3411 4.769688 TGTGTGTTCTGACAGATTGACTT 58.230 39.130 5.87 0.00 36.20 3.01
2845 3413 4.811024 GTGTGTTCTGACAGATTGACTTCA 59.189 41.667 5.87 3.66 36.20 3.02
2846 3414 4.811024 TGTGTTCTGACAGATTGACTTCAC 59.189 41.667 5.87 7.92 36.20 3.18
2847 3415 5.053145 GTGTTCTGACAGATTGACTTCACT 58.947 41.667 5.87 0.00 36.20 3.41
2848 3416 6.183360 TGTGTTCTGACAGATTGACTTCACTA 60.183 38.462 5.87 0.00 36.20 2.74
2849 3417 6.364706 GTGTTCTGACAGATTGACTTCACTAG 59.635 42.308 5.87 0.00 36.20 2.57
2850 3418 5.065704 TCTGACAGATTGACTTCACTAGC 57.934 43.478 0.00 0.00 0.00 3.42
2851 3419 4.769488 TCTGACAGATTGACTTCACTAGCT 59.231 41.667 0.00 0.00 0.00 3.32
2870 3470 5.143916 AGCTTTTATCGTCGCATTTACAG 57.856 39.130 0.00 0.00 0.00 2.74
2924 3524 7.439655 CAGATTCTTTATACTGAGTTACCTGCC 59.560 40.741 0.00 0.00 32.90 4.85
2932 3543 3.765511 ACTGAGTTACCTGCCGTTATGTA 59.234 43.478 0.00 0.00 0.00 2.29
2936 3547 3.131755 AGTTACCTGCCGTTATGTACTCC 59.868 47.826 0.00 0.00 0.00 3.85
2940 3551 2.287427 CCTGCCGTTATGTACTCCTACG 60.287 54.545 0.00 0.00 0.00 3.51
2941 3552 1.066002 TGCCGTTATGTACTCCTACGC 59.934 52.381 0.00 0.00 0.00 4.42
2943 3554 2.857489 GCCGTTATGTACTCCTACGCAG 60.857 54.545 0.00 0.00 0.00 5.18
2946 3557 3.181493 CGTTATGTACTCCTACGCAGGTT 60.181 47.826 0.53 0.00 43.18 3.50
2947 3558 2.961526 ATGTACTCCTACGCAGGTTG 57.038 50.000 0.53 0.00 43.18 3.77
2948 3559 1.624336 TGTACTCCTACGCAGGTTGT 58.376 50.000 0.53 5.09 43.18 3.32
2949 3560 1.271379 TGTACTCCTACGCAGGTTGTG 59.729 52.381 0.53 0.00 43.18 3.33
2950 3561 1.271656 GTACTCCTACGCAGGTTGTGT 59.728 52.381 0.53 0.66 44.22 3.72
2954 3565 2.735134 CTCCTACGCAGGTTGTGTTAAC 59.265 50.000 0.53 0.00 41.83 2.01
2956 3567 3.573538 TCCTACGCAGGTTGTGTTAACTA 59.426 43.478 7.22 0.00 41.83 2.24
2959 3570 3.135994 ACGCAGGTTGTGTTAACTAAGG 58.864 45.455 7.22 0.00 37.97 2.69
2961 3572 3.059188 CGCAGGTTGTGTTAACTAAGGTG 60.059 47.826 7.22 4.36 0.00 4.00
2969 3580 6.177310 TGTGTTAACTAAGGTGTACATGGT 57.823 37.500 7.22 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.756760 GAGCATGCAAGAGGAAATGGAA 59.243 45.455 21.98 0.00 0.00 3.53
142 167 2.163509 CATCGGACGAGGAGTATGGAT 58.836 52.381 0.00 0.00 0.00 3.41
289 319 3.428282 GCCGCGGGAAATGTCGTT 61.428 61.111 29.38 0.00 0.00 3.85
295 325 4.832608 GTCCTCGCCGCGGGAAAT 62.833 66.667 29.38 0.00 33.01 2.17
427 517 4.713792 AAATTGCACCAAATTTACCCCA 57.286 36.364 0.00 0.00 37.84 4.96
433 524 4.506448 CCCACCCTAAATTGCACCAAATTT 60.506 41.667 0.00 0.00 41.45 1.82
434 525 3.008923 CCCACCCTAAATTGCACCAAATT 59.991 43.478 0.00 0.00 0.00 1.82
500 591 6.158520 CCATCCTACATATGGGGTTGATATGA 59.841 42.308 20.28 3.50 40.27 2.15
517 623 1.916181 CATCCCCCATACCCATCCTAC 59.084 57.143 0.00 0.00 0.00 3.18
522 628 1.388654 TGGCATCCCCCATACCCAT 60.389 57.895 0.00 0.00 0.00 4.00
526 632 1.545651 GCTAACTGGCATCCCCCATAC 60.546 57.143 0.00 0.00 33.64 2.39
540 646 2.359478 CAAACGCCCGGGCTAACT 60.359 61.111 41.01 21.10 39.32 2.24
566 672 2.677228 CCCAAACGGGCCTCTCAT 59.323 61.111 0.84 0.00 36.72 2.90
600 707 2.031163 GCCGTCCAGTCACTGCTT 59.969 61.111 0.00 0.00 0.00 3.91
601 708 4.008933 GGCCGTCCAGTCACTGCT 62.009 66.667 0.00 0.00 0.00 4.24
638 745 4.223953 TCTATAATCGGCCCTCTCAAACT 58.776 43.478 0.00 0.00 0.00 2.66
681 791 7.453439 GGTAGGAGGCTCTCTTTCTAGATATTT 59.547 40.741 15.23 0.00 0.00 1.40
690 800 1.406180 GACGGTAGGAGGCTCTCTTTC 59.594 57.143 15.23 6.84 0.00 2.62
695 805 1.482593 CAAATGACGGTAGGAGGCTCT 59.517 52.381 15.23 3.10 0.00 4.09
696 806 1.480954 TCAAATGACGGTAGGAGGCTC 59.519 52.381 5.78 5.78 0.00 4.70
697 807 1.568504 TCAAATGACGGTAGGAGGCT 58.431 50.000 0.00 0.00 0.00 4.58
698 808 2.093658 TCTTCAAATGACGGTAGGAGGC 60.094 50.000 0.00 0.00 0.00 4.70
699 809 3.887621 TCTTCAAATGACGGTAGGAGG 57.112 47.619 0.00 0.00 0.00 4.30
700 810 3.557595 GCATCTTCAAATGACGGTAGGAG 59.442 47.826 0.00 0.00 0.00 3.69
701 811 3.055458 TGCATCTTCAAATGACGGTAGGA 60.055 43.478 0.00 0.00 0.00 2.94
702 812 3.270027 TGCATCTTCAAATGACGGTAGG 58.730 45.455 0.00 0.00 0.00 3.18
703 813 5.490139 AATGCATCTTCAAATGACGGTAG 57.510 39.130 0.00 0.00 0.00 3.18
704 814 6.992123 AGATAATGCATCTTCAAATGACGGTA 59.008 34.615 0.00 0.00 41.49 4.02
705 815 5.824624 AGATAATGCATCTTCAAATGACGGT 59.175 36.000 0.00 0.00 41.49 4.83
706 816 6.140786 CAGATAATGCATCTTCAAATGACGG 58.859 40.000 0.00 0.00 41.49 4.79
729 839 7.329962 CATTTGATCTGAAAATGTGCTTTAGCA 59.670 33.333 0.00 0.00 40.73 3.49
730 840 7.672738 CATTTGATCTGAAAATGTGCTTTAGC 58.327 34.615 8.23 0.00 39.24 3.09
731 841 7.201496 GGCATTTGATCTGAAAATGTGCTTTAG 60.201 37.037 14.85 0.00 43.72 1.85
732 842 6.591062 GGCATTTGATCTGAAAATGTGCTTTA 59.409 34.615 14.85 0.00 43.72 1.85
733 843 5.410439 GGCATTTGATCTGAAAATGTGCTTT 59.590 36.000 14.85 0.00 43.72 3.51
734 844 4.933400 GGCATTTGATCTGAAAATGTGCTT 59.067 37.500 14.85 0.00 43.72 3.91
735 845 4.222145 AGGCATTTGATCTGAAAATGTGCT 59.778 37.500 14.85 0.00 43.72 4.40
736 846 4.501071 AGGCATTTGATCTGAAAATGTGC 58.499 39.130 14.85 6.49 43.72 4.57
737 847 8.437742 GTTTAAGGCATTTGATCTGAAAATGTG 58.562 33.333 14.85 0.00 43.72 3.21
738 848 7.603784 GGTTTAAGGCATTTGATCTGAAAATGT 59.396 33.333 14.85 2.95 43.72 2.71
739 849 7.603404 TGGTTTAAGGCATTTGATCTGAAAATG 59.397 33.333 10.98 10.98 44.34 2.32
740 850 7.678837 TGGTTTAAGGCATTTGATCTGAAAAT 58.321 30.769 0.00 0.00 0.00 1.82
741 851 7.060383 TGGTTTAAGGCATTTGATCTGAAAA 57.940 32.000 0.00 0.00 0.00 2.29
742 852 6.662865 TGGTTTAAGGCATTTGATCTGAAA 57.337 33.333 0.00 0.00 0.00 2.69
743 853 6.855763 ATGGTTTAAGGCATTTGATCTGAA 57.144 33.333 0.00 0.00 0.00 3.02
744 854 7.118723 ACTATGGTTTAAGGCATTTGATCTGA 58.881 34.615 0.00 0.00 0.00 3.27
745 855 7.338800 ACTATGGTTTAAGGCATTTGATCTG 57.661 36.000 0.00 0.00 0.00 2.90
746 856 7.961326 AACTATGGTTTAAGGCATTTGATCT 57.039 32.000 0.00 0.00 30.55 2.75
747 857 9.435688 AAAAACTATGGTTTAAGGCATTTGATC 57.564 29.630 7.69 0.00 43.90 2.92
772 882 7.670916 CAAAAACGTGCTTGAACAGATAAAAA 58.329 30.769 4.27 0.00 0.00 1.94
784 894 3.921969 TTTGATGCAAAAACGTGCTTG 57.078 38.095 0.00 5.68 45.17 4.01
863 973 4.722700 TCTCCGCCCCTGCTTTGC 62.723 66.667 0.00 0.00 34.43 3.68
885 995 4.657814 ACACAGGGTTGGTCTATTTCAT 57.342 40.909 0.00 0.00 0.00 2.57
886 996 4.561938 CGTACACAGGGTTGGTCTATTTCA 60.562 45.833 0.00 0.00 0.00 2.69
887 997 3.930848 CGTACACAGGGTTGGTCTATTTC 59.069 47.826 0.00 0.00 0.00 2.17
888 998 3.579586 TCGTACACAGGGTTGGTCTATTT 59.420 43.478 0.00 0.00 0.00 1.40
889 999 3.056322 GTCGTACACAGGGTTGGTCTATT 60.056 47.826 0.00 0.00 0.00 1.73
890 1000 2.494870 GTCGTACACAGGGTTGGTCTAT 59.505 50.000 0.00 0.00 0.00 1.98
891 1001 1.888512 GTCGTACACAGGGTTGGTCTA 59.111 52.381 0.00 0.00 0.00 2.59
892 1002 0.677842 GTCGTACACAGGGTTGGTCT 59.322 55.000 0.00 0.00 0.00 3.85
1206 1316 3.902086 GCGAGGTAGGGGAGCGAC 61.902 72.222 0.00 0.00 0.00 5.19
1314 1424 2.752640 TCGACGAATGCGAGGGGA 60.753 61.111 0.00 0.00 41.64 4.81
1692 1802 1.302271 GAACGACCCCACCAAGTCC 60.302 63.158 0.00 0.00 0.00 3.85
1696 1806 2.109387 CGTGAACGACCCCACCAA 59.891 61.111 0.00 0.00 43.02 3.67
1944 2054 2.281761 AACTGTGCCGCCAAGAGG 60.282 61.111 0.00 0.00 38.23 3.69
1984 2094 2.665185 ACCTCACGCGTTCTTGGC 60.665 61.111 10.22 0.00 0.00 4.52
2078 2196 2.209838 TTTCGCCGATGATGACTCTC 57.790 50.000 0.00 0.00 0.00 3.20
2109 2227 7.365741 CACAAAGTGCTAATCTGATCAGTTTT 58.634 34.615 21.92 17.80 31.83 2.43
2164 2282 2.004583 TCGAATCGGCCTAACAACAG 57.995 50.000 1.76 0.00 0.00 3.16
2191 2309 3.055094 AGGTACCATGAGATGACAACACC 60.055 47.826 15.94 0.00 0.00 4.16
2208 2326 5.299782 AGAATCGGATACAGAGACAAGGTAC 59.700 44.000 0.00 0.00 0.00 3.34
2329 2447 1.002888 ACCTGAGTCCTGACATTGCAG 59.997 52.381 0.00 2.19 35.66 4.41
2404 2522 5.663106 TGTATTAAGGTCTGAGCTCATCCTT 59.337 40.000 34.61 34.61 40.47 3.36
2466 2585 3.696051 TGATGCTTTTACATCTGCTTCCC 59.304 43.478 6.13 0.00 45.51 3.97
2512 2631 7.031975 GGGATCAGTTGCTTTTGAAGATAAAG 58.968 38.462 0.00 0.00 36.04 1.85
2517 2636 3.569701 GTGGGATCAGTTGCTTTTGAAGA 59.430 43.478 0.00 0.00 0.00 2.87
2525 2644 1.632409 AGTGATGTGGGATCAGTTGCT 59.368 47.619 0.00 0.00 0.00 3.91
2526 2645 2.119801 AGTGATGTGGGATCAGTTGC 57.880 50.000 0.00 0.00 0.00 4.17
2529 2648 3.795688 AACAAGTGATGTGGGATCAGT 57.204 42.857 0.00 0.00 42.99 3.41
2530 2649 4.330250 AGAAACAAGTGATGTGGGATCAG 58.670 43.478 0.00 0.00 42.99 2.90
2573 2692 6.036300 GCCTATATTACAATTGCGCGGTATAA 59.964 38.462 8.83 0.00 0.00 0.98
2578 2697 2.482336 TGCCTATATTACAATTGCGCGG 59.518 45.455 8.83 0.00 0.00 6.46
2580 2699 4.155826 TGGATGCCTATATTACAATTGCGC 59.844 41.667 5.05 0.00 0.00 6.09
2581 2700 5.878332 TGGATGCCTATATTACAATTGCG 57.122 39.130 5.05 0.00 0.00 4.85
2582 2701 7.415989 CCAGATGGATGCCTATATTACAATTGC 60.416 40.741 5.05 0.00 37.39 3.56
2583 2702 7.830697 TCCAGATGGATGCCTATATTACAATTG 59.169 37.037 3.24 3.24 39.78 2.32
2584 2703 7.932134 TCCAGATGGATGCCTATATTACAATT 58.068 34.615 0.00 0.00 39.78 2.32
2585 2704 7.515004 TCCAGATGGATGCCTATATTACAAT 57.485 36.000 0.00 0.00 39.78 2.71
2589 2708 6.501805 ACAGTTCCAGATGGATGCCTATATTA 59.498 38.462 1.61 0.00 44.98 0.98
2590 2709 5.311649 ACAGTTCCAGATGGATGCCTATATT 59.688 40.000 1.61 0.00 44.98 1.28
2591 2710 4.848660 ACAGTTCCAGATGGATGCCTATAT 59.151 41.667 1.61 0.00 44.98 0.86
2592 2711 4.040829 CACAGTTCCAGATGGATGCCTATA 59.959 45.833 1.61 0.00 44.98 1.31
2597 2742 2.012673 GTCACAGTTCCAGATGGATGC 58.987 52.381 1.61 0.00 44.98 3.91
2598 2743 3.339253 TGTCACAGTTCCAGATGGATG 57.661 47.619 1.61 1.66 44.98 3.51
2601 2746 2.154462 GGTTGTCACAGTTCCAGATGG 58.846 52.381 0.00 0.00 0.00 3.51
2603 2748 3.307059 GCTAGGTTGTCACAGTTCCAGAT 60.307 47.826 0.00 0.00 0.00 2.90
2610 2755 2.494073 GAGCTAGCTAGGTTGTCACAGT 59.506 50.000 25.38 0.00 33.58 3.55
2623 2768 0.967887 TGCAGAGAACCGAGCTAGCT 60.968 55.000 19.45 19.45 0.00 3.32
2625 2770 1.470632 CCTTGCAGAGAACCGAGCTAG 60.471 57.143 0.00 0.00 0.00 3.42
2632 2777 3.214328 TGAGTTTTCCTTGCAGAGAACC 58.786 45.455 5.94 0.72 32.66 3.62
2688 2833 2.098443 GCTCGGTGTTCCTTCAACAAAA 59.902 45.455 0.00 0.00 46.90 2.44
2700 2845 0.666577 GAGCTGTTACGCTCGGTGTT 60.667 55.000 11.77 0.00 45.91 3.32
2702 2847 3.768632 GAGCTGTTACGCTCGGTG 58.231 61.111 11.77 0.00 45.91 4.94
2728 3293 8.492673 ACAAAATCATTCTAAGCTCGTTATGA 57.507 30.769 0.00 0.00 0.00 2.15
2734 3299 8.136057 ACATAGACAAAATCATTCTAAGCTCG 57.864 34.615 0.00 0.00 0.00 5.03
2747 3312 5.643379 ATGCCGTTCAACATAGACAAAAT 57.357 34.783 0.00 0.00 0.00 1.82
2748 3313 5.218885 CAATGCCGTTCAACATAGACAAAA 58.781 37.500 0.00 0.00 0.00 2.44
2758 3324 1.249407 TAACCCCAATGCCGTTCAAC 58.751 50.000 0.00 0.00 0.00 3.18
2764 3330 3.243401 GCTTTATCTTAACCCCAATGCCG 60.243 47.826 0.00 0.00 0.00 5.69
2791 3359 4.415881 TTACGGCATACCATGAATGTCT 57.584 40.909 9.86 2.34 34.57 3.41
2803 3371 7.147143 ACACACAATTTTGTATTACGGCATA 57.853 32.000 0.00 0.00 39.91 3.14
2804 3372 6.019779 ACACACAATTTTGTATTACGGCAT 57.980 33.333 0.00 0.00 39.91 4.40
2808 3376 7.853437 TGTCAGAACACACAATTTTGTATTACG 59.147 33.333 0.00 0.00 39.91 3.18
2821 3389 4.406648 AGTCAATCTGTCAGAACACACA 57.593 40.909 6.64 0.00 0.00 3.72
2822 3390 4.811024 TGAAGTCAATCTGTCAGAACACAC 59.189 41.667 6.64 1.94 0.00 3.82
2827 3395 5.244851 AGCTAGTGAAGTCAATCTGTCAGAA 59.755 40.000 6.64 0.00 0.00 3.02
2838 3406 5.093457 CGACGATAAAAGCTAGTGAAGTCA 58.907 41.667 0.00 0.00 0.00 3.41
2839 3407 4.027540 GCGACGATAAAAGCTAGTGAAGTC 60.028 45.833 0.00 0.00 0.00 3.01
2840 3408 3.858238 GCGACGATAAAAGCTAGTGAAGT 59.142 43.478 0.00 0.00 0.00 3.01
2841 3409 3.857665 TGCGACGATAAAAGCTAGTGAAG 59.142 43.478 0.00 0.00 0.00 3.02
2843 3411 3.497297 TGCGACGATAAAAGCTAGTGA 57.503 42.857 0.00 0.00 0.00 3.41
2845 3413 5.808540 TGTAAATGCGACGATAAAAGCTAGT 59.191 36.000 0.00 0.00 0.00 2.57
2846 3414 6.268797 TGTAAATGCGACGATAAAAGCTAG 57.731 37.500 0.00 0.00 0.00 3.42
2847 3415 5.276678 GCTGTAAATGCGACGATAAAAGCTA 60.277 40.000 0.00 0.00 0.00 3.32
2848 3416 4.494199 GCTGTAAATGCGACGATAAAAGCT 60.494 41.667 0.00 0.00 0.00 3.74
2849 3417 3.719352 GCTGTAAATGCGACGATAAAAGC 59.281 43.478 0.00 0.00 0.00 3.51
2850 3418 4.892655 TGCTGTAAATGCGACGATAAAAG 58.107 39.130 0.00 0.00 0.00 2.27
2851 3419 4.726591 GCTGCTGTAAATGCGACGATAAAA 60.727 41.667 0.00 0.00 0.00 1.52
2870 3470 1.339438 TGGGAACTCAATCTCTGCTGC 60.339 52.381 0.00 0.00 0.00 5.25
2918 3518 1.861982 AGGAGTACATAACGGCAGGT 58.138 50.000 0.00 0.00 0.00 4.00
2936 3547 4.387862 CCTTAGTTAACACAACCTGCGTAG 59.612 45.833 8.61 0.00 0.00 3.51
2940 3551 3.881089 ACACCTTAGTTAACACAACCTGC 59.119 43.478 8.61 0.00 0.00 4.85
2941 3552 6.050432 TGTACACCTTAGTTAACACAACCTG 58.950 40.000 8.61 0.00 0.00 4.00
2943 3554 6.072893 CCATGTACACCTTAGTTAACACAACC 60.073 42.308 8.61 0.00 0.00 3.77
2946 3557 6.177310 ACCATGTACACCTTAGTTAACACA 57.823 37.500 8.61 0.98 0.00 3.72
2947 3558 7.500720 AAACCATGTACACCTTAGTTAACAC 57.499 36.000 8.61 0.00 0.00 3.32
2948 3559 6.424509 CGAAACCATGTACACCTTAGTTAACA 59.575 38.462 8.61 0.00 0.00 2.41
2949 3560 6.646240 TCGAAACCATGTACACCTTAGTTAAC 59.354 38.462 0.00 0.00 0.00 2.01
2950 3561 6.757237 TCGAAACCATGTACACCTTAGTTAA 58.243 36.000 0.00 0.00 0.00 2.01
2954 3565 4.992319 TGTTCGAAACCATGTACACCTTAG 59.008 41.667 0.00 0.00 0.00 2.18
2956 3567 3.811083 TGTTCGAAACCATGTACACCTT 58.189 40.909 0.00 0.00 0.00 3.50
2959 3570 5.351233 TTGATGTTCGAAACCATGTACAC 57.649 39.130 0.00 0.00 0.00 2.90
2961 3572 5.851177 CACTTTGATGTTCGAAACCATGTAC 59.149 40.000 0.00 0.00 0.00 2.90
2969 3580 2.948979 ACAGCCACTTTGATGTTCGAAA 59.051 40.909 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.