Multiple sequence alignment - TraesCS1A01G134400

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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 TraesCS1A01G134400 chr1A 100.000 2282 0 0 1 2282 201752131 201754412 0 4215
1 TraesCS1A01G134400 chr5A 96.589 2287 70 5 1 2282 268814512 268812229 0 3784
2 TraesCS1A01G134400 chr5A 96.371 2287 76 4 1 2282 268822486 268820202 0 3757
3 TraesCS1A01G134400 chr5A 94.702 755 33 4 1534 2282 29797114 29797867 0 1166
4 TraesCS1A01G134400 chr5A 94.570 755 34 4 1534 2282 29804790 29805543 0 1160
5 TraesCS1A01G134400 chr4A 93.162 2296 135 19 1 2282 85922179 85924466 0 3350
6 TraesCS1A01G134400 chr4A 92.988 2296 140 18 1 2282 85954392 85956680 0 3328
7 TraesCS1A01G134400 chr2A 91.950 2323 138 30 1 2282 352651382 352653696 0 3208
8 TraesCS1A01G134400 chr2A 91.559 2322 147 30 1 2282 352643372 352645684 0 3157
9 TraesCS1A01G134400 chr2A 88.592 1087 89 23 1207 2279 604016772 604017837 0 1288
10 TraesCS1A01G134400 chr2A 88.511 1088 89 24 1207 2280 604025252 604026317 0 1284
11 TraesCS1A01G134400 chr6A 91.399 2209 136 23 1 2171 216935635 216933443 0 2977
12 TraesCS1A01G134400 chr3A 94.971 1372 64 5 13 1382 701989669 701988301 0 2146
13 TraesCS1A01G134400 chr3A 93.882 1373 76 8 13 1382 701981803 701980436 0 2063


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 TraesCS1A01G134400 chr1A 201752131 201754412 2281 False 4215 4215 100.000 1 2282 1 chr1A.!!$F1 2281
1 TraesCS1A01G134400 chr5A 268812229 268814512 2283 True 3784 3784 96.589 1 2282 1 chr5A.!!$R1 2281
2 TraesCS1A01G134400 chr5A 268820202 268822486 2284 True 3757 3757 96.371 1 2282 1 chr5A.!!$R2 2281
3 TraesCS1A01G134400 chr5A 29797114 29797867 753 False 1166 1166 94.702 1534 2282 1 chr5A.!!$F1 748
4 TraesCS1A01G134400 chr5A 29804790 29805543 753 False 1160 1160 94.570 1534 2282 1 chr5A.!!$F2 748
5 TraesCS1A01G134400 chr4A 85922179 85924466 2287 False 3350 3350 93.162 1 2282 1 chr4A.!!$F1 2281
6 TraesCS1A01G134400 chr4A 85954392 85956680 2288 False 3328 3328 92.988 1 2282 1 chr4A.!!$F2 2281
7 TraesCS1A01G134400 chr2A 352651382 352653696 2314 False 3208 3208 91.950 1 2282 1 chr2A.!!$F2 2281
8 TraesCS1A01G134400 chr2A 352643372 352645684 2312 False 3157 3157 91.559 1 2282 1 chr2A.!!$F1 2281
9 TraesCS1A01G134400 chr2A 604016772 604017837 1065 False 1288 1288 88.592 1207 2279 1 chr2A.!!$F3 1072
10 TraesCS1A01G134400 chr2A 604025252 604026317 1065 False 1284 1284 88.511 1207 2280 1 chr2A.!!$F4 1073
11 TraesCS1A01G134400 chr6A 216933443 216935635 2192 True 2977 2977 91.399 1 2171 1 chr6A.!!$R1 2170
12 TraesCS1A01G134400 chr3A 701988301 701989669 1368 True 2146 2146 94.971 13 1382 1 chr3A.!!$R2 1369
13 TraesCS1A01G134400 chr3A 701980436 701981803 1367 True 2063 2063 93.882 13 1382 1 chr3A.!!$R1 1369

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
525 527 0.252284 TCTCCTCCTCGCTTCCCTTT 60.252 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1870 0.868406 CAAAGGAGAAGTGTGCGGAC 59.132 55.0 0.0 0.0 0.0 4.79 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
96 97 2.237392 CCTTCCTAACCCTCACTTCCTG 59.763 54.545 0.00 0.00 0.00 3.86
525 527 0.252284 TCTCCTCCTCGCTTCCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
624 626 2.606587 ATCCTCCTGCGCCCTTGTT 61.607 57.895 4.18 0.00 0.00 2.83
676 678 0.617820 GCCCTCCTCTACCAACCTGA 60.618 60.000 0.00 0.00 0.00 3.86
894 897 2.483714 GCTCCCTTCGTCATCTGCATTA 60.484 50.000 0.00 0.00 0.00 1.90
1073 1076 2.923035 ACACACGCCCCTGCTAGT 60.923 61.111 0.00 0.00 34.43 2.57
1086 1089 2.353208 CCTGCTAGTTGCTTCGACTCTT 60.353 50.000 0.00 0.00 43.37 2.85
1210 1214 3.577667 GCTACATGTAACACCGTGTACA 58.422 45.455 4.17 9.93 36.11 2.90
1285 1289 0.173708 GACCACGGATCTGTGAGGTC 59.826 60.000 32.02 26.52 42.55 3.85
1286 1290 1.139734 CCACGGATCTGTGAGGTCG 59.860 63.158 32.02 13.82 42.55 4.79
1294 1298 2.904131 TGTGAGGTCGCACAACCA 59.096 55.556 5.11 0.00 45.08 3.67
1317 1321 0.037697 CCGTGGATCCGACAAGTTCA 60.038 55.000 7.39 0.00 0.00 3.18
1450 1454 2.038426 AGGTGGATCACGAATGTTGACA 59.962 45.455 0.00 0.00 34.83 3.58
1467 1471 2.901192 TGACAAGGTTCCGATAAGACCA 59.099 45.455 0.00 0.00 35.89 4.02
1736 1741 0.865769 GTCCGTGAACGAATGCTTGT 59.134 50.000 4.03 0.00 43.02 3.16
2060 2130 7.851387 TCCGCATCATGTTAACAACTTTATA 57.149 32.000 13.23 0.00 0.00 0.98
2135 2205 3.637911 TGTTGTTGGTTATATCCGGCT 57.362 42.857 0.00 0.00 0.00 5.52
2136 2206 3.275143 TGTTGTTGGTTATATCCGGCTG 58.725 45.455 0.00 0.00 0.00 4.85
2147 2217 7.448777 TGGTTATATCCGGCTGCATTTAAATTA 59.551 33.333 0.50 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 527 2.224159 GGGAGAAGGGTGGCTGTGA 61.224 63.158 0.00 0.00 0.00 3.58
624 626 3.760035 GGTTCCCTGCTCGCGAGA 61.760 66.667 38.74 21.90 39.12 4.04
894 897 4.070552 GCTCCGGCGAACTCCAGT 62.071 66.667 9.30 0.00 0.00 4.00
1073 1076 1.227999 CGGGCAAAGAGTCGAAGCAA 61.228 55.000 0.00 0.00 0.00 3.91
1086 1089 2.410466 AAAAACGAAGCTCGGGCAA 58.590 47.368 11.40 0.00 45.59 4.52
1210 1214 1.968493 ACGCATCCCGGATATGTAGTT 59.032 47.619 0.73 0.00 42.52 2.24
1273 1277 1.071605 GTTGTGCGACCTCACAGATC 58.928 55.000 0.00 0.00 46.28 2.75
1277 1281 0.602638 GATGGTTGTGCGACCTCACA 60.603 55.000 9.75 0.00 44.39 3.58
1285 1289 4.444024 CACGGCGATGGTTGTGCG 62.444 66.667 16.62 0.00 0.00 5.34
1286 1290 4.101790 CCACGGCGATGGTTGTGC 62.102 66.667 16.62 0.00 34.77 4.57
1294 1298 2.629050 CTTGTCGGATCCACGGCGAT 62.629 60.000 16.62 0.00 42.29 4.58
1317 1321 0.700564 TGGGAGGTAGTGGTACTCGT 59.299 55.000 0.00 0.00 0.00 4.18
1450 1454 3.454371 CGATGGTCTTATCGGAACCTT 57.546 47.619 0.00 0.00 44.56 3.50
1467 1471 2.877168 GGAGTAGGTCGTACATGTCGAT 59.123 50.000 18.67 9.90 39.45 3.59
1736 1741 1.271325 ACGGGTGCATCTCAAACATCA 60.271 47.619 0.00 0.00 0.00 3.07
1859 1870 0.868406 CAAAGGAGAAGTGTGCGGAC 59.132 55.000 0.00 0.00 0.00 4.79
2060 2130 9.298774 CAATTTGGTGCAACAACAATTTTAAAT 57.701 25.926 18.78 1.19 40.90 1.40


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

AutoCloner maintained by Alex Coulton.