Multiple sequence alignment - TraesCS6B01G288700

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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 TraesCS6B01G288700 chr6B 100.000 2510 0 0 1 2510 519815172 519812663 0.000000e+00 4636
1 TraesCS6B01G288700 chr6B 82.462 325 30 16 1062 1385 156279785 156279487 2.480000e-65 259
2 TraesCS6B01G288700 chr6A 92.345 1842 88 24 1 1817 484849543 484847730 0.000000e+00 2571
3 TraesCS6B01G288700 chr6A 93.740 607 31 5 1903 2505 484847529 484846926 0.000000e+00 904
4 TraesCS6B01G288700 chr6D 91.522 1557 67 27 288 1817 344301116 344299598 0.000000e+00 2084
5 TraesCS6B01G288700 chr6D 96.132 698 20 5 1814 2506 344299571 344298876 0.000000e+00 1133
6 TraesCS6B01G288700 chr6D 94.020 301 14 3 1 299 344301874 344301576 1.060000e-123 453
7 TraesCS6B01G288700 chrUn 89.327 431 34 9 1063 1482 79140674 79141103 4.750000e-147 531
8 TraesCS6B01G288700 chr7A 90.058 171 16 1 1217 1387 648569891 648569722 1.170000e-53 220
9 TraesCS6B01G288700 chr3B 90.000 170 9 6 1218 1387 819915686 819915847 1.960000e-51 213
10 TraesCS6B01G288700 chr2D 76.690 429 62 22 1066 1466 563958633 563959051 1.180000e-48 204
11 TraesCS6B01G288700 chr2B 76.457 429 63 24 1066 1466 674722577 674722995 5.480000e-47 198
12 TraesCS6B01G288700 chr2A 76.212 433 60 25 1066 1466 704004972 704005393 3.300000e-44 189


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 TraesCS6B01G288700 chr6B 519812663 519815172 2509 True 4636.000000 4636 100.000000 1 2510 1 chr6B.!!$R2 2509
1 TraesCS6B01G288700 chr6A 484846926 484849543 2617 True 1737.500000 2571 93.042500 1 2505 2 chr6A.!!$R1 2504
2 TraesCS6B01G288700 chr6D 344298876 344301874 2998 True 1223.333333 2084 93.891333 1 2506 3 chr6D.!!$R1 2505

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
162 166 0.544833 TCCCTAACCCCGTTGCTACA 60.545 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 2472 1.569493 CGTCCACAAGTTTCGCCAG 59.431 57.895 0.0 0.0 0.0 4.85 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
74 76 2.806745 GCTGAGTGACAGGTAGCAAACA 60.807 50.000 0.00 0.00 45.82 2.83
75 77 2.802816 CTGAGTGACAGGTAGCAAACAC 59.197 50.000 0.00 1.23 42.39 3.32
92 95 1.065709 ACACCAACCGAAAGTCTGTGT 60.066 47.619 0.00 0.00 37.94 3.72
162 166 0.544833 TCCCTAACCCCGTTGCTACA 60.545 55.000 0.00 0.00 0.00 2.74
173 177 2.161609 CCGTTGCTACAAGATGGGTTTC 59.838 50.000 0.00 0.00 0.00 2.78
299 781 7.921786 TGACATAATTGAAACTCGGAATCTT 57.078 32.000 0.00 0.00 0.00 2.40
345 839 2.065789 TGATGCAGAGGCCGATGGA 61.066 57.895 11.60 9.35 40.13 3.41
347 841 0.954449 GATGCAGAGGCCGATGGATG 60.954 60.000 19.26 5.02 40.13 3.51
437 931 9.952030 TCTGTACATGGATTACTTACAATTTCA 57.048 29.630 0.00 0.00 0.00 2.69
509 1003 9.628500 ATTTCCTCTACATGGATTACTTTTACC 57.372 33.333 0.00 0.00 33.09 2.85
510 1004 7.743116 TCCTCTACATGGATTACTTTTACCA 57.257 36.000 0.00 0.00 36.83 3.25
511 1005 7.562135 TCCTCTACATGGATTACTTTTACCAC 58.438 38.462 0.00 0.00 35.19 4.16
541 1036 3.508793 CACCTTGTTTCTCTACGACCCTA 59.491 47.826 0.00 0.00 0.00 3.53
641 1136 4.751600 TGACTCTTGTTAAGACATGTGCTG 59.248 41.667 1.15 0.00 35.29 4.41
769 1265 1.254026 CGAACCACTCCACTGACCTA 58.746 55.000 0.00 0.00 0.00 3.08
770 1266 1.067776 CGAACCACTCCACTGACCTAC 60.068 57.143 0.00 0.00 0.00 3.18
771 1267 2.249139 GAACCACTCCACTGACCTACT 58.751 52.381 0.00 0.00 0.00 2.57
772 1268 3.428532 GAACCACTCCACTGACCTACTA 58.571 50.000 0.00 0.00 0.00 1.82
773 1269 3.088789 ACCACTCCACTGACCTACTAG 57.911 52.381 0.00 0.00 0.00 2.57
938 1451 1.379977 ACGACTAGCCAGCCAGCTA 60.380 57.895 5.28 5.28 42.70 3.32
950 1463 4.914420 CAGCTACTCCTCCGCGCG 62.914 72.222 25.67 25.67 0.00 6.86
953 1466 4.492160 CTACTCCTCCGCGCGCAA 62.492 66.667 32.61 17.63 0.00 4.85
954 1467 4.492160 TACTCCTCCGCGCGCAAG 62.492 66.667 32.61 25.74 43.44 4.01
996 1516 3.319198 GAACTCTCCCGGTGCCCA 61.319 66.667 0.00 0.00 0.00 5.36
1312 1835 3.358076 GAGTTCGAGGACGGCCAGG 62.358 68.421 11.69 0.00 40.21 4.45
1398 1921 4.778415 CACTCCTCGTGCCCGTCG 62.778 72.222 0.00 0.00 36.72 5.12
1723 2250 4.678622 TGAAGGCGTGTGTACATACATAG 58.321 43.478 20.85 7.50 38.63 2.23
1882 2472 3.521947 AACTGCCCGTGAGTATAACTC 57.478 47.619 0.01 0.01 45.26 3.01
2011 2689 1.191944 CATAGCGCAGTACTCGTGTG 58.808 55.000 11.47 3.81 0.00 3.82
2012 2690 0.809385 ATAGCGCAGTACTCGTGTGT 59.191 50.000 11.47 0.00 0.00 3.72
2014 2692 0.594602 AGCGCAGTACTCGTGTGTTA 59.405 50.000 11.47 0.00 0.00 2.41
2015 2693 1.201647 AGCGCAGTACTCGTGTGTTAT 59.798 47.619 11.47 0.00 0.00 1.89
2016 2694 1.582502 GCGCAGTACTCGTGTGTTATC 59.417 52.381 0.30 0.00 0.00 1.75
2179 2861 5.411781 GCTACAACTAGAGTACTGCAACAT 58.588 41.667 0.00 0.00 0.00 2.71
2240 2922 5.412286 TCACACATAACACATCATCCACAAG 59.588 40.000 0.00 0.00 0.00 3.16
2241 2923 4.701651 ACACATAACACATCATCCACAAGG 59.298 41.667 0.00 0.00 0.00 3.61
2272 2954 5.534654 TGCAACCTAGATAGCAAACAAAAGT 59.465 36.000 0.00 0.00 33.48 2.66
2355 3037 6.709018 TCTACTTATGTTGATCATCCGTGA 57.291 37.500 0.00 0.00 37.91 4.35
2404 3086 1.677966 CCTGAACGACTCCTCCCGA 60.678 63.158 0.00 0.00 0.00 5.14
2442 3124 1.215647 GACATCGCACGAGAAGGGT 59.784 57.895 0.00 0.00 0.00 4.34
2506 3189 1.072806 TGCTCAGCTTGTCCAGAATGT 59.927 47.619 0.00 0.00 0.00 2.71
2507 3190 2.157738 GCTCAGCTTGTCCAGAATGTT 58.842 47.619 0.00 0.00 0.00 2.71
2508 3191 2.095364 GCTCAGCTTGTCCAGAATGTTG 60.095 50.000 0.00 0.00 0.00 3.33
2509 3192 3.144506 CTCAGCTTGTCCAGAATGTTGT 58.855 45.455 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 2.484241 GGTACACAGACTTTCGGTTGGT 60.484 50.000 0.00 0.00 0.00 3.67
75 77 2.140717 GGTACACAGACTTTCGGTTGG 58.859 52.381 0.00 0.00 0.00 3.77
92 95 3.056458 CAGCACTCCGGTGTGGTA 58.944 61.111 33.39 0.00 45.37 3.25
127 131 2.936032 GAGGGGACAGGTGGCCTT 60.936 66.667 3.32 0.00 44.77 4.35
162 166 1.156736 CGAGCAACGAAACCCATCTT 58.843 50.000 0.00 0.00 45.77 2.40
173 177 1.927174 CCTTGACTTATCCGAGCAACG 59.073 52.381 0.00 0.00 42.18 4.10
299 781 1.146041 GCCGTCCATATGCCACTCA 59.854 57.895 0.00 0.00 0.00 3.41
475 969 8.915057 AATCCATGTAGAGGAAATTAGACATG 57.085 34.615 5.95 5.95 42.34 3.21
508 1002 6.173339 AGAGAAACAAGGTGTATATGTGTGG 58.827 40.000 0.00 0.00 0.00 4.17
509 1003 7.009265 CGTAGAGAAACAAGGTGTATATGTGTG 59.991 40.741 0.00 0.00 0.00 3.82
510 1004 7.033791 CGTAGAGAAACAAGGTGTATATGTGT 58.966 38.462 0.00 0.00 0.00 3.72
511 1005 7.220300 GTCGTAGAGAAACAAGGTGTATATGTG 59.780 40.741 0.00 0.00 36.95 3.21
541 1036 1.065418 CCGCCAGGAAACTAGGATGTT 60.065 52.381 0.00 0.00 40.21 2.71
641 1136 2.597520 GTCACCGTAGTGCTCTCTTTC 58.402 52.381 0.00 0.00 44.16 2.62
841 1346 4.677584 GCTGGCTTATATAGAGATCGTGG 58.322 47.826 0.00 0.00 0.00 4.94
845 1350 4.202070 GGGTCGCTGGCTTATATAGAGATC 60.202 50.000 0.00 0.00 0.00 2.75
950 1463 4.712425 CGCTGGCTTGTGGCTTGC 62.712 66.667 0.00 0.00 41.46 4.01
951 1464 4.047059 CCGCTGGCTTGTGGCTTG 62.047 66.667 0.00 0.00 41.46 4.01
996 1516 1.377725 CCTTCTTGCCGCCATGTCT 60.378 57.895 0.00 0.00 0.00 3.41
1267 1790 4.492160 GATGGCGCACTCGTCCGA 62.492 66.667 10.83 0.00 40.09 4.55
1882 2472 1.569493 CGTCCACAAGTTTCGCCAG 59.431 57.895 0.00 0.00 0.00 4.85
2011 2689 7.417496 ACTTGAAACTTTACCTGTCGATAAC 57.583 36.000 0.00 0.00 0.00 1.89
2012 2690 8.441312 AAACTTGAAACTTTACCTGTCGATAA 57.559 30.769 0.00 0.00 0.00 1.75
2014 2692 6.937436 AAACTTGAAACTTTACCTGTCGAT 57.063 33.333 0.00 0.00 0.00 3.59
2015 2693 7.846644 TTAAACTTGAAACTTTACCTGTCGA 57.153 32.000 0.00 0.00 0.00 4.20
2016 2694 8.953990 CATTTAAACTTGAAACTTTACCTGTCG 58.046 33.333 0.00 0.00 0.00 4.35
2093 2775 5.467035 TTTGATAAAAGTTGAGGCTTGGG 57.533 39.130 0.00 0.00 0.00 4.12
2096 2778 6.462909 CCACCTTTTGATAAAAGTTGAGGCTT 60.463 38.462 11.56 0.00 41.69 4.35
2121 2803 5.898630 AACGGTTTGAATGTTTATTGCAC 57.101 34.783 0.00 0.00 0.00 4.57
2122 2804 6.019479 GTGAAACGGTTTGAATGTTTATTGCA 60.019 34.615 11.43 0.00 36.06 4.08
2179 2861 4.740695 GGCACTTTGCGTTTGTAATTTGTA 59.259 37.500 0.00 0.00 46.21 2.41
2240 2922 5.551233 TGCTATCTAGGTTGCATTCATACC 58.449 41.667 8.11 0.00 0.00 2.73
2241 2923 7.012327 TGTTTGCTATCTAGGTTGCATTCATAC 59.988 37.037 12.95 7.35 35.27 2.39
2272 2954 6.777580 TCTGCTAGGATGTGATAGTGTTGATA 59.222 38.462 0.00 0.00 0.00 2.15
2355 3037 1.063717 CCTAACCCTGCCATTGGATGT 60.064 52.381 6.95 0.00 0.00 3.06
2404 3086 4.099113 TGTCTTCTGCTTCTCGATCATCAT 59.901 41.667 0.00 0.00 0.00 2.45
2442 3124 7.468141 AATTATATCGATGGTGCTCAGTCTA 57.532 36.000 8.54 0.00 0.00 2.59
2477 3160 2.551459 GACAAGCTGAGCACATGTCTTT 59.449 45.455 22.34 0.00 36.61 2.52


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

AutoCloner maintained by Alex Coulton.