Multiple sequence alignment - TraesCS7D01G379200

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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 TraesCS7D01G379200 chr7D 100.000 3421 0 0 1 3421 491245692 491249112 0.000000e+00 6318
1 TraesCS7D01G379200 chr7A 96.692 3446 67 14 1 3421 557552811 557556234 0.000000e+00 5688
2 TraesCS7D01G379200 chr7B 95.434 3460 88 30 2 3421 519783432 519786861 0.000000e+00 5450
3 TraesCS7D01G379200 chr1A 82.126 207 33 4 2 207 373783063 373783266 1.260000e-39 174


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 TraesCS7D01G379200 chr7D 491245692 491249112 3420 False 6318 6318 100.000 1 3421 1 chr7D.!!$F1 3420
1 TraesCS7D01G379200 chr7A 557552811 557556234 3423 False 5688 5688 96.692 1 3421 1 chr7A.!!$F1 3420
2 TraesCS7D01G379200 chr7B 519783432 519786861 3429 False 5450 5450 95.434 2 3421 1 chr7B.!!$F1 3419

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
561 577 0.482887 CACCACCTTTCCCCTTCCTT 59.517 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2525 0.687354 TTCTTCCTCCTGGCACACTC 59.313 55.0 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
415 431 5.583495 CAGCAACTAGTCGTAGAAGCTAAT 58.417 41.667 0.00 0.0 39.69 1.73
518 534 2.997315 CTCGCCACAGTCCAGGGA 60.997 66.667 0.00 0.0 0.00 4.20
559 575 1.076727 CCACCACCTTTCCCCTTCC 59.923 63.158 0.00 0.0 0.00 3.46
560 576 1.435346 CCACCACCTTTCCCCTTCCT 61.435 60.000 0.00 0.0 0.00 3.36
561 577 0.482887 CACCACCTTTCCCCTTCCTT 59.517 55.000 0.00 0.0 0.00 3.36
562 578 0.778083 ACCACCTTTCCCCTTCCTTC 59.222 55.000 0.00 0.0 0.00 3.46
715 733 7.118390 GGCTATGGCTGACATTATTTGTAGTAG 59.882 40.741 0.00 0.0 41.03 2.57
716 734 7.657761 GCTATGGCTGACATTATTTGTAGTAGT 59.342 37.037 0.00 0.0 41.03 2.73
719 737 8.074613 TGGCTGACATTATTTGTAGTAGTAGT 57.925 34.615 0.00 0.0 39.18 2.73
720 738 9.192642 TGGCTGACATTATTTGTAGTAGTAGTA 57.807 33.333 0.00 0.0 39.18 1.82
1006 1024 4.428209 GAGCGAAGAAGAAGACATGATCA 58.572 43.478 0.00 0.0 0.00 2.92
2488 2525 2.103941 GGAGGAGGAGCTAGTTGGATTG 59.896 54.545 0.00 0.0 0.00 2.67
2498 2535 1.901591 AGTTGGATTGAGTGTGCCAG 58.098 50.000 0.00 0.0 0.00 4.85
2559 2596 6.324512 TGATGTTAATTATTCATTGGCTGCCT 59.675 34.615 21.03 0.0 0.00 4.75
2573 2610 1.698506 CTGCCTGGTTGGTTGGTTAA 58.301 50.000 0.00 0.0 38.35 2.01
2593 2630 9.802039 TGGTTAATTACTGTTGATTTAAGACCT 57.198 29.630 0.00 0.0 0.00 3.85
2604 2641 6.743575 TGATTTAAGACCTGAAAGCTTAGC 57.256 37.500 0.00 0.0 0.00 3.09
2619 2656 2.589720 CTTAGCAATGCATGGGGATCA 58.410 47.619 8.35 0.0 0.00 2.92
2629 2666 2.701951 GCATGGGGATCACATTGGATTT 59.298 45.455 0.00 0.0 0.00 2.17
2630 2667 3.896888 GCATGGGGATCACATTGGATTTA 59.103 43.478 0.00 0.0 0.00 1.40
2638 2675 5.221126 GGATCACATTGGATTTAAGAGGTGC 60.221 44.000 0.00 0.0 0.00 5.01
2643 2680 4.864704 TTGGATTTAAGAGGTGCCAAAC 57.135 40.909 0.00 0.0 32.91 2.93
2705 2746 6.803154 ATTTTCCTCTTTCTAGGTTGTTCG 57.197 37.500 0.00 0.0 37.91 3.95
2712 2753 6.158023 TCTTTCTAGGTTGTTCGTTTCTCT 57.842 37.500 0.00 0.0 0.00 3.10
2722 2763 3.979495 TGTTCGTTTCTCTCTTAGTTCGC 59.021 43.478 0.00 0.0 0.00 4.70
2752 2794 7.883833 GGAGTAAAGTTTAGGGAGATTTTGTCT 59.116 37.037 0.00 0.0 40.81 3.41
2925 2971 8.564574 TGCGACCACCAATTATTTTATTCTATC 58.435 33.333 0.00 0.0 0.00 2.08
3346 3394 4.092821 TGTGTTCTTGTTTTCTGTGTCTCG 59.907 41.667 0.00 0.0 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.348666 GCTCACCGCGGCATAAATATAG 59.651 50.000 28.58 10.20 0.00 1.31
141 143 7.937649 AGCTTTTGACGGTTTAAAAGTTATCT 58.062 30.769 21.73 13.34 42.79 1.98
415 431 0.738975 CGAGGTTCATACGCCAGAGA 59.261 55.000 0.00 0.00 0.00 3.10
518 534 2.817844 GAGGGTGGCGTTGTCTTTTATT 59.182 45.455 0.00 0.00 0.00 1.40
559 575 5.954757 TCTCTAACTATGTAGAGGGGGAAG 58.045 45.833 8.89 0.00 44.93 3.46
560 576 5.675421 TCTCTCTAACTATGTAGAGGGGGAA 59.325 44.000 8.81 0.00 45.36 3.97
561 577 5.233143 TCTCTCTAACTATGTAGAGGGGGA 58.767 45.833 8.81 3.90 45.36 4.81
562 578 5.311121 TCTCTCTCTAACTATGTAGAGGGGG 59.689 48.000 8.81 6.05 46.76 5.40
715 733 1.557651 GCAACCAGCTACGCTACTAC 58.442 55.000 0.00 0.00 36.40 2.73
717 735 4.913126 GCAACCAGCTACGCTACT 57.087 55.556 0.00 0.00 36.40 2.57
963 981 2.844839 GCGCCCTGGGACTAGGAT 60.845 66.667 19.27 0.00 40.42 3.24
1006 1024 1.555967 GAGGAAGAGTGGAGTGAGCT 58.444 55.000 0.00 0.00 0.00 4.09
1830 1860 1.252904 CCATGGCCTTCACCCACTTG 61.253 60.000 3.32 0.00 34.68 3.16
1932 1962 2.485302 CGAATAGTGATCCATGGCCACA 60.485 50.000 27.54 16.59 33.53 4.17
2058 2088 4.394712 CACCACCTCCCGCCTGTC 62.395 72.222 0.00 0.00 0.00 3.51
2488 2525 0.687354 TTCTTCCTCCTGGCACACTC 59.313 55.000 0.00 0.00 0.00 3.51
2498 2535 2.276391 AGGGTTAGGGTTTCTTCCTCC 58.724 52.381 0.00 0.00 35.92 4.30
2545 2582 0.899720 CAACCAGGCAGCCAATGAAT 59.100 50.000 15.80 0.00 0.00 2.57
2559 2596 5.892119 TCAACAGTAATTAACCAACCAACCA 59.108 36.000 0.00 0.00 0.00 3.67
2573 2610 8.515414 GCTTTCAGGTCTTAAATCAACAGTAAT 58.485 33.333 0.00 0.00 0.00 1.89
2591 2628 3.444916 CATGCATTGCTAAGCTTTCAGG 58.555 45.455 3.20 1.56 0.00 3.86
2593 2630 2.166870 CCCATGCATTGCTAAGCTTTCA 59.833 45.455 3.20 0.00 0.00 2.69
2604 2641 2.224185 CCAATGTGATCCCCATGCATTG 60.224 50.000 0.00 11.01 43.30 2.82
2619 2656 4.046286 TGGCACCTCTTAAATCCAATGT 57.954 40.909 0.00 0.00 0.00 2.71
2638 2675 2.571212 TGTAGCACTCACAAGGTTTGG 58.429 47.619 0.00 0.00 34.12 3.28
2643 2680 1.865865 ACGTTGTAGCACTCACAAGG 58.134 50.000 6.41 6.41 43.76 3.61
2705 2746 3.121445 CCAACGCGAACTAAGAGAGAAAC 59.879 47.826 15.93 0.00 0.00 2.78
2712 2753 3.921119 TTACTCCAACGCGAACTAAGA 57.079 42.857 15.93 0.00 0.00 2.10
2722 2763 5.143376 TCTCCCTAAACTTTACTCCAACG 57.857 43.478 0.00 0.00 0.00 4.10
2752 2794 6.714810 GGTGCATTAGGTCCAACAATCATATA 59.285 38.462 0.00 0.00 0.00 0.86
3346 3394 3.686726 GCTTACCAGCATATATGGAGCAC 59.313 47.826 14.51 0.00 46.49 4.40


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

AutoCloner maintained by Alex Coulton.