Multiple sequence alignment - TraesCS3B01G236200

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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 TraesCS3B01G236200 chr3B 100.000 2255 0 0 1 2255 368867462 368865208 0 4165
1 TraesCS3B01G236200 chr3B 96.857 891 27 1 1365 2255 368428492 368427603 0 1489
2 TraesCS3B01G236200 chr3B 96.742 890 28 1 1366 2255 649375040 649375928 0 1482
3 TraesCS3B01G236200 chr7B 96.633 1366 45 1 1 1365 644465627 644466992 0 2266
4 TraesCS3B01G236200 chr3A 96.630 1365 46 0 1 1365 633109438 633110802 0 2266
5 TraesCS3B01G236200 chr1B 96.630 1365 46 0 1 1365 668806977 668805613 0 2266
6 TraesCS3B01G236200 chr1B 96.630 1365 46 0 1 1365 672477345 672478709 0 2266
7 TraesCS3B01G236200 chr1B 96.044 1365 54 0 1 1365 638702482 638701118 0 2222
8 TraesCS3B01G236200 chr1D 96.630 1365 45 1 1 1365 141314951 141313588 0 2265
9 TraesCS3B01G236200 chr4B 96.628 1364 45 1 1 1364 209079333 209077971 0 2263
10 TraesCS3B01G236200 chr4B 97.424 893 20 2 1365 2255 142624240 142625131 0 1519
11 TraesCS3B01G236200 chr4B 96.973 892 24 2 1366 2255 556035880 556036770 0 1495
12 TraesCS3B01G236200 chr4B 96.753 893 26 2 1365 2255 439003970 439004861 0 1485
13 TraesCS3B01G236200 chr7A 96.410 1365 49 0 1 1365 60150103 60148739 0 2250
14 TraesCS3B01G236200 chr6B 96.117 1365 53 0 1 1365 306997806 306996442 0 2228
15 TraesCS3B01G236200 chr6B 96.644 894 28 2 1362 2255 669250266 669249375 0 1483
16 TraesCS3B01G236200 chr5B 97.085 892 23 2 1366 2255 662587740 662586850 0 1500
17 TraesCS3B01G236200 chr5B 96.742 890 28 1 1366 2255 494303563 494304451 0 1482
18 TraesCS3B01G236200 chr5B 96.742 890 28 1 1366 2255 538531138 538530250 0 1482


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 TraesCS3B01G236200 chr3B 368865208 368867462 2254 True 4165 4165 100.000 1 2255 1 chr3B.!!$R2 2254
1 TraesCS3B01G236200 chr3B 368427603 368428492 889 True 1489 1489 96.857 1365 2255 1 chr3B.!!$R1 890
2 TraesCS3B01G236200 chr3B 649375040 649375928 888 False 1482 1482 96.742 1366 2255 1 chr3B.!!$F1 889
3 TraesCS3B01G236200 chr7B 644465627 644466992 1365 False 2266 2266 96.633 1 1365 1 chr7B.!!$F1 1364
4 TraesCS3B01G236200 chr3A 633109438 633110802 1364 False 2266 2266 96.630 1 1365 1 chr3A.!!$F1 1364
5 TraesCS3B01G236200 chr1B 668805613 668806977 1364 True 2266 2266 96.630 1 1365 1 chr1B.!!$R2 1364
6 TraesCS3B01G236200 chr1B 672477345 672478709 1364 False 2266 2266 96.630 1 1365 1 chr1B.!!$F1 1364
7 TraesCS3B01G236200 chr1B 638701118 638702482 1364 True 2222 2222 96.044 1 1365 1 chr1B.!!$R1 1364
8 TraesCS3B01G236200 chr1D 141313588 141314951 1363 True 2265 2265 96.630 1 1365 1 chr1D.!!$R1 1364
9 TraesCS3B01G236200 chr4B 209077971 209079333 1362 True 2263 2263 96.628 1 1364 1 chr4B.!!$R1 1363
10 TraesCS3B01G236200 chr4B 142624240 142625131 891 False 1519 1519 97.424 1365 2255 1 chr4B.!!$F1 890
11 TraesCS3B01G236200 chr4B 556035880 556036770 890 False 1495 1495 96.973 1366 2255 1 chr4B.!!$F3 889
12 TraesCS3B01G236200 chr4B 439003970 439004861 891 False 1485 1485 96.753 1365 2255 1 chr4B.!!$F2 890
13 TraesCS3B01G236200 chr7A 60148739 60150103 1364 True 2250 2250 96.410 1 1365 1 chr7A.!!$R1 1364
14 TraesCS3B01G236200 chr6B 306996442 306997806 1364 True 2228 2228 96.117 1 1365 1 chr6B.!!$R1 1364
15 TraesCS3B01G236200 chr6B 669249375 669250266 891 True 1483 1483 96.644 1362 2255 1 chr6B.!!$R2 893
16 TraesCS3B01G236200 chr5B 662586850 662587740 890 True 1500 1500 97.085 1366 2255 1 chr5B.!!$R2 889
17 TraesCS3B01G236200 chr5B 494303563 494304451 888 False 1482 1482 96.742 1366 2255 1 chr5B.!!$F1 889
18 TraesCS3B01G236200 chr5B 538530250 538531138 888 True 1482 1482 96.742 1366 2255 1 chr5B.!!$R1 889

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
511 512 0.108377 TGGCGCGATAAAGAGCTTGA 60.108 50.0 12.1 0.0 37.12 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1557 0.17897 TATAGACACCGGAGAGGGCC 60.179 60.0 9.46 0.0 46.96 5.8 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
195 196 1.272147 ACCCTTCATTTGACCTCTGGC 60.272 52.381 0.00 0.00 0.00 4.85
228 229 9.168451 TGTCAATTGTAAAAAGTAGTTGAGTCA 57.832 29.630 5.13 0.00 0.00 3.41
307 308 8.797438 CCTCTTCCTTCTAAACTAATTGCTTTT 58.203 33.333 0.00 0.00 0.00 2.27
434 435 9.520515 AAATGGACATACAATCAAAGAGTAAGT 57.479 29.630 0.00 0.00 0.00 2.24
471 472 1.561542 GATGGGTGGATTGGTCAGAGT 59.438 52.381 0.00 0.00 0.00 3.24
488 489 1.542030 GAGTTGCAAGGAGAGACTCGA 59.458 52.381 0.00 0.00 0.00 4.04
511 512 0.108377 TGGCGCGATAAAGAGCTTGA 60.108 50.000 12.10 0.00 37.12 3.02
522 523 6.238293 CGATAAAGAGCTTGATTCAATGCTCA 60.238 38.462 30.54 20.57 41.88 4.26
525 526 4.193090 AGAGCTTGATTCAATGCTCAGAG 58.807 43.478 30.54 11.31 41.88 3.35
612 613 2.820197 GGTAGTTGGGAAAAAGCTCTGG 59.180 50.000 0.00 0.00 0.00 3.86
637 638 9.228949 GGATACAGATTCAAAGCATCAAGATAT 57.771 33.333 0.00 0.00 0.00 1.63
664 665 3.069586 TCCTATCATTAGTTGGCCAGTCG 59.930 47.826 5.11 0.00 0.00 4.18
667 668 3.965379 TCATTAGTTGGCCAGTCGTAA 57.035 42.857 5.11 3.06 0.00 3.18
697 698 2.206576 AGAAAGCTTGCTTCGGGATT 57.793 45.000 0.00 0.00 0.00 3.01
724 725 5.376625 TCATTCAACTAAAGCTGTCAGGTT 58.623 37.500 11.52 11.52 37.57 3.50
883 885 2.355108 CCCTTCTCCATTCTTTGCTCGA 60.355 50.000 0.00 0.00 0.00 4.04
899 901 0.726827 TCGAATGATTGCCGCTTGTC 59.273 50.000 0.00 0.00 0.00 3.18
911 913 3.005684 TGCCGCTTGTCTGAATTTCATTT 59.994 39.130 0.00 0.00 0.00 2.32
921 923 5.474876 GTCTGAATTTCATTTCTGTGGGTCT 59.525 40.000 0.00 0.00 0.00 3.85
987 989 1.529152 TTCTTGACTCCGCGGTGCTA 61.529 55.000 27.15 12.48 0.00 3.49
997 999 0.306840 CGCGGTGCTAGTTATCGAGA 59.693 55.000 0.00 0.00 0.00 4.04
1040 1042 4.358851 CAAAAAGTCAAAGATGGCGTCAA 58.641 39.130 9.78 0.00 35.88 3.18
1049 1051 4.946784 AAGATGGCGTCAACATTTACTC 57.053 40.909 9.78 0.00 0.00 2.59
1050 1052 2.930040 AGATGGCGTCAACATTTACTCG 59.070 45.455 9.78 0.00 0.00 4.18
1078 1080 4.279922 GCTCTCTTCTAATAGTGGTCCCTC 59.720 50.000 0.00 0.00 0.00 4.30
1188 1190 8.962884 AGATAAGGATTTTGCAAAACTTTTGT 57.037 26.923 26.05 16.96 0.00 2.83
1230 1232 4.658435 AGAAAACCTTACCATTTTTGGGCT 59.342 37.500 0.00 0.00 0.00 5.19
1237 1239 1.202675 ACCATTTTTGGGCTGCTGTTG 60.203 47.619 0.00 0.00 0.00 3.33
1253 1255 3.195396 GCTGTTGCCATTTCCATTTCCTA 59.805 43.478 0.00 0.00 0.00 2.94
1555 1557 0.966920 ACCGACTCTGTGTAACCCTG 59.033 55.000 0.00 0.00 34.36 4.45
1710 1714 7.064866 ACCCACATCATCAATATCAATCAAGT 58.935 34.615 0.00 0.00 0.00 3.16
1772 1776 3.327172 TGGGTAAAACATCGTGTCCCTTA 59.673 43.478 11.28 1.58 35.00 2.69
1836 1840 1.743995 CCGAGATCCGCCGGTTTTT 60.744 57.895 1.63 0.00 40.78 1.94
2004 2008 2.620251 CCAATTCGTCTGGCCATCTA 57.380 50.000 5.51 0.00 0.00 1.98
2076 2080 0.615331 ACTTCATGGCTGACATCCGT 59.385 50.000 0.00 0.00 37.84 4.69
2111 2115 0.035152 AATGGATTCGAGCCACAGCA 60.035 50.000 10.80 0.00 43.56 4.41
2156 2160 1.948145 GCATGATTTAGCTCTGCTGCT 59.052 47.619 0.00 4.99 46.11 4.24
2229 2233 2.202797 GCTGCGCAGATCGAGGAA 60.203 61.111 40.21 0.00 41.67 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 2.026262 GCCAGAGGTCAAATGAAGGGTA 60.026 50.000 0.00 0.0 0.00 3.69
184 185 0.909610 CAGGGTAGGCCAGAGGTCAA 60.910 60.000 5.01 0.0 36.17 3.18
195 196 6.894339 ACTTTTTACAATTGACAGGGTAGG 57.106 37.500 13.59 0.0 0.00 3.18
228 229 1.808945 CTTTTTGCTCCTGCGAGACAT 59.191 47.619 0.00 0.0 43.34 3.06
434 435 4.955450 ACCCATCATTGCAAATAACTGCTA 59.045 37.500 1.71 0.0 43.07 3.49
471 472 4.442052 CCATAATCGAGTCTCTCCTTGCAA 60.442 45.833 0.00 0.0 0.00 4.08
488 489 3.045601 AGCTCTTTATCGCGCCATAAT 57.954 42.857 8.31 0.0 0.00 1.28
511 512 3.996921 ACCTGACTCTGAGCATTGAAT 57.003 42.857 4.19 0.0 0.00 2.57
522 523 5.326069 TGCTCTTACTTTCTACCTGACTCT 58.674 41.667 0.00 0.0 0.00 3.24
525 526 5.394224 ACTGCTCTTACTTTCTACCTGAC 57.606 43.478 0.00 0.0 0.00 3.51
637 638 4.966168 TGGCCAACTAATGATAGGACTACA 59.034 41.667 0.61 0.0 33.15 2.74
664 665 9.678941 AAGCAAGCTTTCTACTTAAATTGTTAC 57.321 29.630 0.00 0.0 31.29 2.50
667 668 7.078228 CGAAGCAAGCTTTCTACTTAAATTGT 58.922 34.615 8.91 0.0 36.26 2.71
697 698 7.044181 CCTGACAGCTTTAGTTGAATGATCTA 58.956 38.462 0.00 0.0 0.00 1.98
724 725 1.440618 TGTTCCTCAAAGCCTACCCA 58.559 50.000 0.00 0.0 0.00 4.51
883 885 1.825090 TCAGACAAGCGGCAATCATT 58.175 45.000 1.45 0.0 0.00 2.57
899 901 5.391310 CGAGACCCACAGAAATGAAATTCAG 60.391 44.000 1.10 0.0 33.67 3.02
911 913 1.739667 CACACACGAGACCCACAGA 59.260 57.895 0.00 0.0 0.00 3.41
921 923 4.754618 ACAATCTTATTTGAGCACACACGA 59.245 37.500 0.00 0.0 0.00 4.35
987 989 2.671351 CGGCGCCATAATCTCGATAACT 60.671 50.000 28.98 0.0 0.00 2.24
1040 1042 6.868622 AGAAGAGAGCATAACGAGTAAATGT 58.131 36.000 0.00 0.0 0.00 2.71
1049 1051 6.740110 ACCACTATTAGAAGAGAGCATAACG 58.260 40.000 0.00 0.0 0.00 3.18
1050 1052 7.149307 GGACCACTATTAGAAGAGAGCATAAC 58.851 42.308 0.00 0.0 0.00 1.89
1115 1117 8.038351 GGCCATTACAAAAACAAGGTATAACAT 58.962 33.333 0.00 0.0 0.00 2.71
1175 1177 6.484977 AGAAAAAGGAACACAAAAGTTTTGCA 59.515 30.769 24.86 0.0 0.00 4.08
1237 1239 6.538945 TTAGGTTTAGGAAATGGAAATGGC 57.461 37.500 0.00 0.0 0.00 4.40
1555 1557 0.178970 TATAGACACCGGAGAGGGCC 60.179 60.000 9.46 0.0 46.96 5.80
1710 1714 3.365472 GGAGGTAAAACCCTACGTCCTA 58.635 50.000 12.88 0.0 46.43 2.94
2004 2008 2.483583 CGTAGCTTTCGATCTGCTCT 57.516 50.000 9.96 0.0 38.15 4.09
2076 2080 5.705397 ATCCATTGAAGATCAAGTCTCCA 57.295 39.130 0.00 0.0 40.05 3.86
2156 2160 2.930019 CCTCCAGGGCACTGTCCA 60.930 66.667 16.38 0.0 43.36 4.02


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

AutoCloner maintained by Alex Coulton.