Multiple sequence alignment - TraesCS7A01G202600

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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 TraesCS7A01G202600 chr7A 100.000 2627 0 0 1 2627 164396504 164399130 0.000000e+00 4852.0
1 TraesCS7A01G202600 chr7A 78.947 133 26 2 147 278 5154363 5154494 3.600000e-14 89.8
2 TraesCS7A01G202600 chr7B 93.341 1667 80 10 1 1639 125501204 125502867 0.000000e+00 2435.0
3 TraesCS7A01G202600 chr7B 93.687 998 42 9 1640 2627 125502898 125503884 0.000000e+00 1474.0
4 TraesCS7A01G202600 chr7D 92.696 1684 74 11 1 1639 163253345 163255024 0.000000e+00 2383.0
5 TraesCS7A01G202600 chr7D 92.323 1003 47 14 1640 2627 163255061 163256048 0.000000e+00 1399.0


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 TraesCS7A01G202600 chr7A 164396504 164399130 2626 False 4852.0 4852 100.0000 1 2627 1 chr7A.!!$F2 2626
1 TraesCS7A01G202600 chr7B 125501204 125503884 2680 False 1954.5 2435 93.5140 1 2627 2 chr7B.!!$F1 2626
2 TraesCS7A01G202600 chr7D 163253345 163256048 2703 False 1891.0 2383 92.5095 1 2627 2 chr7D.!!$F1 2626

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
988 1021 0.323178 AACAGCTCCCCTTGCATCAG 60.323 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 2604 0.391263 GTGCCGAAGTAGGGAACTGG 60.391 60.0 0.0 0.0 43.88 4.0 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
28 29 7.912056 AGATAACATTGCATTCATAGCGTAT 57.088 32.000 0.00 0.00 33.85 3.06
45 46 6.616774 AGCGTATGTCTAGTTTCCTAGTAC 57.383 41.667 0.00 0.00 41.31 2.73
98 99 5.789643 CTCCAAAATTGAAGGAGTGGAAA 57.210 39.130 11.17 0.00 43.11 3.13
125 141 9.796180 TCTAGAGTAGATTTATCCACTAGGTTC 57.204 37.037 0.00 0.00 28.93 3.62
143 159 2.441164 TGTGGGGCACAAGCGTTT 60.441 55.556 0.00 0.00 41.69 3.60
247 263 6.525976 GCAAATAGAAAGAAGTGTCAAGCATC 59.474 38.462 0.00 0.00 0.00 3.91
340 357 9.023967 CATTCTAGTTGCTTATTTTATTGCCAC 57.976 33.333 0.00 0.00 0.00 5.01
345 362 7.092716 AGTTGCTTATTTTATTGCCACTTCTG 58.907 34.615 0.00 0.00 29.02 3.02
397 414 8.034215 TGACTTGAATTTATTATGGTTTGCAGG 58.966 33.333 0.00 0.00 0.00 4.85
513 530 7.281774 GGATCTGCTACAATCAATTTTCTCTCA 59.718 37.037 0.00 0.00 0.00 3.27
527 544 6.365970 TTTTCTCTCACTTAGGCTCAATCT 57.634 37.500 0.00 0.00 0.00 2.40
528 545 4.998671 TCTCTCACTTAGGCTCAATCTG 57.001 45.455 0.00 0.00 0.00 2.90
657 674 3.002246 CCCAATATTCGTGTCCATGTTCG 59.998 47.826 0.00 0.00 0.00 3.95
745 762 4.643387 GCCACCGGCCTTCACTGT 62.643 66.667 0.00 0.00 44.06 3.55
882 915 4.219944 GGCCCATTACGTGATGACTATAGA 59.780 45.833 20.86 0.00 0.00 1.98
988 1021 0.323178 AACAGCTCCCCTTGCATCAG 60.323 55.000 0.00 0.00 0.00 2.90
1059 1092 3.344515 GGTTGGAAGTGATACTTGGTCC 58.655 50.000 0.00 0.00 38.80 4.46
1109 1142 8.827832 ATAATTCAGATTGTGGAATTCAAGGA 57.172 30.769 7.93 0.00 41.45 3.36
1141 1174 2.283298 CCATGGATCTTCGTCAACAGG 58.717 52.381 5.56 0.00 0.00 4.00
1182 1215 1.003580 CCCAAGCTTAGACTGCAGGAA 59.996 52.381 19.93 8.18 32.20 3.36
1186 1219 5.128919 CCAAGCTTAGACTGCAGGAAATAT 58.871 41.667 19.93 0.00 32.20 1.28
1230 1263 0.178992 CCAAGAGTTGCCAAGACCCA 60.179 55.000 0.00 0.00 0.00 4.51
1431 1464 2.820787 GGGGAGTGATATCAGGAGTACG 59.179 54.545 5.42 0.00 0.00 3.67
1525 1558 5.789574 ACCTTGGAGTGAATATGGGTTAA 57.210 39.130 0.00 0.00 0.00 2.01
1530 1563 4.947388 TGGAGTGAATATGGGTTAAGCAAC 59.053 41.667 7.03 0.00 0.00 4.17
1615 1660 0.315251 CCCGAGCATGCTCTATTCGA 59.685 55.000 37.44 0.00 40.69 3.71
1661 1742 9.408648 TGTATTATTGGGAAATTTCCTCTTCTC 57.591 33.333 31.23 17.05 46.72 2.87
1742 1823 4.271807 TGCATTATATTTTGGTCCCCCA 57.728 40.909 0.00 0.00 39.65 4.96
1776 1857 7.145932 ACTTTGTAAGAGATGTTTATGGTGC 57.854 36.000 0.00 0.00 0.00 5.01
1806 1887 3.583086 ACTGCTTAAGCTGAACCTCCTAA 59.417 43.478 33.10 8.21 41.71 2.69
1855 1944 7.826744 TGTTTAATGTTGCACTGGATAGATGTA 59.173 33.333 0.00 0.00 0.00 2.29
1905 1994 7.152645 TCATTTTCTACTGTCGAGCTTTAAGT 58.847 34.615 0.00 0.00 0.00 2.24
1906 1995 8.301720 TCATTTTCTACTGTCGAGCTTTAAGTA 58.698 33.333 0.00 0.00 0.00 2.24
1909 1998 7.627298 TTCTACTGTCGAGCTTTAAGTATCT 57.373 36.000 0.00 0.00 0.00 1.98
2031 2120 2.548057 TCGAGTTGCATCACCTTGTTTC 59.452 45.455 0.00 0.00 0.00 2.78
2046 2135 6.957077 CACCTTGTTTCCATAATTAACGTACG 59.043 38.462 15.01 15.01 0.00 3.67
2051 2140 8.254178 TGTTTCCATAATTAACGTACGTCATT 57.746 30.769 23.05 22.60 0.00 2.57
2310 2399 0.676466 CGGCAGCCCACAAGATTGTA 60.676 55.000 5.63 0.00 39.91 2.41
2311 2400 0.811281 GGCAGCCCACAAGATTGTAC 59.189 55.000 0.00 0.00 39.91 2.90
2312 2401 1.614317 GGCAGCCCACAAGATTGTACT 60.614 52.381 0.00 0.00 39.91 2.73
2313 2402 1.740025 GCAGCCCACAAGATTGTACTC 59.260 52.381 0.00 0.00 39.91 2.59
2314 2403 2.616510 GCAGCCCACAAGATTGTACTCT 60.617 50.000 0.00 0.00 39.91 3.24
2376 2466 0.755686 GCCCATCACACCAACCAAAA 59.244 50.000 0.00 0.00 0.00 2.44
2402 2492 5.474532 ACAATGACATGAACAGCAGTACAAT 59.525 36.000 0.00 0.00 0.00 2.71
2582 2687 2.626780 GGCACGGCAAAAGAGACCC 61.627 63.158 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.833285 ATCTACTCTAGATTTCCACTCCTTC 57.167 40.000 0.00 0.00 42.70 3.46
118 134 0.400213 TTGTGCCCCACAGAACCTAG 59.600 55.000 0.00 0.00 45.39 3.02
125 141 2.489275 AAACGCTTGTGCCCCACAG 61.489 57.895 0.00 0.00 45.39 3.66
154 170 4.336889 TGTTATCCTAGCCACACTATGC 57.663 45.455 0.00 0.00 0.00 3.14
217 233 7.750229 TGACACTTCTTTCTATTTGCAGATT 57.250 32.000 0.00 0.00 0.00 2.40
228 244 4.965814 TCTGATGCTTGACACTTCTTTCT 58.034 39.130 0.00 0.00 0.00 2.52
340 357 7.488187 TTGAAAGAATGAGTCACTTCAGAAG 57.512 36.000 8.77 8.77 33.98 2.85
345 362 9.741647 AAAGAAATTGAAAGAATGAGTCACTTC 57.258 29.630 0.00 1.19 0.00 3.01
397 414 1.031571 TTTGCATGATGGCGACCTCC 61.032 55.000 0.00 0.00 36.28 4.30
447 464 1.831736 CTTGGAGTCCGAACATAGGGT 59.168 52.381 4.30 0.00 0.00 4.34
481 498 3.031013 TGATTGTAGCAGATCCTTCGGA 58.969 45.455 0.00 0.00 35.55 4.55
494 511 8.394121 GCCTAAGTGAGAGAAAATTGATTGTAG 58.606 37.037 0.00 0.00 0.00 2.74
513 530 3.618690 GGTCACAGATTGAGCCTAAGT 57.381 47.619 0.00 0.00 45.55 2.24
527 544 0.468226 ACAAAGGCGAGAAGGTCACA 59.532 50.000 0.00 0.00 0.00 3.58
528 545 1.264288 CAACAAAGGCGAGAAGGTCAC 59.736 52.381 0.00 0.00 0.00 3.67
657 674 2.936498 CCATTGTTACATGGAGGACGAC 59.064 50.000 0.00 0.00 40.30 4.34
745 762 9.577110 GTCTGCAAAATTTCTTCATCAATATGA 57.423 29.630 0.00 0.00 40.43 2.15
882 915 5.189180 GGAATATCAGACCAGTTGAGCTTT 58.811 41.667 0.00 0.00 0.00 3.51
934 967 7.361885 GCTGCAGTAAGACTCTGTAACTAGTTA 60.362 40.741 16.64 11.38 35.60 2.24
988 1021 5.535157 GCTAACAAGCATATGCGAGTTTGC 61.535 45.833 33.62 33.62 44.92 3.68
1015 1048 3.117851 GGCCAACTAAATAAGGAGAGGCT 60.118 47.826 0.00 0.00 37.47 4.58
1107 1140 2.109774 TCCATGGCAATGAATTGGTCC 58.890 47.619 6.96 0.00 38.21 4.46
1109 1142 3.649843 AGATCCATGGCAATGAATTGGT 58.350 40.909 6.96 0.00 38.21 3.67
1141 1174 3.477530 GGGCCATCTCCAAAGTGTATAC 58.522 50.000 4.39 0.00 0.00 1.47
1182 1215 0.769247 GGGGGCGGTTAGTGGATATT 59.231 55.000 0.00 0.00 0.00 1.28
1230 1263 8.099537 CAGACCACTAGCCATGATATTTTAGAT 58.900 37.037 0.00 0.00 0.00 1.98
1431 1464 4.022068 TCTGGGTTCATGCAAGAAAATGAC 60.022 41.667 5.85 0.00 32.63 3.06
1525 1558 0.179062 GATGGATCTGGCTCGTTGCT 60.179 55.000 0.00 0.00 42.39 3.91
1615 1660 1.064463 ACGTGATGATCAAGGGCCATT 60.064 47.619 12.73 0.00 30.01 3.16
1701 1782 1.534729 AAGGTTGAATTCCGAGTGCC 58.465 50.000 2.27 0.00 0.00 5.01
1776 1857 6.595716 AGGTTCAGCTTAAGCAGTAATACAAG 59.404 38.462 28.39 5.85 45.16 3.16
1962 2051 4.018050 AGTGGCCTTTCTGTCAATAATCCT 60.018 41.667 3.32 0.00 0.00 3.24
2031 2120 9.205916 CAAAAGAATGACGTACGTTAATTATGG 57.794 33.333 23.70 11.70 0.00 2.74
2046 2135 8.369218 ACCAATTGTGAATTCAAAAGAATGAC 57.631 30.769 16.02 0.00 0.00 3.06
2075 2164 3.365969 CGCCAATCAAGTCAAAAGGTACC 60.366 47.826 2.73 2.73 0.00 3.34
2172 2261 4.454678 GGTTGTCATCATGAGGCATTCTA 58.545 43.478 1.57 0.00 0.00 2.10
2310 2399 4.649674 TCGGAGGCAATCAATTAGTAGAGT 59.350 41.667 0.00 0.00 0.00 3.24
2311 2400 5.201713 TCGGAGGCAATCAATTAGTAGAG 57.798 43.478 0.00 0.00 0.00 2.43
2312 2401 5.808366 ATCGGAGGCAATCAATTAGTAGA 57.192 39.130 0.00 0.00 0.00 2.59
2313 2402 7.962964 TTTATCGGAGGCAATCAATTAGTAG 57.037 36.000 0.00 0.00 0.00 2.57
2314 2403 8.918202 AATTTATCGGAGGCAATCAATTAGTA 57.082 30.769 0.00 0.00 0.00 1.82
2326 2415 3.877508 AGTGCTGTTAATTTATCGGAGGC 59.122 43.478 0.00 0.00 0.00 4.70
2376 2466 3.748083 ACTGCTGTTCATGTCATTGTCT 58.252 40.909 0.00 0.00 0.00 3.41
2465 2555 7.307219 GCCACTAAGGAAAATATTACTACGCAG 60.307 40.741 0.00 0.00 41.22 5.18
2514 2604 0.391263 GTGCCGAAGTAGGGAACTGG 60.391 60.000 0.00 0.00 43.88 4.00


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

AutoCloner maintained by Alex Coulton.