Multiple sequence alignment - TraesCS4B01G151100

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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 TraesCS4B01G151100 chr4B 100.000 2246 0 0 1 2246 240016201 240013956 0.000000e+00 4148
1 TraesCS4B01G151100 chr4B 96.621 2249 73 3 1 2246 239620476 239622724 0.000000e+00 3729
2 TraesCS4B01G151100 chr4B 92.857 616 32 6 1234 1845 601914713 601914106 0.000000e+00 883
3 TraesCS4B01G151100 chr3A 93.947 1239 62 10 1 1227 433764527 433765764 0.000000e+00 1860
4 TraesCS4B01G151100 chr3A 91.842 1238 88 6 1 1225 575149668 575150905 0.000000e+00 1714
5 TraesCS4B01G151100 chr4D 93.790 1240 62 9 1 1227 210026561 210025324 0.000000e+00 1849
6 TraesCS4B01G151100 chr7B 93.619 1238 65 8 1 1226 365876219 365874984 0.000000e+00 1836
7 TraesCS4B01G151100 chr7B 92.695 616 33 7 1234 1845 658576787 658576180 0.000000e+00 878
8 TraesCS4B01G151100 chr7B 92.695 616 33 7 1234 1845 658687106 658686499 0.000000e+00 878
9 TraesCS4B01G151100 chr1B 92.799 1236 77 6 1 1224 40282513 40283748 0.000000e+00 1779
10 TraesCS4B01G151100 chr5A 91.613 1240 88 11 1 1225 173529045 173527807 0.000000e+00 1700
11 TraesCS4B01G151100 chr5A 92.193 807 49 9 1 793 683756643 683755837 0.000000e+00 1129
12 TraesCS4B01G151100 chr5A 91.945 807 51 9 1 793 681742545 681743351 0.000000e+00 1118
13 TraesCS4B01G151100 chr5A 93.103 435 30 0 791 1225 683752375 683751941 2.430000e-179 638
14 TraesCS4B01G151100 chr5B 94.039 822 37 7 1 810 415416747 415415926 0.000000e+00 1236
15 TraesCS4B01G151100 chr5B 94.969 477 23 1 1770 2245 599243130 599242654 0.000000e+00 747
16 TraesCS4B01G151100 chr5D 90.649 909 63 14 1 890 68971074 68971979 0.000000e+00 1188
17 TraesCS4B01G151100 chr4A 89.491 904 72 16 1 890 292710046 292709152 0.000000e+00 1122
18 TraesCS4B01G151100 chr4A 92.707 617 31 7 1234 1845 664564527 664565134 0.000000e+00 878
19 TraesCS4B01G151100 chr7A 95.782 569 24 0 659 1227 617960339 617959771 0.000000e+00 918
20 TraesCS4B01G151100 chrUn 92.707 617 31 7 1234 1845 49051120 49051727 0.000000e+00 878
21 TraesCS4B01G151100 chrUn 92.707 617 31 7 1234 1845 49054914 49055521 0.000000e+00 878
22 TraesCS4B01G151100 chrUn 92.707 617 31 7 1234 1845 49106606 49107213 0.000000e+00 878
23 TraesCS4B01G151100 chrUn 92.695 616 33 7 1234 1845 307452866 307452259 0.000000e+00 878
24 TraesCS4B01G151100 chr3D 82.182 275 29 11 1980 2240 600652447 600652179 3.760000e-53 219
25 TraesCS4B01G151100 chr3D 91.089 101 8 1 1882 1981 600652581 600652481 3.890000e-28 135


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 TraesCS4B01G151100 chr4B 240013956 240016201 2245 True 4148.0 4148 100.000 1 2246 1 chr4B.!!$R1 2245
1 TraesCS4B01G151100 chr4B 239620476 239622724 2248 False 3729.0 3729 96.621 1 2246 1 chr4B.!!$F1 2245
2 TraesCS4B01G151100 chr4B 601914106 601914713 607 True 883.0 883 92.857 1234 1845 1 chr4B.!!$R2 611
3 TraesCS4B01G151100 chr3A 433764527 433765764 1237 False 1860.0 1860 93.947 1 1227 1 chr3A.!!$F1 1226
4 TraesCS4B01G151100 chr3A 575149668 575150905 1237 False 1714.0 1714 91.842 1 1225 1 chr3A.!!$F2 1224
5 TraesCS4B01G151100 chr4D 210025324 210026561 1237 True 1849.0 1849 93.790 1 1227 1 chr4D.!!$R1 1226
6 TraesCS4B01G151100 chr7B 365874984 365876219 1235 True 1836.0 1836 93.619 1 1226 1 chr7B.!!$R1 1225
7 TraesCS4B01G151100 chr7B 658576180 658576787 607 True 878.0 878 92.695 1234 1845 1 chr7B.!!$R2 611
8 TraesCS4B01G151100 chr7B 658686499 658687106 607 True 878.0 878 92.695 1234 1845 1 chr7B.!!$R3 611
9 TraesCS4B01G151100 chr1B 40282513 40283748 1235 False 1779.0 1779 92.799 1 1224 1 chr1B.!!$F1 1223
10 TraesCS4B01G151100 chr5A 173527807 173529045 1238 True 1700.0 1700 91.613 1 1225 1 chr5A.!!$R1 1224
11 TraesCS4B01G151100 chr5A 681742545 681743351 806 False 1118.0 1118 91.945 1 793 1 chr5A.!!$F1 792
12 TraesCS4B01G151100 chr5A 683751941 683756643 4702 True 883.5 1129 92.648 1 1225 2 chr5A.!!$R2 1224
13 TraesCS4B01G151100 chr5B 415415926 415416747 821 True 1236.0 1236 94.039 1 810 1 chr5B.!!$R1 809
14 TraesCS4B01G151100 chr5D 68971074 68971979 905 False 1188.0 1188 90.649 1 890 1 chr5D.!!$F1 889
15 TraesCS4B01G151100 chr4A 292709152 292710046 894 True 1122.0 1122 89.491 1 890 1 chr4A.!!$R1 889
16 TraesCS4B01G151100 chr4A 664564527 664565134 607 False 878.0 878 92.707 1234 1845 1 chr4A.!!$F1 611
17 TraesCS4B01G151100 chr7A 617959771 617960339 568 True 918.0 918 95.782 659 1227 1 chr7A.!!$R1 568
18 TraesCS4B01G151100 chrUn 49051120 49055521 4401 False 878.0 878 92.707 1234 1845 2 chrUn.!!$F2 611
19 TraesCS4B01G151100 chrUn 49106606 49107213 607 False 878.0 878 92.707 1234 1845 1 chrUn.!!$F1 611
20 TraesCS4B01G151100 chrUn 307452259 307452866 607 True 878.0 878 92.695 1234 1845 1 chrUn.!!$R1 611

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
997 4487 0.251608 GGGAGCCAAAGCCCTAACAA 60.252 55.0 0.0 0.0 41.31 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 9362 1.213926 AGGATCCCAACAATGCTCTCC 59.786 52.381 8.55 0.0 0.0 3.71 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
70 71 0.758734 TTGTAGGCAGTCTGTGTGCT 59.241 50.000 0.93 0.00 40.97 4.40
79 80 5.048713 AGGCAGTCTGTGTGCTTAAATAAAC 60.049 40.000 0.93 0.00 40.97 2.01
172 173 2.746904 TGCAATCACATCAGGTTTACCG 59.253 45.455 0.00 0.00 42.08 4.02
601 623 1.021390 CGCAAGCTTGACCTGGGTAG 61.021 60.000 30.39 0.00 0.00 3.18
997 4487 0.251608 GGGAGCCAAAGCCCTAACAA 60.252 55.000 0.00 0.00 41.31 2.83
1063 4553 0.324738 CCTCTCAGGGGCTGTAGACA 60.325 60.000 0.00 0.00 32.61 3.41
1149 4639 2.359169 CCTCGCCCTTGAGCTACCA 61.359 63.158 0.00 0.00 34.56 3.25
1156 4646 1.134280 CCCTTGAGCTACCACATCTGG 60.134 57.143 0.00 0.00 44.26 3.86
1169 4659 1.035932 CATCTGGAAGGCAAGGCAGG 61.036 60.000 0.00 0.00 0.00 4.85
1218 4708 1.938577 CAACATGAAGAGGATGAGGCG 59.061 52.381 0.00 0.00 0.00 5.52
1254 4744 3.442273 AGAGGAAGAAGTGACAGATCGAC 59.558 47.826 0.00 0.00 0.00 4.20
1291 8575 2.906897 CAACAGCAGGCAACGGGT 60.907 61.111 0.00 0.00 45.69 5.28
1408 8692 1.529948 CATGCGCCCCCATGAAGAT 60.530 57.895 4.18 0.00 44.12 2.40
1662 8946 0.320374 TACAAGACCTCGCACCAAGG 59.680 55.000 0.00 0.00 39.96 3.61
1675 8959 2.757868 GCACCAAGGCCATTTGTATACA 59.242 45.455 5.01 0.08 0.00 2.29
1944 9232 7.445945 AGAAGTGCAGTACTCAAACTAAGAAT 58.554 34.615 0.00 0.00 39.18 2.40
1957 9245 8.306313 TCAAACTAAGAATAGCATAGAGACCA 57.694 34.615 0.00 0.00 31.96 4.02
2041 9329 9.823647 CAGTAAAAGTATCAACTACATCAGGAT 57.176 33.333 0.00 0.00 33.75 3.24
2045 9333 8.954950 AAAGTATCAACTACATCAGGATTCAG 57.045 34.615 0.00 0.00 33.75 3.02
2050 9338 4.833478 ACTACATCAGGATTCAGCAAGT 57.167 40.909 0.00 0.00 0.00 3.16
2054 9342 5.426689 ACATCAGGATTCAGCAAGTTCTA 57.573 39.130 0.00 0.00 0.00 2.10
2074 9362 3.965379 ATGAGGCTCTGCTATCATCAG 57.035 47.619 16.72 0.00 32.63 2.90
2097 9385 2.512896 AGAGCATTGTTGGGATCCTCAT 59.487 45.455 12.58 0.00 0.00 2.90
2098 9386 2.621998 GAGCATTGTTGGGATCCTCATG 59.378 50.000 12.58 8.03 0.00 3.07
2101 9389 3.623703 CATTGTTGGGATCCTCATGTCA 58.376 45.455 12.58 0.00 0.00 3.58
2115 9403 4.945543 CCTCATGTCAGATTCCAATTGTCA 59.054 41.667 4.43 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 9.912634 TTCTATGCCTCATTTTTCTTGTTTTAG 57.087 29.630 0.00 0.00 0.00 1.85
280 284 6.884832 ACCGGATATGATCTACTTGAACAAA 58.115 36.000 9.46 0.00 31.27 2.83
635 659 6.313658 GCTCAATTGAACTGTTGTTTTCCTTT 59.686 34.615 9.88 0.00 36.39 3.11
997 4487 3.389329 ACTCTTCTATTCGATGCCATGGT 59.611 43.478 14.67 0.00 0.00 3.55
1149 4639 0.323178 CTGCCTTGCCTTCCAGATGT 60.323 55.000 0.00 0.00 0.00 3.06
1156 4646 1.067354 CATGTTTCCTGCCTTGCCTTC 60.067 52.381 0.00 0.00 0.00 3.46
1169 4659 5.633830 TTGCCTCTGATTCTTCATGTTTC 57.366 39.130 0.00 0.00 0.00 2.78
1218 4708 1.153667 CCTCTCGTGAAGCAGAGCC 60.154 63.158 0.00 0.00 35.69 4.70
1254 4744 3.325870 TGCTACTGGTGAGACAATTTCG 58.674 45.455 0.00 0.00 0.00 3.46
1291 8575 0.687354 GCTGACCCTCCTCAACTTCA 59.313 55.000 0.00 0.00 0.00 3.02
1550 8834 8.957466 GGTTCCTTGCTGAATAAATAAGTAACT 58.043 33.333 0.00 0.00 0.00 2.24
1662 8946 6.568462 GCACCATACTCATGTATACAAATGGC 60.568 42.308 21.91 12.76 37.28 4.40
1675 8959 4.399303 GGTAGCTTTTTGCACCATACTCAT 59.601 41.667 0.00 0.00 45.94 2.90
1729 9013 7.278646 CAGCTTAGTAACATCTTGCATTGTCTA 59.721 37.037 0.00 0.00 0.00 2.59
1735 9021 6.825213 TCATTCAGCTTAGTAACATCTTGCAT 59.175 34.615 0.00 0.00 0.00 3.96
1872 9160 3.184581 GGTTAGCACTCAACTTCTGTTCG 59.815 47.826 0.00 0.00 33.52 3.95
1918 9206 7.520451 TCTTAGTTTGAGTACTGCACTTCTA 57.480 36.000 0.00 0.00 37.72 2.10
1944 9232 1.704641 ATGCGGTGGTCTCTATGCTA 58.295 50.000 0.00 0.00 0.00 3.49
1957 9245 3.746045 ATTCGTAATCCAGTATGCGGT 57.254 42.857 0.00 0.00 31.97 5.68
2041 9329 3.517100 AGAGCCTCATAGAACTTGCTGAA 59.483 43.478 0.00 0.00 0.00 3.02
2045 9333 1.939255 GCAGAGCCTCATAGAACTTGC 59.061 52.381 0.00 0.00 0.00 4.01
2050 9338 5.082425 TGATGATAGCAGAGCCTCATAGAA 58.918 41.667 0.00 0.00 33.57 2.10
2054 9342 2.568062 CCTGATGATAGCAGAGCCTCAT 59.432 50.000 0.00 4.85 35.25 2.90
2074 9362 1.213926 AGGATCCCAACAATGCTCTCC 59.786 52.381 8.55 0.00 0.00 3.71
2097 9385 3.073678 CGGTGACAATTGGAATCTGACA 58.926 45.455 10.83 0.00 0.00 3.58
2098 9386 3.334691 TCGGTGACAATTGGAATCTGAC 58.665 45.455 10.83 0.00 0.00 3.51
2101 9389 6.094048 CAGTAATTCGGTGACAATTGGAATCT 59.906 38.462 10.83 1.10 0.00 2.40
2115 9403 2.124411 AGGTATGGCCAGTAATTCGGT 58.876 47.619 13.05 0.00 40.61 4.69


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

AutoCloner maintained by Alex Coulton.