Multiple sequence alignment - TraesCS7A01G186700

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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 TraesCS7A01G186700 chr7A 100.000 2495 0 0 1 2495 141891548 141889054 0.000000e+00 4608
1 TraesCS7A01G186700 chr7A 98.358 2497 37 3 1 2495 140756640 140754146 0.000000e+00 4381
2 TraesCS7A01G186700 chr7A 97.677 2497 47 5 1 2495 141300813 141298326 0.000000e+00 4279
3 TraesCS7A01G186700 chr7A 97.303 2336 56 5 162 2495 141630622 141628292 0.000000e+00 3958
4 TraesCS7A01G186700 chr7A 97.526 1859 44 2 162 2018 141022969 141021111 0.000000e+00 3177
5 TraesCS7A01G186700 chr7A 97.541 122 3 0 2374 2495 141021111 141020990 2.510000e-50 209
6 TraesCS7A01G186700 chr4A 97.757 2497 50 4 1 2495 588598256 588595764 0.000000e+00 4296
7 TraesCS7A01G186700 chr4A 91.787 207 13 1 2287 2493 552914892 552914690 4.060000e-73 285
8 TraesCS7A01G186700 chr7B 97.217 1761 45 3 736 2495 433300752 433302509 0.000000e+00 2977
9 TraesCS7A01G186700 chr5B 90.899 1791 142 16 712 2494 361542933 361544710 0.000000e+00 2385
10 TraesCS7A01G186700 chr2D 90.476 462 42 2 1 461 642833705 642834165 2.120000e-170 608
11 TraesCS7A01G186700 chr2D 89.056 466 45 5 1 461 431918529 431918993 7.740000e-160 573
12 TraesCS7A01G186700 chr7D 89.610 462 47 1 1 461 569024366 569023905 9.940000e-164 586
13 TraesCS7A01G186700 chr7D 83.511 188 25 5 475 658 168430035 168430220 1.190000e-38 171
14 TraesCS7A01G186700 chr6D 88.793 464 48 3 1 461 396520297 396520759 1.300000e-157 566
15 TraesCS7A01G186700 chr6D 84.409 186 23 5 475 656 160568237 160568420 7.090000e-41 178
16 TraesCS7A01G186700 chr1D 84.324 185 24 4 475 655 295181359 295181542 2.550000e-40 176
17 TraesCS7A01G186700 chr3D 83.957 187 24 5 475 656 99875162 99875347 9.170000e-40 174


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 TraesCS7A01G186700 chr7A 141889054 141891548 2494 True 4608 4608 100.0000 1 2495 1 chr7A.!!$R4 2494
1 TraesCS7A01G186700 chr7A 140754146 140756640 2494 True 4381 4381 98.3580 1 2495 1 chr7A.!!$R1 2494
2 TraesCS7A01G186700 chr7A 141298326 141300813 2487 True 4279 4279 97.6770 1 2495 1 chr7A.!!$R2 2494
3 TraesCS7A01G186700 chr7A 141628292 141630622 2330 True 3958 3958 97.3030 162 2495 1 chr7A.!!$R3 2333
4 TraesCS7A01G186700 chr7A 141020990 141022969 1979 True 1693 3177 97.5335 162 2495 2 chr7A.!!$R5 2333
5 TraesCS7A01G186700 chr4A 588595764 588598256 2492 True 4296 4296 97.7570 1 2495 1 chr4A.!!$R2 2494
6 TraesCS7A01G186700 chr7B 433300752 433302509 1757 False 2977 2977 97.2170 736 2495 1 chr7B.!!$F1 1759
7 TraesCS7A01G186700 chr5B 361542933 361544710 1777 False 2385 2385 90.8990 712 2494 1 chr5B.!!$F1 1782

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
260 261 1.692749 GCCATGGGAGGAGGTGGTA 60.693 63.158 15.13 0.0 34.23 3.25 F
730 732 1.904378 TCCGTCCCGTGTGTGATGA 60.904 57.895 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1261 0.390735 GAGCGCCTTTCGTTTCCCTA 60.391 55.000 2.29 0.0 41.07 3.53 R
1841 1850 4.400251 CCTCCCTCGGTCCACCCT 62.400 72.222 0.00 0.0 0.00 4.34 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
260 261 1.692749 GCCATGGGAGGAGGTGGTA 60.693 63.158 15.13 0.0 34.23 3.25
322 323 3.083997 GCCGTCCCACCTCTGGAT 61.084 66.667 0.00 0.0 40.55 3.41
449 450 9.735646 GGCAGCGTTTTTATTTATTTTTAAGTC 57.264 29.630 0.00 0.0 0.00 3.01
628 630 2.701587 CAGCCAAACTGGACGTTCA 58.298 52.632 0.00 0.0 40.96 3.18
728 730 2.654877 GTCCGTCCCGTGTGTGAT 59.345 61.111 0.00 0.0 0.00 3.06
730 732 1.904378 TCCGTCCCGTGTGTGATGA 60.904 57.895 0.00 0.0 0.00 2.92
923 925 2.828868 GTGTGAGTCTGGGGCACA 59.171 61.111 0.00 0.0 39.95 4.57
989 995 2.676471 GCACGGGCATTTGGAGGT 60.676 61.111 3.77 0.0 40.72 3.85
1253 1261 4.536090 TCTGTTTATGTTCCATCAGGAGGT 59.464 41.667 0.00 0.0 46.74 3.85
1841 1850 5.073554 AGCCTCAATCATATTACATGGTCCA 59.926 40.000 0.00 0.0 0.00 4.02
1858 1867 4.400251 AGGGTGGACCGAGGGAGG 62.400 72.222 0.00 0.0 46.96 4.30
2339 2353 8.052748 AGGCAAAACATGTGGAGTAATAATAGA 58.947 33.333 0.00 0.0 0.00 1.98
2340 2354 8.682710 GGCAAAACATGTGGAGTAATAATAGAA 58.317 33.333 0.00 0.0 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 323 2.049767 TCGACATAGTCCAGCGGCA 61.050 57.895 1.45 0.0 0.00 5.69
449 450 3.848272 ACGTCCAGTTTGGCATAATTG 57.152 42.857 0.00 0.0 37.47 2.32
499 501 3.859221 TCCGGAGTGGACGTGAAA 58.141 55.556 0.00 0.0 43.74 2.69
561 563 1.817099 CGCTCATGTCCCCTTCAGC 60.817 63.158 0.00 0.0 0.00 4.26
628 630 0.768622 TTCACCTCACGTCCCCAAAT 59.231 50.000 0.00 0.0 0.00 2.32
728 730 1.342074 CCAGACAGGAGACCAAGTCA 58.658 55.000 12.98 0.0 41.22 3.41
730 732 1.821061 CGCCAGACAGGAGACCAAGT 61.821 60.000 0.00 0.0 40.01 3.16
980 986 0.335019 GCTACCCCCAACCTCCAAAT 59.665 55.000 0.00 0.0 0.00 2.32
989 995 2.006415 CCCTCCATGCTACCCCCAA 61.006 63.158 0.00 0.0 0.00 4.12
1253 1261 0.390735 GAGCGCCTTTCGTTTCCCTA 60.391 55.000 2.29 0.0 41.07 3.53
1841 1850 4.400251 CCTCCCTCGGTCCACCCT 62.400 72.222 0.00 0.0 0.00 4.34


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

AutoCloner maintained by Alex Coulton.