Multiple sequence alignment - TraesCS6B01G031400

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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 TraesCS6B01G031400 chr6B 100.000 2324 0 0 1 2324 18600449 18598126 0.000000e+00 4292
1 TraesCS6B01G031400 chr6B 97.312 1674 39 4 1 1669 573347663 573349335 0.000000e+00 2837
2 TraesCS6B01G031400 chr6B 88.154 650 57 10 1678 2324 18727300 18727932 0.000000e+00 756
3 TraesCS6B01G031400 chr6B 90.115 435 42 1 1678 2111 18720727 18721161 4.340000e-157 564
4 TraesCS6B01G031400 chr6B 84.615 208 30 2 1848 2055 18766301 18766096 3.030000e-49 206
5 TraesCS6B01G031400 chr7B 96.318 1684 58 4 1 1680 484928864 484927181 0.000000e+00 2763
6 TraesCS6B01G031400 chr5B 91.746 1672 131 7 1 1669 364099711 364098044 0.000000e+00 2316
7 TraesCS6B01G031400 chr3B 90.078 1673 156 10 2 1669 629908993 629910660 0.000000e+00 2161
8 TraesCS6B01G031400 chr4A 89.524 1680 167 9 1 1676 700975954 700977628 0.000000e+00 2119
9 TraesCS6B01G031400 chr4A 89.348 1671 171 7 1 1669 632630871 632632536 0.000000e+00 2093
10 TraesCS6B01G031400 chr3A 88.590 1674 179 11 1 1669 702515842 702514176 0.000000e+00 2023
11 TraesCS6B01G031400 chr2A 87.767 1684 192 13 1 1676 179276104 179277781 0.000000e+00 1956
12 TraesCS6B01G031400 chr2A 86.695 1676 211 12 1 1669 673275406 673273736 0.000000e+00 1849
13 TraesCS6B01G031400 chr6A 91.745 642 51 2 1683 2324 11585279 11585918 0.000000e+00 891
14 TraesCS6B01G031400 chr6D 85.670 642 61 17 1688 2324 10116948 10117563 0.000000e+00 647
15 TraesCS6B01G031400 chr6D 92.411 448 30 3 1678 2123 10097874 10098319 9.060000e-179 636
16 TraesCS6B01G031400 chr6D 91.449 421 35 1 1905 2324 10099157 10099577 5.570000e-161 577


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 TraesCS6B01G031400 chr6B 18598126 18600449 2323 True 4292.0 4292 100.000 1 2324 1 chr6B.!!$R1 2323
1 TraesCS6B01G031400 chr6B 573347663 573349335 1672 False 2837.0 2837 97.312 1 1669 1 chr6B.!!$F3 1668
2 TraesCS6B01G031400 chr6B 18727300 18727932 632 False 756.0 756 88.154 1678 2324 1 chr6B.!!$F2 646
3 TraesCS6B01G031400 chr7B 484927181 484928864 1683 True 2763.0 2763 96.318 1 1680 1 chr7B.!!$R1 1679
4 TraesCS6B01G031400 chr5B 364098044 364099711 1667 True 2316.0 2316 91.746 1 1669 1 chr5B.!!$R1 1668
5 TraesCS6B01G031400 chr3B 629908993 629910660 1667 False 2161.0 2161 90.078 2 1669 1 chr3B.!!$F1 1667
6 TraesCS6B01G031400 chr4A 700975954 700977628 1674 False 2119.0 2119 89.524 1 1676 1 chr4A.!!$F2 1675
7 TraesCS6B01G031400 chr4A 632630871 632632536 1665 False 2093.0 2093 89.348 1 1669 1 chr4A.!!$F1 1668
8 TraesCS6B01G031400 chr3A 702514176 702515842 1666 True 2023.0 2023 88.590 1 1669 1 chr3A.!!$R1 1668
9 TraesCS6B01G031400 chr2A 179276104 179277781 1677 False 1956.0 1956 87.767 1 1676 1 chr2A.!!$F1 1675
10 TraesCS6B01G031400 chr2A 673273736 673275406 1670 True 1849.0 1849 86.695 1 1669 1 chr2A.!!$R1 1668
11 TraesCS6B01G031400 chr6A 11585279 11585918 639 False 891.0 891 91.745 1683 2324 1 chr6A.!!$F1 641
12 TraesCS6B01G031400 chr6D 10116948 10117563 615 False 647.0 647 85.670 1688 2324 1 chr6D.!!$F1 636
13 TraesCS6B01G031400 chr6D 10097874 10099577 1703 False 606.5 636 91.930 1678 2324 2 chr6D.!!$F2 646

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
592 593 4.955925 TGTGTCGTGAAAGATTGTTTGT 57.044 36.364 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1790 0.108138 CGCTAGACCCCTCTTTGTGG 60.108 60.0 0.0 0.0 0.0 4.17 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
382 383 5.326283 TGGTAGAGATACAGTAGCCTCAT 57.674 43.478 12.70 4.13 0.00 2.90
592 593 4.955925 TGTGTCGTGAAAGATTGTTTGT 57.044 36.364 0.00 0.00 0.00 2.83
1046 1047 0.819582 AACTTGTGGCAGGCATATGC 59.180 50.000 19.79 19.79 45.74 3.14
1223 1224 0.685097 TGTTACTGGGCAGGACTGAC 59.315 55.000 3.00 0.00 38.06 3.51
1621 1631 6.655078 ATCTGCTGAACTTGGTTGTATTTT 57.345 33.333 0.00 0.00 0.00 1.82
1698 1711 3.185797 AGAAACGCTAACAACGATCAACC 59.814 43.478 0.00 0.00 0.00 3.77
1953 1971 7.765819 TGTGATCAGACTCGATTTTAATCATGT 59.234 33.333 0.00 1.30 35.11 3.21
1990 2008 4.453480 TCCTTGGAATCCAAACTTCTGT 57.547 40.909 16.30 0.00 43.44 3.41
1991 2009 5.576563 TCCTTGGAATCCAAACTTCTGTA 57.423 39.130 16.30 0.00 43.44 2.74
1992 2010 5.947663 TCCTTGGAATCCAAACTTCTGTAA 58.052 37.500 16.30 0.00 43.44 2.41
2048 3125 4.233632 TGCCATGTCATATGTCCTTTCA 57.766 40.909 1.90 0.00 0.00 2.69
2202 3279 2.166459 TCGGCCACAAAAATGAACACAA 59.834 40.909 2.24 0.00 0.00 3.33
2209 3286 3.197549 ACAAAAATGAACACAAGGGCACT 59.802 39.130 0.00 0.00 0.00 4.40
2212 3289 3.733443 AATGAACACAAGGGCACTTTC 57.267 42.857 0.00 0.00 33.81 2.62
2217 3294 3.290948 ACACAAGGGCACTTTCTAACA 57.709 42.857 0.00 0.00 33.81 2.41
2227 3304 5.241728 GGGCACTTTCTAACATTGAAGTTCT 59.758 40.000 4.17 0.00 33.07 3.01
2297 3374 3.958147 TGCAGTCGGTAATAATCTCCAGA 59.042 43.478 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
382 383 5.094387 AGAGTCAGTGATTCTCCCCTTAAA 58.906 41.667 12.12 0.0 0.00 1.52
592 593 8.129280 TCGAAAGAAGGTGATAGGATTAGCCTA 61.129 40.741 0.00 0.0 45.67 3.93
1046 1047 6.715264 ACCTGGAAAGAAAGTATAACACCAAG 59.285 38.462 0.00 0.0 0.00 3.61
1223 1224 1.205655 TCTCAGCATCCTCCTGTTTCG 59.794 52.381 0.00 0.0 0.00 3.46
1277 1278 1.333931 TCCTCATCATACGAGACGCAC 59.666 52.381 0.00 0.0 31.84 5.34
1621 1631 7.341769 CCCCTTTCCATTACTTGAACATAATGA 59.658 37.037 5.72 0.0 39.96 2.57
1691 1704 6.017400 ACTGTGATGTTGATTTGGTTGATC 57.983 37.500 0.00 0.0 0.00 2.92
1693 1706 4.886489 TGACTGTGATGTTGATTTGGTTGA 59.114 37.500 0.00 0.0 0.00 3.18
1736 1749 8.247562 CGTCTCTCTTCCTATATCCTTTATTGG 58.752 40.741 0.00 0.0 0.00 3.16
1743 1756 3.010808 CCCCGTCTCTCTTCCTATATCCT 59.989 52.174 0.00 0.0 0.00 3.24
1777 1790 0.108138 CGCTAGACCCCTCTTTGTGG 60.108 60.000 0.00 0.0 0.00 4.17
1928 1946 8.136057 ACATGATTAAAATCGAGTCTGATCAC 57.864 34.615 0.00 0.0 38.26 3.06
1953 1971 3.519510 CCAAGGATGGGTGAGAGAAGTTA 59.480 47.826 0.00 0.0 43.51 2.24
1956 1974 2.706339 CCAAGGATGGGTGAGAGAAG 57.294 55.000 0.00 0.0 43.51 2.85
2202 3279 4.729868 ACTTCAATGTTAGAAAGTGCCCT 58.270 39.130 0.00 0.0 0.00 5.19
2209 3286 7.498900 TCAAGCTCAGAACTTCAATGTTAGAAA 59.501 33.333 0.00 0.0 0.00 2.52
2212 3289 6.597614 GTCAAGCTCAGAACTTCAATGTTAG 58.402 40.000 0.00 0.0 0.00 2.34
2217 3294 2.481952 GCGTCAAGCTCAGAACTTCAAT 59.518 45.455 0.00 0.0 44.04 2.57
2251 3328 4.970662 AATATGCTGCCACTTGTTACAG 57.029 40.909 0.00 0.0 0.00 2.74
2297 3374 5.362430 TGTCTTGAAGGTGCCATTTTAGTTT 59.638 36.000 0.00 0.0 0.00 2.66


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

AutoCloner maintained by Alex Coulton.