Multiple sequence alignment - TraesCS7D01G306100

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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 TraesCS7D01G306100 chr7D 100.000 4127 0 0 1 4127 387229894 387225768 0.000000e+00 7622
1 TraesCS7D01G306100 chr7B 98.019 3129 51 6 1009 4127 382287575 382284448 0.000000e+00 5424
2 TraesCS7D01G306100 chr7B 88.588 701 62 8 6 703 382327199 382326514 0.000000e+00 835
3 TraesCS7D01G306100 chr7A 97.906 2436 50 1 1046 3480 437079138 437076703 0.000000e+00 4215
4 TraesCS7D01G306100 chr7A 98.313 652 9 2 3477 4127 437074141 437073491 0.000000e+00 1142
5 TraesCS7D01G306100 chr7A 93.457 703 42 4 4 703 437401972 437401271 0.000000e+00 1040
6 TraesCS7D01G306100 chr7A 88.816 304 21 4 716 1008 437079439 437079138 1.090000e-95 361


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 TraesCS7D01G306100 chr7D 387225768 387229894 4126 True 7622 7622 100.000000 1 4127 1 chr7D.!!$R1 4126
1 TraesCS7D01G306100 chr7B 382284448 382287575 3127 True 5424 5424 98.019000 1009 4127 1 chr7B.!!$R1 3118
2 TraesCS7D01G306100 chr7B 382326514 382327199 685 True 835 835 88.588000 6 703 1 chr7B.!!$R2 697
3 TraesCS7D01G306100 chr7A 437073491 437079439 5948 True 1906 4215 95.011667 716 4127 3 chr7A.!!$R2 3411
4 TraesCS7D01G306100 chr7A 437401271 437401972 701 True 1040 1040 93.457000 4 703 1 chr7A.!!$R1 699

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
438 442 0.108992 GCCGTCTTATCGTGGTCACA 60.109 55.0 1.90 0.00 0.00 3.58 F
719 724 0.384309 CGTGACGCAGGCTATAAGGA 59.616 55.0 0.00 0.00 0.00 3.36 F
853 858 0.828022 TAGCGGGTCCTACATGTTGG 59.172 55.0 19.01 19.01 0.00 3.77 F
1007 1023 0.851495 CTCTTCGATCAGATGTGCGC 59.149 55.0 0.00 0.00 0.00 6.09 F
1881 1897 1.135046 CGACACTCTCAGTTGTGCTG 58.865 55.0 0.00 0.00 46.34 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1897 0.964358 AAGCCTCAGCACAAGCATCC 60.964 55.000 0.00 0.00 45.49 3.51 R
2293 2309 1.164041 AACCACCGCACTGCACTTAC 61.164 55.000 1.11 0.00 0.00 2.34 R
2421 2437 3.006110 CCCATCCCATGTTGATTGCATAC 59.994 47.826 0.00 0.00 0.00 2.39 R
2978 2994 3.306989 CCCCGCAGATGAGAGCATATTTA 60.307 47.826 0.00 0.00 34.11 1.40 R
3145 3161 0.620556 TTTGGGTTTTGGCTTGCCAA 59.379 45.000 21.59 21.59 0.00 4.52 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
27 28 1.586028 CAACAAGCCACCCAATCCG 59.414 57.895 0.00 0.00 0.00 4.18
70 71 2.035155 TCGCCCTGACTCGAAGGA 59.965 61.111 3.07 0.00 36.91 3.36
82 83 1.153706 CGAAGGACGCCATACCGTT 60.154 57.895 0.00 0.00 42.24 4.44
96 97 1.071471 CCGTTGGAAGGCAGAGTGT 59.929 57.895 0.00 0.00 0.00 3.55
238 241 4.515028 ATGACCACCACAAGATCATCAT 57.485 40.909 0.00 0.00 0.00 2.45
332 335 2.452006 AACAGAAAAACGAGCACACG 57.548 45.000 0.00 0.00 39.31 4.49
423 427 1.230635 GCAACACACATCTCTGCCGT 61.231 55.000 0.00 0.00 0.00 5.68
427 431 1.893137 ACACACATCTCTGCCGTCTTA 59.107 47.619 0.00 0.00 0.00 2.10
436 440 0.172578 CTGCCGTCTTATCGTGGTCA 59.827 55.000 0.00 0.00 0.00 4.02
438 442 0.108992 GCCGTCTTATCGTGGTCACA 60.109 55.000 1.90 0.00 0.00 3.58
503 507 2.359900 CATTGTAGTTGGGAGCTGGAC 58.640 52.381 0.00 0.00 0.00 4.02
523 527 1.758783 GAGCAAAGAAAAGCACGTGG 58.241 50.000 18.88 0.00 0.00 4.94
548 552 2.095053 GCAAGAAAGAGTTGAGATCGGC 59.905 50.000 0.00 0.00 0.00 5.54
582 586 8.206126 AGAATCCCCAAATCAAAACACTAATT 57.794 30.769 0.00 0.00 0.00 1.40
586 590 8.117813 TCCCCAAATCAAAACACTAATTCTAC 57.882 34.615 0.00 0.00 0.00 2.59
682 686 7.602644 GTCTCACAGTCATTACAAGAAACCATA 59.397 37.037 0.00 0.00 0.00 2.74
687 691 5.351465 AGTCATTACAAGAAACCATAGTGCG 59.649 40.000 0.00 0.00 0.00 5.34
718 723 2.886859 CGTGACGCAGGCTATAAGG 58.113 57.895 0.00 0.00 0.00 2.69
719 724 0.384309 CGTGACGCAGGCTATAAGGA 59.616 55.000 0.00 0.00 0.00 3.36
720 725 1.202371 CGTGACGCAGGCTATAAGGAA 60.202 52.381 0.00 0.00 0.00 3.36
721 726 2.202566 GTGACGCAGGCTATAAGGAAC 58.797 52.381 0.00 0.00 0.00 3.62
729 734 4.517285 CAGGCTATAAGGAACACACACAT 58.483 43.478 0.00 0.00 0.00 3.21
752 757 1.469308 AGAACCGAGTAAGTGAGCGAG 59.531 52.381 0.00 0.00 0.00 5.03
766 771 2.802106 CGAGAGAGGGGAACGAGC 59.198 66.667 0.00 0.00 0.00 5.03
792 797 3.853330 CCGCGTGCACCGATTCAG 61.853 66.667 23.58 5.43 39.56 3.02
804 809 3.739300 CACCGATTCAGTTTTACACGACT 59.261 43.478 0.00 0.00 0.00 4.18
851 856 3.926058 AAATAGCGGGTCCTACATGTT 57.074 42.857 2.30 0.00 0.00 2.71
853 858 0.828022 TAGCGGGTCCTACATGTTGG 59.172 55.000 19.01 19.01 0.00 3.77
868 873 3.715871 TTGGAAACATCCTCACGCA 57.284 47.368 0.00 0.00 42.32 5.24
898 903 5.560966 ACCGATTAGTGGTTTATGCAAAG 57.439 39.130 0.00 0.00 35.82 2.77
956 972 9.444534 AAGAAAATGTGTTTTGTGTTTGAAAAC 57.555 25.926 0.00 0.00 41.63 2.43
982 998 7.425606 GTGTGAAAAATGTGGACAGTAGATTT 58.574 34.615 0.00 0.00 0.00 2.17
996 1012 7.760340 GGACAGTAGATTTGTTAACTCTTCGAT 59.240 37.037 7.22 0.00 0.00 3.59
1007 1023 0.851495 CTCTTCGATCAGATGTGCGC 59.149 55.000 0.00 0.00 0.00 6.09
1018 1034 1.202698 AGATGTGCGCTTATCCCTTCC 60.203 52.381 9.73 0.00 0.00 3.46
1023 1039 1.227973 CGCTTATCCCTTCCCCTGC 60.228 63.158 0.00 0.00 0.00 4.85
1141 1157 4.742201 CTCTCACCGTGGTGCCCG 62.742 72.222 14.25 5.47 45.04 6.13
1156 1172 2.341101 CCCGGTCAGTACGCACTCT 61.341 63.158 0.00 0.00 30.46 3.24
1401 1417 3.997064 CTGGAACGCCCTGCTCTCG 62.997 68.421 0.00 0.00 35.38 4.04
1881 1897 1.135046 CGACACTCTCAGTTGTGCTG 58.865 55.000 0.00 0.00 46.34 4.41
2030 2046 2.173569 GGATGGTTGATGCTAGAAGGGT 59.826 50.000 0.00 0.00 0.00 4.34
2031 2047 2.787473 TGGTTGATGCTAGAAGGGTG 57.213 50.000 0.00 0.00 0.00 4.61
2073 2089 7.125659 TGGAAAGACATAGTATCATGGAACTCA 59.874 37.037 4.40 0.00 0.00 3.41
2204 2220 1.509548 AACAGGGGTTGGATGAGGGG 61.510 60.000 0.00 0.00 35.46 4.79
2293 2309 6.344500 AGTCTTGCTACAAATGGAGACTATG 58.656 40.000 0.00 0.00 41.29 2.23
2394 2410 1.608590 GCTTTGGCTAGCTTGACAACA 59.391 47.619 16.39 7.12 34.27 3.33
2550 2566 4.513318 GCCATTAGCAGTCCAAGTCTTATC 59.487 45.833 0.00 0.00 42.97 1.75
2620 2636 4.737054 AGATGCATTCAAGCTTTTTACCG 58.263 39.130 0.00 0.00 34.99 4.02
2761 2777 1.337118 TGGCATTGAACCAAACCCTC 58.663 50.000 0.00 0.00 33.12 4.30
2978 2994 1.831736 AGCAGCTTATACCGTCCTGTT 59.168 47.619 0.00 0.00 0.00 3.16
3172 3188 6.376864 GGCAAGCCAAAACCCAAAATAATAAT 59.623 34.615 6.14 0.00 35.81 1.28
3244 3261 8.168790 TGATCATGTTGAGACAAGAAAATTGA 57.831 30.769 0.00 0.00 37.09 2.57
3302 3319 4.321899 GCAGTCCCTGTTTTAATGCAATGA 60.322 41.667 0.00 0.00 33.43 2.57
3540 6130 1.969200 GACTTACGGGGAGAAGGGGC 61.969 65.000 0.00 0.00 0.00 5.80
3806 6397 5.694006 CCGTTTGTGCCTGATTCAATAAAAA 59.306 36.000 0.00 0.00 0.00 1.94
4099 6690 4.472691 TTCGCTTCAACTTCATCACTTG 57.527 40.909 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.724061 AGAGGATTATAGTCTTCTTCAGAGGTC 59.276 40.741 4.29 0.00 31.27 3.85
70 71 1.078708 CCTTCCAACGGTATGGCGT 60.079 57.895 0.00 0.00 40.46 5.68
82 83 0.108585 GGTGAACACTCTGCCTTCCA 59.891 55.000 4.96 0.00 0.00 3.53
96 97 2.972713 GGATGGCTCCATACTAGGTGAA 59.027 50.000 3.85 0.00 41.64 3.18
179 181 2.671963 GAGGGTGTTTGGTCGGGC 60.672 66.667 0.00 0.00 0.00 6.13
184 186 1.499007 AGTGAATGGAGGGTGTTTGGT 59.501 47.619 0.00 0.00 0.00 3.67
238 241 5.252547 TGTAAGTTTTGCTGAGCATGGATA 58.747 37.500 8.44 0.00 38.76 2.59
354 357 0.388134 CCTTGCATGTGTTGAGCTGC 60.388 55.000 0.00 0.00 35.21 5.25
436 440 5.886474 TGACCTAGATTTGAGTATCTCGTGT 59.114 40.000 0.00 0.00 36.34 4.49
438 442 7.429633 CATTGACCTAGATTTGAGTATCTCGT 58.570 38.462 0.00 0.00 36.34 4.18
503 507 1.388888 CACGTGCTTTTCTTTGCTCG 58.611 50.000 0.82 7.67 46.87 5.03
520 524 4.096382 TCTCAACTCTTTCTTGCAAACCAC 59.904 41.667 0.00 0.00 0.00 4.16
523 527 5.142962 CGATCTCAACTCTTTCTTGCAAAC 58.857 41.667 0.00 0.00 0.00 2.93
548 552 5.443283 TGATTTGGGGATTCTTCATCTGAG 58.557 41.667 0.00 0.00 31.67 3.35
558 562 8.314021 AGAATTAGTGTTTTGATTTGGGGATTC 58.686 33.333 0.00 0.00 0.00 2.52
582 586 8.684386 TTTATGAGTGGATTTTTGTGTGTAGA 57.316 30.769 0.00 0.00 0.00 2.59
586 590 8.011106 GCATTTTTATGAGTGGATTTTTGTGTG 58.989 33.333 0.00 0.00 0.00 3.82
653 657 7.656137 GGTTTCTTGTAATGACTGTGAGACTAA 59.344 37.037 0.00 0.00 0.00 2.24
703 708 2.202566 GTGTTCCTTATAGCCTGCGTC 58.797 52.381 0.00 0.00 0.00 5.19
704 709 1.553248 TGTGTTCCTTATAGCCTGCGT 59.447 47.619 0.00 0.00 0.00 5.24
705 710 1.933853 GTGTGTTCCTTATAGCCTGCG 59.066 52.381 0.00 0.00 0.00 5.18
706 711 2.678336 GTGTGTGTTCCTTATAGCCTGC 59.322 50.000 0.00 0.00 0.00 4.85
707 712 3.937814 TGTGTGTGTTCCTTATAGCCTG 58.062 45.455 0.00 0.00 0.00 4.85
708 713 4.517285 CATGTGTGTGTTCCTTATAGCCT 58.483 43.478 0.00 0.00 0.00 4.58
709 714 3.627577 CCATGTGTGTGTTCCTTATAGCC 59.372 47.826 0.00 0.00 0.00 3.93
710 715 4.513442 TCCATGTGTGTGTTCCTTATAGC 58.487 43.478 0.00 0.00 0.00 2.97
711 716 5.977635 TCTCCATGTGTGTGTTCCTTATAG 58.022 41.667 0.00 0.00 0.00 1.31
712 717 6.170506 GTTCTCCATGTGTGTGTTCCTTATA 58.829 40.000 0.00 0.00 0.00 0.98
713 718 4.908601 TCTCCATGTGTGTGTTCCTTAT 57.091 40.909 0.00 0.00 0.00 1.73
714 719 4.385825 GTTCTCCATGTGTGTGTTCCTTA 58.614 43.478 0.00 0.00 0.00 2.69
715 720 3.214328 GTTCTCCATGTGTGTGTTCCTT 58.786 45.455 0.00 0.00 0.00 3.36
716 721 2.487265 GGTTCTCCATGTGTGTGTTCCT 60.487 50.000 0.00 0.00 0.00 3.36
717 722 1.880027 GGTTCTCCATGTGTGTGTTCC 59.120 52.381 0.00 0.00 0.00 3.62
718 723 1.531149 CGGTTCTCCATGTGTGTGTTC 59.469 52.381 0.00 0.00 0.00 3.18
719 724 1.140052 TCGGTTCTCCATGTGTGTGTT 59.860 47.619 0.00 0.00 0.00 3.32
720 725 0.756294 TCGGTTCTCCATGTGTGTGT 59.244 50.000 0.00 0.00 0.00 3.72
721 726 1.270305 ACTCGGTTCTCCATGTGTGTG 60.270 52.381 0.00 0.00 0.00 3.82
729 734 1.544691 GCTCACTTACTCGGTTCTCCA 59.455 52.381 0.00 0.00 0.00 3.86
752 757 2.490685 GTCGCTCGTTCCCCTCTC 59.509 66.667 0.00 0.00 0.00 3.20
776 781 2.170260 AAACTGAATCGGTGCACGCG 62.170 55.000 18.07 18.07 43.86 6.01
778 783 2.222213 TGTAAAACTGAATCGGTGCACG 59.778 45.455 11.45 6.55 46.11 5.34
782 787 3.739300 AGTCGTGTAAAACTGAATCGGTG 59.261 43.478 0.00 0.00 0.00 4.94
804 809 0.812014 TGAAGACGCCTTTTGACGCA 60.812 50.000 0.00 0.00 31.62 5.24
833 838 1.416401 CCAACATGTAGGACCCGCTAT 59.584 52.381 0.00 0.00 0.00 2.97
851 856 0.396435 AGTGCGTGAGGATGTTTCCA 59.604 50.000 0.00 0.00 45.30 3.53
853 858 4.946784 AATTAGTGCGTGAGGATGTTTC 57.053 40.909 0.00 0.00 0.00 2.78
857 862 3.245284 CGGTAAATTAGTGCGTGAGGATG 59.755 47.826 0.00 0.00 0.00 3.51
859 864 2.492881 TCGGTAAATTAGTGCGTGAGGA 59.507 45.455 0.00 0.00 0.00 3.71
898 903 4.683320 GGTAAAAGAACACCACGTCTACTC 59.317 45.833 0.00 0.00 34.77 2.59
932 937 7.584485 ACGTTTTCAAACACAAAACACATTTTC 59.416 29.630 8.35 0.00 41.79 2.29
936 941 5.463724 ACACGTTTTCAAACACAAAACACAT 59.536 32.000 8.35 0.00 41.79 3.21
955 971 3.013921 ACTGTCCACATTTTTCACACGT 58.986 40.909 0.00 0.00 0.00 4.49
956 972 3.691049 ACTGTCCACATTTTTCACACG 57.309 42.857 0.00 0.00 0.00 4.49
982 998 4.864806 GCACATCTGATCGAAGAGTTAACA 59.135 41.667 8.61 0.00 43.63 2.41
996 1012 1.123077 AGGGATAAGCGCACATCTGA 58.877 50.000 11.47 0.00 0.00 3.27
1007 1023 1.345715 ACGGCAGGGGAAGGGATAAG 61.346 60.000 0.00 0.00 0.00 1.73
1033 1049 2.751436 CCAGTGGGGGCATGAACG 60.751 66.667 0.00 0.00 0.00 3.95
1052 1068 6.513806 TCATTGAATGAAACCACTGTATGG 57.486 37.500 5.21 0.00 45.10 2.74
1141 1157 1.136984 CCGAGAGTGCGTACTGACC 59.863 63.158 12.07 0.00 37.25 4.02
1881 1897 0.964358 AAGCCTCAGCACAAGCATCC 60.964 55.000 0.00 0.00 45.49 3.51
2030 2046 2.030371 TCCACTTCATGCAAGCAAACA 58.970 42.857 0.00 0.00 35.17 2.83
2031 2047 2.798976 TCCACTTCATGCAAGCAAAC 57.201 45.000 0.00 0.00 35.17 2.93
2073 2089 3.881688 GCTGAACATAGCCTGTGATCAAT 59.118 43.478 0.00 0.00 38.39 2.57
2220 2236 1.541147 TCTTTTCCTGGCATTTGCTCG 59.459 47.619 2.12 0.00 41.70 5.03
2293 2309 1.164041 AACCACCGCACTGCACTTAC 61.164 55.000 1.11 0.00 0.00 2.34
2394 2410 3.371965 AGCTTGCATTCCCTGATTCAAT 58.628 40.909 0.00 0.00 0.00 2.57
2421 2437 3.006110 CCCATCCCATGTTGATTGCATAC 59.994 47.826 0.00 0.00 0.00 2.39
2550 2566 8.694975 ATGCTGTAATCATAGAATTAGTAGCG 57.305 34.615 0.00 0.00 36.37 4.26
2620 2636 3.336468 TGTGGCCATCAATTTGCATTTC 58.664 40.909 9.72 0.00 0.00 2.17
2978 2994 3.306989 CCCCGCAGATGAGAGCATATTTA 60.307 47.826 0.00 0.00 34.11 1.40
3145 3161 0.620556 TTTGGGTTTTGGCTTGCCAA 59.379 45.000 21.59 21.59 0.00 4.52
3172 3188 5.504337 GCATTACAACAGTTGTGGTACGAAA 60.504 40.000 26.42 12.61 45.03 3.46
3244 3261 5.695816 GCGAGCTCTTTCTGAAATCATCTAT 59.304 40.000 12.85 0.00 0.00 1.98
3302 3319 6.265196 TGTGTGCATAGAATCCTCAACTTTTT 59.735 34.615 0.00 0.00 0.00 1.94
3540 6130 2.867287 TGTTCCATGTGTGCTTGTTG 57.133 45.000 0.00 0.00 0.00 3.33
3668 6258 6.037610 GCAAATCTTACTCCAACATCTACCAG 59.962 42.308 0.00 0.00 0.00 4.00
3721 6312 4.679373 AGGTGTTCTACATCTGCCTATG 57.321 45.455 0.00 0.00 38.32 2.23
4099 6690 6.580416 GTCAAGCTTGCTTATGAAAGAAACTC 59.420 38.462 21.99 0.00 34.37 3.01


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

AutoCloner maintained by Alex Coulton.