Multiple sequence alignment - TraesCS2B01G450400

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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 TraesCS2B01G450400 chr2B 100.000 2588 0 0 1 2588 643415168 643417755 0.000000e+00 4780
1 TraesCS2B01G450400 chr2B 96.037 656 17 2 1617 2263 643512647 643513302 0.000000e+00 1059
2 TraesCS2B01G450400 chr2B 95.884 656 18 2 1617 2263 643464754 643465409 0.000000e+00 1053
3 TraesCS2B01G450400 chr2B 99.003 301 3 0 2288 2588 643513419 643513719 8.150000e-150 540
4 TraesCS2B01G450400 chr2B 99.293 283 2 0 2288 2570 643465526 643465808 1.780000e-141 512
5 TraesCS2B01G450400 chr7B 98.025 1620 32 0 1 1620 662932689 662934308 0.000000e+00 2815
6 TraesCS2B01G450400 chr7B 97.409 1621 42 0 1 1621 581899753 581901373 0.000000e+00 2761
7 TraesCS2B01G450400 chr2A 91.739 1622 132 2 1 1621 54668422 54670042 0.000000e+00 2252
8 TraesCS2B01G450400 chr3B 87.963 1620 192 3 1 1619 707144976 707146593 0.000000e+00 1908
9 TraesCS2B01G450400 chr7D 81.813 1622 287 8 2 1620 463860495 463858879 0.000000e+00 1354
10 TraesCS2B01G450400 chr7A 90.900 989 88 2 630 1618 670496879 670497865 0.000000e+00 1327
11 TraesCS2B01G450400 chr5B 80.976 1619 303 5 2 1618 602641161 602642776 0.000000e+00 1279
12 TraesCS2B01G450400 chr1B 80.888 1622 301 7 2 1619 41751512 41753128 0.000000e+00 1269
13 TraesCS2B01G450400 chr1B 85.813 1015 139 5 1 1013 74686587 74685576 0.000000e+00 1072
14 TraesCS2B01G450400 chr1B 87.500 608 74 2 1010 1617 74656453 74655848 0.000000e+00 701
15 TraesCS2B01G450400 chr3A 83.440 936 149 6 54 987 724332888 724333819 0.000000e+00 865
16 TraesCS2B01G450400 chr3A 87.189 523 66 1 1094 1616 724370978 724371499 6.170000e-166 593


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 TraesCS2B01G450400 chr2B 643415168 643417755 2587 False 4780.0 4780 100.0000 1 2588 1 chr2B.!!$F1 2587
1 TraesCS2B01G450400 chr2B 643512647 643513719 1072 False 799.5 1059 97.5200 1617 2588 2 chr2B.!!$F3 971
2 TraesCS2B01G450400 chr2B 643464754 643465808 1054 False 782.5 1053 97.5885 1617 2570 2 chr2B.!!$F2 953
3 TraesCS2B01G450400 chr7B 662932689 662934308 1619 False 2815.0 2815 98.0250 1 1620 1 chr7B.!!$F2 1619
4 TraesCS2B01G450400 chr7B 581899753 581901373 1620 False 2761.0 2761 97.4090 1 1621 1 chr7B.!!$F1 1620
5 TraesCS2B01G450400 chr2A 54668422 54670042 1620 False 2252.0 2252 91.7390 1 1621 1 chr2A.!!$F1 1620
6 TraesCS2B01G450400 chr3B 707144976 707146593 1617 False 1908.0 1908 87.9630 1 1619 1 chr3B.!!$F1 1618
7 TraesCS2B01G450400 chr7D 463858879 463860495 1616 True 1354.0 1354 81.8130 2 1620 1 chr7D.!!$R1 1618
8 TraesCS2B01G450400 chr7A 670496879 670497865 986 False 1327.0 1327 90.9000 630 1618 1 chr7A.!!$F1 988
9 TraesCS2B01G450400 chr5B 602641161 602642776 1615 False 1279.0 1279 80.9760 2 1618 1 chr5B.!!$F1 1616
10 TraesCS2B01G450400 chr1B 41751512 41753128 1616 False 1269.0 1269 80.8880 2 1619 1 chr1B.!!$F1 1617
11 TraesCS2B01G450400 chr1B 74685576 74686587 1011 True 1072.0 1072 85.8130 1 1013 1 chr1B.!!$R2 1012
12 TraesCS2B01G450400 chr1B 74655848 74656453 605 True 701.0 701 87.5000 1010 1617 1 chr1B.!!$R1 607
13 TraesCS2B01G450400 chr3A 724332888 724333819 931 False 865.0 865 83.4400 54 987 1 chr3A.!!$F1 933
14 TraesCS2B01G450400 chr3A 724370978 724371499 521 False 593.0 593 87.1890 1094 1616 1 chr3A.!!$F2 522

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
559 561 0.88515 ATCGGCGTATCGAGCTCTGA 60.885 55.0 12.85 11.22 42.69 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1773 2.093181 AGTTATTCATGCCAGCACCGTA 60.093 45.455 0.0 0.0 0.0 4.02 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
90 91 2.349912 GCGAGTTTTCAACTTGGCTCTC 60.350 50.000 6.10 0.00 43.03 3.20
103 104 1.377856 GCTCTCCTGGGAAAGCACC 60.378 63.158 9.80 0.00 34.86 5.01
445 447 1.478510 GAGAGACCTTCATTGCTCCGA 59.521 52.381 0.00 0.00 0.00 4.55
559 561 0.885150 ATCGGCGTATCGAGCTCTGA 60.885 55.000 12.85 11.22 42.69 3.27
944 947 3.255395 AGAGAACGAGCGATCATCATCAT 59.745 43.478 0.00 0.00 0.00 2.45
951 954 5.105756 ACGAGCGATCATCATCATGGTTATA 60.106 40.000 0.00 0.00 0.00 0.98
965 968 7.043300 TCATGGTTATATGGGCTATTTGGAT 57.957 36.000 0.00 0.00 0.00 3.41
1156 1159 2.358898 GCGGCTACACATTTGGATGATT 59.641 45.455 0.00 0.00 36.73 2.57
1157 1160 3.181487 GCGGCTACACATTTGGATGATTT 60.181 43.478 0.00 0.00 36.73 2.17
1357 1361 2.036862 GTGGTTAACCTCTGGAACTCGT 59.963 50.000 24.78 0.00 36.82 4.18
1489 1493 1.069906 CACACCTTTGTGCTAAGCGAC 60.070 52.381 0.00 0.00 46.60 5.19
1857 1862 1.699656 CGTGCTCCGATGCCTCTTTG 61.700 60.000 0.00 0.00 39.56 2.77
1972 1977 8.928270 ATTTACACATCAACAAACCGTAAAAA 57.072 26.923 0.00 0.00 32.82 1.94
2067 2072 7.624360 AACAAGAGAAAGAAACATGTGTGTA 57.376 32.000 0.00 0.00 37.67 2.90
2164 2169 8.950208 AATCAGATCTAACTAGCTACAAAACC 57.050 34.615 0.00 0.00 0.00 3.27
2172 2177 4.386711 ACTAGCTACAAAACCACAAGTCC 58.613 43.478 0.00 0.00 0.00 3.85
2183 2190 5.413309 AACCACAAGTCCAACAAAAATGA 57.587 34.783 0.00 0.00 0.00 2.57
2189 2196 7.543172 CCACAAGTCCAACAAAAATGATAGATG 59.457 37.037 0.00 0.00 0.00 2.90
2263 2277 3.805108 GCACGCCCAAGATCTGATCTAAT 60.805 47.826 19.82 3.37 39.08 1.73
2264 2278 3.993081 CACGCCCAAGATCTGATCTAATC 59.007 47.826 19.82 9.15 39.08 1.75
2265 2279 3.643320 ACGCCCAAGATCTGATCTAATCA 59.357 43.478 19.82 0.00 39.08 2.57
2280 2294 8.622948 TGATCTAATCAGCGAATAGAGTTCTA 57.377 34.615 8.56 0.00 33.59 2.10
2281 2295 9.067986 TGATCTAATCAGCGAATAGAGTTCTAA 57.932 33.333 8.56 0.00 33.59 2.10
2285 2299 9.340695 CTAATCAGCGAATAGAGTTCTAATCAG 57.659 37.037 5.38 0.68 29.81 2.90
2309 2415 6.465144 GCGAATAAAATCAGATCTATCGCTG 58.535 40.000 15.88 0.00 38.45 5.18
2358 2464 5.583495 ACAGATCTAGTTAAGATGCACGAC 58.417 41.667 0.00 0.00 45.35 4.34
2570 2676 1.415200 GAGGAGGGGGATGAGTGTAC 58.585 60.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.526825 GCATATCGCGAAAACCCAC 57.473 52.632 15.24 0.00 0.00 4.61
90 91 1.750399 CCATCGGTGCTTTCCCAGG 60.750 63.158 0.00 0.00 0.00 4.45
103 104 4.389992 CGGATTGGTCATAAATCTCCATCG 59.610 45.833 0.00 0.00 34.95 3.84
559 561 5.476752 GCTAGTCGCTCTTTTTGATTCAT 57.523 39.130 0.00 0.00 35.14 2.57
944 947 6.212840 ACATCCAAATAGCCCATATAACCA 57.787 37.500 0.00 0.00 0.00 3.67
951 954 1.609208 GCGACATCCAAATAGCCCAT 58.391 50.000 0.00 0.00 0.00 4.00
965 968 4.893601 TCAACCGGTTGCGCGACA 62.894 61.111 37.21 19.84 40.24 4.35
1357 1361 4.351938 CGAACGGTCGGTGAGGCA 62.352 66.667 16.82 0.00 43.81 4.75
1489 1493 2.159707 CGGTCACATTAAGCGAACAAGG 60.160 50.000 0.00 0.00 39.86 3.61
1563 1567 2.123988 AAAACGCATTCGCCGAGCAA 62.124 50.000 0.00 0.00 39.84 3.91
1764 1769 2.168326 TCATGCCAGCACCGTATATG 57.832 50.000 0.00 0.00 0.00 1.78
1768 1773 2.093181 AGTTATTCATGCCAGCACCGTA 60.093 45.455 0.00 0.00 0.00 4.02
2153 2158 3.290948 TGGACTTGTGGTTTTGTAGCT 57.709 42.857 0.00 0.00 0.00 3.32
2164 2169 8.084073 ACATCTATCATTTTTGTTGGACTTGTG 58.916 33.333 0.00 0.00 0.00 3.33
2200 2207 6.662755 TGATTAGAACTCCCATACAGCAAAT 58.337 36.000 0.00 0.00 0.00 2.32
2207 2214 4.585955 TCGCTGATTAGAACTCCCATAC 57.414 45.455 0.00 0.00 0.00 2.39
2263 2277 5.524284 GCTGATTAGAACTCTATTCGCTGA 58.476 41.667 12.74 0.00 33.70 4.26
2264 2278 4.381270 CGCTGATTAGAACTCTATTCGCTG 59.619 45.833 15.28 9.92 33.70 5.18
2265 2279 4.276183 TCGCTGATTAGAACTCTATTCGCT 59.724 41.667 15.28 0.00 33.70 4.93
2266 2280 4.537965 TCGCTGATTAGAACTCTATTCGC 58.462 43.478 0.00 11.32 33.70 4.70
2267 2281 8.729529 TTATTCGCTGATTAGAACTCTATTCG 57.270 34.615 0.00 0.00 33.70 3.34
2272 2286 8.948631 TGATTTTATTCGCTGATTAGAACTCT 57.051 30.769 0.00 0.00 0.00 3.24
2273 2287 9.035607 TCTGATTTTATTCGCTGATTAGAACTC 57.964 33.333 0.00 0.00 0.00 3.01
2274 2288 8.948631 TCTGATTTTATTCGCTGATTAGAACT 57.051 30.769 0.00 0.00 0.00 3.01
2275 2289 9.804547 GATCTGATTTTATTCGCTGATTAGAAC 57.195 33.333 0.00 0.00 0.00 3.01
2276 2290 9.770097 AGATCTGATTTTATTCGCTGATTAGAA 57.230 29.630 0.00 0.00 0.00 2.10
2280 2294 8.867935 CGATAGATCTGATTTTATTCGCTGATT 58.132 33.333 5.18 0.00 39.76 2.57
2281 2295 7.009999 GCGATAGATCTGATTTTATTCGCTGAT 59.990 37.037 5.18 0.00 38.45 2.90
2283 2297 6.465144 GCGATAGATCTGATTTTATTCGCTG 58.535 40.000 5.18 0.00 38.45 5.18
2285 2299 6.309009 TCAGCGATAGATCTGATTTTATTCGC 59.691 38.462 5.18 17.23 41.22 4.70
2309 2415 4.326826 TGTCTGATGTCCCTGATGTTTTC 58.673 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.