Multiple sequence alignment - TraesCS7D01G471200

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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 TraesCS7D01G471200 chr7D 100.000 2456 0 0 1 2456 584851297 584848842 0.000000e+00 4536.0
1 TraesCS7D01G471200 chr7A 95.508 2449 81 5 3 2426 675234556 675237000 0.000000e+00 3886.0
2 TraesCS7D01G471200 chr7B 94.039 2097 86 11 1 2063 653015244 653013153 0.000000e+00 3144.0
3 TraesCS7D01G471200 chr7B 89.744 273 27 1 2183 2455 653004359 653004088 5.030000e-92 348.0
4 TraesCS7D01G471200 chr5B 100.000 30 0 0 2117 2146 158910288 158910317 3.410000e-04 56.5
5 TraesCS7D01G471200 chr5B 94.444 36 2 0 2117 2152 458663520 458663485 3.410000e-04 56.5
6 TraesCS7D01G471200 chr3D 100.000 28 0 0 2117 2144 391258106 391258133 4.000000e-03 52.8


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 TraesCS7D01G471200 chr7D 584848842 584851297 2455 True 4536 4536 100.000 1 2456 1 chr7D.!!$R1 2455
1 TraesCS7D01G471200 chr7A 675234556 675237000 2444 False 3886 3886 95.508 3 2426 1 chr7A.!!$F1 2423
2 TraesCS7D01G471200 chr7B 653013153 653015244 2091 True 3144 3144 94.039 1 2063 1 chr7B.!!$R2 2062

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
896 908 2.490903 GGCTCAAACTCAATCTGCACAT 59.509 45.455 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2183 0.043053 CGTCGATGCACCAAATAGCG 60.043 55.0 0.0 0.0 0.0 4.26 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
61 62 7.258441 TCTTTCTACAAATCTGGTCAGTATCG 58.742 38.462 0.00 0.00 0.00 2.92
62 63 6.525578 TTCTACAAATCTGGTCAGTATCGT 57.474 37.500 0.00 0.00 0.00 3.73
293 304 9.739276 ATACTGACTCCAGATCATTTACAAAAA 57.261 29.630 0.00 0.00 43.02 1.94
444 456 5.528043 AGTTTGATTGCCAACATAACACA 57.472 34.783 0.00 0.00 33.85 3.72
735 747 5.221601 ACAGATATGGCATGAGGACAGTTAG 60.222 44.000 10.98 0.00 38.50 2.34
896 908 2.490903 GGCTCAAACTCAATCTGCACAT 59.509 45.455 0.00 0.00 0.00 3.21
1035 1047 1.206072 GCGCATCATCAATCGGCTC 59.794 57.895 0.30 0.00 0.00 4.70
1697 1715 1.068083 GATGCGGCGAAGAGATCCA 59.932 57.895 12.98 0.00 0.00 3.41
2003 2038 3.302870 CGAATTTCGATCCGGCGTAAATT 60.303 43.478 13.45 16.41 43.74 1.82
2020 2055 2.225068 ATTGTGGCCGTTAGATCTCG 57.775 50.000 0.00 0.00 0.00 4.04
2021 2056 0.459585 TTGTGGCCGTTAGATCTCGC 60.460 55.000 0.00 0.00 0.00 5.03
2025 2060 1.370657 GCCGTTAGATCTCGCTCGG 60.371 63.158 17.48 17.48 40.72 4.63
2029 2064 0.595310 GTTAGATCTCGCTCGGTGGC 60.595 60.000 0.00 0.00 0.00 5.01
2038 2073 0.373716 CGCTCGGTGGCTGTATTTTC 59.626 55.000 0.00 0.00 0.00 2.29
2046 2081 1.022451 GGCTGTATTTTCGCCGTCCA 61.022 55.000 0.00 0.00 33.64 4.02
2055 2090 0.527113 TTCGCCGTCCAATCTTCGTA 59.473 50.000 0.00 0.00 0.00 3.43
2063 2098 3.361414 GTCCAATCTTCGTACTCGCTAC 58.639 50.000 0.00 0.00 36.96 3.58
2083 2118 7.280876 TCGCTACAAGATTTGAGAGCAATATTT 59.719 33.333 15.37 0.00 40.61 1.40
2107 2142 4.056050 ACTTTCACGTATGGTCACTTGTC 58.944 43.478 0.00 0.00 0.00 3.18
2123 2158 7.307811 GGTCACTTGTCCTTGTAAAATCAGTAC 60.308 40.741 0.00 0.00 0.00 2.73
2140 2175 4.705507 TCAGTACAGTTACTAAGCTCCCAG 59.294 45.833 0.00 0.00 36.31 4.45
2148 2183 2.728007 ACTAAGCTCCCAGGAAATTGC 58.272 47.619 0.00 0.00 0.00 3.56
2154 2189 2.301346 CTCCCAGGAAATTGCGCTATT 58.699 47.619 11.38 11.38 0.00 1.73
2166 2201 0.316196 GCGCTATTTGGTGCATCGAC 60.316 55.000 0.00 0.00 41.71 4.20
2178 2213 1.226974 CATCGACGGGTGTAGCAGG 60.227 63.158 0.00 0.00 0.00 4.85
2180 2215 4.063967 CGACGGGTGTAGCAGGCA 62.064 66.667 0.00 0.00 0.00 4.75
2188 2223 1.026718 GTGTAGCAGGCATGTGGGAC 61.027 60.000 0.00 0.00 0.00 4.46
2191 2226 1.913951 TAGCAGGCATGTGGGACCAG 61.914 60.000 0.00 0.00 0.00 4.00
2192 2227 2.759114 CAGGCATGTGGGACCAGT 59.241 61.111 0.00 0.00 0.00 4.00
2227 2262 3.057734 CGAAGAGCTTAACAGTCGGTTT 58.942 45.455 0.00 0.00 40.96 3.27
2239 2274 3.047877 CGGTTTGGTCCACCTCGC 61.048 66.667 0.00 0.00 36.82 5.03
2246 2281 0.981183 TGGTCCACCTCGCAGTTAAT 59.019 50.000 0.00 0.00 36.82 1.40
2248 2283 1.066430 GGTCCACCTCGCAGTTAATCA 60.066 52.381 0.00 0.00 0.00 2.57
2253 2288 2.668457 CACCTCGCAGTTAATCAGTGTC 59.332 50.000 0.00 0.00 0.00 3.67
2263 2298 6.074302 GCAGTTAATCAGTGTCGTATGTATGG 60.074 42.308 0.00 0.00 0.00 2.74
2273 2308 2.038426 TCGTATGTATGGGCATTCCTGG 59.962 50.000 0.00 0.00 36.20 4.45
2294 2329 2.093306 TTAGGTGCCATGTTGTCTCG 57.907 50.000 0.00 0.00 0.00 4.04
2327 2362 4.060038 AGCCAAGCACGCCAATGC 62.060 61.111 0.00 0.00 46.50 3.56
2338 2373 1.343142 ACGCCAATGCCGTATCTATCA 59.657 47.619 0.00 0.00 37.12 2.15
2426 2461 2.562738 TCGTGATGCTTCTCTTCCAAGA 59.437 45.455 0.88 0.00 0.00 3.02
2427 2462 2.670414 CGTGATGCTTCTCTTCCAAGAC 59.330 50.000 0.88 0.00 0.00 3.01
2428 2463 2.670414 GTGATGCTTCTCTTCCAAGACG 59.330 50.000 0.88 0.00 0.00 4.18
2429 2464 2.562738 TGATGCTTCTCTTCCAAGACGA 59.437 45.455 0.88 0.00 0.00 4.20
2430 2465 2.440539 TGCTTCTCTTCCAAGACGAC 57.559 50.000 0.00 0.00 0.00 4.34
2431 2466 1.686587 TGCTTCTCTTCCAAGACGACA 59.313 47.619 0.00 0.00 0.00 4.35
2432 2467 2.300152 TGCTTCTCTTCCAAGACGACAT 59.700 45.455 0.00 0.00 0.00 3.06
2433 2468 3.509967 TGCTTCTCTTCCAAGACGACATA 59.490 43.478 0.00 0.00 0.00 2.29
2434 2469 4.021456 TGCTTCTCTTCCAAGACGACATAA 60.021 41.667 0.00 0.00 0.00 1.90
2435 2470 4.564769 GCTTCTCTTCCAAGACGACATAAG 59.435 45.833 0.00 0.00 0.00 1.73
2436 2471 5.622460 GCTTCTCTTCCAAGACGACATAAGA 60.622 44.000 0.00 0.00 0.00 2.10
2437 2472 5.568685 TCTCTTCCAAGACGACATAAGAG 57.431 43.478 0.00 0.00 40.69 2.85
2438 2473 4.109050 CTCTTCCAAGACGACATAAGAGC 58.891 47.826 0.00 0.00 35.14 4.09
2439 2474 3.509967 TCTTCCAAGACGACATAAGAGCA 59.490 43.478 0.00 0.00 0.00 4.26
2440 2475 3.232213 TCCAAGACGACATAAGAGCAC 57.768 47.619 0.00 0.00 0.00 4.40
2441 2476 2.560981 TCCAAGACGACATAAGAGCACA 59.439 45.455 0.00 0.00 0.00 4.57
2442 2477 3.195610 TCCAAGACGACATAAGAGCACAT 59.804 43.478 0.00 0.00 0.00 3.21
2443 2478 3.553511 CCAAGACGACATAAGAGCACATC 59.446 47.826 0.00 0.00 0.00 3.06
2444 2479 4.176271 CAAGACGACATAAGAGCACATCA 58.824 43.478 0.00 0.00 0.00 3.07
2445 2480 4.662468 AGACGACATAAGAGCACATCAT 57.338 40.909 0.00 0.00 0.00 2.45
2446 2481 4.366586 AGACGACATAAGAGCACATCATG 58.633 43.478 0.00 0.00 0.00 3.07
2447 2482 4.098501 AGACGACATAAGAGCACATCATGA 59.901 41.667 0.00 0.00 0.00 3.07
2448 2483 4.953667 ACGACATAAGAGCACATCATGAT 58.046 39.130 1.18 1.18 0.00 2.45
2449 2484 5.363101 ACGACATAAGAGCACATCATGATT 58.637 37.500 5.16 0.00 0.00 2.57
2450 2485 5.819379 ACGACATAAGAGCACATCATGATTT 59.181 36.000 5.16 0.00 0.00 2.17
2451 2486 6.134061 CGACATAAGAGCACATCATGATTTG 58.866 40.000 16.05 16.05 0.00 2.32
2452 2487 6.387041 ACATAAGAGCACATCATGATTTGG 57.613 37.500 20.54 6.93 0.00 3.28
2453 2488 3.795623 AAGAGCACATCATGATTTGGC 57.204 42.857 20.54 16.49 0.00 4.52
2454 2489 3.014304 AGAGCACATCATGATTTGGCT 57.986 42.857 20.54 20.19 0.00 4.75
2455 2490 4.160642 AGAGCACATCATGATTTGGCTA 57.839 40.909 20.54 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 9.538508 AATATGGTAAGACGGTTATACTTTCAC 57.461 33.333 0.00 0.00 0.00 3.18
444 456 6.096846 AGCTTCCGTTTGCAATTTATATCCTT 59.903 34.615 0.00 0.00 0.00 3.36
598 610 2.039084 AGAGTAAGTTGACCAGGCAAGG 59.961 50.000 0.00 0.00 0.00 3.61
605 617 1.765904 TGTGCCAGAGTAAGTTGACCA 59.234 47.619 0.00 0.00 0.00 4.02
609 621 2.417719 GGAGTGTGCCAGAGTAAGTTG 58.582 52.381 0.00 0.00 0.00 3.16
610 622 1.000955 CGGAGTGTGCCAGAGTAAGTT 59.999 52.381 0.00 0.00 0.00 2.66
680 692 5.771469 TGGAAATGTTTGTGCAAGTAGATG 58.229 37.500 0.00 0.00 0.00 2.90
735 747 3.696548 GGAAGAATGGGAGGTGATTTGTC 59.303 47.826 0.00 0.00 0.00 3.18
896 908 8.251383 TGGGTTTTTATCTTTGGATGTTTGTA 57.749 30.769 0.00 0.00 33.71 2.41
1113 1125 2.744202 GACAACGCTGATGGTGAGAAAT 59.256 45.455 0.00 0.00 0.00 2.17
1697 1715 1.605058 CCCGAGGACGACAATGGAGT 61.605 60.000 0.00 0.00 42.66 3.85
2003 2038 1.141019 GCGAGATCTAACGGCCACA 59.859 57.895 2.24 0.00 0.00 4.17
2020 2055 0.373716 CGAAAATACAGCCACCGAGC 59.626 55.000 0.00 0.00 0.00 5.03
2021 2056 0.373716 GCGAAAATACAGCCACCGAG 59.626 55.000 0.00 0.00 0.00 4.63
2029 2064 2.936498 AGATTGGACGGCGAAAATACAG 59.064 45.455 16.62 0.00 0.00 2.74
2038 2073 0.179145 AGTACGAAGATTGGACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
2046 2081 4.959596 TCTTGTAGCGAGTACGAAGATT 57.040 40.909 0.00 0.00 42.66 2.40
2055 2090 3.056536 TGCTCTCAAATCTTGTAGCGAGT 60.057 43.478 0.00 0.00 40.84 4.18
2063 2098 9.635520 AAAGTGAAATATTGCTCTCAAATCTTG 57.364 29.630 0.00 0.00 35.56 3.02
2083 2118 4.055360 CAAGTGACCATACGTGAAAGTGA 58.945 43.478 0.00 0.00 32.79 3.41
2123 2158 4.553330 TTTCCTGGGAGCTTAGTAACTG 57.447 45.455 0.00 0.00 0.00 3.16
2140 2175 1.926510 GCACCAAATAGCGCAATTTCC 59.073 47.619 11.47 0.00 0.00 3.13
2148 2183 0.043053 CGTCGATGCACCAAATAGCG 60.043 55.000 0.00 0.00 0.00 4.26
2154 2189 1.817911 TACACCCGTCGATGCACCAA 61.818 55.000 0.00 0.00 0.00 3.67
2161 2196 3.077519 GCCTGCTACACCCGTCGAT 62.078 63.158 0.00 0.00 0.00 3.59
2166 2201 2.108514 CACATGCCTGCTACACCCG 61.109 63.158 0.00 0.00 0.00 5.28
2178 2213 0.674895 GACAGACTGGTCCCACATGC 60.675 60.000 7.51 0.00 0.00 4.06
2180 2215 0.979665 CTGACAGACTGGTCCCACAT 59.020 55.000 7.51 0.00 36.97 3.21
2188 2223 4.007644 TGCCGGCTGACAGACTGG 62.008 66.667 29.70 12.81 0.00 4.00
2191 2226 3.858868 TTCGTGCCGGCTGACAGAC 62.859 63.158 29.70 15.36 0.00 3.51
2192 2227 3.573772 CTTCGTGCCGGCTGACAGA 62.574 63.158 29.70 16.19 0.00 3.41
2213 2248 2.546789 GTGGACCAAACCGACTGTTAAG 59.453 50.000 0.00 0.00 35.67 1.85
2216 2251 0.464916 GGTGGACCAAACCGACTGTT 60.465 55.000 0.00 0.00 39.43 3.16
2227 2262 0.981183 ATTAACTGCGAGGTGGACCA 59.019 50.000 0.00 0.00 38.89 4.02
2239 2274 6.420903 CCCATACATACGACACTGATTAACTG 59.579 42.308 0.00 0.00 0.00 3.16
2246 2281 2.104170 TGCCCATACATACGACACTGA 58.896 47.619 0.00 0.00 0.00 3.41
2248 2283 3.494398 GGAATGCCCATACATACGACACT 60.494 47.826 0.00 0.00 34.14 3.55
2253 2288 2.038426 TCCAGGAATGCCCATACATACG 59.962 50.000 0.00 0.00 37.41 3.06
2273 2308 2.609459 CGAGACAACATGGCACCTAATC 59.391 50.000 0.00 0.00 0.00 1.75
2294 2329 0.579156 GGCTGATTGCTCGATCGTTC 59.421 55.000 15.94 8.60 42.39 3.95
2327 2362 6.169094 AGGCAATGAGAATTGATAGATACGG 58.831 40.000 2.69 0.00 33.55 4.02
2338 2373 6.767456 AGATTAGATCGAGGCAATGAGAATT 58.233 36.000 0.00 0.00 0.00 2.17
2426 2461 4.391405 TCATGATGTGCTCTTATGTCGT 57.609 40.909 0.00 0.00 0.00 4.34
2427 2462 5.919272 AATCATGATGTGCTCTTATGTCG 57.081 39.130 9.46 0.00 0.00 4.35
2428 2463 6.436261 CCAAATCATGATGTGCTCTTATGTC 58.564 40.000 19.05 0.00 0.00 3.06
2429 2464 5.221185 GCCAAATCATGATGTGCTCTTATGT 60.221 40.000 19.05 0.00 0.00 2.29
2430 2465 5.009710 AGCCAAATCATGATGTGCTCTTATG 59.990 40.000 19.05 6.09 0.00 1.90
2431 2466 5.138276 AGCCAAATCATGATGTGCTCTTAT 58.862 37.500 19.05 0.00 0.00 1.73
2432 2467 4.529897 AGCCAAATCATGATGTGCTCTTA 58.470 39.130 19.05 0.00 0.00 2.10
2433 2468 3.362706 AGCCAAATCATGATGTGCTCTT 58.637 40.909 19.05 1.45 0.00 2.85
2434 2469 3.014304 AGCCAAATCATGATGTGCTCT 57.986 42.857 19.05 14.58 0.00 4.09


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

AutoCloner maintained by Alex Coulton.