Multiple sequence alignment - TraesCS3D01G226600

Loading Multiple Alignment...

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 TraesCS3D01G226600 chr3D 100.000 3382 0 0 1 3382 308527974 308524593 0 6246
1 TraesCS3D01G226600 chr2D 97.084 3395 85 3 1 3382 200934936 200938329 0 5709
2 TraesCS3D01G226600 chr2D 96.348 3395 108 5 1 3382 604416907 604420298 0 5568
3 TraesCS3D01G226600 chr5D 97.054 3395 85 4 1 3382 562925175 562928567 0 5701
4 TraesCS3D01G226600 chr1A 97.025 3395 82 4 1 3382 94765602 94762214 0 5692
5 TraesCS3D01G226600 chr7A 96.907 3395 91 3 1 3382 211308108 211311501 0 5675
6 TraesCS3D01G226600 chr7A 96.672 3395 99 3 1 3382 563544633 563548026 0 5631
7 TraesCS3D01G226600 chr7A 97.388 2565 54 2 831 3382 60348516 60345952 0 4353
8 TraesCS3D01G226600 chr1D 96.819 3395 92 4 1 3382 185786576 185783185 0 5657
9 TraesCS3D01G226600 chr4A 96.171 3395 110 7 1 3382 275495393 275498780 0 5531
10 TraesCS3D01G226600 chr7D 96.164 3389 116 3 7 3382 307118238 307114851 0 5526
11 TraesCS3D01G226600 chr7D 97.699 2564 46 2 832 3382 382102059 382099496 0 4396
12 TraesCS3D01G226600 chrUn 97.501 2961 61 2 435 3382 189423055 189426015 0 5046
13 TraesCS3D01G226600 chrUn 97.466 2565 52 2 831 3382 182448355 182445791 0 4364
14 TraesCS3D01G226600 chrUn 97.174 1663 34 2 1733 3382 222877108 222875446 0 2798
15 TraesCS3D01G226600 chr4D 97.427 2565 52 3 831 3382 123639682 123642245 0 4359
16 TraesCS3D01G226600 chr7B 97.349 2565 55 2 831 3382 742955280 742957844 0 4348
17 TraesCS3D01G226600 chr5A 97.274 2054 43 2 1342 3382 420179133 420177080 0 3470


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 TraesCS3D01G226600 chr3D 308524593 308527974 3381 True 6246 6246 100.000 1 3382 1 chr3D.!!$R1 3381
1 TraesCS3D01G226600 chr2D 200934936 200938329 3393 False 5709 5709 97.084 1 3382 1 chr2D.!!$F1 3381
2 TraesCS3D01G226600 chr2D 604416907 604420298 3391 False 5568 5568 96.348 1 3382 1 chr2D.!!$F2 3381
3 TraesCS3D01G226600 chr5D 562925175 562928567 3392 False 5701 5701 97.054 1 3382 1 chr5D.!!$F1 3381
4 TraesCS3D01G226600 chr1A 94762214 94765602 3388 True 5692 5692 97.025 1 3382 1 chr1A.!!$R1 3381
5 TraesCS3D01G226600 chr7A 211308108 211311501 3393 False 5675 5675 96.907 1 3382 1 chr7A.!!$F1 3381
6 TraesCS3D01G226600 chr7A 563544633 563548026 3393 False 5631 5631 96.672 1 3382 1 chr7A.!!$F2 3381
7 TraesCS3D01G226600 chr7A 60345952 60348516 2564 True 4353 4353 97.388 831 3382 1 chr7A.!!$R1 2551
8 TraesCS3D01G226600 chr1D 185783185 185786576 3391 True 5657 5657 96.819 1 3382 1 chr1D.!!$R1 3381
9 TraesCS3D01G226600 chr4A 275495393 275498780 3387 False 5531 5531 96.171 1 3382 1 chr4A.!!$F1 3381
10 TraesCS3D01G226600 chr7D 307114851 307118238 3387 True 5526 5526 96.164 7 3382 1 chr7D.!!$R1 3375
11 TraesCS3D01G226600 chr7D 382099496 382102059 2563 True 4396 4396 97.699 832 3382 1 chr7D.!!$R2 2550
12 TraesCS3D01G226600 chrUn 189423055 189426015 2960 False 5046 5046 97.501 435 3382 1 chrUn.!!$F1 2947
13 TraesCS3D01G226600 chrUn 182445791 182448355 2564 True 4364 4364 97.466 831 3382 1 chrUn.!!$R1 2551
14 TraesCS3D01G226600 chrUn 222875446 222877108 1662 True 2798 2798 97.174 1733 3382 1 chrUn.!!$R2 1649
15 TraesCS3D01G226600 chr4D 123639682 123642245 2563 False 4359 4359 97.427 831 3382 1 chr4D.!!$F1 2551
16 TraesCS3D01G226600 chr7B 742955280 742957844 2564 False 4348 4348 97.349 831 3382 1 chr7B.!!$F1 2551
17 TraesCS3D01G226600 chr5A 420177080 420179133 2053 True 3470 3470 97.274 1342 3382 1 chr5A.!!$R1 2040

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
572 573 1.380785 CGGGTGACTAGCCCTACCA 60.381 63.158 2.81 0.0 43.92 3.25 F
1576 1579 1.039233 CGCTTTCTAGGTACCCCCGA 61.039 60.000 8.74 0.0 38.74 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2139 0.807496 GACACTTGCTGCATCCCTTC 59.193 55.0 1.84 0.0 0.00 3.46 R
2420 2435 2.159421 ACAGCTAACCATCGTACTGTCG 60.159 50.0 0.00 0.0 33.25 4.35 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
284 285 6.558909 ACTGCTGCAAAATATTTCTTAGCTC 58.441 36.000 21.16 12.11 0.00 4.09
493 494 1.571457 TCCCCAACCCAAGTTCAAGAA 59.429 47.619 0.00 0.00 32.45 2.52
572 573 1.380785 CGGGTGACTAGCCCTACCA 60.381 63.158 2.81 0.00 43.92 3.25
704 705 4.547406 AAGTTCGTTACCAAAAGCAGAC 57.453 40.909 0.00 0.00 0.00 3.51
705 706 2.876550 AGTTCGTTACCAAAAGCAGACC 59.123 45.455 0.00 0.00 0.00 3.85
733 734 7.317722 AGGGGTTAGTAGCTAAAGGATAATG 57.682 40.000 0.00 0.00 0.00 1.90
821 822 4.632153 CGGACCCTATTGATTCTTACAGG 58.368 47.826 0.00 0.00 0.00 4.00
881 882 4.974368 AGAACAGTCTCGTAGGAAGATG 57.026 45.455 0.00 0.00 0.00 2.90
1258 1260 9.453572 AATGCATATGAGAGAACTTCAAACTAA 57.546 29.630 6.97 0.00 0.00 2.24
1370 1372 5.062308 GGATTAGATGTCGCAATATCGGTTC 59.938 44.000 0.00 0.00 0.00 3.62
1524 1526 3.013219 GGAATCAGAGAAAGGGCTGTTC 58.987 50.000 0.00 0.00 33.90 3.18
1536 1538 1.541588 GGGCTGTTCAGTCAACAATCC 59.458 52.381 6.74 0.00 44.71 3.01
1542 1544 2.455674 TCAGTCAACAATCCTGACCG 57.544 50.000 0.00 0.00 43.53 4.79
1576 1579 1.039233 CGCTTTCTAGGTACCCCCGA 61.039 60.000 8.74 0.00 38.74 5.14
1761 1764 2.380410 CGTACGCTGGCGCTCTTTT 61.380 57.895 15.04 0.00 44.19 2.27
2098 2113 3.550842 GCGTTGAAGCAATGGAAAGAAGT 60.551 43.478 0.00 0.00 37.05 3.01
2182 2197 5.336929 GCCCGGTGAAAATTATAAACAAGGT 60.337 40.000 0.00 0.00 0.00 3.50
2340 2355 4.957759 TTCTTAATAACTGGGCGCTTTC 57.042 40.909 7.64 0.00 0.00 2.62
2420 2435 6.109359 CCATAGATCGAACCTATCCCATTTC 58.891 44.000 7.49 0.00 0.00 2.17
2469 2484 4.811557 GGATTAGCTGTACTGGAATGACAC 59.188 45.833 0.00 0.00 0.00 3.67
2599 2615 5.245526 AGCGTTAGAGAAAGGAAAGGACTTA 59.754 40.000 0.00 0.00 0.00 2.24
2604 2620 6.517013 AGAGAAAGGAAAGGACTTAAGGTT 57.483 37.500 7.53 0.00 0.00 3.50
2653 2669 3.497227 GCCTTTGGGGACTACTACAACAA 60.497 47.826 0.00 0.00 37.23 2.83
2719 2735 3.117888 CCCAGCCCTTAAGAAGCAGAATA 60.118 47.826 16.67 0.00 0.00 1.75
2722 2738 6.479884 CCAGCCCTTAAGAAGCAGAATATAT 58.520 40.000 16.67 0.00 0.00 0.86
2749 2765 4.481368 TGGGATACGTATTTGCAGACTT 57.519 40.909 9.92 0.00 37.60 3.01
2850 2866 1.885163 CTACTGCGAAACTCCCGGGT 61.885 60.000 22.86 0.00 0.00 5.28
2996 3012 7.043961 AGTGAAGACGAATTGCTATCATCTA 57.956 36.000 0.00 0.00 0.00 1.98
3092 3108 4.507710 TGCTTCATTCCTATATCGGCATC 58.492 43.478 0.00 0.00 0.00 3.91
3299 3315 1.268896 CCGTATCGCGTCCAATACAGT 60.269 52.381 5.77 0.00 39.32 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 6.376581 AGAGCTAAGAAATATTTTGCAGCAGT 59.623 34.615 21.19 11.24 0.00 4.40
311 312 5.668471 CAAGAGCTATCATCTGTCTTGGAA 58.332 41.667 0.00 0.00 40.21 3.53
493 494 7.124448 CCATCTTTTGTACTCTTAGGTAGGTCT 59.876 40.741 0.00 0.00 0.00 3.85
572 573 6.137559 ACCTATCTTTCTAAGGAAGACGGAT 58.862 40.000 13.36 7.24 32.51 4.18
704 705 4.439968 CTTTAGCTACTAACCCCTTTCGG 58.560 47.826 0.00 0.00 0.00 4.30
705 706 4.161001 TCCTTTAGCTACTAACCCCTTTCG 59.839 45.833 0.00 0.00 0.00 3.46
725 726 8.940397 TTCCTTCAAAAGTTCTTCATTATCCT 57.060 30.769 0.00 0.00 0.00 3.24
733 734 5.007724 TCTCGCTTTCCTTCAAAAGTTCTTC 59.992 40.000 0.00 0.00 38.30 2.87
743 744 2.494059 CCTTTGTCTCGCTTTCCTTCA 58.506 47.619 0.00 0.00 0.00 3.02
821 822 6.484977 AGAGAACACTTCTTTTCACAGGATTC 59.515 38.462 0.00 0.00 40.87 2.52
938 939 8.201242 GAATTGATTCCTTCTCTAGATAGGGT 57.799 38.462 16.87 9.19 0.00 4.34
1230 1232 9.453572 AGTTTGAAGTTCTCTCATATGCATTTA 57.546 29.630 3.54 0.00 0.00 1.40
1370 1372 8.301002 AGCTTATAGAAAGAGCGGAAATACTAG 58.699 37.037 0.00 0.00 41.19 2.57
1408 1410 5.125356 AGATCATGAACAACCGATTATGCA 58.875 37.500 0.00 0.00 0.00 3.96
1536 1538 1.604604 ACAAATGTTCCCACGGTCAG 58.395 50.000 0.00 0.00 0.00 3.51
1576 1579 5.819901 GCTCAAAGGCAATGACTAGTAGATT 59.180 40.000 3.59 0.00 0.00 2.40
1761 1764 8.721133 TTCAGGGTTGTAGATAATGCTCTATA 57.279 34.615 0.00 0.00 30.75 1.31
1893 1896 2.719426 AGGTTCAAAGTAGGTCGACG 57.281 50.000 9.92 0.00 0.00 5.12
2124 2139 0.807496 GACACTTGCTGCATCCCTTC 59.193 55.000 1.84 0.00 0.00 3.46
2182 2197 4.018506 TGGCAGTATGAAATCCTTCCTCAA 60.019 41.667 0.00 0.00 39.69 3.02
2340 2355 5.611796 TCATCGAGTTGTTCCAAAGAATG 57.388 39.130 0.00 0.00 33.67 2.67
2420 2435 2.159421 ACAGCTAACCATCGTACTGTCG 60.159 50.000 0.00 0.00 33.25 4.35
2469 2484 5.831997 TCGTGTACAGATTCTCATATGTGG 58.168 41.667 0.00 0.00 35.55 4.17
2604 2620 5.186409 AGCTTTATTAGTTGTAGGTGGACGA 59.814 40.000 0.00 0.00 0.00 4.20
2653 2669 4.222810 GGTTTGGTCCTTCAAATGCCTATT 59.777 41.667 0.00 0.00 38.64 1.73
2719 2735 8.911918 TGCAAATACGTATCCCAAAGTTATAT 57.088 30.769 8.86 0.00 0.00 0.86
2722 2738 6.314400 GTCTGCAAATACGTATCCCAAAGTTA 59.686 38.462 8.86 0.00 0.00 2.24
2742 2758 7.854916 GCATTGTATCTATCTTTTGAAGTCTGC 59.145 37.037 0.00 0.00 0.00 4.26
2749 2765 9.109393 GGTAACAGCATTGTATCTATCTTTTGA 57.891 33.333 0.00 0.00 36.23 2.69
2850 2866 4.212636 GCTAAACCAGTTAGAAAAGCGTCA 59.787 41.667 0.00 0.00 41.70 4.35
3092 3108 4.038763 TCACAACCAGCCTACGGATAATAG 59.961 45.833 0.00 0.00 0.00 1.73
3299 3315 4.076394 GGTTAGGTCAACTTGTGGCATAA 58.924 43.478 0.00 0.00 35.82 1.90


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

AutoCloner maintained by Alex Coulton.