Multiple sequence alignment - TraesCS7D01G310500

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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 TraesCS7D01G310500 chr7D 100.000 2924 0 0 1 2924 393951369 393948446 0.000000e+00 5400
1 TraesCS7D01G310500 chr7D 97.445 274 7 0 2081 2354 393942695 393942968 4.410000e-128 468
2 TraesCS7D01G310500 chr7B 99.011 1516 14 1 566 2080 393640972 393639457 0.000000e+00 2715
3 TraesCS7D01G310500 chr7B 91.108 1462 102 13 566 2016 539200583 539199139 0.000000e+00 1954
4 TraesCS7D01G310500 chr7B 96.120 567 20 1 1 567 393641694 393641130 0.000000e+00 924
5 TraesCS7D01G310500 chr7B 94.928 276 13 1 2081 2356 629502280 629502554 5.790000e-117 431
6 TraesCS7D01G310500 chr7B 80.224 536 96 7 1385 1915 639283531 639284061 7.600000e-106 394
7 TraesCS7D01G310500 chr7A 94.474 760 42 0 913 1672 447283307 447282548 0.000000e+00 1171
8 TraesCS7D01G310500 chr7A 98.551 414 5 1 1668 2080 447281927 447281514 0.000000e+00 730
9 TraesCS7D01G310500 chr7A 87.895 380 39 5 1 380 447314499 447314127 9.620000e-120 440
10 TraesCS7D01G310500 chr7A 90.000 200 13 3 374 567 447312408 447312210 4.840000e-63 252
11 TraesCS7D01G310500 chr7A 74.517 569 115 19 1108 1653 668712524 668711963 1.360000e-53 220
12 TraesCS7D01G310500 chr2D 97.821 413 9 0 2097 2509 560217722 560218134 0.000000e+00 713
13 TraesCS7D01G310500 chr2D 93.469 490 10 5 2439 2924 560218093 560218564 0.000000e+00 708
14 TraesCS7D01G310500 chr2D 96.000 275 11 0 2082 2356 560224341 560224067 5.750000e-122 448
15 TraesCS7D01G310500 chr2D 75.965 570 113 16 9 567 626127953 626128509 3.710000e-69 272
16 TraesCS7D01G310500 chr1D 87.340 624 54 9 2081 2684 400415290 400414672 0.000000e+00 691
17 TraesCS7D01G310500 chr1D 92.000 100 8 0 2825 2924 400414602 400414503 1.090000e-29 141
18 TraesCS7D01G310500 chr5B 96.364 275 10 0 2082 2356 604858156 604858430 1.240000e-123 453
19 TraesCS7D01G310500 chr5B 95.635 252 11 0 2086 2337 604872432 604872683 3.510000e-109 405
20 TraesCS7D01G310500 chr4B 95.273 275 13 0 2082 2356 112962055 112962329 1.240000e-118 436
21 TraesCS7D01G310500 chr4B 94.615 260 14 0 2081 2340 112967703 112967444 1.260000e-108 403
22 TraesCS7D01G310500 chr3B 91.273 275 24 0 2081 2355 586152032 586151758 2.750000e-100 375
23 TraesCS7D01G310500 chr3B 74.618 524 101 23 45 553 819380316 819379810 4.940000e-48 202
24 TraesCS7D01G310500 chr3A 78.684 380 69 11 45 417 141912383 141912757 2.910000e-60 243
25 TraesCS7D01G310500 chr6D 79.128 321 56 8 1 321 284397531 284397222 8.210000e-51 211
26 TraesCS7D01G310500 chr5D 83.929 112 15 1 1 112 221596774 221596882 1.430000e-18 104


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 TraesCS7D01G310500 chr7D 393948446 393951369 2923 True 5400.0 5400 100.0000 1 2924 1 chr7D.!!$R1 2923
1 TraesCS7D01G310500 chr7B 539199139 539200583 1444 True 1954.0 1954 91.1080 566 2016 1 chr7B.!!$R1 1450
2 TraesCS7D01G310500 chr7B 393639457 393641694 2237 True 1819.5 2715 97.5655 1 2080 2 chr7B.!!$R2 2079
3 TraesCS7D01G310500 chr7B 639283531 639284061 530 False 394.0 394 80.2240 1385 1915 1 chr7B.!!$F2 530
4 TraesCS7D01G310500 chr7A 447281514 447283307 1793 True 950.5 1171 96.5125 913 2080 2 chr7A.!!$R2 1167
5 TraesCS7D01G310500 chr7A 447312210 447314499 2289 True 346.0 440 88.9475 1 567 2 chr7A.!!$R3 566
6 TraesCS7D01G310500 chr7A 668711963 668712524 561 True 220.0 220 74.5170 1108 1653 1 chr7A.!!$R1 545
7 TraesCS7D01G310500 chr2D 560217722 560218564 842 False 710.5 713 95.6450 2097 2924 2 chr2D.!!$F2 827
8 TraesCS7D01G310500 chr2D 626127953 626128509 556 False 272.0 272 75.9650 9 567 1 chr2D.!!$F1 558
9 TraesCS7D01G310500 chr1D 400414503 400415290 787 True 416.0 691 89.6700 2081 2924 2 chr1D.!!$R1 843
10 TraesCS7D01G310500 chr3B 819379810 819380316 506 True 202.0 202 74.6180 45 553 1 chr3B.!!$R2 508

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
126 127 0.687427 GCCATTACAATGCCCCCACT 60.687 55.000 0.0 0.0 35.08 4.0 F
1267 3176 1.625818 CTGGCTCCACTCTAACAAGGT 59.374 52.381 0.0 0.0 0.00 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 3311 1.750572 CGAGCTCGATTGCACTGCTC 61.751 60.000 32.06 9.78 44.49 4.26 R
2390 4950 1.128692 GTGTTTTCTGAATCGAGGGCG 59.871 52.381 0.00 0.00 39.35 6.13 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
69 70 8.877779 CAAAAACATACATCAAACAACCAGAAA 58.122 29.630 0.00 0.0 0.00 2.52
103 104 4.188462 CACCTACAAACTCAACAGTGTGA 58.812 43.478 0.00 0.0 40.04 3.58
126 127 0.687427 GCCATTACAATGCCCCCACT 60.687 55.000 0.00 0.0 35.08 4.00
158 161 3.153781 TCATCATCGAGCCGCCCA 61.154 61.111 0.00 0.0 0.00 5.36
328 335 2.887360 GATGCCAAACAGCGCCAT 59.113 55.556 2.29 0.0 34.65 4.40
376 383 3.198409 TCCGCCTACGAGACTATGTTA 57.802 47.619 0.00 0.0 43.93 2.41
377 384 3.748083 TCCGCCTACGAGACTATGTTAT 58.252 45.455 0.00 0.0 43.93 1.89
379 2109 3.501062 CCGCCTACGAGACTATGTTATGA 59.499 47.826 0.00 0.0 43.93 2.15
1176 3079 2.358737 CTCCCGTGGTTGGTGCTC 60.359 66.667 0.00 0.0 0.00 4.26
1267 3176 1.625818 CTGGCTCCACTCTAACAAGGT 59.374 52.381 0.00 0.0 0.00 3.50
1313 3232 2.359169 GGCCACCACATCTCCTCGA 61.359 63.158 0.00 0.0 0.00 4.04
1663 3585 3.268965 GAGGACGTGCACGAGCTGA 62.269 63.158 42.94 0.0 43.02 4.26
2049 4599 0.664466 GCAGCTCAAACGGCTTTTCC 60.664 55.000 0.00 0.0 38.03 3.13
2093 4643 9.983804 GCATGTTTACTTTAGAGGTAAATACAC 57.016 33.333 0.00 0.0 39.99 2.90
2117 4667 0.250597 GGTGCCTAAACTTGTCCGGT 60.251 55.000 0.00 0.0 0.00 5.28
2226 4776 1.060308 CCGCCGTATTTGCTTGTCG 59.940 57.895 0.00 0.0 0.00 4.35
2324 4884 3.257375 GCGGTTATTTTCCAGAAAACCCT 59.743 43.478 7.68 0.0 42.32 4.34
2390 4950 0.678684 CGTCCATACCCAAACCACCC 60.679 60.000 0.00 0.0 0.00 4.61
2434 4994 3.595190 ACCAAATCCCTAACCCTATGC 57.405 47.619 0.00 0.0 0.00 3.14
2468 5029 4.324254 GGGGAGGATGTAGTTGATTTGTCA 60.324 45.833 0.00 0.0 0.00 3.58
2755 5349 1.340017 TGGACTATGGCTGAAGGTTGC 60.340 52.381 0.00 0.0 0.00 4.17
2822 5429 3.188460 GCTTCGAGCAAATGTAAGGTTCA 59.812 43.478 2.53 0.0 41.89 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.399376 TGTAGGTGTGGAGTGGTGGT 60.399 55.000 0.00 0.00 0.00 4.16
126 127 1.343580 TGATGACCCCGGTTCTGGATA 60.344 52.381 0.00 0.00 0.00 2.59
158 161 2.421739 GCTCCCGATACGCCATGT 59.578 61.111 0.00 0.00 0.00 3.21
376 383 1.740285 GGTCTCGGCGGTATGTCAT 59.260 57.895 7.21 0.00 0.00 3.06
377 384 2.420568 GGGTCTCGGCGGTATGTCA 61.421 63.158 7.21 0.00 0.00 3.58
379 2109 2.363276 TGGGTCTCGGCGGTATGT 60.363 61.111 7.21 0.00 0.00 2.29
411 2141 2.338984 GAGCGGCCCCGTGTATAG 59.661 66.667 8.66 0.00 42.09 1.31
1054 2957 8.331730 TCTGCATTGATAGAACCATCATTATG 57.668 34.615 0.00 0.00 34.95 1.90
1176 3079 2.482142 GGTAAAGGTCATGAGAGCCTCG 60.482 54.545 3.95 0.00 43.21 4.63
1392 3311 1.750572 CGAGCTCGATTGCACTGCTC 61.751 60.000 32.06 9.78 44.49 4.26
2049 4599 5.531634 ACATGCACAAGTTGGACTAATTTG 58.468 37.500 7.96 5.42 40.61 2.32
2093 4643 2.427506 GACAAGTTTAGGCACCTCTGG 58.572 52.381 0.00 0.00 0.00 3.86
2324 4884 7.485418 TTGCGATAATTAATAAAAGCTCCGA 57.515 32.000 0.00 0.00 0.00 4.55
2390 4950 1.128692 GTGTTTTCTGAATCGAGGGCG 59.871 52.381 0.00 0.00 39.35 6.13
2746 5340 1.832167 GGCAACCCAGCAACCTTCA 60.832 57.895 0.00 0.00 35.83 3.02
2755 5349 2.442236 ACCTCATATTGGCAACCCAG 57.558 50.000 0.00 0.00 43.37 4.45
2822 5429 7.865706 AAAAAGTACTCAGTGTGAAAGACAT 57.134 32.000 0.00 0.00 36.78 3.06


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

AutoCloner maintained by Alex Coulton.