Multiple sequence alignment - TraesCS2D01G387200

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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 TraesCS2D01G387200 chr2D 100.000 6648 0 0 1 6648 492657237 492663884 0.000000e+00 12277.0
1 TraesCS2D01G387200 chr2A 95.234 3525 118 35 2458 5938 637977789 637981307 0.000000e+00 5533.0
2 TraesCS2D01G387200 chr2A 95.373 2183 74 12 6 2181 637975230 637977392 0.000000e+00 3446.0
3 TraesCS2D01G387200 chr2A 92.096 291 13 5 2176 2463 637977463 637977746 1.040000e-107 401.0
4 TraesCS2D01G387200 chr2B 94.771 2142 80 14 42 2176 578595590 578597706 0.000000e+00 3306.0
5 TraesCS2D01G387200 chr2B 96.294 1700 54 6 4308 6002 578599989 578601684 0.000000e+00 2782.0
6 TraesCS2D01G387200 chr2B 92.538 1769 73 29 2466 4207 578598252 578599988 0.000000e+00 2481.0
7 TraesCS2D01G387200 chr2B 88.667 300 20 6 2172 2463 578597908 578598201 2.950000e-93 353.0
8 TraesCS2D01G387200 chrUn 98.831 599 6 1 6050 6648 273399743 273400340 0.000000e+00 1066.0
9 TraesCS2D01G387200 chrUn 89.286 56 4 2 5936 5990 199304433 199304487 1.200000e-07 69.4
10 TraesCS2D01G387200 chr5A 97.496 599 9 3 6051 6648 592852568 592851975 0.000000e+00 1018.0
11 TraesCS2D01G387200 chr5A 96.995 599 12 3 6051 6648 532848399 532847806 0.000000e+00 1002.0
12 TraesCS2D01G387200 chr5A 96.013 602 5 3 6048 6648 469907624 469908207 0.000000e+00 961.0
13 TraesCS2D01G387200 chr6A 96.828 599 12 4 6051 6648 436478025 436477433 0.000000e+00 994.0
14 TraesCS2D01G387200 chr4D 92.807 431 21 7 6221 6648 122260665 122261088 3.410000e-172 616.0
15 TraesCS2D01G387200 chr4D 97.183 355 9 1 6294 6648 332789596 332789243 3.430000e-167 599.0
16 TraesCS2D01G387200 chr4D 95.833 216 9 0 6050 6265 332789810 332789595 3.810000e-92 350.0
17 TraesCS2D01G387200 chr4D 90.805 174 10 3 6051 6218 122259948 122260121 1.870000e-55 228.0
18 TraesCS2D01G387200 chr4B 96.620 355 11 1 6294 6648 411257944 411257591 7.430000e-164 588.0
19 TraesCS2D01G387200 chr4B 91.071 336 18 5 6216 6549 112932681 112933006 1.700000e-120 444.0
20 TraesCS2D01G387200 chr4B 95.833 216 9 0 6050 6265 411258158 411257943 3.810000e-92 350.0
21 TraesCS2D01G387200 chr4B 91.228 114 6 3 6535 6648 112939511 112939620 1.150000e-32 152.0
22 TraesCS2D01G387200 chr4B 96.226 53 2 0 6225 6277 112932746 112932798 3.300000e-13 87.9
23 TraesCS2D01G387200 chr6D 92.073 164 9 2 6048 6207 48117429 48117266 1.870000e-55 228.0
24 TraesCS2D01G387200 chr4A 92.727 55 4 0 5938 5992 636103665 636103611 5.530000e-11 80.5
25 TraesCS2D01G387200 chr5B 100.000 40 0 0 5938 5977 70910322 70910283 2.570000e-09 75.0
26 TraesCS2D01G387200 chr5B 89.286 56 4 2 5936 5990 102433740 102433686 1.200000e-07 69.4
27 TraesCS2D01G387200 chr3A 93.750 48 3 0 5935 5982 79391045 79391092 9.250000e-09 73.1
28 TraesCS2D01G387200 chr1B 93.750 48 3 0 5938 5985 9595451 9595404 9.250000e-09 73.1
29 TraesCS2D01G387200 chr5D 97.500 40 1 0 5938 5977 59829369 59829408 1.200000e-07 69.4
30 TraesCS2D01G387200 chr7D 90.196 51 5 0 5933 5983 76791523 76791573 4.300000e-07 67.6


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 TraesCS2D01G387200 chr2D 492657237 492663884 6647 False 12277.000000 12277 100.000000 1 6648 1 chr2D.!!$F1 6647
1 TraesCS2D01G387200 chr2A 637975230 637981307 6077 False 3126.666667 5533 94.234333 6 5938 3 chr2A.!!$F1 5932
2 TraesCS2D01G387200 chr2B 578595590 578601684 6094 False 2230.500000 3306 93.067500 42 6002 4 chr2B.!!$F1 5960
3 TraesCS2D01G387200 chrUn 273399743 273400340 597 False 1066.000000 1066 98.831000 6050 6648 1 chrUn.!!$F2 598
4 TraesCS2D01G387200 chr5A 592851975 592852568 593 True 1018.000000 1018 97.496000 6051 6648 1 chr5A.!!$R2 597
5 TraesCS2D01G387200 chr5A 532847806 532848399 593 True 1002.000000 1002 96.995000 6051 6648 1 chr5A.!!$R1 597
6 TraesCS2D01G387200 chr5A 469907624 469908207 583 False 961.000000 961 96.013000 6048 6648 1 chr5A.!!$F1 600
7 TraesCS2D01G387200 chr6A 436477433 436478025 592 True 994.000000 994 96.828000 6051 6648 1 chr6A.!!$R1 597
8 TraesCS2D01G387200 chr4D 332789243 332789810 567 True 474.500000 599 96.508000 6050 6648 2 chr4D.!!$R1 598
9 TraesCS2D01G387200 chr4D 122259948 122261088 1140 False 422.000000 616 91.806000 6051 6648 2 chr4D.!!$F1 597
10 TraesCS2D01G387200 chr4B 411257591 411258158 567 True 469.000000 588 96.226500 6050 6648 2 chr4B.!!$R1 598

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
582 591 0.232303 GTGTTGTAGCACACGCAGTC 59.768 55.000 0.00 0.0 41.61 3.51 F
818 829 1.134907 CCATGGGAAGCAATGAACAGC 60.135 52.381 2.85 0.0 0.00 4.40 F
823 834 1.398390 GGAAGCAATGAACAGCTACCG 59.602 52.381 0.00 0.0 40.90 4.02 F
1010 1021 1.813513 AACAAAGAGATGGACGCAGG 58.186 50.000 0.00 0.0 0.00 4.85 F
1623 1634 4.281182 CGGTTTATGGCCTCTACACTAGAT 59.719 45.833 3.32 0.0 33.66 1.98 F
1951 1962 5.620205 GCGACTGTATATATCTGTCTGGTGG 60.620 48.000 14.29 0.0 33.64 4.61 F
3303 3611 2.340328 GGGCGGCTTTACAACCCTG 61.340 63.158 9.56 0.0 37.59 4.45 F
3476 3785 2.638363 ACTCCTCCACAGTTCCCTAAAC 59.362 50.000 0.00 0.0 38.21 2.01 F
4708 5053 1.135972 CGTGGTCTTGATCCAAAAGCG 60.136 52.381 0.00 0.0 36.68 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2698 1.913951 TTCATGCTGCCACGGGAGAT 61.914 55.000 9.03 0.00 35.50 2.75 R
2723 3028 0.390340 GAGACTTCGCATGACCAGCA 60.390 55.000 0.00 0.00 0.00 4.41 R
2877 3182 5.417580 GCCAACACAGACAATCCCTAAAATA 59.582 40.000 0.00 0.00 0.00 1.40 R
2983 3291 6.035650 CCTGCAAAATTATCAATGTTCAGCTG 59.964 38.462 7.63 7.63 0.00 4.24 R
3303 3611 2.684881 CCACTCAACAGCCAATATGTCC 59.315 50.000 0.00 0.00 0.00 4.02 R
3476 3785 3.176552 TGCAAATGTCCAACAACAAGG 57.823 42.857 0.00 0.00 31.81 3.61 R
4278 4623 0.534873 TATGCCACGCTGCACTTCTA 59.465 50.000 1.11 0.00 45.48 2.10 R
5388 5733 1.071542 CAAAAATGAACCCCACCCCAC 59.928 52.381 0.00 0.00 0.00 4.61 R
6229 7134 0.391228 TGGTGTGTCTATGTGCGTGT 59.609 50.000 0.00 0.00 0.00 4.49 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
32 33 6.590234 AGTTCTTGTTTTTACCATCCATCC 57.410 37.500 0.00 0.00 0.00 3.51
35 36 4.941263 TCTTGTTTTTACCATCCATCCGAG 59.059 41.667 0.00 0.00 0.00 4.63
37 38 5.110814 TGTTTTTACCATCCATCCGAGAT 57.889 39.130 0.00 0.00 0.00 2.75
39 40 6.288294 TGTTTTTACCATCCATCCGAGATAG 58.712 40.000 0.00 0.00 0.00 2.08
40 41 6.099125 TGTTTTTACCATCCATCCGAGATAGA 59.901 38.462 0.00 0.00 0.00 1.98
203 212 1.358152 CACCCTCCTGTACCTTTCCA 58.642 55.000 0.00 0.00 0.00 3.53
204 213 1.702957 CACCCTCCTGTACCTTTCCAA 59.297 52.381 0.00 0.00 0.00 3.53
393 402 2.401766 CGCAATCCTGGACACTGGC 61.402 63.158 0.00 0.00 35.80 4.85
469 478 0.249114 AAATTTTTCGCGTGCCGGTT 60.249 45.000 5.77 0.00 37.59 4.44
524 533 3.367806 CGTGCTCCCCATATCTCTGTATG 60.368 52.174 0.00 0.00 32.95 2.39
538 547 6.037786 TCTCTGTATGAAACCACGAATTCT 57.962 37.500 3.52 0.00 0.00 2.40
546 555 4.994852 TGAAACCACGAATTCTAGACCTTG 59.005 41.667 3.52 0.00 0.00 3.61
550 559 2.673368 CACGAATTCTAGACCTTGGTGC 59.327 50.000 13.12 0.00 0.00 5.01
551 560 1.927174 CGAATTCTAGACCTTGGTGCG 59.073 52.381 3.52 0.00 0.00 5.34
582 591 0.232303 GTGTTGTAGCACACGCAGTC 59.768 55.000 0.00 0.00 41.61 3.51
602 611 6.045318 CAGTCGTGGAGATCTGAATTTGTAT 58.955 40.000 0.00 0.00 33.07 2.29
608 617 6.203723 GTGGAGATCTGAATTTGTATGGCTAC 59.796 42.308 0.00 0.00 0.00 3.58
713 723 8.656849 CATCACTTTAGATGTTACAACAGTACC 58.343 37.037 0.84 0.00 43.04 3.34
814 825 3.385314 TGATCCATGGGAAGCAATGAA 57.615 42.857 13.02 0.00 34.34 2.57
818 829 1.134907 CCATGGGAAGCAATGAACAGC 60.135 52.381 2.85 0.00 0.00 4.40
823 834 1.398390 GGAAGCAATGAACAGCTACCG 59.602 52.381 0.00 0.00 40.90 4.02
982 993 2.618053 CGTTCCGATGCTCTTAAGGTT 58.382 47.619 1.85 0.00 0.00 3.50
1009 1020 3.904136 AAAACAAAGAGATGGACGCAG 57.096 42.857 0.00 0.00 0.00 5.18
1010 1021 1.813513 AACAAAGAGATGGACGCAGG 58.186 50.000 0.00 0.00 0.00 4.85
1275 1286 5.389935 CGAAGTCTATTCTGGCAAACTGTTC 60.390 44.000 0.00 0.00 0.00 3.18
1305 1316 9.174166 GACAGGAAAAATAAAAGTATAGGAGCA 57.826 33.333 0.00 0.00 0.00 4.26
1623 1634 4.281182 CGGTTTATGGCCTCTACACTAGAT 59.719 45.833 3.32 0.00 33.66 1.98
1839 1850 7.698130 GGTCGATCAATTAAAGTTTTCCATGAG 59.302 37.037 0.00 0.00 0.00 2.90
1887 1898 9.240159 GTAACTTTTGATGTTTTCACCGTAAAT 57.760 29.630 0.00 0.00 32.84 1.40
1951 1962 5.620205 GCGACTGTATATATCTGTCTGGTGG 60.620 48.000 14.29 0.00 33.64 4.61
2039 2050 7.224297 AGAAGATGATAGTACTCTCCTCTGTC 58.776 42.308 14.12 13.03 0.00 3.51
2192 2441 7.086376 TGATGTACTGACCTAAAACGTCTTAC 58.914 38.462 0.00 0.00 0.00 2.34
2201 2450 7.964011 TGACCTAAAACGTCTTACAAAAGTTTG 59.036 33.333 2.22 2.22 43.62 2.93
2270 2519 9.487790 ACATATTGGTGGTTAATTTTGAGTTTG 57.512 29.630 0.00 0.00 0.00 2.93
2271 2520 9.703892 CATATTGGTGGTTAATTTTGAGTTTGA 57.296 29.630 0.00 0.00 0.00 2.69
2272 2521 9.927668 ATATTGGTGGTTAATTTTGAGTTTGAG 57.072 29.630 0.00 0.00 0.00 3.02
2273 2522 6.783708 TGGTGGTTAATTTTGAGTTTGAGT 57.216 33.333 0.00 0.00 0.00 3.41
2274 2523 7.883391 TGGTGGTTAATTTTGAGTTTGAGTA 57.117 32.000 0.00 0.00 0.00 2.59
2275 2524 7.708998 TGGTGGTTAATTTTGAGTTTGAGTAC 58.291 34.615 0.00 0.00 0.00 2.73
2441 2698 9.135189 AGGCAATATGATTAGCATTTTAACTCA 57.865 29.630 0.00 0.00 38.44 3.41
3303 3611 2.340328 GGGCGGCTTTACAACCCTG 61.340 63.158 9.56 0.00 37.59 4.45
3339 3647 3.338250 TGGCTCCAATCCGGGCTT 61.338 61.111 0.00 0.00 32.99 4.35
3446 3755 9.620660 ATTTTGTTTCACTATTATCACGTTTCC 57.379 29.630 0.00 0.00 0.00 3.13
3476 3785 2.638363 ACTCCTCCACAGTTCCCTAAAC 59.362 50.000 0.00 0.00 38.21 2.01
3632 3970 5.250235 TCGGTTGTCAAAGTTGCATTTTA 57.750 34.783 0.00 0.00 0.00 1.52
3974 4318 8.267620 TCCACAGATAGTCAAATATGAATCCT 57.732 34.615 0.00 0.00 37.30 3.24
4112 4456 5.016051 TGCCTTTTGTAAGTTTGCATTCA 57.984 34.783 0.00 0.00 0.00 2.57
4152 4496 2.789409 ATGGTGTAGCTTTGTCCTCC 57.211 50.000 0.00 0.00 0.00 4.30
4159 4503 4.021368 GTGTAGCTTTGTCCTCCTAAGTCA 60.021 45.833 0.00 0.00 0.00 3.41
4290 4635 4.388773 TCAAGTATTTGTAGAAGTGCAGCG 59.611 41.667 0.00 0.00 35.73 5.18
4708 5053 1.135972 CGTGGTCTTGATCCAAAAGCG 60.136 52.381 0.00 0.00 36.68 4.68
4801 5146 2.290832 TGCATCATACTGGCCAAGAACA 60.291 45.455 7.01 3.34 0.00 3.18
4842 5187 5.586243 CCGATAGAAATTCAGTTGGTGTCAT 59.414 40.000 0.00 0.00 39.76 3.06
4843 5188 6.094048 CCGATAGAAATTCAGTTGGTGTCATT 59.906 38.462 0.00 0.00 39.76 2.57
5021 5366 3.430929 CCACCCTATCGAACTTCCTGAAG 60.431 52.174 5.37 5.37 43.79 3.02
5278 5623 3.641437 TTTGGTCGCCATCTTTCTTTG 57.359 42.857 0.00 0.00 31.53 2.77
5327 5672 1.265365 GCAACTTCTGTCCTTGCTCAC 59.735 52.381 0.00 0.00 35.89 3.51
5347 5692 5.837437 TCACGTTATTTTTCTGCCATGTTT 58.163 33.333 0.00 0.00 0.00 2.83
5383 5728 2.100605 AGAGCTTCCATTTGTCGTCC 57.899 50.000 0.00 0.00 0.00 4.79
5388 5733 2.437716 CCATTTGTCGTCCGGGGG 60.438 66.667 0.00 0.00 0.00 5.40
5485 5832 4.124970 GACTCGGTCTTAACTGTTTGGTT 58.875 43.478 0.00 0.00 33.20 3.67
5557 5904 2.044806 ATGGCTGTGGGATAGACGGC 62.045 60.000 0.00 0.00 43.79 5.68
5650 5997 6.687105 GGCAATGTAAACAGTCTATTTAAGCG 59.313 38.462 0.00 0.00 0.00 4.68
5654 6001 5.878116 TGTAAACAGTCTATTTAAGCGCCAT 59.122 36.000 2.29 0.00 0.00 4.40
5655 6002 4.882671 AACAGTCTATTTAAGCGCCATG 57.117 40.909 2.29 0.00 0.00 3.66
5657 6004 4.513442 ACAGTCTATTTAAGCGCCATGAA 58.487 39.130 2.29 0.00 0.00 2.57
5719 6066 6.112734 TCTGTTGTCACTTGTAACAGTTGAT 58.887 36.000 19.16 0.00 46.91 2.57
5753 6100 8.812147 TGTCTATATTATCGTTTACTTGCCAG 57.188 34.615 0.00 0.00 0.00 4.85
5779 6126 2.627737 GCGAGTGACTGGTCGGTCT 61.628 63.158 10.78 0.00 36.67 3.85
5900 6253 2.094762 TTTCCGCTTCAACCTAGAGC 57.905 50.000 0.00 0.00 0.00 4.09
5922 6275 2.825532 ACTTTGTTGACCACAGCTTGTT 59.174 40.909 0.00 0.00 36.48 2.83
5934 6287 1.273048 CAGCTTGTTAATTGCTGCCCA 59.727 47.619 12.13 0.00 45.76 5.36
5935 6288 2.093869 CAGCTTGTTAATTGCTGCCCAT 60.094 45.455 12.13 0.00 45.76 4.00
5936 6289 2.093869 AGCTTGTTAATTGCTGCCCATG 60.094 45.455 0.00 0.00 35.54 3.66
5939 6292 2.101783 TGTTAATTGCTGCCCATGAGG 58.898 47.619 0.00 0.00 39.47 3.86
5978 6335 5.353400 AGGTGCTTAGTAAAATAAACCGAGC 59.647 40.000 0.00 0.00 0.00 5.03
5980 6337 6.128090 GGTGCTTAGTAAAATAAACCGAGCTT 60.128 38.462 0.00 0.00 0.00 3.74
5983 6340 6.965500 GCTTAGTAAAATAAACCGAGCTTTCC 59.035 38.462 0.00 0.00 0.00 3.13
5986 6343 6.909909 AGTAAAATAAACCGAGCTTTCCTTG 58.090 36.000 0.00 0.00 0.00 3.61
5987 6344 6.713450 AGTAAAATAAACCGAGCTTTCCTTGA 59.287 34.615 0.00 0.00 0.00 3.02
5989 6346 1.239347 AAACCGAGCTTTCCTTGAGC 58.761 50.000 0.00 0.00 40.43 4.26
6002 6359 2.290916 TCCTTGAGCGCTTATCTCTACG 59.709 50.000 13.26 0.00 0.00 3.51
6003 6360 2.605823 CCTTGAGCGCTTATCTCTACGG 60.606 54.545 13.26 0.00 0.00 4.02
6004 6361 1.963172 TGAGCGCTTATCTCTACGGA 58.037 50.000 13.26 0.00 0.00 4.69
6005 6362 2.294979 TGAGCGCTTATCTCTACGGAA 58.705 47.619 13.26 0.00 0.00 4.30
6006 6363 2.290916 TGAGCGCTTATCTCTACGGAAG 59.709 50.000 13.26 0.00 0.00 3.46
6008 6365 3.474600 AGCGCTTATCTCTACGGAAGTA 58.525 45.455 2.64 0.00 46.88 2.24
6031 6388 9.921637 AGTATCTATTCTCTACAAATAAGCAGC 57.078 33.333 0.00 0.00 0.00 5.25
6032 6389 9.698309 GTATCTATTCTCTACAAATAAGCAGCA 57.302 33.333 0.00 0.00 0.00 4.41
6034 6391 9.790344 ATCTATTCTCTACAAATAAGCAGCATT 57.210 29.630 0.00 0.00 0.00 3.56
6035 6392 9.049523 TCTATTCTCTACAAATAAGCAGCATTG 57.950 33.333 0.00 0.00 0.00 2.82
6036 6393 7.870509 ATTCTCTACAAATAAGCAGCATTGA 57.129 32.000 0.00 0.00 0.00 2.57
6037 6394 6.915544 TCTCTACAAATAAGCAGCATTGAG 57.084 37.500 0.00 0.00 0.00 3.02
6038 6395 5.819379 TCTCTACAAATAAGCAGCATTGAGG 59.181 40.000 0.00 0.00 0.00 3.86
6039 6396 3.515330 ACAAATAAGCAGCATTGAGGC 57.485 42.857 0.00 0.00 0.00 4.70
6041 6398 4.272489 ACAAATAAGCAGCATTGAGGCTA 58.728 39.130 0.00 0.00 43.68 3.93
6042 6399 4.706476 ACAAATAAGCAGCATTGAGGCTAA 59.294 37.500 0.00 0.00 43.68 3.09
6043 6400 5.185635 ACAAATAAGCAGCATTGAGGCTAAA 59.814 36.000 0.00 0.00 43.68 1.85
6044 6401 5.511234 AATAAGCAGCATTGAGGCTAAAG 57.489 39.130 0.00 0.00 43.68 1.85
6045 6402 2.795231 AGCAGCATTGAGGCTAAAGA 57.205 45.000 0.00 0.00 43.68 2.52
6046 6403 3.077484 AGCAGCATTGAGGCTAAAGAA 57.923 42.857 0.00 0.00 43.68 2.52
6047 6404 3.424703 AGCAGCATTGAGGCTAAAGAAA 58.575 40.909 0.00 0.00 43.68 2.52
6048 6405 3.828451 AGCAGCATTGAGGCTAAAGAAAA 59.172 39.130 0.00 0.00 43.68 2.29
6069 6426 0.464452 ACTAGTAAGATGCCCGTGCC 59.536 55.000 0.00 0.00 36.33 5.01
6105 6462 5.247862 ACTATGCATGTGTTCAGATTGACA 58.752 37.500 10.16 0.00 0.00 3.58
6234 7139 7.075741 AGAATTTTTCAGTATTACACACACGC 58.924 34.615 0.00 0.00 0.00 5.34
6235 7140 5.736486 TTTTTCAGTATTACACACACGCA 57.264 34.783 0.00 0.00 0.00 5.24
6236 7141 4.718858 TTTCAGTATTACACACACGCAC 57.281 40.909 0.00 0.00 0.00 5.34
6237 7142 3.372660 TCAGTATTACACACACGCACA 57.627 42.857 0.00 0.00 0.00 4.57
6238 7143 3.920446 TCAGTATTACACACACGCACAT 58.080 40.909 0.00 0.00 0.00 3.21
6239 7144 5.061920 TCAGTATTACACACACGCACATA 57.938 39.130 0.00 0.00 0.00 2.29
6240 7145 5.099575 TCAGTATTACACACACGCACATAG 58.900 41.667 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.626302 TGGTAAAAACAAGAACTTTGTGGAG 58.374 36.000 0.00 0.00 32.22 3.86
2 3 6.591750 TGGTAAAAACAAGAACTTTGTGGA 57.408 33.333 0.00 0.00 32.22 4.02
3 4 6.478673 GGATGGTAAAAACAAGAACTTTGTGG 59.521 38.462 0.00 0.00 32.22 4.17
4 5 7.038659 TGGATGGTAAAAACAAGAACTTTGTG 58.961 34.615 0.00 0.00 32.22 3.33
18 19 5.839063 AGTCTATCTCGGATGGATGGTAAAA 59.161 40.000 3.91 0.00 0.00 1.52
32 33 8.750416 CAGAAATTATTGTGTCAGTCTATCTCG 58.250 37.037 0.00 0.00 0.00 4.04
37 38 7.823799 TGCATCAGAAATTATTGTGTCAGTCTA 59.176 33.333 0.00 0.00 31.97 2.59
39 40 6.845302 TGCATCAGAAATTATTGTGTCAGTC 58.155 36.000 0.00 0.00 31.97 3.51
40 41 6.432162 ACTGCATCAGAAATTATTGTGTCAGT 59.568 34.615 0.29 0.00 34.61 3.41
203 212 1.141185 GAAGGGATCGGGGAGGAATT 58.859 55.000 0.00 0.00 0.00 2.17
204 213 0.768609 GGAAGGGATCGGGGAGGAAT 60.769 60.000 0.00 0.00 0.00 3.01
334 343 2.442188 CGCGGTGAAGTAGGAACGC 61.442 63.158 0.00 0.00 43.15 4.84
393 402 3.564225 ACCAAAAGCTCGTACCTCAAAAG 59.436 43.478 0.00 0.00 0.00 2.27
469 478 2.596046 ATTGTTTGGCGGGTGCGA 60.596 55.556 0.00 0.00 44.10 5.10
477 486 1.604278 GGCGGATCTAGATTGTTTGGC 59.396 52.381 6.70 4.35 0.00 4.52
524 533 4.392138 CCAAGGTCTAGAATTCGTGGTTTC 59.608 45.833 12.50 0.00 0.00 2.78
538 547 0.108186 CAGATGCGCACCAAGGTCTA 60.108 55.000 14.90 0.00 0.00 2.59
546 555 0.179156 CACATTTCCAGATGCGCACC 60.179 55.000 14.90 0.66 0.00 5.01
550 559 2.995466 ACAACACATTTCCAGATGCG 57.005 45.000 0.00 0.00 0.00 4.73
551 560 3.191162 TGCTACAACACATTTCCAGATGC 59.809 43.478 0.00 0.00 0.00 3.91
578 587 4.248859 ACAAATTCAGATCTCCACGACTG 58.751 43.478 0.00 0.00 0.00 3.51
582 591 4.024556 GCCATACAAATTCAGATCTCCACG 60.025 45.833 0.00 0.00 0.00 4.94
602 611 3.788227 ACAATTCAACTCCTGTAGCCA 57.212 42.857 0.00 0.00 0.00 4.75
630 639 8.885052 CTAGTACCCTAGAACACCTTTTGTGGA 61.885 44.444 0.00 0.00 44.84 4.02
695 705 6.071560 CCTCACTGGTACTGTTGTAACATCTA 60.072 42.308 0.00 0.00 44.37 1.98
700 710 4.557205 CTCCTCACTGGTACTGTTGTAAC 58.443 47.826 0.00 0.00 38.84 2.50
703 713 1.344763 GCTCCTCACTGGTACTGTTGT 59.655 52.381 0.00 0.00 38.84 3.32
706 716 1.261480 CAGCTCCTCACTGGTACTGT 58.739 55.000 0.00 0.00 42.57 3.55
713 723 0.251077 AAAAGGGCAGCTCCTCACTG 60.251 55.000 3.14 0.00 35.80 3.66
872 883 9.092338 AGGATTGGCATAATTAAATAATCTGCA 57.908 29.630 16.20 0.00 36.64 4.41
944 955 3.515330 ACGGGTAAGGAGTTTGATACG 57.485 47.619 0.00 0.00 0.00 3.06
982 993 5.179368 CGTCCATCTCTTTGTTTTAAGCAGA 59.821 40.000 0.00 0.00 0.00 4.26
1009 1020 5.070981 TGGATGTTGGATTCTCTAGATCACC 59.929 44.000 0.00 0.00 0.00 4.02
1010 1021 6.041409 TCTGGATGTTGGATTCTCTAGATCAC 59.959 42.308 0.00 0.00 0.00 3.06
1305 1316 6.491062 TCTTGTTTGATGACAAATGACCATCT 59.509 34.615 15.64 0.00 45.71 2.90
1887 1898 3.492102 AGCAGTGCAAAAGGTAGAAGA 57.508 42.857 19.20 0.00 0.00 2.87
1951 1962 9.899226 AATAGAAGTTTCATGAAGCAAGTTTAC 57.101 29.630 22.26 9.37 0.00 2.01
1999 2010 9.727859 CTATCATCTTCTTCATGAGATTTCCAT 57.272 33.333 0.00 0.00 33.74 3.41
2192 2441 6.405278 AATTACTCCCTCCACAAACTTTTG 57.595 37.500 0.00 0.00 43.62 2.44
2231 2480 5.526111 CCACCAATATGTTTAAGACTACCCG 59.474 44.000 0.00 0.00 0.00 5.28
2441 2698 1.913951 TTCATGCTGCCACGGGAGAT 61.914 55.000 9.03 0.00 35.50 2.75
2463 2720 2.474410 AGCAGTACCCAAGTTAGCAC 57.526 50.000 0.00 0.00 0.00 4.40
2464 2721 4.469945 AGATTAGCAGTACCCAAGTTAGCA 59.530 41.667 0.00 0.00 0.00 3.49
2723 3028 0.390340 GAGACTTCGCATGACCAGCA 60.390 55.000 0.00 0.00 0.00 4.41
2877 3182 5.417580 GCCAACACAGACAATCCCTAAAATA 59.582 40.000 0.00 0.00 0.00 1.40
2983 3291 6.035650 CCTGCAAAATTATCAATGTTCAGCTG 59.964 38.462 7.63 7.63 0.00 4.24
3303 3611 2.684881 CCACTCAACAGCCAATATGTCC 59.315 50.000 0.00 0.00 0.00 4.02
3339 3647 5.470437 TGAAACAGTTGTGCCGAAATGTATA 59.530 36.000 0.00 0.00 33.20 1.47
3446 3755 5.242838 GGAACTGTGGAGGAGTATATCAGAG 59.757 48.000 0.00 0.00 0.00 3.35
3476 3785 3.176552 TGCAAATGTCCAACAACAAGG 57.823 42.857 0.00 0.00 31.81 3.61
3611 3920 5.277825 TCTAAAATGCAACTTTGACAACCG 58.722 37.500 7.26 0.00 0.00 4.44
3632 3970 6.155910 AGACATTAGACATTGACATGGTCTCT 59.844 38.462 11.52 2.72 34.27 3.10
3873 4214 7.763985 TGGTTATCCATATGCATGTTCGTATAG 59.236 37.037 10.16 0.00 39.03 1.31
3891 4232 8.686334 ACATTTTAGACATTGACATGGTTATCC 58.314 33.333 0.00 0.00 34.27 2.59
4112 4456 5.420104 CCATTTGCTCAGGGAACTTTAGATT 59.580 40.000 0.00 0.00 40.21 2.40
4159 4503 8.180267 CGCAGATCTTGAAACTCATTAAGAATT 58.820 33.333 0.00 0.00 33.39 2.17
4212 4556 3.741344 CAGTTATGGCAGATAAGGTACGC 59.259 47.826 0.00 0.00 0.00 4.42
4213 4557 3.741344 GCAGTTATGGCAGATAAGGTACG 59.259 47.826 0.00 0.00 0.00 3.67
4224 4569 4.486125 TTCTATGTCTGCAGTTATGGCA 57.514 40.909 14.67 0.00 39.32 4.92
4278 4623 0.534873 TATGCCACGCTGCACTTCTA 59.465 50.000 1.11 0.00 45.48 2.10
4290 4635 3.923017 ACTTTTTCAGTGCTATGCCAC 57.077 42.857 0.00 0.00 32.83 5.01
4708 5053 1.334869 CTGCCCATAGATTGCCGTTTC 59.665 52.381 0.00 0.00 0.00 2.78
4842 5187 7.497595 AGATAACCGTGTATCATTAGAAGCAA 58.502 34.615 5.64 0.00 33.60 3.91
4843 5188 7.050970 AGATAACCGTGTATCATTAGAAGCA 57.949 36.000 5.64 0.00 33.60 3.91
4978 5323 2.361737 GGCTCCCAAGTTGGCTCC 60.362 66.667 17.07 12.23 35.79 4.70
5021 5366 5.784177 TCCGATTTCTATATCTTCTGGTGC 58.216 41.667 0.00 0.00 0.00 5.01
5278 5623 5.072741 ACCTTCACATATTCCACATATGGC 58.927 41.667 7.80 0.00 46.80 4.40
5327 5672 6.949578 ATGAAACATGGCAGAAAAATAACG 57.050 33.333 0.00 0.00 0.00 3.18
5347 5692 5.266733 AGCTCTTCAAAAAGCACAAATGA 57.733 34.783 0.00 0.00 41.06 2.57
5388 5733 1.071542 CAAAAATGAACCCCACCCCAC 59.928 52.381 0.00 0.00 0.00 4.61
5485 5832 3.996363 CTGATTTCACCTGTCAATGTCGA 59.004 43.478 0.00 0.00 0.00 4.20
5650 5997 1.099879 AAGCTCGGCAGATTCATGGC 61.100 55.000 0.00 0.00 42.07 4.40
5655 6002 0.458543 TCGTGAAGCTCGGCAGATTC 60.459 55.000 7.64 7.64 44.12 2.52
5657 6004 1.140589 CTCGTGAAGCTCGGCAGAT 59.859 57.895 0.00 0.00 0.00 2.90
5753 6100 1.373497 CAGTCACTCGCACCCTCAC 60.373 63.158 0.00 0.00 0.00 3.51
5779 6126 2.611751 CAGAACCGTCACAACATTGTCA 59.388 45.455 0.00 0.00 39.91 3.58
5900 6253 2.164219 ACAAGCTGTGGTCAACAAAGTG 59.836 45.455 0.00 0.00 38.67 3.16
5931 6284 2.026641 CATTGTACAAGGCCTCATGGG 58.973 52.381 14.65 0.00 38.36 4.00
5934 6287 2.512692 TGCATTGTACAAGGCCTCAT 57.487 45.000 34.56 6.30 46.35 2.90
5935 6288 2.161855 CTTGCATTGTACAAGGCCTCA 58.838 47.619 34.56 21.00 46.35 3.86
5936 6289 2.927553 CTTGCATTGTACAAGGCCTC 57.072 50.000 34.56 14.50 46.35 4.70
5978 6335 3.791245 AGAGATAAGCGCTCAAGGAAAG 58.209 45.455 12.06 0.00 34.85 2.62
5980 6337 3.243101 CGTAGAGATAAGCGCTCAAGGAA 60.243 47.826 12.06 0.00 34.85 3.36
5983 6340 2.290916 TCCGTAGAGATAAGCGCTCAAG 59.709 50.000 12.06 0.00 34.85 3.02
5986 6343 2.291190 ACTTCCGTAGAGATAAGCGCTC 59.709 50.000 12.06 0.00 0.00 5.03
5987 6344 2.299521 ACTTCCGTAGAGATAAGCGCT 58.700 47.619 2.64 2.64 0.00 5.92
5989 6346 5.866335 AGATACTTCCGTAGAGATAAGCG 57.134 43.478 0.00 0.00 0.00 4.68
6005 6362 9.921637 GCTGCTTATTTGTAGAGAATAGATACT 57.078 33.333 0.00 0.00 0.00 2.12
6006 6363 9.698309 TGCTGCTTATTTGTAGAGAATAGATAC 57.302 33.333 0.00 0.00 0.00 2.24
6008 6365 9.790344 AATGCTGCTTATTTGTAGAGAATAGAT 57.210 29.630 0.00 0.00 0.00 1.98
6009 6366 9.049523 CAATGCTGCTTATTTGTAGAGAATAGA 57.950 33.333 0.00 0.00 0.00 1.98
6010 6367 9.049523 TCAATGCTGCTTATTTGTAGAGAATAG 57.950 33.333 0.00 0.00 0.00 1.73
6011 6368 8.962884 TCAATGCTGCTTATTTGTAGAGAATA 57.037 30.769 0.00 0.00 0.00 1.75
6012 6369 7.013083 CCTCAATGCTGCTTATTTGTAGAGAAT 59.987 37.037 0.00 0.00 0.00 2.40
6013 6370 6.317140 CCTCAATGCTGCTTATTTGTAGAGAA 59.683 38.462 0.00 0.00 0.00 2.87
6014 6371 5.819379 CCTCAATGCTGCTTATTTGTAGAGA 59.181 40.000 0.00 0.00 0.00 3.10
6015 6372 5.505324 GCCTCAATGCTGCTTATTTGTAGAG 60.505 44.000 0.00 0.00 0.00 2.43
6016 6373 4.336433 GCCTCAATGCTGCTTATTTGTAGA 59.664 41.667 0.00 0.00 0.00 2.59
6017 6374 4.337555 AGCCTCAATGCTGCTTATTTGTAG 59.662 41.667 0.00 1.13 40.90 2.74
6018 6375 4.272489 AGCCTCAATGCTGCTTATTTGTA 58.728 39.130 0.00 0.00 40.90 2.41
6019 6376 3.094572 AGCCTCAATGCTGCTTATTTGT 58.905 40.909 0.00 0.00 40.90 2.83
6020 6377 3.795623 AGCCTCAATGCTGCTTATTTG 57.204 42.857 0.00 0.40 40.90 2.32
6021 6378 5.653769 TCTTTAGCCTCAATGCTGCTTATTT 59.346 36.000 0.00 0.00 42.77 1.40
6022 6379 5.195940 TCTTTAGCCTCAATGCTGCTTATT 58.804 37.500 0.00 0.00 42.77 1.40
6023 6380 4.785301 TCTTTAGCCTCAATGCTGCTTAT 58.215 39.130 0.00 0.00 42.77 1.73
6024 6381 4.220693 TCTTTAGCCTCAATGCTGCTTA 57.779 40.909 0.00 0.00 42.77 3.09
6025 6382 3.077484 TCTTTAGCCTCAATGCTGCTT 57.923 42.857 0.00 0.00 42.77 3.91
6026 6383 2.795231 TCTTTAGCCTCAATGCTGCT 57.205 45.000 0.00 2.25 42.77 4.24
6027 6384 3.855689 TTTCTTTAGCCTCAATGCTGC 57.144 42.857 0.00 0.00 42.77 5.25
6046 6403 3.439129 GCACGGGCATCTTACTAGTTTTT 59.561 43.478 3.77 0.00 40.72 1.94
6047 6404 3.007635 GCACGGGCATCTTACTAGTTTT 58.992 45.455 3.77 0.00 40.72 2.43
6048 6405 2.629051 GCACGGGCATCTTACTAGTTT 58.371 47.619 3.77 0.00 40.72 2.66
6105 6462 5.549228 ACATACATGGGATGACCTGACATAT 59.451 40.000 14.77 0.00 41.11 1.78
6227 7132 1.497991 GTGTGTCTATGTGCGTGTGT 58.502 50.000 0.00 0.00 0.00 3.72
6228 7133 0.790207 GGTGTGTCTATGTGCGTGTG 59.210 55.000 0.00 0.00 0.00 3.82
6229 7134 0.391228 TGGTGTGTCTATGTGCGTGT 59.609 50.000 0.00 0.00 0.00 4.49
6230 7135 1.725641 ATGGTGTGTCTATGTGCGTG 58.274 50.000 0.00 0.00 0.00 5.34
6231 7136 2.734175 CGTATGGTGTGTCTATGTGCGT 60.734 50.000 0.00 0.00 0.00 5.24
6232 7137 1.852280 CGTATGGTGTGTCTATGTGCG 59.148 52.381 0.00 0.00 0.00 5.34
6233 7138 2.201732 CCGTATGGTGTGTCTATGTGC 58.798 52.381 0.00 0.00 0.00 4.57
6234 7139 2.821546 CCCGTATGGTGTGTCTATGTG 58.178 52.381 0.00 0.00 0.00 3.21
6235 7140 1.138266 GCCCGTATGGTGTGTCTATGT 59.862 52.381 0.00 0.00 36.04 2.29
6236 7141 1.412710 AGCCCGTATGGTGTGTCTATG 59.587 52.381 0.00 0.00 36.04 2.23
6237 7142 1.412710 CAGCCCGTATGGTGTGTCTAT 59.587 52.381 0.00 0.00 36.04 1.98
6238 7143 0.821517 CAGCCCGTATGGTGTGTCTA 59.178 55.000 0.00 0.00 36.04 2.59
6239 7144 1.596934 CAGCCCGTATGGTGTGTCT 59.403 57.895 0.00 0.00 36.04 3.41
6240 7145 1.449601 CCAGCCCGTATGGTGTGTC 60.450 63.158 0.00 0.00 36.04 3.67
6379 7304 1.464997 GGTTGACGATGCTCTTGTTCC 59.535 52.381 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.