Multiple sequence alignment - TraesCS6D01G090500

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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 TraesCS6D01G090500 chr6D 100.000 3322 0 0 1 3322 56297236 56293915 0.000000e+00 6135
1 TraesCS6D01G090500 chr6D 88.450 1013 117 0 1323 2335 47267109 47266097 0.000000e+00 1223
2 TraesCS6D01G090500 chr6B 96.094 2765 89 6 257 3018 126729866 126727118 0.000000e+00 4490
3 TraesCS6D01G090500 chr6B 88.491 1034 104 4 1317 2335 124466096 124467129 0.000000e+00 1236
4 TraesCS6D01G090500 chr6B 95.312 320 13 2 3005 3322 126725984 126725665 1.060000e-139 507
5 TraesCS6D01G090500 chr6B 93.822 259 8 1 1 259 126743119 126742869 1.870000e-102 383
6 TraesCS6D01G090500 chr6A 95.947 2739 99 4 1 2738 70936759 70934032 0.000000e+00 4433
7 TraesCS6D01G090500 chr6A 90.951 1083 90 7 79 1156 60157134 60156055 0.000000e+00 1450
8 TraesCS6D01G090500 chr6A 88.264 1031 103 7 1323 2335 68502114 68503144 0.000000e+00 1218
9 TraesCS6D01G090500 chr6A 93.624 596 26 6 2737 3322 70933928 70933335 0.000000e+00 880
10 TraesCS6D01G090500 chr3A 91.009 1090 87 10 74 1156 715137223 715138308 0.000000e+00 1459
11 TraesCS6D01G090500 chr2A 90.875 1074 84 7 79 1146 758294832 758293767 0.000000e+00 1428
12 TraesCS6D01G090500 chr7A 90.397 1083 95 8 79 1156 672452154 672453232 0.000000e+00 1415
13 TraesCS6D01G090500 chr7D 89.093 1091 83 17 79 1156 325937602 325936535 0.000000e+00 1323
14 TraesCS6D01G090500 chr4A 91.591 880 69 4 281 1156 614522783 614521905 0.000000e+00 1210
15 TraesCS6D01G090500 chr7B 92.197 833 59 5 328 1156 164154010 164154840 0.000000e+00 1173
16 TraesCS6D01G090500 chr1B 91.274 722 52 6 1 721 662455114 662454403 0.000000e+00 974
17 TraesCS6D01G090500 chr5A 86.047 129 9 2 6 134 692233157 692233038 2.690000e-26 130


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 TraesCS6D01G090500 chr6D 56293915 56297236 3321 True 6135.0 6135 100.0000 1 3322 1 chr6D.!!$R2 3321
1 TraesCS6D01G090500 chr6D 47266097 47267109 1012 True 1223.0 1223 88.4500 1323 2335 1 chr6D.!!$R1 1012
2 TraesCS6D01G090500 chr6B 126725665 126729866 4201 True 2498.5 4490 95.7030 257 3322 2 chr6B.!!$R2 3065
3 TraesCS6D01G090500 chr6B 124466096 124467129 1033 False 1236.0 1236 88.4910 1317 2335 1 chr6B.!!$F1 1018
4 TraesCS6D01G090500 chr6A 70933335 70936759 3424 True 2656.5 4433 94.7855 1 3322 2 chr6A.!!$R2 3321
5 TraesCS6D01G090500 chr6A 60156055 60157134 1079 True 1450.0 1450 90.9510 79 1156 1 chr6A.!!$R1 1077
6 TraesCS6D01G090500 chr6A 68502114 68503144 1030 False 1218.0 1218 88.2640 1323 2335 1 chr6A.!!$F1 1012
7 TraesCS6D01G090500 chr3A 715137223 715138308 1085 False 1459.0 1459 91.0090 74 1156 1 chr3A.!!$F1 1082
8 TraesCS6D01G090500 chr2A 758293767 758294832 1065 True 1428.0 1428 90.8750 79 1146 1 chr2A.!!$R1 1067
9 TraesCS6D01G090500 chr7A 672452154 672453232 1078 False 1415.0 1415 90.3970 79 1156 1 chr7A.!!$F1 1077
10 TraesCS6D01G090500 chr7D 325936535 325937602 1067 True 1323.0 1323 89.0930 79 1156 1 chr7D.!!$R1 1077
11 TraesCS6D01G090500 chr4A 614521905 614522783 878 True 1210.0 1210 91.5910 281 1156 1 chr4A.!!$R1 875
12 TraesCS6D01G090500 chr7B 164154010 164154840 830 False 1173.0 1173 92.1970 328 1156 1 chr7B.!!$F1 828
13 TraesCS6D01G090500 chr1B 662454403 662455114 711 True 974.0 974 91.2740 1 721 1 chr1B.!!$R1 720

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
858 864 1.80296 CAGAAGACACACATGCTGGTC 59.197 52.381 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 2518 0.107703 CTGGGTAATGAAGCGGCTCA 60.108 55.0 1.45 3.66 0.0 4.26 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
74 75 3.730761 GCGTGAGGCAGCCACAAG 61.731 66.667 18.32 18.32 42.87 3.16
75 76 3.730761 CGTGAGGCAGCCACAAGC 61.731 66.667 13.83 1.15 44.25 4.01
171 173 6.889177 TGCCCATAGTTAATTCATTCAGTTCA 59.111 34.615 0.00 0.00 0.00 3.18
544 548 3.455910 CTGGAATCATCTACCAACCAGGA 59.544 47.826 0.00 0.00 41.22 3.86
858 864 1.802960 CAGAAGACACACATGCTGGTC 59.197 52.381 0.00 0.00 0.00 4.02
1019 1026 3.266772 ACAATGGCAGAGAAGGTATTCCA 59.733 43.478 0.00 0.00 35.94 3.53
1031 1038 8.482128 AGAGAAGGTATTCCAGAAGAAATACAG 58.518 37.037 7.35 0.00 38.21 2.74
1321 1339 2.744202 CCAGTTCCTCCAAATTCAGTCG 59.256 50.000 0.00 0.00 0.00 4.18
1373 1391 3.256383 CACTTCATGCCAAGAAATCCACA 59.744 43.478 1.40 0.00 0.00 4.17
2438 2474 3.683802 CAATTTCCTCCTCTTGCTGAGT 58.316 45.455 6.56 0.00 41.11 3.41
2447 2483 4.089361 TCCTCTTGCTGAGTAGATTGACA 58.911 43.478 6.56 0.00 41.11 3.58
2482 2518 3.014623 TCAGTGATAGTGACGTCCGATT 58.985 45.455 14.12 0.00 0.00 3.34
2494 2530 0.811616 GTCCGATTGAGCCGCTTCAT 60.812 55.000 0.00 0.00 0.00 2.57
2644 2680 3.430790 CGAACAGTCCATAGGCAAGATGA 60.431 47.826 0.00 0.00 0.00 2.92
2645 2681 3.550437 ACAGTCCATAGGCAAGATGAC 57.450 47.619 0.00 0.00 0.00 3.06
2647 2683 2.171237 CAGTCCATAGGCAAGATGACCA 59.829 50.000 0.00 0.00 0.00 4.02
2680 2717 1.803334 TGGACACGCAGGTATGAAAC 58.197 50.000 0.00 0.00 0.00 2.78
2704 2741 8.421249 ACTATTCAGTGATCCAATTCCAAAAA 57.579 30.769 0.00 0.00 32.25 1.94
2729 2766 2.158475 TGGCACAAACCTGAAGAGGATT 60.158 45.455 0.00 0.00 37.04 3.01
2730 2767 2.893489 GGCACAAACCTGAAGAGGATTT 59.107 45.455 0.00 0.00 42.93 2.17
3002 3144 5.185828 ACAGCCCATAGAATTGGAAAGTTTC 59.814 40.000 7.09 7.09 39.25 2.78
3049 4338 5.032863 AGATTGAGTTGTACGCACGTATAC 58.967 41.667 6.15 7.99 32.82 1.47
3174 4465 1.514678 TTTGACGCAGGACACATGCC 61.515 55.000 2.99 0.00 40.67 4.40
3214 4505 5.691305 GCAGAAAACAAGTGCACATGAATAA 59.309 36.000 27.42 0.00 37.16 1.40
3245 4544 7.011857 CCTTCAGAATATAGGTGCAGAGTTTTC 59.988 40.741 0.00 0.00 0.00 2.29
3254 4553 5.121811 AGGTGCAGAGTTTTCATATAGCTG 58.878 41.667 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.031857 GTCGAGCCGATTACGATTCTCT 60.032 50.000 0.00 0.00 42.66 3.10
70 71 5.115480 CAACTTAAATTGTTGTGGGCTTGT 58.885 37.500 0.00 0.00 39.69 3.16
71 72 4.511082 CCAACTTAAATTGTTGTGGGCTTG 59.489 41.667 6.44 0.00 42.09 4.01
72 73 4.444164 CCCAACTTAAATTGTTGTGGGCTT 60.444 41.667 6.44 0.00 42.09 4.35
73 74 3.070878 CCCAACTTAAATTGTTGTGGGCT 59.929 43.478 6.44 0.00 42.09 5.19
74 75 3.398406 CCCAACTTAAATTGTTGTGGGC 58.602 45.455 6.44 0.00 42.09 5.36
75 76 3.643792 TCCCCAACTTAAATTGTTGTGGG 59.356 43.478 18.11 18.11 45.99 4.61
76 77 4.586841 TCTCCCCAACTTAAATTGTTGTGG 59.413 41.667 3.24 3.24 41.90 4.17
77 78 5.782893 TCTCCCCAACTTAAATTGTTGTG 57.217 39.130 6.44 0.00 42.09 3.33
171 173 2.755952 ACTTTCCTGAAACCCAGCTT 57.244 45.000 0.00 0.00 41.57 3.74
219 221 7.589958 TGTGCCCTTTGTTCTTATTTAAAGA 57.410 32.000 0.00 0.00 33.18 2.52
433 435 3.645884 GCACATTGCATCAGTTTGAAGT 58.354 40.909 0.00 0.00 44.26 3.01
544 548 6.625740 CGCATAGGACAAATTCTCACCAAATT 60.626 38.462 0.00 0.00 0.00 1.82
629 633 6.665992 ATAAAGCGAGGGAATACTGATACA 57.334 37.500 0.00 0.00 0.00 2.29
858 864 3.248266 GCAAACTAAGCCTGAATTGCTG 58.752 45.455 6.82 0.00 39.48 4.41
1007 1014 8.152023 ACTGTATTTCTTCTGGAATACCTTCT 57.848 34.615 5.16 0.00 37.04 2.85
1019 1026 5.013183 AGTTGGCCACTACTGTATTTCTTCT 59.987 40.000 3.88 0.00 31.97 2.85
1321 1339 0.254178 TGGAGGAAGATGGAGCTTGC 59.746 55.000 0.00 0.00 36.59 4.01
1373 1391 3.379445 CACCGTACGAGGCTGGGT 61.379 66.667 18.76 0.39 33.69 4.51
1514 1550 1.293498 GGACTCAAAGAGGCGCTCA 59.707 57.895 7.64 0.00 38.87 4.26
2063 2099 1.660560 ATAGCAGGCCGACGTAACGT 61.661 55.000 0.00 0.00 45.10 3.99
2114 2150 4.074526 AGCTGCTCGGATGTGCGT 62.075 61.111 0.00 0.00 37.41 5.24
2120 2156 2.688666 TTCCCCAGCTGCTCGGAT 60.689 61.111 15.29 0.00 0.00 4.18
2438 2474 3.196469 CCTCCTCAAGCACTGTCAATCTA 59.804 47.826 0.00 0.00 0.00 1.98
2447 2483 0.683973 CACTGACCTCCTCAAGCACT 59.316 55.000 0.00 0.00 0.00 4.40
2482 2518 0.107703 CTGGGTAATGAAGCGGCTCA 60.108 55.000 1.45 3.66 0.00 4.26
2494 2530 4.752879 GGCGCGCTGACTGGGTAA 62.753 66.667 32.29 0.00 0.00 2.85
2644 2680 1.221523 TCCATCCAGGAGCTCTATGGT 59.778 52.381 27.17 17.12 43.07 3.55
2645 2681 2.021262 TCCATCCAGGAGCTCTATGG 57.979 55.000 24.42 24.42 43.07 2.74
2704 2741 4.019174 CCTCTTCAGGTTTGTGCCATTAT 58.981 43.478 0.00 0.00 34.60 1.28
2725 2762 8.094798 TCAAGTACACACATAGAAACAAATCC 57.905 34.615 0.00 0.00 0.00 3.01
2730 2767 9.936759 TGAATATCAAGTACACACATAGAAACA 57.063 29.630 0.00 0.00 0.00 2.83
2752 2894 4.060205 GCACATGTTCTTTTTGGCTGAAT 58.940 39.130 0.00 0.00 0.00 2.57
2889 3031 3.199946 TCCCTATAAACTGGAACCTGCAG 59.800 47.826 6.78 6.78 41.93 4.41
3002 3144 7.777440 TCTGAGCATATAGATCCTACATACTGG 59.223 40.741 0.00 0.00 0.00 4.00
3049 4338 8.155821 AGAGAGATCATACTGCATTTTCAATG 57.844 34.615 0.00 0.00 0.00 2.82
3109 4399 4.518970 GCAACTCCAAACCAAAGACTATGA 59.481 41.667 0.00 0.00 0.00 2.15
3214 4505 7.013220 TCTGCACCTATATTCTGAAGGATAGT 58.987 38.462 15.51 2.04 34.34 2.12


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

AutoCloner maintained by Alex Coulton.