Multiple sequence alignment - TraesCS3D01G260000

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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 TraesCS3D01G260000 chr3D 100.000 3104 0 0 1 3104 362058873 362055770 0 5733
1 TraesCS3D01G260000 chr6A 92.382 3124 207 14 1 3104 508718353 508721465 0 4421
2 TraesCS3D01G260000 chr3A 92.763 2570 162 10 1 2555 52406683 52409243 0 3694
3 TraesCS3D01G260000 chr3A 90.175 570 30 14 2557 3104 52414290 52414855 0 719
4 TraesCS3D01G260000 chr6B 80.284 3165 537 58 4 3104 611338299 611335158 0 2307


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 TraesCS3D01G260000 chr3D 362055770 362058873 3103 True 5733 5733 100.000 1 3104 1 chr3D.!!$R1 3103
1 TraesCS3D01G260000 chr6A 508718353 508721465 3112 False 4421 4421 92.382 1 3104 1 chr6A.!!$F1 3103
2 TraesCS3D01G260000 chr3A 52406683 52409243 2560 False 3694 3694 92.763 1 2555 1 chr3A.!!$F1 2554
3 TraesCS3D01G260000 chr3A 52414290 52414855 565 False 719 719 90.175 2557 3104 1 chr3A.!!$F2 547
4 TraesCS3D01G260000 chr6B 611335158 611338299 3141 True 2307 2307 80.284 4 3104 1 chr6B.!!$R1 3100

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
667 675 0.260816 TATACACCGAGTCCTGGCCT 59.739 55.0 3.32 0.00 0.0 5.19 F
1448 1469 1.942776 TTGGTCAGGCTCAGAGATGA 58.057 50.0 0.00 1.43 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1836 1.531423 CACCACAGCAATCTTCAGCT 58.469 50.0 0.0 0.0 42.94 4.24 R
2935 3008 2.755103 CCTACAGTTCCAAATCAAGCCC 59.245 50.0 0.0 0.0 0.00 5.19 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
83 84 5.046014 AGGTTGACTCTGCAACTGAAGATAT 60.046 40.000 0.00 0.00 45.64 1.63
91 92 7.710044 ACTCTGCAACTGAAGATATAGAACATG 59.290 37.037 0.00 0.00 0.00 3.21
249 253 5.437289 TTGAAGATGTAAACAGGCAAGTG 57.563 39.130 0.00 0.00 0.00 3.16
260 264 1.610522 CAGGCAAGTGAACTTCCCTTG 59.389 52.381 2.75 9.07 41.22 3.61
266 270 4.278419 GCAAGTGAACTTCCCTTGTTGTAT 59.722 41.667 13.52 0.00 38.24 2.29
307 311 3.753815 TCTGCAAGATGTGGTTTGATCA 58.246 40.909 0.00 0.00 38.67 2.92
332 336 8.663025 CAAGGATGATCGATGGTATCAAATTAG 58.337 37.037 0.54 0.00 36.95 1.73
357 361 5.045578 CAGAGGAAGGAAAGTGGATTTAGGA 60.046 44.000 0.00 0.00 0.00 2.94
454 458 1.112113 TGCCCCTCTCTCAATACGAC 58.888 55.000 0.00 0.00 0.00 4.34
459 463 2.423660 CCCTCTCTCAATACGACCTCCT 60.424 54.545 0.00 0.00 0.00 3.69
463 467 2.363680 CTCTCAATACGACCTCCTGCAT 59.636 50.000 0.00 0.00 0.00 3.96
585 592 6.493458 GCCAAATTAAAGGAGATTATGGGCTA 59.507 38.462 0.00 0.00 32.67 3.93
606 614 0.408309 AGGGGGAAAAAGTAGGCCAC 59.592 55.000 5.01 0.54 0.00 5.01
613 621 4.585581 GGGAAAAAGTAGGCCACAAAAGTA 59.414 41.667 5.01 0.00 0.00 2.24
631 639 8.215736 ACAAAAGTAGAGAAAACTTTAGGCCTA 58.784 33.333 8.91 8.91 44.35 3.93
634 642 7.312415 AGTAGAGAAAACTTTAGGCCTACAA 57.688 36.000 13.46 9.38 0.00 2.41
667 675 0.260816 TATACACCGAGTCCTGGCCT 59.739 55.000 3.32 0.00 0.00 5.19
883 891 7.417116 GGGATGCACAATTTGATAGACAAGATT 60.417 37.037 2.79 0.00 39.77 2.40
953 961 6.366061 GGTAATCAATTTCAGAACCACTTTGC 59.634 38.462 0.00 0.00 0.00 3.68
1020 1028 6.025707 GACATGCGTCAGTTTCAGTATAAG 57.974 41.667 0.00 0.00 42.13 1.73
1028 1036 7.360101 GCGTCAGTTTCAGTATAAGTCAACATT 60.360 37.037 0.00 0.00 0.00 2.71
1136 1144 8.212995 TGATATTCAGACATCCAAAGCAATCTA 58.787 33.333 0.00 0.00 0.00 1.98
1166 1174 5.339200 GGGGAGTTCTGAATGGTAATCAAGA 60.339 44.000 0.00 0.00 0.00 3.02
1248 1256 5.983333 AATGTGGAGAGAAGGGTCATAAT 57.017 39.130 0.00 0.00 0.00 1.28
1413 1434 8.914011 GCAAAAGAGTTACCTGGGAATAATAAT 58.086 33.333 0.00 0.00 0.00 1.28
1448 1469 1.942776 TTGGTCAGGCTCAGAGATGA 58.057 50.000 0.00 1.43 0.00 2.92
1473 1494 7.600065 ACTGTGATTTGGAAATTGATTCAGAG 58.400 34.615 0.00 0.00 39.98 3.35
1555 1576 2.485814 GTGTCTGATGGAGTTTTCCTGC 59.514 50.000 0.00 0.00 44.36 4.85
1633 1654 5.945784 CCTCTGAAAGGTGGAAACATAATGA 59.054 40.000 0.00 0.00 46.14 2.57
1698 1719 4.013267 ACTAGCATTGATATGGGTCAGC 57.987 45.455 0.00 0.00 32.15 4.26
1775 1797 7.015779 TGGATCAATGATTGGATATGTGCAAAT 59.984 33.333 5.20 0.00 39.21 2.32
1783 1805 4.731720 TGGATATGTGCAAATTGTTGACG 58.268 39.130 0.00 0.00 36.83 4.35
1799 1821 4.580995 TGTTGACGTGGATTTGGTAAACAT 59.419 37.500 0.00 0.00 31.67 2.71
1807 1829 6.294286 CGTGGATTTGGTAAACATAAGTGGTT 60.294 38.462 0.00 0.00 39.07 3.67
1809 1831 7.383843 GTGGATTTGGTAAACATAAGTGGTTTG 59.616 37.037 0.00 0.00 38.77 2.93
1814 1836 5.892119 TGGTAAACATAAGTGGTTTGGTCAA 59.108 36.000 0.00 0.00 38.77 3.18
1969 1991 7.385267 AGATGAACTATCACAAGGATATGAGC 58.615 38.462 0.00 0.00 38.69 4.26
2040 2063 6.316890 AGAAAGCAAAAACAGATGCAAATGTT 59.683 30.769 12.68 12.68 44.95 2.71
2088 2111 3.133003 GGATGGCACTAGCTAGAAGACAA 59.867 47.826 27.45 11.72 41.70 3.18
2129 2152 3.806507 GCAAGAGGCTGCTGATAAGCTAT 60.807 47.826 3.06 0.00 40.64 2.97
2131 2154 4.005487 AGAGGCTGCTGATAAGCTATTG 57.995 45.455 3.06 0.00 40.64 1.90
2216 2243 4.019860 CAGTCAATGGAGAGGGAGAGAAAA 60.020 45.833 0.00 0.00 0.00 2.29
2217 2244 4.224818 AGTCAATGGAGAGGGAGAGAAAAG 59.775 45.833 0.00 0.00 0.00 2.27
2249 2276 6.549736 TGATGAGATGCAAAAGGATGATTCAT 59.450 34.615 0.00 0.00 0.00 2.57
2425 2456 7.015680 ACAGAGATGACATTCCTATACTGGAT 58.984 38.462 0.00 0.00 35.83 3.41
2491 2522 4.130286 AGGTATGTCTGAAACTGCTAGC 57.870 45.455 8.10 8.10 0.00 3.42
2500 2531 5.696724 GTCTGAAACTGCTAGCACTTCTTAA 59.303 40.000 24.80 13.71 0.00 1.85
2510 2541 8.615878 TGCTAGCACTTCTTAACTTGAAAATA 57.384 30.769 14.93 0.00 0.00 1.40
2530 2561 6.778834 AATATTGAGTTGATTGATGTGGCA 57.221 33.333 0.00 0.00 0.00 4.92
2555 2586 7.544804 AATTTGATAGGAATAGATTTGGGGC 57.455 36.000 0.00 0.00 0.00 5.80
2636 2669 8.465201 CAGGAAAGAAATTTATCTAGCAAGCTT 58.535 33.333 0.00 0.00 0.00 3.74
2722 2755 8.357402 ACATTTTTCTGGACCTGTTGTTATTAC 58.643 33.333 0.00 0.00 0.00 1.89
2918 2969 1.909986 ACTTCCTTACCCTCTGCCTTC 59.090 52.381 0.00 0.00 0.00 3.46
2975 3048 8.875168 ACTGTAGGGGAATTAGAGATAAGAATG 58.125 37.037 0.00 0.00 0.00 2.67
3029 3102 3.817709 ACAACCTTGATTTTGTGGGTG 57.182 42.857 0.00 0.00 42.54 4.61
3043 3116 2.955660 TGTGGGTGTCCAAGAAACAATC 59.044 45.455 0.00 0.00 46.04 2.67
3045 3118 2.955660 TGGGTGTCCAAGAAACAATCAC 59.044 45.455 0.00 0.00 40.73 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 7.292356 TGGCTAGATAAGGATTTCCATGTTCTA 59.708 37.037 0.00 0.26 38.89 2.10
91 92 5.512232 CCAGAGTGGCTAGATAAGGATTTCC 60.512 48.000 0.00 0.00 0.00 3.13
211 212 0.681733 TCAAGCACTCTGTCCCTGTC 59.318 55.000 0.00 0.00 0.00 3.51
249 253 4.403734 TCCCAATACAACAAGGGAAGTTC 58.596 43.478 0.00 0.00 46.94 3.01
260 264 7.514721 TGGTCTCCTATTATTCCCAATACAAC 58.485 38.462 0.00 0.00 0.00 3.32
266 270 5.221925 GCAGATGGTCTCCTATTATTCCCAA 60.222 44.000 0.00 0.00 0.00 4.12
307 311 7.335422 GCTAATTTGATACCATCGATCATCCTT 59.665 37.037 0.00 0.00 33.41 3.36
332 336 2.797177 ATCCACTTTCCTTCCTCTGC 57.203 50.000 0.00 0.00 0.00 4.26
357 361 2.568509 CCAATTGGGTTCAGCTCCATTT 59.431 45.455 17.36 0.00 32.48 2.32
454 458 0.679002 CCCTCACAACATGCAGGAGG 60.679 60.000 4.84 13.53 43.76 4.30
459 463 1.680735 GTTTCACCCTCACAACATGCA 59.319 47.619 0.00 0.00 0.00 3.96
463 467 1.409521 CCCTGTTTCACCCTCACAACA 60.410 52.381 0.00 0.00 0.00 3.33
492 496 9.927668 GAGATAAAACAATCTCCCAAAAATTCA 57.072 29.630 3.01 0.00 44.10 2.57
585 592 1.000496 GGCCTACTTTTTCCCCCTCT 59.000 55.000 0.00 0.00 0.00 3.69
606 614 7.511959 AGGCCTAAAGTTTTCTCTACTTTTG 57.488 36.000 1.29 5.00 41.69 2.44
613 621 6.435292 TCTTGTAGGCCTAAAGTTTTCTCT 57.565 37.500 15.83 0.00 0.00 3.10
631 639 6.429151 GGTGTATATAACCCCCTTTTCTTGT 58.571 40.000 3.85 0.00 0.00 3.16
634 642 4.970640 TCGGTGTATATAACCCCCTTTTCT 59.029 41.667 7.90 0.00 33.88 2.52
656 664 2.069165 AACACCCAAGGCCAGGACTC 62.069 60.000 15.35 0.00 0.00 3.36
659 667 2.067932 CTCAACACCCAAGGCCAGGA 62.068 60.000 15.35 0.00 0.00 3.86
667 675 1.338890 TGGGTCGTCTCAACACCCAA 61.339 55.000 6.59 0.00 45.62 4.12
739 747 1.522569 GAGGGCTGCTGGTATTCGT 59.477 57.895 0.00 0.00 0.00 3.85
883 891 2.138179 GGCGGACATGGTAGCCCTA 61.138 63.158 14.27 0.00 43.54 3.53
921 929 8.869109 TGGTTCTGAAATTGATTACCTTGAAAT 58.131 29.630 0.00 0.00 0.00 2.17
953 961 3.626670 CCAATTGCCAAAGCTCTCTCTAG 59.373 47.826 0.00 0.00 40.80 2.43
1012 1020 7.905604 TGGTCTGAAATGTTGACTTATACTG 57.094 36.000 0.00 0.00 0.00 2.74
1020 1028 4.448732 GGCAAATTGGTCTGAAATGTTGAC 59.551 41.667 0.00 0.00 0.00 3.18
1028 1036 2.978156 AGGAGGCAAATTGGTCTGAA 57.022 45.000 0.00 0.00 0.00 3.02
1136 1144 1.064166 CATTCAGAACTCCCCCTGCAT 60.064 52.381 0.00 0.00 0.00 3.96
1248 1256 1.440618 TAGCTTCACACCCCTTGGAA 58.559 50.000 0.00 0.00 34.81 3.53
1413 1434 4.842574 TGACCAAAGCTACTGCATCATTA 58.157 39.130 0.00 0.00 42.74 1.90
1448 1469 7.309621 CCTCTGAATCAATTTCCAAATCACAGT 60.310 37.037 0.00 0.00 33.04 3.55
1473 1494 6.639632 TTTGCCAAGCTATTGATAAGATCC 57.360 37.500 0.00 0.00 38.83 3.36
1485 1506 2.894765 GGGGTAAGTTTTTGCCAAGCTA 59.105 45.455 0.00 0.00 40.50 3.32
1555 1576 6.690530 TCCTTGCAACAGATGGAAAATTTAG 58.309 36.000 0.00 0.00 39.03 1.85
1633 1654 6.944290 TCATCATTCCAGACTTTCACTTTGAT 59.056 34.615 0.00 0.00 0.00 2.57
1698 1719 1.814394 GTTTTTGGTACCCCCTTAGCG 59.186 52.381 10.07 0.00 0.00 4.26
1775 1797 4.398358 TGTTTACCAAATCCACGTCAACAA 59.602 37.500 0.00 0.00 0.00 2.83
1783 1805 6.584185 ACCACTTATGTTTACCAAATCCAC 57.416 37.500 0.00 0.00 0.00 4.02
1799 1821 3.569194 TCAGCTTGACCAAACCACTTA 57.431 42.857 0.00 0.00 0.00 2.24
1807 1829 2.555325 CAGCAATCTTCAGCTTGACCAA 59.445 45.455 0.00 0.00 39.50 3.67
1809 1831 2.095364 CACAGCAATCTTCAGCTTGACC 60.095 50.000 0.00 0.00 39.50 4.02
1814 1836 1.531423 CACCACAGCAATCTTCAGCT 58.469 50.000 0.00 0.00 42.94 4.24
2078 2101 3.608316 AGCAGCCTCTTTGTCTTCTAG 57.392 47.619 0.00 0.00 0.00 2.43
2079 2102 5.683876 AATAGCAGCCTCTTTGTCTTCTA 57.316 39.130 0.00 0.00 0.00 2.10
2080 2103 4.566426 AATAGCAGCCTCTTTGTCTTCT 57.434 40.909 0.00 0.00 0.00 2.85
2081 2104 6.595716 TCTTTAATAGCAGCCTCTTTGTCTTC 59.404 38.462 0.00 0.00 0.00 2.87
2088 2111 4.494091 TGCTCTTTAATAGCAGCCTCTT 57.506 40.909 8.52 0.00 44.78 2.85
2216 2243 2.113807 TGCATCTCATCATCCTCCCT 57.886 50.000 0.00 0.00 0.00 4.20
2217 2244 2.945080 TTGCATCTCATCATCCTCCC 57.055 50.000 0.00 0.00 0.00 4.30
2249 2276 6.127026 GGTTCTTCCTCATTAGCTTTCTCCTA 60.127 42.308 0.00 0.00 0.00 2.94
2399 2430 6.491745 TCCAGTATAGGAATGTCATCTCTGTC 59.508 42.308 0.00 0.00 33.93 3.51
2425 2456 3.374764 TCTGGCCAAAGTCATAGCTCTA 58.625 45.455 7.01 0.00 0.00 2.43
2510 2541 5.471556 TTTGCCACATCAATCAACTCAAT 57.528 34.783 0.00 0.00 0.00 2.57
2530 2561 7.791282 AGCCCCAAATCTATTCCTATCAAATTT 59.209 33.333 0.00 0.00 0.00 1.82
2636 2669 4.766891 CCTGAGCATTTTTAGTTTCCCTGA 59.233 41.667 0.00 0.00 0.00 3.86
2701 2734 5.613329 ACGTAATAACAACAGGTCCAGAAA 58.387 37.500 0.00 0.00 0.00 2.52
2722 2755 6.094048 ACCTGTTCATCATCCTCATTTTTACG 59.906 38.462 0.00 0.00 0.00 3.18
2887 2938 4.604490 AGGGTAAGGAAGTTTATGTGGGAA 59.396 41.667 0.00 0.00 0.00 3.97
2889 2940 4.227527 AGAGGGTAAGGAAGTTTATGTGGG 59.772 45.833 0.00 0.00 0.00 4.61
2935 3008 2.755103 CCTACAGTTCCAAATCAAGCCC 59.245 50.000 0.00 0.00 0.00 5.19
3007 3080 4.119136 CACCCACAAAATCAAGGTTGTTC 58.881 43.478 0.00 0.00 35.81 3.18
3029 3102 3.882888 TCACCTGTGATTGTTTCTTGGAC 59.117 43.478 0.00 0.00 34.14 4.02


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

AutoCloner maintained by Alex Coulton.