Multiple sequence alignment - TraesCS1D01G112900

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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 TraesCS1D01G112900 chr1D 100.000 3000 0 0 1 3000 109453786 109456785 0.000000e+00 5541
1 TraesCS1D01G112900 chr1B 95.984 2216 57 11 796 3000 165064318 165066512 0.000000e+00 3570
2 TraesCS1D01G112900 chr1B 92.324 469 30 2 2 464 165063507 165063975 0.000000e+00 662
3 TraesCS1D01G112900 chr1B 95.098 306 8 5 496 800 165063963 165064262 2.710000e-130 475
4 TraesCS1D01G112900 chr1A 97.601 1876 39 3 1131 3000 112927784 112929659 0.000000e+00 3210
5 TraesCS1D01G112900 chr1A 96.416 586 11 3 496 1073 112927189 112927772 0.000000e+00 957
6 TraesCS1D01G112900 chr1A 92.781 471 31 1 1 468 112926735 112927205 0.000000e+00 678


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 TraesCS1D01G112900 chr1D 109453786 109456785 2999 False 5541 5541 100.000000 1 3000 1 chr1D.!!$F1 2999
1 TraesCS1D01G112900 chr1B 165063507 165066512 3005 False 1569 3570 94.468667 2 3000 3 chr1B.!!$F1 2998
2 TraesCS1D01G112900 chr1A 112926735 112929659 2924 False 1615 3210 95.599333 1 3000 3 chr1A.!!$F1 2999

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
419 429 2.626840 GCAACCAACTTTGCCTTTTCA 58.373 42.857 0.0 0.0 45.22 2.69 F
1117 1202 0.394899 GGCAATCAACCAGCTAGGCT 60.395 55.000 0.0 0.0 43.14 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1505 1.133407 CCGGTCTTCTTCTTCCTCTCG 59.867 57.143 0.0 0.0 0.0 4.04 R
2120 2210 1.251251 AACTTGTGCTTGGCTCCATC 58.749 50.000 0.0 0.0 0.0 3.51 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
173 174 9.838339 AGTTTATCTTTTAGGATGTATGGACAG 57.162 33.333 0.00 0.00 39.50 3.51
180 181 4.032960 AGGATGTATGGACAGTGCAAAA 57.967 40.909 0.00 0.00 39.50 2.44
217 218 6.486657 ACACTATCTCATAGCTGTTCTCTCTC 59.513 42.308 0.00 0.00 36.30 3.20
312 315 5.046304 TCCAGTGCTAGCTGTTTCTTCTAAT 60.046 40.000 17.23 0.00 34.84 1.73
316 319 6.936900 AGTGCTAGCTGTTTCTTCTAATGAAA 59.063 34.615 17.23 0.00 0.00 2.69
319 322 9.102757 TGCTAGCTGTTTCTTCTAATGAAATAG 57.897 33.333 17.23 8.07 41.98 1.73
419 429 2.626840 GCAACCAACTTTGCCTTTTCA 58.373 42.857 0.00 0.00 45.22 2.69
421 431 3.438434 GCAACCAACTTTGCCTTTTCAAA 59.562 39.130 0.00 0.00 45.22 2.69
423 433 5.730289 GCAACCAACTTTGCCTTTTCAAATC 60.730 40.000 0.00 0.00 45.22 2.17
428 438 5.612725 ACTTTGCCTTTTCAAATCCTTCA 57.387 34.783 0.00 0.00 35.64 3.02
450 460 9.199982 CTTCATAATTCTTTGTGCATTTTCTGT 57.800 29.630 0.00 0.00 0.00 3.41
464 474 6.161381 GCATTTTCTGTGGATCTCATTTGTT 58.839 36.000 0.00 0.00 0.00 2.83
465 475 6.647895 GCATTTTCTGTGGATCTCATTTGTTT 59.352 34.615 0.00 0.00 0.00 2.83
466 476 7.148689 GCATTTTCTGTGGATCTCATTTGTTTC 60.149 37.037 0.00 0.00 0.00 2.78
467 477 7.587037 TTTTCTGTGGATCTCATTTGTTTCT 57.413 32.000 0.00 0.00 0.00 2.52
468 478 7.587037 TTTCTGTGGATCTCATTTGTTTCTT 57.413 32.000 0.00 0.00 0.00 2.52
469 479 7.587037 TTCTGTGGATCTCATTTGTTTCTTT 57.413 32.000 0.00 0.00 0.00 2.52
470 480 7.587037 TCTGTGGATCTCATTTGTTTCTTTT 57.413 32.000 0.00 0.00 0.00 2.27
471 481 8.010733 TCTGTGGATCTCATTTGTTTCTTTTT 57.989 30.769 0.00 0.00 0.00 1.94
507 517 3.903783 CGGGTGGATCGCATTTGT 58.096 55.556 0.00 0.00 0.00 2.83
564 581 4.194640 CAAGGATCAACACCCATCTACAG 58.805 47.826 0.00 0.00 0.00 2.74
675 693 2.760092 GTGGGAATAATTGAGGCAAGCA 59.240 45.455 0.00 0.00 0.00 3.91
1105 1190 0.694771 AAGCAGAGAGGTGGCAATCA 59.305 50.000 0.00 0.00 0.00 2.57
1117 1202 0.394899 GGCAATCAACCAGCTAGGCT 60.395 55.000 0.00 0.00 43.14 4.58
1119 1204 2.487986 GGCAATCAACCAGCTAGGCTAT 60.488 50.000 0.00 0.00 43.14 2.97
1165 1250 7.744087 TTCATAGTATCATACAATGGGCAAC 57.256 36.000 0.00 0.00 0.00 4.17
1594 1679 0.108615 CGGAGAAGAGGTCGTTGCAT 60.109 55.000 0.00 0.00 0.00 3.96
1800 1885 6.625081 GCCCTTTTTGTAAGTGTACATCCATC 60.625 42.308 0.00 0.00 39.96 3.51
1921 2006 2.901192 TGTTGTTCCGTTCTATCCTCCA 59.099 45.455 0.00 0.00 0.00 3.86
1946 2033 4.097551 TGTGGATGAGTGTTTGATTGGA 57.902 40.909 0.00 0.00 0.00 3.53
2120 2210 5.220854 CCCACTGCTTACCTTCAAATAATCG 60.221 44.000 0.00 0.00 0.00 3.34
2141 2231 2.356665 TGGAGCCAAGCACAAGTTTA 57.643 45.000 0.00 0.00 0.00 2.01
2144 2234 2.623416 GGAGCCAAGCACAAGTTTAGTT 59.377 45.455 0.00 0.00 0.00 2.24
2430 2520 3.069443 TGAAAGTTGAAACCATGCCTTCC 59.931 43.478 0.00 0.00 0.00 3.46
2705 2796 4.849329 GCTGCATGCTTCGGCTGC 62.849 66.667 20.33 2.77 45.32 5.25
2850 2942 4.408921 TCTGAGAACTGAAACTCTGGGAAA 59.591 41.667 0.00 0.00 34.47 3.13
2870 2962 6.145534 GGGAAACTCCAAAAGAAATAAAAGCG 59.854 38.462 0.00 0.00 38.64 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 9.757227 GCTATGAGATAGTGTTTAGACAGATTT 57.243 33.333 0.00 0.00 36.20 2.17
270 273 9.374838 AGCACTGGAATGATATTTTTCAAAATC 57.625 29.630 0.69 0.00 39.24 2.17
355 365 5.664294 TTGTGGCAATTGCTCAAAGATAT 57.336 34.783 28.42 0.00 41.70 1.63
419 429 9.729281 AAATGCACAAAGAATTATGAAGGATTT 57.271 25.926 0.00 0.00 0.00 2.17
421 431 9.374838 GAAAATGCACAAAGAATTATGAAGGAT 57.625 29.630 0.00 0.00 0.00 3.24
423 433 8.653338 CAGAAAATGCACAAAGAATTATGAAGG 58.347 33.333 0.00 0.00 0.00 3.46
428 438 7.669427 TCCACAGAAAATGCACAAAGAATTAT 58.331 30.769 0.00 0.00 0.00 1.28
490 500 0.744414 AGACAAATGCGATCCACCCG 60.744 55.000 0.00 0.00 0.00 5.28
491 501 2.325583 TAGACAAATGCGATCCACCC 57.674 50.000 0.00 0.00 0.00 4.61
492 502 4.377021 TGTATAGACAAATGCGATCCACC 58.623 43.478 0.00 0.00 30.68 4.61
493 503 5.984233 TTGTATAGACAAATGCGATCCAC 57.016 39.130 0.00 0.00 42.66 4.02
534 544 2.241176 GGTGTTGATCCTTGGGGTATGA 59.759 50.000 0.00 0.00 0.00 2.15
675 693 2.649742 TGTTCTCTCCCTCCCATCTT 57.350 50.000 0.00 0.00 0.00 2.40
780 799 5.938125 TCTAAAGTACCAATCAAAGGACAGC 59.062 40.000 0.00 0.00 0.00 4.40
963 1042 8.655901 TCATATGTCCAAGGTAGCATACAATTA 58.344 33.333 1.90 0.00 45.43 1.40
1105 1190 4.518249 GTTCAGAAATAGCCTAGCTGGTT 58.482 43.478 0.00 0.00 40.10 3.67
1119 1204 8.195165 TGAATCTTTCTCTCTAGGTTCAGAAA 57.805 34.615 0.00 0.00 36.77 2.52
1420 1505 1.133407 CCGGTCTTCTTCTTCCTCTCG 59.867 57.143 0.00 0.00 0.00 4.04
1576 1661 1.646189 GATGCAACGACCTCTTCTCC 58.354 55.000 0.00 0.00 0.00 3.71
1698 1783 7.148103 CCATGCCAAAGGAAAAAGAAAAGAAAA 60.148 33.333 0.00 0.00 0.00 2.29
1708 1793 1.202746 GCACCCATGCCAAAGGAAAAA 60.203 47.619 0.00 0.00 46.97 1.94
1728 1813 2.030893 TGCGCACAAGAGAGAAAAATGG 60.031 45.455 5.66 0.00 0.00 3.16
1921 2006 6.041865 TCCAATCAAACACTCATCCACAAAAT 59.958 34.615 0.00 0.00 0.00 1.82
1946 2033 7.878621 TTCATATGTTATCCTCCTCCTTGAT 57.121 36.000 1.90 0.00 0.00 2.57
2037 2127 6.962182 AGGATGAACAGATTGAAACTCCATA 58.038 36.000 0.00 0.00 0.00 2.74
2120 2210 1.251251 AACTTGTGCTTGGCTCCATC 58.749 50.000 0.00 0.00 0.00 3.51
2141 2231 6.591935 TGTATCTTGGTTGTGAGAAGAAACT 58.408 36.000 0.00 0.00 29.78 2.66
2144 2234 7.706607 CGATATGTATCTTGGTTGTGAGAAGAA 59.293 37.037 0.00 0.00 29.78 2.52
2184 2274 5.708948 TGATTGGAAATTAAGGCTTCGTTG 58.291 37.500 1.30 0.00 0.00 4.10
2430 2520 4.142447 ACAATGAGTAGTACTACTGGCACG 60.142 45.833 34.67 22.96 45.63 5.34
2850 2942 9.788960 GAATATCGCTTTTATTTCTTTTGGAGT 57.211 29.630 0.00 0.00 0.00 3.85
2870 2962 4.156739 GGATTGGCGAAATGGGAGAATATC 59.843 45.833 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.