Multiple sequence alignment - TraesCS2B01G191400

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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 TraesCS2B01G191400 chr2B 100.000 2540 0 0 1 2540 166614359 166611820 0.000000e+00 4691
1 TraesCS2B01G191400 chr2B 77.391 1464 303 25 210 1663 746154666 746156111 0.000000e+00 845
2 TraesCS2B01G191400 chr3A 93.866 1565 90 4 98 1662 646857386 646858944 0.000000e+00 2353
3 TraesCS2B01G191400 chr2D 92.289 1686 85 10 1 1663 56585088 56586751 0.000000e+00 2351
4 TraesCS2B01G191400 chr2D 95.805 882 30 3 1666 2540 115959552 115958671 0.000000e+00 1417
5 TraesCS2B01G191400 chr6B 92.243 1663 106 6 1 1663 685976635 685974996 0.000000e+00 2335
6 TraesCS2B01G191400 chr6B 91.345 855 68 5 709 1563 618326725 618327573 0.000000e+00 1164
7 TraesCS2B01G191400 chr6B 91.036 859 68 7 709 1566 618138740 618139590 0.000000e+00 1151
8 TraesCS2B01G191400 chr6B 88.387 465 33 6 253 716 618137895 618138339 7.990000e-150 540
9 TraesCS2B01G191400 chr6B 83.668 398 60 4 2130 2526 679365055 679365448 1.110000e-98 370
10 TraesCS2B01G191400 chr6B 93.213 221 14 1 433 652 618326176 618326396 8.760000e-85 324
11 TraesCS2B01G191400 chr5D 92.432 1110 79 4 557 1666 487947164 487948268 0.000000e+00 1580
12 TraesCS2B01G191400 chr4B 89.562 1188 117 6 4 1191 4556072 4554892 0.000000e+00 1500
13 TraesCS2B01G191400 chr2A 96.263 883 24 4 1666 2540 117404184 117403303 0.000000e+00 1439
14 TraesCS2B01G191400 chr5A 93.694 888 53 3 196 1082 582905173 582906058 0.000000e+00 1327
15 TraesCS2B01G191400 chr5A 77.591 1669 349 22 1 1661 704548195 704549846 0.000000e+00 987
16 TraesCS2B01G191400 chr4A 93.773 819 41 7 852 1670 618557737 618558545 0.000000e+00 1221
17 TraesCS2B01G191400 chr5B 77.618 1671 348 22 4 1665 710683764 710682111 0.000000e+00 990
18 TraesCS2B01G191400 chr5B 84.404 109 15 2 2132 2239 607272799 607272906 3.460000e-19 106
19 TraesCS2B01G191400 chr3B 84.383 397 59 3 2130 2526 467068558 467068165 1.100000e-103 387
20 TraesCS2B01G191400 chr7A 86.707 331 42 2 2130 2460 64595519 64595191 1.440000e-97 366
21 TraesCS2B01G191400 chr6A 86.707 331 42 2 2130 2460 580187120 580187448 1.440000e-97 366
22 TraesCS2B01G191400 chr1B 83.123 397 64 3 2130 2526 15690218 15690611 2.400000e-95 359


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 TraesCS2B01G191400 chr2B 166611820 166614359 2539 True 4691.0 4691 100.0000 1 2540 1 chr2B.!!$R1 2539
1 TraesCS2B01G191400 chr2B 746154666 746156111 1445 False 845.0 845 77.3910 210 1663 1 chr2B.!!$F1 1453
2 TraesCS2B01G191400 chr3A 646857386 646858944 1558 False 2353.0 2353 93.8660 98 1662 1 chr3A.!!$F1 1564
3 TraesCS2B01G191400 chr2D 56585088 56586751 1663 False 2351.0 2351 92.2890 1 1663 1 chr2D.!!$F1 1662
4 TraesCS2B01G191400 chr2D 115958671 115959552 881 True 1417.0 1417 95.8050 1666 2540 1 chr2D.!!$R1 874
5 TraesCS2B01G191400 chr6B 685974996 685976635 1639 True 2335.0 2335 92.2430 1 1663 1 chr6B.!!$R1 1662
6 TraesCS2B01G191400 chr6B 618137895 618139590 1695 False 845.5 1151 89.7115 253 1566 2 chr6B.!!$F2 1313
7 TraesCS2B01G191400 chr6B 618326176 618327573 1397 False 744.0 1164 92.2790 433 1563 2 chr6B.!!$F3 1130
8 TraesCS2B01G191400 chr5D 487947164 487948268 1104 False 1580.0 1580 92.4320 557 1666 1 chr5D.!!$F1 1109
9 TraesCS2B01G191400 chr4B 4554892 4556072 1180 True 1500.0 1500 89.5620 4 1191 1 chr4B.!!$R1 1187
10 TraesCS2B01G191400 chr2A 117403303 117404184 881 True 1439.0 1439 96.2630 1666 2540 1 chr2A.!!$R1 874
11 TraesCS2B01G191400 chr5A 582905173 582906058 885 False 1327.0 1327 93.6940 196 1082 1 chr5A.!!$F1 886
12 TraesCS2B01G191400 chr5A 704548195 704549846 1651 False 987.0 987 77.5910 1 1661 1 chr5A.!!$F2 1660
13 TraesCS2B01G191400 chr4A 618557737 618558545 808 False 1221.0 1221 93.7730 852 1670 1 chr4A.!!$F1 818
14 TraesCS2B01G191400 chr5B 710682111 710683764 1653 True 990.0 990 77.6180 4 1665 1 chr5B.!!$R1 1661

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
181 182 0.178967 TGCAAAGTGGCATCCTTCCA 60.179 50.0 0.0 0.0 39.25 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2901 1.838846 GAGGATGGCGAGGGGATCA 60.839 63.158 0.0 0.0 0.0 2.92 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
26 27 5.183530 TCATCCTTCAACCAGAACATGAT 57.816 39.130 0.00 0.00 30.65 2.45
181 182 0.178967 TGCAAAGTGGCATCCTTCCA 60.179 50.000 0.00 0.00 39.25 3.53
185 186 2.426024 CAAAGTGGCATCCTTCCATCAG 59.574 50.000 0.00 0.00 35.81 2.90
195 196 5.363939 CATCCTTCCATCAGTCTTACCTTC 58.636 45.833 0.00 0.00 0.00 3.46
219 220 2.239681 ACCTTTGTCCACCCACAAAA 57.760 45.000 0.82 0.00 43.90 2.44
231 232 7.038445 TGTCCACCCACAAAATCAATATGAAAT 60.038 33.333 0.00 0.00 0.00 2.17
237 238 9.533253 CCCACAAAATCAATATGAAATACTTCC 57.467 33.333 0.00 0.00 0.00 3.46
273 274 1.068281 AGATCGACCGTCGTCTAGCTA 59.932 52.381 19.89 0.00 41.35 3.32
404 417 5.351948 TTGTCCAGGACATCGATAAATGA 57.648 39.130 23.56 0.86 42.40 2.57
417 430 4.816385 TCGATAAATGATGCAGGTCCTTTC 59.184 41.667 0.00 0.00 0.00 2.62
426 439 0.250727 CAGGTCCTTTCTTTGGGCGA 60.251 55.000 0.00 0.00 0.00 5.54
470 483 2.154462 CAGTGTAAAGTGGCTTGGGAG 58.846 52.381 0.00 0.00 0.00 4.30
580 594 8.542497 AATAAACTTCACTCGTACATTGCTTA 57.458 30.769 0.00 0.00 0.00 3.09
723 1417 7.510001 TCCGTTCCATAACTAAGGTGGATATTA 59.490 37.037 0.00 0.00 41.37 0.98
767 1484 7.663493 GCTTTCTGGCTAGATCTATGGTTTAAT 59.337 37.037 0.00 0.00 31.81 1.40
831 1548 2.124403 ATACTCTCGGACCCGCGT 60.124 61.111 4.92 3.71 39.59 6.01
871 1588 1.635487 AGGCTATCCTGCTTTGAACCA 59.365 47.619 0.00 0.00 42.34 3.67
968 1686 3.449737 CCTTGAATTTGCAGGTGATGGAT 59.550 43.478 0.00 0.00 0.00 3.41
978 1696 3.438781 GCAGGTGATGGATAAACGAACAA 59.561 43.478 0.00 0.00 0.00 2.83
1014 1732 4.978083 CAAGCCTATGACTTGCAAATCT 57.022 40.909 9.58 0.00 38.23 2.40
1016 1734 3.960571 AGCCTATGACTTGCAAATCTGT 58.039 40.909 9.58 0.00 0.00 3.41
1060 1778 1.937546 GCCAATTGACCCCTTCGCAG 61.938 60.000 7.12 0.00 0.00 5.18
1063 1781 2.463589 AATTGACCCCTTCGCAGCGA 62.464 55.000 15.11 15.11 0.00 4.93
1244 1962 3.196207 AATGCCACCACCTGCGTCT 62.196 57.895 0.00 0.00 0.00 4.18
1284 2003 1.276705 TCAATTACTGCCACGCTACCA 59.723 47.619 0.00 0.00 0.00 3.25
1338 2057 1.515521 CCAACAAACCTCGCTCCACC 61.516 60.000 0.00 0.00 0.00 4.61
1518 2237 4.695455 CGAGATTGGAGTACCATGTTGTTT 59.305 41.667 0.00 0.00 46.34 2.83
1583 2303 0.044244 CCCCACCCTCCCTTTCTCTA 59.956 60.000 0.00 0.00 0.00 2.43
1599 2319 8.755977 CCCTTTCTCTACCTTGTAAATGTACTA 58.244 37.037 0.00 0.00 0.00 1.82
1657 2377 3.849953 GCCGTAGCGCCGTCAAAG 61.850 66.667 2.29 0.00 0.00 2.77
1745 2470 8.434392 AGTAAATAAATCGCTGTAAATAGGGGA 58.566 33.333 0.00 0.00 0.00 4.81
1749 2474 4.543590 ATCGCTGTAAATAGGGGAGATG 57.456 45.455 0.00 0.00 0.00 2.90
1941 2671 2.203788 TCGCTGACTTCCCCCACT 60.204 61.111 0.00 0.00 0.00 4.00
2018 2748 4.933064 CGGTCGCTGGAGATCGCC 62.933 72.222 8.81 8.81 37.96 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.205464 AGTGTTTGTAGTTGATCATGTTCTGG 59.795 38.462 0.00 0.0 0.00 3.86
26 27 8.375506 AGGATAGATTTGAGTGTTTGTAGTTGA 58.624 33.333 0.00 0.0 0.00 3.18
181 182 4.857679 AGGTAGACGAAGGTAAGACTGAT 58.142 43.478 0.00 0.0 0.00 2.90
185 186 5.131594 ACAAAGGTAGACGAAGGTAAGAC 57.868 43.478 0.00 0.0 0.00 3.01
195 196 0.682852 TGGGTGGACAAAGGTAGACG 59.317 55.000 0.00 0.0 0.00 4.18
237 238 7.810282 ACGGTCGATCTTATCTATGATGAAAAG 59.190 37.037 0.00 0.0 0.00 2.27
273 274 1.988406 GAAGTACCCCTCGCCACCT 60.988 63.158 0.00 0.0 0.00 4.00
404 417 1.928868 CCCAAAGAAAGGACCTGCAT 58.071 50.000 0.00 0.0 0.00 3.96
417 430 1.604604 TTTTCCTGACTCGCCCAAAG 58.395 50.000 0.00 0.0 0.00 2.77
426 439 3.545703 CACCAGACACTTTTTCCTGACT 58.454 45.455 0.00 0.0 0.00 3.41
470 483 2.278531 AACGGCGCACAAACAAGC 60.279 55.556 10.83 0.0 0.00 4.01
471 484 0.657368 GAGAACGGCGCACAAACAAG 60.657 55.000 10.83 0.0 0.00 3.16
580 594 2.903135 GCAAGATGAGAGCTACCCCTAT 59.097 50.000 0.00 0.0 0.00 2.57
681 942 1.209747 ACGGAAGAATTCTAGCCCCAC 59.790 52.381 8.75 0.0 46.56 4.61
723 1417 3.412237 AGCGGTTGTTGTACCATTACT 57.588 42.857 0.00 0.0 38.12 2.24
746 1463 5.645497 GCCATTAAACCATAGATCTAGCCAG 59.355 44.000 8.70 0.0 0.00 4.85
767 1484 1.691196 CAAGGTTTTCAGTGGAGCCA 58.309 50.000 0.00 0.0 0.00 4.75
831 1548 4.293648 CACCCGTGCGACAGTGGA 62.294 66.667 0.00 0.0 0.00 4.02
978 1696 1.067635 GGCTTGCCATCAAAACGTCAT 60.068 47.619 6.79 0.0 0.00 3.06
1014 1732 3.072330 TGATCCAAACAGCCTTGTAGACA 59.928 43.478 0.00 0.0 36.23 3.41
1016 1734 4.072131 GTTGATCCAAACAGCCTTGTAGA 58.928 43.478 0.00 0.0 36.23 2.59
1060 1778 3.487544 GCATAGTTCTTCCAAATGGTCGC 60.488 47.826 0.00 0.0 36.34 5.19
1063 1781 3.763897 GGTGCATAGTTCTTCCAAATGGT 59.236 43.478 0.00 0.0 36.34 3.55
1138 1856 4.142381 CCCCCTTTTGAATCGTCTTTCATC 60.142 45.833 0.00 0.0 35.64 2.92
1199 1917 4.651503 GGAGGAGGTGAGTGATTGATTCTA 59.348 45.833 0.00 0.0 0.00 2.10
1244 1962 6.723298 TTGAATTTAGCTCTTCCCAAAACA 57.277 33.333 0.00 0.0 0.00 2.83
1284 2003 1.972978 GAGCTGGTGTAGGTCCGTT 59.027 57.895 0.00 0.0 45.92 4.44
1518 2237 9.588096 TTAAGCTACCATCTCATAGATAAGTGA 57.412 33.333 0.00 0.0 32.12 3.41
1535 2254 8.718102 TGAGAGTACAAATCAATTAAGCTACC 57.282 34.615 0.00 0.0 0.00 3.18
1568 2288 2.157989 ACAAGGTAGAGAAAGGGAGGGT 60.158 50.000 0.00 0.0 0.00 4.34
1569 2289 2.552367 ACAAGGTAGAGAAAGGGAGGG 58.448 52.381 0.00 0.0 0.00 4.30
1570 2290 5.757099 TTTACAAGGTAGAGAAAGGGAGG 57.243 43.478 0.00 0.0 0.00 4.30
1571 2291 6.712276 ACATTTACAAGGTAGAGAAAGGGAG 58.288 40.000 0.00 0.0 0.00 4.30
1609 2329 3.429410 GCCAGCCTGAACCATTTCATTAC 60.429 47.826 0.00 0.0 41.05 1.89
1691 2411 9.961266 CGATTTACAAAGATTACATTCGTAACA 57.039 29.630 0.00 0.0 40.35 2.41
1777 2505 5.246429 CCCTCTCTGTTTATATAGACCACCC 59.754 48.000 1.24 0.0 0.00 4.61
2171 2901 1.838846 GAGGATGGCGAGGGGATCA 60.839 63.158 0.00 0.0 0.00 2.92


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

AutoCloner maintained by Alex Coulton.