Multiple sequence alignment - TraesCS6B01G154100

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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 TraesCS6B01G154100 chr6B 100.000 2252 0 0 1 2252 157776949 157779200 0.000000e+00 4159
1 TraesCS6B01G154100 chr6B 87.633 1504 122 29 293 1753 157932186 157930704 0.000000e+00 1688
2 TraesCS6B01G154100 chr6B 93.282 521 33 2 1734 2252 157912638 157912118 0.000000e+00 767
3 TraesCS6B01G154100 chr6B 74.927 1707 384 36 564 2243 157902661 157900972 0.000000e+00 741
4 TraesCS6B01G154100 chr6B 76.382 1393 305 19 877 2252 156416409 156417794 0.000000e+00 728
5 TraesCS6B01G154100 chr6B 77.419 1023 216 14 1209 2224 157788721 157789735 1.490000e-166 595
6 TraesCS6B01G154100 chr6D 93.882 2272 92 19 2 2252 82961749 82963994 0.000000e+00 3382
7 TraesCS6B01G154100 chr6D 77.002 1361 291 16 908 2252 81748180 81749534 0.000000e+00 760
8 TraesCS6B01G154100 chr6D 74.503 1510 342 30 741 2234 46903588 46902106 1.140000e-172 616
9 TraesCS6B01G154100 chr6D 83.802 605 92 5 1651 2252 81919528 81920129 9.020000e-159 569
10 TraesCS6B01G154100 chr6A 91.847 2269 147 17 3 2252 99784032 99786281 0.000000e+00 3131
11 TraesCS6B01G154100 chr6A 78.411 1510 293 27 741 2226 99793531 99795031 0.000000e+00 952
12 TraesCS6B01G154100 chr6A 77.046 1503 310 30 745 2226 99929394 99930882 0.000000e+00 832
13 TraesCS6B01G154100 chr6A 75.346 1517 345 25 745 2243 100361296 100362801 0.000000e+00 702
14 TraesCS6B01G154100 chr5D 88.768 1843 160 25 430 2250 372057869 372059686 0.000000e+00 2213
15 TraesCS6B01G154100 chr5D 78.762 1502 284 23 742 2226 372061950 372063433 0.000000e+00 974


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 TraesCS6B01G154100 chr6B 157776949 157779200 2251 False 4159.0 4159 100.000 1 2252 1 chr6B.!!$F2 2251
1 TraesCS6B01G154100 chr6B 157930704 157932186 1482 True 1688.0 1688 87.633 293 1753 1 chr6B.!!$R3 1460
2 TraesCS6B01G154100 chr6B 157912118 157912638 520 True 767.0 767 93.282 1734 2252 1 chr6B.!!$R2 518
3 TraesCS6B01G154100 chr6B 157900972 157902661 1689 True 741.0 741 74.927 564 2243 1 chr6B.!!$R1 1679
4 TraesCS6B01G154100 chr6B 156416409 156417794 1385 False 728.0 728 76.382 877 2252 1 chr6B.!!$F1 1375
5 TraesCS6B01G154100 chr6B 157788721 157789735 1014 False 595.0 595 77.419 1209 2224 1 chr6B.!!$F3 1015
6 TraesCS6B01G154100 chr6D 82961749 82963994 2245 False 3382.0 3382 93.882 2 2252 1 chr6D.!!$F3 2250
7 TraesCS6B01G154100 chr6D 81748180 81749534 1354 False 760.0 760 77.002 908 2252 1 chr6D.!!$F1 1344
8 TraesCS6B01G154100 chr6D 46902106 46903588 1482 True 616.0 616 74.503 741 2234 1 chr6D.!!$R1 1493
9 TraesCS6B01G154100 chr6D 81919528 81920129 601 False 569.0 569 83.802 1651 2252 1 chr6D.!!$F2 601
10 TraesCS6B01G154100 chr6A 99784032 99786281 2249 False 3131.0 3131 91.847 3 2252 1 chr6A.!!$F1 2249
11 TraesCS6B01G154100 chr6A 99793531 99795031 1500 False 952.0 952 78.411 741 2226 1 chr6A.!!$F2 1485
12 TraesCS6B01G154100 chr6A 99929394 99930882 1488 False 832.0 832 77.046 745 2226 1 chr6A.!!$F3 1481
13 TraesCS6B01G154100 chr6A 100361296 100362801 1505 False 702.0 702 75.346 745 2243 1 chr6A.!!$F4 1498
14 TraesCS6B01G154100 chr5D 372057869 372063433 5564 False 1593.5 2213 83.765 430 2250 2 chr5D.!!$F1 1820

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
55 56 0.830444 CGGGGGCTAGGCATGTACTA 60.830 60.0 19.14 0.0 0.0 1.82 F
1044 1128 0.675633 GGTTGTTCAATGCAGCTGGT 59.324 50.0 17.12 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 1296 1.203928 CGAAGTGCTGGATCTAAGCG 58.796 55.000 13.79 0.0 43.88 4.68 R
1955 5819 6.264292 AGTTGCATTTGGACTACAACAACATA 59.736 34.615 6.91 0.0 41.93 2.29 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
55 56 0.830444 CGGGGGCTAGGCATGTACTA 60.830 60.000 19.14 0.00 0.00 1.82
63 64 5.162075 GGCTAGGCATGTACTAGTAAATCG 58.838 45.833 20.42 1.69 40.01 3.34
77 78 3.976490 AATCGGCTCGGGACCCAGA 62.976 63.158 12.15 8.07 0.00 3.86
281 298 3.689347 TGAGATGTGCTGCTTACCAAAT 58.311 40.909 0.00 0.00 0.00 2.32
356 373 6.631971 TTTTGACATGCTGTTCTGTGATAA 57.368 33.333 0.00 0.00 0.00 1.75
387 405 3.040795 CGTCGTATGCACCATACTACAC 58.959 50.000 15.64 8.66 42.99 2.90
448 470 4.534168 CATGAAGCAAAGTGAACTGTGAG 58.466 43.478 4.76 0.00 32.93 3.51
480 530 6.540914 AGTTTCAGTACAGAATTCGTTTTCCA 59.459 34.615 1.13 0.00 0.00 3.53
481 531 5.917541 TCAGTACAGAATTCGTTTTCCAC 57.082 39.130 7.96 1.82 0.00 4.02
482 532 5.607477 TCAGTACAGAATTCGTTTTCCACT 58.393 37.500 7.96 3.66 0.00 4.00
483 533 6.053005 TCAGTACAGAATTCGTTTTCCACTT 58.947 36.000 7.96 0.00 0.00 3.16
484 534 6.540914 TCAGTACAGAATTCGTTTTCCACTTT 59.459 34.615 7.96 0.00 0.00 2.66
485 535 7.066525 TCAGTACAGAATTCGTTTTCCACTTTT 59.933 33.333 7.96 0.00 0.00 2.27
486 536 7.376072 CAGTACAGAATTCGTTTTCCACTTTTC 59.624 37.037 7.96 0.00 0.00 2.29
487 537 5.588240 ACAGAATTCGTTTTCCACTTTTCC 58.412 37.500 0.00 0.00 0.00 3.13
613 666 2.811431 ACGAAATGGAATCACGCTTCAA 59.189 40.909 0.00 0.00 0.00 2.69
614 667 3.120199 ACGAAATGGAATCACGCTTCAAG 60.120 43.478 0.00 0.00 0.00 3.02
953 1037 5.584649 CGAAGCTAGAATTTGGGAATGTGTA 59.415 40.000 0.00 0.00 0.00 2.90
956 1040 7.158099 AGCTAGAATTTGGGAATGTGTAAAC 57.842 36.000 0.00 0.00 0.00 2.01
1044 1128 0.675633 GGTTGTTCAATGCAGCTGGT 59.324 50.000 17.12 0.00 0.00 4.00
1083 1167 3.190744 TGTTGCTAGAGAAGTCCAGTACG 59.809 47.826 0.00 0.00 0.00 3.67
1177 1261 2.830370 GGGATTTCAGCTGGCCGG 60.830 66.667 15.13 7.41 0.00 6.13
1205 1296 7.775561 AGGGATCTCACCAGTTAATTTATTGTC 59.224 37.037 0.00 0.00 0.00 3.18
1293 1384 1.457346 GTAGTTCGAAGACCCTCGGA 58.543 55.000 0.00 0.00 39.35 4.55
1299 1390 2.573369 TCGAAGACCCTCGGATCTAAG 58.427 52.381 0.00 0.00 39.35 2.18
1692 1796 6.881602 AGAGTTTATAGCAAGTGAAAGGAAGG 59.118 38.462 0.00 0.00 0.00 3.46
1955 5819 1.695239 TGATGGCAGCTCCCCTGAT 60.695 57.895 3.69 0.00 44.64 2.90
2157 6023 5.936956 AGTAAGGAAGCATCAAAGAGTTCAG 59.063 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.950205 TTTACTAGTACATGCCTAGCCC 57.050 45.455 16.19 0.00 36.23 5.19
55 56 1.683418 GGGTCCCGAGCCGATTTACT 61.683 60.000 0.00 0.00 39.39 2.24
260 277 2.857186 TTGGTAAGCAGCACATCTCA 57.143 45.000 0.00 0.00 0.00 3.27
267 284 3.485394 TGAACAGATTTGGTAAGCAGCA 58.515 40.909 0.00 0.00 0.00 4.41
281 298 6.208797 AGCACAATAGTACTACACTGAACAGA 59.791 38.462 4.31 0.00 38.24 3.41
387 405 8.088981 ACTACTACACTAAACAAGATGAACTGG 58.911 37.037 0.00 0.00 0.00 4.00
448 470 8.283291 ACGAATTCTGTACTGAAACTTCAATTC 58.717 33.333 17.70 13.43 36.64 2.17
483 533 8.342634 CGTGTATTTTCTTCTTCTTTCAGGAAA 58.657 33.333 0.00 0.00 0.00 3.13
484 534 7.041372 CCGTGTATTTTCTTCTTCTTTCAGGAA 60.041 37.037 0.00 0.00 0.00 3.36
485 535 6.426937 CCGTGTATTTTCTTCTTCTTTCAGGA 59.573 38.462 0.00 0.00 0.00 3.86
486 536 6.426937 TCCGTGTATTTTCTTCTTCTTTCAGG 59.573 38.462 0.00 0.00 0.00 3.86
487 537 7.421530 TCCGTGTATTTTCTTCTTCTTTCAG 57.578 36.000 0.00 0.00 0.00 3.02
591 644 2.415168 TGAAGCGTGATTCCATTTCGTC 59.585 45.455 0.00 0.00 0.00 4.20
727 805 1.827969 CTAGGACTGTCCACCTTCCAG 59.172 57.143 27.48 9.33 39.61 3.86
733 811 2.167398 TTGCGCTAGGACTGTCCACC 62.167 60.000 27.48 14.04 39.61 4.61
953 1037 0.909623 CCCATACGGAGGTCAGGTTT 59.090 55.000 0.00 0.00 0.00 3.27
956 1040 2.171840 CTATCCCATACGGAGGTCAGG 58.828 57.143 0.00 0.00 46.60 3.86
1083 1167 1.337703 TGCAATCTCACAAACCTGCAC 59.662 47.619 0.00 0.00 35.02 4.57
1177 1261 3.567478 ATTAACTGGTGAGATCCCTGC 57.433 47.619 0.00 0.00 0.00 4.85
1205 1296 1.203928 CGAAGTGCTGGATCTAAGCG 58.796 55.000 13.79 0.00 43.88 4.68
1293 1384 5.955355 AGAGAAGACTACAACCAGCTTAGAT 59.045 40.000 0.00 0.00 0.00 1.98
1299 1390 3.257127 AGTCAGAGAAGACTACAACCAGC 59.743 47.826 0.00 0.00 46.52 4.85
1425 1524 4.526262 TGAAAATCAACCACCGGATCAATT 59.474 37.500 9.46 0.00 0.00 2.32
1692 1796 2.716217 AGGCAATCTAAAGCACCTCAC 58.284 47.619 0.00 0.00 0.00 3.51
1955 5819 6.264292 AGTTGCATTTGGACTACAACAACATA 59.736 34.615 6.91 0.00 41.93 2.29


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

AutoCloner maintained by Alex Coulton.