Multiple sequence alignment - TraesCS5B01G462000

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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 TraesCS5B01G462000 chr5B 100.000 3596 0 0 1 3596 637448664 637445069 0.000000e+00 6641.0
1 TraesCS5B01G462000 chr5B 98.810 84 1 0 1 84 5595005 5594922 2.240000e-32 150.0
2 TraesCS5B01G462000 chr5B 100.000 81 0 0 1 81 493459748 493459828 2.240000e-32 150.0
3 TraesCS5B01G462000 chr5A 87.093 1937 167 33 691 2573 634499890 634497983 0.000000e+00 2115.0
4 TraesCS5B01G462000 chr5D 90.736 1414 82 16 1195 2578 507422168 507420774 0.000000e+00 1840.0
5 TraesCS5B01G462000 chr5D 88.557 603 64 2 78 676 130412607 130412006 0.000000e+00 726.0
6 TraesCS5B01G462000 chr5D 77.537 1291 209 48 1313 2568 506949990 506948746 0.000000e+00 702.0
7 TraesCS5B01G462000 chr5D 82.846 787 99 7 2804 3586 108959848 108959094 0.000000e+00 673.0
8 TraesCS5B01G462000 chr5D 88.958 480 43 6 1195 1664 507139620 507139141 5.170000e-163 584.0
9 TraesCS5B01G462000 chr5D 78.322 858 146 24 1738 2568 507138797 507137953 5.320000e-143 518.0
10 TraesCS5B01G462000 chr5D 86.000 200 21 5 2362 2555 507165676 507165478 1.310000e-49 207.0
11 TraesCS5B01G462000 chr5D 82.805 221 27 6 2355 2573 506941352 506941141 1.700000e-43 187.0
12 TraesCS5B01G462000 chr3B 97.482 993 24 1 2605 3596 244629626 244628634 0.000000e+00 1694.0
13 TraesCS5B01G462000 chr3B 84.331 919 102 18 2690 3590 170807909 170807015 0.000000e+00 861.0
14 TraesCS5B01G462000 chr3B 83.306 605 93 5 78 676 157366364 157365762 5.250000e-153 551.0
15 TraesCS5B01G462000 chr3B 100.000 28 0 0 2576 2603 785655357 785655330 6.000000e-03 52.8
16 TraesCS5B01G462000 chr6B 96.065 991 37 2 2607 3596 561643225 561642236 0.000000e+00 1613.0
17 TraesCS5B01G462000 chr7B 95.972 993 22 3 2605 3596 158398277 158397302 0.000000e+00 1596.0
18 TraesCS5B01G462000 chr7B 85.124 242 36 0 2607 2848 440249477 440249718 7.710000e-62 248.0
19 TraesCS5B01G462000 chr7B 82.645 121 16 5 862 979 629027630 629027512 6.350000e-18 102.0
20 TraesCS5B01G462000 chr1B 92.649 993 69 4 2605 3596 326206321 326207310 0.000000e+00 1426.0
21 TraesCS5B01G462000 chr1B 82.578 706 103 14 2618 3307 549031242 549031943 3.970000e-169 604.0
22 TraesCS5B01G462000 chr1B 97.727 88 0 1 1 88 330660103 330660018 2.240000e-32 150.0
23 TraesCS5B01G462000 chr6D 88.867 997 106 4 2604 3596 124640818 124639823 0.000000e+00 1221.0
24 TraesCS5B01G462000 chr6D 90.164 610 54 3 75 680 225076115 225075508 0.000000e+00 789.0
25 TraesCS5B01G462000 chr6D 84.488 606 90 1 75 676 202963711 202964316 2.390000e-166 595.0
26 TraesCS5B01G462000 chr6D 87.952 415 48 2 2607 3020 124639044 124639457 4.170000e-134 488.0
27 TraesCS5B01G462000 chr6D 75.347 288 44 19 855 1125 338738598 338738321 2.930000e-21 113.0
28 TraesCS5B01G462000 chr6D 80.000 100 16 3 858 954 14538943 14539041 1.790000e-08 71.3
29 TraesCS5B01G462000 chr4D 87.753 792 91 6 2804 3590 43404122 43404912 0.000000e+00 920.0
30 TraesCS5B01G462000 chr4D 78.188 298 40 17 843 1131 88148288 88148007 2.220000e-37 167.0
31 TraesCS5B01G462000 chr7D 84.221 976 116 19 2623 3590 404241420 404240475 0.000000e+00 915.0
32 TraesCS5B01G462000 chr7D 85.333 600 86 2 78 676 28197378 28196780 1.420000e-173 619.0
33 TraesCS5B01G462000 chr7D 83.761 117 16 3 862 976 572034884 572034769 1.370000e-19 108.0
34 TraesCS5B01G462000 chr7D 91.892 37 3 0 2575 2611 417794797 417794761 6.000000e-03 52.8
35 TraesCS5B01G462000 chr6A 89.256 605 59 3 75 675 274956083 274955481 0.000000e+00 752.0
36 TraesCS5B01G462000 chr3D 88.779 606 64 1 75 676 231699519 231700124 0.000000e+00 739.0
37 TraesCS5B01G462000 chr3D 76.101 159 22 12 939 1093 178590357 178590211 6.440000e-08 69.4
38 TraesCS5B01G462000 chr2B 83.770 610 91 5 75 678 441074447 441075054 4.030000e-159 571.0
39 TraesCS5B01G462000 chr2B 96.591 88 1 2 1 88 713620986 713620901 1.040000e-30 145.0
40 TraesCS5B01G462000 chr2B 83.846 130 16 3 913 1042 47370366 47370242 6.310000e-23 119.0
41 TraesCS5B01G462000 chr2B 100.000 28 0 0 2575 2602 785955810 785955783 6.000000e-03 52.8
42 TraesCS5B01G462000 chr4B 81.549 607 104 5 75 676 362341202 362341805 8.970000e-136 494.0
43 TraesCS5B01G462000 chr4B 81.407 199 18 12 924 1116 124922801 124922616 1.040000e-30 145.0
44 TraesCS5B01G462000 chr2D 84.581 227 23 7 2624 2842 325652885 325652663 7.820000e-52 215.0
45 TraesCS5B01G462000 chr2D 95.455 88 3 1 1 87 36376253 36376340 4.840000e-29 139.0
46 TraesCS5B01G462000 chr2D 77.570 107 17 6 728 830 423558022 423558125 1.390000e-04 58.4
47 TraesCS5B01G462000 chr4A 78.295 258 38 12 845 1097 4247898 4248142 2.240000e-32 150.0
48 TraesCS5B01G462000 chr4A 98.780 82 1 0 1 82 642008317 642008236 2.890000e-31 147.0
49 TraesCS5B01G462000 chr4A 95.506 89 3 1 1 89 455474400 455474313 1.350000e-29 141.0
50 TraesCS5B01G462000 chr4A 79.630 216 23 14 924 1131 501128834 501128632 6.260000e-28 135.0
51 TraesCS5B01G462000 chr3A 96.552 87 2 1 1 87 176541627 176541542 3.740000e-30 143.0
52 TraesCS5B01G462000 chr7A 94.505 91 3 2 1 91 299032645 299032557 4.840000e-29 139.0
53 TraesCS5B01G462000 chr7A 81.176 170 20 9 924 1087 664370858 664370695 3.770000e-25 126.0
54 TraesCS5B01G462000 chr7A 82.114 123 19 3 856 976 661295709 661295588 6.350000e-18 102.0
55 TraesCS5B01G462000 chrUn 82.400 125 17 5 856 976 90079163 90079040 1.770000e-18 104.0
56 TraesCS5B01G462000 chrUn 100.000 28 0 0 2575 2602 277180054 277180027 6.000000e-03 52.8
57 TraesCS5B01G462000 chrUn 100.000 28 0 0 2575 2602 300679901 300679928 6.000000e-03 52.8
58 TraesCS5B01G462000 chr2A 100.000 28 0 0 2575 2602 42783352 42783379 6.000000e-03 52.8


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 TraesCS5B01G462000 chr5B 637445069 637448664 3595 True 6641 6641 100.000 1 3596 1 chr5B.!!$R2 3595
1 TraesCS5B01G462000 chr5A 634497983 634499890 1907 True 2115 2115 87.093 691 2573 1 chr5A.!!$R1 1882
2 TraesCS5B01G462000 chr5D 507420774 507422168 1394 True 1840 1840 90.736 1195 2578 1 chr5D.!!$R6 1383
3 TraesCS5B01G462000 chr5D 130412006 130412607 601 True 726 726 88.557 78 676 1 chr5D.!!$R2 598
4 TraesCS5B01G462000 chr5D 506948746 506949990 1244 True 702 702 77.537 1313 2568 1 chr5D.!!$R4 1255
5 TraesCS5B01G462000 chr5D 108959094 108959848 754 True 673 673 82.846 2804 3586 1 chr5D.!!$R1 782
6 TraesCS5B01G462000 chr5D 507137953 507139620 1667 True 551 584 83.640 1195 2568 2 chr5D.!!$R7 1373
7 TraesCS5B01G462000 chr3B 244628634 244629626 992 True 1694 1694 97.482 2605 3596 1 chr3B.!!$R3 991
8 TraesCS5B01G462000 chr3B 170807015 170807909 894 True 861 861 84.331 2690 3590 1 chr3B.!!$R2 900
9 TraesCS5B01G462000 chr3B 157365762 157366364 602 True 551 551 83.306 78 676 1 chr3B.!!$R1 598
10 TraesCS5B01G462000 chr6B 561642236 561643225 989 True 1613 1613 96.065 2607 3596 1 chr6B.!!$R1 989
11 TraesCS5B01G462000 chr7B 158397302 158398277 975 True 1596 1596 95.972 2605 3596 1 chr7B.!!$R1 991
12 TraesCS5B01G462000 chr1B 326206321 326207310 989 False 1426 1426 92.649 2605 3596 1 chr1B.!!$F1 991
13 TraesCS5B01G462000 chr1B 549031242 549031943 701 False 604 604 82.578 2618 3307 1 chr1B.!!$F2 689
14 TraesCS5B01G462000 chr6D 124639823 124640818 995 True 1221 1221 88.867 2604 3596 1 chr6D.!!$R1 992
15 TraesCS5B01G462000 chr6D 225075508 225076115 607 True 789 789 90.164 75 680 1 chr6D.!!$R2 605
16 TraesCS5B01G462000 chr6D 202963711 202964316 605 False 595 595 84.488 75 676 1 chr6D.!!$F3 601
17 TraesCS5B01G462000 chr4D 43404122 43404912 790 False 920 920 87.753 2804 3590 1 chr4D.!!$F1 786
18 TraesCS5B01G462000 chr7D 404240475 404241420 945 True 915 915 84.221 2623 3590 1 chr7D.!!$R2 967
19 TraesCS5B01G462000 chr7D 28196780 28197378 598 True 619 619 85.333 78 676 1 chr7D.!!$R1 598
20 TraesCS5B01G462000 chr6A 274955481 274956083 602 True 752 752 89.256 75 675 1 chr6A.!!$R1 600
21 TraesCS5B01G462000 chr3D 231699519 231700124 605 False 739 739 88.779 75 676 1 chr3D.!!$F1 601
22 TraesCS5B01G462000 chr2B 441074447 441075054 607 False 571 571 83.770 75 678 1 chr2B.!!$F1 603
23 TraesCS5B01G462000 chr4B 362341202 362341805 603 False 494 494 81.549 75 676 1 chr4B.!!$F1 601

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
768 774 0.828022 TCAAGCCACTATGTACGGGG 59.172 55.0 0.0 0.0 0.00 5.73 F
1213 1226 0.179129 CTTTGCATGTTGGGCCGATC 60.179 55.0 0.0 0.0 0.00 3.69 F
2092 2439 0.465705 ATGTCTACTGGGCATCCGTG 59.534 55.0 0.0 0.0 35.24 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2420 0.465705 CACGGATGCCCAGTAGACAT 59.534 55.000 0.00 0.0 0.0 3.06 R
2347 2724 0.532862 CACAACCTTCAGTCGTGGCT 60.533 55.000 0.00 0.0 0.0 4.75 R
3316 3730 1.819632 GTTCTCGGCCGCATCCATT 60.820 57.895 23.51 0.0 0.0 3.16 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
73 74 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
90 91 2.422276 ACATTTCTTTGGCTTGCGAC 57.578 45.000 0.00 0.00 0.00 5.19
164 165 2.916703 ACGCATGCCCCTTTTGCA 60.917 55.556 13.15 0.00 43.97 4.08
198 199 4.225984 GAGACCATCGATCATCTTCTTCG 58.774 47.826 8.90 0.00 0.00 3.79
199 200 3.634448 AGACCATCGATCATCTTCTTCGT 59.366 43.478 0.00 0.00 34.60 3.85
205 206 2.736719 CGATCATCTTCTTCGTGGCTGT 60.737 50.000 0.00 0.00 0.00 4.40
356 357 4.234574 CACACGTGCAATCTTACTACTCA 58.765 43.478 17.22 0.00 0.00 3.41
407 408 1.078497 ATTGTCTTCGATGGCGCCA 60.078 52.632 34.80 34.80 37.46 5.69
412 414 3.976701 CTTCGATGGCGCCACCCTT 62.977 63.158 35.50 17.44 37.83 3.95
453 455 2.226330 CAAAATTGACACCGAGGGACA 58.774 47.619 0.00 0.00 0.00 4.02
502 504 3.730269 AGGAAATGTAGAGCCTCTCCTT 58.270 45.455 0.00 0.00 0.00 3.36
533 535 2.367512 GGTGGGCTGAGGGGAGAT 60.368 66.667 0.00 0.00 0.00 2.75
553 555 7.364851 GGGAGATGTTAGGCTAGAGTAGTTTTT 60.365 40.741 0.00 0.00 0.00 1.94
567 573 5.246307 AGTAGTTTTTGGCTATGTGGAGTC 58.754 41.667 0.00 0.00 0.00 3.36
569 575 3.071479 GTTTTTGGCTATGTGGAGTCGA 58.929 45.455 0.00 0.00 0.00 4.20
615 621 2.203437 GCCAACGTGGAGGGGTTT 60.203 61.111 8.04 0.00 40.96 3.27
751 757 6.762702 ACATGCAACTATGTCAATTCATCA 57.237 33.333 0.00 0.00 36.60 3.07
758 764 5.503927 ACTATGTCAATTCATCAAGCCACT 58.496 37.500 0.00 0.00 0.00 4.00
762 768 5.255687 TGTCAATTCATCAAGCCACTATGT 58.744 37.500 0.00 0.00 0.00 2.29
766 772 3.452755 TCATCAAGCCACTATGTACGG 57.547 47.619 0.00 0.00 0.00 4.02
768 774 0.828022 TCAAGCCACTATGTACGGGG 59.172 55.000 0.00 0.00 0.00 5.73
772 778 1.910671 AGCCACTATGTACGGGGAAAA 59.089 47.619 0.00 0.00 0.00 2.29
774 780 2.421073 GCCACTATGTACGGGGAAAAAC 59.579 50.000 0.00 0.00 0.00 2.43
791 797 2.621556 AACCCCACCTTAACATGCAT 57.378 45.000 0.00 0.00 0.00 3.96
812 818 6.555812 CATCATGCATGCTACTTATCTTGT 57.444 37.500 22.25 0.00 0.00 3.16
817 823 8.955388 TCATGCATGCTACTTATCTTGTTAAAA 58.045 29.630 22.25 0.00 0.00 1.52
870 878 1.285280 TGCAACTAGGTATGTGCCCT 58.715 50.000 0.00 0.00 36.04 5.19
881 889 3.910490 GTGCCCTTGCGTTGCCAA 61.910 61.111 0.00 0.00 41.78 4.52
884 892 2.639327 GCCCTTGCGTTGCCAAGAT 61.639 57.895 3.65 0.00 43.79 2.40
885 893 1.312371 GCCCTTGCGTTGCCAAGATA 61.312 55.000 3.65 0.00 43.79 1.98
1034 1043 8.358148 ACTTATAAAGTAGGTATGTGTCGATGG 58.642 37.037 0.00 0.00 40.69 3.51
1046 1055 4.055360 TGTGTCGATGGTTACTCTGTTTG 58.945 43.478 0.00 0.00 0.00 2.93
1071 1083 9.316594 TGGGTTACCGAATATAAGAGATTGATA 57.683 33.333 0.00 0.00 40.75 2.15
1148 1160 1.009449 CTCGAGCGAGTCCGATTCC 60.009 63.158 11.50 0.00 37.47 3.01
1160 1172 5.567138 AGTCCGATTCCACAATGATTTTC 57.433 39.130 0.00 0.00 0.00 2.29
1166 1178 5.959527 CGATTCCACAATGATTTTCGTGTAG 59.040 40.000 0.00 0.00 0.00 2.74
1167 1179 4.678509 TCCACAATGATTTTCGTGTAGC 57.321 40.909 0.00 0.00 0.00 3.58
1170 1182 3.190327 CACAATGATTTTCGTGTAGCCCA 59.810 43.478 0.00 0.00 0.00 5.36
1171 1183 3.440173 ACAATGATTTTCGTGTAGCCCAG 59.560 43.478 0.00 0.00 0.00 4.45
1213 1226 0.179129 CTTTGCATGTTGGGCCGATC 60.179 55.000 0.00 0.00 0.00 3.69
1218 1231 2.735772 ATGTTGGGCCGATCGCTCT 61.736 57.895 10.32 0.00 39.51 4.09
1293 1306 1.377229 CTAACCCTTTCCCGTGGCA 59.623 57.895 0.00 0.00 0.00 4.92
1298 1311 2.354729 CTTTCCCGTGGCATCCCA 59.645 61.111 0.00 0.00 39.32 4.37
1299 1312 1.750399 CTTTCCCGTGGCATCCCAG 60.750 63.158 0.00 0.00 43.18 4.45
1300 1313 3.936772 TTTCCCGTGGCATCCCAGC 62.937 63.158 0.00 0.00 43.18 4.85
1336 1359 4.575973 ATCGCCATGGCCTCCAGC 62.576 66.667 30.79 4.35 36.75 4.85
1713 1931 0.553333 GATGAAGGGGAAGGGGAAGG 59.447 60.000 0.00 0.00 0.00 3.46
1714 1932 0.926220 ATGAAGGGGAAGGGGAAGGG 60.926 60.000 0.00 0.00 0.00 3.95
1715 1933 2.204464 AAGGGGAAGGGGAAGGGG 60.204 66.667 0.00 0.00 0.00 4.79
1716 1934 2.800523 GAAGGGGAAGGGGAAGGGGA 62.801 65.000 0.00 0.00 0.00 4.81
1717 1935 2.204401 GGGGAAGGGGAAGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
1718 1936 2.317378 GGGGAAGGGGAAGGGGAAG 61.317 68.421 0.00 0.00 0.00 3.46
1722 1940 1.151877 AAGGGGAAGGGGAAGACGT 60.152 57.895 0.00 0.00 0.00 4.34
1790 2110 2.474410 GGTTCTCATCAACCGGACTT 57.526 50.000 9.46 0.00 36.69 3.01
1876 2223 4.148825 CCGCCCGGAGAACCAGAG 62.149 72.222 0.73 0.00 37.50 3.35
1880 2227 1.305381 CCCGGAGAACCAGAGGAGT 60.305 63.158 0.73 0.00 35.59 3.85
1977 2324 4.323477 TGGGAAAGTGCGGGTCGG 62.323 66.667 0.00 0.00 0.00 4.79
2008 2355 2.673523 GACAGCAGGGAGTGGCAT 59.326 61.111 0.00 0.00 0.00 4.40
2019 2366 1.202818 GGAGTGGCATATCTCCCCAAC 60.203 57.143 10.72 0.00 42.96 3.77
2073 2420 1.094785 GGTACGCTAGTGAACGGGTA 58.905 55.000 10.99 0.00 0.00 3.69
2092 2439 0.465705 ATGTCTACTGGGCATCCGTG 59.534 55.000 0.00 0.00 35.24 4.94
2320 2697 1.002684 GACGATATCGACAAGCTCCGT 60.003 52.381 30.75 5.27 43.02 4.69
2347 2724 5.046878 ACAGTTTGTAGATCATTACCCACGA 60.047 40.000 0.00 0.00 0.00 4.35
2348 2725 5.520288 CAGTTTGTAGATCATTACCCACGAG 59.480 44.000 0.00 0.00 0.00 4.18
2349 2726 3.728076 TGTAGATCATTACCCACGAGC 57.272 47.619 0.00 0.00 0.00 5.03
2350 2727 2.364324 TGTAGATCATTACCCACGAGCC 59.636 50.000 0.00 0.00 0.00 4.70
2351 2728 1.496060 AGATCATTACCCACGAGCCA 58.504 50.000 0.00 0.00 0.00 4.75
2352 2729 1.139058 AGATCATTACCCACGAGCCAC 59.861 52.381 0.00 0.00 0.00 5.01
2485 2868 1.691434 GAAGGAGGTCTGCCCTATCAG 59.309 57.143 0.00 0.00 46.51 2.90
2537 2920 1.795170 CGTGGCCTCCTGTTTTGGTG 61.795 60.000 3.32 0.00 0.00 4.17
2568 2951 2.750712 GTGAACTCTCTCGGCTAGAAGT 59.249 50.000 0.00 0.00 32.46 3.01
2573 2956 1.212195 TCTCTCGGCTAGAAGTGGCTA 59.788 52.381 0.00 0.00 32.46 3.93
2578 2961 3.147629 TCGGCTAGAAGTGGCTATAGTC 58.852 50.000 0.00 0.00 0.00 2.59
2579 2962 3.150767 CGGCTAGAAGTGGCTATAGTCT 58.849 50.000 5.83 0.67 0.00 3.24
2580 2963 3.570550 CGGCTAGAAGTGGCTATAGTCTT 59.429 47.826 5.83 6.33 0.00 3.01
2581 2964 4.038162 CGGCTAGAAGTGGCTATAGTCTTT 59.962 45.833 5.83 0.23 0.00 2.52
2582 2965 5.241064 CGGCTAGAAGTGGCTATAGTCTTTA 59.759 44.000 5.83 2.77 0.00 1.85
2583 2966 6.071840 CGGCTAGAAGTGGCTATAGTCTTTAT 60.072 42.308 5.83 0.81 0.00 1.40
2584 2967 7.317390 GGCTAGAAGTGGCTATAGTCTTTATC 58.683 42.308 5.83 0.00 0.00 1.75
2585 2968 7.177744 GGCTAGAAGTGGCTATAGTCTTTATCT 59.822 40.741 5.83 6.79 0.00 1.98
2586 2969 8.581578 GCTAGAAGTGGCTATAGTCTTTATCTT 58.418 37.037 5.83 3.11 0.00 2.40
2590 2973 9.478768 GAAGTGGCTATAGTCTTTATCTTTACC 57.521 37.037 5.83 0.00 0.00 2.85
2591 2974 8.785184 AGTGGCTATAGTCTTTATCTTTACCT 57.215 34.615 5.83 0.00 0.00 3.08
2592 2975 9.878737 AGTGGCTATAGTCTTTATCTTTACCTA 57.121 33.333 5.83 0.00 0.00 3.08
3075 3464 0.107703 CTACCGATTTGCCCTGCAGA 60.108 55.000 17.39 0.00 40.61 4.26
3413 3828 2.360852 GTGATGCTGCTGCCACCT 60.361 61.111 13.47 0.00 38.71 4.00
3517 3932 2.355126 CACTGCGTGCGTCTGAGT 60.355 61.111 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.437682 TGTTGGAAATATGCCCTAGAGG 57.562 45.455 0.00 0.00 39.47 3.69
53 54 6.774656 AGAAATGTTGGAAATATGCCCTAGAG 59.225 38.462 0.00 0.00 0.00 2.43
54 55 6.672593 AGAAATGTTGGAAATATGCCCTAGA 58.327 36.000 0.00 0.00 0.00 2.43
55 56 6.966534 AGAAATGTTGGAAATATGCCCTAG 57.033 37.500 0.00 0.00 0.00 3.02
56 57 7.555087 CAAAGAAATGTTGGAAATATGCCCTA 58.445 34.615 0.00 0.00 0.00 3.53
57 58 6.408869 CAAAGAAATGTTGGAAATATGCCCT 58.591 36.000 0.00 0.00 0.00 5.19
58 59 6.667007 CAAAGAAATGTTGGAAATATGCCC 57.333 37.500 0.00 0.00 0.00 5.36
69 70 2.472488 GTCGCAAGCCAAAGAAATGTTG 59.528 45.455 0.00 0.00 37.18 3.33
70 71 2.742774 GTCGCAAGCCAAAGAAATGTT 58.257 42.857 0.00 0.00 37.18 2.71
71 72 1.334960 CGTCGCAAGCCAAAGAAATGT 60.335 47.619 0.00 0.00 37.18 2.71
72 73 1.330306 CGTCGCAAGCCAAAGAAATG 58.670 50.000 0.00 0.00 37.18 2.32
73 74 0.387239 GCGTCGCAAGCCAAAGAAAT 60.387 50.000 13.44 0.00 37.18 2.17
90 91 3.675225 CGAGGTCCAACATCTATTATGCG 59.325 47.826 0.00 0.00 0.00 4.73
164 165 2.417379 CGATGGTCTCCTCGTGTTGATT 60.417 50.000 0.00 0.00 0.00 2.57
198 199 2.355837 TCGCGAAGACACAGCCAC 60.356 61.111 6.20 0.00 0.00 5.01
199 200 2.049156 CTCGCGAAGACACAGCCA 60.049 61.111 11.33 0.00 0.00 4.75
205 206 2.394708 CAAACTTCTCTCGCGAAGACA 58.605 47.619 11.33 6.63 42.29 3.41
306 307 0.034186 CCCTTGGCCATGAGTAGCAA 60.034 55.000 19.85 0.00 0.00 3.91
356 357 3.117398 TGCTTCCAAATCTCCCATAGCAT 60.117 43.478 0.00 0.00 32.94 3.79
453 455 1.271543 TGCTAGCTTGCTTCCATGTGT 60.272 47.619 20.64 0.00 0.00 3.72
502 504 0.909610 CCCACCTGACTAGCCCTTCA 60.910 60.000 0.00 0.00 0.00 3.02
533 535 5.012768 AGCCAAAAACTACTCTAGCCTAACA 59.987 40.000 0.00 0.00 0.00 2.41
553 555 1.040646 GGATCGACTCCACATAGCCA 58.959 55.000 8.48 0.00 44.26 4.75
567 573 6.843069 TGTTACAATGATACATGTGGATCG 57.157 37.500 9.11 0.00 0.00 3.69
741 747 5.523552 CGTACATAGTGGCTTGATGAATTGA 59.476 40.000 0.00 0.00 0.00 2.57
745 751 3.431626 CCCGTACATAGTGGCTTGATGAA 60.432 47.826 0.00 0.00 0.00 2.57
751 757 1.575419 TTCCCCGTACATAGTGGCTT 58.425 50.000 0.00 0.00 0.00 4.35
768 774 3.070302 TGCATGTTAAGGTGGGGTTTTTC 59.930 43.478 0.00 0.00 0.00 2.29
772 778 2.225242 TGATGCATGTTAAGGTGGGGTT 60.225 45.455 2.46 0.00 0.00 4.11
774 780 2.142356 TGATGCATGTTAAGGTGGGG 57.858 50.000 2.46 0.00 0.00 4.96
791 797 8.504812 TTTAACAAGATAAGTAGCATGCATGA 57.495 30.769 30.64 7.50 0.00 3.07
840 846 8.395633 CACATACCTAGTTGCAACTAAAATACC 58.604 37.037 32.86 5.36 40.70 2.73
870 878 1.610363 TTGGTATCTTGGCAACGCAA 58.390 45.000 0.00 0.00 42.51 4.85
901 910 7.115414 TGTCATGTATGGTCCATGTATTTTGA 58.885 34.615 15.10 6.21 40.43 2.69
902 911 7.332213 TGTCATGTATGGTCCATGTATTTTG 57.668 36.000 15.10 4.10 40.43 2.44
911 920 5.814481 TCAAGATTTGTCATGTATGGTCCA 58.186 37.500 0.00 0.00 0.00 4.02
921 930 5.142061 TGCTTTGCATCAAGATTTGTCAT 57.858 34.783 2.23 0.00 31.71 3.06
922 931 4.587584 TGCTTTGCATCAAGATTTGTCA 57.412 36.364 2.23 0.00 31.71 3.58
1011 1020 7.828508 ACCATCGACACATACCTACTTTATA 57.171 36.000 0.00 0.00 0.00 0.98
1017 1026 5.298777 AGAGTAACCATCGACACATACCTAC 59.701 44.000 0.00 0.00 0.00 3.18
1030 1039 4.698780 GGTAACCCAAACAGAGTAACCATC 59.301 45.833 0.00 0.00 0.00 3.51
1034 1043 3.993920 TCGGTAACCCAAACAGAGTAAC 58.006 45.455 0.00 0.00 0.00 2.50
1046 1055 9.804758 CTATCAATCTCTTATATTCGGTAACCC 57.195 37.037 0.00 0.00 0.00 4.11
1071 1083 7.824779 CCCAGAAGCAAAAGTAAATACTCTACT 59.175 37.037 0.00 0.00 34.99 2.57
1073 1085 6.598064 GCCCAGAAGCAAAAGTAAATACTCTA 59.402 38.462 0.00 0.00 34.99 2.43
1074 1086 5.416013 GCCCAGAAGCAAAAGTAAATACTCT 59.584 40.000 0.00 0.00 34.99 3.24
1075 1087 5.393135 GGCCCAGAAGCAAAAGTAAATACTC 60.393 44.000 0.00 0.00 34.99 2.59
1076 1088 4.462834 GGCCCAGAAGCAAAAGTAAATACT 59.537 41.667 0.00 0.00 38.39 2.12
1077 1089 4.674362 CGGCCCAGAAGCAAAAGTAAATAC 60.674 45.833 0.00 0.00 0.00 1.89
1078 1090 3.442273 CGGCCCAGAAGCAAAAGTAAATA 59.558 43.478 0.00 0.00 0.00 1.40
1079 1091 2.231235 CGGCCCAGAAGCAAAAGTAAAT 59.769 45.455 0.00 0.00 0.00 1.40
1083 1095 1.152756 ACGGCCCAGAAGCAAAAGT 60.153 52.632 0.00 0.00 0.00 2.66
1084 1096 1.286880 CACGGCCCAGAAGCAAAAG 59.713 57.895 0.00 0.00 0.00 2.27
1127 1139 1.716826 AATCGGACTCGCTCGAGGTC 61.717 60.000 21.34 12.76 45.88 3.85
1130 1142 1.009449 GGAATCGGACTCGCTCGAG 60.009 63.158 16.71 16.71 46.91 4.04
1148 1160 3.190327 TGGGCTACACGAAAATCATTGTG 59.810 43.478 0.00 0.00 40.03 3.33
1160 1172 2.811431 TGTTGAAAATCTGGGCTACACG 59.189 45.455 0.00 0.00 0.00 4.49
1166 1178 2.669391 CGAGCTTGTTGAAAATCTGGGC 60.669 50.000 0.00 0.00 0.00 5.36
1167 1179 2.813754 TCGAGCTTGTTGAAAATCTGGG 59.186 45.455 0.00 0.00 0.00 4.45
1170 1182 2.485814 GGCTCGAGCTTGTTGAAAATCT 59.514 45.455 34.46 0.00 41.70 2.40
1171 1183 2.414691 GGGCTCGAGCTTGTTGAAAATC 60.415 50.000 34.46 14.53 41.70 2.17
1263 1276 4.477581 GGAAAGGGTTAGGAGAGGGTTATT 59.522 45.833 0.00 0.00 0.00 1.40
1351 1374 3.140144 TGGTGGGACTGGATTTCTTCTTT 59.860 43.478 0.00 0.00 0.00 2.52
1535 1558 3.493334 TGTCGAGGAAGACACCTAGAAA 58.507 45.455 0.00 0.00 45.18 2.52
1599 1622 3.001902 GCGTGGTCTGGATCGGACA 62.002 63.158 15.88 0.00 41.15 4.02
1790 2110 1.523711 GCTTGATGATCCGGCCGAA 60.524 57.895 30.73 6.63 0.00 4.30
1870 2217 2.896685 CTCAACTTCAGACTCCTCTGGT 59.103 50.000 0.00 0.00 43.87 4.00
1876 2223 3.394719 GTGGAACTCAACTTCAGACTCC 58.605 50.000 0.00 0.00 0.00 3.85
1880 2227 2.543031 CGACGTGGAACTCAACTTCAGA 60.543 50.000 0.00 0.00 31.75 3.27
1955 2302 0.822121 ACCCGCACTTTCCCACTTTC 60.822 55.000 0.00 0.00 0.00 2.62
1956 2303 0.822121 GACCCGCACTTTCCCACTTT 60.822 55.000 0.00 0.00 0.00 2.66
1957 2304 1.228154 GACCCGCACTTTCCCACTT 60.228 57.895 0.00 0.00 0.00 3.16
1977 2324 3.358076 CTGTCCGGGGAGAAGACGC 62.358 68.421 0.00 0.00 33.09 5.19
2073 2420 0.465705 CACGGATGCCCAGTAGACAT 59.534 55.000 0.00 0.00 0.00 3.06
2198 2560 1.340991 GGCCAAGCAGAGTTTCCCATA 60.341 52.381 0.00 0.00 0.00 2.74
2345 2722 1.006102 AACCTTCAGTCGTGGCTCG 60.006 57.895 1.94 1.94 41.41 5.03
2347 2724 0.532862 CACAACCTTCAGTCGTGGCT 60.533 55.000 0.00 0.00 0.00 4.75
2348 2725 1.507141 CCACAACCTTCAGTCGTGGC 61.507 60.000 0.00 0.00 40.60 5.01
2349 2726 2.616969 CCACAACCTTCAGTCGTGG 58.383 57.895 0.00 0.00 41.06 4.94
2350 2727 1.507141 GGCCACAACCTTCAGTCGTG 61.507 60.000 0.00 0.00 0.00 4.35
2351 2728 1.227853 GGCCACAACCTTCAGTCGT 60.228 57.895 0.00 0.00 0.00 4.34
2352 2729 0.606401 ATGGCCACAACCTTCAGTCG 60.606 55.000 8.16 0.00 0.00 4.18
2485 2868 4.102367 AGGGATAGGAAGAATCAGAGTTGC 59.898 45.833 0.00 0.00 0.00 4.17
2537 2920 3.536570 GAGAGAGTTCACCTTATTGCCC 58.463 50.000 0.00 0.00 0.00 5.36
2586 2969 9.683069 GACGGACGATTCTTTATTATTAGGTAA 57.317 33.333 0.00 0.00 0.00 2.85
2587 2970 8.017373 CGACGGACGATTCTTTATTATTAGGTA 58.983 37.037 0.00 0.00 45.77 3.08
2588 2971 6.860023 CGACGGACGATTCTTTATTATTAGGT 59.140 38.462 0.00 0.00 45.77 3.08
2589 2972 6.860023 ACGACGGACGATTCTTTATTATTAGG 59.140 38.462 6.90 0.00 45.77 2.69
2590 2973 7.848716 ACGACGGACGATTCTTTATTATTAG 57.151 36.000 6.90 0.00 45.77 1.73
2591 2974 7.306167 GCAACGACGGACGATTCTTTATTATTA 60.306 37.037 6.90 0.00 45.77 0.98
2592 2975 6.509039 GCAACGACGGACGATTCTTTATTATT 60.509 38.462 6.90 0.00 45.77 1.40
2593 2976 5.051240 GCAACGACGGACGATTCTTTATTAT 60.051 40.000 6.90 0.00 45.77 1.28
2594 2977 4.266029 GCAACGACGGACGATTCTTTATTA 59.734 41.667 6.90 0.00 45.77 0.98
2595 2978 3.061697 GCAACGACGGACGATTCTTTATT 59.938 43.478 6.90 0.00 45.77 1.40
2596 2979 2.601763 GCAACGACGGACGATTCTTTAT 59.398 45.455 6.90 0.00 45.77 1.40
2597 2980 1.987770 GCAACGACGGACGATTCTTTA 59.012 47.619 6.90 0.00 45.77 1.85
2598 2981 0.788391 GCAACGACGGACGATTCTTT 59.212 50.000 6.90 0.00 45.77 2.52
2599 2982 1.342082 CGCAACGACGGACGATTCTT 61.342 55.000 6.90 0.00 45.77 2.52
2600 2983 1.800315 CGCAACGACGGACGATTCT 60.800 57.895 6.90 0.00 45.77 2.40
2601 2984 2.687436 CGCAACGACGGACGATTC 59.313 61.111 6.90 0.00 45.77 2.52
3316 3730 1.819632 GTTCTCGGCCGCATCCATT 60.820 57.895 23.51 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.