Multiple sequence alignment - TraesCS5B01G256500

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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 TraesCS5B01G256500 chr5B 100.000 5504 0 0 1 5504 439234941 439229438 0.000000e+00 10165
1 TraesCS5B01G256500 chr5B 92.197 692 50 4 4815 5503 75908396 75909086 0.000000e+00 976
2 TraesCS5B01G256500 chr5B 86.026 687 94 2 4815 5499 206502619 206503305 0.000000e+00 736
3 TraesCS5B01G256500 chr5D 94.286 4305 189 24 534 4810 369875755 369871480 0.000000e+00 6534
4 TraesCS5B01G256500 chr5D 86.301 292 24 9 5 282 369876932 369876643 2.490000e-78 303
5 TraesCS5B01G256500 chr5A 93.596 4294 203 25 529 4810 472347938 472343705 0.000000e+00 6340
6 TraesCS5B01G256500 chr5A 84.888 536 60 16 6 530 472348492 472347967 6.320000e-144 521
7 TraesCS5B01G256500 chr3B 94.509 692 35 3 4815 5504 18494897 18494207 0.000000e+00 1064
8 TraesCS5B01G256500 chr7B 91.582 689 56 2 4816 5503 517626944 517627631 0.000000e+00 950
9 TraesCS5B01G256500 chr4B 91.581 677 52 4 4826 5500 383657165 383657838 0.000000e+00 929
10 TraesCS5B01G256500 chr3D 88.338 686 79 1 4815 5499 445829132 445829817 0.000000e+00 822
11 TraesCS5B01G256500 chr3D 85.239 691 99 3 4815 5503 589322153 589321464 0.000000e+00 708
12 TraesCS5B01G256500 chr1D 86.561 692 90 3 4814 5503 3735864 3735174 0.000000e+00 760
13 TraesCS5B01G256500 chr4A 84.928 690 101 2 4815 5503 455105627 455104940 0.000000e+00 695


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 TraesCS5B01G256500 chr5B 439229438 439234941 5503 True 10165.0 10165 100.0000 1 5504 1 chr5B.!!$R1 5503
1 TraesCS5B01G256500 chr5B 75908396 75909086 690 False 976.0 976 92.1970 4815 5503 1 chr5B.!!$F1 688
2 TraesCS5B01G256500 chr5B 206502619 206503305 686 False 736.0 736 86.0260 4815 5499 1 chr5B.!!$F2 684
3 TraesCS5B01G256500 chr5D 369871480 369876932 5452 True 3418.5 6534 90.2935 5 4810 2 chr5D.!!$R1 4805
4 TraesCS5B01G256500 chr5A 472343705 472348492 4787 True 3430.5 6340 89.2420 6 4810 2 chr5A.!!$R1 4804
5 TraesCS5B01G256500 chr3B 18494207 18494897 690 True 1064.0 1064 94.5090 4815 5504 1 chr3B.!!$R1 689
6 TraesCS5B01G256500 chr7B 517626944 517627631 687 False 950.0 950 91.5820 4816 5503 1 chr7B.!!$F1 687
7 TraesCS5B01G256500 chr4B 383657165 383657838 673 False 929.0 929 91.5810 4826 5500 1 chr4B.!!$F1 674
8 TraesCS5B01G256500 chr3D 445829132 445829817 685 False 822.0 822 88.3380 4815 5499 1 chr3D.!!$F1 684
9 TraesCS5B01G256500 chr3D 589321464 589322153 689 True 708.0 708 85.2390 4815 5503 1 chr3D.!!$R1 688
10 TraesCS5B01G256500 chr1D 3735174 3735864 690 True 760.0 760 86.5610 4814 5503 1 chr1D.!!$R1 689
11 TraesCS5B01G256500 chr4A 455104940 455105627 687 True 695.0 695 84.9280 4815 5503 1 chr4A.!!$R1 688

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
887 1562 0.034059 CCAGGAATTCCCGATCCTCG 59.966 60.0 21.22 0.02 44.26 4.63 F
1764 2463 0.599466 CTGATGGCGATCACAGCGAT 60.599 55.0 7.38 0.00 34.71 4.58 F
2596 3295 0.630673 ACATATGCTTGGCCCCTTCA 59.369 50.0 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 3276 0.630673 TGAAGGGGCCAAGCATATGT 59.369 50.0 4.39 0.0 0.00 2.29 R
3161 3865 0.178990 AAAAGTGGAGAAGCGCCCTT 60.179 50.0 2.29 0.0 0.00 3.95 R
4524 5233 0.387202 CTACACAGAGGCTCATCCGG 59.613 60.0 18.26 0.0 40.77 5.14 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
26 27 2.267642 GCCCGTCATGGTAGTGCA 59.732 61.111 0.00 0.00 35.15 4.57
42 43 2.989639 CATGGTCTGAGCCCCGAA 59.010 61.111 4.17 0.00 0.00 4.30
45 48 0.692419 ATGGTCTGAGCCCCGAAGAT 60.692 55.000 4.17 0.00 0.00 2.40
55 58 0.886490 CCCCGAAGATGTAGCCATGC 60.886 60.000 0.00 0.00 0.00 4.06
103 106 6.368805 AGAGAAACAAAAGAGAAGGGATTGT 58.631 36.000 0.00 0.00 35.86 2.71
107 110 6.544928 AACAAAAGAGAAGGGATTGTGTTT 57.455 33.333 0.00 0.00 34.67 2.83
119 122 3.561503 GATTGTGTTTACGCCAAGGAAC 58.438 45.455 0.00 0.00 0.00 3.62
120 123 2.039818 TGTGTTTACGCCAAGGAACA 57.960 45.000 0.00 0.00 0.00 3.18
121 124 1.671845 TGTGTTTACGCCAAGGAACAC 59.328 47.619 12.20 12.20 44.24 3.32
122 125 1.671845 GTGTTTACGCCAAGGAACACA 59.328 47.619 13.54 0.00 43.84 3.72
156 159 1.600957 CAACGCATGAGAGCATAAGGG 59.399 52.381 2.50 0.00 32.27 3.95
158 161 1.233285 CGCATGAGAGCATAAGGGGC 61.233 60.000 0.00 0.00 32.27 5.80
159 162 0.179009 GCATGAGAGCATAAGGGGCA 60.179 55.000 0.00 0.00 32.27 5.36
160 163 1.751733 GCATGAGAGCATAAGGGGCAA 60.752 52.381 0.00 0.00 32.27 4.52
186 203 2.730094 GGCCATAAAGCCGCATGG 59.270 61.111 0.00 4.22 44.57 3.66
247 265 1.811679 GGCAAGAGACGTAGCTGGC 60.812 63.158 7.76 7.76 0.00 4.85
262 280 2.517875 GGCCAGCCGATGCAGAAT 60.518 61.111 0.00 0.00 41.13 2.40
283 301 8.462016 CAGAATGTTTACCTTCATCTAAAAGGG 58.538 37.037 6.83 0.00 46.32 3.95
309 662 4.201950 GGCAAGCGAACATCATTTGATAGT 60.202 41.667 0.00 0.00 32.63 2.12
337 690 4.590850 AGTTGCAAGGAAAGATCAAACC 57.409 40.909 0.00 0.00 0.00 3.27
342 695 3.378427 GCAAGGAAAGATCAAACCGCTAT 59.622 43.478 0.00 0.00 0.00 2.97
371 724 6.089685 TTTTAAACGAAAATTGCCTTATCGGC 59.910 34.615 0.00 0.00 44.53 5.54
392 745 2.921754 CGAAGAAACTACCATGTCGTCC 59.078 50.000 0.00 0.00 0.00 4.79
394 747 1.891150 AGAAACTACCATGTCGTCCGT 59.109 47.619 0.00 0.00 0.00 4.69
436 1066 6.438763 GTCACTTCCTCACAAATAAAACTGG 58.561 40.000 0.00 0.00 0.00 4.00
443 1073 4.854399 TCACAAATAAAACTGGCACGAAG 58.146 39.130 0.00 0.00 0.00 3.79
460 1090 2.806745 CGAAGTCGTTCCCATATGCCAT 60.807 50.000 0.00 0.00 34.11 4.40
465 1095 1.611673 CGTTCCCATATGCCATCCTCC 60.612 57.143 0.00 0.00 0.00 4.30
466 1096 1.075601 TTCCCATATGCCATCCTCCC 58.924 55.000 0.00 0.00 0.00 4.30
467 1097 0.846427 TCCCATATGCCATCCTCCCC 60.846 60.000 0.00 0.00 0.00 4.81
468 1098 1.693640 CCATATGCCATCCTCCCCC 59.306 63.158 0.00 0.00 0.00 5.40
469 1099 1.142048 CCATATGCCATCCTCCCCCA 61.142 60.000 0.00 0.00 0.00 4.96
470 1100 0.779358 CATATGCCATCCTCCCCCAA 59.221 55.000 0.00 0.00 0.00 4.12
471 1101 1.360162 CATATGCCATCCTCCCCCAAT 59.640 52.381 0.00 0.00 0.00 3.16
485 1115 0.240945 CCCAATGAACGTTCACCAGC 59.759 55.000 31.87 4.17 40.49 4.85
488 1118 2.416547 CCAATGAACGTTCACCAGCTAG 59.583 50.000 31.87 15.81 40.49 3.42
490 1120 0.320374 TGAACGTTCACCAGCTAGGG 59.680 55.000 26.53 0.00 43.89 3.53
491 1121 0.320697 GAACGTTCACCAGCTAGGGT 59.679 55.000 23.12 0.00 43.89 4.34
492 1122 0.320697 AACGTTCACCAGCTAGGGTC 59.679 55.000 0.00 0.00 43.89 4.46
493 1123 0.542232 ACGTTCACCAGCTAGGGTCT 60.542 55.000 7.06 0.00 43.89 3.85
494 1124 1.272313 ACGTTCACCAGCTAGGGTCTA 60.272 52.381 7.06 0.00 43.89 2.59
495 1125 1.822990 CGTTCACCAGCTAGGGTCTAA 59.177 52.381 7.06 0.00 43.89 2.10
496 1126 2.232941 CGTTCACCAGCTAGGGTCTAAA 59.767 50.000 7.06 0.00 43.89 1.85
523 1159 6.363167 TTTCTAAAAGGTGGATCCGACTTA 57.637 37.500 17.95 6.03 41.99 2.24
524 1160 6.555463 TTCTAAAAGGTGGATCCGACTTAT 57.445 37.500 17.95 8.40 41.99 1.73
527 1193 8.081517 TCTAAAAGGTGGATCCGACTTATTAA 57.918 34.615 17.95 5.58 41.99 1.40
554 1220 2.311542 TGTAGAAACCCATGAGGCCATT 59.688 45.455 5.01 0.00 40.58 3.16
555 1221 2.629017 AGAAACCCATGAGGCCATTT 57.371 45.000 5.01 0.00 40.58 2.32
596 1262 1.067416 CGCATTAGCCGTCTAGCCA 59.933 57.895 0.00 0.00 37.52 4.75
597 1263 0.319900 CGCATTAGCCGTCTAGCCAT 60.320 55.000 0.00 0.00 37.52 4.40
598 1264 1.433534 GCATTAGCCGTCTAGCCATC 58.566 55.000 0.00 0.00 33.58 3.51
599 1265 1.702886 CATTAGCCGTCTAGCCATCG 58.297 55.000 0.00 0.00 0.00 3.84
600 1266 0.038159 ATTAGCCGTCTAGCCATCGC 60.038 55.000 0.00 0.00 0.00 4.58
601 1267 2.083835 TTAGCCGTCTAGCCATCGCC 62.084 60.000 0.00 0.00 34.57 5.54
675 1347 2.488355 GATCCGACGGTGCTCGAA 59.512 61.111 14.79 0.00 42.43 3.71
776 1451 6.766467 ACCATAACGATAAGGAAAACTCCATC 59.234 38.462 0.58 0.00 0.00 3.51
777 1452 6.992715 CCATAACGATAAGGAAAACTCCATCT 59.007 38.462 0.00 0.00 0.00 2.90
780 1455 4.469945 ACGATAAGGAAAACTCCATCTCCA 59.530 41.667 0.00 0.00 0.00 3.86
781 1456 5.131142 ACGATAAGGAAAACTCCATCTCCAT 59.869 40.000 0.00 0.00 0.00 3.41
836 1511 1.229529 TCCCCACTTCCACTCCTCC 60.230 63.158 0.00 0.00 0.00 4.30
837 1512 1.229658 CCCCACTTCCACTCCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
838 1513 1.268283 CCCCACTTCCACTCCTCCTC 61.268 65.000 0.00 0.00 0.00 3.71
887 1562 0.034059 CCAGGAATTCCCGATCCTCG 59.966 60.000 21.22 0.02 44.26 4.63
1134 1812 2.885861 GAGCACCACGAGGACGAT 59.114 61.111 5.68 0.00 42.66 3.73
1269 1953 1.224870 GCCTAAGGGGAAGCAGGAC 59.775 63.158 0.00 0.00 37.23 3.85
1567 2266 2.253758 GCTGCTCACGCCAAGAACA 61.254 57.895 0.00 0.00 34.43 3.18
1653 2352 2.569134 GAGAACTCGCGCTCCAGT 59.431 61.111 5.56 1.19 0.00 4.00
1744 2443 2.155155 GGCGTTCACAAGTTTCTCTACG 59.845 50.000 0.00 0.00 0.00 3.51
1764 2463 0.599466 CTGATGGCGATCACAGCGAT 60.599 55.000 7.38 0.00 34.71 4.58
1824 2523 6.209774 TGGAGGTTTCTATAAGGAGAATGGA 58.790 40.000 0.00 0.00 35.41 3.41
1874 2573 2.386779 TGGTGATTTGTATGCCCATGG 58.613 47.619 4.14 4.14 0.00 3.66
1986 2685 1.530293 CAGTCAGCACAAGAAGCACTC 59.470 52.381 0.00 0.00 0.00 3.51
2096 2795 4.870426 TCAATTAGATCGAGCAGGTGTTTC 59.130 41.667 2.38 0.00 0.00 2.78
2106 2805 6.927416 TCGAGCAGGTGTTTCTTACTATTTA 58.073 36.000 0.00 0.00 0.00 1.40
2141 2840 5.989477 TGCATTTCACATAGCCTACTTACT 58.011 37.500 0.00 0.00 0.00 2.24
2157 2856 9.002600 GCCTACTTACTATCTTAGACCTTAGAC 57.997 40.741 0.00 0.00 0.00 2.59
2184 2883 8.186821 GGCGTAGTTCAGAATTTCTACTACTAA 58.813 37.037 24.02 3.22 36.84 2.24
2224 2923 9.241919 TCAGCTATTCATTTTGAGATTAAACCA 57.758 29.630 0.00 0.00 0.00 3.67
2280 2979 6.089954 GCTGGAAATAACTGAAAACTTGATGC 59.910 38.462 0.00 0.00 0.00 3.91
2284 2983 9.638239 GGAAATAACTGAAAACTTGATGCATTA 57.362 29.630 0.00 0.00 0.00 1.90
2286 2985 9.979578 AAATAACTGAAAACTTGATGCATTACA 57.020 25.926 0.00 0.00 0.00 2.41
2313 3012 9.425248 ATAGTGATCAACAATAAATGGGACAAT 57.575 29.630 0.00 0.00 35.50 2.71
2487 3186 4.019231 AGGGAAAAGTGGTCATTCTCCTAC 60.019 45.833 0.00 0.00 0.00 3.18
2506 3205 2.256591 CCTGTTGCTGCTGCTTCGT 61.257 57.895 17.00 0.00 40.48 3.85
2525 3224 2.350804 CGTTCTCATGTTGGATCTGCAG 59.649 50.000 7.63 7.63 0.00 4.41
2562 3261 5.833667 TCAGTCTCTTTCTCTTCTTGGTACA 59.166 40.000 0.00 0.00 0.00 2.90
2576 3275 2.855014 TACACCACCACCCCACCC 60.855 66.667 0.00 0.00 0.00 4.61
2577 3276 3.733681 TACACCACCACCCCACCCA 62.734 63.158 0.00 0.00 0.00 4.51
2595 3294 1.035139 CACATATGCTTGGCCCCTTC 58.965 55.000 0.00 0.00 0.00 3.46
2596 3295 0.630673 ACATATGCTTGGCCCCTTCA 59.369 50.000 0.00 0.00 0.00 3.02
2610 3309 1.815003 CCCTTCAATGCAGTGACTTCC 59.185 52.381 17.75 0.00 0.00 3.46
2618 3317 0.667792 GCAGTGACTTCCTGTCCGAC 60.668 60.000 0.00 0.00 44.75 4.79
2663 3362 2.839486 TGAGGTTCCTAGTTGTGCAG 57.161 50.000 0.00 0.00 0.00 4.41
2778 3478 1.283321 AGCCTTGTCAAGAGGGAATCC 59.717 52.381 14.42 0.00 34.75 3.01
2791 3491 4.103153 AGAGGGAATCCGAATGCTGATTTA 59.897 41.667 0.00 0.00 38.33 1.40
2843 3546 9.481340 GTGATAGTGAGCATATCATTAACAGAA 57.519 33.333 0.00 0.00 40.69 3.02
2848 3551 9.053840 AGTGAGCATATCATTAACAGAATTGAG 57.946 33.333 0.00 0.00 40.92 3.02
2856 3559 7.870509 TCATTAACAGAATTGAGATGGAAGG 57.129 36.000 0.00 0.00 0.00 3.46
2963 3666 1.631388 TGATAGGAAAAGAACCCGGCA 59.369 47.619 0.00 0.00 0.00 5.69
2971 3674 1.605753 AAGAACCCGGCAAAGAAGAC 58.394 50.000 0.00 0.00 0.00 3.01
3007 3710 2.092753 TGGAGATGATGAACTTCCAGCC 60.093 50.000 0.00 0.00 0.00 4.85
3011 3714 3.760684 AGATGATGAACTTCCAGCCAAAC 59.239 43.478 0.00 0.00 0.00 2.93
3020 3723 3.245052 ACTTCCAGCCAAACTTAGAGCAT 60.245 43.478 0.00 0.00 0.00 3.79
3040 3743 5.817296 AGCATACATGATTGCGAGTTAGAAA 59.183 36.000 15.46 0.00 43.61 2.52
3053 3756 5.051641 GCGAGTTAGAAATTAGGACACATCG 60.052 44.000 0.00 0.00 0.00 3.84
3088 3791 1.766059 TGAGGGTGTCAGCTGTGGT 60.766 57.895 14.67 0.00 0.00 4.16
3114 3817 1.973281 CACAGCTTTGGTGGCGGAT 60.973 57.895 0.00 0.00 35.13 4.18
3169 3873 3.787001 GCTACAGGGAAGGGCGCT 61.787 66.667 7.64 0.00 40.97 5.92
3192 3896 3.822735 TCTCCACTTTTCAATGAGCTTGG 59.177 43.478 0.00 0.00 35.43 3.61
3200 3904 0.458669 CAATGAGCTTGGTCCCATGC 59.541 55.000 14.54 14.54 44.29 4.06
3232 3936 3.551846 CAAACCTGGTGTAGAACTTGGT 58.448 45.455 0.00 0.00 36.42 3.67
3249 3953 7.390718 AGAACTTGGTTCACATTATGTTAGGAC 59.609 37.037 12.06 0.00 44.11 3.85
3279 3983 7.546358 TGCCAAAACAGTCCTTATTGATATTG 58.454 34.615 0.00 0.00 0.00 1.90
3313 4017 3.495753 AGTTTTAAGGCGAGGTGTTAACG 59.504 43.478 0.26 0.00 0.00 3.18
3346 4050 9.040939 ACAATGCTTGTTTAAAAAGGAATACAC 57.959 29.630 0.00 0.00 42.22 2.90
3421 4125 6.005823 TGGTGACTTGATGAGTTGATCAATT 58.994 36.000 12.12 7.39 42.53 2.32
3423 4127 6.246449 GTGACTTGATGAGTTGATCAATTCG 58.754 40.000 21.66 12.03 41.51 3.34
3476 4180 3.367292 CCATTGTGGACTTTCCCATTTCG 60.367 47.826 0.00 0.00 40.96 3.46
3561 4270 6.550938 TTCATATCAGATCAAGTGGTCTGT 57.449 37.500 18.68 10.40 41.92 3.41
3564 4273 7.397221 TCATATCAGATCAAGTGGTCTGTTTT 58.603 34.615 18.68 9.51 41.92 2.43
3598 4307 9.875691 AGTTTTAAGAAAGAAAATTTGTGCTCT 57.124 25.926 0.00 0.00 0.00 4.09
3611 4320 1.071987 TGCTCTGCAGTCCACAAGG 59.928 57.895 14.67 0.00 33.32 3.61
3613 4322 0.536006 GCTCTGCAGTCCACAAGGTT 60.536 55.000 14.67 0.00 35.89 3.50
3614 4323 1.270839 GCTCTGCAGTCCACAAGGTTA 60.271 52.381 14.67 0.00 35.89 2.85
3652 4361 5.233083 TCAGTAGCAGCCATTATAGCATT 57.767 39.130 0.00 0.00 0.00 3.56
3706 4415 4.079253 GCATGTTCTGGGAAGTTTCCTTA 58.921 43.478 10.53 0.60 46.72 2.69
3718 4427 6.010850 GGAAGTTTCCTTAGTCCATTTCCTT 58.989 40.000 3.63 0.00 44.11 3.36
3814 4523 7.275888 TCATTATTTGCTTCAGTCAAAGTGT 57.724 32.000 0.00 0.00 36.93 3.55
3815 4524 7.715657 TCATTATTTGCTTCAGTCAAAGTGTT 58.284 30.769 0.00 0.00 36.93 3.32
3816 4525 8.196771 TCATTATTTGCTTCAGTCAAAGTGTTT 58.803 29.630 0.00 0.00 36.93 2.83
3817 4526 8.819974 CATTATTTGCTTCAGTCAAAGTGTTTT 58.180 29.630 0.00 0.00 36.93 2.43
4072 4781 6.257849 TGAACTTGATACACTCAACAAGACAC 59.742 38.462 0.00 0.00 38.97 3.67
4206 4915 0.239347 CTTCAGAAGCTTGGCAACCG 59.761 55.000 2.10 0.00 0.00 4.44
4212 4921 4.043200 GCTTGGCAACCGCAGACC 62.043 66.667 6.59 0.00 41.24 3.85
4228 4937 3.322466 CCGAGGGTCAGGGCACTT 61.322 66.667 0.00 0.00 0.00 3.16
4233 4942 0.178990 AGGGTCAGGGCACTTTTCAC 60.179 55.000 0.00 0.00 0.00 3.18
4239 4948 1.082104 GGGCACTTTTCACGAAGCG 60.082 57.895 0.00 0.00 0.00 4.68
4311 5020 1.309950 CCGAGAATAGAGCGAGGACA 58.690 55.000 0.00 0.00 0.00 4.02
4341 5050 1.464734 TGGTGGAGAAGCTAGAGTCG 58.535 55.000 0.00 0.00 0.00 4.18
4344 5053 1.202582 GTGGAGAAGCTAGAGTCGCAA 59.797 52.381 0.00 0.00 0.00 4.85
4464 5173 1.374252 AGTGTGGACATTCGTCGCC 60.374 57.895 0.00 0.00 43.61 5.54
4524 5233 7.875554 ACTTGATGAGGTTAGAAAGTTTCTCTC 59.124 37.037 21.25 19.90 41.14 3.20
4556 5265 6.820656 AGCCTCTGTGTAGACATTATTGAAAG 59.179 38.462 0.00 0.00 0.00 2.62
4557 5266 6.595716 GCCTCTGTGTAGACATTATTGAAAGT 59.404 38.462 0.00 0.00 0.00 2.66
4561 5270 9.778741 TCTGTGTAGACATTATTGAAAGTTTCT 57.221 29.630 16.33 0.09 0.00 2.52
4782 5491 0.669619 CTGTTTGGATGTGCTGTGCA 59.330 50.000 0.00 0.00 35.60 4.57
4857 5566 5.840243 TGCGTACCTTAGCTTTATAGACA 57.160 39.130 0.00 0.00 0.00 3.41
5029 5742 2.925170 ACAAGGTCGGCTGCTCCT 60.925 61.111 0.00 2.74 0.00 3.69
5047 5760 4.883585 GCTCCTCATTCATTGGTGATGTTA 59.116 41.667 0.00 0.00 37.06 2.41
5063 5776 5.404366 GTGATGTTACTGTTGCGAAAGACTA 59.596 40.000 0.00 0.00 0.00 2.59
5065 5778 4.684877 TGTTACTGTTGCGAAAGACTACA 58.315 39.130 0.00 0.00 0.00 2.74
5083 5796 5.181748 ACTACATCATTTCTCTGCTTCCAC 58.818 41.667 0.00 0.00 0.00 4.02
5093 5806 1.980765 TCTGCTTCCACAGATTCCAGT 59.019 47.619 0.00 0.00 41.72 4.00
5098 5811 4.141711 TGCTTCCACAGATTCCAGTATACC 60.142 45.833 0.00 0.00 0.00 2.73
5120 5833 3.120546 CGAAATGCAGAGTGTGTCGAATT 60.121 43.478 0.00 0.00 0.00 2.17
5125 5838 3.243873 TGCAGAGTGTGTCGAATTCTCTT 60.244 43.478 3.52 0.00 33.92 2.85
5144 5857 4.703897 TCTTCGGTGTCTCTTGTCAATTT 58.296 39.130 0.00 0.00 0.00 1.82
5233 5946 1.610522 CCCAGCCTTCTGAAACACAAG 59.389 52.381 0.00 0.00 42.95 3.16
5239 5952 3.319122 GCCTTCTGAAACACAAGAACCAT 59.681 43.478 0.00 0.00 0.00 3.55
5354 6067 3.695606 GCCTCTGTCTGCGGTCCA 61.696 66.667 0.00 0.00 0.00 4.02
5434 6148 1.605058 AACTACGCCAGACAGCCGAT 61.605 55.000 0.00 0.00 0.00 4.18
5440 6154 2.393768 CCAGACAGCCGATGCACAC 61.394 63.158 0.00 0.00 41.13 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.398554 CCATGACGGGCGTTCCTTG 61.399 63.158 0.00 0.00 0.00 3.61
2 3 1.546589 TACCATGACGGGCGTTCCTT 61.547 55.000 0.00 0.00 40.22 3.36
3 4 1.956629 CTACCATGACGGGCGTTCCT 61.957 60.000 0.00 0.00 40.22 3.36
26 27 0.692419 ATCTTCGGGGCTCAGACCAT 60.692 55.000 0.00 0.00 27.52 3.55
42 43 3.969287 ACATATCGCATGGCTACATCT 57.031 42.857 0.00 0.00 34.35 2.90
45 48 4.556233 GAACTACATATCGCATGGCTACA 58.444 43.478 0.00 0.00 0.00 2.74
55 58 5.817988 TCTTCTCCAACGAACTACATATCG 58.182 41.667 0.00 0.00 44.33 2.92
103 106 2.039818 TGTGTTCCTTGGCGTAAACA 57.960 45.000 0.00 0.00 0.00 2.83
107 110 1.944024 CACTTTGTGTTCCTTGGCGTA 59.056 47.619 0.00 0.00 0.00 4.42
119 122 1.876156 GTTGCTCTCCTCCACTTTGTG 59.124 52.381 0.00 0.00 0.00 3.33
120 123 1.541233 CGTTGCTCTCCTCCACTTTGT 60.541 52.381 0.00 0.00 0.00 2.83
121 124 1.151668 CGTTGCTCTCCTCCACTTTG 58.848 55.000 0.00 0.00 0.00 2.77
122 125 0.603975 GCGTTGCTCTCCTCCACTTT 60.604 55.000 0.00 0.00 0.00 2.66
158 161 1.857318 TTTATGGCCCACACGCGTTG 61.857 55.000 10.22 11.76 0.00 4.10
159 162 1.582610 CTTTATGGCCCACACGCGTT 61.583 55.000 10.22 0.00 0.00 4.84
160 163 2.032834 TTTATGGCCCACACGCGT 59.967 55.556 5.58 5.58 0.00 6.01
204 221 4.485834 CACGAACCGCCCGATCGA 62.486 66.667 18.66 0.00 39.73 3.59
244 262 3.348554 ATTCTGCATCGGCTGGCCA 62.349 57.895 4.71 4.71 41.91 5.36
247 265 0.813184 AAACATTCTGCATCGGCTGG 59.187 50.000 0.00 0.00 41.91 4.85
262 280 6.492087 CCAACCCTTTTAGATGAAGGTAAACA 59.508 38.462 2.57 0.00 41.70 2.83
283 301 2.352503 AATGATGTTCGCTTGCCAAC 57.647 45.000 0.00 0.00 0.00 3.77
309 662 8.458573 TTGATCTTTCCTTGCAACTAAAACTA 57.541 30.769 0.00 0.00 0.00 2.24
321 674 5.817816 ACTATAGCGGTTTGATCTTTCCTTG 59.182 40.000 0.00 0.00 0.00 3.61
322 675 5.990668 ACTATAGCGGTTTGATCTTTCCTT 58.009 37.500 0.00 0.00 0.00 3.36
337 690 8.099704 GGCAATTTTCGTTTAAAAACTATAGCG 58.900 33.333 0.00 0.00 40.37 4.26
366 719 2.093658 ACATGGTAGTTTCTTCGCCGAT 60.094 45.455 0.00 0.00 0.00 4.18
371 724 2.921754 GGACGACATGGTAGTTTCTTCG 59.078 50.000 0.00 0.00 0.00 3.79
392 745 1.379527 GAGGGGTGGCATTTTCTACG 58.620 55.000 0.00 0.00 0.00 3.51
394 747 0.988832 ACGAGGGGTGGCATTTTCTA 59.011 50.000 0.00 0.00 0.00 2.10
443 1073 1.072331 AGGATGGCATATGGGAACGAC 59.928 52.381 0.00 0.00 0.00 4.34
450 1080 1.142048 TGGGGGAGGATGGCATATGG 61.142 60.000 0.00 0.00 0.00 2.74
460 1090 0.326927 GAACGTTCATTGGGGGAGGA 59.673 55.000 23.12 0.00 0.00 3.71
465 1095 0.881118 CTGGTGAACGTTCATTGGGG 59.119 55.000 31.81 16.88 39.73 4.96
466 1096 0.240945 GCTGGTGAACGTTCATTGGG 59.759 55.000 31.81 21.66 39.73 4.12
467 1097 1.238439 AGCTGGTGAACGTTCATTGG 58.762 50.000 31.81 23.18 39.73 3.16
468 1098 2.416547 CCTAGCTGGTGAACGTTCATTG 59.583 50.000 31.81 23.60 39.73 2.82
469 1099 2.615493 CCCTAGCTGGTGAACGTTCATT 60.615 50.000 31.81 17.58 39.73 2.57
470 1100 1.066143 CCCTAGCTGGTGAACGTTCAT 60.066 52.381 31.81 18.81 39.73 2.57
471 1101 0.320374 CCCTAGCTGGTGAACGTTCA 59.680 55.000 26.53 26.53 34.20 3.18
523 1159 8.917088 CCTCATGGGTTTCTACATCATTTTAAT 58.083 33.333 0.00 0.00 0.00 1.40
524 1160 7.147915 GCCTCATGGGTTTCTACATCATTTTAA 60.148 37.037 0.00 0.00 37.43 1.52
527 1193 4.646492 GCCTCATGGGTTTCTACATCATTT 59.354 41.667 0.00 0.00 37.43 2.32
554 1220 0.037590 GGTGCCCTGGTGTATGTCAA 59.962 55.000 0.00 0.00 0.00 3.18
555 1221 0.840288 AGGTGCCCTGGTGTATGTCA 60.840 55.000 0.00 0.00 29.57 3.58
619 1291 2.757508 CAGGAGGAGCGAGCCAGA 60.758 66.667 0.00 0.00 0.00 3.86
622 1294 4.527583 CAGCAGGAGGAGCGAGCC 62.528 72.222 0.00 0.00 37.01 4.70
675 1347 6.721318 TCTACCAAGATCAGTTTATTGCCTT 58.279 36.000 0.00 0.00 0.00 4.35
776 1451 5.325239 AGTAAAGAAAACAGGGGAATGGAG 58.675 41.667 0.00 0.00 0.00 3.86
777 1452 5.321927 GAGTAAAGAAAACAGGGGAATGGA 58.678 41.667 0.00 0.00 0.00 3.41
780 1455 4.510386 GGGGAGTAAAGAAAACAGGGGAAT 60.510 45.833 0.00 0.00 0.00 3.01
781 1456 3.181426 GGGGAGTAAAGAAAACAGGGGAA 60.181 47.826 0.00 0.00 0.00 3.97
1254 1938 2.987125 GCGTCCTGCTTCCCCTTA 59.013 61.111 0.00 0.00 41.73 2.69
1437 2133 3.458579 CGGTCGTCGCTGTTGTCG 61.459 66.667 0.00 0.00 0.00 4.35
1653 2352 2.333417 GCGGAGGTCAGACTCGACA 61.333 63.158 13.06 0.00 38.39 4.35
1744 2443 2.879070 CGCTGTGATCGCCATCAGC 61.879 63.158 3.31 5.07 39.86 4.26
1755 2454 1.472201 GGAGCTTCATCATCGCTGTGA 60.472 52.381 0.00 0.00 33.47 3.58
1824 2523 1.065126 GCCATTCTCCCTACTGCACTT 60.065 52.381 0.00 0.00 0.00 3.16
1986 2685 9.712305 GGGGATTATATAATCATACCATTCTCG 57.288 37.037 28.37 0.00 42.92 4.04
2106 2805 5.471556 TGTGAAATGCAGATTTCCATGTT 57.528 34.783 9.68 0.00 44.83 2.71
2117 2816 6.051717 AGTAAGTAGGCTATGTGAAATGCAG 58.948 40.000 0.00 0.00 0.00 4.41
2141 2840 3.813443 ACGCCGTCTAAGGTCTAAGATA 58.187 45.455 0.00 0.00 0.00 1.98
2157 2856 4.421948 AGTAGAAATTCTGAACTACGCCG 58.578 43.478 5.64 0.00 39.75 6.46
2184 2883 7.667043 TGAATAGCTGAACAAAAATACTCGT 57.333 32.000 0.00 0.00 0.00 4.18
2224 2923 6.301486 AGTAGGTCGTTTTAGGAAACCAAAT 58.699 36.000 0.00 0.00 41.66 2.32
2242 2941 9.614792 CAGTTATTTCCAGCTAATAAAGTAGGT 57.385 33.333 2.44 0.00 31.35 3.08
2272 2971 8.400947 GTTGATCACTATTGTAATGCATCAAGT 58.599 33.333 0.00 0.00 0.00 3.16
2284 2983 8.686334 GTCCCATTTATTGTTGATCACTATTGT 58.314 33.333 0.00 0.00 0.00 2.71
2285 2984 8.685427 TGTCCCATTTATTGTTGATCACTATTG 58.315 33.333 0.00 0.00 0.00 1.90
2286 2985 8.821686 TGTCCCATTTATTGTTGATCACTATT 57.178 30.769 0.00 0.00 0.00 1.73
2487 3186 2.960170 GAAGCAGCAGCAACAGGG 59.040 61.111 3.17 0.00 45.49 4.45
2506 3205 2.573009 TCCTGCAGATCCAACATGAGAA 59.427 45.455 17.39 0.00 0.00 2.87
2576 3275 1.035139 GAAGGGGCCAAGCATATGTG 58.965 55.000 4.39 0.00 0.00 3.21
2577 3276 0.630673 TGAAGGGGCCAAGCATATGT 59.369 50.000 4.39 0.00 0.00 2.29
2711 3410 7.707624 ATTTTCAGTGAAATCAATAGGCAGA 57.292 32.000 18.69 0.20 31.34 4.26
2754 3453 4.657814 TTCCCTCTTGACAAGGCTTAAT 57.342 40.909 15.13 0.00 32.15 1.40
2778 3478 7.707893 AGGGAAATGAAAATAAATCAGCATTCG 59.292 33.333 0.00 0.00 0.00 3.34
2843 3546 4.934797 TCAACTTCCCTTCCATCTCAAT 57.065 40.909 0.00 0.00 0.00 2.57
2848 3551 6.830838 ACTAAATCATCAACTTCCCTTCCATC 59.169 38.462 0.00 0.00 0.00 3.51
2856 3559 7.339466 ACATGGGTTACTAAATCATCAACTTCC 59.661 37.037 0.00 0.00 0.00 3.46
2910 3613 9.799106 AACTTCTTTTCTCTTCCATCTCAATTA 57.201 29.630 0.00 0.00 0.00 1.40
2929 3632 8.820831 TCTTTTCCTATCAGAGATCAACTTCTT 58.179 33.333 0.00 0.00 0.00 2.52
2986 3689 2.092753 GGCTGGAAGTTCATCATCTCCA 60.093 50.000 5.01 0.00 35.30 3.86
2991 3694 3.771216 AGTTTGGCTGGAAGTTCATCAT 58.229 40.909 5.01 0.00 35.30 2.45
3007 3710 5.905733 CGCAATCATGTATGCTCTAAGTTTG 59.094 40.000 18.52 2.14 40.39 2.93
3011 3714 4.987285 ACTCGCAATCATGTATGCTCTAAG 59.013 41.667 18.52 13.65 40.39 2.18
3020 3723 8.201464 TCCTAATTTCTAACTCGCAATCATGTA 58.799 33.333 0.00 0.00 0.00 2.29
3040 3743 5.537300 AAGTAGCATCGATGTGTCCTAAT 57.463 39.130 25.47 14.48 0.00 1.73
3102 3805 1.784301 TTCCCTCATCCGCCACCAAA 61.784 55.000 0.00 0.00 0.00 3.28
3103 3806 1.570857 ATTCCCTCATCCGCCACCAA 61.571 55.000 0.00 0.00 0.00 3.67
3114 3817 1.273838 ACTGTAGCCTCCATTCCCTCA 60.274 52.381 0.00 0.00 0.00 3.86
3149 3853 2.592308 GCCCTTCCCTGTAGCCAG 59.408 66.667 0.00 0.00 38.50 4.85
3161 3865 0.178990 AAAAGTGGAGAAGCGCCCTT 60.179 50.000 2.29 0.00 0.00 3.95
3169 3873 4.279169 CCAAGCTCATTGAAAAGTGGAGAA 59.721 41.667 0.00 0.00 41.83 2.87
3192 3896 3.540314 TGCCATATTTTTGCATGGGAC 57.460 42.857 4.03 0.00 34.86 4.46
3200 3904 4.640364 ACACCAGGTTTGCCATATTTTTG 58.360 39.130 0.00 0.00 37.19 2.44
3232 3936 5.822519 GCAGGATGTCCTAACATAATGTGAA 59.177 40.000 0.32 0.00 46.20 3.18
3249 3953 1.915141 AGGACTGTTTTGGCAGGATG 58.085 50.000 0.00 0.00 40.59 3.51
3279 3983 7.368480 TCGCCTTAAAACTAAACTGGAATAC 57.632 36.000 0.00 0.00 0.00 1.89
3293 3997 2.807392 CCGTTAACACCTCGCCTTAAAA 59.193 45.455 6.39 0.00 0.00 1.52
3421 4125 2.289382 TGCCAGAGCATTGAACTAACGA 60.289 45.455 0.00 0.00 46.52 3.85
3594 4303 0.536006 AACCTTGTGGACTGCAGAGC 60.536 55.000 23.35 11.79 37.04 4.09
3598 4307 4.947388 GGAAATATAACCTTGTGGACTGCA 59.053 41.667 0.00 0.00 37.04 4.41
3614 4323 8.145122 GCTGCTACTGAAACTACTAGGAAATAT 58.855 37.037 0.00 0.00 0.00 1.28
3706 4415 9.238368 TCACGAATTTATAAAAGGAAATGGACT 57.762 29.630 1.21 0.00 0.00 3.85
3718 4427 7.518161 CAACAGAGCACTCACGAATTTATAAA 58.482 34.615 0.00 0.00 0.00 1.40
3790 4499 7.275888 ACACTTTGACTGAAGCAAATAATGA 57.724 32.000 0.00 0.00 35.00 2.57
3975 4684 5.140747 TGGACTCTAGAAGCTTCAACTTC 57.859 43.478 27.57 15.74 45.29 3.01
4072 4781 3.361977 CGCGGTTTCCCCTGGTTG 61.362 66.667 0.00 0.00 0.00 3.77
4212 4921 0.955919 GAAAAGTGCCCTGACCCTCG 60.956 60.000 0.00 0.00 0.00 4.63
4228 4937 0.859232 GTCTTCTGCGCTTCGTGAAA 59.141 50.000 9.73 0.00 0.00 2.69
4233 4942 2.357792 CAGAGTCTTCTGCGCTTCG 58.642 57.895 9.73 0.00 43.98 3.79
4254 4963 1.699083 TCCAGCTGTTTGTGATCCTCA 59.301 47.619 13.81 0.00 0.00 3.86
4299 5008 2.117051 TCCTCTAGTGTCCTCGCTCTA 58.883 52.381 0.00 0.00 35.84 2.43
4311 5020 3.198853 GCTTCTCCACCAAATCCTCTAGT 59.801 47.826 0.00 0.00 0.00 2.57
4341 5050 0.518636 TCGACAGCTCTTTGCATTGC 59.481 50.000 0.46 0.46 45.94 3.56
4344 5053 0.792640 CGTTCGACAGCTCTTTGCAT 59.207 50.000 0.00 0.00 45.94 3.96
4464 5173 2.269241 GGAGAGGGCAAGAACCGG 59.731 66.667 0.00 0.00 0.00 5.28
4524 5233 0.387202 CTACACAGAGGCTCATCCGG 59.613 60.000 18.26 0.00 40.77 5.14
4556 5265 8.204836 TGCCTAATAGATTACAGGAAGAGAAAC 58.795 37.037 0.00 0.00 0.00 2.78
4557 5266 8.319057 TGCCTAATAGATTACAGGAAGAGAAA 57.681 34.615 0.00 0.00 0.00 2.52
4560 5269 7.605691 CCAATGCCTAATAGATTACAGGAAGAG 59.394 40.741 0.00 0.00 0.00 2.85
4561 5270 7.072454 ACCAATGCCTAATAGATTACAGGAAGA 59.928 37.037 0.00 0.00 0.00 2.87
4669 5378 1.074752 GCGAAGAGAGAACCAGCAAG 58.925 55.000 0.00 0.00 0.00 4.01
4782 5491 2.511659 ACTGCTTCATGACTTGCACAT 58.488 42.857 11.67 3.16 0.00 3.21
5029 5742 6.570186 GCAACAGTAACATCACCAATGAATGA 60.570 38.462 0.00 0.00 38.69 2.57
5047 5760 3.990092 TGATGTAGTCTTTCGCAACAGT 58.010 40.909 0.00 0.00 0.00 3.55
5063 5776 4.008330 CTGTGGAAGCAGAGAAATGATGT 58.992 43.478 0.00 0.00 38.70 3.06
5065 5778 4.564782 TCTGTGGAAGCAGAGAAATGAT 57.435 40.909 0.00 0.00 40.23 2.45
5083 5796 5.056480 TGCATTTCGGTATACTGGAATCTG 58.944 41.667 14.40 8.29 27.98 2.90
5093 5806 4.430007 GACACACTCTGCATTTCGGTATA 58.570 43.478 0.00 0.00 0.00 1.47
5098 5811 1.418373 TCGACACACTCTGCATTTCG 58.582 50.000 0.00 0.00 0.00 3.46
5120 5833 2.583143 TGACAAGAGACACCGAAGAGA 58.417 47.619 0.00 0.00 0.00 3.10
5125 5838 2.548057 GCAAATTGACAAGAGACACCGA 59.452 45.455 0.00 0.00 0.00 4.69
5144 5857 4.329545 GGTGTCGGCCAGGAAGCA 62.330 66.667 2.24 0.00 0.00 3.91
5233 5946 6.144080 GTGTATATGCGAGACAAGTATGGTTC 59.856 42.308 0.00 0.00 29.11 3.62
5239 5952 5.462068 GCATTGTGTATATGCGAGACAAGTA 59.538 40.000 0.00 0.00 39.02 2.24
5354 6067 4.040952 ACTTCAGCATAGAGTGTGGACTTT 59.959 41.667 0.00 0.00 30.16 2.66
5434 6148 2.299013 AGGAGTACGATTTCAGTGTGCA 59.701 45.455 0.00 0.00 0.00 4.57
5440 6154 3.024547 TGAGGGAGGAGTACGATTTCAG 58.975 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.