Multiple sequence alignment - TraesCS2B01G307200

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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 TraesCS2B01G307200 chr2B 100.000 3228 0 0 1 3228 439644003 439640776 0 5962
1 TraesCS2B01G307200 chr2B 93.209 589 40 0 1 589 246361224 246361812 0 867
2 TraesCS2B01G307200 chr2D 97.381 1833 33 5 598 2426 370177447 370175626 0 3105
3 TraesCS2B01G307200 chr2A 95.868 1815 34 12 638 2426 501094579 501092780 0 2898
4 TraesCS2B01G307200 chr3B 91.824 795 62 3 2435 3228 735230226 735229434 0 1105
5 TraesCS2B01G307200 chr3B 96.616 591 20 0 1 591 147146603 147146013 0 981
6 TraesCS2B01G307200 chr5D 90.886 801 65 7 2435 3228 526706335 526707134 0 1068
7 TraesCS2B01G307200 chr6B 90.933 761 64 3 2435 3194 700656359 700657115 0 1018
8 TraesCS2B01G307200 chr6B 96.780 590 18 1 1 590 599837658 599838246 0 983
9 TraesCS2B01G307200 chr6B 86.541 795 100 6 2436 3226 483514693 483513902 0 869
10 TraesCS2B01G307200 chr6B 86.087 805 102 9 2429 3226 23028025 23028826 0 857
11 TraesCS2B01G307200 chr5B 97.124 591 14 2 1 591 644933568 644932981 0 994
12 TraesCS2B01G307200 chr5B 96.284 592 22 0 1 592 325538212 325538803 0 972
13 TraesCS2B01G307200 chr5B 95.601 591 26 0 1 591 527185368 527185958 0 948
14 TraesCS2B01G307200 chr4A 96.622 592 20 0 1 592 715769558 715768967 0 983
15 TraesCS2B01G307200 chrUn 95.402 609 24 4 1 609 277776823 277777427 0 966
16 TraesCS2B01G307200 chr4B 96.108 591 23 0 1 591 3869677 3869087 0 965
17 TraesCS2B01G307200 chr4B 87.909 794 93 3 2435 3228 538350465 538349675 0 931
18 TraesCS2B01G307200 chr4B 87.500 800 91 7 2432 3226 562581477 562582272 0 915
19 TraesCS2B01G307200 chr4D 85.947 797 105 7 2433 3228 102403439 102402649 0 845
20 TraesCS2B01G307200 chr1B 85.430 803 105 10 2433 3228 484321049 484320252 0 824


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 TraesCS2B01G307200 chr2B 439640776 439644003 3227 True 5962 5962 100.000 1 3228 1 chr2B.!!$R1 3227
1 TraesCS2B01G307200 chr2B 246361224 246361812 588 False 867 867 93.209 1 589 1 chr2B.!!$F1 588
2 TraesCS2B01G307200 chr2D 370175626 370177447 1821 True 3105 3105 97.381 598 2426 1 chr2D.!!$R1 1828
3 TraesCS2B01G307200 chr2A 501092780 501094579 1799 True 2898 2898 95.868 638 2426 1 chr2A.!!$R1 1788
4 TraesCS2B01G307200 chr3B 735229434 735230226 792 True 1105 1105 91.824 2435 3228 1 chr3B.!!$R2 793
5 TraesCS2B01G307200 chr3B 147146013 147146603 590 True 981 981 96.616 1 591 1 chr3B.!!$R1 590
6 TraesCS2B01G307200 chr5D 526706335 526707134 799 False 1068 1068 90.886 2435 3228 1 chr5D.!!$F1 793
7 TraesCS2B01G307200 chr6B 700656359 700657115 756 False 1018 1018 90.933 2435 3194 1 chr6B.!!$F3 759
8 TraesCS2B01G307200 chr6B 599837658 599838246 588 False 983 983 96.780 1 590 1 chr6B.!!$F2 589
9 TraesCS2B01G307200 chr6B 483513902 483514693 791 True 869 869 86.541 2436 3226 1 chr6B.!!$R1 790
10 TraesCS2B01G307200 chr6B 23028025 23028826 801 False 857 857 86.087 2429 3226 1 chr6B.!!$F1 797
11 TraesCS2B01G307200 chr5B 644932981 644933568 587 True 994 994 97.124 1 591 1 chr5B.!!$R1 590
12 TraesCS2B01G307200 chr5B 325538212 325538803 591 False 972 972 96.284 1 592 1 chr5B.!!$F1 591
13 TraesCS2B01G307200 chr5B 527185368 527185958 590 False 948 948 95.601 1 591 1 chr5B.!!$F2 590
14 TraesCS2B01G307200 chr4A 715768967 715769558 591 True 983 983 96.622 1 592 1 chr4A.!!$R1 591
15 TraesCS2B01G307200 chrUn 277776823 277777427 604 False 966 966 95.402 1 609 1 chrUn.!!$F1 608
16 TraesCS2B01G307200 chr4B 3869087 3869677 590 True 965 965 96.108 1 591 1 chr4B.!!$R1 590
17 TraesCS2B01G307200 chr4B 538349675 538350465 790 True 931 931 87.909 2435 3228 1 chr4B.!!$R2 793
18 TraesCS2B01G307200 chr4B 562581477 562582272 795 False 915 915 87.500 2432 3226 1 chr4B.!!$F1 794
19 TraesCS2B01G307200 chr4D 102402649 102403439 790 True 845 845 85.947 2433 3228 1 chr4D.!!$R1 795
20 TraesCS2B01G307200 chr1B 484320252 484321049 797 True 824 824 85.430 2433 3228 1 chr1B.!!$R1 795

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
622 625 0.323451 GCCCAGGGTAAGGTCCAAAG 60.323 60.000 7.55 0.0 0.00 2.77 F
889 892 1.797933 CGAGGACGAGAACACGCAG 60.798 63.158 0.00 0.0 42.66 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1467 2.202171 GCACATACACACGCACGC 60.202 61.111 0.0 0.0 0.00 5.34 R
2861 2899 0.460284 CGTCTGGCGTCTGGCTTATT 60.460 55.000 0.0 0.0 42.94 1.40 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
33 34 8.455903 AGAACTCTGATCACATCTTTTTCAAA 57.544 30.769 0.00 0.00 0.00 2.69
42 43 6.964908 TCACATCTTTTTCAAATGCGTTCTA 58.035 32.000 0.00 0.00 0.00 2.10
198 199 1.951209 TATGTTGGGCTCTCTGGACA 58.049 50.000 0.00 0.00 0.00 4.02
311 312 6.838090 AGATCATTGACTAAGGAGACTGATCA 59.162 38.462 10.70 0.00 42.68 2.92
475 476 2.113860 TGCCTGTATGTTTCCTGCTC 57.886 50.000 0.00 0.00 0.00 4.26
495 496 4.440880 CTCTGGCTACTCTCATCCTTTTG 58.559 47.826 0.00 0.00 0.00 2.44
616 619 1.616628 CAGGAGCCCAGGGTAAGGT 60.617 63.158 7.55 0.00 0.00 3.50
622 625 0.323451 GCCCAGGGTAAGGTCCAAAG 60.323 60.000 7.55 0.00 0.00 2.77
626 629 2.092914 CCAGGGTAAGGTCCAAAGCTAG 60.093 54.545 0.00 0.00 31.54 3.42
671 674 3.945285 AGAAAACGTCACACAATGGAGTT 59.055 39.130 0.00 0.00 32.29 3.01
729 732 2.433664 AGCGACCGGCCGTTTAAG 60.434 61.111 26.12 10.93 45.17 1.85
758 761 2.720605 GTAGTAGCTCCCGCGGAC 59.279 66.667 30.73 17.08 42.32 4.79
812 815 2.260434 CGTTCCCGTCCACGTCAT 59.740 61.111 0.00 0.00 37.74 3.06
865 868 3.585862 CACCGCCTATATTACATTCGCT 58.414 45.455 0.00 0.00 0.00 4.93
889 892 1.797933 CGAGGACGAGAACACGCAG 60.798 63.158 0.00 0.00 42.66 5.18
1035 1038 4.651008 TTCGTCGTGGTGGTCGCC 62.651 66.667 0.00 0.00 0.00 5.54
1455 1467 4.668576 AGCATGTCGTTTATGAACAGTG 57.331 40.909 0.95 0.00 35.44 3.66
2022 2039 1.690985 GGAGGAGGGGAGTGAAGGG 60.691 68.421 0.00 0.00 0.00 3.95
2229 2246 2.427002 CCAGGGGACTCCTCATGTAGAT 60.427 54.545 0.00 0.00 46.12 1.98
2310 2343 7.601508 AGACTATATGCATCATACATGTGTGTG 59.398 37.037 20.39 17.66 39.39 3.82
2426 2459 4.920828 TGGAACCCCAAGCTTCAC 57.079 55.556 0.00 0.00 40.09 3.18
2427 2460 1.228124 TGGAACCCCAAGCTTCACG 60.228 57.895 0.00 0.00 40.09 4.35
2460 2493 2.167693 TGAGAAAAGACATACGCCCGAT 59.832 45.455 0.00 0.00 0.00 4.18
2533 2567 8.668353 CAACATAGTATCACAGCAACAACTAAT 58.332 33.333 0.00 0.00 0.00 1.73
2637 2675 1.402720 CGCCCAAAATCTTCGCAACAT 60.403 47.619 0.00 0.00 0.00 2.71
2810 2848 5.250200 ACTTGTTTCTAGTGTTCCACAACA 58.750 37.500 0.00 0.00 40.40 3.33
2861 2899 1.428718 AACCCTTTTAGCCACCCCGA 61.429 55.000 0.00 0.00 0.00 5.14
2870 2908 1.823899 GCCACCCCGAATAAGCCAG 60.824 63.158 0.00 0.00 0.00 4.85
2871 2909 1.912220 CCACCCCGAATAAGCCAGA 59.088 57.895 0.00 0.00 0.00 3.86
2872 2910 0.463833 CCACCCCGAATAAGCCAGAC 60.464 60.000 0.00 0.00 0.00 3.51
2964 3002 4.051237 CAAACAAACTTAGCCAAAGAGCC 58.949 43.478 3.55 0.00 38.67 4.70
2990 3028 7.567771 CGTGAAAGAAGATATGCTCGGTATTTC 60.568 40.741 0.00 0.00 30.75 2.17
2991 3029 6.420903 TGAAAGAAGATATGCTCGGTATTTCG 59.579 38.462 0.00 0.00 31.78 3.46
2996 3034 6.025749 AGATATGCTCGGTATTTCGAATGA 57.974 37.500 0.00 0.00 38.77 2.57
3152 3196 1.264295 GAACTTGGACGTAGGGGAGT 58.736 55.000 0.00 0.00 0.00 3.85
3155 3199 0.679002 CTTGGACGTAGGGGAGTCGA 60.679 60.000 0.00 0.00 38.20 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.640732 CAAACTAATTTGGCTAGAACGCAT 58.359 37.500 0.00 0.00 41.39 4.73
311 312 3.415087 GCAGGTCCAGGGCATCCT 61.415 66.667 0.00 0.00 46.26 3.24
465 466 1.552792 AGAGTAGCCAGAGCAGGAAAC 59.447 52.381 0.00 0.00 43.56 2.78
475 476 4.213564 ACAAAAGGATGAGAGTAGCCAG 57.786 45.455 0.00 0.00 0.00 4.85
495 496 2.878406 ACAGGAGCACACACACATAAAC 59.122 45.455 0.00 0.00 0.00 2.01
592 595 0.910088 ACCCTGGGCTCCTGAACTAC 60.910 60.000 14.08 0.00 0.00 2.73
593 596 0.714180 TACCCTGGGCTCCTGAACTA 59.286 55.000 14.08 0.00 0.00 2.24
594 597 0.178873 TTACCCTGGGCTCCTGAACT 60.179 55.000 14.08 0.00 0.00 3.01
595 598 0.253327 CTTACCCTGGGCTCCTGAAC 59.747 60.000 14.08 0.00 0.00 3.18
596 599 0.914417 CCTTACCCTGGGCTCCTGAA 60.914 60.000 14.08 0.00 0.00 3.02
616 619 3.120321 TGCGAGTTTTCTAGCTTTGGA 57.880 42.857 0.00 0.00 46.22 3.53
622 625 3.495001 AGTTGTCTTGCGAGTTTTCTAGC 59.505 43.478 0.00 0.00 46.25 3.42
626 629 2.223249 TGCAGTTGTCTTGCGAGTTTTC 60.223 45.455 0.00 0.00 0.00 2.29
784 787 2.585153 GGGAACGGGAAGAGGAGC 59.415 66.667 0.00 0.00 0.00 4.70
812 815 4.947147 GGGGTGCAACGTGGAGCA 62.947 66.667 6.50 6.50 37.97 4.26
865 868 1.303091 TGTTCTCGTCCTCGCGATCA 61.303 55.000 10.36 0.00 40.29 2.92
889 892 1.145119 AGGTTTGGGGGACTTGACTTC 59.855 52.381 0.00 0.00 0.00 3.01
1035 1038 3.730761 GCAGACGCCACCAAGCAG 61.731 66.667 0.00 0.00 0.00 4.24
1036 1039 4.254709 AGCAGACGCCACCAAGCA 62.255 61.111 0.00 0.00 39.83 3.91
1037 1040 3.426568 GAGCAGACGCCACCAAGC 61.427 66.667 0.00 0.00 39.83 4.01
1455 1467 2.202171 GCACATACACACGCACGC 60.202 61.111 0.00 0.00 0.00 5.34
2022 2039 4.162690 CCACCACTAGCCCCTCGC 62.163 72.222 0.00 0.00 37.98 5.03
2107 2124 4.541482 TCGGGCGTGCGATCGTAC 62.541 66.667 24.21 24.21 0.00 3.67
2215 2232 5.772169 TCGATTGATCATCTACATGAGGAGT 59.228 40.000 0.00 0.00 42.53 3.85
2229 2246 7.385778 TGTATATATGTCCGTCGATTGATCA 57.614 36.000 0.00 0.00 0.00 2.92
2448 2481 8.019094 GCTTTATTTATAAAATCGGGCGTATGT 58.981 33.333 1.21 0.00 32.39 2.29
2460 2493 8.871629 TCTGTCTGGTGGCTTTATTTATAAAA 57.128 30.769 1.21 0.00 32.39 1.52
2533 2567 3.493699 GGTAGCCATGTATGCGAACCTTA 60.494 47.826 10.57 0.00 36.97 2.69
2622 2660 5.389859 TTCATCCATGTTGCGAAGATTTT 57.610 34.783 0.00 0.00 0.00 1.82
2628 2666 0.810648 GGCTTCATCCATGTTGCGAA 59.189 50.000 0.00 0.00 0.00 4.70
2637 2675 0.681887 TCGGTCTACGGCTTCATCCA 60.682 55.000 0.00 0.00 44.45 3.41
2810 2848 1.001378 GTTTGCAGCGATCTGTTGGTT 60.001 47.619 0.00 0.00 42.29 3.67
2861 2899 0.460284 CGTCTGGCGTCTGGCTTATT 60.460 55.000 0.00 0.00 42.94 1.40
2964 3002 3.448686 ACCGAGCATATCTTCTTTCACG 58.551 45.455 0.00 0.00 0.00 4.35
2990 3028 2.477189 GCGTTTTATGTGGGGTCATTCG 60.477 50.000 0.00 0.00 0.00 3.34
2991 3029 2.490115 TGCGTTTTATGTGGGGTCATTC 59.510 45.455 0.00 0.00 0.00 2.67
2996 3034 2.507407 AGATGCGTTTTATGTGGGGT 57.493 45.000 0.00 0.00 0.00 4.95
3152 3196 6.016860 TCTGCCTACGCTAAACTTATATTCGA 60.017 38.462 0.00 0.00 35.36 3.71
3155 3199 7.052142 AGTCTGCCTACGCTAAACTTATATT 57.948 36.000 0.00 0.00 35.36 1.28


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

AutoCloner maintained by Alex Coulton.