Multiple sequence alignment - TraesCS6D01G094000

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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 TraesCS6D01G094000 chr6D 100.000 2645 0 0 1 2645 58463004 58460360 0.000000e+00 4885.0
1 TraesCS6D01G094000 chr6A 94.581 1753 59 11 913 2637 73682636 73680892 0.000000e+00 2678.0
2 TraesCS6D01G094000 chr6A 94.794 826 21 3 1 823 73683480 73682674 0.000000e+00 1267.0
3 TraesCS6D01G094000 chr6A 87.571 177 22 0 1 177 548427639 548427815 3.450000e-49 206.0
4 TraesCS6D01G094000 chr6B 89.576 1487 74 20 609 2067 131932482 131931049 0.000000e+00 1812.0
5 TraesCS6D01G094000 chr6B 95.169 414 18 2 2233 2645 131931013 131930601 0.000000e+00 652.0
6 TraesCS6D01G094000 chr6B 95.000 260 13 0 1104 1363 651661653 651661394 2.450000e-110 409.0
7 TraesCS6D01G094000 chr6B 86.452 155 19 2 396 548 131932650 131932496 4.530000e-38 169.0
8 TraesCS6D01G094000 chr6B 91.379 58 4 1 767 823 27328179 27328122 7.850000e-11 78.7
9 TraesCS6D01G094000 chr6B 89.286 56 5 1 769 823 52146135 52146190 4.720000e-08 69.4
10 TraesCS6D01G094000 chr7D 90.183 927 69 10 997 1909 478414746 478415664 0.000000e+00 1188.0
11 TraesCS6D01G094000 chr7D 88.507 757 73 8 993 1739 223709334 223710086 0.000000e+00 904.0
12 TraesCS6D01G094000 chr2B 88.289 760 65 12 1164 1909 401017632 401018381 0.000000e+00 889.0
13 TraesCS6D01G094000 chr2B 88.745 542 40 9 1382 1909 86848818 86848284 0.000000e+00 643.0
14 TraesCS6D01G094000 chr2B 87.222 180 20 3 1 179 17877223 17877400 4.460000e-48 202.0
15 TraesCS6D01G094000 chr2B 89.683 126 13 0 2520 2645 640338629 640338754 7.580000e-36 161.0
16 TraesCS6D01G094000 chr7B 87.500 760 74 9 1164 1909 8676871 8676119 0.000000e+00 857.0
17 TraesCS6D01G094000 chr7B 89.655 58 5 1 767 823 735982175 735982232 3.650000e-09 73.1
18 TraesCS6D01G094000 chr1A 88.351 558 43 10 1367 1909 365222469 365223019 0.000000e+00 651.0
19 TraesCS6D01G094000 chr5B 88.745 542 40 9 1382 1909 290878565 290879099 0.000000e+00 643.0
20 TraesCS6D01G094000 chr5B 94.553 257 14 0 1104 1360 658346496 658346752 5.300000e-107 398.0
21 TraesCS6D01G094000 chr5B 87.151 179 22 1 1 179 705634681 705634504 4.460000e-48 202.0
22 TraesCS6D01G094000 chr3D 93.774 257 16 0 1104 1360 482588262 482588518 1.150000e-103 387.0
23 TraesCS6D01G094000 chr3D 87.709 179 22 0 1 179 58277537 58277715 2.670000e-50 209.0
24 TraesCS6D01G094000 chr1D 88.636 176 20 0 1 176 455656254 455656079 5.730000e-52 215.0
25 TraesCS6D01G094000 chr1D 88.136 177 18 2 1 177 339566211 339566384 9.600000e-50 207.0
26 TraesCS6D01G094000 chr4D 86.592 179 24 0 1 179 474693193 474693371 5.770000e-47 198.0
27 TraesCS6D01G094000 chr3A 86.188 181 21 4 1 179 584021383 584021561 2.690000e-45 193.0
28 TraesCS6D01G094000 chr2D 89.683 126 13 0 2520 2645 537505226 537505351 7.580000e-36 161.0


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 TraesCS6D01G094000 chr6D 58460360 58463004 2644 True 4885.000000 4885 100.0000 1 2645 1 chr6D.!!$R1 2644
1 TraesCS6D01G094000 chr6A 73680892 73683480 2588 True 1972.500000 2678 94.6875 1 2637 2 chr6A.!!$R1 2636
2 TraesCS6D01G094000 chr6B 131930601 131932650 2049 True 877.666667 1812 90.3990 396 2645 3 chr6B.!!$R3 2249
3 TraesCS6D01G094000 chr7D 478414746 478415664 918 False 1188.000000 1188 90.1830 997 1909 1 chr7D.!!$F2 912
4 TraesCS6D01G094000 chr7D 223709334 223710086 752 False 904.000000 904 88.5070 993 1739 1 chr7D.!!$F1 746
5 TraesCS6D01G094000 chr2B 401017632 401018381 749 False 889.000000 889 88.2890 1164 1909 1 chr2B.!!$F2 745
6 TraesCS6D01G094000 chr2B 86848284 86848818 534 True 643.000000 643 88.7450 1382 1909 1 chr2B.!!$R1 527
7 TraesCS6D01G094000 chr7B 8676119 8676871 752 True 857.000000 857 87.5000 1164 1909 1 chr7B.!!$R1 745
8 TraesCS6D01G094000 chr1A 365222469 365223019 550 False 651.000000 651 88.3510 1367 1909 1 chr1A.!!$F1 542
9 TraesCS6D01G094000 chr5B 290878565 290879099 534 False 643.000000 643 88.7450 1382 1909 1 chr5B.!!$F1 527

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
837 841 0.955919 AAGGCCACTTAAGCTGCGTC 60.956 55.0 5.01 0.0 34.49 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 2483 0.474614 GGGAGAACCTCTAATGGGGC 59.525 60.0 0.0 0.0 35.85 5.8 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
44 45 4.142160 CCATTAGTTCTCGAGGACATGTGA 60.142 45.833 25.58 2.55 0.00 3.58
50 51 2.750166 TCTCGAGGACATGTGAGAAGTC 59.250 50.000 13.56 0.00 34.72 3.01
138 139 3.264193 TCCTCTAGTGGTGTCATGCAAAT 59.736 43.478 10.56 0.00 0.00 2.32
244 245 4.798682 GGGCCGGGAGAAGGGAGA 62.799 72.222 2.18 0.00 0.00 3.71
575 578 8.070034 AGAGTTCAAATGATATGCCATGAAAA 57.930 30.769 0.00 0.00 0.00 2.29
680 683 5.172934 AGTTGTATGAATGCCAAATGCTTG 58.827 37.500 0.00 0.00 42.00 4.01
691 694 3.665060 GCCAAATGCTTGCGAATTTCAAC 60.665 43.478 0.00 0.00 36.87 3.18
818 822 1.141657 GAGTGGCTGATATTGGAGGCA 59.858 52.381 0.00 0.00 42.06 4.75
820 824 1.952296 GTGGCTGATATTGGAGGCAAG 59.048 52.381 0.00 0.00 45.38 4.01
822 826 0.957362 GCTGATATTGGAGGCAAGGC 59.043 55.000 0.00 0.00 0.00 4.35
834 838 1.213799 GCAAGGCCACTTAAGCTGC 59.786 57.895 5.01 5.32 34.49 5.25
835 839 1.503542 CAAGGCCACTTAAGCTGCG 59.496 57.895 5.01 0.00 34.49 5.18
836 840 1.073199 AAGGCCACTTAAGCTGCGT 59.927 52.632 5.01 4.34 34.49 5.24
837 841 0.955919 AAGGCCACTTAAGCTGCGTC 60.956 55.000 5.01 0.00 34.49 5.19
838 842 2.399356 GGCCACTTAAGCTGCGTCC 61.399 63.158 1.29 0.00 0.00 4.79
852 856 2.365068 CGTCCGCGTGAGTGACTTG 61.365 63.158 4.92 0.00 46.66 3.16
872 876 1.795286 GACCTCGCAAAGTCACTGAAG 59.205 52.381 0.00 0.00 33.08 3.02
906 910 1.977293 GAGGCCGCCTCTTCCTGATT 61.977 60.000 29.19 0.00 46.41 2.57
1557 1577 2.271497 GATGTGAGCCTGGCTGCT 59.729 61.111 28.82 7.29 46.37 4.24
1769 1816 8.268850 ACAAATGTAGTGTTAATTCTAGGCAG 57.731 34.615 0.00 0.00 0.00 4.85
1791 1838 6.563381 GCAGATGTTGAGCAAATTTTGAACTG 60.563 38.462 13.26 6.31 0.00 3.16
1807 1854 4.641396 TGAACTGATGGATGAGTTTCGTT 58.359 39.130 0.00 0.00 34.38 3.85
1809 1856 4.271696 ACTGATGGATGAGTTTCGTTGA 57.728 40.909 0.00 0.00 0.00 3.18
1882 1931 3.033909 TGTCTACAGGCAGATACATGCT 58.966 45.455 0.00 0.00 45.75 3.79
1883 1932 3.452264 TGTCTACAGGCAGATACATGCTT 59.548 43.478 0.00 0.00 45.75 3.91
1884 1933 4.080919 TGTCTACAGGCAGATACATGCTTT 60.081 41.667 0.00 0.00 45.75 3.51
1945 1994 3.359950 GGATTCCAATCTTTGCCACTCT 58.640 45.455 0.00 0.00 35.73 3.24
1946 1995 3.129988 GGATTCCAATCTTTGCCACTCTG 59.870 47.826 0.00 0.00 35.73 3.35
1947 1996 1.538047 TCCAATCTTTGCCACTCTGC 58.462 50.000 0.00 0.00 0.00 4.26
2116 2194 0.597637 GGCGCTGCTATACACACGAT 60.598 55.000 7.64 0.00 0.00 3.73
2126 2204 0.948623 TACACACGATGCCTGCACAC 60.949 55.000 0.00 0.00 0.00 3.82
2269 2347 0.606401 ACTTCCGTTGTCCTGGCATG 60.606 55.000 0.00 0.00 0.00 4.06
2302 2380 3.090952 TGTTTTCCTCATTGCAAACCG 57.909 42.857 1.71 0.00 0.00 4.44
2319 2397 3.662247 ACCGAAAGTCGTCTGAATTCT 57.338 42.857 7.05 0.00 38.40 2.40
2377 2455 7.517320 AGTTGGATGTGCCTGAATATATGTAA 58.483 34.615 0.00 0.00 37.63 2.41
2388 2466 7.382110 CCTGAATATATGTAACTAGTGCTGCT 58.618 38.462 0.00 0.00 0.00 4.24
2405 2483 7.983307 AGTGCTGCTATTTTCTTCTTAATGAG 58.017 34.615 0.00 0.00 0.00 2.90
2444 2522 7.988937 TCTCCCCTATGCTATTGTGAATATTT 58.011 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.293735 CCTCGAGAACTAATGGATCTACTCAC 60.294 46.154 15.71 0.00 0.00 3.51
44 45 6.070538 ACATGATTACTAGCAACAGGACTTCT 60.071 38.462 0.00 0.00 0.00 2.85
50 51 5.877012 ACTTCACATGATTACTAGCAACAGG 59.123 40.000 0.00 0.00 0.00 4.00
51 52 6.974932 ACTTCACATGATTACTAGCAACAG 57.025 37.500 0.00 0.00 0.00 3.16
138 139 6.262193 TGATGAAGTGTTATGTACTCGACA 57.738 37.500 0.00 0.00 43.97 4.35
227 228 4.798682 TCTCCCTTCTCCCGGCCC 62.799 72.222 0.00 0.00 0.00 5.80
228 229 3.157949 CTCTCCCTTCTCCCGGCC 61.158 72.222 0.00 0.00 0.00 6.13
229 230 3.157949 CCTCTCCCTTCTCCCGGC 61.158 72.222 0.00 0.00 0.00 6.13
230 231 2.444895 CCCTCTCCCTTCTCCCGG 60.445 72.222 0.00 0.00 0.00 5.73
231 232 2.444895 CCCCTCTCCCTTCTCCCG 60.445 72.222 0.00 0.00 0.00 5.14
232 233 2.040359 CCCCCTCTCCCTTCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
233 234 2.770475 GCCCCCTCTCCCTTCTCC 60.770 72.222 0.00 0.00 0.00 3.71
234 235 3.157949 CGCCCCCTCTCCCTTCTC 61.158 72.222 0.00 0.00 0.00 2.87
235 236 4.806339 CCGCCCCCTCTCCCTTCT 62.806 72.222 0.00 0.00 0.00 2.85
575 578 7.768120 AGCATATCATTCGAACTCTTCTTCTTT 59.232 33.333 0.00 0.00 0.00 2.52
691 694 8.874745 ACACTGAAAATATGAACGAAATAACG 57.125 30.769 0.00 0.00 39.31 3.18
818 822 0.955919 GACGCAGCTTAAGTGGCCTT 60.956 55.000 3.32 0.00 34.56 4.35
820 824 2.399356 GGACGCAGCTTAAGTGGCC 61.399 63.158 4.02 0.00 37.53 5.36
822 826 2.740714 GCGGACGCAGCTTAAGTGG 61.741 63.158 12.31 0.00 41.49 4.00
824 828 2.809601 CGCGGACGCAGCTTAAGT 60.810 61.111 17.35 0.00 42.06 2.24
827 831 3.964221 CTCACGCGGACGCAGCTTA 62.964 63.158 17.35 0.00 45.53 3.09
831 835 4.700365 TCACTCACGCGGACGCAG 62.700 66.667 17.35 11.56 45.53 5.18
832 836 4.994201 GTCACTCACGCGGACGCA 62.994 66.667 17.35 0.00 45.53 5.24
833 837 4.702081 AGTCACTCACGCGGACGC 62.702 66.667 12.47 6.63 45.53 5.19
835 839 1.007734 TCAAGTCACTCACGCGGAC 60.008 57.895 12.47 7.79 0.00 4.79
836 840 1.007734 GTCAAGTCACTCACGCGGA 60.008 57.895 12.47 3.82 0.00 5.54
837 841 2.022129 GGTCAAGTCACTCACGCGG 61.022 63.158 12.47 0.00 0.00 6.46
838 842 1.004277 GAGGTCAAGTCACTCACGCG 61.004 60.000 3.53 3.53 0.00 6.01
852 856 1.795286 CTTCAGTGACTTTGCGAGGTC 59.205 52.381 9.25 9.25 0.00 3.85
890 894 1.524849 GGAATCAGGAAGAGGCGGC 60.525 63.158 0.00 0.00 0.00 6.53
891 895 1.147153 GGGAATCAGGAAGAGGCGG 59.853 63.158 0.00 0.00 0.00 6.13
892 896 1.147153 GGGGAATCAGGAAGAGGCG 59.853 63.158 0.00 0.00 0.00 5.52
893 897 0.625849 TTGGGGAATCAGGAAGAGGC 59.374 55.000 0.00 0.00 0.00 4.70
906 910 4.986708 GGGCAAGCGGTTTGGGGA 62.987 66.667 6.71 0.00 37.26 4.81
1557 1577 2.343758 GCTCTGAACTGTCGGGCA 59.656 61.111 0.00 0.00 0.00 5.36
1563 1583 1.871408 CGAAGCAGTGCTCTGAACTGT 60.871 52.381 20.03 0.00 45.58 3.55
1723 1765 6.704289 TGTACTATGTTATTGTCCGCTAGT 57.296 37.500 0.00 0.00 0.00 2.57
1769 1816 7.359765 CCATCAGTTCAAAATTTGCTCAACATC 60.360 37.037 0.00 0.00 0.00 3.06
1791 1838 3.991069 CGTTCAACGAAACTCATCCATC 58.009 45.455 3.01 0.00 46.05 3.51
1807 1854 4.617520 TGCAGCCCGCTTCGTTCA 62.618 61.111 0.00 0.00 43.06 3.18
1824 1871 2.227036 AGTAGCAGGGGTGCAAGCT 61.227 57.895 0.00 0.00 40.92 3.74
1825 1872 2.042831 CAGTAGCAGGGGTGCAAGC 61.043 63.158 0.00 0.00 37.25 4.01
1837 1884 8.015658 ACATTTAAAGTTCGTTTCATCAGTAGC 58.984 33.333 0.00 0.00 0.00 3.58
1913 1962 5.116084 AGATTGGAATCCGGAGAATTTCA 57.884 39.130 11.34 0.91 36.04 2.69
2132 2210 2.176546 CTGTTGGCATTGCGACGG 59.823 61.111 1.91 5.49 0.00 4.79
2269 2347 5.305585 TGAGGAAAACATCTTGTCCTACAC 58.694 41.667 0.00 0.00 40.67 2.90
2377 2455 8.887717 CATTAAGAAGAAAATAGCAGCACTAGT 58.112 33.333 0.00 0.00 33.29 2.57
2388 2466 9.354673 CTAATGGGGCTCATTAAGAAGAAAATA 57.645 33.333 19.74 0.00 44.82 1.40
2405 2483 0.474614 GGGAGAACCTCTAATGGGGC 59.525 60.000 0.00 0.00 35.85 5.80


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

AutoCloner maintained by Alex Coulton.