Multiple sequence alignment - TraesCS5B01G083200

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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 TraesCS5B01G083200 chr5B 100.000 3438 0 0 1 3438 104504796 104501359 0 6349
1 TraesCS5B01G083200 chr5B 94.870 3450 153 16 1 3438 197387107 197390544 0 5369
2 TraesCS5B01G083200 chr1B 95.622 3449 130 10 1 3438 256706754 256710192 0 5513
3 TraesCS5B01G083200 chr1B 94.910 3458 143 19 1 3438 164401135 164397691 0 5380
4 TraesCS5B01G083200 chr4B 95.395 3453 133 14 1 3438 310225949 310222508 0 5472
5 TraesCS5B01G083200 chr4B 95.019 3453 144 18 1 3438 407695548 407692109 0 5398
6 TraesCS5B01G083200 chr4B 94.958 3451 150 17 1 3438 224372269 224375708 0 5387
7 TraesCS5B01G083200 chr2B 95.226 3435 138 18 17 3438 506424421 506421000 0 5411
8 TraesCS5B01G083200 chr2B 94.878 3456 146 22 1 3438 300243649 300240207 0 5373
9 TraesCS5B01G083200 chr7B 95.019 3453 143 18 1 3438 381026456 381023018 0 5397


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 TraesCS5B01G083200 chr5B 104501359 104504796 3437 True 6349 6349 100.000 1 3438 1 chr5B.!!$R1 3437
1 TraesCS5B01G083200 chr5B 197387107 197390544 3437 False 5369 5369 94.870 1 3438 1 chr5B.!!$F1 3437
2 TraesCS5B01G083200 chr1B 256706754 256710192 3438 False 5513 5513 95.622 1 3438 1 chr1B.!!$F1 3437
3 TraesCS5B01G083200 chr1B 164397691 164401135 3444 True 5380 5380 94.910 1 3438 1 chr1B.!!$R1 3437
4 TraesCS5B01G083200 chr4B 310222508 310225949 3441 True 5472 5472 95.395 1 3438 1 chr4B.!!$R1 3437
5 TraesCS5B01G083200 chr4B 407692109 407695548 3439 True 5398 5398 95.019 1 3438 1 chr4B.!!$R2 3437
6 TraesCS5B01G083200 chr4B 224372269 224375708 3439 False 5387 5387 94.958 1 3438 1 chr4B.!!$F1 3437
7 TraesCS5B01G083200 chr2B 506421000 506424421 3421 True 5411 5411 95.226 17 3438 1 chr2B.!!$R2 3421
8 TraesCS5B01G083200 chr2B 300240207 300243649 3442 True 5373 5373 94.878 1 3438 1 chr2B.!!$R1 3437
9 TraesCS5B01G083200 chr7B 381023018 381026456 3438 True 5397 5397 95.019 1 3438 1 chr7B.!!$R1 3437

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
797 810 0.685785 TGCCACAAGGGACTGCAAAA 60.686 50.000 0.0 0.0 40.86 2.44 F
1150 1165 1.067565 GCAACGAGACACTGGAGATCA 60.068 52.381 0.0 0.0 0.00 2.92 F
1283 1298 1.542375 AACCTCCCCAGATGGCAGT 60.542 57.895 0.0 0.0 0.00 4.40 F
1734 1754 2.024414 GACTTGGTGAAGCACTGGTTT 58.976 47.619 0.0 0.0 34.40 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2047 1.134310 TCATGATGCAGCATCTCGGTT 60.134 47.619 31.02 11.83 41.06 4.44 R
2198 2225 1.852157 AATGGGTGGATGACGCTGGT 61.852 55.000 0.00 0.00 38.35 4.00 R
2277 2304 2.031163 GGTTGTCTGGCAGCTCGT 59.969 61.111 10.34 0.00 0.00 4.18 R
3268 3300 3.148279 CGCTAGTCGAGGGGGCTT 61.148 66.667 0.98 0.00 41.67 4.35 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
226 231 7.819900 ACAAAAGGCATAGTAAAACAAACACAA 59.180 29.630 0.00 0.00 0.00 3.33
227 232 8.660373 CAAAAGGCATAGTAAAACAAACACAAA 58.340 29.630 0.00 0.00 0.00 2.83
228 233 7.764695 AAGGCATAGTAAAACAAACACAAAC 57.235 32.000 0.00 0.00 0.00 2.93
229 234 6.868622 AGGCATAGTAAAACAAACACAAACA 58.131 32.000 0.00 0.00 0.00 2.83
242 247 1.735018 CACAAACACCAGTGAACGACA 59.265 47.619 4.48 0.00 37.97 4.35
312 320 4.289410 TCCCAATTCAGAAAGACCATCAGA 59.711 41.667 0.00 0.00 0.00 3.27
517 529 4.698201 TTACACTTCAATCACCAGTCCA 57.302 40.909 0.00 0.00 0.00 4.02
588 600 1.559219 TGCAAGTGGGATAAGCAGCTA 59.441 47.619 0.00 0.00 0.00 3.32
596 608 7.560796 AGTGGGATAAGCAGCTAATAAGTAT 57.439 36.000 0.00 0.00 0.00 2.12
638 650 2.230992 TGCCACAGTAAAATGCCATCAC 59.769 45.455 0.00 0.00 0.00 3.06
650 662 2.032528 CATCACCACCACCGCAGT 59.967 61.111 0.00 0.00 0.00 4.40
695 707 5.877012 CAGGTCATAAGTACAGCTTGACAAT 59.123 40.000 13.02 0.66 36.93 2.71
797 810 0.685785 TGCCACAAGGGACTGCAAAA 60.686 50.000 0.00 0.00 40.86 2.44
838 852 2.741092 CACTACACACACGCCCCT 59.259 61.111 0.00 0.00 0.00 4.79
970 985 5.102313 CACACAAACCAAAAACTTCTCTCC 58.898 41.667 0.00 0.00 0.00 3.71
1116 1131 2.818751 ACACAACAACCCTCAAAGGA 57.181 45.000 0.00 0.00 37.67 3.36
1140 1155 1.300931 GCTCCACAGCAACGAGACA 60.301 57.895 0.00 0.00 46.06 3.41
1150 1165 1.067565 GCAACGAGACACTGGAGATCA 60.068 52.381 0.00 0.00 0.00 2.92
1283 1298 1.542375 AACCTCCCCAGATGGCAGT 60.542 57.895 0.00 0.00 0.00 4.40
1493 1511 5.163814 GCACTACTGCATTTTCTCAAGTAGG 60.164 44.000 11.60 3.77 43.62 3.18
1528 1546 7.701539 ATGTATTTTTGAACCTGATGCACTA 57.298 32.000 0.00 0.00 0.00 2.74
1734 1754 2.024414 GACTTGGTGAAGCACTGGTTT 58.976 47.619 0.00 0.00 34.40 3.27
1736 1756 3.626930 ACTTGGTGAAGCACTGGTTTTA 58.373 40.909 0.00 0.00 34.40 1.52
1738 1758 4.649218 ACTTGGTGAAGCACTGGTTTTATT 59.351 37.500 0.00 0.00 34.40 1.40
1767 1787 8.161699 TCCCATTTCAACAAAAGTAGACTAAC 57.838 34.615 0.00 0.00 0.00 2.34
2198 2225 3.141398 GACTCCTTGACTGATGTTGCAA 58.859 45.455 0.00 0.00 0.00 4.08
2239 2266 6.899393 TTCTACAAAGGCATGAAGAACAAT 57.101 33.333 0.00 0.00 0.00 2.71
2319 2346 1.941294 CGAGTACGCAGGAGTAGATGT 59.059 52.381 0.00 0.00 0.00 3.06
2431 2458 0.260523 GCCCCTATTGCCCCTTTACA 59.739 55.000 0.00 0.00 0.00 2.41
2473 2500 0.869730 GCCTTCGTTTTACTTCCGCA 59.130 50.000 0.00 0.00 0.00 5.69
2532 2559 2.435372 TGCTCTTGTTGGGTTGAACT 57.565 45.000 0.00 0.00 0.00 3.01
2857 2884 6.775594 ATGCACTATCAGTACAACTCAGTA 57.224 37.500 0.00 0.00 0.00 2.74
2907 2934 3.068732 TGACACCAGAAGACACTTGAGAG 59.931 47.826 0.00 0.00 0.00 3.20
2999 3026 8.561738 AACTGACAAGAACTAGAACAAAAAGA 57.438 30.769 0.00 0.00 0.00 2.52
3235 3267 5.871396 AAGTGTTCAGAGGAGTTTGACTA 57.129 39.130 0.00 0.00 0.00 2.59
3268 3300 3.857052 CTGCACTTATAAACAGGTCCGA 58.143 45.455 0.00 0.00 0.00 4.55
3312 3344 1.080093 CTAAACCCAGAGCGCACGA 60.080 57.895 11.47 0.00 0.00 4.35
3313 3345 0.460284 CTAAACCCAGAGCGCACGAT 60.460 55.000 11.47 0.00 0.00 3.73
3344 3382 2.427740 GCGCGGACGAGCTATCTC 60.428 66.667 8.83 0.00 43.93 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 7.887996 TTCAAATTTATTTGTGACTGCATCC 57.112 32.000 13.28 0.00 45.49 3.51
226 231 2.102070 TTGTGTCGTTCACTGGTGTT 57.898 45.000 12.67 0.00 46.27 3.32
227 232 2.102070 TTTGTGTCGTTCACTGGTGT 57.898 45.000 12.67 0.00 46.27 4.16
228 233 3.479505 TTTTTGTGTCGTTCACTGGTG 57.520 42.857 12.67 0.00 46.27 4.17
352 360 4.848357 AGATTTTCACCAGTACAGGATGG 58.152 43.478 11.86 4.21 43.62 3.51
452 464 6.436218 AGTGAGACTATGTGTGTGGTAATGTA 59.564 38.462 0.00 0.00 0.00 2.29
454 466 5.578336 CAGTGAGACTATGTGTGTGGTAATG 59.422 44.000 0.00 0.00 0.00 1.90
517 529 7.722285 GGTCTGAACTCCTCTACTATCATACTT 59.278 40.741 0.00 0.00 0.00 2.24
596 608 4.556104 GCACCGATTCGTATAGTCAAGCTA 60.556 45.833 5.20 0.00 0.00 3.32
638 650 4.602259 ACGTCACTGCGGTGGTGG 62.602 66.667 25.15 16.15 43.17 4.61
650 662 0.950836 CAAATCCCACTTGCACGTCA 59.049 50.000 0.00 0.00 0.00 4.35
695 707 8.259411 TGGTTTTTACTGTTGAACTGACTAGTA 58.741 33.333 9.24 0.00 35.69 1.82
838 852 3.235481 TGGGAGGCGGTTCGTTCA 61.235 61.111 0.00 0.00 0.00 3.18
894 909 0.816373 GGAACGAGGGAGAGGTGTAC 59.184 60.000 0.00 0.00 0.00 2.90
970 985 3.365265 GCGACTGTGGGCTTTGGG 61.365 66.667 0.00 0.00 0.00 4.12
1092 1107 4.582656 CCTTTGAGGGTTGTTGTGTATTCA 59.417 41.667 0.00 0.00 0.00 2.57
1095 1110 4.141251 ACTCCTTTGAGGGTTGTTGTGTAT 60.141 41.667 0.00 0.00 43.29 2.29
1116 1131 0.882042 CGTTGCTGTGGAGCTCAACT 60.882 55.000 21.84 0.00 46.39 3.16
1129 1144 1.203523 GATCTCCAGTGTCTCGTTGCT 59.796 52.381 0.00 0.00 0.00 3.91
1140 1155 1.485480 CTGGTGCAGATGATCTCCAGT 59.515 52.381 16.51 0.00 38.48 4.00
1150 1165 1.219124 CTGGTACGCTGGTGCAGAT 59.781 57.895 0.00 0.00 39.64 2.90
1283 1298 0.319555 GACGCACAACTGCAGGACTA 60.320 55.000 19.93 0.00 44.50 2.59
1439 1457 6.655848 ACTTTTCACAAACCACACTAGTACAA 59.344 34.615 0.00 0.00 0.00 2.41
1528 1546 8.527810 TCCGCAAAATTTTCCAAATAGTAATCT 58.472 29.630 0.00 0.00 0.00 2.40
1547 1565 7.214467 ACTTCAGAATTTAATCTTCCGCAAA 57.786 32.000 0.00 0.00 0.00 3.68
1738 1758 9.362151 AGTCTACTTTTGTTGAAATGGGATAAA 57.638 29.630 0.00 0.00 36.08 1.40
1767 1787 5.670485 TGTATGTTCTGCATTGGTACTAGG 58.330 41.667 0.00 0.00 38.94 3.02
2020 2047 1.134310 TCATGATGCAGCATCTCGGTT 60.134 47.619 31.02 11.83 41.06 4.44
2078 2105 4.336713 GGACAACTTCAGCTTCTCTTTGTT 59.663 41.667 0.00 0.00 0.00 2.83
2165 2192 4.828387 AGTCAAGGAGTCGTACTCTTTTCT 59.172 41.667 12.62 9.78 41.00 2.52
2198 2225 1.852157 AATGGGTGGATGACGCTGGT 61.852 55.000 0.00 0.00 38.35 4.00
2239 2266 3.508402 TGTAGTCTTCCTGCGTGTTGATA 59.492 43.478 0.00 0.00 0.00 2.15
2277 2304 2.031163 GGTTGTCTGGCAGCTCGT 59.969 61.111 10.34 0.00 0.00 4.18
2431 2458 4.283978 CAGGCTCTGATGTATCTTCATCCT 59.716 45.833 4.59 0.00 42.24 3.24
2473 2500 5.221501 ACAACAAGATAAAAGGCAAGCACAT 60.222 36.000 0.00 0.00 0.00 3.21
2532 2559 6.801575 TGACAAGCACGACATAATCATACTA 58.198 36.000 0.00 0.00 0.00 1.82
2656 2683 8.302438 CCATTCAGAAGCTACTTTTCAATTTCT 58.698 33.333 0.00 0.00 0.00 2.52
2657 2684 8.299570 TCCATTCAGAAGCTACTTTTCAATTTC 58.700 33.333 0.00 0.00 0.00 2.17
2857 2884 5.593679 AGAACTATGGTACTTGCGTGTAT 57.406 39.130 0.00 0.00 0.00 2.29
2880 2907 5.652014 TCAAGTGTCTTCTGGTGTCATTTTT 59.348 36.000 0.00 0.00 0.00 1.94
2999 3026 3.650942 TCCACCAGTAACTTGGACTGATT 59.349 43.478 4.38 0.00 46.01 2.57
3061 3092 4.660938 GCCTGACCTTGGGCGGTT 62.661 66.667 0.09 0.00 38.91 4.44
3268 3300 3.148279 CGCTAGTCGAGGGGGCTT 61.148 66.667 0.98 0.00 41.67 4.35


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

AutoCloner maintained by Alex Coulton.