Multiple sequence alignment - TraesCS4B01G155700

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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 TraesCS4B01G155700 chr4B 100.000 3497 0 0 1 3497 279977881 279981377 0.000000e+00 6458
1 TraesCS4B01G155700 chr4B 94.393 3531 152 24 1 3497 335221381 335224899 0.000000e+00 5382
2 TraesCS4B01G155700 chr4B 94.430 3483 155 20 49 3497 310222108 310218631 0.000000e+00 5321
3 TraesCS4B01G155700 chr4B 94.288 3484 158 22 49 3497 407691711 407688234 0.000000e+00 5293
4 TraesCS4B01G155700 chr4B 93.426 3438 189 23 49 3464 470135780 470139202 0.000000e+00 5062
5 TraesCS4B01G155700 chr5B 95.954 3485 108 18 30 3497 221162655 221159187 0.000000e+00 5624
6 TraesCS4B01G155700 chr7B 94.947 3483 123 26 49 3497 463804551 463808014 0.000000e+00 5408
7 TraesCS4B01G155700 chr7B 93.665 3520 184 26 1 3497 33969096 33972599 0.000000e+00 5228
8 TraesCS4B01G155700 chr1B 94.631 3483 147 21 49 3497 163066912 163063436 0.000000e+00 5360
9 TraesCS4B01G155700 chr1B 94.571 3481 151 20 49 3497 256710757 256714231 0.000000e+00 5347
10 TraesCS4B01G155700 chr1B 93.314 3515 190 26 1 3497 252930188 252933675 0.000000e+00 5147
11 TraesCS4B01G155700 chr1B 93.281 3468 198 24 49 3497 274298011 274301462 0.000000e+00 5081
12 TraesCS4B01G155700 chr1B 95.060 2328 94 11 1187 3497 206326192 206328515 0.000000e+00 3642
13 TraesCS4B01G155700 chr3B 93.835 3520 182 20 1 3497 107250144 107253651 0.000000e+00 5265
14 TraesCS4B01G155700 chr3B 92.978 3475 198 34 49 3497 247151094 247154548 0.000000e+00 5024
15 TraesCS4B01G155700 chr2B 95.195 3018 118 16 1 3001 205272437 205269430 0.000000e+00 4745
16 TraesCS4B01G155700 chr5D 93.300 3194 176 22 49 3218 378821602 378818423 0.000000e+00 4678
17 TraesCS4B01G155700 chr3A 87.692 65 7 1 14 78 204355079 204355016 1.350000e-09 75


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 TraesCS4B01G155700 chr4B 279977881 279981377 3496 False 6458 6458 100.000 1 3497 1 chr4B.!!$F1 3496
1 TraesCS4B01G155700 chr4B 335221381 335224899 3518 False 5382 5382 94.393 1 3497 1 chr4B.!!$F2 3496
2 TraesCS4B01G155700 chr4B 310218631 310222108 3477 True 5321 5321 94.430 49 3497 1 chr4B.!!$R1 3448
3 TraesCS4B01G155700 chr4B 407688234 407691711 3477 True 5293 5293 94.288 49 3497 1 chr4B.!!$R2 3448
4 TraesCS4B01G155700 chr4B 470135780 470139202 3422 False 5062 5062 93.426 49 3464 1 chr4B.!!$F3 3415
5 TraesCS4B01G155700 chr5B 221159187 221162655 3468 True 5624 5624 95.954 30 3497 1 chr5B.!!$R1 3467
6 TraesCS4B01G155700 chr7B 463804551 463808014 3463 False 5408 5408 94.947 49 3497 1 chr7B.!!$F2 3448
7 TraesCS4B01G155700 chr7B 33969096 33972599 3503 False 5228 5228 93.665 1 3497 1 chr7B.!!$F1 3496
8 TraesCS4B01G155700 chr1B 163063436 163066912 3476 True 5360 5360 94.631 49 3497 1 chr1B.!!$R1 3448
9 TraesCS4B01G155700 chr1B 256710757 256714231 3474 False 5347 5347 94.571 49 3497 1 chr1B.!!$F3 3448
10 TraesCS4B01G155700 chr1B 252930188 252933675 3487 False 5147 5147 93.314 1 3497 1 chr1B.!!$F2 3496
11 TraesCS4B01G155700 chr1B 274298011 274301462 3451 False 5081 5081 93.281 49 3497 1 chr1B.!!$F4 3448
12 TraesCS4B01G155700 chr1B 206326192 206328515 2323 False 3642 3642 95.060 1187 3497 1 chr1B.!!$F1 2310
13 TraesCS4B01G155700 chr3B 107250144 107253651 3507 False 5265 5265 93.835 1 3497 1 chr3B.!!$F1 3496
14 TraesCS4B01G155700 chr3B 247151094 247154548 3454 False 5024 5024 92.978 49 3497 1 chr3B.!!$F2 3448
15 TraesCS4B01G155700 chr2B 205269430 205272437 3007 True 4745 4745 95.195 1 3001 1 chr2B.!!$R1 3000
16 TraesCS4B01G155700 chr5D 378818423 378821602 3179 True 4678 4678 93.300 49 3218 1 chr5D.!!$R1 3169

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
675 687 1.899814 AGAGACGTGCAAGTGGGATTA 59.100 47.619 10.87 0.0 0.00 1.75 F
1193 1211 1.215382 CCGACGAGGTGATGAGCAA 59.785 57.895 0.00 0.0 34.51 3.91 F
1565 1585 3.127548 AGCATTCTGAACTTTATGCACCG 59.872 43.478 13.52 0.0 44.38 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2383 0.541063 TGAGGTTGTCTGGTAGCGGA 60.541 55.000 0.0 0.0 0.00 5.54 R
2456 2503 2.464782 AGTTGTAGTGGTAGTAGGGGC 58.535 52.381 0.0 0.0 0.00 5.80 R
2578 2638 5.126067 CACATAGCATAAGGTAGCTGGTTT 58.874 41.667 0.0 0.0 41.97 3.27 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
675 687 1.899814 AGAGACGTGCAAGTGGGATTA 59.100 47.619 10.87 0.00 0.00 1.75
711 723 6.759272 AGTACAGCTTGACAAGACTAATCAA 58.241 36.000 19.51 2.31 0.00 2.57
897 914 5.777732 ACTGCAAAAATACCCCATTGTCTTA 59.222 36.000 0.00 0.00 0.00 2.10
1193 1211 1.215382 CCGACGAGGTGATGAGCAA 59.785 57.895 0.00 0.00 34.51 3.91
1270 1288 3.771577 ACACCGATGAAGAAGAACCTT 57.228 42.857 0.00 0.00 0.00 3.50
1565 1585 3.127548 AGCATTCTGAACTTTATGCACCG 59.872 43.478 13.52 0.00 44.38 4.94
1569 1589 6.458206 GCATTCTGAACTTTATGCACCGAATA 60.458 38.462 7.78 0.00 42.18 1.75
1954 1989 7.611467 AGTTTCTAAACTACATTCATGCATGGA 59.389 33.333 25.97 19.31 46.75 3.41
1989 2026 5.336150 AGCATCTACCTCATGGATTATCG 57.664 43.478 0.00 0.00 37.04 2.92
2114 2159 4.521146 CTGCAGGAGGAGAAATTGTACAT 58.479 43.478 5.57 0.00 34.74 2.29
2304 2350 5.344743 ACGAAGGCATGAAGAAGAAGATA 57.655 39.130 0.00 0.00 0.00 1.98
2501 2549 3.791122 GCGGATGAAGATGCATGAAAGTG 60.791 47.826 2.46 0.00 0.00 3.16
2511 2559 6.106003 AGATGCATGAAAGTGTACATTCGTA 58.894 36.000 2.46 0.00 0.00 3.43
2554 2614 5.815740 TGTCCTTAGTCTTGTTGTTTCAGAC 59.184 40.000 0.00 0.00 0.00 3.51
2576 2636 5.449304 ACTTGTAGTTTGCTTTCGTTATGC 58.551 37.500 0.00 0.00 0.00 3.14
2578 2638 6.425721 ACTTGTAGTTTGCTTTCGTTATGCTA 59.574 34.615 0.00 0.00 0.00 3.49
2685 2756 4.144297 ACAAGTTTGCTAGCTTGATCCAA 58.856 39.130 26.08 0.00 43.29 3.53
3127 3230 4.265073 AGCTTCAGTTCGCATTCCTTAAT 58.735 39.130 0.00 0.00 0.00 1.40
3131 3234 6.403200 GCTTCAGTTCGCATTCCTTAATACAA 60.403 38.462 0.00 0.00 0.00 2.41
3409 3518 7.411588 GCTCAGTACAACTAAGTTTATTCGGTG 60.412 40.741 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 5.460646 GTTGTGGTGTGGACAGATTTTATG 58.539 41.667 0.00 0.00 0.00 1.90
286 291 7.759489 ATGTTGTATGTATGTTTGAACTGGT 57.241 32.000 0.00 0.00 0.00 4.00
287 292 9.773328 CTAATGTTGTATGTATGTTTGAACTGG 57.227 33.333 0.00 0.00 0.00 4.00
675 687 5.814705 GTCAAGCTGTACTTATGATCTGCTT 59.185 40.000 0.00 0.00 42.53 3.91
733 749 4.265073 CTGGAAGAACTAACCATCCAAGG 58.735 47.826 0.00 0.00 39.54 3.61
897 914 2.836372 TCTGTGAATGAGGCAGAGATGT 59.164 45.455 0.00 0.00 34.72 3.06
1024 1042 3.678014 CGAAGTCTCGCCATGGTGACA 62.678 57.143 24.20 11.87 41.41 3.58
1193 1211 2.739996 CCGCCCTTCATCCTGAGCT 61.740 63.158 0.00 0.00 0.00 4.09
1270 1288 2.265739 GACTGCCGCCATCTGTGA 59.734 61.111 0.00 0.00 0.00 3.58
1323 1341 4.471726 GTGGCTGCTGCGATGTGC 62.472 66.667 9.65 0.00 46.70 4.57
1404 1422 9.747898 TCATCTAGCTGGGAAATAAGTTTTAAA 57.252 29.630 0.00 0.00 0.00 1.52
1414 1432 7.863901 ATAGTAGTTCATCTAGCTGGGAAAT 57.136 36.000 0.00 0.00 0.00 2.17
1569 1589 8.621532 TGCTAGTACATCAAGTTCAGAAATTT 57.378 30.769 0.00 0.00 0.00 1.82
2114 2159 5.048364 CCTCCAATGTTGAAACCGACAAATA 60.048 40.000 0.00 0.00 32.14 1.40
2304 2350 1.111277 GTTTGTGGTCTGCCCTGTTT 58.889 50.000 0.00 0.00 0.00 2.83
2337 2383 0.541063 TGAGGTTGTCTGGTAGCGGA 60.541 55.000 0.00 0.00 0.00 5.54
2456 2503 2.464782 AGTTGTAGTGGTAGTAGGGGC 58.535 52.381 0.00 0.00 0.00 5.80
2554 2614 5.689819 AGCATAACGAAAGCAAACTACAAG 58.310 37.500 0.00 0.00 0.00 3.16
2576 2636 6.425114 CACATAGCATAAGGTAGCTGGTTTAG 59.575 42.308 0.00 0.00 41.97 1.85
2578 2638 5.126067 CACATAGCATAAGGTAGCTGGTTT 58.874 41.667 0.00 0.00 41.97 3.27
2685 2756 7.339466 ACTTCAACCTACTTCAACTTCAAATGT 59.661 33.333 0.00 0.00 0.00 2.71
3383 3492 6.589139 ACCGAATAAACTTAGTTGTACTGAGC 59.411 38.462 0.00 0.00 35.47 4.26
3409 3518 8.180267 GCATTAATTGGTATCATCATAGCACTC 58.820 37.037 0.00 0.00 41.66 3.51


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

AutoCloner maintained by Alex Coulton.