Multiple sequence alignment - TraesCS2B01G269900

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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 TraesCS2B01G269900 chr2B 100.000 2387 0 0 1 2387 367850409 367852795 0 4409
1 TraesCS2B01G269900 chr5B 94.105 2392 129 8 1 2387 216109985 216107601 0 3626
2 TraesCS2B01G269900 chr5B 93.344 2404 134 17 1 2387 157357357 157354963 0 3530
3 TraesCS2B01G269900 chr5B 93.331 2399 145 13 1 2387 209747434 209745039 0 3530
4 TraesCS2B01G269900 chr5B 93.203 2398 145 13 1 2387 443756333 443758723 0 3509
5 TraesCS2B01G269900 chr4B 93.659 2397 132 13 1 2387 411911179 411908793 0 3567
6 TraesCS2B01G269900 chr3B 93.589 2402 134 11 1 2387 251544809 251542413 0 3565
7 TraesCS2B01G269900 chr3B 93.408 2397 140 13 1 2387 441312899 441315287 0 3535
8 TraesCS2B01G269900 chr3B 93.408 2397 137 12 1 2387 379742421 379744806 0 3531
9 TraesCS2B01G269900 chr3B 93.311 2392 145 9 1 2387 374176158 374178539 0 3517


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 TraesCS2B01G269900 chr2B 367850409 367852795 2386 False 4409 4409 100.000 1 2387 1 chr2B.!!$F1 2386
1 TraesCS2B01G269900 chr5B 216107601 216109985 2384 True 3626 3626 94.105 1 2387 1 chr5B.!!$R3 2386
2 TraesCS2B01G269900 chr5B 157354963 157357357 2394 True 3530 3530 93.344 1 2387 1 chr5B.!!$R1 2386
3 TraesCS2B01G269900 chr5B 209745039 209747434 2395 True 3530 3530 93.331 1 2387 1 chr5B.!!$R2 2386
4 TraesCS2B01G269900 chr5B 443756333 443758723 2390 False 3509 3509 93.203 1 2387 1 chr5B.!!$F1 2386
5 TraesCS2B01G269900 chr4B 411908793 411911179 2386 True 3567 3567 93.659 1 2387 1 chr4B.!!$R1 2386
6 TraesCS2B01G269900 chr3B 251542413 251544809 2396 True 3565 3565 93.589 1 2387 1 chr3B.!!$R1 2386
7 TraesCS2B01G269900 chr3B 441312899 441315287 2388 False 3535 3535 93.408 1 2387 1 chr3B.!!$F3 2386
8 TraesCS2B01G269900 chr3B 379742421 379744806 2385 False 3531 3531 93.408 1 2387 1 chr3B.!!$F2 2386
9 TraesCS2B01G269900 chr3B 374176158 374178539 2381 False 3517 3517 93.311 1 2387 1 chr3B.!!$F1 2386

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
774 788 0.252197 GCTTCACCGGGACCTACAAT 59.748 55.0 6.32 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2097 0.393077 CAACTGTCCGTCCTCCTTGT 59.607 55.0 0.0 0.0 0.0 3.16 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
36 38 5.540400 ATGACATGCTTAATTGGGATTGG 57.460 39.130 0.00 0.00 0.00 3.16
275 285 3.466836 TGTTGCAGACTTTTCAGACGAT 58.533 40.909 0.00 0.00 0.00 3.73
342 353 5.089970 TGGAGTTGATGGACTCACTTATG 57.910 43.478 7.27 0.00 46.21 1.90
534 546 4.021632 CAGAGATCAGACTGTTTGAGGTCA 60.022 45.833 7.14 0.00 35.18 4.02
580 592 0.313987 CACGCTGACTGTAGGACACA 59.686 55.000 0.00 0.00 35.30 3.72
618 632 4.647399 GCCCTAGATCACTACTCACTCTTT 59.353 45.833 0.00 0.00 0.00 2.52
687 701 0.736053 GGAACAAGTTCACGCAACCA 59.264 50.000 14.25 0.00 41.20 3.67
750 764 5.067936 CACTAGATACCTGAACATCGGAGTT 59.932 44.000 0.00 0.00 0.00 3.01
774 788 0.252197 GCTTCACCGGGACCTACAAT 59.748 55.000 6.32 0.00 0.00 2.71
798 812 2.028930 CACTTTACCTGAAGAGGAGCGT 60.029 50.000 0.00 0.00 42.93 5.07
863 883 4.327680 GTCACTGAGCCCATAGAGTTTTT 58.672 43.478 0.00 0.00 0.00 1.94
892 912 2.472029 CACCAACCTGGAGTCTAGGAT 58.528 52.381 27.89 14.54 40.96 3.24
913 933 3.896133 GCATGGCAGCCCACATCG 61.896 66.667 9.64 0.00 45.77 3.84
938 958 3.670625 TGGGACGTATTGGAGAAGTTTG 58.329 45.455 0.00 0.00 0.00 2.93
988 1008 1.376609 GATTTGTGGGCGCCGAGATT 61.377 55.000 22.54 5.75 0.00 2.40
991 1011 1.895020 TTGTGGGCGCCGAGATTAGT 61.895 55.000 22.54 0.00 0.00 2.24
999 1019 2.673833 CGCCGAGATTAGTAATGGGAC 58.326 52.381 0.00 0.00 0.00 4.46
1079 1099 0.179073 ATTCGATGCCAGGAGAACCG 60.179 55.000 0.00 0.00 41.83 4.44
1149 1169 3.494398 CGGAACTGGAGGAAGAACTCAAA 60.494 47.826 0.00 0.00 39.27 2.69
1180 1200 5.248248 TGCGATGGATATGAGGAGGAAATAA 59.752 40.000 0.00 0.00 0.00 1.40
1204 1224 6.402222 ACAACACTAGTGGAGAAGAATGATC 58.598 40.000 26.12 0.00 34.19 2.92
1370 1399 6.885376 GGAGCAGATATCATGGAATCTTCATT 59.115 38.462 5.32 0.00 29.93 2.57
1463 1493 8.100791 AGCACTTTTGTAATGATAGTTAGACCA 58.899 33.333 0.00 0.00 0.00 4.02
1472 1502 7.658179 AATGATAGTTAGACCATTGTATGCG 57.342 36.000 0.00 0.00 0.00 4.73
1536 1568 5.714333 TCATGTGCATATGGGTAGTGTTTTT 59.286 36.000 21.57 0.00 0.00 1.94
1554 1587 6.309251 GTGTTTTTCTCTCTAGACCTCATTCG 59.691 42.308 0.00 0.00 0.00 3.34
1595 1630 1.839994 CTAAACCCTCAGATGCCTCCA 59.160 52.381 0.00 0.00 0.00 3.86
1598 1633 1.277580 ACCCTCAGATGCCTCCAAGG 61.278 60.000 1.56 1.56 38.80 3.61
1683 1718 3.423539 TGCAATTGCTAGTCCAGAACT 57.576 42.857 29.37 0.00 42.66 3.01
1709 1747 5.722021 ATCAGGGGAACAACAACAATAAC 57.278 39.130 0.00 0.00 0.00 1.89
1710 1748 4.537751 TCAGGGGAACAACAACAATAACA 58.462 39.130 0.00 0.00 0.00 2.41
1711 1749 4.956700 TCAGGGGAACAACAACAATAACAA 59.043 37.500 0.00 0.00 0.00 2.83
1764 1814 5.294734 TCACTTAACCCGTTTTCTTAGGT 57.705 39.130 0.00 0.00 0.00 3.08
1767 1817 4.823442 ACTTAACCCGTTTTCTTAGGTTGG 59.177 41.667 3.58 0.04 42.49 3.77
1796 1846 1.204941 GTGTTCTCCAGTAGCACCGAT 59.795 52.381 0.00 0.00 0.00 4.18
1809 1859 0.801872 CACCGATCCGATTGTTGCAA 59.198 50.000 0.00 0.00 0.00 4.08
1904 1955 1.457346 CACATCAGCTTGAAGGACCC 58.543 55.000 0.00 0.00 0.00 4.46
1913 1964 2.514824 GAAGGACCCGCAGCATCC 60.515 66.667 0.00 0.00 0.00 3.51
1958 2009 2.743636 ACCCTATCAACACTGTCACG 57.256 50.000 0.00 0.00 0.00 4.35
1989 2040 3.370840 TCCAGTAGGCTTTCCGTACTA 57.629 47.619 0.00 0.00 37.47 1.82
2028 2079 2.615912 GCTATGGCCATGAAGAAGTGTC 59.384 50.000 29.04 0.83 0.00 3.67
2265 2317 1.003349 AGCAGCAGCAGATTGAGAACT 59.997 47.619 3.17 0.00 45.49 3.01
2326 2378 2.744202 CTCAGCAGAAGCCACGTTTTAT 59.256 45.455 0.00 0.00 43.56 1.40
2331 2383 1.002773 AGAAGCCACGTTTTATCCCGT 59.997 47.619 0.00 0.00 37.90 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.322828 CCTCCCAATCCCAATTAAGCATG 59.677 47.826 0.00 0.00 0.00 4.06
36 38 0.680280 TGAGAGCGTAGACACCCTCC 60.680 60.000 0.00 0.00 31.05 4.30
106 108 4.630644 TGCATAAAGCCAATTTTTCCCA 57.369 36.364 0.00 0.00 44.83 4.37
275 285 1.822990 CGACCTAAGGCACCTTACTCA 59.177 52.381 5.00 0.00 37.47 3.41
534 546 4.716784 TCTGATACCATCTTGTAGCAACCT 59.283 41.667 0.00 0.00 36.75 3.50
580 592 4.101856 TCTAGGGCTTTAGCTTAGTGGTT 58.898 43.478 0.00 0.00 41.70 3.67
618 632 7.456725 AGAAAAGATGAGGAGTCAGAAATGAA 58.543 34.615 0.00 0.00 35.66 2.57
687 701 4.383118 CGTCCAAAGGGTGTATCTTCATCT 60.383 45.833 0.00 0.00 34.93 2.90
750 764 2.747686 GTCCCGGTGAAGCTTGGA 59.252 61.111 2.10 0.00 0.00 3.53
774 788 2.303022 CTCCTCTTCAGGTAAAGTGGCA 59.697 50.000 0.00 0.00 41.28 4.92
798 812 4.753107 GGTACTTGAACTTGAATCGTCCAA 59.247 41.667 0.00 0.00 0.00 3.53
863 883 1.144708 TCCAGGTTGGTGCATCAAAGA 59.855 47.619 15.37 6.43 39.03 2.52
892 912 1.638679 ATGTGGGCTGCCATGCTCTA 61.639 55.000 22.05 0.00 33.90 2.43
913 933 2.325583 TCTCCAATACGTCCCATTGC 57.674 50.000 0.00 0.00 33.00 3.56
938 958 2.725221 ATCCTTGAGATCCTTGTGGC 57.275 50.000 0.00 0.00 0.00 5.01
988 1008 5.368230 TGGTGCTAATCATGTCCCATTACTA 59.632 40.000 0.00 0.00 0.00 1.82
991 1011 4.446167 CCTGGTGCTAATCATGTCCCATTA 60.446 45.833 0.00 0.00 0.00 1.90
999 1019 3.565764 TCCTTCCTGGTGCTAATCATG 57.434 47.619 0.00 0.00 37.07 3.07
1005 1025 4.199002 TGATCTATCCTTCCTGGTGCTA 57.801 45.455 0.00 0.00 37.07 3.49
1149 1169 4.958581 TCCTCATATCCATCGCATGTAGAT 59.041 41.667 0.00 0.00 0.00 1.98
1180 1200 5.808366 TCATTCTTCTCCACTAGTGTTGT 57.192 39.130 21.18 0.00 0.00 3.32
1204 1224 8.602328 CATAAACACTCTTAGCTTCTTCAGATG 58.398 37.037 0.00 0.00 0.00 2.90
1370 1399 3.554337 GGTCGACTAGAAAAACTGCTCCA 60.554 47.826 16.46 0.00 0.00 3.86
1463 1493 5.058149 TCAATCAAACAAGCGCATACAAT 57.942 34.783 11.47 0.00 0.00 2.71
1472 1502 7.647907 AATCACTTCATTCAATCAAACAAGC 57.352 32.000 0.00 0.00 0.00 4.01
1536 1568 5.935945 AGAATCGAATGAGGTCTAGAGAGA 58.064 41.667 0.00 0.00 0.00 3.10
1595 1630 1.067635 GCAAATCCATTGTCACGCCTT 60.068 47.619 0.00 0.00 41.32 4.35
1598 1633 2.352503 AAGCAAATCCATTGTCACGC 57.647 45.000 0.00 0.00 41.32 5.34
1683 1718 4.715534 TGTTGTTGTTCCCCTGATTCTA 57.284 40.909 0.00 0.00 0.00 2.10
1709 1747 1.435515 CGGTGGTGGGTTGTTGTTG 59.564 57.895 0.00 0.00 0.00 3.33
1710 1748 2.419739 GCGGTGGTGGGTTGTTGTT 61.420 57.895 0.00 0.00 0.00 2.83
1711 1749 2.831284 GCGGTGGTGGGTTGTTGT 60.831 61.111 0.00 0.00 0.00 3.32
1764 1814 1.003580 GGAGAACACCAGCAGATCCAA 59.996 52.381 0.00 0.00 0.00 3.53
1796 1846 3.847542 CCAATCATTTGCAACAATCGGA 58.152 40.909 0.00 0.00 0.00 4.55
1904 1955 4.100084 TCCCACCAGGATGCTGCG 62.100 66.667 9.03 4.98 40.93 5.18
1913 1964 1.815003 GCTGTGAAATTCTCCCACCAG 59.185 52.381 0.00 0.00 0.00 4.00
1974 2025 2.530460 TGGGTAGTACGGAAAGCCTA 57.470 50.000 1.53 0.00 0.00 3.93
1989 2040 0.610232 GCTCCTGCTGAAACATGGGT 60.610 55.000 0.00 0.00 36.03 4.51
2028 2079 1.906757 TGTCGCAAGTTGCAAAACTG 58.093 45.000 26.56 9.97 45.36 3.16
2045 2097 0.393077 CAACTGTCCGTCCTCCTTGT 59.607 55.000 0.00 0.00 0.00 3.16
2265 2317 3.307691 CCTTGTCCATACTTCCTCTTGCA 60.308 47.826 0.00 0.00 0.00 4.08
2331 2383 2.093658 GCTGGAACTGTCTTCCCGATTA 60.094 50.000 0.00 0.00 37.79 1.75
2340 2392 1.656587 TGGGTATGCTGGAACTGTCT 58.343 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.