Multiple sequence alignment - TraesCS7B01G051700

Loading Multiple Alignment...

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 TraesCS7B01G051700 chr7B 100.000 2314 0 0 1 2314 54063138 54065451 0 4274
1 TraesCS7B01G051700 chr7B 97.971 2316 45 2 1 2314 743095874 743098189 0 4015
2 TraesCS7B01G051700 chr7B 97.884 2316 47 2 1 2314 644446411 644448726 0 4004
3 TraesCS7B01G051700 chrUn 97.971 2316 44 3 1 2314 170995033 170992719 0 4013
4 TraesCS7B01G051700 chr6B 97.453 2316 56 3 1 2314 307014539 307012225 0 3947
5 TraesCS7B01G051700 chr1B 97.150 2316 63 3 1 2314 672527984 672525670 0 3908
6 TraesCS7B01G051700 chr7A 96.941 2321 63 5 1 2314 211377602 211379921 0 3886
7 TraesCS7B01G051700 chr1A 96.934 2316 68 3 1 2314 94677202 94679516 0 3880
8 TraesCS7B01G051700 chr4B 96.848 2316 67 6 1 2314 623334090 623331779 0 3868
9 TraesCS7B01G051700 chr2B 96.544 2315 67 5 1 2314 391131375 391129073 0 3819


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 TraesCS7B01G051700 chr7B 54063138 54065451 2313 False 4274 4274 100.000 1 2314 1 chr7B.!!$F1 2313
1 TraesCS7B01G051700 chr7B 743095874 743098189 2315 False 4015 4015 97.971 1 2314 1 chr7B.!!$F3 2313
2 TraesCS7B01G051700 chr7B 644446411 644448726 2315 False 4004 4004 97.884 1 2314 1 chr7B.!!$F2 2313
3 TraesCS7B01G051700 chrUn 170992719 170995033 2314 True 4013 4013 97.971 1 2314 1 chrUn.!!$R1 2313
4 TraesCS7B01G051700 chr6B 307012225 307014539 2314 True 3947 3947 97.453 1 2314 1 chr6B.!!$R1 2313
5 TraesCS7B01G051700 chr1B 672525670 672527984 2314 True 3908 3908 97.150 1 2314 1 chr1B.!!$R1 2313
6 TraesCS7B01G051700 chr7A 211377602 211379921 2319 False 3886 3886 96.941 1 2314 1 chr7A.!!$F1 2313
7 TraesCS7B01G051700 chr1A 94677202 94679516 2314 False 3880 3880 96.934 1 2314 1 chr1A.!!$F1 2313
8 TraesCS7B01G051700 chr4B 623331779 623334090 2311 True 3868 3868 96.848 1 2314 1 chr4B.!!$R1 2313
9 TraesCS7B01G051700 chr2B 391129073 391131375 2302 True 3819 3819 96.544 1 2314 1 chr2B.!!$R1 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
53 54 0.322975 CTGGGAGCACTAGCACAAGT 59.677 55.0 0.0 0.0 45.49 3.16 F
942 949 0.673644 GTGTGCTGTCCCTATTGCGT 60.674 55.0 0.0 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1208 1.651987 CAGTTGTTCCGCGGTGATAT 58.348 50.000 27.15 5.31 0.00 1.63 R
2001 2012 2.097466 GCTATGCCAACTTGCGTACAAT 59.903 45.455 0.00 0.00 34.61 2.71 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
53 54 0.322975 CTGGGAGCACTAGCACAAGT 59.677 55.000 0.00 0.00 45.49 3.16
110 111 7.045416 AGAGTAAAACAACCAAAAATCCCAAC 58.955 34.615 0.00 0.00 0.00 3.77
234 235 0.828343 GACCTACTCCCTCCCATCCG 60.828 65.000 0.00 0.00 0.00 4.18
270 271 6.380079 AGAAAGTTATCTCCAGTCACCAAT 57.620 37.500 0.00 0.00 0.00 3.16
412 414 3.031736 ACATCACTACGGTCAGGCTATT 58.968 45.455 0.00 0.00 0.00 1.73
866 873 2.376165 TGGTTCACCGGTTCCACCA 61.376 57.895 20.71 20.71 38.47 4.17
940 947 1.032114 GGGTGTGCTGTCCCTATTGC 61.032 60.000 3.96 0.00 40.48 3.56
942 949 0.673644 GTGTGCTGTCCCTATTGCGT 60.674 55.000 0.00 0.00 0.00 5.24
982 989 2.582436 CACCGTCGGGGCATAAGT 59.418 61.111 17.28 0.00 40.62 2.24
1047 1054 2.659063 CCAGGATCGCTCCCACACA 61.659 63.158 0.62 0.00 43.21 3.72
1163 1170 1.686325 CCCCTCGATTCCCGACATGT 61.686 60.000 0.00 0.00 43.23 3.21
1201 1208 2.975265 TAGGAGCGGGTCGAGTCCA 61.975 63.158 0.53 0.00 35.08 4.02
1432 1440 4.163458 TGGTGGTCATTATAGTGGTTCCTC 59.837 45.833 0.00 0.00 0.00 3.71
1453 1461 2.481449 CCAGATCCTAGAAAACGTCCGG 60.481 54.545 0.00 0.00 0.00 5.14
1484 1492 3.367087 GCTACAGAACTACCGAGCAAAGA 60.367 47.826 0.00 0.00 0.00 2.52
1594 1604 6.370442 ACGTGTTAAGCATATAAGCACTTTCA 59.630 34.615 2.37 0.00 36.85 2.69
1766 1777 3.695060 GGTCGTCCTCTTATTCACTCTCA 59.305 47.826 0.00 0.00 0.00 3.27
1830 1841 5.299782 GGACTGAGGTATGAGACGATAAAGT 59.700 44.000 0.00 0.00 0.00 2.66
1844 1855 6.212993 AGACGATAAAGTTAAAGAGAAGGGGT 59.787 38.462 0.00 0.00 0.00 4.95
1890 1901 6.990939 TCTTTCCTATCTACGATCTTTCTCGA 59.009 38.462 0.00 0.00 41.12 4.04
2229 2241 6.099413 TCCTAGCAGTCATTGAGATTGAATCT 59.901 38.462 7.53 7.53 43.70 2.40
2300 2312 8.859090 TCAGTTCAACTAAATGGTCAAAATCAT 58.141 29.630 0.00 0.00 33.95 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 5.235186 CGAGTAGGTGATTTTGGATTAGCTG 59.765 44.000 0.00 0.00 0.00 4.24
313 315 0.764369 TGAGGATCCGCATAGCCCTT 60.764 55.000 14.91 0.00 0.00 3.95
412 414 6.757897 AATTCACTTTTGACTCTGTGTTCA 57.242 33.333 0.00 0.00 0.00 3.18
706 708 6.143915 CCATACCTATACCCATATAGTGCCT 58.856 44.000 1.72 0.00 39.06 4.75
713 715 3.134081 GCACGCCATACCTATACCCATAT 59.866 47.826 0.00 0.00 0.00 1.78
866 873 7.341256 TGAATAACTCTATCTAAGGGTGACGTT 59.659 37.037 0.00 0.00 38.26 3.99
982 989 1.421268 CATATGGGTAGCAAGAGGGCA 59.579 52.381 0.00 0.00 35.83 5.36
1201 1208 1.651987 CAGTTGTTCCGCGGTGATAT 58.348 50.000 27.15 5.31 0.00 1.63
1432 1440 2.481449 CCGGACGTTTTCTAGGATCTGG 60.481 54.545 0.00 0.00 0.00 3.86
1453 1461 3.434641 GGTAGTTCTGTAGCCGGTTTTTC 59.565 47.826 1.90 0.00 0.00 2.29
1467 1475 3.746045 TTGTCTTTGCTCGGTAGTTCT 57.254 42.857 0.00 0.00 0.00 3.01
1510 1518 9.751542 TCTGATTTATTTTAAGAGACTCGATCC 57.248 33.333 0.00 0.00 0.00 3.36
1528 1537 5.335897 GGCTGCTTGAACATTGTCTGATTTA 60.336 40.000 0.00 0.00 0.00 1.40
1594 1604 3.290710 ACTGACCACTGCAAATCAAGTT 58.709 40.909 0.00 0.00 0.00 2.66
1766 1777 3.319405 TGTCTCTCTTCTTCTTTGCTCGT 59.681 43.478 0.00 0.00 0.00 4.18
1830 1841 4.131596 CAACAACGACCCCTTCTCTTTAA 58.868 43.478 0.00 0.00 0.00 1.52
1844 1855 2.839975 TCTGTTATGCACCAACAACGA 58.160 42.857 14.65 8.37 35.57 3.85
2001 2012 2.097466 GCTATGCCAACTTGCGTACAAT 59.903 45.455 0.00 0.00 34.61 2.71
2200 2212 7.795047 TCAATCTCAATGACTGCTAGGATTTA 58.205 34.615 0.00 0.00 0.00 1.40
2229 2241 5.763204 GGTAATTGGATTGCGATTTCCTCTA 59.237 40.000 6.56 0.00 32.95 2.43


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

AutoCloner maintained by Alex Coulton.