Multiple sequence alignment - TraesCS7A01G154300

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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 TraesCS7A01G154300 chr7A 100.000 3394 0 0 1 3394 107624237 107620844 0.000000e+00 6268
1 TraesCS7A01G154300 chr7A 94.194 2635 114 27 775 3394 84767716 84765106 0.000000e+00 3982
2 TraesCS7A01G154300 chr7A 93.758 737 34 9 8 740 84768442 84767714 0.000000e+00 1096
3 TraesCS7A01G154300 chr6A 96.683 3407 83 18 1 3394 194725226 194721837 0.000000e+00 5638
4 TraesCS7A01G154300 chr6A 96.438 2583 69 17 1 2572 194776012 194773442 0.000000e+00 4239
5 TraesCS7A01G154300 chr6A 96.400 2583 73 14 1 2572 194748156 194745583 0.000000e+00 4237
6 TraesCS7A01G154300 chr3A 93.669 2638 111 34 775 3394 202638216 202640815 0.000000e+00 3895
7 TraesCS7A01G154300 chr3A 93.011 744 36 9 1 740 202637487 202638218 0.000000e+00 1072
8 TraesCS7A01G154300 chr3B 86.133 3173 297 87 9 3101 757876472 757873363 0.000000e+00 3290
9 TraesCS7A01G154300 chr3B 93.004 243 16 1 3152 3394 757873368 757873127 1.500000e-93 353
10 TraesCS7A01G154300 chr3B 93.004 243 16 1 3152 3394 757884778 757884537 1.500000e-93 353
11 TraesCS7A01G154300 chr3B 80.663 362 34 21 2768 3101 757885126 757884773 7.270000e-62 248
12 TraesCS7A01G154300 chr3D 94.228 1975 71 22 774 2730 591985195 591987144 0.000000e+00 2976
13 TraesCS7A01G154300 chr3D 95.232 734 26 7 9 740 591984474 591985200 0.000000e+00 1153
14 TraesCS7A01G154300 chr3D 96.672 631 15 5 2767 3394 591987139 591987766 0.000000e+00 1044


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 TraesCS7A01G154300 chr7A 107620844 107624237 3393 True 6268.000000 6268 100.000000 1 3394 1 chr7A.!!$R1 3393
1 TraesCS7A01G154300 chr7A 84765106 84768442 3336 True 2539.000000 3982 93.976000 8 3394 2 chr7A.!!$R2 3386
2 TraesCS7A01G154300 chr6A 194721837 194725226 3389 True 5638.000000 5638 96.683000 1 3394 1 chr6A.!!$R1 3393
3 TraesCS7A01G154300 chr6A 194773442 194776012 2570 True 4239.000000 4239 96.438000 1 2572 1 chr6A.!!$R3 2571
4 TraesCS7A01G154300 chr6A 194745583 194748156 2573 True 4237.000000 4237 96.400000 1 2572 1 chr6A.!!$R2 2571
5 TraesCS7A01G154300 chr3A 202637487 202640815 3328 False 2483.500000 3895 93.340000 1 3394 2 chr3A.!!$F1 3393
6 TraesCS7A01G154300 chr3B 757873127 757876472 3345 True 1821.500000 3290 89.568500 9 3394 2 chr3B.!!$R1 3385
7 TraesCS7A01G154300 chr3B 757884537 757885126 589 True 300.500000 353 86.833500 2768 3394 2 chr3B.!!$R2 626
8 TraesCS7A01G154300 chr3D 591984474 591987766 3292 False 1724.333333 2976 95.377333 9 3394 3 chr3D.!!$F1 3385

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
980 1042 1.280982 CGTAGCTCACCGTACGACTA 58.719 55.000 18.76 7.27 43.81 2.59 F
1953 2058 3.062042 CAAGTTTTTCCTGCAAGCATCC 58.938 45.455 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 2504 1.331214 CGGGGTTAACCTATAGGCGA 58.669 55.000 23.69 3.78 40.03 5.54 R
3056 3217 6.534793 GGAAAAACTCAAACATGAGCAAAGAA 59.465 34.615 0.00 0.00 39.42 2.52 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
76 79 2.426738 CAACACAGAAACAGGGAAGCAA 59.573 45.455 0.00 0.00 0.00 3.91
326 336 1.670811 CGCAGACAACACCTGAAGTTT 59.329 47.619 0.00 0.00 33.65 2.66
443 453 6.613153 AGAAGGTAGTTCTGAAATAGCAGT 57.387 37.500 23.48 13.83 44.41 4.40
543 555 5.419471 TGGTTCTATTTTTATGTTTCCCCCG 59.581 40.000 0.00 0.00 0.00 5.73
581 593 9.250246 TGGTTCCAATAATAGGAAAAAGGTTAG 57.750 33.333 0.00 0.00 46.03 2.34
582 594 8.692710 GGTTCCAATAATAGGAAAAAGGTTAGG 58.307 37.037 0.00 0.00 46.03 2.69
583 595 9.251440 GTTCCAATAATAGGAAAAAGGTTAGGT 57.749 33.333 0.00 0.00 46.03 3.08
584 596 9.831682 TTCCAATAATAGGAAAAAGGTTAGGTT 57.168 29.630 0.00 0.00 41.94 3.50
597 609 4.844884 AGGTTAGGTTATTTGCAGAGGAC 58.155 43.478 0.00 0.00 0.00 3.85
624 636 3.576078 TGTCAACAAGAATCCAGTGGT 57.424 42.857 9.54 0.00 0.00 4.16
646 658 5.123979 GGTAGCAAAAGGAATCCAGTACAAG 59.876 44.000 0.61 0.00 0.00 3.16
818 873 6.012113 TCAGGACAACTCAAAATTCATGGAT 58.988 36.000 0.00 0.00 0.00 3.41
909 971 2.628178 GTTAGGAAGGCCAAGCAGTTTT 59.372 45.455 5.01 0.00 36.29 2.43
980 1042 1.280982 CGTAGCTCACCGTACGACTA 58.719 55.000 18.76 7.27 43.81 2.59
1123 1195 9.515226 AATGTTTTTCTTGCCTTATACTCACTA 57.485 29.630 0.00 0.00 0.00 2.74
1197 1271 9.727859 TTTTGTTCTATATGTACAGCAAACCTA 57.272 29.630 0.33 0.00 0.00 3.08
1210 1284 4.984161 CAGCAAACCTACAGTTTTGATTGG 59.016 41.667 3.69 0.00 46.79 3.16
1380 1454 4.846779 TCTGTAAGCAAATGAAACCCAC 57.153 40.909 0.00 0.00 0.00 4.61
1751 1852 7.285629 TCCAAAATGGATGTACACAAGTTGTAA 59.714 33.333 8.49 0.00 42.67 2.41
1781 1882 6.579666 ACACTACACGAGGAACATTACTTA 57.420 37.500 0.00 0.00 0.00 2.24
1948 2053 3.118542 GTCTGCAAGTTTTTCCTGCAAG 58.881 45.455 0.00 0.00 34.96 4.01
1953 2058 3.062042 CAAGTTTTTCCTGCAAGCATCC 58.938 45.455 0.00 0.00 0.00 3.51
2083 2189 6.472887 CCTAAAGTCCCTCAACAAGATAACA 58.527 40.000 0.00 0.00 0.00 2.41
2104 2210 7.739498 AACAAGTACGAAACCAAACATCTAT 57.261 32.000 0.00 0.00 0.00 1.98
2384 2504 2.622064 AGAAGCGTGTGAAGGAGTTT 57.378 45.000 0.00 0.00 0.00 2.66
2403 2523 1.331214 TCGCCTATAGGTTAACCCCG 58.669 55.000 21.30 12.65 37.57 5.73
2495 2616 4.345859 TTGTGTTCTTATCCTTCCGTGT 57.654 40.909 0.00 0.00 0.00 4.49
2554 2676 6.493115 CACCACTCATAGATGATAAGAGGAGT 59.507 42.308 0.00 0.00 36.02 3.85
2694 2818 5.568620 AGACCCTTCTTGTTGTTGTAGAT 57.431 39.130 0.00 0.00 0.00 1.98
2746 2876 1.620822 GTTGGGAAACATGTGCTCCT 58.379 50.000 20.99 0.00 0.00 3.69
2841 2971 7.068103 TGTTTTTCCTCATGTGTTTATGTCTGT 59.932 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 5.962433 TGCTTAGCTCGTAGTTTGAACTAT 58.038 37.500 5.60 0.00 42.88 2.12
251 256 4.968719 AGGAAAAAGTCAACCCTGGAAATT 59.031 37.500 0.00 0.00 0.00 1.82
326 336 4.764823 GTGATTCCACCCAGTTGACATTTA 59.235 41.667 0.00 0.00 37.33 1.40
543 555 1.580059 TGGAACCATGGAGTAGTCCC 58.420 55.000 21.47 8.56 43.15 4.46
581 593 3.751698 ACTTTCGTCCTCTGCAAATAACC 59.248 43.478 0.00 0.00 0.00 2.85
582 594 5.147162 CAACTTTCGTCCTCTGCAAATAAC 58.853 41.667 0.00 0.00 0.00 1.89
583 595 4.819630 ACAACTTTCGTCCTCTGCAAATAA 59.180 37.500 0.00 0.00 0.00 1.40
584 596 4.385825 ACAACTTTCGTCCTCTGCAAATA 58.614 39.130 0.00 0.00 0.00 1.40
585 597 3.214328 ACAACTTTCGTCCTCTGCAAAT 58.786 40.909 0.00 0.00 0.00 2.32
597 609 5.168526 TGGATTCTTGTTGACAACTTTCG 57.831 39.130 18.73 5.39 0.00 3.46
624 636 5.876357 ACTTGTACTGGATTCCTTTTGCTA 58.124 37.500 3.95 0.00 0.00 3.49
690 702 5.779922 ACGATTAACAAACTGAGAGCACTA 58.220 37.500 0.00 0.00 0.00 2.74
818 873 4.614993 GCGCTCTTGCCTAAACATGTTTTA 60.615 41.667 27.66 13.19 33.28 1.52
909 971 4.502950 GGTGGTGCATTTTCTTTTCCATGA 60.503 41.667 0.00 0.00 0.00 3.07
980 1042 1.858739 TATTGGGCCCCTTTCGCTGT 61.859 55.000 22.27 0.00 0.00 4.40
1037 1099 0.776810 TCCTTCAACATTGGCCAGGA 59.223 50.000 5.11 3.33 31.28 3.86
1138 1210 1.002087 AGCTTGCAGGTTAGCTTACGT 59.998 47.619 4.77 0.00 45.03 3.57
1210 1284 2.030981 CCAAATGTGGCAATGGTTTTGC 60.031 45.455 1.76 1.76 44.22 3.68
1615 1711 7.659390 ACTTGTGTTGTGGAAAAATGAAAAGAA 59.341 29.630 0.00 0.00 0.00 2.52
1751 1852 4.062991 GTTCCTCGTGTAGTGTTGGAAAT 58.937 43.478 0.00 0.00 35.68 2.17
1781 1882 2.502213 TGATGTTGACGACGAACAGT 57.498 45.000 0.00 0.00 36.77 3.55
2083 2189 5.938125 AGCATAGATGTTTGGTTTCGTACTT 59.062 36.000 0.00 0.00 0.00 2.24
2104 2210 6.976934 AGGAAGTCAGGAAAAATAAAAGCA 57.023 33.333 0.00 0.00 0.00 3.91
2204 2322 8.851541 AAATGCCACAATCAATACTGAAAAAT 57.148 26.923 0.00 0.00 34.49 1.82
2384 2504 1.331214 CGGGGTTAACCTATAGGCGA 58.669 55.000 23.69 3.78 40.03 5.54
2495 2616 4.214119 GCTGTCAGCACTTTTTCATGTCTA 59.786 41.667 20.16 0.00 41.89 2.59
2554 2676 8.791327 TTTTGCTGATATGACTCTTGATACAA 57.209 30.769 0.00 0.00 0.00 2.41
2719 2849 4.256920 CACATGTTTCCCAACCAAACAAA 58.743 39.130 0.00 0.00 44.73 2.83
2720 2850 3.866651 CACATGTTTCCCAACCAAACAA 58.133 40.909 0.00 0.00 44.73 2.83
2746 2876 4.415224 AACTAGGGGAGAAGTACCTTCA 57.585 45.455 6.74 0.00 42.37 3.02
3056 3217 6.534793 GGAAAAACTCAAACATGAGCAAAGAA 59.465 34.615 0.00 0.00 39.42 2.52


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

AutoCloner maintained by Alex Coulton.