Multiple sequence alignment - TraesCS3D01G101500

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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 TraesCS3D01G101500 chr3D 100.000 3779 0 0 1 3779 54624533 54628311 0.000000e+00 6979.0
1 TraesCS3D01G101500 chr3D 92.408 382 17 5 3405 3779 118538440 118538064 5.560000e-148 534.0
2 TraesCS3D01G101500 chr3D 86.352 381 21 15 3404 3779 602726915 602726561 1.650000e-103 387.0
3 TraesCS3D01G101500 chr3D 97.826 184 3 1 3221 3404 363070739 363070557 2.190000e-82 316.0
4 TraesCS3D01G101500 chr3B 94.036 2515 108 15 733 3224 85054698 85057193 0.000000e+00 3775.0
5 TraesCS3D01G101500 chr3B 94.359 2411 115 12 833 3224 84878788 84881196 0.000000e+00 3679.0
6 TraesCS3D01G101500 chr3B 81.538 260 20 14 2702 2936 84880917 84881173 4.980000e-44 189.0
7 TraesCS3D01G101500 chr3B 81.609 261 18 16 2702 2936 85056914 85057170 4.980000e-44 189.0
8 TraesCS3D01G101500 chr3B 90.278 72 6 1 733 803 84878717 84878788 4.020000e-15 93.5
9 TraesCS3D01G101500 chr3A 95.222 2114 70 12 839 2942 65403612 65405704 0.000000e+00 3315.0
10 TraesCS3D01G101500 chr3A 86.316 95 10 2 3133 3224 65405629 65405723 2.400000e-17 100.0
11 TraesCS3D01G101500 chr1D 86.979 960 98 11 1371 2324 396888326 396889264 0.000000e+00 1055.0
12 TraesCS3D01G101500 chr1D 87.731 595 60 4 1731 2324 396877619 396878201 0.000000e+00 682.0
13 TraesCS3D01G101500 chr1D 90.254 236 20 3 1212 1446 391159466 391159233 4.740000e-79 305.0
14 TraesCS3D01G101500 chr1D 93.122 189 12 1 3216 3404 267388376 267388563 3.720000e-70 276.0
15 TraesCS3D01G101500 chr1D 84.307 274 23 7 3428 3684 411569700 411569430 2.250000e-62 250.0
16 TraesCS3D01G101500 chr1D 87.013 154 20 0 1293 1446 391159232 391159079 1.400000e-39 174.0
17 TraesCS3D01G101500 chr5D 99.109 561 5 0 3219 3779 401761866 401762426 0.000000e+00 1009.0
18 TraesCS3D01G101500 chr2D 98.564 557 8 0 3223 3779 623998395 623998951 0.000000e+00 985.0
19 TraesCS3D01G101500 chr2D 96.283 565 11 4 3215 3779 393687863 393688417 0.000000e+00 918.0
20 TraesCS3D01G101500 chr2D 88.511 618 69 2 6 622 38203883 38203267 0.000000e+00 747.0
21 TraesCS3D01G101500 chr2D 87.379 618 75 3 6 622 38377768 38377153 0.000000e+00 706.0
22 TraesCS3D01G101500 chr7D 92.569 619 45 1 3 620 263526399 263525781 0.000000e+00 887.0
23 TraesCS3D01G101500 chr7D 82.492 297 26 7 3405 3678 280587732 280588025 1.750000e-58 237.0
24 TraesCS3D01G101500 chr7D 94.853 136 7 0 3405 3540 327403405 327403540 2.960000e-51 213.0
25 TraesCS3D01G101500 chr7D 92.857 98 7 0 3682 3779 280588158 280588255 3.930000e-30 143.0
26 TraesCS3D01G101500 chr1A 89.939 656 53 8 2298 2942 494320990 494321643 0.000000e+00 833.0
27 TraesCS3D01G101500 chr1A 85.540 491 54 10 1098 1587 494173801 494174275 7.290000e-137 497.0
28 TraesCS3D01G101500 chr1A 88.049 410 39 4 1862 2271 494320590 494320989 9.500000e-131 477.0
29 TraesCS3D01G101500 chr1A 86.550 342 24 8 1988 2324 494174272 494174596 1.290000e-94 357.0
30 TraesCS3D01G101500 chr1A 80.634 284 32 13 2948 3224 494321395 494321662 8.280000e-47 198.0
31 TraesCS3D01G101500 chr1B 86.824 721 87 2 1008 1720 531858199 531858919 0.000000e+00 798.0
32 TraesCS3D01G101500 chr1B 89.206 630 62 3 1696 2324 532019067 532019691 0.000000e+00 782.0
33 TraesCS3D01G101500 chr1B 87.840 625 70 1 3 621 32076855 32076231 0.000000e+00 728.0
34 TraesCS3D01G101500 chr1B 89.173 508 46 4 1762 2262 531858932 531859437 3.200000e-175 625.0
35 TraesCS3D01G101500 chr1B 97.159 176 4 1 3229 3404 645735713 645735539 2.850000e-76 296.0
36 TraesCS3D01G101500 chr1B 84.231 260 25 8 3428 3684 2119593 2119347 4.880000e-59 239.0
37 TraesCS3D01G101500 chr7B 91.860 516 41 1 96 611 703942104 703942618 0.000000e+00 719.0
38 TraesCS3D01G101500 chr7B 86.074 596 68 8 29 622 40652544 40653126 8.910000e-176 627.0
39 TraesCS3D01G101500 chr7B 85.106 376 30 7 3405 3779 368148225 368147875 9.980000e-96 361.0
40 TraesCS3D01G101500 chr7B 98.370 184 2 1 3221 3404 173302225 173302407 4.710000e-84 322.0
41 TraesCS3D01G101500 chr7B 96.089 179 6 1 3226 3404 552552405 552552228 1.330000e-74 291.0
42 TraesCS3D01G101500 chr7B 96.269 134 5 0 3407 3540 285373272 285373405 1.770000e-53 220.0
43 TraesCS3D01G101500 chr7B 92.053 151 11 1 3391 3540 478471036 478471186 1.060000e-50 211.0
44 TraesCS3D01G101500 chr4A 88.508 583 63 2 3 583 615043601 615044181 0.000000e+00 702.0
45 TraesCS3D01G101500 chr4A 94.215 121 7 0 3659 3779 18305579 18305459 6.450000e-43 185.0
46 TraesCS3D01G101500 chr6A 86.452 620 82 2 3 622 123260788 123261405 0.000000e+00 678.0
47 TraesCS3D01G101500 chr7A 83.144 617 95 8 3 615 183828985 183829596 4.260000e-154 555.0
48 TraesCS3D01G101500 chr5A 83.990 381 20 16 3404 3779 31970421 31970765 1.010000e-85 327.0
49 TraesCS3D01G101500 chr6D 93.956 182 10 1 3223 3404 460766370 460766190 1.340000e-69 274.0
50 TraesCS3D01G101500 chr6B 94.928 138 6 1 3404 3540 331043016 331042879 8.220000e-52 215.0


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 TraesCS3D01G101500 chr3D 54624533 54628311 3778 False 6979.000000 6979 100.000000 1 3779 1 chr3D.!!$F1 3778
1 TraesCS3D01G101500 chr3B 85054698 85057193 2495 False 1982.000000 3775 87.822500 733 3224 2 chr3B.!!$F2 2491
2 TraesCS3D01G101500 chr3B 84878717 84881196 2479 False 1320.500000 3679 88.725000 733 3224 3 chr3B.!!$F1 2491
3 TraesCS3D01G101500 chr3A 65403612 65405723 2111 False 1707.500000 3315 90.769000 839 3224 2 chr3A.!!$F1 2385
4 TraesCS3D01G101500 chr1D 396888326 396889264 938 False 1055.000000 1055 86.979000 1371 2324 1 chr1D.!!$F3 953
5 TraesCS3D01G101500 chr1D 396877619 396878201 582 False 682.000000 682 87.731000 1731 2324 1 chr1D.!!$F2 593
6 TraesCS3D01G101500 chr5D 401761866 401762426 560 False 1009.000000 1009 99.109000 3219 3779 1 chr5D.!!$F1 560
7 TraesCS3D01G101500 chr2D 623998395 623998951 556 False 985.000000 985 98.564000 3223 3779 1 chr2D.!!$F2 556
8 TraesCS3D01G101500 chr2D 393687863 393688417 554 False 918.000000 918 96.283000 3215 3779 1 chr2D.!!$F1 564
9 TraesCS3D01G101500 chr2D 38203267 38203883 616 True 747.000000 747 88.511000 6 622 1 chr2D.!!$R1 616
10 TraesCS3D01G101500 chr2D 38377153 38377768 615 True 706.000000 706 87.379000 6 622 1 chr2D.!!$R2 616
11 TraesCS3D01G101500 chr7D 263525781 263526399 618 True 887.000000 887 92.569000 3 620 1 chr7D.!!$R1 617
12 TraesCS3D01G101500 chr1A 494320590 494321662 1072 False 502.666667 833 86.207333 1862 3224 3 chr1A.!!$F2 1362
13 TraesCS3D01G101500 chr1A 494173801 494174596 795 False 427.000000 497 86.045000 1098 2324 2 chr1A.!!$F1 1226
14 TraesCS3D01G101500 chr1B 532019067 532019691 624 False 782.000000 782 89.206000 1696 2324 1 chr1B.!!$F1 628
15 TraesCS3D01G101500 chr1B 32076231 32076855 624 True 728.000000 728 87.840000 3 621 1 chr1B.!!$R2 618
16 TraesCS3D01G101500 chr1B 531858199 531859437 1238 False 711.500000 798 87.998500 1008 2262 2 chr1B.!!$F2 1254
17 TraesCS3D01G101500 chr7B 703942104 703942618 514 False 719.000000 719 91.860000 96 611 1 chr7B.!!$F5 515
18 TraesCS3D01G101500 chr7B 40652544 40653126 582 False 627.000000 627 86.074000 29 622 1 chr7B.!!$F1 593
19 TraesCS3D01G101500 chr4A 615043601 615044181 580 False 702.000000 702 88.508000 3 583 1 chr4A.!!$F1 580
20 TraesCS3D01G101500 chr6A 123260788 123261405 617 False 678.000000 678 86.452000 3 622 1 chr6A.!!$F1 619
21 TraesCS3D01G101500 chr7A 183828985 183829596 611 False 555.000000 555 83.144000 3 615 1 chr7A.!!$F1 612

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
497 508 0.036388 TTTCTCTTGGAGGCGCGATT 60.036 50.0 12.1 0.0 0.00 3.34 F
1482 1541 0.163788 CGTTCAACACGCTCATCACC 59.836 55.0 0.0 0.0 43.37 4.02 F
2031 2096 0.250770 AGGGTCGGGAGCTTTTCAAC 60.251 55.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2408 0.174845 TTCTCACGCATTAGGTCCCG 59.825 55.000 0.00 0.0 0.00 5.14 R
2490 2566 0.608640 CAGGCACGTAACCTTCCTCT 59.391 55.000 6.57 0.0 34.42 3.69 R
2873 2952 1.227060 CGCCTCGACTCATGCATCA 60.227 57.895 0.00 0.0 0.00 3.07 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
268 272 0.392327 TGCATTTCTTCGCCATCGGA 60.392 50.000 0.00 0.00 36.13 4.55
272 276 1.550130 TTTCTTCGCCATCGGAGGGT 61.550 55.000 10.76 0.00 41.62 4.34
291 295 3.495331 GGTGAGCTCAGATCCTATCTCA 58.505 50.000 18.89 0.00 37.58 3.27
337 342 1.269723 CGATGCCGACAGCTTCCTATA 59.730 52.381 0.00 0.00 41.49 1.31
497 508 0.036388 TTTCTCTTGGAGGCGCGATT 60.036 50.000 12.10 0.00 0.00 3.34
500 511 0.740868 CTCTTGGAGGCGCGATTTCA 60.741 55.000 12.10 0.00 0.00 2.69
541 552 2.224281 GGTGTGTCTTGATGGAGTGTGA 60.224 50.000 0.00 0.00 0.00 3.58
611 624 6.721571 TTTTCTCATCACTTTGTATCGGTC 57.278 37.500 0.00 0.00 0.00 4.79
612 625 5.661056 TTCTCATCACTTTGTATCGGTCT 57.339 39.130 0.00 0.00 0.00 3.85
625 638 2.983592 GGTCTGGCCGTGTTTGGG 60.984 66.667 0.00 0.00 0.00 4.12
626 639 2.983592 GTCTGGCCGTGTTTGGGG 60.984 66.667 0.00 0.00 0.00 4.96
627 640 3.494254 TCTGGCCGTGTTTGGGGT 61.494 61.111 0.00 0.00 0.00 4.95
628 641 3.294493 CTGGCCGTGTTTGGGGTG 61.294 66.667 0.00 0.00 0.00 4.61
629 642 4.904590 TGGCCGTGTTTGGGGTGG 62.905 66.667 0.00 0.00 0.00 4.61
630 643 4.589675 GGCCGTGTTTGGGGTGGA 62.590 66.667 0.00 0.00 0.00 4.02
631 644 2.519780 GCCGTGTTTGGGGTGGAA 60.520 61.111 0.00 0.00 0.00 3.53
632 645 2.561037 GCCGTGTTTGGGGTGGAAG 61.561 63.158 0.00 0.00 0.00 3.46
633 646 1.149627 CCGTGTTTGGGGTGGAAGA 59.850 57.895 0.00 0.00 0.00 2.87
634 647 1.170290 CCGTGTTTGGGGTGGAAGAC 61.170 60.000 0.00 0.00 0.00 3.01
635 648 0.179029 CGTGTTTGGGGTGGAAGACT 60.179 55.000 0.00 0.00 0.00 3.24
636 649 1.749286 CGTGTTTGGGGTGGAAGACTT 60.749 52.381 0.00 0.00 0.00 3.01
637 650 2.384828 GTGTTTGGGGTGGAAGACTTT 58.615 47.619 0.00 0.00 0.00 2.66
638 651 2.764010 GTGTTTGGGGTGGAAGACTTTT 59.236 45.455 0.00 0.00 0.00 2.27
639 652 3.196901 GTGTTTGGGGTGGAAGACTTTTT 59.803 43.478 0.00 0.00 0.00 1.94
640 653 3.449377 TGTTTGGGGTGGAAGACTTTTTC 59.551 43.478 0.00 0.00 0.00 2.29
641 654 1.975660 TGGGGTGGAAGACTTTTTCG 58.024 50.000 0.00 0.00 0.00 3.46
642 655 1.491332 TGGGGTGGAAGACTTTTTCGA 59.509 47.619 0.00 0.00 0.00 3.71
643 656 2.107552 TGGGGTGGAAGACTTTTTCGAT 59.892 45.455 0.00 0.00 0.00 3.59
644 657 3.154710 GGGGTGGAAGACTTTTTCGATT 58.845 45.455 0.00 0.00 0.00 3.34
645 658 3.572682 GGGGTGGAAGACTTTTTCGATTT 59.427 43.478 0.00 0.00 0.00 2.17
646 659 4.546570 GGGTGGAAGACTTTTTCGATTTG 58.453 43.478 0.00 0.00 0.00 2.32
647 660 3.981416 GGTGGAAGACTTTTTCGATTTGC 59.019 43.478 0.00 0.00 0.00 3.68
648 661 4.261614 GGTGGAAGACTTTTTCGATTTGCT 60.262 41.667 0.00 0.00 0.00 3.91
649 662 4.676924 GTGGAAGACTTTTTCGATTTGCTG 59.323 41.667 0.00 0.00 0.00 4.41
650 663 4.578516 TGGAAGACTTTTTCGATTTGCTGA 59.421 37.500 0.00 0.00 0.00 4.26
651 664 5.241506 TGGAAGACTTTTTCGATTTGCTGAT 59.758 36.000 0.00 0.00 0.00 2.90
652 665 5.797434 GGAAGACTTTTTCGATTTGCTGATC 59.203 40.000 0.00 0.00 0.00 2.92
653 666 5.947228 AGACTTTTTCGATTTGCTGATCA 57.053 34.783 0.00 0.00 0.00 2.92
654 667 6.317789 AGACTTTTTCGATTTGCTGATCAA 57.682 33.333 0.00 0.00 0.00 2.57
656 669 6.860023 AGACTTTTTCGATTTGCTGATCAAAG 59.140 34.615 0.00 0.00 46.68 2.77
657 670 6.738114 ACTTTTTCGATTTGCTGATCAAAGA 58.262 32.000 0.00 0.00 46.68 2.52
658 671 6.860023 ACTTTTTCGATTTGCTGATCAAAGAG 59.140 34.615 0.00 11.52 46.68 2.85
659 672 4.952262 TTCGATTTGCTGATCAAAGAGG 57.048 40.909 0.00 0.00 46.68 3.69
660 673 3.942829 TCGATTTGCTGATCAAAGAGGT 58.057 40.909 0.00 0.00 46.68 3.85
661 674 4.326826 TCGATTTGCTGATCAAAGAGGTT 58.673 39.130 0.00 0.00 46.68 3.50
662 675 4.393062 TCGATTTGCTGATCAAAGAGGTTC 59.607 41.667 0.00 0.00 46.68 3.62
663 676 4.394300 CGATTTGCTGATCAAAGAGGTTCT 59.606 41.667 0.00 0.00 46.68 3.01
664 677 5.638783 GATTTGCTGATCAAAGAGGTTCTG 58.361 41.667 0.00 0.00 46.68 3.02
665 678 3.777106 TGCTGATCAAAGAGGTTCTGT 57.223 42.857 0.00 0.00 0.00 3.41
666 679 4.890158 TGCTGATCAAAGAGGTTCTGTA 57.110 40.909 0.00 0.00 0.00 2.74
667 680 5.227569 TGCTGATCAAAGAGGTTCTGTAA 57.772 39.130 0.00 0.00 0.00 2.41
668 681 4.997395 TGCTGATCAAAGAGGTTCTGTAAC 59.003 41.667 0.00 0.00 34.66 2.50
669 682 5.221722 TGCTGATCAAAGAGGTTCTGTAACT 60.222 40.000 0.00 0.00 35.81 2.24
670 683 5.703130 GCTGATCAAAGAGGTTCTGTAACTT 59.297 40.000 0.00 0.00 35.81 2.66
671 684 6.348050 GCTGATCAAAGAGGTTCTGTAACTTG 60.348 42.308 0.00 0.00 35.81 3.16
672 685 6.591935 TGATCAAAGAGGTTCTGTAACTTGT 58.408 36.000 0.00 0.00 35.81 3.16
673 686 7.732025 TGATCAAAGAGGTTCTGTAACTTGTA 58.268 34.615 0.00 0.00 35.81 2.41
674 687 7.872993 TGATCAAAGAGGTTCTGTAACTTGTAG 59.127 37.037 0.00 0.00 35.81 2.74
675 688 7.120923 TCAAAGAGGTTCTGTAACTTGTAGT 57.879 36.000 0.00 0.00 35.81 2.73
676 689 7.208080 TCAAAGAGGTTCTGTAACTTGTAGTC 58.792 38.462 0.00 0.00 35.81 2.59
677 690 6.726490 AAGAGGTTCTGTAACTTGTAGTCA 57.274 37.500 0.00 0.00 35.81 3.41
678 691 6.334102 AGAGGTTCTGTAACTTGTAGTCAG 57.666 41.667 0.00 0.00 35.81 3.51
679 692 5.244178 AGAGGTTCTGTAACTTGTAGTCAGG 59.756 44.000 0.00 0.00 35.81 3.86
680 693 4.900054 AGGTTCTGTAACTTGTAGTCAGGT 59.100 41.667 0.00 0.00 35.81 4.00
681 694 5.010820 AGGTTCTGTAACTTGTAGTCAGGTC 59.989 44.000 0.00 0.00 35.81 3.85
682 695 5.010820 GGTTCTGTAACTTGTAGTCAGGTCT 59.989 44.000 0.00 0.00 35.81 3.85
683 696 6.462628 GGTTCTGTAACTTGTAGTCAGGTCTT 60.463 42.308 0.00 0.00 35.81 3.01
684 697 6.085555 TCTGTAACTTGTAGTCAGGTCTTG 57.914 41.667 0.00 0.00 32.75 3.02
685 698 5.010719 TCTGTAACTTGTAGTCAGGTCTTGG 59.989 44.000 0.00 0.00 32.75 3.61
686 699 4.897076 TGTAACTTGTAGTCAGGTCTTGGA 59.103 41.667 0.00 0.00 32.75 3.53
687 700 5.364446 TGTAACTTGTAGTCAGGTCTTGGAA 59.636 40.000 0.00 0.00 32.75 3.53
688 701 5.568620 AACTTGTAGTCAGGTCTTGGAAT 57.431 39.130 0.00 0.00 32.75 3.01
689 702 5.568620 ACTTGTAGTCAGGTCTTGGAATT 57.431 39.130 0.00 0.00 0.00 2.17
690 703 5.308825 ACTTGTAGTCAGGTCTTGGAATTG 58.691 41.667 0.00 0.00 0.00 2.32
691 704 5.071788 ACTTGTAGTCAGGTCTTGGAATTGA 59.928 40.000 0.00 0.00 0.00 2.57
692 705 5.152623 TGTAGTCAGGTCTTGGAATTGAG 57.847 43.478 0.00 0.00 0.00 3.02
693 706 4.838423 TGTAGTCAGGTCTTGGAATTGAGA 59.162 41.667 0.00 0.00 0.00 3.27
694 707 5.485353 TGTAGTCAGGTCTTGGAATTGAGAT 59.515 40.000 0.00 0.00 0.00 2.75
695 708 6.667848 TGTAGTCAGGTCTTGGAATTGAGATA 59.332 38.462 0.00 0.00 0.00 1.98
696 709 6.821616 AGTCAGGTCTTGGAATTGAGATAT 57.178 37.500 0.00 0.00 0.00 1.63
697 710 7.205515 AGTCAGGTCTTGGAATTGAGATATT 57.794 36.000 0.00 0.00 0.00 1.28
698 711 7.637511 AGTCAGGTCTTGGAATTGAGATATTT 58.362 34.615 0.00 0.00 0.00 1.40
699 712 8.112183 AGTCAGGTCTTGGAATTGAGATATTTT 58.888 33.333 0.00 0.00 0.00 1.82
700 713 8.743714 GTCAGGTCTTGGAATTGAGATATTTTT 58.256 33.333 0.00 0.00 0.00 1.94
701 714 8.742777 TCAGGTCTTGGAATTGAGATATTTTTG 58.257 33.333 0.00 0.00 0.00 2.44
702 715 8.526147 CAGGTCTTGGAATTGAGATATTTTTGT 58.474 33.333 0.00 0.00 0.00 2.83
703 716 9.093458 AGGTCTTGGAATTGAGATATTTTTGTT 57.907 29.630 0.00 0.00 0.00 2.83
704 717 9.710900 GGTCTTGGAATTGAGATATTTTTGTTT 57.289 29.630 0.00 0.00 0.00 2.83
706 719 9.709495 TCTTGGAATTGAGATATTTTTGTTTGG 57.291 29.630 0.00 0.00 0.00 3.28
707 720 8.845413 TTGGAATTGAGATATTTTTGTTTGGG 57.155 30.769 0.00 0.00 0.00 4.12
708 721 8.200024 TGGAATTGAGATATTTTTGTTTGGGA 57.800 30.769 0.00 0.00 0.00 4.37
709 722 8.093927 TGGAATTGAGATATTTTTGTTTGGGAC 58.906 33.333 0.00 0.00 0.00 4.46
710 723 8.093927 GGAATTGAGATATTTTTGTTTGGGACA 58.906 33.333 0.00 0.00 36.19 4.02
711 724 8.831715 AATTGAGATATTTTTGTTTGGGACAC 57.168 30.769 0.00 0.00 39.29 3.67
712 725 6.968263 TGAGATATTTTTGTTTGGGACACA 57.032 33.333 0.00 0.00 39.29 3.72
713 726 6.980593 TGAGATATTTTTGTTTGGGACACAG 58.019 36.000 0.00 0.00 39.29 3.66
714 727 6.549364 TGAGATATTTTTGTTTGGGACACAGT 59.451 34.615 0.00 0.00 39.29 3.55
715 728 7.721842 TGAGATATTTTTGTTTGGGACACAGTA 59.278 33.333 0.00 0.00 39.29 2.74
716 729 8.110860 AGATATTTTTGTTTGGGACACAGTAG 57.889 34.615 0.00 0.00 39.29 2.57
717 730 7.724061 AGATATTTTTGTTTGGGACACAGTAGT 59.276 33.333 0.00 0.00 39.29 2.73
1482 1541 0.163788 CGTTCAACACGCTCATCACC 59.836 55.000 0.00 0.00 43.37 4.02
1550 1609 2.026822 ACGAAATGCCTGAGAGGAATGT 60.027 45.455 0.00 0.00 32.56 2.71
1590 1649 2.045340 AATGGGTACGTGCAGGCC 60.045 61.111 6.26 0.00 0.00 5.19
2031 2096 0.250770 AGGGTCGGGAGCTTTTCAAC 60.251 55.000 0.00 0.00 0.00 3.18
2157 2228 3.237746 TGAGAAAATGCCCATGAAACCA 58.762 40.909 0.00 0.00 0.00 3.67
2199 2270 4.192317 CTCTAATGGCTGGTTGTAGGTTC 58.808 47.826 0.00 0.00 0.00 3.62
2228 2299 1.339055 TGTGGAGTTGGCTGAGTATGC 60.339 52.381 0.00 0.00 0.00 3.14
2332 2408 1.453155 TGCTTCTGCGAGGGAAATTC 58.547 50.000 0.00 0.00 43.34 2.17
2335 2411 0.392461 TTCTGCGAGGGAAATTCGGG 60.392 55.000 0.00 0.00 38.45 5.14
2885 2964 5.295152 TGATACATCAGTGATGCATGAGTC 58.705 41.667 29.10 18.25 43.15 3.36
2906 2985 2.348666 CGAGGCGATAAAGTTGGTGAAG 59.651 50.000 0.00 0.00 0.00 3.02
2987 3071 5.901552 AGATTGAACACGTTTCCATTTGTT 58.098 33.333 7.64 0.00 34.88 2.83
3030 3114 6.238103 CGTGCAAGGATTATTGGTAGTAACTG 60.238 42.308 0.00 0.00 0.00 3.16
3032 3116 6.821665 TGCAAGGATTATTGGTAGTAACTGAC 59.178 38.462 0.00 0.00 0.00 3.51
3036 3120 8.554490 AGGATTATTGGTAGTAACTGACAGAT 57.446 34.615 10.08 0.00 0.00 2.90
3057 3141 7.712205 ACAGATTTATGTATTAACACCGGTACC 59.288 37.037 6.87 0.16 38.78 3.34
3066 3150 1.640917 ACACCGGTACCTGTCTCATT 58.359 50.000 6.87 0.00 0.00 2.57
3097 3181 1.689959 GCTGTTGAGCACCAAAATCG 58.310 50.000 0.00 0.00 45.46 3.34
3175 3262 6.322931 AGGGGATAAAGTTGGTGAAGAAAAT 58.677 36.000 0.00 0.00 0.00 1.82
3176 3263 6.211384 AGGGGATAAAGTTGGTGAAGAAAATG 59.789 38.462 0.00 0.00 0.00 2.32
3433 3537 2.743126 ACGAGTTGAAGGACTAGTCGAG 59.257 50.000 16.56 2.96 45.03 4.04
3434 3538 3.001414 CGAGTTGAAGGACTAGTCGAGA 58.999 50.000 16.56 0.00 45.03 4.04
3435 3539 3.181518 CGAGTTGAAGGACTAGTCGAGAC 60.182 52.174 16.56 10.25 45.03 3.36
3436 3540 4.004982 GAGTTGAAGGACTAGTCGAGACT 58.995 47.826 16.56 14.27 45.02 3.24
3437 3541 5.163281 AGTTGAAGGACTAGTCGAGACTA 57.837 43.478 16.56 11.89 42.54 2.59
3491 3595 1.733912 TGTCGACTGCAAATCTCATGC 59.266 47.619 17.92 0.00 44.08 4.06
3617 3721 0.983378 AGGGGATAACAGAGGCGCTT 60.983 55.000 7.64 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 246 1.668751 GGCGAAGAAATGCAATCGGTA 59.331 47.619 0.00 0.00 35.91 4.02
247 251 1.066002 CCGATGGCGAAGAAATGCAAT 59.934 47.619 0.00 0.00 40.82 3.56
268 272 2.450500 AGATAGGATCTGAGCTCACCCT 59.549 50.000 23.30 23.30 38.44 4.34
272 276 4.039004 GCTTTGAGATAGGATCTGAGCTCA 59.961 45.833 17.19 17.19 40.38 4.26
337 342 3.822996 CTCTCGACGTCATGTGTAAAGT 58.177 45.455 17.16 0.00 0.00 2.66
497 508 5.187186 CCCAAGGCTACTAACTAGAAGTGAA 59.813 44.000 11.27 0.00 0.00 3.18
500 511 4.466726 CACCCAAGGCTACTAACTAGAAGT 59.533 45.833 0.00 2.06 0.00 3.01
569 582 5.535030 AGAAAAACCTCTTACAAAGCGGATT 59.465 36.000 2.82 0.00 36.86 3.01
573 586 5.418310 TGAGAAAAACCTCTTACAAAGCG 57.582 39.130 0.00 0.00 34.38 4.68
611 624 3.294493 CACCCCAAACACGGCCAG 61.294 66.667 2.24 0.00 0.00 4.85
612 625 4.904590 CCACCCCAAACACGGCCA 62.905 66.667 2.24 0.00 0.00 5.36
622 635 1.491332 TCGAAAAAGTCTTCCACCCCA 59.509 47.619 0.00 0.00 0.00 4.96
623 636 2.265589 TCGAAAAAGTCTTCCACCCC 57.734 50.000 0.00 0.00 0.00 4.95
624 637 4.546570 CAAATCGAAAAAGTCTTCCACCC 58.453 43.478 0.00 0.00 0.00 4.61
625 638 3.981416 GCAAATCGAAAAAGTCTTCCACC 59.019 43.478 0.00 0.00 0.00 4.61
626 639 4.676924 CAGCAAATCGAAAAAGTCTTCCAC 59.323 41.667 0.00 0.00 0.00 4.02
627 640 4.578516 TCAGCAAATCGAAAAAGTCTTCCA 59.421 37.500 0.00 0.00 0.00 3.53
628 641 5.108385 TCAGCAAATCGAAAAAGTCTTCC 57.892 39.130 0.00 0.00 0.00 3.46
629 642 6.373779 TGATCAGCAAATCGAAAAAGTCTTC 58.626 36.000 0.00 0.00 0.00 2.87
630 643 6.317789 TGATCAGCAAATCGAAAAAGTCTT 57.682 33.333 0.00 0.00 0.00 3.01
631 644 5.947228 TGATCAGCAAATCGAAAAAGTCT 57.053 34.783 0.00 0.00 0.00 3.24
632 645 6.857964 TCTTTGATCAGCAAATCGAAAAAGTC 59.142 34.615 0.00 0.00 44.90 3.01
633 646 6.738114 TCTTTGATCAGCAAATCGAAAAAGT 58.262 32.000 0.00 0.00 44.90 2.66
634 647 6.307318 CCTCTTTGATCAGCAAATCGAAAAAG 59.693 38.462 0.00 0.00 44.90 2.27
635 648 6.151691 CCTCTTTGATCAGCAAATCGAAAAA 58.848 36.000 0.00 0.00 44.90 1.94
636 649 5.241506 ACCTCTTTGATCAGCAAATCGAAAA 59.758 36.000 0.00 0.00 44.90 2.29
637 650 4.761739 ACCTCTTTGATCAGCAAATCGAAA 59.238 37.500 0.00 0.00 44.90 3.46
638 651 4.326826 ACCTCTTTGATCAGCAAATCGAA 58.673 39.130 0.00 0.00 44.90 3.71
639 652 3.942829 ACCTCTTTGATCAGCAAATCGA 58.057 40.909 0.00 0.00 44.90 3.59
640 653 4.394300 AGAACCTCTTTGATCAGCAAATCG 59.606 41.667 0.00 0.00 44.90 3.34
641 654 5.182760 ACAGAACCTCTTTGATCAGCAAATC 59.817 40.000 0.00 0.00 44.90 2.17
642 655 5.075493 ACAGAACCTCTTTGATCAGCAAAT 58.925 37.500 0.00 0.00 44.90 2.32
643 656 4.464008 ACAGAACCTCTTTGATCAGCAAA 58.536 39.130 0.00 0.00 43.89 3.68
644 657 4.090761 ACAGAACCTCTTTGATCAGCAA 57.909 40.909 0.00 0.00 33.88 3.91
645 658 3.777106 ACAGAACCTCTTTGATCAGCA 57.223 42.857 0.00 0.00 0.00 4.41
646 659 5.241662 AGTTACAGAACCTCTTTGATCAGC 58.758 41.667 0.00 0.00 36.08 4.26
647 660 6.708054 ACAAGTTACAGAACCTCTTTGATCAG 59.292 38.462 0.00 0.00 36.08 2.90
648 661 6.591935 ACAAGTTACAGAACCTCTTTGATCA 58.408 36.000 0.00 0.00 36.08 2.92
649 662 7.873505 ACTACAAGTTACAGAACCTCTTTGATC 59.126 37.037 0.00 0.00 36.08 2.92
650 663 7.736893 ACTACAAGTTACAGAACCTCTTTGAT 58.263 34.615 0.00 0.00 36.08 2.57
651 664 7.120923 ACTACAAGTTACAGAACCTCTTTGA 57.879 36.000 0.00 0.00 36.08 2.69
652 665 6.984474 TGACTACAAGTTACAGAACCTCTTTG 59.016 38.462 0.00 0.00 36.08 2.77
653 666 7.120923 TGACTACAAGTTACAGAACCTCTTT 57.879 36.000 0.00 0.00 36.08 2.52
654 667 6.239345 CCTGACTACAAGTTACAGAACCTCTT 60.239 42.308 0.00 0.00 36.08 2.85
655 668 5.244178 CCTGACTACAAGTTACAGAACCTCT 59.756 44.000 0.00 0.00 36.08 3.69
656 669 5.010820 ACCTGACTACAAGTTACAGAACCTC 59.989 44.000 0.00 0.00 36.08 3.85
657 670 4.900054 ACCTGACTACAAGTTACAGAACCT 59.100 41.667 0.00 0.00 36.08 3.50
658 671 5.010820 AGACCTGACTACAAGTTACAGAACC 59.989 44.000 0.00 0.00 36.08 3.62
659 672 6.086785 AGACCTGACTACAAGTTACAGAAC 57.913 41.667 0.00 0.00 35.64 3.01
660 673 6.462487 CCAAGACCTGACTACAAGTTACAGAA 60.462 42.308 0.00 0.00 0.00 3.02
661 674 5.010719 CCAAGACCTGACTACAAGTTACAGA 59.989 44.000 0.00 0.00 0.00 3.41
662 675 5.010719 TCCAAGACCTGACTACAAGTTACAG 59.989 44.000 0.00 0.00 0.00 2.74
663 676 4.897076 TCCAAGACCTGACTACAAGTTACA 59.103 41.667 0.00 0.00 0.00 2.41
664 677 5.464030 TCCAAGACCTGACTACAAGTTAC 57.536 43.478 0.00 0.00 0.00 2.50
665 678 6.681729 ATTCCAAGACCTGACTACAAGTTA 57.318 37.500 0.00 0.00 0.00 2.24
666 679 5.568620 ATTCCAAGACCTGACTACAAGTT 57.431 39.130 0.00 0.00 0.00 2.66
667 680 5.071788 TCAATTCCAAGACCTGACTACAAGT 59.928 40.000 0.00 0.00 0.00 3.16
668 681 5.551233 TCAATTCCAAGACCTGACTACAAG 58.449 41.667 0.00 0.00 0.00 3.16
669 682 5.306937 TCTCAATTCCAAGACCTGACTACAA 59.693 40.000 0.00 0.00 0.00 2.41
670 683 4.838423 TCTCAATTCCAAGACCTGACTACA 59.162 41.667 0.00 0.00 0.00 2.74
671 684 5.407407 TCTCAATTCCAAGACCTGACTAC 57.593 43.478 0.00 0.00 0.00 2.73
672 685 7.921041 ATATCTCAATTCCAAGACCTGACTA 57.079 36.000 0.00 0.00 0.00 2.59
673 686 6.821616 ATATCTCAATTCCAAGACCTGACT 57.178 37.500 0.00 0.00 0.00 3.41
674 687 7.872113 AAATATCTCAATTCCAAGACCTGAC 57.128 36.000 0.00 0.00 0.00 3.51
675 688 8.742777 CAAAAATATCTCAATTCCAAGACCTGA 58.257 33.333 0.00 0.00 0.00 3.86
676 689 8.526147 ACAAAAATATCTCAATTCCAAGACCTG 58.474 33.333 0.00 0.00 0.00 4.00
677 690 8.655935 ACAAAAATATCTCAATTCCAAGACCT 57.344 30.769 0.00 0.00 0.00 3.85
678 691 9.710900 AAACAAAAATATCTCAATTCCAAGACC 57.289 29.630 0.00 0.00 0.00 3.85
680 693 9.709495 CCAAACAAAAATATCTCAATTCCAAGA 57.291 29.630 0.00 0.00 0.00 3.02
681 694 8.938906 CCCAAACAAAAATATCTCAATTCCAAG 58.061 33.333 0.00 0.00 0.00 3.61
682 695 8.654997 TCCCAAACAAAAATATCTCAATTCCAA 58.345 29.630 0.00 0.00 0.00 3.53
683 696 8.093927 GTCCCAAACAAAAATATCTCAATTCCA 58.906 33.333 0.00 0.00 0.00 3.53
684 697 8.093927 TGTCCCAAACAAAAATATCTCAATTCC 58.906 33.333 0.00 0.00 34.03 3.01
685 698 8.925700 GTGTCCCAAACAAAAATATCTCAATTC 58.074 33.333 0.00 0.00 40.31 2.17
686 699 8.428063 TGTGTCCCAAACAAAAATATCTCAATT 58.572 29.630 0.00 0.00 40.31 2.32
687 700 7.961351 TGTGTCCCAAACAAAAATATCTCAAT 58.039 30.769 0.00 0.00 40.31 2.57
688 701 7.069331 ACTGTGTCCCAAACAAAAATATCTCAA 59.931 33.333 0.00 0.00 40.31 3.02
689 702 6.549364 ACTGTGTCCCAAACAAAAATATCTCA 59.451 34.615 0.00 0.00 40.31 3.27
690 703 6.981722 ACTGTGTCCCAAACAAAAATATCTC 58.018 36.000 0.00 0.00 40.31 2.75
691 704 6.976934 ACTGTGTCCCAAACAAAAATATCT 57.023 33.333 0.00 0.00 40.31 1.98
692 705 7.807907 CACTACTGTGTCCCAAACAAAAATATC 59.192 37.037 0.00 0.00 40.31 1.63
693 706 7.657336 CACTACTGTGTCCCAAACAAAAATAT 58.343 34.615 0.00 0.00 40.31 1.28
694 707 7.033530 CACTACTGTGTCCCAAACAAAAATA 57.966 36.000 0.00 0.00 40.31 1.40
695 708 5.901552 CACTACTGTGTCCCAAACAAAAAT 58.098 37.500 0.00 0.00 40.31 1.82
696 709 5.317733 CACTACTGTGTCCCAAACAAAAA 57.682 39.130 0.00 0.00 40.31 1.94
697 710 4.974368 CACTACTGTGTCCCAAACAAAA 57.026 40.909 0.00 0.00 40.31 2.44
724 737 1.704641 GCCCCAAGAGTGACCTTTTT 58.295 50.000 0.00 0.00 0.00 1.94
725 738 0.178961 GGCCCCAAGAGTGACCTTTT 60.179 55.000 0.00 0.00 0.00 2.27
726 739 1.068352 AGGCCCCAAGAGTGACCTTT 61.068 55.000 0.00 0.00 0.00 3.11
727 740 1.068352 AAGGCCCCAAGAGTGACCTT 61.068 55.000 0.00 0.00 31.38 3.50
728 741 1.464198 AAGGCCCCAAGAGTGACCT 60.464 57.895 0.00 0.00 0.00 3.85
729 742 1.002011 GAAGGCCCCAAGAGTGACC 60.002 63.158 0.00 0.00 0.00 4.02
730 743 1.376037 CGAAGGCCCCAAGAGTGAC 60.376 63.158 0.00 0.00 0.00 3.67
731 744 3.068881 CGAAGGCCCCAAGAGTGA 58.931 61.111 0.00 0.00 0.00 3.41
732 745 2.747855 GCGAAGGCCCCAAGAGTG 60.748 66.667 0.00 0.00 0.00 3.51
733 746 4.394712 CGCGAAGGCCCCAAGAGT 62.395 66.667 0.00 0.00 35.02 3.24
734 747 4.394712 ACGCGAAGGCCCCAAGAG 62.395 66.667 15.93 0.00 35.02 2.85
735 748 4.388499 GACGCGAAGGCCCCAAGA 62.388 66.667 15.93 0.00 35.02 3.02
827 846 4.493747 CGCGACGAGGGGGTTCTC 62.494 72.222 0.00 0.00 0.00 2.87
829 848 4.368543 AACGCGACGAGGGGGTTC 62.369 66.667 15.93 0.00 35.96 3.62
830 849 4.368543 GAACGCGACGAGGGGGTT 62.369 66.667 15.93 0.00 42.35 4.11
1260 1305 2.883253 GCGAGCGACTTGAGGAGC 60.883 66.667 0.00 0.00 0.00 4.70
1550 1609 3.555324 TGGCGCTCCAGGACACAA 61.555 61.111 7.64 0.00 37.47 3.33
1707 1772 2.162906 ATGCACCCACTTCCCCTGT 61.163 57.895 0.00 0.00 0.00 4.00
1903 1968 3.924144 AGAAGAGTGTCAATGAGTCTGC 58.076 45.455 0.00 0.00 0.00 4.26
2031 2096 2.092753 ACCATAGTTGCTCACCATGGAG 60.093 50.000 21.47 11.61 38.77 3.86
2157 2228 1.423161 GCTCCCCAGATTAAGGCATCT 59.577 52.381 0.00 0.00 33.44 2.90
2228 2299 5.991606 TCCAATTCGATCCAGTGCTTTATAG 59.008 40.000 0.00 0.00 0.00 1.31
2244 2315 2.554032 ACTTTTGTCTGGCTCCAATTCG 59.446 45.455 0.00 0.00 0.00 3.34
2332 2408 0.174845 TTCTCACGCATTAGGTCCCG 59.825 55.000 0.00 0.00 0.00 5.14
2335 2411 1.480954 TCCCTTCTCACGCATTAGGTC 59.519 52.381 0.00 0.00 0.00 3.85
2490 2566 0.608640 CAGGCACGTAACCTTCCTCT 59.391 55.000 6.57 0.00 34.42 3.69
2796 2874 6.182507 TGAGACCAAGTACCACTGTTAATT 57.817 37.500 0.00 0.00 0.00 1.40
2856 2935 7.283580 TCATGCATCACTGATGTATCATGAAAA 59.716 33.333 24.28 12.17 41.91 2.29
2873 2952 1.227060 CGCCTCGACTCATGCATCA 60.227 57.895 0.00 0.00 0.00 3.07
2885 2964 2.004583 TCACCAACTTTATCGCCTCG 57.995 50.000 0.00 0.00 0.00 4.63
2968 3052 7.884816 TTTTAAACAAATGGAAACGTGTTCA 57.115 28.000 0.00 0.00 33.07 3.18
2987 3071 3.971150 CACGAACAGGTGCCATTTTTAA 58.029 40.909 0.00 0.00 0.00 1.52
3010 3094 8.375493 TCTGTCAGTTACTACCAATAATCCTT 57.625 34.615 0.00 0.00 0.00 3.36
3030 3114 7.781548 ACCGGTGTTAATACATAAATCTGTC 57.218 36.000 6.12 0.00 36.50 3.51
3032 3116 7.929785 AGGTACCGGTGTTAATACATAAATCTG 59.070 37.037 19.93 0.00 36.50 2.90
3036 3120 6.945218 ACAGGTACCGGTGTTAATACATAAA 58.055 36.000 19.93 0.00 36.50 1.40
3050 3134 4.082679 GCTCTATAATGAGACAGGTACCGG 60.083 50.000 10.83 10.83 36.23 5.28
3057 3141 4.252073 GCCCATGCTCTATAATGAGACAG 58.748 47.826 0.00 0.00 36.23 3.51
3095 3179 4.709886 TGGGAGTATGATGAAAGAGTTCGA 59.290 41.667 0.00 0.00 36.46 3.71
3096 3180 5.011090 TGGGAGTATGATGAAAGAGTTCG 57.989 43.478 0.00 0.00 36.46 3.95
3097 3181 7.687941 TTTTGGGAGTATGATGAAAGAGTTC 57.312 36.000 0.00 0.00 0.00 3.01
3438 3542 4.150980 CGACTCATAGACTAGTCCATCGAC 59.849 50.000 19.38 4.78 39.16 4.20
3439 3543 4.308265 CGACTCATAGACTAGTCCATCGA 58.692 47.826 19.38 9.95 39.16 3.59
3440 3544 3.120477 GCGACTCATAGACTAGTCCATCG 60.120 52.174 19.38 17.89 39.16 3.84
3441 3545 3.815962 TGCGACTCATAGACTAGTCCATC 59.184 47.826 19.38 7.28 39.16 3.51
3442 3546 3.566322 GTGCGACTCATAGACTAGTCCAT 59.434 47.826 19.38 8.73 39.16 3.41
3617 3721 4.056125 CGACAGGCTCGCAGACCA 62.056 66.667 0.00 0.00 35.06 4.02


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

AutoCloner maintained by Alex Coulton.