Multiple sequence alignment - TraesCS5A01G155200

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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 TraesCS5A01G155200 chr5A 100.000 2336 0 0 1 2336 332718506 332720841 0.000000e+00 4314
1 TraesCS5A01G155200 chr5D 95.315 1558 47 10 803 2336 249980877 249982432 0.000000e+00 2449
2 TraesCS5A01G155200 chr5B 95.004 1421 42 10 802 2193 282847158 282848578 0.000000e+00 2204
3 TraesCS5A01G155200 chr5B 85.488 379 48 4 80 458 282845263 282845634 2.810000e-104 388
4 TraesCS5A01G155200 chr5B 97.059 102 3 0 2235 2336 282848580 282848681 3.090000e-39 172
5 TraesCS5A01G155200 chr4D 86.559 372 37 6 973 1338 116153757 116153393 4.680000e-107 398
6 TraesCS5A01G155200 chr4B 86.649 367 36 6 978 1338 177861912 177861553 6.050000e-106 394
7 TraesCS5A01G155200 chr4A 86.290 372 38 6 973 1338 460448871 460449235 2.180000e-105 392


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 TraesCS5A01G155200 chr5A 332718506 332720841 2335 False 4314.000000 4314 100.000 1 2336 1 chr5A.!!$F1 2335
1 TraesCS5A01G155200 chr5D 249980877 249982432 1555 False 2449.000000 2449 95.315 803 2336 1 chr5D.!!$F1 1533
2 TraesCS5A01G155200 chr5B 282845263 282848681 3418 False 921.333333 2204 92.517 80 2336 3 chr5B.!!$F1 2256

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
492 722 0.037232 GTGGTGCCTCTAGCTTCGTT 60.037 55.0 0.0 0.0 44.23 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 3057 0.387929 TAACATAGCTCCTTCCCGCG 59.612 55.0 0.0 0.0 0.0 6.46 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
18 19 3.835686 CGACGCTGTCAGGAGATAG 57.164 57.895 1.14 0.00 36.20 2.08
19 20 1.300481 CGACGCTGTCAGGAGATAGA 58.700 55.000 1.14 0.00 35.20 1.98
20 21 1.262950 CGACGCTGTCAGGAGATAGAG 59.737 57.143 1.14 0.00 38.44 2.43
21 22 1.606668 GACGCTGTCAGGAGATAGAGG 59.393 57.143 1.14 0.00 37.17 3.69
22 23 1.213182 ACGCTGTCAGGAGATAGAGGA 59.787 52.381 1.14 0.00 37.17 3.71
23 24 2.302260 CGCTGTCAGGAGATAGAGGAA 58.698 52.381 1.14 0.00 35.20 3.36
24 25 2.034053 CGCTGTCAGGAGATAGAGGAAC 59.966 54.545 1.14 0.00 35.20 3.62
25 26 2.364002 GCTGTCAGGAGATAGAGGAACC 59.636 54.545 1.14 0.00 35.20 3.62
26 27 2.962421 CTGTCAGGAGATAGAGGAACCC 59.038 54.545 0.00 0.00 35.20 4.11
27 28 2.587777 TGTCAGGAGATAGAGGAACCCT 59.412 50.000 0.00 0.00 36.03 4.34
28 29 3.792114 TGTCAGGAGATAGAGGAACCCTA 59.208 47.826 0.00 0.00 31.76 3.53
29 30 4.232122 TGTCAGGAGATAGAGGAACCCTAA 59.768 45.833 0.00 0.00 31.76 2.69
30 31 4.830600 GTCAGGAGATAGAGGAACCCTAAG 59.169 50.000 0.00 0.00 31.76 2.18
31 32 3.576550 CAGGAGATAGAGGAACCCTAAGC 59.423 52.174 0.00 0.00 31.76 3.09
32 33 3.207777 AGGAGATAGAGGAACCCTAAGCA 59.792 47.826 0.00 0.00 31.76 3.91
33 34 4.140567 AGGAGATAGAGGAACCCTAAGCAT 60.141 45.833 0.00 0.00 31.76 3.79
34 35 4.595350 GGAGATAGAGGAACCCTAAGCATT 59.405 45.833 0.00 0.00 31.76 3.56
35 36 5.072464 GGAGATAGAGGAACCCTAAGCATTT 59.928 44.000 0.00 0.00 31.76 2.32
36 37 6.181206 AGATAGAGGAACCCTAAGCATTTC 57.819 41.667 0.00 0.00 31.76 2.17
37 38 5.908247 AGATAGAGGAACCCTAAGCATTTCT 59.092 40.000 0.00 0.00 31.76 2.52
38 39 4.936685 AGAGGAACCCTAAGCATTTCTT 57.063 40.909 0.00 0.00 38.79 2.52
39 40 4.593956 AGAGGAACCCTAAGCATTTCTTG 58.406 43.478 0.00 0.00 36.25 3.02
40 41 3.696548 GAGGAACCCTAAGCATTTCTTGG 59.303 47.826 0.00 0.00 36.25 3.61
44 45 2.826674 CCTAAGCATTTCTTGGGGGA 57.173 50.000 0.00 0.00 46.34 4.81
45 46 2.659428 CCTAAGCATTTCTTGGGGGAG 58.341 52.381 0.00 0.00 46.34 4.30
46 47 2.659428 CTAAGCATTTCTTGGGGGAGG 58.341 52.381 0.00 0.00 36.25 4.30
47 48 1.084018 AAGCATTTCTTGGGGGAGGA 58.916 50.000 0.00 0.00 32.79 3.71
48 49 0.627986 AGCATTTCTTGGGGGAGGAG 59.372 55.000 0.00 0.00 0.00 3.69
49 50 0.396278 GCATTTCTTGGGGGAGGAGG 60.396 60.000 0.00 0.00 0.00 4.30
50 51 1.298953 CATTTCTTGGGGGAGGAGGA 58.701 55.000 0.00 0.00 0.00 3.71
51 52 1.640670 CATTTCTTGGGGGAGGAGGAA 59.359 52.381 0.00 0.00 0.00 3.36
52 53 1.372501 TTTCTTGGGGGAGGAGGAAG 58.627 55.000 0.00 0.00 0.00 3.46
53 54 1.208165 TTCTTGGGGGAGGAGGAAGC 61.208 60.000 0.00 0.00 0.00 3.86
54 55 1.617839 CTTGGGGGAGGAGGAAGCT 60.618 63.158 0.00 0.00 0.00 3.74
55 56 1.919600 CTTGGGGGAGGAGGAAGCTG 61.920 65.000 0.00 0.00 0.00 4.24
56 57 2.041265 GGGGGAGGAGGAAGCTGA 59.959 66.667 0.00 0.00 0.00 4.26
57 58 1.385206 GGGGGAGGAGGAAGCTGAT 60.385 63.158 0.00 0.00 0.00 2.90
58 59 0.990818 GGGGGAGGAGGAAGCTGATT 60.991 60.000 0.00 0.00 0.00 2.57
59 60 0.922626 GGGGAGGAGGAAGCTGATTT 59.077 55.000 0.00 0.00 0.00 2.17
60 61 1.133945 GGGGAGGAGGAAGCTGATTTC 60.134 57.143 0.00 0.00 0.00 2.17
61 62 1.843206 GGGAGGAGGAAGCTGATTTCT 59.157 52.381 0.00 0.00 0.00 2.52
62 63 2.240921 GGGAGGAGGAAGCTGATTTCTT 59.759 50.000 0.00 0.00 0.00 2.52
63 64 3.277715 GGAGGAGGAAGCTGATTTCTTG 58.722 50.000 0.00 0.00 0.00 3.02
64 65 3.277715 GAGGAGGAAGCTGATTTCTTGG 58.722 50.000 0.00 0.00 0.00 3.61
65 66 2.646798 AGGAGGAAGCTGATTTCTTGGT 59.353 45.455 0.00 0.00 0.00 3.67
66 67 3.013219 GGAGGAAGCTGATTTCTTGGTC 58.987 50.000 0.00 0.00 0.00 4.02
67 68 3.308046 GGAGGAAGCTGATTTCTTGGTCT 60.308 47.826 0.00 0.00 0.00 3.85
68 69 4.080863 GGAGGAAGCTGATTTCTTGGTCTA 60.081 45.833 0.00 0.00 0.00 2.59
69 70 4.837972 AGGAAGCTGATTTCTTGGTCTAC 58.162 43.478 0.00 0.00 0.00 2.59
70 71 4.287067 AGGAAGCTGATTTCTTGGTCTACA 59.713 41.667 0.00 0.00 0.00 2.74
71 72 5.045286 AGGAAGCTGATTTCTTGGTCTACAT 60.045 40.000 0.00 0.00 0.00 2.29
72 73 6.156949 AGGAAGCTGATTTCTTGGTCTACATA 59.843 38.462 0.00 0.00 0.00 2.29
73 74 6.995091 GGAAGCTGATTTCTTGGTCTACATAT 59.005 38.462 0.00 0.00 0.00 1.78
74 75 7.500559 GGAAGCTGATTTCTTGGTCTACATATT 59.499 37.037 0.00 0.00 0.00 1.28
75 76 9.547753 GAAGCTGATTTCTTGGTCTACATATTA 57.452 33.333 0.00 0.00 0.00 0.98
76 77 9.553064 AAGCTGATTTCTTGGTCTACATATTAG 57.447 33.333 0.00 0.00 0.00 1.73
77 78 8.709308 AGCTGATTTCTTGGTCTACATATTAGT 58.291 33.333 0.00 0.00 0.00 2.24
78 79 8.983724 GCTGATTTCTTGGTCTACATATTAGTC 58.016 37.037 0.00 0.00 0.00 2.59
106 107 9.431887 ACGATACTTATTCACACAACTTTGTAT 57.568 29.630 0.00 0.00 39.91 2.29
121 122 8.203485 ACAACTTTGTATTGTGGTCATGATTTT 58.797 29.630 0.00 0.00 40.16 1.82
123 124 7.950512 ACTTTGTATTGTGGTCATGATTTTCA 58.049 30.769 0.00 0.00 0.00 2.69
124 125 8.420222 ACTTTGTATTGTGGTCATGATTTTCAA 58.580 29.630 0.00 3.56 0.00 2.69
125 126 9.258826 CTTTGTATTGTGGTCATGATTTTCAAA 57.741 29.630 0.00 3.36 0.00 2.69
183 184 9.817809 TGAATTGTAATGAGTATAAGAGTGGTC 57.182 33.333 0.00 0.00 0.00 4.02
240 241 2.950877 CGTTGCGCTAAGGAGAGAG 58.049 57.895 9.73 0.00 0.00 3.20
242 243 0.533032 GTTGCGCTAAGGAGAGAGGT 59.467 55.000 9.73 0.00 0.00 3.85
243 244 1.066787 GTTGCGCTAAGGAGAGAGGTT 60.067 52.381 9.73 0.00 0.00 3.50
245 246 0.818296 GCGCTAAGGAGAGAGGTTCA 59.182 55.000 0.00 0.00 0.00 3.18
247 248 2.159028 GCGCTAAGGAGAGAGGTTCATT 60.159 50.000 0.00 0.00 0.00 2.57
257 258 6.441924 AGGAGAGAGGTTCATTCATCTAAACA 59.558 38.462 0.00 0.00 0.00 2.83
267 268 9.213799 GTTCATTCATCTAAACAGAGAGAAAGT 57.786 33.333 0.00 0.00 0.00 2.66
292 293 5.354792 AGAACTAGACGACCACAACTATCTC 59.645 44.000 0.00 0.00 0.00 2.75
300 301 5.924825 ACGACCACAACTATCTCAAGTTAAC 59.075 40.000 0.00 0.00 37.61 2.01
301 302 5.060569 CGACCACAACTATCTCAAGTTAACG 59.939 44.000 0.00 0.00 37.61 3.18
307 308 9.302345 CACAACTATCTCAAGTTAACGATGTAT 57.698 33.333 12.29 10.24 37.61 2.29
315 316 5.517411 TCAAGTTAACGATGTATAAGCCACG 59.483 40.000 12.29 0.00 0.00 4.94
316 317 4.365723 AGTTAACGATGTATAAGCCACGG 58.634 43.478 0.00 0.00 0.00 4.94
330 331 2.607750 ACGGAGGCATGGTGGACT 60.608 61.111 0.00 0.00 0.00 3.85
331 332 2.187946 CGGAGGCATGGTGGACTC 59.812 66.667 0.00 0.00 42.48 3.36
337 338 2.584608 CATGGTGGACTCCGACCC 59.415 66.667 11.90 3.63 0.00 4.46
338 339 2.687566 ATGGTGGACTCCGACCCC 60.688 66.667 11.90 1.60 0.00 4.95
359 360 2.517402 CGGAGGGAGGACTCGAGG 60.517 72.222 18.41 0.00 38.39 4.63
362 363 1.820481 GAGGGAGGACTCGAGGTCG 60.820 68.421 18.41 0.00 45.35 4.79
374 375 4.550422 ACTCGAGGTCGGTTTTTAGTTAC 58.450 43.478 18.41 0.00 40.29 2.50
406 407 1.334384 GGTTTGGGTTGGTGCCTTGT 61.334 55.000 0.00 0.00 0.00 3.16
423 424 3.467226 TTTAGGGAGGCGAGGCGG 61.467 66.667 0.00 0.00 0.00 6.13
439 440 0.598065 GCGGCAACAAACTCCTTGAT 59.402 50.000 0.00 0.00 38.50 2.57
452 453 4.723309 ACTCCTTGATGATGGAATAAGGC 58.277 43.478 0.00 0.00 38.19 4.35
458 688 3.723681 TGATGATGGAATAAGGCCCTTCT 59.276 43.478 0.00 0.00 0.00 2.85
471 701 1.527457 CCCTTCTCATCCCCCATCTT 58.473 55.000 0.00 0.00 0.00 2.40
472 702 1.144503 CCCTTCTCATCCCCCATCTTG 59.855 57.143 0.00 0.00 0.00 3.02
480 710 2.362889 CCCCATCTTGGTGGTGCC 60.363 66.667 0.00 0.00 37.57 5.01
487 717 0.545309 TCTTGGTGGTGCCTCTAGCT 60.545 55.000 0.00 0.00 44.23 3.32
491 721 1.592223 GTGGTGCCTCTAGCTTCGT 59.408 57.895 0.00 0.00 44.23 3.85
492 722 0.037232 GTGGTGCCTCTAGCTTCGTT 60.037 55.000 0.00 0.00 44.23 3.85
493 723 0.037326 TGGTGCCTCTAGCTTCGTTG 60.037 55.000 0.00 0.00 44.23 4.10
494 724 0.246635 GGTGCCTCTAGCTTCGTTGA 59.753 55.000 0.00 0.00 44.23 3.18
501 731 0.642800 CTAGCTTCGTTGAAGAGCGC 59.357 55.000 10.58 0.00 41.71 5.92
502 732 0.038618 TAGCTTCGTTGAAGAGCGCA 60.039 50.000 11.47 0.00 41.71 6.09
503 733 1.154580 GCTTCGTTGAAGAGCGCAC 60.155 57.895 11.47 2.25 41.71 5.34
505 735 1.275471 CTTCGTTGAAGAGCGCACGA 61.275 55.000 11.47 12.69 41.71 4.35
526 757 0.176449 TGTGTGCCTCGATGGATCTG 59.824 55.000 5.24 0.00 38.35 2.90
527 758 0.176680 GTGTGCCTCGATGGATCTGT 59.823 55.000 5.24 0.00 38.35 3.41
529 760 0.596083 GTGCCTCGATGGATCTGTCG 60.596 60.000 12.15 12.15 38.35 4.35
531 762 1.662608 CCTCGATGGATCTGTCGGG 59.337 63.158 16.36 14.05 38.05 5.14
534 765 1.615883 CTCGATGGATCTGTCGGGATT 59.384 52.381 12.77 0.00 40.68 3.01
537 768 1.613925 GATGGATCTGTCGGGATTCGA 59.386 52.381 0.00 0.00 46.77 3.71
552 783 0.245539 TTCGATCGGTGTTGGTCCTC 59.754 55.000 16.41 0.00 0.00 3.71
571 802 2.169352 CTCGGTGGATCTGTTTGGATCT 59.831 50.000 0.00 0.00 41.15 2.75
572 803 3.371034 TCGGTGGATCTGTTTGGATCTA 58.629 45.455 0.00 0.00 41.15 1.98
573 804 3.384789 TCGGTGGATCTGTTTGGATCTAG 59.615 47.826 0.00 0.00 41.15 2.43
583 814 6.263344 TCTGTTTGGATCTAGTATTCGTTCG 58.737 40.000 0.00 0.00 0.00 3.95
589 820 6.147581 TGGATCTAGTATTCGTTCGTATTGC 58.852 40.000 0.00 0.00 0.00 3.56
602 833 3.864243 TCGTATTGCGTTAGGTTGGATT 58.136 40.909 0.00 0.00 42.13 3.01
620 851 9.764363 GGTTGGATTCTTTTGATCTAAGTTTTT 57.236 29.630 0.00 0.00 0.00 1.94
623 854 9.965824 TGGATTCTTTTGATCTAAGTTTTTCAC 57.034 29.630 0.00 0.00 0.00 3.18
633 864 0.872388 AGTTTTTCACCATCGGCGAC 59.128 50.000 13.76 0.00 0.00 5.19
634 865 0.109919 GTTTTTCACCATCGGCGACC 60.110 55.000 13.76 0.00 0.00 4.79
645 876 2.635338 GGCGACCGTTGTTGTTCC 59.365 61.111 0.00 0.00 0.00 3.62
649 880 0.162933 CGACCGTTGTTGTTCCGATG 59.837 55.000 0.00 0.00 0.00 3.84
654 885 1.795872 CGTTGTTGTTCCGATGCACTA 59.204 47.619 0.00 0.00 0.00 2.74
665 896 2.166459 CCGATGCACTAGTCCTTTGAGA 59.834 50.000 0.00 0.00 0.00 3.27
666 897 3.443037 CGATGCACTAGTCCTTTGAGAG 58.557 50.000 0.00 0.00 0.00 3.20
667 898 2.751166 TGCACTAGTCCTTTGAGAGC 57.249 50.000 0.00 0.00 0.00 4.09
671 902 4.081972 TGCACTAGTCCTTTGAGAGCTTAG 60.082 45.833 0.00 0.00 0.00 2.18
674 905 3.608316 AGTCCTTTGAGAGCTTAGCAG 57.392 47.619 7.07 0.00 0.00 4.24
680 911 1.769026 TGAGAGCTTAGCAGGACGAT 58.231 50.000 7.07 0.00 0.00 3.73
684 915 3.935828 GAGAGCTTAGCAGGACGATTTTT 59.064 43.478 7.07 0.00 0.00 1.94
712 943 8.747538 ACTGTTTACCATACCAAGATTTATCC 57.252 34.615 0.00 0.00 0.00 2.59
713 944 8.333235 ACTGTTTACCATACCAAGATTTATCCA 58.667 33.333 0.00 0.00 0.00 3.41
714 945 9.354673 CTGTTTACCATACCAAGATTTATCCAT 57.645 33.333 0.00 0.00 0.00 3.41
715 946 9.349713 TGTTTACCATACCAAGATTTATCCATC 57.650 33.333 0.00 0.00 0.00 3.51
716 947 9.574516 GTTTACCATACCAAGATTTATCCATCT 57.425 33.333 0.00 0.00 34.78 2.90
724 1254 5.936956 CCAAGATTTATCCATCTCACTAGGC 59.063 44.000 0.00 0.00 31.87 3.93
739 1269 2.963782 ACTAGGCGGTCTATAAACCTGG 59.036 50.000 0.00 0.00 37.15 4.45
746 1276 5.121105 GCGGTCTATAAACCTGGTTGTAAT 58.879 41.667 13.79 9.79 37.15 1.89
757 1287 7.758613 AACCTGGTTGTAATTTTTGTTAACG 57.241 32.000 12.11 0.00 0.00 3.18
758 1288 7.098074 ACCTGGTTGTAATTTTTGTTAACGA 57.902 32.000 0.26 0.00 0.00 3.85
759 1289 7.718525 ACCTGGTTGTAATTTTTGTTAACGAT 58.281 30.769 0.26 0.00 0.00 3.73
760 1290 8.848182 ACCTGGTTGTAATTTTTGTTAACGATA 58.152 29.630 0.26 0.00 0.00 2.92
761 1291 9.680315 CCTGGTTGTAATTTTTGTTAACGATAA 57.320 29.630 0.26 1.11 0.00 1.75
787 1317 5.358922 AGATTGAAAATTTGTGTGTGTGGG 58.641 37.500 0.00 0.00 0.00 4.61
788 1318 2.898705 TGAAAATTTGTGTGTGTGGGC 58.101 42.857 0.00 0.00 0.00 5.36
789 1319 2.499289 TGAAAATTTGTGTGTGTGGGCT 59.501 40.909 0.00 0.00 0.00 5.19
790 1320 3.701542 TGAAAATTTGTGTGTGTGGGCTA 59.298 39.130 0.00 0.00 0.00 3.93
791 1321 3.726291 AAATTTGTGTGTGTGGGCTAC 57.274 42.857 0.00 0.00 0.00 3.58
793 1323 1.961793 TTTGTGTGTGTGGGCTACTC 58.038 50.000 1.79 0.00 0.00 2.59
794 1324 0.107831 TTGTGTGTGTGGGCTACTCC 59.892 55.000 1.79 0.00 0.00 3.85
796 1326 0.037232 GTGTGTGTGGGCTACTCCTC 60.037 60.000 1.79 0.00 34.39 3.71
799 1329 1.681327 GTGTGGGCTACTCCTCGGA 60.681 63.158 1.79 0.00 34.39 4.55
800 1330 1.379977 TGTGGGCTACTCCTCGGAG 60.380 63.158 11.35 11.35 46.91 4.63
848 2030 5.490139 AAATGATGTAGATTGCCGTTCAG 57.510 39.130 0.00 0.00 0.00 3.02
879 2062 1.220206 CCACATCCGCTGCTTCTCT 59.780 57.895 0.00 0.00 0.00 3.10
881 2064 0.725686 CACATCCGCTGCTTCTCTTG 59.274 55.000 0.00 0.00 0.00 3.02
1032 2215 4.103103 TCGCAGTCGCAGTCCTCG 62.103 66.667 0.00 0.00 38.40 4.63
1035 2218 2.179517 CAGTCGCAGTCCTCGGTC 59.820 66.667 0.00 0.00 0.00 4.79
1801 2996 3.622166 TTTTGGAGAACCGAGTATCCC 57.378 47.619 0.00 0.00 39.42 3.85
1806 3001 2.764572 GGAGAACCGAGTATCCCTTTCA 59.235 50.000 0.00 0.00 0.00 2.69
1826 3021 6.360370 TTCAAAGTATAGCTCACCTTGTCT 57.640 37.500 0.00 0.00 0.00 3.41
1862 3057 3.219281 AGAGCTAGCCTAGTTGAGCTAC 58.781 50.000 12.13 4.76 45.15 3.58
1915 3124 1.652012 CGTTCAACGCCCACATTGT 59.348 52.632 0.00 0.00 33.65 2.71
1973 3182 0.393537 CCGCTGATTTGGCTCTCCTT 60.394 55.000 0.00 0.00 0.00 3.36
2027 3236 3.719268 TCTTGCCAGGCTCAAGAAATA 57.281 42.857 14.15 0.00 44.70 1.40
2171 3390 0.870307 CTACATCTACGCCGTGCACC 60.870 60.000 12.15 0.00 0.00 5.01
2321 3540 8.749499 GTTGAATCTCTTTGAAAATGTCTTGTG 58.251 33.333 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.262950 CTCTATCTCCTGACAGCGTCG 59.737 57.143 0.00 0.00 34.95 5.12
1 2 1.606668 CCTCTATCTCCTGACAGCGTC 59.393 57.143 0.00 2.32 0.00 5.19
2 3 1.213182 TCCTCTATCTCCTGACAGCGT 59.787 52.381 0.00 0.00 0.00 5.07
3 4 1.974265 TCCTCTATCTCCTGACAGCG 58.026 55.000 0.00 0.00 0.00 5.18
4 5 2.364002 GGTTCCTCTATCTCCTGACAGC 59.636 54.545 0.00 0.00 0.00 4.40
5 6 2.962421 GGGTTCCTCTATCTCCTGACAG 59.038 54.545 0.00 0.00 0.00 3.51
6 7 2.587777 AGGGTTCCTCTATCTCCTGACA 59.412 50.000 0.00 0.00 0.00 3.58
7 8 3.322191 AGGGTTCCTCTATCTCCTGAC 57.678 52.381 0.00 0.00 0.00 3.51
8 9 4.693058 GCTTAGGGTTCCTCTATCTCCTGA 60.693 50.000 0.00 0.00 34.61 3.86
9 10 3.576550 GCTTAGGGTTCCTCTATCTCCTG 59.423 52.174 0.00 0.00 34.61 3.86
10 11 3.207777 TGCTTAGGGTTCCTCTATCTCCT 59.792 47.826 0.00 0.00 34.61 3.69
11 12 3.577919 TGCTTAGGGTTCCTCTATCTCC 58.422 50.000 0.00 0.00 34.61 3.71
12 13 5.816955 AATGCTTAGGGTTCCTCTATCTC 57.183 43.478 0.00 0.00 34.61 2.75
13 14 5.908247 AGAAATGCTTAGGGTTCCTCTATCT 59.092 40.000 0.00 0.00 34.61 1.98
14 15 6.181206 AGAAATGCTTAGGGTTCCTCTATC 57.819 41.667 0.00 0.00 34.61 2.08
15 16 6.360618 CAAGAAATGCTTAGGGTTCCTCTAT 58.639 40.000 0.00 0.00 34.31 1.98
16 17 5.339200 CCAAGAAATGCTTAGGGTTCCTCTA 60.339 44.000 0.00 0.00 34.31 2.43
17 18 4.568592 CCAAGAAATGCTTAGGGTTCCTCT 60.569 45.833 0.00 0.00 34.31 3.69
18 19 3.696548 CCAAGAAATGCTTAGGGTTCCTC 59.303 47.826 0.00 0.00 34.31 3.71
19 20 3.564352 CCCAAGAAATGCTTAGGGTTCCT 60.564 47.826 0.00 0.00 38.80 3.36
20 21 2.760650 CCCAAGAAATGCTTAGGGTTCC 59.239 50.000 0.00 0.00 38.80 3.62
21 22 2.760650 CCCCAAGAAATGCTTAGGGTTC 59.239 50.000 0.00 0.00 46.80 3.62
22 23 2.820178 CCCCAAGAAATGCTTAGGGTT 58.180 47.619 0.00 0.00 46.80 4.11
23 24 2.532250 CCCCAAGAAATGCTTAGGGT 57.468 50.000 0.00 0.00 46.80 4.34
25 26 2.659428 CTCCCCCAAGAAATGCTTAGG 58.341 52.381 0.00 0.00 35.42 2.69
26 27 2.242196 TCCTCCCCCAAGAAATGCTTAG 59.758 50.000 0.00 0.00 34.31 2.18
27 28 2.242196 CTCCTCCCCCAAGAAATGCTTA 59.758 50.000 0.00 0.00 34.31 3.09
28 29 1.006400 CTCCTCCCCCAAGAAATGCTT 59.994 52.381 0.00 0.00 37.29 3.91
29 30 0.627986 CTCCTCCCCCAAGAAATGCT 59.372 55.000 0.00 0.00 0.00 3.79
30 31 0.396278 CCTCCTCCCCCAAGAAATGC 60.396 60.000 0.00 0.00 0.00 3.56
31 32 1.298953 TCCTCCTCCCCCAAGAAATG 58.701 55.000 0.00 0.00 0.00 2.32
32 33 1.925959 CTTCCTCCTCCCCCAAGAAAT 59.074 52.381 0.00 0.00 0.00 2.17
33 34 1.372501 CTTCCTCCTCCCCCAAGAAA 58.627 55.000 0.00 0.00 0.00 2.52
34 35 1.208165 GCTTCCTCCTCCCCCAAGAA 61.208 60.000 0.00 0.00 0.00 2.52
35 36 1.616628 GCTTCCTCCTCCCCCAAGA 60.617 63.158 0.00 0.00 0.00 3.02
36 37 1.617839 AGCTTCCTCCTCCCCCAAG 60.618 63.158 0.00 0.00 0.00 3.61
37 38 1.925455 CAGCTTCCTCCTCCCCCAA 60.925 63.158 0.00 0.00 0.00 4.12
38 39 2.200373 ATCAGCTTCCTCCTCCCCCA 62.200 60.000 0.00 0.00 0.00 4.96
39 40 0.990818 AATCAGCTTCCTCCTCCCCC 60.991 60.000 0.00 0.00 0.00 5.40
40 41 0.922626 AAATCAGCTTCCTCCTCCCC 59.077 55.000 0.00 0.00 0.00 4.81
41 42 1.843206 AGAAATCAGCTTCCTCCTCCC 59.157 52.381 0.00 0.00 0.00 4.30
42 43 3.277715 CAAGAAATCAGCTTCCTCCTCC 58.722 50.000 0.00 0.00 0.00 4.30
43 44 3.277715 CCAAGAAATCAGCTTCCTCCTC 58.722 50.000 0.00 0.00 0.00 3.71
44 45 2.646798 ACCAAGAAATCAGCTTCCTCCT 59.353 45.455 0.00 0.00 0.00 3.69
45 46 3.013219 GACCAAGAAATCAGCTTCCTCC 58.987 50.000 0.00 0.00 0.00 4.30
46 47 3.949132 AGACCAAGAAATCAGCTTCCTC 58.051 45.455 0.00 0.00 0.00 3.71
47 48 4.287067 TGTAGACCAAGAAATCAGCTTCCT 59.713 41.667 0.00 0.00 0.00 3.36
48 49 4.579869 TGTAGACCAAGAAATCAGCTTCC 58.420 43.478 0.00 0.00 0.00 3.46
49 50 8.443953 AATATGTAGACCAAGAAATCAGCTTC 57.556 34.615 0.00 0.00 0.00 3.86
50 51 9.553064 CTAATATGTAGACCAAGAAATCAGCTT 57.447 33.333 0.00 0.00 0.00 3.74
51 52 8.709308 ACTAATATGTAGACCAAGAAATCAGCT 58.291 33.333 0.00 0.00 0.00 4.24
52 53 8.894768 ACTAATATGTAGACCAAGAAATCAGC 57.105 34.615 0.00 0.00 0.00 4.26
57 58 9.399797 TCGTAGACTAATATGTAGACCAAGAAA 57.600 33.333 0.00 0.00 0.00 2.52
58 59 8.969260 TCGTAGACTAATATGTAGACCAAGAA 57.031 34.615 0.00 0.00 0.00 2.52
73 74 9.778993 GTTGTGTGAATAAGTATCGTAGACTAA 57.221 33.333 0.00 0.00 42.51 2.24
74 75 9.170734 AGTTGTGTGAATAAGTATCGTAGACTA 57.829 33.333 0.00 0.00 42.51 2.59
75 76 8.053026 AGTTGTGTGAATAAGTATCGTAGACT 57.947 34.615 0.00 0.00 42.51 3.24
76 77 8.684973 AAGTTGTGTGAATAAGTATCGTAGAC 57.315 34.615 0.00 0.00 42.51 2.59
77 78 9.135843 CAAAGTTGTGTGAATAAGTATCGTAGA 57.864 33.333 0.00 0.00 45.75 2.59
78 79 8.922676 ACAAAGTTGTGTGAATAAGTATCGTAG 58.077 33.333 0.00 0.00 40.49 3.51
79 80 8.821147 ACAAAGTTGTGTGAATAAGTATCGTA 57.179 30.769 0.00 0.00 40.49 3.43
80 81 7.724305 ACAAAGTTGTGTGAATAAGTATCGT 57.276 32.000 0.00 0.00 40.49 3.73
222 223 0.526524 CCTCTCTCCTTAGCGCAACG 60.527 60.000 11.47 0.00 0.00 4.10
228 229 4.744795 TGAATGAACCTCTCTCCTTAGC 57.255 45.455 0.00 0.00 0.00 3.09
240 241 8.553459 TTTCTCTCTGTTTAGATGAATGAACC 57.447 34.615 0.00 0.00 30.69 3.62
247 248 9.303116 AGTTCTACTTTCTCTCTGTTTAGATGA 57.697 33.333 0.00 0.00 31.21 2.92
257 258 5.876460 GGTCGTCTAGTTCTACTTTCTCTCT 59.124 44.000 0.00 0.00 0.00 3.10
267 268 6.413052 AGATAGTTGTGGTCGTCTAGTTCTA 58.587 40.000 0.00 0.00 0.00 2.10
268 269 5.254901 AGATAGTTGTGGTCGTCTAGTTCT 58.745 41.667 0.00 0.00 0.00 3.01
274 275 3.827302 ACTTGAGATAGTTGTGGTCGTCT 59.173 43.478 0.00 0.00 0.00 4.18
292 293 5.276678 CCGTGGCTTATACATCGTTAACTTG 60.277 44.000 3.71 4.12 0.00 3.16
300 301 2.065993 CCTCCGTGGCTTATACATCG 57.934 55.000 0.00 0.00 0.00 3.84
315 316 2.592308 GGAGTCCACCATGCCTCC 59.408 66.667 3.60 0.00 36.98 4.30
316 317 2.187946 CGGAGTCCACCATGCCTC 59.812 66.667 10.49 0.00 0.00 4.70
337 338 4.787280 AGTCCTCCCTCCGGCAGG 62.787 72.222 11.75 11.75 43.01 4.85
338 339 3.151022 GAGTCCTCCCTCCGGCAG 61.151 72.222 0.00 0.00 0.00 4.85
343 344 1.454295 GACCTCGAGTCCTCCCTCC 60.454 68.421 12.31 0.00 39.84 4.30
344 345 1.820481 CGACCTCGAGTCCTCCCTC 60.820 68.421 12.31 0.00 43.08 4.30
356 357 6.609237 AAACTGTAACTAAAAACCGACCTC 57.391 37.500 0.00 0.00 0.00 3.85
394 395 1.886542 CTCCCTAAACAAGGCACCAAC 59.113 52.381 0.00 0.00 45.03 3.77
398 399 1.305930 CGCCTCCCTAAACAAGGCAC 61.306 60.000 12.65 0.00 45.03 5.01
406 407 3.467226 CCGCCTCGCCTCCCTAAA 61.467 66.667 0.00 0.00 0.00 1.85
423 424 3.507233 TCCATCATCAAGGAGTTTGTTGC 59.493 43.478 0.00 0.00 36.74 4.17
428 429 5.595952 GCCTTATTCCATCATCAAGGAGTTT 59.404 40.000 2.91 0.00 38.42 2.66
439 440 3.122480 TGAGAAGGGCCTTATTCCATCA 58.878 45.455 20.97 13.21 0.00 3.07
452 453 1.144503 CAAGATGGGGGATGAGAAGGG 59.855 57.143 0.00 0.00 0.00 3.95
471 701 1.888436 CGAAGCTAGAGGCACCACCA 61.888 60.000 0.00 0.00 44.79 4.17
472 702 1.153549 CGAAGCTAGAGGCACCACC 60.154 63.158 0.00 0.00 44.79 4.61
480 710 2.181205 CGCTCTTCAACGAAGCTAGAG 58.819 52.381 3.48 3.48 39.29 2.43
487 717 1.275471 CTCGTGCGCTCTTCAACGAA 61.275 55.000 17.32 4.40 0.00 3.85
491 721 1.067416 ACACTCGTGCGCTCTTCAA 59.933 52.632 9.73 0.00 0.00 2.69
492 722 1.661509 CACACTCGTGCGCTCTTCA 60.662 57.895 9.73 0.00 36.06 3.02
493 723 3.150895 CACACTCGTGCGCTCTTC 58.849 61.111 9.73 0.00 36.06 2.87
505 735 0.176680 GATCCATCGAGGCACACACT 59.823 55.000 0.00 0.00 37.29 3.55
513 743 0.823769 TCCCGACAGATCCATCGAGG 60.824 60.000 15.79 14.33 40.86 4.63
529 760 0.107848 ACCAACACCGATCGAATCCC 60.108 55.000 18.66 0.00 0.00 3.85
531 762 1.134788 AGGACCAACACCGATCGAATC 60.135 52.381 18.66 2.93 0.00 2.52
534 765 1.888018 GAGGACCAACACCGATCGA 59.112 57.895 18.66 0.00 0.00 3.59
537 768 1.911766 ACCGAGGACCAACACCGAT 60.912 57.895 0.00 0.00 0.00 4.18
552 783 2.698855 AGATCCAAACAGATCCACCG 57.301 50.000 0.00 0.00 43.14 4.94
561 792 5.957798 ACGAACGAATACTAGATCCAAACA 58.042 37.500 0.00 0.00 0.00 2.83
583 814 5.813080 AAGAATCCAACCTAACGCAATAC 57.187 39.130 0.00 0.00 0.00 1.89
589 820 6.743575 AGATCAAAAGAATCCAACCTAACG 57.256 37.500 0.00 0.00 0.00 3.18
602 833 8.289618 CGATGGTGAAAAACTTAGATCAAAAGA 58.710 33.333 13.13 0.00 0.00 2.52
633 864 0.385473 GTGCATCGGAACAACAACGG 60.385 55.000 0.00 0.00 0.00 4.44
634 865 0.586319 AGTGCATCGGAACAACAACG 59.414 50.000 0.00 0.00 0.00 4.10
635 866 2.806244 ACTAGTGCATCGGAACAACAAC 59.194 45.455 0.00 0.00 0.00 3.32
641 872 2.673368 CAAAGGACTAGTGCATCGGAAC 59.327 50.000 17.34 0.00 0.00 3.62
645 876 3.443037 CTCTCAAAGGACTAGTGCATCG 58.557 50.000 17.34 4.01 0.00 3.84
649 880 3.326836 AAGCTCTCAAAGGACTAGTGC 57.673 47.619 6.22 6.22 0.00 4.40
654 885 2.235898 CCTGCTAAGCTCTCAAAGGACT 59.764 50.000 0.00 0.00 0.00 3.85
688 919 8.746052 TGGATAAATCTTGGTATGGTAAACAG 57.254 34.615 0.00 0.00 0.00 3.16
689 920 9.349713 GATGGATAAATCTTGGTATGGTAAACA 57.650 33.333 0.00 0.00 0.00 2.83
690 921 9.574516 AGATGGATAAATCTTGGTATGGTAAAC 57.425 33.333 0.00 0.00 32.88 2.01
691 922 9.793259 GAGATGGATAAATCTTGGTATGGTAAA 57.207 33.333 0.00 0.00 37.03 2.01
692 923 8.944138 TGAGATGGATAAATCTTGGTATGGTAA 58.056 33.333 0.00 0.00 37.03 2.85
693 924 8.375506 GTGAGATGGATAAATCTTGGTATGGTA 58.624 37.037 0.00 0.00 37.03 3.25
694 925 7.072961 AGTGAGATGGATAAATCTTGGTATGGT 59.927 37.037 0.00 0.00 37.03 3.55
695 926 7.456725 AGTGAGATGGATAAATCTTGGTATGG 58.543 38.462 0.00 0.00 37.03 2.74
696 927 9.650539 CTAGTGAGATGGATAAATCTTGGTATG 57.349 37.037 0.00 0.00 37.03 2.39
697 928 8.820831 CCTAGTGAGATGGATAAATCTTGGTAT 58.179 37.037 0.00 0.00 37.03 2.73
698 929 7.256332 GCCTAGTGAGATGGATAAATCTTGGTA 60.256 40.741 0.00 0.00 37.03 3.25
699 930 6.465035 GCCTAGTGAGATGGATAAATCTTGGT 60.465 42.308 0.00 0.00 37.03 3.67
700 931 5.936956 GCCTAGTGAGATGGATAAATCTTGG 59.063 44.000 0.00 0.00 37.03 3.61
701 932 5.636965 CGCCTAGTGAGATGGATAAATCTTG 59.363 44.000 0.00 0.00 37.03 3.02
702 933 5.279708 CCGCCTAGTGAGATGGATAAATCTT 60.280 44.000 0.00 0.00 37.03 2.40
703 934 4.221703 CCGCCTAGTGAGATGGATAAATCT 59.778 45.833 0.00 0.00 39.66 2.40
704 935 4.021016 ACCGCCTAGTGAGATGGATAAATC 60.021 45.833 0.00 0.00 0.00 2.17
705 936 3.904339 ACCGCCTAGTGAGATGGATAAAT 59.096 43.478 0.00 0.00 0.00 1.40
706 937 3.305720 ACCGCCTAGTGAGATGGATAAA 58.694 45.455 0.00 0.00 0.00 1.40
707 938 2.891580 GACCGCCTAGTGAGATGGATAA 59.108 50.000 0.00 0.00 0.00 1.75
708 939 2.108425 AGACCGCCTAGTGAGATGGATA 59.892 50.000 0.00 0.00 0.00 2.59
709 940 1.133325 AGACCGCCTAGTGAGATGGAT 60.133 52.381 0.00 0.00 0.00 3.41
710 941 0.259065 AGACCGCCTAGTGAGATGGA 59.741 55.000 0.00 0.00 0.00 3.41
711 942 1.982660 TAGACCGCCTAGTGAGATGG 58.017 55.000 0.00 0.00 0.00 3.51
712 943 5.462405 GTTTATAGACCGCCTAGTGAGATG 58.538 45.833 0.00 0.00 0.00 2.90
713 944 4.523558 GGTTTATAGACCGCCTAGTGAGAT 59.476 45.833 0.00 0.00 0.00 2.75
714 945 3.887716 GGTTTATAGACCGCCTAGTGAGA 59.112 47.826 0.00 0.00 0.00 3.27
715 946 3.890147 AGGTTTATAGACCGCCTAGTGAG 59.110 47.826 6.79 0.00 44.62 3.51
716 947 3.635373 CAGGTTTATAGACCGCCTAGTGA 59.365 47.826 6.79 0.00 44.62 3.41
724 1254 7.619964 AAATTACAACCAGGTTTATAGACCG 57.380 36.000 0.44 2.74 44.62 4.79
760 1290 9.044150 CCACACACACAAATTTTCAATCTATTT 57.956 29.630 0.00 0.00 0.00 1.40
761 1291 7.656948 CCCACACACACAAATTTTCAATCTATT 59.343 33.333 0.00 0.00 0.00 1.73
762 1292 7.153985 CCCACACACACAAATTTTCAATCTAT 58.846 34.615 0.00 0.00 0.00 1.98
764 1294 5.358922 CCCACACACACAAATTTTCAATCT 58.641 37.500 0.00 0.00 0.00 2.40
765 1295 4.024977 GCCCACACACACAAATTTTCAATC 60.025 41.667 0.00 0.00 0.00 2.67
766 1296 3.876320 GCCCACACACACAAATTTTCAAT 59.124 39.130 0.00 0.00 0.00 2.57
769 1299 3.177997 AGCCCACACACACAAATTTTC 57.822 42.857 0.00 0.00 0.00 2.29
770 1300 3.704061 AGTAGCCCACACACACAAATTTT 59.296 39.130 0.00 0.00 0.00 1.82
771 1301 3.295973 AGTAGCCCACACACACAAATTT 58.704 40.909 0.00 0.00 0.00 1.82
773 1303 2.504367 GAGTAGCCCACACACACAAAT 58.496 47.619 0.00 0.00 0.00 2.32
774 1304 1.476110 GGAGTAGCCCACACACACAAA 60.476 52.381 0.00 0.00 0.00 2.83
775 1305 0.107831 GGAGTAGCCCACACACACAA 59.892 55.000 0.00 0.00 0.00 3.33
777 1307 0.037232 GAGGAGTAGCCCACACACAC 60.037 60.000 0.00 0.00 37.37 3.82
779 1309 1.215647 CGAGGAGTAGCCCACACAC 59.784 63.158 0.00 0.00 37.37 3.82
780 1310 1.982395 CCGAGGAGTAGCCCACACA 60.982 63.158 0.00 0.00 37.37 3.72
781 1311 1.668101 CTCCGAGGAGTAGCCCACAC 61.668 65.000 10.88 0.00 37.47 3.82
782 1312 1.379977 CTCCGAGGAGTAGCCCACA 60.380 63.158 10.88 0.00 37.47 4.17
783 1313 3.527641 CTCCGAGGAGTAGCCCAC 58.472 66.667 10.88 0.00 37.47 4.61
791 1321 4.378774 TCGACTTTAGATACTCCGAGGAG 58.621 47.826 17.01 17.01 46.91 3.69
793 1323 4.815308 TCTTCGACTTTAGATACTCCGAGG 59.185 45.833 0.00 0.00 0.00 4.63
794 1324 5.987777 TCTTCGACTTTAGATACTCCGAG 57.012 43.478 0.00 0.00 0.00 4.63
796 1326 6.037391 ACTCTTCTTCGACTTTAGATACTCCG 59.963 42.308 0.00 0.00 0.00 4.63
879 2062 2.215451 GAGCTGGATGGGAAGGGCAA 62.215 60.000 0.00 0.00 0.00 4.52
881 2064 1.931007 AAGAGCTGGATGGGAAGGGC 61.931 60.000 0.00 0.00 0.00 5.19
989 2172 1.731700 CGAGCCATGGGAATGCTTG 59.268 57.895 15.13 3.75 34.99 4.01
1666 2861 5.820947 ACAAGTAACAAAACTGTACCCTCAG 59.179 40.000 0.00 0.00 40.80 3.35
1801 2996 6.876257 AGACAAGGTGAGCTATACTTTGAAAG 59.124 38.462 23.52 2.89 37.32 2.62
1806 3001 7.906199 AGATAGACAAGGTGAGCTATACTTT 57.094 36.000 0.00 0.00 0.00 2.66
1826 3021 6.273730 AGGCTAGCTCTACTTTCTCCTAGATA 59.726 42.308 15.72 0.00 0.00 1.98
1862 3057 0.387929 TAACATAGCTCCTTCCCGCG 59.612 55.000 0.00 0.00 0.00 6.46
1915 3124 0.391228 TGCTAAGGACACGAACTGCA 59.609 50.000 0.00 0.00 0.00 4.41
1973 3182 4.016444 GACCAAGAAATCATTGCCTGGTA 58.984 43.478 0.00 0.00 0.00 3.25
2171 3390 0.962356 AAGGAAGCACCATCTTGCCG 60.962 55.000 2.96 0.00 44.14 5.69
2289 3508 4.997905 TTCAAAGAGATTCAACTGCTCG 57.002 40.909 0.00 0.00 33.98 5.03


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

AutoCloner maintained by Alex Coulton.