Multiple sequence alignment - TraesCS5B01G292700

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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 TraesCS5B01G292700 chr5B 100.000 2129 0 0 1 2129 478139314 478141442 0.000000e+00 3932
1 TraesCS5B01G292700 chr5B 93.023 86 6 0 2044 2129 478154496 478154581 2.220000e-25 126
2 TraesCS5B01G292700 chr1A 93.823 2137 120 10 1 2129 499296976 499294844 0.000000e+00 3205
3 TraesCS5B01G292700 chr7B 93.779 2138 120 11 1 2129 479639106 479636973 0.000000e+00 3199
4 TraesCS5B01G292700 chrUn 94.205 1553 84 5 1 1551 11755875 11757423 0.000000e+00 2364


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 TraesCS5B01G292700 chr5B 478139314 478141442 2128 False 3932 3932 100.000 1 2129 1 chr5B.!!$F1 2128
1 TraesCS5B01G292700 chr1A 499294844 499296976 2132 True 3205 3205 93.823 1 2129 1 chr1A.!!$R1 2128
2 TraesCS5B01G292700 chr7B 479636973 479639106 2133 True 3199 3199 93.779 1 2129 1 chr7B.!!$R1 2128
3 TraesCS5B01G292700 chrUn 11755875 11757423 1548 False 2364 2364 94.205 1 1551 1 chrUn.!!$F1 1550

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
365 368 2.02902 GGGATGAAGTTTGGTTCAAGGC 60.029 50.0 0.0 0.0 39.84 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1851 0.892814 GCCAGCTAGCCATTCCATCC 60.893 60.0 12.13 0.0 0.0 3.51 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
37 38 7.901029 TCAGATGAAGAAGACAGTGATTACTT 58.099 34.615 0.00 0.00 34.07 2.24
38 39 8.031864 TCAGATGAAGAAGACAGTGATTACTTC 58.968 37.037 0.00 7.42 38.96 3.01
42 43 6.724441 TGAAGAAGACAGTGATTACTTCCCTA 59.276 38.462 0.00 0.00 39.33 3.53
50 51 6.098982 ACAGTGATTACTTCCCTAATGAGGAG 59.901 42.308 0.00 0.00 39.22 3.69
64 65 5.643421 AATGAGGAGGATGCATCTAAAGT 57.357 39.130 25.28 7.63 0.00 2.66
98 99 9.522804 GAATCAGAACAGATAAAGAAGACGTAT 57.477 33.333 0.00 0.00 0.00 3.06
100 101 7.827701 TCAGAACAGATAAAGAAGACGTATGT 58.172 34.615 0.00 0.00 0.00 2.29
192 194 5.954752 AGAGTAGGATCATCAAAGACAGTGA 59.045 40.000 0.00 0.00 0.00 3.41
197 199 6.537355 AGGATCATCAAAGACAGTGAAAGAA 58.463 36.000 0.00 0.00 0.00 2.52
200 202 7.336427 GGATCATCAAAGACAGTGAAAGAAGAT 59.664 37.037 0.00 0.00 0.00 2.40
202 204 8.768957 TCATCAAAGACAGTGAAAGAAGATAG 57.231 34.615 0.00 0.00 0.00 2.08
221 223 8.770438 AAGATAGTTCAGAGAAAGATGACAAC 57.230 34.615 0.00 0.00 0.00 3.32
239 241 4.738124 ACAACGACACTGACTATGATGAG 58.262 43.478 0.00 0.00 0.00 2.90
293 295 2.640316 GTGAAACCAGGGAAGACACT 57.360 50.000 0.00 0.00 0.00 3.55
296 298 2.637872 TGAAACCAGGGAAGACACTAGG 59.362 50.000 0.00 0.00 0.00 3.02
311 313 3.821033 ACACTAGGCGCTTCAAAAGATTT 59.179 39.130 7.64 0.00 0.00 2.17
365 368 2.029020 GGGATGAAGTTTGGTTCAAGGC 60.029 50.000 0.00 0.00 39.84 4.35
377 380 2.820197 GGTTCAAGGCAAGAGTTTAGGG 59.180 50.000 0.00 0.00 0.00 3.53
378 381 3.497942 GGTTCAAGGCAAGAGTTTAGGGA 60.498 47.826 0.00 0.00 0.00 4.20
391 394 6.831976 AGAGTTTAGGGATGCAGTTATAAGG 58.168 40.000 0.00 0.00 0.00 2.69
477 481 3.404224 TGTGATTGGCAAACATGCAAT 57.596 38.095 13.47 0.00 36.33 3.56
483 487 3.037431 TGGCAAACATGCAATTGGTAC 57.963 42.857 7.72 0.00 36.33 3.34
515 519 6.647067 GCTAGTCTGACAAGTAAGTCAAACAT 59.353 38.462 10.88 0.00 46.90 2.71
518 522 7.952671 AGTCTGACAAGTAAGTCAAACATCTA 58.047 34.615 10.88 0.00 46.90 1.98
537 541 8.798859 ACATCTAGCAGATAACAAGTTTCAAT 57.201 30.769 0.00 0.00 32.12 2.57
543 547 5.517770 GCAGATAACAAGTTTCAATGATGCC 59.482 40.000 0.00 0.00 0.00 4.40
548 552 4.406456 ACAAGTTTCAATGATGCCCACTA 58.594 39.130 0.00 0.00 0.00 2.74
574 578 2.814336 CCACCTAGGAAAGACAACAAGC 59.186 50.000 17.98 0.00 41.22 4.01
583 587 4.497507 GGAAAGACAACAAGCTGGTAACAC 60.498 45.833 0.00 0.00 46.17 3.32
609 613 6.040209 ACAAAGATTGCAGCCAAATATGAA 57.960 33.333 0.00 0.00 34.05 2.57
612 616 7.444792 ACAAAGATTGCAGCCAAATATGAAAAA 59.555 29.630 0.00 0.00 34.05 1.94
666 670 4.022935 GCACATCTGAGAAAACACATCCAA 60.023 41.667 0.00 0.00 0.00 3.53
670 674 6.016777 ACATCTGAGAAAACACATCCAAGAAC 60.017 38.462 0.00 0.00 0.00 3.01
710 714 4.956700 CAGTACATCCCAGGTTAAGAGAGA 59.043 45.833 0.00 0.00 0.00 3.10
927 931 7.607991 ACTGGATGTAGAAAAGTAATTGGACTG 59.392 37.037 0.00 0.00 0.00 3.51
967 971 3.118592 AGGTGCAACTAATGGAGAGCTAC 60.119 47.826 0.00 0.00 36.74 3.58
980 984 3.070159 GGAGAGCTACTATGTGCATTGGA 59.930 47.826 0.00 0.00 0.00 3.53
985 989 5.688807 AGCTACTATGTGCATTGGAAAGAT 58.311 37.500 0.00 0.00 0.00 2.40
1008 1012 1.421646 GCCAATAGCCAGATGTACCCT 59.578 52.381 0.00 0.00 34.35 4.34
1144 1148 5.461327 ACCAATAAAGAGGGCATCATCAAT 58.539 37.500 0.58 0.00 0.00 2.57
1146 1150 5.303589 CCAATAAAGAGGGCATCATCAATGT 59.696 40.000 0.58 0.00 37.71 2.71
1205 1209 4.163458 TGTGCAAGACATGTTTATGCTG 57.837 40.909 23.25 7.08 37.85 4.41
1222 1226 2.563179 TGCTGACTGGAGGAAAGAGTAC 59.437 50.000 0.00 0.00 0.00 2.73
1224 1228 3.196685 GCTGACTGGAGGAAAGAGTACAT 59.803 47.826 0.00 0.00 0.00 2.29
1272 1276 2.760092 GGAATTGTGCAAAGGCTCCATA 59.240 45.455 0.00 0.00 41.91 2.74
1320 1324 2.789491 AAGCTTGCAAGAGAAACTGC 57.211 45.000 30.39 12.67 0.00 4.40
1422 1426 4.494484 TCTGTCGACAATAACATCTGTGG 58.506 43.478 20.49 2.96 0.00 4.17
1480 1484 2.992543 GCCGATCATCTCAATGCTAGAC 59.007 50.000 0.00 0.00 32.58 2.59
1495 1499 4.816392 TGCTAGACGCTATCAGACAAAAA 58.184 39.130 0.00 0.00 40.11 1.94
1523 1527 8.501904 TGATGGTTAGAATCCAGGAAATGATTA 58.498 33.333 0.00 0.00 38.42 1.75
1557 1561 9.853177 CCTTAAATGGACAGGAGATATAGTTTT 57.147 33.333 0.00 0.00 0.00 2.43
1563 1567 7.136885 TGGACAGGAGATATAGTTTTCCCTAA 58.863 38.462 0.00 0.00 0.00 2.69
1601 1606 9.941325 AACCAAACAAATGCATTGAATATTCTA 57.059 25.926 13.82 9.43 41.85 2.10
1616 1621 5.818678 ATATTCTACCCAATGCGAACCTA 57.181 39.130 0.00 0.00 0.00 3.08
1672 1677 7.032580 CACAGAACAAAAATCACAGGTTTACA 58.967 34.615 0.00 0.00 0.00 2.41
1699 1704 6.660521 TGGATTTGAATAGACTGAATTGCACT 59.339 34.615 0.00 0.00 0.00 4.40
1716 1722 0.546747 ACTTGGGGTACTGGCAGCTA 60.547 55.000 15.89 3.51 0.00 3.32
1722 1728 1.330655 GGTACTGGCAGCTAGCTGGA 61.331 60.000 38.52 13.53 43.77 3.86
1729 1735 1.542108 GGCAGCTAGCTGGATTACCTG 60.542 57.143 38.52 17.07 43.77 4.00
1759 1768 3.009253 TGCCATTTCAGCAATCCCAAAAT 59.991 39.130 0.00 0.00 37.28 1.82
1814 1823 3.338249 TCTATGTGGCTGCTTTCAAGAC 58.662 45.455 0.00 0.00 0.00 3.01
1842 1851 0.957395 CCTACTGCCTGCAACCTGTG 60.957 60.000 0.00 0.00 0.00 3.66
1906 1915 5.862845 CTGTAGCTCCAGGATATGTGAAAT 58.137 41.667 0.00 0.00 0.00 2.17
1972 1981 7.063426 GTGAGAAGAAAGTTTCCAAAACAAAGG 59.937 37.037 12.05 0.00 0.00 3.11
1984 1993 5.659079 TCCAAAACAAAGGTACCAAAGACAT 59.341 36.000 15.94 0.00 0.00 3.06
1989 1998 2.949177 AGGTACCAAAGACATGCACA 57.051 45.000 15.94 0.00 0.00 4.57
1992 2001 3.326588 AGGTACCAAAGACATGCACAGTA 59.673 43.478 15.94 0.00 0.00 2.74
1995 2004 5.878116 GGTACCAAAGACATGCACAGTAATA 59.122 40.000 7.15 0.00 0.00 0.98
2021 2031 2.954611 GAAGTGCAAAGGACGGGC 59.045 61.111 0.00 0.00 0.00 6.13
2032 2042 4.202212 GCAAAGGACGGGCCATAATAAAAT 60.202 41.667 4.39 0.00 40.02 1.82
2073 2083 1.896220 CAGCCAACCAGCTCAAACTA 58.104 50.000 0.00 0.00 42.61 2.24
2077 2087 3.019564 GCCAACCAGCTCAAACTATGAT 58.980 45.455 0.00 0.00 37.44 2.45
2079 2089 4.012374 CCAACCAGCTCAAACTATGATGT 58.988 43.478 0.00 0.00 37.44 3.06
2088 2098 7.223582 CAGCTCAAACTATGATGTAGGTTAGTG 59.776 40.741 0.00 0.00 37.44 2.74
2102 2112 8.833231 TGTAGGTTAGTGAAAATTCTCTTCAG 57.167 34.615 3.37 0.00 33.56 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.076910 AGTAATCACTGTCTTCTTCATCTGAT 57.923 34.615 0.00 0.00 32.25 2.90
17 18 5.544176 AGGGAAGTAATCACTGTCTTCTTCA 59.456 40.000 0.00 0.00 41.47 3.02
37 38 2.494888 TGCATCCTCCTCATTAGGGA 57.505 50.000 0.00 0.00 43.84 4.20
38 39 2.911636 AGATGCATCCTCCTCATTAGGG 59.088 50.000 23.06 0.00 43.84 3.53
42 43 5.643421 ACTTTAGATGCATCCTCCTCATT 57.357 39.130 23.06 4.58 0.00 2.57
75 76 7.827701 ACATACGTCTTCTTTATCTGTTCTGA 58.172 34.615 0.00 0.00 0.00 3.27
164 166 5.303078 TGTCTTTGATGATCCTACTCTAGGC 59.697 44.000 0.00 0.00 45.82 3.93
192 194 9.651913 GTCATCTTTCTCTGAACTATCTTCTTT 57.348 33.333 0.00 0.00 0.00 2.52
197 199 7.032580 CGTTGTCATCTTTCTCTGAACTATCT 58.967 38.462 0.00 0.00 0.00 1.98
200 202 6.150318 GTCGTTGTCATCTTTCTCTGAACTA 58.850 40.000 0.00 0.00 0.00 2.24
202 204 4.745125 TGTCGTTGTCATCTTTCTCTGAAC 59.255 41.667 0.00 0.00 0.00 3.18
221 223 4.891627 AGACTCATCATAGTCAGTGTCG 57.108 45.455 6.76 0.00 46.89 4.35
239 241 9.376075 TCATAAGAATCATCAAACTGAGAAGAC 57.624 33.333 0.00 0.00 0.00 3.01
291 293 5.488341 TCTAAATCTTTTGAAGCGCCTAGT 58.512 37.500 2.29 0.00 0.00 2.57
292 294 5.812642 TCTCTAAATCTTTTGAAGCGCCTAG 59.187 40.000 2.29 0.00 0.00 3.02
293 295 5.730550 TCTCTAAATCTTTTGAAGCGCCTA 58.269 37.500 2.29 0.00 0.00 3.93
296 298 6.304208 CACTTTCTCTAAATCTTTTGAAGCGC 59.696 38.462 0.00 0.00 0.00 5.92
311 313 5.640158 TTGGGGTTTCTTCACTTTCTCTA 57.360 39.130 0.00 0.00 0.00 2.43
365 368 7.227512 CCTTATAACTGCATCCCTAAACTCTTG 59.772 40.741 0.00 0.00 0.00 3.02
377 380 6.824305 AATGCCATACCTTATAACTGCATC 57.176 37.500 0.00 0.00 37.22 3.91
378 381 7.094205 GCTTAATGCCATACCTTATAACTGCAT 60.094 37.037 0.00 0.00 39.68 3.96
424 428 9.587772 CCTACACCTATTATTATCATTCTTCCG 57.412 37.037 0.00 0.00 0.00 4.30
477 481 2.028112 CAGACTAGCAAGGCAGTACCAA 60.028 50.000 0.00 0.00 43.14 3.67
483 487 2.289320 ACTTGTCAGACTAGCAAGGCAG 60.289 50.000 11.50 0.60 42.60 4.85
515 519 8.886719 CATCATTGAAACTTGTTATCTGCTAGA 58.113 33.333 0.00 0.00 0.00 2.43
518 522 6.327934 GCATCATTGAAACTTGTTATCTGCT 58.672 36.000 0.00 0.00 0.00 4.24
537 541 1.064758 GGTGGACAATAGTGGGCATCA 60.065 52.381 0.00 0.00 0.00 3.07
543 547 4.469945 TCTTTCCTAGGTGGACAATAGTGG 59.530 45.833 9.08 0.00 46.14 4.00
548 552 4.104102 TGTTGTCTTTCCTAGGTGGACAAT 59.896 41.667 29.68 0.00 46.14 2.71
582 586 1.412079 TGGCTGCAATCTTTGTTGGT 58.588 45.000 0.50 0.00 0.00 3.67
583 587 2.529780 TTGGCTGCAATCTTTGTTGG 57.470 45.000 0.50 0.00 0.00 3.77
590 594 6.704310 ACTTTTTCATATTTGGCTGCAATCT 58.296 32.000 0.50 0.00 0.00 2.40
609 613 8.517878 CACATTGGATTAGAACTGATGACTTTT 58.482 33.333 0.00 0.00 0.00 2.27
612 616 6.118170 CCACATTGGATTAGAACTGATGACT 58.882 40.000 0.00 0.00 40.96 3.41
627 631 0.889994 GTGCAATCTGCCACATTGGA 59.110 50.000 0.00 0.00 44.23 3.53
666 670 6.233434 ACTGACATTCACACACATATGTTCT 58.767 36.000 5.37 0.00 36.72 3.01
670 674 6.966435 TGTACTGACATTCACACACATATG 57.034 37.500 0.00 0.00 0.00 1.78
870 874 5.163152 ACCCTCTTTCAGAGAAGTCAAACAT 60.163 40.000 2.13 0.00 45.07 2.71
877 881 5.373812 TTGAAACCCTCTTTCAGAGAAGT 57.626 39.130 2.13 0.00 45.07 3.01
880 884 6.467677 CAGTATTGAAACCCTCTTTCAGAGA 58.532 40.000 2.13 0.00 45.07 3.10
888 892 5.964477 TCTACATCCAGTATTGAAACCCTCT 59.036 40.000 0.00 0.00 30.93 3.69
900 904 8.822805 AGTCCAATTACTTTTCTACATCCAGTA 58.177 33.333 0.00 0.00 0.00 2.74
901 905 7.607991 CAGTCCAATTACTTTTCTACATCCAGT 59.392 37.037 0.00 0.00 0.00 4.00
927 931 3.005791 CACCTTTGAAGAAACACCCATCC 59.994 47.826 0.00 0.00 0.00 3.51
967 971 5.242171 TGGCATATCTTTCCAATGCACATAG 59.758 40.000 8.59 0.00 46.18 2.23
1008 1012 2.297895 AACCACTGCCCAGGCGATA 61.298 57.895 3.83 0.00 45.51 2.92
1020 1024 4.103153 TCATTGGTCTCTTTCTCAACCACT 59.897 41.667 0.00 0.00 41.34 4.00
1126 1130 5.263599 ACAACATTGATGATGCCCTCTTTA 58.736 37.500 0.43 0.00 39.47 1.85
1127 1131 4.091549 ACAACATTGATGATGCCCTCTTT 58.908 39.130 0.43 0.00 39.47 2.52
1130 1134 2.360165 GGACAACATTGATGATGCCCTC 59.640 50.000 0.43 0.00 39.47 4.30
1144 1148 1.547675 GGAGCCCAATTCTGGACAACA 60.548 52.381 0.00 0.00 46.92 3.33
1146 1150 0.039618 GGGAGCCCAATTCTGGACAA 59.960 55.000 0.00 0.00 46.92 3.18
1205 1209 9.886132 TTTAATTATGTACTCTTTCCTCCAGTC 57.114 33.333 0.00 0.00 0.00 3.51
1238 1242 4.402155 TGCACAATTCCAGAACAGTTTCTT 59.598 37.500 0.00 0.00 40.34 2.52
1246 1250 2.036346 AGCCTTTGCACAATTCCAGAAC 59.964 45.455 0.00 0.00 41.13 3.01
1272 1276 6.389830 TTGCATAGTTGAACAAACTCACAT 57.610 33.333 0.00 0.00 46.60 3.21
1363 1367 3.902881 AACCTGAACCATGCTCTAGAG 57.097 47.619 15.85 15.85 0.00 2.43
1434 1438 9.044150 GCAAGAATCTAGCATCTATTATCCATC 57.956 37.037 0.00 0.00 0.00 3.51
1480 1484 4.393062 ACCATCACTTTTTGTCTGATAGCG 59.607 41.667 0.00 0.00 0.00 4.26
1495 1499 5.779241 TTTCCTGGATTCTAACCATCACT 57.221 39.130 0.00 0.00 36.79 3.41
1523 1527 4.837860 TCCTGTCCATTTAAGGCATTTTGT 59.162 37.500 0.00 0.00 0.00 2.83
1578 1583 8.819974 GGGTAGAATATTCAATGCATTTGTTTG 58.180 33.333 17.56 0.00 36.65 2.93
1601 1606 2.158682 TGCATATAGGTTCGCATTGGGT 60.159 45.455 0.24 0.00 0.00 4.51
1609 1614 5.056480 TCTTGACCATTGCATATAGGTTCG 58.944 41.667 0.00 0.00 33.77 3.95
1672 1677 6.660521 TGCAATTCAGTCTATTCAAATCCACT 59.339 34.615 0.00 0.00 0.00 4.00
1699 1704 1.910580 GCTAGCTGCCAGTACCCCAA 61.911 60.000 7.70 0.00 35.15 4.12
1716 1722 2.546899 TGTACACCAGGTAATCCAGCT 58.453 47.619 0.00 0.00 32.72 4.24
1722 1728 3.951563 ATGGCATGTACACCAGGTAAT 57.048 42.857 10.63 0.00 39.88 1.89
1729 1735 1.818060 TGCTGAAATGGCATGTACACC 59.182 47.619 0.00 0.00 34.56 4.16
1759 1768 6.310467 GCTATGTAACGAGACAAATCACTTGA 59.690 38.462 0.00 0.00 38.50 3.02
1842 1851 0.892814 GCCAGCTAGCCATTCCATCC 60.893 60.000 12.13 0.00 0.00 3.51
1972 1981 5.880054 ATTACTGTGCATGTCTTTGGTAC 57.120 39.130 0.00 0.00 0.00 3.34
1984 1993 6.090763 CACTTCGAACATCTTATTACTGTGCA 59.909 38.462 0.00 0.00 0.00 4.57
1989 1998 7.148407 CCTTTGCACTTCGAACATCTTATTACT 60.148 37.037 0.00 0.00 0.00 2.24
1992 2001 5.705441 TCCTTTGCACTTCGAACATCTTATT 59.295 36.000 0.00 0.00 0.00 1.40
1995 2004 3.251004 GTCCTTTGCACTTCGAACATCTT 59.749 43.478 0.00 0.00 0.00 2.40
2032 2042 8.458843 GGCTGCTTTCTTTTATATGACAAGTTA 58.541 33.333 0.00 0.00 0.00 2.24
2073 2083 9.965902 AAGAGAATTTTCACTAACCTACATCAT 57.034 29.630 0.00 0.00 0.00 2.45
2077 2087 8.429641 ACTGAAGAGAATTTTCACTAACCTACA 58.570 33.333 0.00 0.00 31.66 2.74
2079 2089 9.847224 AAACTGAAGAGAATTTTCACTAACCTA 57.153 29.630 0.00 0.00 31.66 3.08


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

AutoCloner maintained by Alex Coulton.