Multiple sequence alignment - TraesCS4B01G092100

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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 TraesCS4B01G092100 chr4B 100.000 3260 0 0 1 3260 95101581 95098322 0 6021
1 TraesCS4B01G092100 chr4B 94.547 3264 172 5 1 3260 11453930 11450669 0 5036
2 TraesCS4B01G092100 chr2B 95.311 3263 148 4 1 3260 381517158 381513898 0 5173
3 TraesCS4B01G092100 chr2B 94.028 3282 161 10 1 3260 39764215 39760947 0 4942
4 TraesCS4B01G092100 chr1B 94.891 3171 157 4 92 3260 6922960 6919793 0 4953
5 TraesCS4B01G092100 chr1B 94.177 3263 164 16 1 3257 50796890 50800132 0 4950
6 TraesCS4B01G092100 chr1B 95.194 3100 144 4 1 3096 444123959 444120861 0 4894
7 TraesCS4B01G092100 chr1B 95.602 2342 100 2 1 2339 6953827 6951486 0 3751
8 TraesCS4B01G092100 chr5B 95.707 2958 111 2 319 3260 668091584 668088627 0 4745
9 TraesCS4B01G092100 chr3B 92.409 3267 231 12 1 3260 629711520 629708264 0 4643
10 TraesCS4B01G092100 chr3B 94.867 2338 113 4 7 2341 284827218 284824885 0 3646
11 TraesCS4B01G092100 chr3B 94.534 2049 107 3 1214 3260 284729043 284726998 0 3158


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 TraesCS4B01G092100 chr4B 95098322 95101581 3259 True 6021 6021 100.000 1 3260 1 chr4B.!!$R2 3259
1 TraesCS4B01G092100 chr4B 11450669 11453930 3261 True 5036 5036 94.547 1 3260 1 chr4B.!!$R1 3259
2 TraesCS4B01G092100 chr2B 381513898 381517158 3260 True 5173 5173 95.311 1 3260 1 chr2B.!!$R2 3259
3 TraesCS4B01G092100 chr2B 39760947 39764215 3268 True 4942 4942 94.028 1 3260 1 chr2B.!!$R1 3259
4 TraesCS4B01G092100 chr1B 6919793 6922960 3167 True 4953 4953 94.891 92 3260 1 chr1B.!!$R1 3168
5 TraesCS4B01G092100 chr1B 50796890 50800132 3242 False 4950 4950 94.177 1 3257 1 chr1B.!!$F1 3256
6 TraesCS4B01G092100 chr1B 444120861 444123959 3098 True 4894 4894 95.194 1 3096 1 chr1B.!!$R3 3095
7 TraesCS4B01G092100 chr1B 6951486 6953827 2341 True 3751 3751 95.602 1 2339 1 chr1B.!!$R2 2338
8 TraesCS4B01G092100 chr5B 668088627 668091584 2957 True 4745 4745 95.707 319 3260 1 chr5B.!!$R1 2941
9 TraesCS4B01G092100 chr3B 629708264 629711520 3256 True 4643 4643 92.409 1 3260 1 chr3B.!!$R3 3259
10 TraesCS4B01G092100 chr3B 284824885 284827218 2333 True 3646 3646 94.867 7 2341 1 chr3B.!!$R2 2334
11 TraesCS4B01G092100 chr3B 284726998 284729043 2045 True 3158 3158 94.534 1214 3260 1 chr3B.!!$R1 2046

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
763 773 0.105194 TCGGATGGGATAAGGCAGGA 60.105 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 2651 0.107897 AACCGCGCAGATCATACCAA 60.108 50.0 8.75 0.0 0.0 3.67 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
28 29 2.565834 CCCTTCTCGGAGGAAGTAACAA 59.434 50.000 4.96 0.00 40.56 2.83
144 146 2.610859 AGGACGCCAAGACCCCAT 60.611 61.111 0.00 0.00 35.19 4.00
674 683 4.561105 GAGATCTTCCGTCTGACAAGTTT 58.439 43.478 8.73 0.00 0.00 2.66
704 713 1.507140 AGCGGATTTAGTGGGATCCA 58.493 50.000 15.23 0.00 41.55 3.41
763 773 0.105194 TCGGATGGGATAAGGCAGGA 60.105 55.000 0.00 0.00 0.00 3.86
780 790 0.108804 GGAACGCCTCGATTCTCACA 60.109 55.000 0.00 0.00 0.00 3.58
1046 1056 3.361977 GCGGGCAAAGAAGGCGAA 61.362 61.111 0.00 0.00 34.40 4.70
1179 1189 2.122167 GGATCTCGACGACCTGGCT 61.122 63.158 0.00 0.00 0.00 4.75
1269 1279 0.106708 GTGAGTGTGTCCTCTTGGCA 59.893 55.000 0.00 0.00 32.50 4.92
1582 1592 1.069935 GCTATGACCCTTCCCGAGC 59.930 63.158 0.00 0.00 0.00 5.03
1744 1769 3.326747 GAGCGTGTAGTCCAGTTGATTT 58.673 45.455 0.00 0.00 0.00 2.17
1993 2019 0.821517 TGATGCGGACAAGGTACGAT 59.178 50.000 4.97 0.00 43.34 3.73
2002 2028 4.201783 CGGACAAGGTACGATCATTTTTCC 60.202 45.833 0.00 0.00 43.34 3.13
2046 2072 6.330278 TGTTTCATCGTAGATCAGTCGATTT 58.670 36.000 13.94 0.00 45.12 2.17
2103 2129 2.906354 GAGTTGTACTCGATGCCCAAT 58.094 47.619 0.00 0.00 35.28 3.16
2205 2243 2.237893 TGATGAAGATGCAGGCTCTGAA 59.762 45.455 6.40 0.00 32.44 3.02
2227 2265 1.725182 AGGAGGAAGAGGAGGAGGAAA 59.275 52.381 0.00 0.00 0.00 3.13
2323 2361 3.695606 GAGTCGTGCCTGCTGGGA 61.696 66.667 12.06 5.61 37.23 4.37
2341 2379 0.942884 GAAGTCGACGAAACGCCCTT 60.943 55.000 10.46 0.00 0.00 3.95
2520 2578 4.035208 GCTGACCGACCGATATTTGAAATT 59.965 41.667 0.00 0.00 0.00 1.82
2593 2651 4.202243 GGAAGATGCTGCTACTTCTCATCT 60.202 45.833 25.27 11.96 43.85 2.90
2996 3054 2.192861 CGAACCACCAGCCAAGCAA 61.193 57.895 0.00 0.00 0.00 3.91
3034 3092 2.097825 GCTCTCCAAAGCAATGTCCAT 58.902 47.619 0.00 0.00 42.05 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.040646 TACTTCCTCCGAGAAGGGCA 59.959 55.000 12.46 0.00 46.24 5.36
28 29 2.439883 GGCTCCGAGACGTAGGGT 60.440 66.667 0.00 0.00 0.00 4.34
144 146 2.283604 TCTGCTACGTGGGCTGGA 60.284 61.111 17.04 11.98 0.00 3.86
248 251 5.598830 TCAGGATCTACTCTGTATCCAAACC 59.401 44.000 0.00 0.00 41.44 3.27
620 628 1.545841 GCTCGGAAATCCCCAAGTTT 58.454 50.000 0.00 0.00 0.00 2.66
674 683 0.988832 AAATCCGCTAACCACAGGGA 59.011 50.000 0.00 0.00 38.05 4.20
704 713 4.990426 CGCTTCACATTCTTCCCAAAATTT 59.010 37.500 0.00 0.00 0.00 1.82
717 727 1.673033 CGGTCTTCTCCGCTTCACATT 60.673 52.381 0.00 0.00 43.96 2.71
718 728 0.108615 CGGTCTTCTCCGCTTCACAT 60.109 55.000 0.00 0.00 43.96 3.21
763 773 0.389948 GGTGTGAGAATCGAGGCGTT 60.390 55.000 0.00 0.00 38.61 4.84
780 790 2.992607 TACGTGGCGAAAAAGGCGGT 62.993 55.000 0.00 0.00 39.82 5.68
1179 1189 1.741401 CGCAATCAGGCCTTCGTCA 60.741 57.895 0.00 0.00 0.00 4.35
1269 1279 4.282496 AGAACCCTCGATCTACATGAGTT 58.718 43.478 0.00 0.00 0.00 3.01
1582 1592 2.177594 GACTGCCACCCTCTGACTGG 62.178 65.000 0.00 0.00 0.00 4.00
1744 1769 2.038814 ATGCCAGTCACACCGTCACA 62.039 55.000 0.00 0.00 0.00 3.58
1993 2019 3.501349 TGGAACAATCGGGGAAAAATGA 58.499 40.909 0.00 0.00 31.92 2.57
2046 2072 7.653713 TGAAAAACAACAAGCAAGACAAAAGTA 59.346 29.630 0.00 0.00 0.00 2.24
2205 2243 0.933700 CCTCCTCCTCTTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
2227 2265 1.003233 GCGCAACTTCCTCCTCCTT 60.003 57.895 0.30 0.00 0.00 3.36
2323 2361 1.068585 AAGGGCGTTTCGTCGACTT 59.931 52.632 14.70 0.00 39.03 3.01
2341 2379 2.280524 CGCCGGTGAAGTTGTCCA 60.281 61.111 10.20 0.00 0.00 4.02
2365 2403 0.668535 GGTTGCTTCAACGCCTTCTT 59.331 50.000 3.93 0.00 44.36 2.52
2375 2413 4.697756 CCGCTCGGGGTTGCTTCA 62.698 66.667 0.00 0.00 0.00 3.02
2421 2459 3.459598 TCGGAATTTCCATCCTCATCCTT 59.540 43.478 15.58 0.00 35.91 3.36
2423 2461 3.142174 GTCGGAATTTCCATCCTCATCC 58.858 50.000 15.58 0.00 35.91 3.51
2507 2563 5.615495 CAGCACTGCAATTTCAAATATCG 57.385 39.130 3.30 0.00 0.00 2.92
2593 2651 0.107897 AACCGCGCAGATCATACCAA 60.108 50.000 8.75 0.00 0.00 3.67
2996 3054 0.526524 GCTGAGCTCGCGTCATAAGT 60.527 55.000 9.64 0.00 0.00 2.24
3022 3080 7.283625 TGTTTAACTAACATGGACATTGCTT 57.716 32.000 0.00 0.00 41.73 3.91
3088 3147 3.521126 AGCAGTCCACCATAGAATTGACT 59.479 43.478 0.00 0.00 33.59 3.41


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

AutoCloner maintained by Alex Coulton.