Multiple sequence alignment - TraesCS2B01G345900

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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 TraesCS2B01G345900 chr2B 100.000 2549 0 0 1 2549 492636099 492638647 0 4708
1 TraesCS2B01G345900 chr2B 95.641 1996 76 7 555 2549 458657413 458659398 0 3193
2 TraesCS2B01G345900 chr2B 95.576 1989 76 9 564 2549 692955894 692957873 0 3175
3 TraesCS2B01G345900 chr2B 95.760 566 24 0 1 566 461547580 461548145 0 913
4 TraesCS2B01G345900 chr1B 96.280 1989 69 5 563 2549 581717565 581715580 0 3258
5 TraesCS2B01G345900 chr1B 95.617 1985 75 9 567 2549 520844119 520842145 0 3173
6 TraesCS2B01G345900 chr4A 95.980 1990 69 8 562 2549 705529256 705527276 0 3221
7 TraesCS2B01G345900 chr4A 95.936 566 23 0 1 566 699669284 699669849 0 918
8 TraesCS2B01G345900 chr7B 95.720 1986 77 8 567 2549 677862790 677860810 0 3190
9 TraesCS2B01G345900 chr7B 95.622 1987 77 8 566 2549 720989191 720987212 0 3179
10 TraesCS2B01G345900 chr5B 95.571 1987 76 11 567 2549 497276165 497278143 0 3171
11 TraesCS2B01G345900 chr5B 95.243 1997 82 11 557 2549 46530261 46528274 0 3149
12 TraesCS2B01G345900 chr5B 96.290 566 20 1 1 566 605037196 605036632 0 928
13 TraesCS2B01G345900 chr5B 96.113 566 22 0 1 566 601002394 601001829 0 924
14 TraesCS2B01G345900 chr5B 95.936 566 23 0 1 566 327830884 327830319 0 918
15 TraesCS2B01G345900 chr5B 95.760 566 24 0 1 566 339507270 339507835 0 913
16 TraesCS2B01G345900 chr4B 95.936 566 23 0 1 566 39370031 39369466 0 918
17 TraesCS2B01G345900 chr4B 95.760 566 24 0 1 566 615119562 615120127 0 913
18 TraesCS2B01G345900 chr6B 95.936 566 22 1 1 566 450014853 450014289 0 917


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 TraesCS2B01G345900 chr2B 492636099 492638647 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F3 2548
1 TraesCS2B01G345900 chr2B 458657413 458659398 1985 False 3193 3193 95.641 555 2549 1 chr2B.!!$F1 1994
2 TraesCS2B01G345900 chr2B 692955894 692957873 1979 False 3175 3175 95.576 564 2549 1 chr2B.!!$F4 1985
3 TraesCS2B01G345900 chr2B 461547580 461548145 565 False 913 913 95.760 1 566 1 chr2B.!!$F2 565
4 TraesCS2B01G345900 chr1B 581715580 581717565 1985 True 3258 3258 96.280 563 2549 1 chr1B.!!$R2 1986
5 TraesCS2B01G345900 chr1B 520842145 520844119 1974 True 3173 3173 95.617 567 2549 1 chr1B.!!$R1 1982
6 TraesCS2B01G345900 chr4A 705527276 705529256 1980 True 3221 3221 95.980 562 2549 1 chr4A.!!$R1 1987
7 TraesCS2B01G345900 chr4A 699669284 699669849 565 False 918 918 95.936 1 566 1 chr4A.!!$F1 565
8 TraesCS2B01G345900 chr7B 677860810 677862790 1980 True 3190 3190 95.720 567 2549 1 chr7B.!!$R1 1982
9 TraesCS2B01G345900 chr7B 720987212 720989191 1979 True 3179 3179 95.622 566 2549 1 chr7B.!!$R2 1983
10 TraesCS2B01G345900 chr5B 497276165 497278143 1978 False 3171 3171 95.571 567 2549 1 chr5B.!!$F2 1982
11 TraesCS2B01G345900 chr5B 46528274 46530261 1987 True 3149 3149 95.243 557 2549 1 chr5B.!!$R1 1992
12 TraesCS2B01G345900 chr5B 605036632 605037196 564 True 928 928 96.290 1 566 1 chr5B.!!$R4 565
13 TraesCS2B01G345900 chr5B 601001829 601002394 565 True 924 924 96.113 1 566 1 chr5B.!!$R3 565
14 TraesCS2B01G345900 chr5B 327830319 327830884 565 True 918 918 95.936 1 566 1 chr5B.!!$R2 565
15 TraesCS2B01G345900 chr5B 339507270 339507835 565 False 913 913 95.760 1 566 1 chr5B.!!$F1 565
16 TraesCS2B01G345900 chr4B 39369466 39370031 565 True 918 918 95.936 1 566 1 chr4B.!!$R1 565
17 TraesCS2B01G345900 chr4B 615119562 615120127 565 False 913 913 95.760 1 566 1 chr4B.!!$F1 565
18 TraesCS2B01G345900 chr6B 450014289 450014853 564 True 917 917 95.936 1 566 1 chr6B.!!$R1 565

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
92 93 0.976073 GATCGTCCTCCACCCAAGGA 60.976 60.0 0.0 0.0 40.67 3.36 F
1137 1141 0.246635 CGAGGAACCACAATCGTCCT 59.753 55.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 1194 0.531974 GCTCAAAGACCACGACCACA 60.532 55.000 0.0 0.0 0.0 4.17 R
2179 2190 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.0 0.0 0.0 4.00 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
56 57 8.410912 GGTTCCTATTTTGAAACACAACTTACT 58.589 33.333 0.00 0.00 38.29 2.24
92 93 0.976073 GATCGTCCTCCACCCAAGGA 60.976 60.000 0.00 0.00 40.67 3.36
256 258 4.040461 ACCGTGCTGCTATTGGATATACTT 59.960 41.667 0.00 0.00 0.00 2.24
291 293 2.706190 GGGCATTAGTCCCACTCTATGT 59.294 50.000 0.00 0.00 43.37 2.29
335 337 3.356529 AGATGCCAAACCAGTTAGAGG 57.643 47.619 0.00 0.00 0.00 3.69
341 343 2.353803 CCAAACCAGTTAGAGGTCCTCG 60.354 54.545 13.41 0.53 38.76 4.63
425 427 5.072600 AGGCAGGTATAATTTATCCCGTTGA 59.927 40.000 0.00 0.00 0.00 3.18
719 721 1.002773 ACGTTTTGACTCGGCCCTTAT 59.997 47.619 0.00 0.00 0.00 1.73
772 774 1.841663 ATTCAGACCGTTGCACGTGC 61.842 55.000 33.11 33.11 40.58 5.34
935 939 1.920325 AAGCTAGCTGTGGAGGGCA 60.920 57.895 20.16 0.00 0.00 5.36
936 940 1.277580 AAGCTAGCTGTGGAGGGCAT 61.278 55.000 20.16 0.00 0.00 4.40
1035 1039 4.201679 CGCGCCACCTCACGGATA 62.202 66.667 0.00 0.00 0.00 2.59
1038 1042 1.441729 CGCCACCTCACGGATACAT 59.558 57.895 0.00 0.00 0.00 2.29
1137 1141 0.246635 CGAGGAACCACAATCGTCCT 59.753 55.000 0.00 0.00 0.00 3.85
1143 1147 4.225267 AGGAACCACAATCGTCCTTTCTAT 59.775 41.667 0.00 0.00 0.00 1.98
1262 1266 1.673923 GGCATGCTTCTTTCTTTGGGC 60.674 52.381 18.92 0.00 0.00 5.36
1347 1351 4.974721 CCCCAAACCGCAGTGGCT 62.975 66.667 0.00 0.00 43.94 4.75
1408 1412 1.204467 GCACTGACAGAGAGCTAGCTT 59.796 52.381 20.42 8.93 35.53 3.74
1490 1494 4.103943 ACCCATTTGCAAATACTTTTGGGT 59.896 37.500 32.30 32.30 42.09 4.51
1509 1513 9.771140 TTTTGGGTATTTGTAGGTATGGTAATT 57.229 29.630 0.00 0.00 0.00 1.40
1527 1531 6.490381 TGGTAATTGCACTGGTTGTAATGTTA 59.510 34.615 0.00 0.00 39.41 2.41
2082 2089 3.256704 AGTTTGACATGGGTAGGGAAGA 58.743 45.455 0.00 0.00 0.00 2.87
2086 2093 4.503714 TGACATGGGTAGGGAAGAAATC 57.496 45.455 0.00 0.00 0.00 2.17
2179 2190 2.342279 CTCGAACCCAAGACCGCA 59.658 61.111 0.00 0.00 0.00 5.69
2291 2302 7.542130 AGTGAGACTGTGAAATTTGTCAAAAAC 59.458 33.333 1.31 0.28 32.41 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.696864 TCATCCTTGGGTGGAGGAC 58.303 57.895 0.00 0.0 45.59 3.85
92 93 3.627395 TTAGCTCAAACACGGGATCAT 57.373 42.857 0.00 0.0 0.00 2.45
256 258 6.266131 ACTAATGCCCTTAAGATCATCCAA 57.734 37.500 3.36 0.0 0.00 3.53
291 293 8.744652 TCTTTCTCCACTTTAATTTTGTGTTGA 58.255 29.630 0.00 0.0 0.00 3.18
341 343 5.585390 TCATCTTAGGGTTTAATCGTCGTC 58.415 41.667 0.00 0.0 0.00 4.20
783 785 1.520342 CAACGGCTCTCTGCTAGGC 60.520 63.158 0.00 0.0 42.39 3.93
786 788 1.250840 TGCTCAACGGCTCTCTGCTA 61.251 55.000 0.00 0.0 42.39 3.49
888 892 1.376037 TCGTGCTCTCGCTCTCTCA 60.376 57.895 0.00 0.0 36.97 3.27
916 920 1.451028 GCCCTCCACAGCTAGCTTG 60.451 63.158 16.46 16.0 0.00 4.01
935 939 2.911143 CTAGCTTCCCACCGCCAT 59.089 61.111 0.00 0.0 0.00 4.40
936 940 4.096003 GCTAGCTTCCCACCGCCA 62.096 66.667 7.70 0.0 0.00 5.69
1085 1089 3.417275 CTCCGATCAACGCTCGCCT 62.417 63.158 0.00 0.0 41.07 5.52
1137 1141 2.741759 TCTCGCTGCACACATAGAAA 57.258 45.000 0.00 0.0 0.00 2.52
1143 1147 1.672030 CCCATTCTCGCTGCACACA 60.672 57.895 0.00 0.0 0.00 3.72
1190 1194 0.531974 GCTCAAAGACCACGACCACA 60.532 55.000 0.00 0.0 0.00 4.17
1198 1202 1.879380 CAACCGATTGCTCAAAGACCA 59.121 47.619 0.00 0.0 0.00 4.02
1262 1266 1.817099 GTCTTGGCCAGAGCATCGG 60.817 63.158 5.11 0.0 42.67 4.18
1355 1359 1.484240 CCATCTCTTCTTCCGGAGCTT 59.516 52.381 3.34 0.0 0.00 3.74
1408 1412 6.533730 TCTTCTTCAACATCCTAAGCTCAAA 58.466 36.000 0.00 0.0 0.00 2.69
1490 1494 7.500892 CCAGTGCAATTACCATACCTACAAATA 59.499 37.037 0.00 0.0 0.00 1.40
1509 1513 7.268586 ACATTTTTAACATTACAACCAGTGCA 58.731 30.769 0.00 0.0 0.00 4.57
1601 1605 8.419076 ACATTTAAACAACTTTGACCAACATC 57.581 30.769 0.00 0.0 0.00 3.06
1635 1640 7.730364 TTAAATGTTGGTCACTTCTTCTCTC 57.270 36.000 0.00 0.0 0.00 3.20
1833 1839 5.931146 GCACATTTTCCATGACATTTTGGTA 59.069 36.000 0.00 0.0 34.48 3.25
1950 1957 2.791383 TGTGCATTTTTCACCCTTCG 57.209 45.000 0.00 0.0 33.71 3.79
2179 2190 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.00 0.0 0.00 4.00
2291 2302 4.488126 AACATTCACGGTCTCACATTTG 57.512 40.909 0.00 0.0 0.00 2.32


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

AutoCloner maintained by Alex Coulton.