Multiple sequence alignment - TraesCS5A01G012000

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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 TraesCS5A01G012000 chr5A 100.000 2885 0 0 1 2885 7678790 7681674 0.000000e+00 5328.0
1 TraesCS5A01G012000 chr5A 85.294 102 10 3 496 597 407950320 407950416 1.830000e-17 100.0
2 TraesCS5A01G012000 chr5D 91.399 1651 80 24 823 2451 9547850 9549460 0.000000e+00 2206.0
3 TraesCS5A01G012000 chr5D 93.793 435 23 2 2455 2885 9549515 9549949 0.000000e+00 651.0
4 TraesCS5A01G012000 chr5D 79.902 408 75 6 2480 2883 37754112 37754516 2.810000e-75 292.0
5 TraesCS5A01G012000 chr5D 88.182 110 10 3 597 706 9531918 9532024 8.390000e-26 128.0
6 TraesCS5A01G012000 chr5B 92.486 1078 61 9 823 1895 9538921 9539983 0.000000e+00 1524.0
7 TraesCS5A01G012000 chr5B 92.188 256 20 0 1649 1904 10338699 10338444 2.110000e-96 363.0
8 TraesCS5A01G012000 chr5B 87.273 110 11 3 597 706 9538073 9538179 3.900000e-24 122.0
9 TraesCS5A01G012000 chr7D 93.644 472 24 6 1 468 37556728 37556259 0.000000e+00 701.0
10 TraesCS5A01G012000 chr7D 84.043 94 9 4 496 588 55924738 55924650 5.120000e-13 86.1
11 TraesCS5A01G012000 chr3A 93.148 467 28 4 1 465 604276808 604277272 0.000000e+00 682.0
12 TraesCS5A01G012000 chr3A 93.148 467 26 6 7 468 60662815 60662350 0.000000e+00 680.0
13 TraesCS5A01G012000 chr3A 93.290 462 24 5 9 465 199768750 199769209 0.000000e+00 675.0
14 TraesCS5A01G012000 chr3A 92.553 470 29 4 1 468 458865031 458864566 0.000000e+00 669.0
15 TraesCS5A01G012000 chr3A 78.670 436 51 28 2045 2450 696706201 696706624 4.770000e-63 252.0
16 TraesCS5A01G012000 chr6A 93.668 458 21 3 14 465 32878695 32879150 0.000000e+00 678.0
17 TraesCS5A01G012000 chr6A 91.379 116 9 1 481 596 32879138 32879252 1.070000e-34 158.0
18 TraesCS5A01G012000 chr6A 86.667 105 10 3 496 599 587419195 587419094 2.350000e-21 113.0
19 TraesCS5A01G012000 chr6A 86.598 97 8 4 501 596 65076432 65076524 5.090000e-18 102.0
20 TraesCS5A01G012000 chrUn 93.074 462 29 3 8 468 347710680 347710221 0.000000e+00 673.0
21 TraesCS5A01G012000 chr1A 93.074 462 29 3 8 468 568106018 568105559 0.000000e+00 673.0
22 TraesCS5A01G012000 chr1A 77.119 354 37 29 2128 2451 548451451 548451112 6.400000e-37 165.0
23 TraesCS5A01G012000 chr1A 85.714 112 16 0 2130 2241 436420048 436419937 5.050000e-23 119.0
24 TraesCS5A01G012000 chr4A 92.521 468 32 2 1 465 334951425 334951892 0.000000e+00 667.0
25 TraesCS5A01G012000 chr1B 76.939 967 165 36 1962 2884 681047673 681048625 5.550000e-137 497.0
26 TraesCS5A01G012000 chr1D 83.716 436 64 5 2454 2883 467409582 467410016 3.460000e-109 405.0
27 TraesCS5A01G012000 chr1D 82.227 422 65 5 2462 2883 6412755 6412344 3.540000e-94 355.0
28 TraesCS5A01G012000 chr1D 79.779 272 24 16 2207 2451 486254717 486254984 4.940000e-38 169.0
29 TraesCS5A01G012000 chr1D 83.824 136 21 1 2748 2883 486255253 486255387 8.390000e-26 128.0
30 TraesCS5A01G012000 chr7A 77.875 574 76 31 1911 2451 83299904 83300459 2.790000e-80 309.0
31 TraesCS5A01G012000 chr7A 82.192 365 33 16 2522 2883 83300567 83300902 4.710000e-73 285.0
32 TraesCS5A01G012000 chr7A 82.857 105 10 5 496 600 632594288 632594384 1.420000e-13 87.9
33 TraesCS5A01G012000 chr2B 85.223 291 39 3 2455 2743 608543086 608542798 2.170000e-76 296.0
34 TraesCS5A01G012000 chr6B 83.974 312 45 3 2575 2883 684145679 684145988 7.820000e-76 294.0
35 TraesCS5A01G012000 chr6B 80.278 360 36 20 2107 2446 684145235 684145579 3.720000e-59 239.0
36 TraesCS5A01G012000 chr2A 84.039 307 40 7 2455 2755 661084973 661084670 1.310000e-73 287.0
37 TraesCS5A01G012000 chr2A 84.167 120 19 0 2122 2241 3506718 3506599 1.820000e-22 117.0
38 TraesCS5A01G012000 chr2A 85.294 102 8 5 496 596 42712529 42712624 6.580000e-17 99.0
39 TraesCS5A01G012000 chr3B 77.471 435 59 23 2045 2451 745551753 745552176 1.040000e-54 224.0
40 TraesCS5A01G012000 chr2D 77.193 399 79 10 2491 2882 8422338 8421945 3.740000e-54 222.0
41 TraesCS5A01G012000 chr2D 88.235 102 7 5 495 595 22946034 22945937 1.820000e-22 117.0
42 TraesCS5A01G012000 chr3D 87.379 103 6 5 496 597 380901967 380902063 8.450000e-21 111.0
43 TraesCS5A01G012000 chr4D 85.714 70 4 6 1467 1535 453516734 453516670 5.160000e-08 69.4


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 TraesCS5A01G012000 chr5A 7678790 7681674 2884 False 5328.0 5328 100.0000 1 2885 1 chr5A.!!$F1 2884
1 TraesCS5A01G012000 chr5D 9547850 9549949 2099 False 1428.5 2206 92.5960 823 2885 2 chr5D.!!$F3 2062
2 TraesCS5A01G012000 chr5B 9538073 9539983 1910 False 823.0 1524 89.8795 597 1895 2 chr5B.!!$F1 1298
3 TraesCS5A01G012000 chr6A 32878695 32879252 557 False 418.0 678 92.5235 14 596 2 chr6A.!!$F2 582
4 TraesCS5A01G012000 chr1B 681047673 681048625 952 False 497.0 497 76.9390 1962 2884 1 chr1B.!!$F1 922
5 TraesCS5A01G012000 chr7A 83299904 83300902 998 False 297.0 309 80.0335 1911 2883 2 chr7A.!!$F2 972
6 TraesCS5A01G012000 chr6B 684145235 684145988 753 False 266.5 294 82.1260 2107 2883 2 chr6B.!!$F1 776

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
762 769 0.043053 CTGACAGTGACAACGCAACG 60.043 55.0 0.0 0.0 0.00 4.10 F
1666 2366 0.179119 GGGGATGTACCGTGAGTTCG 60.179 60.0 0.0 0.0 40.11 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 2482 0.465705 CCGTCATGCTCCCATACACT 59.534 55.000 0.0 0.0 0.0 3.55 R
2846 3641 5.672503 GGACTACTTTACTCTTTCATCCCC 58.327 45.833 0.0 0.0 0.0 4.81 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
117 118 6.761731 TTTGAATAAATTTTGGCACGACAG 57.238 33.333 0.00 0.00 0.00 3.51
120 121 6.686630 TGAATAAATTTTGGCACGACAGAAT 58.313 32.000 0.00 0.00 0.00 2.40
125 126 4.335082 TTTTGGCACGACAGAATAATCG 57.665 40.909 0.00 0.00 43.97 3.34
126 127 2.951457 TGGCACGACAGAATAATCGA 57.049 45.000 0.00 0.00 40.86 3.59
129 130 4.188462 TGGCACGACAGAATAATCGAAAT 58.812 39.130 0.00 0.00 40.86 2.17
276 278 8.668510 ATTAGACTTGCAATAGGAACACATAG 57.331 34.615 0.00 0.00 0.00 2.23
277 279 6.299805 AGACTTGCAATAGGAACACATAGA 57.700 37.500 0.00 0.00 0.00 1.98
285 287 8.461222 TGCAATAGGAACACATAGAAAAATGAG 58.539 33.333 0.00 0.00 0.00 2.90
390 397 3.448660 GCAGGAAAATATGGGCTGACTTT 59.551 43.478 0.00 0.00 0.00 2.66
405 412 1.844497 GACTTTACTGGGCCATAGGGT 59.156 52.381 6.72 3.59 36.17 4.34
437 444 7.202526 CCCATGTACGAAATTCTGCATAAATT 58.797 34.615 0.00 0.00 0.00 1.82
460 467 7.411486 TTGTTTTTCCTTTACCAACAGATGA 57.589 32.000 0.00 0.00 0.00 2.92
465 472 8.754991 TTTTCCTTTACCAACAGATGAAGTAA 57.245 30.769 0.00 0.00 0.00 2.24
466 473 7.979444 TTCCTTTACCAACAGATGAAGTAAG 57.021 36.000 0.00 0.00 0.00 2.34
467 474 7.311092 TCCTTTACCAACAGATGAAGTAAGA 57.689 36.000 0.00 0.00 0.00 2.10
468 475 7.918076 TCCTTTACCAACAGATGAAGTAAGAT 58.082 34.615 0.00 0.00 0.00 2.40
469 476 8.041323 TCCTTTACCAACAGATGAAGTAAGATC 58.959 37.037 0.00 0.00 0.00 2.75
470 477 7.281100 CCTTTACCAACAGATGAAGTAAGATCC 59.719 40.741 0.00 0.00 0.00 3.36
471 478 5.104259 ACCAACAGATGAAGTAAGATCCC 57.896 43.478 0.00 0.00 0.00 3.85
472 479 4.785376 ACCAACAGATGAAGTAAGATCCCT 59.215 41.667 0.00 0.00 0.00 4.20
473 480 5.104735 ACCAACAGATGAAGTAAGATCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
474 481 5.104776 CCAACAGATGAAGTAAGATCCCTCA 60.105 44.000 0.00 0.00 0.00 3.86
475 482 6.409704 CAACAGATGAAGTAAGATCCCTCAA 58.590 40.000 0.00 0.00 0.00 3.02
476 483 6.627087 ACAGATGAAGTAAGATCCCTCAAA 57.373 37.500 0.00 0.00 0.00 2.69
477 484 7.020827 ACAGATGAAGTAAGATCCCTCAAAA 57.979 36.000 0.00 0.00 0.00 2.44
478 485 7.461749 ACAGATGAAGTAAGATCCCTCAAAAA 58.538 34.615 0.00 0.00 0.00 1.94
512 519 8.488668 TGAAGTAAGAAAGTTTAGTACCACCTT 58.511 33.333 0.00 0.00 0.00 3.50
523 530 7.847848 AGTTTAGTACCACCTTGAATATAGGGA 59.152 37.037 0.00 0.00 37.09 4.20
524 531 8.488668 GTTTAGTACCACCTTGAATATAGGGAA 58.511 37.037 0.00 0.00 37.09 3.97
529 536 9.856162 GTACCACCTTGAATATAGGGAAAAATA 57.144 33.333 0.00 0.00 37.09 1.40
555 562 1.814793 TGGCGATGAACGGATGAAAA 58.185 45.000 0.00 0.00 42.83 2.29
613 620 7.292591 AGGTATAGATTTTGCATACTGGTAGGT 59.707 37.037 0.00 0.00 0.00 3.08
617 624 3.799432 TTTGCATACTGGTAGGTTGGT 57.201 42.857 0.00 0.00 0.00 3.67
621 628 5.031066 TGCATACTGGTAGGTTGGTAATC 57.969 43.478 0.00 0.00 0.00 1.75
626 633 3.710165 ACTGGTAGGTTGGTAATCTAGGC 59.290 47.826 0.00 0.00 0.00 3.93
631 638 6.042781 TGGTAGGTTGGTAATCTAGGCTTATG 59.957 42.308 0.00 0.00 0.00 1.90
632 639 6.042897 GGTAGGTTGGTAATCTAGGCTTATGT 59.957 42.308 0.00 0.00 0.00 2.29
640 647 8.330247 TGGTAATCTAGGCTTATGTTTAACCAA 58.670 33.333 0.00 0.00 0.00 3.67
676 683 6.792250 GTGTCTCGTGATGAAATTAAGTTGTG 59.208 38.462 0.00 0.00 0.00 3.33
677 684 6.073276 TGTCTCGTGATGAAATTAAGTTGTGG 60.073 38.462 0.00 0.00 0.00 4.17
682 689 8.788806 TCGTGATGAAATTAAGTTGTGGTAATT 58.211 29.630 0.00 0.00 32.54 1.40
699 706 7.147976 GTGGTAATTTGAACAATTCAGAAGCT 58.852 34.615 0.00 0.00 41.38 3.74
701 708 8.203485 TGGTAATTTGAACAATTCAGAAGCTTT 58.797 29.630 0.00 0.00 41.38 3.51
702 709 8.703336 GGTAATTTGAACAATTCAGAAGCTTTC 58.297 33.333 0.00 0.00 41.38 2.62
703 710 9.468532 GTAATTTGAACAATTCAGAAGCTTTCT 57.531 29.630 0.00 0.00 41.38 2.52
708 715 4.723309 ACAATTCAGAAGCTTTCTCCTGT 58.277 39.130 0.00 0.00 38.11 4.00
709 716 4.518211 ACAATTCAGAAGCTTTCTCCTGTG 59.482 41.667 0.00 0.82 38.11 3.66
711 718 1.349026 TCAGAAGCTTTCTCCTGTGGG 59.651 52.381 0.00 0.00 38.11 4.61
713 720 2.057922 AGAAGCTTTCTCCTGTGGGAA 58.942 47.619 0.00 0.00 41.69 3.97
715 722 3.846588 AGAAGCTTTCTCCTGTGGGAATA 59.153 43.478 0.00 0.00 41.69 1.75
717 724 4.162040 AGCTTTCTCCTGTGGGAATATG 57.838 45.455 0.00 0.00 41.69 1.78
718 725 3.525199 AGCTTTCTCCTGTGGGAATATGT 59.475 43.478 0.00 0.00 41.69 2.29
719 726 3.629398 GCTTTCTCCTGTGGGAATATGTG 59.371 47.826 0.00 0.00 41.69 3.21
720 727 3.281727 TTCTCCTGTGGGAATATGTGC 57.718 47.619 0.00 0.00 41.69 4.57
721 728 1.490490 TCTCCTGTGGGAATATGTGCC 59.510 52.381 0.00 0.00 41.69 5.01
722 729 0.180171 TCCTGTGGGAATATGTGCCG 59.820 55.000 0.00 0.00 41.79 5.69
724 731 3.432186 GTGGGAATATGTGCCGCC 58.568 61.111 0.00 0.00 42.23 6.13
725 732 1.453015 GTGGGAATATGTGCCGCCA 60.453 57.895 0.00 0.00 42.23 5.69
726 733 1.453015 TGGGAATATGTGCCGCCAC 60.453 57.895 0.00 0.00 41.79 5.01
733 740 2.977456 TGTGCCGCCACACATGAC 60.977 61.111 0.00 0.00 46.51 3.06
734 741 2.977456 GTGCCGCCACACATGACA 60.977 61.111 0.00 0.00 41.67 3.58
735 742 2.977456 TGCCGCCACACATGACAC 60.977 61.111 0.00 0.00 0.00 3.67
736 743 2.977456 GCCGCCACACATGACACA 60.977 61.111 0.00 0.00 0.00 3.72
737 744 2.334946 GCCGCCACACATGACACAT 61.335 57.895 0.00 0.00 0.00 3.21
738 745 1.796151 CCGCCACACATGACACATC 59.204 57.895 0.00 0.00 0.00 3.06
739 746 0.954938 CCGCCACACATGACACATCA 60.955 55.000 0.00 0.00 39.83 3.07
740 747 0.873721 CGCCACACATGACACATCAA 59.126 50.000 0.00 0.00 38.69 2.57
741 748 1.469703 CGCCACACATGACACATCAAT 59.530 47.619 0.00 0.00 38.69 2.57
742 749 2.476686 CGCCACACATGACACATCAATC 60.477 50.000 0.00 0.00 38.69 2.67
743 750 2.159338 GCCACACATGACACATCAATCC 60.159 50.000 0.00 0.00 38.69 3.01
744 751 3.349927 CCACACATGACACATCAATCCT 58.650 45.455 0.00 0.00 38.69 3.24
745 752 3.128068 CCACACATGACACATCAATCCTG 59.872 47.826 0.00 0.00 38.69 3.86
746 753 4.004982 CACACATGACACATCAATCCTGA 58.995 43.478 0.00 0.00 38.69 3.86
747 754 4.005650 ACACATGACACATCAATCCTGAC 58.994 43.478 0.00 0.00 38.69 3.51
748 755 4.004982 CACATGACACATCAATCCTGACA 58.995 43.478 0.00 0.00 38.69 3.58
749 756 4.094442 CACATGACACATCAATCCTGACAG 59.906 45.833 0.00 0.00 38.69 3.51
750 757 4.259356 CATGACACATCAATCCTGACAGT 58.741 43.478 0.93 0.00 38.69 3.55
751 758 3.667360 TGACACATCAATCCTGACAGTG 58.333 45.455 0.93 7.58 42.46 3.66
752 759 3.324556 TGACACATCAATCCTGACAGTGA 59.675 43.478 13.38 0.00 40.69 3.41
753 760 3.668447 ACACATCAATCCTGACAGTGAC 58.332 45.455 13.38 0.00 40.69 3.67
754 761 3.071457 ACACATCAATCCTGACAGTGACA 59.929 43.478 13.38 0.00 40.69 3.58
755 762 4.067192 CACATCAATCCTGACAGTGACAA 58.933 43.478 0.00 0.00 40.69 3.18
756 763 4.067896 ACATCAATCCTGACAGTGACAAC 58.932 43.478 0.00 0.00 33.30 3.32
757 764 2.754472 TCAATCCTGACAGTGACAACG 58.246 47.619 0.00 0.00 0.00 4.10
758 765 1.195448 CAATCCTGACAGTGACAACGC 59.805 52.381 0.00 0.00 0.00 4.84
759 766 0.392706 ATCCTGACAGTGACAACGCA 59.607 50.000 0.00 0.00 0.00 5.24
760 767 0.176910 TCCTGACAGTGACAACGCAA 59.823 50.000 0.00 0.00 0.00 4.85
761 768 0.304705 CCTGACAGTGACAACGCAAC 59.695 55.000 0.00 0.00 0.00 4.17
762 769 0.043053 CTGACAGTGACAACGCAACG 60.043 55.000 0.00 0.00 0.00 4.10
763 770 1.367665 GACAGTGACAACGCAACGC 60.368 57.895 0.00 0.00 0.00 4.84
764 771 1.762222 GACAGTGACAACGCAACGCT 61.762 55.000 0.00 0.00 0.00 5.07
765 772 1.368019 CAGTGACAACGCAACGCTG 60.368 57.895 0.00 0.00 36.19 5.18
766 773 2.052237 GTGACAACGCAACGCTGG 60.052 61.111 0.00 0.00 0.00 4.85
767 774 2.512745 TGACAACGCAACGCTGGT 60.513 55.556 0.00 0.00 0.00 4.00
768 775 2.052237 GACAACGCAACGCTGGTG 60.052 61.111 0.00 0.00 0.00 4.17
769 776 2.512745 ACAACGCAACGCTGGTGA 60.513 55.556 0.00 0.00 0.00 4.02
770 777 2.042520 GACAACGCAACGCTGGTGAA 62.043 55.000 0.00 0.00 0.00 3.18
771 778 1.369209 CAACGCAACGCTGGTGAAG 60.369 57.895 0.00 0.00 0.00 3.02
772 779 1.817941 AACGCAACGCTGGTGAAGT 60.818 52.632 0.00 0.00 0.00 3.01
773 780 2.047151 AACGCAACGCTGGTGAAGTG 62.047 55.000 0.00 0.00 42.48 3.16
783 790 2.613977 GCTGGTGAAGTGTGAGTATGCT 60.614 50.000 0.00 0.00 0.00 3.79
784 791 3.668447 CTGGTGAAGTGTGAGTATGCTT 58.332 45.455 0.00 0.00 0.00 3.91
789 796 4.872691 GTGAAGTGTGAGTATGCTTGCTAT 59.127 41.667 0.00 0.00 0.00 2.97
790 797 4.872124 TGAAGTGTGAGTATGCTTGCTATG 59.128 41.667 0.00 0.00 0.00 2.23
802 809 5.726980 TGCTTGCTATGGAATTTGAGTTT 57.273 34.783 0.00 0.00 0.00 2.66
808 815 7.994425 TGCTATGGAATTTGAGTTTAGACAA 57.006 32.000 0.00 0.00 0.00 3.18
809 816 8.402798 TGCTATGGAATTTGAGTTTAGACAAA 57.597 30.769 0.00 0.00 39.67 2.83
810 817 8.296713 TGCTATGGAATTTGAGTTTAGACAAAC 58.703 33.333 0.00 0.00 43.71 2.93
811 818 7.755373 GCTATGGAATTTGAGTTTAGACAAACC 59.245 37.037 0.00 0.00 44.32 3.27
812 819 7.839680 ATGGAATTTGAGTTTAGACAAACCT 57.160 32.000 0.00 0.00 44.32 3.50
814 821 6.017440 TGGAATTTGAGTTTAGACAAACCTCG 60.017 38.462 0.00 0.00 44.32 4.63
815 822 4.806342 TTTGAGTTTAGACAAACCTCGC 57.194 40.909 0.00 0.00 44.32 5.03
818 825 0.794473 GTTTAGACAAACCTCGCCGG 59.206 55.000 0.00 0.00 38.49 6.13
840 1528 2.345991 CCGGCCGGAGTTCTCAAA 59.654 61.111 41.82 0.00 37.50 2.69
846 1534 2.550208 GGCCGGAGTTCTCAAAGAAAGA 60.550 50.000 5.05 0.00 35.75 2.52
862 1550 1.768684 AAGAGGAAGGCGCCAACAGA 61.769 55.000 31.54 0.00 0.00 3.41
865 1553 2.563427 GAAGGCGCCAACAGAAGC 59.437 61.111 31.54 4.11 0.00 3.86
873 1561 1.593196 GCCAACAGAAGCCGCATATA 58.407 50.000 0.00 0.00 0.00 0.86
875 1563 2.838736 CCAACAGAAGCCGCATATACT 58.161 47.619 0.00 0.00 0.00 2.12
880 1568 6.213677 CAACAGAAGCCGCATATACTTACTA 58.786 40.000 0.00 0.00 0.00 1.82
889 1577 7.342284 AGCCGCATATACTTACTACATATTCCT 59.658 37.037 0.00 0.00 0.00 3.36
890 1578 7.435488 GCCGCATATACTTACTACATATTCCTG 59.565 40.741 0.00 0.00 0.00 3.86
924 1616 0.940519 CCAAACATGCACCAACAGCG 60.941 55.000 0.00 0.00 33.85 5.18
952 1644 4.686091 TGTTTGCTTCATCTTGTACGAGAG 59.314 41.667 17.74 10.22 0.00 3.20
980 1677 7.909777 ATGCTATATATACATGAACGCGTAC 57.090 36.000 14.46 0.00 0.00 3.67
1107 1804 3.691342 TACTGCCGTGCCTTCGCT 61.691 61.111 0.00 0.00 35.36 4.93
1189 1886 1.208358 GATGACACCGTCGTCGTCA 59.792 57.895 14.16 14.16 46.68 4.35
1191 1888 0.662374 ATGACACCGTCGTCGTCAAC 60.662 55.000 15.35 0.00 42.53 3.18
1660 2360 1.220749 CAGTGGGGGATGTACCGTG 59.779 63.158 0.00 0.00 40.11 4.94
1666 2366 0.179119 GGGGATGTACCGTGAGTTCG 60.179 60.000 0.00 0.00 40.11 3.95
1788 2488 1.863662 CGCCGCGGGAGATAGTGTAT 61.864 60.000 29.38 0.00 0.00 2.29
1875 2575 4.699522 AGGCGGTTCGGGCTCAAC 62.700 66.667 1.03 0.00 38.65 3.18
1928 2628 2.127646 CACGTCATGTGTGCACGC 60.128 61.111 23.40 23.40 43.88 5.34
1957 2657 4.439305 TGGGATACGTATTATGTACCGC 57.561 45.455 9.92 4.11 37.60 5.68
1959 2659 4.082625 TGGGATACGTATTATGTACCGCTG 60.083 45.833 9.92 0.00 37.60 5.18
1960 2660 3.855950 GGATACGTATTATGTACCGCTGC 59.144 47.826 9.92 0.00 0.00 5.25
1978 2678 3.185188 GCTGCACTATGGATTATGTGACG 59.815 47.826 0.00 0.00 32.72 4.35
1980 2680 2.155732 GCACTATGGATTATGTGACGCG 59.844 50.000 3.53 3.53 32.72 6.01
1985 2685 3.446310 TGGATTATGTGACGCGTGTAT 57.554 42.857 20.70 10.72 0.00 2.29
2004 2704 9.419297 GCGTGTATTATCATATTAACTTCTCCA 57.581 33.333 0.00 0.00 0.00 3.86
2021 2721 0.533978 CCATGTGACGTGTGGGACAA 60.534 55.000 3.87 0.00 44.16 3.18
2119 2822 5.050490 CCAACCCACAAGAGTTATATCTCG 58.950 45.833 5.38 0.00 39.21 4.04
2150 2853 9.168451 TCCACGCTTTTCAGTTTGATTATATAA 57.832 29.630 0.00 0.00 0.00 0.98
2201 2904 7.807433 CCAAATATTCGATTGACAAACTGTTCA 59.193 33.333 0.00 0.00 0.00 3.18
2256 2968 8.977505 TCAAAACAAGAAGAACACTTTTGAAAG 58.022 29.630 2.06 2.06 41.73 2.62
2332 3045 6.903419 TGCATGTGTGTTTCATCGTATTTTA 58.097 32.000 0.00 0.00 0.00 1.52
2392 3112 7.605410 TTTTCATTCCGGATTTCAGTACTAC 57.395 36.000 4.15 0.00 0.00 2.73
2460 3244 8.801882 TGTCAAAATATCTTTCGGTATTTCCT 57.198 30.769 0.00 0.00 31.26 3.36
2641 3433 4.404394 TGGTTCACTCTAGTTTCACTGTCA 59.596 41.667 0.00 0.00 0.00 3.58
2711 3506 6.882610 TGAGCTTGTTTAGAACATGTTCAT 57.117 33.333 33.92 22.73 45.14 2.57
2763 3558 5.336372 GCCAATACCACTAATCTGCAAACAA 60.336 40.000 0.00 0.00 0.00 2.83
2846 3641 8.437274 ACTAAAAGTATGGGTAGATGGATAGG 57.563 38.462 0.00 0.00 0.00 2.57
2869 3664 5.396548 GGGGGATGAAAGAGTAAAGTAGTCC 60.397 48.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 7.643764 CGATTATTCTGTCGTGCCAAAATTTAT 59.356 33.333 0.00 0.00 33.42 1.40
120 121 9.607988 TTCCTACTCTGCAAAATATTTCGATTA 57.392 29.630 0.10 0.00 0.00 1.75
125 126 7.816640 TGTGTTCCTACTCTGCAAAATATTTC 58.183 34.615 0.10 0.00 0.00 2.17
126 127 7.759489 TGTGTTCCTACTCTGCAAAATATTT 57.241 32.000 0.00 0.00 0.00 1.40
129 130 7.759489 AAATGTGTTCCTACTCTGCAAAATA 57.241 32.000 0.00 0.00 0.00 1.40
252 254 7.847096 TCTATGTGTTCCTATTGCAAGTCTAA 58.153 34.615 4.94 0.00 0.00 2.10
276 278 2.079925 AGACTCGGCAGCTCATTTTTC 58.920 47.619 0.00 0.00 0.00 2.29
277 279 2.191128 AGACTCGGCAGCTCATTTTT 57.809 45.000 0.00 0.00 0.00 1.94
364 371 1.221265 AGCCCATATTTTCCTGCCCAT 59.779 47.619 0.00 0.00 0.00 4.00
390 397 2.439960 CGCACCCTATGGCCCAGTA 61.440 63.158 0.00 0.00 33.59 2.74
405 412 3.597675 TTCGTACATGGGCTGCGCA 62.598 57.895 21.86 21.86 0.00 6.09
437 444 7.123547 ACTTCATCTGTTGGTAAAGGAAAAACA 59.876 33.333 0.00 0.00 0.00 2.83
449 456 4.785376 AGGGATCTTACTTCATCTGTTGGT 59.215 41.667 0.00 0.00 0.00 3.67
483 490 9.708092 GTGGTACTAAACTTTCTTACTTCATCT 57.292 33.333 0.00 0.00 0.00 2.90
484 491 8.933807 GGTGGTACTAAACTTTCTTACTTCATC 58.066 37.037 0.00 0.00 0.00 2.92
485 492 8.657712 AGGTGGTACTAAACTTTCTTACTTCAT 58.342 33.333 0.00 0.00 0.00 2.57
486 493 8.026396 AGGTGGTACTAAACTTTCTTACTTCA 57.974 34.615 0.00 0.00 0.00 3.02
487 494 8.771766 CAAGGTGGTACTAAACTTTCTTACTTC 58.228 37.037 0.00 0.00 0.00 3.01
488 495 8.488668 TCAAGGTGGTACTAAACTTTCTTACTT 58.511 33.333 0.00 0.00 0.00 2.24
489 496 8.026396 TCAAGGTGGTACTAAACTTTCTTACT 57.974 34.615 0.00 0.00 0.00 2.24
490 497 8.667076 TTCAAGGTGGTACTAAACTTTCTTAC 57.333 34.615 0.00 0.00 0.00 2.34
523 530 6.310224 CCGTTCATCGCCAAAAGATTATTTTT 59.690 34.615 0.00 0.00 38.35 1.94
524 531 5.804979 CCGTTCATCGCCAAAAGATTATTTT 59.195 36.000 0.00 0.00 38.35 1.82
529 536 2.432444 TCCGTTCATCGCCAAAAGATT 58.568 42.857 0.00 0.00 38.35 2.40
532 539 1.737236 TCATCCGTTCATCGCCAAAAG 59.263 47.619 0.00 0.00 38.35 2.27
555 562 1.892209 AGGTGCGTTTCTCCGATTTT 58.108 45.000 0.00 0.00 33.65 1.82
562 569 6.665465 ACTAATAAAACAAGGTGCGTTTCTC 58.335 36.000 0.00 0.00 35.57 2.87
606 613 4.003584 AGCCTAGATTACCAACCTACCA 57.996 45.455 0.00 0.00 0.00 3.25
607 614 6.042897 ACATAAGCCTAGATTACCAACCTACC 59.957 42.308 0.00 0.00 0.00 3.18
613 620 8.330247 TGGTTAAACATAAGCCTAGATTACCAA 58.670 33.333 0.00 0.00 0.00 3.67
626 633 7.171337 ACTTGCATGCTTTTGGTTAAACATAAG 59.829 33.333 20.33 16.66 34.06 1.73
631 638 4.570369 ACACTTGCATGCTTTTGGTTAAAC 59.430 37.500 20.33 0.00 0.00 2.01
632 639 4.764172 ACACTTGCATGCTTTTGGTTAAA 58.236 34.783 20.33 0.00 0.00 1.52
640 647 1.265095 CACGAGACACTTGCATGCTTT 59.735 47.619 20.33 0.00 0.00 3.51
676 683 8.593492 AAAGCTTCTGAATTGTTCAAATTACC 57.407 30.769 0.00 0.00 39.58 2.85
677 684 9.468532 AGAAAGCTTCTGAATTGTTCAAATTAC 57.531 29.630 0.00 0.00 39.58 1.89
682 689 5.829924 AGGAGAAAGCTTCTGAATTGTTCAA 59.170 36.000 0.00 0.00 40.87 2.69
699 706 3.620488 GCACATATTCCCACAGGAGAAA 58.380 45.455 0.00 0.00 45.19 2.52
701 708 1.490490 GGCACATATTCCCACAGGAGA 59.510 52.381 0.00 0.00 45.19 3.71
702 709 1.811558 CGGCACATATTCCCACAGGAG 60.812 57.143 0.00 0.00 45.19 3.69
703 710 0.180171 CGGCACATATTCCCACAGGA 59.820 55.000 0.00 0.00 41.88 3.86
708 715 1.453015 GTGGCGGCACATATTCCCA 60.453 57.895 34.40 1.70 0.00 4.37
709 716 1.453015 TGTGGCGGCACATATTCCC 60.453 57.895 37.56 12.73 0.00 3.97
711 718 2.476772 TGTGTGGCGGCACATATTC 58.523 52.632 41.71 30.02 43.54 1.75
717 724 2.977456 TGTCATGTGTGGCGGCAC 60.977 61.111 33.07 33.07 39.65 5.01
718 725 2.977456 GTGTCATGTGTGGCGGCA 60.977 61.111 7.97 7.97 30.74 5.69
719 726 2.257286 GATGTGTCATGTGTGGCGGC 62.257 60.000 0.00 0.00 30.74 6.53
720 727 0.954938 TGATGTGTCATGTGTGGCGG 60.955 55.000 0.00 0.00 30.74 6.13
721 728 0.873721 TTGATGTGTCATGTGTGGCG 59.126 50.000 0.00 0.00 33.56 5.69
722 729 2.159338 GGATTGATGTGTCATGTGTGGC 60.159 50.000 0.00 0.00 33.56 5.01
723 730 3.128068 CAGGATTGATGTGTCATGTGTGG 59.872 47.826 0.00 0.00 33.56 4.17
724 731 4.004982 TCAGGATTGATGTGTCATGTGTG 58.995 43.478 0.00 0.00 33.56 3.82
725 732 4.005650 GTCAGGATTGATGTGTCATGTGT 58.994 43.478 0.00 0.00 35.39 3.72
726 733 4.004982 TGTCAGGATTGATGTGTCATGTG 58.995 43.478 0.00 0.00 35.39 3.21
727 734 4.259356 CTGTCAGGATTGATGTGTCATGT 58.741 43.478 0.00 0.00 35.39 3.21
728 735 4.094442 CACTGTCAGGATTGATGTGTCATG 59.906 45.833 4.53 0.00 36.63 3.07
729 736 4.019950 TCACTGTCAGGATTGATGTGTCAT 60.020 41.667 4.53 0.00 39.49 3.06
730 737 3.324556 TCACTGTCAGGATTGATGTGTCA 59.675 43.478 4.53 0.00 39.49 3.58
731 738 3.681897 GTCACTGTCAGGATTGATGTGTC 59.318 47.826 4.53 5.19 39.49 3.67
732 739 3.071457 TGTCACTGTCAGGATTGATGTGT 59.929 43.478 4.53 0.00 39.49 3.72
733 740 3.667360 TGTCACTGTCAGGATTGATGTG 58.333 45.455 4.53 7.07 39.66 3.21
734 741 4.067896 GTTGTCACTGTCAGGATTGATGT 58.932 43.478 4.53 0.00 35.39 3.06
735 742 3.124128 CGTTGTCACTGTCAGGATTGATG 59.876 47.826 4.53 0.00 35.39 3.07
736 743 3.329386 CGTTGTCACTGTCAGGATTGAT 58.671 45.455 4.53 0.00 35.39 2.57
737 744 2.754472 CGTTGTCACTGTCAGGATTGA 58.246 47.619 4.53 0.00 0.00 2.57
738 745 1.195448 GCGTTGTCACTGTCAGGATTG 59.805 52.381 4.53 0.00 0.00 2.67
739 746 1.202639 TGCGTTGTCACTGTCAGGATT 60.203 47.619 4.53 0.00 0.00 3.01
740 747 0.392706 TGCGTTGTCACTGTCAGGAT 59.607 50.000 4.53 0.00 0.00 3.24
741 748 0.176910 TTGCGTTGTCACTGTCAGGA 59.823 50.000 4.53 0.00 0.00 3.86
742 749 0.304705 GTTGCGTTGTCACTGTCAGG 59.695 55.000 4.53 0.00 0.00 3.86
743 750 0.043053 CGTTGCGTTGTCACTGTCAG 60.043 55.000 0.00 0.00 0.00 3.51
744 751 2.002899 CGTTGCGTTGTCACTGTCA 58.997 52.632 0.00 0.00 0.00 3.58
745 752 1.367665 GCGTTGCGTTGTCACTGTC 60.368 57.895 0.00 0.00 0.00 3.51
746 753 1.813753 AGCGTTGCGTTGTCACTGT 60.814 52.632 0.00 0.00 0.00 3.55
747 754 1.368019 CAGCGTTGCGTTGTCACTG 60.368 57.895 0.00 0.00 33.66 3.66
748 755 2.534019 CCAGCGTTGCGTTGTCACT 61.534 57.895 0.00 0.00 36.40 3.41
749 756 2.052237 CCAGCGTTGCGTTGTCAC 60.052 61.111 0.00 0.00 36.40 3.67
750 757 2.512745 ACCAGCGTTGCGTTGTCA 60.513 55.556 0.00 0.00 36.40 3.58
751 758 2.042520 TTCACCAGCGTTGCGTTGTC 62.043 55.000 0.00 0.00 36.40 3.18
752 759 2.047151 CTTCACCAGCGTTGCGTTGT 62.047 55.000 0.00 0.00 36.40 3.32
753 760 1.369209 CTTCACCAGCGTTGCGTTG 60.369 57.895 0.00 0.00 37.79 4.10
754 761 1.817941 ACTTCACCAGCGTTGCGTT 60.818 52.632 0.00 0.00 0.00 4.84
755 762 2.203015 ACTTCACCAGCGTTGCGT 60.203 55.556 0.00 0.00 0.00 5.24
756 763 2.249309 CACTTCACCAGCGTTGCG 59.751 61.111 0.00 0.00 0.00 4.85
757 764 1.009675 CACACTTCACCAGCGTTGC 60.010 57.895 0.00 0.00 0.00 4.17
758 765 0.583438 CTCACACTTCACCAGCGTTG 59.417 55.000 0.00 0.00 0.00 4.10
759 766 0.178068 ACTCACACTTCACCAGCGTT 59.822 50.000 0.00 0.00 0.00 4.84
760 767 1.037493 TACTCACACTTCACCAGCGT 58.963 50.000 0.00 0.00 0.00 5.07
761 768 1.995484 CATACTCACACTTCACCAGCG 59.005 52.381 0.00 0.00 0.00 5.18
762 769 1.734465 GCATACTCACACTTCACCAGC 59.266 52.381 0.00 0.00 0.00 4.85
763 770 3.325293 AGCATACTCACACTTCACCAG 57.675 47.619 0.00 0.00 0.00 4.00
764 771 3.402110 CAAGCATACTCACACTTCACCA 58.598 45.455 0.00 0.00 0.00 4.17
765 772 2.160417 GCAAGCATACTCACACTTCACC 59.840 50.000 0.00 0.00 0.00 4.02
766 773 3.070018 AGCAAGCATACTCACACTTCAC 58.930 45.455 0.00 0.00 0.00 3.18
767 774 3.407424 AGCAAGCATACTCACACTTCA 57.593 42.857 0.00 0.00 0.00 3.02
768 775 4.272018 CCATAGCAAGCATACTCACACTTC 59.728 45.833 0.00 0.00 0.00 3.01
769 776 4.080919 TCCATAGCAAGCATACTCACACTT 60.081 41.667 0.00 0.00 0.00 3.16
770 777 3.452264 TCCATAGCAAGCATACTCACACT 59.548 43.478 0.00 0.00 0.00 3.55
771 778 3.797039 TCCATAGCAAGCATACTCACAC 58.203 45.455 0.00 0.00 0.00 3.82
772 779 4.486125 TTCCATAGCAAGCATACTCACA 57.514 40.909 0.00 0.00 0.00 3.58
773 780 6.038603 TCAAATTCCATAGCAAGCATACTCAC 59.961 38.462 0.00 0.00 0.00 3.51
774 781 6.121590 TCAAATTCCATAGCAAGCATACTCA 58.878 36.000 0.00 0.00 0.00 3.41
783 790 7.994425 TGTCTAAACTCAAATTCCATAGCAA 57.006 32.000 0.00 0.00 0.00 3.91
784 791 7.994425 TTGTCTAAACTCAAATTCCATAGCA 57.006 32.000 0.00 0.00 0.00 3.49
789 796 6.017440 CGAGGTTTGTCTAAACTCAAATTCCA 60.017 38.462 11.78 0.00 44.39 3.53
790 797 6.371389 CGAGGTTTGTCTAAACTCAAATTCC 58.629 40.000 11.78 0.00 44.39 3.01
802 809 2.263540 GCCGGCGAGGTTTGTCTA 59.736 61.111 12.58 0.00 43.70 2.59
835 1523 1.466558 GCGCCTTCCTCTTTCTTTGAG 59.533 52.381 0.00 0.00 0.00 3.02
840 1528 0.606673 GTTGGCGCCTTCCTCTTTCT 60.607 55.000 29.70 0.00 0.00 2.52
846 1534 1.302832 CTTCTGTTGGCGCCTTCCT 60.303 57.895 29.70 0.00 0.00 3.36
862 1550 7.980099 GGAATATGTAGTAAGTATATGCGGCTT 59.020 37.037 0.00 0.00 0.00 4.35
865 1553 7.435488 GCAGGAATATGTAGTAAGTATATGCGG 59.565 40.741 0.00 0.00 0.00 5.69
873 1561 6.583562 GTCAAGGCAGGAATATGTAGTAAGT 58.416 40.000 0.00 0.00 0.00 2.24
875 1563 5.452776 CCGTCAAGGCAGGAATATGTAGTAA 60.453 44.000 0.00 0.00 0.00 2.24
880 1568 1.837439 TCCGTCAAGGCAGGAATATGT 59.163 47.619 0.00 0.00 40.77 2.29
889 1577 0.687920 TTGGTATGTCCGTCAAGGCA 59.312 50.000 0.00 0.00 40.77 4.75
890 1578 1.467342 GTTTGGTATGTCCGTCAAGGC 59.533 52.381 0.00 0.00 40.77 4.35
894 1582 2.080693 GCATGTTTGGTATGTCCGTCA 58.919 47.619 0.00 0.00 39.52 4.35
924 1616 4.045636 ACAAGATGAAGCAAACACCAAC 57.954 40.909 0.00 0.00 0.00 3.77
952 1644 7.856398 ACGCGTTCATGTATATATAGCATACTC 59.144 37.037 5.58 0.00 31.43 2.59
972 1669 5.469084 TGATCTGATACTGATAGTACGCGTT 59.531 40.000 20.78 1.73 32.84 4.84
975 1672 7.975750 TGTATGATCTGATACTGATAGTACGC 58.024 38.462 0.00 0.00 32.84 4.42
980 1677 8.009622 AGCCATGTATGATCTGATACTGATAG 57.990 38.462 0.00 0.00 31.15 2.08
1083 1780 1.213537 GGCACGGCAGTACTCGTAA 59.786 57.895 9.06 0.00 37.88 3.18
1623 2320 4.704833 TGCTGTCCCTGCTTCGCC 62.705 66.667 0.00 0.00 0.00 5.54
1782 2482 0.465705 CCGTCATGCTCCCATACACT 59.534 55.000 0.00 0.00 0.00 3.55
1875 2575 3.614616 CGGCTAGAGTTTGTTAGAGCTTG 59.385 47.826 0.00 0.00 0.00 4.01
1949 2649 1.119684 TCCATAGTGCAGCGGTACAT 58.880 50.000 7.89 0.00 31.27 2.29
1954 2654 2.481568 CACATAATCCATAGTGCAGCGG 59.518 50.000 0.00 0.00 0.00 5.52
1955 2655 3.185188 GTCACATAATCCATAGTGCAGCG 59.815 47.826 0.00 0.00 32.25 5.18
1957 2657 3.185188 GCGTCACATAATCCATAGTGCAG 59.815 47.826 0.00 0.00 32.25 4.41
1959 2659 2.155732 CGCGTCACATAATCCATAGTGC 59.844 50.000 0.00 0.00 32.25 4.40
1960 2660 3.182372 CACGCGTCACATAATCCATAGTG 59.818 47.826 9.86 0.00 0.00 2.74
1978 2678 9.419297 TGGAGAAGTTAATATGATAATACACGC 57.581 33.333 0.00 0.00 0.00 5.34
1985 2685 9.476202 CGTCACATGGAGAAGTTAATATGATAA 57.524 33.333 0.00 0.00 0.00 1.75
2004 2704 0.468226 AGTTGTCCCACACGTCACAT 59.532 50.000 0.00 0.00 0.00 3.21
2082 2783 6.035368 TGTGGGTTGGTTCAAAATATGATG 57.965 37.500 0.00 0.00 38.03 3.07
2119 2822 1.523758 ACTGAAAAGCGTGGATGGAC 58.476 50.000 0.00 0.00 0.00 4.02
2293 3005 8.752005 ACACACATGCAATAGTTTCCTATAAT 57.248 30.769 0.00 0.00 32.57 1.28
2294 3006 8.574251 AACACACATGCAATAGTTTCCTATAA 57.426 30.769 0.00 0.00 32.57 0.98
2295 3007 8.574251 AAACACACATGCAATAGTTTCCTATA 57.426 30.769 0.00 0.00 32.57 1.31
2296 3008 7.176515 TGAAACACACATGCAATAGTTTCCTAT 59.823 33.333 20.65 0.00 42.31 2.57
2392 3112 9.480053 TTTGAAAGCTCCAAAATAGAAATGAAG 57.520 29.630 10.64 0.00 31.36 3.02
2451 3184 9.797556 GTAAAATTGTGGTGATAAGGAAATACC 57.202 33.333 0.00 0.00 39.35 2.73
2579 3370 7.924412 TGACAAAGATAGCGTAATAAACCCTAG 59.076 37.037 0.00 0.00 0.00 3.02
2641 3433 8.975663 AACTCATGTGAAATGTGAGATGATAT 57.024 30.769 8.44 0.00 41.38 1.63
2740 3535 5.895636 TGTTTGCAGATTAGTGGTATTGG 57.104 39.130 0.00 0.00 0.00 3.16
2763 3558 6.703319 TGAACCAATGATCTGATTTGCAATT 58.297 32.000 0.00 0.00 0.00 2.32
2768 3563 8.597662 AACTTTTGAACCAATGATCTGATTTG 57.402 30.769 0.00 0.00 0.00 2.32
2819 3614 6.742559 TCCATCTACCCATACTTTTAGTCC 57.257 41.667 0.00 0.00 0.00 3.85
2846 3641 5.672503 GGACTACTTTACTCTTTCATCCCC 58.327 45.833 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.