Multiple sequence alignment - TraesCS7B01G335100

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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 TraesCS7B01G335100 chr7B 100.000 2285 0 0 1 2285 590103425 590105709 0.000000e+00 4220
1 TraesCS7B01G335100 chr7B 90.732 205 18 1 2081 2285 589943326 589943123 2.890000e-69 272
2 TraesCS7B01G335100 chr7B 86.550 171 23 0 2112 2282 589901162 589900992 3.000000e-44 189
3 TraesCS7B01G335100 chr7A 94.190 2289 105 15 1 2283 628863156 628865422 0.000000e+00 3465
4 TraesCS7B01G335100 chr7A 93.103 203 14 0 2081 2283 628655206 628655004 4.770000e-77 298
5 TraesCS7B01G335100 chr7A 83.600 250 28 10 390 629 628839566 628839812 2.950000e-54 222
6 TraesCS7B01G335100 chr7D 94.516 2261 90 11 24 2283 546125866 546128093 0.000000e+00 3458
7 TraesCS7B01G335100 chr7D 93.069 202 14 0 2081 2282 545662074 545661873 1.720000e-76 296
8 TraesCS7B01G335100 chr7D 92.118 203 16 0 2081 2283 545656791 545656589 1.030000e-73 287
9 TraesCS7B01G335100 chr6B 78.867 918 179 13 955 1863 156372864 156373775 6.980000e-170 606
10 TraesCS7B01G335100 chr6A 78.758 918 180 12 955 1863 98061801 98062712 3.250000e-168 601
11 TraesCS7B01G335100 chr6A 79.808 832 160 7 978 1804 98246862 98247690 1.170000e-167 599
12 TraesCS7B01G335100 chr6A 78.767 876 179 6 978 1848 98306854 98307727 4.230000e-162 580
13 TraesCS7B01G335100 chr6D 79.067 879 171 10 978 1848 81760807 81761680 1.950000e-165 592
14 TraesCS7B01G335100 chr6D 78.812 892 178 10 979 1863 81670746 81671633 7.030000e-165 590
15 TraesCS7B01G335100 chr6D 78.275 893 184 8 978 1862 81770738 81771628 1.180000e-157 566


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 TraesCS7B01G335100 chr7B 590103425 590105709 2284 False 4220 4220 100.000 1 2285 1 chr7B.!!$F1 2284
1 TraesCS7B01G335100 chr7A 628863156 628865422 2266 False 3465 3465 94.190 1 2283 1 chr7A.!!$F2 2282
2 TraesCS7B01G335100 chr7D 546125866 546128093 2227 False 3458 3458 94.516 24 2283 1 chr7D.!!$F1 2259
3 TraesCS7B01G335100 chr6B 156372864 156373775 911 False 606 606 78.867 955 1863 1 chr6B.!!$F1 908
4 TraesCS7B01G335100 chr6A 98061801 98062712 911 False 601 601 78.758 955 1863 1 chr6A.!!$F1 908
5 TraesCS7B01G335100 chr6A 98246862 98247690 828 False 599 599 79.808 978 1804 1 chr6A.!!$F2 826
6 TraesCS7B01G335100 chr6A 98306854 98307727 873 False 580 580 78.767 978 1848 1 chr6A.!!$F3 870
7 TraesCS7B01G335100 chr6D 81760807 81761680 873 False 592 592 79.067 978 1848 1 chr6D.!!$F2 870
8 TraesCS7B01G335100 chr6D 81670746 81671633 887 False 590 590 78.812 979 1863 1 chr6D.!!$F1 884
9 TraesCS7B01G335100 chr6D 81770738 81771628 890 False 566 566 78.275 978 1862 1 chr6D.!!$F3 884

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
192 195 0.036765 TTCCACAGTTCGATTCCCCG 60.037 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2103 0.040958 CAACGGCTGCAACTCAAGAC 60.041 55.0 0.5 0.0 0.0 3.01 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
108 111 4.629065 GAAGAAATCGTTGTTAGTCTGCG 58.371 43.478 0.00 0.00 0.00 5.18
129 132 1.134220 ACAATGTGTTGTCCGTGACCT 60.134 47.619 0.00 0.00 45.14 3.85
134 137 1.597027 GTTGTCCGTGACCTGTGGG 60.597 63.158 2.23 0.00 38.88 4.61
146 149 0.468029 CCTGTGGGTTGCACTCCTTT 60.468 55.000 7.00 0.00 0.00 3.11
147 150 0.954452 CTGTGGGTTGCACTCCTTTC 59.046 55.000 7.00 0.00 0.00 2.62
161 164 1.208052 TCCTTTCGCTCTGGAATCTGG 59.792 52.381 0.00 0.00 0.00 3.86
165 168 1.780503 TCGCTCTGGAATCTGGATCA 58.219 50.000 0.00 0.00 0.00 2.92
166 169 2.110578 TCGCTCTGGAATCTGGATCAA 58.889 47.619 0.00 0.00 0.00 2.57
167 170 2.702478 TCGCTCTGGAATCTGGATCAAT 59.298 45.455 0.00 0.00 0.00 2.57
168 171 2.806818 CGCTCTGGAATCTGGATCAATG 59.193 50.000 0.00 0.00 0.00 2.82
169 172 2.553172 GCTCTGGAATCTGGATCAATGC 59.447 50.000 0.00 0.00 0.00 3.56
170 173 3.147629 CTCTGGAATCTGGATCAATGCC 58.852 50.000 0.00 0.00 0.00 4.40
171 174 1.878088 CTGGAATCTGGATCAATGCCG 59.122 52.381 0.00 0.00 0.00 5.69
172 175 0.595095 GGAATCTGGATCAATGCCGC 59.405 55.000 0.00 0.00 0.00 6.53
173 176 1.602311 GAATCTGGATCAATGCCGCT 58.398 50.000 0.00 0.00 0.00 5.52
174 177 1.952296 GAATCTGGATCAATGCCGCTT 59.048 47.619 0.00 0.00 0.00 4.68
175 178 1.602311 ATCTGGATCAATGCCGCTTC 58.398 50.000 0.00 0.00 0.00 3.86
176 179 0.464373 TCTGGATCAATGCCGCTTCC 60.464 55.000 0.00 0.00 0.00 3.46
177 180 0.749091 CTGGATCAATGCCGCTTCCA 60.749 55.000 0.00 0.00 35.29 3.53
178 181 1.031571 TGGATCAATGCCGCTTCCAC 61.032 55.000 0.00 0.00 31.67 4.02
179 182 1.031571 GGATCAATGCCGCTTCCACA 61.032 55.000 0.00 0.00 0.00 4.17
187 190 1.298859 GCCGCTTCCACAGTTCGATT 61.299 55.000 0.00 0.00 0.00 3.34
192 195 0.036765 TTCCACAGTTCGATTCCCCG 60.037 55.000 0.00 0.00 0.00 5.73
204 207 2.612972 CGATTCCCCGACCTCATATTGG 60.613 54.545 0.00 0.00 0.00 3.16
254 257 4.010349 GCAGCAGTTAGGACTTGGTAAAT 58.990 43.478 0.00 0.00 32.54 1.40
282 285 1.354040 GCGTGATTGTGGTCTCAGAG 58.646 55.000 0.00 0.00 0.00 3.35
285 288 3.181486 GCGTGATTGTGGTCTCAGAGATA 60.181 47.826 2.64 0.00 0.00 1.98
295 298 6.317140 TGTGGTCTCAGAGATAAATTCAATGC 59.683 38.462 2.64 0.00 0.00 3.56
340 343 3.146066 GTGCTGTAATGTTGGACTTCCA 58.854 45.455 0.00 0.00 45.94 3.53
371 374 2.485814 GTGCGCCTTTCTCAGAGAAATT 59.514 45.455 23.24 0.00 42.66 1.82
374 377 3.181512 GCGCCTTTCTCAGAGAAATTGAG 60.182 47.826 23.24 18.99 42.66 3.02
464 468 6.145338 AGCAGCTCAAATAAATGAAGATGG 57.855 37.500 0.00 0.00 0.00 3.51
470 474 8.974238 AGCTCAAATAAATGAAGATGGATTCAA 58.026 29.630 0.00 0.00 42.21 2.69
577 581 1.879380 TGGAGCTGAAATGTTTCCACG 59.121 47.619 0.00 0.00 36.36 4.94
581 585 3.472652 AGCTGAAATGTTTCCACGTACA 58.527 40.909 3.26 0.00 36.36 2.90
616 620 8.854614 AAACTGAATATATGGGCTCATAACTC 57.145 34.615 11.06 8.03 39.10 3.01
709 713 5.011738 AGTTTACACCTAGTCTAGCAAAGCA 59.988 40.000 0.86 0.00 0.00 3.91
711 715 2.263077 CACCTAGTCTAGCAAAGCACG 58.737 52.381 0.86 0.00 0.00 5.34
758 763 2.863809 ACCGAGTTTGGAGCTGAAATT 58.136 42.857 0.00 0.00 0.00 1.82
875 882 8.495949 ACTGTACAATCTGTTAGAAAACAATCG 58.504 33.333 0.00 0.00 44.79 3.34
896 903 7.642082 ATCGTTCTACTCAGTTTACACCTAT 57.358 36.000 0.00 0.00 0.00 2.57
930 937 4.572389 CACAAGATTACCACCTGTATCTGC 59.428 45.833 0.00 0.00 0.00 4.26
1302 1309 3.314331 CCCAGAGTGCCGACCAGT 61.314 66.667 0.00 0.00 0.00 4.00
1314 1321 0.852777 CGACCAGTTCAGTTGTGACG 59.147 55.000 0.00 0.00 30.10 4.35
1617 1627 1.120530 AGTAACCCCATAGAGGCACG 58.879 55.000 0.00 0.00 35.39 5.34
1680 1690 4.096081 GCAGTGAATTCTCTTTCCATCAGG 59.904 45.833 7.30 0.00 0.00 3.86
1785 1795 0.926155 CGATGATGTTCTGCTGGTCG 59.074 55.000 0.00 0.00 0.00 4.79
1878 1891 5.549742 TCACCAAAATGCTTCCTTTCATT 57.450 34.783 0.00 0.00 34.66 2.57
1892 1905 6.403866 TCCTTTCATTACATTGCACAAGTT 57.596 33.333 0.00 0.00 0.00 2.66
1899 1912 7.751732 TCATTACATTGCACAAGTTATCTGAC 58.248 34.615 0.00 0.00 0.00 3.51
1908 1921 2.926200 CAAGTTATCTGACGCAGAGGTG 59.074 50.000 13.55 5.29 44.08 4.00
1918 1931 3.006430 TGACGCAGAGGTGAATGAACTTA 59.994 43.478 0.00 0.00 0.00 2.24
2022 2035 1.000521 CAGAATGGCAAGCCCTCCA 60.001 57.895 8.89 0.00 36.70 3.86
2043 2056 4.582656 CCAAAGAACACACCTAATCCAACA 59.417 41.667 0.00 0.00 0.00 3.33
2067 2080 5.827797 AGCAGTAATGTTCTTCTTGTTCCAA 59.172 36.000 0.00 0.00 0.00 3.53
2073 2086 3.869246 TGTTCTTCTTGTTCCAACGTCTC 59.131 43.478 0.00 0.00 0.00 3.36
2092 2105 1.153349 GGGGACGCTGAAGATGGTC 60.153 63.158 0.00 0.00 0.00 4.02
2104 2117 1.818642 AGATGGTCTTGAGTTGCAGC 58.181 50.000 0.00 0.00 0.00 5.25
2106 2119 0.957395 ATGGTCTTGAGTTGCAGCCG 60.957 55.000 0.00 0.00 0.00 5.52
2109 2122 0.040958 GTCTTGAGTTGCAGCCGTTG 60.041 55.000 0.00 0.00 0.00 4.10
2129 2142 4.787135 TGTTGATCATAGGGCCACATAA 57.213 40.909 6.18 0.00 0.00 1.90
2192 2205 2.104963 ACTGTCCTCCACTTGGAACTTC 59.895 50.000 0.00 0.00 44.91 3.01
2211 2224 4.349930 ACTTCCCCTTCTAGCTTGTTGTTA 59.650 41.667 0.00 0.00 0.00 2.41
2250 2263 2.731572 AGGAAATGCAGACCATTCAGG 58.268 47.619 8.83 0.00 43.22 3.86
2283 2296 1.392589 CACCTGTGAGCTGGTTGTTT 58.607 50.000 0.00 0.00 43.79 2.83
2284 2297 1.066002 CACCTGTGAGCTGGTTGTTTG 59.934 52.381 0.00 0.00 43.79 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.208614 GAAAAGACAGCAGCGCCAG 59.791 57.895 2.29 0.00 0.00 4.85
5 6 0.871057 AGAAGAAAAGACAGCAGCGC 59.129 50.000 0.00 0.00 0.00 5.92
15 16 2.706555 GGGCACCGAAAGAAGAAAAG 57.293 50.000 0.00 0.00 40.86 2.27
134 137 0.514691 CAGAGCGAAAGGAGTGCAAC 59.485 55.000 0.00 0.00 0.00 4.17
138 141 2.093764 AGATTCCAGAGCGAAAGGAGTG 60.094 50.000 0.00 0.00 32.11 3.51
146 149 1.780503 TGATCCAGATTCCAGAGCGA 58.219 50.000 0.00 0.00 0.00 4.93
147 150 2.609427 TTGATCCAGATTCCAGAGCG 57.391 50.000 0.00 0.00 0.00 5.03
161 164 0.379669 CTGTGGAAGCGGCATTGATC 59.620 55.000 1.45 0.00 0.00 2.92
165 168 1.577328 CGAACTGTGGAAGCGGCATT 61.577 55.000 1.45 0.00 0.00 3.56
166 169 2.034879 CGAACTGTGGAAGCGGCAT 61.035 57.895 1.45 0.00 0.00 4.40
167 170 2.449031 ATCGAACTGTGGAAGCGGCA 62.449 55.000 1.45 0.00 0.00 5.69
168 171 1.298859 AATCGAACTGTGGAAGCGGC 61.299 55.000 0.00 0.00 0.00 6.53
169 172 0.721718 GAATCGAACTGTGGAAGCGG 59.278 55.000 0.00 0.00 0.00 5.52
170 173 0.721718 GGAATCGAACTGTGGAAGCG 59.278 55.000 0.00 0.00 0.00 4.68
171 174 1.087501 GGGAATCGAACTGTGGAAGC 58.912 55.000 0.00 0.00 0.00 3.86
172 175 1.739067 GGGGAATCGAACTGTGGAAG 58.261 55.000 0.00 0.00 0.00 3.46
173 176 0.036765 CGGGGAATCGAACTGTGGAA 60.037 55.000 0.00 0.00 0.00 3.53
174 177 0.901114 TCGGGGAATCGAACTGTGGA 60.901 55.000 0.00 0.00 36.12 4.02
175 178 0.739813 GTCGGGGAATCGAACTGTGG 60.740 60.000 0.00 0.00 41.05 4.17
176 179 0.739813 GGTCGGGGAATCGAACTGTG 60.740 60.000 0.00 0.00 42.91 3.66
177 180 1.595357 GGTCGGGGAATCGAACTGT 59.405 57.895 0.00 0.00 42.91 3.55
178 181 4.515404 GGTCGGGGAATCGAACTG 57.485 61.111 0.00 0.00 42.91 3.16
187 190 0.692756 TGCCAATATGAGGTCGGGGA 60.693 55.000 0.00 0.00 0.00 4.81
192 195 4.122776 CAGTACTGTGCCAATATGAGGTC 58.877 47.826 15.06 0.00 0.00 3.85
204 207 4.170256 GAGAGCTAGTTTCAGTACTGTGC 58.830 47.826 21.99 15.97 32.70 4.57
254 257 0.936600 CACAATCACGCGCATATGGA 59.063 50.000 5.73 0.00 0.00 3.41
282 285 8.416329 AGTTGTTCCTATGGCATTGAATTTATC 58.584 33.333 4.78 0.00 0.00 1.75
285 288 6.610075 AGTTGTTCCTATGGCATTGAATTT 57.390 33.333 4.78 0.00 0.00 1.82
295 298 5.643777 CCAAGTTGACTAGTTGTTCCTATGG 59.356 44.000 3.87 0.00 35.74 2.74
340 343 1.928706 AAAGGCGCACAACACAACGT 61.929 50.000 10.83 0.00 0.00 3.99
341 344 1.199852 GAAAGGCGCACAACACAACG 61.200 55.000 10.83 0.00 0.00 4.10
342 345 0.100503 AGAAAGGCGCACAACACAAC 59.899 50.000 10.83 0.00 0.00 3.32
343 346 0.380378 GAGAAAGGCGCACAACACAA 59.620 50.000 10.83 0.00 0.00 3.33
344 347 0.746204 TGAGAAAGGCGCACAACACA 60.746 50.000 10.83 0.00 0.00 3.72
345 348 0.040958 CTGAGAAAGGCGCACAACAC 60.041 55.000 10.83 0.00 0.00 3.32
371 374 8.370182 TGTTGATATGCTAGCAGAATAATCTCA 58.630 33.333 23.89 14.55 32.03 3.27
374 377 8.944029 ACATGTTGATATGCTAGCAGAATAATC 58.056 33.333 23.89 18.23 0.00 1.75
464 468 3.364366 CGGTTCAGAGCTGTTGTTGAATC 60.364 47.826 0.00 0.00 32.76 2.52
470 474 0.753262 AGTCGGTTCAGAGCTGTTGT 59.247 50.000 0.00 0.00 0.00 3.32
531 535 1.060122 CGTTCCACGATTACGGAAAGC 59.940 52.381 0.00 0.00 46.05 3.51
594 598 6.045318 CGGAGTTATGAGCCCATATATTCAG 58.955 44.000 0.00 0.00 35.38 3.02
666 670 9.198475 TGTAAACTGGGTAAAAGGATTGTTTTA 57.802 29.630 0.00 0.00 31.96 1.52
683 687 5.401531 TTGCTAGACTAGGTGTAAACTGG 57.598 43.478 11.48 0.00 0.00 4.00
709 713 6.037830 CCAATTACGGAAAATGGTATTCTCGT 59.962 38.462 7.29 0.00 37.42 4.18
711 715 6.238925 CCCCAATTACGGAAAATGGTATTCTC 60.239 42.308 13.00 0.00 0.00 2.87
775 780 8.000709 TGAGCCCATATATTCAATTTTGTCTCT 58.999 33.333 0.00 0.00 0.00 3.10
779 784 7.658525 TGTGAGCCCATATATTCAATTTTGT 57.341 32.000 0.00 0.00 0.00 2.83
896 903 5.181245 GTGGTAATCTTGTGCTTTGCTAGAA 59.819 40.000 0.00 0.00 0.00 2.10
930 937 8.936864 CAGGTGGAAATGTAGTTAAAAGTAGAG 58.063 37.037 0.00 0.00 0.00 2.43
1302 1309 1.996898 GACACACACGTCACAACTGAA 59.003 47.619 0.00 0.00 35.88 3.02
1314 1321 0.892755 TCCGTCCCTATGACACACAC 59.107 55.000 0.00 0.00 44.71 3.82
1617 1627 2.474526 CGTGGCGAAACATGACAATCTC 60.475 50.000 0.00 0.00 0.00 2.75
1680 1690 1.797537 GCTCAACGGCGAAATGTGC 60.798 57.895 16.62 17.18 0.00 4.57
1785 1795 5.257082 TCTTAAAGGCCACAAACAACTTC 57.743 39.130 5.01 0.00 0.00 3.01
1878 1891 4.092821 GCGTCAGATAACTTGTGCAATGTA 59.907 41.667 0.00 0.00 0.00 2.29
1892 1905 3.023832 TCATTCACCTCTGCGTCAGATA 58.976 45.455 9.47 0.00 39.92 1.98
1899 1912 2.673368 GGTAAGTTCATTCACCTCTGCG 59.327 50.000 0.00 0.00 0.00 5.18
1908 1921 4.745620 GGCGACATAGAGGTAAGTTCATTC 59.254 45.833 0.00 0.00 0.00 2.67
2022 2035 4.278419 GCTGTTGGATTAGGTGTGTTCTTT 59.722 41.667 0.00 0.00 0.00 2.52
2043 2056 5.376625 TGGAACAAGAAGAACATTACTGCT 58.623 37.500 0.00 0.00 31.92 4.24
2073 2086 2.202932 CCATCTTCAGCGTCCCCG 60.203 66.667 0.00 0.00 37.07 5.73
2090 2103 0.040958 CAACGGCTGCAACTCAAGAC 60.041 55.000 0.50 0.00 0.00 3.01
2092 2105 0.381801 AACAACGGCTGCAACTCAAG 59.618 50.000 0.50 0.00 0.00 3.02
2104 2117 1.308998 GGCCCTATGATCAACAACGG 58.691 55.000 0.00 0.00 0.00 4.44
2106 2119 2.722094 TGTGGCCCTATGATCAACAAC 58.278 47.619 0.00 0.00 0.00 3.32
2109 2122 4.718961 AGTTATGTGGCCCTATGATCAAC 58.281 43.478 0.00 0.00 0.00 3.18
2129 2142 2.644798 AGCTACAGTGGGAATCCAAAGT 59.355 45.455 0.09 0.00 46.04 2.66
2192 2205 4.553330 TCTAACAACAAGCTAGAAGGGG 57.447 45.455 0.00 0.00 0.00 4.79
2211 2224 9.059260 CATTTCCTTTCCAAATTTGATGTTTCT 57.941 29.630 19.86 0.00 0.00 2.52
2235 2248 0.395311 CTGCCCTGAATGGTCTGCAT 60.395 55.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.