Multiple sequence alignment - TraesCS2A01G053900

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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 TraesCS2A01G053900 chr2A 100.000 2404 0 0 1 2404 22040423 22038020 0.000000e+00 4440.0
1 TraesCS2A01G053900 chr2A 97.517 1329 29 2 1 1327 95943045 95941719 0.000000e+00 2268.0
2 TraesCS2A01G053900 chr2A 97.059 476 14 0 1351 1826 95922128 95921653 0.000000e+00 802.0
3 TraesCS2A01G053900 chr2A 88.497 539 30 12 59 584 313206703 313206184 7.300000e-175 623.0
4 TraesCS2A01G053900 chr2A 90.909 55 5 0 1 55 313206794 313206740 9.220000e-10 75.0
5 TraesCS2A01G053900 chr5A 98.421 2406 35 3 1 2404 148830953 148828549 0.000000e+00 4229.0
6 TraesCS2A01G053900 chr7A 88.155 1165 90 27 1283 2404 51910872 51909713 0.000000e+00 1343.0
7 TraesCS2A01G053900 chr7A 96.508 630 22 0 1197 1826 613450787 613450158 0.000000e+00 1042.0
8 TraesCS2A01G053900 chr7A 96.747 584 17 2 1823 2404 105796427 105797010 0.000000e+00 972.0
9 TraesCS2A01G053900 chr7A 95.548 584 24 2 1823 2404 613450130 613449547 0.000000e+00 933.0
10 TraesCS2A01G053900 chr7A 94.152 342 11 2 1 333 51912123 51911782 1.650000e-141 512.0
11 TraesCS2A01G053900 chr3A 85.481 1164 116 25 1283 2404 543426214 543427366 0.000000e+00 1164.0
12 TraesCS2A01G053900 chr3A 89.175 582 56 5 1827 2404 500021359 500021937 0.000000e+00 719.0
13 TraesCS2A01G053900 chr2B 94.368 657 32 1 1 652 2004751 2004095 0.000000e+00 1003.0
14 TraesCS2A01G053900 chr2B 92.463 544 40 1 1283 1826 2002671 2002129 0.000000e+00 776.0
15 TraesCS2A01G053900 chr2B 91.408 547 27 5 54 584 298581123 298581665 0.000000e+00 732.0
16 TraesCS2A01G053900 chr2B 90.459 545 49 3 1283 1826 120980295 120979753 0.000000e+00 715.0
17 TraesCS2A01G053900 chr5B 93.760 657 33 4 1 652 606614973 606614320 0.000000e+00 979.0
18 TraesCS2A01G053900 chr5B 91.360 544 46 1 1283 1826 606612896 606612354 0.000000e+00 743.0
19 TraesCS2A01G053900 chrUn 93.760 657 27 5 1 652 68841913 68842560 0.000000e+00 974.0
20 TraesCS2A01G053900 chrUn 92.421 541 41 0 1283 1823 68843977 68844517 0.000000e+00 773.0
21 TraesCS2A01G053900 chr1B 90.311 578 52 3 1828 2404 426934304 426934878 0.000000e+00 754.0
22 TraesCS2A01G053900 chr4B 91.128 541 48 0 1283 1823 264556999 264557539 0.000000e+00 734.0
23 TraesCS2A01G053900 chr4B 90.998 411 32 5 1995 2404 264557713 264558119 1.260000e-152 549.0
24 TraesCS2A01G053900 chr4B 90.741 162 11 1 692 853 256841300 256841457 1.870000e-51 213.0
25 TraesCS2A01G053900 chr4B 100.000 31 0 0 1254 1284 256842362 256842392 9.280000e-05 58.4
26 TraesCS2A01G053900 chr7B 90.959 542 47 2 1286 1826 747297140 747296600 0.000000e+00 728.0
27 TraesCS2A01G053900 chr7B 100.000 34 0 0 1254 1287 672816652 672816685 2.000000e-06 63.9
28 TraesCS2A01G053900 chr5D 85.160 748 62 28 1696 2404 338877564 338876827 0.000000e+00 721.0
29 TraesCS2A01G053900 chr2D 87.823 542 32 13 56 584 257746152 257746672 2.640000e-169 604.0
30 TraesCS2A01G053900 chr2D 83.371 445 29 27 1707 2108 250282285 250281843 1.050000e-98 370.0
31 TraesCS2A01G053900 chr2D 88.927 289 23 6 1828 2109 619155610 619155324 4.920000e-92 348.0
32 TraesCS2A01G053900 chr2D 90.909 55 5 0 1 55 257746064 257746118 9.220000e-10 75.0
33 TraesCS2A01G053900 chr6D 93.466 352 23 0 906 1257 62081525 62081174 7.610000e-145 523.0
34 TraesCS2A01G053900 chr6D 93.466 352 22 1 907 1257 156016776 156016425 2.740000e-144 521.0
35 TraesCS2A01G053900 chr6D 93.182 352 23 1 907 1257 54816822 54817173 1.270000e-142 516.0
36 TraesCS2A01G053900 chr1D 90.441 408 24 10 853 1257 438032857 438032462 7.610000e-145 523.0
37 TraesCS2A01G053900 chr1D 97.222 36 0 1 1252 1287 438031136 438031102 2.580000e-05 60.2
38 TraesCS2A01G053900 chr7D 93.182 352 24 0 906 1257 32520359 32520008 3.540000e-143 518.0
39 TraesCS2A01G053900 chr7D 92.898 352 25 0 906 1257 625868532 625868883 1.650000e-141 512.0
40 TraesCS2A01G053900 chr1A 92.614 352 26 0 906 1257 434044709 434045060 7.670000e-140 507.0


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 TraesCS2A01G053900 chr2A 22038020 22040423 2403 True 4440.0 4440 100.0000 1 2404 1 chr2A.!!$R1 2403
1 TraesCS2A01G053900 chr2A 95941719 95943045 1326 True 2268.0 2268 97.5170 1 1327 1 chr2A.!!$R3 1326
2 TraesCS2A01G053900 chr2A 313206184 313206794 610 True 349.0 623 89.7030 1 584 2 chr2A.!!$R4 583
3 TraesCS2A01G053900 chr5A 148828549 148830953 2404 True 4229.0 4229 98.4210 1 2404 1 chr5A.!!$R1 2403
4 TraesCS2A01G053900 chr7A 613449547 613450787 1240 True 987.5 1042 96.0280 1197 2404 2 chr7A.!!$R2 1207
5 TraesCS2A01G053900 chr7A 105796427 105797010 583 False 972.0 972 96.7470 1823 2404 1 chr7A.!!$F1 581
6 TraesCS2A01G053900 chr7A 51909713 51912123 2410 True 927.5 1343 91.1535 1 2404 2 chr7A.!!$R1 2403
7 TraesCS2A01G053900 chr3A 543426214 543427366 1152 False 1164.0 1164 85.4810 1283 2404 1 chr3A.!!$F2 1121
8 TraesCS2A01G053900 chr3A 500021359 500021937 578 False 719.0 719 89.1750 1827 2404 1 chr3A.!!$F1 577
9 TraesCS2A01G053900 chr2B 2002129 2004751 2622 True 889.5 1003 93.4155 1 1826 2 chr2B.!!$R2 1825
10 TraesCS2A01G053900 chr2B 298581123 298581665 542 False 732.0 732 91.4080 54 584 1 chr2B.!!$F1 530
11 TraesCS2A01G053900 chr2B 120979753 120980295 542 True 715.0 715 90.4590 1283 1826 1 chr2B.!!$R1 543
12 TraesCS2A01G053900 chr5B 606612354 606614973 2619 True 861.0 979 92.5600 1 1826 2 chr5B.!!$R1 1825
13 TraesCS2A01G053900 chrUn 68841913 68844517 2604 False 873.5 974 93.0905 1 1823 2 chrUn.!!$F1 1822
14 TraesCS2A01G053900 chr1B 426934304 426934878 574 False 754.0 754 90.3110 1828 2404 1 chr1B.!!$F1 576
15 TraesCS2A01G053900 chr4B 264556999 264558119 1120 False 641.5 734 91.0630 1283 2404 2 chr4B.!!$F2 1121
16 TraesCS2A01G053900 chr7B 747296600 747297140 540 True 728.0 728 90.9590 1286 1826 1 chr7B.!!$R1 540
17 TraesCS2A01G053900 chr5D 338876827 338877564 737 True 721.0 721 85.1600 1696 2404 1 chr5D.!!$R1 708
18 TraesCS2A01G053900 chr2D 257746064 257746672 608 False 339.5 604 89.3660 1 584 2 chr2D.!!$F1 583
19 TraesCS2A01G053900 chr1D 438031102 438032857 1755 True 291.6 523 93.8315 853 1287 2 chr1D.!!$R1 434

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
476 534 2.996153 ATTGTGGGCATTGCGGCA 60.996 55.556 0.0 0.0 43.6 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 3006 1.073897 GCTTCCACCAGGAGTTGCT 59.926 57.895 0.0 0.0 46.74 3.91 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
476 534 2.996153 ATTGTGGGCATTGCGGCA 60.996 55.556 0.00 0.0 43.60 5.69
574 632 7.180766 TCCTTTTTCCTTATGCATGGAAGAAAT 59.819 33.333 17.36 0.0 42.46 2.17
1065 1126 9.482627 CCTTACTTCATAATCACCTATCTGAAC 57.517 37.037 0.00 0.0 0.00 3.18
1135 1196 3.620488 TGTGTGCAGGAAAGAAAGACTT 58.380 40.909 0.00 0.0 40.98 3.01
1585 3186 4.437239 CTTACTAGTCTTGGCAGGATGTG 58.563 47.826 1.54 0.0 39.31 3.21
1667 3268 1.751927 GGGTGATTCAGCCCAGCAG 60.752 63.158 21.80 0.0 45.22 4.24
1752 3357 8.356657 TGCTTATGCTTTACACATTTACACTTT 58.643 29.630 1.96 0.0 40.48 2.66
1931 3570 0.982673 CGGACAGTTTAGTCTTCGCG 59.017 55.000 0.00 0.0 38.57 5.87
2183 3842 1.072806 ACAAGGATGCTGCAACAGAGA 59.927 47.619 6.36 0.0 32.44 3.10
2194 3853 8.737168 ATGCTGCAACAGAGAACTTTATATTA 57.263 30.769 6.36 0.0 32.44 0.98
2264 3928 2.293955 GGCGCCACCAAAGTAAGTTTTA 59.706 45.455 24.80 0.0 38.86 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
476 534 6.344500 CACCATGACACTTTCTAAGCTAGAT 58.656 40.000 0.00 0.00 34.22 1.98
574 632 4.119862 GCGGTACAGCAAAAGATGATCTA 58.880 43.478 13.42 0.00 37.05 1.98
971 1032 4.218417 CCTTGTGTAAGTAAAGCAGCCATT 59.782 41.667 0.00 0.00 31.80 3.16
975 1036 2.095212 GCCCTTGTGTAAGTAAAGCAGC 60.095 50.000 0.00 0.00 31.80 5.25
1065 1126 0.241749 AGCATTGATGTTGTGCACCG 59.758 50.000 15.69 0.00 41.19 4.94
1135 1196 7.060421 ACTTTCCATCCTTGTTAAGAGAACAA 58.940 34.615 3.11 3.11 37.76 2.83
1411 3006 1.073897 GCTTCCACCAGGAGTTGCT 59.926 57.895 0.00 0.00 46.74 3.91
1585 3186 2.429610 TCCTCATAGTTGTTAGGTCCGC 59.570 50.000 0.00 0.00 0.00 5.54
2183 3842 9.893305 GCCAAACTATTGCGATAATATAAAGTT 57.107 29.630 0.00 0.00 35.10 2.66
2194 3853 1.472480 GTGGTGCCAAACTATTGCGAT 59.528 47.619 0.00 0.00 35.10 4.58
2264 3928 7.624360 TTTCGTGGCAATACTCTATTTCAAT 57.376 32.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.