Multiple sequence alignment - TraesCS7A01G290200

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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 TraesCS7A01G290200 chr7A 100.000 2369 0 0 1 2369 352357903 352360271 0 4375
1 TraesCS7A01G290200 chr7A 95.640 688 29 1 1682 2369 55878424 55877738 0 1103
2 TraesCS7A01G290200 chr7A 94.767 688 35 1 1682 2369 371812597 371811911 0 1070
3 TraesCS7A01G290200 chr5D 95.027 1689 75 7 1 1682 6260993 6262679 0 2645
4 TraesCS7A01G290200 chr5D 94.678 1691 81 7 1 1685 503305782 503304095 0 2615
5 TraesCS7A01G290200 chr5D 94.668 1688 84 4 1 1682 6163000 6164687 0 2614
6 TraesCS7A01G290200 chr5D 93.370 1282 82 3 404 1682 329150344 329151625 0 1893
7 TraesCS7A01G290200 chr1D 94.563 1692 83 7 1 1685 254448949 254447260 0 2606
8 TraesCS7A01G290200 chr1D 93.839 1607 93 5 80 1682 51858203 51859807 0 2414
9 TraesCS7A01G290200 chr6B 94.139 1689 91 5 1 1682 18746153 18747840 0 2564
10 TraesCS7A01G290200 chr4A 92.507 1348 95 5 341 1685 544291389 544290045 0 1925
11 TraesCS7A01G290200 chr4A 92.028 577 42 4 1110 1682 309477518 309478094 0 808
12 TraesCS7A01G290200 chr4D 93.386 1270 76 6 1 1265 206977451 206978717 0 1873
13 TraesCS7A01G290200 chr2A 95.349 688 31 1 1682 2369 511155422 511156108 0 1092
14 TraesCS7A01G290200 chr2A 94.767 688 35 1 1682 2369 508526675 508527361 0 1070
15 TraesCS7A01G290200 chr1A 95.058 688 33 1 1682 2369 234246615 234247301 0 1081
16 TraesCS7A01G290200 chr1A 94.630 689 34 3 1682 2369 247441655 247442341 0 1064
17 TraesCS7A01G290200 chr6A 94.622 688 36 1 1682 2369 198173735 198173049 0 1064
18 TraesCS7A01G290200 chr6A 94.622 688 36 1 1682 2369 281544006 281543320 0 1064
19 TraesCS7A01G290200 chr5A 94.622 688 36 1 1682 2369 330765836 330765150 0 1064
20 TraesCS7A01G290200 chr3D 96.422 531 15 2 1 527 596658727 596658197 0 872


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 TraesCS7A01G290200 chr7A 352357903 352360271 2368 False 4375 4375 100.000 1 2369 1 chr7A.!!$F1 2368
1 TraesCS7A01G290200 chr7A 55877738 55878424 686 True 1103 1103 95.640 1682 2369 1 chr7A.!!$R1 687
2 TraesCS7A01G290200 chr7A 371811911 371812597 686 True 1070 1070 94.767 1682 2369 1 chr7A.!!$R2 687
3 TraesCS7A01G290200 chr5D 6260993 6262679 1686 False 2645 2645 95.027 1 1682 1 chr5D.!!$F2 1681
4 TraesCS7A01G290200 chr5D 503304095 503305782 1687 True 2615 2615 94.678 1 1685 1 chr5D.!!$R1 1684
5 TraesCS7A01G290200 chr5D 6163000 6164687 1687 False 2614 2614 94.668 1 1682 1 chr5D.!!$F1 1681
6 TraesCS7A01G290200 chr5D 329150344 329151625 1281 False 1893 1893 93.370 404 1682 1 chr5D.!!$F3 1278
7 TraesCS7A01G290200 chr1D 254447260 254448949 1689 True 2606 2606 94.563 1 1685 1 chr1D.!!$R1 1684
8 TraesCS7A01G290200 chr1D 51858203 51859807 1604 False 2414 2414 93.839 80 1682 1 chr1D.!!$F1 1602
9 TraesCS7A01G290200 chr6B 18746153 18747840 1687 False 2564 2564 94.139 1 1682 1 chr6B.!!$F1 1681
10 TraesCS7A01G290200 chr4A 544290045 544291389 1344 True 1925 1925 92.507 341 1685 1 chr4A.!!$R1 1344
11 TraesCS7A01G290200 chr4A 309477518 309478094 576 False 808 808 92.028 1110 1682 1 chr4A.!!$F1 572
12 TraesCS7A01G290200 chr4D 206977451 206978717 1266 False 1873 1873 93.386 1 1265 1 chr4D.!!$F1 1264
13 TraesCS7A01G290200 chr2A 511155422 511156108 686 False 1092 1092 95.349 1682 2369 1 chr2A.!!$F2 687
14 TraesCS7A01G290200 chr2A 508526675 508527361 686 False 1070 1070 94.767 1682 2369 1 chr2A.!!$F1 687
15 TraesCS7A01G290200 chr1A 234246615 234247301 686 False 1081 1081 95.058 1682 2369 1 chr1A.!!$F1 687
16 TraesCS7A01G290200 chr1A 247441655 247442341 686 False 1064 1064 94.630 1682 2369 1 chr1A.!!$F2 687
17 TraesCS7A01G290200 chr6A 198173049 198173735 686 True 1064 1064 94.622 1682 2369 1 chr6A.!!$R1 687
18 TraesCS7A01G290200 chr6A 281543320 281544006 686 True 1064 1064 94.622 1682 2369 1 chr6A.!!$R2 687
19 TraesCS7A01G290200 chr5A 330765150 330765836 686 True 1064 1064 94.622 1682 2369 1 chr5A.!!$R1 687
20 TraesCS7A01G290200 chr3D 596658197 596658727 530 True 872 872 96.422 1 527 1 chr3D.!!$R1 526

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
650 656 0.959553 AGACTCTCGCGAAACCTTCA 59.04 50.0 11.33 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2181 0.459899 TCCGTCAAGGTCATCATCGG 59.54 55.0 0.0 0.0 41.99 4.18 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
105 109 5.483811 TCTATTTGCACAAATACCTCGACA 58.516 37.500 10.94 0.00 40.99 4.35
299 305 2.294791 CCGCATTGAAACCCTTACACAA 59.705 45.455 0.00 0.00 0.00 3.33
303 309 5.571357 CGCATTGAAACCCTTACACAATAAC 59.429 40.000 0.00 0.00 31.40 1.89
323 329 9.153721 CAATAACGGGTGTAAAGAAATAGTACA 57.846 33.333 0.00 0.00 0.00 2.90
339 345 8.676397 AAATAGTACACCCCTCTACTAAAGTT 57.324 34.615 0.00 0.00 30.92 2.66
352 358 3.637769 ACTAAAGTTGGTTGAAAGGCCA 58.362 40.909 5.01 0.00 0.00 5.36
587 593 2.286365 AATGAAAGCGAAGGACCCAA 57.714 45.000 0.00 0.00 0.00 4.12
597 603 2.350388 CGAAGGACCCAAAACAATGACG 60.350 50.000 0.00 0.00 0.00 4.35
602 608 2.359531 GACCCAAAACAATGACGGAACA 59.640 45.455 0.00 0.00 0.00 3.18
634 640 1.228154 ACCCGTTTCCCAAGCAGAC 60.228 57.895 0.00 0.00 0.00 3.51
650 656 0.959553 AGACTCTCGCGAAACCTTCA 59.040 50.000 11.33 0.00 0.00 3.02
716 722 1.189524 TGACCATCCCTCGTCGGTTT 61.190 55.000 0.00 0.00 0.00 3.27
719 725 1.614241 CCATCCCTCGTCGGTTTCCT 61.614 60.000 0.00 0.00 0.00 3.36
749 755 5.667626 ACCCACTATCAAGAAGTGTATCCAT 59.332 40.000 2.86 0.00 42.30 3.41
764 770 2.787473 TCCATGGCTTCTTGTACCAG 57.213 50.000 6.96 0.00 36.78 4.00
838 844 9.905713 TTAATAGATAGGCAAGATTGTTGTTCT 57.094 29.630 0.00 0.00 0.00 3.01
851 857 4.594123 TGTTGTTCTGACGGATAACTCA 57.406 40.909 11.17 0.00 0.00 3.41
852 858 5.147330 TGTTGTTCTGACGGATAACTCAT 57.853 39.130 11.17 0.00 0.00 2.90
893 899 7.526142 TGTGTGAAGTCACTACTTTATCTCT 57.474 36.000 12.43 0.00 46.09 3.10
1016 1023 6.455780 CGCAATTGCATGCATCTAATCAAAAA 60.456 34.615 28.77 1.36 46.76 1.94
1048 1055 8.630278 TCTTATTCGTCTTTTTCTATCTTCCG 57.370 34.615 0.00 0.00 0.00 4.30
1144 1152 7.177216 ACAAATCCAATCTGCTAATTGTTCTCA 59.823 33.333 9.71 0.00 35.31 3.27
1250 1261 4.038271 ACAGGATGCAATTTCCTCTTCA 57.962 40.909 4.28 0.00 41.78 3.02
1311 1326 3.356290 GGGCCTAGCAAAAGAGAAATCA 58.644 45.455 0.84 0.00 0.00 2.57
1342 1357 3.193782 AGGCCCTCCAACTTCTTAAGAT 58.806 45.455 5.89 0.00 33.74 2.40
1383 1398 8.985315 TCACGATATAACTAGGAAGACCTTTA 57.015 34.615 0.00 0.00 45.36 1.85
1422 1437 1.086696 CGGGACATGCGAGTTTGATT 58.913 50.000 0.00 0.00 0.00 2.57
1479 1494 4.996758 ACAAATTCTACCCTGCATTTTTGC 59.003 37.500 0.00 0.00 0.00 3.68
1481 1496 1.555967 TCTACCCTGCATTTTTGCCC 58.444 50.000 0.00 0.00 0.00 5.36
1484 1499 1.066471 ACCCTGCATTTTTGCCCAAT 58.934 45.000 0.00 0.00 0.00 3.16
1504 1519 6.363357 CCCAATTCTTTCGTCTTCATTTTCAC 59.637 38.462 0.00 0.00 0.00 3.18
1510 1525 2.036733 TCGTCTTCATTTTCACCTCCGT 59.963 45.455 0.00 0.00 0.00 4.69
1519 1534 2.467946 TTCACCTCCGTTCGCTCGAC 62.468 60.000 0.00 0.00 0.00 4.20
1542 1557 2.929903 GCCACAAGCGCAAATCCCA 61.930 57.895 11.47 0.00 0.00 4.37
1575 1590 5.696270 GGGTTCAAAGATTCTTTCGCAAAAT 59.304 36.000 8.71 0.00 0.00 1.82
1626 1641 8.406297 GTTTTATAATGAAAAGTAGAGGGCCTG 58.594 37.037 12.95 0.00 0.00 4.85
1655 1670 2.289002 CGCCAATGACTTCTCCATTAGC 59.711 50.000 0.00 0.00 36.02 3.09
1722 1738 8.466617 TTTTGGTGGCAAATAGAACTAAGTTA 57.533 30.769 0.00 0.00 0.00 2.24
1866 1882 2.308690 GGAGACATAGGGCGAAGTACT 58.691 52.381 0.00 0.00 0.00 2.73
2057 2073 3.533606 ATGCTCGACTTGAATAGTGCT 57.466 42.857 0.00 0.00 37.17 4.40
2084 2101 3.568007 TCGCTTAGCCATTGAACTTTGTT 59.432 39.130 0.00 0.00 0.00 2.83
2140 2157 3.558931 TGGAGCAAAGTTCTTCACTGA 57.441 42.857 0.00 0.00 35.12 3.41
2164 2181 3.983044 AGTTATGACAACTCCCTCCAC 57.017 47.619 0.00 0.00 0.00 4.02
2310 2327 7.572523 TGAATCTTCATCACAAAAGACTTGT 57.427 32.000 0.00 0.00 34.52 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 133 1.140852 CCCAAGACATGCTTATCGGGA 59.859 52.381 13.79 0.00 34.31 5.14
299 305 8.707938 GTGTACTATTTCTTTACACCCGTTAT 57.292 34.615 0.00 0.00 39.72 1.89
323 329 4.237018 TCAACCAACTTTAGTAGAGGGGT 58.763 43.478 1.77 1.77 0.00 4.95
339 345 1.544724 GCATACTGGCCTTTCAACCA 58.455 50.000 3.32 0.00 0.00 3.67
352 358 4.171234 ACCCTGCATAGATTAGGCATACT 58.829 43.478 0.00 0.00 45.06 2.12
587 593 1.324383 GGGGTGTTCCGTCATTGTTT 58.676 50.000 0.00 0.00 36.01 2.83
597 603 0.819582 TCGATTACTCGGGGTGTTCC 59.180 55.000 2.41 0.00 45.10 3.62
602 608 3.945647 GGGTCGATTACTCGGGGT 58.054 61.111 2.41 0.00 45.10 4.95
634 640 1.068194 AGAGTGAAGGTTTCGCGAGAG 60.068 52.381 9.59 0.00 44.62 3.20
650 656 7.540474 TCAGATGTAACTGAAGGTAAAGAGT 57.460 36.000 0.00 0.00 42.79 3.24
692 698 1.405526 CGACGAGGGATGGTCACAATT 60.406 52.381 0.00 0.00 32.74 2.32
716 722 0.042581 TGATAGTGGGTCCTGCAGGA 59.957 55.000 32.00 32.00 43.08 3.86
719 725 1.951209 TCTTGATAGTGGGTCCTGCA 58.049 50.000 0.00 0.00 0.00 4.41
749 755 3.634910 GGAAAAACTGGTACAAGAAGCCA 59.365 43.478 3.64 0.00 38.70 4.75
775 781 5.989477 AGTGCCAGCAGATTTAGTAATGTA 58.011 37.500 0.00 0.00 0.00 2.29
838 844 9.878667 TGAACTTTATAAATGAGTTATCCGTCA 57.121 29.630 0.00 0.00 34.02 4.35
872 878 8.400186 GGTCTAGAGATAAAGTAGTGACTTCAC 58.600 40.741 0.77 0.77 45.50 3.18
920 926 2.265526 ATTACCGGTTCTTCCTCCCT 57.734 50.000 15.04 0.00 0.00 4.20
966 972 9.579610 CGGAAACATTTTATTCAAACAAATGTC 57.420 29.630 9.33 0.35 45.91 3.06
991 997 3.634283 TGATTAGATGCATGCAATTGCG 58.366 40.909 26.68 12.97 45.77 4.85
992 998 5.977171 TTTGATTAGATGCATGCAATTGC 57.023 34.783 26.68 23.69 43.07 3.56
1048 1055 4.083565 GAGGGGTATAGTGGAGATGAGTC 58.916 52.174 0.00 0.00 0.00 3.36
1250 1261 9.777575 CCATTTTTACGATTACGAGGTTTATTT 57.222 29.630 0.00 0.00 42.66 1.40
1289 1304 2.215942 TTTCTCTTTTGCTAGGCCCC 57.784 50.000 0.00 0.00 0.00 5.80
1311 1326 0.855598 TGGAGGGCCTAGTATACGGT 59.144 55.000 5.73 0.00 34.31 4.83
1356 1371 7.893124 AGGTCTTCCTAGTTATATCGTGAAA 57.107 36.000 0.00 0.00 43.12 2.69
1383 1398 3.751175 CCGTGACTCATGTGTGGTATTTT 59.249 43.478 4.90 0.00 0.00 1.82
1446 1461 6.125029 CAGGGTAGAATTTGTGGATTCTCAT 58.875 40.000 3.60 0.00 43.44 2.90
1479 1494 6.363357 GTGAAAATGAAGACGAAAGAATTGGG 59.637 38.462 0.00 0.00 0.00 4.12
1481 1496 7.141363 AGGTGAAAATGAAGACGAAAGAATTG 58.859 34.615 0.00 0.00 0.00 2.32
1484 1499 5.238650 GGAGGTGAAAATGAAGACGAAAGAA 59.761 40.000 0.00 0.00 0.00 2.52
1504 1519 0.736325 AATTGTCGAGCGAACGGAGG 60.736 55.000 0.00 0.00 0.00 4.30
1510 1525 0.882484 TGTGGCAATTGTCGAGCGAA 60.882 50.000 5.42 0.00 0.00 4.70
1519 1534 4.340076 TTGCGCTTGTGGCAATTG 57.660 50.000 9.73 0.00 44.79 2.32
1542 1557 9.764363 GAAAGAATCTTTGAACCCATAAAAAGT 57.236 29.630 13.55 0.00 32.64 2.66
1555 1570 8.303156 TGGATTATTTTGCGAAAGAATCTTTGA 58.697 29.630 31.30 18.07 45.79 2.69
1575 1590 6.072175 CCGACAAACCAGAAAAAGATGGATTA 60.072 38.462 0.00 0.00 39.02 1.75
1640 1655 6.374417 AAAACCTAGCTAATGGAGAAGTCA 57.626 37.500 6.05 0.00 0.00 3.41
1655 1670 3.056821 GGCTTGGGCTAACAAAAACCTAG 60.057 47.826 0.00 0.00 38.73 3.02
1722 1738 2.932614 CTCCACGATGAGCGAAAAGAAT 59.067 45.455 0.00 0.00 44.57 2.40
1866 1882 7.745717 TCTTCAAGATGAAAGGAAAGGAGTAA 58.254 34.615 0.00 0.00 35.73 2.24
1918 1934 2.223340 GGCAATTTGATACAGGCGTCAG 60.223 50.000 0.00 0.00 0.00 3.51
1923 1939 2.431782 ACCATGGCAATTTGATACAGGC 59.568 45.455 13.04 0.00 0.00 4.85
1927 1943 4.081752 TGGTTGACCATGGCAATTTGATAC 60.082 41.667 19.91 9.46 42.01 2.24
1990 2006 3.391049 GAGCTTACGAAGACACTTTGGT 58.609 45.455 0.00 0.00 0.00 3.67
2057 2073 0.901827 TCAATGGCTAAGCGACTCCA 59.098 50.000 0.00 0.00 0.00 3.86
2084 2101 2.350895 CGAAGCACCCACATCCCA 59.649 61.111 0.00 0.00 0.00 4.37
2140 2157 5.046520 GTGGAGGGAGTTGTCATAACTTAGT 60.047 44.000 0.00 0.00 0.00 2.24
2164 2181 0.459899 TCCGTCAAGGTCATCATCGG 59.540 55.000 0.00 0.00 41.99 4.18
2310 2327 3.498397 GCAAGTGAACGATGAAGAGGAAA 59.502 43.478 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.