Multiple sequence alignment - TraesCS1D01G294600

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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 TraesCS1D01G294600 chr1D 100.000 2702 0 0 1 2702 393751583 393748882 0.000000e+00 4990.0
1 TraesCS1D01G294600 chr1D 87.850 428 46 6 1083 1507 311988748 311988324 5.200000e-137 497.0
2 TraesCS1D01G294600 chr1D 89.231 65 5 2 106 168 393751410 393751346 2.230000e-11 80.5
3 TraesCS1D01G294600 chr1D 89.231 65 5 2 174 238 393751478 393751416 2.230000e-11 80.5
4 TraesCS1D01G294600 chr1B 93.963 2468 70 24 292 2702 529287387 529289832 0.000000e+00 3659.0
5 TraesCS1D01G294600 chr1B 89.109 404 36 6 1108 1507 422563208 422562809 1.870000e-136 496.0
6 TraesCS1D01G294600 chr1B 94.348 230 12 1 78 306 529283954 529284183 4.280000e-93 351.0
7 TraesCS1D01G294600 chr1B 90.769 65 4 2 174 238 529283982 529284044 4.790000e-13 86.1
8 TraesCS1D01G294600 chr1A 90.241 2449 103 38 351 2702 492045251 492047660 0.000000e+00 3073.0
9 TraesCS1D01G294600 chr1A 88.806 402 41 4 1108 1507 392084936 392084537 8.690000e-135 490.0
10 TraesCS1D01G294600 chr3B 88.056 427 47 4 1089 1513 598468534 598468110 1.120000e-138 503.0
11 TraesCS1D01G294600 chr3D 87.119 427 51 4 1089 1513 455106879 455106455 5.230000e-132 481.0
12 TraesCS1D01G294600 chr3A 87.775 409 48 2 1106 1513 597547649 597547242 6.770000e-131 477.0
13 TraesCS1D01G294600 chr6D 85.057 435 55 10 1108 1537 452722164 452721735 4.130000e-118 435.0


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 TraesCS1D01G294600 chr1D 393748882 393751583 2701 True 1717.000000 4990 92.820667 1 2702 3 chr1D.!!$R2 2701
1 TraesCS1D01G294600 chr1B 529283954 529289832 5878 False 1365.366667 3659 93.026667 78 2702 3 chr1B.!!$F1 2624
2 TraesCS1D01G294600 chr1A 492045251 492047660 2409 False 3073.000000 3073 90.241000 351 2702 1 chr1A.!!$F1 2351

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
663 3913 2.06631 CTACGCGCACATGCACTACG 62.066 60.0 5.73 4.57 42.21 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 5047 0.526524 CTCTTGTCGGCGAGGTGATC 60.527 60.0 11.2 0.0 0.0 2.92 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
40 41 6.512514 TTAGGTGTTTTAAGTACTTGGGGA 57.487 37.500 18.56 0.00 0.00 4.81
41 42 5.391577 AGGTGTTTTAAGTACTTGGGGAA 57.608 39.130 18.56 1.25 0.00 3.97
42 43 5.960704 AGGTGTTTTAAGTACTTGGGGAAT 58.039 37.500 18.56 0.00 0.00 3.01
43 44 6.378745 AGGTGTTTTAAGTACTTGGGGAATT 58.621 36.000 18.56 0.00 0.00 2.17
44 45 6.842280 AGGTGTTTTAAGTACTTGGGGAATTT 59.158 34.615 18.56 0.00 0.00 1.82
45 46 7.346175 AGGTGTTTTAAGTACTTGGGGAATTTT 59.654 33.333 18.56 0.00 0.00 1.82
46 47 7.988599 GGTGTTTTAAGTACTTGGGGAATTTTT 59.011 33.333 18.56 0.00 0.00 1.94
52 53 9.657728 TTAAGTACTTGGGGAATTTTTAAAGGA 57.342 29.630 18.56 0.00 0.00 3.36
53 54 7.776618 AGTACTTGGGGAATTTTTAAAGGAG 57.223 36.000 0.00 0.00 0.00 3.69
54 55 7.302948 AGTACTTGGGGAATTTTTAAAGGAGT 58.697 34.615 0.00 0.00 0.00 3.85
55 56 8.450434 AGTACTTGGGGAATTTTTAAAGGAGTA 58.550 33.333 0.00 0.00 0.00 2.59
56 57 9.251440 GTACTTGGGGAATTTTTAAAGGAGTAT 57.749 33.333 0.00 0.00 0.00 2.12
57 58 8.736097 ACTTGGGGAATTTTTAAAGGAGTATT 57.264 30.769 0.00 0.00 0.00 1.89
58 59 9.831682 ACTTGGGGAATTTTTAAAGGAGTATTA 57.168 29.630 0.00 0.00 0.00 0.98
277 279 6.151312 TGGCTAACTTTATTTTGATTACGGCA 59.849 34.615 0.00 0.00 0.00 5.69
309 3529 2.998493 AGGATCTCCCTGTCACACC 58.002 57.895 0.00 0.00 45.61 4.16
337 3557 5.640783 GCAGCTCCAAAAATGCTTTATCTTT 59.359 36.000 0.00 0.00 35.78 2.52
338 3558 6.183360 GCAGCTCCAAAAATGCTTTATCTTTC 60.183 38.462 0.00 0.00 35.78 2.62
339 3559 6.869913 CAGCTCCAAAAATGCTTTATCTTTCA 59.130 34.615 0.00 0.00 34.51 2.69
340 3560 7.548075 CAGCTCCAAAAATGCTTTATCTTTCAT 59.452 33.333 0.00 0.00 34.51 2.57
341 3561 7.763071 AGCTCCAAAAATGCTTTATCTTTCATC 59.237 33.333 0.00 0.00 32.61 2.92
663 3913 2.066310 CTACGCGCACATGCACTACG 62.066 60.000 5.73 4.57 42.21 3.51
1709 5047 5.163933 GCACCTCTCGAGTATAGTAGAATCG 60.164 48.000 13.13 8.25 34.80 3.34
1840 5178 5.381174 TCTCTTGCCATTTGATTTCACTG 57.619 39.130 0.00 0.00 0.00 3.66
1986 5330 0.875059 GGAGTTTTGGGAGCTGAACG 59.125 55.000 0.00 0.00 0.00 3.95
2020 5367 3.570926 AGCTGATGTTTTGCTCATGTG 57.429 42.857 0.00 0.00 30.41 3.21
2182 5535 3.004734 GCAAACATTTGGACACTGCTACT 59.995 43.478 6.49 0.00 38.57 2.57
2195 5548 0.039165 TGCTACTGTGAGACGCTGTG 60.039 55.000 0.00 0.00 0.00 3.66
2240 5593 4.075682 TCACTTCAAGTTTGTGTTCCACA 58.924 39.130 0.00 0.00 43.02 4.17
2241 5594 4.704540 TCACTTCAAGTTTGTGTTCCACAT 59.295 37.500 0.00 0.00 44.16 3.21
2272 5626 1.521681 GGAGACATACGCAGGTGCC 60.522 63.158 0.00 0.00 37.91 5.01
2361 5715 3.054361 ACCTCCTCAACCACATTACCATC 60.054 47.826 0.00 0.00 0.00 3.51
2388 5742 4.037446 CGAATCCCTTTCCAGAGAGAGTAG 59.963 50.000 0.00 0.00 0.00 2.57
2609 5967 2.158519 TGGGACACTGTAGACTCACTGA 60.159 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.838741 TCCCCAAGTACTTAAAACACCTAATAT 58.161 33.333 8.04 0.00 0.00 1.28
15 16 8.217188 TCCCCAAGTACTTAAAACACCTAATA 57.783 34.615 8.04 0.00 0.00 0.98
16 17 7.093965 TCCCCAAGTACTTAAAACACCTAAT 57.906 36.000 8.04 0.00 0.00 1.73
17 18 6.512514 TCCCCAAGTACTTAAAACACCTAA 57.487 37.500 8.04 0.00 0.00 2.69
18 19 6.512514 TTCCCCAAGTACTTAAAACACCTA 57.487 37.500 8.04 0.00 0.00 3.08
19 20 5.391577 TTCCCCAAGTACTTAAAACACCT 57.608 39.130 8.04 0.00 0.00 4.00
20 21 6.659745 AATTCCCCAAGTACTTAAAACACC 57.340 37.500 8.04 0.00 0.00 4.16
21 22 8.951787 AAAAATTCCCCAAGTACTTAAAACAC 57.048 30.769 8.04 0.00 0.00 3.32
26 27 9.657728 TCCTTTAAAAATTCCCCAAGTACTTAA 57.342 29.630 8.04 0.00 0.00 1.85
27 28 9.304335 CTCCTTTAAAAATTCCCCAAGTACTTA 57.696 33.333 8.04 0.00 0.00 2.24
28 29 7.787904 ACTCCTTTAAAAATTCCCCAAGTACTT 59.212 33.333 1.12 1.12 0.00 2.24
29 30 7.302948 ACTCCTTTAAAAATTCCCCAAGTACT 58.697 34.615 0.00 0.00 0.00 2.73
30 31 7.534723 ACTCCTTTAAAAATTCCCCAAGTAC 57.465 36.000 0.00 0.00 0.00 2.73
31 32 9.831682 AATACTCCTTTAAAAATTCCCCAAGTA 57.168 29.630 0.00 0.00 0.00 2.24
32 33 8.736097 AATACTCCTTTAAAAATTCCCCAAGT 57.264 30.769 0.00 0.00 0.00 3.16
67 68 9.834628 CGGTATAATACTTCTTTTCTTGCAAAA 57.165 29.630 0.00 0.00 0.00 2.44
68 69 9.005777 ACGGTATAATACTTCTTTTCTTGCAAA 57.994 29.630 0.00 0.00 0.00 3.68
69 70 8.556213 ACGGTATAATACTTCTTTTCTTGCAA 57.444 30.769 0.00 0.00 0.00 4.08
70 71 8.447833 CAACGGTATAATACTTCTTTTCTTGCA 58.552 33.333 0.00 0.00 0.00 4.08
71 72 8.662141 TCAACGGTATAATACTTCTTTTCTTGC 58.338 33.333 0.00 0.00 0.00 4.01
74 75 9.886132 ACATCAACGGTATAATACTTCTTTTCT 57.114 29.630 0.00 0.00 0.00 2.52
254 256 8.455598 TTTGCCGTAATCAAAATAAAGTTAGC 57.544 30.769 0.00 0.00 31.27 3.09
277 279 9.453830 ACAGGGAGATCCTAATTACTAAGATTT 57.546 33.333 0.00 0.00 46.12 2.17
286 288 4.654262 GGTGTGACAGGGAGATCCTAATTA 59.346 45.833 0.00 0.00 46.12 1.40
309 3529 1.544691 AGCATTTTTGGAGCTGCTGAG 59.455 47.619 7.01 0.00 43.02 3.35
340 3560 9.027129 GCAACAACGTATGTATAGTTAATGAGA 57.973 33.333 0.00 0.00 42.99 3.27
341 3561 8.813282 TGCAACAACGTATGTATAGTTAATGAG 58.187 33.333 0.00 0.00 42.99 2.90
397 3620 7.931275 ACCTGAAACAGTTATCAAACTCTTTC 58.069 34.615 10.31 10.31 44.28 2.62
405 3628 5.924356 TGTCAGACCTGAAACAGTTATCAA 58.076 37.500 0.70 0.00 41.85 2.57
509 3747 2.904131 TGTGTCCAACAGTGGCGA 59.096 55.556 0.00 0.00 45.54 5.54
626 3876 0.111639 AGGGATCGGAGTAGAGGCTC 59.888 60.000 6.34 6.34 34.89 4.70
627 3877 1.074244 GTAGGGATCGGAGTAGAGGCT 59.926 57.143 0.00 0.00 0.00 4.58
628 3878 1.536940 GTAGGGATCGGAGTAGAGGC 58.463 60.000 0.00 0.00 0.00 4.70
629 3879 1.810959 CGTAGGGATCGGAGTAGAGG 58.189 60.000 0.00 0.00 0.00 3.69
630 3880 1.158434 GCGTAGGGATCGGAGTAGAG 58.842 60.000 0.00 0.00 0.00 2.43
631 3881 0.602106 CGCGTAGGGATCGGAGTAGA 60.602 60.000 0.00 0.00 46.37 2.59
663 3913 0.577269 GCGCGTATGGATGAACAGTC 59.423 55.000 8.43 0.00 0.00 3.51
689 3951 1.798735 GTACTCCAGAGCGTACGCA 59.201 57.895 38.58 19.14 44.88 5.24
690 3952 4.686227 GTACTCCAGAGCGTACGC 57.314 61.111 32.17 32.17 42.33 4.42
692 3954 1.004079 GCTACGTACTCCAGAGCGTAC 60.004 57.143 0.00 0.00 38.56 3.67
693 3955 1.293924 GCTACGTACTCCAGAGCGTA 58.706 55.000 0.00 7.15 38.56 4.42
694 3956 2.096596 GCTACGTACTCCAGAGCGT 58.903 57.895 0.00 5.80 40.76 5.07
696 3958 1.298488 GCGCTACGTACTCCAGAGC 60.298 63.158 0.00 0.00 0.00 4.09
697 3959 1.011019 CGCGCTACGTACTCCAGAG 60.011 63.158 5.56 0.00 36.87 3.35
698 3960 3.095911 CGCGCTACGTACTCCAGA 58.904 61.111 5.56 0.00 36.87 3.86
699 3961 2.651232 GCGCGCTACGTACTCCAG 60.651 66.667 26.67 0.00 46.11 3.86
700 3962 3.391160 CTGCGCGCTACGTACTCCA 62.391 63.158 33.29 6.44 46.11 3.86
701 3963 2.651232 CTGCGCGCTACGTACTCC 60.651 66.667 33.29 0.00 46.11 3.85
702 3964 2.651232 CCTGCGCGCTACGTACTC 60.651 66.667 33.29 0.00 46.11 2.59
703 3965 4.189188 CCCTGCGCGCTACGTACT 62.189 66.667 33.29 0.00 46.11 2.73
797 4071 1.537643 GATAGCTGGGGAGGGAGGG 60.538 68.421 0.00 0.00 0.00 4.30
798 4072 1.124477 GTGATAGCTGGGGAGGGAGG 61.124 65.000 0.00 0.00 0.00 4.30
1692 5030 6.699366 AGGTGATCGATTCTACTATACTCGA 58.301 40.000 0.00 0.00 41.91 4.04
1709 5047 0.526524 CTCTTGTCGGCGAGGTGATC 60.527 60.000 11.20 0.00 0.00 2.92
1840 5178 6.954487 TTAAACAAGAAAAGGGAGAAGGAC 57.046 37.500 0.00 0.00 0.00 3.85
1869 5213 4.775058 AATCATAAGGACTCGATCGAGG 57.225 45.455 39.70 25.49 45.88 4.63
2043 5390 2.673862 TGCGGTTAATTATGTCACCACG 59.326 45.455 5.20 0.00 0.00 4.94
2122 5469 8.086851 AGAAAACAATGCATGGTAATCAAAAC 57.913 30.769 7.27 0.00 0.00 2.43
2182 5535 1.592400 CACAGCACAGCGTCTCACA 60.592 57.895 0.00 0.00 0.00 3.58
2240 5593 5.294306 CGTATGTCTCCATTTGCACAGTTAT 59.706 40.000 0.00 0.00 32.29 1.89
2241 5594 4.629634 CGTATGTCTCCATTTGCACAGTTA 59.370 41.667 0.00 0.00 32.29 2.24
2272 5626 6.539324 CACCATTCATGCAAGCTTTTAATTG 58.461 36.000 0.00 0.00 0.00 2.32
2361 5715 4.125703 CTCTCTGGAAAGGGATTCGATTG 58.874 47.826 0.00 0.00 39.05 2.67


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

AutoCloner maintained by Alex Coulton.