Multiple sequence alignment - TraesCS1B01G300400

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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 TraesCS1B01G300400 chr1B 100.000 3922 0 0 688 4609 520900884 520896963 0.000000e+00 7243
1 TraesCS1B01G300400 chr1B 100.000 134 0 0 1 134 520901571 520901438 9.900000e-62 248
2 TraesCS1B01G300400 chr1A 96.295 3914 116 8 711 4609 487314434 487310535 0.000000e+00 6397
3 TraesCS1B01G300400 chr1A 94.262 122 7 0 1 122 487314768 487314647 2.190000e-43 187
4 TraesCS1B01G300400 chr1D 96.331 3870 80 18 702 4553 387554986 387551161 0.000000e+00 6303
5 TraesCS1B01G300400 chr1D 93.860 114 7 0 1 114 387556604 387556491 6.130000e-39 172


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 TraesCS1B01G300400 chr1B 520896963 520901571 4608 True 3745.5 7243 100.0000 1 4609 2 chr1B.!!$R1 4608
1 TraesCS1B01G300400 chr1A 487310535 487314768 4233 True 3292.0 6397 95.2785 1 4609 2 chr1A.!!$R1 4608
2 TraesCS1B01G300400 chr1D 387551161 387556604 5443 True 3237.5 6303 95.0955 1 4553 2 chr1D.!!$R1 4552

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
79 80 0.252197 AGGCCCGTATTTCACAGTCC 59.748 55.0 0.00 0.00 0.0 3.85 F
777 1745 0.478507 CTCCCCTCTCCTCTCCTCTC 59.521 65.0 0.00 0.00 0.0 3.20 F
1310 2287 0.109272 TCATCAGCAACGTCGAGGAC 60.109 55.0 12.85 0.91 0.0 3.85 F
2075 3052 0.622665 AGGCTAAGCTTGACCTGCAT 59.377 50.0 18.42 6.46 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 2120 0.588252 CACGGCCACAGTTTTCAGAG 59.412 55.000 2.24 0.00 0.00 3.35 R
1853 2830 0.895559 GCTGGCCCTGCAAGTTAACT 60.896 55.000 7.85 1.12 31.11 2.24 R
2237 3214 1.205064 CAGGCGCTTGTGAAAGTCG 59.795 57.895 11.99 0.00 0.00 4.18 R
3905 4882 0.668535 GCTTTATGAACGATGCCCCC 59.331 55.000 0.00 0.00 0.00 5.40 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
68 69 0.619255 TTCCAGAATCCAGGCCCGTA 60.619 55.000 0.00 0.00 0.00 4.02
79 80 0.252197 AGGCCCGTATTTCACAGTCC 59.748 55.000 0.00 0.00 0.00 3.85
766 1734 4.400251 CCGACCCACCTCCCCTCT 62.400 72.222 0.00 0.00 0.00 3.69
777 1745 0.478507 CTCCCCTCTCCTCTCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
778 1746 0.996762 TCCCCTCTCCTCTCCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
779 1747 0.998945 CCCCTCTCCTCTCCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
780 1748 0.478507 CCCTCTCCTCTCCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
781 1749 1.522900 CCTCTCCTCTCCTCTCCTCT 58.477 60.000 0.00 0.00 0.00 3.69
848 1816 2.181021 CACACCCCGTCGCTCTAC 59.819 66.667 0.00 0.00 0.00 2.59
862 1830 1.749334 CTCTACCCGCATCCAGTCCC 61.749 65.000 0.00 0.00 0.00 4.46
947 1915 2.445654 GCAGGAGGAGGAGGAGGG 60.446 72.222 0.00 0.00 0.00 4.30
1114 2091 4.540153 CGCATTCGTTCCCCATCT 57.460 55.556 0.00 0.00 0.00 2.90
1143 2120 1.585521 GCATTGCGCACTGCTGATC 60.586 57.895 36.51 14.59 46.63 2.92
1165 2142 1.098712 TGAAAACTGTGGCCGTGACC 61.099 55.000 0.00 0.00 0.00 4.02
1310 2287 0.109272 TCATCAGCAACGTCGAGGAC 60.109 55.000 12.85 0.91 0.00 3.85
1397 2374 2.625823 CCACACCATTGCCACCGTC 61.626 63.158 0.00 0.00 0.00 4.79
1436 2413 1.588239 TCTCCATGCAAGAGGGTGAT 58.412 50.000 15.05 0.00 31.96 3.06
1437 2414 2.763039 TCTCCATGCAAGAGGGTGATA 58.237 47.619 15.05 0.00 31.96 2.15
1755 2732 1.032014 GTTGCAGGAGGAAGTTTGCA 58.968 50.000 0.00 0.00 44.09 4.08
1853 2830 6.992123 CCCTTATGTCTTGTGAGCATACATTA 59.008 38.462 0.00 0.00 35.01 1.90
2005 2982 1.678728 GCCCGATCACCATGAAACAGA 60.679 52.381 0.00 0.00 0.00 3.41
2046 3023 1.138859 CTGTGGATGGTGGCGATTCTA 59.861 52.381 0.00 0.00 0.00 2.10
2075 3052 0.622665 AGGCTAAGCTTGACCTGCAT 59.377 50.000 18.42 6.46 0.00 3.96
2155 3132 3.938963 GACATAGCGGAAAAGGTTGATCA 59.061 43.478 0.00 0.00 0.00 2.92
2237 3214 7.753659 TCGATAGAATGAAATCCGAGATAGAC 58.246 38.462 0.00 0.00 46.15 2.59
2515 3492 0.389817 TCGGAAGATCTTGTGGTGCG 60.390 55.000 14.00 5.76 33.31 5.34
3566 4543 1.997311 CTCCTGCATGGGTCCTGGA 60.997 63.158 0.00 0.00 36.20 3.86
3732 4709 5.770162 GGCTTAAATGTATAGGACCTGCATT 59.230 40.000 3.53 9.28 0.00 3.56
3736 4713 9.209175 CTTAAATGTATAGGACCTGCATTACTC 57.791 37.037 16.13 0.00 0.00 2.59
3782 4759 6.582636 TCAATATACTCCTGCACTAACCTTG 58.417 40.000 0.00 0.00 0.00 3.61
3819 4796 3.931907 TGGTGGGAAGGATAATGTCAG 57.068 47.619 0.00 0.00 0.00 3.51
3842 4819 8.531146 TCAGATTTGTTCATCATACTACTGTCA 58.469 33.333 0.00 0.00 0.00 3.58
3849 4826 7.342026 TGTTCATCATACTACTGTCATGGTACT 59.658 37.037 0.00 0.00 0.00 2.73
3862 4839 5.305902 TGTCATGGTACTGGAAGAAACTGTA 59.694 40.000 0.00 0.00 37.43 2.74
3905 4882 2.229784 GAGGTCAAGTTGGCAATCCTTG 59.770 50.000 19.21 19.21 37.51 3.61
4296 5281 2.755103 CCTTTTCTATGGAAGGTGGTGC 59.245 50.000 0.00 0.00 38.07 5.01
4368 5353 6.095021 CCAGTTTACCATAAGTTTAGGGCTTC 59.905 42.308 2.68 0.00 38.11 3.86
4369 5354 6.657541 CAGTTTACCATAAGTTTAGGGCTTCA 59.342 38.462 2.68 0.00 38.11 3.02
4420 5406 8.081633 GTGACTGTTGGTTTCATTCAATCATTA 58.918 33.333 0.00 0.00 0.00 1.90
4424 5410 9.258826 CTGTTGGTTTCATTCAATCATTAACAA 57.741 29.630 0.00 0.00 0.00 2.83
4447 5433 1.699083 TGGTGTCAGAATCTTGGCTCA 59.301 47.619 0.00 0.00 0.00 4.26
4452 5438 5.423015 GTGTCAGAATCTTGGCTCAGATAA 58.577 41.667 0.88 0.00 32.84 1.75
4498 5484 0.457443 TGCTCTAGACGGCACATCAG 59.543 55.000 2.67 0.00 33.23 2.90
4524 5510 9.331282 GATGAAGTTAATAATGCTACCTTGTCT 57.669 33.333 0.00 0.00 0.00 3.41
4534 5520 2.226674 GCTACCTTGTCTGTTCTTTGCC 59.773 50.000 0.00 0.00 0.00 4.52
4553 5539 8.434661 TCTTTGCCGTATTTACTTTTTAGTACG 58.565 33.333 0.00 0.00 35.86 3.67
4556 5542 8.168681 TGCCGTATTTACTTTTTAGTACGTAC 57.831 34.615 18.10 18.10 34.71 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.004044 CCCAGAGCAGGACTGTGAAAT 59.996 52.381 0.82 0.00 42.26 2.17
79 80 2.509916 GATCCAGGCCCAGAGCAG 59.490 66.667 0.00 0.00 46.50 4.24
766 1734 1.850345 GAAGGAGAGGAGAGGAGAGGA 59.150 57.143 0.00 0.00 0.00 3.71
777 1745 1.681486 GGAAGCCGGAGAAGGAGAGG 61.681 65.000 5.05 0.00 0.00 3.69
778 1746 1.819905 GGAAGCCGGAGAAGGAGAG 59.180 63.158 5.05 0.00 0.00 3.20
779 1747 2.052690 CGGAAGCCGGAGAAGGAGA 61.053 63.158 5.05 0.00 44.15 3.71
780 1748 2.496817 CGGAAGCCGGAGAAGGAG 59.503 66.667 5.05 0.00 44.15 3.69
830 1798 2.282674 TAGAGCGACGGGGTGTGT 60.283 61.111 0.00 0.00 0.00 3.72
837 1805 3.825833 GATGCGGGTAGAGCGACGG 62.826 68.421 0.00 0.00 37.44 4.79
844 1812 1.760875 GGGACTGGATGCGGGTAGA 60.761 63.158 0.00 0.00 0.00 2.59
931 1899 0.637195 TTACCCTCCTCCTCCTCCTG 59.363 60.000 0.00 0.00 0.00 3.86
1104 2081 3.782443 ACGCCGGAGATGGGGAAC 61.782 66.667 13.83 0.00 44.30 3.62
1135 2112 3.436015 CCACAGTTTTCAGAGATCAGCAG 59.564 47.826 0.00 0.00 0.00 4.24
1139 2116 2.783135 GGCCACAGTTTTCAGAGATCA 58.217 47.619 0.00 0.00 0.00 2.92
1143 2120 0.588252 CACGGCCACAGTTTTCAGAG 59.412 55.000 2.24 0.00 0.00 3.35
1165 2142 2.598205 CGCACGATGCAGATACAACATG 60.598 50.000 9.95 0.00 45.36 3.21
1310 2287 2.868583 CGCTTGGTAGGATCTGAACATG 59.131 50.000 0.00 0.00 0.00 3.21
1436 2413 0.616679 CCTTGGGGACTCCTTCGGTA 60.617 60.000 0.00 0.00 36.20 4.02
1437 2414 1.918800 CCTTGGGGACTCCTTCGGT 60.919 63.158 0.00 0.00 36.20 4.69
1755 2732 5.006386 AGTGCTAAAAGTATCTTGCAAGCT 58.994 37.500 21.99 14.99 32.10 3.74
1853 2830 0.895559 GCTGGCCCTGCAAGTTAACT 60.896 55.000 7.85 1.12 31.11 2.24
2005 2982 2.224695 GGTGGCAGTACTTGGGTAAGTT 60.225 50.000 0.00 0.00 44.57 2.66
2046 3023 3.055819 TCAAGCTTAGCCTCGTTCTGAAT 60.056 43.478 0.00 0.00 0.00 2.57
2155 3132 4.444449 GGTTGACTACCTTCTCCACAAGTT 60.444 45.833 0.00 0.00 44.10 2.66
2237 3214 1.205064 CAGGCGCTTGTGAAAGTCG 59.795 57.895 11.99 0.00 0.00 4.18
2582 3559 7.340487 TGCTCTGTATCTTTGTAGATCTGAAGA 59.660 37.037 5.18 12.16 41.38 2.87
3732 4709 4.853196 CGTAAACCAAATTCGAGTCGAGTA 59.147 41.667 15.88 1.88 37.14 2.59
3736 4713 4.835199 ATCGTAAACCAAATTCGAGTCG 57.165 40.909 6.09 6.09 34.20 4.18
3782 4759 3.578688 CACCAAATTTAGTTCTGGCAGC 58.421 45.455 10.34 0.00 31.74 5.25
3819 4796 8.554528 CCATGACAGTAGTATGATGAACAAATC 58.445 37.037 0.00 0.00 0.00 2.17
3842 4819 6.151144 GCAAATACAGTTTCTTCCAGTACCAT 59.849 38.462 0.00 0.00 0.00 3.55
3849 4826 5.136828 TGAAGGCAAATACAGTTTCTTCCA 58.863 37.500 0.00 0.00 0.00 3.53
3862 4839 4.344679 TCAGTTTGACCATTGAAGGCAAAT 59.655 37.500 0.00 0.00 37.18 2.32
3905 4882 0.668535 GCTTTATGAACGATGCCCCC 59.331 55.000 0.00 0.00 0.00 5.40
4420 5406 4.763793 CCAAGATTCTGACACCATCTTGTT 59.236 41.667 20.22 0.00 46.81 2.83
4424 5410 2.575279 AGCCAAGATTCTGACACCATCT 59.425 45.455 0.00 0.00 0.00 2.90
4447 5433 9.911788 ATGAAACATACCTGATCAAGTTTATCT 57.088 29.630 1.50 0.00 30.23 1.98
4498 5484 9.331282 AGACAAGGTAGCATTATTAACTTCATC 57.669 33.333 0.00 0.00 0.00 2.92
4524 5510 8.623030 ACTAAAAAGTAAATACGGCAAAGAACA 58.377 29.630 0.00 0.00 0.00 3.18
4556 5542 9.143631 CAGCCCAATTTCTGTTTTCTAAATAAG 57.856 33.333 0.00 0.00 0.00 1.73
4559 5545 6.930722 CACAGCCCAATTTCTGTTTTCTAAAT 59.069 34.615 2.90 0.00 41.19 1.40
4560 5546 6.097554 TCACAGCCCAATTTCTGTTTTCTAAA 59.902 34.615 2.90 0.00 41.19 1.85
4561 5547 5.596361 TCACAGCCCAATTTCTGTTTTCTAA 59.404 36.000 2.90 0.00 41.19 2.10
4562 5548 5.136828 TCACAGCCCAATTTCTGTTTTCTA 58.863 37.500 2.90 0.00 41.19 2.10
4564 5550 4.301628 CTCACAGCCCAATTTCTGTTTTC 58.698 43.478 2.90 0.00 41.19 2.29
4565 5551 3.070015 CCTCACAGCCCAATTTCTGTTTT 59.930 43.478 2.90 0.00 41.19 2.43
4566 5552 2.629617 CCTCACAGCCCAATTTCTGTTT 59.370 45.455 2.90 0.00 41.19 2.83
4567 5553 2.242043 CCTCACAGCCCAATTTCTGTT 58.758 47.619 2.90 0.00 41.19 3.16
4568 5554 1.145738 ACCTCACAGCCCAATTTCTGT 59.854 47.619 0.35 0.35 43.67 3.41
4569 5555 1.542915 CACCTCACAGCCCAATTTCTG 59.457 52.381 0.00 0.00 36.45 3.02
4570 5556 1.548582 CCACCTCACAGCCCAATTTCT 60.549 52.381 0.00 0.00 0.00 2.52
4575 5561 3.496309 CTGCCACCTCACAGCCCAA 62.496 63.158 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.