Multiple sequence alignment - TraesCS5D01G079500

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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 TraesCS5D01G079500 chr5D 100.000 2660 0 0 1 2660 80019581 80016922 0 4913
1 TraesCS5D01G079500 chr4D 95.284 2693 92 8 1 2660 123348976 123351666 0 4237
2 TraesCS5D01G079500 chr4D 94.879 2695 101 9 1 2660 134978278 134980970 0 4178
3 TraesCS5D01G079500 chr4D 93.943 2691 120 12 1 2660 240995916 240993238 0 4026
4 TraesCS5D01G079500 chr4D 92.804 945 35 8 1747 2660 123561662 123562604 0 1338
5 TraesCS5D01G079500 chr2D 94.790 2668 112 6 1 2660 39655508 39658156 0 4132
6 TraesCS5D01G079500 chr1D 94.649 2691 94 9 1 2660 269427894 269425223 0 4126
7 TraesCS5D01G079500 chr1D 95.218 2384 82 5 1 2353 185744906 185742524 0 3742
8 TraesCS5D01G079500 chr6D 94.277 2691 104 14 1 2660 370021376 370024047 0 4071
9 TraesCS5D01G079500 chr7B 95.725 2456 73 5 1 2425 742949883 742947429 0 3925
10 TraesCS5D01G079500 chr7B 95.475 2453 79 5 1 2422 716783462 716785913 0 3886
11 TraesCS5D01G079500 chr7A 95.760 2453 71 6 1 2422 60083792 60086242 0 3923
12 TraesCS5D01G079500 chr7A 95.643 2456 75 5 1 2425 60169912 60167458 0 3914
13 TraesCS5D01G079500 chr5A 95.638 2453 75 5 1 2422 16543409 16545860 0 3908
14 TraesCS5D01G079500 chr5A 95.597 2453 75 6 1 2422 420184558 420187008 0 3901
15 TraesCS5D01G079500 chr2A 95.556 2453 77 5 1 2422 755479404 755481855 0 3897
16 TraesCS5D01G079500 chr7D 96.162 495 17 2 2166 2660 382029145 382028653 0 808


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 TraesCS5D01G079500 chr5D 80016922 80019581 2659 True 4913 4913 100.000 1 2660 1 chr5D.!!$R1 2659
1 TraesCS5D01G079500 chr4D 123348976 123351666 2690 False 4237 4237 95.284 1 2660 1 chr4D.!!$F1 2659
2 TraesCS5D01G079500 chr4D 134978278 134980970 2692 False 4178 4178 94.879 1 2660 1 chr4D.!!$F3 2659
3 TraesCS5D01G079500 chr4D 240993238 240995916 2678 True 4026 4026 93.943 1 2660 1 chr4D.!!$R1 2659
4 TraesCS5D01G079500 chr4D 123561662 123562604 942 False 1338 1338 92.804 1747 2660 1 chr4D.!!$F2 913
5 TraesCS5D01G079500 chr2D 39655508 39658156 2648 False 4132 4132 94.790 1 2660 1 chr2D.!!$F1 2659
6 TraesCS5D01G079500 chr1D 269425223 269427894 2671 True 4126 4126 94.649 1 2660 1 chr1D.!!$R2 2659
7 TraesCS5D01G079500 chr1D 185742524 185744906 2382 True 3742 3742 95.218 1 2353 1 chr1D.!!$R1 2352
8 TraesCS5D01G079500 chr6D 370021376 370024047 2671 False 4071 4071 94.277 1 2660 1 chr6D.!!$F1 2659
9 TraesCS5D01G079500 chr7B 742947429 742949883 2454 True 3925 3925 95.725 1 2425 1 chr7B.!!$R1 2424
10 TraesCS5D01G079500 chr7B 716783462 716785913 2451 False 3886 3886 95.475 1 2422 1 chr7B.!!$F1 2421
11 TraesCS5D01G079500 chr7A 60083792 60086242 2450 False 3923 3923 95.760 1 2422 1 chr7A.!!$F1 2421
12 TraesCS5D01G079500 chr7A 60167458 60169912 2454 True 3914 3914 95.643 1 2425 1 chr7A.!!$R1 2424
13 TraesCS5D01G079500 chr5A 16543409 16545860 2451 False 3908 3908 95.638 1 2422 1 chr5A.!!$F1 2421
14 TraesCS5D01G079500 chr5A 420184558 420187008 2450 False 3901 3901 95.597 1 2422 1 chr5A.!!$F2 2421
15 TraesCS5D01G079500 chr2A 755479404 755481855 2451 False 3897 3897 95.556 1 2422 1 chr2A.!!$F1 2421

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
994 997 0.553819 TAAACAGGCGGGGGCATATT 59.446 50.0 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 1897 0.902048 GGTATAGGTAGGGGGTCCGC 60.902 65.0 0.0 0.0 38.33 5.54 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
74 75 7.758980 CGGTTCACCAAATGATAATTCAAATCA 59.241 33.333 0.00 0.00 37.11 2.57
135 136 7.446625 CGGATTTCTCCCTTCAAAATATCATCT 59.553 37.037 0.00 0.00 38.45 2.90
280 281 1.718757 GGAGATGGGATTGCACGTGC 61.719 60.000 33.11 33.11 42.50 5.34
293 294 3.016031 TGCACGTGCTTATGGATTGAAT 58.984 40.909 37.59 0.00 42.66 2.57
331 332 3.680156 GGTGGAATTTGCCAGCGA 58.320 55.556 0.00 0.00 45.32 4.93
455 456 4.445448 GGATCTATTGTGGATGTTCCTGCT 60.445 45.833 0.00 0.00 37.46 4.24
488 489 4.760047 GGCCGTGTGGTCGATGCT 62.760 66.667 0.00 0.00 37.67 3.79
568 569 1.566231 AGTGAAAGCCCCAGGGATTAG 59.434 52.381 7.25 0.00 43.82 1.73
585 586 5.293569 GGGATTAGTGAACGTAAATCTGTGG 59.706 44.000 0.00 0.00 0.00 4.17
670 671 3.119029 CGAGAACTTATAACCGGGGACAA 60.119 47.826 6.32 0.00 0.00 3.18
737 738 2.978156 AGCAAATGAACTCAAGGGGA 57.022 45.000 0.00 0.00 0.00 4.81
791 794 1.066303 TGCGATTGGACAAAAACGCTT 59.934 42.857 23.16 0.00 39.77 4.68
857 860 7.768582 TGCTTTCGAATATTCCATTCTTGTAGA 59.231 33.333 9.87 0.00 0.00 2.59
865 868 2.642311 TCCATTCTTGTAGAAGCCACCA 59.358 45.455 0.00 0.00 37.69 4.17
905 908 3.113824 TGCAATTTCTGGCCCCATATTT 58.886 40.909 0.00 0.00 0.00 1.40
916 919 1.499007 CCCCATATTTAGGGTGTGCCT 59.501 52.381 0.00 0.00 45.28 4.75
948 951 2.183478 TCCGCGATAATGGAATGCAT 57.817 45.000 8.23 0.00 0.00 3.96
986 989 3.536956 TGATCTAAGTAAACAGGCGGG 57.463 47.619 0.00 0.00 0.00 6.13
994 997 0.553819 TAAACAGGCGGGGGCATATT 59.446 50.000 0.00 0.00 0.00 1.28
1070 1073 7.654022 GGGATGTTTTCTATTTACATTCCCA 57.346 36.000 0.00 0.00 40.58 4.37
1124 1127 1.066303 GACAGGTGCAGGTATCTCGAG 59.934 57.143 5.93 5.93 0.00 4.04
1128 1131 0.173481 GTGCAGGTATCTCGAGTGCA 59.827 55.000 20.06 20.06 41.72 4.57
1163 1166 3.402628 AACACAAGCTGGAGACGTATT 57.597 42.857 0.00 0.00 0.00 1.89
1235 1238 8.862325 TGTTTGGAAATAGAGCTCTTTTATCA 57.138 30.769 23.84 17.38 0.00 2.15
1267 1270 5.823045 AGACCAGCTATTAATGTTGGCTTAC 59.177 40.000 15.57 8.69 39.03 2.34
1271 1274 3.304458 GCTATTAATGTTGGCTTACCCGC 60.304 47.826 0.00 0.00 35.87 6.13
1289 1292 4.039357 CAGTCGCGTCGGGTCTGT 62.039 66.667 22.19 0.37 0.00 3.41
1359 1362 2.588027 TGGCACAATATCGCGAAGTA 57.412 45.000 15.24 1.35 31.92 2.24
1520 1523 1.571460 CTGTCAACGGCTTCTGTGC 59.429 57.895 0.00 0.00 0.00 4.57
1523 1526 0.880278 GTCAACGGCTTCTGTGCTCA 60.880 55.000 0.00 0.00 0.00 4.26
1657 1660 6.916360 TGGAACCAGATGCTTCTTTAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
1731 1734 5.186198 GCAGATGTAGGAAGAAGGCTTTTA 58.814 41.667 0.00 0.00 33.61 1.52
1772 1775 3.913089 AGGCTATTTTGGACTTTTTGCG 58.087 40.909 0.00 0.00 0.00 4.85
1855 1858 2.204059 ACAAGGGGGAGCTGCTCT 60.204 61.111 27.09 6.46 0.00 4.09
1877 1880 2.318207 AGTAGTTCAGGATACCCCACCT 59.682 50.000 0.00 0.00 37.41 4.00
2102 2122 5.360714 ACAAGAAATCCAAGAAAGAACAGCA 59.639 36.000 0.00 0.00 0.00 4.41
2112 2132 6.539826 CCAAGAAAGAACAGCAAAGGAAAAAT 59.460 34.615 0.00 0.00 0.00 1.82
2120 2140 5.486526 ACAGCAAAGGAAAAATGTGACAAA 58.513 33.333 0.00 0.00 0.00 2.83
2123 2143 7.121020 ACAGCAAAGGAAAAATGTGACAAAAAT 59.879 29.630 0.00 0.00 0.00 1.82
2127 2147 9.919348 CAAAGGAAAAATGTGACAAAAATAGTG 57.081 29.630 0.00 0.00 0.00 2.74
2128 2149 9.665719 AAAGGAAAAATGTGACAAAAATAGTGT 57.334 25.926 0.00 0.00 0.00 3.55
2151 2178 5.723672 TTTCTCGAGATGTTAGAAGGTGT 57.276 39.130 17.44 0.00 31.30 4.16
2353 2404 5.219768 CGTTTTCCAATCGCATAAAAAGTCG 60.220 40.000 0.00 0.00 0.00 4.18
2355 2406 6.483385 TTTCCAATCGCATAAAAAGTCGTA 57.517 33.333 0.00 0.00 0.00 3.43
2433 2485 2.159240 CGTTCTCTTGGTCGATGATGGA 60.159 50.000 0.00 0.00 0.00 3.41
2478 2530 8.921353 ATTGGATCTCTCTATGAATGGAAAAG 57.079 34.615 0.00 0.00 0.00 2.27
2487 2539 1.713647 TGAATGGAAAAGGGGGTGCTA 59.286 47.619 0.00 0.00 0.00 3.49
2519 2571 4.027437 AGTAACCACTTTTGAAAGGGCAA 58.973 39.130 8.23 0.00 38.11 4.52
2621 2678 6.728164 TGATTCTTGTTTTTATCAATGGGGGA 59.272 34.615 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
293 294 4.263639 ACCATTTCTCCTGCTTGAATCTCA 60.264 41.667 0.00 0.00 0.00 3.27
488 489 6.395780 TTTCCATCAATAGGTACTCCCAAA 57.604 37.500 0.00 0.00 41.75 3.28
568 569 5.390567 GGTTCATCCACAGATTTACGTTCAC 60.391 44.000 0.00 0.00 35.97 3.18
585 586 1.404583 GCCTGTTTGCATGGGTTCATC 60.405 52.381 0.00 0.00 0.00 2.92
661 662 0.466555 TCCAGTTTGTTTGTCCCCGG 60.467 55.000 0.00 0.00 0.00 5.73
670 671 8.007405 AGCTATTGTAGTTTTTCCAGTTTGTT 57.993 30.769 0.00 0.00 0.00 2.83
791 794 3.814625 TGAACTAATTGTGCCACAGTCA 58.185 40.909 0.00 0.00 0.00 3.41
837 840 6.483307 TGGCTTCTACAAGAATGGAATATTCG 59.517 38.462 9.32 0.00 33.13 3.34
857 860 1.201429 AGGATCCGAAGTGGTGGCTT 61.201 55.000 5.98 0.00 39.52 4.35
865 868 0.032615 AGAGGAGCAGGATCCGAAGT 60.033 55.000 5.98 0.00 44.65 3.01
905 908 2.938798 CCCCCAAGGCACACCCTA 60.939 66.667 0.00 0.00 45.62 3.53
1124 1127 3.057876 TGTTTCAATCACGGGTAATGCAC 60.058 43.478 0.00 0.00 0.00 4.57
1128 1131 4.320935 GCTTGTGTTTCAATCACGGGTAAT 60.321 41.667 0.00 0.00 38.48 1.89
1163 1166 1.710244 CATTGGTGGGGATATAGGCCA 59.290 52.381 5.01 0.00 0.00 5.36
1235 1238 9.113838 CAACATTAATAGCTGGTCTAATTCTGT 57.886 33.333 0.00 0.00 0.00 3.41
1271 1274 4.778415 CAGACCCGACGCGACTGG 62.778 72.222 15.93 16.25 0.00 4.00
1289 1292 3.592898 TCATAGCTTTCAACTGAGCGA 57.407 42.857 0.00 0.00 43.53 4.93
1500 1503 0.882042 CACAGAAGCCGTTGACAGCT 60.882 55.000 0.00 0.00 42.40 4.24
1520 1523 6.373774 AGAAATTCTGTCTAGTGGCATTTGAG 59.626 38.462 0.00 0.00 0.00 3.02
1523 1526 6.240894 TGAGAAATTCTGTCTAGTGGCATTT 58.759 36.000 0.00 0.00 0.00 2.32
1657 1660 3.568007 CACAGGTAAGGCAAAGTGCTTTA 59.432 43.478 1.12 1.12 41.04 1.85
1731 1734 2.028561 ATTGGGGTTCAGTTGGCAAT 57.971 45.000 1.92 0.00 0.00 3.56
1855 1858 3.534747 AGGTGGGGTATCCTGAACTACTA 59.465 47.826 0.00 0.00 36.20 1.82
1894 1897 0.902048 GGTATAGGTAGGGGGTCCGC 60.902 65.000 0.00 0.00 38.33 5.54
2102 2122 9.665719 ACACTATTTTTGTCACATTTTTCCTTT 57.334 25.926 0.00 0.00 0.00 3.11
2112 2132 7.279090 TCTCGAGAAAACACTATTTTTGTCACA 59.721 33.333 14.01 0.00 38.19 3.58
2120 2140 9.706691 TTCTAACATCTCGAGAAAACACTATTT 57.293 29.630 20.91 4.91 0.00 1.40
2123 2143 7.039923 ACCTTCTAACATCTCGAGAAAACACTA 60.040 37.037 20.91 4.77 0.00 2.74
2127 2147 5.927115 ACACCTTCTAACATCTCGAGAAAAC 59.073 40.000 20.91 0.00 0.00 2.43
2128 2149 6.097915 ACACCTTCTAACATCTCGAGAAAA 57.902 37.500 20.91 4.28 0.00 2.29
2151 2178 3.118038 AGCTCCGGCACCTATTGATTTAA 60.118 43.478 0.00 0.00 41.70 1.52
2178 2229 2.103537 AAGGACGTTTCCAATACCGG 57.896 50.000 0.00 0.00 45.72 5.28
2433 2485 9.927668 ATCCAATCGTCAAAATCAATAAAAAGT 57.072 25.926 0.00 0.00 0.00 2.66
2478 2530 2.192175 CCAATCCGTAGCACCCCC 59.808 66.667 0.00 0.00 0.00 5.40
2487 2539 1.652947 AGTGGTTACTCCCAATCCGT 58.347 50.000 0.00 0.00 35.92 4.69
2543 2596 5.798125 TTTCCTTTTTGTGCCATATGTCA 57.202 34.783 1.24 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.