Multiple sequence alignment - TraesCS6D01G371000

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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 TraesCS6D01G371000 chr6D 100.000 2459 0 0 1 2459 456545516 456547974 0.000000e+00 4542.0
1 TraesCS6D01G371000 chr6B 91.134 1534 95 21 391 1912 694345481 694346985 0.000000e+00 2041.0
2 TraesCS6D01G371000 chr6B 88.991 327 23 8 1 319 694342669 694342990 2.290000e-105 392.0
3 TraesCS6D01G371000 chr6B 87.791 344 26 7 1981 2309 694347276 694347618 2.970000e-104 388.0
4 TraesCS6D01G371000 chr6A 88.228 1665 134 30 333 1976 603271392 603273015 0.000000e+00 1932.0
5 TraesCS6D01G371000 chr6A 90.683 483 41 3 1981 2459 603273055 603273537 7.410000e-180 640.0
6 TraesCS6D01G371000 chr6A 90.196 204 13 5 118 319 603268957 603269155 2.430000e-65 259.0
7 TraesCS6D01G371000 chr6A 91.803 61 5 0 1 61 603268911 603268971 4.360000e-13 86.1


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 TraesCS6D01G371000 chr6D 456545516 456547974 2458 False 4542.000000 4542 100.000000 1 2459 1 chr6D.!!$F1 2458
1 TraesCS6D01G371000 chr6B 694342669 694347618 4949 False 940.333333 2041 89.305333 1 2309 3 chr6B.!!$F1 2308
2 TraesCS6D01G371000 chr6A 603268911 603273537 4626 False 729.275000 1932 90.227500 1 2459 4 chr6A.!!$F1 2458

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
621 3491 0.108585 GTGTCTCCTCCTTGTTGGCA 59.891 55.0 0.0 0.0 35.26 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 4358 0.031994 GGCCAGCAAAAACATCACGT 59.968 50.0 0.0 0.0 0.0 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
65 66 6.405065 GCAATCATGACAGTGACAATTATGGT 60.405 38.462 0.00 0.00 0.00 3.55
162 169 4.039124 ACCTTTTCTTGGTTTGATTGCGAT 59.961 37.500 0.00 0.00 33.34 4.58
319 329 8.131100 GCTCATAGCTGCTTTTATGTTTTGATA 58.869 33.333 7.79 0.00 38.45 2.15
320 330 9.443283 CTCATAGCTGCTTTTATGTTTTGATAC 57.557 33.333 7.79 0.00 0.00 2.24
322 332 9.443283 CATAGCTGCTTTTATGTTTTGATACTC 57.557 33.333 7.79 0.00 0.00 2.59
324 334 7.756558 AGCTGCTTTTATGTTTTGATACTCTC 58.243 34.615 0.00 0.00 0.00 3.20
325 335 6.684555 GCTGCTTTTATGTTTTGATACTCTCG 59.315 38.462 0.00 0.00 0.00 4.04
326 336 7.413000 GCTGCTTTTATGTTTTGATACTCTCGA 60.413 37.037 0.00 0.00 0.00 4.04
328 338 7.064609 TGCTTTTATGTTTTGATACTCTCGAGG 59.935 37.037 13.56 5.96 0.00 4.63
329 339 7.466050 GCTTTTATGTTTTGATACTCTCGAGGG 60.466 40.741 11.78 11.78 0.00 4.30
331 341 5.677319 ATGTTTTGATACTCTCGAGGGAA 57.323 39.130 21.80 0.00 0.00 3.97
363 2892 5.193679 GTTTGAGACCAGGTATATTTGGCT 58.806 41.667 0.00 4.55 38.03 4.75
371 2900 9.203163 AGACCAGGTATATTTGGCTATCTATAC 57.797 37.037 0.00 0.00 38.03 1.47
383 2912 8.677148 TTGGCTATCTATACAAATTCAACCTC 57.323 34.615 0.00 0.00 0.00 3.85
384 2913 7.801104 TGGCTATCTATACAAATTCAACCTCA 58.199 34.615 0.00 0.00 0.00 3.86
386 2915 7.934120 GGCTATCTATACAAATTCAACCTCAGT 59.066 37.037 0.00 0.00 0.00 3.41
387 2916 9.331282 GCTATCTATACAAATTCAACCTCAGTT 57.669 33.333 0.00 0.00 36.33 3.16
400 3263 5.355910 TCAACCTCAGTTTTGTAGTCCAAAC 59.644 40.000 0.00 0.00 42.63 2.93
529 3399 6.470557 TCGAAAATAAAGTAAACAGGGACG 57.529 37.500 0.00 0.00 0.00 4.79
590 3460 2.354704 CCAAATCAAGTCGGAGCCACTA 60.355 50.000 0.00 0.00 0.00 2.74
621 3491 0.108585 GTGTCTCCTCCTTGTTGGCA 59.891 55.000 0.00 0.00 35.26 4.92
622 3492 1.067295 TGTCTCCTCCTTGTTGGCAT 58.933 50.000 0.00 0.00 35.26 4.40
718 3588 6.921307 CCCAAAAAGTGTTAGTAACATGAACC 59.079 38.462 18.35 5.82 44.35 3.62
779 3651 7.382110 TGAAAATGAAAATAAATCAAGCGGGA 58.618 30.769 0.00 0.00 0.00 5.14
1463 4344 3.611674 GCCCGAGGCCTAGAGAGC 61.612 72.222 15.38 10.32 44.06 4.09
1465 4346 1.456705 CCCGAGGCCTAGAGAGCTT 60.457 63.158 15.38 0.00 0.00 3.74
1567 4450 3.376859 TGTTCATGACTTTGTGGTGTGAC 59.623 43.478 0.00 0.00 0.00 3.67
1625 4508 7.279981 TGCTCATGGTTCAACTATGTTATGTAC 59.720 37.037 13.13 0.00 38.13 2.90
1626 4509 7.516785 GCTCATGGTTCAACTATGTTATGTACG 60.517 40.741 13.13 0.00 38.13 3.67
1627 4510 6.759356 TCATGGTTCAACTATGTTATGTACGG 59.241 38.462 13.13 0.00 38.13 4.02
1628 4511 6.283544 TGGTTCAACTATGTTATGTACGGA 57.716 37.500 0.00 0.00 0.00 4.69
1629 4512 6.334989 TGGTTCAACTATGTTATGTACGGAG 58.665 40.000 0.00 0.00 0.00 4.63
1631 4514 7.122501 TGGTTCAACTATGTTATGTACGGAGTA 59.877 37.037 0.00 0.00 45.11 2.59
1672 4555 6.060788 TGCAAATTGCTTTGTAGGGAATTTT 58.939 32.000 19.34 0.00 45.31 1.82
1688 4571 5.687285 GGGAATTTTCGCTGCATTAATGTAG 59.313 40.000 24.42 24.42 42.44 2.74
1690 4573 6.414987 GGAATTTTCGCTGCATTAATGTAGAC 59.585 38.462 30.55 21.38 42.19 2.59
1722 4605 7.069950 ACATTGTCTCATGATGCTAAGTACCTA 59.930 37.037 0.00 0.00 0.00 3.08
1759 4643 5.572896 CCAACGCAAGAAATAATCCTCAAAC 59.427 40.000 0.00 0.00 43.62 2.93
1797 4681 2.695359 CTTCCATCTTCCCGACGAAAA 58.305 47.619 0.00 0.00 0.00 2.29
1828 4712 1.247567 AAGAACCATTCGGCAACAGG 58.752 50.000 0.00 0.00 34.57 4.00
1880 4764 2.747446 CTGGTAGCCGCTTAACATGTTT 59.253 45.455 17.78 0.00 0.00 2.83
1959 5038 5.922546 TGGTACGAATCATTTTCTTTCACG 58.077 37.500 0.00 0.00 0.00 4.35
2055 5170 1.067495 GCTAACTTCACGGAGCTGACT 60.067 52.381 0.00 0.00 32.04 3.41
2076 5191 0.321298 GTTTGGCCCAGCTTCGTCTA 60.321 55.000 0.00 0.00 0.00 2.59
2084 5199 2.028930 CCCAGCTTCGTCTACTGACTTT 60.029 50.000 0.00 0.00 40.86 2.66
2089 5204 4.083003 AGCTTCGTCTACTGACTTTGAGAG 60.083 45.833 0.00 0.00 40.86 3.20
2116 5232 1.003118 AGTTGGGCAGTTGCGAATAGA 59.997 47.619 0.00 0.00 43.26 1.98
2119 5235 1.429148 GGGCAGTTGCGAATAGACCG 61.429 60.000 0.00 0.00 43.26 4.79
2142 5258 6.262496 CCGTAAGAGTATGATTGGACACTCTA 59.738 42.308 3.70 0.00 45.33 2.43
2178 5294 8.702438 CAACTTGTGATGGTTTGATAACAATTC 58.298 33.333 0.00 0.00 35.92 2.17
2215 5332 0.673985 GTGGAGCTTGTTTGGGGAAC 59.326 55.000 0.00 0.00 38.78 3.62
2312 5441 5.245531 TCGAAAATGACAATCAACTAGCCT 58.754 37.500 0.00 0.00 0.00 4.58
2314 5443 6.876789 TCGAAAATGACAATCAACTAGCCTAA 59.123 34.615 0.00 0.00 0.00 2.69
2319 5448 5.168569 TGACAATCAACTAGCCTAACTTCG 58.831 41.667 0.00 0.00 0.00 3.79
2323 5452 5.854010 ATCAACTAGCCTAACTTCGATCA 57.146 39.130 0.00 0.00 0.00 2.92
2346 5475 6.017523 TCACTTTGACAATGAGTAATCGCAAA 60.018 34.615 7.99 0.00 0.00 3.68
2348 5477 5.940192 TTGACAATGAGTAATCGCAAACT 57.060 34.783 0.00 0.00 0.00 2.66
2363 5492 4.515191 TCGCAAACTTTCTAGCTCAAATGT 59.485 37.500 0.00 0.00 0.00 2.71
2366 5495 5.560953 GCAAACTTTCTAGCTCAAATGTCGT 60.561 40.000 0.00 0.00 0.00 4.34
2386 5515 7.406553 TGTCGTCTTCTTAACATGTTGAAAAG 58.593 34.615 21.42 14.97 0.00 2.27
2390 5519 7.112148 CGTCTTCTTAACATGTTGAAAAGAAGC 59.888 37.037 33.51 28.85 42.44 3.86
2393 5522 8.633075 TTCTTAACATGTTGAAAAGAAGCAAG 57.367 30.769 22.46 14.22 31.76 4.01
2409 5538 0.179156 CAAGCCATGACGCAATCCAC 60.179 55.000 0.00 0.00 0.00 4.02
2436 5565 4.513318 GGTCTTACATATCAAGAGCTTGGC 59.487 45.833 10.09 0.00 43.74 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 248 6.405278 TTCCTTTTTGGGAAGTCATCTTTC 57.595 37.500 0.00 0.00 40.08 2.62
308 318 6.785337 TTCCCTCGAGAGTATCAAAACATA 57.215 37.500 15.71 0.00 37.82 2.29
347 2876 8.911018 TGTATAGATAGCCAAATATACCTGGT 57.089 34.615 4.05 4.05 34.97 4.00
371 2900 6.918022 GGACTACAAAACTGAGGTTGAATTTG 59.082 38.462 5.32 0.00 35.63 2.32
448 3313 0.454620 CTCGACGACTCTTTGGACCG 60.455 60.000 0.00 0.00 0.00 4.79
503 3373 7.148540 CGTCCCTGTTTACTTTATTTTCGATCA 60.149 37.037 0.00 0.00 0.00 2.92
504 3374 7.148523 ACGTCCCTGTTTACTTTATTTTCGATC 60.149 37.037 0.00 0.00 0.00 3.69
505 3375 6.652062 ACGTCCCTGTTTACTTTATTTTCGAT 59.348 34.615 0.00 0.00 0.00 3.59
506 3376 5.990996 ACGTCCCTGTTTACTTTATTTTCGA 59.009 36.000 0.00 0.00 0.00 3.71
507 3377 6.146673 AGACGTCCCTGTTTACTTTATTTTCG 59.853 38.462 13.01 0.00 0.00 3.46
508 3378 7.430992 AGACGTCCCTGTTTACTTTATTTTC 57.569 36.000 13.01 0.00 0.00 2.29
513 3383 4.060205 GCAAGACGTCCCTGTTTACTTTA 58.940 43.478 13.01 0.00 0.00 1.85
517 3387 2.165319 AGCAAGACGTCCCTGTTTAC 57.835 50.000 13.01 0.00 0.00 2.01
562 3432 4.559153 CTCCGACTTGATTTGGCATTTTT 58.441 39.130 0.00 0.00 0.00 1.94
564 3434 2.094545 GCTCCGACTTGATTTGGCATTT 60.095 45.455 0.00 0.00 0.00 2.32
565 3435 1.474077 GCTCCGACTTGATTTGGCATT 59.526 47.619 0.00 0.00 0.00 3.56
567 3437 0.960364 GGCTCCGACTTGATTTGGCA 60.960 55.000 0.00 0.00 0.00 4.92
568 3438 0.960364 TGGCTCCGACTTGATTTGGC 60.960 55.000 0.00 0.00 0.00 4.52
590 3460 0.669077 GGAGACACGTCACTCACACT 59.331 55.000 16.74 0.00 35.17 3.55
621 3491 1.880027 GTTTTGGTTGCTCCTCGTGAT 59.120 47.619 0.80 0.00 37.07 3.06
622 3492 1.305201 GTTTTGGTTGCTCCTCGTGA 58.695 50.000 0.80 0.00 37.07 4.35
863 3738 2.592308 GGCTGGGAGGATGTGGTC 59.408 66.667 0.00 0.00 0.00 4.02
910 3785 3.750373 GAGTGGTGGTGTGTGGCGT 62.750 63.158 0.00 0.00 0.00 5.68
1428 4309 0.674895 GCTTGAGGATGCCGTTGACT 60.675 55.000 0.00 0.00 0.00 3.41
1463 4344 3.958147 ATCACGTGCCGAGCCCAAG 62.958 63.158 11.67 0.00 0.00 3.61
1465 4346 4.758251 CATCACGTGCCGAGCCCA 62.758 66.667 11.67 0.00 0.00 5.36
1475 4358 0.031994 GGCCAGCAAAAACATCACGT 59.968 50.000 0.00 0.00 0.00 4.49
1479 4362 1.405933 GGATGGGCCAGCAAAAACATC 60.406 52.381 25.00 6.78 36.34 3.06
1480 4363 0.614812 GGATGGGCCAGCAAAAACAT 59.385 50.000 25.00 0.00 36.34 2.71
1625 4508 4.682787 TGATCTTGTTGCATACTACTCCG 58.317 43.478 0.00 0.00 0.00 4.63
1626 4509 5.049818 GCATGATCTTGTTGCATACTACTCC 60.050 44.000 10.05 0.00 36.40 3.85
1627 4510 5.525012 TGCATGATCTTGTTGCATACTACTC 59.475 40.000 10.05 0.00 41.18 2.59
1628 4511 5.430886 TGCATGATCTTGTTGCATACTACT 58.569 37.500 10.05 0.00 41.18 2.57
1629 4512 5.739752 TGCATGATCTTGTTGCATACTAC 57.260 39.130 10.05 0.00 41.18 2.73
1630 4513 6.756299 TTTGCATGATCTTGTTGCATACTA 57.244 33.333 10.05 0.00 45.04 1.82
1631 4514 5.648178 TTTGCATGATCTTGTTGCATACT 57.352 34.783 10.05 0.00 45.04 2.12
1672 4555 4.503910 AGTTGTCTACATTAATGCAGCGA 58.496 39.130 15.48 5.81 0.00 4.93
1690 4573 6.432607 AGCATCATGAGACAATGTAAGTTG 57.567 37.500 0.09 0.00 35.25 3.16
1703 4586 6.096036 CCGAATAGGTACTTAGCATCATGAG 58.904 44.000 0.09 0.00 41.75 2.90
1743 4627 5.196695 GAGCTGGGTTTGAGGATTATTTCT 58.803 41.667 0.00 0.00 0.00 2.52
1744 4628 4.339530 GGAGCTGGGTTTGAGGATTATTTC 59.660 45.833 0.00 0.00 0.00 2.17
1745 4629 4.017130 AGGAGCTGGGTTTGAGGATTATTT 60.017 41.667 0.00 0.00 0.00 1.40
1746 4630 3.529319 AGGAGCTGGGTTTGAGGATTATT 59.471 43.478 0.00 0.00 0.00 1.40
1747 4631 3.126453 AGGAGCTGGGTTTGAGGATTAT 58.874 45.455 0.00 0.00 0.00 1.28
1748 4632 2.505819 GAGGAGCTGGGTTTGAGGATTA 59.494 50.000 0.00 0.00 0.00 1.75
1759 4643 3.038280 CGAGATCGAGGAGCTGGG 58.962 66.667 0.00 0.00 43.02 4.45
1828 4712 1.337635 GCGATCATGGATCTGGGAGTC 60.338 57.143 4.86 0.00 36.96 3.36
1880 4764 1.123077 ACCATGCCAGAATCGAGCTA 58.877 50.000 0.00 0.00 0.00 3.32
1921 5000 3.388676 TCGTACCAGGGAAGAAAAGAACA 59.611 43.478 0.00 0.00 0.00 3.18
1959 5038 1.516603 GAAGAGCTACCACCGCGAC 60.517 63.158 8.23 0.00 0.00 5.19
2055 5170 1.452145 GACGAAGCTGGGCCAAACAA 61.452 55.000 8.04 0.00 0.00 2.83
2076 5191 0.689623 CCTGGCCTCTCAAAGTCAGT 59.310 55.000 3.32 0.00 0.00 3.41
2084 5199 1.920325 CCCAACTCCTGGCCTCTCA 60.920 63.158 3.32 0.00 44.90 3.27
2116 5232 4.710375 AGTGTCCAATCATACTCTTACGGT 59.290 41.667 0.00 0.00 0.00 4.83
2119 5235 9.871238 TTTTAGAGTGTCCAATCATACTCTTAC 57.129 33.333 10.56 0.00 45.48 2.34
2142 5258 6.036577 ACCATCACAAGTTGTTCTGTTTTT 57.963 33.333 5.57 0.00 0.00 1.94
2178 5294 5.393461 GCTCCACTTGGTTCATTTCCATTAG 60.393 44.000 0.00 0.00 34.75 1.73
2205 5321 2.430248 ATATCCCACGTTCCCCAAAC 57.570 50.000 0.00 0.00 34.31 2.93
2255 5373 7.097834 GTCCTACCCAATGTAGCATCTATTAC 58.902 42.308 0.00 0.00 44.77 1.89
2287 5416 6.375455 AGGCTAGTTGATTGTCATTTTCGAAT 59.625 34.615 0.00 0.00 0.00 3.34
2291 5420 8.045176 AGTTAGGCTAGTTGATTGTCATTTTC 57.955 34.615 0.00 0.00 0.00 2.29
2303 5432 5.000012 AGTGATCGAAGTTAGGCTAGTTG 58.000 43.478 0.00 0.00 0.00 3.16
2312 5441 6.929049 ACTCATTGTCAAAGTGATCGAAGTTA 59.071 34.615 0.00 0.00 0.00 2.24
2314 5443 5.300752 ACTCATTGTCAAAGTGATCGAAGT 58.699 37.500 0.00 0.00 0.00 3.01
2319 5448 6.183360 TGCGATTACTCATTGTCAAAGTGATC 60.183 38.462 10.20 10.20 34.45 2.92
2323 5452 5.940192 TTGCGATTACTCATTGTCAAAGT 57.060 34.783 0.00 0.00 0.00 2.66
2346 5475 5.140747 AGACGACATTTGAGCTAGAAAGT 57.859 39.130 0.00 0.00 0.00 2.66
2348 5477 5.784177 AGAAGACGACATTTGAGCTAGAAA 58.216 37.500 0.00 0.00 0.00 2.52
2363 5492 7.780008 TCTTTTCAACATGTTAAGAAGACGA 57.220 32.000 16.40 9.61 0.00 4.20
2386 5515 0.171903 ATTGCGTCATGGCTTGCTTC 59.828 50.000 0.00 0.00 0.00 3.86
2390 5519 0.179156 GTGGATTGCGTCATGGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
2393 5522 0.243365 TTTGTGGATTGCGTCATGGC 59.757 50.000 0.00 0.00 0.00 4.40
2409 5538 7.201679 CCAAGCTCTTGATATGTAAGACCTTTG 60.202 40.741 10.94 5.64 42.93 2.77


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

AutoCloner maintained by Alex Coulton.