Multiple sequence alignment - TraesCS2A01G334300

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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 TraesCS2A01G334300 chr2A 100.000 3649 0 0 1 3649 568289515 568285867 0.000000e+00 6739.0
1 TraesCS2A01G334300 chr2B 96.149 3635 92 19 1 3615 494269128 494265522 0.000000e+00 5893.0
2 TraesCS2A01G334300 chr2D 97.173 2087 47 5 1570 3649 421796863 421794782 0.000000e+00 3517.0
3 TraesCS2A01G334300 chr2D 93.970 1509 56 23 13 1502 421798587 421797095 0.000000e+00 2250.0
4 TraesCS2A01G334300 chr5D 96.552 58 2 0 3586 3643 395735715 395735772 3.000000e-16 97.1
5 TraesCS2A01G334300 chr3B 96.364 55 2 0 3592 3646 118739146 118739200 1.400000e-14 91.6
6 TraesCS2A01G334300 chr1B 96.296 54 2 0 3595 3648 239780289 239780236 5.020000e-14 89.8
7 TraesCS2A01G334300 chr5B 98.000 50 1 0 3595 3644 429789905 429789954 1.810000e-13 87.9
8 TraesCS2A01G334300 chr5A 98.000 50 1 0 3595 3644 464575956 464576005 1.810000e-13 87.9
9 TraesCS2A01G334300 chr4D 98.000 50 1 0 3595 3644 4772132 4772181 1.810000e-13 87.9
10 TraesCS2A01G334300 chr4A 98.000 50 1 0 3595 3644 598724455 598724504 1.810000e-13 87.9
11 TraesCS2A01G334300 chr7D 92.982 57 2 1 3595 3649 375400916 375400860 8.400000e-12 82.4


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 TraesCS2A01G334300 chr2A 568285867 568289515 3648 True 6739.0 6739 100.0000 1 3649 1 chr2A.!!$R1 3648
1 TraesCS2A01G334300 chr2B 494265522 494269128 3606 True 5893.0 5893 96.1490 1 3615 1 chr2B.!!$R1 3614
2 TraesCS2A01G334300 chr2D 421794782 421798587 3805 True 2883.5 3517 95.5715 13 3649 2 chr2D.!!$R1 3636

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
195 198 0.038801 GCTTGGAGCTTTTGGAGTGC 60.039 55.000 0.0 0.0 38.45 4.40 F
605 614 0.811616 CTCTGCTATGCCCGAACCAC 60.812 60.000 0.0 0.0 0.00 4.16 F
720 729 2.094417 GGTATGACAGAGCAAGAAACGC 59.906 50.000 0.0 0.0 0.00 4.84 F
1476 1498 2.187958 TGAACCAGATAGGACCACAGG 58.812 52.381 0.0 0.0 41.22 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1408 1.545428 GCAATTCCCTGCCCGATGATA 60.545 52.381 0.00 0.0 36.25 2.15 R
1417 1438 3.958147 TCCTGAATCGGCTAGTATTGTCA 59.042 43.478 0.00 0.0 0.00 3.58 R
2027 2221 4.269363 GGCATTACTTGAATTTGCAGATGC 59.731 41.667 0.00 0.0 42.50 3.91 R
3415 3616 0.251297 TTGGCAGAGTGAACCATGGG 60.251 55.000 18.09 0.0 32.39 4.00 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 67 4.651778 TGTCTTATCCTTGGAAACCACAG 58.348 43.478 0.00 0.00 30.78 3.66
195 198 0.038801 GCTTGGAGCTTTTGGAGTGC 60.039 55.000 0.00 0.00 38.45 4.40
224 233 7.399245 TTTTACAGTAGCTTTTGGAGTGTTT 57.601 32.000 0.00 0.00 0.00 2.83
227 236 4.576463 ACAGTAGCTTTTGGAGTGTTTCTG 59.424 41.667 0.00 0.00 0.00 3.02
268 277 9.733556 TTGGCAAACTTGACTAGATAATCTTAA 57.266 29.630 0.00 0.00 37.03 1.85
269 278 9.905713 TGGCAAACTTGACTAGATAATCTTAAT 57.094 29.630 0.00 0.00 37.03 1.40
346 355 5.772521 AGTAAAAGCAAACTGATCGCAAAT 58.227 33.333 0.00 0.00 0.00 2.32
605 614 0.811616 CTCTGCTATGCCCGAACCAC 60.812 60.000 0.00 0.00 0.00 4.16
720 729 2.094417 GGTATGACAGAGCAAGAAACGC 59.906 50.000 0.00 0.00 0.00 4.84
740 749 5.640732 ACGCCACAAGAATATGACAAAATC 58.359 37.500 0.00 0.00 0.00 2.17
776 794 4.330944 AACCAGTGACGTAACATGAGAA 57.669 40.909 5.68 0.00 0.00 2.87
789 807 4.283363 ACATGAGAACTCAGTTGATGCT 57.717 40.909 10.26 0.00 43.61 3.79
792 810 4.871933 TGAGAACTCAGTTGATGCTGTA 57.128 40.909 0.00 0.00 37.70 2.74
800 818 5.187772 ACTCAGTTGATGCTGTATTCTGGTA 59.812 40.000 0.00 0.00 37.70 3.25
859 877 2.224426 TGCTTTGGCTTCTTCCGTTCTA 60.224 45.455 0.00 0.00 39.59 2.10
932 950 5.702865 CGAGTGGCCATGATATTAATTTGG 58.297 41.667 9.72 0.00 0.00 3.28
1145 1166 3.689161 TGATCATCGGGTTTGTTGTCATC 59.311 43.478 0.00 0.00 0.00 2.92
1216 1237 6.542370 AGGGATATTGGTAATTTCACAACTCG 59.458 38.462 0.00 0.00 0.00 4.18
1255 1276 4.320870 TGCTGGTAGCTTTTACTTGGTAC 58.679 43.478 0.00 0.00 42.97 3.34
1387 1408 7.277760 GCAACTGAAAACTTACACCTTTCAAAT 59.722 33.333 0.00 0.00 38.30 2.32
1417 1438 3.490348 GCAGGGAATTGCAGGTACATAT 58.510 45.455 0.00 0.00 43.53 1.78
1418 1439 3.254166 GCAGGGAATTGCAGGTACATATG 59.746 47.826 0.00 0.00 43.53 1.78
1440 1461 4.202121 TGACAATACTAGCCGATTCAGGAC 60.202 45.833 0.00 0.00 0.00 3.85
1476 1498 2.187958 TGAACCAGATAGGACCACAGG 58.812 52.381 0.00 0.00 41.22 4.00
1540 1613 7.316544 GGTAATAACCACATTCAGTAGGTTG 57.683 40.000 5.98 0.00 45.98 3.77
2008 2202 3.432252 CGAGACATCAAGGTTGGTTACAC 59.568 47.826 0.00 0.00 0.00 2.90
2035 2229 3.822167 TGAAAGATTCAAGTGCATCTGCA 59.178 39.130 0.00 0.00 42.25 4.41
2058 2252 7.148390 TGCAAATTCAAGTAATGCCAATTCATG 60.148 33.333 0.00 0.00 36.20 3.07
2063 2257 3.724374 AGTAATGCCAATTCATGCATGC 58.276 40.909 22.25 11.82 46.97 4.06
2358 2552 5.221682 TGGTAAGACCGTAATTTCTGGAACA 60.222 40.000 0.00 0.00 42.58 3.18
2363 2557 5.591067 AGACCGTAATTTCTGGAACAAAACA 59.409 36.000 0.00 0.00 38.70 2.83
2369 2563 8.977505 CGTAATTTCTGGAACAAAACAATCAAT 58.022 29.630 0.00 0.00 38.70 2.57
2374 2568 5.523188 TCTGGAACAAAACAATCAATTGTGC 59.477 36.000 9.03 0.00 44.60 4.57
2389 2583 8.681486 ATCAATTGTGCTTAAGCTGATATACA 57.319 30.769 26.90 18.46 42.66 2.29
2390 2584 8.681486 TCAATTGTGCTTAAGCTGATATACAT 57.319 30.769 26.90 6.37 42.66 2.29
2671 2865 5.841783 AGTGTTTTAAGAGAGGGAAGAGAGT 59.158 40.000 0.00 0.00 0.00 3.24
2849 3044 2.684881 GGAGGTAATGTCAACATGCTGG 59.315 50.000 0.00 0.00 36.56 4.85
2936 3137 9.277565 CAGCAACAACAACAATAATGATAGTAC 57.722 33.333 0.00 0.00 0.00 2.73
2972 3173 4.904116 AGTAACACAACAACAACATCGTG 58.096 39.130 0.00 0.00 0.00 4.35
3000 3201 6.200878 ACTTTCCTGACCTCTTTATTTCCA 57.799 37.500 0.00 0.00 0.00 3.53
3421 3622 1.625315 TCAGTCACTGACTTCCCATGG 59.375 52.381 2.36 4.14 41.37 3.66
3495 3697 4.630894 TGTTTTCGACAAAGCACAGAAT 57.369 36.364 0.00 0.00 34.69 2.40
3618 3820 8.723365 TGTACTCCCTCCATTCACAAATATAAT 58.277 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.375455 AGGTCATCAAACTTGCATAAACTAGG 59.625 38.462 0.00 0.00 0.00 3.02
65 67 5.851047 AGTTACGTGCAGGTTACATTAAC 57.149 39.130 25.10 18.02 37.94 2.01
202 211 6.260050 CAGAAACACTCCAAAAGCTACTGTAA 59.740 38.462 0.00 0.00 0.00 2.41
268 277 2.039418 TGGGCATGTAGACGCTAAGAT 58.961 47.619 0.00 0.00 0.00 2.40
269 278 1.480789 TGGGCATGTAGACGCTAAGA 58.519 50.000 0.00 0.00 0.00 2.10
270 279 1.933853 GTTGGGCATGTAGACGCTAAG 59.066 52.381 0.00 0.00 0.00 2.18
271 280 1.737696 CGTTGGGCATGTAGACGCTAA 60.738 52.381 0.00 0.00 0.00 3.09
272 281 0.179121 CGTTGGGCATGTAGACGCTA 60.179 55.000 0.00 0.00 0.00 4.26
273 282 1.447838 CGTTGGGCATGTAGACGCT 60.448 57.895 0.00 0.00 0.00 5.07
274 283 1.017177 TTCGTTGGGCATGTAGACGC 61.017 55.000 0.00 0.00 34.04 5.19
275 284 1.651987 ATTCGTTGGGCATGTAGACG 58.348 50.000 0.00 0.76 35.24 4.18
276 285 5.295787 TGATTAATTCGTTGGGCATGTAGAC 59.704 40.000 0.00 0.00 0.00 2.59
346 355 6.411376 TGTTCTTTCCAAGTAACTTCTGTCA 58.589 36.000 0.00 0.00 0.00 3.58
720 729 9.655769 CTAATCGATTTTGTCATATTCTTGTGG 57.344 33.333 17.19 0.00 0.00 4.17
740 749 7.434307 ACGTCACTGGTTTACATAATCTAATCG 59.566 37.037 0.00 0.00 0.00 3.34
776 794 4.019860 ACCAGAATACAGCATCAACTGAGT 60.020 41.667 0.00 0.00 40.25 3.41
875 893 6.090763 TCGTTATTAGCAATGATGAATAGCCG 59.909 38.462 0.00 0.00 0.00 5.52
945 963 4.637483 TGCCTTTTCTTTCACTGTGAAG 57.363 40.909 21.13 15.64 37.70 3.02
1145 1166 2.762887 TCTTCTCCTGATGTGGCAGTAG 59.237 50.000 0.00 0.00 34.06 2.57
1216 1237 3.304257 CCAGCATCTGCAATTCGATTACC 60.304 47.826 4.79 0.00 45.16 2.85
1255 1276 6.052840 AGATGAACAATTGCATAGCGTTAG 57.947 37.500 5.05 0.00 0.00 2.34
1387 1408 1.545428 GCAATTCCCTGCCCGATGATA 60.545 52.381 0.00 0.00 36.25 2.15
1417 1438 3.958147 TCCTGAATCGGCTAGTATTGTCA 59.042 43.478 0.00 0.00 0.00 3.58
1418 1439 4.202121 TGTCCTGAATCGGCTAGTATTGTC 60.202 45.833 0.00 0.00 0.00 3.18
1451 1473 4.161565 TGTGGTCCTATCTGGTTCATGTAC 59.838 45.833 0.00 0.00 37.07 2.90
1476 1498 9.360093 GTTATATGTATATCACAGTTCTGCTCC 57.640 37.037 0.00 0.00 41.51 4.70
1540 1613 5.008613 TGCATCCAACTCTTAGAACAACAAC 59.991 40.000 0.00 0.00 0.00 3.32
2008 2202 7.631822 CAGATGCACTTGAATCTTTCAGATAG 58.368 38.462 0.00 0.00 38.37 2.08
2027 2221 4.269363 GGCATTACTTGAATTTGCAGATGC 59.731 41.667 0.00 0.00 42.50 3.91
2030 2224 5.465532 TTGGCATTACTTGAATTTGCAGA 57.534 34.783 0.00 0.00 0.00 4.26
2035 2229 6.879993 TGCATGAATTGGCATTACTTGAATTT 59.120 30.769 0.00 0.00 34.58 1.82
2063 2257 8.268850 AGAAGTATGTTTGTTGGCTACAATAG 57.731 34.615 14.92 0.00 45.72 1.73
2080 2274 5.940617 TCCATATCAACCCCAAGAAGTATG 58.059 41.667 0.00 0.00 0.00 2.39
2363 2557 9.123902 TGTATATCAGCTTAAGCACAATTGATT 57.876 29.630 28.39 17.93 45.16 2.57
2389 2583 6.043706 AGCCTGAGAGCAAAAGGTATGTATAT 59.956 38.462 0.00 0.00 33.34 0.86
2390 2584 5.366768 AGCCTGAGAGCAAAAGGTATGTATA 59.633 40.000 0.00 0.00 33.34 1.47
2849 3044 7.992180 AAAATGTGAAGTCAAGTGTCAAATC 57.008 32.000 0.00 0.00 0.00 2.17
2906 3107 2.965572 ATTGTTGTTGTTGCTGCTGT 57.034 40.000 0.00 0.00 0.00 4.40
2909 3110 6.808212 ACTATCATTATTGTTGTTGTTGCTGC 59.192 34.615 0.00 0.00 0.00 5.25
2972 3173 2.849294 AGAGGTCAGGAAAGTTCAGC 57.151 50.000 0.00 0.00 0.00 4.26
3415 3616 0.251297 TTGGCAGAGTGAACCATGGG 60.251 55.000 18.09 0.00 32.39 4.00
3421 3622 8.677300 TCAAATCTATATTTTGGCAGAGTGAAC 58.323 33.333 7.89 0.00 32.87 3.18
3495 3697 5.394224 TGTCACTGTATGTTACGAATCCA 57.606 39.130 0.00 0.00 0.00 3.41
3537 3739 6.877611 ACTTTGTTGGTCTATACTTGTTGG 57.122 37.500 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.