Multiple sequence alignment - TraesCS7B01G366000

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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 TraesCS7B01G366000 chr7B 100.000 4463 0 0 1 4463 629987631 629992093 0.000000e+00 8242
1 TraesCS7B01G366000 chr7B 94.388 392 22 0 4072 4463 750156248 750155857 1.780000e-168 603
2 TraesCS7B01G366000 chr6B 96.791 4487 118 7 1 4463 572516258 572511774 0.000000e+00 7465
3 TraesCS7B01G366000 chr6B 95.846 4478 158 13 1 4463 82736864 82732400 0.000000e+00 7214
4 TraesCS7B01G366000 chr1B 96.725 4488 122 5 1 4463 567735555 567731068 0.000000e+00 7450
5 TraesCS7B01G366000 chr1B 96.458 4489 129 10 1 4463 676864369 676859885 0.000000e+00 7382
6 TraesCS7B01G366000 chr1B 96.101 4488 148 7 1 4462 7902781 7898295 0.000000e+00 7293
7 TraesCS7B01G366000 chr4A 96.636 4489 124 8 1 4463 673171250 673166763 0.000000e+00 7428
8 TraesCS7B01G366000 chr4A 96.205 4479 133 13 1 4463 645851501 645855958 0.000000e+00 7295
9 TraesCS7B01G366000 chr2B 96.523 4487 129 7 1 4463 785300733 785296250 0.000000e+00 7396
10 TraesCS7B01G366000 chr2B 96.314 4476 127 15 1 4463 662568097 662572547 0.000000e+00 7317
11 TraesCS7B01G366000 chr5B 96.301 4488 136 6 1 4463 18261490 18257008 0.000000e+00 7341
12 TraesCS7B01G366000 chr5B 96.569 2011 58 2 2464 4463 568809872 568811882 0.000000e+00 3321
13 TraesCS7B01G366000 chr3B 96.234 4487 139 7 1 4463 667633221 667637701 0.000000e+00 7323
14 TraesCS7B01G366000 chr3B 93.333 150 9 1 3921 4070 13141456 13141604 2.090000e-53 220
15 TraesCS7B01G366000 chr2A 94.576 3927 209 4 1 3924 773697662 773693737 0.000000e+00 6069


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 TraesCS7B01G366000 chr7B 629987631 629992093 4462 False 8242 8242 100.000 1 4463 1 chr7B.!!$F1 4462
1 TraesCS7B01G366000 chr6B 572511774 572516258 4484 True 7465 7465 96.791 1 4463 1 chr6B.!!$R2 4462
2 TraesCS7B01G366000 chr6B 82732400 82736864 4464 True 7214 7214 95.846 1 4463 1 chr6B.!!$R1 4462
3 TraesCS7B01G366000 chr1B 567731068 567735555 4487 True 7450 7450 96.725 1 4463 1 chr1B.!!$R2 4462
4 TraesCS7B01G366000 chr1B 676859885 676864369 4484 True 7382 7382 96.458 1 4463 1 chr1B.!!$R3 4462
5 TraesCS7B01G366000 chr1B 7898295 7902781 4486 True 7293 7293 96.101 1 4462 1 chr1B.!!$R1 4461
6 TraesCS7B01G366000 chr4A 673166763 673171250 4487 True 7428 7428 96.636 1 4463 1 chr4A.!!$R1 4462
7 TraesCS7B01G366000 chr4A 645851501 645855958 4457 False 7295 7295 96.205 1 4463 1 chr4A.!!$F1 4462
8 TraesCS7B01G366000 chr2B 785296250 785300733 4483 True 7396 7396 96.523 1 4463 1 chr2B.!!$R1 4462
9 TraesCS7B01G366000 chr2B 662568097 662572547 4450 False 7317 7317 96.314 1 4463 1 chr2B.!!$F1 4462
10 TraesCS7B01G366000 chr5B 18257008 18261490 4482 True 7341 7341 96.301 1 4463 1 chr5B.!!$R1 4462
11 TraesCS7B01G366000 chr5B 568809872 568811882 2010 False 3321 3321 96.569 2464 4463 1 chr5B.!!$F1 1999
12 TraesCS7B01G366000 chr3B 667633221 667637701 4480 False 7323 7323 96.234 1 4463 1 chr3B.!!$F2 4462
13 TraesCS7B01G366000 chr2A 773693737 773697662 3925 True 6069 6069 94.576 1 3924 1 chr2A.!!$R1 3923

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
307 308 0.541863 CATTACCTCGCCCCAAGACT 59.458 55.000 0.0 0.0 0.00 3.24 F
1126 1129 1.296727 GGCCGTACTGGTTCTTATGC 58.703 55.000 0.0 0.0 41.21 3.14 F
1777 1792 2.711542 GTCAGGGGTTTCATCGAACAT 58.288 47.619 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1183 1.298859 GCGTTCATGTCCTCCACCAC 61.299 60.0 0.00 0.0 0.00 4.16 R
2620 2639 0.826715 TCTGGCTGCCTCTATGTGAC 59.173 55.0 21.03 0.0 0.00 3.67 R
3614 3637 0.442310 CGACAATACGTGGCCTTGTG 59.558 55.0 11.70 0.6 33.46 3.33 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
125 126 9.939802 AAGAAAACTATATAAAGGAGTCAACGT 57.060 29.630 0.00 0.00 0.00 3.99
307 308 0.541863 CATTACCTCGCCCCAAGACT 59.458 55.000 0.00 0.00 0.00 3.24
313 314 1.899437 CTCGCCCCAAGACTGCCTAA 61.899 60.000 0.00 0.00 0.00 2.69
354 355 4.385740 TCACCCGTCCCCGATCCA 62.386 66.667 0.00 0.00 35.63 3.41
391 392 2.067197 CCGTCCAAACTCCCTTCCT 58.933 57.895 0.00 0.00 0.00 3.36
750 751 5.982356 TGAATTGGTGGAAAAATTCACACA 58.018 33.333 6.70 0.00 44.05 3.72
758 759 4.704540 TGGAAAAATTCACACACAGACAGT 59.295 37.500 0.00 0.00 0.00 3.55
870 872 7.993101 ACAACGTATGATAGTACTAGAAAGCA 58.007 34.615 8.85 0.00 0.00 3.91
1126 1129 1.296727 GGCCGTACTGGTTCTTATGC 58.703 55.000 0.00 0.00 41.21 3.14
1221 1224 6.767902 ACGCTATCAAGTCATACAATTGGAAT 59.232 34.615 10.83 0.00 0.00 3.01
1450 1456 6.853041 GCCAATTGGTGTGGATACATTTGATT 60.853 38.462 25.19 0.00 43.83 2.57
1728 1739 6.261603 AGAAACGAAGAAACCTAAACGGAAAT 59.738 34.615 0.00 0.00 36.31 2.17
1777 1792 2.711542 GTCAGGGGTTTCATCGAACAT 58.288 47.619 0.00 0.00 0.00 2.71
2109 2124 5.479306 GTGGAGCTAGTAACATCTTTCACA 58.521 41.667 0.00 0.00 0.00 3.58
2225 2240 5.714806 ACGATAATGAAAAGTCCCCATGTTT 59.285 36.000 0.00 0.00 0.00 2.83
2270 2286 2.764572 AGTTTCCGTCTATGTCCCGAAT 59.235 45.455 0.00 0.00 0.00 3.34
2316 2332 3.248024 TGAGTCTATGGGTGGTTTGTCT 58.752 45.455 0.00 0.00 0.00 3.41
2421 2437 3.634568 AAACGCAAACGAAATCCATCA 57.365 38.095 0.00 0.00 43.93 3.07
2617 2636 7.561722 TCTGGCAAGTACTCTTAATATGACTCT 59.438 37.037 0.00 0.00 32.07 3.24
2620 2639 6.926272 GCAAGTACTCTTAATATGACTCTGGG 59.074 42.308 0.00 0.00 32.07 4.45
2659 2678 4.806247 CAGAGTTTTTGTTGAGACTCTCGT 59.194 41.667 3.68 0.00 45.10 4.18
2773 2792 4.186856 AGTTTAAATGGTTGAATGGCGG 57.813 40.909 0.00 0.00 0.00 6.13
2779 2798 1.240256 TGGTTGAATGGCGGTGTAAC 58.760 50.000 0.00 0.00 0.00 2.50
2931 2950 2.561419 TCAACAACGTGGTTCCCAAAAA 59.439 40.909 5.02 0.00 34.18 1.94
2934 2953 4.209307 ACAACGTGGTTCCCAAAAATTT 57.791 36.364 0.00 0.00 34.18 1.82
3280 3299 5.128008 GGCACCCTGGTATGCTAAAATTTTA 59.872 40.000 16.88 10.16 41.74 1.52
3501 3524 7.072263 AGAAAGTGCATGCTATATCCTAAGT 57.928 36.000 20.33 0.00 0.00 2.24
3614 3637 6.500684 TTTGACCAGCAAGAGATTAATGAC 57.499 37.500 0.00 0.00 37.87 3.06
3615 3638 5.164620 TGACCAGCAAGAGATTAATGACA 57.835 39.130 0.00 0.00 0.00 3.58
3739 3763 3.562609 GCATTGGTAGGGTTTTAGTCCCA 60.563 47.826 3.79 0.00 46.82 4.37
4029 4056 0.035439 GGTTAGGCTTGCCACAGCTA 60.035 55.000 14.54 0.00 39.97 3.32
4171 4243 3.290948 AAAAATATGCCCGCTGTCCTA 57.709 42.857 0.00 0.00 0.00 2.94
4186 4258 0.470766 TCCTAAGTTGGTGCGGTGTT 59.529 50.000 0.00 0.00 0.00 3.32
4197 4269 2.295070 GGTGCGGTGTTGATAAAACCTT 59.705 45.455 0.00 0.00 0.00 3.50
4218 4290 4.131649 TCACAATATCCCACGTCGATTT 57.868 40.909 0.00 0.00 0.00 2.17
4397 4469 4.337060 CACGCACGTCTCGTCCCA 62.337 66.667 9.15 0.00 38.32 4.37
4400 4472 3.986006 GCACGTCTCGTCCCACCA 61.986 66.667 0.00 0.00 38.32 4.17
4409 4481 4.269523 GTCCCACCACAGCCAGCA 62.270 66.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.820871 GAGTCTTCACCTGCTCCGAT 59.179 55.000 0.00 0.00 0.00 4.18
19 20 3.523806 GTGAGTCTTCACCTGCTCC 57.476 57.895 0.00 0.00 46.47 4.70
161 162 9.327628 CCCATGATGCATTTATTAAAAACATGA 57.672 29.630 15.39 4.91 35.09 3.07
326 327 1.940883 GACGGGTGAGGATGTGCGTA 61.941 60.000 0.00 0.00 0.00 4.42
660 661 8.786898 GCATTCTAAATAAGATGCCAGTTATCA 58.213 33.333 0.00 0.00 34.93 2.15
787 788 5.411361 CACGGAAGGAATTCTCAACATACAA 59.589 40.000 5.23 0.00 0.00 2.41
941 943 2.167693 TGACATCATCACCCTCGTTACC 59.832 50.000 0.00 0.00 29.99 2.85
1126 1129 2.717580 TGTGGTGCTAAGACTGTACG 57.282 50.000 0.00 0.00 0.00 3.67
1180 1183 1.298859 GCGTTCATGTCCTCCACCAC 61.299 60.000 0.00 0.00 0.00 4.16
1221 1224 2.550606 GCACACCCTCAACGTAAAATCA 59.449 45.455 0.00 0.00 0.00 2.57
1450 1456 5.762179 AGTGGGTATTCATGAGACAAAGA 57.238 39.130 10.88 0.00 0.00 2.52
1728 1739 1.347707 CTTTCTACTCCTGCCACCACA 59.652 52.381 0.00 0.00 0.00 4.17
1777 1792 3.057104 CACACGGTCCATACTGTTAGTCA 60.057 47.826 0.00 0.00 42.83 3.41
2011 2026 1.630369 CTCCATCCCAACTCCTTGACA 59.370 52.381 0.00 0.00 0.00 3.58
2109 2124 3.063452 GCACGTCCGTATCATTGAAACAT 59.937 43.478 0.00 0.00 0.00 2.71
2178 2193 7.014326 TCGTGTATAATGAAAGGATCAGTAGCT 59.986 37.037 0.00 0.00 41.47 3.32
2225 2240 6.274579 TCTTTTGTACGTACAGTTGATGACA 58.725 36.000 26.04 7.61 37.52 3.58
2316 2332 4.780815 ACATGTCTTCAGACTTTGTTGGA 58.219 39.130 8.41 0.00 44.99 3.53
2421 2437 5.295045 GTCGTACGGGGATTGACAATATTTT 59.705 40.000 16.52 0.00 0.00 1.82
2617 2636 1.626356 GGCTGCCTCTATGTGACCCA 61.626 60.000 12.43 0.00 0.00 4.51
2620 2639 0.826715 TCTGGCTGCCTCTATGTGAC 59.173 55.000 21.03 0.00 0.00 3.67
2659 2678 3.125146 GTGTGCATGCTTCTTTGTCGATA 59.875 43.478 20.33 0.00 0.00 2.92
2931 2950 2.024369 CCCTAGCCCTACCCAACAAAAT 60.024 50.000 0.00 0.00 0.00 1.82
2934 2953 0.917333 CCCCTAGCCCTACCCAACAA 60.917 60.000 0.00 0.00 0.00 2.83
3280 3299 7.592938 TCAATAATTTTCTGAATGCGAGTGTT 58.407 30.769 0.00 0.00 0.00 3.32
3406 3427 3.558931 AATTGGCCACGATGAGACATA 57.441 42.857 3.88 0.00 0.00 2.29
3501 3524 6.207221 ACTCTGCAATAAACATGTGTGATCAA 59.793 34.615 0.00 0.00 0.00 2.57
3614 3637 0.442310 CGACAATACGTGGCCTTGTG 59.558 55.000 11.70 0.60 33.46 3.33
3615 3638 1.296056 GCGACAATACGTGGCCTTGT 61.296 55.000 3.32 5.52 43.06 3.16
4006 4033 2.945890 GCTGTGGCAAGCCTAACCTTAT 60.946 50.000 12.96 0.00 37.20 1.73
4029 4056 4.357918 TTCTACAGCAAAAGCCTCTTCT 57.642 40.909 0.00 0.00 0.00 2.85
4171 4243 2.264005 TATCAACACCGCACCAACTT 57.736 45.000 0.00 0.00 0.00 2.66
4186 4258 6.317642 CGTGGGATATTGTGAAGGTTTTATCA 59.682 38.462 0.00 0.00 0.00 2.15
4197 4269 3.812156 AATCGACGTGGGATATTGTGA 57.188 42.857 0.00 0.00 0.00 3.58
4409 4481 1.750399 GGGATCGTTGCATGTGCCT 60.750 57.895 2.07 0.00 41.18 4.75


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

AutoCloner maintained by Alex Coulton.