Multiple sequence alignment - TraesCS1B01G235800

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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 TraesCS1B01G235800 chr1B 100.000 3098 0 0 1 3098 422564411 422561314 0.000000e+00 5722
1 TraesCS1B01G235800 chr1B 87.871 404 41 6 1204 1603 529288210 529288609 4.680000e-128 468
2 TraesCS1B01G235800 chr1D 95.581 2987 74 30 148 3098 311989781 311986817 0.000000e+00 4732
3 TraesCS1B01G235800 chr1D 89.109 404 36 6 1204 1603 393750476 393750077 2.150000e-136 496
4 TraesCS1B01G235800 chr1D 86.047 172 10 4 1 162 311989974 311989807 4.110000e-39 172
5 TraesCS1B01G235800 chr1A 94.082 3160 96 44 1 3098 392086154 392083024 0.000000e+00 4715
6 TraesCS1B01G235800 chr1A 88.614 404 38 6 1204 1603 492046063 492046462 4.640000e-133 484
7 TraesCS1B01G235800 chr3B 88.942 416 42 4 1204 1617 598468515 598468102 7.660000e-141 510
8 TraesCS1B01G235800 chr3D 88.221 416 45 4 1204 1617 455106860 455106447 7.720000e-136 494
9 TraesCS1B01G235800 chr3A 87.981 416 46 4 1204 1617 597547647 597547234 3.590000e-134 488
10 TraesCS1B01G235800 chr6B 86.967 399 48 4 1204 1600 687525401 687525005 2.190000e-121 446


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 TraesCS1B01G235800 chr1B 422561314 422564411 3097 True 5722 5722 100.000 1 3098 1 chr1B.!!$R1 3097
1 TraesCS1B01G235800 chr1D 311986817 311989974 3157 True 2452 4732 90.814 1 3098 2 chr1D.!!$R2 3097
2 TraesCS1B01G235800 chr1A 392083024 392086154 3130 True 4715 4715 94.082 1 3098 1 chr1A.!!$R1 3097

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
517 572 0.106569 TTCAGGGGTATGCATGCAGG 60.107 55.0 26.69 8.99 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2380 1.678728 GCGTGATGAATGGGACCAAGA 60.679 52.381 0.0 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
29 30 4.223144 GGCCTCTTCTCCTCTCTAATCTT 58.777 47.826 0.00 0.00 0.00 2.40
141 151 3.635331 GCATGCACACCTATGCTATTTG 58.365 45.455 14.21 0.00 46.28 2.32
189 243 4.215827 CCGTATATCTATAAGCTAGCGGGG 59.784 50.000 9.55 0.00 32.85 5.73
190 244 4.215827 CGTATATCTATAAGCTAGCGGGGG 59.784 50.000 9.55 0.36 0.00 5.40
289 343 4.201940 GCCAAAAAGAACAAAAGCAGCAAT 60.202 37.500 0.00 0.00 0.00 3.56
422 476 3.485463 ACAGGGACACGATCTTTTTCA 57.515 42.857 0.00 0.00 0.00 2.69
517 572 0.106569 TTCAGGGGTATGCATGCAGG 60.107 55.000 26.69 8.99 0.00 4.85
520 575 0.855598 AGGGGTATGCATGCAGGAAT 59.144 50.000 26.69 11.76 0.00 3.01
521 576 1.218704 AGGGGTATGCATGCAGGAATT 59.781 47.619 26.69 11.35 0.00 2.17
522 577 2.446666 AGGGGTATGCATGCAGGAATTA 59.553 45.455 26.69 10.24 0.00 1.40
523 578 3.117169 AGGGGTATGCATGCAGGAATTAA 60.117 43.478 26.69 0.00 0.00 1.40
524 579 3.834231 GGGGTATGCATGCAGGAATTAAT 59.166 43.478 26.69 9.00 0.00 1.40
525 580 4.284234 GGGGTATGCATGCAGGAATTAATT 59.716 41.667 26.69 8.22 0.00 1.40
559 622 1.142870 GGCTGCATGGTGGGATACTTA 59.857 52.381 0.50 0.00 0.00 2.24
564 627 5.380043 CTGCATGGTGGGATACTTATTTCT 58.620 41.667 0.00 0.00 0.00 2.52
606 669 0.249120 GGGCCGGGGAAAAAGAAATG 59.751 55.000 2.18 0.00 0.00 2.32
644 709 2.486013 GGAACAACAAGGACGGGTACTT 60.486 50.000 0.00 0.00 33.02 2.24
645 710 3.244181 GGAACAACAAGGACGGGTACTTA 60.244 47.826 0.00 0.00 31.24 2.24
646 711 4.564199 GGAACAACAAGGACGGGTACTTAT 60.564 45.833 0.00 0.00 31.24 1.73
854 930 2.158534 CCCTTCTCTCTCTAGCTGCCTA 60.159 54.545 0.00 0.00 0.00 3.93
876 956 2.686715 GCCAGGTAGCTTCTCTCTCTCT 60.687 54.545 0.00 0.00 0.00 3.10
877 957 3.214328 CCAGGTAGCTTCTCTCTCTCTC 58.786 54.545 0.00 0.00 0.00 3.20
919 999 2.787601 ACAAGAAACGACGTAGCAGA 57.212 45.000 0.00 0.00 0.00 4.26
921 1001 2.292569 ACAAGAAACGACGTAGCAGAGA 59.707 45.455 0.00 0.00 0.00 3.10
922 1002 2.904011 AGAAACGACGTAGCAGAGAG 57.096 50.000 0.00 0.00 0.00 3.20
923 1003 2.424557 AGAAACGACGTAGCAGAGAGA 58.575 47.619 0.00 0.00 0.00 3.10
924 1004 2.417239 AGAAACGACGTAGCAGAGAGAG 59.583 50.000 0.00 0.00 0.00 3.20
927 1007 1.205179 ACGACGTAGCAGAGAGAGAGA 59.795 52.381 0.00 0.00 0.00 3.10
928 1008 1.858458 CGACGTAGCAGAGAGAGAGAG 59.142 57.143 0.00 0.00 0.00 3.20
1142 1225 3.279504 AAGGAGGAGGCCAGCAAGC 62.280 63.158 5.01 0.00 0.00 4.01
1482 1565 3.138798 GCCGCCTACGAGGAGTCA 61.139 66.667 5.24 0.00 43.93 3.41
2395 2487 8.492415 AGGCCTCAGTTATATATACAGTTTCA 57.508 34.615 0.00 0.00 0.00 2.69
2425 2517 1.281287 AGCTGAGATGTCCTTGCACAT 59.719 47.619 0.00 0.00 39.84 3.21
2485 2577 6.647067 AGACAATGAGCAGTACTCTTAACAAC 59.353 38.462 0.00 0.00 46.41 3.32
2523 2615 5.835257 ACAATTTTCATGTGGTCTGTGAAG 58.165 37.500 0.00 0.00 33.82 3.02
2635 2727 9.477484 GCTTTCTCGAATCCATATACTTTCTTA 57.523 33.333 0.00 0.00 0.00 2.10
2754 2846 5.300286 CCTTTCTTTTCTCATCTGTGGTTGT 59.700 40.000 0.00 0.00 0.00 3.32
2812 2904 4.769688 TGTGCTTACACCTGGAATATCTG 58.230 43.478 0.00 0.00 46.86 2.90
2837 2950 9.462606 TGTTATACTTACTCAGAGAGTTCATGA 57.537 33.333 3.79 0.00 40.28 3.07
3008 3126 8.870160 TGGAGATTTTTGTGAGTGTTAATTTG 57.130 30.769 0.00 0.00 0.00 2.32
3090 3211 2.982488 CCCTCCAAATATGTAGAGCCCT 59.018 50.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.304391 GCTACGTGGCAGTTTTTGATTGA 60.304 43.478 19.95 0.00 0.00 2.57
102 112 4.357142 CATGCTTTGCCTTGTGATGATAC 58.643 43.478 0.00 0.00 0.00 2.24
104 114 2.418197 GCATGCTTTGCCTTGTGATGAT 60.418 45.455 11.37 0.00 46.15 2.45
141 151 6.143118 GCGCGATATTTGATATATCAGAGTCC 59.857 42.308 12.10 6.11 38.19 3.85
189 243 2.202837 GGTGTCGCGTATGACCCC 60.203 66.667 5.77 0.00 38.11 4.95
190 244 1.226888 GAGGTGTCGCGTATGACCC 60.227 63.158 5.77 0.58 38.11 4.46
199 253 1.226888 GGGTACGATGAGGTGTCGC 60.227 63.158 0.00 0.00 42.56 5.19
289 343 7.545265 GCCTATGTATGCTTTTGTTTCATTTCA 59.455 33.333 0.00 0.00 0.00 2.69
336 390 0.678048 GATGCTTCCGCTTCCAGGTT 60.678 55.000 0.00 0.00 35.05 3.50
364 418 3.682718 GCTCAATGGCTTTCCTGCTACTA 60.683 47.826 0.00 0.00 0.00 1.82
517 572 9.659830 CAGCCTACGGTTATGTTTAATTAATTC 57.340 33.333 3.39 0.00 0.00 2.17
520 575 6.598457 TGCAGCCTACGGTTATGTTTAATTAA 59.402 34.615 0.00 0.00 0.00 1.40
521 576 6.114089 TGCAGCCTACGGTTATGTTTAATTA 58.886 36.000 0.00 0.00 0.00 1.40
522 577 4.944930 TGCAGCCTACGGTTATGTTTAATT 59.055 37.500 0.00 0.00 0.00 1.40
523 578 4.519213 TGCAGCCTACGGTTATGTTTAAT 58.481 39.130 0.00 0.00 0.00 1.40
524 579 3.940319 TGCAGCCTACGGTTATGTTTAA 58.060 40.909 0.00 0.00 0.00 1.52
525 580 3.613494 TGCAGCCTACGGTTATGTTTA 57.387 42.857 0.00 0.00 0.00 2.01
550 609 9.930693 ATTCGTATCTTCAGAAATAAGTATCCC 57.069 33.333 0.00 0.00 0.00 3.85
559 622 8.122952 CGGCTTTTTATTCGTATCTTCAGAAAT 58.877 33.333 0.00 0.00 0.00 2.17
564 627 5.522460 CCTCGGCTTTTTATTCGTATCTTCA 59.478 40.000 0.00 0.00 0.00 3.02
606 669 6.147000 TGTTGTTCCTTTCTCTTTGCAAAAAC 59.853 34.615 13.84 11.94 0.00 2.43
644 709 5.979993 TGGTTCTTAGTGTTCGGCATAATA 58.020 37.500 0.00 0.00 0.00 0.98
645 710 4.839121 TGGTTCTTAGTGTTCGGCATAAT 58.161 39.130 0.00 0.00 0.00 1.28
646 711 4.274602 TGGTTCTTAGTGTTCGGCATAA 57.725 40.909 0.00 0.00 0.00 1.90
854 930 1.287739 AGAGAGAGAAGCTACCTGGCT 59.712 52.381 0.00 0.00 45.30 4.75
919 999 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
921 1001 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
922 1002 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
923 1003 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
924 1004 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
927 1007 3.964031 GGTCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
928 1008 3.706594 TGGTCTCTCTCTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
1494 1577 2.434359 GCGAAGGGGTTGGACTCG 60.434 66.667 0.00 0.00 0.00 4.18
2118 2210 3.548818 GCGTGATTGAGCAGAACAAACTT 60.549 43.478 0.00 0.00 0.00 2.66
2288 2380 1.678728 GCGTGATGAATGGGACCAAGA 60.679 52.381 0.00 0.00 0.00 3.02
2635 2727 9.956720 CTTGAAAAAGAAGTAAGATGACAACAT 57.043 29.630 0.00 0.00 39.67 2.71
2754 2846 3.829886 AACAAGAACGTATCGTACCGA 57.170 42.857 0.00 0.00 39.99 4.69
2826 2918 2.001812 TGCGAGCTTCATGAACTCTC 57.998 50.000 23.56 20.54 0.00 3.20
2837 2950 2.937379 CTAGGCCTGCATGCGAGCTT 62.937 60.000 25.35 21.82 34.99 3.74
3008 3126 7.382488 ACATCGAGTAATACACACATCTTATGC 59.618 37.037 0.00 0.00 0.00 3.14
3064 3184 4.042187 GCTCTACATATTTGGAGGGATGGT 59.958 45.833 0.00 0.00 36.20 3.55
3067 3187 3.589288 GGGCTCTACATATTTGGAGGGAT 59.411 47.826 0.00 0.00 36.20 3.85


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

AutoCloner maintained by Alex Coulton.