Multiple sequence alignment - TraesCS6D01G351600

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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 TraesCS6D01G351600 chr6D 100.000 3079 0 0 1 3079 448617455 448614377 0.000000e+00 5686
1 TraesCS6D01G351600 chr6D 99.025 2052 10 2 375 2426 448902209 448904250 0.000000e+00 3670
2 TraesCS6D01G351600 chr6D 98.333 240 3 1 23 261 448901521 448901760 1.320000e-113 420
3 TraesCS6D01G351600 chr6A 91.721 1981 99 21 256 2198 594978506 594980459 0.000000e+00 2689
4 TraesCS6D01G351600 chr6A 98.253 229 3 1 23 250 594977866 594978094 1.720000e-107 399
5 TraesCS6D01G351600 chr6A 77.565 575 85 26 1040 1606 595171977 595171439 1.070000e-79 307
6 TraesCS6D01G351600 chr2B 93.874 653 35 4 2431 3079 38022678 38022027 0.000000e+00 979
7 TraesCS6D01G351600 chr7A 93.558 652 35 6 2430 3079 1911168 1910522 0.000000e+00 965
8 TraesCS6D01G351600 chr7A 73.050 423 83 23 2492 2905 533501274 533500874 1.500000e-23 121
9 TraesCS6D01G351600 chr1A 90.867 646 49 8 2437 3076 71083310 71083951 0.000000e+00 857
10 TraesCS6D01G351600 chr1A 90.000 650 54 9 2437 3079 389796697 389796052 0.000000e+00 830
11 TraesCS6D01G351600 chr6B 87.682 755 39 18 1459 2195 680726831 680727549 0.000000e+00 830
12 TraesCS6D01G351600 chr6B 93.069 202 8 3 1088 1289 680726634 680726829 1.080000e-74 291
13 TraesCS6D01G351600 chr6B 93.750 160 10 0 2200 2359 680727640 680727799 1.100000e-59 241
14 TraesCS6D01G351600 chr1D 84.762 210 24 6 23 232 452588745 452588544 1.450000e-48 204
15 TraesCS6D01G351600 chr1B 84.286 210 24 6 23 231 622608387 622608186 2.420000e-46 196
16 TraesCS6D01G351600 chr5D 93.590 78 4 1 476 553 120801761 120801837 6.980000e-22 115


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 TraesCS6D01G351600 chr6D 448614377 448617455 3078 True 5686 5686 100.000000 1 3079 1 chr6D.!!$R1 3078
1 TraesCS6D01G351600 chr6D 448901521 448904250 2729 False 2045 3670 98.679000 23 2426 2 chr6D.!!$F1 2403
2 TraesCS6D01G351600 chr6A 594977866 594980459 2593 False 1544 2689 94.987000 23 2198 2 chr6A.!!$F1 2175
3 TraesCS6D01G351600 chr6A 595171439 595171977 538 True 307 307 77.565000 1040 1606 1 chr6A.!!$R1 566
4 TraesCS6D01G351600 chr2B 38022027 38022678 651 True 979 979 93.874000 2431 3079 1 chr2B.!!$R1 648
5 TraesCS6D01G351600 chr7A 1910522 1911168 646 True 965 965 93.558000 2430 3079 1 chr7A.!!$R1 649
6 TraesCS6D01G351600 chr1A 71083310 71083951 641 False 857 857 90.867000 2437 3076 1 chr1A.!!$F1 639
7 TraesCS6D01G351600 chr1A 389796052 389796697 645 True 830 830 90.000000 2437 3079 1 chr1A.!!$R1 642
8 TraesCS6D01G351600 chr6B 680726634 680727799 1165 False 454 830 91.500333 1088 2359 3 chr6B.!!$F1 1271

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
757 1166 1.003718 GGCACCAAGGCGTTCTACT 60.004 57.895 0.0 0.0 33.57 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 3128 2.806244 CTCGGGTTCAAAGTTACCACAG 59.194 50.0 0.0 0.0 36.1 3.66 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
250 252 4.673580 CGCTACTCGCTACCTTTAGTTTCA 60.674 45.833 0.00 0.00 36.13 2.69
251 253 5.166398 GCTACTCGCTACCTTTAGTTTCAA 58.834 41.667 0.00 0.00 35.14 2.69
285 694 1.620589 ACCCCATCTGGCACCATCT 60.621 57.895 0.00 0.00 0.00 2.90
343 752 1.918293 TCCCCGCACAATCTCTGGT 60.918 57.895 0.00 0.00 0.00 4.00
497 906 6.605594 GGTTGTGACCCCATAGATAAAAATGA 59.394 38.462 0.00 0.00 40.25 2.57
757 1166 1.003718 GGCACCAAGGCGTTCTACT 60.004 57.895 0.00 0.00 33.57 2.57
793 1202 7.307989 GCCGTAAAGATACCGTAGAGTGTTATA 60.308 40.741 0.00 0.00 0.00 0.98
2426 2981 6.531503 TTTGTTGGACTGGAAATGTGTAAA 57.468 33.333 0.00 0.00 0.00 2.01
2427 2982 6.723298 TTGTTGGACTGGAAATGTGTAAAT 57.277 33.333 0.00 0.00 0.00 1.40
2428 2983 6.083098 TGTTGGACTGGAAATGTGTAAATG 57.917 37.500 0.00 0.00 0.00 2.32
2434 2989 3.911868 TGGAAATGTGTAAATGCTGCAC 58.088 40.909 3.57 0.00 40.79 4.57
2572 3128 6.913873 ACCCAATGACATACGTATAAACAC 57.086 37.500 7.96 0.00 0.00 3.32
2622 3179 9.733219 CAAAAATTGTTGCAAAAACATATCCTT 57.267 25.926 3.61 0.00 0.00 3.36
2623 3180 9.949174 AAAAATTGTTGCAAAAACATATCCTTC 57.051 25.926 3.61 0.00 0.00 3.46
2755 3315 5.952347 ACCCCCTCTAACTTATGTGTAAG 57.048 43.478 0.00 0.00 42.45 2.34
2863 3424 8.655651 TTGAAAACATTCATGGTAACTTTTCC 57.344 30.769 0.00 0.00 31.88 3.13
2975 3540 6.425735 TGGAACATACCAACATGAGATTGAT 58.574 36.000 0.00 0.00 36.96 2.57
2999 3564 3.793797 TGAAGGTCTTAATCGCGATGA 57.206 42.857 24.47 13.39 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.156000 AGAACACTAGTAGAAAAAGAGGCTTC 58.844 38.462 3.59 0.00 0.00 3.86
1 2 7.068686 AGAACACTAGTAGAAAAAGAGGCTT 57.931 36.000 3.59 0.00 0.00 4.35
2 3 6.295405 GGAGAACACTAGTAGAAAAAGAGGCT 60.295 42.308 3.59 0.00 0.00 4.58
3 4 5.870433 GGAGAACACTAGTAGAAAAAGAGGC 59.130 44.000 3.59 0.00 0.00 4.70
4 5 7.234661 AGGAGAACACTAGTAGAAAAAGAGG 57.765 40.000 3.59 0.00 0.00 3.69
6 7 9.756571 AGATAGGAGAACACTAGTAGAAAAAGA 57.243 33.333 3.59 0.00 0.00 2.52
212 214 2.076863 GTAGCGATAATGGCCACCATC 58.923 52.381 8.16 13.14 44.40 3.51
250 252 3.338250 TGGCCGGGATGGAAGCTT 61.338 61.111 2.18 0.00 42.00 3.74
251 253 4.115199 GTGGCCGGGATGGAAGCT 62.115 66.667 2.18 0.00 42.00 3.74
285 694 1.404181 GCTGGTGCACATCTTCGACTA 60.404 52.381 20.43 0.00 39.41 2.59
343 752 4.308458 CACCCTGTTCGGCGTGGA 62.308 66.667 6.85 0.00 33.11 4.02
528 937 4.142816 CGATTTCTTTCTCGTTCAATGCCT 60.143 41.667 0.00 0.00 0.00 4.75
561 970 1.153229 GGGCGGTTCCTGACATACC 60.153 63.158 0.00 0.00 34.39 2.73
751 1160 1.684734 GGCCCCCTCGACAGTAGAA 60.685 63.158 0.00 0.00 0.00 2.10
757 1166 2.604079 TTTACGGCCCCCTCGACA 60.604 61.111 0.00 0.00 0.00 4.35
793 1202 5.503662 TGCGATCTTTGTGCATGAAATAT 57.496 34.783 0.00 0.00 32.86 1.28
2426 2981 3.641434 AAGTTATCAGAGGTGCAGCAT 57.359 42.857 19.63 5.14 0.00 3.79
2427 2982 3.260632 TGTAAGTTATCAGAGGTGCAGCA 59.739 43.478 19.63 0.00 0.00 4.41
2428 2983 3.861840 TGTAAGTTATCAGAGGTGCAGC 58.138 45.455 8.11 8.11 0.00 5.25
2434 2989 7.382488 CGGTGTTCATATGTAAGTTATCAGAGG 59.618 40.741 1.90 0.00 0.00 3.69
2469 3024 8.710749 TCAATATTATTTTCCCCAAGGATCAG 57.289 34.615 0.00 0.00 43.54 2.90
2502 3058 4.942483 TCTTTACGCAAAAATTATCGGGGA 59.058 37.500 0.00 0.00 0.00 4.81
2572 3128 2.806244 CTCGGGTTCAAAGTTACCACAG 59.194 50.000 0.00 0.00 36.10 3.66
2623 3180 9.871238 ACCATACTATTTACACAGAAACTACTG 57.129 33.333 0.00 0.00 42.78 2.74
2694 3253 5.900865 TTTTACCGCGGGAAAAAGATTAT 57.099 34.783 39.31 13.51 0.00 1.28
2755 3315 2.931969 GGCGTGTATGTTACCAAGGTAC 59.068 50.000 0.00 0.00 0.00 3.34
2882 3445 2.271821 TCACGTCATCGGTGTGTATG 57.728 50.000 0.00 0.00 41.85 2.39
2975 3540 5.410132 TCATCGCGATTAAGACCTTCAAAAA 59.590 36.000 21.14 0.00 0.00 1.94
3012 3578 8.941977 GTCGGCCCTATTCAAAAATTTAATTTT 58.058 29.630 9.58 9.58 43.83 1.82
3019 3585 4.086457 ACTGTCGGCCCTATTCAAAAATT 58.914 39.130 0.00 0.00 0.00 1.82
3030 3596 2.224670 TGTAATTCAAACTGTCGGCCCT 60.225 45.455 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.