Multiple sequence alignment - TraesCS6B01G264700

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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 TraesCS6B01G264700 chr6B 100.000 2668 0 0 1 2668 476127521 476124854 0.000000e+00 4927
1 TraesCS6B01G264700 chr6D 90.523 2733 108 62 1 2666 308902254 308899606 0.000000e+00 3472
2 TraesCS6B01G264700 chr6A 93.069 1688 63 18 811 2462 445561947 445563616 0.000000e+00 2420
3 TraesCS6B01G264700 chr6A 92.466 438 24 8 347 781 445559908 445560339 3.770000e-173 617
4 TraesCS6B01G264700 chr6A 85.227 176 3 5 2453 2605 445569980 445570155 2.750000e-35 159


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 TraesCS6B01G264700 chr6B 476124854 476127521 2667 True 4927.0 4927 100.0000 1 2668 1 chr6B.!!$R1 2667
1 TraesCS6B01G264700 chr6D 308899606 308902254 2648 True 3472.0 3472 90.5230 1 2666 1 chr6D.!!$R1 2665
2 TraesCS6B01G264700 chr6A 445559908 445563616 3708 False 1518.5 2420 92.7675 347 2462 2 chr6A.!!$F2 2115

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
127 128 0.167033 CACTCCGTCGTCTCAGACAG 59.833 60.0 5.45 0.0 40.98 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 3543 1.474478 CTCGCTCTAGTGGCTTCTTCA 59.526 52.381 8.32 0.0 0.0 3.02 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
30 31 3.185391 ACGCAAACCAAATTTAAATGGCG 59.815 39.130 18.17 18.17 41.16 5.69
81 82 0.171903 CAGCAGCAGCAACCAATACC 59.828 55.000 3.17 0.00 45.49 2.73
88 89 2.783135 CAGCAACCAATACCAGTCAGT 58.217 47.619 0.00 0.00 0.00 3.41
89 90 3.868369 GCAGCAACCAATACCAGTCAGTA 60.868 47.826 0.00 0.00 0.00 2.74
90 91 3.935203 CAGCAACCAATACCAGTCAGTAG 59.065 47.826 0.00 0.00 0.00 2.57
91 92 3.838317 AGCAACCAATACCAGTCAGTAGA 59.162 43.478 0.00 0.00 0.00 2.59
127 128 0.167033 CACTCCGTCGTCTCAGACAG 59.833 60.000 5.45 0.00 40.98 3.51
198 199 4.496507 GCTCCCGTTTTAATCAAGAGCATC 60.497 45.833 4.33 0.00 43.62 3.91
200 201 3.621268 CCCGTTTTAATCAAGAGCATCGA 59.379 43.478 0.00 0.00 42.67 3.59
201 202 4.260375 CCCGTTTTAATCAAGAGCATCGAG 60.260 45.833 0.00 0.00 42.67 4.04
202 203 4.330074 CCGTTTTAATCAAGAGCATCGAGT 59.670 41.667 0.00 0.00 42.67 4.18
203 204 5.251081 CGTTTTAATCAAGAGCATCGAGTG 58.749 41.667 0.00 0.00 42.67 3.51
313 341 4.884668 AATCTTCCGTAGTGTCCAAGAA 57.115 40.909 0.00 0.00 0.00 2.52
341 369 2.128729 GAGTCCTCGATTCCCAGGG 58.871 63.158 0.00 0.00 0.00 4.45
342 370 2.034048 GAGTCCTCGATTCCCAGGGC 62.034 65.000 0.00 0.00 34.25 5.19
343 371 2.768344 TCCTCGATTCCCAGGGCC 60.768 66.667 0.00 0.00 0.00 5.80
344 372 3.089874 CCTCGATTCCCAGGGCCA 61.090 66.667 6.18 0.00 0.00 5.36
345 373 2.507944 CTCGATTCCCAGGGCCAG 59.492 66.667 6.18 0.00 0.00 4.85
453 483 3.511934 AGTCTACTGAGAAGACGCCAAAT 59.488 43.478 0.00 0.00 46.46 2.32
567 600 0.179124 GCTACTCAAGTCTCAGCCCG 60.179 60.000 0.00 0.00 0.00 6.13
571 604 2.125912 CAAGTCTCAGCCCGTCCG 60.126 66.667 0.00 0.00 0.00 4.79
624 657 1.066286 ACTGCATCTCTCAGCTGAACC 60.066 52.381 18.85 3.24 35.04 3.62
743 776 8.699283 AGTAAATAACAGGAATTACTGACGAC 57.301 34.615 24.82 11.95 40.97 4.34
766 799 1.272816 TGGTCTCACGATCCAAGGGTA 60.273 52.381 0.00 0.00 0.00 3.69
783 816 5.687166 AGGGTATTGGAATTCAAGTACGA 57.313 39.130 7.93 0.00 38.95 3.43
792 2373 4.499758 GGAATTCAAGTACGATCTCACGAC 59.500 45.833 7.93 0.00 37.03 4.34
815 2396 6.930731 ACGCAAGGTGTTGGAATTTATTTAT 58.069 32.000 0.00 0.00 46.39 1.40
863 2471 1.678635 CAGCTTTCCCGATTGGCCA 60.679 57.895 0.00 0.00 0.00 5.36
945 2553 0.908198 GACATCTGTCTGGCCTCCTT 59.092 55.000 3.32 0.00 41.65 3.36
1056 2664 4.052518 AATCCGCTGCCCTGCCTT 62.053 61.111 0.00 0.00 0.00 4.35
1067 2675 1.606531 CCTGCCTTAGCCAAGCTCT 59.393 57.895 0.00 0.00 40.44 4.09
1428 3041 0.316854 GGCGAGCTAGCAGTACGTAC 60.317 60.000 20.82 18.10 39.27 3.67
1429 3042 0.656785 GCGAGCTAGCAGTACGTACT 59.343 55.000 22.45 22.45 36.90 2.73
1430 3043 1.863454 GCGAGCTAGCAGTACGTACTA 59.137 52.381 26.95 11.87 34.13 1.82
1634 3265 4.242475 CGAGATTGTTGTACTAGTGCCAA 58.758 43.478 5.39 5.41 0.00 4.52
1652 3289 8.635765 AGTGCCAAGTGATCTTCTAAAATTAA 57.364 30.769 0.00 0.00 0.00 1.40
1653 3290 9.077885 AGTGCCAAGTGATCTTCTAAAATTAAA 57.922 29.630 0.00 0.00 0.00 1.52
1654 3291 9.860898 GTGCCAAGTGATCTTCTAAAATTAAAT 57.139 29.630 0.00 0.00 0.00 1.40
1764 3409 4.382793 GCTCGGTGTTTATTACTCCCTCTT 60.383 45.833 0.00 0.00 37.15 2.85
1813 3458 5.987953 GGGCCTAGACTTAGGTAAAATAACG 59.012 44.000 0.84 0.00 46.96 3.18
1856 3501 4.679331 ACAGAGGGAGTATATCTTAGGGC 58.321 47.826 0.00 0.00 0.00 5.19
1932 3577 2.094442 AGAGCGAGCTGGTTTAGAAGAC 60.094 50.000 0.84 0.00 0.00 3.01
1945 3590 5.220796 GGTTTAGAAGACGAGCAACAAAGTT 60.221 40.000 0.00 0.00 0.00 2.66
2105 3753 0.684805 AAGGTGAGTAGGGCCTCTCG 60.685 60.000 10.74 0.00 33.88 4.04
2150 3798 0.030369 ATTTACCGTCGCGAGCTAGG 59.970 55.000 10.24 13.70 0.00 3.02
2162 3810 1.000896 AGCTAGGGCCAACGCAAAT 60.001 52.632 6.18 0.00 39.73 2.32
2462 4117 4.839121 TGGAAAGGCGTCATAAACAGTAT 58.161 39.130 0.00 0.00 0.00 2.12
2553 4223 6.660521 ACTTCTAACATGATTGATGAAGCCAA 59.339 34.615 0.00 0.00 35.80 4.52
2557 4227 5.068234 ACATGATTGATGAAGCCAAACTG 57.932 39.130 0.00 0.00 35.80 3.16
2586 4256 7.581213 TCAGCTCAAAAGGAACAGATAAAAA 57.419 32.000 0.00 0.00 0.00 1.94
2597 4267 7.886338 AGGAACAGATAAAAATCCAAAGTGAC 58.114 34.615 0.00 0.00 32.47 3.67
2640 4310 9.280174 AGGAAAAATTGACTGAGTTTCGTATTA 57.720 29.630 0.00 0.00 0.00 0.98
2666 4336 2.686405 TGCATGAGATGGTGATTCAAGC 59.314 45.455 0.00 0.00 36.43 4.01
2667 4337 2.034305 GCATGAGATGGTGATTCAAGCC 59.966 50.000 0.00 0.00 31.43 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.386049 CGCCATTTAAATTTGGTTTGCGTA 59.614 37.500 9.13 0.00 34.47 4.42
10 11 4.665394 CGACGCCATTTAAATTTGGTTTGC 60.665 41.667 9.13 0.00 35.34 3.68
30 31 2.845752 TTATGTGGCTGCCGGTCGAC 62.846 60.000 14.98 7.13 0.00 4.20
42 43 2.492881 TGCTGCTGTCCAATTTATGTGG 59.507 45.455 0.00 0.00 37.51 4.17
81 82 3.355270 CGTGCGTTCTATCTACTGACTG 58.645 50.000 0.00 0.00 0.00 3.51
88 89 0.728542 TCGTGCGTGCGTTCTATCTA 59.271 50.000 1.25 0.00 0.00 1.98
89 90 0.797249 GTCGTGCGTGCGTTCTATCT 60.797 55.000 1.25 0.00 0.00 1.98
90 91 1.068832 TGTCGTGCGTGCGTTCTATC 61.069 55.000 1.25 0.00 0.00 2.08
91 92 1.081041 TGTCGTGCGTGCGTTCTAT 60.081 52.632 1.25 0.00 0.00 1.98
127 128 2.660236 CGACGTAACAGTTGGCTCTAAC 59.340 50.000 0.00 0.00 0.00 2.34
198 199 1.073216 CTGGAGTTAGTGCGCACTCG 61.073 60.000 43.74 21.09 42.54 4.18
200 201 1.374758 GCTGGAGTTAGTGCGCACT 60.375 57.895 41.46 41.46 45.02 4.40
201 202 0.951040 AAGCTGGAGTTAGTGCGCAC 60.951 55.000 32.79 32.79 0.00 5.34
202 203 0.606096 TAAGCTGGAGTTAGTGCGCA 59.394 50.000 5.66 5.66 0.00 6.09
203 204 1.722011 TTAAGCTGGAGTTAGTGCGC 58.278 50.000 0.00 0.00 0.00 6.09
204 205 2.030946 GCATTAAGCTGGAGTTAGTGCG 59.969 50.000 0.00 0.00 41.15 5.34
205 206 3.682372 GCATTAAGCTGGAGTTAGTGC 57.318 47.619 0.00 0.00 41.15 4.40
247 272 4.916183 AGTATGCTGAGCCTTTTCTCTTT 58.084 39.130 0.23 0.00 34.29 2.52
250 275 4.808364 CACTAGTATGCTGAGCCTTTTCTC 59.192 45.833 0.23 0.00 0.00 2.87
252 277 3.311048 GCACTAGTATGCTGAGCCTTTTC 59.689 47.826 0.23 0.00 42.62 2.29
257 282 2.208431 CTTGCACTAGTATGCTGAGCC 58.792 52.381 0.23 0.00 46.28 4.70
259 284 4.047822 GCTACTTGCACTAGTATGCTGAG 58.952 47.826 6.85 7.14 46.28 3.35
261 286 4.047822 GAGCTACTTGCACTAGTATGCTG 58.952 47.826 18.83 3.88 46.28 4.41
267 292 0.888619 TGCGAGCTACTTGCACTAGT 59.111 50.000 5.40 0.00 44.84 2.57
299 327 0.782384 GCGTGTTCTTGGACACTACG 59.218 55.000 10.09 0.00 45.96 3.51
313 341 1.428219 CGAGGACTCGTATGCGTGT 59.572 57.895 10.66 10.66 46.99 4.49
331 359 0.694444 TACTCCTGGCCCTGGGAATC 60.694 60.000 19.27 5.54 0.00 2.52
341 369 0.972983 TCTCACCTGCTACTCCTGGC 60.973 60.000 0.00 0.00 0.00 4.85
342 370 0.820871 GTCTCACCTGCTACTCCTGG 59.179 60.000 0.00 0.00 0.00 4.45
343 371 1.550327 TGTCTCACCTGCTACTCCTG 58.450 55.000 0.00 0.00 0.00 3.86
344 372 2.310779 TTGTCTCACCTGCTACTCCT 57.689 50.000 0.00 0.00 0.00 3.69
345 373 4.342378 TGATATTGTCTCACCTGCTACTCC 59.658 45.833 0.00 0.00 0.00 3.85
453 483 2.741985 CGCGCACTGGATGTCCAA 60.742 61.111 8.75 0.00 46.97 3.53
505 535 2.800544 CGACAAAATTCTGGTCAGACGT 59.199 45.455 0.00 0.00 37.14 4.34
567 600 0.391263 AAAGGCTGATTCGGTCGGAC 60.391 55.000 0.00 0.00 42.03 4.79
571 604 0.035439 TGGGAAAGGCTGATTCGGTC 60.035 55.000 0.00 0.00 0.00 4.79
612 645 1.290324 GCTCACGGTTCAGCTGAGA 59.710 57.895 17.43 9.40 34.46 3.27
704 737 7.436673 CCTGTTATTTACTGAATCTTCCTCTCG 59.563 40.741 0.00 0.00 0.00 4.04
743 776 2.036475 CCCTTGGATCGTGAGACCATAG 59.964 54.545 0.00 0.00 46.97 2.23
766 799 5.520288 CGTGAGATCGTACTTGAATTCCAAT 59.480 40.000 2.27 0.00 33.68 3.16
783 816 0.033504 AACACCTTGCGTCGTGAGAT 59.966 50.000 4.11 0.00 45.19 2.75
792 2373 8.402472 TCTATAAATAAATTCCAACACCTTGCG 58.598 33.333 0.00 0.00 0.00 4.85
815 2396 1.210870 AACGAAGCAAACGCGTTCTA 58.789 45.000 26.77 0.00 43.87 2.10
843 2451 2.418083 GCCAATCGGGAAAGCTGGG 61.418 63.158 0.00 0.00 40.01 4.45
970 2578 1.006832 GAGTTGTCTGCGTTGTGTGT 58.993 50.000 0.00 0.00 0.00 3.72
1203 2811 4.197498 GCTACCGCGTCCGCCTTA 62.197 66.667 4.92 0.00 37.98 2.69
1503 3119 2.032528 TGCTCTTCGGCACAAGGG 59.967 61.111 0.00 0.00 37.29 3.95
1586 3216 2.222027 CCTTGATCGATTTGCCCTACC 58.778 52.381 0.00 0.00 0.00 3.18
1652 3289 6.095440 GCCATAGGTGTCAACATACAAAGATT 59.905 38.462 0.00 0.00 0.00 2.40
1653 3290 5.590259 GCCATAGGTGTCAACATACAAAGAT 59.410 40.000 0.00 0.00 0.00 2.40
1654 3291 4.941263 GCCATAGGTGTCAACATACAAAGA 59.059 41.667 0.00 0.00 0.00 2.52
1655 3292 4.943705 AGCCATAGGTGTCAACATACAAAG 59.056 41.667 0.00 0.00 0.00 2.77
1656 3293 4.917385 AGCCATAGGTGTCAACATACAAA 58.083 39.130 0.00 0.00 0.00 2.83
1657 3294 4.568072 AGCCATAGGTGTCAACATACAA 57.432 40.909 0.00 0.00 0.00 2.41
1659 3296 4.513442 TCAAGCCATAGGTGTCAACATAC 58.487 43.478 0.00 0.00 0.00 2.39
1660 3297 4.835284 TCAAGCCATAGGTGTCAACATA 57.165 40.909 0.00 0.00 0.00 2.29
1661 3298 3.719268 TCAAGCCATAGGTGTCAACAT 57.281 42.857 0.00 0.00 0.00 2.71
1671 3312 8.649841 CACAACATAACAAAAATCAAGCCATAG 58.350 33.333 0.00 0.00 0.00 2.23
1673 3314 6.073112 GCACAACATAACAAAAATCAAGCCAT 60.073 34.615 0.00 0.00 0.00 4.40
1856 3501 7.171502 AGCATGTTACAAAGAACACTTTGCTG 61.172 38.462 18.46 11.33 45.04 4.41
1898 3543 1.474478 CTCGCTCTAGTGGCTTCTTCA 59.526 52.381 8.32 0.00 0.00 3.02
1932 3577 1.535462 CCCTACCAACTTTGTTGCTCG 59.465 52.381 5.04 0.00 0.00 5.03
1945 3590 2.035626 GCTTTGCTGCCCCTACCA 59.964 61.111 0.00 0.00 0.00 3.25
2105 3753 2.109425 ACCTCACCGCAAGATAAACC 57.891 50.000 0.00 0.00 43.02 3.27
2150 3798 3.380142 CCATATAACATTTGCGTTGGCC 58.620 45.455 0.00 0.00 38.85 5.36
2162 3810 3.491276 CCGTGAGCGTAACCCATATAACA 60.491 47.826 0.00 0.00 36.15 2.41
2273 3921 4.655762 AACTTTGCAAGAAAAGGGACTC 57.344 40.909 0.00 0.00 38.49 3.36
2356 4007 7.548780 TCTGCTTTTGACTTTTTATTGCACTTT 59.451 29.630 0.00 0.00 0.00 2.66
2553 4223 4.526970 TCCTTTTGAGCTGAAAGTCAGTT 58.473 39.130 14.68 0.70 45.94 3.16
2557 4227 4.576463 TCTGTTCCTTTTGAGCTGAAAGTC 59.424 41.667 14.68 8.02 35.30 3.01
2613 4283 6.061231 ACGAAACTCAGTCAATTTTTCCTC 57.939 37.500 0.00 0.00 0.00 3.71
2640 4310 7.591421 TTGAATCACCATCTCATGCAAATAT 57.409 32.000 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.