Multiple sequence alignment - TraesCS3A01G062100

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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 TraesCS3A01G062100 chr3A 100.000 2387 0 0 1 2387 37296167 37298553 0.000000e+00 4409
1 TraesCS3A01G062100 chr3A 96.463 1442 45 5 758 2195 37189112 37190551 0.000000e+00 2375
2 TraesCS3A01G062100 chr3A 87.945 1659 170 16 744 2384 36921632 36923278 0.000000e+00 1929
3 TraesCS3A01G062100 chr3A 92.202 731 46 6 1 726 634686024 634686748 0.000000e+00 1024
4 TraesCS3A01G062100 chr3A 97.449 196 5 0 2192 2387 37193528 37193723 3.800000e-88 335
5 TraesCS3A01G062100 chr3D 88.802 1661 158 14 744 2387 27059799 27058150 0.000000e+00 2012
6 TraesCS3A01G062100 chr3D 93.673 1217 58 10 726 1929 26678077 26679287 0.000000e+00 1803
7 TraesCS3A01G062100 chr3D 92.224 733 47 6 1 729 8293399 8292673 0.000000e+00 1029
8 TraesCS3A01G062100 chrUn 89.332 1481 126 15 745 2200 267178820 267177347 0.000000e+00 1832
9 TraesCS3A01G062100 chrUn 90.887 1229 82 9 729 1941 38679580 38678366 0.000000e+00 1622
10 TraesCS3A01G062100 chrUn 90.068 443 42 2 1947 2387 38673588 38673146 7.400000e-160 573
11 TraesCS3A01G062100 chrUn 89.474 190 13 4 2198 2385 267176743 267176559 1.430000e-57 233
12 TraesCS3A01G062100 chr3B 89.332 1481 126 15 745 2200 45282302 45283775 0.000000e+00 1832
13 TraesCS3A01G062100 chr3B 89.691 1426 124 14 791 2200 45285558 45286976 0.000000e+00 1797
14 TraesCS3A01G062100 chr3B 89.474 190 13 4 2198 2385 45284379 45284563 1.430000e-57 233
15 TraesCS3A01G062100 chr3B 89.474 190 13 4 2198 2385 45287713 45287897 1.430000e-57 233
16 TraesCS3A01G062100 chr1A 93.570 731 39 5 1 727 94476203 94475477 0.000000e+00 1083
17 TraesCS3A01G062100 chr7D 93.306 732 42 5 1 726 592631449 592632179 0.000000e+00 1074
18 TraesCS3A01G062100 chr7D 92.381 735 43 8 1 725 108617139 108616408 0.000000e+00 1035
19 TraesCS3A01G062100 chr7D 91.837 735 49 6 1 725 79171547 79170814 0.000000e+00 1014
20 TraesCS3A01G062100 chr7D 91.929 731 48 6 1 726 599906093 599906817 0.000000e+00 1013
21 TraesCS3A01G062100 chr4D 93.333 720 42 4 1 715 449911129 449911847 0.000000e+00 1059
22 TraesCS3A01G062100 chr4D 91.803 732 54 5 1 726 480852350 480851619 0.000000e+00 1014
23 TraesCS3A01G062100 chr5D 78.606 1047 181 24 744 1759 523452757 523451723 0.000000e+00 652


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 TraesCS3A01G062100 chr3A 37296167 37298553 2386 False 4409.00 4409 100.00000 1 2387 1 chr3A.!!$F2 2386
1 TraesCS3A01G062100 chr3A 36921632 36923278 1646 False 1929.00 1929 87.94500 744 2384 1 chr3A.!!$F1 1640
2 TraesCS3A01G062100 chr3A 37189112 37193723 4611 False 1355.00 2375 96.95600 758 2387 2 chr3A.!!$F4 1629
3 TraesCS3A01G062100 chr3A 634686024 634686748 724 False 1024.00 1024 92.20200 1 726 1 chr3A.!!$F3 725
4 TraesCS3A01G062100 chr3D 27058150 27059799 1649 True 2012.00 2012 88.80200 744 2387 1 chr3D.!!$R2 1643
5 TraesCS3A01G062100 chr3D 26678077 26679287 1210 False 1803.00 1803 93.67300 726 1929 1 chr3D.!!$F1 1203
6 TraesCS3A01G062100 chr3D 8292673 8293399 726 True 1029.00 1029 92.22400 1 729 1 chr3D.!!$R1 728
7 TraesCS3A01G062100 chrUn 38678366 38679580 1214 True 1622.00 1622 90.88700 729 1941 1 chrUn.!!$R2 1212
8 TraesCS3A01G062100 chrUn 267176559 267178820 2261 True 1032.50 1832 89.40300 745 2385 2 chrUn.!!$R3 1640
9 TraesCS3A01G062100 chr3B 45282302 45287897 5595 False 1023.75 1832 89.49275 745 2385 4 chr3B.!!$F1 1640
10 TraesCS3A01G062100 chr1A 94475477 94476203 726 True 1083.00 1083 93.57000 1 727 1 chr1A.!!$R1 726
11 TraesCS3A01G062100 chr7D 592631449 592632179 730 False 1074.00 1074 93.30600 1 726 1 chr7D.!!$F1 725
12 TraesCS3A01G062100 chr7D 108616408 108617139 731 True 1035.00 1035 92.38100 1 725 1 chr7D.!!$R2 724
13 TraesCS3A01G062100 chr7D 79170814 79171547 733 True 1014.00 1014 91.83700 1 725 1 chr7D.!!$R1 724
14 TraesCS3A01G062100 chr7D 599906093 599906817 724 False 1013.00 1013 91.92900 1 726 1 chr7D.!!$F2 725
15 TraesCS3A01G062100 chr4D 449911129 449911847 718 False 1059.00 1059 93.33300 1 715 1 chr4D.!!$F1 714
16 TraesCS3A01G062100 chr4D 480851619 480852350 731 True 1014.00 1014 91.80300 1 726 1 chr4D.!!$R1 725
17 TraesCS3A01G062100 chr5D 523451723 523452757 1034 True 652.00 652 78.60600 744 1759 1 chr5D.!!$R1 1015

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
699 716 0.182061 TCATTCTGATGCAGAGGCCC 59.818 55.0 0.0 0.0 41.75 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 8753 1.153353 CGCCTATTGTCAACGGTGTT 58.847 50.0 0.0 0.0 0.0 3.32 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
56 57 9.535878 TGGTTTGTCCATAAACAAGTTATTTTC 57.464 29.630 0.00 0.00 41.93 2.29
155 156 3.037549 ACACCTTTTTCTTGATTGCCCA 58.962 40.909 0.00 0.00 0.00 5.36
159 160 6.013466 ACACCTTTTTCTTGATTGCCCATTAT 60.013 34.615 0.00 0.00 0.00 1.28
178 179 3.644966 ATCCAAAGTTCTATGGCGGAA 57.355 42.857 0.00 0.00 36.62 4.30
232 233 5.813157 TGAGTTCTGTCAACACGTTATTTGA 59.187 36.000 0.00 0.00 0.00 2.69
387 389 1.079875 TATTTTCCGAGCCACGACGC 61.080 55.000 0.00 0.00 45.77 5.19
445 447 1.053424 AGGGAGCGTTTGGTTACTGA 58.947 50.000 0.00 0.00 0.00 3.41
558 560 0.616371 TTATGCTAGCCGGTTGTGGT 59.384 50.000 13.29 0.00 0.00 4.16
640 656 8.637281 TTTCGTTTGGAAAATTTAAGACCTTC 57.363 30.769 0.00 0.00 41.55 3.46
682 699 7.501892 TGTTTAATAAGATGGCTGTATGCATCA 59.498 33.333 0.19 0.10 45.15 3.07
699 716 0.182061 TCATTCTGATGCAGAGGCCC 59.818 55.000 0.00 0.00 41.75 5.80
793 819 1.425267 CGGTGCAACAGACACGTCAA 61.425 55.000 0.98 0.00 39.98 3.18
810 836 5.803461 CACGTCAACTAATGTCCTCGAATTA 59.197 40.000 0.00 0.00 0.00 1.40
828 854 4.778213 ATTAACCTTGGCTGAGCTCATA 57.222 40.909 18.63 4.01 0.00 2.15
860 886 3.441572 CACTTCATGGGAAAGCTACAAGG 59.558 47.826 0.00 0.00 31.35 3.61
880 906 3.946558 AGGTGAAGTGAGGAGTATCGTAC 59.053 47.826 0.00 0.00 34.37 3.67
984 1011 5.074746 TGTATCCTATTGCACCTCTCCTA 57.925 43.478 0.00 0.00 0.00 2.94
985 1012 5.655394 TGTATCCTATTGCACCTCTCCTAT 58.345 41.667 0.00 0.00 0.00 2.57
1034 1061 2.035961 CCATCGACGGATACATGGTTCT 59.964 50.000 0.00 0.00 32.49 3.01
1089 1116 1.371467 TTGGGAGGGATTCAAGCTCA 58.629 50.000 0.00 0.00 0.00 4.26
1113 1140 3.204526 GGAGGATGCTGAAGAGTTCATG 58.795 50.000 0.00 0.00 39.30 3.07
1214 4442 0.603975 GGACGAAGGATATGCCCTGC 60.604 60.000 0.00 0.00 36.49 4.85
1722 4994 9.489084 TGTTATCTTATACAGCATAACATCCAC 57.511 33.333 0.00 0.00 36.99 4.02
1861 5146 4.100707 CTGGAAAACATACCAGCACATG 57.899 45.455 0.00 0.00 45.30 3.21
2124 5413 4.460034 AGAGACTCCGAAACCTAGAAGAAC 59.540 45.833 0.00 0.00 0.00 3.01
2189 5478 3.463944 CAACTGGTGGGTATAATCGGTC 58.536 50.000 0.00 0.00 0.00 4.79
2242 8723 2.351924 ATCCAACAACCACCACCGCT 62.352 55.000 0.00 0.00 0.00 5.52
2272 8753 0.880278 GTCTGCACGCAAGACCTTGA 60.880 55.000 13.44 0.00 42.93 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.803778 GCTTTGTCAAATTGTCCTTGGTG 59.196 43.478 0.00 0.00 0.00 4.17
155 156 5.304686 TCCGCCATAGAACTTTGGATAAT 57.695 39.130 13.78 0.00 34.19 1.28
159 160 3.244770 ACTTTCCGCCATAGAACTTTGGA 60.245 43.478 13.78 0.00 34.19 3.53
232 233 2.234414 TCTATCCCGTTAAGCCACGTTT 59.766 45.455 0.00 0.00 38.57 3.60
387 389 0.670546 AGCGACCACAAACGGATCAG 60.671 55.000 0.00 0.00 0.00 2.90
445 447 2.975489 ACCATCTTCCAGCGGATAGATT 59.025 45.455 13.77 5.06 31.93 2.40
558 560 5.475564 GGACAAACTAGCCATAAAAAGGACA 59.524 40.000 0.00 0.00 0.00 4.02
682 699 1.147824 CGGGCCTCTGCATCAGAAT 59.852 57.895 0.84 0.00 40.18 2.40
793 819 6.113411 CCAAGGTTAATTCGAGGACATTAGT 58.887 40.000 0.00 0.00 0.00 2.24
810 836 2.356535 CCTTATGAGCTCAGCCAAGGTT 60.357 50.000 29.44 14.21 32.77 3.50
828 854 0.038744 CCATGAAGTGTGGCCTCCTT 59.961 55.000 3.32 6.27 0.00 3.36
860 886 3.066481 GGGTACGATACTCCTCACTTCAC 59.934 52.174 0.00 0.00 0.00 3.18
880 906 0.970427 CAATTTCTTGTCCCCGGGGG 60.970 60.000 39.51 27.32 46.11 5.40
984 1011 1.452651 CATGGCAAGGTGCGGAGAT 60.453 57.895 0.00 0.00 46.21 2.75
985 1012 2.046023 CATGGCAAGGTGCGGAGA 60.046 61.111 0.00 0.00 46.21 3.71
1089 1116 1.890552 ACTCTTCAGCATCCTCCCAT 58.109 50.000 0.00 0.00 0.00 4.00
1113 1140 5.449725 GCCTTCATCTGTAAATCTTTCAGGC 60.450 44.000 0.00 0.00 0.00 4.85
1214 4442 3.662247 AGGCGATTCCGAGGTTTATAG 57.338 47.619 0.00 0.00 40.77 1.31
1722 4994 7.382218 GTGAGTTTTCATTTTGTATTGTCCCAG 59.618 37.037 0.00 0.00 35.39 4.45
1861 5146 3.614159 TGGTAGATGCGTGTACGATAC 57.386 47.619 8.82 5.10 43.02 2.24
1966 5251 1.378531 TTTGTGCCATCGTAGATGCC 58.621 50.000 4.60 0.00 45.12 4.40
2242 8723 1.368950 GTGCAGACACAGAGAGGCA 59.631 57.895 0.00 0.00 46.61 4.75
2267 8748 3.188460 CCTATTGTCAACGGTGTTCAAGG 59.812 47.826 15.76 10.53 0.00 3.61
2272 8753 1.153353 CGCCTATTGTCAACGGTGTT 58.847 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.