Multiple sequence alignment - TraesCS1B01G163300

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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 TraesCS1B01G163300 chr1B 100.000 2828 0 0 1 2828 284054962 284052135 0 5223
1 TraesCS1B01G163300 chr1B 94.558 2830 151 3 1 2828 291466722 291463894 0 4370
2 TraesCS1B01G163300 chr1B 94.493 2833 148 7 1 2828 81030683 81033512 0 4361
3 TraesCS1B01G163300 chr6B 95.131 2834 130 7 1 2828 505750211 505747380 0 4462
4 TraesCS1B01G163300 chr6B 95.094 2833 130 7 1 2828 416260008 416262836 0 4453
5 TraesCS1B01G163300 chr6B 94.415 2829 151 2 1 2828 311693326 311696148 0 4342
6 TraesCS1B01G163300 chr6B 94.346 2830 152 3 1 2828 370079323 370082146 0 4333
7 TraesCS1B01G163300 chr6B 94.307 2828 151 5 3 2828 258238153 258240972 0 4322
8 TraesCS1B01G163300 chr3B 94.356 2835 152 7 1 2828 412041189 412044022 0 4342
9 TraesCS1B01G163300 chr7B 94.207 2831 157 7 1 2828 207619470 207616644 0 4313


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 TraesCS1B01G163300 chr1B 284052135 284054962 2827 True 5223 5223 100.000 1 2828 1 chr1B.!!$R1 2827
1 TraesCS1B01G163300 chr1B 291463894 291466722 2828 True 4370 4370 94.558 1 2828 1 chr1B.!!$R2 2827
2 TraesCS1B01G163300 chr1B 81030683 81033512 2829 False 4361 4361 94.493 1 2828 1 chr1B.!!$F1 2827
3 TraesCS1B01G163300 chr6B 505747380 505750211 2831 True 4462 4462 95.131 1 2828 1 chr6B.!!$R1 2827
4 TraesCS1B01G163300 chr6B 416260008 416262836 2828 False 4453 4453 95.094 1 2828 1 chr6B.!!$F4 2827
5 TraesCS1B01G163300 chr6B 311693326 311696148 2822 False 4342 4342 94.415 1 2828 1 chr6B.!!$F2 2827
6 TraesCS1B01G163300 chr6B 370079323 370082146 2823 False 4333 4333 94.346 1 2828 1 chr6B.!!$F3 2827
7 TraesCS1B01G163300 chr6B 258238153 258240972 2819 False 4322 4322 94.307 3 2828 1 chr6B.!!$F1 2825
8 TraesCS1B01G163300 chr3B 412041189 412044022 2833 False 4342 4342 94.356 1 2828 1 chr3B.!!$F1 2827
9 TraesCS1B01G163300 chr7B 207616644 207619470 2826 True 4313 4313 94.207 1 2828 1 chr7B.!!$R1 2827

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
586 587 0.855349 CTGTTATGAGCGCGGTGATC 59.145 55.0 18.92 1.89 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2208 0.248907 GACGTATGCCGCTTAGAGCA 60.249 55.0 0.0 0.09 42.58 4.26 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
505 506 2.513259 GGTGACCTCCGTCCAACCA 61.513 63.158 0.00 0.00 38.32 3.67
512 513 4.003788 CCGTCCAACCAGAGGCGT 62.004 66.667 0.00 0.00 0.00 5.68
516 517 4.760047 CCAACCAGAGGCGTCGGG 62.760 72.222 21.78 21.78 43.36 5.14
577 578 1.021390 AGCACCGCACTGTTATGAGC 61.021 55.000 0.00 0.00 0.00 4.26
586 587 0.855349 CTGTTATGAGCGCGGTGATC 59.145 55.000 18.92 1.89 0.00 2.92
799 802 3.668141 TGTCAATATGGGAATGCAGGT 57.332 42.857 0.00 0.00 0.00 4.00
1001 1009 0.478507 GTGGGTATTGCAGGGGCTAT 59.521 55.000 0.00 0.00 41.91 2.97
1014 1022 1.220749 GGCTATGAACGAGGTGGCA 59.779 57.895 0.00 0.00 0.00 4.92
1029 1037 1.228552 GGCAACCCTGAAGGAAGCA 60.229 57.895 0.00 0.00 39.62 3.91
1206 1216 1.881498 GCTCTTGAGAGTGCCAAAGCT 60.881 52.381 9.58 0.00 43.85 3.74
1235 1246 0.831711 GAAGCCCAAAAAGCCCTCCA 60.832 55.000 0.00 0.00 0.00 3.86
1238 1249 0.831711 GCCCAAAAAGCCCTCCAGAA 60.832 55.000 0.00 0.00 0.00 3.02
1304 1315 0.848305 CAAAGCAAGCACGTGAAAGC 59.152 50.000 22.23 18.28 0.00 3.51
1359 1370 4.075682 CTCCAGGAGTATTCGCAGATCTA 58.924 47.826 8.54 0.00 35.04 1.98
1379 1390 2.261361 CCGCAGTGTGTCCGATGA 59.739 61.111 2.46 0.00 0.00 2.92
1392 1403 1.276138 TCCGATGATGCCGCATTCTAT 59.724 47.619 7.43 3.06 0.00 1.98
1653 1665 3.346631 CTGCATTGAAGGTGCCCGC 62.347 63.158 0.00 0.00 41.83 6.13
1753 1765 3.825833 GAGTATCGCACGCCCGAGG 62.826 68.421 4.37 0.00 40.97 4.63
1784 1796 2.449518 TGTCCTGAAGGGTGCCCA 60.450 61.111 10.26 0.00 38.92 5.36
2039 2053 1.758514 TCCTTCTAGGGAGGCGCTG 60.759 63.158 7.64 0.00 35.59 5.18
2067 2081 1.289800 GAACGAGGCAACCGGACTTC 61.290 60.000 9.46 1.84 31.94 3.01
2192 2208 2.034221 GGACAAAGCCGGCTCCTT 59.966 61.111 32.93 19.55 0.00 3.36
2208 2224 1.202533 TCCTTGCTCTAAGCGGCATAC 60.203 52.381 1.45 0.00 46.26 2.39
2425 2441 3.694043 TTGACCCAAGACATGATTCGA 57.306 42.857 0.00 0.00 0.00 3.71
2562 2578 4.033472 CGTACGGATGCAACATGTCATAAA 59.967 41.667 7.57 0.00 0.00 1.40
2682 2699 3.329300 CGATAAGCAAGGGATGGGG 57.671 57.895 0.00 0.00 0.00 4.96
2757 2775 6.211584 ACAGGTATAATGCTCGTAATGGAGAT 59.788 38.462 0.00 0.00 36.08 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
505 506 0.743345 GCAAATTACCCGACGCCTCT 60.743 55.000 0.00 0.00 0.00 3.69
512 513 0.393808 GCCTCCAGCAAATTACCCGA 60.394 55.000 0.00 0.00 42.97 5.14
516 517 0.378610 GAGCGCCTCCAGCAAATTAC 59.621 55.000 2.29 0.00 44.04 1.89
577 578 0.721718 GAACTTTCTGGATCACCGCG 59.278 55.000 0.00 0.00 39.42 6.46
586 587 0.250295 TGGCGGACTGAACTTTCTGG 60.250 55.000 1.54 0.00 0.00 3.86
673 675 7.148120 GGGCTACTGTCTATGCGATACTATTTA 60.148 40.741 0.00 0.00 0.00 1.40
682 684 0.106167 AGGGGCTACTGTCTATGCGA 60.106 55.000 0.00 0.00 0.00 5.10
799 802 2.357881 CAGAGGTCAGCAGCGCAA 60.358 61.111 11.47 0.00 0.00 4.85
1001 1009 2.112297 GGGTTGCCACCTCGTTCA 59.888 61.111 6.95 0.00 43.65 3.18
1014 1022 0.846693 ACACTGCTTCCTTCAGGGTT 59.153 50.000 0.00 0.00 45.14 4.11
1029 1037 4.052229 CGTTCGGCCTCGGACACT 62.052 66.667 0.00 0.00 44.78 3.55
1235 1246 6.227298 TCTTCTTTATCGCCTCAATCTTCT 57.773 37.500 0.00 0.00 0.00 2.85
1238 1249 7.151308 CACTATCTTCTTTATCGCCTCAATCT 58.849 38.462 0.00 0.00 0.00 2.40
1304 1315 6.949578 TTCGGGTAAGTAACAAGTAATTCG 57.050 37.500 0.00 0.00 0.00 3.34
1346 1357 0.601558 GCGGGGTAGATCTGCGAATA 59.398 55.000 5.18 0.00 0.00 1.75
1379 1390 1.672356 GCCCGATAGAATGCGGCAT 60.672 57.895 10.23 10.23 45.93 4.40
1753 1765 5.163437 CCTTCAGGACACCCTTATAGTACAC 60.163 48.000 0.00 0.00 42.02 2.90
1787 1799 0.737715 GGAGCATTCGCCCGCTATAG 60.738 60.000 0.00 0.00 38.99 1.31
2039 2053 0.653636 TTGCCTCGTTCGTTGTGTTC 59.346 50.000 0.00 0.00 0.00 3.18
2067 2081 3.679389 AGTGGGAGTGTTCAAGCATTAG 58.321 45.455 0.00 0.00 0.00 1.73
2192 2208 0.248907 GACGTATGCCGCTTAGAGCA 60.249 55.000 0.00 0.09 42.58 4.26
2366 2382 4.278310 GCTCCCATGTTTTGGTACCTTAT 58.722 43.478 14.36 0.00 44.83 1.73
2682 2699 3.117663 TGGAGGGGGACATGTTAAATAGC 60.118 47.826 0.00 0.00 0.00 2.97
2757 2775 2.558378 CTACGTCGAGTATCCAGGTGA 58.442 52.381 0.00 0.00 34.34 4.02


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

AutoCloner maintained by Alex Coulton.