Multiple sequence alignment - TraesCS7A01G038200

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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 TraesCS7A01G038200 chr7A 100.000 2447 0 0 1 2447 17207181 17209627 0.000000e+00 4519.0
1 TraesCS7A01G038200 chr7A 73.004 263 64 7 889 1148 11991422 11991164 4.340000e-13 86.1
2 TraesCS7A01G038200 chrUn 95.610 2460 88 15 1 2447 89799856 89802308 0.000000e+00 3927.0
3 TraesCS7A01G038200 chr4A 73.736 811 184 23 898 1690 715954937 715955736 8.560000e-75 291.0
4 TraesCS7A01G038200 chr4A 74.573 586 135 13 1113 1691 715931732 715931154 6.760000e-61 244.0
5 TraesCS7A01G038200 chr6A 77.928 222 45 3 1926 2144 151721615 151721835 4.240000e-28 135.0
6 TraesCS7A01G038200 chr4D 77.489 231 48 3 1926 2153 501256301 501256530 4.240000e-28 135.0
7 TraesCS7A01G038200 chr7D 71.455 536 138 12 806 1338 17664927 17664404 7.100000e-26 128.0
8 TraesCS7A01G038200 chr7D 73.764 263 62 7 889 1148 12380765 12380507 2.000000e-16 97.1
9 TraesCS7A01G038200 chr6B 76.856 229 46 7 1929 2153 411823277 411823052 3.300000e-24 122.0
10 TraesCS7A01G038200 chr1B 76.415 212 43 5 1926 2133 191312077 191312285 9.250000e-20 108.0
11 TraesCS7A01G038200 chr6D 79.851 134 25 2 2260 2391 267807956 267808089 2.000000e-16 97.1
12 TraesCS7A01G038200 chr5D 80.488 123 21 3 2260 2380 147555968 147555847 9.320000e-15 91.6
13 TraesCS7A01G038200 chr4B 78.195 133 28 1 2260 2391 340826133 340826265 1.560000e-12 84.2
14 TraesCS7A01G038200 chr3B 92.308 39 3 0 2266 2304 716934927 716934889 3.400000e-04 56.5


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 TraesCS7A01G038200 chr7A 17207181 17209627 2446 False 4519 4519 100.000 1 2447 1 chr7A.!!$F1 2446
1 TraesCS7A01G038200 chrUn 89799856 89802308 2452 False 3927 3927 95.610 1 2447 1 chrUn.!!$F1 2446
2 TraesCS7A01G038200 chr4A 715954937 715955736 799 False 291 291 73.736 898 1690 1 chr4A.!!$F1 792
3 TraesCS7A01G038200 chr4A 715931154 715931732 578 True 244 244 74.573 1113 1691 1 chr4A.!!$R1 578

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
802 810 2.129607 GGCACAAACACTCAAATGCAG 58.87 47.619 0.0 0.0 34.73 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1826 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.0 0.0 0.0 0.0 4.57 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
72 73 5.276440 TCCAAAGTGGGCATTAATACCATT 58.724 37.500 12.62 7.26 38.32 3.16
73 74 5.723887 TCCAAAGTGGGCATTAATACCATTT 59.276 36.000 12.62 11.84 38.32 2.32
77 78 7.436320 AAGTGGGCATTAATACCATTTCATT 57.564 32.000 12.62 3.58 36.54 2.57
163 164 5.050490 ACGATATCTAAAACAAGAGCGCAT 58.950 37.500 11.47 0.00 0.00 4.73
230 231 7.042187 CCAAAATGATCACTAGTGTATCTCTGC 60.042 40.741 21.99 5.25 0.00 4.26
366 373 2.290577 GGGCATGAATACCAGGAGATCC 60.291 54.545 0.00 0.00 0.00 3.36
439 446 3.119849 ACTTGACACAACTTCACAAGTGC 60.120 43.478 0.00 0.00 45.70 4.40
463 471 6.316140 GCATGTCATTGGTTACAAGAGATACA 59.684 38.462 0.00 0.00 40.49 2.29
498 506 8.810427 ACACTACATTTACGGAAATTACATACG 58.190 33.333 1.85 0.00 32.73 3.06
530 538 6.521527 AGGAGATGCCCTCTATGTTAATTT 57.478 37.500 3.66 0.00 41.66 1.82
597 605 4.067192 TGAATCCATCTATGCCAACATCG 58.933 43.478 0.00 0.00 37.74 3.84
610 618 3.485743 GCCAACATCGTTTTGAGTTCAAC 59.514 43.478 0.00 0.00 35.28 3.18
621 629 5.471556 TTTGAGTTCAACCCATCTACGTA 57.528 39.130 0.00 0.00 35.28 3.57
627 635 8.262227 TGAGTTCAACCCATCTACGTAAATTAT 58.738 33.333 0.00 0.00 0.00 1.28
764 772 4.491234 ACTACGAGATCCTAAATGAGCG 57.509 45.455 0.00 0.00 0.00 5.03
783 791 8.939201 ATGAGCGTTGATATTCATAGATTAGG 57.061 34.615 0.00 0.00 0.00 2.69
787 795 6.368791 GCGTTGATATTCATAGATTAGGCACA 59.631 38.462 0.00 0.00 0.00 4.57
790 798 9.884465 GTTGATATTCATAGATTAGGCACAAAC 57.116 33.333 0.00 0.00 0.00 2.93
797 805 6.939730 TCATAGATTAGGCACAAACACTCAAA 59.060 34.615 0.00 0.00 0.00 2.69
802 810 2.129607 GGCACAAACACTCAAATGCAG 58.870 47.619 0.00 0.00 34.73 4.41
960 968 5.505181 ACATTCAGTTCCACCTATCTTGT 57.495 39.130 0.00 0.00 0.00 3.16
991 999 2.422832 AGTTCGAGGTTTCTAGGTAGCG 59.577 50.000 0.00 0.00 0.00 4.26
1036 1044 1.751351 CGACCACCATCAGCTTCTCTA 59.249 52.381 0.00 0.00 0.00 2.43
1098 1106 2.621070 ACCAATGACTCTGGTAGTGGT 58.379 47.619 0.00 0.00 45.58 4.16
1358 1368 1.192534 GGCAATGCGCGATCTTAGTAC 59.807 52.381 12.10 0.00 43.84 2.73
1373 1383 6.415206 TCTTAGTACTTGCAAGGTGTACTT 57.585 37.500 29.18 14.81 42.65 2.24
1502 1522 0.317479 GCTACCCAGTTGACGAGTGT 59.683 55.000 0.00 0.00 0.00 3.55
1519 1539 4.312443 GAGTGTTGGTTCGGTCTTCAATA 58.688 43.478 0.00 0.00 0.00 1.90
1799 1822 3.612423 CCATGTATCTACACACACACACG 59.388 47.826 0.00 0.00 39.30 4.49
1801 1824 1.647213 GTATCTACACACACACACGCG 59.353 52.381 3.53 3.53 0.00 6.01
1803 1826 3.263171 CTACACACACACACGCGCG 62.263 63.158 30.96 30.96 0.00 6.86
1844 1885 4.094294 ACACACACACACACACACTATTTC 59.906 41.667 0.00 0.00 0.00 2.17
1914 1955 1.532868 CAGCACTAGTTGAACTGCACC 59.467 52.381 8.33 0.00 0.00 5.01
1969 2010 1.369692 CGGGGCTTGCGATATACCA 59.630 57.895 0.00 0.00 0.00 3.25
1985 2026 6.367695 CGATATACCATGCGAAAACTATGGAA 59.632 38.462 9.28 0.00 43.15 3.53
2019 2060 3.256631 AACCTATGTTGAGGCTTTTGCAG 59.743 43.478 0.00 0.00 40.65 4.41
2035 2076 7.138736 GCTTTTGCAGAATCTACACAGTTTAA 58.861 34.615 0.00 0.00 46.58 1.52
2094 2135 5.786401 ACATGAAGTGTATTTTCGAGCTC 57.214 39.130 2.73 2.73 39.91 4.09
2133 2174 6.889301 ATCGGAATGAAGCAATTCATATGT 57.111 33.333 1.90 0.00 40.51 2.29
2254 2295 1.007849 CTTCAAACCAAACGGCCCG 60.008 57.895 0.00 0.00 0.00 6.13
2315 2356 3.524763 AAATGCGCTTGTTTTTCATGC 57.475 38.095 9.73 0.00 41.74 4.06
2324 2365 5.108254 CGCTTGTTTTTCATGCAGAAAGTAC 60.108 40.000 10.02 11.78 46.24 2.73
2372 2413 8.593492 AAGCAATTTGAAATAGGTTGAAGTTC 57.407 30.769 0.00 0.00 0.00 3.01
2393 2434 1.094785 ACCGAGAATGCATTTTCCCG 58.905 50.000 20.78 16.60 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.825143 TGCTCATTTCGGATCTCATGA 57.175 42.857 0.00 0.00 0.00 3.07
25 26 2.677836 TCGTGGCAGTAATGCTCATTTC 59.322 45.455 15.61 0.00 34.73 2.17
29 30 0.894835 TCTCGTGGCAGTAATGCTCA 59.105 50.000 15.61 8.58 34.73 4.26
30 31 2.131183 GATCTCGTGGCAGTAATGCTC 58.869 52.381 15.61 5.93 34.73 4.26
44 45 1.755179 AATGCCCACTTTGGATCTCG 58.245 50.000 0.00 0.00 40.96 4.04
45 46 5.241728 GGTATTAATGCCCACTTTGGATCTC 59.758 44.000 11.29 0.00 40.96 2.75
163 164 6.969828 TGTGTAACGTGCATAAATGTGATA 57.030 33.333 0.00 0.00 42.39 2.15
250 251 8.924511 ATATCTTGATCACCCGTATTCAAATT 57.075 30.769 0.00 0.00 0.00 1.82
254 255 7.549134 GCAATATATCTTGATCACCCGTATTCA 59.451 37.037 5.09 0.00 0.00 2.57
334 335 8.328758 CCTGGTATTCATGCCCTCTATAAATAA 58.671 37.037 0.00 0.00 0.00 1.40
357 364 4.730949 AATGCAAACATTGGATCTCCTG 57.269 40.909 0.00 0.00 44.90 3.86
366 373 6.550843 TCTCGTGGTATTAATGCAAACATTG 58.449 36.000 5.87 0.00 46.08 2.82
414 421 5.580691 CACTTGTGAAGTTGTGTCAAGTCTA 59.419 40.000 5.99 0.00 44.11 2.59
430 437 2.585330 ACCAATGACATGCACTTGTGA 58.415 42.857 4.79 0.00 0.00 3.58
439 446 7.848223 TGTATCTCTTGTAACCAATGACATG 57.152 36.000 0.00 0.00 0.00 3.21
463 471 5.589452 TCCGTAAATGTAGTGTGGTTGTTTT 59.411 36.000 0.00 0.00 0.00 2.43
530 538 9.585369 TGGATATCCAATTGCTATTGTGAAATA 57.415 29.630 22.52 10.75 44.35 1.40
549 557 1.302033 CAGCCTGGCCGTGGATATC 60.302 63.158 16.57 0.00 0.00 1.63
597 605 4.514066 ACGTAGATGGGTTGAACTCAAAAC 59.486 41.667 0.33 0.00 37.63 2.43
764 772 9.884465 GTTTGTGCCTAATCTATGAATATCAAC 57.116 33.333 0.00 0.00 0.00 3.18
783 791 3.082698 TCTGCATTTGAGTGTTTGTGC 57.917 42.857 0.00 0.00 0.00 4.57
802 810 3.984633 GGATCTCGTGCTACTAATGCTTC 59.015 47.826 0.00 0.00 0.00 3.86
852 860 8.593945 ATTATTTATAGTGCATGTATTGGGGG 57.406 34.615 0.00 0.00 0.00 5.40
960 968 4.099573 AGAAACCTCGAACTGTCTTGAAGA 59.900 41.667 0.00 0.00 0.00 2.87
991 999 2.886081 TGTTGTTGTCATTGGTGCAAC 58.114 42.857 0.00 0.00 40.05 4.17
1036 1044 6.888632 ACAGAAAGCAAGATGAATAGAATGGT 59.111 34.615 0.00 0.00 0.00 3.55
1098 1106 1.600107 GTTGGTCACCCTCGCCATA 59.400 57.895 0.00 0.00 31.71 2.74
1358 1368 5.940192 TGTATCAAAGTACACCTTGCAAG 57.060 39.130 19.93 19.93 32.32 4.01
1502 1522 3.663995 TCGTATTGAAGACCGAACCAA 57.336 42.857 0.00 0.00 0.00 3.67
1640 1661 5.155509 TGCTACAACATCATTTATCGCAC 57.844 39.130 0.00 0.00 0.00 5.34
1751 1774 9.099454 GAGAAAGAGAGAGTAGAACAACAAAAA 57.901 33.333 0.00 0.00 0.00 1.94
1752 1775 7.711339 GGAGAAAGAGAGAGTAGAACAACAAAA 59.289 37.037 0.00 0.00 0.00 2.44
1753 1776 7.147724 TGGAGAAAGAGAGAGTAGAACAACAAA 60.148 37.037 0.00 0.00 0.00 2.83
1754 1777 6.323996 TGGAGAAAGAGAGAGTAGAACAACAA 59.676 38.462 0.00 0.00 0.00 2.83
1755 1778 5.833667 TGGAGAAAGAGAGAGTAGAACAACA 59.166 40.000 0.00 0.00 0.00 3.33
1756 1779 6.334102 TGGAGAAAGAGAGAGTAGAACAAC 57.666 41.667 0.00 0.00 0.00 3.32
1757 1780 6.495181 ACATGGAGAAAGAGAGAGTAGAACAA 59.505 38.462 0.00 0.00 0.00 2.83
1758 1781 6.013379 ACATGGAGAAAGAGAGAGTAGAACA 58.987 40.000 0.00 0.00 0.00 3.18
1759 1782 6.524101 ACATGGAGAAAGAGAGAGTAGAAC 57.476 41.667 0.00 0.00 0.00 3.01
1760 1783 8.278639 AGATACATGGAGAAAGAGAGAGTAGAA 58.721 37.037 0.00 0.00 0.00 2.10
1761 1784 7.811282 AGATACATGGAGAAAGAGAGAGTAGA 58.189 38.462 0.00 0.00 0.00 2.59
1762 1785 8.999431 GTAGATACATGGAGAAAGAGAGAGTAG 58.001 40.741 0.00 0.00 0.00 2.57
1801 1824 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1803 1826 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
1914 1955 3.857010 GCCGAAGTTCAATTTGTCCTTGG 60.857 47.826 3.32 6.83 0.00 3.61
1969 2010 3.374058 CCTCGTTTCCATAGTTTTCGCAT 59.626 43.478 0.00 0.00 0.00 4.73
1985 2026 4.553330 AACATAGGTTGTGATCCTCGTT 57.447 40.909 0.00 0.00 38.99 3.85
2094 2135 7.614908 TCATTCCGATAAACGTTTTAGAATCG 58.385 34.615 25.93 25.93 40.78 3.34
2133 2174 3.334691 CCTTGTAGCATCTTTCCAACGA 58.665 45.455 0.00 0.00 0.00 3.85
2198 2239 7.817478 AGTTCGAAAGTTTGGTTTGAGAAATTT 59.183 29.630 0.00 0.00 0.00 1.82
2254 2295 5.051508 GCCATATCATTTGCGTCAATCAAAC 60.052 40.000 0.00 0.00 36.40 2.93
2256 2297 4.097589 TGCCATATCATTTGCGTCAATCAA 59.902 37.500 0.00 0.00 0.00 2.57
2315 2356 8.844441 TGTTTAAAATTGGAACGTACTTTCTG 57.156 30.769 11.43 0.00 0.00 3.02
2372 2413 1.134946 GGGAAAATGCATTCTCGGTGG 59.865 52.381 13.38 0.00 0.00 4.61
2393 2434 4.270808 CCAGCAAACCATTGAGAAACAAAC 59.729 41.667 0.00 0.00 42.03 2.93


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

AutoCloner maintained by Alex Coulton.