Multiple sequence alignment - TraesCS5A01G343300

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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 TraesCS5A01G343300 chr5A 100.000 2354 0 0 1 2354 548232435 548234788 0.000000e+00 4348
1 TraesCS5A01G343300 chr5A 84.354 1828 196 41 584 2354 549161730 549159936 0.000000e+00 1709
2 TraesCS5A01G343300 chr5A 84.298 1815 211 47 584 2354 549158798 549157014 0.000000e+00 1705
3 TraesCS5A01G343300 chr5A 84.587 1077 105 25 1299 2354 549163997 549162961 0.000000e+00 1013
4 TraesCS5A01G343300 chr5A 82.254 834 99 22 1551 2354 547636296 547637110 0.000000e+00 675
5 TraesCS5A01G343300 chr5A 81.941 814 98 27 1569 2354 547643283 547644075 0.000000e+00 643
6 TraesCS5A01G343300 chr5A 89.216 306 21 6 24 323 549165269 549164970 2.860000e-99 372
7 TraesCS5A01G343300 chr5A 81.179 441 56 16 428 843 549164912 549164474 1.740000e-86 329
8 TraesCS5A01G343300 chr5D 93.713 2370 115 10 1 2354 434395365 434397716 0.000000e+00 3520
9 TraesCS5A01G343300 chr5D 92.517 1724 95 16 657 2354 434327764 434326049 0.000000e+00 2438
10 TraesCS5A01G343300 chr5D 82.734 1836 222 40 584 2354 435249940 435248135 0.000000e+00 1546
11 TraesCS5A01G343300 chr5D 83.301 1545 191 39 861 2354 433018103 433019631 0.000000e+00 1362
12 TraesCS5A01G343300 chr5D 82.895 1064 138 31 580 1627 435252899 435251864 0.000000e+00 917
13 TraesCS5A01G343300 chr5D 90.111 718 50 5 1658 2354 435251867 435251150 0.000000e+00 913
14 TraesCS5A01G343300 chr5D 91.452 620 25 9 1 596 434328369 434327754 0.000000e+00 826
15 TraesCS5A01G343300 chr5D 82.290 655 88 14 1112 1742 434399344 434399994 2.060000e-150 542
16 TraesCS5A01G343300 chr5D 84.742 485 51 10 100 578 435253401 435252934 4.580000e-127 464
17 TraesCS5A01G343300 chr5D 81.685 546 66 14 39 574 435250506 435249985 7.780000e-115 424
18 TraesCS5A01G343300 chr5D 85.172 290 34 3 98 387 433017779 433018059 2.960000e-74 289
19 TraesCS5A01G343300 chr5B 95.175 1368 40 3 1 1368 527051414 527052755 0.000000e+00 2137
20 TraesCS5A01G343300 chr5B 86.976 1789 176 34 616 2354 528546119 528544338 0.000000e+00 1960
21 TraesCS5A01G343300 chr5B 95.572 926 33 2 1430 2354 527052759 527053677 0.000000e+00 1476
22 TraesCS5A01G343300 chr5B 81.398 1559 191 68 861 2354 526584291 526585815 0.000000e+00 1181
23 TraesCS5A01G343300 chr5B 87.879 726 69 10 763 1486 528543003 528542295 0.000000e+00 835
24 TraesCS5A01G343300 chr5B 85.549 519 56 13 13 519 528546982 528546471 2.070000e-145 525
25 TraesCS5A01G343300 chr5B 86.972 284 24 2 41 320 528543677 528543403 8.170000e-80 307
26 TraesCS5A01G343300 chr5B 83.162 291 39 4 98 387 526583966 526584247 8.350000e-65 257


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 TraesCS5A01G343300 chr5A 548232435 548234788 2353 False 4348.00 4348 100.0000 1 2354 1 chr5A.!!$F3 2353
1 TraesCS5A01G343300 chr5A 549157014 549165269 8255 True 1025.60 1709 84.7268 24 2354 5 chr5A.!!$R1 2330
2 TraesCS5A01G343300 chr5A 547636296 547637110 814 False 675.00 675 82.2540 1551 2354 1 chr5A.!!$F1 803
3 TraesCS5A01G343300 chr5A 547643283 547644075 792 False 643.00 643 81.9410 1569 2354 1 chr5A.!!$F2 785
4 TraesCS5A01G343300 chr5D 434395365 434399994 4629 False 2031.00 3520 88.0015 1 2354 2 chr5D.!!$F2 2353
5 TraesCS5A01G343300 chr5D 434326049 434328369 2320 True 1632.00 2438 91.9845 1 2354 2 chr5D.!!$R1 2353
6 TraesCS5A01G343300 chr5D 435248135 435253401 5266 True 852.80 1546 84.4334 39 2354 5 chr5D.!!$R2 2315
7 TraesCS5A01G343300 chr5D 433017779 433019631 1852 False 825.50 1362 84.2365 98 2354 2 chr5D.!!$F1 2256
8 TraesCS5A01G343300 chr5B 527051414 527053677 2263 False 1806.50 2137 95.3735 1 2354 2 chr5B.!!$F2 2353
9 TraesCS5A01G343300 chr5B 528542295 528546982 4687 True 906.75 1960 86.8440 13 2354 4 chr5B.!!$R1 2341
10 TraesCS5A01G343300 chr5B 526583966 526585815 1849 False 719.00 1181 82.2800 98 2354 2 chr5B.!!$F1 2256

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
328 388 0.250295 TTGAGAGTTTCCAGGCCACG 60.25 55.0 5.01 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 5155 0.749818 TGTGCAGGCGAGTTTTCCAA 60.75 50.0 0.0 0.0 0.0 3.53 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
328 388 0.250295 TTGAGAGTTTCCAGGCCACG 60.250 55.000 5.01 0.00 0.00 4.94
332 392 0.392461 GAGTTTCCAGGCCACGCATA 60.392 55.000 5.01 0.00 0.00 3.14
333 393 0.255890 AGTTTCCAGGCCACGCATAT 59.744 50.000 5.01 0.00 0.00 1.78
440 523 6.840780 ATGCAAGGCTTATTTGTTAGTCTT 57.159 33.333 0.00 0.00 36.80 3.01
497 587 6.618287 TTACTTTGACTTCCATGACACAAG 57.382 37.500 0.00 0.00 0.00 3.16
653 1028 2.568956 TCCCATCTCCAGCTGCATATAC 59.431 50.000 8.66 0.00 0.00 1.47
672 1047 1.139058 ACTCTATCATGGGTTGTCGGC 59.861 52.381 0.00 0.00 0.00 5.54
677 1052 0.327924 TCATGGGTTGTCGGCTGAAT 59.672 50.000 0.00 0.00 0.00 2.57
1039 1438 1.039068 CTCCATCTCTGAGGACGCAT 58.961 55.000 4.59 0.00 0.00 4.73
1148 1547 1.761784 CTCCTCTTGGGACATCCTCAG 59.238 57.143 0.00 0.00 39.58 3.35
1200 1599 0.535102 CAAGTGGCACCTCGAACCTT 60.535 55.000 15.27 0.00 0.00 3.50
1642 5155 1.302033 CACTTCCTGGAGCTTGCGT 60.302 57.895 0.00 0.00 0.00 5.24
1647 5160 1.600636 CCTGGAGCTTGCGTTGGAA 60.601 57.895 0.00 0.00 0.00 3.53
1649 5162 0.667993 CTGGAGCTTGCGTTGGAAAA 59.332 50.000 0.00 0.00 0.00 2.29
1830 5390 1.077663 ACTCATGGCATTGTCCCCTTT 59.922 47.619 0.00 0.00 0.00 3.11
1835 5395 1.203288 TGGCATTGTCCCCTTTCCAAT 60.203 47.619 0.00 0.00 0.00 3.16
1847 5407 2.163815 CCTTTCCAATGCTCTTGCTGAG 59.836 50.000 3.46 3.46 45.33 3.35
2043 5621 2.291153 ACTCAACCATGACCCATCCAAG 60.291 50.000 0.00 0.00 0.00 3.61
2197 8843 0.036483 ACTGCATGATGTACACCGCA 60.036 50.000 0.00 3.92 37.74 5.69
2252 8898 1.091771 CGGGACTACGGTCTTCGCTA 61.092 60.000 0.00 0.00 43.89 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
328 388 8.481314 TCACTGGATAGATTCAAGGATATATGC 58.519 37.037 0.00 0.00 28.44 3.14
332 392 8.373981 CAAGTCACTGGATAGATTCAAGGATAT 58.626 37.037 0.00 0.00 28.44 1.63
333 393 7.345653 ACAAGTCACTGGATAGATTCAAGGATA 59.654 37.037 0.00 0.00 28.44 2.59
440 523 5.450818 AGGCCAGGTTCATTGTCTAATAA 57.549 39.130 5.01 0.00 0.00 1.40
497 587 5.796437 GGCAAAACAAAATTTCATGCTATGC 59.204 36.000 11.06 8.57 33.09 3.14
653 1028 1.414181 AGCCGACAACCCATGATAGAG 59.586 52.381 0.00 0.00 0.00 2.43
761 1151 6.344572 TCCAAAGACAAATATTCGATCACG 57.655 37.500 0.00 0.00 41.26 4.35
776 1166 8.673711 TGTATGCATATACTTTGTTCCAAAGAC 58.326 33.333 20.26 7.70 39.90 3.01
1039 1438 2.156917 CATGTGCTTGCTCAGGAGAAA 58.843 47.619 0.00 0.00 0.00 2.52
1200 1599 1.171549 TGTACACTACCGACGGTGCA 61.172 55.000 29.55 9.71 36.19 4.57
1412 4868 2.079925 CCAGCCTTGAACTAGCAGAAC 58.920 52.381 0.00 0.00 0.00 3.01
1642 5155 0.749818 TGTGCAGGCGAGTTTTCCAA 60.750 50.000 0.00 0.00 0.00 3.53
1647 5160 2.980233 GGCTGTGCAGGCGAGTTT 60.980 61.111 9.93 0.00 44.15 2.66
1830 5390 2.398252 CTCTCAGCAAGAGCATTGGA 57.602 50.000 3.50 0.00 44.95 3.53
1847 5407 1.616865 TGTGTGGGTAGTGTGTAGCTC 59.383 52.381 0.00 0.00 0.00 4.09
2197 8843 2.524887 TCCAACCGGGTTCCGTCT 60.525 61.111 10.04 0.00 46.80 4.18
2212 8858 2.043248 TACGCCAGAGGGACCTCC 60.043 66.667 14.55 0.00 43.70 4.30
2252 8898 2.109774 CTCAGACATCCTCAGGAGCTT 58.890 52.381 0.00 0.00 34.05 3.74


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

AutoCloner maintained by Alex Coulton.