Multiple sequence alignment - TraesCS3B01G364200

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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 TraesCS3B01G364200 chr3B 100.000 2243 0 0 1 2243 575839742 575837500 0 4143
1 TraesCS3B01G364200 chr3B 96.791 2244 69 3 1 2243 483333212 483335453 0 3742
2 TraesCS3B01G364200 chr4B 96.881 2244 67 3 1 2243 209242557 209244798 0 3753
3 TraesCS3B01G364200 chr2A 96.610 2242 74 2 1 2241 750453591 750451351 0 3718
4 TraesCS3B01G364200 chr6A 96.253 2242 81 3 1 2241 155857299 155859538 0 3672
5 TraesCS3B01G364200 chr6A 95.986 2242 86 3 1 2241 375860759 375858521 0 3639
6 TraesCS3B01G364200 chr4A 95.897 2242 89 3 1 2241 350172240 350174479 0 3627
7 TraesCS3B01G364200 chr3A 95.639 2018 73 8 235 2241 230228527 230226514 0 3225
8 TraesCS3B01G364200 chr7B 97.477 1308 32 1 1 1308 742948738 742947432 0 2231
9 TraesCS3B01G364200 chr7B 97.401 1308 33 1 1 1308 716784607 716785913 0 2226
10 TraesCS3B01G364200 chrUn 98.084 1044 19 1 1201 2243 171017238 171018281 0 1816
11 TraesCS3B01G364200 chr5B 97.985 1042 19 2 1201 2241 439641088 439642128 0 1807


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 TraesCS3B01G364200 chr3B 575837500 575839742 2242 True 4143 4143 100.000 1 2243 1 chr3B.!!$R1 2242
1 TraesCS3B01G364200 chr3B 483333212 483335453 2241 False 3742 3742 96.791 1 2243 1 chr3B.!!$F1 2242
2 TraesCS3B01G364200 chr4B 209242557 209244798 2241 False 3753 3753 96.881 1 2243 1 chr4B.!!$F1 2242
3 TraesCS3B01G364200 chr2A 750451351 750453591 2240 True 3718 3718 96.610 1 2241 1 chr2A.!!$R1 2240
4 TraesCS3B01G364200 chr6A 155857299 155859538 2239 False 3672 3672 96.253 1 2241 1 chr6A.!!$F1 2240
5 TraesCS3B01G364200 chr6A 375858521 375860759 2238 True 3639 3639 95.986 1 2241 1 chr6A.!!$R1 2240
6 TraesCS3B01G364200 chr4A 350172240 350174479 2239 False 3627 3627 95.897 1 2241 1 chr4A.!!$F1 2240
7 TraesCS3B01G364200 chr3A 230226514 230228527 2013 True 3225 3225 95.639 235 2241 1 chr3A.!!$R1 2006
8 TraesCS3B01G364200 chr7B 742947432 742948738 1306 True 2231 2231 97.477 1 1308 1 chr7B.!!$R1 1307
9 TraesCS3B01G364200 chr7B 716784607 716785913 1306 False 2226 2226 97.401 1 1308 1 chr7B.!!$F1 1307
10 TraesCS3B01G364200 chrUn 171017238 171018281 1043 False 1816 1816 98.084 1201 2243 1 chrUn.!!$F1 1042
11 TraesCS3B01G364200 chr5B 439641088 439642128 1040 False 1807 1807 97.985 1201 2241 1 chr5B.!!$F1 1040

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
220 221 0.107897 ACAATATCGCGAAGTGGCCA 60.108 50.0 15.24 0.0 39.32 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1434 0.685097 TTGACCGCTCTTAAGGTGCT 59.315 50.0 15.61 2.68 41.51 4.4 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 1.200252 CTGGAGACGTATCGGCCTATG 59.800 57.143 3.77 0.00 34.11 2.23
49 50 0.921896 CCCCACCAATGTGATCTCCT 59.078 55.000 0.00 0.00 45.76 3.69
129 130 6.037172 CAGCTATTAACGTTGGCTTATCTGTT 59.963 38.462 11.99 0.00 0.00 3.16
136 137 3.259064 GTTGGCTTATCTGTTAGTCGCA 58.741 45.455 0.00 0.00 0.00 5.10
220 221 0.107897 ACAATATCGCGAAGTGGCCA 60.108 50.000 15.24 0.00 39.32 5.36
257 258 2.355513 GGTCAGACCTTGATGCTGTGAT 60.356 50.000 12.94 0.00 38.29 3.06
477 478 5.934935 TCTTAGAAAAAGGTGGCTTAACG 57.065 39.130 0.00 0.00 0.00 3.18
568 569 1.302993 GGTTGCCCCTTACTCGCAA 60.303 57.895 0.00 0.00 40.06 4.85
665 668 2.572191 AGATTTTCGTGCCATGCATG 57.428 45.000 20.19 20.19 45.79 4.06
1053 1056 3.350833 AGCTGCTACAATTGCTTTAGCT 58.649 40.909 20.79 19.00 42.66 3.32
1249 1253 7.376435 TCGCATAAAAAGTCATGAGATCAAA 57.624 32.000 0.00 0.00 0.00 2.69
1333 1337 2.923035 ATGGGGCGTCCTATCCGG 60.923 66.667 5.77 0.00 36.20 5.14
1430 1434 1.442769 GATTCAAGCCAAGAGTGCGA 58.557 50.000 0.00 0.00 0.00 5.10
1457 1461 4.442192 CCTTAAGAGCGGTCAAAGCTAGAT 60.442 45.833 18.15 0.00 46.13 1.98
1571 1575 5.462405 GCGAGACATAAGTTATCGGAATCT 58.538 41.667 5.93 0.00 37.58 2.40
1879 1885 1.300620 GCTGCATCGCCACCGTATA 60.301 57.895 0.00 0.00 35.54 1.47
1991 1998 3.776969 ACCTCTCTCTATCAACCATTGCA 59.223 43.478 0.00 0.00 0.00 4.08
2066 2073 2.554032 GGCCTACAATCCATGGAAATCG 59.446 50.000 20.67 9.89 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.408822 GGAGATCACATTGGTGGGGAC 60.409 57.143 0.00 0.00 45.32 4.46
87 88 2.029828 AGCTGGTCTAATTCCGCGATAG 60.030 50.000 8.23 4.74 32.79 2.08
129 130 2.782222 GGCAGACCCGATGCGACTA 61.782 63.158 0.00 0.00 44.80 2.59
220 221 1.202879 TGACCCAAATTGAGCGAAGGT 60.203 47.619 0.00 0.00 46.54 3.50
257 258 5.674525 CACCTCTATTGAGTAATGCCTGAA 58.325 41.667 3.47 0.00 38.61 3.02
447 448 6.209589 AGCCACCTTTTTCTAAGAAGGATTTC 59.790 38.462 16.55 5.22 44.15 2.17
477 478 4.755123 TCTGGTTCCATCTTTCTTTCGTTC 59.245 41.667 0.00 0.00 0.00 3.95
568 569 4.938226 CGAGAAAAGCCTTCTTCCTACATT 59.062 41.667 0.51 0.00 0.00 2.71
665 668 1.001860 AGACTCTCAGCAGCTTGGTTC 59.998 52.381 0.00 0.00 0.00 3.62
795 798 5.988310 TGAGCTGTGGATTGAAAATCATT 57.012 34.783 0.00 0.00 0.00 2.57
991 994 3.119459 GCACCTTCTAACATCTCGAGTCA 60.119 47.826 13.13 0.00 0.00 3.41
1053 1056 1.614051 CCAATACCAACAGCAGCTCCA 60.614 52.381 0.00 0.00 0.00 3.86
1065 1068 4.927267 ACTGAGGATGTTTCCAATACCA 57.073 40.909 0.00 0.00 45.30 3.25
1197 1200 3.902881 ACGAATGAGATCAGAAAGGCT 57.097 42.857 0.00 0.00 0.00 4.58
1249 1253 9.349713 TGTAACTACATCCTCACATTTCTTTTT 57.650 29.630 0.00 0.00 0.00 1.94
1310 1314 2.180276 GATAGGACGCCCCATCTATGT 58.820 52.381 0.00 0.00 37.41 2.29
1333 1337 3.072184 ACATAGGCTCCTCATTCATCCAC 59.928 47.826 0.00 0.00 0.00 4.02
1430 1434 0.685097 TTGACCGCTCTTAAGGTGCT 59.315 50.000 15.61 2.68 41.51 4.40
1457 1461 4.635223 GTTCCAGCAGTCATGATATAGCA 58.365 43.478 0.00 0.00 0.00 3.49
1571 1575 4.552674 GAAATAGGGAAAAATAGGCCCCA 58.447 43.478 0.00 0.00 43.08 4.96
1649 1653 2.102252 TGAAAACGGCAGCTCCATTTTT 59.898 40.909 9.34 9.38 40.01 1.94
1879 1885 2.614057 CAGTTCGAAAAGCAAGTCAGGT 59.386 45.455 0.00 0.00 0.00 4.00
1974 1981 9.851686 ACTATTTAATGCAATGGTTGATAGAGA 57.148 29.630 0.00 0.00 0.00 3.10
2066 2073 2.910688 TTCCCAGTGATCGGAATAGC 57.089 50.000 0.00 0.00 33.14 2.97
2189 2204 8.481492 TGGCATATTTCCTATCATTTCACAAT 57.519 30.769 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.