Multiple sequence alignment - TraesCS6A01G297200

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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 TraesCS6A01G297200 chr6A 100.000 2620 0 0 1 2620 530618272 530620891 0.000000e+00 4839
1 TraesCS6A01G297200 chr6A 86.505 289 23 9 971 1247 530597478 530597762 1.180000e-78 303
2 TraesCS6A01G297200 chr6A 92.661 109 7 1 667 774 528215306 528215414 3.490000e-34 156
3 TraesCS6A01G297200 chr6A 90.909 110 8 2 667 774 528432397 528432506 2.100000e-31 147
4 TraesCS6A01G297200 chr6D 92.657 2465 107 21 1 2436 386085906 386088325 0.000000e+00 3482
5 TraesCS6A01G297200 chr6D 81.447 760 59 34 544 1259 386063268 386063989 4.930000e-152 547
6 TraesCS6A01G297200 chr6D 90.816 294 25 2 201 494 386062651 386062942 2.440000e-105 392
7 TraesCS6A01G297200 chr6D 77.827 681 93 38 971 1630 386068005 386068648 4.120000e-98 368
8 TraesCS6A01G297200 chr6D 92.391 184 11 2 2434 2617 386088448 386088628 2.590000e-65 259
9 TraesCS6A01G297200 chr6B 93.559 1770 76 13 1 1763 576607722 576609460 0.000000e+00 2603
10 TraesCS6A01G297200 chr6B 92.839 391 23 2 1883 2271 576609698 576610085 1.760000e-156 562
11 TraesCS6A01G297200 chr6B 94.540 348 12 2 2273 2620 576610883 576611223 4.960000e-147 531
12 TraesCS6A01G297200 chr6B 77.101 690 95 47 971 1630 576452903 576453559 8.980000e-90 340
13 TraesCS6A01G297200 chr6B 84.615 299 25 11 972 1259 576441493 576441781 7.140000e-71 278


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 TraesCS6A01G297200 chr6A 530618272 530620891 2619 False 4839.0 4839 100.0000 1 2620 1 chr6A.!!$F4 2619
1 TraesCS6A01G297200 chr6D 386085906 386088628 2722 False 1870.5 3482 92.5240 1 2617 2 chr6D.!!$F3 2616
2 TraesCS6A01G297200 chr6D 386062651 386063989 1338 False 469.5 547 86.1315 201 1259 2 chr6D.!!$F2 1058
3 TraesCS6A01G297200 chr6D 386068005 386068648 643 False 368.0 368 77.8270 971 1630 1 chr6D.!!$F1 659
4 TraesCS6A01G297200 chr6B 576607722 576611223 3501 False 1232.0 2603 93.6460 1 2620 3 chr6B.!!$F3 2619
5 TraesCS6A01G297200 chr6B 576452903 576453559 656 False 340.0 340 77.1010 971 1630 1 chr6B.!!$F2 659

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
451 452 0.034863 GGGGGTGTTCGGCTATTTGA 60.035 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2312 0.246635 CAGTAGAGTTGACACCCCGG 59.753 60.0 0.0 0.0 0.0 5.73 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
23 24 6.679327 GGACTTATGTAAATCCCTCAACAC 57.321 41.667 0.00 0.00 0.00 3.32
43 44 1.336887 CCAGTAGGGTCAGACAACGTG 60.337 57.143 2.17 0.00 0.00 4.49
89 90 3.185594 TGGTGCGTATTCTCAAAAAGACG 59.814 43.478 0.00 0.00 44.36 4.18
101 102 4.509616 TCAAAAAGACGTGACCTTCTTGA 58.490 39.130 0.00 0.00 30.69 3.02
102 103 4.331717 TCAAAAAGACGTGACCTTCTTGAC 59.668 41.667 0.00 0.00 28.85 3.18
116 117 4.717280 CCTTCTTGACCATACCTAGGACTT 59.283 45.833 17.98 0.00 0.00 3.01
167 168 1.868997 GTCGGACGACGTGGAGTTA 59.131 57.895 4.58 0.00 44.69 2.24
231 232 0.947180 TGAGCCGCGACAAGGTTTAC 60.947 55.000 8.23 0.00 0.00 2.01
367 368 0.980754 TGGTGGTGATCCTATGCGGT 60.981 55.000 0.00 0.00 34.23 5.68
368 369 0.532862 GGTGGTGATCCTATGCGGTG 60.533 60.000 0.00 0.00 34.23 4.94
395 396 6.032094 CAGACATTGCATATTTGTCTTCCAC 58.968 40.000 15.40 0.00 45.88 4.02
411 412 0.179111 CCACTGCTCGCCTTCGAATA 60.179 55.000 0.00 0.00 44.98 1.75
420 421 2.362397 TCGCCTTCGAATAAGAGATGCT 59.638 45.455 0.00 0.00 42.44 3.79
440 441 3.306379 GCTACTAGCGGGGGTGTT 58.694 61.111 0.00 0.00 0.00 3.32
451 452 0.034863 GGGGGTGTTCGGCTATTTGA 60.035 55.000 0.00 0.00 0.00 2.69
562 839 4.214119 CGATGGTGAAATTGAGTGACTTGT 59.786 41.667 0.00 0.00 0.00 3.16
603 880 0.966920 ACACTTGTTCCGACCTCGAT 59.033 50.000 0.00 0.00 43.02 3.59
605 882 2.163815 ACACTTGTTCCGACCTCGATAG 59.836 50.000 0.00 0.00 43.02 2.08
618 895 6.153067 CGACCTCGATAGCATATTTCTTCTT 58.847 40.000 0.00 0.00 43.02 2.52
632 909 0.314935 CTTCTTGGCGGCATGTGTTT 59.685 50.000 21.71 0.00 0.00 2.83
647 924 0.250124 TGTTTAGTGTGCCTCGGTGG 60.250 55.000 0.00 0.00 39.35 4.61
870 1150 8.398665 AGAAAGCCGAAACAAGATCAATTATAC 58.601 33.333 0.00 0.00 0.00 1.47
871 1151 7.865706 AAGCCGAAACAAGATCAATTATACT 57.134 32.000 0.00 0.00 0.00 2.12
872 1152 8.958119 AAGCCGAAACAAGATCAATTATACTA 57.042 30.769 0.00 0.00 0.00 1.82
962 1266 9.270640 CTATCTGAAACCATAAAATCTCCTCTG 57.729 37.037 0.00 0.00 0.00 3.35
1154 1466 2.517166 GATGGAAGAAGGCCGGCC 60.517 66.667 39.29 39.29 0.00 6.13
1247 1583 4.547671 TCCTTGGTCGATCCTCTTATCTT 58.452 43.478 0.00 0.00 37.07 2.40
1249 1585 5.535406 TCCTTGGTCGATCCTCTTATCTTAC 59.465 44.000 0.00 0.00 37.07 2.34
1250 1586 5.536916 CCTTGGTCGATCCTCTTATCTTACT 59.463 44.000 0.00 0.00 37.07 2.24
1251 1587 6.715718 CCTTGGTCGATCCTCTTATCTTACTA 59.284 42.308 0.00 0.00 37.07 1.82
1280 1630 2.607635 GCAGAGTTCACAGACGTTTCAA 59.392 45.455 0.00 0.00 0.00 2.69
1369 1722 2.099141 ATGTATGATGGGAATCGGCG 57.901 50.000 0.00 0.00 0.00 6.46
1403 1756 1.276844 GAGTGGTGCGCGATTATGC 59.723 57.895 12.10 0.00 0.00 3.14
1421 1774 0.304098 GCATGCGCTCTGACAGATTC 59.696 55.000 9.73 0.33 34.30 2.52
1486 1839 2.919494 CGGTTTGGCTCTTGGTGGC 61.919 63.158 0.00 0.00 0.00 5.01
1757 2110 4.335594 GCATACAGAACCTACATTGTTCCC 59.664 45.833 0.00 0.00 42.41 3.97
1795 2312 3.282021 TCTGCTATCCCAGATTTGCAAC 58.718 45.455 0.00 0.00 36.96 4.17
1796 2313 2.360165 CTGCTATCCCAGATTTGCAACC 59.640 50.000 0.00 0.00 34.77 3.77
1834 2351 2.092323 GCATTTAGTCTCGGGGCTTTT 58.908 47.619 0.00 0.00 0.00 2.27
1874 2406 8.214364 TCATGTTATGCATATGTTTAGGTGGTA 58.786 33.333 7.36 0.00 35.74 3.25
2022 2554 5.509501 GCAAAAGACAAGTTTCCATGGATCA 60.510 40.000 17.06 2.15 0.00 2.92
2128 2660 4.043750 CACACATTTGTCGTTTGATTGCT 58.956 39.130 0.00 0.00 31.66 3.91
2136 2668 0.725784 CGTTTGATTGCTGACGGTGC 60.726 55.000 0.00 0.00 32.29 5.01
2203 2735 5.067413 TGTTCTCCTAGTTGCTTATACCTCG 59.933 44.000 0.00 0.00 0.00 4.63
2267 2800 7.271868 GGGTTAGTACAAATTTCGCAAATGTAC 59.728 37.037 14.77 14.77 33.68 2.90
2271 2804 5.881637 ACAAATTTCGCAAATGTACACAC 57.118 34.783 0.00 0.00 0.00 3.82
2315 3644 1.906574 AGAGGCAAGAATTCGTACCCA 59.093 47.619 6.99 0.00 0.00 4.51
2316 3645 2.505819 AGAGGCAAGAATTCGTACCCAT 59.494 45.455 6.99 0.00 0.00 4.00
2317 3646 3.709653 AGAGGCAAGAATTCGTACCCATA 59.290 43.478 6.99 0.00 0.00 2.74
2318 3647 4.348168 AGAGGCAAGAATTCGTACCCATAT 59.652 41.667 6.99 0.00 0.00 1.78
2319 3648 4.642429 AGGCAAGAATTCGTACCCATATC 58.358 43.478 6.99 0.00 0.00 1.63
2320 3649 3.751698 GGCAAGAATTCGTACCCATATCC 59.248 47.826 0.00 0.00 0.00 2.59
2321 3650 4.385825 GCAAGAATTCGTACCCATATCCA 58.614 43.478 0.00 0.00 0.00 3.41
2322 3651 4.213482 GCAAGAATTCGTACCCATATCCAC 59.787 45.833 0.00 0.00 0.00 4.02
2333 3662 6.153851 CGTACCCATATCCACTATCCAATACA 59.846 42.308 0.00 0.00 0.00 2.29
2424 3753 4.809958 CCAGTGAGAGAACATGATGATGTC 59.190 45.833 0.00 0.00 42.30 3.06
2577 4031 0.387878 GCATACTGCTCCTCGATCCG 60.388 60.000 0.00 0.00 40.96 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.966920 ACGTTGTCTGACCCTACTGG 59.033 55.000 5.17 0.00 41.37 4.00
89 90 3.983044 AGGTATGGTCAAGAAGGTCAC 57.017 47.619 0.00 0.00 0.00 3.67
101 102 4.162320 CACACATCAAGTCCTAGGTATGGT 59.838 45.833 9.08 0.00 0.00 3.55
102 103 4.162320 ACACACATCAAGTCCTAGGTATGG 59.838 45.833 9.08 0.00 0.00 2.74
158 159 2.380410 GCACCACGCTAACTCCACG 61.380 63.158 0.00 0.00 37.77 4.94
186 187 1.058404 GCTCAACACCGTCGTAGTTC 58.942 55.000 0.00 0.00 0.00 3.01
411 412 3.254657 CCGCTAGTAGCTAAGCATCTCTT 59.745 47.826 19.66 0.00 39.60 2.85
420 421 0.032813 ACACCCCCGCTAGTAGCTAA 60.033 55.000 19.66 0.00 39.60 3.09
440 441 0.465460 GGCCCATGTCAAATAGCCGA 60.465 55.000 0.00 0.00 0.00 5.54
451 452 2.837031 GAATCCACACCGGCCCATGT 62.837 60.000 0.00 0.00 33.14 3.21
562 839 7.229506 AGTGTCATCATCATACTTATCTCGTGA 59.770 37.037 0.00 0.00 0.00 4.35
603 880 2.878406 GCCGCCAAGAAGAAATATGCTA 59.122 45.455 0.00 0.00 0.00 3.49
605 882 1.405105 TGCCGCCAAGAAGAAATATGC 59.595 47.619 0.00 0.00 0.00 3.14
618 895 0.536233 ACACTAAACACATGCCGCCA 60.536 50.000 0.00 0.00 0.00 5.69
841 1121 5.108385 TGATCTTGTTTCGGCTTTCTTTC 57.892 39.130 0.00 0.00 0.00 2.62
870 1150 3.372206 CGGCTTGACTTCATGGTTTCTAG 59.628 47.826 0.00 0.00 0.00 2.43
871 1151 3.007506 TCGGCTTGACTTCATGGTTTCTA 59.992 43.478 0.00 0.00 0.00 2.10
872 1152 2.154462 CGGCTTGACTTCATGGTTTCT 58.846 47.619 0.00 0.00 0.00 2.52
1247 1583 5.193679 TGTGAACTCTGCAGAGCTATAGTA 58.806 41.667 37.78 18.69 45.79 1.82
1249 1585 4.337836 TCTGTGAACTCTGCAGAGCTATAG 59.662 45.833 37.78 28.67 45.79 1.31
1250 1586 4.097135 GTCTGTGAACTCTGCAGAGCTATA 59.903 45.833 37.78 22.55 45.79 1.31
1251 1587 3.095332 TCTGTGAACTCTGCAGAGCTAT 58.905 45.455 37.78 26.10 45.79 2.97
1280 1630 5.067273 TGTTCGGTTCAACCACTGAATATT 58.933 37.500 7.52 0.00 45.74 1.28
1300 1650 7.201644 CGAGTAAATTCAGGCATTGAGTATGTT 60.202 37.037 0.00 0.00 37.07 2.71
1403 1756 1.326852 GTGAATCTGTCAGAGCGCATG 59.673 52.381 11.47 8.44 36.74 4.06
1421 1774 2.236489 AACCCTGGGAAATCATGGTG 57.764 50.000 22.23 0.00 36.13 4.17
1486 1839 1.127951 GATTCTGGTACACAAACCGCG 59.872 52.381 0.00 0.00 42.91 6.46
1490 1843 6.363357 GCAATTCTTGATTCTGGTACACAAAC 59.637 38.462 0.00 0.00 0.00 2.93
1594 1947 2.453521 ACGGAGTAGGTGTCTGCATAA 58.546 47.619 0.00 0.00 41.94 1.90
1722 2075 4.403453 GTTCTGTATGCAAACGATTCACC 58.597 43.478 0.00 0.00 0.00 4.02
1783 2300 1.606313 ACCCCGGTTGCAAATCTGG 60.606 57.895 0.00 4.08 30.11 3.86
1795 2312 0.246635 CAGTAGAGTTGACACCCCGG 59.753 60.000 0.00 0.00 0.00 5.73
1796 2313 0.389948 GCAGTAGAGTTGACACCCCG 60.390 60.000 0.00 0.00 0.00 5.73
1834 2351 5.356751 GCATAACATGATAAACCTGACACCA 59.643 40.000 0.00 0.00 0.00 4.17
1868 2400 1.816835 GCCTTTAACTTGCCTACCACC 59.183 52.381 0.00 0.00 0.00 4.61
1874 2406 1.244816 GAACCGCCTTTAACTTGCCT 58.755 50.000 0.00 0.00 0.00 4.75
1899 2431 4.266714 GACCCCCGATTTCTGTCAATTTA 58.733 43.478 0.00 0.00 0.00 1.40
1901 2433 2.620627 GGACCCCCGATTTCTGTCAATT 60.621 50.000 0.00 0.00 0.00 2.32
1902 2434 1.064685 GGACCCCCGATTTCTGTCAAT 60.065 52.381 0.00 0.00 0.00 2.57
1951 2483 9.657121 GCTATAAACTGCTTATGTGAATTCTTC 57.343 33.333 7.05 0.90 32.28 2.87
2022 2554 6.172630 TGTGTGATACTGATGCATGTAGTTT 58.827 36.000 15.95 9.94 0.00 2.66
2128 2660 2.543578 GCAAGAAGATGCACCGTCA 58.456 52.632 0.00 0.00 45.70 4.35
2136 2668 3.119459 AGCTGCTTTCATGCAAGAAGATG 60.119 43.478 16.46 1.53 42.83 2.90
2203 2735 2.107950 TGCAGTGTTGTATGGTAGGC 57.892 50.000 0.00 0.00 0.00 3.93
2267 2800 9.891828 TTGCTCTTTATACTGTTTATTTGTGTG 57.108 29.630 0.00 0.00 0.00 3.82
2315 3644 6.253758 TCCTCGTGTATTGGATAGTGGATAT 58.746 40.000 0.00 0.00 0.00 1.63
2316 3645 5.637127 TCCTCGTGTATTGGATAGTGGATA 58.363 41.667 0.00 0.00 0.00 2.59
2317 3646 4.480115 TCCTCGTGTATTGGATAGTGGAT 58.520 43.478 0.00 0.00 0.00 3.41
2318 3647 3.905968 TCCTCGTGTATTGGATAGTGGA 58.094 45.455 0.00 0.00 0.00 4.02
2319 3648 4.621991 CTTCCTCGTGTATTGGATAGTGG 58.378 47.826 0.00 0.00 0.00 4.00
2320 3649 4.051922 GCTTCCTCGTGTATTGGATAGTG 58.948 47.826 0.00 0.00 0.00 2.74
2321 3650 3.704566 TGCTTCCTCGTGTATTGGATAGT 59.295 43.478 0.00 0.00 0.00 2.12
2322 3651 4.322080 TGCTTCCTCGTGTATTGGATAG 57.678 45.455 0.00 0.00 0.00 2.08
2349 3678 1.002134 GCTTTCCTAGTGCTGGCCA 60.002 57.895 4.71 4.71 0.00 5.36
2357 3686 1.004745 CACCATGTGGGCTTTCCTAGT 59.995 52.381 3.77 0.00 42.05 2.57
2577 4031 2.048503 CCTTGTCCGGACGGTCAC 60.049 66.667 28.70 5.90 33.38 3.67


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

AutoCloner maintained by Alex Coulton.