Multiple sequence alignment - TraesCS7A01G418400

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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 TraesCS7A01G418400 chr7A 100.000 2752 0 0 1 2752 610421467 610424218 0 5083
1 TraesCS7A01G418400 chr7A 98.560 903 12 1 1851 2752 610429024 610429926 0 1594
2 TraesCS7A01G418400 chr7A 96.452 902 32 0 1851 2752 69325603 69326504 0 1489
3 TraesCS7A01G418400 chr5D 95.366 1856 78 3 1 1855 363005584 363007432 0 2944
4 TraesCS7A01G418400 chr4B 94.779 1858 89 6 1 1855 525388660 525386808 0 2887
5 TraesCS7A01G418400 chr4B 94.774 1856 92 4 1 1855 525305993 525307844 0 2885
6 TraesCS7A01G418400 chr5A 94.624 1860 90 4 1 1855 573662464 573660610 0 2872
7 TraesCS7A01G418400 chr5A 94.235 1856 99 3 1 1855 524632902 524631054 0 2828
8 TraesCS7A01G418400 chr5A 94.645 1662 75 4 200 1854 673390640 673388986 0 2564
9 TraesCS7A01G418400 chr1A 94.215 1867 95 6 1 1855 50971146 50969281 0 2837
10 TraesCS7A01G418400 chr1A 96.563 902 31 0 1851 2752 486094045 486094946 0 1495
11 TraesCS7A01G418400 chr1A 96.552 899 31 0 1854 2752 461790644 461789746 0 1489
12 TraesCS7A01G418400 chr2D 95.624 1554 56 5 303 1854 82210877 82209334 0 2483
13 TraesCS7A01G418400 chr1D 94.882 1563 69 5 1 1560 309985170 309983616 0 2433
14 TraesCS7A01G418400 chr3A 97.511 884 22 0 1869 2752 628228613 628229496 0 1511
15 TraesCS7A01G418400 chr3A 96.663 899 30 0 1854 2752 380884453 380883555 0 1495
16 TraesCS7A01G418400 chr6A 96.885 899 28 0 1854 2752 399227475 399226577 0 1506
17 TraesCS7A01G418400 chr6A 96.563 902 30 1 1851 2752 497812269 497813169 0 1493
18 TraesCS7A01G418400 chr4A 96.785 902 28 1 1851 2752 512519123 512520023 0 1504
19 TraesCS7A01G418400 chr2B 94.558 588 29 2 1270 1854 33503334 33502747 0 905


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 TraesCS7A01G418400 chr7A 610421467 610424218 2751 False 5083 5083 100.000 1 2752 1 chr7A.!!$F2 2751
1 TraesCS7A01G418400 chr7A 610429024 610429926 902 False 1594 1594 98.560 1851 2752 1 chr7A.!!$F3 901
2 TraesCS7A01G418400 chr7A 69325603 69326504 901 False 1489 1489 96.452 1851 2752 1 chr7A.!!$F1 901
3 TraesCS7A01G418400 chr5D 363005584 363007432 1848 False 2944 2944 95.366 1 1855 1 chr5D.!!$F1 1854
4 TraesCS7A01G418400 chr4B 525386808 525388660 1852 True 2887 2887 94.779 1 1855 1 chr4B.!!$R1 1854
5 TraesCS7A01G418400 chr4B 525305993 525307844 1851 False 2885 2885 94.774 1 1855 1 chr4B.!!$F1 1854
6 TraesCS7A01G418400 chr5A 573660610 573662464 1854 True 2872 2872 94.624 1 1855 1 chr5A.!!$R2 1854
7 TraesCS7A01G418400 chr5A 524631054 524632902 1848 True 2828 2828 94.235 1 1855 1 chr5A.!!$R1 1854
8 TraesCS7A01G418400 chr5A 673388986 673390640 1654 True 2564 2564 94.645 200 1854 1 chr5A.!!$R3 1654
9 TraesCS7A01G418400 chr1A 50969281 50971146 1865 True 2837 2837 94.215 1 1855 1 chr1A.!!$R1 1854
10 TraesCS7A01G418400 chr1A 486094045 486094946 901 False 1495 1495 96.563 1851 2752 1 chr1A.!!$F1 901
11 TraesCS7A01G418400 chr1A 461789746 461790644 898 True 1489 1489 96.552 1854 2752 1 chr1A.!!$R2 898
12 TraesCS7A01G418400 chr2D 82209334 82210877 1543 True 2483 2483 95.624 303 1854 1 chr2D.!!$R1 1551
13 TraesCS7A01G418400 chr1D 309983616 309985170 1554 True 2433 2433 94.882 1 1560 1 chr1D.!!$R1 1559
14 TraesCS7A01G418400 chr3A 628228613 628229496 883 False 1511 1511 97.511 1869 2752 1 chr3A.!!$F1 883
15 TraesCS7A01G418400 chr3A 380883555 380884453 898 True 1495 1495 96.663 1854 2752 1 chr3A.!!$R1 898
16 TraesCS7A01G418400 chr6A 399226577 399227475 898 True 1506 1506 96.885 1854 2752 1 chr6A.!!$R1 898
17 TraesCS7A01G418400 chr6A 497812269 497813169 900 False 1493 1493 96.563 1851 2752 1 chr6A.!!$F1 901
18 TraesCS7A01G418400 chr4A 512519123 512520023 900 False 1504 1504 96.785 1851 2752 1 chr4A.!!$F1 901
19 TraesCS7A01G418400 chr2B 33502747 33503334 587 True 905 905 94.558 1270 1854 1 chr2B.!!$R1 584

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
936 961 0.109342 AGCCAACTACTGCTGCTGTT 59.891 50.0 17.29 6.33 36.23 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1833 0.178975 CAACACCCTGGGCCTTGTTA 60.179 55.0 17.04 0.0 31.0 2.41 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 4.069232 CTCCCCTCGTGCGAGCAA 62.069 66.667 15.32 3.05 40.69 3.91
147 148 2.695585 CTATTTAGCCCCTCCCTCACT 58.304 52.381 0.00 0.00 0.00 3.41
185 186 3.927163 TTCTTCCTCCGTTCGCGCC 62.927 63.158 0.00 0.00 39.70 6.53
225 226 2.273179 ACCGACGAGCAGGTAAGCA 61.273 57.895 0.00 0.00 39.30 3.91
226 227 1.080093 CCGACGAGCAGGTAAGCAA 60.080 57.895 0.00 0.00 36.85 3.91
245 246 2.108976 GCATCTTCATCGGCCGGA 59.891 61.111 27.83 14.94 0.00 5.14
359 361 1.561542 TCAATCCCCCTTTCTCTCTGC 59.438 52.381 0.00 0.00 0.00 4.26
375 377 5.546110 TCTCTCTGCTCCTTCTAGCTAGATA 59.454 44.000 23.81 13.46 43.19 1.98
409 411 5.840693 TCTAGGGTTTGATCTAGATGCATGA 59.159 40.000 10.74 0.00 37.60 3.07
488 491 4.650972 TTTGTGGTAGGGCTAGATGTTT 57.349 40.909 0.00 0.00 0.00 2.83
489 492 3.627395 TGTGGTAGGGCTAGATGTTTG 57.373 47.619 0.00 0.00 0.00 2.93
514 518 4.381079 GCATGTGGTAGGCTAGATAGTAGC 60.381 50.000 0.00 0.00 39.70 3.58
590 594 5.685520 TTGTAGCTATTGGTGGTCATGTA 57.314 39.130 0.00 0.00 0.00 2.29
716 726 2.254546 TCATGGATTGTCCGGTATGC 57.745 50.000 0.00 0.00 40.17 3.14
732 742 1.664873 ATGCTGTGTGCTATGCTCAG 58.335 50.000 0.00 0.00 43.37 3.35
741 751 3.005554 GTGCTATGCTCAGTGTCAATGT 58.994 45.455 0.00 0.00 0.00 2.71
795 805 2.700897 GCAAGATCTTAGTCAGGCCCTA 59.299 50.000 7.86 0.00 0.00 3.53
796 806 3.134804 GCAAGATCTTAGTCAGGCCCTAA 59.865 47.826 7.86 0.00 0.00 2.69
933 958 0.397941 TTGAGCCAACTACTGCTGCT 59.602 50.000 0.00 0.00 38.11 4.24
934 959 0.321034 TGAGCCAACTACTGCTGCTG 60.321 55.000 4.89 4.89 38.11 4.41
935 960 0.321122 GAGCCAACTACTGCTGCTGT 60.321 55.000 16.37 16.37 38.11 4.40
936 961 0.109342 AGCCAACTACTGCTGCTGTT 59.891 50.000 17.29 6.33 36.23 3.16
937 962 0.239347 GCCAACTACTGCTGCTGTTG 59.761 55.000 17.29 16.93 39.35 3.33
938 963 1.597742 CCAACTACTGCTGCTGTTGT 58.402 50.000 17.29 17.56 38.35 3.32
1146 1172 2.808933 CGAGTTTTGTGGGCAAGAGGTA 60.809 50.000 0.00 0.00 35.82 3.08
1394 1421 1.082194 TCTTAGGACCACCCAAGGGAT 59.918 52.381 13.15 0.00 38.96 3.85
1406 1433 1.005215 CCAAGGGATGCTGAGTTCCTT 59.995 52.381 4.08 0.00 38.25 3.36
1411 1438 3.525199 AGGGATGCTGAGTTCCTTAACAT 59.475 43.478 4.08 0.00 38.12 2.71
1421 1448 5.251932 TGAGTTCCTTAACATACCCATCCAA 59.748 40.000 0.00 0.00 38.12 3.53
1524 1551 1.225704 CCCATGCCTGACTTCCCTC 59.774 63.158 0.00 0.00 0.00 4.30
1612 1642 2.759355 TGACCCCGTTGATAGGAAGAT 58.241 47.619 0.00 0.00 0.00 2.40
1616 1646 3.521937 ACCCCGTTGATAGGAAGATGAAA 59.478 43.478 0.00 0.00 0.00 2.69
1688 1719 1.966451 GGTGAAGGAGGTGGCAACG 60.966 63.158 0.00 0.00 42.51 4.10
1837 1877 1.151679 TTGGGTTCGTTGCCATGGA 59.848 52.632 18.40 0.00 0.00 3.41
1872 1912 2.560105 GTGCCAGAAATCCTTCTTGCTT 59.440 45.455 10.99 0.00 45.96 3.91
1923 1963 2.108075 TGAAGAGGAAAGGGTGATGCAA 59.892 45.455 0.00 0.00 0.00 4.08
2417 2458 3.181455 ACCGCTATCCAACATGCATCTAA 60.181 43.478 0.00 0.00 0.00 2.10
2574 2615 2.057922 ACTGTCACTGGGAAAGGACAT 58.942 47.619 1.50 0.00 36.28 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.187946 CGAGGGGAGAAATGCGCT 59.812 61.111 9.73 0.00 0.00 5.92
24 25 2.125106 ACGAGGGGAGAAATGCGC 60.125 61.111 0.00 0.00 0.00 6.09
28 29 3.708210 TCGCACGAGGGGAGAAAT 58.292 55.556 0.00 0.00 33.99 2.17
79 80 0.254747 ATCCTCCCGCCGATTTTTCA 59.745 50.000 0.00 0.00 0.00 2.69
165 166 1.359459 GCGCGAACGGAGGAAGAATT 61.359 55.000 12.10 0.00 40.57 2.17
225 226 2.173669 CGGCCGATGAAGATGCGTT 61.174 57.895 24.07 0.00 0.00 4.84
226 227 2.586079 CGGCCGATGAAGATGCGT 60.586 61.111 24.07 0.00 0.00 5.24
245 246 2.970639 CTCCGACACCGTGGACAT 59.029 61.111 3.03 0.00 0.00 3.06
255 256 2.636412 CGGTGAAGGAGCTCCGACA 61.636 63.158 26.95 25.18 45.07 4.35
307 309 0.752009 CATGGCTGCAGCTTGAGGAT 60.752 55.000 35.82 16.20 41.70 3.24
375 377 2.507058 TCAAACCCTAGATGCAGCTCAT 59.493 45.455 8.28 0.00 38.32 2.90
409 411 6.550938 TCACAGATCAGACCACTAATCAAT 57.449 37.500 0.00 0.00 0.00 2.57
488 491 2.159179 TCTAGCCTACCACATGCTCA 57.841 50.000 0.00 0.00 36.57 4.26
489 492 3.829601 ACTATCTAGCCTACCACATGCTC 59.170 47.826 0.00 0.00 36.57 4.26
514 518 5.335127 CACAAGGTTCAACTTCAAACTCTG 58.665 41.667 0.00 0.00 0.00 3.35
590 594 6.239217 TGGTTCATCACTATCATAGCAAGT 57.761 37.500 0.00 0.00 0.00 3.16
716 726 1.998315 GACACTGAGCATAGCACACAG 59.002 52.381 0.00 0.00 34.68 3.66
732 742 3.186409 ACAATCGTAGCACACATTGACAC 59.814 43.478 14.51 0.00 33.51 3.67
795 805 0.615331 ACTGGCTGTCGGACATGATT 59.385 50.000 11.86 0.00 29.39 2.57
796 806 0.615331 AACTGGCTGTCGGACATGAT 59.385 50.000 11.86 0.00 29.39 2.45
1108 1134 0.602638 TCGAACACCTGCTTCGCAAT 60.603 50.000 0.52 0.00 40.29 3.56
1268 1294 4.452733 GGCCGGCGTAGTGCTCTT 62.453 66.667 22.54 0.00 45.43 2.85
1394 1421 3.585289 TGGGTATGTTAAGGAACTCAGCA 59.415 43.478 0.00 0.00 38.49 4.41
1406 1433 6.660094 GGTTGTAGTTTTGGATGGGTATGTTA 59.340 38.462 0.00 0.00 0.00 2.41
1411 1438 4.351407 TCTGGTTGTAGTTTTGGATGGGTA 59.649 41.667 0.00 0.00 0.00 3.69
1421 1448 3.951037 TGTGTTGCATCTGGTTGTAGTTT 59.049 39.130 0.00 0.00 0.00 2.66
1612 1642 1.283029 CCATCAGGCCTCCTCTTTTCA 59.717 52.381 0.00 0.00 0.00 2.69
1616 1646 0.693767 CCTCCATCAGGCCTCCTCTT 60.694 60.000 0.00 0.00 34.56 2.85
1688 1719 1.751927 CTTGCACTCCCTGATGGCC 60.752 63.158 0.00 0.00 0.00 5.36
1802 1833 0.178975 CAACACCCTGGGCCTTGTTA 60.179 55.000 17.04 0.00 31.00 2.41
1837 1877 4.664677 GCACCCTGTGAGCGTCGT 62.665 66.667 0.00 0.00 35.23 4.34
1872 1912 2.156917 CAATGCAAGTGCTCAAGAGGA 58.843 47.619 4.69 0.00 42.66 3.71
1923 1963 4.954826 AGGGAAATACTTACGCTACTCTGT 59.045 41.667 0.00 0.00 0.00 3.41
2050 2090 1.640917 AGTGACCGTGTAGGGATTGT 58.359 50.000 0.00 0.00 46.96 2.71
2330 2371 1.406219 CTTGTCTCGGACGTGATGCG 61.406 60.000 0.00 0.00 44.87 4.73
2574 2615 1.269448 GCTTTGGGTTCAATCTTGCGA 59.731 47.619 0.00 0.00 32.28 5.10


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

AutoCloner maintained by Alex Coulton.