Multiple sequence alignment - TraesCS5B01G455000

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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 TraesCS5B01G455000 chr5B 100.000 2819 0 0 1 2819 629227929 629225111 0 5206
1 TraesCS5B01G455000 chr7D 97.161 2149 52 7 675 2819 474678255 474680398 0 3622
2 TraesCS5B01G455000 chr1B 96.324 2149 67 6 675 2819 530762815 530760675 0 3520
3 TraesCS5B01G455000 chr1B 96.229 2148 67 6 675 2819 95493351 95495487 0 3506
4 TraesCS5B01G455000 chr2A 95.996 2148 75 5 675 2819 628646903 628644764 0 3480
5 TraesCS5B01G455000 chr2A 95.905 2149 75 7 675 2819 374484984 374487123 0 3469
6 TraesCS5B01G455000 chr2A 95.903 2148 76 6 675 2819 628571116 628573254 0 3469
7 TraesCS5B01G455000 chr2A 95.765 2149 73 8 675 2819 161528180 161530314 0 3448
8 TraesCS5B01G455000 chr1A 95.905 2149 76 6 675 2819 409610544 409612684 0 3470
9 TraesCS5B01G455000 chr2B 95.907 2150 72 7 675 2819 424683707 424681569 0 3469
10 TraesCS5B01G455000 chrUn 94.675 676 35 1 1 675 124316160 124316835 0 1048
11 TraesCS5B01G455000 chrUn 94.083 676 39 1 1 675 4668153 4668828 0 1026
12 TraesCS5B01G455000 chr6B 94.667 675 35 1 1 674 404170541 404171215 0 1046
13 TraesCS5B01G455000 chr6B 94.092 677 36 2 1 676 337992295 337991622 0 1026
14 TraesCS5B01G455000 chr7B 94.527 676 33 3 1 675 402654664 402655336 0 1040
15 TraesCS5B01G455000 chr7B 94.222 675 38 1 1 674 22421503 22422177 0 1029
16 TraesCS5B01G455000 chr6D 94.231 676 37 2 1 675 465595765 465595091 0 1031
17 TraesCS5B01G455000 chr4B 94.231 676 35 3 1 675 346782219 346781547 0 1029
18 TraesCS5B01G455000 chr2D 94.469 669 35 2 7 674 610759523 610758856 0 1029


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 TraesCS5B01G455000 chr5B 629225111 629227929 2818 True 5206 5206 100.000 1 2819 1 chr5B.!!$R1 2818
1 TraesCS5B01G455000 chr7D 474678255 474680398 2143 False 3622 3622 97.161 675 2819 1 chr7D.!!$F1 2144
2 TraesCS5B01G455000 chr1B 530760675 530762815 2140 True 3520 3520 96.324 675 2819 1 chr1B.!!$R1 2144
3 TraesCS5B01G455000 chr1B 95493351 95495487 2136 False 3506 3506 96.229 675 2819 1 chr1B.!!$F1 2144
4 TraesCS5B01G455000 chr2A 628644764 628646903 2139 True 3480 3480 95.996 675 2819 1 chr2A.!!$R1 2144
5 TraesCS5B01G455000 chr2A 374484984 374487123 2139 False 3469 3469 95.905 675 2819 1 chr2A.!!$F2 2144
6 TraesCS5B01G455000 chr2A 628571116 628573254 2138 False 3469 3469 95.903 675 2819 1 chr2A.!!$F3 2144
7 TraesCS5B01G455000 chr2A 161528180 161530314 2134 False 3448 3448 95.765 675 2819 1 chr2A.!!$F1 2144
8 TraesCS5B01G455000 chr1A 409610544 409612684 2140 False 3470 3470 95.905 675 2819 1 chr1A.!!$F1 2144
9 TraesCS5B01G455000 chr2B 424681569 424683707 2138 True 3469 3469 95.907 675 2819 1 chr2B.!!$R1 2144
10 TraesCS5B01G455000 chrUn 124316160 124316835 675 False 1048 1048 94.675 1 675 1 chrUn.!!$F2 674
11 TraesCS5B01G455000 chrUn 4668153 4668828 675 False 1026 1026 94.083 1 675 1 chrUn.!!$F1 674
12 TraesCS5B01G455000 chr6B 404170541 404171215 674 False 1046 1046 94.667 1 674 1 chr6B.!!$F1 673
13 TraesCS5B01G455000 chr6B 337991622 337992295 673 True 1026 1026 94.092 1 676 1 chr6B.!!$R1 675
14 TraesCS5B01G455000 chr7B 402654664 402655336 672 False 1040 1040 94.527 1 675 1 chr7B.!!$F2 674
15 TraesCS5B01G455000 chr7B 22421503 22422177 674 False 1029 1029 94.222 1 674 1 chr7B.!!$F1 673
16 TraesCS5B01G455000 chr6D 465595091 465595765 674 True 1031 1031 94.231 1 675 1 chr6D.!!$R1 674
17 TraesCS5B01G455000 chr4B 346781547 346782219 672 True 1029 1029 94.231 1 675 1 chr4B.!!$R1 674
18 TraesCS5B01G455000 chr2D 610758856 610759523 667 True 1029 1029 94.469 7 674 1 chr2D.!!$R1 667

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
247 251 0.669318 GTCCCGATCTGTGCGTCAAA 60.669 55.0 0.00 0.00 0.0 2.69 F
548 553 0.748005 GGATCGCCAAGCTTGCCTTA 60.748 55.0 21.43 6.23 31.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1229 1.541147 TGCAATTCTCCCAAAGCTTCG 59.459 47.619 0.0 0.0 0.0 3.79 R
2516 2537 1.961394 TCTTCCACGCTACAGTCAGTT 59.039 47.619 0.0 0.0 0.0 3.16 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
39 40 1.227205 CTGCCGATCTGCTCCAGAC 60.227 63.158 10.62 0.00 43.63 3.51
79 80 4.404654 GGCAAAGCCGCCGAACAG 62.405 66.667 0.00 0.00 43.52 3.16
155 159 2.165998 GAAGGAGCCATTGAGCTTTGT 58.834 47.619 0.00 0.00 45.15 2.83
247 251 0.669318 GTCCCGATCTGTGCGTCAAA 60.669 55.000 0.00 0.00 0.00 2.69
324 328 3.703052 TCGATGGAGGTAAAACCCTACTC 59.297 47.826 0.00 0.00 39.75 2.59
328 332 3.340664 TGGAGGTAAAACCCTACTCCCTA 59.659 47.826 6.57 0.00 39.75 3.53
408 412 2.434702 GGCTAAACCCTAAGAGCTAGCA 59.565 50.000 18.83 0.00 34.72 3.49
548 553 0.748005 GGATCGCCAAGCTTGCCTTA 60.748 55.000 21.43 6.23 31.00 2.69
616 621 7.268586 AGTCTTGTATCTTCACGCTTCAATAT 58.731 34.615 0.00 0.00 0.00 1.28
941 947 9.104713 AGAAATTCCACCAAAAGAATCCTTATT 57.895 29.630 0.00 0.00 31.54 1.40
1045 1052 1.375523 GGCGTTTCATGGGACGACT 60.376 57.895 20.74 0.00 43.69 4.18
1079 1086 1.906574 TCTAGCGGATCCACCACTTTT 59.093 47.619 13.41 0.00 38.90 2.27
1189 1196 2.736144 TGTAGTCACACCCTAAAGCG 57.264 50.000 0.00 0.00 0.00 4.68
1222 1229 3.891977 AGACAAAAGCCTTCCCTCTTTTC 59.108 43.478 0.00 0.00 39.63 2.29
1445 1452 1.583556 TGGAGGAGCTGGCAAGAATA 58.416 50.000 0.00 0.00 0.00 1.75
1522 1529 5.426509 TGATGAAGATGTTGAGGAGGTGTAT 59.573 40.000 0.00 0.00 0.00 2.29
1593 1600 1.251251 ACTGCACCCTCAAGAAATGC 58.749 50.000 0.00 0.00 36.81 3.56
1643 1652 1.026182 GCGAATGGTGATGTGGCTGA 61.026 55.000 0.00 0.00 0.00 4.26
1753 1762 3.844577 ACTGCATTGATCTGCTGAAAC 57.155 42.857 17.16 0.00 41.92 2.78
1754 1763 3.151554 ACTGCATTGATCTGCTGAAACA 58.848 40.909 17.16 0.00 41.92 2.83
1767 1776 3.635836 TGCTGAAACAAATGGACATCACA 59.364 39.130 0.00 0.00 0.00 3.58
1808 1822 3.368948 GCTTTCCGAGTCTTCAAGATCCT 60.369 47.826 0.00 0.00 0.00 3.24
1978 1995 2.886523 TGCTGCTGCAGTAAAGACATTT 59.113 40.909 28.50 0.00 45.31 2.32
2218 2237 8.697507 ATTATGCCTTGTCCCTAGAAAATAAG 57.302 34.615 0.00 0.00 0.00 1.73
2299 2319 9.619316 CGTATGTTTTTCTCATTGTTTCCATTA 57.381 29.630 0.00 0.00 0.00 1.90
2391 2411 6.529220 GGAGTTCTACATAAGAATGCTCCAT 58.471 40.000 14.74 0.00 46.87 3.41
2745 2766 6.367695 TGTCATTACTACACGAGAATTGTTGG 59.632 38.462 0.00 0.00 0.00 3.77
2787 2808 5.871524 TCTGTTTGCATCTCTGTCAATACTC 59.128 40.000 0.00 0.00 0.00 2.59
2789 2810 6.935167 TGTTTGCATCTCTGTCAATACTCTA 58.065 36.000 0.00 0.00 0.00 2.43
2794 2815 5.300539 GCATCTCTGTCAATACTCTAGTCCA 59.699 44.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.397254 TCTCCCCGGACAGATCTTCC 60.397 60.000 0.73 11.74 0.00 3.46
155 159 2.812591 GAGTTCCTCTGTGTCGTCACTA 59.187 50.000 13.77 1.92 44.14 2.74
247 251 1.630369 TGCTTCCTGTTACCATCAGCT 59.370 47.619 0.00 0.00 0.00 4.24
548 553 1.067295 TGGGACTCTCCTTTGCATGT 58.933 50.000 0.00 0.00 36.57 3.21
582 587 6.642950 CGTGAAGATACAAGACTCAAGACTTT 59.357 38.462 0.00 0.00 0.00 2.66
616 621 2.164219 GGACTATGTACAACGTCCGGAA 59.836 50.000 23.13 0.00 36.88 4.30
941 947 5.647225 GGACTTTCTTCTTCTCGTACCTAGA 59.353 44.000 0.00 0.00 0.00 2.43
962 968 9.647797 TTTTAACTCTTTTTCCTTTTCTTGGAC 57.352 29.630 0.00 0.00 32.65 4.02
1045 1052 1.742761 GCTAGAATCTTGCACTGCCA 58.257 50.000 11.58 0.00 32.87 4.92
1189 1196 3.384789 AGGCTTTTGTCTTGAACTTTCCC 59.615 43.478 0.00 0.00 0.00 3.97
1222 1229 1.541147 TGCAATTCTCCCAAAGCTTCG 59.459 47.619 0.00 0.00 0.00 3.79
1593 1600 6.204495 CCTTCTCTTTGGTTCTTTCTCTTCTG 59.796 42.308 0.00 0.00 0.00 3.02
1643 1652 9.753674 TTATTTCCAAGTACTTCTCCATCATTT 57.246 29.630 4.77 0.00 0.00 2.32
1753 1762 4.074259 TCTTCAGGTGTGATGTCCATTTG 58.926 43.478 0.00 0.00 30.85 2.32
1754 1763 4.371624 TCTTCAGGTGTGATGTCCATTT 57.628 40.909 0.00 0.00 30.85 2.32
1767 1776 2.708325 AGCCTTGACTTCTTCTTCAGGT 59.292 45.455 0.00 0.00 0.00 4.00
1808 1822 6.071672 ACTCATGAAAATCTCTCAGTTCTCGA 60.072 38.462 0.00 0.00 0.00 4.04
1921 1935 5.278061 TGGACTAAATGGCTAGTAAGGAGT 58.722 41.667 0.00 0.00 32.14 3.85
1928 1942 5.179452 ACAACATGGACTAAATGGCTAGT 57.821 39.130 0.00 0.00 34.76 2.57
1978 1995 7.288810 ACAACTATCCATTTCAGCAGAAAAA 57.711 32.000 8.45 0.00 46.06 1.94
2097 2114 4.219725 TCAACCTGTGTCGATACATCAAGA 59.780 41.667 15.75 9.07 38.08 3.02
2188 2207 3.951563 AGGGACAAGGCATAATAGCAA 57.048 42.857 0.00 0.00 35.83 3.91
2195 2214 7.446106 TCTTATTTTCTAGGGACAAGGCATA 57.554 36.000 0.00 0.00 0.00 3.14
2218 2237 9.784531 TCTGATCTATGTTAAAATCATCCCTTC 57.215 33.333 0.00 0.00 0.00 3.46
2299 2319 7.539034 AATACTTGCCAGTTTTATTTCCAGT 57.461 32.000 0.00 0.00 34.06 4.00
2315 2335 9.899226 AAATTAGTTTGAGAGTGAAATACTTGC 57.101 29.630 0.00 0.00 40.53 4.01
2516 2537 1.961394 TCTTCCACGCTACAGTCAGTT 59.039 47.619 0.00 0.00 0.00 3.16
2745 2766 8.979574 GCAAACAGAAGTGGTACATATAGATAC 58.020 37.037 0.00 0.00 44.52 2.24
2787 2808 0.179100 CGCTGGACCACATGGACTAG 60.179 60.000 4.53 7.15 40.29 2.57
2789 2810 2.665000 CGCTGGACCACATGGACT 59.335 61.111 4.53 0.00 38.94 3.85


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

AutoCloner maintained by Alex Coulton.