Multiple sequence alignment - TraesCS7D01G361900

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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 TraesCS7D01G361900 chr7D 100.000 2726 0 0 1 2726 464362365 464359640 0.000000e+00 5035.0
1 TraesCS7D01G361900 chr7D 79.331 1166 131 55 791 1887 464948052 464946928 0.000000e+00 717.0
2 TraesCS7D01G361900 chr7A 92.223 2546 95 29 1 2473 535271820 535274335 0.000000e+00 3509.0
3 TraesCS7D01G361900 chr7A 78.877 1193 137 64 767 1887 534766041 534767190 0.000000e+00 701.0
4 TraesCS7D01G361900 chr7A 87.109 256 10 7 2471 2726 535319102 535319334 4.470000e-68 268.0
5 TraesCS7D01G361900 chr7A 96.667 60 1 1 563 621 535272329 535272388 6.210000e-17 99.0
6 TraesCS7D01G361900 chr7B 94.173 1802 50 22 943 2726 489781330 489779566 0.000000e+00 2695.0
7 TraesCS7D01G361900 chr7B 93.075 852 48 7 1 849 489782601 489781758 0.000000e+00 1236.0
8 TraesCS7D01G361900 chr7B 84.514 762 89 16 944 1692 489552299 489551554 0.000000e+00 726.0
9 TraesCS7D01G361900 chr3B 87.991 458 25 14 2271 2725 49098296 49098726 5.210000e-142 514.0
10 TraesCS7D01G361900 chr2B 84.173 278 27 8 2449 2726 773937801 773938061 1.250000e-63 254.0
11 TraesCS7D01G361900 chr2B 95.238 42 2 0 2685 2726 110017187 110017228 1.750000e-07 67.6


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 TraesCS7D01G361900 chr7D 464359640 464362365 2725 True 5035.0 5035 100.000 1 2726 1 chr7D.!!$R1 2725
1 TraesCS7D01G361900 chr7D 464946928 464948052 1124 True 717.0 717 79.331 791 1887 1 chr7D.!!$R2 1096
2 TraesCS7D01G361900 chr7A 535271820 535274335 2515 False 1804.0 3509 94.445 1 2473 2 chr7A.!!$F3 2472
3 TraesCS7D01G361900 chr7A 534766041 534767190 1149 False 701.0 701 78.877 767 1887 1 chr7A.!!$F1 1120
4 TraesCS7D01G361900 chr7B 489779566 489782601 3035 True 1965.5 2695 93.624 1 2726 2 chr7B.!!$R2 2725
5 TraesCS7D01G361900 chr7B 489551554 489552299 745 True 726.0 726 84.514 944 1692 1 chr7B.!!$R1 748

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
374 384 0.325296 TGCCCTTCCATCCGTCTAGT 60.325 55.0 0.0 0.0 0.0 2.57 F
460 472 0.755686 GCGGAACCCTCTCTCATGAT 59.244 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1953 0.114168 CCTGGATCTCCTCCTCCGAT 59.886 60.0 0.0 0.0 45.21 4.18 R
2034 2479 0.165944 CAAACCCGCACGAGATCAAC 59.834 55.0 0.0 0.0 0.00 3.18 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
49 50 4.932200 CGCAAATGATATAGTTCTCCCTCC 59.068 45.833 0.00 0.00 0.00 4.30
144 154 3.313274 ACTTTTACAACGCTCACAACG 57.687 42.857 0.00 0.00 0.00 4.10
206 216 5.536554 AGTATTTCTCACATTGAGTTGCG 57.463 39.130 3.19 0.00 44.58 4.85
210 220 2.832563 TCTCACATTGAGTTGCGACAA 58.167 42.857 6.90 0.00 44.58 3.18
267 277 6.849588 TGAGAACATGTATCCATCATTTCG 57.150 37.500 0.00 0.00 0.00 3.46
374 384 0.325296 TGCCCTTCCATCCGTCTAGT 60.325 55.000 0.00 0.00 0.00 2.57
430 440 1.538419 GGCGCGCTATCCTAAAGAACT 60.538 52.381 32.29 0.00 0.00 3.01
460 472 0.755686 GCGGAACCCTCTCTCATGAT 59.244 55.000 0.00 0.00 0.00 2.45
507 519 5.758296 GCTATATCGGTCCACAAAATTCTCA 59.242 40.000 0.00 0.00 0.00 3.27
656 668 3.713936 GATCGACATCCACGTGTGA 57.286 52.632 15.65 11.79 31.16 3.58
661 673 1.282248 GACATCCACGTGTGACACCG 61.282 60.000 15.65 7.99 31.16 4.94
892 921 2.665603 GGCTGTCCGCTTCTCCTT 59.334 61.111 0.00 0.00 39.13 3.36
897 926 1.446272 GTCCGCTTCTCCTTCCACG 60.446 63.158 0.00 0.00 0.00 4.94
921 965 1.295020 AATAACCAGCAGCCCCACTA 58.705 50.000 0.00 0.00 0.00 2.74
977 1331 0.756294 CAAAACCCAAACCCCACTCC 59.244 55.000 0.00 0.00 0.00 3.85
1104 1461 1.211969 CGTCGTCCTCACCATCGTT 59.788 57.895 0.00 0.00 0.00 3.85
1120 1477 2.040544 GTTGTCACCTCCATGGCCG 61.041 63.158 6.96 1.05 40.22 6.13
1763 2166 2.906458 CGGGAGCTCCTTGATGCT 59.094 61.111 31.36 0.00 42.82 3.79
1805 2223 3.436015 GCTAGTAGCCGAGTCGATGAATA 59.564 47.826 15.64 1.05 34.48 1.75
1806 2224 4.083431 GCTAGTAGCCGAGTCGATGAATAA 60.083 45.833 15.64 0.00 34.48 1.40
2013 2458 5.174943 CACAAAAACAGTTATTCTTTCCCGC 59.825 40.000 0.00 0.00 0.00 6.13
2034 2479 0.647410 CGGCTATTCTGTTCTGCACG 59.353 55.000 0.00 0.00 0.00 5.34
2168 2613 6.808829 TGTTTCAGTCATTTGCTCAGAAATT 58.191 32.000 0.00 0.00 0.00 1.82
2184 2629 2.596904 AATTCATTGCAGAGCATGGC 57.403 45.000 0.00 0.00 38.76 4.40
2194 2639 1.153086 GAGCATGGCTACAGGGGTG 60.153 63.158 0.00 0.00 39.88 4.61
2239 2685 0.109551 CTAGATCATCGATGGCGCGT 60.110 55.000 24.61 8.43 37.46 6.01
2530 3001 8.706035 GCGAGTTAGAAACAAAGTAGATTGTAA 58.294 33.333 0.00 0.00 42.49 2.41
2537 3008 7.606839 AGAAACAAAGTAGATTGTAACCTAGGC 59.393 37.037 9.30 0.00 42.49 3.93
2538 3009 6.368779 ACAAAGTAGATTGTAACCTAGGCA 57.631 37.500 9.30 0.00 41.56 4.75
2539 3010 6.775708 ACAAAGTAGATTGTAACCTAGGCAA 58.224 36.000 9.30 5.68 41.56 4.52
2542 3013 6.808321 AGTAGATTGTAACCTAGGCAATGA 57.192 37.500 15.42 3.73 33.56 2.57
2543 3014 6.583562 AGTAGATTGTAACCTAGGCAATGAC 58.416 40.000 15.42 12.84 33.56 3.06
2544 3015 5.435686 AGATTGTAACCTAGGCAATGACA 57.564 39.130 15.42 7.54 33.56 3.58
2545 3016 6.006275 AGATTGTAACCTAGGCAATGACAT 57.994 37.500 15.42 0.00 33.56 3.06
2546 3017 7.136822 AGATTGTAACCTAGGCAATGACATA 57.863 36.000 15.42 3.49 33.56 2.29
2547 3018 6.992715 AGATTGTAACCTAGGCAATGACATAC 59.007 38.462 15.42 7.47 33.56 2.39
2548 3019 5.950544 TGTAACCTAGGCAATGACATACT 57.049 39.130 9.30 0.00 0.00 2.12
2549 3020 6.308015 TGTAACCTAGGCAATGACATACTT 57.692 37.500 9.30 0.00 0.00 2.24
2550 3021 6.112734 TGTAACCTAGGCAATGACATACTTG 58.887 40.000 9.30 0.00 0.00 3.16
2551 3022 4.844349 ACCTAGGCAATGACATACTTGT 57.156 40.909 9.30 0.00 39.32 3.16
2552 3023 4.517285 ACCTAGGCAATGACATACTTGTG 58.483 43.478 9.30 0.00 35.79 3.33
2553 3024 4.019321 ACCTAGGCAATGACATACTTGTGT 60.019 41.667 9.30 0.00 35.79 3.72
2554 3025 5.188948 ACCTAGGCAATGACATACTTGTGTA 59.811 40.000 9.30 0.00 35.79 2.90
2555 3026 6.112734 CCTAGGCAATGACATACTTGTGTAA 58.887 40.000 0.00 0.00 35.79 2.41
2556 3027 5.880054 AGGCAATGACATACTTGTGTAAC 57.120 39.130 0.00 0.00 35.79 2.50
2599 3070 5.474578 TCTAAGCAGGCATAACTATGAGG 57.525 43.478 0.77 0.00 35.75 3.86
2627 3098 4.096382 TGACTTCACTGGTTCAAAAGCTTC 59.904 41.667 0.00 0.00 0.00 3.86
2632 3103 2.689983 ACTGGTTCAAAAGCTTCTGTGG 59.310 45.455 0.00 0.00 0.00 4.17
2712 3183 0.529378 GCATGGTTGAAGGCTTGGAG 59.471 55.000 3.46 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.877779 AGAACTATATCATTTGCGCATTATCTC 58.122 33.333 12.75 0.00 0.00 2.75
25 26 4.319177 AGGGAGAACTATATCATTTGCGC 58.681 43.478 0.00 0.00 0.00 6.09
112 122 6.537660 AGCGTTGTAAAAGTTACTTTCTCTGT 59.462 34.615 10.98 0.00 31.99 3.41
267 277 3.660865 AGATGAAAAGGACACGGTGTAC 58.339 45.455 15.79 15.79 0.00 2.90
327 337 8.514330 ACTTTTGTTGTGAGTTATTTCTACCA 57.486 30.769 0.00 0.00 0.00 3.25
374 384 4.075682 TCCGCCAAATGTTATTTCAGTGA 58.924 39.130 0.00 0.00 0.00 3.41
460 472 5.743467 CGTCATTAGTGCGGCATTTTAATA 58.257 37.500 5.72 0.00 0.00 0.98
523 535 9.634163 ACGTAAAAAGAGAAACAACTTTTGATT 57.366 25.926 0.00 0.00 42.80 2.57
533 545 3.803778 GGACGGACGTAAAAAGAGAAACA 59.196 43.478 0.00 0.00 0.00 2.83
546 558 4.295119 AAGCGCTTGGACGGACGT 62.295 61.111 24.40 0.00 0.00 4.34
661 673 4.265556 CGATTTCTACAACATCGACTGGAC 59.734 45.833 0.00 0.00 41.96 4.02
705 718 6.934056 TGCAAATATCTAAATGGTTGTTGCT 58.066 32.000 0.00 0.00 39.56 3.91
706 719 7.775397 ATGCAAATATCTAAATGGTTGTTGC 57.225 32.000 0.00 0.00 39.35 4.17
892 921 3.189702 GCTGCTGGTTATTTAAACGTGGA 59.810 43.478 0.00 0.00 0.00 4.02
897 926 2.829120 TGGGGCTGCTGGTTATTTAAAC 59.171 45.455 0.00 0.00 0.00 2.01
921 965 2.622447 CGGGGTTGGGGAAGGGAAT 61.622 63.158 0.00 0.00 0.00 3.01
941 1293 2.116556 GGCGTTTTGGGGGAGGAA 59.883 61.111 0.00 0.00 0.00 3.36
1104 1461 4.408821 GCGGCCATGGAGGTGACA 62.409 66.667 18.40 0.00 40.61 3.58
1309 1666 4.637489 CTCCATCTCGAGCGGCGG 62.637 72.222 9.78 5.26 41.33 6.13
1531 1918 3.249189 TTTCGCCACCAGGGAGCT 61.249 61.111 0.00 0.00 40.01 4.09
1534 1924 4.323477 CGGTTTCGCCACCAGGGA 62.323 66.667 4.00 0.00 40.01 4.20
1560 1953 0.114168 CCTGGATCTCCTCCTCCGAT 59.886 60.000 0.00 0.00 45.21 4.18
1750 2153 0.252479 CTGTGGAGCATCAAGGAGCT 59.748 55.000 0.00 0.00 45.25 4.09
1762 2165 1.078567 GGGAAGCAGCTCTGTGGAG 60.079 63.158 0.00 0.00 42.18 3.86
1763 2166 2.947532 CGGGAAGCAGCTCTGTGGA 61.948 63.158 0.00 0.00 0.00 4.02
1764 2167 2.435586 CGGGAAGCAGCTCTGTGG 60.436 66.667 0.00 0.00 0.00 4.17
1805 2223 8.625651 GCCAGGTTTTGTTTGGTTATTTATTTT 58.374 29.630 0.00 0.00 34.43 1.82
1806 2224 7.996066 AGCCAGGTTTTGTTTGGTTATTTATTT 59.004 29.630 0.00 0.00 34.43 1.40
2013 2458 1.929836 GTGCAGAACAGAATAGCCGAG 59.070 52.381 0.00 0.00 0.00 4.63
2034 2479 0.165944 CAAACCCGCACGAGATCAAC 59.834 55.000 0.00 0.00 0.00 3.18
2168 2613 1.065272 TGTAGCCATGCTCTGCAATGA 60.065 47.619 0.00 0.00 43.62 2.57
2184 2629 1.831736 CTGAACTACCCACCCCTGTAG 59.168 57.143 0.00 0.00 40.21 2.74
2194 2639 7.544915 GTGAACTGAATTAGTACTGAACTACCC 59.455 40.741 5.39 0.00 40.48 3.69
2239 2685 2.605837 TTATAGATGGGCGCGACAAA 57.394 45.000 17.00 0.00 0.00 2.83
2530 3001 4.019321 ACACAAGTATGTCATTGCCTAGGT 60.019 41.667 11.31 0.00 37.82 3.08
2532 3003 6.593770 TGTTACACAAGTATGTCATTGCCTAG 59.406 38.462 0.00 0.00 37.82 3.02
2534 3005 5.312895 TGTTACACAAGTATGTCATTGCCT 58.687 37.500 0.00 0.00 37.82 4.75
2535 3006 5.621197 TGTTACACAAGTATGTCATTGCC 57.379 39.130 0.00 0.00 37.82 4.52
2536 3007 7.359595 TCTTTGTTACACAAGTATGTCATTGC 58.640 34.615 0.00 0.00 39.53 3.56
2537 3008 9.897744 ATTCTTTGTTACACAAGTATGTCATTG 57.102 29.630 0.00 0.00 39.53 2.82
2542 3013 8.615878 TGCTATTCTTTGTTACACAAGTATGT 57.384 30.769 0.00 0.00 39.53 2.29
2543 3014 7.693951 GCTGCTATTCTTTGTTACACAAGTATG 59.306 37.037 0.00 0.00 39.53 2.39
2544 3015 7.148239 GGCTGCTATTCTTTGTTACACAAGTAT 60.148 37.037 0.00 0.00 39.53 2.12
2545 3016 6.148811 GGCTGCTATTCTTTGTTACACAAGTA 59.851 38.462 0.00 0.00 39.53 2.24
2546 3017 5.048713 GGCTGCTATTCTTTGTTACACAAGT 60.049 40.000 0.00 0.00 39.53 3.16
2547 3018 5.393962 GGCTGCTATTCTTTGTTACACAAG 58.606 41.667 0.00 0.00 39.53 3.16
2548 3019 4.217550 GGGCTGCTATTCTTTGTTACACAA 59.782 41.667 0.00 0.00 36.11 3.33
2549 3020 3.756434 GGGCTGCTATTCTTTGTTACACA 59.244 43.478 0.00 0.00 0.00 3.72
2550 3021 3.756434 TGGGCTGCTATTCTTTGTTACAC 59.244 43.478 0.00 0.00 0.00 2.90
2551 3022 4.027674 TGGGCTGCTATTCTTTGTTACA 57.972 40.909 0.00 0.00 0.00 2.41
2552 3023 5.582689 ATTGGGCTGCTATTCTTTGTTAC 57.417 39.130 0.00 0.00 0.00 2.50
2553 3024 7.779798 AGATTATTGGGCTGCTATTCTTTGTTA 59.220 33.333 0.00 0.00 0.00 2.41
2554 3025 6.608808 AGATTATTGGGCTGCTATTCTTTGTT 59.391 34.615 0.00 0.00 0.00 2.83
2555 3026 6.131961 AGATTATTGGGCTGCTATTCTTTGT 58.868 36.000 0.00 0.00 0.00 2.83
2556 3027 6.645790 AGATTATTGGGCTGCTATTCTTTG 57.354 37.500 0.00 0.00 0.00 2.77
2557 3028 7.040132 GCTTAGATTATTGGGCTGCTATTCTTT 60.040 37.037 0.00 0.00 0.00 2.52
2558 3029 6.432472 GCTTAGATTATTGGGCTGCTATTCTT 59.568 38.462 0.00 0.00 0.00 2.52
2566 3037 2.555757 GCCTGCTTAGATTATTGGGCTG 59.444 50.000 0.00 0.00 35.92 4.85
2599 3070 3.334583 TGAACCAGTGAAGTCATAGCC 57.665 47.619 0.00 0.00 0.00 3.93
2627 3098 1.310933 GCTGCCCTTGATCACCACAG 61.311 60.000 0.00 2.35 0.00 3.66
2632 3103 4.580167 TGTATATTTGCTGCCCTTGATCAC 59.420 41.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.