Multiple sequence alignment - TraesCS3B01G217700

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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 TraesCS3B01G217700 chr3B 100.000 2246 0 0 1 2246 260376727 260378972 0.000000e+00 4148
1 TraesCS3B01G217700 chr3B 92.714 1743 68 19 136 1822 201559165 201557426 0.000000e+00 2460
2 TraesCS3B01G217700 chr3D 92.501 2067 74 29 1 2021 182097004 182099035 0.000000e+00 2883
3 TraesCS3B01G217700 chr3D 95.122 246 11 1 2001 2246 182100725 182100969 9.730000e-104 387
4 TraesCS3B01G217700 chr3D 91.597 119 9 1 2128 2246 48838297 48838414 1.780000e-36 163
5 TraesCS3B01G217700 chr3D 98.765 81 1 0 1824 1904 24157366 24157446 6.460000e-31 145
6 TraesCS3B01G217700 chr3D 98.765 81 1 0 1824 1904 608536361 608536441 6.460000e-31 145
7 TraesCS3B01G217700 chr5B 92.089 1757 62 23 136 1820 413609046 413610797 0.000000e+00 2403
8 TraesCS3B01G217700 chr5B 90.930 1742 83 13 136 1818 432878330 432880055 0.000000e+00 2272
9 TraesCS3B01G217700 chr5B 90.293 1741 74 36 136 1821 429038290 429039990 0.000000e+00 2191
10 TraesCS3B01G217700 chr2D 91.732 1778 53 24 136 1821 33935419 33937194 0.000000e+00 2383
11 TraesCS3B01G217700 chr2D 91.718 1775 54 25 136 1819 630271895 630273667 0.000000e+00 2377
12 TraesCS3B01G217700 chr2D 90.535 243 22 1 1912 2154 391397657 391397416 1.000000e-83 320
13 TraesCS3B01G217700 chr4A 90.719 1724 99 28 136 1806 310764015 310765730 0.000000e+00 2241
14 TraesCS3B01G217700 chr4A 90.448 513 36 4 349 850 219308174 219307664 0.000000e+00 664
15 TraesCS3B01G217700 chr4D 91.598 1583 77 14 136 1667 245650290 245651867 0.000000e+00 2135
16 TraesCS3B01G217700 chr4D 90.184 163 11 4 2087 2246 362412219 362412379 8.130000e-50 207
17 TraesCS3B01G217700 chr5A 92.677 1311 46 17 555 1819 482027333 482026027 0.000000e+00 1844
18 TraesCS3B01G217700 chr1D 94.060 926 35 4 911 1818 254419186 254420109 0.000000e+00 1387
19 TraesCS3B01G217700 chr1D 88.142 253 28 2 1903 2154 458822857 458823108 1.300000e-77 300
20 TraesCS3B01G217700 chr1D 91.558 154 10 3 2092 2244 65844692 65844541 2.260000e-50 209
21 TraesCS3B01G217700 chr1D 98.795 83 1 0 1822 1904 68411218 68411136 5.000000e-32 148
22 TraesCS3B01G217700 chr1D 98.765 81 1 0 1824 1904 180376015 180375935 6.460000e-31 145
23 TraesCS3B01G217700 chrUn 89.845 1034 32 13 136 1096 371050056 371051089 0.000000e+00 1260
24 TraesCS3B01G217700 chrUn 95.249 442 11 2 136 567 449931931 449932372 0.000000e+00 691
25 TraesCS3B01G217700 chrUn 91.614 477 12 10 296 744 451362693 451362217 3.150000e-178 634
26 TraesCS3B01G217700 chrUn 89.047 493 26 5 555 1019 451362730 451363222 8.940000e-164 586
27 TraesCS3B01G217700 chrUn 95.425 153 6 1 1670 1821 390488681 390488529 2.230000e-60 243
28 TraesCS3B01G217700 chrUn 98.765 81 1 0 1824 1904 438111605 438111525 6.460000e-31 145
29 TraesCS3B01G217700 chr3A 89.764 889 32 19 136 968 672876825 672875940 0.000000e+00 1083
30 TraesCS3B01G217700 chr3A 88.439 346 36 3 1903 2246 706192193 706192536 4.460000e-112 414
31 TraesCS3B01G217700 chr3A 88.957 163 14 3 2087 2246 596497660 596497821 4.890000e-47 198
32 TraesCS3B01G217700 chr3A 88.820 161 14 3 2087 2244 673464409 673464568 6.330000e-46 195
33 TraesCS3B01G217700 chr7D 90.551 762 25 12 136 850 231585280 231586041 0.000000e+00 965
34 TraesCS3B01G217700 chr7D 88.764 356 30 4 142 491 127764087 127764438 5.730000e-116 427
35 TraesCS3B01G217700 chr4B 90.632 459 14 11 258 687 1 459 1.160000e-162 582
36 TraesCS3B01G217700 chr2B 91.483 317 9 11 1522 1820 363495212 363495528 9.590000e-114 420
37 TraesCS3B01G217700 chr1A 87.608 347 40 3 1901 2246 151351327 151350983 1.250000e-107 399
38 TraesCS3B01G217700 chr1A 89.431 246 25 1 1909 2154 49290275 49290519 2.170000e-80 309
39 TraesCS3B01G217700 chr1A 88.128 219 25 1 1936 2154 536202764 536202981 2.210000e-65 259
40 TraesCS3B01G217700 chr5D 88.889 243 26 1 1912 2154 477177315 477177074 4.690000e-77 298
41 TraesCS3B01G217700 chr5D 90.184 163 12 3 2087 2246 327733971 327734132 2.260000e-50 209
42 TraesCS3B01G217700 chr6D 88.938 226 21 3 1932 2154 315628605 315628381 2.200000e-70 276
43 TraesCS3B01G217700 chr1B 87.234 235 28 2 1921 2154 138736814 138737047 1.320000e-67 267
44 TraesCS3B01G217700 chr7B 98.765 81 1 0 1824 1904 622427279 622427359 6.460000e-31 145
45 TraesCS3B01G217700 chr7A 98.765 81 1 0 1824 1904 12219619 12219539 6.460000e-31 145
46 TraesCS3B01G217700 chr6A 98.765 81 1 0 1824 1904 602046733 602046653 6.460000e-31 145


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 TraesCS3B01G217700 chr3B 260376727 260378972 2245 False 4148 4148 100.0000 1 2246 1 chr3B.!!$F1 2245
1 TraesCS3B01G217700 chr3B 201557426 201559165 1739 True 2460 2460 92.7140 136 1822 1 chr3B.!!$R1 1686
2 TraesCS3B01G217700 chr3D 182097004 182100969 3965 False 1635 2883 93.8115 1 2246 2 chr3D.!!$F4 2245
3 TraesCS3B01G217700 chr5B 413609046 413610797 1751 False 2403 2403 92.0890 136 1820 1 chr5B.!!$F1 1684
4 TraesCS3B01G217700 chr5B 432878330 432880055 1725 False 2272 2272 90.9300 136 1818 1 chr5B.!!$F3 1682
5 TraesCS3B01G217700 chr5B 429038290 429039990 1700 False 2191 2191 90.2930 136 1821 1 chr5B.!!$F2 1685
6 TraesCS3B01G217700 chr2D 33935419 33937194 1775 False 2383 2383 91.7320 136 1821 1 chr2D.!!$F1 1685
7 TraesCS3B01G217700 chr2D 630271895 630273667 1772 False 2377 2377 91.7180 136 1819 1 chr2D.!!$F2 1683
8 TraesCS3B01G217700 chr4A 310764015 310765730 1715 False 2241 2241 90.7190 136 1806 1 chr4A.!!$F1 1670
9 TraesCS3B01G217700 chr4A 219307664 219308174 510 True 664 664 90.4480 349 850 1 chr4A.!!$R1 501
10 TraesCS3B01G217700 chr4D 245650290 245651867 1577 False 2135 2135 91.5980 136 1667 1 chr4D.!!$F1 1531
11 TraesCS3B01G217700 chr5A 482026027 482027333 1306 True 1844 1844 92.6770 555 1819 1 chr5A.!!$R1 1264
12 TraesCS3B01G217700 chr1D 254419186 254420109 923 False 1387 1387 94.0600 911 1818 1 chr1D.!!$F1 907
13 TraesCS3B01G217700 chrUn 371050056 371051089 1033 False 1260 1260 89.8450 136 1096 1 chrUn.!!$F1 960
14 TraesCS3B01G217700 chr3A 672875940 672876825 885 True 1083 1083 89.7640 136 968 1 chr3A.!!$R1 832
15 TraesCS3B01G217700 chr7D 231585280 231586041 761 False 965 965 90.5510 136 850 1 chr7D.!!$F2 714

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
491 518 0.181114 TGCTGAAGCCGCTATTGGAT 59.819 50.0 0.0 0.0 41.18 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 3944 0.035458 GGGAGATCTAACGGCATGGG 59.965 60.0 0.0 0.0 0.0 4.0 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
369 371 7.847711 ACATGGTTAGAGCTCTAATATGTCT 57.152 36.000 34.96 25.14 40.70 3.41
370 372 8.256356 ACATGGTTAGAGCTCTAATATGTCTT 57.744 34.615 34.96 24.72 40.70 3.01
371 373 8.147058 ACATGGTTAGAGCTCTAATATGTCTTG 58.853 37.037 34.96 27.76 40.70 3.02
372 374 7.898014 TGGTTAGAGCTCTAATATGTCTTGA 57.102 36.000 32.99 9.58 40.20 3.02
373 375 8.306313 TGGTTAGAGCTCTAATATGTCTTGAA 57.694 34.615 32.99 10.77 40.20 2.69
374 376 8.198109 TGGTTAGAGCTCTAATATGTCTTGAAC 58.802 37.037 32.99 20.28 40.20 3.18
375 377 8.417884 GGTTAGAGCTCTAATATGTCTTGAACT 58.582 37.037 32.99 2.63 40.20 3.01
376 378 9.810545 GTTAGAGCTCTAATATGTCTTGAACTT 57.189 33.333 32.99 2.28 40.20 2.66
491 518 0.181114 TGCTGAAGCCGCTATTGGAT 59.819 50.000 0.00 0.00 41.18 3.41
493 520 1.002033 GCTGAAGCCGCTATTGGATTG 60.002 52.381 0.00 0.00 37.85 2.67
791 874 8.602328 CAATTTATTGGCTAATTCGAATTTGCA 58.398 29.630 38.71 27.94 44.96 4.08
923 1037 1.726791 CGTCTGGTGTCTACAATGCAC 59.273 52.381 0.00 0.00 0.00 4.57
1096 1211 8.982471 TGTATTAGAAATGATACCCTGGGATA 57.018 34.615 22.23 8.62 0.00 2.59
1166 1281 5.473504 GTGTGGGTTGTAAGAGATGTGAATT 59.526 40.000 0.00 0.00 0.00 2.17
1237 1353 0.107848 AACACGTAGCATGGCCCTAC 60.108 55.000 0.00 3.72 33.50 3.18
1422 1538 3.951775 TTTGCCGATATTTGCAGGTTT 57.048 38.095 0.00 0.00 38.95 3.27
1684 1819 1.331756 GCTGCTACACGGAATTCATGG 59.668 52.381 7.93 0.00 0.00 3.66
1859 1995 3.578716 TGAAGTGTCCTTCCTTCCTACAG 59.421 47.826 0.38 0.00 45.45 2.74
1873 2009 5.339200 CCTTCCTACAGCTGATAGGGAAAAA 60.339 44.000 27.72 19.02 39.87 1.94
1874 2010 5.975988 TCCTACAGCTGATAGGGAAAAAT 57.024 39.130 27.72 6.45 39.87 1.82
1875 2011 5.930135 TCCTACAGCTGATAGGGAAAAATC 58.070 41.667 27.72 0.00 39.87 2.17
1876 2012 5.428457 TCCTACAGCTGATAGGGAAAAATCA 59.572 40.000 27.72 13.26 39.87 2.57
1878 2014 6.774656 CCTACAGCTGATAGGGAAAAATCATT 59.225 38.462 23.35 0.00 36.33 2.57
1879 2015 6.461110 ACAGCTGATAGGGAAAAATCATTG 57.539 37.500 23.35 0.00 31.95 2.82
1892 2028 7.064134 GGGAAAAATCATTGTTTTTACGATCCC 59.936 37.037 17.00 17.00 40.97 3.85
1893 2029 7.817478 GGAAAAATCATTGTTTTTACGATCCCT 59.183 33.333 6.00 0.00 40.35 4.20
1894 2030 9.849166 GAAAAATCATTGTTTTTACGATCCCTA 57.151 29.630 6.00 0.00 40.35 3.53
1896 2032 9.801873 AAAATCATTGTTTTTACGATCCCTATG 57.198 29.630 4.08 0.00 0.00 2.23
1897 2033 8.519799 AATCATTGTTTTTACGATCCCTATGT 57.480 30.769 0.00 0.00 0.00 2.29
1898 2034 9.621629 AATCATTGTTTTTACGATCCCTATGTA 57.378 29.630 0.00 0.00 0.00 2.29
1899 2035 8.657074 TCATTGTTTTTACGATCCCTATGTAG 57.343 34.615 0.00 0.00 0.00 2.74
1900 2036 8.479689 TCATTGTTTTTACGATCCCTATGTAGA 58.520 33.333 0.00 0.00 0.00 2.59
1901 2037 9.104965 CATTGTTTTTACGATCCCTATGTAGAA 57.895 33.333 0.00 0.00 0.00 2.10
1902 2038 9.675464 ATTGTTTTTACGATCCCTATGTAGAAA 57.325 29.630 0.00 0.00 0.00 2.52
1903 2039 8.712285 TGTTTTTACGATCCCTATGTAGAAAG 57.288 34.615 0.00 0.00 0.00 2.62
1945 2083 5.124936 GCCGGTGGATTAGTTAAAAACATCT 59.875 40.000 1.90 0.00 0.00 2.90
1952 2090 1.544246 AGTTAAAAACATCTGCCGCCC 59.456 47.619 0.00 0.00 0.00 6.13
2038 3885 2.292916 GCAACAAGCGCGGTGTTTC 61.293 57.895 24.21 18.16 37.09 2.78
2053 3900 1.029681 GTTTCAGAAACAAGGGGCGT 58.970 50.000 19.46 0.00 41.04 5.68
2060 3907 1.170290 AAACAAGGGGCGTGCTACAC 61.170 55.000 0.00 0.00 0.00 2.90
2081 3928 0.673644 ACCGCCGATTGAAGTTCAGG 60.674 55.000 5.56 5.51 0.00 3.86
2097 3944 3.208747 TCAGGAAAGAACAACCACCTC 57.791 47.619 0.00 0.00 0.00 3.85
2104 3951 1.228862 AACAACCACCTCCCATGCC 60.229 57.895 0.00 0.00 0.00 4.40
2175 4022 2.355756 GCTGAAACAGAGACTTTGTGCA 59.644 45.455 0.00 1.26 32.44 4.57
2201 4048 5.238432 AGACGTGATGTATCTTTTGCAACAA 59.762 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
370 372 9.653287 ACGAGAATTGAATTCAGTATAAGTTCA 57.347 29.630 19.02 0.00 41.71 3.18
399 426 9.202273 AGCGACTATCAAATAGATCAGAAAATC 57.798 33.333 0.00 0.00 38.19 2.17
452 479 3.206150 CAGTCGCAAGGGCTATAACAAT 58.794 45.455 0.00 0.00 38.10 2.71
491 518 4.996793 TGGATGGAAGAAAGAATGGACAA 58.003 39.130 0.00 0.00 0.00 3.18
493 520 4.274459 CGATGGATGGAAGAAAGAATGGAC 59.726 45.833 0.00 0.00 0.00 4.02
1096 1211 4.248058 GCAATTTGCTTGGCTTTACATCT 58.752 39.130 14.11 0.00 40.96 2.90
1260 1376 6.337853 GAATCAGACGATTCGAGTGAATTT 57.662 37.500 13.95 6.95 46.01 1.82
1261 1377 5.957910 GAATCAGACGATTCGAGTGAATT 57.042 39.130 13.95 10.15 46.01 2.17
1324 1440 2.375146 ACGTTTTGACCAGAAAAGCCT 58.625 42.857 0.00 0.00 0.00 4.58
1588 1705 5.937975 TTCCCAATCTCCATTGAAAATCC 57.062 39.130 0.00 0.00 41.97 3.01
1594 1711 4.392047 CATCGATTCCCAATCTCCATTGA 58.608 43.478 0.00 0.00 41.97 2.57
1684 1819 5.466728 TGCGAGCATGAGGAAATAGAATAAC 59.533 40.000 0.00 0.00 0.00 1.89
1789 1925 7.563556 CCCCCACATGGATAAAAGTAAGTAAAT 59.436 37.037 0.00 0.00 37.39 1.40
1859 1995 8.552083 AAAAACAATGATTTTTCCCTATCAGC 57.448 30.769 0.00 0.00 37.21 4.26
1873 2009 9.273016 CTACATAGGGATCGTAAAAACAATGAT 57.727 33.333 0.00 0.00 0.00 2.45
1874 2010 8.479689 TCTACATAGGGATCGTAAAAACAATGA 58.520 33.333 0.00 0.00 0.00 2.57
1875 2011 8.657074 TCTACATAGGGATCGTAAAAACAATG 57.343 34.615 0.00 0.00 0.00 2.82
1876 2012 9.675464 TTTCTACATAGGGATCGTAAAAACAAT 57.325 29.630 0.00 0.00 0.00 2.71
1878 2014 7.767198 CCTTTCTACATAGGGATCGTAAAAACA 59.233 37.037 0.00 0.00 0.00 2.83
1879 2015 8.139521 CCTTTCTACATAGGGATCGTAAAAAC 57.860 38.462 0.00 0.00 0.00 2.43
1920 2056 4.400120 TGTTTTTAACTAATCCACCGGCT 58.600 39.130 0.00 0.00 0.00 5.52
1922 2058 6.551736 CAGATGTTTTTAACTAATCCACCGG 58.448 40.000 0.00 0.00 0.00 5.28
1952 2090 4.609018 CCATCCTACGGCCAGGCG 62.609 72.222 12.45 12.45 35.49 5.52
1962 2100 3.147595 AGCAGCGCGTCCATCCTA 61.148 61.111 8.43 0.00 0.00 2.94
1963 2101 4.827087 CAGCAGCGCGTCCATCCT 62.827 66.667 8.43 0.00 0.00 3.24
2038 3885 0.605319 TAGCACGCCCCTTGTTTCTG 60.605 55.000 0.00 0.00 0.00 3.02
2053 3900 2.997075 AATCGGCGGTCGTGTAGCA 61.997 57.895 7.21 0.00 40.32 3.49
2060 3907 1.011968 TGAACTTCAATCGGCGGTCG 61.012 55.000 7.21 0.00 40.90 4.79
2081 3928 2.358322 TGGGAGGTGGTTGTTCTTTC 57.642 50.000 0.00 0.00 0.00 2.62
2089 3936 1.493854 TAACGGCATGGGAGGTGGTT 61.494 55.000 0.00 0.00 0.00 3.67
2097 3944 0.035458 GGGAGATCTAACGGCATGGG 59.965 60.000 0.00 0.00 0.00 4.00
2104 3951 2.546795 GCTCATGTGGGGAGATCTAACG 60.547 54.545 0.00 0.00 34.24 3.18
2175 4022 4.820897 TGCAAAAGATACATCACGTCTCT 58.179 39.130 0.00 0.00 32.68 3.10
2201 4048 7.721402 TGTAAAGTTTTCTGCAACAATACCAT 58.279 30.769 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.