Multiple sequence alignment - TraesCS7B01G175900

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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 TraesCS7B01G175900 chr7B 100.000 2411 0 0 1 2411 247459879 247462289 0 4453
1 TraesCS7B01G175900 chr7B 96.275 2416 85 2 1 2411 743004893 743007308 0 3958
2 TraesCS7B01G175900 chrUn 96.853 2415 72 2 1 2411 221549587 221547173 0 4036
3 TraesCS7B01G175900 chrUn 96.605 2415 78 2 1 2411 186192585 186190171 0 4002
4 TraesCS7B01G175900 chr7A 95.939 2413 88 3 1 2411 120879287 120881691 0 3904
5 TraesCS7B01G175900 chr3A 95.618 2419 95 7 1 2411 51914989 51917404 0 3869
6 TraesCS7B01G175900 chr6A 95.362 2415 105 7 1 2411 79142508 79144919 0 3832
7 TraesCS7B01G175900 chr6D 96.678 2288 70 3 1 2283 458963780 458966066 0 3799
8 TraesCS7B01G175900 chr1B 94.242 2414 131 7 1 2411 499826020 499828428 0 3681
9 TraesCS7B01G175900 chr2B 92.467 2416 170 8 1 2411 343521092 343523500 0 3443
10 TraesCS7B01G175900 chr2B 90.757 1439 113 16 1 1423 357246209 357244775 0 1903


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 TraesCS7B01G175900 chr7B 247459879 247462289 2410 False 4453 4453 100.000 1 2411 1 chr7B.!!$F1 2410
1 TraesCS7B01G175900 chr7B 743004893 743007308 2415 False 3958 3958 96.275 1 2411 1 chr7B.!!$F2 2410
2 TraesCS7B01G175900 chrUn 221547173 221549587 2414 True 4036 4036 96.853 1 2411 1 chrUn.!!$R2 2410
3 TraesCS7B01G175900 chrUn 186190171 186192585 2414 True 4002 4002 96.605 1 2411 1 chrUn.!!$R1 2410
4 TraesCS7B01G175900 chr7A 120879287 120881691 2404 False 3904 3904 95.939 1 2411 1 chr7A.!!$F1 2410
5 TraesCS7B01G175900 chr3A 51914989 51917404 2415 False 3869 3869 95.618 1 2411 1 chr3A.!!$F1 2410
6 TraesCS7B01G175900 chr6A 79142508 79144919 2411 False 3832 3832 95.362 1 2411 1 chr6A.!!$F1 2410
7 TraesCS7B01G175900 chr6D 458963780 458966066 2286 False 3799 3799 96.678 1 2283 1 chr6D.!!$F1 2282
8 TraesCS7B01G175900 chr1B 499826020 499828428 2408 False 3681 3681 94.242 1 2411 1 chr1B.!!$F1 2410
9 TraesCS7B01G175900 chr2B 343521092 343523500 2408 False 3443 3443 92.467 1 2411 1 chr2B.!!$F1 2410
10 TraesCS7B01G175900 chr2B 357244775 357246209 1434 True 1903 1903 90.757 1 1423 1 chr2B.!!$R1 1422

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
603 604 0.972983 CTTCTCTTCCAGCCCCTCGA 60.973 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1669 1.278127 CGGGTCGGGCTAATTCCATAT 59.722 52.381 0.0 0.0 0.0 1.78 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
77 78 2.953453 AGGGGTGGTTTTCTGTTTACC 58.047 47.619 0.00 0.00 0.00 2.85
152 153 7.646922 GTCTGAAGTTTCATGATGAATATTGGC 59.353 37.037 8.90 0.00 36.11 4.52
246 247 2.677836 TGAGGTAGATTCGCATTGTTGC 59.322 45.455 0.00 0.00 45.78 4.17
270 271 4.279420 AGAAAGCGAAGAAAAAGGATGCTT 59.721 37.500 0.00 0.00 42.46 3.91
351 352 4.680440 ATTTCTTTTGGAAAGCAAGTGCGT 60.680 37.500 0.00 0.00 45.61 5.24
455 456 8.829746 AGCATCCAGAAATATCATAGAATGGTA 58.170 33.333 0.00 0.00 0.00 3.25
574 575 4.557205 GTTCTTCTCTTCCAGCGTTTAGA 58.443 43.478 0.00 0.00 0.00 2.10
603 604 0.972983 CTTCTCTTCCAGCCCCTCGA 60.973 60.000 0.00 0.00 0.00 4.04
623 624 4.287585 TCGACCCCTCTTTGATAAGGAAAA 59.712 41.667 0.00 0.00 34.35 2.29
846 869 7.070074 TCCTTCATTATTACTCTTCCTCCAGAC 59.930 40.741 0.00 0.00 0.00 3.51
904 927 5.070580 GGGCTAAACTTCTATCTGAGCCTTA 59.929 44.000 9.67 0.00 45.89 2.69
1025 1048 5.011635 TGGAAGAACAACTGTCTAGTATGCA 59.988 40.000 0.00 0.00 35.69 3.96
1145 1168 1.670811 GGACCATATTCACGCAACTGG 59.329 52.381 0.00 0.00 0.00 4.00
1154 1177 2.571212 TCACGCAACTGGTTCTTTCAT 58.429 42.857 0.00 0.00 0.00 2.57
1180 1203 5.344743 TCTCCAAGCGTCTTATCAAGATT 57.655 39.130 0.00 0.00 40.18 2.40
1183 1206 5.245531 TCCAAGCGTCTTATCAAGATTTGT 58.754 37.500 0.00 0.00 40.18 2.83
1222 1245 8.083828 AGGATCTGTTTTCTTTAGAGATGCTA 57.916 34.615 0.00 0.00 39.30 3.49
1293 1316 3.812167 GCTTGGAAGTGGAACAGAGGATT 60.812 47.826 0.00 0.00 41.80 3.01
1322 1345 1.995542 AGAAATCCCCAAGAGCAAGGA 59.004 47.619 0.00 0.00 0.00 3.36
1347 1370 0.528017 TCGAAAGAGCTGAGCACGAT 59.472 50.000 7.39 0.00 34.84 3.73
1360 1383 0.654683 GCACGATCATGCTCTTGACC 59.345 55.000 6.50 0.00 42.62 4.02
1370 1393 5.376625 TCATGCTCTTGACCTGTTTAAGTT 58.623 37.500 0.00 0.00 0.00 2.66
1371 1394 6.530120 TCATGCTCTTGACCTGTTTAAGTTA 58.470 36.000 0.00 0.00 0.00 2.24
1564 1593 2.753452 TGGCTCTTCTCTACTAACCACG 59.247 50.000 0.00 0.00 0.00 4.94
1594 1623 6.874278 TTGGGACTCTCTATTTCATCTTCA 57.126 37.500 0.00 0.00 0.00 3.02
1640 1669 3.195610 ACATGCTTCTCCGTACTGATTCA 59.804 43.478 0.00 0.00 0.00 2.57
1888 1918 6.071051 GCTCCTATTAAGCTCAGCCTTAGTAT 60.071 42.308 0.00 0.00 36.80 2.12
1923 1953 2.567169 CACTTGGTGGACAGTCTATCCA 59.433 50.000 0.00 0.00 44.20 3.41
2142 2172 1.855295 TATCACTTCCGGTACTGGCA 58.145 50.000 16.58 4.05 0.00 4.92
2166 2196 7.632680 GCAGGGGCAATTACAATGTTATTAACT 60.633 37.037 7.99 0.00 40.72 2.24
2257 2287 2.178912 TTGGTTCTTCGGTCATCCAC 57.821 50.000 0.00 0.00 0.00 4.02
2259 2289 1.628340 TGGTTCTTCGGTCATCCACAT 59.372 47.619 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 6.742718 CCTCACGTAAGCAATAAAATGTGAAG 59.257 38.462 0.00 0.00 45.62 3.02
246 247 3.916776 GCATCCTTTTTCTTCGCTTTCTG 59.083 43.478 0.00 0.00 0.00 3.02
270 271 2.872408 GCCACAAGCAAGCCATAGA 58.128 52.632 0.00 0.00 42.97 1.98
351 352 9.185680 TGCTATTACTAACACTTATGACTGAGA 57.814 33.333 0.00 0.00 0.00 3.27
455 456 1.137086 CCCGTGAAGGTGATCTCGATT 59.863 52.381 0.00 0.00 38.27 3.34
574 575 4.764308 GGCTGGAAGAGAAGAACTTGAATT 59.236 41.667 0.00 0.00 34.07 2.17
603 604 7.512402 TGAAAATTTTCCTTATCAAAGAGGGGT 59.488 33.333 24.51 0.00 36.36 4.95
782 789 7.479352 TTGCAAATTGGGAGAAGAATAATCA 57.521 32.000 0.00 0.00 0.00 2.57
846 869 1.493871 AGAGCTTGGGGATCCTGAATG 59.506 52.381 12.58 1.48 0.00 2.67
904 927 0.467384 CATCCAGGATCCTGCTCGTT 59.533 55.000 32.97 13.99 42.35 3.85
978 1001 1.205893 AGGAAGAGCTTAAGCCGTCTG 59.794 52.381 23.71 0.00 43.38 3.51
1009 1032 6.369890 ACATCTTGTTGCATACTAGACAGTTG 59.630 38.462 12.49 10.34 40.57 3.16
1011 1034 6.042638 ACATCTTGTTGCATACTAGACAGT 57.957 37.500 12.49 11.59 40.57 3.55
1025 1048 7.149973 CACAAATTCCTGAATGACATCTTGTT 58.850 34.615 3.74 0.00 27.89 2.83
1145 1168 4.222114 CGCTTGGAGAACAATGAAAGAAC 58.778 43.478 0.00 0.00 38.65 3.01
1154 1177 4.265904 TGATAAGACGCTTGGAGAACAA 57.734 40.909 2.86 0.00 37.55 2.83
1180 1203 1.203428 TCCTCCCTCATTCTCCCACAA 60.203 52.381 0.00 0.00 0.00 3.33
1183 1206 1.582624 AGATCCTCCCTCATTCTCCCA 59.417 52.381 0.00 0.00 0.00 4.37
1273 1296 3.557054 CGAATCCTCTGTTCCACTTCCAA 60.557 47.826 0.00 0.00 0.00 3.53
1322 1345 2.036475 TGCTCAGCTCTTTCGAGACTTT 59.964 45.455 0.00 0.00 39.74 2.66
1347 1370 4.973168 ACTTAAACAGGTCAAGAGCATGA 58.027 39.130 0.00 0.00 0.00 3.07
1360 1383 9.810545 CCTTCTAAGATCCTCTAACTTAAACAG 57.189 37.037 0.00 0.00 0.00 3.16
1370 1393 9.953429 TTTCTAATTCCCTTCTAAGATCCTCTA 57.047 33.333 0.00 0.00 0.00 2.43
1371 1394 8.862091 TTTCTAATTCCCTTCTAAGATCCTCT 57.138 34.615 0.00 0.00 0.00 3.69
1414 1442 9.224267 CTGGAAGAGAAAAGAATCAGAATTACA 57.776 33.333 0.00 0.00 34.07 2.41
1458 1486 3.435275 GGGGCTGGAAGAGAAAAGAAAT 58.565 45.455 0.00 0.00 34.07 2.17
1564 1593 7.546250 TGAAATAGAGAGTCCCAATATCCTC 57.454 40.000 0.00 0.00 0.00 3.71
1640 1669 1.278127 CGGGTCGGGCTAATTCCATAT 59.722 52.381 0.00 0.00 0.00 1.78
1747 1777 3.494924 CCAAATCCACCTATCATCGCTGA 60.495 47.826 0.00 0.00 35.41 4.26
1855 1885 4.100189 TGAGCTTAATAGGAGCAAGAGACC 59.900 45.833 0.00 0.00 42.56 3.85
1888 1918 1.752198 AAGTGTCGCTGCCCACTTA 59.248 52.632 23.06 0.00 46.97 2.24
1923 1953 3.201487 GGCTGGTAATACCACTTAAGGGT 59.799 47.826 8.27 16.71 44.79 4.34
2142 2172 7.617723 TCAGTTAATAACATTGTAATTGCCCCT 59.382 33.333 5.89 0.00 0.00 4.79
2210 2240 7.017551 AGAGATGCTGGTATAATATTGGGTCAA 59.982 37.037 0.00 0.00 0.00 3.18
2211 2241 6.501805 AGAGATGCTGGTATAATATTGGGTCA 59.498 38.462 0.00 0.00 0.00 4.02
2257 2287 6.148976 CCAGGCAGAATGAGAATATACACATG 59.851 42.308 0.00 0.00 39.69 3.21
2259 2289 5.366477 TCCAGGCAGAATGAGAATATACACA 59.634 40.000 0.00 0.00 39.69 3.72
2309 2339 5.432885 GACCGATTTTCTTGAAAAGGTCA 57.567 39.130 25.67 5.21 46.79 4.02
2326 2356 1.816961 GCCTAGATACCCGAAGACCGA 60.817 57.143 0.00 0.00 41.76 4.69


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

AutoCloner maintained by Alex Coulton.