Multiple sequence alignment - TraesCS7D01G265900

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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 TraesCS7D01G265900 chr7D 100.000 2159 0 0 1 2159 247883080 247885238 0.000000e+00 3988.0
1 TraesCS7D01G265900 chr7D 95.717 1471 53 6 697 2159 248466116 248467584 0.000000e+00 2359.0
2 TraesCS7D01G265900 chr7D 100.000 475 0 0 2593 3067 247885672 247886146 0.000000e+00 878.0
3 TraesCS7D01G265900 chr7D 80.962 520 70 20 9 516 102629098 102628596 4.800000e-103 385.0
4 TraesCS7D01G265900 chr7D 91.176 204 8 5 2593 2793 248467613 248467809 5.040000e-68 268.0
5 TraesCS7D01G265900 chr7D 92.593 108 4 3 2940 3046 248468076 248468180 5.300000e-33 152.0
6 TraesCS7D01G265900 chr7D 95.652 46 2 0 2956 3001 247885978 247886023 1.180000e-09 75.0
7 TraesCS7D01G265900 chr7D 95.652 46 2 0 2899 2944 247886035 247886080 1.180000e-09 75.0
8 TraesCS7D01G265900 chr7D 95.652 46 2 0 2899 2944 248468092 248468137 1.180000e-09 75.0
9 TraesCS7D01G265900 chr7A 94.644 1419 64 6 691 2102 265501726 265503139 0.000000e+00 2189.0
10 TraesCS7D01G265900 chr7A 94.683 1373 54 11 805 2159 265926559 265927930 0.000000e+00 2113.0
11 TraesCS7D01G265900 chr7A 93.231 458 18 7 2593 3046 265503207 265503655 0.000000e+00 662.0
12 TraesCS7D01G265900 chr7A 96.178 157 1 4 2593 2746 265927962 265928116 5.080000e-63 252.0
13 TraesCS7D01G265900 chr7A 91.509 106 4 4 2941 3046 265928297 265928397 1.150000e-29 141.0
14 TraesCS7D01G265900 chr7B 95.200 1375 46 10 805 2159 225507322 225508696 0.000000e+00 2156.0
15 TraesCS7D01G265900 chr7B 95.062 1377 46 12 805 2159 225390299 225391675 0.000000e+00 2146.0
16 TraesCS7D01G265900 chr7B 90.391 281 19 8 1 278 290068772 290069047 2.250000e-96 363.0
17 TraesCS7D01G265900 chr7B 93.229 192 7 4 2855 3046 225391882 225392067 8.380000e-71 278.0
18 TraesCS7D01G265900 chr7B 92.188 192 9 4 2855 3046 225508903 225509088 1.810000e-67 267.0
19 TraesCS7D01G265900 chr7B 93.605 172 5 4 2593 2760 225391704 225391873 5.080000e-63 252.0
20 TraesCS7D01G265900 chr7B 93.605 172 5 4 2593 2760 225508725 225508894 5.080000e-63 252.0
21 TraesCS7D01G265900 chr7B 93.204 103 2 4 2944 3046 225509149 225509246 2.460000e-31 147.0
22 TraesCS7D01G265900 chr7B 91.262 103 4 4 2944 3046 225392128 225392225 5.330000e-28 135.0
23 TraesCS7D01G265900 chr7B 97.826 46 1 0 2899 2944 225391983 225392028 2.540000e-11 80.5
24 TraesCS7D01G265900 chr7B 97.826 46 1 0 2899 2944 225392140 225392185 2.540000e-11 80.5
25 TraesCS7D01G265900 chr7B 97.826 46 1 0 2899 2944 225509004 225509049 2.540000e-11 80.5
26 TraesCS7D01G265900 chr7B 97.826 46 1 0 2899 2944 225509161 225509206 2.540000e-11 80.5
27 TraesCS7D01G265900 chrUn 98.082 417 8 0 937 1353 477095380 477094964 0.000000e+00 726.0
28 TraesCS7D01G265900 chrUn 77.551 343 61 13 284 617 30701837 30702172 3.120000e-45 193.0
29 TraesCS7D01G265900 chr2B 83.231 650 91 12 3 644 599200991 599201630 5.700000e-162 580.0
30 TraesCS7D01G265900 chr2B 84.014 588 65 18 1 578 233561850 233561282 3.480000e-149 538.0
31 TraesCS7D01G265900 chr2B 90.282 319 26 4 1 317 317251075 317251390 2.200000e-111 412.0
32 TraesCS7D01G265900 chr2B 88.344 326 29 8 1 322 237157751 237158071 1.730000e-102 383.0
33 TraesCS7D01G265900 chr2B 83.133 83 11 3 2729 2809 800419179 800419260 4.240000e-09 73.1
34 TraesCS7D01G265900 chr4B 82.317 656 83 24 1 643 87615911 87616546 3.480000e-149 538.0
35 TraesCS7D01G265900 chr4D 82.464 633 88 15 1 625 328074027 328074644 1.620000e-147 532.0
36 TraesCS7D01G265900 chr4D 85.714 70 10 0 386 455 13213962 13214031 1.180000e-09 75.0
37 TraesCS7D01G265900 chr3B 85.084 476 55 13 1 472 623638775 623638312 3.580000e-129 472.0
38 TraesCS7D01G265900 chr3A 92.500 80 4 2 2732 2809 491189505 491189426 2.500000e-21 113.0
39 TraesCS7D01G265900 chr3D 91.667 72 6 0 2733 2804 327568894 327568965 1.950000e-17 100.0
40 TraesCS7D01G265900 chr3D 85.227 88 9 3 2725 2810 565081591 565081506 1.510000e-13 87.9
41 TraesCS7D01G265900 chr6A 86.747 83 5 6 2729 2809 530600117 530600195 1.510000e-13 87.9
42 TraesCS7D01G265900 chr1B 85.882 85 9 3 2731 2812 211325039 211324955 1.510000e-13 87.9
43 TraesCS7D01G265900 chr1A 87.143 70 6 3 2732 2799 494443766 494443698 3.280000e-10 76.8
44 TraesCS7D01G265900 chr6D 100.000 30 0 0 389 418 36618655 36618626 4.270000e-04 56.5
45 TraesCS7D01G265900 chr6D 100.000 30 0 0 389 418 463780213 463780184 4.270000e-04 56.5


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 TraesCS7D01G265900 chr7D 247883080 247886146 3066 False 1254.000000 3988 97.826000 1 3067 4 chr7D.!!$F1 3066
1 TraesCS7D01G265900 chr7D 248466116 248468180 2064 False 713.500000 2359 93.784500 697 3046 4 chr7D.!!$F2 2349
2 TraesCS7D01G265900 chr7D 102628596 102629098 502 True 385.000000 385 80.962000 9 516 1 chr7D.!!$R1 507
3 TraesCS7D01G265900 chr7A 265501726 265503655 1929 False 1425.500000 2189 93.937500 691 3046 2 chr7A.!!$F1 2355
4 TraesCS7D01G265900 chr7A 265926559 265928397 1838 False 835.333333 2113 94.123333 805 3046 3 chr7A.!!$F2 2241
5 TraesCS7D01G265900 chr7B 225507322 225509246 1924 False 497.166667 2156 94.974833 805 3046 6 chr7B.!!$F3 2241
6 TraesCS7D01G265900 chr7B 225390299 225392225 1926 False 495.333333 2146 94.801667 805 3046 6 chr7B.!!$F2 2241
7 TraesCS7D01G265900 chr2B 599200991 599201630 639 False 580.000000 580 83.231000 3 644 1 chr2B.!!$F3 641
8 TraesCS7D01G265900 chr2B 233561282 233561850 568 True 538.000000 538 84.014000 1 578 1 chr2B.!!$R1 577
9 TraesCS7D01G265900 chr4B 87615911 87616546 635 False 538.000000 538 82.317000 1 643 1 chr4B.!!$F1 642
10 TraesCS7D01G265900 chr4D 328074027 328074644 617 False 532.000000 532 82.464000 1 625 1 chr4D.!!$F2 624

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
517 535 0.101040 CCGTTACACCTATCGCCGAA 59.899 55.0 0.0 0.0 0.00 4.30 F
545 567 0.108138 AGGGTGTGTGAAGCTATCGC 60.108 55.0 0.0 0.0 39.09 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1627 0.244994 GCTTCTCGAACAGCTCCTGA 59.755 55.0 8.02 0.0 35.18 3.86 R
2117 2191 0.257328 TGCTCCCTGTGTTGAAACCA 59.743 50.0 0.00 0.0 0.00 3.67 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
176 183 4.959723 ACATGATTCCAACCAACCAAAAG 58.040 39.130 0.00 0.00 0.00 2.27
177 184 4.653341 ACATGATTCCAACCAACCAAAAGA 59.347 37.500 0.00 0.00 0.00 2.52
182 189 2.023888 TCCAACCAACCAAAAGAAGGGA 60.024 45.455 0.00 0.00 0.00 4.20
183 190 2.365293 CCAACCAACCAAAAGAAGGGAG 59.635 50.000 0.00 0.00 0.00 4.30
185 192 3.680777 ACCAACCAAAAGAAGGGAGAA 57.319 42.857 0.00 0.00 0.00 2.87
188 195 3.259123 CCAACCAAAAGAAGGGAGAATGG 59.741 47.826 0.00 0.00 0.00 3.16
260 267 5.563592 TCAAGCAAATGAGAGAGATTTGGA 58.436 37.500 0.00 0.00 39.97 3.53
291 304 1.093408 TGAGGAAGAGAGGGGGAGAA 58.907 55.000 0.00 0.00 0.00 2.87
322 335 1.573108 GGGTGAGTGGAGGAGAATGA 58.427 55.000 0.00 0.00 0.00 2.57
326 339 0.467804 GAGTGGAGGAGAATGAGGGC 59.532 60.000 0.00 0.00 0.00 5.19
329 342 0.399091 TGGAGGAGAATGAGGGCGAT 60.399 55.000 0.00 0.00 0.00 4.58
339 352 0.888736 TGAGGGCGATTGGTTGTGTG 60.889 55.000 0.00 0.00 0.00 3.82
340 353 1.586154 GAGGGCGATTGGTTGTGTGG 61.586 60.000 0.00 0.00 0.00 4.17
341 354 2.635443 GGGCGATTGGTTGTGTGGG 61.635 63.158 0.00 0.00 0.00 4.61
342 355 2.635443 GGCGATTGGTTGTGTGGGG 61.635 63.158 0.00 0.00 0.00 4.96
343 356 1.901464 GCGATTGGTTGTGTGGGGT 60.901 57.895 0.00 0.00 0.00 4.95
344 357 1.956043 CGATTGGTTGTGTGGGGTG 59.044 57.895 0.00 0.00 0.00 4.61
388 406 2.419673 CACAATCTTATCCACTGCGCAA 59.580 45.455 13.05 0.00 0.00 4.85
436 454 0.109226 GCCTAATAGAGCCTACCGCG 60.109 60.000 0.00 0.00 44.76 6.46
476 494 0.517316 CCTTTGCCTCGTTAGCACAC 59.483 55.000 0.00 0.00 40.69 3.82
517 535 0.101040 CCGTTACACCTATCGCCGAA 59.899 55.000 0.00 0.00 0.00 4.30
519 537 1.064505 CGTTACACCTATCGCCGAAGA 59.935 52.381 0.00 0.00 0.00 2.87
522 540 0.968901 ACACCTATCGCCGAAGACCA 60.969 55.000 0.00 0.00 0.00 4.02
535 557 2.699954 GAAGACCATGTAGGGTGTGTG 58.300 52.381 0.00 0.00 42.53 3.82
542 564 3.118261 CCATGTAGGGTGTGTGAAGCTAT 60.118 47.826 0.00 0.00 0.00 2.97
545 567 0.108138 AGGGTGTGTGAAGCTATCGC 60.108 55.000 0.00 0.00 39.09 4.58
548 570 0.457853 GTGTGTGAAGCTATCGCCGA 60.458 55.000 0.00 0.00 37.78 5.54
554 576 1.236628 GAAGCTATCGCCGAGGACTA 58.763 55.000 0.00 0.00 36.60 2.59
560 582 0.955178 ATCGCCGAGGACTATGACAG 59.045 55.000 0.00 0.00 0.00 3.51
567 589 3.489398 CCGAGGACTATGACAGTAGCAAC 60.489 52.174 0.00 0.00 37.72 4.17
569 591 4.380550 CGAGGACTATGACAGTAGCAACAA 60.381 45.833 0.00 0.00 37.72 2.83
578 601 3.579709 ACAGTAGCAACAAGTCAGATCG 58.420 45.455 0.00 0.00 0.00 3.69
579 602 2.926200 CAGTAGCAACAAGTCAGATCGG 59.074 50.000 0.00 0.00 0.00 4.18
586 609 4.201822 GCAACAAGTCAGATCGGGAAATAC 60.202 45.833 0.00 0.00 0.00 1.89
590 613 5.875359 ACAAGTCAGATCGGGAAATACTTTC 59.125 40.000 0.00 0.00 38.94 2.62
591 614 5.677319 AGTCAGATCGGGAAATACTTTCA 57.323 39.130 2.39 0.00 41.43 2.69
592 615 5.665459 AGTCAGATCGGGAAATACTTTCAG 58.335 41.667 2.39 0.00 41.43 3.02
594 617 6.098982 AGTCAGATCGGGAAATACTTTCAGAT 59.901 38.462 8.53 8.53 41.43 2.90
595 618 6.201806 GTCAGATCGGGAAATACTTTCAGATG 59.798 42.308 11.74 4.39 41.43 2.90
596 619 6.098266 TCAGATCGGGAAATACTTTCAGATGA 59.902 38.462 11.74 5.95 41.43 2.92
598 621 7.280876 CAGATCGGGAAATACTTTCAGATGAAA 59.719 37.037 7.71 7.71 41.43 2.69
648 674 7.686438 AAATCAAACCATTAAATTTGGCTCC 57.314 32.000 0.00 0.00 37.81 4.70
649 675 4.815269 TCAAACCATTAAATTTGGCTCCG 58.185 39.130 0.00 0.00 37.81 4.63
650 676 4.282195 TCAAACCATTAAATTTGGCTCCGT 59.718 37.500 0.00 0.00 37.81 4.69
651 677 3.866883 ACCATTAAATTTGGCTCCGTG 57.133 42.857 0.00 0.00 37.81 4.94
652 678 3.161866 ACCATTAAATTTGGCTCCGTGT 58.838 40.909 0.00 0.00 37.81 4.49
653 679 4.337145 ACCATTAAATTTGGCTCCGTGTA 58.663 39.130 0.00 0.00 37.81 2.90
654 680 4.398044 ACCATTAAATTTGGCTCCGTGTAG 59.602 41.667 0.00 0.00 37.81 2.74
655 681 4.398044 CCATTAAATTTGGCTCCGTGTAGT 59.602 41.667 0.00 0.00 0.00 2.73
656 682 5.587043 CCATTAAATTTGGCTCCGTGTAGTA 59.413 40.000 0.00 0.00 0.00 1.82
657 683 6.262273 CCATTAAATTTGGCTCCGTGTAGTAT 59.738 38.462 0.00 0.00 0.00 2.12
658 684 7.442969 CCATTAAATTTGGCTCCGTGTAGTATA 59.557 37.037 0.00 0.00 0.00 1.47
659 685 8.495949 CATTAAATTTGGCTCCGTGTAGTATAG 58.504 37.037 0.00 0.00 0.00 1.31
660 686 4.602340 ATTTGGCTCCGTGTAGTATAGG 57.398 45.455 0.00 0.00 0.00 2.57
661 687 1.325355 TGGCTCCGTGTAGTATAGGC 58.675 55.000 0.00 0.00 0.00 3.93
662 688 0.602060 GGCTCCGTGTAGTATAGGCC 59.398 60.000 0.00 0.00 0.00 5.19
663 689 1.325355 GCTCCGTGTAGTATAGGCCA 58.675 55.000 5.01 0.00 0.00 5.36
664 690 1.893801 GCTCCGTGTAGTATAGGCCAT 59.106 52.381 5.01 0.00 0.00 4.40
665 691 2.352814 GCTCCGTGTAGTATAGGCCATG 60.353 54.545 5.01 0.00 0.00 3.66
666 692 1.616865 TCCGTGTAGTATAGGCCATGC 59.383 52.381 5.01 0.00 0.00 4.06
667 693 1.618837 CCGTGTAGTATAGGCCATGCT 59.381 52.381 5.01 8.23 33.66 3.79
668 694 2.352814 CCGTGTAGTATAGGCCATGCTC 60.353 54.545 5.01 1.54 31.32 4.26
669 695 2.558795 CGTGTAGTATAGGCCATGCTCT 59.441 50.000 5.01 0.00 31.32 4.09
670 696 3.612717 CGTGTAGTATAGGCCATGCTCTG 60.613 52.174 5.01 0.00 31.32 3.35
671 697 3.574396 GTGTAGTATAGGCCATGCTCTGA 59.426 47.826 5.01 0.00 31.32 3.27
672 698 4.039245 GTGTAGTATAGGCCATGCTCTGAA 59.961 45.833 5.01 0.00 31.32 3.02
673 699 4.840680 TGTAGTATAGGCCATGCTCTGAAT 59.159 41.667 5.01 0.00 31.32 2.57
674 700 4.283363 AGTATAGGCCATGCTCTGAATG 57.717 45.455 5.01 0.00 0.00 2.67
675 701 1.906990 ATAGGCCATGCTCTGAATGC 58.093 50.000 5.01 0.00 0.00 3.56
676 702 0.841961 TAGGCCATGCTCTGAATGCT 59.158 50.000 5.01 0.00 0.00 3.79
677 703 0.841961 AGGCCATGCTCTGAATGCTA 59.158 50.000 5.01 0.00 0.00 3.49
678 704 1.424302 AGGCCATGCTCTGAATGCTAT 59.576 47.619 5.01 0.00 0.00 2.97
679 705 1.540267 GGCCATGCTCTGAATGCTATG 59.460 52.381 0.00 0.00 0.00 2.23
680 706 1.540267 GCCATGCTCTGAATGCTATGG 59.460 52.381 12.05 12.05 39.62 2.74
681 707 2.812983 GCCATGCTCTGAATGCTATGGA 60.813 50.000 16.82 0.00 39.31 3.41
682 708 2.812591 CCATGCTCTGAATGCTATGGAC 59.187 50.000 11.44 0.00 39.31 4.02
683 709 3.473625 CATGCTCTGAATGCTATGGACA 58.526 45.455 0.00 0.00 0.00 4.02
684 710 2.910199 TGCTCTGAATGCTATGGACAC 58.090 47.619 0.00 0.00 0.00 3.67
685 711 1.863454 GCTCTGAATGCTATGGACACG 59.137 52.381 0.00 0.00 0.00 4.49
686 712 2.739932 GCTCTGAATGCTATGGACACGT 60.740 50.000 0.00 0.00 0.00 4.49
687 713 2.862536 CTCTGAATGCTATGGACACGTG 59.137 50.000 15.48 15.48 0.00 4.49
688 714 2.495669 TCTGAATGCTATGGACACGTGA 59.504 45.455 25.01 0.00 0.00 4.35
689 715 2.604914 CTGAATGCTATGGACACGTGAC 59.395 50.000 25.01 16.95 0.00 3.67
693 719 1.940883 GCTATGGACACGTGACCGGA 61.941 60.000 27.55 18.35 38.78 5.14
706 732 2.548480 GTGACCGGAAAGAAGACAAAGG 59.452 50.000 9.46 0.00 0.00 3.11
755 781 3.175710 AAAGCGGTGGGTGGTCCT 61.176 61.111 0.00 0.00 36.20 3.85
803 829 3.211963 GCCGATGCAGCCCGATTT 61.212 61.111 0.00 0.00 37.47 2.17
889 923 4.526262 CACACATCCCCAAGAATAAAACCA 59.474 41.667 0.00 0.00 0.00 3.67
1086 1123 4.292178 GAGCAGGCGGGGATCTCG 62.292 72.222 0.00 0.00 0.00 4.04
1560 1597 1.068588 GGCACCTACGATGCAGTGATA 59.931 52.381 5.76 0.00 45.27 2.15
1584 1621 2.599677 GATTCCTCCGATCCAGTAGGT 58.400 52.381 0.00 0.00 35.89 3.08
1590 1627 0.757188 CCGATCCAGTAGGTCCTGCT 60.757 60.000 3.18 3.18 35.89 4.24
1764 1801 2.042686 ACTACGCATGGACTACGGTA 57.957 50.000 0.00 0.00 0.00 4.02
1786 1823 0.108520 CACATACCCAAGGTACGCGT 60.109 55.000 19.17 19.17 41.31 6.01
1825 1863 1.967779 TGTGATCGAACTGGGTTCTCA 59.032 47.619 8.46 4.21 40.05 3.27
1845 1895 6.299141 TCTCATTTCTTTAGCCACTGAGTTT 58.701 36.000 0.00 0.00 32.49 2.66
1846 1896 7.450074 TCTCATTTCTTTAGCCACTGAGTTTA 58.550 34.615 0.00 0.00 32.49 2.01
1854 1904 9.905713 TCTTTAGCCACTGAGTTTATATGATTT 57.094 29.630 0.00 0.00 0.00 2.17
1861 1911 9.927668 CCACTGAGTTTATATGATTTTTGGTTT 57.072 29.630 0.00 0.00 0.00 3.27
1901 1951 0.807496 GTTTCATGCTCTGCTCCACC 59.193 55.000 0.00 0.00 0.00 4.61
1978 2028 0.189574 TCCACAAAATCCAAGGGGCA 59.810 50.000 0.00 0.00 0.00 5.36
2102 2176 1.067060 GTCACTGAAACCAAGGCCAAC 59.933 52.381 5.01 0.00 0.00 3.77
2103 2177 1.064017 TCACTGAAACCAAGGCCAACT 60.064 47.619 5.01 0.00 0.00 3.16
2104 2178 2.173782 TCACTGAAACCAAGGCCAACTA 59.826 45.455 5.01 0.00 0.00 2.24
2105 2179 2.554032 CACTGAAACCAAGGCCAACTAG 59.446 50.000 5.01 0.00 0.00 2.57
2106 2180 2.441750 ACTGAAACCAAGGCCAACTAGA 59.558 45.455 5.01 0.00 0.00 2.43
2107 2181 3.117663 ACTGAAACCAAGGCCAACTAGAA 60.118 43.478 5.01 0.00 0.00 2.10
2108 2182 3.486383 TGAAACCAAGGCCAACTAGAAG 58.514 45.455 5.01 0.00 0.00 2.85
2109 2183 3.137544 TGAAACCAAGGCCAACTAGAAGA 59.862 43.478 5.01 0.00 0.00 2.87
2110 2184 3.425162 AACCAAGGCCAACTAGAAGAG 57.575 47.619 5.01 0.00 0.00 2.85
2111 2185 1.003696 ACCAAGGCCAACTAGAAGAGC 59.996 52.381 5.01 0.00 0.00 4.09
2112 2186 1.280421 CCAAGGCCAACTAGAAGAGCT 59.720 52.381 5.01 0.00 0.00 4.09
2113 2187 2.354259 CAAGGCCAACTAGAAGAGCTG 58.646 52.381 5.01 0.00 0.00 4.24
2114 2188 0.908198 AGGCCAACTAGAAGAGCTGG 59.092 55.000 5.01 0.00 0.00 4.85
2115 2189 0.615850 GGCCAACTAGAAGAGCTGGT 59.384 55.000 0.00 0.00 40.42 4.00
2117 2191 2.553247 GGCCAACTAGAAGAGCTGGTTT 60.553 50.000 0.00 0.00 44.80 3.27
2118 2192 2.485814 GCCAACTAGAAGAGCTGGTTTG 59.514 50.000 0.00 0.00 44.80 2.93
2119 2193 3.077359 CCAACTAGAAGAGCTGGTTTGG 58.923 50.000 0.00 0.00 44.80 3.28
2129 2203 2.165437 GAGCTGGTTTGGTTTCAACACA 59.835 45.455 0.00 0.00 31.78 3.72
2631 2705 7.630242 AATTATTGGTACCTGTGATTCTGTG 57.370 36.000 14.36 0.00 0.00 3.66
2843 2921 3.602946 CGAACGAAGCGAGCAGTTTTTAA 60.603 43.478 0.00 0.00 0.00 1.52
2846 2924 3.250040 ACGAAGCGAGCAGTTTTTAATGT 59.750 39.130 0.00 0.00 0.00 2.71
2852 2930 6.677913 AGCGAGCAGTTTTTAATGTGTTTAT 58.322 32.000 0.00 0.00 0.00 1.40
2853 2931 7.812648 AGCGAGCAGTTTTTAATGTGTTTATA 58.187 30.769 0.00 0.00 0.00 0.98
2854 2932 8.458843 AGCGAGCAGTTTTTAATGTGTTTATAT 58.541 29.630 0.00 0.00 0.00 0.86
2855 2933 9.710979 GCGAGCAGTTTTTAATGTGTTTATATA 57.289 29.630 0.00 0.00 0.00 0.86
2949 3170 7.660617 TGGACACAACACGGTTAGATTAAATTA 59.339 33.333 0.00 0.00 0.00 1.40
3059 3436 9.243105 AGTATATGCTTGTTACATCAAAAAGGT 57.757 29.630 0.00 0.00 0.00 3.50
3060 3437 9.289303 GTATATGCTTGTTACATCAAAAAGGTG 57.711 33.333 0.00 0.00 0.00 4.00
3061 3438 5.843673 TGCTTGTTACATCAAAAAGGTGA 57.156 34.783 0.00 0.00 0.00 4.02
3062 3439 5.587289 TGCTTGTTACATCAAAAAGGTGAC 58.413 37.500 0.00 0.00 0.00 3.67
3063 3440 4.982295 GCTTGTTACATCAAAAAGGTGACC 59.018 41.667 0.00 0.00 0.00 4.02
3064 3441 5.451242 GCTTGTTACATCAAAAAGGTGACCA 60.451 40.000 3.63 0.00 0.00 4.02
3065 3442 5.508200 TGTTACATCAAAAAGGTGACCAC 57.492 39.130 3.63 0.00 0.00 4.16
3066 3443 5.197451 TGTTACATCAAAAAGGTGACCACT 58.803 37.500 3.63 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 83 9.407380 TGTGGTAAAATCAAGTTATATGATGCT 57.593 29.630 0.00 0.00 37.58 3.79
89 95 7.866898 TCATCATTGTGTTGTGGTAAAATCAAG 59.133 33.333 0.00 0.00 0.00 3.02
97 103 5.937540 CCTAGTTCATCATTGTGTTGTGGTA 59.062 40.000 0.00 0.00 0.00 3.25
176 183 1.886422 ACCTCTCCCATTCTCCCTTC 58.114 55.000 0.00 0.00 0.00 3.46
177 184 2.629909 GGTACCTCTCCCATTCTCCCTT 60.630 54.545 4.06 0.00 0.00 3.95
182 189 2.482494 CCAAGGTACCTCTCCCATTCT 58.518 52.381 16.64 0.00 0.00 2.40
183 190 1.490910 CCCAAGGTACCTCTCCCATTC 59.509 57.143 16.64 0.00 0.00 2.67
185 192 0.421904 ACCCAAGGTACCTCTCCCAT 59.578 55.000 16.64 0.00 32.11 4.00
188 195 1.486726 CATCACCCAAGGTACCTCTCC 59.513 57.143 16.64 0.00 32.11 3.71
260 267 0.695347 CTTCCTCACTCAAGGGCCTT 59.305 55.000 14.48 14.48 37.02 4.35
291 304 2.604686 TCACCCGAGCTCAAGCCT 60.605 61.111 15.40 0.00 43.38 4.58
322 335 1.603455 CCACACAACCAATCGCCCT 60.603 57.895 0.00 0.00 0.00 5.19
326 339 1.523154 CCACCCCACACAACCAATCG 61.523 60.000 0.00 0.00 0.00 3.34
329 342 2.280416 CCCACCCCACACAACCAA 59.720 61.111 0.00 0.00 0.00 3.67
341 354 4.678743 GTTGTGCCCCTCCCCACC 62.679 72.222 0.00 0.00 0.00 4.61
342 355 4.678743 GGTTGTGCCCCTCCCCAC 62.679 72.222 0.00 0.00 0.00 4.61
436 454 1.400530 CCCTACCGACATGGACCCTC 61.401 65.000 0.00 0.00 42.00 4.30
444 462 1.607612 CAAAGGGCCCTACCGACAT 59.392 57.895 28.96 3.77 40.62 3.06
476 494 2.704193 GCACGAACGGACGTCTTCG 61.704 63.158 28.10 28.10 44.76 3.79
489 507 2.356553 GTGTAACGGCAGGCACGA 60.357 61.111 8.69 0.00 34.93 4.35
517 535 2.024176 TCACACACCCTACATGGTCT 57.976 50.000 0.00 0.00 36.12 3.85
519 537 1.271379 GCTTCACACACCCTACATGGT 60.271 52.381 0.00 0.00 39.96 3.55
522 540 3.181475 CGATAGCTTCACACACCCTACAT 60.181 47.826 0.00 0.00 0.00 2.29
542 564 0.393944 ACTGTCATAGTCCTCGGCGA 60.394 55.000 10.14 10.14 33.17 5.54
545 567 2.298610 TGCTACTGTCATAGTCCTCGG 58.701 52.381 0.00 0.00 40.89 4.63
548 570 4.528596 ACTTGTTGCTACTGTCATAGTCCT 59.471 41.667 0.00 0.00 40.89 3.85
554 576 4.607293 TCTGACTTGTTGCTACTGTCAT 57.393 40.909 20.07 0.00 37.59 3.06
560 582 2.094182 TCCCGATCTGACTTGTTGCTAC 60.094 50.000 0.00 0.00 0.00 3.58
586 609 4.024218 GCCGGATCTGATTTCATCTGAAAG 60.024 45.833 5.05 0.00 45.87 2.62
590 613 3.123157 AGCCGGATCTGATTTCATCTG 57.877 47.619 5.05 0.00 0.00 2.90
591 614 4.963318 TTAGCCGGATCTGATTTCATCT 57.037 40.909 5.05 0.00 0.00 2.90
592 615 5.059833 AGTTTAGCCGGATCTGATTTCATC 58.940 41.667 5.05 0.00 0.00 2.92
594 617 4.487714 AGTTTAGCCGGATCTGATTTCA 57.512 40.909 5.05 0.00 0.00 2.69
595 618 5.573146 CAAAGTTTAGCCGGATCTGATTTC 58.427 41.667 5.05 0.00 0.00 2.17
596 619 4.142381 GCAAAGTTTAGCCGGATCTGATTT 60.142 41.667 5.05 0.00 0.00 2.17
598 621 2.945668 GCAAAGTTTAGCCGGATCTGAT 59.054 45.455 5.05 0.00 0.00 2.90
632 658 3.866883 ACACGGAGCCAAATTTAATGG 57.133 42.857 0.00 0.00 41.08 3.16
635 661 6.987992 CCTATACTACACGGAGCCAAATTTAA 59.012 38.462 0.00 0.00 0.00 1.52
636 662 6.518493 CCTATACTACACGGAGCCAAATTTA 58.482 40.000 0.00 0.00 0.00 1.40
643 669 0.602060 GGCCTATACTACACGGAGCC 59.398 60.000 0.00 0.00 0.00 4.70
644 670 1.325355 TGGCCTATACTACACGGAGC 58.675 55.000 3.32 0.00 0.00 4.70
645 671 2.352814 GCATGGCCTATACTACACGGAG 60.353 54.545 3.32 0.00 0.00 4.63
646 672 1.616865 GCATGGCCTATACTACACGGA 59.383 52.381 3.32 0.00 0.00 4.69
647 673 1.618837 AGCATGGCCTATACTACACGG 59.381 52.381 3.32 0.00 0.00 4.94
648 674 2.558795 AGAGCATGGCCTATACTACACG 59.441 50.000 3.32 0.00 0.00 4.49
649 675 3.574396 TCAGAGCATGGCCTATACTACAC 59.426 47.826 3.32 0.00 0.00 2.90
650 676 3.844640 TCAGAGCATGGCCTATACTACA 58.155 45.455 3.32 0.00 0.00 2.74
651 677 4.873746 TTCAGAGCATGGCCTATACTAC 57.126 45.455 3.32 0.00 0.00 2.73
652 678 4.323028 GCATTCAGAGCATGGCCTATACTA 60.323 45.833 3.32 0.00 0.00 1.82
653 679 3.558746 GCATTCAGAGCATGGCCTATACT 60.559 47.826 3.32 0.00 0.00 2.12
654 680 2.746362 GCATTCAGAGCATGGCCTATAC 59.254 50.000 3.32 0.00 0.00 1.47
655 681 2.641321 AGCATTCAGAGCATGGCCTATA 59.359 45.455 3.32 0.00 0.00 1.31
656 682 1.424302 AGCATTCAGAGCATGGCCTAT 59.576 47.619 3.32 0.00 0.00 2.57
657 683 0.841961 AGCATTCAGAGCATGGCCTA 59.158 50.000 3.32 0.00 0.00 3.93
658 684 0.841961 TAGCATTCAGAGCATGGCCT 59.158 50.000 3.32 0.00 0.00 5.19
659 685 1.540267 CATAGCATTCAGAGCATGGCC 59.460 52.381 0.00 0.00 0.00 5.36
660 686 1.540267 CCATAGCATTCAGAGCATGGC 59.460 52.381 0.00 0.00 35.50 4.40
661 687 2.812591 GTCCATAGCATTCAGAGCATGG 59.187 50.000 0.00 0.00 39.68 3.66
662 688 3.250280 GTGTCCATAGCATTCAGAGCATG 59.750 47.826 0.00 0.00 0.00 4.06
663 689 3.474600 GTGTCCATAGCATTCAGAGCAT 58.525 45.455 0.00 0.00 0.00 3.79
664 690 2.739609 CGTGTCCATAGCATTCAGAGCA 60.740 50.000 0.00 0.00 0.00 4.26
665 691 1.863454 CGTGTCCATAGCATTCAGAGC 59.137 52.381 0.00 0.00 0.00 4.09
666 692 2.862536 CACGTGTCCATAGCATTCAGAG 59.137 50.000 7.58 0.00 0.00 3.35
667 693 2.495669 TCACGTGTCCATAGCATTCAGA 59.504 45.455 16.51 0.00 0.00 3.27
668 694 2.604914 GTCACGTGTCCATAGCATTCAG 59.395 50.000 16.51 0.00 0.00 3.02
669 695 2.616960 GTCACGTGTCCATAGCATTCA 58.383 47.619 16.51 0.00 0.00 2.57
670 696 1.933853 GGTCACGTGTCCATAGCATTC 59.066 52.381 24.29 0.00 0.00 2.67
671 697 1.739035 CGGTCACGTGTCCATAGCATT 60.739 52.381 27.41 0.00 34.81 3.56
672 698 0.179111 CGGTCACGTGTCCATAGCAT 60.179 55.000 27.41 0.00 34.81 3.79
673 699 1.214325 CGGTCACGTGTCCATAGCA 59.786 57.895 27.41 0.00 34.81 3.49
674 700 1.518572 CCGGTCACGTGTCCATAGC 60.519 63.158 27.41 12.15 38.78 2.97
675 701 0.528924 TTCCGGTCACGTGTCCATAG 59.471 55.000 27.41 16.93 38.78 2.23
676 702 0.967662 TTTCCGGTCACGTGTCCATA 59.032 50.000 27.41 14.25 38.78 2.74
677 703 0.320421 CTTTCCGGTCACGTGTCCAT 60.320 55.000 27.41 0.00 38.78 3.41
678 704 1.068417 CTTTCCGGTCACGTGTCCA 59.932 57.895 27.41 9.83 38.78 4.02
679 705 0.249573 TTCTTTCCGGTCACGTGTCC 60.250 55.000 20.24 20.24 38.78 4.02
680 706 1.137513 CTTCTTTCCGGTCACGTGTC 58.862 55.000 16.51 10.16 38.78 3.67
681 707 0.748450 TCTTCTTTCCGGTCACGTGT 59.252 50.000 16.51 0.00 38.78 4.49
682 708 1.137513 GTCTTCTTTCCGGTCACGTG 58.862 55.000 9.94 9.94 38.78 4.49
683 709 0.748450 TGTCTTCTTTCCGGTCACGT 59.252 50.000 0.00 0.00 38.78 4.49
684 710 1.860676 TTGTCTTCTTTCCGGTCACG 58.139 50.000 0.00 0.00 40.55 4.35
685 711 2.548480 CCTTTGTCTTCTTTCCGGTCAC 59.452 50.000 0.00 0.00 0.00 3.67
686 712 2.486548 CCCTTTGTCTTCTTTCCGGTCA 60.487 50.000 0.00 0.00 0.00 4.02
687 713 2.152016 CCCTTTGTCTTCTTTCCGGTC 58.848 52.381 0.00 0.00 0.00 4.79
688 714 1.772453 TCCCTTTGTCTTCTTTCCGGT 59.228 47.619 0.00 0.00 0.00 5.28
689 715 2.561478 TCCCTTTGTCTTCTTTCCGG 57.439 50.000 0.00 0.00 0.00 5.14
693 719 4.338400 CCGAGTTTTCCCTTTGTCTTCTTT 59.662 41.667 0.00 0.00 0.00 2.52
706 732 3.064134 GCTTATCTCTTGCCGAGTTTTCC 59.936 47.826 0.73 0.00 40.75 3.13
803 829 1.002430 GCATCCGGCTGATATTCTGGA 59.998 52.381 10.06 4.31 41.57 3.86
974 1011 3.561213 CCTAGAGCGCGACGACGA 61.561 66.667 12.10 0.00 42.66 4.20
1068 1105 3.157252 GAGATCCCCGCCTGCTCA 61.157 66.667 0.00 0.00 0.00 4.26
1560 1597 1.323412 CTGGATCGGAGGAATCGACT 58.677 55.000 0.00 0.00 39.55 4.18
1590 1627 0.244994 GCTTCTCGAACAGCTCCTGA 59.755 55.000 8.02 0.00 35.18 3.86
1764 1801 0.906775 CGTACCTTGGGTATGTGGGT 59.093 55.000 7.56 0.00 40.54 4.51
1786 1823 7.255277 CGATCACATAGAAGACAGGATCAGTTA 60.255 40.741 0.00 0.00 32.16 2.24
1825 1863 9.905713 TCATATAAACTCAGTGGCTAAAGAAAT 57.094 29.630 0.00 0.00 0.00 2.17
1845 1895 8.502387 GCTGCAACAAAAACCAAAAATCATATA 58.498 29.630 0.00 0.00 0.00 0.86
1846 1896 7.361894 GCTGCAACAAAAACCAAAAATCATAT 58.638 30.769 0.00 0.00 0.00 1.78
1854 1904 1.066858 TCCGCTGCAACAAAAACCAAA 60.067 42.857 0.00 0.00 0.00 3.28
1861 1911 2.076100 CTATCACTCCGCTGCAACAAA 58.924 47.619 0.00 0.00 0.00 2.83
1901 1951 0.541863 AATCAACACTAGGCCCCTCG 59.458 55.000 0.00 0.00 0.00 4.63
1978 2028 2.891580 TCGGAGTTGTAGAACTTGAGCT 59.108 45.455 6.73 0.00 42.80 4.09
2102 2176 4.389374 TGAAACCAAACCAGCTCTTCTAG 58.611 43.478 0.00 0.00 0.00 2.43
2103 2177 4.431416 TGAAACCAAACCAGCTCTTCTA 57.569 40.909 0.00 0.00 0.00 2.10
2104 2178 3.297134 TGAAACCAAACCAGCTCTTCT 57.703 42.857 0.00 0.00 0.00 2.85
2105 2179 3.130340 TGTTGAAACCAAACCAGCTCTTC 59.870 43.478 0.00 0.00 0.00 2.87
2106 2180 3.096092 TGTTGAAACCAAACCAGCTCTT 58.904 40.909 0.00 0.00 0.00 2.85
2107 2181 2.427095 GTGTTGAAACCAAACCAGCTCT 59.573 45.455 0.00 0.00 0.00 4.09
2108 2182 2.165437 TGTGTTGAAACCAAACCAGCTC 59.835 45.455 0.00 0.00 0.00 4.09
2109 2183 2.166254 CTGTGTTGAAACCAAACCAGCT 59.834 45.455 0.00 0.00 0.00 4.24
2110 2184 2.539476 CTGTGTTGAAACCAAACCAGC 58.461 47.619 0.00 0.00 0.00 4.85
2111 2185 2.159114 CCCTGTGTTGAAACCAAACCAG 60.159 50.000 0.00 0.00 0.00 4.00
2112 2186 1.827969 CCCTGTGTTGAAACCAAACCA 59.172 47.619 0.00 0.00 0.00 3.67
2113 2187 2.100749 CTCCCTGTGTTGAAACCAAACC 59.899 50.000 0.00 0.00 0.00 3.27
2114 2188 2.481276 GCTCCCTGTGTTGAAACCAAAC 60.481 50.000 0.00 0.00 0.00 2.93
2115 2189 1.754226 GCTCCCTGTGTTGAAACCAAA 59.246 47.619 0.00 0.00 0.00 3.28
2116 2190 1.341482 TGCTCCCTGTGTTGAAACCAA 60.341 47.619 0.00 0.00 0.00 3.67
2117 2191 0.257328 TGCTCCCTGTGTTGAAACCA 59.743 50.000 0.00 0.00 0.00 3.67
2118 2192 1.398692 TTGCTCCCTGTGTTGAAACC 58.601 50.000 0.00 0.00 0.00 3.27
2119 2193 2.887152 AGATTGCTCCCTGTGTTGAAAC 59.113 45.455 0.00 0.00 0.00 2.78
2129 2203 1.137872 CGCTAAGACAGATTGCTCCCT 59.862 52.381 0.00 0.00 0.00 4.20
2631 2705 6.879458 AGGAAATACAACCTGAGACATACAAC 59.121 38.462 0.00 0.00 34.99 3.32
2660 2736 8.564023 CAGAAGGTTCTCATACCACCAGGTATA 61.564 44.444 6.84 0.00 46.03 1.47
2843 2921 4.264352 CCCTGCCCCCATATATAAACACAT 60.264 45.833 0.00 0.00 0.00 3.21
2846 2924 2.652348 CCCCTGCCCCCATATATAAACA 59.348 50.000 0.00 0.00 0.00 2.83
2852 2930 0.770557 GTCACCCCTGCCCCCATATA 60.771 60.000 0.00 0.00 0.00 0.86
2853 2931 2.084930 GTCACCCCTGCCCCCATAT 61.085 63.158 0.00 0.00 0.00 1.78
2854 2932 2.694616 GTCACCCCTGCCCCCATA 60.695 66.667 0.00 0.00 0.00 2.74
2963 3184 2.504175 GTCCACAAGGCAGGGTCTTATA 59.496 50.000 0.00 0.00 33.74 0.98
3034 3411 9.289303 CACCTTTTTGATGTAACAAGCATATAC 57.711 33.333 0.00 0.00 0.00 1.47
3035 3412 9.237187 TCACCTTTTTGATGTAACAAGCATATA 57.763 29.630 0.00 0.00 0.00 0.86
3036 3413 8.028938 GTCACCTTTTTGATGTAACAAGCATAT 58.971 33.333 0.00 0.00 0.00 1.78
3037 3414 7.367285 GTCACCTTTTTGATGTAACAAGCATA 58.633 34.615 0.00 0.00 0.00 3.14
3038 3415 6.215845 GTCACCTTTTTGATGTAACAAGCAT 58.784 36.000 0.00 0.00 0.00 3.79
3040 3417 4.982295 GGTCACCTTTTTGATGTAACAAGC 59.018 41.667 0.00 0.00 0.00 4.01
3041 3418 5.977129 GTGGTCACCTTTTTGATGTAACAAG 59.023 40.000 0.00 0.00 0.00 3.16
3043 3420 5.197451 AGTGGTCACCTTTTTGATGTAACA 58.803 37.500 0.00 0.00 0.00 2.41
3044 3421 5.767816 AGTGGTCACCTTTTTGATGTAAC 57.232 39.130 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.