Multiple sequence alignment - TraesCS7D01G045800

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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 TraesCS7D01G045800 chr7D 100.000 2136 0 0 387 2522 23095678 23093543 0.000000e+00 3945.0
1 TraesCS7D01G045800 chr7D 100.000 31 0 0 1 31 23096064 23096034 9.740000e-05 58.4
2 TraesCS7D01G045800 chr7A 94.938 1778 66 15 519 2283 23692544 23690778 0.000000e+00 2763.0
3 TraesCS7D01G045800 chr7A 91.960 199 16 0 2324 2522 23690781 23690583 1.910000e-71 279.0
4 TraesCS7D01G045800 chr7A 95.489 133 6 0 387 519 23699319 23699187 1.970000e-51 213.0
5 TraesCS7D01G045800 chr4A 93.548 1488 83 8 387 1867 706536900 706538381 0.000000e+00 2204.0
6 TraesCS7D01G045800 chr4A 85.562 658 73 9 1875 2522 706545413 706546058 0.000000e+00 669.0


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 TraesCS7D01G045800 chr7D 23093543 23096064 2521 True 2001.7 3945 100.000 1 2522 2 chr7D.!!$R1 2521
1 TraesCS7D01G045800 chr7A 23690583 23692544 1961 True 1521.0 2763 93.449 519 2522 2 chr7A.!!$R2 2003
2 TraesCS7D01G045800 chr4A 706536900 706538381 1481 False 2204.0 2204 93.548 387 1867 1 chr4A.!!$F1 1480
3 TraesCS7D01G045800 chr4A 706545413 706546058 645 False 669.0 669 85.562 1875 2522 1 chr4A.!!$F2 647

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
723 724 2.713967 GCAAGGCACGGGCATTCAT 61.714 57.895 13.89 0.0 43.08 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2328 0.172578 CCTTCGGTGATCGTAGCACA 59.827 55.0 0.0 0.0 37.99 4.57 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
22 23 3.614616 GCCAAGCTACGTATAGATGATGC 59.385 47.826 0.00 0.00 0.00 3.91
23 24 4.809673 CCAAGCTACGTATAGATGATGCA 58.190 43.478 0.00 0.00 0.00 3.96
24 25 5.230182 CCAAGCTACGTATAGATGATGCAA 58.770 41.667 0.00 0.00 0.00 4.08
25 26 5.871524 CCAAGCTACGTATAGATGATGCAAT 59.128 40.000 0.00 0.00 0.00 3.56
26 27 7.035612 CCAAGCTACGTATAGATGATGCAATA 58.964 38.462 0.00 0.00 0.00 1.90
27 28 7.708322 CCAAGCTACGTATAGATGATGCAATAT 59.292 37.037 0.00 0.00 0.00 1.28
28 29 9.091784 CAAGCTACGTATAGATGATGCAATATT 57.908 33.333 0.00 0.00 0.00 1.28
29 30 8.864069 AGCTACGTATAGATGATGCAATATTC 57.136 34.615 0.00 0.00 0.00 1.75
30 31 8.470002 AGCTACGTATAGATGATGCAATATTCA 58.530 33.333 0.00 0.00 0.00 2.57
466 467 4.048504 GTGGGTTGATACAAAGTGCAAAC 58.951 43.478 0.00 0.00 0.00 2.93
629 630 5.801444 CGCAACACAATCATCATACACATTT 59.199 36.000 0.00 0.00 0.00 2.32
723 724 2.713967 GCAAGGCACGGGCATTCAT 61.714 57.895 13.89 0.00 43.08 2.57
870 872 8.700051 CACCTTAATTCCATCTCTCTTCTCTTA 58.300 37.037 0.00 0.00 0.00 2.10
937 939 4.642885 TCCTCGAAAACAAAACCAATCACT 59.357 37.500 0.00 0.00 0.00 3.41
1485 1491 2.806745 CGACTTCAAGGAGTTCAGCCAA 60.807 50.000 0.00 0.00 0.00 4.52
1617 1623 7.201688 CCAACGATTCAATGTGGATTGTATACA 60.202 37.037 0.08 0.08 40.09 2.29
1618 1624 8.344831 CAACGATTCAATGTGGATTGTATACAT 58.655 33.333 6.36 0.00 40.09 2.29
1619 1625 9.554395 AACGATTCAATGTGGATTGTATACATA 57.446 29.630 6.36 0.00 40.09 2.29
1620 1626 9.725019 ACGATTCAATGTGGATTGTATACATAT 57.275 29.630 6.36 3.52 40.09 1.78
1729 1738 8.495160 TTTTGGCTGGATTGGATTCATTATAT 57.505 30.769 0.00 0.00 0.00 0.86
1781 1790 5.394883 CGGTAGGGTGAAGAAGCAAGTATTA 60.395 44.000 0.00 0.00 0.00 0.98
1783 1792 5.763876 AGGGTGAAGAAGCAAGTATTACT 57.236 39.130 0.00 0.00 0.00 2.24
1795 1804 6.136857 AGCAAGTATTACTCCTATCCACTCA 58.863 40.000 0.00 0.00 0.00 3.41
1800 1809 7.967908 AGTATTACTCCTATCCACTCATTTGG 58.032 38.462 0.00 0.00 38.10 3.28
1871 1880 1.380515 CTCCTTCCTCCTCTCGGCA 60.381 63.158 0.00 0.00 0.00 5.69
1958 1987 2.964925 GTTGTCGCGACAGTGGCA 60.965 61.111 37.06 22.72 42.94 4.92
2133 2162 2.202797 CTCCTGTCGTGGATGGCG 60.203 66.667 0.00 0.00 35.30 5.69
2187 2216 2.125673 CCTTCCTACGGCGTGGTG 60.126 66.667 24.86 13.82 0.00 4.17
2204 2233 0.535335 GTGGCTCCACGGTAGATCAA 59.465 55.000 2.97 0.00 37.19 2.57
2279 2308 2.501610 GCCTAGTTCGGCCCTCAG 59.498 66.667 0.00 0.00 44.41 3.35
2280 2309 2.359967 GCCTAGTTCGGCCCTCAGT 61.360 63.158 0.00 0.00 44.41 3.41
2281 2310 1.817209 CCTAGTTCGGCCCTCAGTC 59.183 63.158 0.00 0.00 0.00 3.51
2282 2311 1.677637 CCTAGTTCGGCCCTCAGTCC 61.678 65.000 0.00 0.00 0.00 3.85
2283 2312 0.684805 CTAGTTCGGCCCTCAGTCCT 60.685 60.000 0.00 0.00 0.00 3.85
2284 2313 0.970937 TAGTTCGGCCCTCAGTCCTG 60.971 60.000 0.00 0.00 0.00 3.86
2285 2314 3.706373 TTCGGCCCTCAGTCCTGC 61.706 66.667 0.00 0.00 0.00 4.85
2290 2319 3.086600 CCCTCAGTCCTGCCCCTC 61.087 72.222 0.00 0.00 0.00 4.30
2291 2320 3.086600 CCTCAGTCCTGCCCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
2292 2321 2.040278 CTCAGTCCTGCCCCTCCT 59.960 66.667 0.00 0.00 0.00 3.69
2293 2322 1.311403 CTCAGTCCTGCCCCTCCTA 59.689 63.158 0.00 0.00 0.00 2.94
2294 2323 0.105246 CTCAGTCCTGCCCCTCCTAT 60.105 60.000 0.00 0.00 0.00 2.57
2295 2324 0.343372 TCAGTCCTGCCCCTCCTATT 59.657 55.000 0.00 0.00 0.00 1.73
2296 2325 0.471617 CAGTCCTGCCCCTCCTATTG 59.528 60.000 0.00 0.00 0.00 1.90
2297 2326 1.149401 GTCCTGCCCCTCCTATTGC 59.851 63.158 0.00 0.00 0.00 3.56
2298 2327 2.111878 CCTGCCCCTCCTATTGCG 59.888 66.667 0.00 0.00 0.00 4.85
2299 2328 2.746375 CCTGCCCCTCCTATTGCGT 61.746 63.158 0.00 0.00 0.00 5.24
2300 2329 1.524621 CTGCCCCTCCTATTGCGTG 60.525 63.158 0.00 0.00 0.00 5.34
2301 2330 2.257409 CTGCCCCTCCTATTGCGTGT 62.257 60.000 0.00 0.00 0.00 4.49
2302 2331 1.819632 GCCCCTCCTATTGCGTGTG 60.820 63.158 0.00 0.00 0.00 3.82
2303 2332 1.819632 CCCCTCCTATTGCGTGTGC 60.820 63.158 0.00 0.00 43.20 4.57
2304 2333 1.221840 CCCTCCTATTGCGTGTGCT 59.778 57.895 0.00 0.00 43.34 4.40
2305 2334 0.464036 CCCTCCTATTGCGTGTGCTA 59.536 55.000 0.00 0.00 43.34 3.49
2306 2335 1.571919 CCTCCTATTGCGTGTGCTAC 58.428 55.000 0.00 0.00 43.34 3.58
2316 2345 3.411808 GTGTGCTACGATCACCGAA 57.588 52.632 0.00 0.00 41.76 4.30
2317 2346 1.269166 GTGTGCTACGATCACCGAAG 58.731 55.000 0.00 0.00 41.76 3.79
2356 2429 1.820906 CCGTCCATCATGGTGGCTG 60.821 63.158 21.00 14.11 39.03 4.85
2396 2469 2.365617 GGGATCTTCCGCTCATCACTTA 59.634 50.000 0.00 0.00 37.43 2.24
2404 2477 1.202256 CGCTCATCACTTACGCCAGTA 60.202 52.381 0.00 0.00 0.00 2.74
2450 2523 0.394352 GTTGGGATCTTGGATGCCGT 60.394 55.000 12.15 0.00 31.57 5.68
2477 2550 2.520536 GCCTGGTGGTGAGAGGTGT 61.521 63.158 0.00 0.00 35.27 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.809673 TGCATCATCTATACGTAGCTTGG 58.190 43.478 0.08 0.00 0.00 3.61
2 3 6.957984 ATTGCATCATCTATACGTAGCTTG 57.042 37.500 0.08 0.00 0.00 4.01
3 4 9.307121 GAATATTGCATCATCTATACGTAGCTT 57.693 33.333 0.08 0.00 0.00 3.74
5 6 8.634475 TGAATATTGCATCATCTATACGTAGC 57.366 34.615 0.08 0.00 0.00 3.58
386 387 1.384222 GAACCTCCCTCCCTACCCC 60.384 68.421 0.00 0.00 0.00 4.95
387 388 1.384222 GGAACCTCCCTCCCTACCC 60.384 68.421 0.00 0.00 0.00 3.69
388 389 0.981801 GTGGAACCTCCCTCCCTACC 60.982 65.000 0.00 0.00 35.03 3.18
389 390 1.328430 CGTGGAACCTCCCTCCCTAC 61.328 65.000 0.00 0.00 35.03 3.18
390 391 1.001248 CGTGGAACCTCCCTCCCTA 59.999 63.158 0.00 0.00 35.03 3.53
391 392 2.284699 CGTGGAACCTCCCTCCCT 60.285 66.667 0.00 0.00 35.03 4.20
392 393 3.400054 CCGTGGAACCTCCCTCCC 61.400 72.222 0.00 0.00 35.03 4.30
466 467 2.266055 GGAGAGAAGGTGCCCACG 59.734 66.667 0.00 0.00 0.00 4.94
552 553 4.577283 GCAAAACCCAAGTGACTTGTACTA 59.423 41.667 22.40 0.00 39.58 1.82
553 554 3.380320 GCAAAACCCAAGTGACTTGTACT 59.620 43.478 22.40 4.73 39.58 2.73
686 687 8.097038 TGCCTTGCCACAAAACAATAAATATAA 58.903 29.630 0.00 0.00 0.00 0.98
698 699 2.790791 CCCGTGCCTTGCCACAAAA 61.791 57.895 0.00 0.00 35.47 2.44
769 771 9.831737 CACACCTTTTTGTCTATTTCTTATCTG 57.168 33.333 0.00 0.00 0.00 2.90
870 872 0.035056 AATAGCGGTGCCTCTTTGCT 60.035 50.000 0.00 0.00 39.59 3.91
937 939 0.386352 CGACGTTGGCGAAGTAGTCA 60.386 55.000 10.56 0.00 42.00 3.41
1347 1353 2.554142 CGCAGCTCTTCAATGGTGATA 58.446 47.619 0.00 0.00 32.48 2.15
1511 1517 7.356680 TCCCATTCAATAAAGTCAATCCTCAT 58.643 34.615 0.00 0.00 0.00 2.90
1530 1536 3.519667 ACCACAATGAACCATTCCCATT 58.480 40.909 0.00 0.00 31.05 3.16
1579 1585 4.793071 TGAATCGTTGGCATGTTAAAGTG 58.207 39.130 0.00 0.00 0.00 3.16
1781 1790 2.158900 CGCCAAATGAGTGGATAGGAGT 60.159 50.000 0.00 0.00 41.65 3.85
1783 1792 2.115427 TCGCCAAATGAGTGGATAGGA 58.885 47.619 0.00 0.00 41.65 2.94
1795 1804 0.546122 TGCCTACAGGATCGCCAAAT 59.454 50.000 0.00 0.00 37.39 2.32
1800 1809 1.593750 CTGCTGCCTACAGGATCGC 60.594 63.158 0.00 0.00 43.99 4.58
1940 1969 2.964925 GCCACTGTCGCGACAACA 60.965 61.111 38.11 20.07 41.33 3.33
2047 2076 1.377366 ATGCGTCGGATCTGTCGAGT 61.377 55.000 22.66 8.72 37.31 4.18
2103 2132 1.677966 CAGGAGCAGCAGCCACATT 60.678 57.895 0.00 0.00 43.56 2.71
2187 2216 0.535335 TGTTGATCTACCGTGGAGCC 59.465 55.000 4.82 0.00 0.00 4.70
2204 2233 0.596082 GTTGCCGTAGCCAAACATGT 59.404 50.000 0.00 0.00 38.69 3.21
2278 2307 1.348775 GCAATAGGAGGGGCAGGACT 61.349 60.000 0.00 0.00 0.00 3.85
2279 2308 1.149401 GCAATAGGAGGGGCAGGAC 59.851 63.158 0.00 0.00 0.00 3.85
2280 2309 2.443394 CGCAATAGGAGGGGCAGGA 61.443 63.158 0.00 0.00 0.00 3.86
2281 2310 2.111878 CGCAATAGGAGGGGCAGG 59.888 66.667 0.00 0.00 0.00 4.85
2282 2311 1.524621 CACGCAATAGGAGGGGCAG 60.525 63.158 0.00 0.00 0.00 4.85
2283 2312 2.297895 ACACGCAATAGGAGGGGCA 61.298 57.895 0.00 0.00 0.00 5.36
2284 2313 1.819632 CACACGCAATAGGAGGGGC 60.820 63.158 0.00 0.00 0.00 5.80
2285 2314 1.819632 GCACACGCAATAGGAGGGG 60.820 63.158 0.00 0.00 38.36 4.79
2286 2315 0.464036 TAGCACACGCAATAGGAGGG 59.536 55.000 0.00 0.00 42.27 4.30
2287 2316 1.571919 GTAGCACACGCAATAGGAGG 58.428 55.000 0.00 0.00 42.27 4.30
2288 2317 1.200483 CGTAGCACACGCAATAGGAG 58.800 55.000 0.00 0.00 45.03 3.69
2289 2318 3.339061 CGTAGCACACGCAATAGGA 57.661 52.632 0.00 0.00 45.03 2.94
2298 2327 1.269166 CTTCGGTGATCGTAGCACAC 58.731 55.000 0.00 0.00 37.99 3.82
2299 2328 0.172578 CCTTCGGTGATCGTAGCACA 59.827 55.000 0.00 0.00 37.99 4.57
2300 2329 0.527817 CCCTTCGGTGATCGTAGCAC 60.528 60.000 0.00 0.00 40.32 4.40
2301 2330 0.968901 ACCCTTCGGTGATCGTAGCA 60.969 55.000 0.00 0.00 42.48 3.49
2302 2331 0.175073 AACCCTTCGGTGATCGTAGC 59.825 55.000 0.00 0.00 43.71 3.58
2303 2332 2.686915 ACTAACCCTTCGGTGATCGTAG 59.313 50.000 0.00 0.00 43.71 3.51
2304 2333 2.684881 GACTAACCCTTCGGTGATCGTA 59.315 50.000 0.00 0.00 43.71 3.43
2305 2334 1.475682 GACTAACCCTTCGGTGATCGT 59.524 52.381 0.00 0.00 43.71 3.73
2306 2335 1.202382 GGACTAACCCTTCGGTGATCG 60.202 57.143 0.00 0.00 43.71 3.69
2307 2336 1.829222 TGGACTAACCCTTCGGTGATC 59.171 52.381 0.00 0.00 43.71 2.92
2308 2337 1.553704 GTGGACTAACCCTTCGGTGAT 59.446 52.381 0.00 0.00 43.71 3.06
2309 2338 0.971386 GTGGACTAACCCTTCGGTGA 59.029 55.000 0.00 0.00 43.71 4.02
2310 2339 0.974383 AGTGGACTAACCCTTCGGTG 59.026 55.000 0.00 0.00 43.71 4.94
2312 2341 0.535797 GGAGTGGACTAACCCTTCGG 59.464 60.000 0.00 0.00 38.00 4.30
2313 2342 0.535797 GGGAGTGGACTAACCCTTCG 59.464 60.000 0.00 0.00 39.28 3.79
2314 2343 0.910338 GGGGAGTGGACTAACCCTTC 59.090 60.000 10.46 0.00 41.79 3.46
2315 2344 0.195096 TGGGGAGTGGACTAACCCTT 59.805 55.000 16.18 0.00 41.39 3.95
2316 2345 0.421904 ATGGGGAGTGGACTAACCCT 59.578 55.000 16.18 4.05 41.39 4.34
2317 2346 0.837940 GATGGGGAGTGGACTAACCC 59.162 60.000 10.71 10.71 41.27 4.11
2318 2347 1.209747 GTGATGGGGAGTGGACTAACC 59.790 57.143 0.00 0.00 39.54 2.85
2319 2348 1.209747 GGTGATGGGGAGTGGACTAAC 59.790 57.143 0.00 0.00 0.00 2.34
2320 2349 1.580059 GGTGATGGGGAGTGGACTAA 58.420 55.000 0.00 0.00 0.00 2.24
2321 2350 0.686441 CGGTGATGGGGAGTGGACTA 60.686 60.000 0.00 0.00 0.00 2.59
2322 2351 1.990060 CGGTGATGGGGAGTGGACT 60.990 63.158 0.00 0.00 0.00 3.85
2370 2443 2.522271 GAGCGGAAGATCCCTCCTT 58.478 57.895 9.24 0.00 41.55 3.36
2457 2530 2.608988 CCTCTCACCACCAGGCCT 60.609 66.667 0.00 0.00 39.06 5.19
2470 2543 1.251527 CCCACGAGCACTACACCTCT 61.252 60.000 0.00 0.00 0.00 3.69
2499 2572 4.275508 CCAGCCCACACCTGTGCT 62.276 66.667 0.00 0.00 44.34 4.40


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

AutoCloner maintained by Alex Coulton.