Multiple sequence alignment - TraesCS2A01G528000

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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 TraesCS2A01G528000 chr2A 100.000 2366 0 0 1 2366 747152535 747154900 0.000000e+00 4370
1 TraesCS2A01G528000 chr2A 90.334 1469 115 10 5 1453 746980893 746982354 0.000000e+00 1901
2 TraesCS2A01G528000 chr2B 90.576 1910 145 16 13 1899 752833504 752835401 0.000000e+00 2497
3 TraesCS2A01G528000 chr2B 82.592 517 29 20 1907 2364 752836238 752836752 1.320000e-107 399
4 TraesCS2A01G528000 chr2D 89.848 1448 119 12 14 1440 617076497 617077937 0.000000e+00 1834
5 TraesCS2A01G528000 chr2D 85.507 414 36 10 1797 2191 617078029 617078437 6.090000e-111 411
6 TraesCS2A01G528000 chr5A 85.694 1377 166 16 64 1413 584458231 584456859 0.000000e+00 1423
7 TraesCS2A01G528000 chr5D 84.933 1427 168 24 62 1454 464075090 464073677 0.000000e+00 1400
8 TraesCS2A01G528000 chr5B 84.853 1426 174 20 62 1454 570932496 570931080 0.000000e+00 1399
9 TraesCS2A01G528000 chr5B 79.036 1307 221 37 82 1352 687161559 687160270 0.000000e+00 846
10 TraesCS2A01G528000 chr1B 83.013 1042 158 10 326 1352 10084760 10085797 0.000000e+00 926
11 TraesCS2A01G528000 chr1B 82.263 1043 165 9 326 1352 10074729 10075767 0.000000e+00 883
12 TraesCS2A01G528000 chr3D 82.037 1041 171 6 326 1352 4971870 4972908 0.000000e+00 872
13 TraesCS2A01G528000 chr3D 85.926 270 32 3 1444 1711 152168974 152169239 1.380000e-72 283
14 TraesCS2A01G528000 chr4A 79.423 1283 215 34 104 1352 624631817 624633084 0.000000e+00 861
15 TraesCS2A01G528000 chr3A 82.335 968 149 12 401 1352 11382692 11383653 0.000000e+00 821
16 TraesCS2A01G528000 chr7D 86.312 263 28 5 1454 1714 436499200 436498944 1.790000e-71 279
17 TraesCS2A01G528000 chr7D 86.154 260 30 3 1457 1714 204871003 204870748 2.320000e-70 276
18 TraesCS2A01G528000 chr6D 85.932 263 32 4 1454 1714 123159231 123158972 2.320000e-70 276
19 TraesCS2A01G528000 chr7A 85.393 267 31 6 1451 1714 486156530 486156791 1.080000e-68 270
20 TraesCS2A01G528000 chr1A 86.220 254 28 6 1453 1703 498534237 498534486 3.880000e-68 268
21 TraesCS2A01G528000 chr6B 85.283 265 32 4 1454 1714 217169259 217168998 1.390000e-67 267
22 TraesCS2A01G528000 chr7B 85.171 263 32 4 1454 1714 169295739 169295482 1.800000e-66 263


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 TraesCS2A01G528000 chr2A 747152535 747154900 2365 False 4370.0 4370 100.0000 1 2366 1 chr2A.!!$F2 2365
1 TraesCS2A01G528000 chr2A 746980893 746982354 1461 False 1901.0 1901 90.3340 5 1453 1 chr2A.!!$F1 1448
2 TraesCS2A01G528000 chr2B 752833504 752836752 3248 False 1448.0 2497 86.5840 13 2364 2 chr2B.!!$F1 2351
3 TraesCS2A01G528000 chr2D 617076497 617078437 1940 False 1122.5 1834 87.6775 14 2191 2 chr2D.!!$F1 2177
4 TraesCS2A01G528000 chr5A 584456859 584458231 1372 True 1423.0 1423 85.6940 64 1413 1 chr5A.!!$R1 1349
5 TraesCS2A01G528000 chr5D 464073677 464075090 1413 True 1400.0 1400 84.9330 62 1454 1 chr5D.!!$R1 1392
6 TraesCS2A01G528000 chr5B 570931080 570932496 1416 True 1399.0 1399 84.8530 62 1454 1 chr5B.!!$R1 1392
7 TraesCS2A01G528000 chr5B 687160270 687161559 1289 True 846.0 846 79.0360 82 1352 1 chr5B.!!$R2 1270
8 TraesCS2A01G528000 chr1B 10084760 10085797 1037 False 926.0 926 83.0130 326 1352 1 chr1B.!!$F2 1026
9 TraesCS2A01G528000 chr1B 10074729 10075767 1038 False 883.0 883 82.2630 326 1352 1 chr1B.!!$F1 1026
10 TraesCS2A01G528000 chr3D 4971870 4972908 1038 False 872.0 872 82.0370 326 1352 1 chr3D.!!$F1 1026
11 TraesCS2A01G528000 chr4A 624631817 624633084 1267 False 861.0 861 79.4230 104 1352 1 chr4A.!!$F1 1248
12 TraesCS2A01G528000 chr3A 11382692 11383653 961 False 821.0 821 82.3350 401 1352 1 chr3A.!!$F1 951

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
379 409 0.391597 TCTTCTGTTGACGGTGGTCC 59.608 55.0 0.0 0.0 42.73 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 3257 0.250727 CCCCGGCTGTCTCAAGAAAA 60.251 55.0 0.0 0.0 0.0 2.29 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
54 55 7.072177 TGTTGGATCTAACTTTTATCGCTTG 57.928 36.000 20.91 0.00 0.00 4.01
57 58 6.640518 TGGATCTAACTTTTATCGCTTGAGT 58.359 36.000 0.00 0.00 0.00 3.41
59 60 8.255206 TGGATCTAACTTTTATCGCTTGAGTTA 58.745 33.333 0.00 0.00 33.13 2.24
108 109 7.698970 ACGTACTAAACAAACAACCAAATCTTG 59.301 33.333 0.00 0.00 0.00 3.02
121 122 4.278170 ACCAAATCTTGTTCGCATCTTTGA 59.722 37.500 0.00 0.00 0.00 2.69
135 136 4.736793 GCATCTTTGATATTTGCAGGTTCG 59.263 41.667 0.00 0.00 33.58 3.95
165 166 5.700402 AAATCATTGCAGGTACTACTCCT 57.300 39.130 0.00 0.00 36.02 3.69
179 180 9.503369 AGGTACTACTCCTATCCAAACTTTTAT 57.497 33.333 0.00 0.00 36.02 1.40
239 257 7.224753 TCTGCTGCACATAAAGTAATTAGCTAC 59.775 37.037 0.00 0.00 0.00 3.58
312 332 6.239317 GGCAATTTCCAACCCTAAGGAATATC 60.239 42.308 0.00 0.00 43.02 1.63
377 407 1.208535 TGTTCTTCTGTTGACGGTGGT 59.791 47.619 0.00 0.00 0.00 4.16
379 409 0.391597 TCTTCTGTTGACGGTGGTCC 59.608 55.000 0.00 0.00 42.73 4.46
441 471 9.695884 GAAGAGATACATTTGAAAGTCGAAATC 57.304 33.333 0.00 0.00 0.00 2.17
507 537 5.671493 TCCTCCGAAATCAAGAAGATAACC 58.329 41.667 0.00 0.00 35.39 2.85
546 576 0.616371 TAGGACGTGGTGGATTTGGG 59.384 55.000 0.00 0.00 0.00 4.12
547 577 1.074248 GGACGTGGTGGATTTGGGT 59.926 57.895 0.00 0.00 0.00 4.51
583 613 4.081087 GTGAGCTACCAAATGGAGTTCCTA 60.081 45.833 6.42 0.00 38.94 2.94
598 628 3.389329 AGTTCCTATGGCGATCAAGATGT 59.611 43.478 0.00 0.00 0.00 3.06
606 636 5.084818 TGGCGATCAAGATGTTAGAGAAA 57.915 39.130 0.00 0.00 0.00 2.52
678 708 6.916360 AGAATCCACCATACAAACATTGTT 57.084 33.333 0.54 0.00 42.22 2.83
1114 1169 0.836400 GGTGAGTGGGAGGAGGAACA 60.836 60.000 0.00 0.00 0.00 3.18
1236 1291 3.562973 CAGCAGAAGAGCAAGAAAAGACA 59.437 43.478 0.00 0.00 36.85 3.41
1292 1347 1.529713 GGAACCCAAGAAACCGGCA 60.530 57.895 0.00 0.00 0.00 5.69
1420 1486 6.879993 AGATCGTATCACCATAGTGTACTAGG 59.120 42.308 0.00 0.00 44.83 3.02
1427 1493 4.833380 CACCATAGTGTACTAGGCCTACAT 59.167 45.833 8.91 2.38 39.30 2.29
1489 1555 8.662141 GTTTCTTTTTACTCCGCATACAAGATA 58.338 33.333 0.00 0.00 0.00 1.98
1530 1596 9.567848 CTACGCAAAGTTTGACCAAATTTATAT 57.432 29.630 19.82 0.00 31.37 0.86
1561 1627 6.354794 TGTCAGCACCTACAATACTAAAGT 57.645 37.500 0.00 0.00 0.00 2.66
1608 1674 9.952188 CATGATGCATCTAATGATATTGATTCC 57.048 33.333 26.32 0.00 0.00 3.01
1714 1780 5.066913 ACTGAAAAGAAATGGAGGGAGTT 57.933 39.130 0.00 0.00 0.00 3.01
1730 1796 7.610305 TGGAGGGAGTTTTAAATGCTAAACTAG 59.390 37.037 0.00 0.00 42.82 2.57
1772 1843 6.845758 TGGTAGCAGTAGTATGTACAACTT 57.154 37.500 13.48 0.13 0.00 2.66
1778 1849 6.874134 AGCAGTAGTATGTACAACTTGAAAGG 59.126 38.462 13.48 0.00 0.00 3.11
1781 1852 8.709646 CAGTAGTATGTACAACTTGAAAGGTTC 58.290 37.037 13.48 0.00 0.00 3.62
1802 1890 2.480419 CGTTGTTTAGTCAGCTTCCTGG 59.520 50.000 0.00 0.00 39.61 4.45
1805 1893 1.807142 GTTTAGTCAGCTTCCTGGTGC 59.193 52.381 6.38 6.38 43.32 5.01
1807 1895 1.279496 TAGTCAGCTTCCTGGTGCAT 58.721 50.000 14.47 3.37 43.32 3.96
1877 1966 8.937884 TGTAATTGGATTTGATTTGCAATGAAG 58.062 29.630 0.00 0.00 35.62 3.02
1883 1972 8.801299 TGGATTTGATTTGCAATGAAGTAGTTA 58.199 29.630 0.00 0.00 36.15 2.24
1901 2819 5.584551 AGTTAAAGAATGAGGAACCTGGT 57.415 39.130 0.00 0.00 0.00 4.00
1903 2821 6.712276 AGTTAAAGAATGAGGAACCTGGTAG 58.288 40.000 0.00 0.00 0.00 3.18
1905 2823 5.584551 AAAGAATGAGGAACCTGGTAGTT 57.415 39.130 0.00 0.00 0.00 2.24
1910 2828 6.215636 AGAATGAGGAACCTGGTAGTTATTGT 59.784 38.462 0.00 0.00 0.00 2.71
1987 2920 5.297776 AGTTCCTCATTCCGAATGCAATTAG 59.702 40.000 15.21 7.75 36.07 1.73
2028 2963 6.522054 TGAGGTTATGTATACCTAAGCAAGC 58.478 40.000 23.35 15.71 45.88 4.01
2033 2968 3.380393 TGTATACCTAAGCAAGCCCAGA 58.620 45.455 0.00 0.00 0.00 3.86
2174 3119 2.909662 AGAAAGGAAGACAGAAGGGGAG 59.090 50.000 0.00 0.00 0.00 4.30
2178 3123 2.200955 GGAAGACAGAAGGGGAGGAAT 58.799 52.381 0.00 0.00 0.00 3.01
2217 3162 3.669122 GCTAACATAAGATACCACGCGAG 59.331 47.826 15.93 4.16 0.00 5.03
2348 3326 1.153529 CAACTACGCGGCCCATACA 60.154 57.895 12.47 0.00 0.00 2.29
2349 3327 0.741574 CAACTACGCGGCCCATACAA 60.742 55.000 12.47 0.00 0.00 2.41
2350 3328 0.036199 AACTACGCGGCCCATACAAA 60.036 50.000 12.47 0.00 0.00 2.83
2351 3329 0.461339 ACTACGCGGCCCATACAAAG 60.461 55.000 12.47 0.00 0.00 2.77
2352 3330 0.461339 CTACGCGGCCCATACAAAGT 60.461 55.000 12.47 0.00 0.00 2.66
2364 3342 7.205992 GGCCCATACAAAGTAAGTAGTAGTAC 58.794 42.308 0.00 0.00 0.00 2.73
2365 3343 7.147846 GGCCCATACAAAGTAAGTAGTAGTACA 60.148 40.741 10.33 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 4.736793 CCTGCAAATATCAAAGATGCGAAC 59.263 41.667 0.00 0.00 39.81 3.95
121 122 1.448985 ACACGCGAACCTGCAAATAT 58.551 45.000 15.93 0.00 34.15 1.28
135 136 3.574614 ACCTGCAATGATTTTTACACGC 58.425 40.909 0.00 0.00 0.00 5.34
201 219 9.777297 TTTATGTGCAGCAGATATATACTTCAA 57.223 29.630 12.81 0.00 0.00 2.69
239 257 4.282195 AGAGAATGTAAGAGCGGGAATAGG 59.718 45.833 0.00 0.00 0.00 2.57
289 308 7.014615 CAGGATATTCCTTAGGGTTGGAAATTG 59.985 40.741 0.00 0.00 46.91 2.32
292 311 5.734140 TCAGGATATTCCTTAGGGTTGGAAA 59.266 40.000 0.00 0.00 46.91 3.13
312 332 6.057533 TGTAGCTGAATACATGGAAATCAGG 58.942 40.000 20.05 7.36 38.32 3.86
377 407 2.501723 AGCGAAAGATAAAGAGCAGGGA 59.498 45.455 0.00 0.00 0.00 4.20
379 409 3.525537 TCAGCGAAAGATAAAGAGCAGG 58.474 45.455 0.00 0.00 0.00 4.85
441 471 8.722480 TTGATGTACCATATGTCTTGAGAAAG 57.278 34.615 1.24 0.00 0.00 2.62
485 515 5.428253 TGGTTATCTTCTTGATTTCGGAGG 58.572 41.667 0.00 0.00 36.65 4.30
507 537 7.096023 CGTCCTAATTTATCCTTGAATCGTCTG 60.096 40.741 0.00 0.00 0.00 3.51
546 576 2.561569 AGCTCACCTTTGTACACACAC 58.438 47.619 0.00 0.00 33.30 3.82
547 577 3.493699 GGTAGCTCACCTTTGTACACACA 60.494 47.826 0.00 0.00 44.79 3.72
583 613 4.944619 TCTCTAACATCTTGATCGCCAT 57.055 40.909 0.00 0.00 0.00 4.40
598 628 5.308237 GCCCCTCTCCATTAGATTTCTCTAA 59.692 44.000 0.00 0.00 45.61 2.10
606 636 1.224120 TCCTGCCCCTCTCCATTAGAT 59.776 52.381 0.00 0.00 32.41 1.98
901 932 6.228258 TCTTCGGATTAAAGCTGTAGTTGTT 58.772 36.000 0.00 0.00 0.00 2.83
958 1013 1.676006 GGTAATGATGCTTTGGTCCCG 59.324 52.381 0.00 0.00 0.00 5.14
1236 1291 1.952367 GCCACAATAGCCAGCTGTCTT 60.952 52.381 13.81 0.00 0.00 3.01
1292 1347 5.067273 TGTTTACCACCTTTGTCATCGATT 58.933 37.500 0.00 0.00 0.00 3.34
1420 1486 3.710209 ATATCCCTCAAGCATGTAGGC 57.290 47.619 0.00 0.00 0.00 3.93
1427 1493 9.812347 ACATGAATTAAATATATCCCTCAAGCA 57.188 29.630 0.00 0.00 0.00 3.91
1689 1755 5.536538 ACTCCCTCCATTTCTTTTCAGTTTC 59.463 40.000 0.00 0.00 0.00 2.78
1691 1757 5.066913 ACTCCCTCCATTTCTTTTCAGTT 57.933 39.130 0.00 0.00 0.00 3.16
1730 1796 5.835113 ACCAATTGCACTACCATGTAATC 57.165 39.130 0.00 0.00 34.28 1.75
1772 1843 4.034742 GCTGACTAAACAACGAACCTTTCA 59.965 41.667 0.00 0.00 0.00 2.69
1778 1849 3.808174 AGGAAGCTGACTAAACAACGAAC 59.192 43.478 0.00 0.00 0.00 3.95
1781 1852 2.480419 CCAGGAAGCTGACTAAACAACG 59.520 50.000 0.00 0.00 0.00 4.10
1802 1890 6.652481 ACAATATAGTGGCTCATAAGATGCAC 59.348 38.462 5.03 0.00 0.00 4.57
1807 1895 9.929180 GTTATCACAATATAGTGGCTCATAAGA 57.071 33.333 5.03 0.00 39.93 2.10
1850 1938 9.451002 TTCATTGCAAATCAAATCCAATTACAT 57.549 25.926 1.71 0.00 38.34 2.29
1852 1940 8.938906 ACTTCATTGCAAATCAAATCCAATTAC 58.061 29.630 1.71 0.00 38.34 1.89
1877 1966 6.473758 ACCAGGTTCCTCATTCTTTAACTAC 58.526 40.000 0.00 0.00 0.00 2.73
1883 1972 5.584551 AACTACCAGGTTCCTCATTCTTT 57.415 39.130 0.00 0.00 0.00 2.52
1903 2821 9.065871 GTGCTGAAGATAATTCACAACAATAAC 57.934 33.333 0.00 0.00 0.00 1.89
1905 2823 8.565896 AGTGCTGAAGATAATTCACAACAATA 57.434 30.769 0.00 0.00 0.00 1.90
2003 2938 7.162082 GCTTGCTTAGGTATACATAACCTCAT 58.838 38.462 5.90 0.00 44.20 2.90
2028 2963 4.161295 TCCTCCGCGCAATCTGGG 62.161 66.667 8.75 0.00 0.00 4.45
2033 2968 3.729965 CTCAGCTCCTCCGCGCAAT 62.730 63.158 8.75 0.00 34.40 3.56
2108 3043 1.427819 CGGCGCTGGTGGTTAATTC 59.572 57.895 8.83 0.00 0.00 2.17
2129 3064 3.735097 GGGGGCGGTACCATTGGT 61.735 66.667 13.94 13.94 42.05 3.67
2143 3078 0.332972 CTTCCTTTCTTCCCTGGGGG 59.667 60.000 14.00 4.90 46.11 5.40
2200 3145 1.053048 CGCTCGCGTGGTATCTTATG 58.947 55.000 5.77 0.00 34.35 1.90
2280 3257 0.250727 CCCCGGCTGTCTCAAGAAAA 60.251 55.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.