Multiple sequence alignment - TraesCS7B01G086600

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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 TraesCS7B01G086600 chr7B 100.000 2517 0 0 1 2517 99704696 99707212 0 4649
1 TraesCS7B01G086600 chr7B 93.985 2527 137 11 1 2517 657413366 657410845 0 3810
2 TraesCS7B01G086600 chr3B 96.117 2524 91 5 1 2517 103304294 103306817 0 4111
3 TraesCS7B01G086600 chr3B 95.802 2525 98 5 1 2517 694799523 694802047 0 4069
4 TraesCS7B01G086600 chr3B 94.022 2526 139 9 1 2517 177753549 177751027 0 3818
5 TraesCS7B01G086600 chr3B 93.819 2524 140 14 1 2517 756002615 756005129 0 3783
6 TraesCS7B01G086600 chr4D 94.614 2525 121 12 1 2517 65869132 65871649 0 3895
7 TraesCS7B01G086600 chr5B 94.486 2521 128 9 1 2517 12563428 12560915 0 3875
8 TraesCS7B01G086600 chr1D 94.293 2523 132 10 1 2517 108782091 108784607 0 3851
9 TraesCS7B01G086600 chr7D 94.013 2522 137 12 1 2517 54980078 54977566 0 3808


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 TraesCS7B01G086600 chr7B 99704696 99707212 2516 False 4649 4649 100.000 1 2517 1 chr7B.!!$F1 2516
1 TraesCS7B01G086600 chr7B 657410845 657413366 2521 True 3810 3810 93.985 1 2517 1 chr7B.!!$R1 2516
2 TraesCS7B01G086600 chr3B 103304294 103306817 2523 False 4111 4111 96.117 1 2517 1 chr3B.!!$F1 2516
3 TraesCS7B01G086600 chr3B 694799523 694802047 2524 False 4069 4069 95.802 1 2517 1 chr3B.!!$F2 2516
4 TraesCS7B01G086600 chr3B 177751027 177753549 2522 True 3818 3818 94.022 1 2517 1 chr3B.!!$R1 2516
5 TraesCS7B01G086600 chr3B 756002615 756005129 2514 False 3783 3783 93.819 1 2517 1 chr3B.!!$F3 2516
6 TraesCS7B01G086600 chr4D 65869132 65871649 2517 False 3895 3895 94.614 1 2517 1 chr4D.!!$F1 2516
7 TraesCS7B01G086600 chr5B 12560915 12563428 2513 True 3875 3875 94.486 1 2517 1 chr5B.!!$R1 2516
8 TraesCS7B01G086600 chr1D 108782091 108784607 2516 False 3851 3851 94.293 1 2517 1 chr1D.!!$F1 2516
9 TraesCS7B01G086600 chr7D 54977566 54980078 2512 True 3808 3808 94.013 1 2517 1 chr7D.!!$R1 2516

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
293 294 0.038744 CCAGAGAATTGCCACACCCT 59.961 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1693 0.179009 ATGTGCCACTCTGCAACTGT 60.179 50.0 0.0 0.0 44.11 3.55 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
202 203 1.208706 TGAGTGTGAGTTGGACCCAA 58.791 50.000 0.00 0.00 0.00 4.12
293 294 0.038744 CCAGAGAATTGCCACACCCT 59.961 55.000 0.00 0.00 0.00 4.34
326 327 1.962822 CAGAAGCTGGCACGAGCAA 60.963 57.895 7.26 0.00 44.61 3.91
479 483 1.656652 CTCTTGTATTGGGTCAGGCG 58.343 55.000 0.00 0.00 0.00 5.52
628 633 3.447229 AGGCTTTTAGTTGCACACTGTTT 59.553 39.130 10.59 0.00 35.97 2.83
823 834 4.556233 TGTTGAGACTGGAATCTTACACG 58.444 43.478 0.00 0.00 0.00 4.49
880 891 3.071479 GTTATGCCACTGAGGTTTTCGA 58.929 45.455 0.00 0.00 40.61 3.71
1133 1146 3.769844 TCTTTTTAGTTTGGCACCCACAA 59.230 39.130 0.00 0.00 30.78 3.33
1140 1153 1.198713 TTGGCACCCACAACATGTTT 58.801 45.000 8.77 0.00 30.78 2.83
1185 1198 3.321682 AGTTGGCACATACTTGTTGCAAT 59.678 39.130 0.59 0.00 39.30 3.56
1189 1202 3.057315 GGCACATACTTGTTGCAATCTGT 60.057 43.478 0.59 4.44 33.96 3.41
1202 1217 7.093354 TGTTGCAATCTGTTTTTAACTTGACA 58.907 30.769 0.59 0.00 0.00 3.58
1353 1369 3.503748 GTCTTCAATGTCAACTTGAGGGG 59.496 47.826 0.00 0.00 34.33 4.79
1434 1450 2.838225 CTCTACCATCGCGGGGGT 60.838 66.667 22.69 22.69 40.22 4.95
1505 1521 6.127925 GCACTTCCAGATTATTGACATTGACA 60.128 38.462 0.00 0.00 0.00 3.58
1514 1530 7.987458 AGATTATTGACATTGACATACCGAAGT 59.013 33.333 0.00 0.00 0.00 3.01
1643 1660 6.425114 CACAGTACTAGTCTGCAATCTGTTTT 59.575 38.462 17.17 0.00 36.50 2.43
1644 1661 7.598869 CACAGTACTAGTCTGCAATCTGTTTTA 59.401 37.037 17.17 0.00 36.50 1.52
1645 1662 8.314751 ACAGTACTAGTCTGCAATCTGTTTTAT 58.685 33.333 17.17 0.00 36.50 1.40
1646 1663 8.812329 CAGTACTAGTCTGCAATCTGTTTTATC 58.188 37.037 0.00 0.00 0.00 1.75
1647 1664 8.531982 AGTACTAGTCTGCAATCTGTTTTATCA 58.468 33.333 0.00 0.00 0.00 2.15
1765 1782 5.707298 AGCAGTTGCACAGTAGAACATAAAT 59.293 36.000 6.90 0.00 45.16 1.40
1793 1810 8.504005 GTTGCACAGTAGAACATAAATAGTTGT 58.496 33.333 0.00 0.00 0.00 3.32
1875 1894 1.134818 CGCAGTAATGAGTGTGGGCTA 60.135 52.381 0.00 0.00 33.56 3.93
1891 1910 2.006888 GGCTATTCGCACTGCTTAACA 58.993 47.619 0.00 0.00 41.67 2.41
1916 1935 0.034337 GAGTGGAACGGTAGCCAACA 59.966 55.000 4.45 0.00 45.86 3.33
1967 1986 1.676529 CATCAGGAAGAAGCTGGCATG 59.323 52.381 0.00 0.00 0.00 4.06
2007 2026 2.933287 AACACCGCCCCATGGAGA 60.933 61.111 15.22 0.00 32.25 3.71
2466 2492 5.294060 TGGCTGCATTTGTTTTTCTTCTTTC 59.706 36.000 0.50 0.00 0.00 2.62
2483 2509 1.045407 TTCGGTGTAACTCCAGTGCT 58.955 50.000 0.00 0.00 36.74 4.40
2508 2534 0.243095 GTACCGTCGACTCTTTGCCT 59.757 55.000 14.70 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 3.136763 CGCATCCTTCATTCATAGCTGT 58.863 45.455 0.00 0.00 0.00 4.40
293 294 2.554142 CTTCTGGTTCTGCGCATATCA 58.446 47.619 12.24 8.09 0.00 2.15
326 327 2.421529 GCAATAGGTGGTCCCGAAGAAT 60.422 50.000 0.00 0.00 38.74 2.40
377 378 6.813293 TGAATGGAGACCTTTGAGATGATA 57.187 37.500 0.00 0.00 0.00 2.15
379 380 5.705397 ATGAATGGAGACCTTTGAGATGA 57.295 39.130 0.00 0.00 0.00 2.92
479 483 3.002791 TCATCATTTGCTCCTTCGTGAC 58.997 45.455 0.00 0.00 0.00 3.67
715 726 6.904626 AGAAAGCACCATACCTGATTATCTT 58.095 36.000 0.00 0.00 0.00 2.40
789 800 5.598005 TCCAGTCTCAACAACAATTTTGGAT 59.402 36.000 0.00 0.00 0.00 3.41
792 803 7.205297 AGATTCCAGTCTCAACAACAATTTTG 58.795 34.615 0.00 0.00 0.00 2.44
802 813 4.557205 ACGTGTAAGATTCCAGTCTCAAC 58.443 43.478 0.00 0.00 0.00 3.18
823 834 5.368989 CCCTTCTGGTAAGTTATCCATGAC 58.631 45.833 0.00 0.00 33.01 3.06
937 949 0.786435 AAGGCCTCCCTCAATTGGTT 59.214 50.000 5.23 0.00 41.90 3.67
1158 1171 5.734786 GCAACAAGTATGTGCCAACTAACAA 60.735 40.000 0.00 0.00 40.46 2.83
1185 1198 9.974980 AAAAGACTTTGTCAAGTTAAAAACAGA 57.025 25.926 0.06 0.00 43.79 3.41
1353 1369 1.282930 AAGAACTTCGAAGCGTCCGC 61.283 55.000 24.86 2.94 42.33 5.54
1434 1450 2.359981 ACTCCATAGCTGGCGTACTA 57.640 50.000 0.00 0.00 38.71 1.82
1453 1469 4.402829 TGCTGAACTTTGGGTAATGCTTA 58.597 39.130 0.00 0.00 0.00 3.09
1505 1521 3.015327 ACTTGTCGAGCTACTTCGGTAT 58.985 45.455 0.00 0.00 40.83 2.73
1514 1530 6.034591 GCTTATTGTCTTACTTGTCGAGCTA 58.965 40.000 0.00 0.00 0.00 3.32
1676 1693 0.179009 ATGTGCCACTCTGCAACTGT 60.179 50.000 0.00 0.00 44.11 3.55
1765 1782 9.938280 AACTATTTATGTTCTACTGTGCAACTA 57.062 29.630 0.00 0.00 38.04 2.24
1793 1810 9.461312 AAACCAATAAAGATAATGCACTCTGTA 57.539 29.630 0.00 0.00 0.00 2.74
1836 1854 2.731451 GCGATGGGCAAGAAAAGAAAAC 59.269 45.455 0.00 0.00 42.87 2.43
1875 1894 1.535462 GTGGTGTTAAGCAGTGCGAAT 59.465 47.619 10.00 2.80 33.61 3.34
1916 1935 1.280998 CCTTGGGATCGTAGTTGGGTT 59.719 52.381 0.00 0.00 0.00 4.11
2007 2026 6.070309 AGTCCTTCTCATATCTCAGCAACTTT 60.070 38.462 0.00 0.00 0.00 2.66
2050 2069 0.539051 CCTCCGTGGAGCAGAGAAAT 59.461 55.000 10.53 0.00 40.69 2.17
2372 2396 6.774084 ACTGTGATTTTGTTTCATTGTTTGC 58.226 32.000 0.00 0.00 0.00 3.68
2387 2411 2.906389 TCCACTCAGGCTACTGTGATTT 59.094 45.455 13.04 0.00 45.14 2.17
2466 2492 0.317160 TCAGCACTGGAGTTACACCG 59.683 55.000 0.00 0.00 0.00 4.94
2483 2509 3.928727 AAGAGTCGACGGTACAAATCA 57.071 42.857 10.46 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.