Multiple sequence alignment - TraesCS7B01G173100

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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 TraesCS7B01G173100 chr7B 100.000 2708 0 0 1 2708 244692354 244695061 0.000000e+00 5001
1 TraesCS7B01G173100 chr7B 97.042 1758 37 6 144 1887 244715971 244717727 0.000000e+00 2944
2 TraesCS7B01G173100 chr7B 95.381 1667 60 7 340 1990 244644891 244646556 0.000000e+00 2636
3 TraesCS7B01G173100 chr7B 92.130 1817 118 15 688 2487 244651643 244653451 0.000000e+00 2540
4 TraesCS7B01G173100 chr7B 90.416 553 28 9 1991 2543 244646607 244647134 0.000000e+00 704
5 TraesCS7B01G173100 chr7B 93.913 345 17 2 1 342 244644263 244644606 4.000000e-143 518
6 TraesCS7B01G173100 chr7B 82.593 563 54 22 2 559 244651039 244651562 8.840000e-125 457
7 TraesCS7B01G173100 chr7B 97.436 117 3 0 1 117 244715864 244715980 1.640000e-47 200
8 TraesCS7B01G173100 chr7D 95.817 2008 61 6 1 1990 264360349 264362351 0.000000e+00 3221
9 TraesCS7B01G173100 chr7D 96.581 1901 48 2 1 1887 264370220 264372117 0.000000e+00 3134
10 TraesCS7B01G173100 chr7D 91.957 2064 126 17 455 2487 264338738 264340792 0.000000e+00 2856
11 TraesCS7B01G173100 chr7D 92.346 1620 100 19 394 1994 264325902 264327516 0.000000e+00 2283
12 TraesCS7B01G173100 chr7D 96.936 718 13 3 1991 2708 264362402 264363110 0.000000e+00 1195
13 TraesCS7B01G173100 chr7D 93.677 427 24 1 1 427 264338317 264338740 1.060000e-178 636
14 TraesCS7B01G173100 chr7D 80.851 329 22 16 60 388 264325488 264325775 1.260000e-53 220
15 TraesCS7B01G173100 chr7D 88.554 166 18 1 1991 2156 264327563 264327727 1.640000e-47 200
16 TraesCS7B01G173100 chr7D 92.661 109 6 2 2586 2693 264330411 264330518 3.610000e-34 156
17 TraesCS7B01G173100 chr7A 89.608 2117 160 38 422 2487 287889479 287891586 0.000000e+00 2636
18 TraesCS7B01G173100 chr7A 95.268 803 37 1 1192 1994 287862649 287863450 0.000000e+00 1271
19 TraesCS7B01G173100 chr7A 87.917 240 23 5 1991 2229 287863497 287863731 7.380000e-71 278
20 TraesCS7B01G173100 chr7A 93.085 188 12 1 2510 2696 287895920 287896107 9.550000e-70 274
21 TraesCS7B01G173100 chr7A 81.044 364 19 10 1 364 287889160 287889473 7.490000e-61 244
22 TraesCS7B01G173100 chr7A 81.373 306 37 12 220 521 287862381 287862670 5.830000e-57 231
23 TraesCS7B01G173100 chr7A 87.135 171 6 5 1 171 287862228 287862382 2.140000e-41 180
24 TraesCS7B01G173100 chr7A 93.578 109 5 2 2586 2693 287883556 287883663 7.760000e-36 161


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 TraesCS7B01G173100 chr7B 244692354 244695061 2707 False 5001.00 5001 100.00000 1 2708 1 chr7B.!!$F1 2707
1 TraesCS7B01G173100 chr7B 244715864 244717727 1863 False 1572.00 2944 97.23900 1 1887 2 chr7B.!!$F3 1886
2 TraesCS7B01G173100 chr7B 244644263 244653451 9188 False 1371.00 2636 90.88660 1 2543 5 chr7B.!!$F2 2542
3 TraesCS7B01G173100 chr7D 264370220 264372117 1897 False 3134.00 3134 96.58100 1 1887 1 chr7D.!!$F1 1886
4 TraesCS7B01G173100 chr7D 264360349 264363110 2761 False 2208.00 3221 96.37650 1 2708 2 chr7D.!!$F4 2707
5 TraesCS7B01G173100 chr7D 264338317 264340792 2475 False 1746.00 2856 92.81700 1 2487 2 chr7D.!!$F3 2486
6 TraesCS7B01G173100 chr7D 264325488 264330518 5030 False 714.75 2283 88.60300 60 2693 4 chr7D.!!$F2 2633
7 TraesCS7B01G173100 chr7A 287889160 287891586 2426 False 1440.00 2636 85.32600 1 2487 2 chr7A.!!$F4 2486
8 TraesCS7B01G173100 chr7A 287862228 287863731 1503 False 490.00 1271 87.92325 1 2229 4 chr7A.!!$F3 2228

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
51 52 2.526304 TGTCTCCAAGAAGTTCCACG 57.474 50.000 0.00 0.0 0.0 4.94 F
1429 1893 1.404986 CCGCGAAGAAGGTTACATCCA 60.405 52.381 8.23 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1927 0.178987 GGTGATCTCCCTAGCCTCGA 60.179 60.0 2.14 0.0 0.0 4.04 R
2503 9797 0.933097 CAAGAGATTCATCACCGCCG 59.067 55.0 0.00 0.0 0.0 6.46 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
51 52 2.526304 TGTCTCCAAGAAGTTCCACG 57.474 50.000 0.00 0.00 0.00 4.94
158 162 5.163364 GGAGATTGATCCAGAGCAGAGTTTA 60.163 44.000 0.00 0.00 39.34 2.01
665 1128 9.123902 CAATTATGTCAAGATCCACCAATAGAA 57.876 33.333 0.00 0.00 0.00 2.10
841 1305 3.698040 GTGGAGATGAGTTGGCATGATTT 59.302 43.478 0.00 0.00 0.00 2.17
886 1350 5.221185 GGCGTTGTATCATACAGTTCCTCTA 60.221 44.000 0.00 0.00 40.24 2.43
953 1417 3.611530 GCGCTCTCTCATTCTCATACCTC 60.612 52.174 0.00 0.00 0.00 3.85
1429 1893 1.404986 CCGCGAAGAAGGTTACATCCA 60.405 52.381 8.23 0.00 0.00 3.41
1463 1927 1.064906 CAGGATGGTCAGGCTGTTGAT 60.065 52.381 15.27 4.56 0.00 2.57
1782 2246 8.408043 TTTAAAGGATTGCTGATCTTTCTCAA 57.592 30.769 0.00 0.00 33.37 3.02
1855 8710 9.965824 AAACAAAAGTTTTGATCGAACTCATAT 57.034 25.926 30.20 4.65 36.38 1.78
2012 8920 0.171231 GGCCAGATTTTCTTCACGGC 59.829 55.000 0.00 0.00 36.33 5.68
2033 8941 1.065491 CACACAGCCTGGCCTGTTATA 60.065 52.381 16.57 0.00 43.19 0.98
2057 9006 3.685139 TTGTTTTTGTTTGCACCCAGA 57.315 38.095 0.00 0.00 0.00 3.86
2086 9035 4.558538 ACACAATTGCAGTGAAAGAGAC 57.441 40.909 11.19 0.00 40.16 3.36
2185 9135 8.622157 TGTACTTCTAATGATACTCAGTACTGC 58.378 37.037 18.45 4.27 34.81 4.40
2186 9136 7.889873 ACTTCTAATGATACTCAGTACTGCT 57.110 36.000 18.45 7.97 0.00 4.24
2187 9137 7.711846 ACTTCTAATGATACTCAGTACTGCTG 58.288 38.462 18.45 14.80 46.34 4.41
2188 9138 7.340743 ACTTCTAATGATACTCAGTACTGCTGT 59.659 37.037 18.45 19.29 45.23 4.40
2189 9139 7.032377 TCTAATGATACTCAGTACTGCTGTG 57.968 40.000 18.45 10.11 45.23 3.66
2190 9140 3.510388 TGATACTCAGTACTGCTGTGC 57.490 47.619 18.45 14.34 45.23 4.57
2240 9190 1.378382 TGCAATATGGCGTGGCTGT 60.378 52.632 0.00 0.00 36.28 4.40
2311 9504 6.857964 AGAAATTATATGCAGCGCACATAAAC 59.142 34.615 22.03 12.23 40.50 2.01
2503 9797 3.695816 GGTGGCTTCAAAAGATAATCGC 58.304 45.455 0.00 0.00 0.00 4.58
2531 9968 5.994054 GGTGATGAATCTCTTGCTTATGCTA 59.006 40.000 1.96 0.00 40.48 3.49
2590 11834 1.270907 GAAGCCTTGGACTGGAGAGA 58.729 55.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.836125 TGTTGCATGGAAGTCTTTTCTC 57.164 40.909 0.00 0.00 0.00 2.87
158 162 6.830873 ACAAGCTTAGAGCATTCAGAAAAT 57.169 33.333 0.00 0.00 45.56 1.82
627 1067 7.312154 TCTTGACATAATTGCGTGCTATTTTT 58.688 30.769 6.82 0.00 0.00 1.94
628 1068 6.851609 TCTTGACATAATTGCGTGCTATTTT 58.148 32.000 6.82 0.00 0.00 1.82
629 1069 6.435430 TCTTGACATAATTGCGTGCTATTT 57.565 33.333 6.82 0.00 0.00 1.40
630 1070 6.293626 GGATCTTGACATAATTGCGTGCTATT 60.294 38.462 6.74 6.74 0.00 1.73
787 1251 7.981789 TGTATATCAAGTTTGTGAGATCTGGTC 59.018 37.037 0.00 0.00 31.99 4.02
886 1350 6.716284 GCCTTCTTCTGAGGCCTATTTATAT 58.284 40.000 4.42 0.00 42.52 0.86
953 1417 4.196193 TGTGTTGAGTACTTGAGGTTTGG 58.804 43.478 0.00 0.00 0.00 3.28
1429 1893 1.004044 CATCCTGCAGTCCTCCTTGTT 59.996 52.381 13.81 0.00 0.00 2.83
1463 1927 0.178987 GGTGATCTCCCTAGCCTCGA 60.179 60.000 2.14 0.00 0.00 4.04
1736 2200 3.430862 TGGAAGCCAATCGCACGC 61.431 61.111 0.00 0.00 41.38 5.34
1855 8710 3.808726 GCATGCAAAGGTTGAATTCACAA 59.191 39.130 14.21 0.00 0.00 3.33
2012 8920 2.410322 TAACAGGCCAGGCTGTGTGG 62.410 60.000 25.35 0.00 38.21 4.17
2033 8941 2.682352 GGGTGCAAACAAAAACAATGCT 59.318 40.909 0.00 0.00 37.86 3.79
2057 9006 9.160496 TCTTTCACTGCAATTGTGTTTTAAATT 57.840 25.926 7.40 0.00 36.83 1.82
2086 9035 6.128336 TGCCAACAGAAAAATTGAAGTTGTTG 60.128 34.615 12.47 12.47 41.96 3.33
2185 9135 5.704053 TGCTCAAATGATATGGATAGCACAG 59.296 40.000 0.00 0.00 34.05 3.66
2186 9136 5.623169 TGCTCAAATGATATGGATAGCACA 58.377 37.500 0.00 0.00 34.05 4.57
2188 9138 5.623169 TGTGCTCAAATGATATGGATAGCA 58.377 37.500 0.00 0.00 36.45 3.49
2189 9139 6.754702 ATGTGCTCAAATGATATGGATAGC 57.245 37.500 0.00 0.00 0.00 2.97
2190 9140 8.782339 TGTATGTGCTCAAATGATATGGATAG 57.218 34.615 0.00 0.00 0.00 2.08
2240 9190 4.562757 GGTGTCAGTAATGAAGGTAGTGCA 60.563 45.833 0.00 0.00 0.00 4.57
2311 9504 1.205064 CCACGCGCTCAGTTCAAAG 59.795 57.895 5.73 0.00 0.00 2.77
2503 9797 0.933097 CAAGAGATTCATCACCGCCG 59.067 55.000 0.00 0.00 0.00 6.46
2531 9968 5.431765 AGCATGGACGAGATTATCTTTTGT 58.568 37.500 0.00 0.00 0.00 2.83
2590 11834 2.181975 CCAATCTTTCAGCCACCCAAT 58.818 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.