Multiple sequence alignment - TraesCS6B01G207900

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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 TraesCS6B01G207900 chr6B 100.000 2314 0 0 1 2314 264960615 264962928 0 4274
1 TraesCS6B01G207900 chr6B 97.149 2315 64 2 1 2314 307014538 307012225 0 3908
2 TraesCS6B01G207900 chrUn 97.710 2314 53 0 1 2314 170995032 170992719 0 3980
3 TraesCS6B01G207900 chr7B 97.538 2315 56 1 1 2314 644446412 644448726 0 3958
4 TraesCS6B01G207900 chr7B 97.495 2315 57 1 1 2314 743095875 743098189 0 3952
5 TraesCS6B01G207900 chr7B 96.371 2315 81 3 1 2314 54063139 54065451 0 3807
6 TraesCS6B01G207900 chr4B 97.063 2315 63 5 1 2314 623334089 623331779 0 3893
7 TraesCS6B01G207900 chr1B 96.889 2314 72 0 1 2314 672527983 672525670 0 3875
8 TraesCS6B01G207900 chr1A 96.544 2315 78 2 1 2314 94677203 94679516 0 3831
9 TraesCS6B01G207900 chr7A 96.379 2320 77 4 1 2314 211377603 211379921 0 3812


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 TraesCS6B01G207900 chr6B 264960615 264962928 2313 False 4274 4274 100.000 1 2314 1 chr6B.!!$F1 2313
1 TraesCS6B01G207900 chr6B 307012225 307014538 2313 True 3908 3908 97.149 1 2314 1 chr6B.!!$R1 2313
2 TraesCS6B01G207900 chrUn 170992719 170995032 2313 True 3980 3980 97.710 1 2314 1 chrUn.!!$R1 2313
3 TraesCS6B01G207900 chr7B 644446412 644448726 2314 False 3958 3958 97.538 1 2314 1 chr7B.!!$F2 2313
4 TraesCS6B01G207900 chr7B 743095875 743098189 2314 False 3952 3952 97.495 1 2314 1 chr7B.!!$F3 2313
5 TraesCS6B01G207900 chr7B 54063139 54065451 2312 False 3807 3807 96.371 1 2314 1 chr7B.!!$F1 2313
6 TraesCS6B01G207900 chr4B 623331779 623334089 2310 True 3893 3893 97.063 1 2314 1 chr4B.!!$R1 2313
7 TraesCS6B01G207900 chr1B 672525670 672527983 2313 True 3875 3875 96.889 1 2314 1 chr1B.!!$R1 2313
8 TraesCS6B01G207900 chr1A 94677203 94679516 2313 False 3831 3831 96.544 1 2314 1 chr1A.!!$F1 2313
9 TraesCS6B01G207900 chr7A 211377603 211379921 2318 False 3812 3812 96.379 1 2314 1 chr7A.!!$F1 2313

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
235 236 0.194587 CCTACTCCCTCCCATCCCAT 59.805 60.0 0.00 0.0 0.00 4.00 F
1065 1070 0.109919 CCTGTCACGTTCGTGATCGA 60.110 55.0 26.32 14.8 45.28 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 1215 1.236616 CGGATGCTGCAGTTGTTCCA 61.237 55.000 16.64 3.54 0.0 3.53 R
2020 2029 2.349886 GAGCGAGATTGATTGAAAGCGT 59.650 45.455 0.00 0.00 0.0 5.07 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
45 46 3.629398 CCATTCATTTCTGGGAGCACTAC 59.371 47.826 0.00 0.00 0.00 2.73
46 47 4.521146 CATTCATTTCTGGGAGCACTACT 58.479 43.478 0.00 0.00 0.00 2.57
90 91 9.535878 AAAAGTCTACTGTTTGAAAGAGAGTAG 57.464 33.333 9.20 9.91 38.21 2.57
127 128 4.706476 CCCAAGAGCTAATCCAAAATCACA 59.294 41.667 0.00 0.00 0.00 3.58
173 174 5.531122 TTATAGCAGCTTTATCCGTCTGT 57.469 39.130 0.00 0.00 0.00 3.41
188 189 3.366679 CCGTCTGTAGTCGTGTAAACCAT 60.367 47.826 0.00 0.00 0.00 3.55
235 236 0.194587 CCTACTCCCTCCCATCCCAT 59.805 60.000 0.00 0.00 0.00 4.00
328 329 1.557099 AATCGAGGGCTATGCGGATA 58.443 50.000 0.00 0.00 0.00 2.59
455 456 1.078918 CGAGTCAGGCCAATCTGCA 60.079 57.895 5.01 0.00 34.91 4.41
460 461 1.820519 GTCAGGCCAATCTGCAAATCA 59.179 47.619 5.01 0.00 34.91 2.57
641 642 3.788227 TCCTTTGCCACTCAAGTGTAT 57.212 42.857 9.19 0.00 44.21 2.29
719 720 1.300963 CTGCCTGGCACTGTATGGT 59.699 57.895 19.30 0.00 33.79 3.55
730 731 5.605069 TGGCACTGTATGGTTATAGGTATGT 59.395 40.000 0.00 0.00 0.00 2.29
772 773 8.053355 CCCTTGGATTTTAGGTGATTAACTACT 58.947 37.037 0.00 0.00 0.00 2.57
861 866 3.273834 CGCGTGGTTCACCGGTTT 61.274 61.111 2.97 0.00 39.43 3.27
901 906 9.961266 CTTAGATAGAGTTATTCAGTCGATACG 57.039 37.037 0.00 0.00 0.00 3.06
1037 1042 2.001803 CCTTGCCTTCCCAGGATCA 58.998 57.895 0.00 0.00 44.19 2.92
1065 1070 0.109919 CCTGTCACGTTCGTGATCGA 60.110 55.000 26.32 14.80 45.28 3.59
1210 1215 1.372087 GGTCGAGTCCGTATCACCGT 61.372 60.000 0.00 0.00 37.05 4.83
1225 1230 2.186160 CCGTGGAACAACTGCAGCA 61.186 57.895 15.27 0.00 44.16 4.41
1449 1455 4.124851 TCCTTCAGATCCTAGAAAACGC 57.875 45.455 0.00 0.00 0.00 4.84
1458 1464 2.549329 TCCTAGAAAACGCCCGAAAAAC 59.451 45.455 0.00 0.00 0.00 2.43
1562 1571 1.377725 AAGCGGCCTGTCATTGAGG 60.378 57.895 0.00 0.00 0.00 3.86
1570 1579 3.731652 CCTGTCATTGAGGCAAAAACA 57.268 42.857 0.00 0.00 0.00 2.83
1718 1727 0.259938 GATGGTTGATCCCCTTGCCT 59.740 55.000 0.00 0.00 34.77 4.75
1720 1729 0.918983 TGGTTGATCCCCTTGCCTAG 59.081 55.000 0.00 0.00 34.77 3.02
1754 1763 1.075525 CCCGGTGGGTCATCCTCTA 60.076 63.158 0.00 0.00 38.25 2.43
1821 1830 3.972638 AGCAATGGACTGAGGTATGAGAT 59.027 43.478 0.00 0.00 0.00 2.75
1984 1993 8.166422 ACGAAATAACTTGTGAAGAGGATTTT 57.834 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 7.492344 AGACTTTTCAACCATTTTTGCTTGTAG 59.508 33.333 0.00 0.00 0.00 2.74
46 47 7.327214 AGACTTTTCAACCATTTTTGCTTGTA 58.673 30.769 0.00 0.00 0.00 2.41
90 91 4.058124 GCTCTTGGGATTTTTGGTTGTTC 58.942 43.478 0.00 0.00 0.00 3.18
127 128 5.207110 AGCTATGCTTGTCAATCGAGTAT 57.793 39.130 0.00 0.00 33.89 2.12
169 170 7.604549 TCATTTATGGTTTACACGACTACAGA 58.395 34.615 0.00 0.00 0.00 3.41
455 456 0.329596 AAGGGGAGCTCGCTTGATTT 59.670 50.000 27.60 13.03 45.32 2.17
503 504 2.029290 GGTTCGGAGAGCACTAAAGACA 60.029 50.000 0.00 0.00 40.41 3.41
719 720 3.201045 TGGCCTGCACAACATACCTATAA 59.799 43.478 3.32 0.00 0.00 0.98
772 773 1.202758 TCCAGCCTTTTCTTCGCTTCA 60.203 47.619 0.00 0.00 0.00 3.02
861 866 0.250858 TCTAAGGGTGACGTCGGTGA 60.251 55.000 11.62 0.00 0.00 4.02
901 906 1.017387 CCCACTTTAAGCGCATCTCC 58.983 55.000 11.47 0.00 0.00 3.71
1037 1042 1.335132 AACGTGACAGGTGTGGGAGT 61.335 55.000 0.75 0.00 0.00 3.85
1065 1070 2.803956 TCGATACACAGTTGAGGAGGT 58.196 47.619 0.00 0.00 0.00 3.85
1120 1125 4.880696 GGACATACTGGACGTAACTACTCT 59.119 45.833 0.00 0.00 0.00 3.24
1210 1215 1.236616 CGGATGCTGCAGTTGTTCCA 61.237 55.000 16.64 3.54 0.00 3.53
1225 1230 5.364778 CGAGTAGATAGATCAGATCCGGAT 58.635 45.833 19.21 19.21 0.00 4.18
1402 1408 1.448985 ATAATGACCACCACGTGTGC 58.551 50.000 15.65 2.43 44.01 4.57
1449 1455 2.392974 CGTAGCCGGGTTTTTCGGG 61.393 63.158 13.43 0.00 46.86 5.14
1562 1571 8.110002 GTGCTTATATGCTTAACATGTTTTTGC 58.890 33.333 17.78 17.59 40.06 3.68
1570 1579 7.495934 AGTCGAAAGTGCTTATATGCTTAACAT 59.504 33.333 11.48 0.00 43.18 2.71
1718 1727 2.118403 GGGGGAGGATGGAATGACTA 57.882 55.000 0.00 0.00 0.00 2.59
1821 1830 5.105064 CGACCCCTTCTCTTTACCTTTATCA 60.105 44.000 0.00 0.00 0.00 2.15
1984 1993 7.823665 TGCGTACAAGATTTTTAGACTCTAGA 58.176 34.615 0.00 0.00 0.00 2.43
2020 2029 2.349886 GAGCGAGATTGATTGAAAGCGT 59.650 45.455 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.