Multiple sequence alignment - TraesCS4D01G220400

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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 TraesCS4D01G220400 chr4D 100.000 2640 0 0 1 2640 375507800 375510439 0.000000e+00 4876.0
1 TraesCS4D01G220400 chr4D 81.383 188 32 2 1076 1263 375445379 375445563 1.640000e-32 150.0
2 TraesCS4D01G220400 chr4D 86.420 81 10 1 416 496 473978004 473978083 1.300000e-13 87.9
3 TraesCS4D01G220400 chr4D 95.833 48 2 0 416 463 452388997 452389044 7.830000e-11 78.7
4 TraesCS4D01G220400 chr4B 93.721 2166 96 22 1 2142 462695803 462697952 0.000000e+00 3210.0
5 TraesCS4D01G220400 chr4B 93.399 303 14 4 2270 2570 462698039 462698337 6.710000e-121 444.0
6 TraesCS4D01G220400 chr4B 77.020 557 89 26 1046 1597 462592291 462592813 1.550000e-72 283.0
7 TraesCS4D01G220400 chr4A 92.716 1414 55 17 563 1961 88541829 88540449 0.000000e+00 1997.0
8 TraesCS4D01G220400 chr4A 93.353 662 31 5 1987 2640 88540453 88539797 0.000000e+00 966.0
9 TraesCS4D01G220400 chr4A 87.645 259 15 8 155 398 88542420 88542164 4.300000e-73 285.0
10 TraesCS4D01G220400 chr4A 76.619 556 98 22 1046 1597 88705013 88704486 7.200000e-71 278.0
11 TraesCS4D01G220400 chr6D 95.294 85 3 1 416 499 315956188 315956104 1.650000e-27 134.0
12 TraesCS4D01G220400 chr3A 89.320 103 7 2 398 496 653979036 653979138 2.760000e-25 126.0
13 TraesCS4D01G220400 chr7B 90.323 93 9 0 407 499 234907794 234907702 3.570000e-24 122.0
14 TraesCS4D01G220400 chr2B 88.043 92 8 2 391 480 794231012 794230922 3.590000e-19 106.0
15 TraesCS4D01G220400 chr2B 100.000 28 0 0 51 78 116390726 116390699 5.000000e-03 52.8
16 TraesCS4D01G220400 chr6B 91.892 74 6 0 416 489 4869055 4868982 1.290000e-18 104.0
17 TraesCS4D01G220400 chr5A 94.444 36 2 0 51 86 290394515 290394480 3.670000e-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 TraesCS4D01G220400 chr4D 375507800 375510439 2639 False 4876.000000 4876 100.000 1 2640 1 chr4D.!!$F2 2639
1 TraesCS4D01G220400 chr4B 462695803 462698337 2534 False 1827.000000 3210 93.560 1 2570 2 chr4B.!!$F2 2569
2 TraesCS4D01G220400 chr4B 462592291 462592813 522 False 283.000000 283 77.020 1046 1597 1 chr4B.!!$F1 551
3 TraesCS4D01G220400 chr4A 88539797 88542420 2623 True 1082.666667 1997 91.238 155 2640 3 chr4A.!!$R2 2485
4 TraesCS4D01G220400 chr4A 88704486 88705013 527 True 278.000000 278 76.619 1046 1597 1 chr4A.!!$R1 551

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
457 488 0.593008 CATCCGACAAATGCATGCGG 60.593 55.0 14.09 18.79 39.62 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2593 0.17668 GCCGACATGTCTCCATCAGT 59.823 55.0 22.95 0.0 0.0 3.41 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
91 95 7.439056 CCCATATTAATTGGCACTGATGTTTTC 59.561 37.037 9.79 0.00 32.60 2.29
102 106 7.119699 TGGCACTGATGTTTTCTACTAAATCAG 59.880 37.037 8.52 8.52 39.87 2.90
125 129 8.200120 TCAGCGATAATTATTATGGATCAGAGG 58.800 37.037 10.44 0.00 0.00 3.69
126 130 8.200120 CAGCGATAATTATTATGGATCAGAGGA 58.800 37.037 10.44 0.00 0.00 3.71
128 132 7.170658 GCGATAATTATTATGGATCAGAGGAGC 59.829 40.741 10.44 0.00 0.00 4.70
133 137 5.736951 ATTATGGATCAGAGGAGCACTAC 57.263 43.478 0.00 0.00 0.00 2.73
387 412 9.431887 TCAAACCAGTGTGAGTATTACTTTATC 57.568 33.333 0.00 0.00 0.00 1.75
447 478 2.268920 GGCCTCTGCATCCGACAA 59.731 61.111 0.00 0.00 40.13 3.18
457 488 0.593008 CATCCGACAAATGCATGCGG 60.593 55.000 14.09 18.79 39.62 5.69
472 503 6.035368 TGCATGCGGCCATATTATTAAAAT 57.965 33.333 14.09 0.00 43.89 1.82
476 507 5.226396 TGCGGCCATATTATTAAAATGTGC 58.774 37.500 2.24 0.00 0.00 4.57
499 530 5.276820 GCCAACAAAATACAAAGTCTGCAAC 60.277 40.000 0.00 0.00 0.00 4.17
509 540 5.181748 ACAAAGTCTGCAACCTAGATGATC 58.818 41.667 0.00 0.00 0.00 2.92
545 576 9.823647 ATGACTGTCAAAATCTAAATCGTAGAT 57.176 29.630 15.31 0.00 45.12 1.98
546 577 9.302345 TGACTGTCAAAATCTAAATCGTAGATC 57.698 33.333 8.27 0.00 45.12 2.75
547 578 9.302345 GACTGTCAAAATCTAAATCGTAGATCA 57.698 33.333 2.24 0.00 45.12 2.92
548 579 9.088512 ACTGTCAAAATCTAAATCGTAGATCAC 57.911 33.333 0.00 0.00 45.12 3.06
549 580 9.307121 CTGTCAAAATCTAAATCGTAGATCACT 57.693 33.333 0.00 0.00 45.12 3.41
551 582 9.522804 GTCAAAATCTAAATCGTAGATCACTCT 57.477 33.333 0.00 0.00 45.12 3.24
618 938 4.437239 AGATCACTCCAAGTAATCTTGCG 58.563 43.478 0.00 0.00 46.74 4.85
623 943 3.502211 ACTCCAAGTAATCTTGCGGTTTG 59.498 43.478 2.85 0.00 46.74 2.93
722 1043 7.148018 ACCATTAAATGAGCACACTCTAAATGG 60.148 37.037 16.64 16.64 43.95 3.16
810 1134 6.042777 GCAGATTGCAGTAACTGACAGTATA 58.957 40.000 8.91 1.25 44.26 1.47
811 1135 6.019479 GCAGATTGCAGTAACTGACAGTATAC 60.019 42.308 8.91 12.80 44.26 1.47
843 1167 1.335689 ACTGTCGAGTAGGAAACGCAC 60.336 52.381 0.00 0.00 0.00 5.34
845 1169 1.335597 TGTCGAGTAGGAAACGCACTG 60.336 52.381 0.00 0.00 31.71 3.66
862 1186 2.047560 GGAGTAAGCAACCGCCGT 60.048 61.111 0.00 0.00 39.83 5.68
959 1283 3.009916 ACCAGATCAAAGCCTTCTGTCAT 59.990 43.478 0.00 0.00 36.06 3.06
1089 1420 2.033602 GCTAACAACTGGGCGGGT 59.966 61.111 0.00 0.00 0.00 5.28
1275 1606 2.046411 TACGCACAGGGCACATGG 60.046 61.111 0.00 0.00 45.17 3.66
1306 1641 9.674068 GGTTAGAAACTTAGAATCTGAAATCCT 57.326 33.333 0.00 0.00 0.00 3.24
1310 1645 7.826744 AGAAACTTAGAATCTGAAATCCTGGTC 59.173 37.037 0.00 0.00 0.00 4.02
1313 1648 3.866651 AGAATCTGAAATCCTGGTCGTG 58.133 45.455 0.00 0.00 0.00 4.35
1314 1649 2.029838 ATCTGAAATCCTGGTCGTGC 57.970 50.000 0.00 0.00 0.00 5.34
1315 1650 0.389817 TCTGAAATCCTGGTCGTGCG 60.390 55.000 0.00 0.00 0.00 5.34
1339 1676 1.667724 CGTTCCTTGACTGATGGCATC 59.332 52.381 20.52 20.52 0.00 3.91
1417 1754 1.402787 TGATGATGACGCTGAGCCTA 58.597 50.000 0.00 0.00 0.00 3.93
1591 1928 4.148825 ATCAGCGTCCGCCCTGAC 62.149 66.667 8.23 0.00 40.55 3.51
1636 1973 3.020026 CTGCTGCAACCGCGAGAAG 62.020 63.158 8.23 1.65 42.97 2.85
1654 1992 2.046314 TGACGCCCCAAGCTTAGC 60.046 61.111 0.00 0.00 40.39 3.09
1674 2012 2.668457 GCGTTCTCATGTCTTTGTCGAT 59.332 45.455 0.00 0.00 0.00 3.59
1704 2042 5.163713 ACTGCTGTGAGTTCAGAACTTTTTC 60.164 40.000 17.19 5.38 43.03 2.29
1714 2052 6.198591 AGTTCAGAACTTTTTCGTCGTCTAAG 59.801 38.462 10.27 0.00 39.04 2.18
1757 2096 8.362639 ACTTTGTTTAGACTCGGAGTAATAACA 58.637 33.333 11.27 16.45 0.00 2.41
1761 2100 9.199982 TGTTTAGACTCGGAGTAATAACAAAAG 57.800 33.333 20.06 0.00 0.00 2.27
1774 2113 0.838987 ACAAAAGGGGGACGCCTAGA 60.839 55.000 8.45 0.00 44.92 2.43
1792 2131 8.139989 ACGCCTAGACGTCACTTATATTAATTT 58.860 33.333 19.50 0.00 44.43 1.82
1793 2132 8.975439 CGCCTAGACGTCACTTATATTAATTTT 58.025 33.333 19.50 0.00 0.00 1.82
1840 2179 1.812571 AGCCGTTTGGATTTACTGCTG 59.187 47.619 0.00 0.00 34.24 4.41
1881 2220 3.390639 AGCCACTATTCATCTTCCTCCTG 59.609 47.826 0.00 0.00 0.00 3.86
1912 2251 2.293318 ATTCTGCCGAGCCTGACCA 61.293 57.895 0.00 0.00 0.00 4.02
2001 2340 2.290367 CCTTCACGCACTCAAACAATCA 59.710 45.455 0.00 0.00 0.00 2.57
2021 2360 1.821332 GCTTCTGATTGGCCTCCGG 60.821 63.158 3.32 0.00 0.00 5.14
2124 2463 1.335689 GGCTACACGAACACGAGAACT 60.336 52.381 0.00 0.00 0.00 3.01
2128 2467 1.404391 ACACGAACACGAGAACTGACT 59.596 47.619 0.00 0.00 0.00 3.41
2133 2472 3.643763 GAACACGAGAACTGACTGATGT 58.356 45.455 0.00 0.00 0.00 3.06
2142 2481 7.226720 ACGAGAACTGACTGATGTAAACAAAAT 59.773 33.333 0.00 0.00 0.00 1.82
2189 2588 7.411274 TGTGTAAGTAACAAAATGGAACTTCG 58.589 34.615 3.77 0.00 40.63 3.79
2194 2593 8.441312 AAGTAACAAAATGGAACTTCGAGTTA 57.559 30.769 1.08 0.00 38.80 2.24
2247 2646 0.682209 AGCGCCATTGCTGGAATTCT 60.682 50.000 2.29 0.00 46.37 2.40
2290 2689 3.520569 CCTTTTTGTGGTGGTTGACAAG 58.479 45.455 0.00 0.00 33.73 3.16
2395 2801 3.502164 CCCAACAAGGCCTATGAGG 57.498 57.895 5.16 13.44 38.80 3.86
2595 3002 6.987992 GGATGCCACATGACAATGAAAATTAT 59.012 34.615 0.00 0.00 37.24 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 106 7.170658 GCTCCTCTGATCCATAATAATTATCGC 59.829 40.741 0.00 0.00 0.00 4.58
122 126 4.689612 TGGGATTAATGTAGTGCTCCTC 57.310 45.455 0.00 0.00 0.00 3.71
125 129 7.801716 TGTATTTGGGATTAATGTAGTGCTC 57.198 36.000 0.00 0.00 0.00 4.26
363 388 8.380099 TGGATAAAGTAATACTCACACTGGTTT 58.620 33.333 0.00 0.00 0.00 3.27
366 391 8.204160 TGATGGATAAAGTAATACTCACACTGG 58.796 37.037 0.00 0.00 0.00 4.00
428 459 4.899239 GTCGGATGCAGAGGCCGG 62.899 72.222 16.62 0.00 44.87 6.13
429 460 3.664025 TTGTCGGATGCAGAGGCCG 62.664 63.158 12.24 12.24 46.08 6.13
447 478 5.657826 TTAATAATATGGCCGCATGCATT 57.342 34.783 19.57 10.95 43.89 3.56
457 488 8.430801 TTGTTGGCACATTTTAATAATATGGC 57.569 30.769 8.01 7.83 39.30 4.40
472 503 5.347342 CAGACTTTGTATTTTGTTGGCACA 58.653 37.500 0.00 0.00 0.00 4.57
476 507 5.234116 GGTTGCAGACTTTGTATTTTGTTGG 59.766 40.000 0.00 0.00 0.00 3.77
538 569 4.882427 CCCTTGAGTAAGAGTGATCTACGA 59.118 45.833 0.00 0.00 35.92 3.43
545 576 3.391296 ACAAAGCCCTTGAGTAAGAGTGA 59.609 43.478 3.27 0.00 38.50 3.41
546 577 3.744660 ACAAAGCCCTTGAGTAAGAGTG 58.255 45.455 3.27 0.00 38.50 3.51
547 578 4.439253 AACAAAGCCCTTGAGTAAGAGT 57.561 40.909 3.27 0.00 38.50 3.24
548 579 4.938226 CCTAACAAAGCCCTTGAGTAAGAG 59.062 45.833 3.27 0.00 38.50 2.85
549 580 4.349930 ACCTAACAAAGCCCTTGAGTAAGA 59.650 41.667 3.27 0.00 38.50 2.10
551 582 4.103469 TGACCTAACAAAGCCCTTGAGTAA 59.897 41.667 3.27 0.00 38.50 2.24
552 583 3.649023 TGACCTAACAAAGCCCTTGAGTA 59.351 43.478 3.27 0.00 38.50 2.59
553 584 2.441750 TGACCTAACAAAGCCCTTGAGT 59.558 45.455 3.27 0.00 38.50 3.41
722 1043 3.216800 TCCAAATCAGGTGATATGCTGC 58.783 45.455 0.00 0.00 33.73 5.25
810 1134 1.669115 GACAGTGTGATGCAGGCGT 60.669 57.895 0.00 0.00 0.00 5.68
811 1135 2.733671 CGACAGTGTGATGCAGGCG 61.734 63.158 0.00 0.00 0.00 5.52
843 1167 2.100631 CGGCGGTTGCTTACTCCAG 61.101 63.158 0.00 0.00 42.25 3.86
845 1169 2.047560 ACGGCGGTTGCTTACTCC 60.048 61.111 13.24 0.00 42.25 3.85
862 1186 1.007734 GCGAAGTCACGGTCAGACA 60.008 57.895 2.17 0.00 38.46 3.41
898 1222 2.104111 CTGTGTTTATAGGATGGGCGGA 59.896 50.000 0.00 0.00 0.00 5.54
905 1229 3.199071 TGGAACGGCTGTGTTTATAGGAT 59.801 43.478 0.00 0.00 30.75 3.24
959 1283 0.659417 GTCGAGTGACAACGAGCGAA 60.659 55.000 5.29 0.00 44.82 4.70
1074 1405 0.320596 CGTTACCCGCCCAGTTGTTA 60.321 55.000 0.00 0.00 0.00 2.41
1089 1420 2.027897 AGCGTGTTGGCGTCGTTA 59.972 55.556 0.00 0.00 38.18 3.18
1275 1606 7.612677 TCAGATTCTAAGTTTCTAACCAGGAC 58.387 38.462 0.00 0.00 0.00 3.85
1313 1648 2.027625 CAGTCAAGGAACGTCCCGC 61.028 63.158 0.00 0.00 37.19 6.13
1314 1649 0.246635 ATCAGTCAAGGAACGTCCCG 59.753 55.000 0.00 0.00 37.19 5.14
1315 1650 1.676014 CCATCAGTCAAGGAACGTCCC 60.676 57.143 0.00 0.00 37.19 4.46
1339 1676 2.108514 CCAGTACCTGCACGCATGG 61.109 63.158 0.00 0.00 0.00 3.66
1591 1928 2.838225 AGGATACGCTCCCGGTGG 60.838 66.667 0.00 0.00 46.27 4.61
1599 1936 2.100989 AGAAGAAACGGAGGATACGCT 58.899 47.619 0.00 0.00 46.39 5.07
1654 1992 4.910746 AATCGACAAAGACATGAGAACG 57.089 40.909 0.00 0.00 0.00 3.95
1674 2012 7.217200 AGTTCTGAACTCACAGCAGTTTATAA 58.783 34.615 17.00 0.00 37.02 0.98
1704 2042 4.785417 ACTTCTGAACTTCTTAGACGACG 58.215 43.478 0.00 0.00 0.00 5.12
1757 2096 1.896122 CGTCTAGGCGTCCCCCTTTT 61.896 60.000 9.00 0.00 36.41 2.27
1808 2147 3.131223 TCCAAACGGCTTTGACAAAATCA 59.869 39.130 1.62 0.00 39.43 2.57
1838 2177 1.215647 CGGAAGGAGGACGAACCAG 59.784 63.158 0.00 0.00 42.04 4.00
1840 2179 2.125633 GCGGAAGGAGGACGAACC 60.126 66.667 0.00 0.00 39.35 3.62
1881 2220 1.483424 GCAGAATGTCGACTAGCGGC 61.483 60.000 17.92 13.22 46.88 6.53
2001 2340 0.393537 CGGAGGCCAATCAGAAGCTT 60.394 55.000 5.01 0.00 0.00 3.74
2113 2452 3.735237 ACATCAGTCAGTTCTCGTGTT 57.265 42.857 0.00 0.00 0.00 3.32
2124 2463 9.681692 CAATTGAGATTTTGTTTACATCAGTCA 57.318 29.630 0.00 0.00 0.00 3.41
2128 2467 8.927721 CATGCAATTGAGATTTTGTTTACATCA 58.072 29.630 10.34 0.00 0.00 3.07
2133 2472 7.894708 TCCTCATGCAATTGAGATTTTGTTTA 58.105 30.769 17.15 0.00 44.88 2.01
2142 2481 7.123098 ACACATTTATTCCTCATGCAATTGAGA 59.877 33.333 17.15 2.60 44.88 3.27
2182 2581 5.096849 GTCTCCATCAGTAACTCGAAGTTC 58.903 45.833 3.94 0.00 39.51 3.01
2189 2588 4.355437 CGACATGTCTCCATCAGTAACTC 58.645 47.826 22.95 0.00 0.00 3.01
2194 2593 0.176680 GCCGACATGTCTCCATCAGT 59.823 55.000 22.95 0.00 0.00 3.41
2242 2641 0.676782 CCGCGTGGGGAAGAAGAATT 60.677 55.000 7.26 0.00 0.00 2.17
2300 2699 4.157840 GGTTAGTTGTCAACCATCATTCCC 59.842 45.833 12.17 0.00 44.12 3.97
2301 2700 4.142687 CGGTTAGTTGTCAACCATCATTCC 60.143 45.833 12.17 5.20 44.80 3.01
2461 2868 5.180680 GCCAAACTAGGTGTAGGTAAAAGTG 59.819 44.000 0.00 0.00 0.00 3.16
2609 3016 7.646130 TGTGAACACGGAATTCAAATTCTTAAC 59.354 33.333 7.93 5.87 43.33 2.01


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

AutoCloner maintained by Alex Coulton.