Multiple sequence alignment - TraesCS1B01G057100

Loading Multiple Alignment...

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 TraesCS1B01G057100 chr1B 100.000 2615 0 0 1 2615 39657411 39654797 0.000000e+00 4830.0
1 TraesCS1B01G057100 chr1B 97.436 585 9 4 1448 2026 39582056 39582640 0.000000e+00 992.0
2 TraesCS1B01G057100 chr1D 95.545 1616 56 5 1 1614 23999799 23998198 0.000000e+00 2571.0
3 TraesCS1B01G057100 chr1D 94.146 1025 37 11 1608 2615 24123770 24122752 0.000000e+00 1539.0
4 TraesCS1B01G057100 chr1D 94.592 980 38 3 638 1614 24126079 24125112 0.000000e+00 1502.0
5 TraesCS1B01G057100 chr1D 95.538 650 23 2 1 650 24126841 24126198 0.000000e+00 1035.0
6 TraesCS1B01G057100 chr1D 95.050 404 17 2 1608 2011 23435772 23436172 1.320000e-177 632.0
7 TraesCS1B01G057100 chr1D 90.625 64 6 0 2368 2431 23996483 23996420 4.640000e-13 86.1
8 TraesCS1B01G057100 chr1A 92.634 1629 98 11 8 1614 24945727 24944099 0.000000e+00 2324.0
9 TraesCS1B01G057100 chr1A 93.501 1031 41 11 1608 2615 24942405 24941378 0.000000e+00 1509.0
10 TraesCS1B01G057100 chr1A 95.332 407 13 4 1608 2011 24561796 24562199 2.190000e-180 641.0
11 TraesCS1B01G057100 chr1A 94.802 404 16 4 1608 2011 24772986 24772588 2.210000e-175 625.0
12 TraesCS1B01G057100 chr1A 81.279 219 21 8 2211 2428 24562514 24562713 2.690000e-35 159.0
13 TraesCS1B01G057100 chr1A 80.392 204 20 8 2211 2413 24772277 24772093 1.260000e-28 137.0
14 TraesCS1B01G057100 chr5A 87.247 792 91 7 832 1614 656936984 656936194 0.000000e+00 894.0
15 TraesCS1B01G057100 chr5B 87.105 791 83 11 832 1614 665811625 665810846 0.000000e+00 878.0
16 TraesCS1B01G057100 chr3D 88.630 686 68 4 932 1614 108571255 108571933 0.000000e+00 826.0
17 TraesCS1B01G057100 chr3B 89.029 556 61 0 1059 1614 160138195 160138750 0.000000e+00 689.0
18 TraesCS1B01G057100 chr3B 94.253 174 10 0 2115 2288 26533930 26534103 1.540000e-67 267.0
19 TraesCS1B01G057100 chr3B 94.915 59 3 0 2038 2096 26533888 26533946 2.770000e-15 93.5
20 TraesCS1B01G057100 chr6B 92.529 174 13 0 2115 2288 1947240 1947413 1.550000e-62 250.0
21 TraesCS1B01G057100 chr6B 94.915 59 3 0 2038 2096 1947198 1947256 2.770000e-15 93.5


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 TraesCS1B01G057100 chr1B 39654797 39657411 2614 True 4830.000000 4830 100.000000 1 2615 1 chr1B.!!$R1 2614
1 TraesCS1B01G057100 chr1B 39582056 39582640 584 False 992.000000 992 97.436000 1448 2026 1 chr1B.!!$F1 578
2 TraesCS1B01G057100 chr1D 24122752 24126841 4089 True 1358.666667 1539 94.758667 1 2615 3 chr1D.!!$R2 2614
3 TraesCS1B01G057100 chr1D 23996420 23999799 3379 True 1328.550000 2571 93.085000 1 2431 2 chr1D.!!$R1 2430
4 TraesCS1B01G057100 chr1A 24941378 24945727 4349 True 1916.500000 2324 93.067500 8 2615 2 chr1A.!!$R2 2607
5 TraesCS1B01G057100 chr1A 24561796 24562713 917 False 400.000000 641 88.305500 1608 2428 2 chr1A.!!$F1 820
6 TraesCS1B01G057100 chr1A 24772093 24772986 893 True 381.000000 625 87.597000 1608 2413 2 chr1A.!!$R1 805
7 TraesCS1B01G057100 chr5A 656936194 656936984 790 True 894.000000 894 87.247000 832 1614 1 chr5A.!!$R1 782
8 TraesCS1B01G057100 chr5B 665810846 665811625 779 True 878.000000 878 87.105000 832 1614 1 chr5B.!!$R1 782
9 TraesCS1B01G057100 chr3D 108571255 108571933 678 False 826.000000 826 88.630000 932 1614 1 chr3D.!!$F1 682
10 TraesCS1B01G057100 chr3B 160138195 160138750 555 False 689.000000 689 89.029000 1059 1614 1 chr3B.!!$F1 555

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
550 560 6.540551 GGATGTCTAAGTTTCTTCCTTGGATC 59.459 42.308 0.0 0.0 32.94 3.36 F
1161 1333 0.537143 TTGCCACTTTGAGCGGACAT 60.537 50.000 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1630 1.205460 GGGCCCAGGAAACAGAGGTA 61.205 60.000 19.95 0.0 0.0 3.08 R
2042 4410 2.633488 GGTAGGCTTCACTGGAACATC 58.367 52.381 0.00 0.0 38.2 3.06 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
169 170 9.509855 TTGACGGTTGCAAATGTTATATTTATC 57.490 29.630 0.00 0.00 0.00 1.75
236 237 7.920738 ACTTTCTAAGAAGTTGTGATGTTGAC 58.079 34.615 0.00 0.00 36.49 3.18
550 560 6.540551 GGATGTCTAAGTTTCTTCCTTGGATC 59.459 42.308 0.00 0.00 32.94 3.36
817 970 9.268268 TGTAACTTCTAATTGTAACAACTCAGG 57.732 33.333 0.00 0.00 0.00 3.86
820 973 7.736893 ACTTCTAATTGTAACAACTCAGGTCT 58.263 34.615 0.00 0.00 0.00 3.85
1146 1318 3.259425 CTCGCACCAGCAACTTGCC 62.259 63.158 10.25 0.00 46.52 4.52
1161 1333 0.537143 TTGCCACTTTGAGCGGACAT 60.537 50.000 0.00 0.00 0.00 3.06
1206 1378 3.027419 GGCTCATCCCAAGTATGGC 57.973 57.895 0.00 0.00 46.09 4.40
1383 1555 3.372349 CCTGTGGTTCATCTGATGGGAAT 60.372 47.826 17.06 0.00 0.00 3.01
1386 1558 5.624159 TGTGGTTCATCTGATGGGAATATC 58.376 41.667 17.06 4.18 0.00 1.63
1410 1582 1.996191 GTCTTCATGGCTCGTTCTGAC 59.004 52.381 0.00 0.00 0.00 3.51
2027 4381 2.352960 GGCTCTTGAGCGTCAATAAAGG 59.647 50.000 15.30 0.00 35.59 3.11
2028 4382 2.352960 GCTCTTGAGCGTCAATAAAGGG 59.647 50.000 6.88 0.00 35.59 3.95
2030 4384 2.083774 CTTGAGCGTCAATAAAGGGCA 58.916 47.619 1.76 0.00 35.59 5.36
2031 4385 2.418368 TGAGCGTCAATAAAGGGCAT 57.582 45.000 0.00 0.00 0.00 4.40
2032 4386 2.722094 TGAGCGTCAATAAAGGGCATT 58.278 42.857 0.00 0.00 0.00 3.56
2033 4387 2.423185 TGAGCGTCAATAAAGGGCATTG 59.577 45.455 0.00 0.00 35.19 2.82
2034 4388 2.682856 GAGCGTCAATAAAGGGCATTGA 59.317 45.455 0.00 0.00 39.48 2.57
2036 4390 2.682856 GCGTCAATAAAGGGCATTGAGA 59.317 45.455 0.00 0.00 41.73 3.27
2040 4408 6.294176 GCGTCAATAAAGGGCATTGAGATATT 60.294 38.462 0.00 0.00 41.73 1.28
2042 4410 8.446273 CGTCAATAAAGGGCATTGAGATATTAG 58.554 37.037 0.00 0.00 41.73 1.73
2048 4416 7.992754 AAGGGCATTGAGATATTAGATGTTC 57.007 36.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 4.505808 TGCATTCAAATGGTGCATTAAGG 58.494 39.130 9.32 0.0 43.30 2.69
321 330 3.782889 AACAAAGGACAAGACAGCAAC 57.217 42.857 0.00 0.0 0.00 4.17
647 658 7.693951 GCTTATTATAATCATGGTGATCGCAAC 59.306 37.037 8.82 0.0 35.76 4.17
792 937 9.269453 ACCTGAGTTGTTACAATTAGAAGTTAC 57.731 33.333 0.00 0.0 0.00 2.50
803 948 7.554835 ACAACATAAAGACCTGAGTTGTTACAA 59.445 33.333 0.00 0.0 44.86 2.41
946 1104 1.502231 CAACTGTTCTGTCCTGACCG 58.498 55.000 0.00 0.0 0.00 4.79
1146 1318 1.081892 CCTCATGTCCGCTCAAAGTG 58.918 55.000 0.00 0.0 0.00 3.16
1362 1534 3.354948 TTCCCATCAGATGAACCACAG 57.645 47.619 12.41 0.0 0.00 3.66
1383 1555 3.291584 ACGAGCCATGAAGACTGAGATA 58.708 45.455 0.00 0.0 0.00 1.98
1386 1558 2.094286 AGAACGAGCCATGAAGACTGAG 60.094 50.000 0.00 0.0 0.00 3.35
1410 1582 3.450115 GTCGTCTCCCACCCTCCG 61.450 72.222 0.00 0.0 0.00 4.63
1458 1630 1.205460 GGGCCCAGGAAACAGAGGTA 61.205 60.000 19.95 0.0 0.00 3.08
1772 4117 1.901085 GTCGAGGATGGGTCTGCTT 59.099 57.895 0.00 0.0 0.00 3.91
2027 4381 6.939163 ACTGGAACATCTAATATCTCAATGCC 59.061 38.462 0.00 0.0 38.20 4.40
2028 4382 7.658982 TCACTGGAACATCTAATATCTCAATGC 59.341 37.037 0.00 0.0 38.20 3.56
2030 4384 9.775854 CTTCACTGGAACATCTAATATCTCAAT 57.224 33.333 0.00 0.0 38.20 2.57
2031 4385 7.712639 GCTTCACTGGAACATCTAATATCTCAA 59.287 37.037 0.00 0.0 38.20 3.02
2032 4386 7.212976 GCTTCACTGGAACATCTAATATCTCA 58.787 38.462 0.00 0.0 38.20 3.27
2033 4387 6.648725 GGCTTCACTGGAACATCTAATATCTC 59.351 42.308 0.00 0.0 38.20 2.75
2034 4388 6.328672 AGGCTTCACTGGAACATCTAATATCT 59.671 38.462 0.00 0.0 38.20 1.98
2036 4390 6.506538 AGGCTTCACTGGAACATCTAATAT 57.493 37.500 0.00 0.0 38.20 1.28
2040 4408 3.451178 GGTAGGCTTCACTGGAACATCTA 59.549 47.826 0.00 0.0 38.20 1.98
2042 4410 2.633488 GGTAGGCTTCACTGGAACATC 58.367 52.381 0.00 0.0 38.20 3.06


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

AutoCloner maintained by Alex Coulton.