Multiple sequence alignment - TraesCS1B01G164600

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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 TraesCS1B01G164600 chr1B 100.000 3485 0 0 1 3485 287515419 287518903 0.000000e+00 6436
1 TraesCS1B01G164600 chr1B 89.736 2952 253 36 548 3466 200994715 200997649 0.000000e+00 3727
2 TraesCS1B01G164600 chr1B 87.753 2964 295 48 558 3485 307385940 307383009 0.000000e+00 3400
3 TraesCS1B01G164600 chr1B 98.848 521 6 0 298 818 287531550 287532070 0.000000e+00 929
4 TraesCS1B01G164600 chr1B 95.329 578 21 4 298 875 524763353 524763924 0.000000e+00 913
5 TraesCS1B01G164600 chr1B 94.627 335 14 2 332 666 524768284 524768614 1.850000e-142 516
6 TraesCS1B01G164600 chr1B 96.220 291 11 0 5 295 287531222 287531512 8.750000e-131 477
7 TraesCS1B01G164600 chr3B 98.092 3197 50 6 298 3485 195664618 195667812 0.000000e+00 5555
8 TraesCS1B01G164600 chr3B 91.729 2950 176 47 568 3466 288474737 288477669 0.000000e+00 4034
9 TraesCS1B01G164600 chr3B 87.880 2962 291 46 537 3466 331024461 331027386 0.000000e+00 3419
10 TraesCS1B01G164600 chr3B 96.949 295 9 0 1 295 195664286 195664580 2.420000e-136 496
11 TraesCS1B01G164600 chr3B 96.271 295 11 0 1 295 195668616 195668910 5.230000e-133 484
12 TraesCS1B01G164600 chr3B 95.254 295 14 0 1 295 40494150 40494444 5.270000e-128 468
13 TraesCS1B01G164600 chr3B 94.237 295 17 0 1 295 40498531 40498825 5.300000e-123 451
14 TraesCS1B01G164600 chr2B 93.993 2647 135 15 674 3306 762705861 762708497 0.000000e+00 3986
15 TraesCS1B01G164600 chr2B 90.807 2676 222 18 674 3335 388225730 388228395 0.000000e+00 3557
16 TraesCS1B01G164600 chr2B 89.242 2835 251 31 677 3466 556544439 556547264 0.000000e+00 3496
17 TraesCS1B01G164600 chr2B 94.095 525 22 4 298 818 263665774 263665255 0.000000e+00 789
18 TraesCS1B01G164600 chr2B 94.932 296 15 0 3190 3485 545609926 545609631 6.810000e-127 464
19 TraesCS1B01G164600 chr2B 95.189 291 14 0 5 295 588899325 588899615 8.810000e-126 460
20 TraesCS1B01G164600 chr2B 94.576 295 13 1 1 295 588900434 588900143 1.470000e-123 453
21 TraesCS1B01G164600 chr2B 85.572 402 47 8 418 818 297404194 297404585 9.000000e-111 411
22 TraesCS1B01G164600 chr2B 95.359 237 3 2 298 528 588899653 588899887 1.530000e-98 370
23 TraesCS1B01G164600 chr2B 94.393 214 2 1 298 501 588900105 588899892 1.560000e-83 320
24 TraesCS1B01G164600 chr2B 88.066 243 23 5 3245 3485 465449102 465448864 2.050000e-72 283
25 TraesCS1B01G164600 chr2B 79.511 327 52 8 494 818 115606298 115605985 5.860000e-53 219
26 TraesCS1B01G164600 chr2A 89.699 2961 265 28 549 3485 267980099 267983043 0.000000e+00 3742
27 TraesCS1B01G164600 chr4B 85.071 1266 130 30 298 1532 277835428 277834191 0.000000e+00 1236
28 TraesCS1B01G164600 chr4B 94.915 295 15 0 1 295 443183473 443183179 2.450000e-126 462
29 TraesCS1B01G164600 chr4B 93.960 298 15 2 1 295 443188069 443187772 6.860000e-122 448
30 TraesCS1B01G164600 chr4B 89.796 147 14 1 3340 3485 376030388 376030534 1.650000e-43 187
31 TraesCS1B01G164600 chr5B 80.072 552 58 27 298 821 343407683 343407156 2.560000e-96 363


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 TraesCS1B01G164600 chr1B 287515419 287518903 3484 False 6436.000000 6436 100.0000 1 3485 1 chr1B.!!$F2 3484
1 TraesCS1B01G164600 chr1B 200994715 200997649 2934 False 3727.000000 3727 89.7360 548 3466 1 chr1B.!!$F1 2918
2 TraesCS1B01G164600 chr1B 307383009 307385940 2931 True 3400.000000 3400 87.7530 558 3485 1 chr1B.!!$R1 2927
3 TraesCS1B01G164600 chr1B 524763353 524763924 571 False 913.000000 913 95.3290 298 875 1 chr1B.!!$F3 577
4 TraesCS1B01G164600 chr1B 287531222 287532070 848 False 703.000000 929 97.5340 5 818 2 chr1B.!!$F5 813
5 TraesCS1B01G164600 chr3B 288474737 288477669 2932 False 4034.000000 4034 91.7290 568 3466 1 chr3B.!!$F3 2898
6 TraesCS1B01G164600 chr3B 331024461 331027386 2925 False 3419.000000 3419 87.8800 537 3466 1 chr3B.!!$F4 2929
7 TraesCS1B01G164600 chr3B 195664286 195668910 4624 False 2178.333333 5555 97.1040 1 3485 3 chr3B.!!$F5 3484
8 TraesCS1B01G164600 chr2B 762705861 762708497 2636 False 3986.000000 3986 93.9930 674 3306 1 chr2B.!!$F4 2632
9 TraesCS1B01G164600 chr2B 388225730 388228395 2665 False 3557.000000 3557 90.8070 674 3335 1 chr2B.!!$F2 2661
10 TraesCS1B01G164600 chr2B 556544439 556547264 2825 False 3496.000000 3496 89.2420 677 3466 1 chr2B.!!$F3 2789
11 TraesCS1B01G164600 chr2B 263665255 263665774 519 True 789.000000 789 94.0950 298 818 1 chr2B.!!$R2 520
12 TraesCS1B01G164600 chr2B 588899325 588899887 562 False 415.000000 460 95.2740 5 528 2 chr2B.!!$F5 523
13 TraesCS1B01G164600 chr2B 588899892 588900434 542 True 386.500000 453 94.4845 1 501 2 chr2B.!!$R5 500
14 TraesCS1B01G164600 chr2A 267980099 267983043 2944 False 3742.000000 3742 89.6990 549 3485 1 chr2A.!!$F1 2936
15 TraesCS1B01G164600 chr4B 277834191 277835428 1237 True 1236.000000 1236 85.0710 298 1532 1 chr4B.!!$R1 1234
16 TraesCS1B01G164600 chr5B 343407156 343407683 527 True 363.000000 363 80.0720 298 821 1 chr5B.!!$R1 523

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
148 149 0.178873 TCCCTTCCCTACCTTGCTGT 60.179 55.0 0.0 0.0 0.0 4.40 F
250 251 0.987294 AGAGTGCTGCCAACCTGTAT 59.013 50.0 0.0 0.0 0.0 2.29 F
1586 1686 1.063806 CTCGCACTTTTGAGTCTCGG 58.936 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2102 2.439880 TGGGTAAACCTGACACATCACA 59.560 45.455 0.00 0.0 41.11 3.58 R
2144 2248 8.429493 GTGATCATCACAAATGAGAGTAATGA 57.571 34.615 13.26 0.0 46.22 2.57 R
3375 3541 0.599728 GAGAGCATGATCCCGAGCAC 60.600 60.000 7.49 0.0 0.00 4.40 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
43 44 1.078567 CTGCTGCTCCTCCACTTCC 60.079 63.158 0.00 0.0 0.00 3.46
81 82 1.349026 TCCTCTTCCCTGCTGTTCTTG 59.651 52.381 0.00 0.0 0.00 3.02
148 149 0.178873 TCCCTTCCCTACCTTGCTGT 60.179 55.000 0.00 0.0 0.00 4.40
164 165 4.071961 TGCTGTTGTTGCTCTCTTTCTA 57.928 40.909 0.00 0.0 0.00 2.10
240 241 9.657121 GTAATATTCAGATTTTAAGAGTGCTGC 57.343 33.333 0.00 0.0 0.00 5.25
250 251 0.987294 AGAGTGCTGCCAACCTGTAT 59.013 50.000 0.00 0.0 0.00 2.29
441 493 9.515020 TGATATATATATACATGTGTGTGTGCG 57.485 33.333 9.11 0.0 39.39 5.34
540 614 6.651975 TTTTTAATTCCCTAGCCGTTTGAA 57.348 33.333 0.00 0.0 0.00 2.69
1443 1537 2.370281 ACTATGCTCCACAACAGTCG 57.630 50.000 0.00 0.0 0.00 4.18
1448 1542 3.120321 TGCTCCACAACAGTCGTATTT 57.880 42.857 0.00 0.0 0.00 1.40
1586 1686 1.063806 CTCGCACTTTTGAGTCTCGG 58.936 55.000 0.00 0.0 0.00 4.63
1999 2102 5.372343 TTGGCCTATTGTCATACATGAGT 57.628 39.130 3.32 0.0 37.51 3.41
2222 2326 8.579006 GCTTAATGAAACATATCATTCCCATGA 58.421 33.333 5.85 0.0 44.64 3.07
2428 2532 1.066215 TGCACGATCCACTACATGCTT 60.066 47.619 0.00 0.0 34.18 3.91
2429 2533 1.328680 GCACGATCCACTACATGCTTG 59.671 52.381 0.00 0.0 0.00 4.01
2745 2864 3.888583 TGGTGCTTGATGAGAATATGCA 58.111 40.909 0.00 0.0 0.00 3.96
2764 2884 2.409378 GCAAACTGATTGTTGAATGCCG 59.591 45.455 0.00 0.0 41.32 5.69
2972 3092 2.771089 ACCACTATGGATTAGCATGCG 58.229 47.619 13.01 0.0 40.96 4.73
3144 3267 1.304052 TGAAATCGGGTGCTTGGGG 60.304 57.895 0.00 0.0 0.00 4.96
3316 3446 5.769367 TCCTTTGGTGAGATCGATAATACG 58.231 41.667 0.00 0.0 0.00 3.06
3400 3566 3.300388 TCGGGATCATGCTCTCTTTAGT 58.700 45.455 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.188207 GCGAGGGAAGAAGGAGCC 59.812 66.667 0.00 0.0 0.00 4.70
43 44 1.294659 GAGCAGCTGGTTCGAGTTGG 61.295 60.000 21.18 0.0 0.00 3.77
81 82 3.435186 GCAGCAAGGCGAGGGAAC 61.435 66.667 0.00 0.0 0.00 3.62
148 149 4.835615 AGAGAGGTAGAAAGAGAGCAACAA 59.164 41.667 0.00 0.0 0.00 2.83
164 165 8.477256 CAGAAAATTCAGAGAAGATAGAGAGGT 58.523 37.037 0.00 0.0 0.00 3.85
240 241 5.278463 CCAAACAGAACAAGATACAGGTTGG 60.278 44.000 0.00 0.0 0.00 3.77
250 251 9.787435 ATATTACAACTACCAAACAGAACAAGA 57.213 29.630 0.00 0.0 0.00 3.02
295 296 5.296283 GCAGATTACTCAATCACAGAGCATT 59.704 40.000 0.65 0.0 42.66 3.56
296 297 4.815308 GCAGATTACTCAATCACAGAGCAT 59.185 41.667 0.65 0.0 42.66 3.79
441 493 7.312657 AGAACATGAACATATCACATCACAC 57.687 36.000 0.00 0.0 41.93 3.82
1448 1542 6.378564 GTGCTGAGGTATATGAATAGGAGCTA 59.621 42.308 0.00 0.0 0.00 3.32
1999 2102 2.439880 TGGGTAAACCTGACACATCACA 59.560 45.455 0.00 0.0 41.11 3.58
2144 2248 8.429493 GTGATCATCACAAATGAGAGTAATGA 57.571 34.615 13.26 0.0 46.22 2.57
2428 2532 2.768253 ATGTCATCTCGAACTTGGCA 57.232 45.000 0.00 0.0 0.00 4.92
2429 2533 2.352960 GGAATGTCATCTCGAACTTGGC 59.647 50.000 0.00 0.0 0.00 4.52
2745 2864 3.068024 ACACGGCATTCAACAATCAGTTT 59.932 39.130 0.00 0.0 38.74 2.66
2764 2884 9.751542 AGCAATATGTAGATCACTAGTTTACAC 57.248 33.333 0.00 0.0 0.00 2.90
2972 3092 1.270358 GCTACCGATCCAGGGAACATC 60.270 57.143 0.00 0.0 35.02 3.06
3260 3389 4.261867 CGATCCCGAGAACATGGTATACAA 60.262 45.833 5.01 0.0 38.22 2.41
3375 3541 0.599728 GAGAGCATGATCCCGAGCAC 60.600 60.000 7.49 0.0 0.00 4.40
3400 3566 4.406456 AGTGATGATTGTGCCAAAGGTTA 58.594 39.130 0.00 0.0 0.00 2.85
3421 3589 8.352201 TGATAAAAGTGGATCAACAAGTTCAAG 58.648 33.333 2.34 0.0 0.00 3.02


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

AutoCloner maintained by Alex Coulton.