Multiple sequence alignment - TraesCS6A01G219400

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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 TraesCS6A01G219400 chr6A 100.000 2257 0 0 1 2257 407084218 407086474 0.000000e+00 4169
1 TraesCS6A01G219400 chr6D 94.349 2265 89 16 9 2257 285868350 285870591 0.000000e+00 3437
2 TraesCS6A01G219400 chr6B 93.789 2270 103 15 9 2257 446834893 446837145 0.000000e+00 3376
3 TraesCS6A01G219400 chr2B 82.305 859 144 6 1400 2254 531466730 531467584 0.000000e+00 737
4 TraesCS6A01G219400 chr2B 82.877 146 18 4 994 1138 531466328 531466467 8.460000e-25 124
5 TraesCS6A01G219400 chr2D 82.176 864 142 11 1400 2257 451287829 451288686 0.000000e+00 732
6 TraesCS6A01G219400 chr2D 82.877 146 18 4 994 1138 451287397 451287536 8.460000e-25 124


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 TraesCS6A01G219400 chr6A 407084218 407086474 2256 False 4169.0 4169 100.0000 1 2257 1 chr6A.!!$F1 2256
1 TraesCS6A01G219400 chr6D 285868350 285870591 2241 False 3437.0 3437 94.3490 9 2257 1 chr6D.!!$F1 2248
2 TraesCS6A01G219400 chr6B 446834893 446837145 2252 False 3376.0 3376 93.7890 9 2257 1 chr6B.!!$F1 2248
3 TraesCS6A01G219400 chr2B 531466328 531467584 1256 False 430.5 737 82.5910 994 2254 2 chr2B.!!$F1 1260
4 TraesCS6A01G219400 chr2D 451287397 451288686 1289 False 428.0 732 82.5265 994 2257 2 chr2D.!!$F1 1263

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
527 549 0.175073 GGTAGGCGTCTTTGATCCGT 59.825 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1451 0.109597 GCAGAGACGGCCATTGTTTG 60.11 55.0 2.24 0.0 0.0 2.93 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
252 266 3.505680 TGCAAGTCGCCTCATTTGTTTAT 59.494 39.130 0.00 0.00 41.33 1.40
253 267 4.098416 GCAAGTCGCCTCATTTGTTTATC 58.902 43.478 0.00 0.00 32.94 1.75
254 268 4.379394 GCAAGTCGCCTCATTTGTTTATCA 60.379 41.667 0.00 0.00 32.94 2.15
255 269 5.327091 CAAGTCGCCTCATTTGTTTATCAG 58.673 41.667 0.00 0.00 0.00 2.90
256 270 4.579869 AGTCGCCTCATTTGTTTATCAGT 58.420 39.130 0.00 0.00 0.00 3.41
343 358 2.155155 GTGAGATTGTGTTCGTCCGTTC 59.845 50.000 0.00 0.00 0.00 3.95
364 379 2.917971 CGCTTTCGTTTCTTCGAGATCT 59.082 45.455 0.00 0.00 40.86 2.75
421 436 1.537348 CCTGTTCGAGGTTTGTGACGA 60.537 52.381 0.00 0.00 37.02 4.20
422 437 1.787155 CTGTTCGAGGTTTGTGACGAG 59.213 52.381 0.00 0.00 36.22 4.18
423 438 1.137513 GTTCGAGGTTTGTGACGAGG 58.862 55.000 0.00 0.00 36.22 4.63
424 439 1.034356 TTCGAGGTTTGTGACGAGGA 58.966 50.000 0.00 0.00 36.22 3.71
425 440 0.313043 TCGAGGTTTGTGACGAGGAC 59.687 55.000 0.00 0.00 0.00 3.85
426 441 1.002250 CGAGGTTTGTGACGAGGACG 61.002 60.000 0.00 0.00 45.75 4.79
427 442 0.313043 GAGGTTTGTGACGAGGACGA 59.687 55.000 0.00 0.00 42.66 4.20
428 443 0.314302 AGGTTTGTGACGAGGACGAG 59.686 55.000 0.00 0.00 42.66 4.18
429 444 1.282930 GGTTTGTGACGAGGACGAGC 61.283 60.000 0.00 0.00 42.66 5.03
509 531 4.631377 TCAGCTCATGTTGTTTCTATTCGG 59.369 41.667 0.00 0.00 0.00 4.30
513 535 5.006746 GCTCATGTTGTTTCTATTCGGTAGG 59.993 44.000 0.00 0.00 0.00 3.18
515 537 3.255725 TGTTGTTTCTATTCGGTAGGCG 58.744 45.455 0.00 0.00 0.00 5.52
520 542 4.179298 GTTTCTATTCGGTAGGCGTCTTT 58.821 43.478 0.00 0.00 0.00 2.52
527 549 0.175073 GGTAGGCGTCTTTGATCCGT 59.825 55.000 0.00 0.00 0.00 4.69
543 565 7.747155 TTGATCCGTGGTAGAAATTTGTTTA 57.253 32.000 0.00 0.00 0.00 2.01
565 587 5.017093 ACTGTGCCTAGTAGGGATCATAT 57.983 43.478 18.13 5.24 38.26 1.78
575 597 6.749036 AGTAGGGATCATATTCCTTTTCGT 57.251 37.500 0.00 0.00 35.97 3.85
580 602 3.899052 TCATATTCCTTTTCGTCCCGT 57.101 42.857 0.00 0.00 0.00 5.28
582 604 5.341872 TCATATTCCTTTTCGTCCCGTTA 57.658 39.130 0.00 0.00 0.00 3.18
585 607 6.824704 TCATATTCCTTTTCGTCCCGTTAATT 59.175 34.615 0.00 0.00 0.00 1.40
586 608 7.986320 TCATATTCCTTTTCGTCCCGTTAATTA 59.014 33.333 0.00 0.00 0.00 1.40
613 635 6.910972 GCTGGATAGGAAAAGTAAATAAACGC 59.089 38.462 0.00 0.00 0.00 4.84
751 773 3.700538 TGGCTGACCTGAATATTGCTTT 58.299 40.909 0.00 0.00 36.63 3.51
770 792 9.722056 ATTGCTTTATGTCAATTCGTTTCTATC 57.278 29.630 0.00 0.00 29.34 2.08
779 801 7.765819 TGTCAATTCGTTTCTATCTCATGATGT 59.234 33.333 0.00 0.00 34.32 3.06
808 836 3.633986 CCCTTTCTGTTATGCCTGGAATC 59.366 47.826 0.00 0.00 0.00 2.52
809 837 4.530875 CCTTTCTGTTATGCCTGGAATCT 58.469 43.478 0.00 0.00 0.00 2.40
836 864 7.439356 TCATCTTCAAATCAGGTCGAATATCAC 59.561 37.037 0.00 0.00 0.00 3.06
837 865 6.049149 TCTTCAAATCAGGTCGAATATCACC 58.951 40.000 0.00 0.00 0.00 4.02
891 919 9.998106 GAAATATTCCTCTACTTTATGTGCCTA 57.002 33.333 0.00 0.00 0.00 3.93
930 959 7.123847 TCCCAGAAGGATGTTAGTACTACTTTC 59.876 40.741 0.91 3.82 40.93 2.62
947 976 8.004087 ACTACTTTCTACCTCGCAATATGTTA 57.996 34.615 0.00 0.00 0.00 2.41
951 980 7.224753 ACTTTCTACCTCGCAATATGTTATGTG 59.775 37.037 0.00 0.00 0.00 3.21
973 1003 4.873827 TGCTTCATCGTTTCTAACCCATAC 59.126 41.667 0.00 0.00 0.00 2.39
1156 1186 8.397906 CAAACGTATGTATCCAATCAATTGAGT 58.602 33.333 14.54 8.63 40.14 3.41
1271 1304 0.389166 CCTGATAATCCCTCTCGCGC 60.389 60.000 0.00 0.00 0.00 6.86
1301 1334 7.213178 TCCTAATTGCTTAGAATTCCCTTCT 57.787 36.000 0.65 0.00 46.16 2.85
1302 1335 7.056635 TCCTAATTGCTTAGAATTCCCTTCTG 58.943 38.462 0.65 0.00 44.12 3.02
1366 1409 1.538950 CTCTGACCAGCAAAGCCTTTC 59.461 52.381 0.00 0.00 0.00 2.62
1385 1451 3.103080 TCCTCCTCTACCAACCTTCTC 57.897 52.381 0.00 0.00 0.00 2.87
1561 1633 3.181467 GCACCATTGTATCTGAGCTCTCT 60.181 47.826 16.19 1.88 0.00 3.10
1567 1639 6.867816 CCATTGTATCTGAGCTCTCTAATGAC 59.132 42.308 16.19 4.71 0.00 3.06
1571 1643 6.830838 TGTATCTGAGCTCTCTAATGACAAGA 59.169 38.462 16.19 5.41 0.00 3.02
1588 1660 5.000012 ACAAGATTGACTCGTATGTCCTC 58.000 43.478 0.00 0.00 36.21 3.71
1643 1715 0.396435 TGTGATCAAGACCTGCGGTT 59.604 50.000 0.00 0.00 35.25 4.44
1644 1716 1.621317 TGTGATCAAGACCTGCGGTTA 59.379 47.619 0.00 0.00 35.25 2.85
1694 1766 1.346062 TCTTGAGCTTGCTGAGGAGT 58.654 50.000 0.00 0.00 0.00 3.85
1783 1855 4.590647 TCTCCACACAAGAACTTCTCTGAT 59.409 41.667 0.00 0.00 33.37 2.90
1991 2063 0.252479 CAAGACCTCTGCTGATGGCT 59.748 55.000 0.00 0.00 42.39 4.75
2137 2209 4.330250 CTTTCTCCACCATTCATGTCACT 58.670 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.821589 CCAGGAGGCTTCGGACGC 62.822 72.222 0.00 0.00 0.00 5.19
4 5 4.148825 CCCAGGAGGCTTCGGACG 62.149 72.222 5.39 0.00 0.00 4.79
211 225 1.355720 CAAGATGGGAAAGTCACCCCT 59.644 52.381 0.00 0.00 46.21 4.79
252 266 3.766676 TTGCGTTTGTGCTAAAACTGA 57.233 38.095 11.39 0.00 37.80 3.41
253 267 3.857093 AGTTTGCGTTTGTGCTAAAACTG 59.143 39.130 11.39 7.38 38.73 3.16
254 268 4.102649 GAGTTTGCGTTTGTGCTAAAACT 58.897 39.130 11.39 4.50 41.19 2.66
255 269 3.242016 GGAGTTTGCGTTTGTGCTAAAAC 59.758 43.478 5.14 5.14 36.81 2.43
256 270 3.440228 GGAGTTTGCGTTTGTGCTAAAA 58.560 40.909 0.00 0.00 31.70 1.52
343 358 2.917971 AGATCTCGAAGAAACGAAAGCG 59.082 45.455 0.00 0.00 41.67 4.68
377 392 0.736053 AAGCGACGGATCTGTCTCTC 59.264 55.000 27.81 17.89 33.03 3.20
421 436 1.140589 CGAATCTGCTGCTCGTCCT 59.859 57.895 0.00 0.00 0.00 3.85
422 437 1.139734 TCGAATCTGCTGCTCGTCC 59.860 57.895 8.54 0.00 34.27 4.79
423 438 1.467556 CGTCGAATCTGCTGCTCGTC 61.468 60.000 8.54 3.28 34.27 4.20
424 439 1.515088 CGTCGAATCTGCTGCTCGT 60.515 57.895 8.54 0.00 34.27 4.18
425 440 2.854214 GCGTCGAATCTGCTGCTCG 61.854 63.158 0.00 1.57 0.00 5.03
426 441 2.854214 CGCGTCGAATCTGCTGCTC 61.854 63.158 0.00 0.00 0.00 4.26
427 442 2.882777 CGCGTCGAATCTGCTGCT 60.883 61.111 0.00 0.00 0.00 4.24
428 443 4.565704 GCGCGTCGAATCTGCTGC 62.566 66.667 8.43 0.00 0.00 5.25
429 444 4.257376 CGCGCGTCGAATCTGCTG 62.257 66.667 24.19 0.00 41.67 4.41
509 531 1.278238 CACGGATCAAAGACGCCTAC 58.722 55.000 0.00 0.00 0.00 3.18
513 535 1.135199 TCTACCACGGATCAAAGACGC 60.135 52.381 0.00 0.00 0.00 5.19
515 537 6.072673 ACAAATTTCTACCACGGATCAAAGAC 60.073 38.462 0.00 0.00 0.00 3.01
520 542 6.938030 AGTAAACAAATTTCTACCACGGATCA 59.062 34.615 0.00 0.00 0.00 2.92
527 549 5.830991 AGGCACAGTAAACAAATTTCTACCA 59.169 36.000 0.00 0.00 0.00 3.25
543 565 2.848678 TGATCCCTACTAGGCACAGT 57.151 50.000 0.00 0.00 32.73 3.55
575 597 3.581332 CCTATCCAGCCTAATTAACGGGA 59.419 47.826 8.74 8.74 32.15 5.14
585 607 9.623000 GTTTATTTACTTTTCCTATCCAGCCTA 57.377 33.333 0.00 0.00 0.00 3.93
586 608 7.282450 CGTTTATTTACTTTTCCTATCCAGCCT 59.718 37.037 0.00 0.00 0.00 4.58
613 635 8.074370 TGAAATTACAGATAATCTAGACGACGG 58.926 37.037 0.00 0.00 30.27 4.79
751 773 9.987272 ATCATGAGATAGAAACGAATTGACATA 57.013 29.630 0.09 0.00 31.14 2.29
770 792 5.125097 CAGAAAGGGAGGAAAACATCATGAG 59.875 44.000 0.09 0.00 0.00 2.90
779 801 4.086457 GGCATAACAGAAAGGGAGGAAAA 58.914 43.478 0.00 0.00 0.00 2.29
808 836 6.674694 ATTCGACCTGATTTGAAGATGAAG 57.325 37.500 0.00 0.00 0.00 3.02
809 837 7.986889 TGATATTCGACCTGATTTGAAGATGAA 59.013 33.333 0.00 0.00 0.00 2.57
864 892 8.494433 AGGCACATAAAGTAGAGGAATATTTCA 58.506 33.333 0.00 0.00 0.00 2.69
887 915 2.026262 TGGGATTCCAGTTTCACTAGGC 60.026 50.000 4.80 0.00 38.32 3.93
916 945 6.428385 TGCGAGGTAGAAAGTAGTACTAAC 57.572 41.667 3.61 0.00 0.00 2.34
930 959 4.991056 AGCACATAACATATTGCGAGGTAG 59.009 41.667 0.00 0.00 40.04 3.18
947 976 3.689649 GGGTTAGAAACGATGAAGCACAT 59.310 43.478 0.00 0.00 42.47 3.21
951 980 4.272748 GGTATGGGTTAGAAACGATGAAGC 59.727 45.833 0.00 0.00 0.00 3.86
973 1003 1.962807 TCAAATTCTGCAGTGGGTTGG 59.037 47.619 14.67 2.75 0.00 3.77
1271 1304 4.453480 TTCTAAGCAATTAGGATGGGGG 57.547 45.455 0.00 0.00 0.00 5.40
1366 1409 2.821437 TGAGAAGGTTGGTAGAGGAGG 58.179 52.381 0.00 0.00 0.00 4.30
1385 1451 0.109597 GCAGAGACGGCCATTGTTTG 60.110 55.000 2.24 0.00 0.00 2.93
1561 1633 6.978659 GGACATACGAGTCAATCTTGTCATTA 59.021 38.462 0.00 0.00 40.81 1.90
1567 1639 5.067153 AGAGAGGACATACGAGTCAATCTTG 59.933 44.000 0.00 0.00 40.29 3.02
1571 1643 4.527944 TCAGAGAGGACATACGAGTCAAT 58.472 43.478 0.00 0.00 40.29 2.57
1588 1660 5.026038 AGATGAAGAGGCTTGATTCAGAG 57.974 43.478 13.69 0.00 36.47 3.35
1783 1855 1.272092 CCATTCAGGAAGGCAACCTCA 60.272 52.381 0.00 0.00 41.22 3.86
2137 2209 2.650116 GCTGAAGCCGTCCTCAGGA 61.650 63.158 0.00 0.00 34.31 3.86


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

AutoCloner maintained by Alex Coulton.