Multiple sequence alignment - TraesCS7B01G048600

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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 TraesCS7B01G048600 chr7B 100.000 2780 0 0 1 2780 48456383 48453604 0.000000e+00 5134
1 TraesCS7B01G048600 chr7D 92.438 2129 73 41 695 2777 94435006 94432920 0.000000e+00 2959
2 TraesCS7B01G048600 chr7D 94.671 319 13 4 1 318 94435635 94435320 2.490000e-135 492
3 TraesCS7B01G048600 chr7D 87.616 323 26 10 338 651 94435333 94435016 2.040000e-96 363
4 TraesCS7B01G048600 chr7A 90.045 2240 95 58 587 2780 97874254 97872097 0.000000e+00 2784
5 TraesCS7B01G048600 chr7A 93.146 321 17 4 1 320 97876968 97876652 1.510000e-127 466
6 TraesCS7B01G048600 chr7A 95.092 163 6 1 417 579 97876553 97876393 3.550000e-64 255
7 TraesCS7B01G048600 chr7A 97.561 82 2 0 338 419 97876667 97876586 1.040000e-29 141


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 TraesCS7B01G048600 chr7B 48453604 48456383 2779 True 5134.000000 5134 100.000 1 2780 1 chr7B.!!$R1 2779
1 TraesCS7B01G048600 chr7D 94432920 94435635 2715 True 1271.333333 2959 91.575 1 2777 3 chr7D.!!$R1 2776
2 TraesCS7B01G048600 chr7A 97872097 97876968 4871 True 911.500000 2784 93.961 1 2780 4 chr7A.!!$R1 2779

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
319 321 0.109689 GCAGAGAGTACACGACGCTT 60.11 55.0 0.0 0.0 38.47 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 4409 0.181587 TCCAAACAAGACTTCGGCCA 59.818 50.0 2.24 0.0 0.0 5.36 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
36 37 1.136147 CAAGCGCAGACTGCCAATC 59.864 57.895 21.55 8.46 41.12 2.67
106 107 8.652810 ATCACAGGCAAATTTATATTTTCTGC 57.347 30.769 13.62 5.91 36.69 4.26
107 108 7.839907 TCACAGGCAAATTTATATTTTCTGCT 58.160 30.769 13.62 4.76 36.69 4.24
174 176 3.457234 CTGCATGTTAGTTCGAGCCATA 58.543 45.455 0.00 0.00 0.00 2.74
304 306 2.101750 TGACTAGGTTTTGACGTGCAGA 59.898 45.455 0.00 0.00 0.00 4.26
305 307 2.731976 GACTAGGTTTTGACGTGCAGAG 59.268 50.000 0.00 0.00 0.00 3.35
306 308 2.364324 ACTAGGTTTTGACGTGCAGAGA 59.636 45.455 0.00 0.00 0.00 3.10
307 309 1.871080 AGGTTTTGACGTGCAGAGAG 58.129 50.000 0.00 0.00 0.00 3.20
308 310 1.139058 AGGTTTTGACGTGCAGAGAGT 59.861 47.619 0.00 0.00 0.00 3.24
309 311 2.364324 AGGTTTTGACGTGCAGAGAGTA 59.636 45.455 0.00 0.00 0.00 2.59
310 312 2.475487 GGTTTTGACGTGCAGAGAGTAC 59.525 50.000 0.00 0.00 0.00 2.73
311 313 3.120792 GTTTTGACGTGCAGAGAGTACA 58.879 45.455 0.00 0.00 32.52 2.90
312 314 2.417339 TTGACGTGCAGAGAGTACAC 57.583 50.000 0.00 0.00 32.52 2.90
316 318 3.002990 GTGCAGAGAGTACACGACG 57.997 57.895 0.00 0.00 32.52 5.12
317 319 1.066114 GTGCAGAGAGTACACGACGC 61.066 60.000 0.00 0.00 32.52 5.19
318 320 1.235281 TGCAGAGAGTACACGACGCT 61.235 55.000 0.00 0.00 41.47 5.07
319 321 0.109689 GCAGAGAGTACACGACGCTT 60.110 55.000 0.00 0.00 38.47 4.68
320 322 1.129998 GCAGAGAGTACACGACGCTTA 59.870 52.381 0.00 0.00 38.47 3.09
321 323 2.771689 CAGAGAGTACACGACGCTTAC 58.228 52.381 0.00 0.00 38.47 2.34
322 324 1.736681 AGAGAGTACACGACGCTTACC 59.263 52.381 0.00 0.00 38.47 2.85
323 325 0.807496 AGAGTACACGACGCTTACCC 59.193 55.000 0.00 0.00 33.94 3.69
324 326 0.179153 GAGTACACGACGCTTACCCC 60.179 60.000 0.00 0.00 0.00 4.95
325 327 1.514873 GTACACGACGCTTACCCCG 60.515 63.158 0.00 0.00 0.00 5.73
326 328 3.340953 TACACGACGCTTACCCCGC 62.341 63.158 0.00 0.00 0.00 6.13
329 331 4.745751 CGACGCTTACCCCGCCAA 62.746 66.667 0.00 0.00 0.00 4.52
330 332 2.358984 GACGCTTACCCCGCCAAA 60.359 61.111 0.00 0.00 0.00 3.28
331 333 1.967494 GACGCTTACCCCGCCAAAA 60.967 57.895 0.00 0.00 0.00 2.44
332 334 1.517210 GACGCTTACCCCGCCAAAAA 61.517 55.000 0.00 0.00 0.00 1.94
379 381 0.777446 AGGCCAACACCCAACAGTAT 59.223 50.000 5.01 0.00 0.00 2.12
570 1021 3.245016 ACAGGAATTGAGAGTTGATGGCA 60.245 43.478 0.00 0.00 0.00 4.92
572 1023 2.096496 GGAATTGAGAGTTGATGGCACG 59.904 50.000 0.00 0.00 0.00 5.34
649 2817 8.472683 TTCGGAAATTATTAAACAAATGGCAG 57.527 30.769 0.00 0.00 0.00 4.85
670 2838 7.232534 TGGCAGTGACCAAAATAAGATTTTACT 59.767 33.333 0.00 0.00 36.55 2.24
671 2839 7.542130 GGCAGTGACCAAAATAAGATTTTACTG 59.458 37.037 14.98 14.98 35.14 2.74
672 2840 7.062255 GCAGTGACCAAAATAAGATTTTACTGC 59.938 37.037 22.08 22.08 45.85 4.40
868 3040 4.657436 AAGAAACCCACATAAAAACGCA 57.343 36.364 0.00 0.00 0.00 5.24
925 3097 4.083862 GGGGGTGTCTGCGTCTCC 62.084 72.222 0.00 0.00 0.00 3.71
926 3098 2.997897 GGGGTGTCTGCGTCTCCT 60.998 66.667 0.00 0.00 0.00 3.69
933 3105 1.271652 TGTCTGCGTCTCCTTCTCTCT 60.272 52.381 0.00 0.00 0.00 3.10
934 3106 1.400494 GTCTGCGTCTCCTTCTCTCTC 59.600 57.143 0.00 0.00 0.00 3.20
937 3109 0.395173 GCGTCTCCTTCTCTCTCCCT 60.395 60.000 0.00 0.00 0.00 4.20
938 3110 1.675552 CGTCTCCTTCTCTCTCCCTC 58.324 60.000 0.00 0.00 0.00 4.30
944 3116 1.476833 CCTTCTCTCTCCCTCCTCTCG 60.477 61.905 0.00 0.00 0.00 4.04
1009 3193 4.856801 CCGAGGGAATGGCCACCG 62.857 72.222 8.16 5.00 38.95 4.94
1035 3225 3.519930 GCCTCCTCGTCCTCGTCC 61.520 72.222 0.00 0.00 38.33 4.79
1036 3226 2.272797 CCTCCTCGTCCTCGTCCT 59.727 66.667 0.00 0.00 38.33 3.85
1037 3227 1.820481 CCTCCTCGTCCTCGTCCTC 60.820 68.421 0.00 0.00 38.33 3.71
1541 3731 2.046023 CTGCGTCATCCCCAGCAA 60.046 61.111 0.00 0.00 39.26 3.91
1543 3733 3.499737 GCGTCATCCCCAGCAACG 61.500 66.667 0.00 0.00 36.48 4.10
1544 3734 2.819595 CGTCATCCCCAGCAACGG 60.820 66.667 0.00 0.00 0.00 4.44
1545 3735 3.134127 GTCATCCCCAGCAACGGC 61.134 66.667 0.00 0.00 41.61 5.68
1546 3736 3.645660 TCATCCCCAGCAACGGCA 61.646 61.111 0.00 0.00 44.61 5.69
1547 3737 3.136123 CATCCCCAGCAACGGCAG 61.136 66.667 0.00 0.00 44.61 4.85
1820 4014 2.548067 CGTTTACAGCTCACACCTTCCT 60.548 50.000 0.00 0.00 0.00 3.36
1854 4048 5.666969 TCGACAGTTACCTGAATTTTGTG 57.333 39.130 0.00 0.00 41.50 3.33
1864 4060 6.743575 ACCTGAATTTTGTGCATAGTACTC 57.256 37.500 0.00 0.00 0.00 2.59
1866 4062 5.066505 CCTGAATTTTGTGCATAGTACTCCC 59.933 44.000 0.00 0.00 0.00 4.30
1992 4200 0.394565 CTAGATACACCTGGCTGGCC 59.605 60.000 10.71 4.43 40.22 5.36
2008 4216 2.108976 CCGTGTGCCTGTGTCACT 59.891 61.111 4.27 0.00 35.58 3.41
2009 4217 1.956170 CCGTGTGCCTGTGTCACTC 60.956 63.158 4.27 0.00 35.58 3.51
2060 4268 0.604243 ATTTGGGTCGCTGTTACGCA 60.604 50.000 0.00 0.00 37.94 5.24
2063 4271 1.213537 GGGTCGCTGTTACGCACTA 59.786 57.895 1.04 0.00 0.00 2.74
2112 4322 7.807433 GTCTATCATGCAATTGTTTGTTGTGTA 59.193 33.333 7.40 0.00 35.17 2.90
2200 4414 8.915871 CATTCTTTGGAGTAAACAACCATATG 57.084 34.615 0.00 0.00 33.56 1.78
2203 4417 3.626930 TGGAGTAAACAACCATATGGCC 58.373 45.455 22.18 11.50 39.32 5.36
2208 4422 2.507407 AACAACCATATGGCCGAAGT 57.493 45.000 22.18 10.09 39.32 3.01
2239 4456 9.912634 TTTGGATTTTCAACTAGATAAAAGCTG 57.087 29.630 0.00 0.00 31.14 4.24
2244 4463 6.875948 TTCAACTAGATAAAAGCTGCACAA 57.124 33.333 1.02 0.00 0.00 3.33
2257 4476 2.399356 GCACAAGCTAAGCCCCGAC 61.399 63.158 0.00 0.00 37.91 4.79
2260 4479 2.682494 AAGCTAAGCCCCGACCGA 60.682 61.111 0.00 0.00 0.00 4.69
2261 4480 2.064581 AAGCTAAGCCCCGACCGAT 61.065 57.895 0.00 0.00 0.00 4.18
2607 4827 3.141488 CACCGACGGGAGGAGGAG 61.141 72.222 20.00 0.00 36.97 3.69
2608 4828 4.444081 ACCGACGGGAGGAGGAGG 62.444 72.222 20.00 0.00 36.97 4.30
2609 4829 4.124943 CCGACGGGAGGAGGAGGA 62.125 72.222 5.81 0.00 34.06 3.71
2626 4846 1.026718 GGACTCGCATTTGTGGAGGG 61.027 60.000 5.98 0.00 0.00 4.30
2677 4897 1.141881 CTTGACCCGTCCGATCAGG 59.858 63.158 0.00 0.00 42.97 3.86
2686 4906 3.766644 TCCGATCAGGATGCACAAG 57.233 52.632 0.00 0.00 45.98 3.16
2706 4941 1.668919 GCATTATCGATCCTTCGGCGA 60.669 52.381 4.99 4.99 45.53 5.54
2707 4942 2.881074 CATTATCGATCCTTCGGCGAT 58.119 47.619 11.76 0.00 45.53 4.58
2708 4943 2.631418 TTATCGATCCTTCGGCGATC 57.369 50.000 11.76 3.97 45.53 3.69
2709 4944 1.530323 TATCGATCCTTCGGCGATCA 58.470 50.000 11.76 0.00 45.53 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.034179 TCAGTCACCTCGTGTGTACTTG 59.966 50.000 7.51 3.85 45.61 3.16
159 161 6.074463 CCGTAGAAATTATGGCTCGAACTAAC 60.074 42.308 0.00 0.00 0.00 2.34
174 176 0.743345 GCAGCCCGACCGTAGAAATT 60.743 55.000 0.00 0.00 0.00 1.82
272 274 1.535833 ACCTAGTCACGACACTGAGG 58.464 55.000 0.00 3.46 0.00 3.86
304 306 0.807496 GGGTAAGCGTCGTGTACTCT 59.193 55.000 0.00 0.00 0.00 3.24
305 307 0.179153 GGGGTAAGCGTCGTGTACTC 60.179 60.000 0.00 0.00 0.00 2.59
306 308 1.885871 GGGGTAAGCGTCGTGTACT 59.114 57.895 0.00 0.00 0.00 2.73
307 309 1.514873 CGGGGTAAGCGTCGTGTAC 60.515 63.158 0.00 0.00 0.00 2.90
308 310 2.876955 CGGGGTAAGCGTCGTGTA 59.123 61.111 0.00 0.00 0.00 2.90
309 311 4.729856 GCGGGGTAAGCGTCGTGT 62.730 66.667 0.00 0.00 0.00 4.49
312 314 4.745751 TTGGCGGGGTAAGCGTCG 62.746 66.667 0.00 0.00 35.00 5.12
313 315 1.517210 TTTTTGGCGGGGTAAGCGTC 61.517 55.000 0.00 0.00 35.00 5.19
314 316 1.528776 TTTTTGGCGGGGTAAGCGT 60.529 52.632 0.00 0.00 35.00 5.07
315 317 3.356837 TTTTTGGCGGGGTAAGCG 58.643 55.556 0.00 0.00 35.00 4.68
333 335 3.450578 TCAAGCGTCGTGTACTCTTTTT 58.549 40.909 0.00 0.00 30.67 1.94
334 336 3.088194 TCAAGCGTCGTGTACTCTTTT 57.912 42.857 0.00 0.00 30.67 2.27
335 337 2.787601 TCAAGCGTCGTGTACTCTTT 57.212 45.000 0.00 0.00 30.67 2.52
336 338 2.728225 CGATCAAGCGTCGTGTACTCTT 60.728 50.000 0.00 0.00 33.37 2.85
379 381 1.451927 GATGTGCGCCCCTGATGAA 60.452 57.895 4.18 0.00 0.00 2.57
482 519 4.507756 GGTTTTGACCAGACTTTGCAATTC 59.492 41.667 0.00 0.00 0.00 2.17
570 1021 2.081462 GCTTACTAAATGGCACCACGT 58.919 47.619 0.00 0.00 0.00 4.49
572 1023 2.352388 TCGCTTACTAAATGGCACCAC 58.648 47.619 0.00 0.00 0.00 4.16
585 1036 3.487544 GCTCCCATTTGAACATCGCTTAC 60.488 47.826 0.00 0.00 0.00 2.34
641 2809 6.610075 ATCTTATTTTGGTCACTGCCATTT 57.390 33.333 0.00 0.00 38.48 2.32
670 2838 6.205784 CCATGAACGACTTTTTCTTTTAGCA 58.794 36.000 0.00 0.00 0.00 3.49
671 2839 5.629435 CCCATGAACGACTTTTTCTTTTAGC 59.371 40.000 0.00 0.00 0.00 3.09
672 2840 5.629435 GCCCATGAACGACTTTTTCTTTTAG 59.371 40.000 0.00 0.00 0.00 1.85
678 2846 3.363341 TTGCCCATGAACGACTTTTTC 57.637 42.857 0.00 0.00 0.00 2.29
925 3097 1.967319 CGAGAGGAGGGAGAGAGAAG 58.033 60.000 0.00 0.00 0.00 2.85
1035 3225 3.151022 GCCGAGGAGGAGGTGGAG 61.151 72.222 0.00 0.00 45.00 3.86
1036 3226 4.779733 GGCCGAGGAGGAGGTGGA 62.780 72.222 0.00 0.00 45.00 4.02
1728 3921 2.649034 GTCAACGTCAGAGCGGGA 59.351 61.111 0.00 0.00 35.98 5.14
1854 4048 4.765856 TCTTAATCTCGGGGAGTACTATGC 59.234 45.833 0.00 0.00 0.00 3.14
1864 4060 3.545703 AGCACAAATCTTAATCTCGGGG 58.454 45.455 0.00 0.00 0.00 5.73
1866 4062 4.260538 GCAGAGCACAAATCTTAATCTCGG 60.261 45.833 0.00 0.00 0.00 4.63
1992 4200 0.941463 GAGAGTGACACAGGCACACG 60.941 60.000 8.59 0.00 38.70 4.49
2000 4208 2.340078 GCAGCGGAGAGTGACACA 59.660 61.111 8.59 0.00 0.00 3.72
2008 4216 2.819595 GCGATTTGGCAGCGGAGA 60.820 61.111 8.21 0.00 0.00 3.71
2009 4217 3.880846 GGCGATTTGGCAGCGGAG 61.881 66.667 8.21 0.00 44.08 4.63
2060 4268 4.143347 CGTTAACCGCAACGTAAATGTAGT 60.143 41.667 0.00 0.00 44.77 2.73
2063 4271 3.172000 CGTTAACCGCAACGTAAATGT 57.828 42.857 0.00 0.00 44.77 2.71
2112 4322 4.810033 GCCAGATAGAATTGGATCCATGCT 60.810 45.833 17.06 15.05 36.55 3.79
2161 4371 2.879103 AGAATGGGCGAAAGGAAGAA 57.121 45.000 0.00 0.00 0.00 2.52
2164 4374 1.892474 CCAAAGAATGGGCGAAAGGAA 59.108 47.619 0.00 0.00 46.27 3.36
2198 4408 1.202879 TCCAAACAAGACTTCGGCCAT 60.203 47.619 2.24 0.00 0.00 4.40
2199 4409 0.181587 TCCAAACAAGACTTCGGCCA 59.818 50.000 2.24 0.00 0.00 5.36
2200 4414 1.534729 ATCCAAACAAGACTTCGGCC 58.465 50.000 0.00 0.00 0.00 6.13
2203 4417 6.265577 AGTTGAAAATCCAAACAAGACTTCG 58.734 36.000 0.00 0.00 0.00 3.79
2239 4456 2.046314 TCGGGGCTTAGCTTGTGC 60.046 61.111 3.59 0.00 40.05 4.57
2244 4463 2.444140 ATCGGTCGGGGCTTAGCT 60.444 61.111 3.59 0.00 0.00 3.32
2257 4476 2.802247 TCAGCAAAAGCATATCGATCGG 59.198 45.455 16.41 0.00 0.00 4.18
2260 4479 4.156664 GCATCAGCAAAAGCATATCGAT 57.843 40.909 2.16 2.16 41.58 3.59
2261 4480 3.614159 GCATCAGCAAAAGCATATCGA 57.386 42.857 0.00 0.00 41.58 3.59
2397 4616 2.016318 CGCATTTCCAGATAGGCACAA 58.984 47.619 0.00 0.00 37.29 3.33
2545 4764 4.838152 CCTCCACCGGCATGGACG 62.838 72.222 9.69 3.01 44.14 4.79
2607 4827 1.026718 CCCTCCACAAATGCGAGTCC 61.027 60.000 0.00 0.00 0.00 3.85
2608 4828 1.648467 GCCCTCCACAAATGCGAGTC 61.648 60.000 0.00 0.00 0.00 3.36
2609 4829 1.675641 GCCCTCCACAAATGCGAGT 60.676 57.895 0.00 0.00 0.00 4.18
2628 4848 4.996434 ACTGTGCTGCGAGGTGGC 62.996 66.667 0.00 0.00 0.00 5.01
2648 4868 1.586154 CGGGTCAAGGTCAATGTGGC 61.586 60.000 0.00 0.00 0.00 5.01
2680 4900 4.139183 GAAGGATCGATAATGCTTGTGC 57.861 45.455 0.00 0.00 45.12 4.57
2706 4941 3.771160 GGGGTCCAGCGACGTGAT 61.771 66.667 0.00 0.00 40.17 3.06


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

AutoCloner maintained by Alex Coulton.