Multiple sequence alignment - TraesCS6D01G263800

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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 TraesCS6D01G263800 chr6D 100.000 3723 0 0 1 3723 372615765 372612043 0.000000e+00 6876
1 TraesCS6D01G263800 chr6D 95.308 1087 48 3 583 1667 163424609 163425694 0.000000e+00 1722
2 TraesCS6D01G263800 chr6D 95.455 176 4 2 3551 3723 440540916 440540742 1.020000e-70 278
3 TraesCS6D01G263800 chr3D 97.186 3731 90 6 7 3723 10935455 10931726 0.000000e+00 6294
4 TraesCS6D01G263800 chr3D 97.377 3355 71 8 1 3339 588694111 588697464 0.000000e+00 5692
5 TraesCS6D01G263800 chr3D 96.055 659 24 2 2894 3552 564469363 564468707 0.000000e+00 1072
6 TraesCS6D01G263800 chr3D 92.708 288 16 5 1 285 45395504 45395789 9.620000e-111 411
7 TraesCS6D01G263800 chr5A 95.815 3154 104 13 1 3134 155589641 155592786 0.000000e+00 5068
8 TraesCS6D01G263800 chr5A 95.664 1084 43 4 1 1082 497932885 497933966 0.000000e+00 1738
9 TraesCS6D01G263800 chr5D 96.151 2364 72 8 1377 3723 556579374 556577013 0.000000e+00 3843
10 TraesCS6D01G263800 chr5D 90.970 299 16 1 283 581 287878938 287878651 3.490000e-105 392
11 TraesCS6D01G263800 chr2D 96.149 2363 73 7 1377 3723 586830299 586832659 0.000000e+00 3843
12 TraesCS6D01G263800 chr1B 94.657 2433 103 10 1314 3723 137870254 137872682 0.000000e+00 3747
13 TraesCS6D01G263800 chr1B 97.297 111 3 0 1680 1790 619350111 619350001 4.910000e-44 189
14 TraesCS6D01G263800 chr1B 96.396 111 4 0 1680 1790 616650862 616650972 2.280000e-42 183
15 TraesCS6D01G263800 chr1A 94.975 1632 79 2 2095 3723 379647386 379649017 0.000000e+00 2556
16 TraesCS6D01G263800 chr7B 94.745 1237 49 6 1667 2890 97120866 97119633 0.000000e+00 1910
17 TraesCS6D01G263800 chr7B 93.800 1242 52 8 1667 2895 89870745 89869516 0.000000e+00 1844
18 TraesCS6D01G263800 chr7B 95.803 834 31 2 2894 3723 97118343 97117510 0.000000e+00 1343
19 TraesCS6D01G263800 chr7B 98.198 111 2 0 1680 1790 679351599 679351709 1.060000e-45 195
20 TraesCS6D01G263800 chr4D 95.492 1087 44 5 583 1667 500937159 500936076 0.000000e+00 1731
21 TraesCS6D01G263800 chr4D 95.400 1087 45 5 583 1667 500975893 500974810 0.000000e+00 1725
22 TraesCS6D01G263800 chr4D 95.124 1087 45 6 583 1667 500899303 500898223 0.000000e+00 1707
23 TraesCS6D01G263800 chr4D 91.329 865 40 11 1893 2743 437505704 437506547 0.000000e+00 1149
24 TraesCS6D01G263800 chr4D 90.970 299 16 3 283 581 457303348 457303061 3.490000e-105 392
25 TraesCS6D01G263800 chr6B 94.931 1085 53 2 583 1667 628512109 628513191 0.000000e+00 1698
26 TraesCS6D01G263800 chr6B 94.841 659 32 2 2894 3552 693678162 693678818 0.000000e+00 1027
27 TraesCS6D01G263800 chr6B 94.983 299 13 2 287 584 552851222 552850925 5.630000e-128 468
28 TraesCS6D01G263800 chr6B 94.649 299 15 1 283 581 628511741 628512038 2.620000e-126 462
29 TraesCS6D01G263800 chr3A 94.751 1086 53 4 583 1667 401133458 401134540 0.000000e+00 1687
30 TraesCS6D01G263800 chr2B 95.000 300 15 0 283 582 553516217 553515918 4.350000e-129 472
31 TraesCS6D01G263800 chr2B 95.098 204 10 0 1680 1883 43958051 43958254 4.640000e-84 322
32 TraesCS6D01G263800 chr5B 89.967 299 19 1 283 581 40567788 40568075 3.510000e-100 375
33 TraesCS6D01G263800 chr4B 89.933 298 19 1 283 580 70197092 70196806 1.260000e-99 374


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 TraesCS6D01G263800 chr6D 372612043 372615765 3722 True 6876.0 6876 100.000 1 3723 1 chr6D.!!$R1 3722
1 TraesCS6D01G263800 chr6D 163424609 163425694 1085 False 1722.0 1722 95.308 583 1667 1 chr6D.!!$F1 1084
2 TraesCS6D01G263800 chr3D 10931726 10935455 3729 True 6294.0 6294 97.186 7 3723 1 chr3D.!!$R1 3716
3 TraesCS6D01G263800 chr3D 588694111 588697464 3353 False 5692.0 5692 97.377 1 3339 1 chr3D.!!$F2 3338
4 TraesCS6D01G263800 chr3D 564468707 564469363 656 True 1072.0 1072 96.055 2894 3552 1 chr3D.!!$R2 658
5 TraesCS6D01G263800 chr5A 155589641 155592786 3145 False 5068.0 5068 95.815 1 3134 1 chr5A.!!$F1 3133
6 TraesCS6D01G263800 chr5A 497932885 497933966 1081 False 1738.0 1738 95.664 1 1082 1 chr5A.!!$F2 1081
7 TraesCS6D01G263800 chr5D 556577013 556579374 2361 True 3843.0 3843 96.151 1377 3723 1 chr5D.!!$R2 2346
8 TraesCS6D01G263800 chr2D 586830299 586832659 2360 False 3843.0 3843 96.149 1377 3723 1 chr2D.!!$F1 2346
9 TraesCS6D01G263800 chr1B 137870254 137872682 2428 False 3747.0 3747 94.657 1314 3723 1 chr1B.!!$F1 2409
10 TraesCS6D01G263800 chr1A 379647386 379649017 1631 False 2556.0 2556 94.975 2095 3723 1 chr1A.!!$F1 1628
11 TraesCS6D01G263800 chr7B 89869516 89870745 1229 True 1844.0 1844 93.800 1667 2895 1 chr7B.!!$R1 1228
12 TraesCS6D01G263800 chr7B 97117510 97120866 3356 True 1626.5 1910 95.274 1667 3723 2 chr7B.!!$R2 2056
13 TraesCS6D01G263800 chr4D 500936076 500937159 1083 True 1731.0 1731 95.492 583 1667 1 chr4D.!!$R3 1084
14 TraesCS6D01G263800 chr4D 500974810 500975893 1083 True 1725.0 1725 95.400 583 1667 1 chr4D.!!$R4 1084
15 TraesCS6D01G263800 chr4D 500898223 500899303 1080 True 1707.0 1707 95.124 583 1667 1 chr4D.!!$R2 1084
16 TraesCS6D01G263800 chr4D 437505704 437506547 843 False 1149.0 1149 91.329 1893 2743 1 chr4D.!!$F1 850
17 TraesCS6D01G263800 chr6B 628511741 628513191 1450 False 1080.0 1698 94.790 283 1667 2 chr6B.!!$F2 1384
18 TraesCS6D01G263800 chr6B 693678162 693678818 656 False 1027.0 1027 94.841 2894 3552 1 chr6B.!!$F1 658
19 TraesCS6D01G263800 chr3A 401133458 401134540 1082 False 1687.0 1687 94.751 583 1667 1 chr3A.!!$F1 1084

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
770 841 0.685097 GCACTGGTGGTCCTTACTCA 59.315 55.0 2.84 0.0 34.23 3.41 F
1934 2021 0.106149 GATCCCAACCCGCGTTAGAT 59.894 55.0 4.92 0.0 30.59 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2487 1.426251 AACCACATCAGCCCCACAGA 61.426 55.0 0.0 0.00 0.00 3.41 R
2839 2946 1.103803 TCTACGAGCAGTGCTTAGGG 58.896 55.0 20.8 11.53 39.88 3.53 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
374 375 1.071699 TCGGCTTTATGGGCATAGTCC 59.928 52.381 0.00 0.00 0.00 3.85
375 376 1.202758 CGGCTTTATGGGCATAGTCCA 60.203 52.381 0.00 0.00 43.40 4.02
403 404 2.812011 GGAATGCTACACCGTTGAAGTT 59.188 45.455 0.00 0.00 0.00 2.66
730 801 2.616960 TCCAAGCATGATGTGTACGTC 58.383 47.619 0.00 0.00 0.00 4.34
770 841 0.685097 GCACTGGTGGTCCTTACTCA 59.315 55.000 2.84 0.00 34.23 3.41
893 964 1.089481 CACTGTGCGACCACACTGTT 61.089 55.000 4.70 0.00 46.61 3.16
1073 1146 6.427853 TCTGTGTTGAGAACATGTAGAAATGG 59.572 38.462 0.00 0.00 44.35 3.16
1351 1424 5.005094 GTGCTAACCCAACATGTACCTAAA 58.995 41.667 0.00 0.00 0.00 1.85
1436 1509 0.603065 GTCTGTGGGAAATTGGGCAC 59.397 55.000 0.00 0.00 0.00 5.01
1748 1835 3.627577 ACTGATTAAAATCTCCGCGCAAT 59.372 39.130 8.75 0.00 36.39 3.56
1934 2021 0.106149 GATCCCAACCCGCGTTAGAT 59.894 55.000 4.92 0.00 30.59 1.98
2013 2109 0.108207 AGCTTCACTGCTGCTTCTGT 59.892 50.000 0.00 0.00 42.33 3.41
2388 2487 3.071602 TGTCTCTGCAAGGAGCTAACTTT 59.928 43.478 0.61 0.00 45.94 2.66
2436 2535 3.231734 CGAACAGCAAGACCATGGA 57.768 52.632 21.47 0.00 0.00 3.41
2666 2772 0.739112 GCTTGTCTCTGCTTCCTCCG 60.739 60.000 0.00 0.00 0.00 4.63
2733 2840 2.182842 GTCCCTGATGATGCACCGC 61.183 63.158 0.00 0.00 0.00 5.68
2890 2997 1.202698 GCCGCTGTTGATTCCTCCTAT 60.203 52.381 0.00 0.00 0.00 2.57
2982 4375 9.485206 GTCTTTAAAGAAGTCAATGTACCTACA 57.515 33.333 19.30 0.00 37.42 2.74
3010 4405 8.693542 ATTTTGTGCTCTGTTATTATCTTTGC 57.306 30.769 0.00 0.00 0.00 3.68
3032 4427 6.159293 TGCTTAGTATCAGTTGTGTCTCTTG 58.841 40.000 0.00 0.00 0.00 3.02
3127 4524 8.907222 AAAATCTTTGAATTTGGTACTGCATT 57.093 26.923 0.00 0.00 0.00 3.56
3148 4545 9.226606 TGCATTAGTTTTTACTACTGCTTACAT 57.773 29.630 20.76 0.00 44.24 2.29
3404 4802 1.053424 GGTACCCCCATAATCGAGCA 58.947 55.000 0.00 0.00 0.00 4.26
3538 4936 9.132923 CTCTCCTACCTTTGTGATGTTAGTATA 57.867 37.037 0.00 0.00 0.00 1.47
3542 4940 9.886132 CCTACCTTTGTGATGTTAGTATACTTT 57.114 33.333 11.40 0.00 0.00 2.66
3585 4983 3.354948 ACAATTCCTAGCTGTGCATGA 57.645 42.857 0.00 0.00 0.00 3.07
3701 5102 8.884323 ACTATGTGTAATGGATCCATGACTTAT 58.116 33.333 33.40 28.02 38.35 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.359009 CAGCCATTTCAATAGTTGAGGATGT 59.641 40.000 6.56 0.00 41.38 3.06
374 375 2.350522 GGTGTAGCATTCCAGAGTGTG 58.649 52.381 0.00 0.00 0.00 3.82
375 376 1.066858 CGGTGTAGCATTCCAGAGTGT 60.067 52.381 0.00 0.00 0.00 3.55
426 427 8.157476 AGACACCAGTAAAATAGAAGACAACAT 58.843 33.333 0.00 0.00 0.00 2.71
648 718 1.735559 GGTCAGTGCGTTCGTACCC 60.736 63.158 9.49 1.51 0.00 3.69
770 841 2.975489 TGAGCACTTCTTTTCCTCTCCT 59.025 45.455 0.00 0.00 0.00 3.69
893 964 0.832135 GACCTCCCCGCATATCCTGA 60.832 60.000 0.00 0.00 0.00 3.86
1052 1125 6.768483 TCTCCATTTCTACATGTTCTCAACA 58.232 36.000 2.30 0.00 46.94 3.33
1053 1126 6.876257 ACTCTCCATTTCTACATGTTCTCAAC 59.124 38.462 2.30 0.00 0.00 3.18
1073 1146 5.164954 CCTAAGTGTCAAGCTACAACTCTC 58.835 45.833 0.00 0.00 0.00 3.20
1123 1196 2.283884 GCTTCGCTGCTAGAATTCACTC 59.716 50.000 8.44 0.00 0.00 3.51
1155 1228 0.755079 AATCAGGCTATCGCTGCTCA 59.245 50.000 0.00 0.00 36.09 4.26
1436 1509 8.519799 ACAGTTCTATATTTACCAACCCAATG 57.480 34.615 0.00 0.00 0.00 2.82
1748 1835 1.675714 CGGCCACTGATTACTTGCTCA 60.676 52.381 2.24 0.00 0.00 4.26
1934 2021 5.181009 CAAGAGGAAATCATAGTGTGCAGA 58.819 41.667 0.00 0.00 0.00 4.26
2285 2383 6.215636 AGGACTGGATATTGTAGAGGTTGTTT 59.784 38.462 0.00 0.00 0.00 2.83
2388 2487 1.426251 AACCACATCAGCCCCACAGA 61.426 55.000 0.00 0.00 0.00 3.41
2432 2531 1.992519 GCTGATGGCTGGACCTCCAT 61.993 60.000 15.78 15.78 46.46 3.41
2436 2535 3.790437 CCGCTGATGGCTGGACCT 61.790 66.667 0.00 0.00 40.22 3.85
2666 2772 1.953559 TGCCACAACTCTGAACTCAC 58.046 50.000 0.00 0.00 0.00 3.51
2733 2840 2.485426 CTGATGGTTGGTAGTGCAACAG 59.515 50.000 0.00 0.00 41.43 3.16
2839 2946 1.103803 TCTACGAGCAGTGCTTAGGG 58.896 55.000 20.80 11.53 39.88 3.53
3010 4405 6.925211 TCCAAGAGACACAACTGATACTAAG 58.075 40.000 0.00 0.00 0.00 2.18
3347 4745 4.882842 ACAAAATCACCACATTAACCCC 57.117 40.909 0.00 0.00 0.00 4.95
3585 4983 5.279006 CCACACTACAGTCAACAGTCTACAT 60.279 44.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.