Multiple sequence alignment - TraesCS7A01G171300

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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 TraesCS7A01G171300 chr7A 100.000 3094 0 0 1 3094 126907611 126910704 0 5714
1 TraesCS7A01G171300 chr4A 91.008 3114 241 25 4 3094 544610261 544607164 0 4163
2 TraesCS7A01G171300 chr2A 89.578 2984 254 34 3 2941 756204022 756206993 0 3735
3 TraesCS7A01G171300 chr6A 86.220 2997 338 38 4 2939 42515370 42518352 0 3177
4 TraesCS7A01G171300 chr6A 86.153 2997 340 37 4 2939 42537745 42540727 0 3166
5 TraesCS7A01G171300 chr6A 84.784 3194 366 53 4 3094 42568448 42571624 0 3096
6 TraesCS7A01G171300 chr6A 85.634 3014 340 46 4 2939 42603064 42606062 0 3081
7 TraesCS7A01G171300 chr6A 85.506 3015 342 48 4 2939 42636658 42639656 0 3059
8 TraesCS7A01G171300 chr6A 85.283 3017 348 46 4 2939 42349311 42352312 0 3024
9 TraesCS7A01G171300 chr6A 88.070 2280 244 14 4 2264 42315061 42317331 0 2678
10 TraesCS7A01G171300 chr6A 88.273 1569 162 11 712 2264 42671064 42672626 0 1858
11 TraesCS7A01G171300 chr6A 81.651 872 112 19 2263 3094 42317359 42318222 0 680
12 TraesCS7A01G171300 chrUn 87.457 2017 209 19 283 2264 355072518 355074525 0 2283


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 TraesCS7A01G171300 chr7A 126907611 126910704 3093 False 5714 5714 100.0000 1 3094 1 chr7A.!!$F1 3093
1 TraesCS7A01G171300 chr4A 544607164 544610261 3097 True 4163 4163 91.0080 4 3094 1 chr4A.!!$R1 3090
2 TraesCS7A01G171300 chr2A 756204022 756206993 2971 False 3735 3735 89.5780 3 2941 1 chr2A.!!$F1 2938
3 TraesCS7A01G171300 chr6A 42515370 42518352 2982 False 3177 3177 86.2200 4 2939 1 chr6A.!!$F2 2935
4 TraesCS7A01G171300 chr6A 42537745 42540727 2982 False 3166 3166 86.1530 4 2939 1 chr6A.!!$F3 2935
5 TraesCS7A01G171300 chr6A 42568448 42571624 3176 False 3096 3096 84.7840 4 3094 1 chr6A.!!$F4 3090
6 TraesCS7A01G171300 chr6A 42603064 42606062 2998 False 3081 3081 85.6340 4 2939 1 chr6A.!!$F5 2935
7 TraesCS7A01G171300 chr6A 42636658 42639656 2998 False 3059 3059 85.5060 4 2939 1 chr6A.!!$F6 2935
8 TraesCS7A01G171300 chr6A 42349311 42352312 3001 False 3024 3024 85.2830 4 2939 1 chr6A.!!$F1 2935
9 TraesCS7A01G171300 chr6A 42671064 42672626 1562 False 1858 1858 88.2730 712 2264 1 chr6A.!!$F7 1552
10 TraesCS7A01G171300 chr6A 42315061 42318222 3161 False 1679 2678 84.8605 4 3094 2 chr6A.!!$F8 3090
11 TraesCS7A01G171300 chrUn 355072518 355074525 2007 False 2283 2283 87.4570 283 2264 1 chrUn.!!$F1 1981

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
592 596 0.108377 AAGCACACTGTGACACACGA 60.108 50.0 15.86 0.0 37.14 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2379 0.744281 TCGCACTTCTGTCAGACACA 59.256 50.0 0.78 0.0 0.0 3.72 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
48 49 3.138884 TGCTTTTGTGGCTCATGAGTA 57.861 42.857 23.38 10.77 0.00 2.59
141 143 1.285667 TGAATGATGGGTCAGCCACAT 59.714 47.619 0.00 1.05 37.87 3.21
208 210 5.431765 TGCCAAAAATGGTAAAACACACAT 58.568 33.333 0.00 0.00 0.00 3.21
235 237 2.099405 TGCAGACATGACCGATACAGA 58.901 47.619 0.00 0.00 0.00 3.41
268 270 1.734477 CAGTGGACCAAGTCGCTCG 60.734 63.158 0.00 0.00 32.65 5.03
305 307 3.733443 GTTGAGCAAACCAGAACCAAT 57.267 42.857 0.00 0.00 32.13 3.16
311 313 5.163322 TGAGCAAACCAGAACCAATGAAAAT 60.163 36.000 0.00 0.00 0.00 1.82
375 379 1.740664 GGTCCTTCTTTCCGGCGTC 60.741 63.158 6.01 0.00 0.00 5.19
384 388 3.793775 TTCCGGCGTCACGAAGCAA 62.794 57.895 0.00 0.00 37.55 3.91
399 403 6.480651 TCACGAAGCAAGTACTTTAACATGAA 59.519 34.615 5.07 0.00 0.00 2.57
434 438 9.840427 CAACTGTATATCTTGGTAAACCTTTTG 57.160 33.333 0.02 0.00 36.82 2.44
441 445 4.888823 TCTTGGTAAACCTTTTGTACCCAC 59.111 41.667 0.02 0.00 37.13 4.61
446 450 4.513406 AAACCTTTTGTACCCACTGAGA 57.487 40.909 0.00 0.00 0.00 3.27
533 537 3.235200 ACTGGCTCACTGACTAACTTCT 58.765 45.455 0.00 0.00 0.00 2.85
534 538 3.006323 ACTGGCTCACTGACTAACTTCTG 59.994 47.826 0.00 0.00 0.00 3.02
548 552 4.487714 AACTTCTGACAAGTTGTCCTCA 57.512 40.909 28.67 13.43 46.40 3.86
557 561 5.304357 TGACAAGTTGTCCTCACTTATCTGA 59.696 40.000 28.67 6.64 46.40 3.27
592 596 0.108377 AAGCACACTGTGACACACGA 60.108 50.000 15.86 0.00 37.14 4.35
606 610 1.258982 CACACGACAGCAAGAGACAAC 59.741 52.381 0.00 0.00 0.00 3.32
709 713 2.243736 GGTTGAACCATTCCCATCCCTA 59.756 50.000 9.98 0.00 38.42 3.53
779 801 5.715279 GGGTGGGATTTTAAAGAAGTAAGCT 59.285 40.000 0.00 0.00 0.00 3.74
1082 1115 1.987855 CGACAGGTTCAGGGGGCTA 60.988 63.158 0.00 0.00 0.00 3.93
1150 1183 7.367285 TGTGGACAAAGAATTAATGTTAGCAC 58.633 34.615 0.00 0.00 0.00 4.40
1183 1218 6.183360 TGTTTTGCTTGTTGGTGAGGAATAAT 60.183 34.615 0.00 0.00 0.00 1.28
1213 1248 5.664457 TGTGTGTGGCATTTACATTTTCAA 58.336 33.333 0.00 0.00 0.00 2.69
1237 1272 2.700773 GGTTTGCAGGGATGACGGC 61.701 63.158 0.00 0.00 0.00 5.68
1242 1277 1.819632 GCAGGGATGACGGCGAAAT 60.820 57.895 16.62 6.30 0.00 2.17
1370 1416 1.078759 CGTCGCTTCCTGTGGCTAAG 61.079 60.000 0.00 0.00 0.00 2.18
1371 1417 0.037232 GTCGCTTCCTGTGGCTAAGT 60.037 55.000 0.00 0.00 0.00 2.24
1379 1425 3.740115 TCCTGTGGCTAAGTTGAAGTTC 58.260 45.455 0.00 0.00 0.00 3.01
1391 1437 8.394121 GCTAAGTTGAAGTTCTTATTCTCATGG 58.606 37.037 4.17 0.00 0.00 3.66
1399 1445 5.639506 AGTTCTTATTCTCATGGTGTGAACG 59.360 40.000 0.00 0.00 36.14 3.95
1404 1450 3.893326 TCTCATGGTGTGAACGATGAT 57.107 42.857 4.37 0.00 35.03 2.45
1409 1455 5.487433 TCATGGTGTGAACGATGATAGTTT 58.513 37.500 0.00 0.00 31.51 2.66
1443 1489 4.264253 TGATTTTATGGACTGCTGGTCAG 58.736 43.478 11.29 0.00 46.16 3.51
1478 1524 4.003648 ACAAGGATGAAAAGACGGTGATC 58.996 43.478 0.00 0.00 0.00 2.92
1682 1728 0.802494 GCGTGTCACATAAACCCCAG 59.198 55.000 3.42 0.00 0.00 4.45
1754 1800 1.409790 CACATATGGGGCAATGTGGTG 59.590 52.381 7.80 0.00 45.94 4.17
1757 1803 0.395586 TATGGGGCAATGTGGTGAGC 60.396 55.000 0.00 0.00 0.00 4.26
1759 1805 2.345760 GGGGCAATGTGGTGAGCAG 61.346 63.158 0.00 0.00 0.00 4.24
1873 1922 2.519377 TGTACCTCCGTTCAACACTG 57.481 50.000 0.00 0.00 0.00 3.66
1886 1935 0.466189 AACACTGAGCCAGGTTGGTG 60.466 55.000 7.06 4.97 40.46 4.17
1926 1976 7.865707 AGGATCATATTTTTAGACGCATCAAC 58.134 34.615 0.00 0.00 0.00 3.18
2063 2114 0.669625 GGAACAAGGGAGACGTTCCG 60.670 60.000 4.90 0.00 46.63 4.30
2117 2168 2.366533 CCTGAAGATGAGCATGCAAGT 58.633 47.619 21.98 4.25 0.00 3.16
2121 2172 2.634815 AGATGAGCATGCAAGTAGGG 57.365 50.000 21.98 0.00 0.00 3.53
2147 2198 2.752238 AGACCGACTCCAGGCTCG 60.752 66.667 0.00 0.31 0.00 5.03
2187 2238 3.181493 CCTCGTGGTATTAGTAGTTGCGT 60.181 47.826 0.00 0.00 0.00 5.24
2189 2240 5.160699 TCGTGGTATTAGTAGTTGCGTAG 57.839 43.478 0.00 0.00 0.00 3.51
2246 2297 4.434713 AAACCACTAAGGCGCAAAATAG 57.565 40.909 10.83 8.06 43.14 1.73
2299 2379 8.785184 AGTATGACCTTAAGACCTATAAGCTT 57.215 34.615 3.48 3.48 0.00 3.74
2311 2391 4.772624 ACCTATAAGCTTGTGTCTGACAGA 59.227 41.667 11.41 7.21 35.44 3.41
2318 2398 0.744281 TGTGTCTGACAGAAGTGCGA 59.256 50.000 11.41 0.00 0.00 5.10
2374 2454 3.058016 CACTATCACTTTGTGGCTGTTGG 60.058 47.826 0.00 0.00 33.87 3.77
2387 2467 0.929824 CTGTTGGCAGTCGTTTTGCG 60.930 55.000 0.00 0.00 42.42 4.85
2390 2470 2.725815 GGCAGTCGTTTTGCGTGC 60.726 61.111 0.00 0.00 42.42 5.34
2451 2531 6.713792 TTGTTTGTGAAAAACAAAGTAGGC 57.286 33.333 11.03 0.00 44.97 3.93
2462 2542 4.546829 ACAAAGTAGGCGGATCAGTTTA 57.453 40.909 0.00 0.00 0.00 2.01
2493 2573 6.091441 GCGATTTACCTGATAATGAGGATGTC 59.909 42.308 0.00 0.00 34.37 3.06
2568 2656 2.798847 GTCGTGTTCCCTTGTTGTAGAC 59.201 50.000 0.00 0.00 0.00 2.59
2571 2659 3.139077 GTGTTCCCTTGTTGTAGACCTG 58.861 50.000 0.00 0.00 0.00 4.00
2645 2734 7.323656 CGTTTAGAAGCCAGAAAAACATAAGTG 59.676 37.037 0.00 0.00 31.85 3.16
2769 2862 3.312697 AGGTGCTCGAACTTTGAACTTTC 59.687 43.478 0.00 0.00 0.00 2.62
2771 2864 2.616842 TGCTCGAACTTTGAACTTTCCC 59.383 45.455 0.00 0.00 0.00 3.97
2797 2890 5.388890 GCGACAAAGTCACTCAGTTATCAAG 60.389 44.000 0.00 0.00 32.09 3.02
2832 2925 3.691575 TCATTTGGGGAAATGCTACGAA 58.308 40.909 0.00 0.00 39.39 3.85
2886 2981 7.113658 TGAGATTATTTGGTGAGGAGTAGAC 57.886 40.000 0.00 0.00 0.00 2.59
2899 2994 6.096987 GTGAGGAGTAGACAAGATCATGGTTA 59.903 42.308 2.59 0.00 0.00 2.85
2977 3099 5.266242 CGTGATGCAGGAAGCTAAAAATAC 58.734 41.667 0.00 0.00 45.94 1.89
3005 3127 3.303791 GCAGAACTTCCATTTTCGTTCGT 60.304 43.478 0.00 0.00 40.36 3.85
3026 3148 3.825908 TGAAGCTATTTCCCAAACCCT 57.174 42.857 0.00 0.00 34.77 4.34
3081 3203 4.922206 ACATGTCATATGGACCTTGTTGT 58.078 39.130 2.13 0.00 46.38 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.665745 TGGGATCAAGCTTTCTTTTGC 57.334 42.857 0.00 0.00 0.00 3.68
1 2 6.051074 AGTTTTGGGATCAAGCTTTCTTTTG 58.949 36.000 0.00 0.00 33.98 2.44
17 18 3.427368 GCCACAAAAGCAAAAGTTTTGGG 60.427 43.478 25.65 17.91 45.33 4.12
73 75 5.545588 CTTCACCATCATCCGAATCTACAT 58.454 41.667 0.00 0.00 0.00 2.29
158 160 5.582550 TCACAGTCATGAAGATACGTGATC 58.417 41.667 0.00 0.00 37.96 2.92
208 210 1.405463 CGGTCATGTCTGCAGCTACTA 59.595 52.381 9.47 0.00 0.00 1.82
235 237 1.228245 ACTGCTGCACCCATTTCGT 60.228 52.632 0.00 0.00 0.00 3.85
268 270 0.675633 AACCACCACATTTGCTGCTC 59.324 50.000 0.00 0.00 0.00 4.26
276 278 2.888834 GTTTGCTCAACCACCACATT 57.111 45.000 0.00 0.00 0.00 2.71
305 307 2.070783 GTTGGACGAGCCGTATTTTCA 58.929 47.619 0.09 0.00 41.37 2.69
311 313 1.287815 CACAGTTGGACGAGCCGTA 59.712 57.895 0.09 0.00 41.37 4.02
375 379 6.223138 TCATGTTAAAGTACTTGCTTCGTG 57.777 37.500 9.34 11.34 0.00 4.35
434 438 6.622896 GCACACATATTTTTCTCAGTGGGTAC 60.623 42.308 0.00 0.00 33.19 3.34
441 445 5.050644 TGCAGCACACATATTTTTCTCAG 57.949 39.130 0.00 0.00 0.00 3.35
446 450 4.751060 CCATCTGCAGCACACATATTTTT 58.249 39.130 9.47 0.00 0.00 1.94
481 485 2.193536 AAAACCCTGTGCACGAGCC 61.194 57.895 13.13 0.00 41.13 4.70
534 538 5.784177 TCAGATAAGTGAGGACAACTTGTC 58.216 41.667 12.81 12.81 46.23 3.18
592 596 4.392047 TGATTCATGTTGTCTCTTGCTGT 58.608 39.130 0.00 0.00 0.00 4.40
606 610 1.064906 ACCAGTCCCTGCTGATTCATG 60.065 52.381 0.00 0.00 38.70 3.07
709 713 4.834496 TGAACCTTGAAATTGCTTCAGGAT 59.166 37.500 4.38 0.00 44.84 3.24
779 801 6.671614 AACGATGAATTGTATCCGCTTTTA 57.328 33.333 0.00 0.00 0.00 1.52
784 806 5.339611 GCAATAAACGATGAATTGTATCCGC 59.660 40.000 0.00 0.00 33.96 5.54
818 840 7.496529 TTCTTTCTCATCGATGTTTTCTTGT 57.503 32.000 24.09 0.00 0.00 3.16
885 910 5.790593 TGCAAAAGTCCTGGTAGTTAGTAG 58.209 41.667 0.00 0.00 0.00 2.57
897 922 2.250924 CCCATTTCCTGCAAAAGTCCT 58.749 47.619 0.00 0.00 0.00 3.85
944 969 0.532573 ATGTCTTGTCCTGACGCGAT 59.467 50.000 15.93 0.00 37.26 4.58
946 971 0.388520 TGATGTCTTGTCCTGACGCG 60.389 55.000 3.53 3.53 37.26 6.01
1082 1115 1.005394 AACGAAGCGTGGGTCGAAT 60.005 52.632 0.00 0.00 39.99 3.34
1123 1156 8.584157 TGCTAACATTAATTCTTTGTCCACATT 58.416 29.630 0.00 0.00 0.00 2.71
1150 1183 3.556775 CCAACAAGCAAAACAATCAGTGG 59.443 43.478 0.00 0.00 0.00 4.00
1183 1218 0.751452 AATGCCACACACAACATGCA 59.249 45.000 0.00 0.00 0.00 3.96
1213 1248 1.988107 TCATCCCTGCAAACCTCTTCT 59.012 47.619 0.00 0.00 0.00 2.85
1237 1272 5.853936 TCTATGTAATCCCAGTCCATTTCG 58.146 41.667 0.00 0.00 0.00 3.46
1242 1277 7.567250 TCATAGTTTCTATGTAATCCCAGTCCA 59.433 37.037 13.95 0.00 0.00 4.02
1370 1416 7.173218 TCACACCATGAGAATAAGAACTTCAAC 59.827 37.037 0.00 0.00 31.91 3.18
1371 1417 7.223584 TCACACCATGAGAATAAGAACTTCAA 58.776 34.615 0.00 0.00 31.91 2.69
1379 1425 5.812127 TCATCGTTCACACCATGAGAATAAG 59.188 40.000 0.00 0.00 38.99 1.73
1391 1437 5.607119 ACCAAAACTATCATCGTTCACAC 57.393 39.130 0.00 0.00 0.00 3.82
1443 1489 3.260884 TCATCCTTGTCCAGAAGGTACAC 59.739 47.826 2.60 0.00 42.89 2.90
1478 1524 2.280524 TCGGTTGGGTCAAGCACG 60.281 61.111 9.90 2.86 41.25 5.34
1696 1742 1.780860 GCACGATTTTGTGTGTTCTGC 59.219 47.619 0.00 0.00 41.94 4.26
1914 1963 4.123506 TCACAACAAAGTTGATGCGTCTA 58.876 39.130 15.99 0.00 34.71 2.59
1926 1976 8.450964 TCTCTTTGTAGACTTTTCACAACAAAG 58.549 33.333 15.92 15.92 42.12 2.77
2117 2168 4.103928 GGTCTCCCCAGGGCCCTA 62.104 72.222 28.13 8.17 34.68 3.53
2147 2198 4.054671 CGAGGATAGACAAAAGATCTGCC 58.945 47.826 0.00 0.00 0.00 4.85
2187 2238 6.374417 AATGAAACCTTAGTCCTTCAGCTA 57.626 37.500 0.00 0.00 28.78 3.32
2189 2240 5.966742 AAATGAAACCTTAGTCCTTCAGC 57.033 39.130 0.00 0.00 28.78 4.26
2246 2297 5.163824 GGGTTACATCGCTGGTTAAAACTAC 60.164 44.000 0.00 0.00 0.00 2.73
2299 2379 0.744281 TCGCACTTCTGTCAGACACA 59.256 50.000 0.78 0.00 0.00 3.72
2311 2391 0.810031 ACAAGCAGTCGTTCGCACTT 60.810 50.000 0.00 0.00 0.00 3.16
2387 2467 1.215655 ATTCTCTAATCGCGCCGCAC 61.216 55.000 10.75 0.00 0.00 5.34
2390 2470 1.858458 TCAAATTCTCTAATCGCGCCG 59.142 47.619 0.00 0.00 0.00 6.46
2443 2523 3.930848 CGTTAAACTGATCCGCCTACTTT 59.069 43.478 0.00 0.00 0.00 2.66
2451 2531 2.256174 TCGCTTCGTTAAACTGATCCG 58.744 47.619 0.00 0.00 0.00 4.18
2462 2542 6.046593 TCATTATCAGGTAAATCGCTTCGTT 58.953 36.000 0.00 0.00 0.00 3.85
2493 2573 1.107945 ACTTTCCCCACCAACAAACG 58.892 50.000 0.00 0.00 0.00 3.60
2571 2659 6.799512 ACAATTTCTATTAGACTGCAATGGC 58.200 36.000 0.00 0.00 41.68 4.40
2736 2829 4.156556 AGTTCGAGCACCTACACGTATTTA 59.843 41.667 1.01 0.00 0.00 1.40
2769 2862 2.027625 GAGTGACTTTGTCGCCGGG 61.028 63.158 2.18 0.00 43.20 5.73
2771 2864 0.597637 ACTGAGTGACTTTGTCGCCG 60.598 55.000 7.52 0.92 43.20 6.46
2797 2890 4.038402 CCCCAAATGAGGATGCATTTCTAC 59.962 45.833 0.00 0.00 44.30 2.59
2832 2925 3.055385 ACAATCCAGTATGTAGCAACCGT 60.055 43.478 0.00 0.00 0.00 4.83
2886 2981 3.270027 TGACCGCTTAACCATGATCTTG 58.730 45.455 0.00 1.60 0.00 3.02
2899 2994 6.797454 TGTAAAATTTACAGTTTGACCGCTT 58.203 32.000 13.93 0.00 0.00 4.68
2977 3099 4.855388 CGAAAATGGAAGTTCTGCTCAATG 59.145 41.667 2.25 0.00 0.00 2.82
3005 3127 4.126520 AGGGTTTGGGAAATAGCTTCAA 57.873 40.909 0.00 0.00 35.55 2.69
3060 3182 5.879777 TGTACAACAAGGTCCATATGACATG 59.120 40.000 3.65 6.55 46.38 3.21


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

AutoCloner maintained by Alex Coulton.