Multiple sequence alignment - TraesCS2A01G293000

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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 TraesCS2A01G293000 chr2A 100.000 2276 0 0 1 2276 504280703 504278428 0.000000e+00 4204
1 TraesCS2A01G293000 chr7D 95.579 1312 48 4 1 1306 535846417 535847724 0.000000e+00 2093
2 TraesCS2A01G293000 chr1D 93.135 1311 67 9 1 1305 479322493 479321200 0.000000e+00 1901
3 TraesCS2A01G293000 chr6D 92.835 1312 74 4 2 1307 138913013 138911716 0.000000e+00 1884
4 TraesCS2A01G293000 chr6D 82.473 1318 210 14 1 1304 453448181 453446871 0.000000e+00 1134
5 TraesCS2A01G293000 chr1B 91.318 1313 104 5 1 1306 473558158 473556849 0.000000e+00 1784
6 TraesCS2A01G293000 chr3D 90.000 1310 121 5 1 1303 44971313 44972619 0.000000e+00 1685
7 TraesCS2A01G293000 chr3D 84.692 1313 185 11 1 1304 284850705 284849400 0.000000e+00 1297
8 TraesCS2A01G293000 chr5B 89.605 1318 127 5 1 1310 540319748 540321063 0.000000e+00 1666
9 TraesCS2A01G293000 chr5B 86.252 1302 166 8 1 1292 503775913 503777211 0.000000e+00 1400
10 TraesCS2A01G293000 chr6A 87.490 1311 154 5 1 1304 13040042 13041349 0.000000e+00 1504
11 TraesCS2A01G293000 chr6B 86.357 1312 162 9 1 1304 63785029 63786331 0.000000e+00 1415
12 TraesCS2A01G293000 chr3B 85.779 1322 163 12 1 1305 573992613 573993926 0.000000e+00 1376
13 TraesCS2A01G293000 chr3B 74.347 651 143 17 2 635 810305364 810306007 2.900000e-64 255
14 TraesCS2A01G293000 chr2B 91.650 1006 28 13 1306 2274 442791719 442792705 0.000000e+00 1341
15 TraesCS2A01G293000 chr2D 91.463 984 20 16 1306 2258 373221661 373222611 0.000000e+00 1293


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 TraesCS2A01G293000 chr2A 504278428 504280703 2275 True 4204 4204 100.000 1 2276 1 chr2A.!!$R1 2275
1 TraesCS2A01G293000 chr7D 535846417 535847724 1307 False 2093 2093 95.579 1 1306 1 chr7D.!!$F1 1305
2 TraesCS2A01G293000 chr1D 479321200 479322493 1293 True 1901 1901 93.135 1 1305 1 chr1D.!!$R1 1304
3 TraesCS2A01G293000 chr6D 138911716 138913013 1297 True 1884 1884 92.835 2 1307 1 chr6D.!!$R1 1305
4 TraesCS2A01G293000 chr6D 453446871 453448181 1310 True 1134 1134 82.473 1 1304 1 chr6D.!!$R2 1303
5 TraesCS2A01G293000 chr1B 473556849 473558158 1309 True 1784 1784 91.318 1 1306 1 chr1B.!!$R1 1305
6 TraesCS2A01G293000 chr3D 44971313 44972619 1306 False 1685 1685 90.000 1 1303 1 chr3D.!!$F1 1302
7 TraesCS2A01G293000 chr3D 284849400 284850705 1305 True 1297 1297 84.692 1 1304 1 chr3D.!!$R1 1303
8 TraesCS2A01G293000 chr5B 540319748 540321063 1315 False 1666 1666 89.605 1 1310 1 chr5B.!!$F2 1309
9 TraesCS2A01G293000 chr5B 503775913 503777211 1298 False 1400 1400 86.252 1 1292 1 chr5B.!!$F1 1291
10 TraesCS2A01G293000 chr6A 13040042 13041349 1307 False 1504 1504 87.490 1 1304 1 chr6A.!!$F1 1303
11 TraesCS2A01G293000 chr6B 63785029 63786331 1302 False 1415 1415 86.357 1 1304 1 chr6B.!!$F1 1303
12 TraesCS2A01G293000 chr3B 573992613 573993926 1313 False 1376 1376 85.779 1 1305 1 chr3B.!!$F1 1304
13 TraesCS2A01G293000 chr3B 810305364 810306007 643 False 255 255 74.347 2 635 1 chr3B.!!$F2 633
14 TraesCS2A01G293000 chr2B 442791719 442792705 986 False 1341 1341 91.650 1306 2274 1 chr2B.!!$F1 968
15 TraesCS2A01G293000 chr2D 373221661 373222611 950 False 1293 1293 91.463 1306 2258 1 chr2D.!!$F1 952

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
993 1013 1.006832 AACTTCGTGGCATATCGCAC 58.993 50.0 0.0 0.0 45.17 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2173 1.066645 ACCGACCGAAATACTCCAACC 60.067 52.381 0.0 0.0 0.0 3.77 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
83 84 6.927936 CAGACAGTTTCGGATCTCATTGATAT 59.072 38.462 0.00 0.00 35.14 1.63
598 616 4.699192 TCCTATGTGGAGACCGGG 57.301 61.111 6.32 0.00 40.56 5.73
957 976 3.243670 TGGAAGCTCTATCATTGCGAGAG 60.244 47.826 9.22 9.22 39.82 3.20
993 1013 1.006832 AACTTCGTGGCATATCGCAC 58.993 50.000 0.00 0.00 45.17 5.34
1068 1088 0.802494 ATTCACGTTCGATTGTGGCC 59.198 50.000 15.11 0.00 36.74 5.36
1110 1139 6.903419 AGGAGAGCTAGTTTTTGATTTTTCG 58.097 36.000 0.00 0.00 0.00 3.46
1127 1156 4.735662 TTTCGGTATTTGAGGTTCAACG 57.264 40.909 0.00 0.00 35.89 4.10
1147 1176 2.668279 CGTGTAAACAGGGCAGCAAATC 60.668 50.000 0.00 0.00 0.00 2.17
1185 1214 1.678360 CAAAACGTGCATGCACTCTC 58.322 50.000 39.46 20.47 44.16 3.20
1210 1239 1.003839 ACCGATTGCTGGCTCGAAA 60.004 52.632 5.93 0.00 37.05 3.46
1239 1268 0.538287 GCTTCTTGGTGACCAGCCTT 60.538 55.000 3.77 0.00 33.81 4.35
1282 1311 7.706607 AGAACACTTTTGTTGAATAAAAGCTCC 59.293 33.333 21.82 11.76 46.43 4.70
1299 1328 1.474077 CTCCCTGATTTGCCCGAAAAG 59.526 52.381 0.00 0.00 0.00 2.27
1357 1399 3.411418 ATCGAGGCGTGGCGTGTAG 62.411 63.158 0.00 0.00 0.00 2.74
1370 1412 0.247735 CGTGTAGACGGAGAGAAGCG 60.248 60.000 4.16 0.00 42.18 4.68
1559 1616 1.786928 GCTTTTGCGGTTCGATTCGAG 60.787 52.381 8.98 0.00 34.35 4.04
1665 1722 4.400251 CCTCCCTCAGGGTCGGGT 62.400 72.222 10.50 0.00 44.74 5.28
1670 1727 3.771160 CTCAGGGTCGGGTTCGGG 61.771 72.222 0.00 0.00 36.95 5.14
1704 1761 4.798682 GGAGGAAGGGCGGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
1752 1809 2.115695 TGCATCCCAGCAGCAACA 59.884 55.556 0.00 0.00 40.11 3.33
1777 1834 4.388499 GCACGACCATGACCCCGT 62.388 66.667 0.00 0.00 35.46 5.28
2110 2173 1.065418 GGTCACCCACCCTTCATACTG 60.065 57.143 0.00 0.00 39.69 2.74
2113 2176 1.354368 CACCCACCCTTCATACTGGTT 59.646 52.381 0.00 0.00 0.00 3.67
2169 2232 5.246203 ACAGATGCTCCTCTTACTTGTGTTA 59.754 40.000 0.00 0.00 0.00 2.41
2201 2267 6.477360 TGTGTATGCAATTGAATCATTCATGC 59.523 34.615 16.15 16.15 42.88 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.541868 CAGAGGTGACATAGATATGGTTCCT 59.458 44.000 4.93 7.84 38.00 3.36
83 84 1.066430 GCCTCCACGTCCAGTTATCAA 60.066 52.381 0.00 0.00 0.00 2.57
598 616 3.706802 TGCTCGATCTTCATCTCTGAC 57.293 47.619 0.00 0.00 0.00 3.51
981 1001 2.517650 TTATCACGTGCGATATGCCA 57.482 45.000 11.67 0.00 45.60 4.92
993 1013 2.099263 ACAGTCGGTCTCCATTATCACG 59.901 50.000 0.00 0.00 0.00 4.35
1068 1088 6.323739 GCTCTCCTATTTCATCTAGGATAGGG 59.676 46.154 11.49 0.00 42.93 3.53
1110 1139 5.927954 TTACACGTTGAACCTCAAATACC 57.072 39.130 0.00 0.00 38.22 2.73
1127 1156 2.558359 AGATTTGCTGCCCTGTTTACAC 59.442 45.455 0.00 0.00 0.00 2.90
1147 1176 1.150567 GCACAGAGATGCGCCAGTAG 61.151 60.000 4.18 0.00 35.50 2.57
1185 1214 1.063006 CCAGCAATCGGTCGCATTG 59.937 57.895 9.47 9.47 34.80 2.82
1210 1239 3.259625 GTCACCAAGAAGCTAGGAGTCTT 59.740 47.826 0.00 0.00 31.76 3.01
1282 1311 3.658757 TTTCTTTTCGGGCAAATCAGG 57.341 42.857 0.00 0.00 0.00 3.86
1299 1328 7.303634 TGCCTCTATGAACGTTATCTTTTTC 57.696 36.000 0.00 0.00 0.00 2.29
1357 1399 3.743091 CTCGGCGCTTCTCTCCGTC 62.743 68.421 7.64 0.00 43.35 4.79
1393 1435 2.195139 GACGGGGAGGATCGGAGA 59.805 66.667 0.00 0.00 45.75 3.71
1394 1436 3.288290 CGACGGGGAGGATCGGAG 61.288 72.222 0.00 0.00 34.37 4.63
1670 1727 1.595382 CCTCGCATGGGATCCGAAC 60.595 63.158 13.45 0.00 0.00 3.95
1752 1809 3.749064 ATGGTCGTGCGCTCTCGT 61.749 61.111 9.73 0.00 38.14 4.18
2110 2173 1.066645 ACCGACCGAAATACTCCAACC 60.067 52.381 0.00 0.00 0.00 3.77
2113 2176 1.066716 CCAACCGACCGAAATACTCCA 60.067 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.