Multiple sequence alignment - TraesCS6B01G332200

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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 TraesCS6B01G332200 chr6B 100.000 2472 0 0 1 2472 583511303 583508832 0.000000e+00 4566.0
1 TraesCS6B01G332200 chr6B 82.456 399 40 21 1943 2315 658406432 658406038 3.660000e-84 322.0
2 TraesCS6B01G332200 chr6B 100.000 66 0 0 2877 2942 583508427 583508362 3.980000e-24 122.0
3 TraesCS6B01G332200 chr6A 89.859 1982 110 43 1 1946 536228204 536226278 0.000000e+00 2462.0
4 TraesCS6B01G332200 chr6D 90.817 1383 74 24 606 1946 389918228 389916857 0.000000e+00 1801.0
5 TraesCS6B01G332200 chr6D 88.987 227 8 7 356 577 389919883 389919669 6.250000e-67 265.0
6 TraesCS6B01G332200 chr3B 95.652 529 23 0 1944 2472 1022234 1021706 0.000000e+00 850.0
7 TraesCS6B01G332200 chr3B 98.333 60 1 0 2883 2942 1021622 1021563 4.010000e-19 106.0
8 TraesCS6B01G332200 chr5A 90.625 480 23 7 1946 2425 130528815 130528358 4.170000e-173 617.0
9 TraesCS6B01G332200 chr5A 95.000 60 3 0 2883 2942 130528263 130528204 8.680000e-16 95.3
10 TraesCS6B01G332200 chr2B 84.708 497 53 10 1941 2417 424522265 424521772 2.650000e-130 475.0
11 TraesCS6B01G332200 chr2B 96.667 60 2 0 2883 2942 424521676 424521617 1.870000e-17 100.0
12 TraesCS6B01G332200 chr7B 84.810 474 60 8 1942 2414 657611012 657610550 1.600000e-127 466.0
13 TraesCS6B01G332200 chr5D 82.667 375 52 11 1943 2312 435542893 435542527 1.320000e-83 320.0
14 TraesCS6B01G332200 chr5D 86.567 268 28 4 2147 2411 437458626 437458888 3.710000e-74 289.0
15 TraesCS6B01G332200 chr1B 81.299 385 52 15 1947 2313 470719262 470719644 7.970000e-76 294.0
16 TraesCS6B01G332200 chr3D 82.759 319 52 3 1946 2263 117319834 117319518 6.210000e-72 281.0
17 TraesCS6B01G332200 chr7A 93.023 172 9 1 1943 2111 7966009 7965838 6.300000e-62 248.0
18 TraesCS6B01G332200 chr7A 92.442 172 10 1 1943 2111 8105227 8105056 2.930000e-60 243.0


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 TraesCS6B01G332200 chr6B 583508362 583511303 2941 True 2344.00 4566 100.0000 1 2942 2 chr6B.!!$R2 2941
1 TraesCS6B01G332200 chr6A 536226278 536228204 1926 True 2462.00 2462 89.8590 1 1946 1 chr6A.!!$R1 1945
2 TraesCS6B01G332200 chr6D 389916857 389919883 3026 True 1033.00 1801 89.9020 356 1946 2 chr6D.!!$R1 1590
3 TraesCS6B01G332200 chr3B 1021563 1022234 671 True 478.00 850 96.9925 1944 2942 2 chr3B.!!$R1 998
4 TraesCS6B01G332200 chr5A 130528204 130528815 611 True 356.15 617 92.8125 1946 2942 2 chr5A.!!$R1 996
5 TraesCS6B01G332200 chr2B 424521617 424522265 648 True 287.50 475 90.6875 1941 2942 2 chr2B.!!$R1 1001

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
353 357 0.095935 CAACTGCGATGAAGGCGAAG 59.904 55.0 0.0 0.0 40.27 3.79 F
603 2044 0.692419 ATCTGGAACGGGATGGAGCT 60.692 55.0 0.0 0.0 33.92 4.09 F
988 2475 1.151083 CCCATCCCATCCCATCCCAT 61.151 60.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 3097 0.320374 ACGTCCTCGAAGCATCCAAA 59.680 50.0 0.00 0.0 40.62 3.28 R
1606 3098 0.389817 CACGTCCTCGAAGCATCCAA 60.390 55.0 0.00 0.0 40.62 3.53 R
2881 4477 0.456221 CTGGGTAGTACACAGGAGCG 59.544 60.0 22.77 0.0 45.63 5.03 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
47 48 8.814038 ATGAAACTAATCAGCCTTGACTTAAT 57.186 30.769 0.00 0.00 35.83 1.40
51 52 9.696917 AAACTAATCAGCCTTGACTTAATTTTG 57.303 29.630 0.00 0.00 35.83 2.44
84 85 6.683974 ATATAAATGGTCAATCTATGCCGC 57.316 37.500 0.00 0.00 0.00 6.53
91 92 3.181476 GGTCAATCTATGCCGCCAAAATT 60.181 43.478 0.00 0.00 0.00 1.82
98 99 0.321021 TGCCGCCAAAATTGCAGAAT 59.679 45.000 0.00 0.00 0.00 2.40
105 106 5.221224 CCGCCAAAATTGCAGAATAATAGGA 60.221 40.000 0.00 0.00 0.00 2.94
109 110 6.183360 CCAAAATTGCAGAATAATAGGAGCCA 60.183 38.462 0.00 0.00 0.00 4.75
118 119 7.254932 GCAGAATAATAGGAGCCACAACTTAAG 60.255 40.741 0.00 0.00 0.00 1.85
122 123 1.774856 AGGAGCCACAACTTAAGGTGT 59.225 47.619 20.61 20.61 33.19 4.16
124 125 3.072211 GGAGCCACAACTTAAGGTGTAC 58.928 50.000 25.27 19.44 33.19 2.90
126 127 4.020839 GGAGCCACAACTTAAGGTGTACTA 60.021 45.833 25.27 0.00 33.19 1.82
127 128 5.148651 AGCCACAACTTAAGGTGTACTAG 57.851 43.478 25.27 13.10 33.19 2.57
132 135 7.519488 GCCACAACTTAAGGTGTACTAGTTTTC 60.519 40.741 25.27 4.18 33.19 2.29
133 136 7.713942 CCACAACTTAAGGTGTACTAGTTTTCT 59.286 37.037 25.27 0.00 33.19 2.52
145 148 9.296400 GTGTACTAGTTTTCTTTTTGCATGAAA 57.704 29.630 0.00 0.00 0.00 2.69
146 149 9.862371 TGTACTAGTTTTCTTTTTGCATGAAAA 57.138 25.926 0.00 0.00 36.60 2.29
175 178 5.636121 ACTTAACGCGAAGTTGATATCACAA 59.364 36.000 15.93 0.00 44.01 3.33
176 179 6.146510 ACTTAACGCGAAGTTGATATCACAAA 59.853 34.615 15.93 0.00 44.01 2.83
196 200 7.753132 TCACAAAATCGTTTAAAGCATGGTATC 59.247 33.333 0.00 0.00 0.00 2.24
198 202 7.540745 ACAAAATCGTTTAAAGCATGGTATCAC 59.459 33.333 0.00 0.00 0.00 3.06
200 204 8.500753 AAATCGTTTAAAGCATGGTATCACTA 57.499 30.769 0.00 0.00 0.00 2.74
230 234 3.376546 GGAGACATGGCTTCTTGTGAATC 59.623 47.826 0.41 0.00 0.00 2.52
231 235 4.005650 GAGACATGGCTTCTTGTGAATCA 58.994 43.478 0.41 0.00 0.00 2.57
232 236 4.597004 AGACATGGCTTCTTGTGAATCAT 58.403 39.130 0.00 0.00 31.19 2.45
233 237 4.398358 AGACATGGCTTCTTGTGAATCATG 59.602 41.667 0.00 14.50 42.53 3.07
234 238 3.446161 ACATGGCTTCTTGTGAATCATGG 59.554 43.478 17.56 7.70 41.93 3.66
235 239 3.159213 TGGCTTCTTGTGAATCATGGT 57.841 42.857 0.00 0.00 0.00 3.55
239 243 4.022068 GGCTTCTTGTGAATCATGGTGAAA 60.022 41.667 0.00 0.00 0.00 2.69
260 264 0.395724 GGGCTGAAATAGTGTGGGGG 60.396 60.000 0.00 0.00 0.00 5.40
292 296 1.304052 CCATTTGGGCCTGTCCGAA 60.304 57.895 4.53 0.00 34.90 4.30
298 302 2.115291 GGGCCTGTCCGAATGCTTC 61.115 63.158 0.84 0.00 34.94 3.86
328 332 1.153289 ACTGAGCCCATCGTGATGC 60.153 57.895 4.29 0.00 37.49 3.91
332 336 1.098050 GAGCCCATCGTGATGCTTTT 58.902 50.000 4.29 0.00 37.49 2.27
338 342 3.057315 CCCATCGTGATGCTTTTTCAACT 60.057 43.478 4.29 0.00 37.49 3.16
353 357 0.095935 CAACTGCGATGAAGGCGAAG 59.904 55.000 0.00 0.00 40.27 3.79
563 578 2.202810 CGAGCTTCTCCGCCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
587 2024 7.039504 TCCTGTAAACAAACTTACTCCGTATCT 60.040 37.037 0.00 0.00 33.67 1.98
599 2040 3.588277 CGTATCTGGAACGGGATGG 57.412 57.895 0.00 0.00 36.71 3.51
600 2041 1.037493 CGTATCTGGAACGGGATGGA 58.963 55.000 0.00 0.00 36.71 3.41
601 2042 1.000163 CGTATCTGGAACGGGATGGAG 60.000 57.143 0.00 0.00 36.71 3.86
602 2043 1.048601 TATCTGGAACGGGATGGAGC 58.951 55.000 0.00 0.00 33.92 4.70
603 2044 0.692419 ATCTGGAACGGGATGGAGCT 60.692 55.000 0.00 0.00 33.92 4.09
729 2174 1.313091 TGATCGGTCGGGTGAGTCTG 61.313 60.000 0.00 0.00 0.00 3.51
731 2176 3.760035 CGGTCGGGTGAGTCTGGG 61.760 72.222 0.00 0.00 0.00 4.45
732 2177 2.283676 GGTCGGGTGAGTCTGGGA 60.284 66.667 0.00 0.00 0.00 4.37
745 2190 2.364842 TGGGAGAGAGAGGCCTGC 60.365 66.667 12.00 0.80 0.00 4.85
926 2412 2.606519 CGTCAACCCTCCCCTCCA 60.607 66.667 0.00 0.00 0.00 3.86
988 2475 1.151083 CCCATCCCATCCCATCCCAT 61.151 60.000 0.00 0.00 0.00 4.00
1012 2499 3.148279 CTCGCCCTACCGCCTCTT 61.148 66.667 0.00 0.00 0.00 2.85
1013 2500 2.682494 TCGCCCTACCGCCTCTTT 60.682 61.111 0.00 0.00 0.00 2.52
1061 2550 4.129148 GGCCGCCCCTCCAAATCT 62.129 66.667 0.00 0.00 0.00 2.40
1265 2757 2.686835 GAGGGCTGCTGGGTCTCT 60.687 66.667 0.00 0.00 0.00 3.10
1539 3031 4.514577 ATCGGGCCGACGAAGCTG 62.515 66.667 33.71 0.00 46.92 4.24
1560 3052 2.967397 CGGTGCAGGGAGACGTAA 59.033 61.111 0.00 0.00 0.00 3.18
1714 3206 1.153168 ATCGATCGCCAAAGGTGGG 60.153 57.895 11.09 0.00 46.09 4.61
1869 3369 5.750352 AAAATCAGCCCATGAATCAAGTT 57.250 34.783 0.00 0.00 42.53 2.66
2084 3585 6.984474 GGAATATTCGCTCATTATCCGGAATA 59.016 38.462 9.01 0.00 0.00 1.75
2200 3701 4.431131 CCGCCACCCTCCTGCATT 62.431 66.667 0.00 0.00 0.00 3.56
2233 3734 1.773653 GATCTGCCTTCTCCATCCCTT 59.226 52.381 0.00 0.00 0.00 3.95
2278 3779 1.087501 CGTCGTCTCCTCTGTGATGA 58.912 55.000 0.00 0.00 0.00 2.92
2357 3876 2.228480 GGTTACCACTCAGGGGGCA 61.228 63.158 0.00 0.00 43.89 5.36
2450 4046 5.046663 TCCTGTTTGGGCAGATTTTATTTCC 60.047 40.000 0.00 0.00 38.70 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.428457 TCAAGGCTGATTAGTTTCATCCCTA 59.572 40.000 0.00 0.00 33.30 3.53
18 19 4.228210 TCAAGGCTGATTAGTTTCATCCCT 59.772 41.667 0.00 0.00 33.30 4.20
20 21 5.189180 AGTCAAGGCTGATTAGTTTCATCC 58.811 41.667 0.00 0.00 33.05 3.51
65 66 1.956477 GGCGGCATAGATTGACCATTT 59.044 47.619 3.07 0.00 0.00 2.32
66 67 1.133823 TGGCGGCATAGATTGACCATT 60.134 47.619 7.97 0.00 0.00 3.16
68 69 0.254462 TTGGCGGCATAGATTGACCA 59.746 50.000 14.32 0.00 0.00 4.02
70 71 3.715628 ATTTTGGCGGCATAGATTGAC 57.284 42.857 14.32 0.00 0.00 3.18
71 72 3.737663 GCAATTTTGGCGGCATAGATTGA 60.738 43.478 29.49 9.30 0.00 2.57
72 73 2.540931 GCAATTTTGGCGGCATAGATTG 59.459 45.455 24.95 24.95 0.00 2.67
73 74 2.168106 TGCAATTTTGGCGGCATAGATT 59.832 40.909 14.32 10.62 0.00 2.40
74 75 1.755959 TGCAATTTTGGCGGCATAGAT 59.244 42.857 14.32 4.36 0.00 1.98
75 76 1.134753 CTGCAATTTTGGCGGCATAGA 59.865 47.619 14.32 1.70 35.45 1.98
76 77 1.134753 TCTGCAATTTTGGCGGCATAG 59.865 47.619 14.32 2.28 37.56 2.23
77 78 1.180907 TCTGCAATTTTGGCGGCATA 58.819 45.000 14.32 4.90 37.56 3.14
78 79 0.321021 TTCTGCAATTTTGGCGGCAT 59.679 45.000 14.32 0.00 37.56 4.40
79 80 0.321021 ATTCTGCAATTTTGGCGGCA 59.679 45.000 7.97 7.97 37.56 5.69
80 81 2.292103 TATTCTGCAATTTTGGCGGC 57.708 45.000 0.00 0.00 37.56 6.53
81 82 4.984161 CCTATTATTCTGCAATTTTGGCGG 59.016 41.667 0.00 0.00 39.01 6.13
82 83 5.830912 TCCTATTATTCTGCAATTTTGGCG 58.169 37.500 0.00 0.00 0.00 5.69
83 84 5.693555 GCTCCTATTATTCTGCAATTTTGGC 59.306 40.000 0.00 0.00 0.00 4.52
84 85 6.183360 TGGCTCCTATTATTCTGCAATTTTGG 60.183 38.462 0.00 0.00 0.00 3.28
91 92 4.080356 AGTTGTGGCTCCTATTATTCTGCA 60.080 41.667 0.00 0.00 0.00 4.41
98 99 5.249852 ACACCTTAAGTTGTGGCTCCTATTA 59.750 40.000 4.67 0.00 36.80 0.98
105 106 4.591924 ACTAGTACACCTTAAGTTGTGGCT 59.408 41.667 15.29 14.23 36.80 4.75
109 110 9.676861 AAAGAAAACTAGTACACCTTAAGTTGT 57.323 29.630 10.72 10.72 31.09 3.32
118 119 7.422399 TCATGCAAAAAGAAAACTAGTACACC 58.578 34.615 0.00 0.00 0.00 4.16
156 159 5.545658 ATTTTGTGATATCAACTTCGCGT 57.454 34.783 7.07 0.00 0.00 6.01
157 160 4.661776 CGATTTTGTGATATCAACTTCGCG 59.338 41.667 7.07 0.00 30.90 5.87
175 178 7.391148 AGTGATACCATGCTTTAAACGATTT 57.609 32.000 0.00 0.00 0.00 2.17
176 179 8.677148 ATAGTGATACCATGCTTTAAACGATT 57.323 30.769 0.00 0.00 0.00 3.34
196 200 3.495100 GCCATGTCTCCTTGGGTATAGTG 60.495 52.174 0.00 0.00 36.60 2.74
198 202 2.975489 AGCCATGTCTCCTTGGGTATAG 59.025 50.000 0.00 0.00 42.80 1.31
200 204 1.898863 AGCCATGTCTCCTTGGGTAT 58.101 50.000 0.00 0.00 42.80 2.73
230 234 3.899052 ATTTCAGCCCATTTCACCATG 57.101 42.857 0.00 0.00 0.00 3.66
231 235 4.403432 CACTATTTCAGCCCATTTCACCAT 59.597 41.667 0.00 0.00 0.00 3.55
232 236 3.763360 CACTATTTCAGCCCATTTCACCA 59.237 43.478 0.00 0.00 0.00 4.17
233 237 3.763897 ACACTATTTCAGCCCATTTCACC 59.236 43.478 0.00 0.00 0.00 4.02
234 238 4.380867 CCACACTATTTCAGCCCATTTCAC 60.381 45.833 0.00 0.00 0.00 3.18
235 239 3.763360 CCACACTATTTCAGCCCATTTCA 59.237 43.478 0.00 0.00 0.00 2.69
239 243 1.063717 CCCCACACTATTTCAGCCCAT 60.064 52.381 0.00 0.00 0.00 4.00
260 264 0.251341 AAATGGCTGTCTCCACCCAC 60.251 55.000 0.00 0.00 39.25 4.61
281 285 3.502572 GAAGCATTCGGACAGGCC 58.497 61.111 0.00 0.00 34.17 5.19
292 296 1.160137 GTCCAGCAGAAACGAAGCAT 58.840 50.000 0.00 0.00 0.00 3.79
298 302 1.294659 GGCTCAGTCCAGCAGAAACG 61.295 60.000 0.00 0.00 41.65 3.60
328 332 2.982470 GCCTTCATCGCAGTTGAAAAAG 59.018 45.455 0.00 0.00 32.98 2.27
332 336 0.320334 TCGCCTTCATCGCAGTTGAA 60.320 50.000 0.00 0.00 0.00 2.69
338 342 2.047370 TGCTTCGCCTTCATCGCA 60.047 55.556 0.00 0.00 0.00 5.10
353 357 0.665298 GGGAAAATGATCGCTCCTGC 59.335 55.000 0.00 0.00 0.00 4.85
354 358 0.940126 CGGGAAAATGATCGCTCCTG 59.060 55.000 0.00 0.00 0.00 3.86
587 2024 0.032515 TCTAGCTCCATCCCGTTCCA 60.033 55.000 0.00 0.00 0.00 3.53
598 2039 1.970092 TCGAGTTAGGCTCTAGCTCC 58.030 55.000 15.40 0.00 41.98 4.70
599 2040 2.946990 AGTTCGAGTTAGGCTCTAGCTC 59.053 50.000 12.81 12.81 41.98 4.09
600 2041 2.946990 GAGTTCGAGTTAGGCTCTAGCT 59.053 50.000 1.39 0.00 41.98 3.32
601 2042 2.286536 CGAGTTCGAGTTAGGCTCTAGC 60.287 54.545 0.00 0.00 41.98 3.42
602 2043 3.196463 TCGAGTTCGAGTTAGGCTCTAG 58.804 50.000 0.00 0.00 44.22 2.43
603 2044 3.257469 TCGAGTTCGAGTTAGGCTCTA 57.743 47.619 0.00 0.00 44.22 2.43
729 2174 3.535962 CGCAGGCCTCTCTCTCCC 61.536 72.222 0.00 0.00 0.00 4.30
731 2176 0.459411 GTTTCGCAGGCCTCTCTCTC 60.459 60.000 0.00 0.00 0.00 3.20
732 2177 1.594310 GTTTCGCAGGCCTCTCTCT 59.406 57.895 0.00 0.00 0.00 3.10
873 2355 2.391389 CGTTTGCTCTCCGGGAAGC 61.391 63.158 18.66 18.66 0.00 3.86
908 2394 2.284405 GGAGGGGAGGGTTGACGA 60.284 66.667 0.00 0.00 0.00 4.20
926 2412 1.299926 GGCTATCGGTTGCGATCGT 60.300 57.895 17.81 0.00 0.00 3.73
1044 2531 4.129148 AGATTTGGAGGGGCGGCC 62.129 66.667 22.00 22.00 0.00 6.13
1051 2538 3.055530 CGGATAGGGATGAGATTTGGAGG 60.056 52.174 0.00 0.00 0.00 4.30
1053 2540 3.856900 TCGGATAGGGATGAGATTTGGA 58.143 45.455 0.00 0.00 0.00 3.53
1056 2543 3.843027 AGCATCGGATAGGGATGAGATTT 59.157 43.478 6.00 0.00 43.07 2.17
1057 2544 3.197333 CAGCATCGGATAGGGATGAGATT 59.803 47.826 6.00 0.00 43.07 2.40
1061 2550 0.610174 GCAGCATCGGATAGGGATGA 59.390 55.000 6.00 0.00 43.07 2.92
1230 2722 3.126225 GTCCTCCTCGTCGACGCT 61.126 66.667 32.19 0.00 39.60 5.07
1352 2844 1.679305 GACGAGCCTCCTGTCCTCA 60.679 63.158 0.00 0.00 0.00 3.86
1560 3052 2.026734 CGCCTGCTCGTCATCGAT 59.973 61.111 0.00 0.00 45.21 3.59
1605 3097 0.320374 ACGTCCTCGAAGCATCCAAA 59.680 50.000 0.00 0.00 40.62 3.28
1606 3098 0.389817 CACGTCCTCGAAGCATCCAA 60.390 55.000 0.00 0.00 40.62 3.53
1789 3283 3.838244 TGGAGGCATATTGACCACTAC 57.162 47.619 0.00 0.00 0.00 2.73
1869 3369 8.246180 GTCAAGAAATAGATGGAGCAATTTCAA 58.754 33.333 8.77 0.00 39.63 2.69
1970 3471 2.104967 TCGGACCCATGACGTTCTATT 58.895 47.619 0.00 0.00 0.00 1.73
2450 4046 4.749245 AAACAAATTGAGGAGCGTACAG 57.251 40.909 0.00 0.00 0.00 2.74
2879 4475 1.226603 GGTAGTACACAGGAGCGCG 60.227 63.158 0.00 0.00 0.00 6.86
2881 4477 0.456221 CTGGGTAGTACACAGGAGCG 59.544 60.000 22.77 0.00 45.63 5.03


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

AutoCloner maintained by Alex Coulton.