Multiple sequence alignment - TraesCS5A01G015900

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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 TraesCS5A01G015900 chr5A 100.000 4636 0 0 1001 5636 11514972 11519607 0.000000e+00 8562.0
1 TraesCS5A01G015900 chr5A 100.000 404 0 0 1 404 11513972 11514375 0.000000e+00 747.0
2 TraesCS5A01G015900 chr5A 88.235 153 13 5 1006 1155 11371727 11371877 1.610000e-40 178.0
3 TraesCS5A01G015900 chr5A 85.294 102 7 6 2834 2927 30409871 30409770 1.290000e-16 99.0
4 TraesCS5A01G015900 chr5D 96.516 4650 125 13 1001 5636 14965340 14969966 0.000000e+00 7655.0
5 TraesCS5A01G015900 chr5D 92.365 406 25 5 1 404 14964881 14965282 1.760000e-159 573.0
6 TraesCS5A01G015900 chr5D 81.698 377 52 9 1001 1363 14928225 14928598 1.190000e-76 298.0
7 TraesCS5A01G015900 chr5D 75.598 418 81 18 1 404 14910525 14910935 2.680000e-43 187.0
8 TraesCS5A01G015900 chr5D 92.381 105 7 1 1 104 14942953 14943057 1.270000e-31 148.0
9 TraesCS5A01G015900 chr5D 84.466 103 15 1 1614 1715 14717018 14717120 3.590000e-17 100.0
10 TraesCS5A01G015900 chr5D 85.882 85 8 1 2834 2914 42032250 42032166 2.800000e-13 87.9
11 TraesCS5A01G015900 chr5B 91.605 4693 236 53 1001 5636 13699077 13703668 0.000000e+00 6338.0
12 TraesCS5A01G015900 chr5B 84.135 416 51 7 1 404 13698607 13699019 6.850000e-104 388.0
13 TraesCS5A01G015900 chr5B 82.493 377 50 9 1001 1363 13689931 13690305 3.280000e-82 316.0
14 TraesCS5A01G015900 chr5B 82.143 364 50 6 1017 1369 13680279 13680638 1.190000e-76 298.0
15 TraesCS5A01G015900 chr5B 85.470 234 28 6 1014 1243 13683388 13683619 7.300000e-59 239.0
16 TraesCS5A01G015900 chr5B 76.812 414 81 11 1 404 13689466 13689874 9.510000e-53 219.0
17 TraesCS5A01G015900 chr5B 80.612 294 44 10 1 290 13693087 13693371 1.230000e-51 215.0
18 TraesCS5A01G015900 chr5B 76.471 408 87 8 1 404 13695517 13695919 4.420000e-51 213.0
19 TraesCS5A01G015900 chr6D 85.680 412 51 6 3846 4256 317121265 317121669 1.450000e-115 427.0
20 TraesCS5A01G015900 chrUn 78.261 391 54 18 2157 2523 144747155 144746772 7.350000e-54 222.0
21 TraesCS5A01G015900 chrUn 78.149 389 58 21 2157 2523 144816745 144816362 7.350000e-54 222.0
22 TraesCS5A01G015900 chrUn 78.261 391 54 18 2157 2523 144899099 144898716 7.350000e-54 222.0
23 TraesCS5A01G015900 chrUn 78.261 391 54 20 2157 2523 144935778 144935395 7.350000e-54 222.0
24 TraesCS5A01G015900 chrUn 78.005 391 55 18 2157 2523 12073708 12073325 3.420000e-52 217.0
25 TraesCS5A01G015900 chrUn 78.005 391 55 20 2157 2523 144784224 144783841 3.420000e-52 217.0
26 TraesCS5A01G015900 chrUn 87.857 140 13 3 2157 2293 144894644 144894506 1.620000e-35 161.0
27 TraesCS5A01G015900 chr7D 80.377 265 48 2 5192 5455 411021054 411021315 1.240000e-46 198.0


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 TraesCS5A01G015900 chr5A 11513972 11519607 5635 False 4654.5 8562 100.000000 1 5636 2 chr5A.!!$F2 5635
1 TraesCS5A01G015900 chr5D 14964881 14969966 5085 False 4114.0 7655 94.440500 1 5636 2 chr5D.!!$F5 5635
2 TraesCS5A01G015900 chr5B 13689466 13703668 14202 False 1281.5 6338 82.021333 1 5636 6 chr5B.!!$F2 5635
3 TraesCS5A01G015900 chr5B 13680279 13683619 3340 False 268.5 298 83.806500 1014 1369 2 chr5B.!!$F1 355

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
308 9451 1.005867 CACACTGCAAATGTGGCCC 60.006 57.895 18.78 0.0 43.11 5.80 F
1336 13612 0.396060 GGAATTTGTTGCCTTGGCCA 59.604 50.000 0.00 0.0 0.00 5.36 F
1492 13781 0.960364 TTTGTCCTGCAGATTCGGCC 60.960 55.000 17.39 0.0 0.00 6.13 F
2039 14342 1.003233 GCGGCTCTTCTTCAAGGGT 60.003 57.895 0.00 0.0 31.84 4.34 F
3222 15527 1.133199 AGCTATGAGTCCCTGGAGAGG 60.133 57.143 0.00 0.0 39.42 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 13678 0.462759 CGCTAAAAGCCCCAGAGAGG 60.463 60.000 0.00 0.0 38.18 3.69 R
3054 15359 2.134346 CAAAATTTGTGGGAACAGCCG 58.866 47.619 0.00 0.0 44.46 5.52 R
3468 15773 1.202698 AGCCGATGCAAAGATAGGTCC 60.203 52.381 0.00 0.0 41.13 4.46 R
3513 15818 1.751437 TCCGTCGACATCTCTGACAT 58.249 50.000 17.16 0.0 32.91 3.06 R
4906 17229 0.738975 CGAGTGGCTACCGAAGATCA 59.261 55.000 0.00 0.0 0.00 2.92 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
41 43 2.961977 GCCCCCTACTCCATTCTCTCTT 60.962 54.545 0.00 0.00 0.00 2.85
129 9272 3.063997 CCACACTCGTAAATCATCTTGGC 59.936 47.826 0.00 0.00 0.00 4.52
156 9299 1.413812 ACAATATTACCCCGACGGTCC 59.586 52.381 13.94 0.00 43.58 4.46
182 9325 9.906660 CTGAAGCCTATCACTAAATCTTACTAG 57.093 37.037 0.00 0.00 0.00 2.57
201 9344 4.838986 ACTAGTTAAGTCTCCCAAGCTTCA 59.161 41.667 0.00 0.00 30.33 3.02
238 9381 2.738846 GCAGAGAAAAACATGAGCGAGA 59.261 45.455 0.00 0.00 0.00 4.04
308 9451 1.005867 CACACTGCAAATGTGGCCC 60.006 57.895 18.78 0.00 43.11 5.80
323 9466 1.154035 GCCCGTCAAAGCCGAAATG 60.154 57.895 0.00 0.00 0.00 2.32
329 9472 3.425193 CCGTCAAAGCCGAAATGAAAAAG 59.575 43.478 0.00 0.00 0.00 2.27
1155 13425 3.215245 CTCCCCTCCGAGCTGAAG 58.785 66.667 0.00 0.00 0.00 3.02
1161 13431 3.068691 TCCGAGCTGAAGTCCGGG 61.069 66.667 0.00 0.00 42.03 5.73
1163 13433 3.382832 CGAGCTGAAGTCCGGGGT 61.383 66.667 0.00 0.00 0.00 4.95
1250 13524 1.059942 CTTGCAAATTCCGCGGTTTC 58.940 50.000 27.15 7.40 0.00 2.78
1336 13612 0.396060 GGAATTTGTTGCCTTGGCCA 59.604 50.000 0.00 0.00 0.00 5.36
1374 13650 3.224007 ATCTGCCAGGCCGGGTTTT 62.224 57.895 23.81 3.45 34.06 2.43
1376 13652 4.986708 TGCCAGGCCGGGTTTTCC 62.987 66.667 23.81 6.66 39.75 3.13
1377 13653 4.986708 GCCAGGCCGGGTTTTCCA 62.987 66.667 23.81 0.00 42.91 3.53
1385 13661 2.477880 CGGGTTTTCCAGGAATCGG 58.522 57.895 1.58 0.00 42.91 4.18
1402 13678 2.486966 GCGGCTGATTTGTGGCTC 59.513 61.111 0.00 0.00 0.00 4.70
1492 13781 0.960364 TTTGTCCTGCAGATTCGGCC 60.960 55.000 17.39 0.00 0.00 6.13
1506 13795 4.467084 GGCCGCGGGTGATTCTCA 62.467 66.667 29.38 0.00 0.00 3.27
1590 13879 1.304134 GAATTTGGTGGCGGTCCCT 60.304 57.895 0.00 0.00 0.00 4.20
1610 13899 2.760159 CCAATTTCGCCATCGCCGT 61.760 57.895 0.00 0.00 35.26 5.68
1664 13953 2.203126 CCTGGCCATCTTCTCCGC 60.203 66.667 5.51 0.00 0.00 5.54
1726 14028 1.679944 CCTGTCGGTGCAGATTGGATT 60.680 52.381 0.00 0.00 38.70 3.01
1868 14171 1.068753 CAATCCGAGCGCTGAGGAT 59.931 57.895 28.62 28.62 45.88 3.24
2039 14342 1.003233 GCGGCTCTTCTTCAAGGGT 60.003 57.895 0.00 0.00 31.84 4.34
2056 14359 2.976350 TGTGTCGAGCTCGGACGT 60.976 61.111 33.98 0.00 40.29 4.34
2120 14423 2.352805 CCTGGGGTGCCTCTTCAC 59.647 66.667 0.00 0.00 36.28 3.18
2243 14546 5.344743 AGATCTTCGCCTTCACTAATTCA 57.655 39.130 0.00 0.00 0.00 2.57
2281 14584 4.363138 CAGGCAAGAGTTTCTGGTTTTTC 58.637 43.478 0.00 0.00 0.00 2.29
2541 14846 8.034313 ACCATAAGCTAATTCTGACCTATTGA 57.966 34.615 0.00 0.00 0.00 2.57
2647 14952 3.372206 GTGAATATGGAGTGAGTGTGCAC 59.628 47.826 10.75 10.75 39.05 4.57
3054 15359 5.221342 ACGAGGTTCTCATATGATCAAGGTC 60.221 44.000 5.72 2.01 0.00 3.85
3222 15527 1.133199 AGCTATGAGTCCCTGGAGAGG 60.133 57.143 0.00 0.00 39.42 3.69
3457 15762 2.125350 GCCTGCCTGTCGAGGAAG 60.125 66.667 0.00 0.00 44.42 3.46
3468 15773 2.993853 GAGGAAGGAGGTGCAGGG 59.006 66.667 0.00 0.00 0.00 4.45
3513 15818 3.252215 CACAAAACAATAGTTGGAGGCGA 59.748 43.478 0.00 0.00 38.17 5.54
3613 15918 5.163519 CGTTCCCTGCATTTTCCAGATATTT 60.164 40.000 0.00 0.00 32.03 1.40
3621 15926 7.483307 TGCATTTTCCAGATATTTGTAGCTTC 58.517 34.615 0.00 0.00 0.00 3.86
3632 15937 9.378551 AGATATTTGTAGCTTCAATTTGTCGTA 57.621 29.630 6.60 0.00 0.00 3.43
3647 15952 8.665685 CAATTTGTCGTATAGTAAAGCCTTCTT 58.334 33.333 0.00 0.00 0.00 2.52
3693 15998 4.082665 TCCCTGAGATGCATGAGATTTC 57.917 45.455 2.46 0.00 0.00 2.17
3804 16109 6.769822 CACAGAGCCTCAAATAATGTTCCTAT 59.230 38.462 0.00 0.00 0.00 2.57
4322 16627 3.119743 CCTACAACGACGACTACATCCAA 60.120 47.826 0.00 0.00 0.00 3.53
4466 16772 2.621055 TCGAAAATTGGTTGACACTGGG 59.379 45.455 0.00 0.00 0.00 4.45
4514 16829 3.820777 TTGTTTGTTTTGTTTGGCTGC 57.179 38.095 0.00 0.00 0.00 5.25
4712 17035 6.969993 TGTGAAAAGTAAGGCATAAAGGTT 57.030 33.333 0.00 0.00 0.00 3.50
4902 17225 5.491982 ACGGCAAGAGAGAAGAAATAATGT 58.508 37.500 0.00 0.00 0.00 2.71
4906 17229 6.183360 GGCAAGAGAGAAGAAATAATGTGCAT 60.183 38.462 0.00 0.00 0.00 3.96
4915 17238 6.309712 AGAAATAATGTGCATGATCTTCGG 57.690 37.500 0.00 0.00 0.00 4.30
4950 17273 4.593206 CAGTAATATCCAGACTTGGCCCTA 59.407 45.833 0.00 0.00 44.63 3.53
5348 17674 0.605589 GAACCCGCCAAAGTAGCTGT 60.606 55.000 0.00 0.00 0.00 4.40
5551 17878 4.870426 TGTGAGAACAGAACAGAACAGAAC 59.130 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 43 4.047166 AGACATTATGGTGGGAGAATGGA 58.953 43.478 0.00 0.00 34.30 3.41
129 9272 1.603678 CGGGGTAATATTGTCGGGTCG 60.604 57.143 0.00 0.00 0.00 4.79
156 9299 9.906660 CTAGTAAGATTTAGTGATAGGCTTCAG 57.093 37.037 0.00 0.00 0.00 3.02
182 9325 5.966742 AAATGAAGCTTGGGAGACTTAAC 57.033 39.130 2.10 0.00 0.00 2.01
186 9329 3.615155 GCTAAATGAAGCTTGGGAGACT 58.385 45.455 2.10 0.00 39.50 3.24
201 9344 2.101582 CTCTGCGTCTACCCAGCTAAAT 59.898 50.000 0.00 0.00 0.00 1.40
304 9447 2.340328 ATTTCGGCTTTGACGGGCC 61.340 57.895 0.00 0.00 44.43 5.80
308 9451 4.286910 TCTTTTTCATTTCGGCTTTGACG 58.713 39.130 0.00 0.00 34.09 4.35
329 9472 8.375465 CGTGGAAATGATTTGCTTCTATTTTTC 58.625 33.333 10.69 0.00 31.65 2.29
366 9519 4.701651 AGAACCCTAATAATTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
367 9520 4.275196 GCAAGAACCCTAATAATTCCGTCC 59.725 45.833 0.00 0.00 0.00 4.79
1067 10220 4.320456 CGGGATCATCGGGGGCAG 62.320 72.222 0.00 0.00 0.00 4.85
1155 13425 3.819877 AACGAACAGCACCCCGGAC 62.820 63.158 0.73 0.00 0.00 4.79
1161 13431 1.192534 CGAGAAAGAACGAACAGCACC 59.807 52.381 0.00 0.00 0.00 5.01
1163 13433 2.502213 TCGAGAAAGAACGAACAGCA 57.498 45.000 0.00 0.00 35.62 4.41
1204 13478 4.391869 GGGGAAAGAACCACGGAC 57.608 61.111 0.00 0.00 0.00 4.79
1215 13489 1.160145 AAGGAGGAGGTCGGGGAAA 59.840 57.895 0.00 0.00 0.00 3.13
1216 13490 1.612442 CAAGGAGGAGGTCGGGGAA 60.612 63.158 0.00 0.00 0.00 3.97
1336 13612 6.765512 GCAGATCTAGAAAAGTAGGAGCATTT 59.234 38.462 0.00 0.00 0.00 2.32
1374 13650 4.161295 CAGCCGCCGATTCCTGGA 62.161 66.667 0.00 0.00 0.00 3.86
1376 13652 1.097547 AAATCAGCCGCCGATTCCTG 61.098 55.000 2.29 0.00 31.90 3.86
1377 13653 1.097547 CAAATCAGCCGCCGATTCCT 61.098 55.000 2.29 0.00 31.90 3.36
1385 13661 2.486966 GAGCCACAAATCAGCCGC 59.513 61.111 0.00 0.00 0.00 6.53
1402 13678 0.462759 CGCTAAAAGCCCCAGAGAGG 60.463 60.000 0.00 0.00 38.18 3.69
1458 13734 6.095377 GCAGGACAAAAATCACCAGAATTAG 58.905 40.000 0.00 0.00 0.00 1.73
1459 13735 5.538053 TGCAGGACAAAAATCACCAGAATTA 59.462 36.000 0.00 0.00 0.00 1.40
1460 13736 4.344679 TGCAGGACAAAAATCACCAGAATT 59.655 37.500 0.00 0.00 0.00 2.17
1461 13737 3.896888 TGCAGGACAAAAATCACCAGAAT 59.103 39.130 0.00 0.00 0.00 2.40
1462 13738 3.295093 TGCAGGACAAAAATCACCAGAA 58.705 40.909 0.00 0.00 0.00 3.02
1492 13781 2.202932 CCCTGAGAATCACCCGCG 60.203 66.667 0.00 0.00 42.56 6.46
1505 13794 1.958205 GCTCGATGATTCGGCCCTG 60.958 63.158 0.00 0.00 45.53 4.45
1506 13795 2.423446 GCTCGATGATTCGGCCCT 59.577 61.111 0.00 0.00 45.53 5.19
1610 13899 2.031919 ACAGCGCGAATTCCACCA 59.968 55.556 12.10 0.00 0.00 4.17
1686 13975 1.880027 GTTGGGAATCAGAAACAGCGT 59.120 47.619 0.00 0.00 0.00 5.07
1714 14016 3.887110 CAGCAATCCTAATCCAATCTGCA 59.113 43.478 0.00 0.00 0.00 4.41
1726 14028 2.513738 AGCCCCAATTACAGCAATCCTA 59.486 45.455 0.00 0.00 0.00 2.94
1880 14183 1.376942 GACGTCCTCACCTCTCGGA 60.377 63.158 3.51 0.00 0.00 4.55
1881 14184 2.751913 CGACGTCCTCACCTCTCGG 61.752 68.421 10.58 0.00 0.00 4.63
1889 14192 3.611674 TTGGCAGCGACGTCCTCA 61.612 61.111 10.58 1.11 0.00 3.86
2039 14342 2.976350 ACGTCCGAGCTCGACACA 60.976 61.111 36.59 14.73 43.02 3.72
2056 14359 0.620556 GGACAGCTTCTTCCCATCCA 59.379 55.000 0.00 0.00 0.00 3.41
2120 14423 0.959372 CCAGCTTCTTCTGCACCCTG 60.959 60.000 0.00 0.00 32.87 4.45
2317 14620 6.914757 GCTGACTGAAACCAATATCTTAATGC 59.085 38.462 0.00 0.00 0.00 3.56
3054 15359 2.134346 CAAAATTTGTGGGAACAGCCG 58.866 47.619 0.00 0.00 44.46 5.52
3325 15630 2.179517 CGACTGACTGGACGAGCC 59.820 66.667 0.00 0.00 37.10 4.70
3457 15762 1.384643 ATAGGTCCCCTGCACCTCC 60.385 63.158 0.00 0.00 43.68 4.30
3468 15773 1.202698 AGCCGATGCAAAGATAGGTCC 60.203 52.381 0.00 0.00 41.13 4.46
3513 15818 1.751437 TCCGTCGACATCTCTGACAT 58.249 50.000 17.16 0.00 32.91 3.06
3613 15918 9.642327 TTTACTATACGACAAATTGAAGCTACA 57.358 29.630 0.00 0.00 0.00 2.74
3621 15926 8.197988 AGAAGGCTTTACTATACGACAAATTG 57.802 34.615 0.00 0.00 0.00 2.32
3632 15937 6.465084 AGAAACGACAAGAAGGCTTTACTAT 58.535 36.000 0.00 0.00 30.14 2.12
3647 15952 4.124238 CTGAGGGTTAACAAGAAACGACA 58.876 43.478 8.10 0.00 0.00 4.35
3693 15998 9.559958 AGATTCACTATTTTTATGCTTTTGTCG 57.440 29.630 0.00 0.00 0.00 4.35
3804 16109 1.974957 TGCCCAGTAGTCTGCACTAAA 59.025 47.619 0.00 0.00 36.84 1.85
4220 16525 1.392853 GTGTCGACGATGTACGAGTCT 59.607 52.381 11.62 0.00 45.77 3.24
4466 16772 8.764287 CAAAGGTGGAAGTATCATTTTGTTTTC 58.236 33.333 0.00 0.00 0.00 2.29
4514 16829 6.041296 CCAAAAGAGAATGAATAATGGAGGGG 59.959 42.308 0.00 0.00 0.00 4.79
4678 16997 7.029563 GCCTTACTTTTCACATCAAATCGAAT 58.970 34.615 0.00 0.00 0.00 3.34
4679 16998 6.016693 TGCCTTACTTTTCACATCAAATCGAA 60.017 34.615 0.00 0.00 0.00 3.71
4680 16999 5.471797 TGCCTTACTTTTCACATCAAATCGA 59.528 36.000 0.00 0.00 0.00 3.59
4681 17000 5.698832 TGCCTTACTTTTCACATCAAATCG 58.301 37.500 0.00 0.00 0.00 3.34
4682 17001 9.638239 TTTATGCCTTACTTTTCACATCAAATC 57.362 29.630 0.00 0.00 0.00 2.17
4712 17035 1.561643 TGTTGGGGTTGCTTTTGTCA 58.438 45.000 0.00 0.00 0.00 3.58
4792 17115 7.928908 TTGCTTTTGTCTACTTTTATGCTTG 57.071 32.000 0.00 0.00 0.00 4.01
4881 17204 5.124457 TGCACATTATTTCTTCTCTCTTGCC 59.876 40.000 0.00 0.00 0.00 4.52
4902 17225 0.829990 TGGCTACCGAAGATCATGCA 59.170 50.000 0.00 0.00 0.00 3.96
4906 17229 0.738975 CGAGTGGCTACCGAAGATCA 59.261 55.000 0.00 0.00 0.00 2.92
4915 17238 4.277672 TGGATATTACTGTCGAGTGGCTAC 59.722 45.833 0.00 0.00 33.21 3.58
5299 17625 0.249238 CTATCGTGCTGCTCCTGGAC 60.249 60.000 0.00 0.00 0.00 4.02
5348 17674 4.986774 AGGCGGTGGGGGTGGTAA 62.987 66.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.