Multiple sequence alignment - TraesCS6A01G066400

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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 TraesCS6A01G066400 chr6A 100.000 4542 0 0 1 4542 35543118 35547659 0.000000e+00 8388.0
1 TraesCS6A01G066400 chrUn 90.550 3725 224 51 693 4336 101365107 101361430 0.000000e+00 4811.0
2 TraesCS6A01G066400 chrUn 86.574 216 13 2 4336 4542 101361389 101361181 1.640000e-54 224.0
3 TraesCS6A01G066400 chr6B 90.299 2742 169 57 693 3395 64966129 64968812 0.000000e+00 3500.0
4 TraesCS6A01G066400 chr6B 91.828 722 44 10 3346 4061 64968815 64969527 0.000000e+00 992.0
5 TraesCS6A01G066400 chr6B 84.956 226 25 5 1566 1791 219880303 219880519 2.130000e-53 220.0
6 TraesCS6A01G066400 chr5A 96.705 698 20 2 3 697 635793865 635793168 0.000000e+00 1158.0
7 TraesCS6A01G066400 chr5A 84.956 226 25 5 1566 1791 702048463 702048247 2.130000e-53 220.0
8 TraesCS6A01G066400 chr5A 82.743 226 30 5 1566 1791 3470869 3470653 4.640000e-45 193.0
9 TraesCS6A01G066400 chr7D 96.115 695 22 4 3 693 232925615 232926308 0.000000e+00 1129.0
10 TraesCS6A01G066400 chr7D 95.971 695 24 2 3 693 497911815 497911121 0.000000e+00 1125.0
11 TraesCS6A01G066400 chr7D 95.578 701 26 4 3 699 149106310 149105611 0.000000e+00 1118.0
12 TraesCS6A01G066400 chr3D 95.965 694 25 2 3 693 87390704 87391397 0.000000e+00 1123.0
13 TraesCS6A01G066400 chr3D 83.333 156 26 0 1566 1721 440212541 440212386 1.320000e-30 145.0
14 TraesCS6A01G066400 chr3D 88.889 90 8 2 963 1052 30771958 30772045 4.800000e-20 110.0
15 TraesCS6A01G066400 chr3D 97.143 35 1 0 1050 1084 30773706 30773740 4.910000e-05 60.2
16 TraesCS6A01G066400 chr2D 95.833 696 24 4 3 693 273018579 273019274 0.000000e+00 1120.0
17 TraesCS6A01G066400 chr2D 85.417 144 21 0 1566 1709 571965565 571965708 2.830000e-32 150.0
18 TraesCS6A01G066400 chr2D 85.106 141 21 0 1581 1721 29674426 29674286 1.320000e-30 145.0
19 TraesCS6A01G066400 chr1D 95.702 698 23 4 3 693 407809755 407810452 0.000000e+00 1116.0
20 TraesCS6A01G066400 chr2A 95.136 699 27 6 1 693 742308642 742307945 0.000000e+00 1096.0
21 TraesCS6A01G066400 chr2A 94.676 695 33 2 3 693 713914694 713915388 0.000000e+00 1075.0
22 TraesCS6A01G066400 chr2A 83.843 229 28 5 1566 1794 416626613 416626394 4.600000e-50 209.0
23 TraesCS6A01G066400 chr3B 84.956 226 25 5 1566 1791 56461345 56461129 2.130000e-53 220.0
24 TraesCS6A01G066400 chr3B 84.513 226 26 4 1566 1791 17969501 17969717 9.900000e-52 215.0
25 TraesCS6A01G066400 chr6D 84.615 221 25 5 1566 1786 133887166 133886955 1.280000e-50 211.0
26 TraesCS6A01G066400 chr6D 94.444 36 2 0 1048 1083 133887307 133887272 6.350000e-04 56.5
27 TraesCS6A01G066400 chr7A 83.628 226 28 5 1566 1791 103919899 103920115 2.140000e-48 204.0
28 TraesCS6A01G066400 chr4B 83.628 226 28 5 1566 1791 597481456 597481672 2.140000e-48 204.0
29 TraesCS6A01G066400 chr4B 97.059 34 1 0 1051 1084 604276851 604276884 1.760000e-04 58.4
30 TraesCS6A01G066400 chr5D 84.722 144 22 0 1566 1709 12363534 12363677 1.320000e-30 145.0
31 TraesCS6A01G066400 chr1A 97.297 37 1 0 1048 1084 536835201 536835165 3.790000e-06 63.9
32 TraesCS6A01G066400 chr2B 97.143 35 1 0 1050 1084 625470116 625470082 4.910000e-05 60.2


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 TraesCS6A01G066400 chr6A 35543118 35547659 4541 False 8388.0 8388 100.0000 1 4542 1 chr6A.!!$F1 4541
1 TraesCS6A01G066400 chrUn 101361181 101365107 3926 True 2517.5 4811 88.5620 693 4542 2 chrUn.!!$R1 3849
2 TraesCS6A01G066400 chr6B 64966129 64969527 3398 False 2246.0 3500 91.0635 693 4061 2 chr6B.!!$F2 3368
3 TraesCS6A01G066400 chr5A 635793168 635793865 697 True 1158.0 1158 96.7050 3 697 1 chr5A.!!$R2 694
4 TraesCS6A01G066400 chr7D 232925615 232926308 693 False 1129.0 1129 96.1150 3 693 1 chr7D.!!$F1 690
5 TraesCS6A01G066400 chr7D 497911121 497911815 694 True 1125.0 1125 95.9710 3 693 1 chr7D.!!$R2 690
6 TraesCS6A01G066400 chr7D 149105611 149106310 699 True 1118.0 1118 95.5780 3 699 1 chr7D.!!$R1 696
7 TraesCS6A01G066400 chr3D 87390704 87391397 693 False 1123.0 1123 95.9650 3 693 1 chr3D.!!$F1 690
8 TraesCS6A01G066400 chr2D 273018579 273019274 695 False 1120.0 1120 95.8330 3 693 1 chr2D.!!$F1 690
9 TraesCS6A01G066400 chr1D 407809755 407810452 697 False 1116.0 1116 95.7020 3 693 1 chr1D.!!$F1 690
10 TraesCS6A01G066400 chr2A 742307945 742308642 697 True 1096.0 1096 95.1360 1 693 1 chr2A.!!$R2 692
11 TraesCS6A01G066400 chr2A 713914694 713915388 694 False 1075.0 1075 94.6760 3 693 1 chr2A.!!$F1 690

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
985 1015 0.526524 CACCCGCTTCAGATCTCGAC 60.527 60.0 3.30 0.00 0.00 4.20 F
1309 1352 0.595095 GGATTCTGGGCGCAATCATC 59.405 55.0 10.83 11.23 31.58 2.92 F
2865 2972 0.185901 TTTCCTGCTGTGGCCTTCTT 59.814 50.0 3.32 0.00 37.74 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 1981 0.175531 AACAAACAAGCACCTGCACC 59.824 50.0 0.00 0.00 45.16 5.01 R
3213 3321 1.573829 GCATCCGCACCTTTCAACGA 61.574 55.0 0.00 0.00 38.36 3.85 R
4096 4258 0.037605 ACTGACGGCGTTTAAGGAGG 60.038 55.0 16.19 1.22 0.00 4.30 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
35 36 6.771267 TGTTCGAGAAATGGTAGCTATCTCTA 59.229 38.462 15.78 5.83 35.50 2.43
60 61 6.011981 ACTTGGTATCTATGGTGGGAAAGAAA 60.012 38.462 0.00 0.00 0.00 2.52
249 254 1.751927 CCATGACTTGCTGGAGGGC 60.752 63.158 0.00 0.00 34.24 5.19
259 265 4.731853 TGGAGGGCACGATGGGGA 62.732 66.667 0.00 0.00 0.00 4.81
286 292 1.544691 TGAGAGACGACAAAGGTAGGC 59.455 52.381 0.00 0.00 0.00 3.93
315 321 4.141390 GCAGGAGGGAATGGAAAGATAGAA 60.141 45.833 0.00 0.00 0.00 2.10
427 433 1.186200 CTCTGACAATCGGGAGGTGA 58.814 55.000 0.00 0.00 0.00 4.02
582 591 7.278868 GCACATGAACTTGTTAGATTAGCTAGT 59.721 37.037 0.00 0.00 0.00 2.57
634 646 9.297037 AGCCTATTAGTGAAATTGTAACACTTT 57.703 29.630 0.00 0.00 43.27 2.66
791 809 1.741770 CCGAGAAGGCGACCCAAAG 60.742 63.158 0.00 0.00 0.00 2.77
800 818 2.680913 CGACCCAAAGAGGCAAGCG 61.681 63.158 0.00 0.00 35.39 4.68
852 870 2.308866 TCAATCCTTTCCCCTCCAGAAC 59.691 50.000 0.00 0.00 0.00 3.01
853 871 1.299939 ATCCTTTCCCCTCCAGAACC 58.700 55.000 0.00 0.00 0.00 3.62
854 872 0.845102 TCCTTTCCCCTCCAGAACCC 60.845 60.000 0.00 0.00 0.00 4.11
855 873 0.846870 CCTTTCCCCTCCAGAACCCT 60.847 60.000 0.00 0.00 0.00 4.34
985 1015 0.526524 CACCCGCTTCAGATCTCGAC 60.527 60.000 3.30 0.00 0.00 4.20
1114 1157 0.983481 GTTCGTTTTTGCGACGGACG 60.983 55.000 0.00 0.00 39.00 4.79
1115 1158 1.144565 TTCGTTTTTGCGACGGACGA 61.145 50.000 3.67 0.00 45.77 4.20
1116 1159 1.154908 CGTTTTTGCGACGGACGAG 60.155 57.895 3.67 0.00 45.77 4.18
1117 1160 1.438222 GTTTTTGCGACGGACGAGC 60.438 57.895 3.67 4.41 45.77 5.03
1128 1171 1.867919 CGGACGAGCCTCACTTGAGT 61.868 60.000 5.53 0.00 40.48 3.41
1149 1192 1.949631 CCGAATCTTAGGCGTCGGC 60.950 63.158 11.43 11.43 45.74 5.54
1257 1300 1.423845 GATTGCGCGTGAAATCGGT 59.576 52.632 13.77 0.00 30.50 4.69
1307 1350 0.836606 TAGGATTCTGGGCGCAATCA 59.163 50.000 10.83 3.16 31.58 2.57
1309 1352 0.595095 GGATTCTGGGCGCAATCATC 59.405 55.000 10.83 11.23 31.58 2.92
1340 1385 4.648307 TGGGTTTTTGGTATTTGTACGGTT 59.352 37.500 0.00 0.00 0.00 4.44
1341 1386 5.221204 TGGGTTTTTGGTATTTGTACGGTTC 60.221 40.000 0.00 0.00 0.00 3.62
1343 1388 6.448852 GGTTTTTGGTATTTGTACGGTTCAT 58.551 36.000 0.00 0.00 0.00 2.57
1352 1397 7.113825 GGTATTTGTACGGTTCATTTGTTTGTC 59.886 37.037 0.00 0.00 0.00 3.18
1355 1400 3.078594 ACGGTTCATTTGTTTGTCAGC 57.921 42.857 0.00 0.00 0.00 4.26
1356 1401 2.223711 ACGGTTCATTTGTTTGTCAGCC 60.224 45.455 0.00 0.00 0.00 4.85
1358 1403 2.547855 GGTTCATTTGTTTGTCAGCCCC 60.548 50.000 0.00 0.00 0.00 5.80
1364 1409 1.303317 GTTTGTCAGCCCCGTGGAT 60.303 57.895 0.00 0.00 0.00 3.41
1410 1464 2.005606 TTTTCTGAGCCCTGGCACCA 62.006 55.000 11.38 6.99 44.88 4.17
1411 1465 2.005606 TTTCTGAGCCCTGGCACCAA 62.006 55.000 11.38 0.00 44.88 3.67
1431 1485 1.407979 ACCGTAATCAGTTAGCCCTCG 59.592 52.381 0.00 0.00 0.00 4.63
1451 1505 2.096909 CGGCGTGTTTCTGTTTCAGTAG 60.097 50.000 0.00 0.00 32.61 2.57
1453 1507 4.053295 GGCGTGTTTCTGTTTCAGTAGTA 58.947 43.478 0.00 0.00 32.61 1.82
1463 1523 8.638685 TTCTGTTTCAGTAGTAACAGTGTAAC 57.361 34.615 12.93 0.00 46.80 2.50
1507 1567 7.661040 AGTATTTTGTGCTGCTTTTATCTGTT 58.339 30.769 0.00 0.00 0.00 3.16
1531 1591 6.225981 GGGTAATTTAGAAGACCCGTAGAA 57.774 41.667 0.00 0.00 42.16 2.10
1547 1607 2.597578 AGAACATTTAGGGCGGGTTT 57.402 45.000 0.00 0.00 0.00 3.27
1555 1615 5.070714 ACATTTAGGGCGGGTTTTTACTTTT 59.929 36.000 0.00 0.00 0.00 2.27
1556 1616 4.852134 TTAGGGCGGGTTTTTACTTTTC 57.148 40.909 0.00 0.00 0.00 2.29
1557 1617 2.668625 AGGGCGGGTTTTTACTTTTCA 58.331 42.857 0.00 0.00 0.00 2.69
1559 1619 4.409187 AGGGCGGGTTTTTACTTTTCATA 58.591 39.130 0.00 0.00 0.00 2.15
1610 1671 3.959573 CAACTATGCTTGCTTAGAGCC 57.040 47.619 18.29 0.00 41.51 4.70
1618 1679 2.514824 GCTTAGAGCCGCCCTTGG 60.515 66.667 0.00 0.00 34.48 3.61
1645 1706 3.207265 ACATTATTGCGATGGCCTGTA 57.793 42.857 3.32 0.00 38.85 2.74
1671 1732 5.240623 TGTTCTTAGGTGTGCTACAAAATGG 59.759 40.000 0.00 0.00 0.00 3.16
1682 1743 3.692593 GCTACAAAATGGGTTCCGTGTAT 59.307 43.478 0.00 0.00 0.00 2.29
1695 1756 5.450826 GGTTCCGTGTATTTTGGACTTGTTT 60.451 40.000 0.00 0.00 0.00 2.83
1697 1758 4.882427 TCCGTGTATTTTGGACTTGTTTGA 59.118 37.500 0.00 0.00 0.00 2.69
1709 1770 4.148696 GGACTTGTTTGACAAATCATTGCG 59.851 41.667 3.49 0.00 36.18 4.85
1710 1771 4.681744 ACTTGTTTGACAAATCATTGCGT 58.318 34.783 3.49 0.00 37.69 5.24
1847 1908 6.644592 TGCTTGCCACATTTTATTAAAGACAC 59.355 34.615 0.00 0.00 0.00 3.67
1899 1962 4.467735 GAAGCCTTGAAATCGTCACTTTC 58.532 43.478 0.00 0.00 35.39 2.62
2065 2138 7.282675 GTGGATGAAGATGATGTCAAAGAATCT 59.717 37.037 0.00 0.00 0.00 2.40
2094 2167 4.034410 GAGGAGGAAGAGGTACTGGAAAT 58.966 47.826 0.00 0.00 41.55 2.17
2164 2238 8.915654 CCACATTTTTGTAGCTCTTCATTTTAC 58.084 33.333 0.00 0.00 0.00 2.01
2202 2276 5.016831 GGGAATCACCTGGTTATTTTCAGT 58.983 41.667 7.62 0.00 38.98 3.41
2207 2281 8.887036 AATCACCTGGTTATTTTCAGTTTTTC 57.113 30.769 0.00 0.00 0.00 2.29
2222 2297 8.816640 TTCAGTTTTTCTCATTTATTTCTGGC 57.183 30.769 0.00 0.00 0.00 4.85
2384 2478 7.447374 CAAGTAATCCTTGGTGTTCATTGTA 57.553 36.000 0.00 0.00 45.70 2.41
2399 2493 6.867816 TGTTCATTGTAGCCATGAATTTCAAC 59.132 34.615 2.68 0.00 36.79 3.18
2432 2526 9.613428 CACTTTAATGTGTAGATGAATCCCTAA 57.387 33.333 12.21 0.00 33.61 2.69
2439 2533 7.861629 TGTGTAGATGAATCCCTAACAAATCT 58.138 34.615 0.00 0.00 0.00 2.40
2445 2539 8.772250 AGATGAATCCCTAACAAATCTAACTGA 58.228 33.333 0.00 0.00 0.00 3.41
2500 2606 8.931385 ATTCATTTTGCCACAAGTATATGTTC 57.069 30.769 0.00 0.00 0.00 3.18
2598 2705 7.864108 AACTTCATGTTTATGCTATGCTGTA 57.136 32.000 0.00 0.00 34.84 2.74
2775 2882 1.135257 CAGCCCTCAACGAGTACTGAG 60.135 57.143 0.00 0.98 39.06 3.35
2865 2972 0.185901 TTTCCTGCTGTGGCCTTCTT 59.814 50.000 3.32 0.00 37.74 2.52
2952 3059 1.882623 GCTGACTTTAAGGCAACAGCT 59.117 47.619 19.33 0.00 44.51 4.24
3063 3170 0.661780 TCGCAAACAAAATTCGCCCG 60.662 50.000 0.00 0.00 0.00 6.13
3112 3220 7.624549 AGAGCTCTCTGTTTGGTTTATATTCA 58.375 34.615 11.45 0.00 38.75 2.57
3331 3440 2.843113 AGAAAGGAGGTGAGATTCTGGG 59.157 50.000 0.00 0.00 0.00 4.45
3343 3452 3.517500 GAGATTCTGGGCCTAATCTAGGG 59.482 52.174 25.12 0.00 46.32 3.53
3344 3453 2.118403 TTCTGGGCCTAATCTAGGGG 57.882 55.000 4.53 0.00 46.32 4.79
3358 3467 2.087646 CTAGGGGCTTTCTGTTTCTGC 58.912 52.381 0.00 0.00 0.00 4.26
3367 3476 4.696455 CTTTCTGTTTCTGCCCAAACATT 58.304 39.130 9.95 0.00 43.63 2.71
3435 3592 5.651576 TCTGTGCTGATGTTTGCCATAAATA 59.348 36.000 0.00 0.00 32.56 1.40
3448 3605 4.828939 TGCCATAAATATCCAGGAGCAAAG 59.171 41.667 0.00 0.00 0.00 2.77
3555 3712 0.920763 ATGTGATTGGCTGGGAGGGA 60.921 55.000 0.00 0.00 0.00 4.20
3697 3856 1.880027 AGGTTGATTTTGACACTCGGC 59.120 47.619 0.00 0.00 0.00 5.54
3747 3906 4.338118 TGAGGCGTTTTTCTTGTTCAAGAT 59.662 37.500 14.67 0.00 0.00 2.40
3864 4023 5.491982 TGCAAGTAAATTTTTGGTGGTTGT 58.508 33.333 0.00 0.00 0.00 3.32
3868 4027 6.783708 AGTAAATTTTTGGTGGTTGTCTCA 57.216 33.333 0.00 0.00 0.00 3.27
3882 4042 6.202188 GTGGTTGTCTCAGTTAAATTCTCGAA 59.798 38.462 0.00 0.00 0.00 3.71
3890 4050 8.926710 TCTCAGTTAAATTCTCGAATTCTTGTC 58.073 33.333 3.52 0.00 39.88 3.18
3929 4089 6.525121 CGAATATCTCGTTATTCCAGCAAA 57.475 37.500 8.74 0.00 42.89 3.68
3933 4093 9.173939 GAATATCTCGTTATTCCAGCAAATTTG 57.826 33.333 14.03 14.03 34.07 2.32
3980 4142 7.886338 AGTATCTCAAGTCGTATGATGCATAA 58.114 34.615 0.00 0.00 0.00 1.90
4001 4163 1.845809 GCTCAGGACAAGTTGCACGG 61.846 60.000 1.81 0.00 0.00 4.94
4021 4183 2.260869 GGCAGGCTCGTTTGCAGAA 61.261 57.895 0.00 0.00 42.02 3.02
4033 4195 3.706698 GTTTGCAGAAAAAGAGGTCACC 58.293 45.455 0.00 0.00 0.00 4.02
4034 4196 2.727123 TGCAGAAAAAGAGGTCACCA 57.273 45.000 0.00 0.00 0.00 4.17
4051 4213 2.813754 CACCATTTTCTGTCATGTCCGT 59.186 45.455 0.00 0.00 0.00 4.69
4069 4231 1.075226 TCCTGCGGCCTCCTAAGAT 60.075 57.895 0.00 0.00 0.00 2.40
4096 4258 3.706373 TCGGCTGCCTCAACCCTC 61.706 66.667 17.92 0.00 0.00 4.30
4097 4259 4.785453 CGGCTGCCTCAACCCTCC 62.785 72.222 17.92 0.00 0.00 4.30
4098 4260 3.334054 GGCTGCCTCAACCCTCCT 61.334 66.667 12.43 0.00 0.00 3.69
4099 4261 2.270527 GCTGCCTCAACCCTCCTC 59.729 66.667 0.00 0.00 0.00 3.71
4100 4262 2.993853 CTGCCTCAACCCTCCTCC 59.006 66.667 0.00 0.00 0.00 4.30
4101 4263 1.614824 CTGCCTCAACCCTCCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
4102 4264 1.151810 TGCCTCAACCCTCCTCCTT 60.152 57.895 0.00 0.00 0.00 3.36
4103 4265 0.118346 TGCCTCAACCCTCCTCCTTA 59.882 55.000 0.00 0.00 0.00 2.69
4104 4266 1.286248 GCCTCAACCCTCCTCCTTAA 58.714 55.000 0.00 0.00 0.00 1.85
4109 4271 0.327259 AACCCTCCTCCTTAAACGCC 59.673 55.000 0.00 0.00 0.00 5.68
4116 4278 1.347320 CTCCTTAAACGCCGTCAGTC 58.653 55.000 0.00 0.00 0.00 3.51
4123 4285 0.949105 AACGCCGTCAGTCACCAATC 60.949 55.000 0.00 0.00 0.00 2.67
4127 4289 1.606668 GCCGTCAGTCACCAATCAAAA 59.393 47.619 0.00 0.00 0.00 2.44
4168 4330 2.125106 AAACGCTCGGGGCTGATC 60.125 61.111 0.00 0.00 39.13 2.92
4178 4340 2.512896 GGCTGATCGGCATCCCTT 59.487 61.111 27.26 0.00 38.25 3.95
4194 4356 5.221126 GCATCCCTTGTATTCAGTCCAAATC 60.221 44.000 0.00 0.00 0.00 2.17
4199 4361 7.622081 TCCCTTGTATTCAGTCCAAATCTAGTA 59.378 37.037 0.00 0.00 0.00 1.82
4208 4370 8.459911 TCAGTCCAAATCTAGTACGAATATGA 57.540 34.615 0.00 0.00 0.00 2.15
4221 4383 2.760374 GAATATGAAGTGGCTCGGGAG 58.240 52.381 0.00 0.00 0.00 4.30
4256 4418 0.617413 CCACTCTGGCTCACCTCAAT 59.383 55.000 0.00 0.00 36.63 2.57
4258 4420 1.554160 CACTCTGGCTCACCTCAATCT 59.446 52.381 0.00 0.00 36.63 2.40
4261 4425 1.552337 TCTGGCTCACCTCAATCTCAC 59.448 52.381 0.00 0.00 36.63 3.51
4271 4435 6.115446 TCACCTCAATCTCACATATTTGTCC 58.885 40.000 0.00 0.00 32.34 4.02
4273 4437 4.512944 CCTCAATCTCACATATTTGTCCCG 59.487 45.833 0.00 0.00 32.34 5.14
4282 4446 5.188163 TCACATATTTGTCCCGGTTCTCTTA 59.812 40.000 0.00 0.00 32.34 2.10
4311 4475 5.134661 CCAAAACCTAACCACTCCACTTTA 58.865 41.667 0.00 0.00 0.00 1.85
4329 4493 2.741878 TACCACCCAAGCTCCCGTCT 62.742 60.000 0.00 0.00 0.00 4.18
4330 4494 1.987855 CCACCCAAGCTCCCGTCTA 60.988 63.158 0.00 0.00 0.00 2.59
4352 4557 0.319900 CTTGTGTCGTCCAGTGAGGG 60.320 60.000 0.00 0.00 38.24 4.30
4369 4574 0.111253 GGGTTGGAGGATGCTATGGG 59.889 60.000 0.00 0.00 0.00 4.00
4370 4575 0.538287 GGTTGGAGGATGCTATGGGC 60.538 60.000 0.00 0.00 42.22 5.36
4371 4576 0.475906 GTTGGAGGATGCTATGGGCT 59.524 55.000 0.00 0.00 42.39 5.19
4372 4577 1.699634 GTTGGAGGATGCTATGGGCTA 59.300 52.381 0.00 0.00 42.39 3.93
4373 4578 2.307098 GTTGGAGGATGCTATGGGCTAT 59.693 50.000 0.00 0.00 42.39 2.97
4374 4579 1.911357 TGGAGGATGCTATGGGCTATG 59.089 52.381 0.00 0.00 42.39 2.23
4375 4580 2.191400 GGAGGATGCTATGGGCTATGA 58.809 52.381 0.00 0.00 42.39 2.15
4380 4585 0.679505 TGCTATGGGCTATGACCGTC 59.320 55.000 0.00 0.00 42.39 4.79
4440 4645 1.221414 CGATGAGGGATCTTTTCGGC 58.779 55.000 0.00 0.00 0.00 5.54
4447 4652 0.377203 GGATCTTTTCGGCGCGAATT 59.623 50.000 12.10 2.60 45.28 2.17
4458 4663 0.857311 GCGCGAATTCATTGTGTCGG 60.857 55.000 12.10 0.00 34.13 4.79
4471 4685 4.057428 GTCGGCGCAGAGGACACT 62.057 66.667 11.47 0.00 32.73 3.55
4487 4701 1.273098 ACACTGGGGTAGGATCTTCGT 60.273 52.381 0.00 0.00 0.00 3.85
4497 4711 1.038280 GGATCTTCGTGGTCCGGTAT 58.962 55.000 0.00 0.00 37.11 2.73
4507 4721 0.767060 GGTCCGGTATCCTCCCCATT 60.767 60.000 0.00 0.00 0.00 3.16
4510 4724 1.061657 TCCGGTATCCTCCCCATTTCT 60.062 52.381 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.036916 TCTTTCCCACCATAGATACCAAGT 58.963 41.667 0.00 0.00 0.00 3.16
249 254 2.430694 TCTCAATACTGTCCCCATCGTG 59.569 50.000 0.00 0.00 0.00 4.35
259 265 4.281182 ACCTTTGTCGTCTCTCAATACTGT 59.719 41.667 0.00 0.00 0.00 3.55
286 292 3.582998 TCCATTCCCTCCTGCAATAAG 57.417 47.619 0.00 0.00 0.00 1.73
315 321 0.885879 TGAGAACGTCCGCACAGTAT 59.114 50.000 0.00 0.00 0.00 2.12
343 349 2.428530 GGCCAAATTTGAGAGCTAAGGG 59.571 50.000 19.86 0.00 0.00 3.95
427 433 3.005554 CTCCGTCTTGCATTGTCTCAAT 58.994 45.455 0.00 0.00 0.00 2.57
468 477 1.135717 CAGTCATCGAAAATTGCCGCA 60.136 47.619 0.00 0.00 0.00 5.69
593 605 0.555769 AGGCTCCTCAAACCAAACCA 59.444 50.000 0.00 0.00 0.00 3.67
634 646 6.804295 GCAATAACCAATACATCGTTTGTGAA 59.196 34.615 4.39 0.00 39.48 3.18
1100 1139 2.600475 GGCTCGTCCGTCGCAAAAA 61.600 57.895 0.00 0.00 39.67 1.94
1116 1159 2.765250 TTCGGCGACTCAAGTGAGGC 62.765 60.000 10.16 8.67 46.66 4.70
1117 1160 0.108615 ATTCGGCGACTCAAGTGAGG 60.109 55.000 10.16 0.00 46.13 3.86
1121 1164 2.159226 CCTAAGATTCGGCGACTCAAGT 60.159 50.000 25.82 14.44 0.00 3.16
1212 1255 3.701241 GCCCGAAATTTGCGATTATGAA 58.299 40.909 0.00 0.00 0.00 2.57
1223 1266 1.933115 AATCGCAGCGCCCGAAATTT 61.933 50.000 21.88 11.12 38.31 1.82
1251 1294 1.897398 GCAGCGAACGTGAACCGATT 61.897 55.000 0.00 0.00 40.70 3.34
1257 1300 0.038251 ATCTCAGCAGCGAACGTGAA 60.038 50.000 0.00 0.00 0.00 3.18
1307 1350 6.950860 ATACCAAAAACCCAAATTCCTGAT 57.049 33.333 0.00 0.00 0.00 2.90
1309 1352 6.770303 ACAAATACCAAAAACCCAAATTCCTG 59.230 34.615 0.00 0.00 0.00 3.86
1340 1385 0.958091 CGGGGCTGACAAACAAATGA 59.042 50.000 0.00 0.00 0.00 2.57
1341 1386 0.673437 ACGGGGCTGACAAACAAATG 59.327 50.000 0.00 0.00 0.00 2.32
1343 1388 1.388065 CCACGGGGCTGACAAACAAA 61.388 55.000 0.00 0.00 0.00 2.83
1352 1397 1.450312 GAACTGATCCACGGGGCTG 60.450 63.158 0.00 0.00 0.00 4.85
1364 1409 4.704833 GCCTGCGCCTGGAACTGA 62.705 66.667 18.93 0.00 0.00 3.41
1384 1438 2.420022 CCAGGGCTCAGAAAACAATACG 59.580 50.000 0.00 0.00 0.00 3.06
1387 1441 1.260544 GCCAGGGCTCAGAAAACAAT 58.739 50.000 2.30 0.00 38.26 2.71
1410 1464 2.159142 CGAGGGCTAACTGATTACGGTT 60.159 50.000 0.00 0.00 45.93 4.44
1411 1465 1.407979 CGAGGGCTAACTGATTACGGT 59.592 52.381 0.00 0.00 37.19 4.83
1431 1485 2.870411 ACTACTGAAACAGAAACACGCC 59.130 45.455 5.76 0.00 35.18 5.68
1463 1523 2.096909 ACTTGACGAAAGCACGAAATCG 60.097 45.455 0.48 0.48 41.63 3.34
1477 1537 3.542712 AGCAGCACAAAATACTTGACG 57.457 42.857 0.00 0.00 0.00 4.35
1480 1540 7.596248 ACAGATAAAAGCAGCACAAAATACTTG 59.404 33.333 0.00 0.00 0.00 3.16
1525 1585 1.134610 ACCCGCCCTAAATGTTCTACG 60.135 52.381 0.00 0.00 0.00 3.51
1531 1591 3.770046 AGTAAAAACCCGCCCTAAATGT 58.230 40.909 0.00 0.00 0.00 2.71
1559 1619 9.555727 TGCAAATTTTACAGTCTAGTTTCTACT 57.444 29.630 0.00 0.00 38.44 2.57
1618 1679 3.853307 GCCATCGCAATAATGTAACCTGC 60.853 47.826 0.00 0.00 34.03 4.85
1645 1706 4.682778 TTGTAGCACACCTAAGAACAGT 57.317 40.909 0.00 0.00 0.00 3.55
1671 1732 3.566742 ACAAGTCCAAAATACACGGAACC 59.433 43.478 0.00 0.00 0.00 3.62
1682 1743 7.413877 GCAATGATTTGTCAAACAAGTCCAAAA 60.414 33.333 11.32 0.00 42.10 2.44
1695 1756 3.812609 ACTGTGTACGCAATGATTTGTCA 59.187 39.130 10.85 0.00 35.17 3.58
1697 1758 6.494893 AATACTGTGTACGCAATGATTTGT 57.505 33.333 10.85 5.59 35.17 2.83
1709 1770 7.428183 CGCATTAACCATCAAAATACTGTGTAC 59.572 37.037 0.00 0.00 0.00 2.90
1710 1771 7.334671 TCGCATTAACCATCAAAATACTGTGTA 59.665 33.333 0.00 0.00 0.00 2.90
1799 1860 5.070180 CACCATCAGATATCACTCAACCTCT 59.930 44.000 5.32 0.00 0.00 3.69
1847 1908 5.882557 ACCTGTTCTGATAATGCACTAAAGG 59.117 40.000 0.00 0.00 0.00 3.11
1899 1962 9.903682 CCTGCACCATATAGATTCAATAAAAAG 57.096 33.333 0.00 0.00 0.00 2.27
1916 1979 0.390124 CAAACAAGCACCTGCACCAT 59.610 50.000 0.00 0.00 45.16 3.55
1917 1980 0.969917 ACAAACAAGCACCTGCACCA 60.970 50.000 0.00 0.00 45.16 4.17
1918 1981 0.175531 AACAAACAAGCACCTGCACC 59.824 50.000 0.00 0.00 45.16 5.01
1919 1982 1.134946 AGAACAAACAAGCACCTGCAC 59.865 47.619 0.00 0.00 45.16 4.57
1920 1983 1.134753 CAGAACAAACAAGCACCTGCA 59.865 47.619 0.00 0.00 45.16 4.41
1921 1984 1.405105 TCAGAACAAACAAGCACCTGC 59.595 47.619 0.00 0.00 42.49 4.85
1922 1985 2.423185 TGTCAGAACAAACAAGCACCTG 59.577 45.455 0.00 0.00 30.70 4.00
1923 1986 2.423538 GTGTCAGAACAAACAAGCACCT 59.576 45.455 0.00 0.00 37.08 4.00
2065 2138 1.152271 ACCTCTTCCTCCTCTTCCCAA 59.848 52.381 0.00 0.00 0.00 4.12
2164 2238 7.653311 CAGGTGATTCCCTTTTTAAACTTTCTG 59.347 37.037 0.00 0.00 36.75 3.02
2222 2297 9.800433 TTCACATATTTGCAGTGTTAATAATGG 57.200 29.630 1.84 0.00 34.94 3.16
2250 2325 8.652290 ACCCTCAGATTGGATATTACTTTCTAC 58.348 37.037 0.00 0.00 0.00 2.59
2261 2355 4.846367 CCCTGATAACCCTCAGATTGGATA 59.154 45.833 2.73 0.00 44.48 2.59
2301 2395 3.684305 GGAATTAATGTTTGGCAAGTGGC 59.316 43.478 0.00 0.00 43.74 5.01
2384 2478 8.701908 AGTGATATATGTTGAAATTCATGGCT 57.298 30.769 0.00 0.00 0.00 4.75
2415 2509 9.832445 TTAGATTTGTTAGGGATTCATCTACAC 57.168 33.333 0.00 0.00 0.00 2.90
2428 2522 9.823647 ACATAGTGATCAGTTAGATTTGTTAGG 57.176 33.333 8.68 0.00 37.00 2.69
2432 2526 9.376075 CAGAACATAGTGATCAGTTAGATTTGT 57.624 33.333 8.68 1.53 37.00 2.83
2439 2533 7.468141 ACAGACAGAACATAGTGATCAGTTA 57.532 36.000 8.68 0.00 0.00 2.24
2445 2539 4.177026 GCGAACAGACAGAACATAGTGAT 58.823 43.478 0.00 0.00 0.00 3.06
2500 2606 4.035792 TGGTCACTGTTAAACAATTCACCG 59.964 41.667 0.00 0.00 0.00 4.94
2751 2858 2.895404 AGTACTCGTTGAGGGCTGTTTA 59.105 45.455 0.00 0.00 33.35 2.01
2775 2882 3.802948 AGAACATCATCGTCCACTACC 57.197 47.619 0.00 0.00 0.00 3.18
2865 2972 4.164030 ACTGAATGGTAGGCACATCATACA 59.836 41.667 0.00 0.00 33.86 2.29
2952 3059 3.489059 CGTCCTTCTTTGCAAAAAGCTCA 60.489 43.478 13.84 4.58 45.94 4.26
3063 3170 4.610680 GCAAACGTTGAACAGACCTCATAC 60.611 45.833 0.00 0.00 0.00 2.39
3106 3214 5.131809 CCTGAAGGAAAGGGAGTCTGAATAT 59.868 44.000 0.00 0.00 37.39 1.28
3111 3219 2.260822 TCCTGAAGGAAAGGGAGTCTG 58.739 52.381 0.00 0.00 42.18 3.51
3112 3220 2.723530 TCCTGAAGGAAAGGGAGTCT 57.276 50.000 0.00 0.00 42.18 3.24
3138 3246 6.682423 TTTCTGTATACATGAGCCAATGTG 57.318 37.500 5.91 0.00 40.93 3.21
3139 3247 6.183360 GCTTTTCTGTATACATGAGCCAATGT 60.183 38.462 5.91 7.03 43.21 2.71
3141 3249 6.125029 AGCTTTTCTGTATACATGAGCCAAT 58.875 36.000 18.41 5.79 0.00 3.16
3213 3321 1.573829 GCATCCGCACCTTTCAACGA 61.574 55.000 0.00 0.00 38.36 3.85
3331 3440 2.439880 ACAGAAAGCCCCTAGATTAGGC 59.560 50.000 0.00 0.00 44.86 3.93
3343 3452 1.039856 TTGGGCAGAAACAGAAAGCC 58.960 50.000 0.00 0.00 44.48 4.35
3344 3453 2.159114 TGTTTGGGCAGAAACAGAAAGC 60.159 45.455 9.31 0.00 40.18 3.51
3358 3467 6.012858 TCCTAGGGCTACATATAATGTTTGGG 60.013 42.308 9.46 0.00 41.63 4.12
3435 3592 2.040813 TGCTTCTTCTTTGCTCCTGGAT 59.959 45.455 0.00 0.00 0.00 3.41
3448 3605 5.720371 TCTCTATATGGAGCTGCTTCTTC 57.280 43.478 11.09 0.00 33.70 2.87
3555 3712 5.365895 AGGTATTACACGGAAGAGGCTATTT 59.634 40.000 0.00 0.00 0.00 1.40
3697 3856 2.534939 CCGCAAGCGTTCTTCTTATTCG 60.535 50.000 13.80 0.00 37.81 3.34
3794 3953 5.941647 ACGTTATAGTACAGTTGGCCAAAAT 59.058 36.000 22.47 9.46 0.00 1.82
3855 4014 5.690865 AGAATTTAACTGAGACAACCACCA 58.309 37.500 0.00 0.00 0.00 4.17
3864 4023 8.833231 ACAAGAATTCGAGAATTTAACTGAGA 57.167 30.769 11.77 0.00 40.77 3.27
3868 4027 8.499162 CACTGACAAGAATTCGAGAATTTAACT 58.501 33.333 11.77 3.20 40.77 2.24
3882 4042 5.581126 TTTCAAAGCACACTGACAAGAAT 57.419 34.783 0.00 0.00 0.00 2.40
3934 4094 1.153208 GAGTCAGAGCCATGCCAGG 60.153 63.158 0.00 0.00 0.00 4.45
3935 4095 0.462225 CAGAGTCAGAGCCATGCCAG 60.462 60.000 0.00 0.00 0.00 4.85
3950 4110 6.852858 TCATACGACTTGAGATACTCAGAG 57.147 41.667 0.00 0.00 41.75 3.35
3980 4142 1.242076 GTGCAACTTGTCCTGAGCAT 58.758 50.000 0.00 0.00 34.24 3.79
4001 4163 2.669569 TGCAAACGAGCCTGCCTC 60.670 61.111 0.00 0.00 37.79 4.70
4021 4183 5.200483 TGACAGAAAATGGTGACCTCTTTT 58.800 37.500 12.95 12.95 0.00 2.27
4033 4195 3.125829 CAGGACGGACATGACAGAAAATG 59.874 47.826 0.00 0.00 31.40 2.32
4034 4196 3.338249 CAGGACGGACATGACAGAAAAT 58.662 45.455 0.00 0.00 31.40 1.82
4069 4231 0.684479 AGGCAGCCGACTGTAGATGA 60.684 55.000 5.55 0.00 46.30 2.92
4096 4258 0.037605 ACTGACGGCGTTTAAGGAGG 60.038 55.000 16.19 1.22 0.00 4.30
4097 4259 1.336517 TGACTGACGGCGTTTAAGGAG 60.337 52.381 16.19 6.30 0.00 3.69
4098 4260 0.675083 TGACTGACGGCGTTTAAGGA 59.325 50.000 16.19 1.40 0.00 3.36
4099 4261 0.788391 GTGACTGACGGCGTTTAAGG 59.212 55.000 16.19 5.58 0.00 2.69
4100 4262 0.788391 GGTGACTGACGGCGTTTAAG 59.212 55.000 16.19 14.98 0.00 1.85
4101 4263 0.104487 TGGTGACTGACGGCGTTTAA 59.896 50.000 16.19 2.00 0.00 1.52
4102 4264 0.104487 TTGGTGACTGACGGCGTTTA 59.896 50.000 16.19 5.81 0.00 2.01
4103 4265 0.534203 ATTGGTGACTGACGGCGTTT 60.534 50.000 16.19 0.82 0.00 3.60
4104 4266 0.949105 GATTGGTGACTGACGGCGTT 60.949 55.000 16.19 0.00 0.00 4.84
4127 4289 5.184892 AGGCAACCATCTAGATCACTTTT 57.815 39.130 1.03 0.00 37.17 2.27
4141 4303 2.250939 CGAGCGTTTGAGGCAACCA 61.251 57.895 0.00 0.00 37.17 3.67
4168 4330 2.213499 GACTGAATACAAGGGATGCCG 58.787 52.381 0.00 0.00 0.00 5.69
4178 4340 7.634671 TCGTACTAGATTTGGACTGAATACA 57.365 36.000 0.00 0.00 0.00 2.29
4194 4356 5.147865 CGAGCCACTTCATATTCGTACTAG 58.852 45.833 0.00 0.00 0.00 2.57
4199 4361 1.202533 CCCGAGCCACTTCATATTCGT 60.203 52.381 0.00 0.00 0.00 3.85
4238 4400 1.554160 AGATTGAGGTGAGCCAGAGTG 59.446 52.381 0.00 0.00 37.19 3.51
4256 4418 3.517901 AGAACCGGGACAAATATGTGAGA 59.482 43.478 6.32 0.00 40.74 3.27
4258 4420 3.517901 AGAGAACCGGGACAAATATGTGA 59.482 43.478 6.32 0.00 40.74 3.58
4261 4425 4.814771 GGTAAGAGAACCGGGACAAATATG 59.185 45.833 6.32 0.00 0.00 1.78
4273 4437 2.810274 GTTTTGGTCCGGTAAGAGAACC 59.190 50.000 0.00 0.00 36.08 3.62
4282 4446 0.845337 TGGTTAGGTTTTGGTCCGGT 59.155 50.000 0.00 0.00 0.00 5.28
4285 4449 2.158579 TGGAGTGGTTAGGTTTTGGTCC 60.159 50.000 0.00 0.00 0.00 4.46
4311 4475 2.741878 TAGACGGGAGCTTGGGTGGT 62.742 60.000 0.00 0.00 0.00 4.16
4329 4493 0.317160 CACTGGACGACACAAGGCTA 59.683 55.000 0.00 0.00 0.00 3.93
4330 4494 1.069765 CACTGGACGACACAAGGCT 59.930 57.895 0.00 0.00 0.00 4.58
4352 4557 3.027419 GCCCATAGCATCCTCCAAC 57.973 57.895 0.00 0.00 42.97 3.77
4369 4574 1.934463 CAATGCGGACGGTCATAGC 59.066 57.895 10.76 12.19 0.00 2.97
4370 4575 1.498865 GGCAATGCGGACGGTCATAG 61.499 60.000 10.76 1.99 0.00 2.23
4371 4576 1.522806 GGCAATGCGGACGGTCATA 60.523 57.895 10.76 0.00 0.00 2.15
4372 4577 2.824041 GGCAATGCGGACGGTCAT 60.824 61.111 10.76 0.00 0.00 3.06
4374 4579 4.778143 AGGGCAATGCGGACGGTC 62.778 66.667 0.00 0.00 0.00 4.79
4375 4580 3.860930 AAAGGGCAATGCGGACGGT 62.861 57.895 0.00 0.00 0.00 4.83
4417 4622 2.474816 GAAAAGATCCCTCATCGGTCG 58.525 52.381 0.00 0.00 36.50 4.79
4424 4629 1.449601 GCGCCGAAAAGATCCCTCA 60.450 57.895 0.00 0.00 0.00 3.86
4426 4631 2.511600 CGCGCCGAAAAGATCCCT 60.512 61.111 0.00 0.00 0.00 4.20
4440 4645 0.857311 GCCGACACAATGAATTCGCG 60.857 55.000 0.00 0.00 0.00 5.87
4447 4652 1.737735 CTCTGCGCCGACACAATGA 60.738 57.895 4.18 0.00 0.00 2.57
4458 4663 4.767255 CCCCAGTGTCCTCTGCGC 62.767 72.222 0.00 0.00 34.47 6.09
4471 4685 0.042131 ACCACGAAGATCCTACCCCA 59.958 55.000 0.00 0.00 0.00 4.96
4487 4701 1.968541 ATGGGGAGGATACCGGACCA 61.969 60.000 9.46 3.37 37.17 4.02
4507 4721 0.250727 CTTCTTCCAACGGCCCAGAA 60.251 55.000 0.00 0.00 0.00 3.02
4510 4724 1.374947 CTCTTCTTCCAACGGCCCA 59.625 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.