Multiple sequence alignment - TraesCS5D01G188600

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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 TraesCS5D01G188600 chr5D 100.000 3050 0 0 1 3050 291083764 291086813 0.000000e+00 5633.0
1 TraesCS5D01G188600 chr5B 93.329 3073 108 32 1 3050 331372965 331375963 0.000000e+00 4449.0
2 TraesCS5D01G188600 chr5A 93.237 2351 86 22 76 2402 383417433 383419734 0.000000e+00 3393.0
3 TraesCS5D01G188600 chr5A 84.870 575 28 31 2521 3050 383419852 383420412 2.690000e-145 525.0
4 TraesCS5D01G188600 chr3D 84.906 159 22 2 1772 1929 467750243 467750400 3.150000e-35 159.0
5 TraesCS5D01G188600 chr3A 84.277 159 23 2 1772 1929 610368482 610368639 1.460000e-33 154.0
6 TraesCS5D01G188600 chr1D 79.121 182 23 11 1758 1929 81485492 81485316 8.940000e-21 111.0
7 TraesCS5D01G188600 chr7A 82.258 124 18 4 1545 1666 22543196 22543075 1.500000e-18 104.0
8 TraesCS5D01G188600 chr7A 84.615 91 12 2 1545 1634 22332289 22332200 4.190000e-14 89.8
9 TraesCS5D01G188600 chr7D 81.452 124 19 4 1545 1666 21836566 21836445 6.960000e-17 99.0
10 TraesCS5D01G188600 chr4A 85.714 91 11 2 1547 1636 711974362 711974451 9.000000e-16 95.3
11 TraesCS5D01G188600 chr4A 82.727 110 14 5 1539 1645 711880571 711880678 3.240000e-15 93.5
12 TraesCS5D01G188600 chr4A 84.615 91 12 2 1547 1636 711957604 711957693 4.190000e-14 89.8
13 TraesCS5D01G188600 chr2A 76.829 164 21 16 1513 1666 280198 280354 3.260000e-10 76.8


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 TraesCS5D01G188600 chr5D 291083764 291086813 3049 False 5633 5633 100.0000 1 3050 1 chr5D.!!$F1 3049
1 TraesCS5D01G188600 chr5B 331372965 331375963 2998 False 4449 4449 93.3290 1 3050 1 chr5B.!!$F1 3049
2 TraesCS5D01G188600 chr5A 383417433 383420412 2979 False 1959 3393 89.0535 76 3050 2 chr5A.!!$F1 2974

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
911 941 0.741221 CTTCTTGTAGCCACCGAGCC 60.741 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2617 2767 0.684805 TTTTTGGGTGCTCCGGTTGT 60.685 50.0 0.0 0.0 38.76 3.32 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
116 117 2.989824 CGTGTCACGTCTCCCCCT 60.990 66.667 17.30 0.00 36.74 4.79
911 941 0.741221 CTTCTTGTAGCCACCGAGCC 60.741 60.000 0.00 0.00 0.00 4.70
976 1006 3.483421 TCAGACGGTGTTCTTGTCTAGA 58.517 45.455 0.00 0.00 40.83 2.43
1857 1893 1.513158 CGACGAGTGCCTGATCCTT 59.487 57.895 0.00 0.00 0.00 3.36
2090 2126 5.039333 GTGATCTTCCATTGCAACAATAGC 58.961 41.667 0.00 0.00 0.00 2.97
2101 2137 7.442364 CCATTGCAACAATAGCAGTATAGTAGT 59.558 37.037 0.00 0.00 43.75 2.73
2102 2138 9.476202 CATTGCAACAATAGCAGTATAGTAGTA 57.524 33.333 0.00 0.00 43.75 1.82
2103 2139 9.698309 ATTGCAACAATAGCAGTATAGTAGTAG 57.302 33.333 0.00 0.00 43.75 2.57
2222 2259 2.354259 CTGGATCAAGTTCAGTGGAGC 58.646 52.381 0.00 0.00 0.00 4.70
2244 2281 4.792068 CACATAGATTATGGTGGGGTTGT 58.208 43.478 1.61 0.00 40.47 3.32
2365 2404 2.429971 TCGATTCAGATCTGCAGCTTCT 59.570 45.455 18.36 10.94 0.00 2.85
2370 2409 2.566279 TCAGATCTGCAGCTTCTGTTCT 59.434 45.455 29.81 14.03 38.39 3.01
2381 2420 5.353678 GCAGCTTCTGTTCTCATCAGTAATT 59.646 40.000 0.00 0.00 33.43 1.40
2385 2424 6.456718 GCTTCTGTTCTCATCAGTAATTCTGC 60.457 42.308 0.00 0.00 43.32 4.26
2418 2457 4.993584 GGATGATGCGTATCTCATGTCTTT 59.006 41.667 14.76 0.00 32.36 2.52
2419 2458 5.468072 GGATGATGCGTATCTCATGTCTTTT 59.532 40.000 14.76 0.00 32.36 2.27
2420 2459 6.646653 GGATGATGCGTATCTCATGTCTTTTA 59.353 38.462 14.76 0.00 32.36 1.52
2421 2460 7.171508 GGATGATGCGTATCTCATGTCTTTTAA 59.828 37.037 14.76 0.00 32.36 1.52
2422 2461 7.234187 TGATGCGTATCTCATGTCTTTTAAC 57.766 36.000 14.76 0.00 34.31 2.01
2423 2462 7.041721 TGATGCGTATCTCATGTCTTTTAACT 58.958 34.615 14.76 0.00 34.31 2.24
2424 2463 7.549134 TGATGCGTATCTCATGTCTTTTAACTT 59.451 33.333 14.76 0.00 34.31 2.66
2426 2465 6.034577 TGCGTATCTCATGTCTTTTAACTTCG 59.965 38.462 0.00 0.00 0.00 3.79
2427 2466 6.034683 GCGTATCTCATGTCTTTTAACTTCGT 59.965 38.462 0.00 0.00 0.00 3.85
2428 2467 7.219535 GCGTATCTCATGTCTTTTAACTTCGTA 59.780 37.037 0.00 0.00 0.00 3.43
2429 2468 9.234384 CGTATCTCATGTCTTTTAACTTCGTAT 57.766 33.333 0.00 0.00 0.00 3.06
2455 2494 6.360618 AGTTCAGATTAGATGGGTGATTTCC 58.639 40.000 0.00 0.00 0.00 3.13
2474 2514 2.159099 TCCCGGATCTTCATCAACTTCG 60.159 50.000 0.73 0.00 0.00 3.79
2491 2531 5.924475 ACTTCGTAAGTTCATGAAACCTG 57.076 39.130 10.35 0.00 39.04 4.00
2492 2532 4.755123 ACTTCGTAAGTTCATGAAACCTGG 59.245 41.667 10.35 0.32 39.04 4.45
2493 2533 4.345859 TCGTAAGTTCATGAAACCTGGT 57.654 40.909 10.35 0.00 38.76 4.00
2494 2534 5.471556 TCGTAAGTTCATGAAACCTGGTA 57.528 39.130 10.35 0.00 38.76 3.25
2495 2535 5.232463 TCGTAAGTTCATGAAACCTGGTAC 58.768 41.667 10.35 4.20 38.76 3.34
2496 2536 4.992319 CGTAAGTTCATGAAACCTGGTACA 59.008 41.667 10.35 4.33 38.76 2.90
2501 2541 5.707298 AGTTCATGAAACCTGGTACAGATTG 59.293 40.000 10.35 0.27 44.71 2.67
2502 2542 6.691491 AGTTCATGAAACCTGGTACAGATTGT 60.691 38.462 10.35 0.00 44.71 2.71
2503 2543 8.438047 AGTTCATGAAACCTGGTACAGATTGTC 61.438 40.741 10.35 0.00 44.71 3.18
2536 2682 7.393796 CCGACCTGTTAGTAGGACTCAATATAT 59.606 40.741 0.00 0.00 40.42 0.86
2617 2767 9.419297 GCACAAACTATATCGAATATCTTGGTA 57.581 33.333 0.00 0.00 0.00 3.25
2782 2956 4.388499 GGCTCCCAAGGACGCGAA 62.388 66.667 15.93 0.00 30.49 4.70
2825 3007 3.832237 AAGCACGACACCTGCCCTG 62.832 63.158 0.00 0.00 35.01 4.45
2830 3012 4.729918 GACACCTGCCCTGCCCAG 62.730 72.222 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 404 2.203070 CGGAGCCAGGAATTCCCG 60.203 66.667 21.22 11.04 40.87 5.14
458 482 4.969196 CGATGGGGATGGCGACGG 62.969 72.222 0.00 0.00 0.00 4.79
465 489 4.552365 AGGTGCGCGATGGGGATG 62.552 66.667 12.10 0.00 0.00 3.51
466 490 4.552365 CAGGTGCGCGATGGGGAT 62.552 66.667 12.10 0.00 0.00 3.85
588 612 8.504409 ACACCCTCACTAATCTACTAATCTACT 58.496 37.037 0.00 0.00 0.00 2.57
589 613 8.694581 ACACCCTCACTAATCTACTAATCTAC 57.305 38.462 0.00 0.00 0.00 2.59
599 623 4.099573 CCACGATAACACCCTCACTAATCT 59.900 45.833 0.00 0.00 0.00 2.40
606 630 1.600107 GGCCACGATAACACCCTCA 59.400 57.895 0.00 0.00 0.00 3.86
927 957 0.385390 ATGAAATGGAAATCGCCGCC 59.615 50.000 0.00 0.00 0.00 6.13
1116 1152 3.161557 GTGACCTTCCACCTGGCT 58.838 61.111 0.00 0.00 34.44 4.75
1458 1494 2.508439 GCGTCCATCCTCGCGAAA 60.508 61.111 11.33 0.90 42.79 3.46
1869 1905 1.597027 GTTGACCACGTCCCACAGG 60.597 63.158 0.00 0.00 0.00 4.00
2222 2259 4.580167 CACAACCCCACCATAATCTATGTG 59.420 45.833 0.00 0.00 34.36 3.21
2244 2281 7.201839 GGTTACACCAGTTGTTATTTCTTTCCA 60.202 37.037 0.00 0.00 39.91 3.53
2365 2404 7.840931 TCTAAGCAGAATTACTGATGAGAACA 58.159 34.615 7.40 0.00 45.98 3.18
2370 2409 7.365497 TCCATCTAAGCAGAATTACTGATGA 57.635 36.000 8.52 0.00 44.93 2.92
2381 2420 3.007723 GCATCATCCTCCATCTAAGCAGA 59.992 47.826 0.00 0.00 34.56 4.26
2385 2424 3.674528 ACGCATCATCCTCCATCTAAG 57.325 47.619 0.00 0.00 0.00 2.18
2420 2459 9.751542 CCATCTAATCTGAACTTATACGAAGTT 57.248 33.333 2.43 2.43 37.78 2.66
2422 2461 8.361139 ACCCATCTAATCTGAACTTATACGAAG 58.639 37.037 0.00 0.00 0.00 3.79
2423 2462 8.141909 CACCCATCTAATCTGAACTTATACGAA 58.858 37.037 0.00 0.00 0.00 3.85
2424 2463 7.504574 TCACCCATCTAATCTGAACTTATACGA 59.495 37.037 0.00 0.00 0.00 3.43
2428 2467 9.566432 GAAATCACCCATCTAATCTGAACTTAT 57.434 33.333 0.00 0.00 0.00 1.73
2429 2468 7.993183 GGAAATCACCCATCTAATCTGAACTTA 59.007 37.037 0.00 0.00 0.00 2.24
2452 2491 3.678806 CGAAGTTGATGAAGATCCGGGAA 60.679 47.826 0.00 0.00 0.00 3.97
2455 2494 2.893637 ACGAAGTTGATGAAGATCCGG 58.106 47.619 0.00 0.00 37.78 5.14
2474 2514 6.228258 TCTGTACCAGGTTTCATGAACTTAC 58.772 40.000 7.89 3.82 38.35 2.34
2481 2521 4.396166 GGACAATCTGTACCAGGTTTCATG 59.604 45.833 0.00 0.00 31.84 3.07
2482 2522 4.289672 AGGACAATCTGTACCAGGTTTCAT 59.710 41.667 0.00 0.00 31.84 2.57
2486 2526 3.521727 AGAGGACAATCTGTACCAGGTT 58.478 45.455 0.00 0.00 34.88 3.50
2487 2527 3.191888 AGAGGACAATCTGTACCAGGT 57.808 47.619 0.00 0.00 29.22 4.00
2488 2528 4.141914 GGTTAGAGGACAATCTGTACCAGG 60.142 50.000 0.00 0.00 36.29 4.45
2489 2529 4.440250 CGGTTAGAGGACAATCTGTACCAG 60.440 50.000 0.00 0.00 36.15 4.00
2490 2530 3.446161 CGGTTAGAGGACAATCTGTACCA 59.554 47.826 0.00 0.00 36.15 3.25
2491 2531 3.698040 TCGGTTAGAGGACAATCTGTACC 59.302 47.826 0.00 0.00 29.22 3.34
2492 2532 4.439837 GGTCGGTTAGAGGACAATCTGTAC 60.440 50.000 0.00 0.00 34.87 2.90
2493 2533 3.698040 GGTCGGTTAGAGGACAATCTGTA 59.302 47.826 0.00 0.00 34.87 2.74
2494 2534 2.496470 GGTCGGTTAGAGGACAATCTGT 59.504 50.000 0.00 0.00 34.87 3.41
2495 2535 2.761208 AGGTCGGTTAGAGGACAATCTG 59.239 50.000 0.00 0.00 34.87 2.90
2496 2536 2.761208 CAGGTCGGTTAGAGGACAATCT 59.239 50.000 0.00 0.00 34.87 2.40
2497 2537 2.496470 ACAGGTCGGTTAGAGGACAATC 59.504 50.000 0.00 0.00 34.87 2.67
2498 2538 2.537143 ACAGGTCGGTTAGAGGACAAT 58.463 47.619 0.00 0.00 34.87 2.71
2499 2539 2.005370 ACAGGTCGGTTAGAGGACAA 57.995 50.000 0.00 0.00 34.87 3.18
2500 2540 2.005370 AACAGGTCGGTTAGAGGACA 57.995 50.000 0.00 0.00 34.87 4.02
2507 2547 4.263462 TGAGTCCTACTAACAGGTCGGTTA 60.263 45.833 0.00 0.00 36.99 2.85
2543 2689 9.823647 ACCTAGTGTAATAGATTTGAACAGATG 57.176 33.333 0.00 0.00 0.00 2.90
2617 2767 0.684805 TTTTTGGGTGCTCCGGTTGT 60.685 50.000 0.00 0.00 38.76 3.32
2782 2956 7.356680 TCCAGATGAATCCCACAAGAAATATT 58.643 34.615 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.