Multiple sequence alignment - TraesCS7A01G483900

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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 TraesCS7A01G483900 chr7A 100.000 2456 0 0 1 2456 675234560 675237015 0.000000e+00 4536
1 TraesCS7A01G483900 chr7D 95.501 2445 81 5 1 2441 584851291 584848872 0.000000e+00 3879
2 TraesCS7A01G483900 chr7B 94.357 2091 100 8 1 2078 653015238 653013153 0.000000e+00 3192
3 TraesCS7A01G483900 chr7B 90.625 224 21 0 2218 2441 653004339 653004116 5.130000e-77 298


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 TraesCS7A01G483900 chr7A 675234560 675237015 2455 False 4536 4536 100.000 1 2456 1 chr7A.!!$F1 2455
1 TraesCS7A01G483900 chr7D 584848872 584851291 2419 True 3879 3879 95.501 1 2441 1 chr7D.!!$R1 2440
2 TraesCS7A01G483900 chr7B 653013153 653015238 2085 True 3192 3192 94.357 1 2078 1 chr7B.!!$R2 2077

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
897 904 2.663879 GCTCAAACTCAATCTGCACACG 60.664 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2223 0.537188 GACAGGATGATCCCACACGT 59.463 55.0 8.08 0.0 39.69 4.49 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
202 203 6.018343 GGAAACTCATCTGATAGTTTAGCAGC 60.018 42.308 17.37 9.89 43.97 5.25
263 264 9.838339 ACCTTGGAAAGTTAGATATTCTATGTG 57.162 33.333 0.00 0.00 44.25 3.21
324 326 8.818141 TGCATATCAGCTTATAACACTAGAAC 57.182 34.615 0.00 0.00 34.99 3.01
464 470 6.374333 ACACACGAGGATATAAATTGCAAACT 59.626 34.615 1.71 0.00 0.00 2.66
529 535 8.752005 TTATTTATCAAGTCTAAAGCAGGCAT 57.248 30.769 0.00 0.00 0.00 4.40
533 539 4.655963 TCAAGTCTAAAGCAGGCATTCTT 58.344 39.130 0.00 0.00 0.00 2.52
534 540 5.804639 TCAAGTCTAAAGCAGGCATTCTTA 58.195 37.500 0.00 0.00 0.00 2.10
548 554 8.742777 GCAGGCATTCTTATATCATCCAAATAA 58.257 33.333 0.00 0.00 0.00 1.40
621 628 4.381079 CCTTGTCCAGTAGACTTACTCTGC 60.381 50.000 0.00 0.00 46.46 4.26
629 636 2.883026 AGACTTACTCTGCCACACTCT 58.117 47.619 0.00 0.00 0.00 3.24
642 649 3.758554 GCCACACTCTGATGTATTTGGTT 59.241 43.478 0.00 0.00 0.00 3.67
653 660 7.549134 TCTGATGTATTTGGTTACTAGTTGCAG 59.451 37.037 0.00 0.00 0.00 4.41
654 661 5.873179 TGTATTTGGTTACTAGTTGCAGC 57.127 39.130 0.00 0.00 0.00 5.25
671 678 7.697691 AGTTGCAGCAAATACAAGTATATCAC 58.302 34.615 10.11 0.00 0.00 3.06
747 754 5.530915 TGAGGACAGTTAAACAAATCACCTG 59.469 40.000 0.00 0.00 0.00 4.00
897 904 2.663879 GCTCAAACTCAATCTGCACACG 60.664 50.000 0.00 0.00 0.00 4.49
1034 1041 3.563088 GCGCGTCATCAATCGGCA 61.563 61.111 8.43 0.00 0.00 5.69
1035 1042 2.622629 CGCGTCATCAATCGGCAG 59.377 61.111 0.00 0.00 0.00 4.85
1680 1693 4.473520 ACGGCCGGCAGAAGATGG 62.474 66.667 33.66 10.64 0.00 3.51
2044 2074 2.879026 CCGTTAGATCTCAGTCGATGGA 59.121 50.000 0.00 0.00 0.00 3.41
2065 2095 3.804786 TGTATTTTAGCCGTCCGATCA 57.195 42.857 0.00 0.00 0.00 2.92
2068 2098 2.971660 TTTTAGCCGTCCGATCATCA 57.028 45.000 0.00 0.00 0.00 3.07
2078 2108 3.497118 GTCCGATCATCATTCTCGCTAG 58.503 50.000 0.00 0.00 0.00 3.42
2098 2128 7.383572 TCGCTAGAAGATTTGAGAGCAATATTC 59.616 37.037 0.00 0.00 33.25 1.75
2122 2152 3.807622 ACTTTCACGTATGGTCACTTGTG 59.192 43.478 0.00 0.00 0.00 3.33
2138 2168 7.308589 GGTCACTTGTGCTTGTAAAATCAGTAT 60.309 37.037 0.00 0.00 0.00 2.12
2155 2185 6.956202 TCAGTATAGTTACTAAGCTCCCAC 57.044 41.667 0.00 0.00 36.50 4.61
2163 2193 3.695830 ACTAAGCTCCCACGAAATTGA 57.304 42.857 0.00 0.00 0.00 2.57
2169 2199 2.545946 GCTCCCACGAAATTGAGCTATC 59.454 50.000 6.07 0.00 45.21 2.08
2176 2206 2.033407 CGAAATTGAGCTATCTGGTGCG 60.033 50.000 0.00 0.00 0.00 5.34
2181 2211 0.317436 GAGCTATCTGGTGCGTCGAG 60.317 60.000 0.00 0.00 0.00 4.04
2193 2223 2.044555 CGTCGAGGGGTGTAGCAGA 61.045 63.158 0.00 0.00 0.00 4.26
2195 2225 2.044555 TCGAGGGGTGTAGCAGACG 61.045 63.158 0.00 0.00 0.00 4.18
2203 2233 0.246635 GTGTAGCAGACGTGTGGGAT 59.753 55.000 15.19 0.00 0.00 3.85
2206 2236 1.137086 GTAGCAGACGTGTGGGATCAT 59.863 52.381 15.19 0.00 0.00 2.45
2207 2237 0.176680 AGCAGACGTGTGGGATCATC 59.823 55.000 15.19 0.00 0.00 2.92
2242 2272 2.405172 GAAGAGGTTGACAGTCGGTTC 58.595 52.381 0.00 0.00 0.00 3.62
2254 2284 3.677648 CGGTTCGGTCCACCTCGT 61.678 66.667 0.00 0.00 31.32 4.18
2261 2291 1.812571 TCGGTCCACCTCGTAGTTAAC 59.187 52.381 0.00 0.00 0.00 2.01
2263 2293 1.205655 GGTCCACCTCGTAGTTAACCC 59.794 57.143 0.88 0.00 0.00 4.11
2268 2298 1.963515 ACCTCGTAGTTAACCCGTGTT 59.036 47.619 13.11 0.00 38.52 3.32
2278 2308 6.040209 AGTTAACCCGTGTTGTATGTATGA 57.960 37.500 0.88 0.00 35.87 2.15
2288 2318 5.817296 GTGTTGTATGTATGAGCATTCCTGA 59.183 40.000 0.00 0.00 0.00 3.86
2309 2339 7.020040 CCTGAATTAGGTGACATGTTGTCTCA 61.020 42.308 0.00 0.00 41.83 3.27
2326 2356 3.367932 GTCTCAAACGATCGAGCAATCAA 59.632 43.478 24.34 0.00 0.00 2.57
2342 2372 1.106351 TCAACCAAGCACGCCAATGT 61.106 50.000 0.00 0.00 0.00 2.71
2353 2383 2.987149 CACGCCAATGTCGTATCTATCC 59.013 50.000 0.00 0.00 38.19 2.59
2441 2471 2.300152 TCGTGATGCTTCTCTTCCAAGT 59.700 45.455 0.88 0.00 0.00 3.16
2442 2472 3.070018 CGTGATGCTTCTCTTCCAAGTT 58.930 45.455 0.88 0.00 0.00 2.66
2443 2473 4.021456 TCGTGATGCTTCTCTTCCAAGTTA 60.021 41.667 0.88 0.00 0.00 2.24
2444 2474 4.872691 CGTGATGCTTCTCTTCCAAGTTAT 59.127 41.667 0.88 0.00 0.00 1.89
2445 2475 5.220548 CGTGATGCTTCTCTTCCAAGTTATG 60.221 44.000 0.88 0.00 0.00 1.90
2446 2476 5.877012 GTGATGCTTCTCTTCCAAGTTATGA 59.123 40.000 0.88 0.00 0.00 2.15
2447 2477 6.541641 GTGATGCTTCTCTTCCAAGTTATGAT 59.458 38.462 0.88 0.00 0.00 2.45
2448 2478 6.541278 TGATGCTTCTCTTCCAAGTTATGATG 59.459 38.462 0.88 0.00 0.00 3.07
2449 2479 5.809001 TGCTTCTCTTCCAAGTTATGATGT 58.191 37.500 0.00 0.00 0.00 3.06
2450 2480 6.240894 TGCTTCTCTTCCAAGTTATGATGTT 58.759 36.000 0.00 0.00 0.00 2.71
2451 2481 6.149973 TGCTTCTCTTCCAAGTTATGATGTTG 59.850 38.462 0.00 0.00 0.00 3.33
2452 2482 6.500684 TTCTCTTCCAAGTTATGATGTTGC 57.499 37.500 0.00 0.00 0.00 4.17
2453 2483 4.943705 TCTCTTCCAAGTTATGATGTTGCC 59.056 41.667 0.00 0.00 0.00 4.52
2454 2484 4.661222 TCTTCCAAGTTATGATGTTGCCA 58.339 39.130 0.00 0.00 0.00 4.92
2455 2485 4.701651 TCTTCCAAGTTATGATGTTGCCAG 59.298 41.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 3.132289 TCGACCTGGCTGATAAGGTTAAG 59.868 47.826 0.00 0.00 46.97 1.85
353 356 7.662258 TGGTCGAAAAGGTATTTGTAGATTTGA 59.338 33.333 0.00 0.00 0.00 2.69
360 363 4.880759 TCGTGGTCGAAAAGGTATTTGTA 58.119 39.130 0.00 0.00 43.34 2.41
521 527 5.509832 TGGATGATATAAGAATGCCTGCT 57.490 39.130 0.00 0.00 0.00 4.24
534 540 9.927081 GGGTCCATATCTTTATTTGGATGATAT 57.073 33.333 1.69 0.00 42.79 1.63
548 554 4.389374 CTTGCGTAATGGGTCCATATCTT 58.611 43.478 2.56 0.00 35.31 2.40
597 603 3.764972 AGAGTAAGTCTACTGGACAAGGC 59.235 47.826 0.00 0.00 46.72 4.35
598 604 4.381079 GCAGAGTAAGTCTACTGGACAAGG 60.381 50.000 0.00 0.00 46.72 3.61
603 610 3.090037 GTGGCAGAGTAAGTCTACTGGA 58.910 50.000 0.00 0.00 38.55 3.86
606 613 3.759618 GAGTGTGGCAGAGTAAGTCTACT 59.240 47.826 0.00 0.00 41.28 2.57
621 628 6.173339 AGTAACCAAATACATCAGAGTGTGG 58.827 40.000 0.00 0.00 33.62 4.17
629 636 6.093495 GCTGCAACTAGTAACCAAATACATCA 59.907 38.462 0.00 0.00 0.00 3.07
671 678 9.409312 TGTTTGTGCAAATAGATATTTTCTGTG 57.591 29.630 0.46 0.00 33.88 3.66
686 693 2.503356 ACCCTGGAAATGTTTGTGCAAA 59.497 40.909 0.00 0.00 0.00 3.68
747 754 0.394899 CCAGGACCAGGAAGAATGGC 60.395 60.000 0.00 0.00 41.87 4.40
897 904 5.994668 TGGGTTTTTATCTTTGGATGTTTGC 59.005 36.000 0.00 0.00 33.71 3.68
1021 1028 1.026182 TGCCACTGCCGATTGATGAC 61.026 55.000 0.00 0.00 36.33 3.06
1680 1693 2.956964 CGGATCTCTTCGCCGCAC 60.957 66.667 0.00 0.00 38.46 5.34
2044 2074 4.330944 TGATCGGACGGCTAAAATACAT 57.669 40.909 0.00 0.00 0.00 2.29
2065 2095 7.048629 TCTCAAATCTTCTAGCGAGAATGAT 57.951 36.000 9.85 11.43 40.95 2.45
2068 2098 5.163468 TGCTCTCAAATCTTCTAGCGAGAAT 60.163 40.000 9.85 0.00 40.95 2.40
2078 2108 7.565323 AGTGGAATATTGCTCTCAAATCTTC 57.435 36.000 8.53 0.00 35.56 2.87
2098 2128 3.040147 AGTGACCATACGTGAAAGTGG 57.960 47.619 0.00 1.18 37.74 4.00
2138 2168 5.927281 ATTTCGTGGGAGCTTAGTAACTA 57.073 39.130 0.00 0.00 0.00 2.24
2155 2185 2.033407 CGCACCAGATAGCTCAATTTCG 60.033 50.000 0.00 0.00 0.00 3.46
2163 2193 1.729470 CCTCGACGCACCAGATAGCT 61.729 60.000 0.00 0.00 0.00 3.32
2169 2199 4.742201 CACCCCTCGACGCACCAG 62.742 72.222 0.00 0.00 0.00 4.00
2176 2206 1.511768 GTCTGCTACACCCCTCGAC 59.488 63.158 0.00 0.00 0.00 4.20
2181 2211 1.374252 CACACGTCTGCTACACCCC 60.374 63.158 0.00 0.00 0.00 4.95
2193 2223 0.537188 GACAGGATGATCCCACACGT 59.463 55.000 8.08 0.00 39.69 4.49
2195 2225 1.745141 GCTGACAGGATGATCCCACAC 60.745 57.143 8.08 0.00 39.69 3.82
2203 2233 3.002583 TGCCGGCTGACAGGATGA 61.003 61.111 29.70 0.00 39.69 2.92
2207 2237 4.680237 TTCGTGCCGGCTGACAGG 62.680 66.667 29.70 13.08 0.00 4.00
2228 2258 0.942884 GGACCGAACCGACTGTCAAC 60.943 60.000 8.73 0.00 0.00 3.18
2231 2261 1.372623 GTGGACCGAACCGACTGTC 60.373 63.158 0.00 0.00 0.00 3.51
2242 2272 1.135286 GGTTAACTACGAGGTGGACCG 60.135 57.143 5.42 0.00 42.08 4.79
2254 2284 7.167924 TCATACATACAACACGGGTTAACTA 57.832 36.000 0.85 0.00 34.87 2.24
2261 2291 2.899976 TGCTCATACATACAACACGGG 58.100 47.619 0.00 0.00 0.00 5.28
2263 2293 4.811024 AGGAATGCTCATACATACAACACG 59.189 41.667 0.00 0.00 0.00 4.49
2268 2298 8.837788 CTAATTCAGGAATGCTCATACATACA 57.162 34.615 0.00 0.00 0.00 2.29
2297 2327 3.649073 TCGATCGTTTGAGACAACATGT 58.351 40.909 15.94 0.00 0.00 3.21
2309 2339 2.422597 TGGTTGATTGCTCGATCGTTT 58.577 42.857 15.94 0.00 0.00 3.60
2326 2356 2.616330 CGACATTGGCGTGCTTGGT 61.616 57.895 3.04 0.00 0.00 3.67
2342 2372 5.481824 AGGCAATGAGAATGGATAGATACGA 59.518 40.000 0.00 0.00 0.00 3.43
2353 2383 6.164876 AGATTAGATCGAGGCAATGAGAATG 58.835 40.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.