Multiple sequence alignment - TraesCS2B01G360800

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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 TraesCS2B01G360800 chr2B 100.000 3685 0 0 1 3685 513705531 513709215 0.000000e+00 6806.0
1 TraesCS2B01G360800 chr2B 92.800 750 47 5 1 743 669239792 669239043 0.000000e+00 1079.0
2 TraesCS2B01G360800 chr2B 84.839 653 37 32 886 1515 513695206 513695819 5.890000e-168 601.0
3 TraesCS2B01G360800 chr2B 84.672 548 38 18 787 1290 513680595 513681140 4.750000e-139 505.0
4 TraesCS2B01G360800 chr2B 82.505 463 51 17 3038 3481 513696723 513697174 3.010000e-101 379.0
5 TraesCS2B01G360800 chr2B 80.591 474 47 24 3038 3479 513681654 513682114 1.430000e-84 324.0
6 TraesCS2B01G360800 chr2B 76.730 636 68 26 2271 2892 799710897 799711466 8.720000e-72 281.0
7 TraesCS2B01G360800 chr2B 88.079 151 17 1 2754 2904 184769139 184769288 1.180000e-40 178.0
8 TraesCS2B01G360800 chr2B 81.564 179 28 5 2724 2901 412657106 412656932 4.290000e-30 143.0
9 TraesCS2B01G360800 chr2B 81.006 179 29 5 2724 2901 412704614 412704440 2.000000e-28 137.0
10 TraesCS2B01G360800 chr2B 92.553 94 7 0 787 880 513695079 513695172 7.190000e-28 135.0
11 TraesCS2B01G360800 chr2B 100.000 61 0 0 4061 4121 513709591 513709651 3.370000e-21 113.0
12 TraesCS2B01G360800 chr2B 94.340 53 2 1 3489 3541 513682148 513682199 3.410000e-11 80.5
13 TraesCS2B01G360800 chr7D 96.875 1280 32 3 1623 2895 631181309 631182587 0.000000e+00 2135.0
14 TraesCS2B01G360800 chr3A 91.451 1275 76 8 1620 2892 106430252 106431495 0.000000e+00 1720.0
15 TraesCS2B01G360800 chr3A 93.405 743 45 2 1 739 100864403 100863661 0.000000e+00 1098.0
16 TraesCS2B01G360800 chr3A 92.608 744 51 2 1 740 127190104 127190847 0.000000e+00 1066.0
17 TraesCS2B01G360800 chr3A 91.620 358 19 5 2396 2742 43141805 43141448 6.190000e-133 484.0
18 TraesCS2B01G360800 chr3A 91.061 358 21 5 2396 2742 43731813 43731456 1.340000e-129 473.0
19 TraesCS2B01G360800 chr3A 88.608 158 16 2 1936 2091 43732377 43732220 1.510000e-44 191.0
20 TraesCS2B01G360800 chr3A 87.975 158 17 2 1936 2091 43142369 43142212 7.030000e-43 185.0
21 TraesCS2B01G360800 chr3A 90.984 122 11 0 1619 1740 7508871 7508750 9.160000e-37 165.0
22 TraesCS2B01G360800 chr3A 85.517 145 19 2 1619 1762 736477508 736477651 2.570000e-32 150.0
23 TraesCS2B01G360800 chr3A 87.912 91 9 1 2089 2177 43141897 43141807 5.630000e-19 106.0
24 TraesCS2B01G360800 chr2A 90.879 899 49 16 744 1622 551373658 551372773 0.000000e+00 1175.0
25 TraesCS2B01G360800 chr2A 88.007 592 40 15 749 1314 551463423 551462837 0.000000e+00 671.0
26 TraesCS2B01G360800 chr2A 85.162 647 47 24 938 1573 551451640 551451032 5.850000e-173 617.0
27 TraesCS2B01G360800 chr2A 89.813 481 38 6 3149 3622 551372004 551371528 1.270000e-169 606.0
28 TraesCS2B01G360800 chr2A 84.163 663 44 25 745 1349 551469509 551468850 1.650000e-163 586.0
29 TraesCS2B01G360800 chr2A 80.499 841 92 33 2030 2841 759857101 759857898 2.760000e-161 579.0
30 TraesCS2B01G360800 chr2A 81.935 620 40 33 787 1345 551482682 551482074 3.750000e-125 459.0
31 TraesCS2B01G360800 chr2A 81.023 469 56 14 3038 3481 551461908 551461448 3.940000e-90 342.0
32 TraesCS2B01G360800 chr2A 79.744 469 56 19 3038 3479 551481264 551480808 1.860000e-78 303.0
33 TraesCS2B01G360800 chr2A 96.970 99 3 0 3038 3136 551372154 551372056 2.550000e-37 167.0
34 TraesCS2B01G360800 chr2A 83.333 168 15 6 3215 3374 551446501 551446339 4.290000e-30 143.0
35 TraesCS2B01G360800 chr2A 87.850 107 6 2 745 844 551451849 551451743 7.240000e-23 119.0
36 TraesCS2B01G360800 chr2A 90.361 83 7 1 2911 2992 551372751 551372669 1.570000e-19 108.0
37 TraesCS2B01G360800 chr7B 93.154 745 45 4 1 740 721206776 721207519 0.000000e+00 1088.0
38 TraesCS2B01G360800 chr1B 93.145 744 46 3 1 739 651902329 651903072 0.000000e+00 1086.0
39 TraesCS2B01G360800 chr1B 85.276 163 23 1 1616 1777 440744307 440744469 2.550000e-37 167.0
40 TraesCS2B01G360800 chr1B 89.683 126 13 0 1613 1738 58020702 58020827 1.190000e-35 161.0
41 TraesCS2B01G360800 chr1B 88.976 127 14 0 1612 1738 58021814 58021688 1.530000e-34 158.0
42 TraesCS2B01G360800 chr4B 92.790 749 45 6 1 743 573398598 573397853 0.000000e+00 1075.0
43 TraesCS2B01G360800 chr4B 84.906 159 24 0 1622 1780 65594680 65594522 1.190000e-35 161.0
44 TraesCS2B01G360800 chr6B 92.732 743 49 3 1 739 682644049 682643308 0.000000e+00 1068.0
45 TraesCS2B01G360800 chr6B 92.598 743 52 1 1 740 29973226 29973968 0.000000e+00 1064.0
46 TraesCS2B01G360800 chr2D 92.722 742 49 3 1 738 546411442 546412182 0.000000e+00 1066.0
47 TraesCS2B01G360800 chr2D 88.795 589 34 14 787 1349 435221661 435222243 0.000000e+00 693.0
48 TraesCS2B01G360800 chr2D 88.676 521 34 10 787 1290 435196604 435197116 2.720000e-171 612.0
49 TraesCS2B01G360800 chr2D 85.327 443 26 14 744 1165 435275290 435275714 4.930000e-114 422.0
50 TraesCS2B01G360800 chr2D 79.957 469 55 21 3038 3479 435197633 435198089 4.000000e-80 309.0
51 TraesCS2B01G360800 chr2D 79.916 478 50 24 3038 3482 435325721 435326185 4.000000e-80 309.0
52 TraesCS2B01G360800 chr2D 78.017 464 58 21 3038 3481 435224824 435225263 6.840000e-63 252.0
53 TraesCS2B01G360800 chr5D 89.523 754 70 5 1623 2374 238394695 238393949 0.000000e+00 946.0
54 TraesCS2B01G360800 chr5D 89.722 360 26 7 2544 2893 238393900 238393542 2.260000e-122 449.0
55 TraesCS2B01G360800 chr5D 90.000 60 5 1 2387 2445 238393954 238393895 4.420000e-10 76.8
56 TraesCS2B01G360800 chr3B 89.209 139 14 1 2754 2892 599095886 599096023 5.480000e-39 172.0
57 TraesCS2B01G360800 chr1A 84.884 172 19 6 2725 2894 28618354 28618188 2.550000e-37 167.0


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 TraesCS2B01G360800 chr2B 513705531 513709651 4120 False 3459.500000 6806 100.000000 1 4121 2 chr2B.!!$F5 4120
1 TraesCS2B01G360800 chr2B 669239043 669239792 749 True 1079.000000 1079 92.800000 1 743 1 chr2B.!!$R3 742
2 TraesCS2B01G360800 chr2B 513695079 513697174 2095 False 371.666667 601 86.632333 787 3481 3 chr2B.!!$F4 2694
3 TraesCS2B01G360800 chr2B 513680595 513682199 1604 False 303.166667 505 86.534333 787 3541 3 chr2B.!!$F3 2754
4 TraesCS2B01G360800 chr2B 799710897 799711466 569 False 281.000000 281 76.730000 2271 2892 1 chr2B.!!$F2 621
5 TraesCS2B01G360800 chr7D 631181309 631182587 1278 False 2135.000000 2135 96.875000 1623 2895 1 chr7D.!!$F1 1272
6 TraesCS2B01G360800 chr3A 106430252 106431495 1243 False 1720.000000 1720 91.451000 1620 2892 1 chr3A.!!$F1 1272
7 TraesCS2B01G360800 chr3A 100863661 100864403 742 True 1098.000000 1098 93.405000 1 739 1 chr3A.!!$R2 738
8 TraesCS2B01G360800 chr3A 127190104 127190847 743 False 1066.000000 1066 92.608000 1 740 1 chr3A.!!$F2 739
9 TraesCS2B01G360800 chr3A 43731456 43732377 921 True 332.000000 473 89.834500 1936 2742 2 chr3A.!!$R4 806
10 TraesCS2B01G360800 chr3A 43141448 43142369 921 True 258.333333 484 89.169000 1936 2742 3 chr3A.!!$R3 806
11 TraesCS2B01G360800 chr2A 551468850 551469509 659 True 586.000000 586 84.163000 745 1349 1 chr2A.!!$R2 604
12 TraesCS2B01G360800 chr2A 759857101 759857898 797 False 579.000000 579 80.499000 2030 2841 1 chr2A.!!$F1 811
13 TraesCS2B01G360800 chr2A 551371528 551373658 2130 True 514.000000 1175 92.005750 744 3622 4 chr2A.!!$R3 2878
14 TraesCS2B01G360800 chr2A 551461448 551463423 1975 True 506.500000 671 84.515000 749 3481 2 chr2A.!!$R5 2732
15 TraesCS2B01G360800 chr2A 551480808 551482682 1874 True 381.000000 459 80.839500 787 3479 2 chr2A.!!$R6 2692
16 TraesCS2B01G360800 chr2A 551451032 551451849 817 True 368.000000 617 86.506000 745 1573 2 chr2A.!!$R4 828
17 TraesCS2B01G360800 chr7B 721206776 721207519 743 False 1088.000000 1088 93.154000 1 740 1 chr7B.!!$F1 739
18 TraesCS2B01G360800 chr1B 651902329 651903072 743 False 1086.000000 1086 93.145000 1 739 1 chr1B.!!$F3 738
19 TraesCS2B01G360800 chr4B 573397853 573398598 745 True 1075.000000 1075 92.790000 1 743 1 chr4B.!!$R2 742
20 TraesCS2B01G360800 chr6B 682643308 682644049 741 True 1068.000000 1068 92.732000 1 739 1 chr6B.!!$R1 738
21 TraesCS2B01G360800 chr6B 29973226 29973968 742 False 1064.000000 1064 92.598000 1 740 1 chr6B.!!$F1 739
22 TraesCS2B01G360800 chr2D 546411442 546412182 740 False 1066.000000 1066 92.722000 1 738 1 chr2D.!!$F3 737
23 TraesCS2B01G360800 chr2D 435221661 435225263 3602 False 472.500000 693 83.406000 787 3481 2 chr2D.!!$F5 2694
24 TraesCS2B01G360800 chr2D 435196604 435198089 1485 False 460.500000 612 84.316500 787 3479 2 chr2D.!!$F4 2692
25 TraesCS2B01G360800 chr5D 238393542 238394695 1153 True 490.600000 946 89.748333 1623 2893 3 chr5D.!!$R1 1270

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
426 429 0.868602 CATAGTTTGGCGCTGCATGC 60.869 55.0 11.82 11.82 38.57 4.06 F
1845 2542 0.032130 GCGGCAGTGTGCTATAGCTA 59.968 55.0 24.61 11.67 44.28 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 3590 1.221466 TTTCGCTCTTGTCACTGCCG 61.221 55.0 0.0 0.0 0.0 5.69 R
3466 5769 0.107017 AGTCCCCATCCAAGATTGCG 60.107 55.0 0.0 0.0 0.0 4.85 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
53 54 7.386299 ACTGTGAAGAGAGTGTGAATCATTTAC 59.614 37.037 0.00 0.00 0.00 2.01
54 55 6.650807 TGTGAAGAGAGTGTGAATCATTTACC 59.349 38.462 0.00 0.00 0.00 2.85
92 93 9.778741 CCTTAGCTAAGTTCATGTGGAATATTA 57.221 33.333 27.54 0.00 37.93 0.98
168 169 4.040952 CCAGAACTGGTTGCCTAGCTATAT 59.959 45.833 12.21 0.00 45.53 0.86
172 173 3.716872 ACTGGTTGCCTAGCTATATTGGT 59.283 43.478 0.00 0.00 0.00 3.67
180 181 9.720769 GTTGCCTAGCTATATTGGTAAAGATAA 57.279 33.333 0.00 0.00 0.00 1.75
226 227 6.012745 TGCTGCTCTCTTATGGTCTATATGA 58.987 40.000 0.00 0.00 0.00 2.15
262 265 9.665719 AACAAATCCTGTTTTCAAAGTGTTATT 57.334 25.926 0.00 0.00 46.49 1.40
410 413 4.774726 GTGATATCTTCAGAGGAGGGCATA 59.225 45.833 3.98 0.00 34.17 3.14
426 429 0.868602 CATAGTTTGGCGCTGCATGC 60.869 55.000 11.82 11.82 38.57 4.06
444 447 4.797471 CATGCGAGAAGGATTTTGTGAAA 58.203 39.130 0.00 0.00 0.00 2.69
552 555 2.326428 GTAGCACTAGGCCCTTCCATA 58.674 52.381 0.00 0.00 46.50 2.74
562 565 6.675303 ACTAGGCCCTTCCATAGTTAGTTTTA 59.325 38.462 0.00 0.00 37.29 1.52
632 635 3.978164 GGCTGGATAGGCTGGAGT 58.022 61.111 0.00 0.00 45.44 3.85
635 638 1.981495 GGCTGGATAGGCTGGAGTATT 59.019 52.381 0.00 0.00 45.44 1.89
656 659 3.334583 TTGGTGTGGCTTCTAGATCAC 57.665 47.619 11.94 11.94 0.00 3.06
670 674 6.709018 TCTAGATCACCGATGTAATGTTGA 57.291 37.500 0.00 0.00 0.00 3.18
702 706 6.146021 GCCTTGTAAACAACTCCATTTTCATG 59.854 38.462 0.00 0.00 0.00 3.07
706 714 9.658799 TTGTAAACAACTCCATTTTCATGAAAA 57.341 25.926 30.27 30.27 43.48 2.29
785 800 5.036117 AGGAACACTTTCACAAGCTCTTA 57.964 39.130 0.00 0.00 32.57 2.10
793 815 3.671008 TCACAAGCTCTTACCGCTTTA 57.329 42.857 0.00 0.00 44.76 1.85
828 850 2.047844 CTGTCGCAGTGTCCCCTG 60.048 66.667 0.00 0.00 35.49 4.45
865 887 3.052082 CAGGTGCACGCTCCCAAG 61.052 66.667 11.45 0.00 0.00 3.61
1359 1531 6.477669 TCGAGAATAGTATACGGACATGAC 57.522 41.667 0.00 0.00 0.00 3.06
1363 1535 7.544915 CGAGAATAGTATACGGACATGACTAGA 59.455 40.741 0.00 0.00 0.00 2.43
1369 1541 3.992260 ACGGACATGACTAGATAGTGC 57.008 47.619 0.00 0.00 36.50 4.40
1377 1549 4.307443 TGACTAGATAGTGCGTGATTGG 57.693 45.455 0.00 0.00 36.50 3.16
1395 1567 6.761242 GTGATTGGTAGTAGAATGCATGTGTA 59.239 38.462 0.00 0.00 0.00 2.90
1396 1568 7.279981 GTGATTGGTAGTAGAATGCATGTGTAA 59.720 37.037 0.00 0.00 0.00 2.41
1399 1571 6.649155 TGGTAGTAGAATGCATGTGTAATGT 58.351 36.000 0.00 0.00 0.00 2.71
1400 1572 6.538381 TGGTAGTAGAATGCATGTGTAATGTG 59.462 38.462 0.00 0.00 0.00 3.21
1401 1573 6.538742 GGTAGTAGAATGCATGTGTAATGTGT 59.461 38.462 0.00 0.00 0.00 3.72
1402 1574 7.065803 GGTAGTAGAATGCATGTGTAATGTGTT 59.934 37.037 0.00 0.00 0.00 3.32
1403 1575 6.845302 AGTAGAATGCATGTGTAATGTGTTG 58.155 36.000 0.00 0.00 0.00 3.33
1404 1576 5.710513 AGAATGCATGTGTAATGTGTTGT 57.289 34.783 0.00 0.00 0.00 3.32
1405 1577 6.088016 AGAATGCATGTGTAATGTGTTGTT 57.912 33.333 0.00 0.00 0.00 2.83
1424 1596 1.808411 TCTGCGAAAGTGGTTCATCC 58.192 50.000 0.00 0.00 35.83 3.51
1426 1598 0.034198 TGCGAAAGTGGTTCATCCGA 59.966 50.000 0.00 0.00 39.52 4.55
1427 1599 0.442699 GCGAAAGTGGTTCATCCGAC 59.557 55.000 0.00 0.00 39.52 4.79
1436 1608 2.505407 TGGTTCATCCGACCATGATTCT 59.495 45.455 0.00 0.00 42.06 2.40
1655 2027 7.761038 ATATTTTTCGTCCCTCAACTCTTTT 57.239 32.000 0.00 0.00 0.00 2.27
1698 2395 6.279882 CCTCAACTTCAAAACCAGCAAAATA 58.720 36.000 0.00 0.00 0.00 1.40
1710 2407 8.838649 AAACCAGCAAAATATAGTCCCTTAAT 57.161 30.769 0.00 0.00 0.00 1.40
1845 2542 0.032130 GCGGCAGTGTGCTATAGCTA 59.968 55.000 24.61 11.67 44.28 3.32
1873 2570 2.935955 CACCGACACCGAGCAAAC 59.064 61.111 0.00 0.00 38.22 2.93
1902 2599 2.986311 CACCGTGTGCTACAACTGT 58.014 52.632 0.00 0.00 0.00 3.55
1926 2623 2.009774 GTCTATGGCATGTCGCACTTT 58.990 47.619 10.98 0.00 45.17 2.66
2086 2925 2.122413 AGGCCACAGGACTGGACA 60.122 61.111 5.01 0.00 41.17 4.02
2299 3457 1.073474 CCCCTCCATCCATCCCAGA 60.073 63.158 0.00 0.00 0.00 3.86
2450 3623 0.889186 GCGAAAGAGCACCTTTGGGA 60.889 55.000 8.55 0.00 44.63 4.37
2451 3624 0.875059 CGAAAGAGCACCTTTGGGAC 59.125 55.000 8.55 0.00 44.63 4.46
2452 3625 1.248486 GAAAGAGCACCTTTGGGACC 58.752 55.000 8.55 0.00 44.63 4.46
2453 3626 0.853530 AAAGAGCACCTTTGGGACCT 59.146 50.000 3.71 0.00 43.10 3.85
2454 3627 0.853530 AAGAGCACCTTTGGGACCTT 59.146 50.000 0.00 0.00 36.25 3.50
2455 3628 0.402121 AGAGCACCTTTGGGACCTTC 59.598 55.000 0.00 0.00 36.25 3.46
2456 3629 0.110486 GAGCACCTTTGGGACCTTCA 59.890 55.000 0.00 0.00 36.25 3.02
2457 3630 0.178990 AGCACCTTTGGGACCTTCAC 60.179 55.000 0.00 0.00 36.25 3.18
2458 3631 1.515521 GCACCTTTGGGACCTTCACG 61.516 60.000 0.00 0.00 36.25 4.35
2459 3632 1.228154 ACCTTTGGGACCTTCACGC 60.228 57.895 0.00 0.00 36.25 5.34
2460 3633 1.971695 CCTTTGGGACCTTCACGCC 60.972 63.158 0.00 0.00 33.58 5.68
2461 3634 2.281208 TTTGGGACCTTCACGCCG 60.281 61.111 0.00 0.00 0.00 6.46
2462 3635 3.109592 TTTGGGACCTTCACGCCGT 62.110 57.895 0.00 0.00 0.00 5.68
2463 3636 2.612095 TTTGGGACCTTCACGCCGTT 62.612 55.000 0.00 0.00 0.00 4.44
2464 3637 3.047877 GGGACCTTCACGCCGTTG 61.048 66.667 0.00 0.00 0.00 4.10
2677 3885 0.185901 AGTGTGCCACCTCCAATGTT 59.814 50.000 0.00 0.00 34.49 2.71
2758 4256 5.376625 ACCACTCTGCATAAGAAGAAAACA 58.623 37.500 3.43 0.00 33.37 2.83
2778 4276 4.279326 CCTAAGGGAGACGAGGGG 57.721 66.667 0.00 0.00 33.58 4.79
2962 4471 8.576442 TCAATTTTACTTCCATTTCTCCAAGTC 58.424 33.333 0.00 0.00 31.52 3.01
2997 4514 0.036858 GCGAGCTCCTGAACCTTCTT 60.037 55.000 8.47 0.00 0.00 2.52
3019 4538 3.198409 TGGTGATGTGGAGATATGCAC 57.802 47.619 4.87 4.87 0.00 4.57
3209 5499 7.927092 AGAGTTACTAAAAGAACTGAACCTGAC 59.073 37.037 0.00 0.00 36.04 3.51
3212 5502 1.217882 AAAGAACTGAACCTGACGCG 58.782 50.000 3.53 3.53 0.00 6.01
3213 5503 1.222115 AAGAACTGAACCTGACGCGC 61.222 55.000 5.73 0.00 0.00 6.86
3310 5601 5.462405 GTGTGAGAGTTTGAGTACTACCAG 58.538 45.833 0.00 0.00 0.00 4.00
3362 5653 3.254657 TGTGCAATTTGTACCTAGTTGCC 59.745 43.478 13.97 11.53 43.24 4.52
3466 5769 5.665459 TCTTAGCAAGTTAGATTGGAGAGC 58.335 41.667 0.00 0.00 0.00 4.09
3536 5863 6.710278 TCTGTTGTGGATGAGATGTATCAAA 58.290 36.000 0.00 0.00 31.76 2.69
3537 5864 7.341030 TCTGTTGTGGATGAGATGTATCAAAT 58.659 34.615 0.00 0.00 31.76 2.32
3538 5865 7.281549 TCTGTTGTGGATGAGATGTATCAAATG 59.718 37.037 0.00 0.00 31.76 2.32
3539 5866 6.885918 TGTTGTGGATGAGATGTATCAAATGT 59.114 34.615 0.00 0.00 31.76 2.71
3540 5867 8.046107 TGTTGTGGATGAGATGTATCAAATGTA 58.954 33.333 0.00 0.00 31.76 2.29
3595 5926 7.496346 TTCTATACATTTGTTCTGGAGGAGT 57.504 36.000 0.00 0.00 0.00 3.85
3604 5935 3.117888 TGTTCTGGAGGAGTCTGCTTTTT 60.118 43.478 0.00 0.00 32.15 1.94
3611 5942 7.016153 TGGAGGAGTCTGCTTTTTCTTATAA 57.984 36.000 0.00 0.00 32.15 0.98
3612 5943 6.879458 TGGAGGAGTCTGCTTTTTCTTATAAC 59.121 38.462 0.00 0.00 32.15 1.89
3616 5947 7.939588 AGGAGTCTGCTTTTTCTTATAACAACT 59.060 33.333 0.00 0.00 0.00 3.16
3635 5966 7.499321 ACAACTATAGTACTTCCTCTGATCG 57.501 40.000 5.65 0.00 0.00 3.69
3636 5967 7.281098 ACAACTATAGTACTTCCTCTGATCGA 58.719 38.462 5.65 0.00 0.00 3.59
3637 5968 7.774157 ACAACTATAGTACTTCCTCTGATCGAA 59.226 37.037 5.65 0.00 0.00 3.71
3638 5969 8.622157 CAACTATAGTACTTCCTCTGATCGAAA 58.378 37.037 5.65 0.00 0.00 3.46
3639 5970 8.749026 ACTATAGTACTTCCTCTGATCGAAAA 57.251 34.615 2.75 0.00 0.00 2.29
3640 5971 9.186837 ACTATAGTACTTCCTCTGATCGAAAAA 57.813 33.333 2.75 0.00 0.00 1.94
3663 5994 9.581099 AAAAAGTGTCGTGACTTTAATTCAATT 57.419 25.926 12.76 0.00 43.83 2.32
3664 5995 8.782533 AAAGTGTCGTGACTTTAATTCAATTC 57.217 30.769 11.29 0.00 43.00 2.17
3665 5996 7.490962 AGTGTCGTGACTTTAATTCAATTCA 57.509 32.000 1.23 0.00 0.00 2.57
3666 5997 8.099364 AGTGTCGTGACTTTAATTCAATTCAT 57.901 30.769 1.23 0.00 0.00 2.57
3667 5998 8.567948 AGTGTCGTGACTTTAATTCAATTCATT 58.432 29.630 1.23 0.00 0.00 2.57
3668 5999 9.180678 GTGTCGTGACTTTAATTCAATTCATTT 57.819 29.630 1.23 0.00 0.00 2.32
3669 6000 9.743057 TGTCGTGACTTTAATTCAATTCATTTT 57.257 25.926 1.23 0.00 0.00 1.82
4082 6413 3.914426 AAGTGGTAAGTATGCCAGAGG 57.086 47.619 0.00 0.00 42.45 3.69
4083 6414 3.116096 AGTGGTAAGTATGCCAGAGGA 57.884 47.619 0.00 0.00 42.45 3.71
4084 6415 3.034635 AGTGGTAAGTATGCCAGAGGAG 58.965 50.000 0.00 0.00 42.45 3.69
4085 6416 2.766828 GTGGTAAGTATGCCAGAGGAGT 59.233 50.000 0.00 0.00 42.45 3.85
4086 6417 3.197983 GTGGTAAGTATGCCAGAGGAGTT 59.802 47.826 0.00 0.00 42.45 3.01
4087 6418 4.404715 GTGGTAAGTATGCCAGAGGAGTTA 59.595 45.833 0.00 0.00 42.45 2.24
4088 6419 5.070580 GTGGTAAGTATGCCAGAGGAGTTAT 59.929 44.000 0.00 0.00 42.45 1.89
4089 6420 5.304614 TGGTAAGTATGCCAGAGGAGTTATC 59.695 44.000 0.00 0.00 36.27 1.75
4090 6421 7.651043 TGGTAAGTATGCCAGAGGAGTTATCC 61.651 46.154 0.00 0.00 40.17 2.59
4091 6422 9.948120 TGGTAAGTATGCCAGAGGAGTTATCCA 62.948 44.444 0.00 0.00 41.38 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.468543 ACTTAGCTAAGGAACAAGAGAAAGG 58.531 40.000 31.67 7.42 37.62 3.11
54 55 7.657761 TGAACTTAGCTAAGGAACAAGAGAAAG 59.342 37.037 31.67 9.59 37.62 2.62
92 93 1.727062 CTCCCTAGAGCACATCCCAT 58.273 55.000 0.00 0.00 32.13 4.00
180 181 7.002276 AGCAGTACCCAATAAAACAACTACTT 58.998 34.615 0.00 0.00 0.00 2.24
262 265 8.225863 AGATAATGTCAGTAGGATCTCTAGGA 57.774 38.462 0.00 0.00 0.00 2.94
322 325 0.538287 GCACCCCTCTTTTCTGCAGT 60.538 55.000 14.67 0.00 0.00 4.40
420 423 2.095110 CACAAAATCCTTCTCGCATGCA 60.095 45.455 19.57 4.02 0.00 3.96
426 429 5.390991 GGCTAGTTTCACAAAATCCTTCTCG 60.391 44.000 0.00 0.00 0.00 4.04
444 447 0.035056 AAGCATTTCCAGCGGCTAGT 60.035 50.000 0.26 0.00 35.11 2.57
552 555 5.592688 TGCTTCAAACTGCCTAAAACTAACT 59.407 36.000 0.00 0.00 0.00 2.24
562 565 1.074405 TCAGGATGCTTCAAACTGCCT 59.926 47.619 1.64 0.00 34.76 4.75
585 588 6.267496 TCACACCACTGATATATATCACCG 57.733 41.667 19.44 13.96 37.76 4.94
632 635 5.880332 GTGATCTAGAAGCCACACCAAAATA 59.120 40.000 14.56 0.00 0.00 1.40
635 638 3.559171 GGTGATCTAGAAGCCACACCAAA 60.559 47.826 20.69 0.00 44.58 3.28
656 659 4.977963 GGCATCAAATCAACATTACATCGG 59.022 41.667 0.00 0.00 0.00 4.18
670 674 5.304101 TGGAGTTGTTTACAAGGCATCAAAT 59.696 36.000 0.00 0.00 36.39 2.32
702 706 2.969827 CCACACGGCCCCATTTTC 59.030 61.111 0.00 0.00 0.00 2.29
741 751 6.150474 TCCTCGACAAAAGAAAAAGTGAAGTT 59.850 34.615 0.00 0.00 0.00 2.66
743 753 6.119144 TCCTCGACAAAAGAAAAAGTGAAG 57.881 37.500 0.00 0.00 0.00 3.02
757 767 3.254470 TGTGAAAGTGTTCCTCGACAA 57.746 42.857 0.00 0.00 32.28 3.18
785 800 0.107831 TTGGCACAGTCTAAAGCGGT 59.892 50.000 0.00 0.00 42.39 5.68
793 815 1.598130 GGCGAACTTGGCACAGTCT 60.598 57.895 0.00 0.00 42.39 3.24
1337 1502 6.483385 AGTCATGTCCGTATACTATTCTCG 57.517 41.667 0.56 0.00 0.00 4.04
1350 1522 2.290916 ACGCACTATCTAGTCATGTCCG 59.709 50.000 0.00 0.00 33.46 4.79
1359 1531 5.440234 ACTACCAATCACGCACTATCTAG 57.560 43.478 0.00 0.00 0.00 2.43
1363 1535 5.847111 TTCTACTACCAATCACGCACTAT 57.153 39.130 0.00 0.00 0.00 2.12
1369 1541 4.811024 ACATGCATTCTACTACCAATCACG 59.189 41.667 0.00 0.00 0.00 4.35
1377 1549 7.539712 ACACATTACACATGCATTCTACTAC 57.460 36.000 0.00 0.00 0.00 2.73
1395 1567 3.489059 CCACTTTCGCAGAACAACACATT 60.489 43.478 0.00 0.00 45.90 2.71
1396 1568 2.033299 CCACTTTCGCAGAACAACACAT 59.967 45.455 0.00 0.00 45.90 3.21
1399 1571 1.745232 ACCACTTTCGCAGAACAACA 58.255 45.000 0.00 0.00 45.90 3.33
1400 1572 2.096819 TGAACCACTTTCGCAGAACAAC 59.903 45.455 0.00 0.00 45.90 3.32
1401 1573 2.360844 TGAACCACTTTCGCAGAACAA 58.639 42.857 0.00 0.00 45.90 2.83
1402 1574 2.031258 TGAACCACTTTCGCAGAACA 57.969 45.000 0.00 0.00 45.90 3.18
1403 1575 2.095718 GGATGAACCACTTTCGCAGAAC 60.096 50.000 0.00 0.00 39.53 3.01
1404 1576 2.151202 GGATGAACCACTTTCGCAGAA 58.849 47.619 0.00 0.00 39.53 3.02
1405 1577 1.808411 GGATGAACCACTTTCGCAGA 58.192 50.000 0.00 0.00 36.97 4.26
1424 1596 5.953183 TCCAATCAAAAAGAATCATGGTCG 58.047 37.500 0.00 0.00 0.00 4.79
1426 1598 5.482878 AGCTCCAATCAAAAAGAATCATGGT 59.517 36.000 0.00 0.00 0.00 3.55
1427 1599 5.974108 AGCTCCAATCAAAAAGAATCATGG 58.026 37.500 0.00 0.00 0.00 3.66
1436 1608 5.771666 ACATGAGAGAAGCTCCAATCAAAAA 59.228 36.000 0.00 0.00 43.26 1.94
1655 2027 6.884472 TGAGGGACCATTTCTATACTTTCA 57.116 37.500 0.00 0.00 0.00 2.69
1728 2425 4.991472 CCTAACTAACGTGAGGGACTAAC 58.009 47.826 4.57 0.00 41.55 2.34
1845 2542 4.250305 GTCGGTGCACTGGGTGGT 62.250 66.667 25.15 0.00 33.64 4.16
1902 2599 2.034685 GTGCGACATGCCATAGACTCTA 59.965 50.000 0.00 0.00 45.60 2.43
1926 2623 1.658596 GCGATAACGTTGCTGATGTCA 59.341 47.619 11.99 0.00 41.98 3.58
2086 2925 2.579860 AGTTCCATGGCTCCTCTTCATT 59.420 45.455 6.96 0.00 0.00 2.57
2299 3457 3.545703 GTTGGGCTTGACATAGCTGTAT 58.454 45.455 0.00 0.00 40.99 2.29
2417 3590 1.221466 TTTCGCTCTTGTCACTGCCG 61.221 55.000 0.00 0.00 0.00 5.69
2450 3623 2.280592 GGTCAACGGCGTGAAGGT 60.281 61.111 15.70 0.00 0.00 3.50
2451 3624 3.047877 GGGTCAACGGCGTGAAGG 61.048 66.667 15.70 3.90 0.00 3.46
2452 3625 2.030562 AGGGTCAACGGCGTGAAG 59.969 61.111 15.70 7.23 0.00 3.02
2453 3626 2.280524 CAGGGTCAACGGCGTGAA 60.281 61.111 15.70 0.86 0.00 3.18
2454 3627 4.980805 GCAGGGTCAACGGCGTGA 62.981 66.667 15.70 10.85 0.00 4.35
2459 3632 3.190738 TTGGAGGCAGGGTCAACGG 62.191 63.158 0.00 0.00 0.00 4.44
2460 3633 1.966451 GTTGGAGGCAGGGTCAACG 60.966 63.158 0.00 0.00 31.77 4.10
2461 3634 1.150536 TGTTGGAGGCAGGGTCAAC 59.849 57.895 0.00 0.00 39.68 3.18
2462 3635 1.150536 GTGTTGGAGGCAGGGTCAA 59.849 57.895 0.00 0.00 0.00 3.18
2463 3636 1.768684 GAGTGTTGGAGGCAGGGTCA 61.769 60.000 0.00 0.00 0.00 4.02
2464 3637 1.003233 GAGTGTTGGAGGCAGGGTC 60.003 63.158 0.00 0.00 0.00 4.46
2647 3838 2.595463 GCACACTCAAGCAGGGCA 60.595 61.111 0.00 0.00 0.00 5.36
2677 3885 4.147449 CCCATCGAGCGGCAGTGA 62.147 66.667 1.45 0.00 0.00 3.41
2758 4256 0.325390 CCCTCGTCTCCCTTAGGGTT 60.325 60.000 18.01 0.00 44.74 4.11
2778 4276 6.675026 ACTTTTGAAACCGGATAAGTTTAGC 58.325 36.000 9.46 0.00 37.55 3.09
2905 4403 1.227556 GTGTGAACAGGGACGTGCT 60.228 57.895 7.11 0.00 0.00 4.40
2997 4514 4.561326 CGTGCATATCTCCACATCACCATA 60.561 45.833 0.00 0.00 32.37 2.74
3019 4538 1.482593 AGGAGACCTTGCTAATGGACG 59.517 52.381 0.00 0.00 0.00 4.79
3138 5391 1.669265 GCGGTTGATTTACCCTACTGC 59.331 52.381 0.00 0.00 34.56 4.40
3221 5511 1.648504 TGATGATCAACAGCAGCGAG 58.351 50.000 0.00 0.00 40.09 5.03
3389 5683 0.471617 AGGCTAGCGCTTCCATCATT 59.528 50.000 18.68 0.00 36.09 2.57
3466 5769 0.107017 AGTCCCCATCCAAGATTGCG 60.107 55.000 0.00 0.00 0.00 4.85
3561 5888 7.947890 AGAACAAATGTATAGAAAAGGACCCAA 59.052 33.333 0.00 0.00 0.00 4.12
3562 5889 7.393234 CAGAACAAATGTATAGAAAAGGACCCA 59.607 37.037 0.00 0.00 0.00 4.51
3563 5890 7.148069 CCAGAACAAATGTATAGAAAAGGACCC 60.148 40.741 0.00 0.00 0.00 4.46
3564 5891 7.610305 TCCAGAACAAATGTATAGAAAAGGACC 59.390 37.037 0.00 0.00 0.00 4.46
3574 5901 6.630413 GCAGACTCCTCCAGAACAAATGTATA 60.630 42.308 0.00 0.00 0.00 1.47
3611 5942 7.281098 TCGATCAGAGGAAGTACTATAGTTGT 58.719 38.462 11.40 0.00 0.00 3.32
3612 5943 7.731882 TCGATCAGAGGAAGTACTATAGTTG 57.268 40.000 11.40 0.57 0.00 3.16
3637 5968 9.581099 AATTGAATTAAAGTCACGACACTTTTT 57.419 25.926 17.54 9.81 42.81 1.94
3638 5969 9.233232 GAATTGAATTAAAGTCACGACACTTTT 57.767 29.630 17.54 4.73 42.81 2.27
3639 5970 8.402472 TGAATTGAATTAAAGTCACGACACTTT 58.598 29.630 16.83 16.83 46.27 2.66
3640 5971 7.925993 TGAATTGAATTAAAGTCACGACACTT 58.074 30.769 1.43 0.00 38.30 3.16
3641 5972 7.490962 TGAATTGAATTAAAGTCACGACACT 57.509 32.000 1.43 0.00 29.80 3.55
3642 5973 8.728088 AATGAATTGAATTAAAGTCACGACAC 57.272 30.769 7.83 0.00 37.01 3.67
3643 5974 9.743057 AAAATGAATTGAATTAAAGTCACGACA 57.257 25.926 7.83 0.00 37.01 4.35
4060 6391 4.081087 TCCTCTGGCATACTTACCACTTTC 60.081 45.833 0.00 0.00 0.00 2.62
4061 6392 3.844211 TCCTCTGGCATACTTACCACTTT 59.156 43.478 0.00 0.00 0.00 2.66
4062 6393 3.450904 TCCTCTGGCATACTTACCACTT 58.549 45.455 0.00 0.00 0.00 3.16
4063 6394 3.034635 CTCCTCTGGCATACTTACCACT 58.965 50.000 0.00 0.00 0.00 4.00
4064 6395 2.766828 ACTCCTCTGGCATACTTACCAC 59.233 50.000 0.00 0.00 0.00 4.16
4065 6396 3.116096 ACTCCTCTGGCATACTTACCA 57.884 47.619 0.00 0.00 0.00 3.25
4066 6397 5.279556 GGATAACTCCTCTGGCATACTTACC 60.280 48.000 0.00 0.00 38.65 2.85
4067 6398 5.304614 TGGATAACTCCTCTGGCATACTTAC 59.695 44.000 0.00 0.00 42.59 2.34
4068 6399 5.464069 TGGATAACTCCTCTGGCATACTTA 58.536 41.667 0.00 0.00 42.59 2.24
4069 6400 4.298626 TGGATAACTCCTCTGGCATACTT 58.701 43.478 0.00 0.00 42.59 2.24
4070 6401 3.928754 TGGATAACTCCTCTGGCATACT 58.071 45.455 0.00 0.00 42.59 2.12
4071 6402 4.689612 TTGGATAACTCCTCTGGCATAC 57.310 45.455 0.00 0.00 42.59 2.39
4072 6403 5.912149 AATTGGATAACTCCTCTGGCATA 57.088 39.130 0.00 0.00 42.59 3.14
4073 6404 4.803329 AATTGGATAACTCCTCTGGCAT 57.197 40.909 0.00 0.00 42.59 4.40
4074 6405 4.591321 AAATTGGATAACTCCTCTGGCA 57.409 40.909 0.00 0.00 42.59 4.92
4075 6406 8.691661 TTTATAAATTGGATAACTCCTCTGGC 57.308 34.615 0.00 0.00 42.59 4.85


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

AutoCloner maintained by Alex Coulton.