Multiple sequence alignment - TraesCS4B01G249600

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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 TraesCS4B01G249600 chr4B 100.000 5975 0 0 1 5975 515139156 515145130 0.000000e+00 11034
1 TraesCS4B01G249600 chr4D 94.540 4011 141 26 1128 5079 418744449 418740458 0.000000e+00 6122
2 TraesCS4B01G249600 chr4D 91.457 1112 70 8 1 1112 418745992 418744906 0.000000e+00 1504
3 TraesCS4B01G249600 chr4D 84.071 904 81 31 5095 5975 418740244 418739381 0.000000e+00 813
4 TraesCS4B01G249600 chr4A 87.631 2199 156 52 3616 5772 46143221 46141097 0.000000e+00 2447
5 TraesCS4B01G249600 chr4A 92.834 1228 77 8 2287 3507 46144446 46143223 0.000000e+00 1770
6 TraesCS4B01G249600 chr4A 89.168 1394 110 14 215 1595 46146385 46145020 0.000000e+00 1700
7 TraesCS4B01G249600 chr4A 89.144 654 57 7 1648 2289 46145018 46144367 0.000000e+00 802
8 TraesCS4B01G249600 chr7B 96.403 278 6 2 1376 1650 597763566 597763842 7.060000e-124 455
9 TraesCS4B01G249600 chr7B 96.629 89 3 0 1562 1650 709579215 709579127 1.340000e-31 148
10 TraesCS4B01G249600 chr2B 77.817 568 112 12 28 590 736884975 736885533 7.420000e-89 339
11 TraesCS4B01G249600 chr2B 76.617 603 125 11 15 614 767741373 767740784 9.660000e-83 318
12 TraesCS4B01G249600 chr1B 77.219 597 118 17 28 615 156840417 156841004 3.450000e-87 333
13 TraesCS4B01G249600 chr1B 77.874 348 73 4 278 623 567980751 567980406 4.690000e-51 213
14 TraesCS4B01G249600 chr3B 76.721 610 125 14 30 631 764815657 764815057 2.080000e-84 324
15 TraesCS4B01G249600 chr2A 77.515 507 101 11 128 629 193586000 193586498 5.860000e-75 292
16 TraesCS4B01G249600 chr6A 79.293 396 72 10 192 584 615562231 615562619 9.870000e-68 268
17 TraesCS4B01G249600 chr3D 75.424 590 109 24 51 627 601862108 601862674 2.760000e-63 254
18 TraesCS4B01G249600 chr5D 74.375 480 109 13 148 623 515796644 515797113 6.110000e-45 193


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 TraesCS4B01G249600 chr4B 515139156 515145130 5974 False 11034.00 11034 100.000000 1 5975 1 chr4B.!!$F1 5974
1 TraesCS4B01G249600 chr4D 418739381 418745992 6611 True 2813.00 6122 90.022667 1 5975 3 chr4D.!!$R1 5974
2 TraesCS4B01G249600 chr4A 46141097 46146385 5288 True 1679.75 2447 89.694250 215 5772 4 chr4A.!!$R1 5557
3 TraesCS4B01G249600 chr2B 736884975 736885533 558 False 339.00 339 77.817000 28 590 1 chr2B.!!$F1 562
4 TraesCS4B01G249600 chr2B 767740784 767741373 589 True 318.00 318 76.617000 15 614 1 chr2B.!!$R1 599
5 TraesCS4B01G249600 chr1B 156840417 156841004 587 False 333.00 333 77.219000 28 615 1 chr1B.!!$F1 587
6 TraesCS4B01G249600 chr3B 764815057 764815657 600 True 324.00 324 76.721000 30 631 1 chr3B.!!$R1 601
7 TraesCS4B01G249600 chr3D 601862108 601862674 566 False 254.00 254 75.424000 51 627 1 chr3D.!!$F1 576

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
310 319 0.105194 TATCATCTCCTTGGGGGCGA 60.105 55.0 0.00 0.0 32.90 5.54 F
1188 1663 0.249238 CAGCGAGATGGGCTCTGTAC 60.249 60.0 0.00 0.0 41.66 2.90 F
2828 3354 0.247419 GCATCTTGATGCGTGTGACG 60.247 55.0 18.06 0.0 45.88 4.35 F
4023 4556 0.319405 ACCTGTAAACTTCCGTCCCG 59.681 55.0 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 2090 1.003851 GCGCATCGTAAACTAGGCAA 58.996 50.000 0.30 0.0 0.0 4.52 R
3017 3543 3.018856 TGGATGTCTTGCCATGTTCATC 58.981 45.455 0.00 0.0 0.0 2.92 R
4079 4612 0.318762 ACTGCAGAGAAAGGACGGAC 59.681 55.000 23.35 0.0 0.0 4.79 R
5617 6376 0.321021 CTGGCTCTCACTTCACTGCT 59.679 55.000 0.00 0.0 0.0 4.24 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
43 44 1.209504 CGATTAGGGCAAACTCTCCCA 59.790 52.381 0.00 0.00 45.07 4.37
64 65 0.529337 CCATGCTTCATCGACGAGCT 60.529 55.000 14.98 0.00 37.32 4.09
91 92 2.947532 CGTCTTCCCTCTGCCTGCA 61.948 63.158 0.00 0.00 0.00 4.41
140 141 3.314388 CTCGGTGCCTTCGCTTTGC 62.314 63.158 0.00 0.00 35.36 3.68
259 266 2.670592 TCGAGTTCGTCCGCCTGA 60.671 61.111 1.07 0.00 40.80 3.86
310 319 0.105194 TATCATCTCCTTGGGGGCGA 60.105 55.000 0.00 0.00 32.90 5.54
315 324 2.040442 TCCTTGGGGGCGATGAGA 59.960 61.111 0.00 0.00 34.39 3.27
348 357 4.323417 TCGACATGTGGCAAGATTTAGTT 58.677 39.130 1.15 0.00 0.00 2.24
351 360 5.046910 ACATGTGGCAAGATTTAGTTTCG 57.953 39.130 0.00 0.00 0.00 3.46
432 449 1.374252 GGGACACGTGCACGAAGAT 60.374 57.895 42.94 24.70 43.02 2.40
455 473 1.280982 CCGGATGTCATCGTCAAGTG 58.719 55.000 0.00 0.00 0.00 3.16
580 600 9.243637 GTTTGTTATGTTTGAGATGCTTTGTAA 57.756 29.630 0.00 0.00 0.00 2.41
590 610 4.526970 AGATGCTTTGTAATTCCGGTGAT 58.473 39.130 0.00 0.00 0.00 3.06
618 638 9.838339 TTTCATAATAGACCTGATCCTTTTCTC 57.162 33.333 0.00 0.00 0.00 2.87
623 643 8.572855 AATAGACCTGATCCTTTTCTCAAAAG 57.427 34.615 2.29 2.29 45.78 2.27
710 730 1.267533 GAACGTGGCCAAATTAACCGT 59.732 47.619 7.24 8.52 0.00 4.83
730 750 3.760035 ATCACCGGTCGCTCGCTT 61.760 61.111 2.59 0.00 0.00 4.68
862 882 1.519751 CGGGAGGGATCGTGAGCTAG 61.520 65.000 0.00 0.00 0.00 3.42
1098 1124 1.271271 ACGGTGAAGAGAGACGGTACT 60.271 52.381 0.00 0.00 0.00 2.73
1188 1663 0.249238 CAGCGAGATGGGCTCTGTAC 60.249 60.000 0.00 0.00 41.66 2.90
1189 1664 0.396417 AGCGAGATGGGCTCTGTACT 60.396 55.000 0.00 0.00 41.66 2.73
1190 1665 1.133761 AGCGAGATGGGCTCTGTACTA 60.134 52.381 0.00 0.00 41.66 1.82
1255 1730 1.304381 TGCATTCCCCTGCTGGTTC 60.304 57.895 9.00 0.00 42.75 3.62
1286 1761 2.282180 AATTGGGCGTCCGCTTGT 60.282 55.556 11.82 0.00 41.60 3.16
1301 1776 2.351350 CGCTTGTTAGGTTGCCGAATTT 60.351 45.455 0.00 0.00 0.00 1.82
1311 1786 3.924507 CCGAATTTGGCTCCCTGG 58.075 61.111 0.00 0.00 0.00 4.45
1356 1831 1.066286 AGCATCTGTGAAGCTGAGACC 60.066 52.381 0.00 0.00 35.24 3.85
1365 1840 3.005539 GCTGAGACCCTGCCTGGA 61.006 66.667 0.00 0.00 38.35 3.86
1506 1986 3.755378 TCTCTGAAAGAAAATGAGCTGGC 59.245 43.478 0.00 0.00 46.34 4.85
1658 2138 6.597562 TGGTGTAGTATGTATCATTTTCCCC 58.402 40.000 0.00 0.00 0.00 4.81
1781 2267 3.611674 TTGCTCGGCGACTGTCCA 61.612 61.111 4.99 0.00 0.00 4.02
2381 2899 4.652822 ACCATGACCAGGACTAGAAAAAC 58.347 43.478 0.00 0.00 0.00 2.43
2828 3354 0.247419 GCATCTTGATGCGTGTGACG 60.247 55.000 18.06 0.00 45.88 4.35
2902 3428 3.345508 TCACCGCTACTCTGTCTTCTA 57.654 47.619 0.00 0.00 0.00 2.10
2964 3490 7.417116 GGCATGATTGAAGTGATGGATTTACTT 60.417 37.037 0.00 0.00 37.36 2.24
3010 3536 3.746751 GCATAACCATCACTCCATCAGCT 60.747 47.826 0.00 0.00 0.00 4.24
3017 3543 4.370049 CATCACTCCATCAGCTCAAGTAG 58.630 47.826 0.00 0.00 0.00 2.57
3136 3666 6.561519 TTAGCCAGAATTTAGGAACTAGCT 57.438 37.500 0.00 0.00 44.25 3.32
3139 3669 6.350103 AGCCAGAATTTAGGAACTAGCTTAC 58.650 40.000 0.00 0.00 44.25 2.34
3164 3694 8.985805 ACTCTGAAAACATTACCTAACTTAACG 58.014 33.333 0.00 0.00 0.00 3.18
3218 3748 9.743057 CTTTTCTGTGTACCAAATGTTTATTCA 57.257 29.630 0.00 0.00 0.00 2.57
3250 3780 5.486735 TTGTAGAAGTATCGTTTTCCCCA 57.513 39.130 0.00 0.00 0.00 4.96
3496 4029 7.509546 ACACCTCAAGATATTGTAAGTATGGG 58.490 38.462 0.00 0.00 0.00 4.00
3513 4046 6.779860 AGTATGGGATGTCTTTGTGTTTACT 58.220 36.000 0.00 0.00 0.00 2.24
3520 4053 6.879458 GGATGTCTTTGTGTTTACTGAGGTAT 59.121 38.462 0.00 0.00 0.00 2.73
3538 4071 6.486657 TGAGGTATATTTGGATGCTAGTTTGC 59.513 38.462 0.00 0.00 0.00 3.68
3999 4532 5.471456 TGAGCTTGGAACTCTCAAAAATCTC 59.529 40.000 0.00 0.00 34.30 2.75
4018 4551 1.000060 TCCGTCACCTGTAAACTTCCG 60.000 52.381 0.00 0.00 0.00 4.30
4023 4556 0.319405 ACCTGTAAACTTCCGTCCCG 59.681 55.000 0.00 0.00 0.00 5.14
4054 4587 7.251704 TCTCTCTCAAGTTCACATGAAAAAC 57.748 36.000 0.00 0.47 35.58 2.43
4055 4588 7.050377 TCTCTCTCAAGTTCACATGAAAAACT 58.950 34.615 0.00 3.00 35.58 2.66
4098 4631 0.318762 GTCCGTCCTTTCTCTGCAGT 59.681 55.000 14.67 0.00 0.00 4.40
4103 4636 4.278669 TCCGTCCTTTCTCTGCAGTATATC 59.721 45.833 14.67 0.00 0.00 1.63
4111 4644 9.064706 CCTTTCTCTGCAGTATATCATGAATTT 57.935 33.333 14.67 0.00 0.00 1.82
4280 4819 1.936547 GAATGCTGTCTTCCTAAGCCG 59.063 52.381 0.00 0.00 36.05 5.52
4322 4861 4.465632 TGTGGTCTGCAGATACGTTAAT 57.534 40.909 21.47 0.00 0.00 1.40
4471 5010 2.792635 CCCCTGGGAAGACCTCTTT 58.207 57.895 16.20 0.00 41.11 2.52
4603 5144 5.366460 CAAGATTGACATATCTGTGAGCCT 58.634 41.667 0.00 0.00 35.12 4.58
4605 5146 6.737720 AGATTGACATATCTGTGAGCCTTA 57.262 37.500 0.00 0.00 35.14 2.69
4615 5156 4.968259 TCTGTGAGCCTTACTGCTTAAAA 58.032 39.130 0.00 0.00 42.95 1.52
4624 5165 9.561270 GAGCCTTACTGCTTAAAATTTCTAAAG 57.439 33.333 0.00 0.00 42.95 1.85
4630 5171 8.803201 ACTGCTTAAAATTTCTAAAGTTCTGC 57.197 30.769 0.00 0.00 0.00 4.26
4643 5184 7.224297 TCTAAAGTTCTGCCTAGTGTTTGATT 58.776 34.615 0.00 0.00 0.00 2.57
4676 5217 3.251484 TCCTCTTTCATCTGGTTCTGGT 58.749 45.455 0.00 0.00 0.00 4.00
4685 5226 5.982356 TCATCTGGTTCTGGTATTCTCAAG 58.018 41.667 0.00 0.00 0.00 3.02
4686 5227 5.485353 TCATCTGGTTCTGGTATTCTCAAGT 59.515 40.000 0.00 0.00 0.00 3.16
4689 5230 5.778241 TCTGGTTCTGGTATTCTCAAGTACA 59.222 40.000 0.00 0.00 0.00 2.90
4693 5234 6.316390 GGTTCTGGTATTCTCAAGTACAATGG 59.684 42.308 0.00 0.00 0.00 3.16
4716 5257 4.329462 TTTTGGCAGGTATTTGGACAAC 57.671 40.909 0.00 0.00 0.00 3.32
4792 5333 2.924290 GAGCTGTACGTTGGCTTTAGAG 59.076 50.000 0.00 0.00 36.37 2.43
4810 5351 8.398665 GCTTTAGAGTCTCAACTTTTTCTCAAA 58.601 33.333 0.00 0.00 35.28 2.69
4828 5369 5.990996 TCTCAAAACAAATTCCTTTCATGCC 59.009 36.000 0.00 0.00 0.00 4.40
4847 5388 7.420002 TCATGCCATCGAAAAGAATTATTCTG 58.580 34.615 8.34 0.00 40.59 3.02
4848 5389 6.757897 TGCCATCGAAAAGAATTATTCTGT 57.242 33.333 8.34 0.00 40.59 3.41
4853 5394 8.344831 CCATCGAAAAGAATTATTCTGTATGCA 58.655 33.333 8.34 0.00 40.59 3.96
4930 5472 3.015327 CCAGGAAGCAGATCAAAAGGAG 58.985 50.000 0.00 0.00 0.00 3.69
5074 5626 2.211803 CACGCGTATTTTAGGACGTACG 59.788 50.000 13.44 15.01 41.13 3.67
5079 5631 6.015504 CGCGTATTTTAGGACGTACGTATAT 58.984 40.000 22.87 12.51 41.26 0.86
5080 5632 6.023026 CGCGTATTTTAGGACGTACGTATATG 60.023 42.308 22.87 18.66 41.26 1.78
5081 5633 7.015289 GCGTATTTTAGGACGTACGTATATGA 58.985 38.462 22.87 6.60 41.26 2.15
5082 5634 7.693951 GCGTATTTTAGGACGTACGTATATGAT 59.306 37.037 22.87 13.26 41.26 2.45
5088 5640 9.440773 TTTAGGACGTACGTATATGATATCTGT 57.559 33.333 22.87 0.00 0.00 3.41
5091 5643 9.440773 AGGACGTACGTATATGATATCTGTAAA 57.559 33.333 22.87 0.00 0.00 2.01
5130 5880 1.154580 GTTTCTCGCTGCGCTGTTC 60.155 57.895 18.65 3.99 0.00 3.18
5135 5885 2.202388 CGCTGCGCTGTTCAATGG 60.202 61.111 9.88 0.00 0.00 3.16
5155 5905 3.492756 TGGTAAGTTTACGCGTACAAACC 59.507 43.478 26.00 23.06 35.66 3.27
5158 5908 2.548875 AGTTTACGCGTACAAACCACA 58.451 42.857 26.00 6.48 35.66 4.17
5159 5909 2.935201 AGTTTACGCGTACAAACCACAA 59.065 40.909 26.00 11.70 35.66 3.33
5162 5912 0.028374 ACGCGTACAAACCACAAAGC 59.972 50.000 11.67 0.00 0.00 3.51
5163 5913 0.659123 CGCGTACAAACCACAAAGCC 60.659 55.000 0.00 0.00 0.00 4.35
5164 5914 0.659123 GCGTACAAACCACAAAGCCG 60.659 55.000 0.00 0.00 0.00 5.52
5165 5915 0.659123 CGTACAAACCACAAAGCCGC 60.659 55.000 0.00 0.00 0.00 6.53
5166 5916 0.666374 GTACAAACCACAAAGCCGCT 59.334 50.000 0.00 0.00 0.00 5.52
5178 5928 3.065371 ACAAAGCCGCTTGCATAGAATAC 59.935 43.478 6.34 0.00 44.83 1.89
5179 5929 2.620251 AGCCGCTTGCATAGAATACA 57.380 45.000 0.00 0.00 44.83 2.29
5186 5936 6.264832 CCGCTTGCATAGAATACAAAAATCA 58.735 36.000 0.00 0.00 0.00 2.57
5202 5952 0.179073 ATCAGTGAAATCCGGAGCCG 60.179 55.000 11.34 1.06 39.44 5.52
5257 6007 1.866880 GCTGTGCTGCTTTTTCCTGTG 60.867 52.381 0.00 0.00 0.00 3.66
5303 6053 0.529337 AGAATCAGATGCGTCGCCAG 60.529 55.000 15.88 1.80 0.00 4.85
5304 6054 2.098842 GAATCAGATGCGTCGCCAGC 62.099 60.000 15.88 5.79 0.00 4.85
5305 6055 2.584261 AATCAGATGCGTCGCCAGCT 62.584 55.000 15.88 8.15 35.28 4.24
5306 6056 3.561213 CAGATGCGTCGCCAGCTG 61.561 66.667 15.88 16.20 42.02 4.24
5425 6182 2.426522 TGATCTGGACTTTTGGAAGCG 58.573 47.619 0.00 0.00 36.29 4.68
5431 6188 1.194772 GGACTTTTGGAAGCGAACTCG 59.805 52.381 0.00 0.00 43.27 4.18
5458 6215 2.031919 AATGCACGCTCGGAACCA 59.968 55.556 0.00 0.00 0.00 3.67
5515 6272 4.832608 GCCGTAAGACCTGCCCCG 62.833 72.222 0.00 0.00 43.02 5.73
5571 6328 5.314923 ACCATGATGACACAATTTACAGC 57.685 39.130 0.00 0.00 0.00 4.40
5585 6343 3.632643 TTACAGCCTGCATCAATCAGA 57.367 42.857 0.00 0.00 33.54 3.27
5606 6364 0.182061 AGATGGCGATGATGCAGGTT 59.818 50.000 0.00 0.00 36.28 3.50
5615 6374 4.094887 GCGATGATGCAGGTTAGAAAAGAA 59.905 41.667 0.00 0.00 34.15 2.52
5617 6376 6.611381 CGATGATGCAGGTTAGAAAAGAAAA 58.389 36.000 0.00 0.00 0.00 2.29
5619 6378 5.772521 TGATGCAGGTTAGAAAAGAAAAGC 58.227 37.500 0.00 0.00 0.00 3.51
5621 6380 5.186996 TGCAGGTTAGAAAAGAAAAGCAG 57.813 39.130 0.00 0.00 0.00 4.24
5625 6384 6.680378 GCAGGTTAGAAAAGAAAAGCAGTGAA 60.680 38.462 0.00 0.00 0.00 3.18
5656 6415 0.815213 GACACCAGTGTGCAGCTTCA 60.815 55.000 8.43 0.00 46.86 3.02
5657 6416 0.816825 ACACCAGTGTGCAGCTTCAG 60.817 55.000 1.88 0.00 46.86 3.02
5661 6426 2.113986 GTGTGCAGCTTCAGGGGT 59.886 61.111 0.00 0.00 0.00 4.95
5665 6430 2.045536 GCAGCTTCAGGGGTCAGG 60.046 66.667 0.00 0.00 0.00 3.86
5666 6431 2.673523 CAGCTTCAGGGGTCAGGG 59.326 66.667 0.00 0.00 0.00 4.45
5684 6449 1.505353 GCAGAAGAGCCACATGCAC 59.495 57.895 0.00 0.00 44.83 4.57
5728 6494 2.086869 CAGTTTGATTGGATGAGCGGT 58.913 47.619 0.00 0.00 0.00 5.68
5742 6512 1.444895 GCGGTTGCAGCAAGGAATG 60.445 57.895 8.49 0.00 42.15 2.67
5759 6529 5.371526 AGGAATGCATACATACTGTCAAGG 58.628 41.667 0.00 0.00 34.62 3.61
5774 6544 0.899720 CAAGGGCACATGCATTTCCT 59.100 50.000 6.15 0.00 44.36 3.36
5776 6546 1.767759 AGGGCACATGCATTTCCTAC 58.232 50.000 6.15 0.00 44.36 3.18
5777 6547 1.285962 AGGGCACATGCATTTCCTACT 59.714 47.619 6.15 0.00 44.36 2.57
5781 6551 3.012518 GCACATGCATTTCCTACTCTGT 58.987 45.455 0.00 0.00 41.59 3.41
5784 6554 4.940046 CACATGCATTTCCTACTCTGTTCT 59.060 41.667 0.00 0.00 0.00 3.01
5785 6555 6.108687 CACATGCATTTCCTACTCTGTTCTA 58.891 40.000 0.00 0.00 0.00 2.10
5788 6558 8.486210 ACATGCATTTCCTACTCTGTTCTATTA 58.514 33.333 0.00 0.00 0.00 0.98
5789 6559 8.768955 CATGCATTTCCTACTCTGTTCTATTAC 58.231 37.037 0.00 0.00 0.00 1.89
5791 6564 8.540388 TGCATTTCCTACTCTGTTCTATTACTT 58.460 33.333 0.00 0.00 0.00 2.24
5823 6596 8.746052 TGACCTTAATAACATGGATACCTTTG 57.254 34.615 0.00 0.00 0.00 2.77
5824 6597 7.284489 TGACCTTAATAACATGGATACCTTTGC 59.716 37.037 0.00 0.00 0.00 3.68
5825 6598 7.354312 ACCTTAATAACATGGATACCTTTGCT 58.646 34.615 0.00 0.00 0.00 3.91
5826 6599 7.285401 ACCTTAATAACATGGATACCTTTGCTG 59.715 37.037 0.00 0.00 0.00 4.41
5827 6600 5.520376 AATAACATGGATACCTTTGCTGC 57.480 39.130 0.00 0.00 0.00 5.25
5828 6601 1.767759 ACATGGATACCTTTGCTGCC 58.232 50.000 0.00 0.00 0.00 4.85
5848 6621 2.194597 GCTGGTGTTGGTGGTCCA 59.805 61.111 0.00 0.00 42.66 4.02
5854 6627 2.913617 TGGTGTTGGTGGTCCATGTATA 59.086 45.455 0.00 0.00 43.91 1.47
5858 6631 5.114081 GTGTTGGTGGTCCATGTATAGTAC 58.886 45.833 0.00 0.00 43.91 2.73
5918 6711 2.420642 CCAGGCGGTTATGATCATCTG 58.579 52.381 12.53 11.68 0.00 2.90
5919 6712 1.802960 CAGGCGGTTATGATCATCTGC 59.197 52.381 12.53 14.89 0.00 4.26
5920 6713 0.792640 GGCGGTTATGATCATCTGCG 59.207 55.000 12.53 0.46 33.57 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.083164 GCCCTAATCGTCTAGAGTTAGAGC 60.083 50.000 15.82 12.43 36.61 4.09
25 26 2.175715 GGATGGGAGAGTTTGCCCTAAT 59.824 50.000 0.00 0.00 44.96 1.73
43 44 1.871408 GCTCGTCGATGAAGCATGGAT 60.871 52.381 18.31 0.00 31.85 3.41
64 65 0.902531 GAGGGAAGACGAATCCACCA 59.097 55.000 0.00 0.00 38.80 4.17
114 115 0.035439 GAAGGCACCGAGATTTCCCA 60.035 55.000 0.00 0.00 0.00 4.37
204 211 6.017109 CCCGAAAGACAATCTCAAAGAAGAAA 60.017 38.462 0.00 0.00 0.00 2.52
310 319 6.038603 CACATGTCGAAAACCCATAATCTCAT 59.961 38.462 0.00 0.00 0.00 2.90
315 324 3.130340 GCCACATGTCGAAAACCCATAAT 59.870 43.478 0.00 0.00 0.00 1.28
348 357 1.818060 CATGGATTTGAAGCACCCGAA 59.182 47.619 0.00 0.00 0.00 4.30
351 360 0.896923 TGCATGGATTTGAAGCACCC 59.103 50.000 0.00 0.00 0.00 4.61
410 421 0.104487 TTCGTGCACGTGTCCCTAAA 59.896 50.000 35.74 19.03 40.80 1.85
432 449 0.899019 TGACGATGACATCCGGGAAA 59.101 50.000 9.87 0.00 0.00 3.13
580 600 7.998964 AGGTCTATTATGAAAAATCACCGGAAT 59.001 33.333 9.46 0.00 31.51 3.01
710 730 4.794439 CGAGCGACCGGTGATGCA 62.794 66.667 14.63 0.00 0.00 3.96
737 757 3.893399 GGTTGGGTTGGGTCGGGT 61.893 66.667 0.00 0.00 0.00 5.28
983 1003 0.899717 CATGGGTGGGTTGAAGTGGG 60.900 60.000 0.00 0.00 0.00 4.61
989 1009 4.358841 CGGCCATGGGTGGGTTGA 62.359 66.667 15.13 0.00 46.14 3.18
1098 1124 1.374252 GCGGAAGAGGAACGAGCAA 60.374 57.895 0.00 0.00 0.00 3.91
1255 1730 2.009774 CCCAATTCAGCACCTCTAACG 58.990 52.381 0.00 0.00 0.00 3.18
1301 1776 3.640407 GTCAGTGCCAGGGAGCCA 61.640 66.667 0.00 0.00 0.00 4.75
1311 1786 2.288640 ACTAACCTACAACCGTCAGTGC 60.289 50.000 0.00 0.00 0.00 4.40
1356 1831 1.448540 CGCTAAGTGTCCAGGCAGG 60.449 63.158 0.00 0.00 39.47 4.85
1400 1875 8.784043 GCGAATTTAACCACCTAATAATGAGAT 58.216 33.333 0.00 0.00 0.00 2.75
1610 2090 1.003851 GCGCATCGTAAACTAGGCAA 58.996 50.000 0.30 0.00 0.00 4.52
1617 2097 2.218759 CACCAGATAGCGCATCGTAAAC 59.781 50.000 11.47 0.00 38.81 2.01
1658 2138 6.658831 CACCAAGTAATATCTTATGCAACCG 58.341 40.000 0.00 0.00 0.00 4.44
1781 2267 4.236935 CAGCACAAACACAACTTCAGTTT 58.763 39.130 0.00 0.00 35.83 2.66
1907 2393 1.691434 TGCTGAGTACATGTCACACCA 59.309 47.619 0.00 0.00 0.00 4.17
2399 2925 6.485171 AGGTTTGAAGTACAAGGCAAGATAT 58.515 36.000 0.00 0.00 39.77 1.63
2667 3193 7.017254 AGACTTCCCTGAAATAAGGTAAAGTGA 59.983 37.037 11.03 0.00 39.60 3.41
2828 3354 7.092716 AGATACAAAAATGCCAACAGTTCATC 58.907 34.615 0.00 0.00 31.74 2.92
2902 3428 5.635280 GCTATGTGCATCACGACACTTATAT 59.365 40.000 0.00 0.00 42.31 0.86
2964 3490 7.549842 TGCTAAAACACTACAAACTTGACAGTA 59.450 33.333 0.00 0.00 30.68 2.74
3010 3536 4.937620 GTCTTGCCATGTTCATCTACTTGA 59.062 41.667 0.00 0.00 0.00 3.02
3017 3543 3.018856 TGGATGTCTTGCCATGTTCATC 58.981 45.455 0.00 0.00 0.00 2.92
3139 3669 8.985805 ACGTTAAGTTAGGTAATGTTTTCAGAG 58.014 33.333 0.00 0.00 28.41 3.35
3496 4029 7.907214 ATACCTCAGTAAACACAAAGACATC 57.093 36.000 0.00 0.00 30.59 3.06
3513 4046 6.486657 GCAAACTAGCATCCAAATATACCTCA 59.513 38.462 0.00 0.00 0.00 3.86
3520 4053 3.879998 TCGGCAAACTAGCATCCAAATA 58.120 40.909 0.00 0.00 35.83 1.40
3538 4071 4.084013 ACAGCGAGAACTAAAACAATTCGG 60.084 41.667 0.00 0.00 0.00 4.30
3824 4357 2.042464 AGAGGCACAGAAACTGAGACA 58.958 47.619 5.76 0.00 32.55 3.41
3999 4532 1.269936 ACGGAAGTTTACAGGTGACGG 60.270 52.381 0.00 0.00 46.40 4.79
4018 4551 0.818938 GAGAGAGAAGGAACCGGGAC 59.181 60.000 6.32 0.00 0.00 4.46
4023 4556 4.202264 TGTGAACTTGAGAGAGAAGGAACC 60.202 45.833 0.00 0.00 0.00 3.62
4076 4609 2.231478 CTGCAGAGAAAGGACGGACTAA 59.769 50.000 8.42 0.00 0.00 2.24
4077 4610 1.819288 CTGCAGAGAAAGGACGGACTA 59.181 52.381 8.42 0.00 0.00 2.59
4078 4611 0.605589 CTGCAGAGAAAGGACGGACT 59.394 55.000 8.42 0.00 0.00 3.85
4079 4612 0.318762 ACTGCAGAGAAAGGACGGAC 59.681 55.000 23.35 0.00 0.00 4.79
4080 4613 1.919240 TACTGCAGAGAAAGGACGGA 58.081 50.000 23.35 0.00 0.00 4.69
4081 4614 2.969628 ATACTGCAGAGAAAGGACGG 57.030 50.000 23.35 0.00 0.00 4.79
4082 4615 5.188327 TGATATACTGCAGAGAAAGGACG 57.812 43.478 23.35 0.00 0.00 4.79
4103 4636 8.876790 GCAAAAGGAGAGGATTTAAAATTCATG 58.123 33.333 0.00 0.00 0.00 3.07
4111 4644 5.630121 TCACTGCAAAAGGAGAGGATTTAA 58.370 37.500 0.00 0.00 0.00 1.52
4116 4649 2.373169 ACATCACTGCAAAAGGAGAGGA 59.627 45.455 0.00 0.00 0.00 3.71
4322 4861 5.593909 CACCACTCCAGCCAATTGATTATTA 59.406 40.000 7.12 0.00 0.00 0.98
4605 5146 7.867909 GGCAGAACTTTAGAAATTTTAAGCAGT 59.132 33.333 0.00 0.00 0.00 4.40
4615 5156 7.719633 TCAAACACTAGGCAGAACTTTAGAAAT 59.280 33.333 0.00 0.00 0.00 2.17
4624 5165 7.023575 CACATTAATCAAACACTAGGCAGAAC 58.976 38.462 0.00 0.00 0.00 3.01
4630 5171 9.994432 GAAGATTCACATTAATCAAACACTAGG 57.006 33.333 0.00 0.00 38.16 3.02
4643 5184 7.772292 CCAGATGAAAGAGGAAGATTCACATTA 59.228 37.037 0.00 0.00 36.03 1.90
4676 5217 7.014711 TGCCAAAAACCATTGTACTTGAGAATA 59.985 33.333 0.00 0.00 0.00 1.75
4685 5226 3.744238 ACCTGCCAAAAACCATTGTAC 57.256 42.857 0.00 0.00 0.00 2.90
4686 5227 6.226787 CAAATACCTGCCAAAAACCATTGTA 58.773 36.000 0.00 0.00 0.00 2.41
4689 5230 4.349342 TCCAAATACCTGCCAAAAACCATT 59.651 37.500 0.00 0.00 0.00 3.16
4693 5234 4.329462 TGTCCAAATACCTGCCAAAAAC 57.671 40.909 0.00 0.00 0.00 2.43
4792 5333 9.958285 GAATTTGTTTTGAGAAAAAGTTGAGAC 57.042 29.630 0.00 0.00 31.13 3.36
4810 5351 4.220382 TCGATGGCATGAAAGGAATTTGTT 59.780 37.500 3.81 0.00 0.00 2.83
4826 5367 7.324616 GCATACAGAATAATTCTTTTCGATGGC 59.675 37.037 0.00 0.00 38.11 4.40
4828 5369 9.162793 GTGCATACAGAATAATTCTTTTCGATG 57.837 33.333 0.00 0.00 38.11 3.84
4944 5486 1.518774 GTCGGCCTCGGGTAATTCA 59.481 57.895 0.00 0.00 36.95 2.57
4947 5489 2.042230 AGGTCGGCCTCGGGTAAT 60.042 61.111 0.35 0.00 42.67 1.89
5022 5565 1.443194 GCGTCGTGTAGAAAGGCGA 60.443 57.895 0.00 0.00 0.00 5.54
5024 5567 0.666577 ACTGCGTCGTGTAGAAAGGC 60.667 55.000 0.00 0.00 33.97 4.35
5079 5631 9.967346 GATGTGCTACTAGTTTTACAGATATCA 57.033 33.333 0.00 0.00 0.00 2.15
5080 5632 9.967346 TGATGTGCTACTAGTTTTACAGATATC 57.033 33.333 0.00 0.00 0.00 1.63
5082 5634 9.582431 GTTGATGTGCTACTAGTTTTACAGATA 57.418 33.333 0.00 0.00 0.00 1.98
5083 5635 8.314751 AGTTGATGTGCTACTAGTTTTACAGAT 58.685 33.333 0.00 0.00 30.67 2.90
5084 5636 7.667557 AGTTGATGTGCTACTAGTTTTACAGA 58.332 34.615 0.00 0.00 30.67 3.41
5085 5637 7.891183 AGTTGATGTGCTACTAGTTTTACAG 57.109 36.000 0.00 0.00 30.67 2.74
5086 5638 9.366216 CATAGTTGATGTGCTACTAGTTTTACA 57.634 33.333 0.00 4.48 38.04 2.41
5130 5880 4.907188 TGTACGCGTAAACTTACCATTG 57.093 40.909 22.44 0.00 0.00 2.82
5135 5885 4.026145 TGTGGTTTGTACGCGTAAACTTAC 60.026 41.667 27.46 25.07 37.07 2.34
5155 5905 0.804364 TCTATGCAAGCGGCTTTGTG 59.196 50.000 13.53 3.94 45.15 3.33
5158 5908 3.278574 TGTATTCTATGCAAGCGGCTTT 58.721 40.909 13.53 1.12 45.15 3.51
5159 5909 2.917933 TGTATTCTATGCAAGCGGCTT 58.082 42.857 9.94 9.94 45.15 4.35
5162 5912 6.264832 TGATTTTTGTATTCTATGCAAGCGG 58.735 36.000 0.00 0.00 36.27 5.52
5163 5913 6.968904 ACTGATTTTTGTATTCTATGCAAGCG 59.031 34.615 0.00 0.00 36.27 4.68
5164 5914 7.970061 TCACTGATTTTTGTATTCTATGCAAGC 59.030 33.333 0.00 0.00 36.27 4.01
5165 5915 9.844790 TTCACTGATTTTTGTATTCTATGCAAG 57.155 29.630 0.00 0.00 36.27 4.01
5178 5928 4.168760 GCTCCGGATTTCACTGATTTTTG 58.831 43.478 3.57 0.00 0.00 2.44
5179 5929 3.193479 GGCTCCGGATTTCACTGATTTTT 59.807 43.478 3.57 0.00 0.00 1.94
5196 5946 1.499049 GATCGTAATTCACCGGCTCC 58.501 55.000 0.00 0.00 0.00 4.70
5355 6105 0.800300 GTTGGCCACACACACAAACG 60.800 55.000 3.88 0.00 0.00 3.60
5425 6182 1.303309 CATTCATGCCCTCCGAGTTC 58.697 55.000 0.00 0.00 0.00 3.01
5453 6210 1.074951 CCCACTTGTCCCCTGGTTC 59.925 63.158 0.00 0.00 0.00 3.62
5458 6215 3.322466 CGCTCCCACTTGTCCCCT 61.322 66.667 0.00 0.00 0.00 4.79
5515 6272 2.644798 AGTATATGGTGCCCCTTCATCC 59.355 50.000 0.00 0.00 0.00 3.51
5571 6328 3.243434 GCCATCTTTCTGATTGATGCAGG 60.243 47.826 12.17 4.12 37.01 4.85
5585 6343 1.315690 CCTGCATCATCGCCATCTTT 58.684 50.000 0.00 0.00 0.00 2.52
5606 6364 7.047891 TCTCACTTCACTGCTTTTCTTTTCTA 58.952 34.615 0.00 0.00 0.00 2.10
5615 6374 1.141657 TGGCTCTCACTTCACTGCTTT 59.858 47.619 0.00 0.00 0.00 3.51
5617 6376 0.321021 CTGGCTCTCACTTCACTGCT 59.679 55.000 0.00 0.00 0.00 4.24
5619 6378 0.972134 TCCTGGCTCTCACTTCACTG 59.028 55.000 0.00 0.00 0.00 3.66
5621 6380 0.681733 TGTCCTGGCTCTCACTTCAC 59.318 55.000 0.00 0.00 0.00 3.18
5625 6384 1.152247 TGGTGTCCTGGCTCTCACT 60.152 57.895 0.00 0.00 0.00 3.41
5652 6411 1.492133 TTCTGCCCTGACCCCTGAAG 61.492 60.000 0.00 0.00 0.00 3.02
5653 6412 1.463214 TTCTGCCCTGACCCCTGAA 60.463 57.895 0.00 0.00 0.00 3.02
5656 6415 1.614824 CTCTTCTGCCCTGACCCCT 60.615 63.158 0.00 0.00 0.00 4.79
5657 6416 2.993853 CTCTTCTGCCCTGACCCC 59.006 66.667 0.00 0.00 0.00 4.95
5666 6431 1.239296 TGTGCATGTGGCTCTTCTGC 61.239 55.000 0.00 0.00 45.15 4.26
5682 6447 3.787805 GCAGCAGACGATCATTTCATGTG 60.788 47.826 0.00 0.00 0.00 3.21
5684 6449 2.286831 GGCAGCAGACGATCATTTCATG 60.287 50.000 0.00 0.00 0.00 3.07
5697 6463 1.985473 ATCAAACTGTTGGCAGCAGA 58.015 45.000 33.65 14.99 46.30 4.26
5759 6529 2.357009 CAGAGTAGGAAATGCATGTGCC 59.643 50.000 4.50 4.75 41.18 5.01
5807 6580 3.053693 AGGCAGCAAAGGTATCCATGTTA 60.054 43.478 0.00 0.00 0.00 2.41
5808 6581 2.102578 GGCAGCAAAGGTATCCATGTT 58.897 47.619 0.00 0.00 0.00 2.71
5809 6582 1.285962 AGGCAGCAAAGGTATCCATGT 59.714 47.619 0.00 0.00 0.00 3.21
5811 6584 2.381911 CAAGGCAGCAAAGGTATCCAT 58.618 47.619 0.00 0.00 0.00 3.41
5812 6585 1.838112 CAAGGCAGCAAAGGTATCCA 58.162 50.000 0.00 0.00 0.00 3.41
5813 6586 0.457443 GCAAGGCAGCAAAGGTATCC 59.543 55.000 0.00 0.00 0.00 2.59
5821 6594 1.757731 AACACCAGCAAGGCAGCAA 60.758 52.632 4.78 0.00 43.14 3.91
5822 6595 2.123769 AACACCAGCAAGGCAGCA 60.124 55.556 4.78 0.00 43.14 4.41
5823 6596 2.337532 CAACACCAGCAAGGCAGC 59.662 61.111 0.00 0.00 43.14 5.25
5824 6597 1.829533 ACCAACACCAGCAAGGCAG 60.830 57.895 0.00 0.00 43.14 4.85
5825 6598 2.126596 CACCAACACCAGCAAGGCA 61.127 57.895 0.00 0.00 43.14 4.75
5826 6599 2.730094 CACCAACACCAGCAAGGC 59.270 61.111 0.00 0.00 43.14 4.35
5827 6600 1.455383 GACCACCAACACCAGCAAGG 61.455 60.000 0.00 0.00 45.67 3.61
5828 6601 1.455383 GGACCACCAACACCAGCAAG 61.455 60.000 0.00 0.00 35.97 4.01
5848 6621 8.657387 ATCATGCTACAAGGAGTACTATACAT 57.343 34.615 0.00 0.00 0.00 2.29
5854 6627 5.423610 ACTGAATCATGCTACAAGGAGTACT 59.576 40.000 0.00 0.00 0.00 2.73
5858 6631 5.021033 AGACTGAATCATGCTACAAGGAG 57.979 43.478 0.00 0.00 0.00 3.69
5918 6711 1.623973 CCTCGTCGTTTTTCCCTCGC 61.624 60.000 0.00 0.00 0.00 5.03
5919 6712 1.623973 GCCTCGTCGTTTTTCCCTCG 61.624 60.000 0.00 0.00 0.00 4.63
5920 6713 1.623973 CGCCTCGTCGTTTTTCCCTC 61.624 60.000 0.00 0.00 0.00 4.30
5954 6747 1.391157 GGCAACAGCAACCAGGACAA 61.391 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.