Multiple sequence alignment - TraesCS7B01G397200

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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 TraesCS7B01G397200 chr7B 100.000 3245 0 0 1 3245 663596932 663600176 0.000000e+00 5993.0
1 TraesCS7B01G397200 chr7B 98.524 3253 36 5 1 3245 663629747 663632995 0.000000e+00 5731.0
2 TraesCS7B01G397200 chr7B 98.100 3263 42 7 1 3245 663682896 663686156 0.000000e+00 5664.0
3 TraesCS7B01G397200 chr7B 99.382 1942 12 0 1304 3245 663706720 663708661 0.000000e+00 3520.0
4 TraesCS7B01G397200 chr7B 98.664 1347 18 0 983 2329 663652792 663654138 0.000000e+00 2388.0
5 TraesCS7B01G397200 chr7B 97.004 1235 26 4 1 1224 663705430 663706664 0.000000e+00 2065.0
6 TraesCS7B01G397200 chr7B 96.804 970 20 5 1 960 663651836 663652804 0.000000e+00 1609.0
7 TraesCS7B01G397200 chr7B 100.000 28 0 0 1908 1935 226333862 226333889 6.000000e-03 52.8
8 TraesCS7B01G397200 chr7D 77.962 1148 196 30 993 2107 589195246 589196369 0.000000e+00 665.0
9 TraesCS7B01G397200 chr7D 87.108 574 60 5 774 1336 589338038 589338608 3.530000e-179 638.0
10 TraesCS7B01G397200 chr7D 76.250 240 48 6 1054 1293 609947236 609947006 5.690000e-23 119.0
11 TraesCS7B01G397200 chr7D 83.621 116 19 0 1045 1160 607931246 607931361 3.420000e-20 110.0
12 TraesCS7B01G397200 chr7D 100.000 28 0 0 1908 1935 249375643 249375670 6.000000e-03 52.8
13 TraesCS7B01G397200 chr1B 74.308 253 58 3 1046 1292 632209438 632209689 2.060000e-17 100.0
14 TraesCS7B01G397200 chr7A 100.000 28 0 0 1908 1935 271792932 271792905 6.000000e-03 52.8


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 TraesCS7B01G397200 chr7B 663596932 663600176 3244 False 5993.0 5993 100.000 1 3245 1 chr7B.!!$F2 3244
1 TraesCS7B01G397200 chr7B 663629747 663632995 3248 False 5731.0 5731 98.524 1 3245 1 chr7B.!!$F3 3244
2 TraesCS7B01G397200 chr7B 663682896 663686156 3260 False 5664.0 5664 98.100 1 3245 1 chr7B.!!$F4 3244
3 TraesCS7B01G397200 chr7B 663705430 663708661 3231 False 2792.5 3520 98.193 1 3245 2 chr7B.!!$F6 3244
4 TraesCS7B01G397200 chr7B 663651836 663654138 2302 False 1998.5 2388 97.734 1 2329 2 chr7B.!!$F5 2328
5 TraesCS7B01G397200 chr7D 589195246 589196369 1123 False 665.0 665 77.962 993 2107 1 chr7D.!!$F2 1114
6 TraesCS7B01G397200 chr7D 589338038 589338608 570 False 638.0 638 87.108 774 1336 1 chr7D.!!$F3 562

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
413 414 0.107897 AACATCGCTGCCAACGGATA 60.108 50.000 0.0 0.0 0.0 2.59 F
416 417 0.392706 ATCGCTGCCAACGGATATGA 59.607 50.000 0.0 0.0 0.0 2.15 F
1149 1174 1.073199 CACCGGCAACTCCTTCCTT 59.927 57.895 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1654 1.672030 TCTTGCACTGTGCCATCCG 60.672 57.895 28.17 12.64 44.23 4.18 R
1906 1966 3.316573 CTTCCCCTGCCTCCACGAC 62.317 68.421 0.00 0.00 0.00 4.34 R
2785 2845 0.101759 CCTTGAGGATGCAATTGCCG 59.898 55.000 26.94 5.71 37.59 5.69 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
42 43 5.815581 AGTAATCCTACTCATGGCAAACAA 58.184 37.500 0.00 0.00 32.61 2.83
318 319 4.711949 CCAGCGAGCTTGGCCACT 62.712 66.667 3.88 0.00 0.00 4.00
373 374 1.359459 GCGTCGACATTTGGGGAGAC 61.359 60.000 17.16 0.00 0.00 3.36
407 408 1.438651 GAGTACAACATCGCTGCCAA 58.561 50.000 0.00 0.00 0.00 4.52
413 414 0.107897 AACATCGCTGCCAACGGATA 60.108 50.000 0.00 0.00 0.00 2.59
416 417 0.392706 ATCGCTGCCAACGGATATGA 59.607 50.000 0.00 0.00 0.00 2.15
572 575 2.430921 GCGTGTGTGGTCGAGAGG 60.431 66.667 0.00 0.00 0.00 3.69
576 579 2.179517 GTGTGGTCGAGAGGAGCG 59.820 66.667 0.00 0.00 46.20 5.03
667 670 1.351017 AGCGGTGAGGAGAAATGGAAA 59.649 47.619 0.00 0.00 0.00 3.13
1035 1060 2.765250 CTTCCACCACAGACGACCGG 62.765 65.000 0.00 0.00 0.00 5.28
1036 1061 3.612681 CCACCACAGACGACCGGT 61.613 66.667 6.92 6.92 0.00 5.28
1149 1174 1.073199 CACCGGCAACTCCTTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
1258 1283 1.153086 CCCATAGCCAGTGCAGTCC 60.153 63.158 0.00 0.00 41.13 3.85
1742 1799 6.766944 TCTTTGAAATACCGTTTGTTCTACCA 59.233 34.615 0.00 0.00 0.00 3.25
1906 1966 2.359975 GAGGGTTCCAGGTTGGCG 60.360 66.667 0.00 0.00 37.47 5.69
2785 2845 1.028868 GGGCTTCAGATGGCTGTCAC 61.029 60.000 9.44 0.00 42.84 3.67
3013 3073 5.936686 ATCTTATCAGTTTCATGCATCCG 57.063 39.130 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.839134 TCCATGAGTAGGAGTACATGTTGTAT 59.161 38.462 2.30 0.00 38.56 2.29
233 234 4.006319 GCTACAAAATCTCAAGGTGAGCT 58.994 43.478 0.17 0.00 43.95 4.09
318 319 3.118000 TCCTCAGAACTCATCTACGGCTA 60.118 47.826 0.00 0.00 36.32 3.93
373 374 0.384309 TACTCGCTATTGCCCAGTCG 59.616 55.000 2.32 0.00 32.83 4.18
407 408 2.431057 GTCACCTGGAAGTCATATCCGT 59.569 50.000 0.00 0.00 39.98 4.69
413 414 0.544357 TCCGGTCACCTGGAAGTCAT 60.544 55.000 0.00 0.00 0.00 3.06
416 417 0.252284 AGATCCGGTCACCTGGAAGT 60.252 55.000 10.90 0.00 37.90 3.01
667 670 2.285442 CCCTTCCCCCTTCCTCGT 60.285 66.667 0.00 0.00 0.00 4.18
709 712 7.223971 GGTAACTGTCAATTTGGGAAGAAAAAC 59.776 37.037 0.00 0.00 0.00 2.43
1022 1047 2.357034 CCAACCGGTCGTCTGTGG 60.357 66.667 8.04 7.02 0.00 4.17
1035 1060 3.316573 CTCCAGGAGGACGGCCAAC 62.317 68.421 11.69 0.00 39.61 3.77
1036 1061 3.003173 CTCCAGGAGGACGGCCAA 61.003 66.667 11.69 0.00 39.61 4.52
1149 1174 2.638354 TTCCTTACGGAAGCGGCGA 61.638 57.895 12.98 0.00 44.28 5.54
1597 1654 1.672030 TCTTGCACTGTGCCATCCG 60.672 57.895 28.17 12.64 44.23 4.18
1906 1966 3.316573 CTTCCCCTGCCTCCACGAC 62.317 68.421 0.00 0.00 0.00 4.34
2785 2845 0.101759 CCTTGAGGATGCAATTGCCG 59.898 55.000 26.94 5.71 37.59 5.69
3013 3073 1.076727 CCCCAGACCCCAAGTTTCC 59.923 63.158 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.