Multiple sequence alignment - TraesCS3A01G246800

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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 TraesCS3A01G246800 chr3A 100.000 2840 0 0 1 2840 464895735 464898574 0.000000e+00 5245.0
1 TraesCS3A01G246800 chr3A 84.783 92 12 2 2745 2835 323102598 323102508 1.080000e-14 91.6
2 TraesCS3A01G246800 chr3D 94.597 1925 57 22 673 2572 339862162 339860260 0.000000e+00 2935.0
3 TraesCS3A01G246800 chr3D 97.637 677 13 2 1 675 339862960 339862285 0.000000e+00 1158.0
4 TraesCS3A01G246800 chr3D 85.201 1169 96 29 12 1125 482834163 482833017 0.000000e+00 1129.0
5 TraesCS3A01G246800 chr3D 95.283 212 9 1 2629 2840 339860258 339860048 4.530000e-88 335.0
6 TraesCS3A01G246800 chr3D 89.024 82 9 0 2745 2826 225524814 225524895 5.010000e-18 102.0
7 TraesCS3A01G246800 chr3B 94.125 1651 56 12 696 2324 438580916 438579285 0.000000e+00 2473.0
8 TraesCS3A01G246800 chr3B 91.189 715 32 7 12 698 438581708 438580997 0.000000e+00 942.0
9 TraesCS3A01G246800 chr3B 88.994 318 27 3 2506 2816 438578970 438578654 1.230000e-103 387.0
10 TraesCS3A01G246800 chr2D 85.666 1179 104 15 9 1125 564471657 564472832 0.000000e+00 1181.0
11 TraesCS3A01G246800 chr2D 89.932 586 44 10 549 1125 601805779 601805200 0.000000e+00 741.0
12 TraesCS3A01G246800 chr2D 87.255 408 21 14 1020 1416 43956494 43956107 1.210000e-118 436.0
13 TraesCS3A01G246800 chr2D 84.444 450 43 16 12 445 601806449 601806011 4.380000e-113 418.0
14 TraesCS3A01G246800 chr2D 100.000 29 0 0 1144 1172 564472830 564472858 1.000000e-03 54.7
15 TraesCS3A01G246800 chr4B 85.823 1178 85 26 12 1125 22446305 22445146 0.000000e+00 1175.0
16 TraesCS3A01G246800 chr4A 85.166 1173 102 30 9 1125 30779118 30780274 0.000000e+00 1136.0
17 TraesCS3A01G246800 chr2B 84.923 1174 102 33 9 1125 675715048 675716203 0.000000e+00 1118.0
18 TraesCS3A01G246800 chr2B 89.096 697 46 15 440 1125 601737587 601738264 0.000000e+00 839.0
19 TraesCS3A01G246800 chr2B 91.111 270 19 4 12 277 601734866 601735134 7.480000e-96 361.0
20 TraesCS3A01G246800 chr2B 88.172 93 11 0 2746 2838 113275026 113275118 8.320000e-21 111.0
21 TraesCS3A01G246800 chr2A 88.995 209 16 5 552 755 46318502 46318296 4.700000e-63 252.0
22 TraesCS3A01G246800 chr2A 91.358 81 7 0 2746 2826 73540767 73540847 8.320000e-21 111.0
23 TraesCS3A01G246800 chr1D 81.111 180 24 6 1665 1841 469834438 469834610 4.940000e-28 135.0
24 TraesCS3A01G246800 chr1B 82.993 147 21 2 1698 1841 651544322 651544467 2.300000e-26 130.0
25 TraesCS3A01G246800 chr7D 91.139 79 7 0 2747 2825 8735130 8735052 1.080000e-19 108.0
26 TraesCS3A01G246800 chr7A 87.778 90 9 2 2747 2835 616806955 616806867 1.390000e-18 104.0
27 TraesCS3A01G246800 chr6B 88.000 75 9 0 2747 2821 51987049 51987123 3.900000e-14 89.8


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 TraesCS3A01G246800 chr3A 464895735 464898574 2839 False 5245.000000 5245 100.0000 1 2840 1 chr3A.!!$F1 2839
1 TraesCS3A01G246800 chr3D 339860048 339862960 2912 True 1476.000000 2935 95.8390 1 2840 3 chr3D.!!$R2 2839
2 TraesCS3A01G246800 chr3D 482833017 482834163 1146 True 1129.000000 1129 85.2010 12 1125 1 chr3D.!!$R1 1113
3 TraesCS3A01G246800 chr3B 438578654 438581708 3054 True 1267.333333 2473 91.4360 12 2816 3 chr3B.!!$R1 2804
4 TraesCS3A01G246800 chr2D 564471657 564472858 1201 False 617.850000 1181 92.8330 9 1172 2 chr2D.!!$F1 1163
5 TraesCS3A01G246800 chr2D 601805200 601806449 1249 True 579.500000 741 87.1880 12 1125 2 chr2D.!!$R2 1113
6 TraesCS3A01G246800 chr4B 22445146 22446305 1159 True 1175.000000 1175 85.8230 12 1125 1 chr4B.!!$R1 1113
7 TraesCS3A01G246800 chr4A 30779118 30780274 1156 False 1136.000000 1136 85.1660 9 1125 1 chr4A.!!$F1 1116
8 TraesCS3A01G246800 chr2B 675715048 675716203 1155 False 1118.000000 1118 84.9230 9 1125 1 chr2B.!!$F2 1116
9 TraesCS3A01G246800 chr2B 601734866 601738264 3398 False 600.000000 839 90.1035 12 1125 2 chr2B.!!$F3 1113

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
785 3458 4.023279 TGTTACGCGTCTACTTTTACTCCA 60.023 41.667 18.63 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 4956 0.030101 GGCCGTCGATCAAGAGAGAG 59.97 60.0 0.0 0.0 0.0 3.2 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
254 259 9.476202 ACTAAGCATCTTGGTTTGAAATTTTAC 57.524 29.630 7.64 0.00 39.08 2.01
349 2668 7.581011 AATAATGGCTTCATTCGAAAAACAC 57.419 32.000 0.00 0.00 41.04 3.32
785 3458 4.023279 TGTTACGCGTCTACTTTTACTCCA 60.023 41.667 18.63 0.00 0.00 3.86
851 3525 6.531594 TCAGCAATCTATGAAACACTTAGACG 59.468 38.462 0.00 0.00 37.83 4.18
897 3571 6.649557 GCAAGGTGCTACTCTTTTAAAGACTA 59.350 38.462 2.94 0.00 40.96 2.59
1662 4341 1.636340 CCGTGATGATTTCCGTCGC 59.364 57.895 0.00 0.00 37.81 5.19
1873 4558 1.766059 TCTGGGTGTGTCCTGTGCT 60.766 57.895 0.00 0.00 36.25 4.40
1891 4576 7.071196 TCCTGTGCTGTTCTTCTATATATTGGT 59.929 37.037 0.00 0.00 0.00 3.67
1956 4641 7.458397 TGTTCCTGTAATTTAGGTGACTTCAT 58.542 34.615 7.95 0.00 43.67 2.57
2001 4686 1.225376 TGTGCTGCCGGAAACTTACG 61.225 55.000 5.05 0.00 0.00 3.18
2025 4710 7.103021 CGTTTTAGCTACTTCGAACTTAATCG 58.897 38.462 0.00 0.00 44.04 3.34
2031 4716 8.152309 AGCTACTTCGAACTTAATCGTACTAT 57.848 34.615 0.00 0.00 43.19 2.12
2032 4717 9.265901 AGCTACTTCGAACTTAATCGTACTATA 57.734 33.333 0.00 0.00 43.19 1.31
2033 4718 9.527566 GCTACTTCGAACTTAATCGTACTATAG 57.472 37.037 0.00 0.00 43.19 1.31
2117 4805 0.389025 CTGGTTGCACTTTGGTTCCC 59.611 55.000 0.00 0.00 0.00 3.97
2136 4824 3.511146 TCCCTTCTGTTTGATTGGAATGC 59.489 43.478 0.00 0.00 0.00 3.56
2150 4838 0.947244 GAATGCCCTTGCTATCGGTG 59.053 55.000 0.00 0.00 38.71 4.94
2151 4839 0.466189 AATGCCCTTGCTATCGGTGG 60.466 55.000 0.00 0.00 38.71 4.61
2152 4840 1.635817 ATGCCCTTGCTATCGGTGGT 61.636 55.000 0.00 0.00 38.71 4.16
2165 4858 6.661805 TGCTATCGGTGGTATCATATAAGACA 59.338 38.462 0.00 0.00 0.00 3.41
2249 4956 4.072088 CTGCGACGCCACGGTTTC 62.072 66.667 18.69 0.00 0.00 2.78
2324 5031 9.483062 CGATTTCTGAATTTCATCACTCTAAAC 57.517 33.333 0.00 0.00 0.00 2.01
2342 5065 9.274206 ACTCTAAACATTTCTCTTGTTAACCTC 57.726 33.333 2.48 0.00 36.32 3.85
2407 5130 6.276847 AGTTCTATAAAGAAGATGAGCACGG 58.723 40.000 0.00 0.00 42.40 4.94
2408 5131 6.096987 AGTTCTATAAAGAAGATGAGCACGGA 59.903 38.462 0.00 0.00 42.40 4.69
2409 5132 5.833082 TCTATAAAGAAGATGAGCACGGAC 58.167 41.667 0.00 0.00 0.00 4.79
2410 5133 1.714794 AAAGAAGATGAGCACGGACG 58.285 50.000 0.00 0.00 0.00 4.79
2413 5136 2.564553 GAAGATGAGCACGGACGGCT 62.565 60.000 7.27 7.27 46.07 5.52
2419 5142 0.651031 GAGCACGGACGGCTTAATTC 59.349 55.000 8.61 0.00 42.78 2.17
2431 5154 3.618150 CGGCTTAATTCTGGGCATTTTTG 59.382 43.478 0.00 0.00 0.00 2.44
2434 5157 4.392754 GCTTAATTCTGGGCATTTTTGTGG 59.607 41.667 0.00 0.00 0.00 4.17
2470 5195 8.548877 AGGCATTCTAACTCTTCTACCAATTTA 58.451 33.333 0.00 0.00 0.00 1.40
2594 5484 6.714810 TCACAAGCTGTTAATCCAAATAGTGT 59.285 34.615 0.00 0.00 0.00 3.55
2595 5485 7.023575 CACAAGCTGTTAATCCAAATAGTGTC 58.976 38.462 0.00 0.00 0.00 3.67
2606 5496 3.954258 CCAAATAGTGTCCCATCTTTCCC 59.046 47.826 0.00 0.00 0.00 3.97
2607 5497 4.569653 CCAAATAGTGTCCCATCTTTCCCA 60.570 45.833 0.00 0.00 0.00 4.37
2608 5498 4.510167 AATAGTGTCCCATCTTTCCCAG 57.490 45.455 0.00 0.00 0.00 4.45
2625 5515 0.389817 CAGTGGATTTGGCTCGACGA 60.390 55.000 0.00 0.00 0.00 4.20
2703 5598 8.773645 CCAGCTATCATATTTTGTTTATCGTCA 58.226 33.333 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 227 1.630369 ACCAAGATGCTTAGTGCCTCA 59.370 47.619 0.00 0.00 42.00 3.86
240 245 8.831550 TGCATAAACAAGGTAAAATTTCAAACC 58.168 29.630 8.55 8.55 0.00 3.27
897 3571 3.495806 GCTCCAGTATGCATAAGGCTCTT 60.496 47.826 17.59 0.00 45.15 2.85
1891 4576 6.090358 GCATAGTAGCAACTACAGAACGAAAA 59.910 38.462 7.45 0.00 40.98 2.29
1956 4641 5.684704 AGTGACAATTTCAAAGTCTCAGGA 58.315 37.500 0.00 0.00 35.39 3.86
2001 4686 7.947090 ACGATTAAGTTCGAAGTAGCTAAAAC 58.053 34.615 5.80 0.00 41.62 2.43
2031 4716 5.506649 GCGTCAGAAAAATGGGAAACAACTA 60.507 40.000 0.00 0.00 0.00 2.24
2032 4717 4.736464 GCGTCAGAAAAATGGGAAACAACT 60.736 41.667 0.00 0.00 0.00 3.16
2033 4718 3.489416 GCGTCAGAAAAATGGGAAACAAC 59.511 43.478 0.00 0.00 0.00 3.32
2034 4719 3.383185 AGCGTCAGAAAAATGGGAAACAA 59.617 39.130 0.00 0.00 0.00 2.83
2035 4720 2.955660 AGCGTCAGAAAAATGGGAAACA 59.044 40.909 0.00 0.00 0.00 2.83
2117 4805 3.512724 AGGGCATTCCAATCAAACAGAAG 59.487 43.478 0.00 0.00 38.24 2.85
2136 4824 1.691976 TGATACCACCGATAGCAAGGG 59.308 52.381 0.00 0.00 0.00 3.95
2150 4838 5.183331 TCGACAGCCTGTCTTATATGATACC 59.817 44.000 21.72 0.00 44.85 2.73
2151 4839 6.255596 TCGACAGCCTGTCTTATATGATAC 57.744 41.667 21.72 0.00 44.85 2.24
2152 4840 6.625960 GCATCGACAGCCTGTCTTATATGATA 60.626 42.308 21.72 0.00 44.85 2.15
2165 4858 1.047596 ATCCTCAGCATCGACAGCCT 61.048 55.000 7.97 0.00 0.00 4.58
2172 4868 5.183713 AGAGAAGAGAATATCCTCAGCATCG 59.816 44.000 0.00 0.00 35.68 3.84
2249 4956 0.030101 GGCCGTCGATCAAGAGAGAG 59.970 60.000 0.00 0.00 0.00 3.20
2324 5031 4.666655 CGTGCGAGGTTAACAAGAGAAATG 60.667 45.833 8.10 0.00 0.00 2.32
2326 5033 2.798283 CGTGCGAGGTTAACAAGAGAAA 59.202 45.455 8.10 0.00 0.00 2.52
2327 5034 2.223876 ACGTGCGAGGTTAACAAGAGAA 60.224 45.455 8.10 0.00 0.00 2.87
2329 5036 1.779569 ACGTGCGAGGTTAACAAGAG 58.220 50.000 8.10 0.00 0.00 2.85
2331 5038 2.915463 CTCTACGTGCGAGGTTAACAAG 59.085 50.000 8.10 0.00 0.00 3.16
2332 5039 2.352030 CCTCTACGTGCGAGGTTAACAA 60.352 50.000 21.23 0.00 42.47 2.83
2333 5040 1.200716 CCTCTACGTGCGAGGTTAACA 59.799 52.381 21.23 0.00 42.47 2.41
2353 5076 2.789491 CCCCCTAAATAGACGTCGTC 57.211 55.000 17.70 17.70 0.00 4.20
2381 5104 8.085296 CCGTGCTCATCTTCTTTATAGAACTAT 58.915 37.037 0.00 0.00 35.49 2.12
2387 5110 4.677378 CGTCCGTGCTCATCTTCTTTATAG 59.323 45.833 0.00 0.00 0.00 1.31
2400 5123 0.651031 GAATTAAGCCGTCCGTGCTC 59.349 55.000 3.74 0.00 38.34 4.26
2401 5124 0.249398 AGAATTAAGCCGTCCGTGCT 59.751 50.000 0.00 0.00 41.89 4.40
2402 5125 0.373716 CAGAATTAAGCCGTCCGTGC 59.626 55.000 0.00 0.00 0.00 5.34
2403 5126 1.006832 CCAGAATTAAGCCGTCCGTG 58.993 55.000 0.00 0.00 0.00 4.94
2404 5127 0.107848 CCCAGAATTAAGCCGTCCGT 60.108 55.000 0.00 0.00 0.00 4.69
2405 5128 1.436983 GCCCAGAATTAAGCCGTCCG 61.437 60.000 0.00 0.00 0.00 4.79
2407 5130 1.680338 ATGCCCAGAATTAAGCCGTC 58.320 50.000 0.00 0.00 0.00 4.79
2408 5131 2.143876 AATGCCCAGAATTAAGCCGT 57.856 45.000 0.00 0.00 0.00 5.68
2409 5132 3.525268 AAAATGCCCAGAATTAAGCCG 57.475 42.857 0.00 0.00 0.00 5.52
2410 5133 4.392754 CACAAAAATGCCCAGAATTAAGCC 59.607 41.667 0.00 0.00 0.00 4.35
2413 5136 4.263243 CCCCACAAAAATGCCCAGAATTAA 60.263 41.667 0.00 0.00 0.00 1.40
2419 5142 1.678724 CCCCCACAAAAATGCCCAG 59.321 57.895 0.00 0.00 0.00 4.45
2434 5157 2.959030 GTTAGAATGCCTGAATTCCCCC 59.041 50.000 2.27 0.00 37.28 5.40
2447 5172 9.110502 GGGTAAATTGGTAGAAGAGTTAGAATG 57.889 37.037 0.00 0.00 0.00 2.67
2470 5195 3.322254 TCGTTGTTAAATTGCCATTGGGT 59.678 39.130 4.53 0.00 36.17 4.51
2501 5386 6.408035 TCTTGCATGCATGTAAATTCCATTT 58.592 32.000 26.87 0.00 32.12 2.32
2561 5451 6.719370 TGGATTAACAGCTTGTGAGGTAAATT 59.281 34.615 0.00 0.00 31.08 1.82
2594 5484 3.511552 TCCACTGGGAAAGATGGGA 57.488 52.632 0.00 0.00 41.32 4.37
2606 5496 0.389817 TCGTCGAGCCAAATCCACTG 60.390 55.000 0.00 0.00 0.00 3.66
2607 5497 0.108615 CTCGTCGAGCCAAATCCACT 60.109 55.000 9.74 0.00 0.00 4.00
2608 5498 1.084370 CCTCGTCGAGCCAAATCCAC 61.084 60.000 17.02 0.00 0.00 4.02
2625 5515 4.703897 TCAACATCTTGTTTCGAAGTCCT 58.296 39.130 0.00 0.00 38.77 3.85


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

AutoCloner maintained by Alex Coulton.