Multiple sequence alignment - TraesCS6B01G263600

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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 TraesCS6B01G263600 chr6B 100.000 2660 0 0 1 2660 474438476 474435817 0.000000 4913.0
1 TraesCS6B01G263600 chr6A 88.183 2801 171 68 1 2659 443423536 443420754 0.000000 3192.0
2 TraesCS6B01G263600 chr6D 91.920 2005 92 32 634 2586 307118735 307116749 0.000000 2741.0
3 TraesCS6B01G263600 chr6D 94.590 647 22 7 1 637 307119458 307118815 0.000000 989.0
4 TraesCS6B01G263600 chr6D 94.872 39 0 2 595 631 413075594 413075632 0.000029 60.2
5 TraesCS6B01G263600 chr1D 100.000 32 0 0 597 628 64895567 64895536 0.000029 60.2
6 TraesCS6B01G263600 chr7A 89.583 48 0 3 584 626 85209346 85209299 0.000370 56.5
7 TraesCS6B01G263600 chr2D 89.583 48 0 2 584 626 564920711 564920758 0.000370 56.5
8 TraesCS6B01G263600 chr2B 89.583 48 0 2 584 626 676588041 676588088 0.000370 56.5
9 TraesCS6B01G263600 chr3A 88.000 50 0 4 581 624 621664492 621664443 0.001000 54.7
10 TraesCS6B01G263600 chr2A 100.000 29 0 0 597 625 475557182 475557154 0.001000 54.7


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 TraesCS6B01G263600 chr6B 474435817 474438476 2659 True 4913 4913 100.000 1 2660 1 chr6B.!!$R1 2659
1 TraesCS6B01G263600 chr6A 443420754 443423536 2782 True 3192 3192 88.183 1 2659 1 chr6A.!!$R1 2658
2 TraesCS6B01G263600 chr6D 307116749 307119458 2709 True 1865 2741 93.255 1 2586 2 chr6D.!!$R1 2585

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
960 1120 0.672342 GCCCTCGGAAGCTTACGATA 59.328 55.0 32.71 13.25 43.55 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 2850 0.326264 ACCTTCGCATTGCCTTCTCT 59.674 50.0 2.41 0.0 0.0 3.1 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
53 54 6.183360 GCAGCAGAGATTATCGAAAAAGTCTT 60.183 38.462 0.00 0.00 0.00 3.01
245 248 5.888691 TTTCAGTAAGCACACACTTTTCA 57.111 34.783 0.00 0.00 0.00 2.69
306 309 7.259290 TGTGTACAAAATGACTTCTCCTTTC 57.741 36.000 0.00 0.00 0.00 2.62
310 313 4.275936 ACAAAATGACTTCTCCTTTCGGTG 59.724 41.667 0.00 0.00 0.00 4.94
399 402 6.176975 TCGTTGCTGTGGATAATTAAGTTG 57.823 37.500 0.00 0.00 0.00 3.16
475 478 8.795842 TGTAGGAACAATTATACGAACCATTT 57.204 30.769 0.00 0.00 30.91 2.32
632 676 2.301009 TCGGAGGGAGTAGAAAAACACC 59.699 50.000 0.00 0.00 0.00 4.16
642 769 6.072673 GGAGTAGAAAAACACCAGTATTGTGG 60.073 42.308 0.00 0.00 44.01 4.17
831 984 8.986477 AAATATGCCTTTTACTGTTTGATGAC 57.014 30.769 0.00 0.00 0.00 3.06
908 1061 3.364023 CACGGTCTGTTGAGTATTTCGTC 59.636 47.826 0.00 0.00 0.00 4.20
913 1066 5.812642 GGTCTGTTGAGTATTTCGTCATCAT 59.187 40.000 0.00 0.00 0.00 2.45
914 1067 6.313905 GGTCTGTTGAGTATTTCGTCATCATT 59.686 38.462 0.00 0.00 0.00 2.57
931 1084 2.293122 TCATTTGCACCGTTTTCTGAGG 59.707 45.455 0.00 0.00 0.00 3.86
946 1099 2.501723 TCTGAGGTTGATAACAGCCCTC 59.498 50.000 11.59 11.59 46.34 4.30
960 1120 0.672342 GCCCTCGGAAGCTTACGATA 59.328 55.000 32.71 13.25 43.55 2.92
968 1128 3.489398 CGGAAGCTTACGATAACAGAGCT 60.489 47.826 27.24 0.00 44.95 4.09
969 1129 4.261072 CGGAAGCTTACGATAACAGAGCTA 60.261 45.833 27.24 0.00 42.44 3.32
970 1130 5.216648 GGAAGCTTACGATAACAGAGCTAG 58.783 45.833 0.00 0.00 42.44 3.42
981 1141 8.251721 ACGATAACAGAGCTAGTACAAAATTCT 58.748 33.333 0.00 0.00 0.00 2.40
1096 1265 0.832135 TTCCTCCACCTCTCGTTGCT 60.832 55.000 0.00 0.00 0.00 3.91
1260 1439 1.308326 CTCCTCGGTCCTCCTCCTT 59.692 63.158 0.00 0.00 0.00 3.36
1614 1793 0.890996 CCAAGCCGGTCAAGCTCTTT 60.891 55.000 1.90 0.00 40.49 2.52
1772 1953 2.605818 CGTGTGTATATTGTTCCGGTGG 59.394 50.000 0.00 0.00 0.00 4.61
1773 1954 3.676598 CGTGTGTATATTGTTCCGGTGGA 60.677 47.826 0.00 0.00 0.00 4.02
1784 1979 1.070615 CCGGTGGATGTGTGTGTGA 59.929 57.895 0.00 0.00 0.00 3.58
1920 2115 3.411446 TCTCAGATGTGCGGAATTGTTT 58.589 40.909 0.00 0.00 0.00 2.83
1925 2120 3.129287 AGATGTGCGGAATTGTTTGGATC 59.871 43.478 0.00 0.00 0.00 3.36
1928 2123 4.013050 TGTGCGGAATTGTTTGGATCATA 58.987 39.130 0.00 0.00 0.00 2.15
1931 2126 5.687285 GTGCGGAATTGTTTGGATCATAATC 59.313 40.000 0.00 0.00 0.00 1.75
1977 2175 0.467844 TTTGCTCTTCCTTGCAGCCA 60.468 50.000 0.00 0.00 40.46 4.75
2006 2204 8.028938 GCTTGATAATTTTGTTCCAAGAGCTTA 58.971 33.333 0.00 0.00 34.57 3.09
2018 2216 7.766278 TGTTCCAAGAGCTTATCTTAATCTGAC 59.234 37.037 0.00 0.00 46.91 3.51
2123 2323 9.273016 GATATTTTCTGTTATGAGGGAATTCGA 57.727 33.333 0.00 0.00 0.00 3.71
2132 2332 4.437682 TGAGGGAATTCGATTAGGCAAT 57.562 40.909 0.00 0.00 0.00 3.56
2159 2359 7.803724 AGTATCTTGTTTTTGGACAATACGAC 58.196 34.615 0.00 0.00 38.71 4.34
2301 2529 9.581289 TTCATGAAATAACTTCTCTAAACCCAA 57.419 29.630 5.45 0.00 34.86 4.12
2307 2535 8.762481 AATAACTTCTCTAAACCCAACTTGTT 57.238 30.769 0.00 0.00 0.00 2.83
2350 2578 3.069872 GCTAAGGCTCTAAGGTAGGTTCC 59.930 52.174 0.00 0.00 35.22 3.62
2389 2617 8.967918 GGTAATCCTAAAATTTAGTTGCTTCCT 58.032 33.333 11.34 0.00 0.00 3.36
2405 2633 6.932356 TGCTTCCTTTCATCATCAATCTAC 57.068 37.500 0.00 0.00 0.00 2.59
2460 2693 9.881529 CGAGTAACCTCATAGAGTTCTTTATAC 57.118 37.037 0.00 0.00 37.59 1.47
2483 2716 4.885907 CCAGCTCATACTTCCACATTGAAT 59.114 41.667 0.00 0.00 0.00 2.57
2516 2749 6.594788 AAACAGCACATTGGACAGATTTAT 57.405 33.333 0.00 0.00 0.00 1.40
2577 2811 8.762645 ACTGTACCTAGTTAATAAACTTACCCC 58.237 37.037 0.00 0.00 43.60 4.95
2578 2812 8.915813 TGTACCTAGTTAATAAACTTACCCCT 57.084 34.615 0.00 0.00 43.60 4.79
2579 2813 8.761689 TGTACCTAGTTAATAAACTTACCCCTG 58.238 37.037 0.00 0.00 43.60 4.45
2580 2814 8.981659 GTACCTAGTTAATAAACTTACCCCTGA 58.018 37.037 0.00 0.00 43.60 3.86
2581 2815 8.087303 ACCTAGTTAATAAACTTACCCCTGAG 57.913 38.462 0.00 0.00 43.60 3.35
2583 2817 5.752650 AGTTAATAAACTTACCCCTGAGCC 58.247 41.667 0.00 0.00 43.60 4.70
2597 2850 4.721776 CCCCTGAGCCTGGCTTATTATATA 59.278 45.833 24.26 1.68 39.88 0.86
2600 2853 6.183360 CCCTGAGCCTGGCTTATTATATAGAG 60.183 46.154 24.26 3.16 39.88 2.43
2604 2857 7.124901 TGAGCCTGGCTTATTATATAGAGAAGG 59.875 40.741 24.26 0.00 39.88 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.199719 CACACTAGATACACGACGACTATACA 59.800 42.308 0.00 0.00 0.00 2.29
180 183 1.810151 TCATTACGGCACAAAAGGAGC 59.190 47.619 0.00 0.00 0.00 4.70
306 309 1.657181 GCCGAAACAAACAGCACCG 60.657 57.895 0.00 0.00 0.00 4.94
310 313 0.863144 TCTACGCCGAAACAAACAGC 59.137 50.000 0.00 0.00 0.00 4.40
360 363 5.121611 CAGCAACGAAACACATTGGATACTA 59.878 40.000 0.00 0.00 37.61 1.82
361 364 4.072131 AGCAACGAAACACATTGGATACT 58.928 39.130 0.00 0.00 37.61 2.12
362 365 4.158384 CAGCAACGAAACACATTGGATAC 58.842 43.478 0.00 0.00 0.00 2.24
377 380 6.176975 TCAACTTAATTATCCACAGCAACG 57.823 37.500 0.00 0.00 0.00 4.10
591 612 9.155975 CCTCCGATCCATATTAATTGTCTTTAG 57.844 37.037 0.00 0.00 0.00 1.85
605 649 4.464652 TTTCTACTCCCTCCGATCCATA 57.535 45.455 0.00 0.00 0.00 2.74
632 676 2.401583 TAGCACAGGCCACAATACTG 57.598 50.000 5.01 0.00 42.56 2.74
642 769 3.990318 ACTTGTTTTCTTAGCACAGGC 57.010 42.857 0.00 0.00 41.61 4.85
828 981 4.704833 GCCTTGGCTCCGCAGTCA 62.705 66.667 4.11 0.00 29.99 3.41
850 1003 2.231235 AGAATTGTGAAATTCGTGGGGC 59.769 45.455 5.74 0.00 42.44 5.80
853 1006 4.984161 AGCAAAGAATTGTGAAATTCGTGG 59.016 37.500 14.35 7.93 42.44 4.94
856 1009 8.451687 TCATAAGCAAAGAATTGTGAAATTCG 57.548 30.769 5.74 0.00 42.44 3.34
908 1061 3.899734 TCAGAAAACGGTGCAAATGATG 58.100 40.909 0.00 0.00 0.00 3.07
913 1066 1.757682 ACCTCAGAAAACGGTGCAAA 58.242 45.000 0.00 0.00 0.00 3.68
914 1067 1.403679 CAACCTCAGAAAACGGTGCAA 59.596 47.619 0.00 0.00 0.00 4.08
931 1084 2.280628 CTTCCGAGGGCTGTTATCAAC 58.719 52.381 0.00 0.00 0.00 3.18
946 1099 2.789893 GCTCTGTTATCGTAAGCTTCCG 59.210 50.000 0.00 2.74 37.18 4.30
960 1120 6.651225 GTCCAGAATTTTGTACTAGCTCTGTT 59.349 38.462 0.00 0.00 0.00 3.16
968 1128 6.790285 GGAAACGTCCAGAATTTTGTACTA 57.210 37.500 0.00 0.00 44.26 1.82
969 1129 5.684550 GGAAACGTCCAGAATTTTGTACT 57.315 39.130 0.00 0.00 44.26 2.73
1096 1265 2.524394 GCAGGATAGGGAGCCCGA 60.524 66.667 0.00 0.00 41.95 5.14
1614 1793 2.034532 TCCTCGCGTAGGTGGACA 59.965 61.111 19.53 2.72 46.62 4.02
1772 1953 2.138320 CTCACCACTCACACACACATC 58.862 52.381 0.00 0.00 0.00 3.06
1773 1954 1.762370 TCTCACCACTCACACACACAT 59.238 47.619 0.00 0.00 0.00 3.21
1784 1979 1.577736 CCTTCATCCCTCTCACCACT 58.422 55.000 0.00 0.00 0.00 4.00
1910 2105 6.299023 TCGATTATGATCCAAACAATTCCG 57.701 37.500 0.00 0.00 0.00 4.30
1928 2123 9.760077 ATCGGTGTTATTTTAGAACTATCGATT 57.240 29.630 1.71 0.00 34.10 3.34
1993 2191 7.984617 AGTCAGATTAAGATAAGCTCTTGGAAC 59.015 37.037 0.00 0.00 44.12 3.62
2018 2216 7.325660 AGAAGCAACAATGTGATTATACCAG 57.674 36.000 0.00 0.00 0.00 4.00
2097 2297 9.273016 TCGAATTCCCTCATAACAGAAAATATC 57.727 33.333 0.00 0.00 0.00 1.63
2102 2302 7.715249 CCTAATCGAATTCCCTCATAACAGAAA 59.285 37.037 0.00 0.00 0.00 2.52
2132 2332 9.491675 TCGTATTGTCCAAAAACAAGATACTTA 57.508 29.630 0.00 0.00 42.09 2.24
2159 2359 4.836125 AGCATTACACTCCAAACACTTG 57.164 40.909 0.00 0.00 0.00 3.16
2207 2417 5.211174 AGTTCACAGGGTTACAGTAAGAC 57.789 43.478 0.00 0.00 0.00 3.01
2297 2525 3.003689 CACTCTACAAGCAACAAGTTGGG 59.996 47.826 14.16 0.00 40.74 4.12
2301 2529 4.513442 TGTTCACTCTACAAGCAACAAGT 58.487 39.130 0.00 0.00 31.37 3.16
2307 2535 3.312421 GCTGTTTGTTCACTCTACAAGCA 59.688 43.478 0.00 0.00 42.06 3.91
2342 2570 2.372852 TGGTCAGCCAGGAACCTAC 58.627 57.895 0.00 0.00 40.46 3.18
2350 2578 2.975489 AGGATTACCTATGGTCAGCCAG 59.025 50.000 7.78 0.00 45.83 4.85
2460 2693 3.877559 TCAATGTGGAAGTATGAGCTGG 58.122 45.455 0.00 0.00 0.00 4.85
2564 2798 3.053619 CCAGGCTCAGGGGTAAGTTTATT 60.054 47.826 0.00 0.00 0.00 1.40
2577 2811 7.652524 TCTCTATATAATAAGCCAGGCTCAG 57.347 40.000 16.53 2.49 38.25 3.35
2578 2812 7.124901 CCTTCTCTATATAATAAGCCAGGCTCA 59.875 40.741 16.53 0.00 38.25 4.26
2579 2813 7.496747 CCTTCTCTATATAATAAGCCAGGCTC 58.503 42.308 16.53 0.00 38.25 4.70
2580 2814 6.126911 GCCTTCTCTATATAATAAGCCAGGCT 60.127 42.308 8.70 8.70 42.56 4.58
2581 2815 6.052360 GCCTTCTCTATATAATAAGCCAGGC 58.948 44.000 1.84 1.84 35.49 4.85
2583 2817 9.107177 CATTGCCTTCTCTATATAATAAGCCAG 57.893 37.037 0.00 0.00 0.00 4.85
2597 2850 0.326264 ACCTTCGCATTGCCTTCTCT 59.674 50.000 2.41 0.00 0.00 3.10
2600 2853 0.733150 GGTACCTTCGCATTGCCTTC 59.267 55.000 4.06 0.00 0.00 3.46
2604 2857 1.423845 CACGGTACCTTCGCATTGC 59.576 57.895 10.90 0.00 0.00 3.56
2637 2890 2.364973 TCTGCCTACCCGCATCCA 60.365 61.111 0.00 0.00 38.30 3.41
2638 2891 2.423446 CTCTGCCTACCCGCATCC 59.577 66.667 0.00 0.00 38.30 3.51
2641 2894 4.082523 GCACTCTGCCTACCCGCA 62.083 66.667 0.00 0.00 37.42 5.69


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

AutoCloner maintained by Alex Coulton.