Multiple sequence alignment - TraesCS7D01G304300

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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 TraesCS7D01G304300 chr7D 100.000 2993 0 0 1 2993 386360392 386357400 0.000000e+00 5528
1 TraesCS7D01G304300 chr7A 96.230 2997 73 8 1 2993 434741288 434738328 0.000000e+00 4872
2 TraesCS7D01G304300 chr7B 94.753 1963 81 8 378 2333 380538653 380536706 0.000000e+00 3035
3 TraesCS7D01G304300 chr7B 94.726 493 20 3 2501 2993 380511800 380511314 0.000000e+00 761
4 TraesCS7D01G304300 chr7B 92.793 333 12 3 1 330 380538965 380538642 3.490000e-129 472


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 TraesCS7D01G304300 chr7D 386357400 386360392 2992 True 5528.0 5528 100.000 1 2993 1 chr7D.!!$R1 2992
1 TraesCS7D01G304300 chr7A 434738328 434741288 2960 True 4872.0 4872 96.230 1 2993 1 chr7A.!!$R1 2992
2 TraesCS7D01G304300 chr7B 380536706 380538965 2259 True 1753.5 3035 93.773 1 2333 2 chr7B.!!$R2 2332

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
698 703 0.244721 AAGAATCTGCAAAAGCGGCC 59.755 50.0 0.0 0.0 0.0 6.13 F
700 705 0.457337 GAATCTGCAAAAGCGGCCTG 60.457 55.0 0.0 0.0 0.0 4.85 F
704 709 0.810648 CTGCAAAAGCGGCCTGAATA 59.189 50.0 0.0 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1579 0.586802 GAAGCGACACTTTCCCACAC 59.413 55.000 0.00 0.00 39.29 3.82 R
1801 1839 0.869068 ACGATGAGAGCGATCCTACG 59.131 55.000 0.00 1.21 0.00 3.51 R
2006 2044 1.079681 CCAAAAGCATGGCACGCAT 60.080 52.632 8.75 0.00 32.78 4.73 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
59 60 9.506018 TTCTGAAGTATTGAATGTGAAATCTGA 57.494 29.630 0.00 0.00 0.00 3.27
474 479 9.810545 TTTGGAAAGGTAAATTACAAGTTTGAG 57.189 29.630 5.45 0.00 0.00 3.02
523 528 6.262273 GTGTCTTTCCTTGTTATTTCACTGGA 59.738 38.462 0.00 0.00 0.00 3.86
582 587 7.438459 CGTCTTATCACTCTTAACCTTTATGGG 59.562 40.741 0.00 0.00 41.11 4.00
636 641 6.240549 ACATCAGATCGATACTTTTCCCTT 57.759 37.500 0.00 0.00 31.20 3.95
644 649 4.692155 TCGATACTTTTCCCTTCGTTTTCC 59.308 41.667 0.00 0.00 0.00 3.13
687 692 6.382869 AACCTTGTGTGAAAGAAGAATCTG 57.617 37.500 0.00 0.00 35.59 2.90
688 693 4.276926 ACCTTGTGTGAAAGAAGAATCTGC 59.723 41.667 0.00 0.00 35.59 4.26
689 694 4.276678 CCTTGTGTGAAAGAAGAATCTGCA 59.723 41.667 0.00 0.00 35.59 4.41
690 695 5.221106 CCTTGTGTGAAAGAAGAATCTGCAA 60.221 40.000 0.00 0.00 35.59 4.08
691 696 5.833406 TGTGTGAAAGAAGAATCTGCAAA 57.167 34.783 0.00 0.00 35.59 3.68
692 697 6.206395 TGTGTGAAAGAAGAATCTGCAAAA 57.794 33.333 0.00 0.00 35.59 2.44
693 698 6.267817 TGTGTGAAAGAAGAATCTGCAAAAG 58.732 36.000 0.00 0.00 35.59 2.27
694 699 5.174579 GTGTGAAAGAAGAATCTGCAAAAGC 59.825 40.000 0.00 0.00 35.59 3.51
695 700 4.380974 GTGAAAGAAGAATCTGCAAAAGCG 59.619 41.667 0.00 0.00 35.59 4.68
696 701 3.565905 AAGAAGAATCTGCAAAAGCGG 57.434 42.857 0.00 0.00 35.59 5.52
697 702 1.200948 AGAAGAATCTGCAAAAGCGGC 59.799 47.619 0.00 0.00 33.59 6.53
698 703 0.244721 AAGAATCTGCAAAAGCGGCC 59.755 50.000 0.00 0.00 0.00 6.13
699 704 0.610232 AGAATCTGCAAAAGCGGCCT 60.610 50.000 0.00 0.00 0.00 5.19
700 705 0.457337 GAATCTGCAAAAGCGGCCTG 60.457 55.000 0.00 0.00 0.00 4.85
701 706 0.895100 AATCTGCAAAAGCGGCCTGA 60.895 50.000 0.00 0.00 0.00 3.86
702 707 0.895100 ATCTGCAAAAGCGGCCTGAA 60.895 50.000 0.00 0.00 0.00 3.02
703 708 0.895100 TCTGCAAAAGCGGCCTGAAT 60.895 50.000 0.00 0.00 0.00 2.57
704 709 0.810648 CTGCAAAAGCGGCCTGAATA 59.189 50.000 0.00 0.00 0.00 1.75
705 710 1.406539 CTGCAAAAGCGGCCTGAATAT 59.593 47.619 0.00 0.00 0.00 1.28
706 711 1.134753 TGCAAAAGCGGCCTGAATATG 59.865 47.619 0.00 0.00 0.00 1.78
707 712 1.134946 GCAAAAGCGGCCTGAATATGT 59.865 47.619 0.00 0.00 0.00 2.29
708 713 2.801063 CAAAAGCGGCCTGAATATGTG 58.199 47.619 0.00 0.00 0.00 3.21
709 714 2.418368 AAAGCGGCCTGAATATGTGA 57.582 45.000 0.00 0.00 0.00 3.58
710 715 2.645838 AAGCGGCCTGAATATGTGAT 57.354 45.000 0.00 0.00 0.00 3.06
711 716 1.888215 AGCGGCCTGAATATGTGATG 58.112 50.000 0.00 0.00 0.00 3.07
777 807 4.263462 TGCAAGGAAGGAATAAAGCTCAGA 60.263 41.667 0.00 0.00 0.00 3.27
938 968 3.572255 GCCACAACTCCCTTCATTGTAAA 59.428 43.478 0.00 0.00 34.84 2.01
1243 1274 3.831715 AAAGGTGCTTCAAACGATAGC 57.168 42.857 0.00 0.00 42.67 2.97
1461 1492 2.827921 GGCATCCATCAACAGGAAACTT 59.172 45.455 0.00 0.00 40.21 2.66
1545 1579 9.393249 TGCAAATCTATAAACGACTTGAAAAAG 57.607 29.630 0.00 0.00 0.00 2.27
1560 1594 3.127895 TGAAAAAGTGTGGGAAAGTGTCG 59.872 43.478 0.00 0.00 0.00 4.35
1635 1671 2.544267 CTCGAGAACACACAAAAGGGTC 59.456 50.000 6.58 0.00 0.00 4.46
1801 1839 7.480810 GGTAATAACCATTGTTGGATGTTCTC 58.519 38.462 0.00 0.00 46.92 2.87
1802 1840 5.818136 ATAACCATTGTTGGATGTTCTCG 57.182 39.130 0.00 0.00 46.92 4.04
2113 2152 6.094325 TGTTGTTCCGTATCTTTCAGTTTGTT 59.906 34.615 0.00 0.00 0.00 2.83
2120 2159 5.277154 CGTATCTTTCAGTTTGTTGTTCGGT 60.277 40.000 0.00 0.00 0.00 4.69
2327 2366 7.982354 GTGGTATCAAATAGCTCAAAGTAGTCT 59.018 37.037 0.00 0.00 34.47 3.24
2395 2434 8.856490 AGCACCGAATCAAAATTATAAACATC 57.144 30.769 0.00 0.00 0.00 3.06
2397 2436 7.431084 GCACCGAATCAAAATTATAAACATCGT 59.569 33.333 0.00 0.00 0.00 3.73
2428 2467 1.026182 CGCTATGCAGAAACTGGCCA 61.026 55.000 4.71 4.71 31.21 5.36
2462 2501 5.936956 ACTGATCTGTGATTCAACCTTCTTC 59.063 40.000 4.21 0.00 0.00 2.87
2463 2502 5.868454 TGATCTGTGATTCAACCTTCTTCA 58.132 37.500 0.00 0.00 0.00 3.02
2481 2520 7.445402 CCTTCTTCACCAAACAGAAGATCTTTA 59.555 37.037 9.87 0.00 46.72 1.85
2514 2553 3.366374 GCAAGGCAGTTGTATGAAAGGAC 60.366 47.826 0.54 0.00 38.55 3.85
2557 2596 6.835174 AGTGCAACATATAGACCAGATGATT 58.165 36.000 0.00 0.00 41.43 2.57
2715 2754 3.521126 AGTTCCATGCTTGATCAGGTACT 59.479 43.478 6.70 5.66 43.88 2.73
2784 2823 1.358152 CAGGAACAACAGTAGGGGGA 58.642 55.000 0.00 0.00 0.00 4.81
2875 2914 1.070445 CCAGAGGCAGATGACTGATCC 59.930 57.143 0.00 0.00 46.03 3.36
2966 3005 1.280746 CTGCTGTGGCTGTGTTTCG 59.719 57.895 0.00 0.00 39.59 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.624159 ACTCTGGTTCAGATTTCACATTCA 58.376 37.500 0.00 0.00 39.92 2.57
58 59 4.044426 GTCAATTGCAACAACTCTGGTTC 58.956 43.478 0.00 0.00 32.73 3.62
59 60 3.181476 GGTCAATTGCAACAACTCTGGTT 60.181 43.478 0.00 0.00 35.86 3.67
305 310 0.754472 TTCAGAACCTCCGAACCGTT 59.246 50.000 0.00 0.00 0.00 4.44
307 312 1.014564 GCTTCAGAACCTCCGAACCG 61.015 60.000 0.00 0.00 0.00 4.44
368 373 6.959639 TGTTTAGCTTCAGAACCTTCAAAT 57.040 33.333 0.00 0.00 0.00 2.32
474 479 7.166970 CACAGCAAACATGCATATTAATGAGAC 59.833 37.037 0.00 0.00 34.84 3.36
482 487 5.395682 AAGACACAGCAAACATGCATATT 57.604 34.783 0.00 0.00 37.25 1.28
523 528 5.329035 AGACATGCAAACAAGTTTTGACT 57.671 34.783 0.00 0.00 0.00 3.41
644 649 3.701532 TTGTAAAGCCAGTGGAAAACG 57.298 42.857 15.20 0.00 0.00 3.60
687 692 1.134946 ACATATTCAGGCCGCTTTTGC 59.865 47.619 0.00 0.00 43.23 3.68
688 693 2.423185 TCACATATTCAGGCCGCTTTTG 59.577 45.455 0.00 0.00 0.00 2.44
689 694 2.722094 TCACATATTCAGGCCGCTTTT 58.278 42.857 0.00 0.00 0.00 2.27
690 695 2.418368 TCACATATTCAGGCCGCTTT 57.582 45.000 0.00 0.00 0.00 3.51
691 696 2.224606 CATCACATATTCAGGCCGCTT 58.775 47.619 0.00 0.00 0.00 4.68
692 697 1.544093 CCATCACATATTCAGGCCGCT 60.544 52.381 0.00 0.00 0.00 5.52
693 698 0.877071 CCATCACATATTCAGGCCGC 59.123 55.000 0.00 0.00 0.00 6.53
694 699 1.527034 CCCATCACATATTCAGGCCG 58.473 55.000 0.00 0.00 0.00 6.13
695 700 1.145738 ACCCCATCACATATTCAGGCC 59.854 52.381 0.00 0.00 0.00 5.19
696 701 2.233271 CACCCCATCACATATTCAGGC 58.767 52.381 0.00 0.00 0.00 4.85
697 702 2.867624 CCACCCCATCACATATTCAGG 58.132 52.381 0.00 0.00 0.00 3.86
698 703 2.158564 AGCCACCCCATCACATATTCAG 60.159 50.000 0.00 0.00 0.00 3.02
699 704 1.852309 AGCCACCCCATCACATATTCA 59.148 47.619 0.00 0.00 0.00 2.57
700 705 2.664402 AGCCACCCCATCACATATTC 57.336 50.000 0.00 0.00 0.00 1.75
701 706 3.299503 GAAAGCCACCCCATCACATATT 58.700 45.455 0.00 0.00 0.00 1.28
702 707 2.749466 CGAAAGCCACCCCATCACATAT 60.749 50.000 0.00 0.00 0.00 1.78
703 708 1.408127 CGAAAGCCACCCCATCACATA 60.408 52.381 0.00 0.00 0.00 2.29
704 709 0.680921 CGAAAGCCACCCCATCACAT 60.681 55.000 0.00 0.00 0.00 3.21
705 710 1.303236 CGAAAGCCACCCCATCACA 60.303 57.895 0.00 0.00 0.00 3.58
706 711 0.035820 TACGAAAGCCACCCCATCAC 60.036 55.000 0.00 0.00 0.00 3.06
707 712 0.035820 GTACGAAAGCCACCCCATCA 60.036 55.000 0.00 0.00 0.00 3.07
708 713 0.252197 AGTACGAAAGCCACCCCATC 59.748 55.000 0.00 0.00 0.00 3.51
709 714 0.035439 CAGTACGAAAGCCACCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
710 715 1.373435 CAGTACGAAAGCCACCCCA 59.627 57.895 0.00 0.00 0.00 4.96
711 716 1.376812 CCAGTACGAAAGCCACCCC 60.377 63.158 0.00 0.00 0.00 4.95
777 807 3.071874 TCCTTCGATCCTTTGTTGCAT 57.928 42.857 0.00 0.00 0.00 3.96
938 968 0.332972 GGGGAGGAAAGATTGCCTGT 59.667 55.000 0.00 0.00 33.84 4.00
1196 1227 3.005155 ACTCTACAGTAACAACCGTCCAC 59.995 47.826 0.00 0.00 0.00 4.02
1243 1274 3.202097 TGAGAGCAGACGTCAGATAGAG 58.798 50.000 19.50 0.00 0.00 2.43
1461 1492 6.643388 TGAGAGAATTATAAGAGTTGCTGCA 58.357 36.000 0.00 0.00 0.00 4.41
1532 1563 2.993937 TCCCACACTTTTTCAAGTCGT 58.006 42.857 0.00 0.00 41.69 4.34
1545 1579 0.586802 GAAGCGACACTTTCCCACAC 59.413 55.000 0.00 0.00 39.29 3.82
1560 1594 6.500684 TGATTCTACTTCCACAAATGAAGC 57.499 37.500 0.00 0.00 42.35 3.86
1635 1671 2.129607 GGCTTAATGAAATGGCATGCG 58.870 47.619 12.44 0.00 0.00 4.73
1801 1839 0.869068 ACGATGAGAGCGATCCTACG 59.131 55.000 0.00 1.21 0.00 3.51
1802 1840 1.136197 CGACGATGAGAGCGATCCTAC 60.136 57.143 0.00 0.00 0.00 3.18
2006 2044 1.079681 CCAAAAGCATGGCACGCAT 60.080 52.632 8.75 0.00 32.78 4.73
2327 2366 4.025229 CAGACAAAATTCGTTCGGAGTTCA 60.025 41.667 0.00 0.00 0.00 3.18
2367 2406 9.482627 TGTTTATAATTTTGATTCGGTGCTTTT 57.517 25.926 0.00 0.00 0.00 2.27
2395 2434 4.843147 TGCATAGCGAAAATGGAAATACG 58.157 39.130 0.00 0.00 0.00 3.06
2397 2436 6.691754 TTCTGCATAGCGAAAATGGAAATA 57.308 33.333 0.00 0.00 0.00 1.40
2462 2501 7.862873 GGAAAAGTAAAGATCTTCTGTTTGGTG 59.137 37.037 8.78 0.00 0.00 4.17
2463 2502 7.780271 AGGAAAAGTAAAGATCTTCTGTTTGGT 59.220 33.333 8.78 0.00 0.00 3.67
2514 2553 5.980698 CACTAGATGATGTGCTGGTTTAG 57.019 43.478 0.00 0.00 0.00 1.85
2762 2801 0.322546 CCCTACTGTTGTTCCTGGCC 60.323 60.000 0.00 0.00 0.00 5.36
2784 2823 7.145323 CGTCTGATGGAAACTAACCAAAATTT 58.855 34.615 0.00 0.00 40.93 1.82
2875 2914 2.289882 TGTTGACCTTGAGGCATCAGAG 60.290 50.000 0.00 2.55 39.32 3.35
2926 2965 1.424302 AGGAATCATCATGGCAGGAGG 59.576 52.381 7.58 7.58 0.00 4.30


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

AutoCloner maintained by Alex Coulton.