Multiple sequence alignment - TraesCS4B01G090200

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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 TraesCS4B01G090200 chr4B 100.000 2456 0 0 1 2456 92463061 92465516 0.000000e+00 4536.0
1 TraesCS4B01G090200 chr4A 92.269 2186 152 14 281 2456 534259374 534257196 0.000000e+00 3085.0
2 TraesCS4B01G090200 chr4A 95.109 184 8 1 48 231 534259554 534259372 3.090000e-74 289.0
3 TraesCS4B01G090200 chr4A 77.193 114 18 7 144 252 472266958 472266848 2.640000e-05 60.2
4 TraesCS4B01G090200 chr4A 100.000 29 0 0 1 29 534259586 534259558 1.000000e-03 54.7
5 TraesCS4B01G090200 chr4D 95.007 1522 74 1 937 2456 62549446 62550967 0.000000e+00 2388.0
6 TraesCS4B01G090200 chr4D 95.304 937 36 6 1 930 62548404 62549339 0.000000e+00 1480.0
7 TraesCS4B01G090200 chr3B 81.982 111 16 3 144 252 822182333 822182225 9.350000e-15 91.6
8 TraesCS4B01G090200 chr5A 86.301 73 8 2 183 253 331121866 331121794 7.280000e-11 78.7
9 TraesCS4B01G090200 chr1B 75.706 177 32 11 82 252 426784593 426784422 7.280000e-11 78.7
10 TraesCS4B01G090200 chr2A 79.487 117 16 7 145 256 578787423 578787536 2.620000e-10 76.8
11 TraesCS4B01G090200 chr3D 79.091 110 20 3 145 252 537904640 537904748 3.390000e-09 73.1
12 TraesCS4B01G090200 chr7A 81.609 87 15 1 167 252 157390829 157390743 1.220000e-08 71.3
13 TraesCS4B01G090200 chr5D 100.000 29 0 0 2216 2244 101455026 101454998 1.000000e-03 54.7


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 TraesCS4B01G090200 chr4B 92463061 92465516 2455 False 4536.0 4536 100.000000 1 2456 1 chr4B.!!$F1 2455
1 TraesCS4B01G090200 chr4A 534257196 534259586 2390 True 1142.9 3085 95.792667 1 2456 3 chr4A.!!$R2 2455
2 TraesCS4B01G090200 chr4D 62548404 62550967 2563 False 1934.0 2388 95.155500 1 2456 2 chr4D.!!$F1 2455

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
300 302 0.116940 ATGCCAACCCTGGTTTGGAT 59.883 50.000 25.40 13.15 45.53 3.41 F
1057 1165 1.376553 GCCTCTGTTGTGGCCTCTC 60.377 63.158 3.32 0.00 44.54 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1199 1307 0.036388 ATTGATCTCACAACCGCCGT 60.036 50.0 0.00 0.00 32.50 5.68 R
2203 2323 0.818040 AACCAAACCTGCAGGACGTC 60.818 55.0 39.19 7.13 38.94 4.34 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
70 72 5.221925 TGGATTGACTAGCTGAAGGAAGTTT 60.222 40.000 0.00 0.00 0.00 2.66
71 73 6.013725 TGGATTGACTAGCTGAAGGAAGTTTA 60.014 38.462 0.00 0.00 0.00 2.01
159 161 4.036144 ACGCCGAGTTAATAGGTTAGTCTC 59.964 45.833 0.00 0.00 0.00 3.36
164 166 6.911511 CCGAGTTAATAGGTTAGTCTCGAAAG 59.088 42.308 12.14 0.00 42.12 2.62
264 266 1.410517 ACGTATCAGAGGCACATGAGG 59.589 52.381 0.00 0.00 0.00 3.86
274 276 4.164796 AGAGGCACATGAGGATGTTGATTA 59.835 41.667 0.00 0.00 41.12 1.75
283 285 9.770097 ACATGAGGATGTTGATTAGTAAGTATG 57.230 33.333 0.00 0.00 40.05 2.39
300 302 0.116940 ATGCCAACCCTGGTTTGGAT 59.883 50.000 25.40 13.15 45.53 3.41
338 340 4.518970 AGTGAAAGAACGGTGTTATGCATT 59.481 37.500 3.54 0.00 0.00 3.56
407 415 3.149196 CAGCTTTCAAGGGTTAGCAAGA 58.851 45.455 0.00 0.00 36.11 3.02
511 519 7.986320 TGCCATCAAAATATGTTATTTCCCTTG 59.014 33.333 0.00 0.00 0.00 3.61
831 839 8.764287 CATTCAAGATAAACACTACGCATGATA 58.236 33.333 0.00 0.00 0.00 2.15
848 856 8.214364 ACGCATGATAGGATATCTCTCTATGTA 58.786 37.037 2.05 0.00 0.00 2.29
855 863 7.538327 AGGATATCTCTCTATGTATGGTCCT 57.462 40.000 2.05 0.00 0.00 3.85
895 903 6.652481 GCATTATACTCCACATTGCAGTCTAT 59.348 38.462 0.00 0.00 0.00 1.98
930 938 7.001674 CAGGTAGACCTATATATGAGGCTAGG 58.998 46.154 0.00 0.00 46.65 3.02
956 1064 6.711277 ACTGCCTTTAGTCACAATCATCTTA 58.289 36.000 0.00 0.00 0.00 2.10
1057 1165 1.376553 GCCTCTGTTGTGGCCTCTC 60.377 63.158 3.32 0.00 44.54 3.20
1288 1396 3.863424 CCAGTCTATGTTGATTAACGCGT 59.137 43.478 5.58 5.58 39.71 6.01
1293 1401 2.953640 TGTTGATTAACGCGTTGACC 57.046 45.000 33.40 18.54 39.71 4.02
1324 1432 2.562298 GTCAAGGTTGCATTCCAATGGA 59.438 45.455 0.00 0.00 36.90 3.41
1356 1464 1.167851 CAGTTGAACGGCATGGTGAT 58.832 50.000 0.00 0.00 0.00 3.06
1363 1471 2.242572 CGGCATGGTGATCAGCTCG 61.243 63.158 24.30 17.68 0.00 5.03
1380 1488 0.602638 TCGTCTTCAATGCAGCCGTT 60.603 50.000 0.00 0.00 0.00 4.44
1397 1505 6.482835 CAGCCGTTATATCAAAATCGTTTCA 58.517 36.000 0.00 0.00 0.00 2.69
1440 1548 4.845580 CGCTGCAGCCGAATCCCT 62.846 66.667 32.07 0.00 37.91 4.20
1476 1584 8.644374 AGTAGATTAATGGGTTAGCAACAAAA 57.356 30.769 0.00 0.00 0.00 2.44
1524 1633 3.886505 TCAACGGGCTCAATTGTTACTTT 59.113 39.130 5.13 0.00 0.00 2.66
1535 1644 8.082242 GCTCAATTGTTACTTTATTCTTGTGGT 58.918 33.333 5.13 0.00 0.00 4.16
1658 1768 8.736244 GGCATAGTTTATGTTACTCCTGAAAAA 58.264 33.333 0.00 0.00 38.43 1.94
1679 1789 2.311542 AGGGGTAGCAAATCATGTTCCA 59.688 45.455 0.00 0.00 0.00 3.53
1700 1812 2.893489 AGCCCTTCACAAAGAAATCACC 59.107 45.455 0.00 0.00 35.40 4.02
1722 1834 5.588648 ACCGAACCATGGAAATGTATACAAG 59.411 40.000 21.47 0.00 0.00 3.16
1741 1853 5.196695 ACAAGATTTCCCTAAAGGCATCTC 58.803 41.667 4.81 0.00 35.39 2.75
1742 1854 5.044550 ACAAGATTTCCCTAAAGGCATCTCT 60.045 40.000 4.81 0.00 35.39 3.10
1749 1861 4.968719 TCCCTAAAGGCATCTCTAACATGA 59.031 41.667 0.00 0.00 34.51 3.07
1760 1872 7.415653 GGCATCTCTAACATGAACCCTTAAAAG 60.416 40.741 0.00 0.00 0.00 2.27
1805 1917 2.027625 GTCCGAAAGCGTCTGTGGG 61.028 63.158 0.00 0.00 35.23 4.61
1813 1925 0.105593 AGCGTCTGTGGGCATGATAG 59.894 55.000 0.00 0.00 0.00 2.08
1900 2013 7.308951 GCATTAACCTTCTGCTAAACAACCTAA 60.309 37.037 0.00 0.00 33.15 2.69
1912 2025 2.627933 ACAACCTAACCTAGCCTTCCA 58.372 47.619 0.00 0.00 0.00 3.53
2067 2186 0.804989 CAACCTTCCGCCATGTCTTC 59.195 55.000 0.00 0.00 0.00 2.87
2076 2195 2.103094 CCGCCATGTCTTCTAATCCTGA 59.897 50.000 0.00 0.00 0.00 3.86
2083 2202 7.412853 CCATGTCTTCTAATCCTGAAAAATCG 58.587 38.462 0.00 0.00 0.00 3.34
2177 2297 7.361371 GCATGAAAAATCATGGCTTTTGATTGA 60.361 33.333 17.69 0.00 45.48 2.57
2203 2323 1.021390 GGATGTCCGAACACCTGCAG 61.021 60.000 6.78 6.78 38.48 4.41
2220 2340 1.071471 AGACGTCCTGCAGGTTTGG 59.929 57.895 31.58 20.19 36.34 3.28
2224 2344 1.515521 CGTCCTGCAGGTTTGGTTCC 61.516 60.000 31.58 9.82 36.34 3.62
2231 2351 1.107945 CAGGTTTGGTTCCGGTTTGT 58.892 50.000 0.00 0.00 0.00 2.83
2247 2367 4.440802 CGGTTTGTGGAATTTTGGACAAGA 60.441 41.667 0.00 0.00 30.37 3.02
2252 2372 3.058224 GTGGAATTTTGGACAAGAGGACG 60.058 47.826 0.00 0.00 0.00 4.79
2256 2376 0.179067 TTTGGACAAGAGGACGCGTT 60.179 50.000 15.53 0.00 0.00 4.84
2297 2417 3.301379 CACATTGGATGAAAAATGCGTCG 59.699 43.478 0.00 0.00 37.30 5.12
2348 2468 1.550072 CGGGCCCAAGACAAAAATGAT 59.450 47.619 24.92 0.00 0.00 2.45
2349 2469 2.028203 CGGGCCCAAGACAAAAATGATT 60.028 45.455 24.92 0.00 0.00 2.57
2364 2484 2.559698 TGATTCGGTGTCCACATGTT 57.440 45.000 0.00 0.00 0.00 2.71
2377 2497 4.637534 GTCCACATGTTCATCACTTATGCT 59.362 41.667 0.00 0.00 35.38 3.79
2444 2565 9.739786 CAAATTAAAATGTCTGGCGATAAAAAC 57.260 29.630 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 9.877178 AGTTGTTGTTTTATGTTATTTTGGACA 57.123 25.926 0.00 0.00 0.00 4.02
159 161 3.438360 GCACCCATTTTATCAGCTTTCG 58.562 45.455 0.00 0.00 0.00 3.46
164 166 3.608316 TTTGGCACCCATTTTATCAGC 57.392 42.857 0.00 0.00 31.53 4.26
248 250 2.125233 ACATCCTCATGTGCCTCTGAT 58.875 47.619 0.00 0.00 42.05 2.90
250 252 2.014857 CAACATCCTCATGTGCCTCTG 58.985 52.381 0.00 0.00 42.89 3.35
264 266 7.255139 GGGTTGGCATACTTACTAATCAACATC 60.255 40.741 0.00 0.00 36.10 3.06
300 302 7.358600 CGTTCTTTCACTACTACAAAACGCATA 60.359 37.037 0.00 0.00 31.97 3.14
407 415 9.807649 GGCTAAAAATATCTCAATGATTGTGTT 57.192 29.630 4.93 0.93 36.65 3.32
546 554 6.642430 ACCCCATATTTGAACAACATTGATG 58.358 36.000 0.00 0.00 0.00 3.07
810 818 7.050970 TCCTATCATGCGTAGTGTTTATCTT 57.949 36.000 0.00 0.00 0.00 2.40
831 839 7.538327 AGGACCATACATAGAGAGATATCCT 57.462 40.000 0.00 0.00 0.00 3.24
930 938 3.674997 TGATTGTGACTAAAGGCAGTCC 58.325 45.455 1.51 0.00 43.63 3.85
956 1064 7.822334 TGTTGATATCCTTTTCGAAGTATGTGT 59.178 33.333 0.00 0.00 0.00 3.72
1057 1165 4.742201 CGAGGTGACGGTGGCTGG 62.742 72.222 0.00 0.00 0.00 4.85
1199 1307 0.036388 ATTGATCTCACAACCGCCGT 60.036 50.000 0.00 0.00 32.50 5.68
1206 1314 1.065491 CCCCCGACATTGATCTCACAA 60.065 52.381 0.00 0.00 0.00 3.33
1288 1396 3.998672 GACGCTCACCCCGGTCAA 61.999 66.667 0.00 0.00 0.00 3.18
1293 1401 3.530910 AACCTTGACGCTCACCCCG 62.531 63.158 0.00 0.00 0.00 5.73
1356 1464 1.718396 CTGCATTGAAGACGAGCTGA 58.282 50.000 0.00 0.00 0.00 4.26
1363 1471 4.511454 TGATATAACGGCTGCATTGAAGAC 59.489 41.667 0.50 0.00 0.00 3.01
1397 1505 3.746492 GCTCACGGAGAAGTTGTTAACAT 59.254 43.478 9.56 0.00 0.00 2.71
1430 1538 1.037030 TGCAATTCCAGGGATTCGGC 61.037 55.000 0.00 0.00 0.00 5.54
1440 1548 6.667414 ACCCATTAATCTACTTTGCAATTCCA 59.333 34.615 0.00 0.00 0.00 3.53
1476 1584 9.768662 ATCTAACAAAATCAAGAAGCAATTGTT 57.231 25.926 7.40 0.00 41.05 2.83
1524 1633 8.564574 GTCACAATAGACAAAACCACAAGAATA 58.435 33.333 0.00 0.00 38.40 1.75
1535 1644 8.898761 ACACATAACAAGTCACAATAGACAAAA 58.101 29.630 0.00 0.00 40.98 2.44
1658 1768 2.311542 TGGAACATGATTTGCTACCCCT 59.688 45.455 0.00 0.00 0.00 4.79
1679 1789 2.893489 GGTGATTTCTTTGTGAAGGGCT 59.107 45.455 0.00 0.00 35.89 5.19
1700 1812 6.918892 TCTTGTATACATTTCCATGGTTCG 57.081 37.500 12.58 1.64 34.27 3.95
1722 1834 6.357367 TGTTAGAGATGCCTTTAGGGAAATC 58.643 40.000 0.00 0.00 39.60 2.17
1760 1872 4.509737 GGACGGCTAGCGTGTCCC 62.510 72.222 32.34 20.82 45.14 4.46
1805 1917 3.281727 TGGTTGGTTCCTCTATCATGC 57.718 47.619 0.00 0.00 0.00 4.06
1813 1925 1.545841 GGTTGGATGGTTGGTTCCTC 58.454 55.000 0.00 0.00 32.95 3.71
1900 2013 3.190439 ACTATTTGGTGGAAGGCTAGGT 58.810 45.455 0.00 0.00 0.00 3.08
1912 2025 5.243507 TGTTGTGCATGATCAACTATTTGGT 59.756 36.000 23.57 0.00 42.71 3.67
2029 2148 2.371306 TGTGCATGAGAATCCATGTGG 58.629 47.619 0.00 0.00 44.25 4.17
2067 2186 4.786609 GCGAAGGCGATTTTTCAGGATTAG 60.787 45.833 0.00 0.00 40.82 1.73
2203 2323 0.818040 AACCAAACCTGCAGGACGTC 60.818 55.000 39.19 7.13 38.94 4.34
2220 2340 3.127589 CCAAAATTCCACAAACCGGAAC 58.872 45.455 9.46 0.00 45.11 3.62
2224 2344 3.444703 TGTCCAAAATTCCACAAACCG 57.555 42.857 0.00 0.00 0.00 4.44
2231 2351 3.146066 CGTCCTCTTGTCCAAAATTCCA 58.854 45.455 0.00 0.00 0.00 3.53
2252 2372 2.124903 CCTGTATATGTCCACGAACGC 58.875 52.381 0.00 0.00 0.00 4.84
2276 2396 3.500982 CGACGCATTTTTCATCCAATGT 58.499 40.909 0.00 0.00 33.58 2.71
2297 2417 1.738432 GTCCGGACCGAACTATCCC 59.262 63.158 24.75 0.00 0.00 3.85
2348 2468 2.224402 TGATGAACATGTGGACACCGAA 60.224 45.455 0.00 0.00 0.00 4.30
2349 2469 1.346068 TGATGAACATGTGGACACCGA 59.654 47.619 0.00 0.00 0.00 4.69
2364 2484 7.386059 TGTCTGTTTCTTAGCATAAGTGATGA 58.614 34.615 0.00 0.00 37.82 2.92
2411 2532 6.586082 CGCCAGACATTTTAATTTGCTAAGTT 59.414 34.615 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.