Multiple sequence alignment - TraesCS4B01G043900

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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 TraesCS4B01G043900 chr4B 100.000 4529 0 0 1 4529 31878685 31874157 0.000000e+00 8364
1 TraesCS4B01G043900 chr4D 94.648 4204 146 35 12 4154 19411017 19406832 0.000000e+00 6444
2 TraesCS4B01G043900 chr4D 79.882 338 44 13 4208 4527 19406814 19406483 4.560000e-55 226
3 TraesCS4B01G043900 chr4D 98.485 66 1 0 5 70 19411592 19411527 2.860000e-22 117
4 TraesCS4B01G043900 chr4A 95.628 3797 125 24 586 4362 581481110 581484885 0.000000e+00 6054
5 TraesCS4B01G043900 chr4A 87.981 208 15 4 188 394 581480792 581480990 2.110000e-58 237
6 TraesCS4B01G043900 chr4A 88.525 122 11 3 4397 4515 581484969 581485090 1.310000e-30 145
7 TraesCS4B01G043900 chr5B 81.930 1876 296 26 1373 3231 96757757 96755908 0.000000e+00 1546
8 TraesCS4B01G043900 chr6B 81.518 1423 256 5 1816 3233 636212529 636213949 0.000000e+00 1164
9 TraesCS4B01G043900 chr6B 81.237 1423 260 5 1816 3233 636186101 636187521 0.000000e+00 1142
10 TraesCS4B01G043900 chr5A 83.679 1207 161 23 1373 2567 85148277 85147095 0.000000e+00 1105
11 TraesCS4B01G043900 chr1A 79.636 275 31 12 1452 1712 574392957 574393220 1.670000e-39 174
12 TraesCS4B01G043900 chr1D 78.909 275 30 14 1457 1712 478181116 478181381 1.300000e-35 161
13 TraesCS4B01G043900 chr1B 79.839 248 29 11 1476 1712 665437643 665437880 1.300000e-35 161


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 TraesCS4B01G043900 chr4B 31874157 31878685 4528 True 8364.000000 8364 100.000000 1 4529 1 chr4B.!!$R1 4528
1 TraesCS4B01G043900 chr4D 19406483 19411592 5109 True 2262.333333 6444 91.005000 5 4527 3 chr4D.!!$R1 4522
2 TraesCS4B01G043900 chr4A 581480792 581485090 4298 False 2145.333333 6054 90.711333 188 4515 3 chr4A.!!$F1 4327
3 TraesCS4B01G043900 chr5B 96755908 96757757 1849 True 1546.000000 1546 81.930000 1373 3231 1 chr5B.!!$R1 1858
4 TraesCS4B01G043900 chr6B 636212529 636213949 1420 False 1164.000000 1164 81.518000 1816 3233 1 chr6B.!!$F2 1417
5 TraesCS4B01G043900 chr6B 636186101 636187521 1420 False 1142.000000 1142 81.237000 1816 3233 1 chr6B.!!$F1 1417
6 TraesCS4B01G043900 chr5A 85147095 85148277 1182 True 1105.000000 1105 83.679000 1373 2567 1 chr5A.!!$R1 1194

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
697 1269 0.902531 ATCGACCGGTTCAGGACAAT 59.097 50.000 9.42 0.0 34.73 2.71 F
2597 3250 2.034687 ACCATGCCACCTGCTGTC 59.965 61.111 0.00 0.0 42.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3050 3706 6.875726 TGTTATCCAGAGTCAAGAATGAAGTG 59.124 38.462 0.0 0.0 37.30 3.16 R
4199 4869 1.003464 GCCAAATGGGTCAGCCAAAAT 59.997 47.619 0.0 0.0 39.65 1.82 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
71 640 1.354031 AGTGGCCCATTGACACATACA 59.646 47.619 0.00 0.00 37.58 2.29
82 651 9.001542 CCCATTGACACATACATTTTCAAAAAT 57.998 29.630 0.00 0.00 39.07 1.82
368 938 8.758829 TGTGTGTATCTTGAAGAGTAATATGGT 58.241 33.333 0.00 0.00 0.00 3.55
497 1069 7.628234 AGAAAAGATCTTCATGTACTCACCAT 58.372 34.615 8.78 0.00 33.39 3.55
650 1222 4.329545 GACTGGGTGGCTTCGGCA 62.330 66.667 0.00 0.00 43.96 5.69
655 1227 4.660938 GGTGGCTTCGGCAAGGGT 62.661 66.667 0.00 0.00 43.96 4.34
697 1269 0.902531 ATCGACCGGTTCAGGACAAT 59.097 50.000 9.42 0.00 34.73 2.71
710 1282 4.450976 TCAGGACAATGAACATAATCCCG 58.549 43.478 11.29 4.75 0.00 5.14
728 1300 5.277857 TCCCGAGGACTTTGATCTATTTC 57.722 43.478 0.00 0.00 0.00 2.17
837 1412 2.044352 GGCCGGCCCAATAACACT 60.044 61.111 36.64 0.00 0.00 3.55
851 1426 2.172483 AACACTACGCTCCAGGCTGG 62.172 60.000 28.01 28.01 39.43 4.85
1367 1972 4.117661 GACCGCGACGAGCCTTCT 62.118 66.667 8.23 0.00 44.76 2.85
2597 3250 2.034687 ACCATGCCACCTGCTGTC 59.965 61.111 0.00 0.00 42.00 3.51
3255 3912 0.107945 GCCGCAGAAGAGGTGAGATT 60.108 55.000 0.00 0.00 37.01 2.40
3309 3966 8.877779 TCTACTGTGTCGAGATTTAGTACTTAC 58.122 37.037 0.00 0.00 0.00 2.34
3360 4017 7.452562 ACCATTATCTTTTCCTGTTTGCAAAT 58.547 30.769 16.21 0.00 0.00 2.32
3381 4039 8.193438 GCAAATCAGCCTTTCTATTTCTGTAAT 58.807 33.333 0.00 0.00 0.00 1.89
3634 4300 8.306761 GGAGATTTATGTGGTTCTTTCAACATT 58.693 33.333 0.00 0.00 0.00 2.71
3666 4332 5.966742 AGAGGTGCCAACTTTCTTATTTC 57.033 39.130 0.00 0.00 0.00 2.17
3668 4334 4.740902 AGGTGCCAACTTTCTTATTTCCT 58.259 39.130 0.00 0.00 0.00 3.36
3709 4375 6.039616 GCACTTCAGTATTCAGTTCTAGAGG 58.960 44.000 0.00 0.00 0.00 3.69
3762 4428 7.657336 TGTAAAATGAGACTTGAAAATGACCC 58.343 34.615 0.00 0.00 0.00 4.46
3773 4439 1.767759 AAATGACCCAGCTACCATGC 58.232 50.000 0.00 0.00 0.00 4.06
3868 4535 2.535574 GCTTTTGTTTGGCTCAACTTCG 59.464 45.455 2.52 0.00 0.00 3.79
3878 4545 2.417515 GGCTCAACTTCGGAGTTCTAGG 60.418 54.545 5.99 0.00 44.14 3.02
3898 4565 2.355756 GGCAATGATTATGAGTGTGCGT 59.644 45.455 0.00 0.00 0.00 5.24
3984 4651 8.335356 CCATTACTTATAGTCATTCGTTGTTGG 58.665 37.037 0.00 0.00 0.00 3.77
3999 4666 5.180492 TCGTTGTTGGTTCTATGGATTGAAC 59.820 40.000 5.65 5.65 40.28 3.18
4106 4776 2.522836 TTGCGTTTGTTGATTGCCAT 57.477 40.000 0.00 0.00 0.00 4.40
4134 4804 7.257003 TGATAAAATATGTGTCACAATGTGCC 58.743 34.615 10.28 0.00 32.98 5.01
4146 4816 4.018870 TCACAATGTGCCTGAGGGTAATAA 60.019 41.667 8.78 0.00 32.98 1.40
4149 4819 3.627395 TGTGCCTGAGGGTAATAACTG 57.373 47.619 0.00 0.00 34.45 3.16
4163 4833 9.448587 AGGGTAATAACTGGTAAGAGTAATGAT 57.551 33.333 0.00 0.00 0.00 2.45
4203 4873 7.965718 TGGAAGTTCCATCTGATTGAAATTTT 58.034 30.769 21.05 7.39 42.67 1.82
4206 4876 6.168389 AGTTCCATCTGATTGAAATTTTGGC 58.832 36.000 5.81 0.00 0.00 4.52
4270 4950 3.253188 TGCATACTGCTGAAACCAAAGAC 59.747 43.478 0.00 0.00 45.31 3.01
4289 4969 5.636903 AGACATTGTGCTGGATAACCTAT 57.363 39.130 0.00 0.00 37.04 2.57
4314 4994 9.897744 ATTCTGTTGTGTGTTTATGATGTAAAG 57.102 29.630 0.00 0.00 0.00 1.85
4357 5038 2.683968 TCAGATCGTAGGTGTTTGTGC 58.316 47.619 0.00 0.00 0.00 4.57
4362 5043 1.141645 CGTAGGTGTTTGTGCGCTTA 58.858 50.000 9.73 0.00 0.00 3.09
4363 5044 1.126113 CGTAGGTGTTTGTGCGCTTAG 59.874 52.381 9.73 0.00 0.00 2.18
4366 5047 0.941542 GGTGTTTGTGCGCTTAGACA 59.058 50.000 9.73 6.34 0.00 3.41
4368 5049 2.031157 GGTGTTTGTGCGCTTAGACAAT 60.031 45.455 9.73 0.00 32.27 2.71
4383 5093 7.201350 CGCTTAGACAATTTTAGAAATTGCACC 60.201 37.037 20.23 12.59 40.35 5.01
4390 5100 4.390129 TTTAGAAATTGCACCCCCACTA 57.610 40.909 0.00 0.00 0.00 2.74
4402 5112 2.585432 ACCCCCACTATTGCCTGTTAAT 59.415 45.455 0.00 0.00 0.00 1.40
4403 5113 3.789274 ACCCCCACTATTGCCTGTTAATA 59.211 43.478 0.00 0.00 0.00 0.98
4404 5114 4.418863 ACCCCCACTATTGCCTGTTAATAT 59.581 41.667 0.00 0.00 0.00 1.28
4405 5115 5.103258 ACCCCCACTATTGCCTGTTAATATT 60.103 40.000 0.00 0.00 0.00 1.28
4406 5116 5.838521 CCCCCACTATTGCCTGTTAATATTT 59.161 40.000 0.00 0.00 0.00 1.40
4407 5117 6.015434 CCCCCACTATTGCCTGTTAATATTTC 60.015 42.308 0.00 0.00 0.00 2.17
4408 5118 6.777580 CCCCACTATTGCCTGTTAATATTTCT 59.222 38.462 0.00 0.00 0.00 2.52
4417 5149 9.474920 TTGCCTGTTAATATTTCTGAGTTTTTG 57.525 29.630 0.00 0.00 0.00 2.44
4458 5190 3.020984 TGGCATTTTTAAGACGGATCCC 58.979 45.455 6.06 0.00 0.00 3.85
4479 5212 7.265599 TCCCATTTTCAACTATAGTCCTTCA 57.734 36.000 5.70 0.00 0.00 3.02
4517 5251 1.479757 GCTGGAAACCCTAAACCCACA 60.480 52.381 0.00 0.00 0.00 4.17
4518 5252 2.821625 GCTGGAAACCCTAAACCCACAT 60.822 50.000 0.00 0.00 0.00 3.21
4520 5254 4.668636 CTGGAAACCCTAAACCCACATAA 58.331 43.478 0.00 0.00 0.00 1.90
4527 5261 3.245839 CCCTAAACCCACATAACCCCTTT 60.246 47.826 0.00 0.00 0.00 3.11
4528 5262 4.021229 CCTAAACCCACATAACCCCTTTC 58.979 47.826 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.627699 CAGGCTTCCTCTCATCTACTCC 59.372 54.545 0.00 0.00 0.00 3.85
1 2 2.035832 GCAGGCTTCCTCTCATCTACTC 59.964 54.545 0.00 0.00 0.00 2.59
2 3 2.038659 GCAGGCTTCCTCTCATCTACT 58.961 52.381 0.00 0.00 0.00 2.57
3 4 1.069978 GGCAGGCTTCCTCTCATCTAC 59.930 57.143 0.00 0.00 0.00 2.59
650 1222 1.066573 CGCTGAAGATGTCTCACCCTT 60.067 52.381 0.00 0.00 0.00 3.95
655 1227 1.153765 CGCCGCTGAAGATGTCTCA 60.154 57.895 0.00 0.00 0.00 3.27
697 1269 4.224147 TCAAAGTCCTCGGGATTATGTTCA 59.776 41.667 0.00 0.00 32.73 3.18
706 1278 4.101119 GGAAATAGATCAAAGTCCTCGGGA 59.899 45.833 0.00 0.00 0.00 5.14
710 1282 4.819088 GCCTGGAAATAGATCAAAGTCCTC 59.181 45.833 0.00 0.00 0.00 3.71
728 1300 2.029623 ACTAGTGGTACATACGCCTGG 58.970 52.381 0.00 0.00 44.52 4.45
793 1368 9.783256 CAATAACTAGGTACTTTGCCATTTTAC 57.217 33.333 0.00 0.00 41.75 2.01
794 1369 8.962679 CCAATAACTAGGTACTTTGCCATTTTA 58.037 33.333 0.00 0.00 41.75 1.52
851 1426 0.668535 GGGCCGCATTAGATTGGAAC 59.331 55.000 0.00 0.00 0.00 3.62
878 1457 1.025113 GCTTGGGCCGTAAGAGGAAC 61.025 60.000 19.30 1.13 43.02 3.62
957 1540 2.983592 GTTTGCGGACAGGTGGGG 60.984 66.667 0.00 0.00 0.00 4.96
1002 1586 2.657944 GCAGAGCGAGGAGATGCG 60.658 66.667 0.00 0.00 35.87 4.73
1046 1630 1.218047 CTCCATGGCGTCGAAGGAA 59.782 57.895 6.96 0.00 0.00 3.36
3050 3706 6.875726 TGTTATCCAGAGTCAAGAATGAAGTG 59.124 38.462 0.00 0.00 37.30 3.16
3255 3912 3.561313 GCCCTGAATTGTACCCAAGAAGA 60.561 47.826 0.00 0.00 33.17 2.87
3309 3966 7.747888 TCAATTGTTATGATGTTTGTACCTCG 58.252 34.615 5.13 0.00 0.00 4.63
3360 4017 9.823647 CTTAGATTACAGAAATAGAAAGGCTGA 57.176 33.333 0.00 0.00 0.00 4.26
3634 4300 4.353777 AGTTGGCACCTCTTGAGACTATA 58.646 43.478 0.00 0.00 0.00 1.31
3635 4301 3.177228 AGTTGGCACCTCTTGAGACTAT 58.823 45.455 0.00 0.00 0.00 2.12
3675 4341 7.225538 ACTGAATACTGAAGTGCATATAACAGC 59.774 37.037 0.00 0.00 0.00 4.40
3676 4342 8.654230 ACTGAATACTGAAGTGCATATAACAG 57.346 34.615 0.00 0.00 0.00 3.16
3678 4344 9.319143 AGAACTGAATACTGAAGTGCATATAAC 57.681 33.333 0.00 0.00 0.00 1.89
3681 4347 8.918116 TCTAGAACTGAATACTGAAGTGCATAT 58.082 33.333 0.00 0.00 0.00 1.78
3738 4404 7.657336 TGGGTCATTTTCAAGTCTCATTTTAC 58.343 34.615 0.00 0.00 0.00 2.01
3756 4422 1.281199 TGGCATGGTAGCTGGGTCAT 61.281 55.000 0.00 0.00 34.17 3.06
3785 4452 8.821686 ATTATAATGAGACCCAACACAATCAA 57.178 30.769 0.00 0.00 0.00 2.57
3786 4453 8.821686 AATTATAATGAGACCCAACACAATCA 57.178 30.769 0.00 0.00 0.00 2.57
3825 4492 9.466497 AAAGCACTTTCTATCCATTCTTGAATA 57.534 29.630 0.00 0.00 0.00 1.75
3868 4535 6.426328 CACTCATAATCATTGCCTAGAACTCC 59.574 42.308 0.00 0.00 0.00 3.85
3878 4545 3.680642 ACGCACACTCATAATCATTGC 57.319 42.857 0.00 0.00 0.00 3.56
3898 4565 1.055849 TCAACAGGCTTCAGCACCTA 58.944 50.000 0.30 0.00 44.36 3.08
3977 4644 6.575162 AGTTCAATCCATAGAACCAACAAC 57.425 37.500 0.00 0.00 43.89 3.32
3984 4651 9.003658 TCTCTCAAAAAGTTCAATCCATAGAAC 57.996 33.333 0.00 0.00 43.33 3.01
3999 4666 6.919721 ACTCTAGCTGTACTCTCTCAAAAAG 58.080 40.000 0.00 0.00 0.00 2.27
4063 4733 1.206610 ACAGAGCAGAGCACGATCAAT 59.793 47.619 0.00 0.00 0.00 2.57
4106 4776 9.623350 CACATTGTGACACATATTTTATCAACA 57.377 29.630 11.45 0.00 35.23 3.33
4134 4804 6.793505 ACTCTTACCAGTTATTACCCTCAG 57.206 41.667 0.00 0.00 0.00 3.35
4163 4833 7.689299 TGGAACTTCCAATTCTCTCTGATAAA 58.311 34.615 8.15 0.00 45.00 1.40
4166 4836 5.768980 TGGAACTTCCAATTCTCTCTGAT 57.231 39.130 8.15 0.00 45.00 2.90
4198 4868 2.552809 GCCAAATGGGTCAGCCAAAATT 60.553 45.455 0.00 0.00 39.65 1.82
4199 4869 1.003464 GCCAAATGGGTCAGCCAAAAT 59.997 47.619 0.00 0.00 39.65 1.82
4203 4873 2.283821 GGCCAAATGGGTCAGCCA 60.284 61.111 0.00 0.00 42.53 4.75
4270 4950 5.824624 ACAGAATAGGTTATCCAGCACAATG 59.175 40.000 0.00 0.00 35.89 2.82
4289 4969 8.898761 ACTTTACATCATAAACACACAACAGAA 58.101 29.630 0.00 0.00 0.00 3.02
4314 4994 6.697455 TGATCTTCACAAAGTATATCTGCGAC 59.303 38.462 0.00 0.00 33.95 5.19
4326 5006 5.518128 CACCTACGATCTGATCTTCACAAAG 59.482 44.000 15.16 0.88 0.00 2.77
4357 5038 7.201350 GGTGCAATTTCTAAAATTGTCTAAGCG 60.201 37.037 20.33 0.82 39.25 4.68
4362 5043 5.279960 GGGGGTGCAATTTCTAAAATTGTCT 60.280 40.000 20.33 0.00 39.25 3.41
4363 5044 4.935205 GGGGGTGCAATTTCTAAAATTGTC 59.065 41.667 20.33 14.91 39.25 3.18
4366 5047 4.597075 AGTGGGGGTGCAATTTCTAAAATT 59.403 37.500 0.00 0.00 0.00 1.82
4368 5049 3.582164 AGTGGGGGTGCAATTTCTAAAA 58.418 40.909 0.00 0.00 0.00 1.52
4383 5093 6.777580 AGAAATATTAACAGGCAATAGTGGGG 59.222 38.462 0.00 0.00 0.00 4.96
4402 5112 9.559732 TCACTGAAGATCAAAAACTCAGAAATA 57.440 29.630 4.49 0.00 0.00 1.40
4403 5113 8.455903 TCACTGAAGATCAAAAACTCAGAAAT 57.544 30.769 4.49 0.00 0.00 2.17
4404 5114 7.864108 TCACTGAAGATCAAAAACTCAGAAA 57.136 32.000 4.49 0.00 0.00 2.52
4405 5115 7.770433 TCTTCACTGAAGATCAAAAACTCAGAA 59.230 33.333 16.22 0.00 42.78 3.02
4406 5116 7.275183 TCTTCACTGAAGATCAAAAACTCAGA 58.725 34.615 16.22 0.00 42.78 3.27
4407 5117 7.488187 TCTTCACTGAAGATCAAAAACTCAG 57.512 36.000 16.22 0.00 42.78 3.35
4408 5118 7.864108 TTCTTCACTGAAGATCAAAAACTCA 57.136 32.000 19.96 1.18 46.20 3.41
4417 5149 5.356190 TGCCATCATTTCTTCACTGAAGATC 59.644 40.000 19.96 5.54 46.20 2.75
4452 5184 6.842676 AGGACTATAGTTGAAAATGGGATCC 58.157 40.000 6.88 1.92 0.00 3.36
4453 5185 7.993183 TGAAGGACTATAGTTGAAAATGGGATC 59.007 37.037 6.88 0.00 0.00 3.36
4458 5190 8.237267 GGTGTTGAAGGACTATAGTTGAAAATG 58.763 37.037 6.88 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.