Multiple sequence alignment - TraesCS7B01G423600

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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 TraesCS7B01G423600 chr7B 100.000 2549 0 0 1 2549 692880880 692883428 0.000000e+00 4708
1 TraesCS7B01G423600 chr7B 98.587 1982 23 3 572 2549 552932144 552930164 0.000000e+00 3500
2 TraesCS7B01G423600 chr7B 83.303 551 86 5 1 548 750438796 750439343 1.050000e-138 503
3 TraesCS7B01G423600 chr7B 83.002 553 84 8 1 548 750173396 750173943 2.280000e-135 492
4 TraesCS7B01G423600 chr7B 82.994 541 82 6 37 573 720161140 720160606 4.930000e-132 481
5 TraesCS7B01G423600 chr7B 82.983 523 77 10 32 548 750149651 750150167 1.790000e-126 462
6 TraesCS7B01G423600 chr7A 98.890 1982 18 3 568 2546 701581936 701583916 0.000000e+00 3535
7 TraesCS7B01G423600 chr7A 83.394 548 87 4 1 546 733275096 733275641 2.930000e-139 505
8 TraesCS7B01G423600 chr7A 82.584 534 83 6 22 548 733062348 733061818 1.790000e-126 462
9 TraesCS7B01G423600 chr6B 98.787 1979 20 4 573 2549 660437743 660435767 0.000000e+00 3518
10 TraesCS7B01G423600 chr6A 98.739 1982 22 2 559 2538 617222883 617220903 0.000000e+00 3518
11 TraesCS7B01G423600 chr3B 98.734 1975 23 2 573 2546 379294093 379296066 0.000000e+00 3507
12 TraesCS7B01G423600 chr1A 98.633 1975 24 3 573 2546 22791529 22793501 0.000000e+00 3494
13 TraesCS7B01G423600 chr5A 98.534 1978 26 2 571 2546 459744879 459746855 0.000000e+00 3489
14 TraesCS7B01G423600 chr5B 98.435 1981 26 4 572 2549 206051426 206049448 0.000000e+00 3482
15 TraesCS7B01G423600 chr4A 98.290 1988 27 5 567 2549 661625049 661623064 0.000000e+00 3476
16 TraesCS7B01G423600 chr2A 82.682 537 87 6 1 534 716477654 716478187 2.970000e-129 472
17 TraesCS7B01G423600 chr6D 81.919 542 90 8 1 538 464347539 464347002 3.870000e-123 451
18 TraesCS7B01G423600 chr7D 81.569 548 93 7 1 544 633671047 633671590 1.800000e-121 446


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 TraesCS7B01G423600 chr7B 692880880 692883428 2548 False 4708 4708 100.000 1 2549 1 chr7B.!!$F1 2548
1 TraesCS7B01G423600 chr7B 552930164 552932144 1980 True 3500 3500 98.587 572 2549 1 chr7B.!!$R1 1977
2 TraesCS7B01G423600 chr7B 750438796 750439343 547 False 503 503 83.303 1 548 1 chr7B.!!$F4 547
3 TraesCS7B01G423600 chr7B 750173396 750173943 547 False 492 492 83.002 1 548 1 chr7B.!!$F3 547
4 TraesCS7B01G423600 chr7B 720160606 720161140 534 True 481 481 82.994 37 573 1 chr7B.!!$R2 536
5 TraesCS7B01G423600 chr7B 750149651 750150167 516 False 462 462 82.983 32 548 1 chr7B.!!$F2 516
6 TraesCS7B01G423600 chr7A 701581936 701583916 1980 False 3535 3535 98.890 568 2546 1 chr7A.!!$F1 1978
7 TraesCS7B01G423600 chr7A 733275096 733275641 545 False 505 505 83.394 1 546 1 chr7A.!!$F2 545
8 TraesCS7B01G423600 chr7A 733061818 733062348 530 True 462 462 82.584 22 548 1 chr7A.!!$R1 526
9 TraesCS7B01G423600 chr6B 660435767 660437743 1976 True 3518 3518 98.787 573 2549 1 chr6B.!!$R1 1976
10 TraesCS7B01G423600 chr6A 617220903 617222883 1980 True 3518 3518 98.739 559 2538 1 chr6A.!!$R1 1979
11 TraesCS7B01G423600 chr3B 379294093 379296066 1973 False 3507 3507 98.734 573 2546 1 chr3B.!!$F1 1973
12 TraesCS7B01G423600 chr1A 22791529 22793501 1972 False 3494 3494 98.633 573 2546 1 chr1A.!!$F1 1973
13 TraesCS7B01G423600 chr5A 459744879 459746855 1976 False 3489 3489 98.534 571 2546 1 chr5A.!!$F1 1975
14 TraesCS7B01G423600 chr5B 206049448 206051426 1978 True 3482 3482 98.435 572 2549 1 chr5B.!!$R1 1977
15 TraesCS7B01G423600 chr4A 661623064 661625049 1985 True 3476 3476 98.290 567 2549 1 chr4A.!!$R1 1982
16 TraesCS7B01G423600 chr2A 716477654 716478187 533 False 472 472 82.682 1 534 1 chr2A.!!$F1 533
17 TraesCS7B01G423600 chr6D 464347002 464347539 537 True 451 451 81.919 1 538 1 chr6D.!!$R1 537
18 TraesCS7B01G423600 chr7D 633671047 633671590 543 False 446 446 81.569 1 544 1 chr7D.!!$F1 543

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
404 409 0.182775 AACCGAGTTGGCTCAAAGGT 59.817 50.0 0.0 0.0 43.94 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2293 0.688087 GATCCTGGGTTCGAGTCCCT 60.688 60.0 22.42 7.77 44.84 4.2 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
61 62 5.530543 GGATGAATTTGAAGAGCTAGGAAGG 59.469 44.000 0.00 0.00 0.00 3.46
80 81 5.648092 GGAAGGAAGCTAGCAAAGAAATGTA 59.352 40.000 18.83 0.00 0.00 2.29
151 156 6.703607 AGAATCTATCTTTACAAGCATGGTCG 59.296 38.462 0.00 0.00 33.39 4.79
154 159 2.695359 TCTTTACAAGCATGGTCGGAC 58.305 47.619 0.00 0.00 0.00 4.79
199 204 2.548875 AGAAAGACAGAGATGATGCGC 58.451 47.619 0.00 0.00 0.00 6.09
206 211 3.736720 ACAGAGATGATGCGCAACATAT 58.263 40.909 29.92 27.50 39.84 1.78
227 232 0.969894 AGCTCGCAGTTACAAGGACT 59.030 50.000 0.00 0.00 0.00 3.85
229 234 2.561419 AGCTCGCAGTTACAAGGACTTA 59.439 45.455 0.00 0.00 0.00 2.24
237 242 5.390567 GCAGTTACAAGGACTTACCAAATCG 60.391 44.000 0.00 0.00 42.04 3.34
351 356 3.635373 AGCTTCATTCCATATGCACCAAG 59.365 43.478 0.00 0.00 0.00 3.61
352 357 3.633525 GCTTCATTCCATATGCACCAAGA 59.366 43.478 0.00 0.00 0.00 3.02
400 405 0.390124 ACGTAACCGAGTTGGCTCAA 59.610 50.000 0.00 0.00 43.94 3.02
403 408 1.804748 GTAACCGAGTTGGCTCAAAGG 59.195 52.381 0.00 0.00 43.94 3.11
404 409 0.182775 AACCGAGTTGGCTCAAAGGT 59.817 50.000 0.00 0.00 43.94 3.50
412 417 0.823356 TGGCTCAAAGGTGCTTGGTC 60.823 55.000 0.00 0.00 34.07 4.02
430 435 2.680339 GGTCCAAGCTGTTGATAGAAGC 59.320 50.000 0.00 0.00 35.46 3.86
433 438 4.216257 GTCCAAGCTGTTGATAGAAGCAAA 59.784 41.667 0.00 0.00 39.47 3.68
453 458 2.928334 AGCACATGGATGGATTGAGAC 58.072 47.619 0.00 0.00 0.00 3.36
478 483 9.155975 ACAATAAGGATTCATGATATCTTACGC 57.844 33.333 3.98 0.00 0.00 4.42
536 541 9.515020 GTTTTCTTGATGTCATTGACAAAACTA 57.485 29.630 22.44 12.64 45.96 2.24
548 553 4.065088 TGACAAAACTACAGGTCATGCTC 58.935 43.478 0.00 0.00 35.51 4.26
549 554 3.412386 ACAAAACTACAGGTCATGCTCC 58.588 45.455 0.00 0.00 0.00 4.70
550 555 3.073062 ACAAAACTACAGGTCATGCTCCT 59.927 43.478 3.89 3.89 35.45 3.69
551 556 4.074970 CAAAACTACAGGTCATGCTCCTT 58.925 43.478 6.55 3.05 32.37 3.36
552 557 4.373156 AAACTACAGGTCATGCTCCTTT 57.627 40.909 6.55 4.20 32.37 3.11
553 558 3.618690 ACTACAGGTCATGCTCCTTTC 57.381 47.619 6.55 0.00 32.37 2.62
554 559 2.093973 ACTACAGGTCATGCTCCTTTCG 60.094 50.000 6.55 1.27 32.37 3.46
555 560 0.687354 ACAGGTCATGCTCCTTTCGT 59.313 50.000 6.55 1.03 32.37 3.85
556 561 1.072331 ACAGGTCATGCTCCTTTCGTT 59.928 47.619 6.55 0.00 32.37 3.85
557 562 1.466167 CAGGTCATGCTCCTTTCGTTG 59.534 52.381 6.55 0.00 32.37 4.10
565 570 5.523552 TCATGCTCCTTTCGTTGTATGTATG 59.476 40.000 0.00 0.00 0.00 2.39
993 1000 1.762460 GAGATCCCCTTCGGCTCCA 60.762 63.158 0.00 0.00 0.00 3.86
1042 1049 1.986757 ACCTCGTGGATGCAGAGCT 60.987 57.895 11.17 0.00 37.04 4.09
1334 1379 4.345962 GTTGCGCATGCTGCCACA 62.346 61.111 24.60 10.14 41.12 4.17
1361 1406 4.008933 GGCCACACCACGAGCTCT 62.009 66.667 12.85 0.00 38.86 4.09
1527 1572 5.352016 GGTAATCGCACTGGTTGTAATGTTA 59.648 40.000 0.00 0.00 0.00 2.41
2546 2676 3.616219 TCACCCCCTACGATTTTCATTG 58.384 45.455 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.565305 CAGCTCTTCTGTACGATGGC 58.435 55.000 0.00 0.00 38.02 4.40
20 21 0.950555 TCCACATCACGCAAGACAGC 60.951 55.000 0.00 0.00 43.62 4.40
26 27 3.505293 TCAAATTCATCCACATCACGCAA 59.495 39.130 0.00 0.00 0.00 4.85
61 62 7.088589 TCCATTACATTTCTTTGCTAGCTTC 57.911 36.000 17.23 0.00 0.00 3.86
67 68 5.046448 TGGCAATCCATTACATTTCTTTGCT 60.046 36.000 0.00 0.00 37.47 3.91
137 142 0.319083 ACGTCCGACCATGCTTGTAA 59.681 50.000 0.00 0.00 0.00 2.41
151 156 0.108472 GCCAACCCAGTAGTACGTCC 60.108 60.000 0.00 0.00 0.00 4.79
154 159 1.976898 TGGCCAACCCAGTAGTACG 59.023 57.895 0.61 0.00 39.18 3.67
178 183 3.131046 TGCGCATCATCTCTGTCTTTCTA 59.869 43.478 5.66 0.00 0.00 2.10
180 185 2.274437 TGCGCATCATCTCTGTCTTTC 58.726 47.619 5.66 0.00 0.00 2.62
184 189 1.362768 TGTTGCGCATCATCTCTGTC 58.637 50.000 16.92 0.00 0.00 3.51
199 204 5.966636 TGTAACTGCGAGCTAATATGTTG 57.033 39.130 0.00 0.00 0.00 3.33
206 211 2.561419 AGTCCTTGTAACTGCGAGCTAA 59.439 45.455 0.00 0.00 0.00 3.09
341 346 7.847096 TCTTCTAGTTTATGTCTTGGTGCATA 58.153 34.615 0.00 0.00 0.00 3.14
344 349 7.041372 TGTTTCTTCTAGTTTATGTCTTGGTGC 60.041 37.037 0.00 0.00 0.00 5.01
351 356 6.526222 CGTGCTGTTTCTTCTAGTTTATGTC 58.474 40.000 0.00 0.00 0.00 3.06
352 357 5.107065 GCGTGCTGTTTCTTCTAGTTTATGT 60.107 40.000 0.00 0.00 0.00 2.29
382 387 1.459592 CTTTGAGCCAACTCGGTTACG 59.540 52.381 0.00 0.00 46.69 3.18
412 417 4.730657 CTTTGCTTCTATCAACAGCTTGG 58.269 43.478 0.00 0.00 34.42 3.61
417 422 4.754372 TGTGCTTTGCTTCTATCAACAG 57.246 40.909 0.00 0.00 0.00 3.16
430 435 3.697542 TCTCAATCCATCCATGTGCTTTG 59.302 43.478 0.00 0.00 0.00 2.77
433 438 2.240414 TGTCTCAATCCATCCATGTGCT 59.760 45.455 0.00 0.00 0.00 4.40
453 458 8.323854 CGCGTAAGATATCATGAATCCTTATTG 58.676 37.037 5.32 6.02 43.02 1.90
478 483 2.938451 TGCTTCTTCTATGCACCAATCG 59.062 45.455 0.00 0.00 33.60 3.34
526 531 4.065088 GAGCATGACCTGTAGTTTTGTCA 58.935 43.478 0.00 0.00 41.52 3.58
536 541 0.687354 ACGAAAGGAGCATGACCTGT 59.313 50.000 11.65 7.13 37.85 4.00
548 553 9.582431 CCCTATATACATACATACAACGAAAGG 57.418 37.037 0.00 0.00 0.00 3.11
993 1000 2.617532 GCTTGAGGAAGACATGGAGCTT 60.618 50.000 0.00 0.00 0.00 3.74
1030 1037 4.478371 CGCCCAGCTCTGCATCCA 62.478 66.667 4.97 0.00 0.00 3.41
1361 1406 2.199208 TGCCATCCATCTCTTCTTCCA 58.801 47.619 0.00 0.00 0.00 3.53
2026 2152 2.434428 CAGAGCTGAGGCACATTTTCT 58.566 47.619 0.00 0.00 41.70 2.52
2059 2185 3.172339 TCATTTATTTTGGCACCTGGCT 58.828 40.909 0.00 0.00 44.01 4.75
2165 2293 0.688087 GATCCTGGGTTCGAGTCCCT 60.688 60.000 22.42 7.77 44.84 4.20


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

AutoCloner maintained by Alex Coulton.