Multiple sequence alignment - TraesCS2B01G200000

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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 TraesCS2B01G200000 chr2B 100.000 3140 0 0 1 3140 178722855 178725994 0.000000e+00 5799
1 TraesCS2B01G200000 chr2B 95.842 1443 48 3 688 2130 762181785 762180355 0.000000e+00 2322
2 TraesCS2B01G200000 chr2B 95.917 1396 51 4 1 1391 64308867 64307473 0.000000e+00 2257
3 TraesCS2B01G200000 chr2B 95.593 1316 54 2 80 1391 573900604 573901919 0.000000e+00 2106
4 TraesCS2B01G200000 chr5B 96.882 3015 90 4 127 3140 23837509 23840520 0.000000e+00 5044
5 TraesCS2B01G200000 chr5B 95.670 1940 73 7 637 2568 432685019 432686955 0.000000e+00 3107
6 TraesCS2B01G200000 chr5B 96.391 1053 36 1 662 1714 695585234 695584184 0.000000e+00 1733
7 TraesCS2B01G200000 chr3B 96.181 2854 83 5 1 2834 18314309 18317156 0.000000e+00 4643
8 TraesCS2B01G200000 chr3B 97.436 351 1 2 1 343 821806791 821806441 2.700000e-165 592
9 TraesCS2B01G200000 chr3B 95.522 335 3 2 1 323 731043588 731043922 2.770000e-145 525
10 TraesCS2B01G200000 chr3B 97.468 158 0 2 1 154 555102111 555101954 1.860000e-67 267
11 TraesCS2B01G200000 chr3B 95.062 162 0 3 1 154 17005159 17005320 6.720000e-62 248
12 TraesCS2B01G200000 chr3B 93.210 162 3 5 1 154 37410981 37410820 6.770000e-57 231
13 TraesCS2B01G200000 chr3B 92.771 166 0 2 1 154 686906372 686906207 2.440000e-56 230
14 TraesCS2B01G200000 chr3B 92.771 166 0 2 1 154 720579922 720580087 2.440000e-56 230
15 TraesCS2B01G200000 chr3B 91.566 166 2 5 1 154 772283678 772283843 5.270000e-53 219
16 TraesCS2B01G200000 chr6B 97.428 1944 35 6 1198 3140 704576183 704578112 0.000000e+00 3299
17 TraesCS2B01G200000 chr6B 97.109 1833 53 0 601 2433 10842073 10843905 0.000000e+00 3092
18 TraesCS2B01G200000 chr6B 97.037 1755 40 9 1389 3140 158272786 158271041 0.000000e+00 2942
19 TraesCS2B01G200000 chr6B 95.630 1396 53 2 4 1391 158274410 158273015 0.000000e+00 2233
20 TraesCS2B01G200000 chr6B 95.568 1399 53 4 1 1391 78759876 78761273 0.000000e+00 2231
21 TraesCS2B01G200000 chr4B 96.982 1756 48 3 1389 3140 619809083 619810837 0.000000e+00 2944
22 TraesCS2B01G200000 chr4B 97.034 1753 46 6 1389 3140 661862937 661864684 0.000000e+00 2944
23 TraesCS2B01G200000 chr7B 96.920 1753 47 5 1389 3140 179705807 179704061 0.000000e+00 2931
24 TraesCS2B01G200000 chr7B 95.354 1399 57 2 1 1391 179707434 179706036 0.000000e+00 2217


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 TraesCS2B01G200000 chr2B 178722855 178725994 3139 False 5799.0 5799 100.0000 1 3140 1 chr2B.!!$F1 3139
1 TraesCS2B01G200000 chr2B 762180355 762181785 1430 True 2322.0 2322 95.8420 688 2130 1 chr2B.!!$R2 1442
2 TraesCS2B01G200000 chr2B 64307473 64308867 1394 True 2257.0 2257 95.9170 1 1391 1 chr2B.!!$R1 1390
3 TraesCS2B01G200000 chr2B 573900604 573901919 1315 False 2106.0 2106 95.5930 80 1391 1 chr2B.!!$F2 1311
4 TraesCS2B01G200000 chr5B 23837509 23840520 3011 False 5044.0 5044 96.8820 127 3140 1 chr5B.!!$F1 3013
5 TraesCS2B01G200000 chr5B 432685019 432686955 1936 False 3107.0 3107 95.6700 637 2568 1 chr5B.!!$F2 1931
6 TraesCS2B01G200000 chr5B 695584184 695585234 1050 True 1733.0 1733 96.3910 662 1714 1 chr5B.!!$R1 1052
7 TraesCS2B01G200000 chr3B 18314309 18317156 2847 False 4643.0 4643 96.1810 1 2834 1 chr3B.!!$F2 2833
8 TraesCS2B01G200000 chr6B 704576183 704578112 1929 False 3299.0 3299 97.4280 1198 3140 1 chr6B.!!$F3 1942
9 TraesCS2B01G200000 chr6B 10842073 10843905 1832 False 3092.0 3092 97.1090 601 2433 1 chr6B.!!$F1 1832
10 TraesCS2B01G200000 chr6B 158271041 158274410 3369 True 2587.5 2942 96.3335 4 3140 2 chr6B.!!$R1 3136
11 TraesCS2B01G200000 chr6B 78759876 78761273 1397 False 2231.0 2231 95.5680 1 1391 1 chr6B.!!$F2 1390
12 TraesCS2B01G200000 chr4B 619809083 619810837 1754 False 2944.0 2944 96.9820 1389 3140 1 chr4B.!!$F1 1751
13 TraesCS2B01G200000 chr4B 661862937 661864684 1747 False 2944.0 2944 97.0340 1389 3140 1 chr4B.!!$F2 1751
14 TraesCS2B01G200000 chr7B 179704061 179707434 3373 True 2574.0 2931 96.1370 1 3140 2 chr7B.!!$R1 3139

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
291 313 1.141657 TCAGCTGCTGAAGAACACCTT 59.858 47.619 28.72 0.0 37.57 3.50 F
1036 1058 0.683504 GAGCAACTCCCCTCCGTCTA 60.684 60.000 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1183 1.136891 CTGGTGCATACGACATCCAGA 59.863 52.381 9.52 0.0 43.28 3.86 R
2640 2905 1.148759 GCTACTAAGCTGTCGCAGGC 61.149 60.000 8.57 0.0 45.85 4.85 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
291 313 1.141657 TCAGCTGCTGAAGAACACCTT 59.858 47.619 28.72 0.00 37.57 3.50
292 314 1.952296 CAGCTGCTGAAGAACACCTTT 59.048 47.619 24.88 0.00 34.68 3.11
351 373 6.115446 TGTCAGTTTCATCAGAGAAGTTTGT 58.885 36.000 0.00 0.00 0.00 2.83
377 399 5.245531 TCAGTTTCAAATAATCCGAGCTGT 58.754 37.500 0.00 0.00 0.00 4.40
471 493 4.306967 TGCATCGCGGGTGACACA 62.307 61.111 6.13 0.00 0.00 3.72
523 545 1.829222 CCGGAAGTGGCCTAGTTTCTA 59.171 52.381 3.32 0.00 0.00 2.10
571 593 8.134895 CGCTGAATAAGAAGAGAAATAGAGAGT 58.865 37.037 0.00 0.00 0.00 3.24
695 717 2.919602 TCTAGAGTTTTCAAGGGCCCAT 59.080 45.455 27.56 10.06 0.00 4.00
774 796 3.953775 ACTGGCAACTCCCCACGG 61.954 66.667 0.00 0.00 37.61 4.94
808 830 1.719529 TCTTCCCACGTCCAGGTAAA 58.280 50.000 0.00 0.00 0.00 2.01
869 891 1.849039 CCTCCCTCCTCATTCCATTGT 59.151 52.381 0.00 0.00 0.00 2.71
871 893 2.776536 CTCCCTCCTCATTCCATTGTCT 59.223 50.000 0.00 0.00 0.00 3.41
925 947 3.882131 GCATCAAGCAACTCCCCTA 57.118 52.632 0.00 0.00 44.79 3.53
1003 1025 1.205655 CTCCGTCTGCCAAGAGAATGA 59.794 52.381 0.00 0.00 31.37 2.57
1036 1058 0.683504 GAGCAACTCCCCTCCGTCTA 60.684 60.000 0.00 0.00 0.00 2.59
1161 1183 2.334023 GATATCCACCTGAAGGAGCCT 58.666 52.381 2.62 0.00 38.83 4.58
1275 1297 2.286831 CGGCGTTGATGTCGAGTATACT 60.287 50.000 4.68 4.68 39.90 2.12
1279 1301 4.212847 GCGTTGATGTCGAGTATACTAGGA 59.787 45.833 5.09 3.70 0.00 2.94
1293 1315 6.958192 AGTATACTAGGAAAGACAAACCTCCA 59.042 38.462 2.75 0.00 35.52 3.86
1464 1724 7.843490 TTAGTAGCTGTTATGAATGTTGTCC 57.157 36.000 0.00 0.00 0.00 4.02
1477 1737 6.757237 TGAATGTTGTCCTGTAATGCAAAAT 58.243 32.000 0.00 0.00 0.00 1.82
1571 1835 8.774586 AGTTGTTGTGATCATTTAGTAGTTGTC 58.225 33.333 0.00 0.00 0.00 3.18
1576 1840 6.584942 TGTGATCATTTAGTAGTTGTCGTGAC 59.415 38.462 0.00 0.00 0.00 3.67
1840 2105 2.232941 GAGATCAACCCCGACAAGTACA 59.767 50.000 0.00 0.00 0.00 2.90
2689 2954 1.542547 GGCCGAAGTTGAGGAAGACAA 60.543 52.381 0.00 0.00 0.00 3.18
3030 3300 0.105913 AGAGGGTCGAAGGGGATCTC 60.106 60.000 0.00 0.00 0.00 2.75
3081 3352 0.739813 GTTCTAATGGCGCACCGTCT 60.740 55.000 10.83 0.00 39.70 4.18
3101 3372 4.067192 TCTAGTCGTGCGCCATAAGTATA 58.933 43.478 4.18 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
291 313 8.743085 ACTACACCTATATCTGACGAAACTAA 57.257 34.615 0.00 0.0 0.00 2.24
292 314 8.743085 AACTACACCTATATCTGACGAAACTA 57.257 34.615 0.00 0.0 0.00 2.24
351 373 7.083858 CAGCTCGGATTATTTGAAACTGAAAA 58.916 34.615 0.00 0.0 0.00 2.29
377 399 0.390124 AACAAACTACGACCGAGGCA 59.610 50.000 0.00 0.0 0.00 4.75
523 545 5.107065 GCGATTACACAGCTAACAGAAAACT 60.107 40.000 0.00 0.0 0.00 2.66
571 593 3.059868 CGTTCAACTTCGCAGCTTTTCTA 60.060 43.478 0.00 0.0 0.00 2.10
774 796 1.587043 GAAGAAAACCCCCTCTGCGC 61.587 60.000 0.00 0.0 0.00 6.09
808 830 1.713078 GGCAATGGAATAGGAGGGGAT 59.287 52.381 0.00 0.0 0.00 3.85
869 891 2.222271 AGAGGGAGGAAGATGGAGAGA 58.778 52.381 0.00 0.0 0.00 3.10
871 893 2.178106 GGTAGAGGGAGGAAGATGGAGA 59.822 54.545 0.00 0.0 0.00 3.71
925 947 2.191375 CAGCGATGGTGGAGGCAT 59.809 61.111 0.00 0.0 0.00 4.40
1003 1025 4.148825 GCTCCACGATGCCTCCGT 62.149 66.667 0.00 0.0 41.36 4.69
1161 1183 1.136891 CTGGTGCATACGACATCCAGA 59.863 52.381 9.52 0.0 43.28 3.86
1275 1297 4.781775 TTGTGGAGGTTTGTCTTTCCTA 57.218 40.909 0.00 0.0 0.00 2.94
1279 1301 4.162131 AGCAATTTGTGGAGGTTTGTCTTT 59.838 37.500 0.00 0.0 0.00 2.52
1571 1835 6.533819 TTCAGTTAAAACAGTATGGTCACG 57.466 37.500 0.00 0.0 27.21 4.35
1576 1840 9.191995 GACCAAAATTCAGTTAAAACAGTATGG 57.808 33.333 0.00 0.0 43.62 2.74
2640 2905 1.148759 GCTACTAAGCTGTCGCAGGC 61.149 60.000 8.57 0.0 45.85 4.85
2689 2954 1.961180 CTTCTTCCTCGGGTCGCCAT 61.961 60.000 0.00 0.0 0.00 4.40
2817 3087 3.160047 CCAGCCCTCGAGCTCCAT 61.160 66.667 6.99 0.0 42.61 3.41
3030 3300 2.413211 TATCCTCCCTCCCTCTCGCG 62.413 65.000 0.00 0.0 0.00 5.87
3081 3352 4.276678 AGTTATACTTATGGCGCACGACTA 59.723 41.667 10.83 0.0 0.00 2.59
3101 3372 3.275617 TGGTGCGCCATTAGAATAGTT 57.724 42.857 16.89 0.0 40.46 2.24


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

AutoCloner maintained by Alex Coulton.