Multiple sequence alignment - TraesCS6B01G110900

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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 TraesCS6B01G110900 chr6B 100.000 1822 0 0 1 1822 93100928 93102749 0.000000e+00 3365.0
1 TraesCS6B01G110900 chr6B 100.000 1815 0 0 2597 4411 93103524 93105338 0.000000e+00 3352.0
2 TraesCS6B01G110900 chr6B 98.898 1815 7 2 2597 4411 93018027 93019828 0.000000e+00 3229.0
3 TraesCS6B01G110900 chr6B 98.303 884 12 2 1 883 93016562 93017443 0.000000e+00 1546.0
4 TraesCS6B01G110900 chr6B 99.659 586 2 0 1237 1822 93017440 93018025 0.000000e+00 1072.0
5 TraesCS6B01G110900 chr6B 79.795 391 47 17 3660 4024 589500405 589500789 5.660000e-64 255.0
6 TraesCS6B01G110900 chr6B 91.429 105 9 0 73 177 678542355 678542251 1.280000e-30 145.0
7 TraesCS6B01G110900 chr6B 87.931 116 14 0 62 177 397518305 397518420 2.140000e-28 137.0
8 TraesCS6B01G110900 chr6B 87.826 115 12 2 59 173 624018537 624018649 2.770000e-27 134.0
9 TraesCS6B01G110900 chr6B 94.667 75 4 0 3029 3103 93104016 93104090 2.790000e-22 117.0
10 TraesCS6B01G110900 chr6B 93.333 75 5 0 3029 3103 93018507 93018581 1.300000e-20 111.0
11 TraesCS6B01G110900 chrUn 87.881 1279 84 20 570 1822 19785387 19784154 0.000000e+00 1437.0
12 TraesCS6B01G110900 chrUn 90.287 1081 73 14 2597 3661 19742406 19741342 0.000000e+00 1386.0
13 TraesCS6B01G110900 chrUn 86.275 816 49 15 570 1366 19743931 19743160 0.000000e+00 828.0
14 TraesCS6B01G110900 chrUn 89.348 629 32 7 3052 3661 19783646 19783034 0.000000e+00 758.0
15 TraesCS6B01G110900 chrUn 85.353 751 79 20 2599 3335 19784150 19783417 0.000000e+00 749.0
16 TraesCS6B01G110900 chrUn 88.835 412 38 5 1418 1822 19742818 19742408 2.370000e-137 499.0
17 TraesCS6B01G110900 chrUn 84.436 257 20 10 177 418 19798000 19797749 7.380000e-58 235.0
18 TraesCS6B01G110900 chrUn 79.646 226 36 7 1268 1491 19784792 19784575 2.120000e-33 154.0
19 TraesCS6B01G110900 chrUn 95.000 60 2 1 1 60 19798067 19798009 4.700000e-15 93.5
20 TraesCS6B01G110900 chr6A 89.823 1071 64 19 2599 3663 57424695 57425726 0.000000e+00 1332.0
21 TraesCS6B01G110900 chr6A 84.920 935 70 22 571 1488 57423387 57424267 0.000000e+00 880.0
22 TraesCS6B01G110900 chr6A 89.736 682 62 5 1148 1822 57424011 57424691 0.000000e+00 865.0
23 TraesCS6B01G110900 chr6A 95.238 42 2 0 4370 4411 540130818 540130777 2.850000e-07 67.6
24 TraesCS6B01G110900 chr3D 86.328 1280 96 23 570 1822 40773569 40774796 0.000000e+00 1321.0
25 TraesCS6B01G110900 chr3D 90.379 1029 65 11 2599 3617 40774800 40775804 0.000000e+00 1321.0
26 TraesCS6B01G110900 chr3D 89.558 249 25 1 1148 1395 40774200 40774448 9.210000e-82 315.0
27 TraesCS6B01G110900 chr3D 92.500 80 6 0 1268 1347 40774164 40774243 1.000000e-21 115.0
28 TraesCS6B01G110900 chr3D 96.721 61 1 1 4312 4372 8988638 8988579 2.810000e-17 100.0
29 TraesCS6B01G110900 chr7D 76.842 665 111 29 3659 4288 95475626 95474970 7.070000e-88 335.0
30 TraesCS6B01G110900 chr7D 95.349 43 2 0 4369 4411 18841987 18841945 7.920000e-08 69.4
31 TraesCS6B01G110900 chr7A 75.934 669 110 34 3660 4285 219508007 219508667 3.340000e-76 296.0
32 TraesCS6B01G110900 chr7A 93.478 138 9 0 3661 3798 618423187 618423050 5.780000e-49 206.0
33 TraesCS6B01G110900 chr7A 96.721 61 1 1 4312 4372 683606425 683606484 2.810000e-17 100.0
34 TraesCS6B01G110900 chr7A 89.091 55 3 3 3661 3715 179250975 179250924 1.020000e-06 65.8
35 TraesCS6B01G110900 chr3B 79.949 389 50 17 3658 4024 86656388 86656006 1.220000e-65 261.0
36 TraesCS6B01G110900 chr3B 91.346 104 9 0 73 176 738378168 738378065 4.600000e-30 143.0
37 TraesCS6B01G110900 chr6D 95.620 137 6 0 3662 3798 333513807 333513671 2.070000e-53 220.0
38 TraesCS6B01G110900 chr6D 92.537 67 3 2 4306 4372 251639900 251639836 1.310000e-15 95.3
39 TraesCS6B01G110900 chr1B 91.667 108 9 0 70 177 405127361 405127468 2.750000e-32 150.0
40 TraesCS6B01G110900 chr4A 91.589 107 9 0 70 176 718207455 718207561 9.880000e-32 148.0
41 TraesCS6B01G110900 chr4A 92.537 67 3 2 4307 4373 719715099 719715035 1.310000e-15 95.3
42 TraesCS6B01G110900 chr4B 89.524 105 11 0 73 177 657171592 657171488 2.770000e-27 134.0
43 TraesCS6B01G110900 chr4B 95.349 43 2 0 4369 4411 141353892 141353850 7.920000e-08 69.4
44 TraesCS6B01G110900 chr4B 95.238 42 2 0 4370 4411 222693284 222693243 2.850000e-07 67.6
45 TraesCS6B01G110900 chr3A 89.524 105 11 0 73 177 22437301 22437197 2.770000e-27 134.0
46 TraesCS6B01G110900 chr3A 86.441 59 6 2 4354 4411 568030419 568030362 3.680000e-06 63.9
47 TraesCS6B01G110900 chr2B 98.361 61 0 1 4312 4372 735243104 735243163 6.030000e-19 106.0
48 TraesCS6B01G110900 chr2B 90.741 54 2 3 3662 3715 219493607 219493657 7.920000e-08 69.4
49 TraesCS6B01G110900 chr2B 95.238 42 2 0 4370 4411 414808494 414808535 2.850000e-07 67.6
50 TraesCS6B01G110900 chr2B 91.489 47 3 1 4365 4411 795060060 795060015 3.680000e-06 63.9
51 TraesCS6B01G110900 chr5A 96.774 62 1 1 4311 4372 267216071 267216131 7.810000e-18 102.0
52 TraesCS6B01G110900 chr5B 96.721 61 1 1 4312 4372 531652471 531652412 2.810000e-17 100.0
53 TraesCS6B01G110900 chr1A 95.161 62 2 1 4311 4372 566885337 566885277 3.630000e-16 97.1
54 TraesCS6B01G110900 chr2A 95.238 42 2 0 4370 4411 21190757 21190798 2.850000e-07 67.6


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 TraesCS6B01G110900 chr6B 93100928 93105338 4410 False 2278.000000 3365 98.222333 1 4411 3 chr6B.!!$F5 4410
1 TraesCS6B01G110900 chr6B 93016562 93019828 3266 False 1489.500000 3229 97.548250 1 4411 4 chr6B.!!$F4 4410
2 TraesCS6B01G110900 chrUn 19741342 19743931 2589 True 904.333333 1386 88.465667 570 3661 3 chrUn.!!$R1 3091
3 TraesCS6B01G110900 chrUn 19783034 19785387 2353 True 774.500000 1437 85.557000 570 3661 4 chrUn.!!$R2 3091
4 TraesCS6B01G110900 chr6A 57423387 57425726 2339 False 1025.666667 1332 88.159667 571 3663 3 chr6A.!!$F1 3092
5 TraesCS6B01G110900 chr3D 40773569 40775804 2235 False 768.000000 1321 89.691250 570 3617 4 chr3D.!!$F1 3047
6 TraesCS6B01G110900 chr7D 95474970 95475626 656 True 335.000000 335 76.842000 3659 4288 1 chr7D.!!$R2 629
7 TraesCS6B01G110900 chr7A 219508007 219508667 660 False 296.000000 296 75.934000 3660 4285 1 chr7A.!!$F1 625

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
935 950 0.035036 AGCGATCATGGCCATCAGAG 59.965 55.0 17.61 9.32 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3799 4304 6.032042 GCACGTATTGTCGAACTAAATTTTGG 59.968 38.462 0.0 0.0 34.7 3.28 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
97 98 5.240844 CCCTCCGTTTGAAATTACTTGTCTT 59.759 40.000 0.00 0.00 0.00 3.01
99 100 6.017440 CCTCCGTTTGAAATTACTTGTCTTGA 60.017 38.462 0.00 0.00 0.00 3.02
294 296 4.528596 AGGTTTCTCTCGGAAAATCTCAGA 59.471 41.667 0.00 0.00 44.34 3.27
440 442 0.108851 TCGCGACTTCTAATGCTGCA 60.109 50.000 3.71 4.13 0.00 4.41
905 920 2.520979 GCGGTCTCTGCGCTATATAAG 58.479 52.381 9.73 0.00 0.00 1.73
908 923 4.407818 CGGTCTCTGCGCTATATAAGAAG 58.592 47.826 9.73 0.00 0.00 2.85
909 924 4.083217 CGGTCTCTGCGCTATATAAGAAGT 60.083 45.833 9.73 0.00 0.00 3.01
910 925 5.395642 GGTCTCTGCGCTATATAAGAAGTC 58.604 45.833 9.73 0.00 0.00 3.01
911 926 5.048643 GGTCTCTGCGCTATATAAGAAGTCA 60.049 44.000 9.73 0.00 0.00 3.41
912 927 6.083630 GTCTCTGCGCTATATAAGAAGTCAG 58.916 44.000 9.73 0.00 0.00 3.51
927 942 0.948141 GTCAGGCTAGCGATCATGGC 60.948 60.000 9.00 0.07 0.00 4.40
935 950 0.035036 AGCGATCATGGCCATCAGAG 59.965 55.000 17.61 9.32 0.00 3.35
950 969 1.687493 AGAGCACCCAGAGCTACCC 60.687 63.158 0.00 0.00 43.58 3.69
954 973 1.626356 GCACCCAGAGCTACCCATCA 61.626 60.000 0.00 0.00 0.00 3.07
960 979 2.971330 CCAGAGCTACCCATCATCTTCT 59.029 50.000 0.00 0.00 0.00 2.85
970 989 2.507058 CCATCATCTTCTTCCCTCCACA 59.493 50.000 0.00 0.00 0.00 4.17
1011 1032 2.488355 CTTGCAATGGCGCCTCAG 59.512 61.111 29.70 17.63 45.35 3.35
1012 1033 2.033911 TTGCAATGGCGCCTCAGA 59.966 55.556 29.70 7.47 45.35 3.27
1013 1034 1.989966 CTTGCAATGGCGCCTCAGAG 61.990 60.000 29.70 13.74 45.35 3.35
1230 1251 0.809385 GCTACACTGACTCTACGCCA 59.191 55.000 0.00 0.00 0.00 5.69
1237 1258 3.759766 GACTCTACGCCAGCCGAGC 62.760 68.421 0.00 0.00 41.02 5.03
4009 4536 0.739112 GCTCTGTTCGAGGCCTCTTG 60.739 60.000 29.73 15.90 40.25 3.02
4090 4631 6.260936 CCTGTAGTCTGATGTCACTTGTTTTT 59.739 38.462 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 5.773176 ACAAGTAATTTCAAACGGAGGGAAT 59.227 36.000 0.00 0.00 0.00 3.01
160 161 3.726557 TTACCTACTCCCTCTGTTCGA 57.273 47.619 0.00 0.00 0.00 3.71
734 736 1.452651 ATGCATCAACAGCTCCCCG 60.453 57.895 0.00 0.00 0.00 5.73
735 737 1.389609 CCATGCATCAACAGCTCCCC 61.390 60.000 0.00 0.00 0.00 4.81
736 738 2.012902 GCCATGCATCAACAGCTCCC 62.013 60.000 0.00 0.00 0.00 4.30
895 910 5.336744 GCTAGCCTGACTTCTTATATAGCG 58.663 45.833 2.29 0.00 0.00 4.26
899 914 5.712446 TGATCGCTAGCCTGACTTCTTATAT 59.288 40.000 9.66 0.00 0.00 0.86
905 920 2.402305 CATGATCGCTAGCCTGACTTC 58.598 52.381 9.66 0.00 0.00 3.01
908 923 0.948141 GCCATGATCGCTAGCCTGAC 60.948 60.000 9.66 0.00 0.00 3.51
909 924 1.368950 GCCATGATCGCTAGCCTGA 59.631 57.895 9.66 1.39 0.00 3.86
910 925 1.670406 GGCCATGATCGCTAGCCTG 60.670 63.158 9.66 0.00 40.57 4.85
911 926 1.486997 ATGGCCATGATCGCTAGCCT 61.487 55.000 20.04 0.00 44.19 4.58
912 927 1.002868 ATGGCCATGATCGCTAGCC 60.003 57.895 20.04 8.48 44.13 3.93
927 942 1.153208 GCTCTGGGTGCTCTGATGG 60.153 63.158 0.00 0.00 0.00 3.51
935 950 1.147153 GATGGGTAGCTCTGGGTGC 59.853 63.158 0.00 0.00 0.00 5.01
950 969 3.453717 TCTGTGGAGGGAAGAAGATGATG 59.546 47.826 0.00 0.00 0.00 3.07
954 973 2.907892 TGTCTGTGGAGGGAAGAAGAT 58.092 47.619 0.00 0.00 0.00 2.40
960 979 0.615331 GCAGATGTCTGTGGAGGGAA 59.385 55.000 11.35 0.00 45.45 3.97
970 989 0.469070 GCTGGATGGAGCAGATGTCT 59.531 55.000 0.00 0.00 38.95 3.41
1184 1205 3.234630 TTCTTGGAGGGTGACGCCG 62.235 63.158 0.00 0.00 42.78 6.46
1185 1206 1.376037 CTTCTTGGAGGGTGACGCC 60.376 63.158 0.00 0.00 39.86 5.68
1186 1207 1.376037 CCTTCTTGGAGGGTGACGC 60.376 63.158 0.00 0.00 38.35 5.19
1187 1208 1.376037 GCCTTCTTGGAGGGTGACG 60.376 63.158 0.00 0.00 37.29 4.35
1188 1209 1.376037 CGCCTTCTTGGAGGGTGAC 60.376 63.158 3.63 0.00 40.99 3.67
1189 1210 3.068881 CGCCTTCTTGGAGGGTGA 58.931 61.111 3.63 0.00 40.99 4.02
3799 4304 6.032042 GCACGTATTGTCGAACTAAATTTTGG 59.968 38.462 0.00 0.00 34.70 3.28
4009 4536 3.482156 TGGAGAATAGCTTCATGGCTC 57.518 47.619 0.00 0.00 42.97 4.70


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

AutoCloner maintained by Alex Coulton.