Multiple sequence alignment - TraesCS6A01G067000

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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 TraesCS6A01G067000 chr6A 100.000 4780 0 0 1 4780 35641690 35636911 0.000000e+00 8828
1 TraesCS6A01G067000 chrUn 92.127 3709 173 61 678 4326 100836151 100839800 0.000000e+00 5121
2 TraesCS6A01G067000 chrUn 89.955 448 36 7 1 446 100833814 100834254 1.930000e-158 569
3 TraesCS6A01G067000 chrUn 90.867 427 19 9 4354 4780 100839796 100840202 5.400000e-154 555
4 TraesCS6A01G067000 chrUn 91.322 242 20 1 436 676 100835874 100836115 3.570000e-86 329
5 TraesCS6A01G067000 chr6B 91.924 1944 122 20 2316 4239 65734058 65732130 0.000000e+00 2687
6 TraesCS6A01G067000 chr6B 85.663 1116 83 42 681 1756 65735675 65734597 0.000000e+00 1103
7 TraesCS6A01G067000 chr6B 92.511 454 33 1 1751 2204 65734571 65734119 0.000000e+00 649
8 TraesCS6A01G067000 chr6B 85.835 593 52 22 106 676 65736296 65735714 6.840000e-168 601
9 TraesCS6A01G067000 chr6B 87.662 308 32 6 4239 4541 65732252 65731946 2.120000e-93 353
10 TraesCS6A01G067000 chr6B 94.624 93 5 0 4688 4780 65731791 65731699 1.390000e-30 145


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 TraesCS6A01G067000 chr6A 35636911 35641690 4779 True 8828.0 8828 100.000000 1 4780 1 chr6A.!!$R1 4779
1 TraesCS6A01G067000 chrUn 100833814 100840202 6388 False 1643.5 5121 91.067750 1 4780 4 chrUn.!!$F1 4779
2 TraesCS6A01G067000 chr6B 65731699 65736296 4597 True 923.0 2687 89.703167 106 4780 6 chr6B.!!$R1 4674

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
540 2184 0.404040 CTTGCCTTCCACCCACCTAA 59.596 55.0 0.0 0.0 0.00 2.69 F
1715 3445 0.244994 CAGCAGTCAAGCGAGGTAGT 59.755 55.0 0.0 0.0 40.15 2.73 F
1941 3732 0.744874 TCTACGAATCCCTCAAGCCG 59.255 55.0 0.0 0.0 0.00 5.52 F
3556 5373 0.036732 ACCTGGTGTGATGACGCAAT 59.963 50.0 0.0 0.0 38.28 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 3594 0.109153 ACATGGTGTTCTGCAGAGCA 59.891 50.000 27.10 27.1 36.92 4.26 R
3353 5163 1.152383 GCCCAGAGTAATTCCGCGAC 61.152 60.000 8.23 0.0 0.00 5.19 R
3744 5561 1.002773 GTAGGGCTCGAAAAGGGTTGA 59.997 52.381 0.00 0.0 0.00 3.18 R
4733 6596 0.802494 CTCCAACGGGCATGTTGTAC 59.198 55.000 17.13 0.0 46.08 2.90 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
40 41 0.541863 CAGGATTCTAAGCCCCACGT 59.458 55.000 0.00 0.00 34.20 4.49
56 57 3.308530 CCACGTGAGGAAAATCTTTTGC 58.691 45.455 19.30 0.00 38.57 3.68
60 61 5.043248 ACGTGAGGAAAATCTTTTGCTTTG 58.957 37.500 10.22 6.65 46.67 2.77
65 66 5.295152 AGGAAAATCTTTTGCTTTGCAGAG 58.705 37.500 0.00 0.00 44.83 3.35
70 71 8.699283 AAAATCTTTTGCTTTGCAGAGATATC 57.301 30.769 8.73 0.00 40.05 1.63
148 150 5.603596 ACTTGAGCATTGATTTTCTTGCAA 58.396 33.333 0.00 0.00 37.56 4.08
165 167 2.032799 TGCAATGAGAAAACCGTGACAC 59.967 45.455 0.00 0.00 0.00 3.67
167 169 3.617669 CAATGAGAAAACCGTGACACAC 58.382 45.455 6.37 0.00 0.00 3.82
179 181 1.396996 GTGACACACGGGTTATGCATC 59.603 52.381 0.19 0.00 0.00 3.91
185 187 3.440173 CACACGGGTTATGCATCTTTCTT 59.560 43.478 0.19 0.00 0.00 2.52
212 216 7.718334 TCTACTATGTGTTTCCAAGAGATGA 57.282 36.000 0.00 0.00 0.00 2.92
359 364 1.940613 GAAGGCATTGTATCCACGGTC 59.059 52.381 0.00 0.00 0.00 4.79
360 365 0.908910 AGGCATTGTATCCACGGTCA 59.091 50.000 0.00 0.00 0.00 4.02
361 366 1.490490 AGGCATTGTATCCACGGTCAT 59.510 47.619 0.00 0.00 0.00 3.06
362 367 1.603802 GGCATTGTATCCACGGTCATG 59.396 52.381 0.00 0.00 0.00 3.07
403 409 4.612614 CGTAACAAAGTAACGCGTCTAGAA 59.387 41.667 14.44 0.00 0.00 2.10
480 2116 6.273825 ACTTCCTGTTTATGACTGCTATACG 58.726 40.000 0.00 0.00 0.00 3.06
482 2118 4.647853 TCCTGTTTATGACTGCTATACGGT 59.352 41.667 0.00 0.00 42.04 4.83
513 2149 8.451908 ACAACTAAGCTTAAATCTTGAAGTGT 57.548 30.769 7.74 0.00 0.00 3.55
524 2168 1.542915 CTTGAAGTGTCATGGGCCTTG 59.457 52.381 13.02 13.02 32.48 3.61
540 2184 0.404040 CTTGCCTTCCACCCACCTAA 59.596 55.000 0.00 0.00 0.00 2.69
568 2212 4.666532 GCTTGACGCCACGTGTGC 62.667 66.667 15.65 15.97 41.37 4.57
602 2246 7.660208 AGACGGATTTATATCATTACAACACCC 59.340 37.037 0.00 0.00 32.09 4.61
649 2298 6.939622 TGACTGAATCTATGTGAGATGTGTT 58.060 36.000 0.00 0.00 44.68 3.32
737 2422 0.604578 TACTCGGTGTTTCTTCGGGG 59.395 55.000 0.00 0.00 0.00 5.73
742 2427 1.002142 CGGTGTTTCTTCGGGGAAAAC 60.002 52.381 5.56 0.00 37.02 2.43
743 2428 2.025898 GGTGTTTCTTCGGGGAAAACA 58.974 47.619 5.56 0.00 37.02 2.83
748 2433 4.758165 TGTTTCTTCGGGGAAAACATCTAC 59.242 41.667 5.56 0.00 37.02 2.59
752 2437 3.992943 TCGGGGAAAACATCTACATGT 57.007 42.857 2.69 2.69 45.89 3.21
826 2513 5.684704 TGGAGATGGTTCTATTTCCATGAC 58.315 41.667 0.00 0.00 43.45 3.06
851 2538 1.569548 TCGATAGAGAGGGGGTTGACT 59.430 52.381 0.00 0.00 42.67 3.41
852 2539 1.683917 CGATAGAGAGGGGGTTGACTG 59.316 57.143 0.00 0.00 39.76 3.51
853 2540 2.687014 CGATAGAGAGGGGGTTGACTGA 60.687 54.545 0.00 0.00 39.76 3.41
854 2541 2.233305 TAGAGAGGGGGTTGACTGAC 57.767 55.000 0.00 0.00 0.00 3.51
881 2568 2.736531 GGCAAGCAACCCAACCAG 59.263 61.111 0.00 0.00 0.00 4.00
953 2645 3.462678 GACCTCACGCCTCCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
991 2683 2.359478 AATCGCGAACCACCACCC 60.359 61.111 15.24 0.00 0.00 4.61
1237 2964 3.958860 AGCCGCAGCACCCTTTCT 61.959 61.111 0.00 0.00 43.56 2.52
1500 3230 4.475135 GCCGTGGAGAGGAAGGGC 62.475 72.222 0.00 0.00 39.87 5.19
1503 3233 3.706373 GTGGAGAGGAAGGGCGCA 61.706 66.667 10.83 0.00 0.00 6.09
1665 3395 2.093537 ATTCTCTCCTCATCGCCGGC 62.094 60.000 19.07 19.07 0.00 6.13
1686 3416 1.669779 GATCAAGAGTGCCATGACAGC 59.330 52.381 0.00 0.00 0.00 4.40
1715 3445 0.244994 CAGCAGTCAAGCGAGGTAGT 59.755 55.000 0.00 0.00 40.15 2.73
1770 3561 3.586174 TGATCATGATTTGCCCCCAAAAA 59.414 39.130 10.14 0.00 43.58 1.94
1774 3565 3.872459 TGATTTGCCCCCAAAAACAAT 57.128 38.095 0.00 0.00 43.58 2.71
1803 3594 4.210331 AGCTCAACTGGTCATGTTTCTTT 58.790 39.130 0.00 0.00 0.00 2.52
1845 3636 0.806102 AATCGAATCAGTCACGGCGG 60.806 55.000 13.24 0.00 0.00 6.13
1866 3657 2.642995 CTGCAAATCAGAACACACACG 58.357 47.619 0.00 0.00 45.72 4.49
1941 3732 0.744874 TCTACGAATCCCTCAAGCCG 59.255 55.000 0.00 0.00 0.00 5.52
2194 3985 3.118223 GGAGGTAAGCAAGCCTTCACTAT 60.118 47.826 0.00 0.00 34.81 2.12
2208 3999 5.125417 GCCTTCACTATATGGAACTTTGCAA 59.875 40.000 0.00 0.00 30.51 4.08
2215 4006 9.289303 CACTATATGGAACTTTGCAATTTGTAC 57.711 33.333 0.00 0.00 30.51 2.90
2237 4028 9.729023 TGTACAATTCTGTTGTAAAATTCACTG 57.271 29.630 0.00 0.00 36.74 3.66
2244 4035 9.781834 TTCTGTTGTAAAATTCACTGTAAACTG 57.218 29.630 0.00 0.00 0.00 3.16
2246 4037 9.438291 CTGTTGTAAAATTCACTGTAAACTGAG 57.562 33.333 0.00 0.00 0.00 3.35
2247 4038 8.402472 TGTTGTAAAATTCACTGTAAACTGAGG 58.598 33.333 0.00 0.00 0.00 3.86
2285 4082 8.769891 GGTTGTAAAAATTCACTGTAAATTGGG 58.230 33.333 0.00 0.00 0.00 4.12
2298 4095 4.469227 TGTAAATTGGGGCTGTGCATAATT 59.531 37.500 0.00 0.00 0.00 1.40
2442 4239 5.224135 TGTGACATTTGCATCAACAATCTG 58.776 37.500 0.00 0.00 0.00 2.90
2481 4278 3.060003 CGAAGCTTCTCAAGGATTATGCG 60.060 47.826 23.50 2.57 0.00 4.73
2596 4393 2.921754 AGCTATGCGTGAGTTAAACGAC 59.078 45.455 2.45 0.00 43.68 4.34
2729 4528 1.140652 CTGAGGGAGCCCAAGATTCTC 59.859 57.143 8.53 0.00 38.92 2.87
2814 4613 1.929836 GCCGATGCAGAAACTACTGAG 59.070 52.381 0.00 0.00 39.94 3.35
2836 4635 4.342092 AGCTTCCAAGTGCACTTTGTAAAT 59.658 37.500 29.23 11.77 33.11 1.40
2842 4641 9.606631 TTCCAAGTGCACTTTGTAAATTTTATT 57.393 25.926 29.23 0.16 33.11 1.40
2984 4792 4.642885 TGTGCATGCATATGATATGGATGG 59.357 41.667 33.31 21.59 44.58 3.51
3016 4824 3.369242 TGGCTCATCACCATCATTCAA 57.631 42.857 0.00 0.00 30.29 2.69
3049 4858 6.735130 TGTCGATTTTCTTTTCTTCTTTCCC 58.265 36.000 0.00 0.00 0.00 3.97
3061 4870 9.435688 CTTTTCTTCTTTCCCTTTTCTTTTCAA 57.564 29.630 0.00 0.00 0.00 2.69
3225 5035 6.608405 TCCATTTCATCCTGATGCAACTAATT 59.392 34.615 2.18 0.00 38.65 1.40
3259 5069 3.364549 CCCACATTTTCAGGCTATGGAA 58.635 45.455 0.49 0.00 0.00 3.53
3353 5163 0.875059 GGCTGAAAACAAGGAGACCG 59.125 55.000 0.00 0.00 0.00 4.79
3382 5192 5.129320 GGAATTACTCTGGGCATTTTTCCAT 59.871 40.000 0.00 0.00 32.32 3.41
3556 5373 0.036732 ACCTGGTGTGATGACGCAAT 59.963 50.000 0.00 0.00 38.28 3.56
3596 5413 0.603569 AGAACTGGACGACTCGCATT 59.396 50.000 0.00 0.00 0.00 3.56
3705 5522 3.190383 TCATCAGGGAGGAGTTTGAGA 57.810 47.619 0.00 0.00 0.00 3.27
3707 5524 3.102972 CATCAGGGAGGAGTTTGAGAGA 58.897 50.000 0.00 0.00 0.00 3.10
3744 5561 3.149981 CAGCATGATGATGATCCTTGCT 58.850 45.455 4.56 12.02 43.04 3.91
3745 5562 3.189495 CAGCATGATGATGATCCTTGCTC 59.811 47.826 4.56 0.00 41.58 4.26
3746 5563 3.146847 GCATGATGATGATCCTTGCTCA 58.853 45.455 0.00 0.00 35.41 4.26
3755 5572 3.157087 TGATCCTTGCTCAACCCTTTTC 58.843 45.455 0.00 0.00 0.00 2.29
3773 5590 5.588648 CCTTTTCGAGCCCTACAATTATGAA 59.411 40.000 0.00 0.00 0.00 2.57
3786 5603 9.716507 CCTACAATTATGAAAACTAAACATCGG 57.283 33.333 0.00 0.00 0.00 4.18
3833 5650 0.111253 CTGCCAGGAAGGTGAAGGTT 59.889 55.000 0.00 0.00 40.61 3.50
3835 5652 0.402121 GCCAGGAAGGTGAAGGTTCT 59.598 55.000 0.00 0.00 40.61 3.01
3885 5702 8.455682 TGGTAAACGGAATAAATGAATGAACTC 58.544 33.333 0.00 0.00 0.00 3.01
3984 5803 8.606830 AGAGAAAACTGATTTGGTAGGACTATT 58.393 33.333 0.00 0.00 0.00 1.73
4058 5877 4.830600 TGACCAGTACACACTCATGTTCTA 59.169 41.667 0.00 0.00 36.72 2.10
4063 5882 5.290400 CAGTACACACTCATGTTCTATGCTG 59.710 44.000 0.00 0.00 36.72 4.41
4074 5893 0.904649 TCTATGCTGTGGTCACCTGG 59.095 55.000 0.00 0.00 0.00 4.45
4134 5953 5.210430 TGCATGGATTCACAATAGGGAAAT 58.790 37.500 0.00 0.00 0.00 2.17
4137 5956 6.480981 GCATGGATTCACAATAGGGAAATTTG 59.519 38.462 0.00 0.00 0.00 2.32
4167 5987 7.265673 TCTCACTCTCCAGGATATTTTTAACG 58.734 38.462 0.00 0.00 0.00 3.18
4170 5990 6.816640 CACTCTCCAGGATATTTTTAACGTCA 59.183 38.462 0.00 0.00 0.00 4.35
4245 6066 8.344831 TGTAATTCTGAAACAGACAATTCACAG 58.655 33.333 0.74 0.00 40.46 3.66
4261 6082 8.434392 ACAATTCACAGTAGGTAAACTTAAGGA 58.566 33.333 7.53 0.00 0.00 3.36
4272 6093 7.395617 AGGTAAACTTAAGGATCTCACTTTCC 58.604 38.462 7.53 0.90 0.00 3.13
4276 6097 5.094387 ACTTAAGGATCTCACTTTCCAGGA 58.906 41.667 7.53 0.00 34.27 3.86
4294 6115 8.463930 TTCCAGGATAATTTCAACATCCATAC 57.536 34.615 6.90 0.00 40.67 2.39
4297 6118 8.571336 CCAGGATAATTTCAACATCCATACTTC 58.429 37.037 6.90 0.00 40.67 3.01
4298 6119 8.571336 CAGGATAATTTCAACATCCATACTTCC 58.429 37.037 6.90 0.00 40.67 3.46
4306 6127 8.421249 TTCAACATCCATACTTCCTTCATTTT 57.579 30.769 0.00 0.00 0.00 1.82
4334 6155 3.982576 AAAACTTGGACATCGTTGACC 57.017 42.857 7.88 7.88 38.06 4.02
4335 6156 2.631160 AACTTGGACATCGTTGACCA 57.369 45.000 12.69 12.69 44.32 4.02
4336 6157 2.859165 ACTTGGACATCGTTGACCAT 57.141 45.000 16.51 2.54 45.12 3.55
4337 6158 3.140325 ACTTGGACATCGTTGACCATT 57.860 42.857 16.51 6.25 45.12 3.16
4338 6159 3.486383 ACTTGGACATCGTTGACCATTT 58.514 40.909 16.51 5.94 45.12 2.32
4339 6160 3.888930 ACTTGGACATCGTTGACCATTTT 59.111 39.130 16.51 3.84 45.12 1.82
4340 6161 3.913548 TGGACATCGTTGACCATTTTG 57.086 42.857 12.69 0.00 41.75 2.44
4341 6162 3.218453 TGGACATCGTTGACCATTTTGT 58.782 40.909 12.69 0.00 41.75 2.83
4342 6163 4.390264 TGGACATCGTTGACCATTTTGTA 58.610 39.130 12.69 0.00 41.75 2.41
4343 6164 4.822350 TGGACATCGTTGACCATTTTGTAA 59.178 37.500 12.69 0.00 41.75 2.41
4344 6165 5.475220 TGGACATCGTTGACCATTTTGTAAT 59.525 36.000 12.69 0.00 41.75 1.89
4345 6166 6.015856 TGGACATCGTTGACCATTTTGTAATT 60.016 34.615 12.69 0.00 41.75 1.40
4346 6167 6.526674 GGACATCGTTGACCATTTTGTAATTC 59.473 38.462 9.66 0.00 37.58 2.17
4347 6168 7.214467 ACATCGTTGACCATTTTGTAATTCT 57.786 32.000 0.00 0.00 0.00 2.40
4348 6169 7.657336 ACATCGTTGACCATTTTGTAATTCTT 58.343 30.769 0.00 0.00 0.00 2.52
4349 6170 8.788806 ACATCGTTGACCATTTTGTAATTCTTA 58.211 29.630 0.00 0.00 0.00 2.10
4350 6171 9.619316 CATCGTTGACCATTTTGTAATTCTTAA 57.381 29.630 0.00 0.00 0.00 1.85
4351 6172 9.840427 ATCGTTGACCATTTTGTAATTCTTAAG 57.160 29.630 0.00 0.00 0.00 1.85
4352 6173 7.806014 TCGTTGACCATTTTGTAATTCTTAAGC 59.194 33.333 0.00 0.00 0.00 3.09
4481 6303 7.016268 AGGACAAAAAGATACTACAAGAGACCA 59.984 37.037 0.00 0.00 0.00 4.02
4507 6329 0.919710 ACCCTAGAGCCAAATGGACC 59.080 55.000 2.98 0.00 37.39 4.46
4515 6337 2.505819 GAGCCAAATGGACCTTCCTAGA 59.494 50.000 2.98 0.00 37.46 2.43
4571 6431 2.953648 CCAATCTTATCATGTGCAGCCA 59.046 45.455 0.00 0.00 0.00 4.75
4572 6432 3.382227 CCAATCTTATCATGTGCAGCCAA 59.618 43.478 0.00 0.00 0.00 4.52
4575 6435 3.623703 TCTTATCATGTGCAGCCAATGT 58.376 40.909 0.00 0.00 0.00 2.71
4576 6436 4.779696 TCTTATCATGTGCAGCCAATGTA 58.220 39.130 0.00 0.00 0.00 2.29
4577 6437 5.192176 TCTTATCATGTGCAGCCAATGTAA 58.808 37.500 0.00 3.38 0.00 2.41
4579 6439 4.579454 ATCATGTGCAGCCAATGTAATC 57.421 40.909 0.00 0.00 0.00 1.75
4580 6440 3.623703 TCATGTGCAGCCAATGTAATCT 58.376 40.909 0.00 0.00 0.00 2.40
4581 6441 3.628942 TCATGTGCAGCCAATGTAATCTC 59.371 43.478 0.00 0.00 0.00 2.75
4582 6442 3.070476 TGTGCAGCCAATGTAATCTCA 57.930 42.857 0.00 0.00 0.00 3.27
4583 6443 3.623703 TGTGCAGCCAATGTAATCTCAT 58.376 40.909 0.00 0.00 0.00 2.90
4584 6444 3.379057 TGTGCAGCCAATGTAATCTCATG 59.621 43.478 0.00 0.00 0.00 3.07
4585 6445 3.628942 GTGCAGCCAATGTAATCTCATGA 59.371 43.478 0.00 0.00 0.00 3.07
4586 6446 3.628942 TGCAGCCAATGTAATCTCATGAC 59.371 43.478 0.00 0.00 0.00 3.06
4587 6447 3.004106 GCAGCCAATGTAATCTCATGACC 59.996 47.826 0.00 0.00 0.00 4.02
4588 6448 4.201657 CAGCCAATGTAATCTCATGACCA 58.798 43.478 0.00 0.00 0.00 4.02
4589 6449 4.641541 CAGCCAATGTAATCTCATGACCAA 59.358 41.667 0.00 0.00 0.00 3.67
4590 6450 4.641989 AGCCAATGTAATCTCATGACCAAC 59.358 41.667 0.00 0.00 0.00 3.77
4591 6451 4.398988 GCCAATGTAATCTCATGACCAACA 59.601 41.667 0.00 0.00 0.00 3.33
4592 6452 5.677091 GCCAATGTAATCTCATGACCAACAC 60.677 44.000 0.00 0.00 0.00 3.32
4593 6453 5.415389 CCAATGTAATCTCATGACCAACACA 59.585 40.000 0.00 0.00 0.00 3.72
4594 6454 6.095860 CCAATGTAATCTCATGACCAACACAT 59.904 38.462 0.00 0.00 0.00 3.21
4595 6455 7.363181 CCAATGTAATCTCATGACCAACACATT 60.363 37.037 10.12 10.12 35.17 2.71
4596 6456 8.676401 CAATGTAATCTCATGACCAACACATTA 58.324 33.333 13.42 0.00 33.59 1.90
4597 6457 7.609760 TGTAATCTCATGACCAACACATTAC 57.390 36.000 0.00 0.00 0.00 1.89
4598 6458 7.164803 TGTAATCTCATGACCAACACATTACA 58.835 34.615 0.00 0.00 33.15 2.41
4599 6459 7.663493 TGTAATCTCATGACCAACACATTACAA 59.337 33.333 0.00 0.00 32.93 2.41
4600 6460 5.940192 TCTCATGACCAACACATTACAAC 57.060 39.130 0.00 0.00 0.00 3.32
4601 6461 4.759693 TCTCATGACCAACACATTACAACC 59.240 41.667 0.00 0.00 0.00 3.77
4602 6462 3.500299 TCATGACCAACACATTACAACCG 59.500 43.478 0.00 0.00 0.00 4.44
4640 6500 5.475909 ACAGACAATGCTGAATGATGTTTCT 59.524 36.000 10.68 0.00 39.20 2.52
4674 6534 0.515564 GCGTGTATTTGTTGTCGCCT 59.484 50.000 0.00 0.00 38.16 5.52
4683 6543 1.370609 TGTTGTCGCCTCGTTTCAAA 58.629 45.000 0.00 0.00 0.00 2.69
4730 6593 3.243839 GCTCAGGCTGGTTGAAATTTTCA 60.244 43.478 15.73 7.74 35.02 2.69
4733 6596 5.299148 TCAGGCTGGTTGAAATTTTCATTG 58.701 37.500 15.73 5.15 39.84 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.541863 ACGTGGGGCTTAGAATCCTG 59.458 55.000 0.00 0.00 0.00 3.86
22 23 0.541863 CACGTGGGGCTTAGAATCCT 59.458 55.000 7.95 0.00 0.00 3.24
40 41 5.021033 TGCAAAGCAAAAGATTTTCCTCA 57.979 34.783 0.00 0.00 34.76 3.86
84 85 8.153411 GGATGTTTCACGTGATTTTTAAAATCG 58.847 33.333 20.80 14.97 0.00 3.34
159 161 1.396996 GATGCATAACCCGTGTGTCAC 59.603 52.381 0.00 0.00 0.00 3.67
165 167 4.701956 AAAGAAAGATGCATAACCCGTG 57.298 40.909 0.00 0.00 0.00 4.94
167 169 6.867662 AGATAAAGAAAGATGCATAACCCG 57.132 37.500 0.00 0.00 0.00 5.28
270 274 8.340618 AGTATGATTTGTGCATTAAGACACTT 57.659 30.769 10.86 0.00 37.68 3.16
359 364 1.133976 CCTAGAGTTTGGCCCCTCATG 60.134 57.143 14.48 7.73 0.00 3.07
360 365 1.216990 CCTAGAGTTTGGCCCCTCAT 58.783 55.000 14.48 4.86 0.00 2.90
361 366 1.562672 GCCTAGAGTTTGGCCCCTCA 61.563 60.000 14.48 2.94 43.11 3.86
362 367 1.224870 GCCTAGAGTTTGGCCCCTC 59.775 63.158 0.00 2.82 43.11 4.30
403 409 2.885135 TCACATGATCTTGGTTGCCT 57.115 45.000 12.76 0.00 0.00 4.75
524 2168 0.035343 GAGTTAGGTGGGTGGAAGGC 60.035 60.000 0.00 0.00 0.00 4.35
540 2184 2.753029 GTCAAGCAGGGGCAGAGT 59.247 61.111 0.00 0.00 44.61 3.24
649 2298 1.135489 CGAAGGTCGACGATCCTTTCA 60.135 52.381 23.49 0.00 43.74 2.69
676 2325 6.631971 TCACACACAAACACACATTCATAT 57.368 33.333 0.00 0.00 0.00 1.78
807 2494 5.066593 GGGAGTCATGGAAATAGAACCATC 58.933 45.833 0.00 0.00 43.89 3.51
869 2556 1.507141 CGTGACTCTGGTTGGGTTGC 61.507 60.000 0.00 0.00 0.00 4.17
953 2645 4.605967 GAGAGCGAGCGAGCGAGG 62.606 72.222 1.41 0.00 43.00 4.63
1155 2882 1.590259 GATGAAGAGGCGCTCGTCC 60.590 63.158 7.64 0.00 38.01 4.79
1219 2946 3.741476 GAAAGGGTGCTGCGGCTG 61.741 66.667 20.27 1.15 39.59 4.85
1226 2953 0.474660 AGGGACTGAGAAAGGGTGCT 60.475 55.000 0.00 0.00 37.18 4.40
1229 2956 0.905337 CGGAGGGACTGAGAAAGGGT 60.905 60.000 0.00 0.00 41.55 4.34
1665 3395 1.931841 CTGTCATGGCACTCTTGATCG 59.068 52.381 0.00 0.00 33.08 3.69
1725 3456 4.307032 TTGAAGAGGAGGAGGATTTTGG 57.693 45.455 0.00 0.00 0.00 3.28
1726 3457 5.948162 TCATTTGAAGAGGAGGAGGATTTTG 59.052 40.000 0.00 0.00 0.00 2.44
1733 3464 5.926663 TCATGATCATTTGAAGAGGAGGAG 58.073 41.667 5.16 0.00 0.00 3.69
1795 3586 3.016031 TGTTCTGCAGAGCAAAGAAACA 58.984 40.909 28.39 18.39 38.41 2.83
1796 3587 3.366719 GTGTTCTGCAGAGCAAAGAAAC 58.633 45.455 31.41 17.71 38.41 2.78
1803 3594 0.109153 ACATGGTGTTCTGCAGAGCA 59.891 50.000 27.10 27.10 36.92 4.26
1836 3627 3.667429 GATTTGCAGCCGCCGTGAC 62.667 63.158 0.00 0.00 37.32 3.67
1845 3636 2.388121 GTGTGTGTTCTGATTTGCAGC 58.612 47.619 0.00 0.00 44.52 5.25
1866 3657 2.519302 CGGCATTCCATCCACCCC 60.519 66.667 0.00 0.00 0.00 4.95
1906 3697 1.402896 TAGATGGAGAGCAAGCCGGG 61.403 60.000 2.18 0.00 0.00 5.73
1912 3703 2.365617 GGGATTCGTAGATGGAGAGCAA 59.634 50.000 0.00 0.00 35.04 3.91
1941 3732 3.529533 CTTGGACATGTGATCCTCTGAC 58.470 50.000 1.15 0.00 37.13 3.51
1950 3741 0.321919 GGCTCTGCTTGGACATGTGA 60.322 55.000 1.15 0.00 0.00 3.58
2109 3900 0.459411 GAAGAAGCTCCACCTCGCTC 60.459 60.000 0.00 0.00 34.96 5.03
2169 3960 0.771127 AAGGCTTGCTTACCTCCACA 59.229 50.000 0.00 0.00 34.31 4.17
2194 3985 9.202273 GAATTGTACAAATTGCAAAGTTCCATA 57.798 29.630 13.23 0.00 27.89 2.74
2233 4024 6.204688 TCAATTTACAGCCTCAGTTTACAGTG 59.795 38.462 0.00 0.00 0.00 3.66
2234 4025 6.296026 TCAATTTACAGCCTCAGTTTACAGT 58.704 36.000 0.00 0.00 0.00 3.55
2235 4026 6.128172 CCTCAATTTACAGCCTCAGTTTACAG 60.128 42.308 0.00 0.00 0.00 2.74
2236 4027 5.705441 CCTCAATTTACAGCCTCAGTTTACA 59.295 40.000 0.00 0.00 0.00 2.41
2237 4028 5.705905 ACCTCAATTTACAGCCTCAGTTTAC 59.294 40.000 0.00 0.00 0.00 2.01
2239 4030 4.729868 ACCTCAATTTACAGCCTCAGTTT 58.270 39.130 0.00 0.00 0.00 2.66
2240 4031 4.373156 ACCTCAATTTACAGCCTCAGTT 57.627 40.909 0.00 0.00 0.00 3.16
2241 4032 4.074970 CAACCTCAATTTACAGCCTCAGT 58.925 43.478 0.00 0.00 0.00 3.41
2242 4033 4.074970 ACAACCTCAATTTACAGCCTCAG 58.925 43.478 0.00 0.00 0.00 3.35
2243 4034 4.098914 ACAACCTCAATTTACAGCCTCA 57.901 40.909 0.00 0.00 0.00 3.86
2244 4035 6.569179 TTTACAACCTCAATTTACAGCCTC 57.431 37.500 0.00 0.00 0.00 4.70
2246 4037 8.601845 AATTTTTACAACCTCAATTTACAGCC 57.398 30.769 0.00 0.00 0.00 4.85
2247 4038 9.255304 TGAATTTTTACAACCTCAATTTACAGC 57.745 29.630 0.00 0.00 0.00 4.40
2285 4082 2.412770 GCAACAACAATTATGCACAGCC 59.587 45.455 0.00 0.00 38.63 4.85
2481 4278 5.545588 TGAAGCAATCTACCATCTATCTGC 58.454 41.667 0.00 0.00 0.00 4.26
2814 4613 3.708563 TTACAAAGTGCACTTGGAAGC 57.291 42.857 35.38 0.00 36.12 3.86
2984 4792 4.202050 GGTGATGAGCCATCCAAATACAAC 60.202 45.833 11.25 2.66 39.87 3.32
3016 4824 9.981114 AAGAAAAGAAAATCGACAAACCATAAT 57.019 25.926 0.00 0.00 0.00 1.28
3049 4858 9.040939 ACATCGGGTAAAAATTGAAAAGAAAAG 57.959 29.630 0.00 0.00 0.00 2.27
3061 4870 9.910267 AAATAACCTACTACATCGGGTAAAAAT 57.090 29.630 0.00 0.00 0.00 1.82
3067 4876 5.121105 GCAAAATAACCTACTACATCGGGT 58.879 41.667 0.00 0.00 0.00 5.28
3068 4877 4.514066 GGCAAAATAACCTACTACATCGGG 59.486 45.833 0.00 0.00 0.00 5.14
3115 4924 8.426569 ACTTACCTGGTAACTACAAATACAGA 57.573 34.615 15.15 0.00 37.61 3.41
3124 4933 4.401837 CCCTCTGACTTACCTGGTAACTAC 59.598 50.000 15.15 9.78 37.61 2.73
3225 5035 4.946160 AAATGTGGGGAAATGAGGTAGA 57.054 40.909 0.00 0.00 0.00 2.59
3259 5069 4.017958 TCAACAACCATGGTATATGTGGGT 60.018 41.667 20.12 1.28 37.33 4.51
3324 5134 4.505390 CCTTGTTTTCAGCCCCAAAATCAT 60.505 41.667 0.00 0.00 0.00 2.45
3353 5163 1.152383 GCCCAGAGTAATTCCGCGAC 61.152 60.000 8.23 0.00 0.00 5.19
3361 5171 6.897413 AGTAATGGAAAAATGCCCAGAGTAAT 59.103 34.615 0.00 0.00 35.67 1.89
3400 5210 6.156775 TGGAGATGACATCTTTCCTGTAATCA 59.843 38.462 18.89 0.00 40.38 2.57
3463 5273 5.200368 TGAATTCTTGGTTTGGAAGAAGC 57.800 39.130 7.05 0.00 41.53 3.86
3518 5335 6.324770 ACCAGGTGAGAAAGAAATGTTTCAAT 59.675 34.615 8.09 0.00 38.66 2.57
3521 5338 5.067805 ACACCAGGTGAGAAAGAAATGTTTC 59.932 40.000 27.39 0.00 36.96 2.78
3556 5373 4.528206 TCTTCTCCTTCTTGCTACATGTCA 59.472 41.667 0.00 0.00 0.00 3.58
3596 5413 1.375396 CAGATGGCGGTCGTTTCCA 60.375 57.895 0.00 0.00 0.00 3.53
3731 5548 1.918262 AGGGTTGAGCAAGGATCATCA 59.082 47.619 0.00 0.00 0.00 3.07
3737 5554 1.142060 TCGAAAAGGGTTGAGCAAGGA 59.858 47.619 0.00 0.00 0.00 3.36
3744 5561 1.002773 GTAGGGCTCGAAAAGGGTTGA 59.997 52.381 0.00 0.00 0.00 3.18
3745 5562 1.271163 TGTAGGGCTCGAAAAGGGTTG 60.271 52.381 0.00 0.00 0.00 3.77
3746 5563 1.061546 TGTAGGGCTCGAAAAGGGTT 58.938 50.000 0.00 0.00 0.00 4.11
3755 5572 7.548196 TTAGTTTTCATAATTGTAGGGCTCG 57.452 36.000 0.00 0.00 0.00 5.03
3773 5590 5.127491 TCAGGTGTTTCCGATGTTTAGTTT 58.873 37.500 0.00 0.00 41.99 2.66
3833 5650 7.446319 AGAATGTTCAAACAGTTCATCATCAGA 59.554 33.333 14.61 0.00 43.04 3.27
3835 5652 7.364970 CAGAATGTTCAAACAGTTCATCATCA 58.635 34.615 14.61 0.00 43.04 3.07
3885 5702 7.636259 TTTCATCTTTTCTTTAATGCAACCG 57.364 32.000 0.00 0.00 0.00 4.44
3984 5803 1.481363 CAGCTCATCTTCCAGCAGAGA 59.519 52.381 0.00 0.00 38.18 3.10
4047 5866 3.261643 TGACCACAGCATAGAACATGAGT 59.738 43.478 0.00 0.00 0.00 3.41
4058 5877 0.478072 TTTCCAGGTGACCACAGCAT 59.522 50.000 3.63 0.00 45.57 3.79
4063 5882 0.108585 TGCTCTTTCCAGGTGACCAC 59.891 55.000 3.63 0.00 0.00 4.16
4074 5893 5.956068 AGAAGGTTTGAGATTGCTCTTTC 57.044 39.130 0.00 0.00 41.84 2.62
4134 5953 4.356436 TCCTGGAGAGTGAGATCATCAAA 58.644 43.478 0.00 0.00 40.43 2.69
4137 5956 6.855763 AATATCCTGGAGAGTGAGATCATC 57.144 41.667 1.52 0.00 0.00 2.92
4228 6049 7.724305 TTACCTACTGTGAATTGTCTGTTTC 57.276 36.000 0.00 0.00 0.00 2.78
4245 6066 9.368674 GAAAGTGAGATCCTTAAGTTTACCTAC 57.631 37.037 0.97 0.00 0.00 3.18
4261 6082 7.890127 TGTTGAAATTATCCTGGAAAGTGAGAT 59.110 33.333 0.00 0.00 0.00 2.75
4272 6093 8.571336 GGAAGTATGGATGTTGAAATTATCCTG 58.429 37.037 5.91 0.00 40.77 3.86
4276 6097 9.699410 TGAAGGAAGTATGGATGTTGAAATTAT 57.301 29.630 0.00 0.00 0.00 1.28
4321 6142 3.915437 ACAAAATGGTCAACGATGTCC 57.085 42.857 2.04 2.04 35.57 4.02
4322 6143 7.305474 AGAATTACAAAATGGTCAACGATGTC 58.695 34.615 0.00 0.00 0.00 3.06
4323 6144 7.214467 AGAATTACAAAATGGTCAACGATGT 57.786 32.000 0.00 0.00 0.00 3.06
4324 6145 9.619316 TTAAGAATTACAAAATGGTCAACGATG 57.381 29.630 0.00 0.00 0.00 3.84
4325 6146 9.840427 CTTAAGAATTACAAAATGGTCAACGAT 57.160 29.630 0.00 0.00 0.00 3.73
4326 6147 7.806014 GCTTAAGAATTACAAAATGGTCAACGA 59.194 33.333 6.67 0.00 0.00 3.85
4327 6148 7.593273 TGCTTAAGAATTACAAAATGGTCAACG 59.407 33.333 6.67 0.00 0.00 4.10
4328 6149 8.810652 TGCTTAAGAATTACAAAATGGTCAAC 57.189 30.769 6.67 0.00 0.00 3.18
4329 6150 8.855110 TCTGCTTAAGAATTACAAAATGGTCAA 58.145 29.630 6.67 0.00 29.54 3.18
4330 6151 8.296713 GTCTGCTTAAGAATTACAAAATGGTCA 58.703 33.333 6.67 0.00 36.40 4.02
4331 6152 8.296713 TGTCTGCTTAAGAATTACAAAATGGTC 58.703 33.333 6.67 0.00 36.40 4.02
4332 6153 8.177119 TGTCTGCTTAAGAATTACAAAATGGT 57.823 30.769 6.67 0.00 36.40 3.55
4333 6154 9.474920 TTTGTCTGCTTAAGAATTACAAAATGG 57.525 29.630 16.47 0.00 36.40 3.16
4345 6166 9.897744 CATGTAAAGAATTTTGTCTGCTTAAGA 57.102 29.630 6.67 0.00 40.09 2.10
4346 6167 8.642020 GCATGTAAAGAATTTTGTCTGCTTAAG 58.358 33.333 0.00 0.00 40.09 1.85
4347 6168 8.359642 AGCATGTAAAGAATTTTGTCTGCTTAA 58.640 29.630 0.00 0.00 40.09 1.85
4348 6169 7.885297 AGCATGTAAAGAATTTTGTCTGCTTA 58.115 30.769 0.00 0.00 40.09 3.09
4349 6170 6.752168 AGCATGTAAAGAATTTTGTCTGCTT 58.248 32.000 0.00 0.00 40.09 3.91
4350 6171 6.336842 AGCATGTAAAGAATTTTGTCTGCT 57.663 33.333 0.00 0.00 40.09 4.24
4351 6172 6.617105 GCAAGCATGTAAAGAATTTTGTCTGC 60.617 38.462 0.00 0.00 40.09 4.26
4352 6173 6.399249 CGCAAGCATGTAAAGAATTTTGTCTG 60.399 38.462 0.00 0.00 40.09 3.51
4481 6303 5.193728 TCCATTTGGCTCTAGGGTAGAATTT 59.806 40.000 0.00 0.00 33.75 1.82
4507 6329 5.659463 CTCAATGTCTTCAGGTCTAGGAAG 58.341 45.833 0.00 0.00 41.42 3.46
4515 6337 2.486472 CCTGCTCAATGTCTTCAGGT 57.514 50.000 0.00 0.00 39.45 4.00
4571 6431 7.707624 AATGTGTTGGTCATGAGATTACATT 57.292 32.000 14.54 14.54 33.03 2.71
4572 6432 7.828717 TGTAATGTGTTGGTCATGAGATTACAT 59.171 33.333 0.00 1.30 0.00 2.29
4575 6435 7.120579 GGTTGTAATGTGTTGGTCATGAGATTA 59.879 37.037 0.00 0.00 0.00 1.75
4576 6436 6.071952 GGTTGTAATGTGTTGGTCATGAGATT 60.072 38.462 0.00 0.00 0.00 2.40
4577 6437 5.415701 GGTTGTAATGTGTTGGTCATGAGAT 59.584 40.000 0.00 0.00 0.00 2.75
4579 6439 4.378356 CGGTTGTAATGTGTTGGTCATGAG 60.378 45.833 0.00 0.00 0.00 2.90
4580 6440 3.500299 CGGTTGTAATGTGTTGGTCATGA 59.500 43.478 0.00 0.00 0.00 3.07
4581 6441 3.500299 TCGGTTGTAATGTGTTGGTCATG 59.500 43.478 0.00 0.00 0.00 3.07
4582 6442 3.745799 TCGGTTGTAATGTGTTGGTCAT 58.254 40.909 0.00 0.00 0.00 3.06
4583 6443 3.195471 TCGGTTGTAATGTGTTGGTCA 57.805 42.857 0.00 0.00 0.00 4.02
4584 6444 3.119990 CCATCGGTTGTAATGTGTTGGTC 60.120 47.826 0.00 0.00 0.00 4.02
4585 6445 2.817258 CCATCGGTTGTAATGTGTTGGT 59.183 45.455 0.00 0.00 0.00 3.67
4586 6446 2.817258 ACCATCGGTTGTAATGTGTTGG 59.183 45.455 0.00 0.00 27.29 3.77
4587 6447 3.365868 CCACCATCGGTTGTAATGTGTTG 60.366 47.826 0.00 0.00 31.02 3.33
4588 6448 2.817258 CCACCATCGGTTGTAATGTGTT 59.183 45.455 0.00 0.00 31.02 3.32
4589 6449 2.224670 ACCACCATCGGTTGTAATGTGT 60.225 45.455 0.00 0.00 34.91 3.72
4590 6450 2.432444 ACCACCATCGGTTGTAATGTG 58.568 47.619 0.00 0.00 34.91 3.21
4591 6451 2.871096 ACCACCATCGGTTGTAATGT 57.129 45.000 0.00 0.00 34.91 2.71
4599 6459 2.635915 TCTGTTTCTAACCACCATCGGT 59.364 45.455 0.00 0.00 42.71 4.69
4600 6460 3.000727 GTCTGTTTCTAACCACCATCGG 58.999 50.000 0.00 0.00 0.00 4.18
4601 6461 3.659786 TGTCTGTTTCTAACCACCATCG 58.340 45.455 0.00 0.00 0.00 3.84
4602 6462 5.619981 GCATTGTCTGTTTCTAACCACCATC 60.620 44.000 0.00 0.00 0.00 3.51
4674 6534 1.606668 GGCCACATGAGTTTGAAACGA 59.393 47.619 0.00 0.00 36.23 3.85
4730 6593 1.543802 CCAACGGGCATGTTGTACAAT 59.456 47.619 12.26 0.00 46.08 2.71
4733 6596 0.802494 CTCCAACGGGCATGTTGTAC 59.198 55.000 17.13 0.00 46.08 2.90


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

AutoCloner maintained by Alex Coulton.