Multiple sequence alignment - TraesCS4D01G042900

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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 TraesCS4D01G042900 chr4D 100.000 2576 0 0 1 2576 19902472 19905047 0.000000e+00 4758
1 TraesCS4D01G042900 chr1A 96.832 2588 70 8 1 2576 554483770 554486357 0.000000e+00 4314
2 TraesCS4D01G042900 chr2B 96.676 2587 75 7 1 2576 683729190 683731776 0.000000e+00 4290
3 TraesCS4D01G042900 chr2B 98.947 95 1 0 1 95 297685371 297685277 1.230000e-38 171
4 TraesCS4D01G042900 chr5D 96.673 2585 76 8 1 2576 6251527 6248944 0.000000e+00 4289
5 TraesCS4D01G042900 chr5D 96.478 2584 81 8 1 2576 503315252 503317833 0.000000e+00 4259
6 TraesCS4D01G042900 chr3A 96.404 2586 83 7 1 2576 105555211 105552626 0.000000e+00 4252
7 TraesCS4D01G042900 chr1D 96.060 2589 89 8 1 2576 254461150 254463738 0.000000e+00 4204
8 TraesCS4D01G042900 chr1D 95.551 2585 99 10 1 2576 51830216 51827639 0.000000e+00 4122
9 TraesCS4D01G042900 chr7A 95.048 2585 108 11 1 2576 537839663 537837090 0.000000e+00 4047
10 TraesCS4D01G042900 chr7B 96.537 2368 76 6 215 2576 662753104 662750737 0.000000e+00 3914


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 TraesCS4D01G042900 chr4D 19902472 19905047 2575 False 4758 4758 100.000 1 2576 1 chr4D.!!$F1 2575
1 TraesCS4D01G042900 chr1A 554483770 554486357 2587 False 4314 4314 96.832 1 2576 1 chr1A.!!$F1 2575
2 TraesCS4D01G042900 chr2B 683729190 683731776 2586 False 4290 4290 96.676 1 2576 1 chr2B.!!$F1 2575
3 TraesCS4D01G042900 chr5D 6248944 6251527 2583 True 4289 4289 96.673 1 2576 1 chr5D.!!$R1 2575
4 TraesCS4D01G042900 chr5D 503315252 503317833 2581 False 4259 4259 96.478 1 2576 1 chr5D.!!$F1 2575
5 TraesCS4D01G042900 chr3A 105552626 105555211 2585 True 4252 4252 96.404 1 2576 1 chr3A.!!$R1 2575
6 TraesCS4D01G042900 chr1D 254461150 254463738 2588 False 4204 4204 96.060 1 2576 1 chr1D.!!$F1 2575
7 TraesCS4D01G042900 chr1D 51827639 51830216 2577 True 4122 4122 95.551 1 2576 1 chr1D.!!$R1 2575
8 TraesCS4D01G042900 chr7A 537837090 537839663 2573 True 4047 4047 95.048 1 2576 1 chr7A.!!$R1 2575
9 TraesCS4D01G042900 chr7B 662750737 662753104 2367 True 3914 3914 96.537 215 2576 1 chr7B.!!$R1 2361

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
677 681 0.250234 CGGTCAAAGAGCATCCTCCA 59.75 55.0 0.0 0.0 38.96 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2296 1.736645 ACGCCTTCATCGACGTTGG 60.737 57.895 2.2 0.0 34.62 3.77 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
106 107 7.749126 GTCAACGAAATTCATAAAATTCTCCGT 59.251 33.333 0.00 0.00 0.00 4.69
155 159 4.160329 AGGGATTGAGAATATAGGTCGCA 58.840 43.478 0.00 0.00 0.00 5.10
169 173 0.727398 GTCGCATAGTTCAAGTGGGC 59.273 55.000 0.00 0.00 0.00 5.36
251 255 4.368067 TGCAGAAGGTACTAGGGGTATTT 58.632 43.478 0.00 0.00 38.49 1.40
254 258 5.130643 GCAGAAGGTACTAGGGGTATTTCTT 59.869 44.000 0.00 0.00 38.49 2.52
367 371 1.476891 GCTCAGATACCCGTGAGTGAA 59.523 52.381 1.61 0.00 41.99 3.18
412 416 3.873910 TGCTCTGGCTAAACCTATTGAC 58.126 45.455 0.00 0.00 40.22 3.18
414 418 3.679083 GCTCTGGCTAAACCTATTGACGT 60.679 47.826 0.00 0.00 40.22 4.34
442 446 4.434330 GGCGAAATTATAGCTTCCGAATCG 60.434 45.833 0.00 0.00 0.00 3.34
444 448 4.386049 CGAAATTATAGCTTCCGAATCGCT 59.614 41.667 0.00 1.02 37.77 4.93
453 457 3.309954 GCTTCCGAATCGCTCTTAATTGT 59.690 43.478 0.00 0.00 0.00 2.71
467 471 6.166984 TCTTAATTGTATCTCCTGCTCCAG 57.833 41.667 0.00 0.00 0.00 3.86
517 521 3.690460 ACCTCTTCAAACAGGGCTTATG 58.310 45.455 0.00 0.00 33.57 1.90
534 538 4.864806 GCTTATGGCTATCGATTCGATGAA 59.135 41.667 27.35 10.92 46.43 2.57
578 582 6.525629 CGAGAGTTAATTATTGGGGACAGAT 58.474 40.000 0.00 0.00 44.54 2.90
640 644 4.864704 TCAAAAAGGGCAAGGTGTAATC 57.135 40.909 0.00 0.00 0.00 1.75
677 681 0.250234 CGGTCAAAGAGCATCCTCCA 59.750 55.000 0.00 0.00 38.96 3.86
681 685 3.135530 GGTCAAAGAGCATCCTCCATAGT 59.864 47.826 0.00 0.00 38.96 2.12
695 699 7.642082 TCCTCCATAGTTCAAGTAGTAACTC 57.358 40.000 0.00 0.00 37.19 3.01
753 757 2.237643 TGGTAGCTGAAAAGGCGGATTA 59.762 45.455 0.00 0.00 34.52 1.75
784 788 5.598769 ACATTACAATACCTCGCTCCTTAC 58.401 41.667 0.00 0.00 0.00 2.34
1035 1041 6.578023 ACCAATAGTTGAGACTCAATCTAGC 58.422 40.000 20.43 7.78 38.79 3.42
1156 1162 6.503589 TTAATGTGGGTATTTCTGTTTCCG 57.496 37.500 0.00 0.00 0.00 4.30
1525 1531 1.002430 TCACCGAGCAAGCAGAAATCT 59.998 47.619 0.00 0.00 0.00 2.40
1537 1543 6.258507 GCAAGCAGAAATCTTTTTGAAGGAAA 59.741 34.615 7.49 0.00 0.00 3.13
1554 1560 6.013725 TGAAGGAAACTATTCAGGAACAGCTA 60.014 38.462 0.00 0.00 42.68 3.32
1646 1652 9.774413 ATTGAGAAAGCTTTTTCATTTGAATCT 57.226 25.926 27.33 10.38 32.30 2.40
1723 1729 9.424319 GATAGAAATAAGATTGCGTCCAATAGA 57.576 33.333 0.00 0.00 41.60 1.98
2279 2296 3.432592 GCTCTAGGTCTTCGGTCAAAAAC 59.567 47.826 0.00 0.00 0.00 2.43
2340 2357 1.919918 GGGATTGCAATTTTTCTCGCG 59.080 47.619 14.33 0.00 0.00 5.87
2346 2363 2.792116 TGCAATTTTTCTCGCGTTTTCC 59.208 40.909 5.77 0.00 0.00 3.13
2381 2399 5.048846 ACTCAAGGGAGAAACTTTGCTTA 57.951 39.130 0.00 0.00 44.26 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 159 1.134098 CCCATCGCCCACTTGAACTAT 60.134 52.381 0.00 0.00 0.00 2.12
169 173 5.043903 CCTATAATACGAGCAATCCCATCG 58.956 45.833 0.00 0.00 42.04 3.84
208 212 5.647658 TGCAAATTCGACTAATTCACCTGAT 59.352 36.000 0.00 0.00 36.76 2.90
367 371 1.140252 ACAACACGACCCAAGTAAGCT 59.860 47.619 0.00 0.00 0.00 3.74
412 416 4.795970 AGCTATAATTTCGCCTTTCACG 57.204 40.909 0.00 0.00 0.00 4.35
414 418 4.272504 CGGAAGCTATAATTTCGCCTTTCA 59.727 41.667 0.00 0.00 0.00 2.69
442 446 4.994217 GGAGCAGGAGATACAATTAAGAGC 59.006 45.833 0.00 0.00 0.00 4.09
444 448 6.166984 CTGGAGCAGGAGATACAATTAAGA 57.833 41.667 0.00 0.00 0.00 2.10
467 471 4.813296 CAGAACGCCTGGAAATTATACC 57.187 45.455 0.00 0.00 39.23 2.73
517 521 2.028930 AGGGTTCATCGAATCGATAGCC 60.029 50.000 22.11 22.11 45.19 3.93
578 582 2.638480 ACTGCTGTTTTGCCAGTCTA 57.362 45.000 0.00 0.00 34.84 2.59
640 644 5.588240 TGACCGATAGCTACATAAACACAG 58.412 41.667 0.00 0.00 0.00 3.66
677 681 8.431910 TGGAAAGGAGTTACTACTTGAACTAT 57.568 34.615 10.99 0.00 34.47 2.12
681 685 7.311092 TCATGGAAAGGAGTTACTACTTGAA 57.689 36.000 10.99 0.17 34.47 2.69
695 699 1.925888 CCCCCTCCTCATGGAAAGG 59.074 63.158 0.00 0.00 42.66 3.11
733 737 1.751437 AATCCGCCTTTTCAGCTACC 58.249 50.000 0.00 0.00 0.00 3.18
744 748 1.200519 TGTAGCAGGTTAATCCGCCT 58.799 50.000 0.00 0.00 41.99 5.52
753 757 5.357257 CGAGGTATTGTAATGTAGCAGGTT 58.643 41.667 0.00 0.00 0.00 3.50
909 913 2.362369 CCTGGATCAGCCTCACGGT 61.362 63.158 0.00 0.00 37.63 4.83
932 936 5.783100 AAGGCGTGAATGCAAATAAAATG 57.217 34.783 0.00 0.00 36.28 2.32
933 937 6.799926 AAAAGGCGTGAATGCAAATAAAAT 57.200 29.167 0.00 0.00 36.28 1.82
1097 1103 3.072915 TCCGGCATTGAATAGATCCACAT 59.927 43.478 0.00 0.00 0.00 3.21
1100 1106 3.855255 TTCCGGCATTGAATAGATCCA 57.145 42.857 0.00 0.00 0.00 3.41
1156 1162 2.913060 AGCCGCGGATCCTACTCC 60.913 66.667 33.48 7.54 0.00 3.85
1492 1498 2.675317 GCTCGGTGAATGTCTTGCTAGT 60.675 50.000 0.00 0.00 0.00 2.57
1525 1531 8.299990 TGTTCCTGAATAGTTTCCTTCAAAAA 57.700 30.769 0.00 0.00 31.40 1.94
1537 1543 4.142138 CCGTTCTAGCTGTTCCTGAATAGT 60.142 45.833 0.00 0.00 32.90 2.12
1554 1560 5.667466 TGTTACTGAAGAGAAAACCGTTCT 58.333 37.500 0.00 0.00 0.00 3.01
2000 2016 6.709281 AGTTACCCCTCTTTAGTTTAAGAGC 58.291 40.000 7.66 0.00 46.32 4.09
2279 2296 1.736645 ACGCCTTCATCGACGTTGG 60.737 57.895 2.20 0.00 34.62 3.77
2340 2357 7.063426 CCTTGAGTTTGAGTGAAAAAGGAAAAC 59.937 37.037 0.00 0.00 33.44 2.43
2346 2363 5.590259 TCTCCCTTGAGTTTGAGTGAAAAAG 59.410 40.000 0.00 0.00 39.75 2.27
2421 2441 2.673368 AGAAGCGGCAGAAATTAGAACG 59.327 45.455 1.45 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.