Multiple sequence alignment - TraesCS3B01G173700

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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 TraesCS3B01G173700 chr3B 100.000 2234 0 0 1 2234 173945276 173943043 0 4126
1 TraesCS3B01G173700 chr6B 96.323 2257 57 10 1 2234 596601816 596604069 0 3685
2 TraesCS3B01G173700 chr6B 95.596 1862 60 5 395 2234 715991687 715993548 0 2964
3 TraesCS3B01G173700 chr6B 95.337 1823 61 9 435 2234 307027422 307025601 0 2874
4 TraesCS3B01G173700 chr7A 96.226 2252 62 8 1 2230 638507622 638509872 0 3666
5 TraesCS3B01G173700 chr7A 95.881 2258 65 11 1 2234 708245667 708243414 0 3629
6 TraesCS3B01G173700 chrUn 96.099 2256 64 8 1 2234 171008328 171006075 0 3657
7 TraesCS3B01G173700 chrUn 94.808 1040 31 8 1 1018 432742396 432741358 0 1600
8 TraesCS3B01G173700 chr5B 95.835 2257 70 9 1 2234 567280038 567277783 0 3626
9 TraesCS3B01G173700 chr1B 95.700 2256 71 9 1 2234 672541264 672539013 0 3605
10 TraesCS3B01G173700 chr2B 95.525 2257 78 9 1 2234 391225199 391227455 0 3587
11 TraesCS3B01G173700 chr7D 95.567 2256 71 10 1 2234 382089841 382087593 0 3585
12 TraesCS3B01G173700 chr4B 95.483 2258 71 13 1 2234 495568004 495565754 0 3576
13 TraesCS3B01G173700 chr4B 95.570 1964 61 9 294 2234 623347112 623345152 0 3121
14 TraesCS3B01G173700 chr4D 95.434 2256 74 11 1 2234 123401561 123399313 0 3568


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 TraesCS3B01G173700 chr3B 173943043 173945276 2233 True 4126 4126 100.000 1 2234 1 chr3B.!!$R1 2233
1 TraesCS3B01G173700 chr6B 596601816 596604069 2253 False 3685 3685 96.323 1 2234 1 chr6B.!!$F1 2233
2 TraesCS3B01G173700 chr6B 715991687 715993548 1861 False 2964 2964 95.596 395 2234 1 chr6B.!!$F2 1839
3 TraesCS3B01G173700 chr6B 307025601 307027422 1821 True 2874 2874 95.337 435 2234 1 chr6B.!!$R1 1799
4 TraesCS3B01G173700 chr7A 638507622 638509872 2250 False 3666 3666 96.226 1 2230 1 chr7A.!!$F1 2229
5 TraesCS3B01G173700 chr7A 708243414 708245667 2253 True 3629 3629 95.881 1 2234 1 chr7A.!!$R1 2233
6 TraesCS3B01G173700 chrUn 171006075 171008328 2253 True 3657 3657 96.099 1 2234 1 chrUn.!!$R1 2233
7 TraesCS3B01G173700 chrUn 432741358 432742396 1038 True 1600 1600 94.808 1 1018 1 chrUn.!!$R2 1017
8 TraesCS3B01G173700 chr5B 567277783 567280038 2255 True 3626 3626 95.835 1 2234 1 chr5B.!!$R1 2233
9 TraesCS3B01G173700 chr1B 672539013 672541264 2251 True 3605 3605 95.700 1 2234 1 chr1B.!!$R1 2233
10 TraesCS3B01G173700 chr2B 391225199 391227455 2256 False 3587 3587 95.525 1 2234 1 chr2B.!!$F1 2233
11 TraesCS3B01G173700 chr7D 382087593 382089841 2248 True 3585 3585 95.567 1 2234 1 chr7D.!!$R1 2233
12 TraesCS3B01G173700 chr4B 495565754 495568004 2250 True 3576 3576 95.483 1 2234 1 chr4B.!!$R1 2233
13 TraesCS3B01G173700 chr4B 623345152 623347112 1960 True 3121 3121 95.570 294 2234 1 chr4B.!!$R2 1940
14 TraesCS3B01G173700 chr4D 123399313 123401561 2248 True 3568 3568 95.434 1 2234 1 chr4D.!!$R1 2233

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
858 883 0.178929 AAGGGTCGTCTGAGGGTTCT 60.179 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1693 0.185175 TCCATCCTAGAGTAGCCGCA 59.815 55.0 0.0 0.0 0.0 5.69 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
177 178 1.464734 ATCTCGTCTTTCTCTCGGCA 58.535 50.000 0.00 0.00 0.00 5.69
180 181 1.176619 TCGTCTTTCTCTCGGCACCA 61.177 55.000 0.00 0.00 0.00 4.17
189 190 2.813754 TCTCTCGGCACCAAGAATTTTG 59.186 45.455 0.00 0.00 0.00 2.44
198 199 3.315191 CACCAAGAATTTTGGACGTGTCT 59.685 43.478 19.74 0.87 42.06 3.41
229 230 1.302511 GGTTCGGCTTGCTTCTCCA 60.303 57.895 0.00 0.00 0.00 3.86
266 267 0.929244 ATGGATAACCCTTGCTGCCT 59.071 50.000 0.00 0.00 35.38 4.75
292 293 4.526970 CAGCAGGATTTTAAGGGCTTCTA 58.473 43.478 0.00 0.00 0.00 2.10
516 519 2.606519 TTAGGGTGCGCCTCCTGT 60.607 61.111 23.57 12.11 34.75 4.00
553 556 0.613012 AATTGGCTGGCTTCCCTCAC 60.613 55.000 2.00 0.00 0.00 3.51
582 585 4.459089 GTCGCCACCTCTCCCAGC 62.459 72.222 0.00 0.00 0.00 4.85
585 588 3.325753 GCCACCTCTCCCAGCACT 61.326 66.667 0.00 0.00 0.00 4.40
769 793 4.567747 CCCCCAGGTTCCATATATAAGCAC 60.568 50.000 1.43 0.00 0.00 4.40
819 843 3.008049 GTCAAAGGGTCACCACTACTGAT 59.992 47.826 0.00 0.00 40.13 2.90
858 883 0.178929 AAGGGTCGTCTGAGGGTTCT 60.179 55.000 0.00 0.00 0.00 3.01
861 886 0.898789 GGTCGTCTGAGGGTTCTCCA 60.899 60.000 0.00 0.00 39.23 3.86
997 1022 1.379044 CCGCAGAGGAAAGCCCAAT 60.379 57.895 0.00 0.00 45.00 3.16
1263 1289 5.012768 CACCCTAACCGTCCTAAATATGGAT 59.987 44.000 0.00 0.00 35.87 3.41
1389 1416 2.461695 TCATCTTTTCGAGAGCCTCCT 58.538 47.619 0.00 0.00 37.93 3.69
1414 1441 2.183409 CCGTCAAGGGGCATTTGAG 58.817 57.895 3.52 0.12 35.39 3.02
1417 1444 1.402968 CGTCAAGGGGCATTTGAGATG 59.597 52.381 3.52 0.00 35.39 2.90
1573 1600 6.524545 AGCCTCTAAAGACTCTACTCCTAT 57.475 41.667 0.00 0.00 0.00 2.57
1706 1738 3.806949 TCAAGGTTTAGGCCAACAGAT 57.193 42.857 5.01 0.00 0.00 2.90
1928 1961 2.005971 AACAATAAGGAGACGCGGTC 57.994 50.000 12.47 6.63 0.00 4.79
1942 1975 0.739462 GCGGTCATGTCGTCATCCAA 60.739 55.000 11.42 0.00 31.15 3.53
2175 2211 6.970484 TCTAACTTGAGCAGAAAAATTGGTC 58.030 36.000 0.00 0.00 41.99 4.02
2201 2237 6.583806 GCATTTGACATCTAAAGTTTCACCAG 59.416 38.462 0.00 0.00 0.00 4.00
2222 2258 2.040178 CCCTACTACTGCCCGAAATCT 58.960 52.381 0.00 0.00 0.00 2.40
2230 2266 0.038343 TGCCCGAAATCTTGCTTTGC 60.038 50.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 3.315191 CAGACACGTCCAAAATTCTTGGT 59.685 43.478 14.88 1.44 40.40 3.67
180 181 2.884639 CCCAGACACGTCCAAAATTCTT 59.115 45.455 0.00 0.00 0.00 2.52
189 190 1.139095 GATCGACCCAGACACGTCC 59.861 63.158 0.00 0.00 0.00 4.79
198 199 1.320344 CCGAACCTCTGATCGACCCA 61.320 60.000 1.01 0.00 41.43 4.51
229 230 1.134098 CATTTCATAGGCGAGGGTGGT 60.134 52.381 0.00 0.00 0.00 4.16
266 267 3.023832 GCCCTTAAAATCCTGCTGCTAA 58.976 45.455 0.00 0.00 0.00 3.09
292 293 3.209410 CTTCCTCCTATTGCGCTTCAAT 58.791 45.455 9.73 2.34 46.48 2.57
301 302 2.353357 TGCATGGCTTCCTCCTATTG 57.647 50.000 0.00 0.00 0.00 1.90
516 519 2.971660 TTGAGTCACTGAAACGACCA 57.028 45.000 0.00 0.00 32.33 4.02
553 556 2.262915 GGCGACACCAGTCTGAGG 59.737 66.667 0.00 0.00 42.73 3.86
582 585 2.154462 GCGGGGATAATCATTCCAGTG 58.846 52.381 0.00 0.00 34.77 3.66
585 588 0.404040 GGGCGGGGATAATCATTCCA 59.596 55.000 0.00 0.00 34.77 3.53
636 639 1.263356 CGGGGAAGTGAAGAGTACCA 58.737 55.000 0.00 0.00 0.00 3.25
697 700 1.612442 GTCCACTCTAGGGGGTGCA 60.612 63.158 0.00 0.00 32.68 4.57
751 754 4.838986 ACCGAGTGCTTATATATGGAACCT 59.161 41.667 0.00 0.00 0.00 3.50
764 788 7.230913 ACTGACTTATATATGTACCGAGTGCTT 59.769 37.037 1.48 0.00 0.00 3.91
769 793 7.683437 TCCACTGACTTATATATGTACCGAG 57.317 40.000 1.48 0.18 0.00 4.63
819 843 5.407049 CCTTCTAAGATAAGGGGGAGATCA 58.593 45.833 0.00 0.00 39.94 2.92
858 883 2.596346 AGCACAACAATGAACCATGGA 58.404 42.857 21.47 0.00 0.00 3.41
861 886 4.870363 GTGTAAGCACAACAATGAACCAT 58.130 39.130 0.00 0.00 44.64 3.55
997 1022 1.820519 GGGCTTTGCATCTGACATTCA 59.179 47.619 0.00 0.00 0.00 2.57
1240 1266 4.559726 TCCATATTTAGGACGGTTAGGGT 58.440 43.478 0.00 0.00 0.00 4.34
1263 1289 0.894184 AAACTCGAGACCGCTCTCCA 60.894 55.000 21.68 0.00 40.10 3.86
1287 1313 1.115467 AAATGCGATCTCGAGGACCT 58.885 50.000 13.56 0.00 43.02 3.85
1414 1441 2.161211 GGACTGCTTTTGTCTCTGCATC 59.839 50.000 0.00 0.00 34.79 3.91
1417 1444 0.877743 GGGACTGCTTTTGTCTCTGC 59.122 55.000 0.00 0.00 32.53 4.26
1532 1559 5.071115 AGAGGCTCGCTTAGAAGGAATAAAT 59.929 40.000 9.22 0.00 0.00 1.40
1589 1616 6.777091 TGTCTTTGGAAGAATTGGAAGAATCA 59.223 34.615 0.00 0.00 39.67 2.57
1666 1693 0.185175 TCCATCCTAGAGTAGCCGCA 59.815 55.000 0.00 0.00 0.00 5.69
1678 1705 2.175715 GGCCTAAACCTTGATCCATCCT 59.824 50.000 0.00 0.00 0.00 3.24
1942 1975 5.505780 CCTTTGGGGTTTTCTTTTTCCTTT 58.494 37.500 0.00 0.00 0.00 3.11
2123 2159 4.116238 GTTTTTCGAAGTGAATTGGCCAA 58.884 39.130 23.00 23.00 36.22 4.52
2175 2211 5.569059 GGTGAAACTTTAGATGTCAAATGCG 59.431 40.000 0.00 0.00 36.74 4.73
2201 2237 0.468648 ATTTCGGGCAGTAGTAGGGC 59.531 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.