Multiple sequence alignment - TraesCS7A01G368700

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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 TraesCS7A01G368700 chr7A 100.000 2544 0 0 1 2544 542605515 542608058 0 4698
1 TraesCS7A01G368700 chr7A 91.747 1878 131 14 1 1859 412882646 412880774 0 2588
2 TraesCS7A01G368700 chr7A 96.637 684 23 0 1861 2544 641023104 641023787 0 1136
3 TraesCS7A01G368700 chr7A 96.366 688 25 0 1857 2544 476210165 476210852 0 1133
4 TraesCS7A01G368700 chr7A 96.496 685 22 2 1861 2544 80160589 80159906 0 1131
5 TraesCS7A01G368700 chr2A 92.059 1889 115 19 1 1858 90138926 90137042 0 2625
6 TraesCS7A01G368700 chr2A 90.461 1604 121 14 272 1859 529894336 529895923 0 2085
7 TraesCS7A01G368700 chr2A 96.491 684 24 0 1861 2544 564275952 564276635 0 1131
8 TraesCS7A01G368700 chr4A 92.250 1871 110 16 1 1852 317061125 317062979 0 2619
9 TraesCS7A01G368700 chr4A 88.677 733 63 9 1 714 705684397 705685128 0 876
10 TraesCS7A01G368700 chr6D 91.968 1880 125 13 1 1859 200593755 200595629 0 2612
11 TraesCS7A01G368700 chr5D 91.919 1881 128 12 1 1859 256499979 256498101 0 2610
12 TraesCS7A01G368700 chr1A 91.755 1880 127 19 1 1856 298162809 298164684 0 2588
13 TraesCS7A01G368700 chr1A 96.496 685 22 2 1861 2544 308613836 308614519 0 1131
14 TraesCS7A01G368700 chr1A 95.954 692 26 1 1853 2544 8949766 8950455 0 1122
15 TraesCS7A01G368700 chr2D 91.339 1882 134 18 1 1859 377095354 377097229 0 2545
16 TraesCS7A01G368700 chr2D 90.798 1880 146 17 1 1859 72328182 72326309 0 2488
17 TraesCS7A01G368700 chr2D 89.466 731 58 9 1 714 6325387 6324659 0 905
18 TraesCS7A01G368700 chr2D 89.008 746 57 15 1 723 159831090 159831833 0 900
19 TraesCS7A01G368700 chr2D 88.980 735 57 12 1 714 54649851 54650582 0 887
20 TraesCS7A01G368700 chr2D 89.056 731 59 11 1 714 188460900 188461626 0 887
21 TraesCS7A01G368700 chr2B 90.058 1881 155 21 1 1859 109029302 109027432 0 2409
22 TraesCS7A01G368700 chr6A 96.930 684 20 1 1861 2544 466756029 466755347 0 1146
23 TraesCS7A01G368700 chr6A 96.507 687 24 0 1858 2544 59792607 59793293 0 1136
24 TraesCS7A01G368700 chr5A 95.702 698 25 4 1848 2544 470406329 470407022 0 1118
25 TraesCS7A01G368700 chr1B 89.617 732 56 10 1 714 288456773 288456044 0 913


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 TraesCS7A01G368700 chr7A 542605515 542608058 2543 False 4698 4698 100.000 1 2544 1 chr7A.!!$F2 2543
1 TraesCS7A01G368700 chr7A 412880774 412882646 1872 True 2588 2588 91.747 1 1859 1 chr7A.!!$R2 1858
2 TraesCS7A01G368700 chr7A 641023104 641023787 683 False 1136 1136 96.637 1861 2544 1 chr7A.!!$F3 683
3 TraesCS7A01G368700 chr7A 476210165 476210852 687 False 1133 1133 96.366 1857 2544 1 chr7A.!!$F1 687
4 TraesCS7A01G368700 chr7A 80159906 80160589 683 True 1131 1131 96.496 1861 2544 1 chr7A.!!$R1 683
5 TraesCS7A01G368700 chr2A 90137042 90138926 1884 True 2625 2625 92.059 1 1858 1 chr2A.!!$R1 1857
6 TraesCS7A01G368700 chr2A 529894336 529895923 1587 False 2085 2085 90.461 272 1859 1 chr2A.!!$F1 1587
7 TraesCS7A01G368700 chr2A 564275952 564276635 683 False 1131 1131 96.491 1861 2544 1 chr2A.!!$F2 683
8 TraesCS7A01G368700 chr4A 317061125 317062979 1854 False 2619 2619 92.250 1 1852 1 chr4A.!!$F1 1851
9 TraesCS7A01G368700 chr4A 705684397 705685128 731 False 876 876 88.677 1 714 1 chr4A.!!$F2 713
10 TraesCS7A01G368700 chr6D 200593755 200595629 1874 False 2612 2612 91.968 1 1859 1 chr6D.!!$F1 1858
11 TraesCS7A01G368700 chr5D 256498101 256499979 1878 True 2610 2610 91.919 1 1859 1 chr5D.!!$R1 1858
12 TraesCS7A01G368700 chr1A 298162809 298164684 1875 False 2588 2588 91.755 1 1856 1 chr1A.!!$F2 1855
13 TraesCS7A01G368700 chr1A 308613836 308614519 683 False 1131 1131 96.496 1861 2544 1 chr1A.!!$F3 683
14 TraesCS7A01G368700 chr1A 8949766 8950455 689 False 1122 1122 95.954 1853 2544 1 chr1A.!!$F1 691
15 TraesCS7A01G368700 chr2D 377095354 377097229 1875 False 2545 2545 91.339 1 1859 1 chr2D.!!$F4 1858
16 TraesCS7A01G368700 chr2D 72326309 72328182 1873 True 2488 2488 90.798 1 1859 1 chr2D.!!$R2 1858
17 TraesCS7A01G368700 chr2D 6324659 6325387 728 True 905 905 89.466 1 714 1 chr2D.!!$R1 713
18 TraesCS7A01G368700 chr2D 159831090 159831833 743 False 900 900 89.008 1 723 1 chr2D.!!$F2 722
19 TraesCS7A01G368700 chr2D 54649851 54650582 731 False 887 887 88.980 1 714 1 chr2D.!!$F1 713
20 TraesCS7A01G368700 chr2D 188460900 188461626 726 False 887 887 89.056 1 714 1 chr2D.!!$F3 713
21 TraesCS7A01G368700 chr2B 109027432 109029302 1870 True 2409 2409 90.058 1 1859 1 chr2B.!!$R1 1858
22 TraesCS7A01G368700 chr6A 466755347 466756029 682 True 1146 1146 96.930 1861 2544 1 chr6A.!!$R1 683
23 TraesCS7A01G368700 chr6A 59792607 59793293 686 False 1136 1136 96.507 1858 2544 1 chr6A.!!$F1 686
24 TraesCS7A01G368700 chr5A 470406329 470407022 693 False 1118 1118 95.702 1848 2544 1 chr5A.!!$F1 696
25 TraesCS7A01G368700 chr1B 288456044 288456773 729 True 913 913 89.617 1 714 1 chr1B.!!$R1 713

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
96 98 0.251787 GAAGTGCCACCCCTGGATTT 60.252 55.0 0.00 0.0 40.55 2.17 F
621 668 0.742635 TCGCTGCGCATGGTGAATTA 60.743 50.0 18.65 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1513 0.445436 CTCGACAACCATTGCAGCTC 59.555 55.0 0.0 0.0 0.0 4.09 R
1919 2002 1.154430 AACCCCTTCAAGCTAACCCA 58.846 50.0 0.0 0.0 0.0 4.51 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
21 22 3.718210 GACGATGTCCTCACGGGGC 62.718 68.421 0.00 0.0 40.85 5.80
89 91 2.736670 ATCATTAGAAGTGCCACCCC 57.263 50.000 0.00 0.0 0.00 4.95
90 92 1.668826 TCATTAGAAGTGCCACCCCT 58.331 50.000 0.00 0.0 0.00 4.79
92 94 0.625849 ATTAGAAGTGCCACCCCTGG 59.374 55.000 0.00 0.0 41.13 4.45
93 95 0.474854 TTAGAAGTGCCACCCCTGGA 60.475 55.000 0.00 0.0 40.55 3.86
94 96 0.253160 TAGAAGTGCCACCCCTGGAT 60.253 55.000 0.00 0.0 40.55 3.41
96 98 0.251787 GAAGTGCCACCCCTGGATTT 60.252 55.000 0.00 0.0 40.55 2.17
212 216 2.687370 GCATTTTGGAAATGCGAGGTT 58.313 42.857 18.93 0.0 42.79 3.50
328 332 5.339177 CAGCCATGCGTCATTTATGTTTTA 58.661 37.500 0.00 0.0 0.00 1.52
329 333 5.978919 CAGCCATGCGTCATTTATGTTTTAT 59.021 36.000 0.00 0.0 0.00 1.40
432 464 2.577449 ATGTGATGCGACATACGTCA 57.423 45.000 0.00 0.0 42.74 4.35
533 566 5.710513 TCAACAGGCATATGGATATTTGC 57.289 39.130 4.56 0.0 39.58 3.68
621 668 0.742635 TCGCTGCGCATGGTGAATTA 60.743 50.000 18.65 0.0 0.00 1.40
681 733 8.946085 TCTTGTTGTACATATTTCTTCCATGTC 58.054 33.333 0.00 0.0 34.78 3.06
702 754 4.216257 GTCATGTTTTGTCAGTAGCCATGT 59.784 41.667 0.00 0.0 32.24 3.21
755 807 8.770438 AAATATGTTTGACCGTTTAATGCAAT 57.230 26.923 0.00 0.0 0.00 3.56
786 838 7.117667 GTGCAAAGTTCACTTAAAATATTGGGG 59.882 37.037 0.00 0.0 34.61 4.96
915 970 4.816385 CCTGTTACTGCATCCGACAATATT 59.184 41.667 0.00 0.0 0.00 1.28
1030 1091 1.153066 TTCCACGAGCTTGCACCAA 60.153 52.632 0.00 0.0 0.00 3.67
1102 1163 3.208747 AGAACCAACGATTTGAGGTGT 57.791 42.857 0.00 0.0 34.24 4.16
1446 1513 1.509923 GACGGGTCCCTGTCGTTAG 59.490 63.158 14.50 0.0 41.68 2.34
1459 1534 2.076863 GTCGTTAGAGCTGCAATGGTT 58.923 47.619 1.02 0.0 0.00 3.67
1532 1607 3.943034 CGCGGGCAAACACACGAA 61.943 61.111 0.00 0.0 0.00 3.85
1541 1616 4.320935 GGGCAAACACACGAAAGTTCATAT 60.321 41.667 0.00 0.0 46.40 1.78
1579 1654 2.287608 GGCCAACAAGAAGTACAAGTGC 60.288 50.000 0.00 0.0 0.00 4.40
1640 1716 7.120923 TCTATGGTTGAGGAATGTAAGGTAC 57.879 40.000 0.00 0.0 0.00 3.34
1859 1942 5.059161 GCTTGAATGTGTCTATGATGCCTA 58.941 41.667 0.00 0.0 0.00 3.93
1919 2002 1.781786 AGTCGTGGAGCCATCACTAT 58.218 50.000 0.00 0.0 33.31 2.12
1956 2039 2.551032 GGTTAAACTGGACAAAGGGACG 59.449 50.000 0.00 0.0 0.00 4.79
1957 2040 3.208594 GTTAAACTGGACAAAGGGACGT 58.791 45.455 0.00 0.0 0.00 4.34
1975 2060 8.757982 AGGGACGTGAGATTTTATACTAGTTA 57.242 34.615 0.00 0.0 0.00 2.24
2069 2154 1.541588 GAATCCGCTTTGTCTGGCTTT 59.458 47.619 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.755103 GTTAGAACTTGATTGCCCCTGG 59.245 50.000 0.00 0.0 0.00 4.45
50 51 5.631119 TGATATCCTCGGATACAGACTCAA 58.369 41.667 7.78 0.0 39.56 3.02
89 91 5.661759 ACTACCCTGTTCTACCTAAATCCAG 59.338 44.000 0.00 0.0 0.00 3.86
90 92 5.596763 ACTACCCTGTTCTACCTAAATCCA 58.403 41.667 0.00 0.0 0.00 3.41
92 94 7.040494 GTGAACTACCCTGTTCTACCTAAATC 58.960 42.308 8.52 0.0 44.63 2.17
93 95 6.350780 CGTGAACTACCCTGTTCTACCTAAAT 60.351 42.308 8.52 0.0 44.63 1.40
94 96 5.047802 CGTGAACTACCCTGTTCTACCTAAA 60.048 44.000 8.52 0.0 44.63 1.85
96 98 4.012374 CGTGAACTACCCTGTTCTACCTA 58.988 47.826 8.52 0.0 44.63 3.08
212 216 1.610038 CCTTCATGTGCTTGCTGTTCA 59.390 47.619 0.00 0.0 0.00 3.18
410 442 2.857748 GACGTATGTCGCATCACATTGA 59.142 45.455 0.00 0.0 44.19 2.57
432 464 2.912956 TCTTAGCAAGATCACCCAGGTT 59.087 45.455 0.00 0.0 31.20 3.50
471 504 6.012658 TGCAACTACATTCTTGGACATTTC 57.987 37.500 0.00 0.0 0.00 2.17
533 566 2.868583 CTGCATAATCGTCTTGTCAGGG 59.131 50.000 0.00 0.0 0.00 4.45
621 668 6.712095 TCACATATTTCTTCAGTGTGAGCTTT 59.288 34.615 2.68 0.0 42.82 3.51
681 733 4.771590 ACATGGCTACTGACAAAACATG 57.228 40.909 0.00 0.0 39.88 3.21
764 816 9.154632 AGTTCCCCAATATTTTAAGTGAACTTT 57.845 29.630 0.21 0.0 37.27 2.66
786 838 6.781138 TGCCATCGATGTATAAACAAAGTTC 58.219 36.000 23.27 0.0 39.58 3.01
803 857 7.081349 TGTGTAATTAAAAGAAGTTGCCATCG 58.919 34.615 0.00 0.0 0.00 3.84
1017 1078 0.594796 GGTTGTTTGGTGCAAGCTCG 60.595 55.000 0.00 0.0 40.11 5.03
1030 1091 2.951642 CACACTTGTCATCTGGGTTGTT 59.048 45.455 0.00 0.0 0.00 2.83
1102 1163 3.424829 GCTTCTGAACGCATTGAATCGAA 60.425 43.478 0.00 0.0 0.00 3.71
1160 1221 4.580167 TCCATGTCTCTTTCAAGTTGTTGG 59.420 41.667 2.11 0.0 34.09 3.77
1345 1409 3.936564 AGAATCAGGTGAACTCAAGAGC 58.063 45.455 0.00 0.0 0.00 4.09
1444 1511 1.275010 TCGACAACCATTGCAGCTCTA 59.725 47.619 0.00 0.0 0.00 2.43
1446 1513 0.445436 CTCGACAACCATTGCAGCTC 59.555 55.000 0.00 0.0 0.00 4.09
1459 1534 5.163632 TGTGTATATTTTACGGAGCTCGACA 60.164 40.000 7.83 0.0 42.43 4.35
1532 1607 8.635765 TTTTTCACAGCTTCCTATATGAACTT 57.364 30.769 0.00 0.0 0.00 2.66
1541 1616 2.158534 TGGCCTTTTTCACAGCTTCCTA 60.159 45.455 3.32 0.0 0.00 2.94
1579 1654 5.885022 TGCGGTATGGAGCATCACGTAAG 62.885 52.174 0.00 0.0 38.59 2.34
1640 1716 9.244799 GGACATAGTTTTAAAAGAACAAGTTGG 57.755 33.333 7.96 0.0 0.00 3.77
1797 1878 5.706369 ACCAACCACAAACGCATAATAGTAA 59.294 36.000 0.00 0.0 0.00 2.24
1919 2002 1.154430 AACCCCTTCAAGCTAACCCA 58.846 50.000 0.00 0.0 0.00 4.51
1956 2039 7.016366 AGGGGCCTAACTAGTATAAAATCTCAC 59.984 40.741 0.84 0.0 0.00 3.51
1957 2040 7.080353 AGGGGCCTAACTAGTATAAAATCTCA 58.920 38.462 0.84 0.0 0.00 3.27
2135 2221 1.681327 GGACTCTGTAGACCGGCCA 60.681 63.158 0.00 0.0 0.00 5.36
2364 2450 7.256547 GGCCTAATGTTGAGGATATAACCACTA 60.257 40.741 0.00 0.0 35.99 2.74


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

AutoCloner maintained by Alex Coulton.