Multiple sequence alignment - TraesCS7D01G051900

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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 TraesCS7D01G051900 chr7D 100.000 2591 0 0 1 2591 27114036 27111446 0 4785
1 TraesCS7D01G051900 chr5D 83.206 2626 342 53 2 2586 482840364 482837797 0 2314
2 TraesCS7D01G051900 chr2A 90.411 1387 121 8 1 1376 738302428 738301043 0 1814
3 TraesCS7D01G051900 chr2A 90.822 1144 98 4 1452 2591 738300988 738299848 0 1524
4 TraesCS7D01G051900 chr3A 76.997 1765 314 65 36 1749 743325897 743324174 0 926
5 TraesCS7D01G051900 chr3D 76.998 1739 304 71 36 1726 343472920 343474610 0 907
6 TraesCS7D01G051900 chr3D 76.980 1742 299 76 36 1726 64827826 64826136 0 902


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 TraesCS7D01G051900 chr7D 27111446 27114036 2590 True 4785 4785 100.0000 1 2591 1 chr7D.!!$R1 2590
1 TraesCS7D01G051900 chr5D 482837797 482840364 2567 True 2314 2314 83.2060 2 2586 1 chr5D.!!$R1 2584
2 TraesCS7D01G051900 chr2A 738299848 738302428 2580 True 1669 1814 90.6165 1 2591 2 chr2A.!!$R1 2590
3 TraesCS7D01G051900 chr3A 743324174 743325897 1723 True 926 926 76.9970 36 1749 1 chr3A.!!$R1 1713
4 TraesCS7D01G051900 chr3D 343472920 343474610 1690 False 907 907 76.9980 36 1726 1 chr3D.!!$F1 1690
5 TraesCS7D01G051900 chr3D 64826136 64827826 1690 True 902 902 76.9800 36 1726 1 chr3D.!!$R1 1690

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
31 33 0.321919 GCATCTGCCTGTGAGAACCA 60.322 55.0 0.00 0.0 34.31 3.67 F
269 271 0.998928 TTGGGATAGCAAGGCCTGAA 59.001 50.0 5.69 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1409 0.109597 CATTTCGCACCTCACCAAGC 60.110 55.0 0.0 0.0 0.0 4.01 R
2162 2221 0.103208 ATCAATCGACACGCCTCTCC 59.897 55.0 0.0 0.0 0.0 3.71 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
31 33 0.321919 GCATCTGCCTGTGAGAACCA 60.322 55.000 0.00 0.00 34.31 3.67
78 80 1.068474 GTTTCACACGCGAGCTACAT 58.932 50.000 15.93 0.00 0.00 2.29
190 192 4.065789 GGGTTACTCACTGACAAAGAAGG 58.934 47.826 0.00 0.00 0.00 3.46
209 211 1.412343 GGAAATGTTGGTTGTGCAGGT 59.588 47.619 0.00 0.00 0.00 4.00
269 271 0.998928 TTGGGATAGCAAGGCCTGAA 59.001 50.000 5.69 0.00 0.00 3.02
316 318 4.075793 TGGGAGAGCCGGCCTAGT 62.076 66.667 26.15 3.43 33.83 2.57
405 407 2.568090 GCGACAAGTGGGCATTGG 59.432 61.111 0.00 0.00 31.76 3.16
409 411 1.883275 CGACAAGTGGGCATTGGTAAA 59.117 47.619 0.00 0.00 31.76 2.01
449 454 6.789262 AGTACATGTGATTTCTTTGCTATGC 58.211 36.000 9.11 0.00 0.00 3.14
631 642 4.740268 AGTAAAGATGCACGAATGTACGA 58.260 39.130 0.00 0.00 37.03 3.43
633 644 1.545759 AGATGCACGAATGTACGACG 58.454 50.000 0.00 0.00 37.03 5.12
770 782 8.134895 GGAGTCAATTTGTAACATCAGTCAAAA 58.865 33.333 0.00 0.00 34.32 2.44
827 839 2.912956 GGATGACCTGGATTATGGCCTA 59.087 50.000 3.32 0.00 0.00 3.93
854 866 4.454847 GCAAGTATGATGGATGAGGATGTG 59.545 45.833 0.00 0.00 0.00 3.21
1133 1156 6.888088 GGTAATGTGACCCAGGTACTAAAAAT 59.112 38.462 0.00 0.00 34.60 1.82
1136 1159 3.442625 GTGACCCAGGTACTAAAAATGCC 59.557 47.826 0.00 0.00 36.02 4.40
1140 1163 3.370103 CCCAGGTACTAAAAATGCCTCGA 60.370 47.826 0.00 0.00 36.02 4.04
1286 1309 4.100498 AGGCCTGCAAGAAAAATATCCATG 59.900 41.667 3.11 0.00 34.07 3.66
1292 1317 6.416415 TGCAAGAAAAATATCCATGGCATTT 58.584 32.000 6.96 12.14 0.00 2.32
1293 1318 6.885376 TGCAAGAAAAATATCCATGGCATTTT 59.115 30.769 21.84 21.84 34.24 1.82
1304 1329 7.860649 ATCCATGGCATTTTATCCATAACTT 57.139 32.000 6.96 0.00 40.88 2.66
1354 1379 2.400467 ACCTTGGTCACTACTGGAGT 57.600 50.000 0.00 0.00 39.82 3.85
1399 1424 2.031012 CAGCTTGGTGAGGTGCGA 59.969 61.111 0.00 0.00 45.85 5.10
1403 1428 0.109597 GCTTGGTGAGGTGCGAAATG 60.110 55.000 0.00 0.00 0.00 2.32
1423 1449 6.877611 AATGAAAAACTGTAACTCGTGGAT 57.122 33.333 0.00 0.00 0.00 3.41
1517 1563 3.815401 GCTTACCTGAAGAAGCAGTTTGA 59.185 43.478 1.86 0.00 45.99 2.69
1539 1585 6.042777 TGAGTATGAGGTGATTTCGATGAAC 58.957 40.000 0.00 0.00 0.00 3.18
1596 1646 2.421619 GAAGTCCTGTTCTGAGCAAGG 58.578 52.381 0.00 0.39 0.00 3.61
1627 1677 9.303537 CTTGGCTCTTTATCTACTAGTGTAAAC 57.696 37.037 5.39 0.00 0.00 2.01
1713 1767 5.865085 AGTAGTGGTGATTGTTTTAGCTCA 58.135 37.500 0.00 0.00 0.00 4.26
1769 1823 2.694829 GATATGCCGGCGTCGACCTT 62.695 60.000 27.77 4.05 39.00 3.50
1801 1855 2.445525 AGGGTGAGGGTGTGTATTTTGT 59.554 45.455 0.00 0.00 0.00 2.83
1868 1922 1.117150 CAGGCCATCTCATTTTGGGG 58.883 55.000 5.01 0.00 33.40 4.96
1938 1992 3.813166 AGATGGAATGTGACGACGTTTTT 59.187 39.130 0.13 0.00 31.06 1.94
2014 2068 3.552132 TCTGCAACAACAGAGTTGGTA 57.448 42.857 13.71 0.00 46.81 3.25
2026 2080 7.709613 ACAACAGAGTTGGTAAACTTACTACTG 59.290 37.037 13.71 0.00 46.84 2.74
2069 2123 3.165071 CTGGAGTTAAGCATTTTGGGGT 58.835 45.455 0.00 0.00 0.00 4.95
2087 2141 1.152777 TTGCTGTGTGGTTGGAGGG 60.153 57.895 0.00 0.00 0.00 4.30
2098 2152 1.369625 GTTGGAGGGAGTACATTGCG 58.630 55.000 0.00 0.00 0.00 4.85
2154 2209 1.663695 AAATAGGATGGTTGCCGTCG 58.336 50.000 1.78 0.00 40.24 5.12
2178 2237 0.608640 AAAGGAGAGGCGTGTCGATT 59.391 50.000 0.00 0.00 0.00 3.34
2185 2244 0.999406 AGGCGTGTCGATTGATTTCG 59.001 50.000 0.00 0.00 40.46 3.46
2194 2253 2.866156 TCGATTGATTTCGTGATGCCTC 59.134 45.455 0.00 0.00 40.03 4.70
2263 2324 7.488792 TCACATATGCAAAATACTGTGAAATGC 59.511 33.333 1.58 0.00 39.80 3.56
2286 2347 9.723601 ATGCATAATAACAACCATTGAAAAGTT 57.276 25.926 0.00 0.00 0.00 2.66
2303 2364 5.388225 AAAGTTTGCACATTTAACAAGCG 57.612 34.783 1.37 0.00 30.84 4.68
2367 2444 7.972277 GCATATGTAGGCATTTCAGGATTTATG 59.028 37.037 4.29 0.00 36.58 1.90
2398 2475 2.280524 CGCACCCAACTGAACGGA 60.281 61.111 0.00 0.00 0.00 4.69
2453 2530 5.048013 TCTGTATATTACATGGTCGAGCAGG 60.048 44.000 25.86 25.86 38.15 4.85
2537 2614 4.594123 TCCAGTGATCAAACTACGACAA 57.406 40.909 0.00 0.00 0.00 3.18
2552 2629 2.293399 ACGACAAATGGAGCTTGGTTTC 59.707 45.455 0.00 0.00 0.00 2.78
2554 2631 3.243367 CGACAAATGGAGCTTGGTTTCAA 60.243 43.478 0.00 0.00 0.00 2.69
2588 2665 1.300971 GGAAATGCAGCTCTCGCACA 61.301 55.000 0.00 0.00 43.35 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.483877 CTCACAGGCAGATGCGTTAAAA 59.516 45.455 0.00 0.00 43.26 1.52
15 17 0.247460 CGATGGTTCTCACAGGCAGA 59.753 55.000 0.00 0.00 0.00 4.26
78 80 6.464892 CCTGTTCCTCTGCCAGAATTATGATA 60.465 42.308 0.54 0.00 0.00 2.15
190 192 2.545742 GGACCTGCACAACCAACATTTC 60.546 50.000 0.00 0.00 0.00 2.17
209 211 2.367241 TGACATTCTTTCCGACACAGGA 59.633 45.455 0.00 0.00 38.79 3.86
269 271 2.225650 ACTACCCATCTCACCCTTCACT 60.226 50.000 0.00 0.00 0.00 3.41
316 318 5.781210 TTGTGCAGTTGGAATTTCATGTA 57.219 34.783 0.00 0.00 0.00 2.29
409 411 8.399425 TCACATGTACTTTACAAATTTGTCGTT 58.601 29.630 26.46 12.35 42.76 3.85
449 454 1.209747 GGTGGGGTAGAGCTGTTTAGG 59.790 57.143 0.00 0.00 0.00 2.69
631 642 3.134804 CCTCCACCTTATCTTCCATTCGT 59.865 47.826 0.00 0.00 0.00 3.85
633 644 3.117888 TGCCTCCACCTTATCTTCCATTC 60.118 47.826 0.00 0.00 0.00 2.67
827 839 3.244009 CCTCATCCATCATACTTGCGAGT 60.244 47.826 12.27 12.27 39.97 4.18
854 866 8.755696 TTGTTCATTGTAATTTGTATCCAAGC 57.244 30.769 0.00 0.00 0.00 4.01
941 962 3.414269 TGCAAAGCAATCATGAGTCAGA 58.586 40.909 0.09 0.00 34.76 3.27
943 964 4.794278 AATGCAAAGCAATCATGAGTCA 57.206 36.364 0.09 0.00 43.62 3.41
1121 1144 4.901868 TGTTCGAGGCATTTTTAGTACCT 58.098 39.130 0.00 0.00 0.00 3.08
1133 1156 2.636412 CGGAGGACTGTTCGAGGCA 61.636 63.158 0.00 0.00 0.00 4.75
1136 1159 2.422479 TGATTACGGAGGACTGTTCGAG 59.578 50.000 0.00 0.00 36.89 4.04
1140 1163 3.367087 CGAAGTGATTACGGAGGACTGTT 60.367 47.826 0.00 0.00 36.89 3.16
1286 1309 9.768662 AATGATCAAAGTTATGGATAAAATGCC 57.231 29.630 0.00 0.00 0.00 4.40
1292 1317 7.922278 GCTGCAAATGATCAAAGTTATGGATAA 59.078 33.333 0.00 0.00 0.00 1.75
1293 1318 7.428020 GCTGCAAATGATCAAAGTTATGGATA 58.572 34.615 0.00 0.00 0.00 2.59
1304 1329 1.739466 GTCCTCGCTGCAAATGATCAA 59.261 47.619 0.00 0.00 0.00 2.57
1354 1379 4.830600 TCGAGATACAGGCCATTGTATGTA 59.169 41.667 19.45 11.75 42.68 2.29
1384 1409 0.109597 CATTTCGCACCTCACCAAGC 60.110 55.000 0.00 0.00 0.00 4.01
1396 1421 5.113529 CACGAGTTACAGTTTTTCATTTCGC 59.886 40.000 0.00 0.00 0.00 4.70
1399 1424 6.687081 TCCACGAGTTACAGTTTTTCATTT 57.313 33.333 0.00 0.00 0.00 2.32
1403 1428 6.721321 TGAAATCCACGAGTTACAGTTTTTC 58.279 36.000 0.00 0.00 0.00 2.29
1447 1473 6.861065 TGAACAAGTTACTCACTCCAATTC 57.139 37.500 0.00 0.00 32.94 2.17
1448 1474 8.918202 TTATGAACAAGTTACTCACTCCAATT 57.082 30.769 0.00 0.00 32.94 2.32
1449 1475 8.918202 TTTATGAACAAGTTACTCACTCCAAT 57.082 30.769 0.00 0.00 32.94 3.16
1450 1476 8.918202 ATTTATGAACAAGTTACTCACTCCAA 57.082 30.769 0.00 0.00 32.94 3.53
1517 1563 5.043903 CGTTCATCGAAATCACCTCATACT 58.956 41.667 0.00 0.00 42.86 2.12
1539 1585 1.515521 GGAGTTCACCCTTGTTGCCG 61.516 60.000 0.00 0.00 0.00 5.69
1596 1646 5.017294 AGTAGATAAAGAGCCAAGTCTGC 57.983 43.478 0.00 0.00 0.00 4.26
1627 1677 7.141363 GCATTTCATAAACCCTTAGCACATAG 58.859 38.462 0.00 0.00 0.00 2.23
1713 1767 1.539869 ACACCAGCAGGAGGGATGT 60.540 57.895 0.35 0.00 38.69 3.06
1818 1872 1.888512 CACACAGGTTCCATCCCAAAG 59.111 52.381 0.00 0.00 0.00 2.77
1868 1922 1.398390 GATTCGATCCAACCACACAGC 59.602 52.381 0.00 0.00 0.00 4.40
1938 1992 6.702716 ACCAAACGGAAGAACAAGAATTTA 57.297 33.333 0.00 0.00 0.00 1.40
1982 2036 6.014242 TCTGTTGTTGCAGATAGGATATAGGG 60.014 42.308 0.00 0.00 40.23 3.53
2026 2080 9.391006 TCCAGTCCACTAAAAATTGTACATATC 57.609 33.333 0.00 0.00 0.00 1.63
2069 2123 1.152777 CCCTCCAACCACACAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
2087 2141 3.064207 TCAACAAGGACGCAATGTACTC 58.936 45.455 0.00 0.00 42.62 2.59
2098 2152 1.609072 GCCTTTCCAGTCAACAAGGAC 59.391 52.381 0.83 0.00 38.52 3.85
2138 2193 1.184431 TTACGACGGCAACCATCCTA 58.816 50.000 0.00 0.00 0.00 2.94
2162 2221 0.103208 ATCAATCGACACGCCTCTCC 59.897 55.000 0.00 0.00 0.00 3.71
2164 2223 2.271800 GAAATCAATCGACACGCCTCT 58.728 47.619 0.00 0.00 0.00 3.69
2178 2237 4.218200 ACAAATTGAGGCATCACGAAATCA 59.782 37.500 0.00 0.00 34.35 2.57
2185 2244 7.887996 TCAAAATAACAAATTGAGGCATCAC 57.112 32.000 0.00 0.00 34.35 3.06
2252 2313 7.225784 TGGTTGTTATTATGCATTTCACAGT 57.774 32.000 3.54 0.00 0.00 3.55
2263 2324 9.810231 GCAAACTTTTCAATGGTTGTTATTATG 57.190 29.630 5.41 0.00 34.36 1.90
2286 2347 2.881513 TCCTCGCTTGTTAAATGTGCAA 59.118 40.909 0.00 0.00 0.00 4.08
2303 2364 4.687483 CCAGCAACATCAACATTTTTCCTC 59.313 41.667 0.00 0.00 0.00 3.71
2367 2444 3.427425 TGCGCCACGGCATGTTAC 61.427 61.111 4.18 0.00 42.06 2.50
2398 2475 6.646240 GCACATCATCTGTTTACACCAAAAAT 59.354 34.615 0.00 0.00 35.29 1.82
2453 2530 6.100714 TCAGGTTTTAATCTATCACCCTACCC 59.899 42.308 0.00 0.00 0.00 3.69
2516 2593 4.594123 TTGTCGTAGTTTGATCACTGGA 57.406 40.909 0.00 0.00 0.00 3.86
2537 2614 5.574188 AGTCTATTGAAACCAAGCTCCATT 58.426 37.500 0.00 0.00 0.00 3.16
2552 2629 6.994496 TGCATTTCCCTTATGAGAGTCTATTG 59.006 38.462 0.00 0.00 0.00 1.90
2554 2631 6.743773 GCTGCATTTCCCTTATGAGAGTCTAT 60.744 42.308 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.