Multiple sequence alignment - TraesCS7A01G263700

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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 TraesCS7A01G263700 chr7A 100.000 3876 0 0 1 3876 261882131 261878256 0.000000e+00 7158.0
1 TraesCS7A01G263700 chr7D 94.749 3923 116 34 1 3876 245486495 245482616 0.000000e+00 6021.0
2 TraesCS7A01G263700 chr7B 94.773 2927 91 32 712 3598 221915519 221912615 0.000000e+00 4501.0
3 TraesCS7A01G263700 chr7B 94.437 719 22 6 1 717 221919346 221918644 0.000000e+00 1090.0
4 TraesCS7A01G263700 chr7B 90.714 140 10 1 3737 3876 221912615 221912479 2.380000e-42 183.0
5 TraesCS7A01G263700 chr5D 77.206 272 41 18 1701 1960 397425887 397425625 5.220000e-29 139.0
6 TraesCS7A01G263700 chr5D 93.976 83 5 0 1549 1631 397426069 397425987 4.070000e-25 126.0
7 TraesCS7A01G263700 chr5D 85.106 94 7 6 3483 3573 562647616 562647527 5.330000e-14 89.8
8 TraesCS7A01G263700 chr5A 76.512 281 39 19 1701 1966 502787402 502787134 1.130000e-25 128.0
9 TraesCS7A01G263700 chr5A 93.827 81 5 0 1551 1631 502787582 502787502 5.260000e-24 122.0
10 TraesCS7A01G263700 chr5B 76.259 278 38 21 1701 1960 477611046 477610779 5.260000e-24 122.0
11 TraesCS7A01G263700 chr5B 91.566 83 7 0 1549 1631 477611226 477611144 8.800000e-22 115.0


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 TraesCS7A01G263700 chr7A 261878256 261882131 3875 True 7158.000000 7158 100.000 1 3876 1 chr7A.!!$R1 3875
1 TraesCS7A01G263700 chr7D 245482616 245486495 3879 True 6021.000000 6021 94.749 1 3876 1 chr7D.!!$R1 3875
2 TraesCS7A01G263700 chr7B 221912479 221919346 6867 True 1924.666667 4501 93.308 1 3876 3 chr7B.!!$R1 3875

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
397 398 0.392998 GCAGTGATTCGGTGTGGGAT 60.393 55.0 0.00 0.00 0.00 3.85 F
415 416 0.969894 ATCGGTAGCTGCTCCCATAC 59.030 55.0 12.02 1.48 0.00 2.39 F
1893 5040 0.459489 TTGCTTTTGTGCAGGTCACC 59.541 50.0 0.00 0.00 45.03 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 5040 0.040425 CCAAAACGAGTGCCTTTCCG 60.040 55.000 0.00 0.00 0.00 4.30 R
2036 5185 1.069978 TGATTTGGTCAGCGACACTCA 59.930 47.619 10.14 5.03 33.68 3.41 R
3340 6544 0.106569 TGCCCATAACTGATGCAGGG 60.107 55.000 0.00 0.00 39.33 4.45 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
118 119 5.012664 TGTCATCTTTTTGCCCTACTACTGA 59.987 40.000 0.00 0.00 0.00 3.41
298 299 2.315925 TGCAGAGCCCTCTTATTTCG 57.684 50.000 0.00 0.00 37.98 3.46
397 398 0.392998 GCAGTGATTCGGTGTGGGAT 60.393 55.000 0.00 0.00 0.00 3.85
413 414 1.476007 GGATCGGTAGCTGCTCCCAT 61.476 60.000 12.02 5.20 0.00 4.00
415 416 0.969894 ATCGGTAGCTGCTCCCATAC 59.030 55.000 12.02 1.48 0.00 2.39
635 645 4.898328 GCATGAAACAAAATGCAGAGAC 57.102 40.909 0.00 0.00 46.75 3.36
647 658 2.422597 TGCAGAGACGGGTACATTTTG 58.577 47.619 0.00 0.00 0.00 2.44
672 683 4.685924 CATTGAGTTGGCAAAGACTTTGT 58.314 39.130 24.98 8.48 42.56 2.83
717 728 5.826208 AGTTTGTTTCCTCGGAATGTTAGTT 59.174 36.000 0.00 0.00 33.79 2.24
718 729 6.993902 AGTTTGTTTCCTCGGAATGTTAGTTA 59.006 34.615 0.00 0.00 33.79 2.24
719 730 7.172703 AGTTTGTTTCCTCGGAATGTTAGTTAG 59.827 37.037 0.00 0.00 33.79 2.34
720 731 4.933400 TGTTTCCTCGGAATGTTAGTTAGC 59.067 41.667 0.00 0.00 33.79 3.09
721 732 3.814005 TCCTCGGAATGTTAGTTAGCC 57.186 47.619 0.00 0.00 0.00 3.93
722 733 3.101437 TCCTCGGAATGTTAGTTAGCCA 58.899 45.455 0.00 0.00 0.00 4.75
723 734 3.709653 TCCTCGGAATGTTAGTTAGCCAT 59.290 43.478 0.00 0.00 0.00 4.40
724 735 3.809832 CCTCGGAATGTTAGTTAGCCATG 59.190 47.826 0.00 0.00 0.00 3.66
725 736 3.804036 TCGGAATGTTAGTTAGCCATGG 58.196 45.455 7.63 7.63 0.00 3.66
779 3918 4.579869 AGTCAAAGTCGGCATACTGAAAT 58.420 39.130 0.00 0.00 31.36 2.17
807 3946 1.341209 CCAGAAAGAAACTGGCCCAAC 59.659 52.381 0.00 0.00 46.30 3.77
1038 4181 1.354168 TACTCCTCCTCTCCCCCGAG 61.354 65.000 0.00 0.00 37.48 4.63
1121 4268 2.373169 ACAATGGCAGACTTCTCCTCAA 59.627 45.455 0.00 0.00 0.00 3.02
1150 4297 1.138661 CACTCTCTCCTCAAGATGCCC 59.861 57.143 0.00 0.00 32.19 5.36
1153 4300 1.964608 CTCTCCTCAAGATGCCCGCA 61.965 60.000 0.00 0.00 32.19 5.69
1172 4319 1.800586 CAGTCTTCACCACCAATGACG 59.199 52.381 0.00 0.00 0.00 4.35
1476 4623 9.387123 GCGATTAAGAATTGTATTTCCTTGATC 57.613 33.333 0.00 0.00 0.00 2.92
1641 4788 3.739519 GCAGAGAGGGTATGTACAGCAAG 60.740 52.174 0.33 0.00 0.00 4.01
1684 4831 5.762179 TTTCTCTTTCTCCTGGCATCTTA 57.238 39.130 0.00 0.00 0.00 2.10
1801 4948 5.712152 AGGTCAAAATTAGCCTGTTTCTG 57.288 39.130 0.00 0.00 0.00 3.02
1824 4971 6.207928 TGTTGTCATTTACATGTCTTGCTTG 58.792 36.000 0.00 0.00 38.10 4.01
1829 4976 1.155889 TACATGTCTTGCTTGGTGCG 58.844 50.000 0.00 0.00 46.63 5.34
1893 5040 0.459489 TTGCTTTTGTGCAGGTCACC 59.541 50.000 0.00 0.00 45.03 4.02
1975 5122 5.199982 TGAGGTAATTAAGCCAAATGGGA 57.800 39.130 0.90 0.00 40.01 4.37
2002 5151 6.874288 ACAAAAGAGAGAAAGATGTCAAGG 57.126 37.500 0.00 0.00 0.00 3.61
2043 5192 7.826260 TTTGACATTTTCCTTTTTGAGTGTC 57.174 32.000 0.00 0.00 36.26 3.67
2057 5208 1.461127 GAGTGTCGCTGACCAAATCAC 59.539 52.381 6.30 0.00 32.37 3.06
2088 5240 7.497595 TGTAATGAGAAGTTCACTGTTGTACT 58.502 34.615 5.50 0.00 38.99 2.73
2149 5301 2.760092 CCCAGTGTTGTATGGATTTGGG 59.240 50.000 0.00 0.00 39.02 4.12
2194 5346 1.890174 GGCACAAGTATGGGGCAAC 59.110 57.895 0.00 0.00 43.92 4.17
2356 5550 0.392863 TCAAGCCATGATGGACACCG 60.393 55.000 17.22 0.00 40.96 4.94
2367 5561 1.065928 GGACACCGCATCCTACTCG 59.934 63.158 0.00 0.00 33.03 4.18
2512 5706 1.881973 GTCCGTTTTACCCCAACTTCC 59.118 52.381 0.00 0.00 0.00 3.46
2513 5707 1.202915 TCCGTTTTACCCCAACTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
2521 5715 1.303236 CCCAACTTCCCGTGCATCA 60.303 57.895 0.00 0.00 0.00 3.07
3194 6395 4.732938 GCATCAAGAGCTGCTTACCATTTC 60.733 45.833 2.53 0.00 34.18 2.17
3340 6544 4.396478 GCTTAGTTCATTTTCCCTGTCTCC 59.604 45.833 0.00 0.00 0.00 3.71
3438 6642 4.038402 CAGTTGGATATGGCCTTTGAATCC 59.962 45.833 3.32 8.11 37.27 3.01
3539 6743 1.358152 TGGGAATTTCAGAGGGACGT 58.642 50.000 0.00 0.00 0.00 4.34
3541 6745 1.679032 GGGAATTTCAGAGGGACGTGG 60.679 57.143 0.00 0.00 0.00 4.94
3646 6850 3.334691 TGCCTCGTCCTGTTAATTCAAG 58.665 45.455 0.00 0.00 0.00 3.02
3707 6912 1.668419 GACACATAGCCCTCGCAAAT 58.332 50.000 0.00 0.00 37.52 2.32
3708 6913 2.017049 GACACATAGCCCTCGCAAATT 58.983 47.619 0.00 0.00 37.52 1.82
3710 6915 2.825532 ACACATAGCCCTCGCAAATTTT 59.174 40.909 0.00 0.00 37.52 1.82
3711 6916 3.258123 ACACATAGCCCTCGCAAATTTTT 59.742 39.130 0.00 0.00 37.52 1.94
3809 7014 5.536497 ATCCCACTTCTAAACTCCCATTT 57.464 39.130 0.00 0.00 0.00 2.32
3825 7030 3.418047 CCATTTCCTTTCCCGTTGTAGT 58.582 45.455 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 255 6.554419 TGCCTCATTAACTTCAAATTGATCG 58.446 36.000 0.00 0.00 0.00 3.69
298 299 3.440522 GTGCAGAGAGGTTAAATGGGAAC 59.559 47.826 0.00 0.00 0.00 3.62
397 398 1.452953 CGTATGGGAGCAGCTACCGA 61.453 60.000 19.66 6.58 37.26 4.69
413 414 8.774890 TTTTATTTCACAGGCAAGTATACGTA 57.225 30.769 0.00 0.00 0.00 3.57
415 416 8.394877 TCATTTTATTTCACAGGCAAGTATACG 58.605 33.333 0.00 0.00 0.00 3.06
635 645 3.440173 ACTCAATGCTCAAAATGTACCCG 59.560 43.478 0.00 0.00 0.00 5.28
647 658 2.555757 AGTCTTTGCCAACTCAATGCTC 59.444 45.455 0.00 0.00 0.00 4.26
672 683 2.445145 TGAATCCTGAACCCCAACTCAA 59.555 45.455 0.00 0.00 0.00 3.02
717 728 1.014804 AACCATTTCCCCCATGGCTA 58.985 50.000 6.09 0.00 44.69 3.93
718 729 1.014804 TAACCATTTCCCCCATGGCT 58.985 50.000 6.09 0.00 44.69 4.75
719 730 1.119684 GTAACCATTTCCCCCATGGC 58.880 55.000 6.09 0.00 44.69 4.40
720 731 1.788229 GGTAACCATTTCCCCCATGG 58.212 55.000 4.14 4.14 46.07 3.66
748 3887 3.932710 TGCCGACTTTGACTACAATCATC 59.067 43.478 0.00 0.00 35.85 2.92
807 3946 1.938585 TAAGAGAGGGTCCCTGTGTG 58.061 55.000 17.72 0.00 31.76 3.82
1121 4268 1.536662 GGAGAGAGTGGTGGTGGGT 60.537 63.158 0.00 0.00 0.00 4.51
1150 4297 0.518636 CATTGGTGGTGAAGACTGCG 59.481 55.000 0.00 0.00 0.00 5.18
1153 4300 1.878102 GCGTCATTGGTGGTGAAGACT 60.878 52.381 0.00 0.00 0.00 3.24
1172 4319 2.124695 GATGTTCGGGGTGGAGGC 60.125 66.667 0.00 0.00 0.00 4.70
1229 4376 1.888018 CATTTGCTGGTGCTGGAGG 59.112 57.895 0.00 0.00 40.48 4.30
1407 4554 5.957774 AGTGGATGGCAAATGGTAGTTAATT 59.042 36.000 0.00 0.00 0.00 1.40
1416 4563 4.081531 ACATACAAAGTGGATGGCAAATGG 60.082 41.667 5.48 0.00 43.00 3.16
1641 4788 2.844146 GTGTGTACGTGTGCGAGC 59.156 61.111 0.00 0.00 42.00 5.03
1684 4831 3.011032 AGAGAAAGGCCACCAAGATCAAT 59.989 43.478 5.01 0.00 0.00 2.57
1801 4948 5.630680 CCAAGCAAGACATGTAAATGACAAC 59.369 40.000 0.00 0.00 42.78 3.32
1893 5040 0.040425 CCAAAACGAGTGCCTTTCCG 60.040 55.000 0.00 0.00 0.00 4.30
1975 5122 9.578439 CTTGACATCTTTCTCTCTTTTGTTTTT 57.422 29.630 0.00 0.00 0.00 1.94
2002 5151 6.012658 TGTCAAATTAAGCATCAGGTGTTC 57.987 37.500 0.00 0.00 0.00 3.18
2036 5185 1.069978 TGATTTGGTCAGCGACACTCA 59.930 47.619 10.14 5.03 33.68 3.41
2037 5186 1.461127 GTGATTTGGTCAGCGACACTC 59.539 52.381 10.14 3.07 37.56 3.51
2043 5192 4.985413 ACATTAATGTGATTTGGTCAGCG 58.015 39.130 20.19 0.00 40.03 5.18
2075 5226 3.753797 TGCACAACAAGTACAACAGTGAA 59.246 39.130 0.00 0.00 0.00 3.18
2149 5301 1.451028 GAGGCCATCACTGTCCAGC 60.451 63.158 5.01 0.00 0.00 4.85
2607 5801 1.517832 CCCTACTGGAAGGAGCACG 59.482 63.158 0.29 0.00 46.40 5.34
2714 5913 3.299503 ACAAGCCAATGGAAACTCAGTT 58.700 40.909 2.05 0.00 0.00 3.16
2773 5972 5.347907 GTCGTCGGTAATCATGGATAATTCC 59.652 44.000 0.00 0.00 42.94 3.01
3340 6544 0.106569 TGCCCATAACTGATGCAGGG 60.107 55.000 0.00 0.00 39.33 4.45
3438 6642 0.871722 TTGGTGGATTTCTTGCGACG 59.128 50.000 0.00 0.00 0.00 5.12
3529 6733 3.589988 GATTATATGCCACGTCCCTCTG 58.410 50.000 0.00 0.00 0.00 3.35
3646 6850 8.871125 TGAATTAGAGAGGAAGTATTATCCCAC 58.129 37.037 0.00 0.00 37.71 4.61
3718 6923 2.164422 TGTTGGATGTGTCGTGCAAAAA 59.836 40.909 0.00 0.00 32.92 1.94
3719 6924 1.745653 TGTTGGATGTGTCGTGCAAAA 59.254 42.857 0.00 0.00 32.92 2.44
3720 6925 1.383523 TGTTGGATGTGTCGTGCAAA 58.616 45.000 0.00 0.00 32.92 3.68
3809 7014 3.118334 TGTTTGACTACAACGGGAAAGGA 60.118 43.478 0.00 0.00 35.63 3.36


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

AutoCloner maintained by Alex Coulton.