Multiple sequence alignment - TraesCS3B01G112000

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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 TraesCS3B01G112000 chr3B 100.000 4000 0 0 1 4000 78391181 78395180 0 7387
1 TraesCS3B01G112000 chr3A 96.278 4003 125 12 1 4000 61341400 61345381 0 6545
2 TraesCS3B01G112000 chr3D 94.964 4031 144 31 1 4000 48859579 48863581 0 6264


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 TraesCS3B01G112000 chr3B 78391181 78395180 3999 False 7387 7387 100.000 1 4000 1 chr3B.!!$F1 3999
1 TraesCS3B01G112000 chr3A 61341400 61345381 3981 False 6545 6545 96.278 1 4000 1 chr3A.!!$F1 3999
2 TraesCS3B01G112000 chr3D 48859579 48863581 4002 False 6264 6264 94.964 1 4000 1 chr3D.!!$F1 3999

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
381 383 0.250081 TTGCGCTGTGGTGTGTGATA 60.250 50.000 9.73 0.0 0.0 2.15 F
382 384 0.250081 TGCGCTGTGGTGTGTGATAA 60.250 50.000 9.73 0.0 0.0 1.75 F
383 385 0.443869 GCGCTGTGGTGTGTGATAAG 59.556 55.000 0.00 0.0 0.0 1.73 F
384 386 0.443869 CGCTGTGGTGTGTGATAAGC 59.556 55.000 0.00 0.0 0.0 3.09 F
385 387 1.813513 GCTGTGGTGTGTGATAAGCT 58.186 50.000 0.00 0.0 0.0 3.74 F
2125 2136 1.696336 AGAGAAGTTGCAGCTTGAGGA 59.304 47.619 21.32 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1612 1.071542 TGGTTCGCTTCATCAACCTCA 59.928 47.619 1.98 0.0 40.37 3.86 R
1644 1655 1.419374 ACTCGTTCGTTCAGTGCATC 58.581 50.000 0.00 0.0 0.00 3.91 R
2084 2095 2.096248 TCCGACAGTTTTGCCAAGTTT 58.904 42.857 0.00 0.0 0.00 2.66 R
2125 2136 4.098914 TGTTCAAGCTCCATAACCTGTT 57.901 40.909 0.00 0.0 0.00 3.16 R
2367 2378 5.180117 CCAACATCGATTTCTCTTGAAGTGT 59.820 40.000 0.00 0.0 33.28 3.55 R
3234 3249 0.874175 TCAGACTCACGGCAACAACG 60.874 55.000 0.00 0.0 37.36 4.10 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
71 73 4.929211 TGAGTTGTCGTATGTTGATTCCTG 59.071 41.667 0.00 0.00 0.00 3.86
72 74 5.147330 AGTTGTCGTATGTTGATTCCTGA 57.853 39.130 0.00 0.00 0.00 3.86
274 276 1.710244 TGGGGTCAGGACAAATGTGAT 59.290 47.619 1.41 0.00 0.00 3.06
377 379 1.029408 TCTTTTGCGCTGTGGTGTGT 61.029 50.000 9.73 0.00 0.00 3.72
378 380 0.866906 CTTTTGCGCTGTGGTGTGTG 60.867 55.000 9.73 0.00 0.00 3.82
379 381 1.308783 TTTTGCGCTGTGGTGTGTGA 61.309 50.000 9.73 0.00 0.00 3.58
380 382 1.100463 TTTGCGCTGTGGTGTGTGAT 61.100 50.000 9.73 0.00 0.00 3.06
381 383 0.250081 TTGCGCTGTGGTGTGTGATA 60.250 50.000 9.73 0.00 0.00 2.15
382 384 0.250081 TGCGCTGTGGTGTGTGATAA 60.250 50.000 9.73 0.00 0.00 1.75
383 385 0.443869 GCGCTGTGGTGTGTGATAAG 59.556 55.000 0.00 0.00 0.00 1.73
384 386 0.443869 CGCTGTGGTGTGTGATAAGC 59.556 55.000 0.00 0.00 0.00 3.09
385 387 1.813513 GCTGTGGTGTGTGATAAGCT 58.186 50.000 0.00 0.00 0.00 3.74
399 409 4.508124 GTGATAAGCTGATAACCAAGTCCG 59.492 45.833 0.00 0.00 0.00 4.79
423 433 5.392811 GGCCATGCTTCTATGATGAATTAGC 60.393 44.000 0.00 0.00 0.00 3.09
465 475 7.012894 GGTACCCACAATATTCGATCAATTTCA 59.987 37.037 0.00 0.00 0.00 2.69
527 537 6.494893 TTTACGCATGAATAATGATAGGCC 57.505 37.500 0.00 0.00 38.72 5.19
561 571 7.074653 TGGTAGTTAATCAGTTTTCTGGTCT 57.925 36.000 0.00 0.00 46.94 3.85
1196 1207 6.855763 ATCTTTAGCACCATGGAAATTTCA 57.144 33.333 21.47 6.65 0.00 2.69
1198 1209 6.632909 TCTTTAGCACCATGGAAATTTCATG 58.367 36.000 21.47 17.99 41.04 3.07
1382 1393 4.830600 ACCCATGTTGAAAATTTCTACCGT 59.169 37.500 15.43 4.31 35.06 4.83
1536 1547 3.325135 TCCTGAGTCTGAAAAGAAGACCC 59.675 47.826 0.00 0.00 44.27 4.46
1601 1612 8.814931 TCTTCTTCTTCTTCTGATTCTGATTCT 58.185 33.333 1.76 0.00 0.00 2.40
1644 1655 4.467769 AGAGAATGGCAATGGGATTACTG 58.532 43.478 0.00 0.00 0.00 2.74
1815 1826 7.976135 CTTCAGAAGGATCTTGAAGAAAAGA 57.024 36.000 17.23 0.00 40.00 2.52
1840 1851 4.572389 CCGTTCATTGGAGAGTATCAAAGG 59.428 45.833 0.00 0.00 37.82 3.11
1890 1901 2.099756 GCTGCAGTTCTGGAAAACAAGT 59.900 45.455 16.64 0.00 0.00 3.16
2049 2060 5.407407 GTCTACCCTTGAGACTGAAATCA 57.593 43.478 0.00 0.00 40.23 2.57
2084 2095 2.777692 AGTGGTCAAGAACTTGGAAGGA 59.222 45.455 13.46 0.00 40.78 3.36
2125 2136 1.696336 AGAGAAGTTGCAGCTTGAGGA 59.304 47.619 21.32 0.00 0.00 3.71
2160 2171 3.004106 GCTTGAACAAACATCTCACAGCT 59.996 43.478 0.00 0.00 0.00 4.24
2367 2378 3.328931 ACTCAAAGCTGATCTGGAAGGAA 59.671 43.478 1.46 0.00 0.00 3.36
2702 2713 0.368227 GTTTGCTGAGTGATCTCGCG 59.632 55.000 0.00 0.00 43.09 5.87
2870 2881 2.576298 GCAGAAGCTCATGGCCTTT 58.424 52.632 3.32 0.00 43.05 3.11
2876 2887 0.403271 AGCTCATGGCCTTTGACAGT 59.597 50.000 3.32 0.00 43.05 3.55
2948 2959 2.954868 CGCGACGGGTATCAGCAC 60.955 66.667 0.00 0.00 0.00 4.40
3122 3135 2.657143 AGCTTCGGTCTACTCCTTAGG 58.343 52.381 0.00 0.00 0.00 2.69
3234 3249 4.806640 TCCTTTTTCAATCAATCTGCCC 57.193 40.909 0.00 0.00 0.00 5.36
3445 3469 7.121168 TGTGAACTTGCCCTTCTATTTCTATTG 59.879 37.037 0.00 0.00 0.00 1.90
3477 3508 7.839680 AGTCTGAAATTGTATTCAAAAGGGT 57.160 32.000 0.00 0.00 38.75 4.34
3485 3516 6.817765 TTGTATTCAAAAGGGTAGCAAGAG 57.182 37.500 0.00 0.00 0.00 2.85
3563 3606 0.320247 GACCACCTGTCTGCTGTCTG 60.320 60.000 0.00 0.00 41.03 3.51
3573 3616 0.317799 CTGCTGTCTGCTGTCTCTGT 59.682 55.000 3.20 0.00 43.37 3.41
3656 3699 7.313951 AGAAAAGCTTACATAGTGCATTCTC 57.686 36.000 0.00 0.00 33.25 2.87
3708 3752 3.669536 AGCTGCAAGAGAAGTTTACTCC 58.330 45.455 1.02 0.00 34.07 3.85
3739 3788 6.374333 AGAAACACGGCATAATTATCACAACT 59.626 34.615 0.00 0.00 0.00 3.16
3742 3791 7.246674 ACACGGCATAATTATCACAACTTAG 57.753 36.000 0.00 0.00 0.00 2.18
3786 3835 4.012374 CACTAAAATGGGAGACAGCACAT 58.988 43.478 0.00 0.00 0.00 3.21
3836 3886 5.359860 CAGGGATTGGACCATTAGTTTAACC 59.640 44.000 0.00 0.00 0.00 2.85
3853 3903 5.585820 TTAACCGATTCTTTTAATGCCCC 57.414 39.130 0.00 0.00 0.00 5.80
3886 3936 2.105006 TCAGAAGCTTCACATGGCTC 57.895 50.000 27.57 0.00 37.87 4.70
3943 3993 2.358898 GCAAGTTTCAGGCTTTCAGACA 59.641 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 8.425491 CAACATACGACAACTCAACTAGTAAAG 58.575 37.037 0.00 0.00 37.50 1.85
167 169 3.464720 TCCAACCAATAATTGAGGCCA 57.535 42.857 5.01 0.00 0.00 5.36
214 216 5.523552 CAGGGTTCAAGGTGAAATTTGAAAC 59.476 40.000 0.00 6.48 45.67 2.78
274 276 2.655090 TTCAATCACAGGCAAGGACA 57.345 45.000 0.00 0.00 0.00 4.02
377 379 4.442893 CCGGACTTGGTTATCAGCTTATCA 60.443 45.833 0.00 0.00 0.00 2.15
378 380 4.058817 CCGGACTTGGTTATCAGCTTATC 58.941 47.826 0.00 0.00 0.00 1.75
379 381 3.744530 GCCGGACTTGGTTATCAGCTTAT 60.745 47.826 5.05 0.00 0.00 1.73
380 382 2.419574 GCCGGACTTGGTTATCAGCTTA 60.420 50.000 5.05 0.00 0.00 3.09
381 383 1.679032 GCCGGACTTGGTTATCAGCTT 60.679 52.381 5.05 0.00 0.00 3.74
382 384 0.107654 GCCGGACTTGGTTATCAGCT 60.108 55.000 5.05 0.00 0.00 4.24
383 385 1.095807 GGCCGGACTTGGTTATCAGC 61.096 60.000 5.05 0.00 0.00 4.26
384 386 0.251916 TGGCCGGACTTGGTTATCAG 59.748 55.000 9.82 0.00 0.00 2.90
385 387 0.916086 ATGGCCGGACTTGGTTATCA 59.084 50.000 9.82 0.00 0.00 2.15
399 409 5.392811 GCTAATTCATCATAGAAGCATGGCC 60.393 44.000 0.00 0.00 0.00 5.36
465 475 8.246180 CAGCCAATCATGAAAAACTATTACAGT 58.754 33.333 0.00 0.00 40.05 3.55
527 537 5.812642 ACTGATTAACTACCAAGAAGATGCG 59.187 40.000 0.00 0.00 0.00 4.73
561 571 1.565759 AGGCAACCTCCATAATGCAGA 59.434 47.619 0.00 0.00 40.51 4.26
621 631 7.522725 GCACCGCCTATGTATAGAAAAGTACTA 60.523 40.741 0.00 0.00 32.05 1.82
633 643 1.675552 GGTTTGCACCGCCTATGTAT 58.324 50.000 0.00 0.00 31.60 2.29
1008 1019 4.037222 TCCTTGTGGGCATTCTACTCATA 58.963 43.478 0.00 0.00 34.39 2.15
1189 1200 7.039882 GGATGAAACATCAGAGCATGAAATTT 58.960 34.615 12.66 0.00 42.53 1.82
1196 1207 2.950309 GCAGGATGAAACATCAGAGCAT 59.050 45.455 12.66 0.00 39.69 3.79
1198 1209 2.362736 TGCAGGATGAAACATCAGAGC 58.637 47.619 12.66 12.28 39.69 4.09
1382 1393 3.969899 CTCAGCAAGAGCACGATACATA 58.030 45.455 0.00 0.00 45.49 2.29
1536 1547 4.651962 TCCCTTTTTACCCTTCTGTTTTGG 59.348 41.667 0.00 0.00 0.00 3.28
1577 1588 8.591940 TCAGAATCAGAATCAGAAGAAGAAGAA 58.408 33.333 0.00 0.00 0.00 2.52
1601 1612 1.071542 TGGTTCGCTTCATCAACCTCA 59.928 47.619 1.98 0.00 40.37 3.86
1644 1655 1.419374 ACTCGTTCGTTCAGTGCATC 58.581 50.000 0.00 0.00 0.00 3.91
1815 1826 5.614324 TTGATACTCTCCAATGAACGGAT 57.386 39.130 0.00 0.00 0.00 4.18
1840 1851 6.765915 AATCCTCCTTTTCACTGCTAATTC 57.234 37.500 0.00 0.00 0.00 2.17
1890 1901 7.673180 TCTCCTTTTAATTCCTCGAACTTGTA 58.327 34.615 0.00 0.00 0.00 2.41
2033 2044 4.081531 AGCTCTCTGATTTCAGTCTCAAGG 60.082 45.833 7.42 0.00 44.12 3.61
2084 2095 2.096248 TCCGACAGTTTTGCCAAGTTT 58.904 42.857 0.00 0.00 0.00 2.66
2125 2136 4.098914 TGTTCAAGCTCCATAACCTGTT 57.901 40.909 0.00 0.00 0.00 3.16
2367 2378 5.180117 CCAACATCGATTTCTCTTGAAGTGT 59.820 40.000 0.00 0.00 33.28 3.55
2465 2476 3.771479 ACAGTTGTAGGATCTCAGCATCA 59.229 43.478 0.00 0.00 0.00 3.07
2702 2713 6.652481 TCTCCTTCATCTTTTCATCACAAGTC 59.348 38.462 0.00 0.00 0.00 3.01
2825 2836 0.455410 CCTCTTCCTCGAGCTCACAG 59.545 60.000 15.40 8.60 0.00 3.66
2826 2837 0.251386 ACCTCTTCCTCGAGCTCACA 60.251 55.000 15.40 0.00 0.00 3.58
2870 2881 2.061220 CTTCCCCTCTGCACTGTCA 58.939 57.895 0.00 0.00 0.00 3.58
3026 3037 4.405358 ACTTTAGGCATCCAGAGAGAAGAG 59.595 45.833 0.00 0.00 0.00 2.85
3027 3038 4.357325 ACTTTAGGCATCCAGAGAGAAGA 58.643 43.478 0.00 0.00 0.00 2.87
3122 3135 3.544356 GCACAAGCTTTACCAAGACTC 57.456 47.619 0.00 0.00 37.91 3.36
3196 3210 3.686227 AGGAATGGCATAATGGTCCAA 57.314 42.857 15.57 0.00 33.04 3.53
3209 3223 5.583457 GGCAGATTGATTGAAAAAGGAATGG 59.417 40.000 0.00 0.00 0.00 3.16
3234 3249 0.874175 TCAGACTCACGGCAACAACG 60.874 55.000 0.00 0.00 37.36 4.10
3445 3469 6.655003 TGAATACAATTTCAGACTTCTGGGAC 59.345 38.462 6.40 0.00 43.91 4.46
3563 3606 2.346099 GTCACAGAGACAGAGACAGC 57.654 55.000 0.00 0.00 46.77 4.40
3656 3699 3.250762 TGCAGTCATCTCCAAAACTTTCG 59.749 43.478 0.00 0.00 0.00 3.46
3697 3741 2.450609 TCTGCCACGGAGTAAACTTC 57.549 50.000 0.00 0.00 41.61 3.01
3786 3835 6.878923 CACACATCTCCTTGTATTTTAGTGGA 59.121 38.462 0.00 0.00 0.00 4.02
3836 3886 2.290641 CTCCGGGGCATTAAAAGAATCG 59.709 50.000 0.00 0.00 0.00 3.34
3853 3903 3.129871 GCTTCTGAATTCCTGATCTCCG 58.870 50.000 2.27 0.00 0.00 4.63
3886 3936 1.082756 GCCGTGAAAACTGACGCTG 60.083 57.895 0.00 0.00 34.18 5.18
3943 3993 6.880529 CCAATTAAATGGGCAAGAAACTGAAT 59.119 34.615 1.16 0.00 36.79 2.57


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

AutoCloner maintained by Alex Coulton.