Multiple sequence alignment - TraesCS5A01G101400

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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 TraesCS5A01G101400 chr5A 100.000 2404 0 0 1 2404 148830954 148828551 0.000000e+00 4440.0
1 TraesCS5A01G101400 chr2A 98.420 2405 35 3 1 2404 22040424 22038022 0.000000e+00 4228.0
2 TraesCS5A01G101400 chr2A 97.519 1330 28 3 1 1327 95943046 95941719 0.000000e+00 2268.0
3 TraesCS5A01G101400 chr2A 97.899 476 10 0 1351 1826 95922128 95921653 0.000000e+00 824.0
4 TraesCS5A01G101400 chr2A 88.497 539 30 12 60 585 313206703 313206184 7.300000e-175 623.0
5 TraesCS5A01G101400 chr7A 88.220 1163 91 25 1283 2404 51910872 51909715 0.000000e+00 1347.0
6 TraesCS5A01G101400 chr7A 97.143 630 18 0 1197 1826 613450787 613450158 0.000000e+00 1064.0
7 TraesCS5A01G101400 chr7A 96.735 582 19 0 1823 2404 105796427 105797008 0.000000e+00 970.0
8 TraesCS5A01G101400 chr7A 95.361 582 27 0 1823 2404 613450130 613449549 0.000000e+00 926.0
9 TraesCS5A01G101400 chr7A 93.878 343 12 2 1 334 51912124 51911782 2.130000e-140 508.0
10 TraesCS5A01G101400 chr3A 85.628 1162 116 23 1283 2404 543426214 543427364 0.000000e+00 1173.0
11 TraesCS5A01G101400 chr3A 89.157 581 56 5 1827 2404 500021359 500021935 0.000000e+00 717.0
12 TraesCS5A01G101400 chr2B 94.225 658 33 1 1 653 2004752 2004095 0.000000e+00 1000.0
13 TraesCS5A01G101400 chr2B 92.831 544 38 1 1283 1826 2002671 2002129 0.000000e+00 787.0
14 TraesCS5A01G101400 chr2B 91.773 547 25 5 55 585 298581123 298581665 0.000000e+00 743.0
15 TraesCS5A01G101400 chr2B 90.642 545 48 3 1283 1826 120980295 120979753 0.000000e+00 721.0
16 TraesCS5A01G101400 chr5B 93.617 658 34 5 1 653 606614974 606614320 0.000000e+00 976.0
17 TraesCS5A01G101400 chr5B 91.728 544 44 1 1283 1826 606612896 606612354 0.000000e+00 754.0
18 TraesCS5A01G101400 chrUn 93.617 658 28 5 1 653 68841912 68842560 0.000000e+00 970.0
19 TraesCS5A01G101400 chrUn 92.791 541 39 0 1283 1823 68843977 68844517 0.000000e+00 784.0
20 TraesCS5A01G101400 chrUn 90.119 587 46 4 1828 2404 68844553 68845137 0.000000e+00 752.0
21 TraesCS5A01G101400 chr4B 91.682 541 45 0 1283 1823 264556999 264557539 0.000000e+00 750.0
22 TraesCS5A01G101400 chr4B 90.732 410 33 5 1995 2404 264557713 264558117 2.100000e-150 542.0
23 TraesCS5A01G101400 chr4B 90.741 162 11 1 693 854 256841300 256841457 1.870000e-51 213.0
24 TraesCS5A01G101400 chr4B 100.000 31 0 0 1254 1284 256842362 256842392 9.280000e-05 58.4
25 TraesCS5A01G101400 chr7B 91.144 542 46 2 1286 1826 747297140 747296600 0.000000e+00 734.0
26 TraesCS5A01G101400 chr7B 100.000 34 0 0 1254 1287 672816652 672816685 2.000000e-06 63.9
27 TraesCS5A01G101400 chr5D 85.121 746 64 26 1696 2404 338877564 338876829 0.000000e+00 719.0
28 TraesCS5A01G101400 chr2D 87.823 542 32 13 57 585 257746152 257746672 2.640000e-169 604.0
29 TraesCS5A01G101400 chr2D 82.735 446 32 27 1707 2110 250282285 250281843 2.940000e-94 355.0
30 TraesCS5A01G101400 chr2D 88.581 289 26 4 1828 2111 619155610 619155324 6.360000e-91 344.0
31 TraesCS5A01G101400 chr6D 94.602 352 19 0 906 1257 62081525 62081174 1.630000e-151 545.0
32 TraesCS5A01G101400 chr6D 94.602 352 18 1 907 1257 156016776 156016425 5.840000e-151 544.0
33 TraesCS5A01G101400 chr7D 94.318 352 20 0 906 1257 32520359 32520008 7.560000e-150 540.0
34 TraesCS5A01G101400 chr7D 94.034 352 21 0 906 1257 625868532 625868883 3.520000e-148 534.0
35 TraesCS5A01G101400 chr7D 88.927 289 24 5 1828 2111 531608274 531608559 1.370000e-92 350.0
36 TraesCS5A01G101400 chr1D 91.155 407 22 10 854 1257 438032857 438032462 7.560000e-150 540.0
37 TraesCS5A01G101400 chr1D 97.222 36 0 1 1252 1287 438031136 438031102 2.580000e-05 60.2
38 TraesCS5A01G101400 chr1A 94.034 352 21 0 906 1257 434044709 434045060 3.520000e-148 534.0
39 TraesCS5A01G101400 chr1A 93.750 352 22 0 906 1257 379474538 379474889 1.640000e-146 529.0


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 TraesCS5A01G101400 chr5A 148828551 148830954 2403 True 4440.000000 4440 100.000000 1 2404 1 chr5A.!!$R1 2403
1 TraesCS5A01G101400 chr2A 22038022 22040424 2402 True 4228.000000 4228 98.420000 1 2404 1 chr2A.!!$R1 2403
2 TraesCS5A01G101400 chr2A 95941719 95943046 1327 True 2268.000000 2268 97.519000 1 1327 1 chr2A.!!$R3 1326
3 TraesCS5A01G101400 chr2A 313206184 313206703 519 True 623.000000 623 88.497000 60 585 1 chr2A.!!$R4 525
4 TraesCS5A01G101400 chr7A 613449549 613450787 1238 True 995.000000 1064 96.252000 1197 2404 2 chr7A.!!$R2 1207
5 TraesCS5A01G101400 chr7A 105796427 105797008 581 False 970.000000 970 96.735000 1823 2404 1 chr7A.!!$F1 581
6 TraesCS5A01G101400 chr7A 51909715 51912124 2409 True 927.500000 1347 91.049000 1 2404 2 chr7A.!!$R1 2403
7 TraesCS5A01G101400 chr3A 543426214 543427364 1150 False 1173.000000 1173 85.628000 1283 2404 1 chr3A.!!$F2 1121
8 TraesCS5A01G101400 chr3A 500021359 500021935 576 False 717.000000 717 89.157000 1827 2404 1 chr3A.!!$F1 577
9 TraesCS5A01G101400 chr2B 2002129 2004752 2623 True 893.500000 1000 93.528000 1 1826 2 chr2B.!!$R2 1825
10 TraesCS5A01G101400 chr2B 298581123 298581665 542 False 743.000000 743 91.773000 55 585 1 chr2B.!!$F1 530
11 TraesCS5A01G101400 chr2B 120979753 120980295 542 True 721.000000 721 90.642000 1283 1826 1 chr2B.!!$R1 543
12 TraesCS5A01G101400 chr5B 606612354 606614974 2620 True 865.000000 976 92.672500 1 1826 2 chr5B.!!$R1 1825
13 TraesCS5A01G101400 chrUn 68841912 68845137 3225 False 835.333333 970 92.175667 1 2404 3 chrUn.!!$F1 2403
14 TraesCS5A01G101400 chr4B 264556999 264558117 1118 False 646.000000 750 91.207000 1283 2404 2 chr4B.!!$F2 1121
15 TraesCS5A01G101400 chr7B 747296600 747297140 540 True 734.000000 734 91.144000 1286 1826 1 chr7B.!!$R1 540
16 TraesCS5A01G101400 chr5D 338876829 338877564 735 True 719.000000 719 85.121000 1696 2404 1 chr5D.!!$R1 708
17 TraesCS5A01G101400 chr2D 257746152 257746672 520 False 604.000000 604 87.823000 57 585 1 chr2D.!!$F1 528
18 TraesCS5A01G101400 chr1D 438031102 438032857 1755 True 300.100000 540 94.188500 854 1287 2 chr1D.!!$R1 433

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
936 961 8.480501 ACTGATTTGATTTTATGCCTGCTTTAT 58.519 29.63 0.0 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 3550 8.092687 TCCTAATTAACTGCGAAGACTAAACTT 58.907 33.333 0.0 0.0 0.0 2.66 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
26 27 9.601810 ATCAAATTAAGGTTTCTAGACCCTTTT 57.398 29.630 21.99 12.31 40.73 2.27
936 961 8.480501 ACTGATTTGATTTTATGCCTGCTTTAT 58.519 29.630 0.00 0.00 0.00 1.40
1354 2914 0.734889 GACTCCATTGCAATGTCCCG 59.265 55.000 31.87 19.59 34.60 5.14
1434 2994 1.002868 CTCCTGGTGGAAGCACTGG 60.003 63.158 0.00 0.00 40.88 4.00
1916 3550 3.280295 GACTGGACTCTAGATCACGGAA 58.720 50.000 0.00 0.00 0.00 4.30
2113 3765 1.475751 GCCACATGCTAGCACCACTAT 60.476 52.381 22.07 0.00 36.87 2.12
2364 4021 9.131791 GTGATACCTATTTATCACCACCAAAAT 57.868 33.333 10.82 0.00 46.99 1.82
2381 4038 7.440856 CCACCAAAATAAGTATGTTGCAGTTTT 59.559 33.333 0.00 0.00 31.07 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
577 599 3.867857 TGCGGTACAGCAAAAGATGATA 58.132 40.909 18.65 0.0 45.06 2.15
1434 2994 5.154932 CGACGAGTCCACCTTATTGATATC 58.845 45.833 0.00 0.0 0.00 1.63
1569 3135 0.249120 CCGTACATCCTGCCAAGACA 59.751 55.000 0.00 0.0 0.00 3.41
1916 3550 8.092687 TCCTAATTAACTGCGAAGACTAAACTT 58.907 33.333 0.00 0.0 0.00 2.66
2364 4021 9.278978 TCATAACAGAAAACTGCAACATACTTA 57.721 29.630 0.00 0.0 0.00 2.24


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

AutoCloner maintained by Alex Coulton.