Multiple sequence alignment - TraesCS6D01G191700

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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 TraesCS6D01G191700 chr6D 100.000 2398 0 0 1 2398 264450622 264448225 0.000000e+00 4429.0
1 TraesCS6D01G191700 chr6B 91.505 1495 50 25 942 2398 408246313 408244858 0.000000e+00 1986.0
2 TraesCS6D01G191700 chr6B 89.956 677 52 5 94 754 408260823 408260147 0.000000e+00 859.0
3 TraesCS6D01G191700 chr6B 90.404 198 6 2 754 951 408259767 408259583 5.120000e-62 248.0
4 TraesCS6D01G191700 chr6A 90.507 1559 58 28 877 2398 373120633 373119128 0.000000e+00 1977.0
5 TraesCS6D01G191700 chr6A 91.657 899 53 7 1 882 373137729 373136836 0.000000e+00 1225.0
6 TraesCS6D01G191700 chr4B 93.421 76 3 2 2239 2312 22844032 22844107 7.010000e-21 111.0
7 TraesCS6D01G191700 chr7B 76.442 208 43 6 1 205 748773482 748773686 9.060000e-20 108.0
8 TraesCS6D01G191700 chr7B 89.474 76 5 3 2239 2312 705867438 705867512 2.540000e-15 93.5
9 TraesCS6D01G191700 chr7B 100.000 32 0 0 2244 2275 420591033 420591002 2.570000e-05 60.2
10 TraesCS6D01G191700 chr7A 92.857 70 3 2 2245 2312 50004226 50004295 1.520000e-17 100.0
11 TraesCS6D01G191700 chr3D 92.308 65 3 2 2249 2312 15968456 15968393 9.130000e-15 91.6
12 TraesCS6D01G191700 chr3D 90.909 44 0 4 2237 2276 28047215 28047258 3.330000e-04 56.5
13 TraesCS6D01G191700 chr1D 82.653 98 10 5 609 699 362575866 362575769 1.980000e-11 80.5
14 TraesCS6D01G191700 chr4A 86.364 66 7 2 2245 2308 17481969 17481904 1.190000e-08 71.3
15 TraesCS6D01G191700 chr5B 91.111 45 0 1 2242 2282 685949265 685949309 9.260000e-05 58.4
16 TraesCS6D01G191700 chr2A 92.500 40 1 2 2241 2279 391897127 391897165 3.330000e-04 56.5


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 TraesCS6D01G191700 chr6D 264448225 264450622 2397 True 4429.0 4429 100.000 1 2398 1 chr6D.!!$R1 2397
1 TraesCS6D01G191700 chr6B 408244858 408246313 1455 True 1986.0 1986 91.505 942 2398 1 chr6B.!!$R1 1456
2 TraesCS6D01G191700 chr6B 408259583 408260823 1240 True 553.5 859 90.180 94 951 2 chr6B.!!$R2 857
3 TraesCS6D01G191700 chr6A 373119128 373120633 1505 True 1977.0 1977 90.507 877 2398 1 chr6A.!!$R1 1521
4 TraesCS6D01G191700 chr6A 373136836 373137729 893 True 1225.0 1225 91.657 1 882 1 chr6A.!!$R2 881

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
279 283 0.034059 CCCAGAACGACAAGCTGTCT 59.966 55.0 12.45 0.00 44.85 3.41 F
629 649 0.611200 TGGAAACCACCATCGTCGAT 59.389 50.0 0.75 0.75 34.77 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1711 0.739561 GCGTCGTACTCCTCCTTGAT 59.260 55.000 0.0 0.0 0.00 2.57 R
1910 2320 1.468520 CTACTTGGCACCCATGTTTCG 59.531 52.381 7.9 0.0 41.24 3.46 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
26 27 2.848887 TCGAACGCATTTTTGTTGTGTG 59.151 40.909 0.00 0.00 37.83 3.82
39 40 1.003116 GTTGTGTGAGCACTGAAGCTG 60.003 52.381 4.28 0.00 46.75 4.24
71 72 1.415289 GGTGGGAGTAAGGATAACCGG 59.585 57.143 0.00 0.00 41.83 5.28
82 83 1.816224 GGATAACCGGCAACACATGTT 59.184 47.619 0.00 0.00 39.12 2.71
163 166 3.143728 GTCAGGGACGTGTGGTATTTTT 58.856 45.455 0.00 0.00 0.00 1.94
186 189 0.319469 TCTCTCGTTGCAATGCACGA 60.319 50.000 23.35 23.35 38.71 4.35
279 283 0.034059 CCCAGAACGACAAGCTGTCT 59.966 55.000 12.45 0.00 44.85 3.41
301 305 2.102252 GGACATTTTGCACAAAGGACCA 59.898 45.455 16.03 0.00 0.00 4.02
333 338 4.301072 AATATTACATCCATCCCCGTGG 57.699 45.455 0.00 0.00 40.76 4.94
457 462 1.747325 TTCCTTGCAACCAAGCTGCC 61.747 55.000 0.00 0.00 45.65 4.85
483 488 2.125912 CTCTTGTGCTCCCCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
629 649 0.611200 TGGAAACCACCATCGTCGAT 59.389 50.000 0.75 0.75 34.77 3.59
634 654 0.824109 ACCACCATCGTCGATGTCAT 59.176 50.000 28.46 14.36 38.28 3.06
692 712 2.510238 CCTGTAGCAGCGCCAGAC 60.510 66.667 2.29 0.00 0.00 3.51
699 719 3.114616 CAGCGCCAGACCGAACAG 61.115 66.667 2.29 0.00 0.00 3.16
705 725 1.668419 GCCAGACCGAACAGCAATAT 58.332 50.000 0.00 0.00 0.00 1.28
711 731 0.947244 CCGAACAGCAATATGGCCTC 59.053 55.000 3.32 0.00 0.00 4.70
752 1154 3.696548 CAGCTATTTCCTCTGAAAACCCC 59.303 47.826 0.00 0.00 43.37 4.95
753 1155 3.024547 GCTATTTCCTCTGAAAACCCCC 58.975 50.000 0.00 0.00 43.37 5.40
777 1179 6.006449 CCCATAAAATCATCGAATTCCTCCT 58.994 40.000 0.00 0.00 0.00 3.69
867 1269 2.223249 CCACTGTGTTGGAACGAAACAG 60.223 50.000 7.08 5.47 43.07 3.16
1162 1568 1.846712 GCTGCTCTTCCCCTTCCTGT 61.847 60.000 0.00 0.00 0.00 4.00
1175 1581 1.111116 TTCCTGTCCGTGTCCTTCGT 61.111 55.000 0.00 0.00 0.00 3.85
1176 1582 1.080705 CCTGTCCGTGTCCTTCGTC 60.081 63.158 0.00 0.00 0.00 4.20
1177 1583 1.080705 CTGTCCGTGTCCTTCGTCC 60.081 63.158 0.00 0.00 0.00 4.79
1178 1584 2.260743 GTCCGTGTCCTTCGTCCC 59.739 66.667 0.00 0.00 0.00 4.46
1179 1585 2.993264 TCCGTGTCCTTCGTCCCC 60.993 66.667 0.00 0.00 0.00 4.81
1247 1653 1.943116 TTGCTCTCGCCTCTCAGCTC 61.943 60.000 0.00 0.00 34.43 4.09
1305 1711 2.904866 GCAAGCCCACCAACGACA 60.905 61.111 0.00 0.00 0.00 4.35
1328 1734 2.402787 GAGGAGTACGACGCGGAC 59.597 66.667 12.47 6.51 41.59 4.79
1440 1846 3.379445 TCCCGAGACGTTGCCCTC 61.379 66.667 0.00 0.00 0.00 4.30
1514 1920 9.303116 TCTCTAGTTATTAGATCAATCTGTCCC 57.697 37.037 2.72 0.00 37.75 4.46
1831 2241 3.042733 TTGTGGATGGCCGCCCTAG 62.043 63.158 7.03 0.00 44.26 3.02
1878 2288 9.224267 AGATTGGATTGTATCATTTCGATTAGG 57.776 33.333 0.00 0.00 35.39 2.69
1910 2320 7.307811 GGTTCAATGTTTGACTACTCCAGTTAC 60.308 40.741 0.00 0.00 39.87 2.50
1946 2356 7.596995 GTGCCAAGTAGATCATCTCTATGTAAC 59.403 40.741 0.00 0.00 38.71 2.50
1947 2357 7.287696 TGCCAAGTAGATCATCTCTATGTAACA 59.712 37.037 0.00 0.00 38.71 2.41
1955 2365 5.907207 TCATCTCTATGTAACAGGAAGCAC 58.093 41.667 0.00 0.00 34.50 4.40
1985 2395 5.461327 AGTATTGGGAAGCAATGGATCAAT 58.539 37.500 0.00 0.00 0.00 2.57
1986 2396 5.901276 AGTATTGGGAAGCAATGGATCAATT 59.099 36.000 0.00 0.00 0.00 2.32
1987 2397 4.475051 TTGGGAAGCAATGGATCAATTG 57.525 40.909 17.26 17.26 39.98 2.32
1997 2409 6.558771 CAATGGATCAATTGCGGACTTATA 57.441 37.500 9.90 0.00 31.19 0.98
2006 2418 8.902540 TCAATTGCGGACTTATAGTTATTGAT 57.097 30.769 0.00 0.00 0.00 2.57
2075 2492 0.984230 CTGCCTAGGTTTGACTCCCA 59.016 55.000 11.31 0.00 0.00 4.37
2076 2493 1.351017 CTGCCTAGGTTTGACTCCCAA 59.649 52.381 11.31 0.00 0.00 4.12
2094 2511 4.224594 TCCCAATGGATGCAAAATTTAGCA 59.775 37.500 0.00 5.58 45.92 3.49
2095 2512 4.573201 CCCAATGGATGCAAAATTTAGCAG 59.427 41.667 0.00 0.00 44.94 4.24
2098 2515 2.984879 GATGCAAAATTTAGCAGCGC 57.015 45.000 0.00 0.00 44.94 5.92
2150 2567 7.173722 CAGGGCCTCTCATTCTCATTAATAAT 58.826 38.462 0.95 0.00 0.00 1.28
2151 2568 8.324306 CAGGGCCTCTCATTCTCATTAATAATA 58.676 37.037 0.95 0.00 0.00 0.98
2154 2571 8.672815 GGCCTCTCATTCTCATTAATAATAAGC 58.327 37.037 0.00 0.00 0.00 3.09
2194 2611 0.036732 ATGCAGGAAGAAGCGGAACA 59.963 50.000 0.00 0.00 0.00 3.18
2220 2637 2.555199 ACAGCAATGATCGAGTAAGCC 58.445 47.619 0.00 0.00 0.00 4.35
2237 2654 0.108756 GCCGTGAAGTAGTGGAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
2243 2660 5.103000 CGTGAAGTAGTGGAGGACATAAAG 58.897 45.833 0.00 0.00 0.00 1.85
2254 2671 3.978610 AGGACATAAAGTACTCCTCCGT 58.021 45.455 0.00 0.00 36.33 4.69
2257 2674 3.029570 ACATAAAGTACTCCTCCGTCCC 58.970 50.000 0.00 0.00 0.00 4.46
2259 2676 2.249309 AAAGTACTCCTCCGTCCCAT 57.751 50.000 0.00 0.00 0.00 4.00
2261 2678 3.393426 AAGTACTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
2262 2679 3.614568 AGTACTCCTCCGTCCCATAAT 57.385 47.619 0.00 0.00 0.00 1.28
2263 2680 4.736611 AGTACTCCTCCGTCCCATAATA 57.263 45.455 0.00 0.00 0.00 0.98
2264 2681 5.272405 AGTACTCCTCCGTCCCATAATAT 57.728 43.478 0.00 0.00 0.00 1.28
2265 2682 6.398655 AGTACTCCTCCGTCCCATAATATA 57.601 41.667 0.00 0.00 0.00 0.86
2266 2683 6.797707 AGTACTCCTCCGTCCCATAATATAA 58.202 40.000 0.00 0.00 0.00 0.98
2267 2684 6.890814 AGTACTCCTCCGTCCCATAATATAAG 59.109 42.308 0.00 0.00 0.00 1.73
2268 2685 5.900437 ACTCCTCCGTCCCATAATATAAGA 58.100 41.667 0.00 0.00 0.00 2.10
2269 2686 5.715753 ACTCCTCCGTCCCATAATATAAGAC 59.284 44.000 0.00 0.00 0.00 3.01
2312 2729 7.241376 AGCTTACAAAAACGTCTATATTGTGC 58.759 34.615 11.96 8.97 35.89 4.57
2313 2730 7.119262 AGCTTACAAAAACGTCTATATTGTGCT 59.881 33.333 11.96 10.43 35.89 4.40
2315 2732 5.390613 ACAAAAACGTCTATATTGTGCTGC 58.609 37.500 0.00 0.00 33.29 5.25
2316 2733 5.181245 ACAAAAACGTCTATATTGTGCTGCT 59.819 36.000 0.00 0.00 33.29 4.24
2318 2735 7.065803 ACAAAAACGTCTATATTGTGCTGCTAT 59.934 33.333 0.00 0.00 33.29 2.97
2371 2812 1.159285 CATGGCTACATACATGGGCG 58.841 55.000 0.00 0.00 40.50 6.13
2384 2825 2.047655 GGGCGTCACCGTTGATGA 60.048 61.111 6.33 0.00 40.78 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.034675 GTGCTCACACAACAAAAATGCG 60.035 45.455 0.00 0.00 46.61 4.73
26 27 2.358003 ACGGCAGCTTCAGTGCTC 60.358 61.111 0.00 0.00 41.98 4.26
58 59 2.702261 TGTGTTGCCGGTTATCCTTAC 58.298 47.619 1.90 0.00 0.00 2.34
59 60 3.275143 CATGTGTTGCCGGTTATCCTTA 58.725 45.455 1.90 0.00 0.00 2.69
82 83 4.460731 TCCGTTATTTCAACATGGCATTCA 59.539 37.500 0.00 0.00 0.00 2.57
163 166 2.224079 GTGCATTGCAACGAGAGAGAAA 59.776 45.455 13.94 0.00 41.47 2.52
279 283 2.102252 GGTCCTTTGTGCAAAATGTCCA 59.898 45.455 0.00 0.00 0.00 4.02
301 305 8.695456 GGATGGATGTAATATTTTGTTCTTGGT 58.305 33.333 0.00 0.00 0.00 3.67
333 338 0.107459 GTGATCTGTTCAGGGGGCTC 60.107 60.000 0.00 0.00 34.17 4.70
383 388 0.321741 TCTTCTCTGTCGGCGTCTCT 60.322 55.000 6.85 0.00 0.00 3.10
457 462 1.517242 GAGCACAAGAGGTCCACAAG 58.483 55.000 0.00 0.00 0.00 3.16
483 488 2.746277 ATGGGCCTCGTCGTTTGC 60.746 61.111 4.53 0.00 0.00 3.68
606 626 0.762418 ACGATGGTGGTTTCCAGACA 59.238 50.000 0.00 0.00 41.05 3.41
629 649 2.782222 GGCGGCGTCCTCTATGACA 61.782 63.158 9.37 0.00 34.88 3.58
634 654 4.435970 TCTGGGCGGCGTCCTCTA 62.436 66.667 32.34 14.03 0.00 2.43
692 712 0.947244 GAGGCCATATTGCTGTTCGG 59.053 55.000 5.01 0.00 0.00 4.30
699 719 2.557920 ACTAGCAGAGGCCATATTGC 57.442 50.000 5.01 9.17 42.56 3.56
705 725 5.280164 CCATATTGATAACTAGCAGAGGCCA 60.280 44.000 5.01 0.00 42.56 5.36
752 1154 5.183904 GGAGGAATTCGATGATTTTATGGGG 59.816 44.000 0.00 0.00 0.00 4.96
753 1155 6.006449 AGGAGGAATTCGATGATTTTATGGG 58.994 40.000 0.00 0.00 0.00 4.00
777 1179 4.435970 CCAGCCCCAGCATGCAGA 62.436 66.667 21.98 0.00 43.56 4.26
1162 1568 2.993264 GGGGACGAAGGACACGGA 60.993 66.667 0.00 0.00 34.93 4.69
1305 1711 0.739561 GCGTCGTACTCCTCCTTGAT 59.260 55.000 0.00 0.00 0.00 2.57
1328 1734 3.036783 GACGTCGTCCTCCTCCACG 62.037 68.421 14.60 0.00 37.36 4.94
1440 1846 1.920574 CGTACAGATTGGTTCGCAGAG 59.079 52.381 0.00 0.00 38.43 3.35
1514 1920 8.648557 TGTAGCAAAGTAAAGTATGATAGCTG 57.351 34.615 0.00 0.00 0.00 4.24
1831 2241 7.707624 ATCTCTGTCTCTGATATTCCATCTC 57.292 40.000 0.00 0.00 0.00 2.75
1878 2288 6.415573 AGTAGTCAAACATTGAACCCTATCC 58.584 40.000 0.00 0.00 42.15 2.59
1910 2320 1.468520 CTACTTGGCACCCATGTTTCG 59.531 52.381 7.90 0.00 41.24 3.46
1946 2356 4.396166 CCAATACTTGGTAAGTGCTTCCTG 59.604 45.833 4.56 0.00 45.93 3.86
1947 2357 4.589908 CCAATACTTGGTAAGTGCTTCCT 58.410 43.478 4.56 0.00 45.93 3.36
1985 2395 6.929049 CCTCATCAATAACTATAAGTCCGCAA 59.071 38.462 0.00 0.00 0.00 4.85
1986 2396 6.266786 TCCTCATCAATAACTATAAGTCCGCA 59.733 38.462 0.00 0.00 0.00 5.69
1987 2397 6.586844 GTCCTCATCAATAACTATAAGTCCGC 59.413 42.308 0.00 0.00 0.00 5.54
1988 2398 7.091443 GGTCCTCATCAATAACTATAAGTCCG 58.909 42.308 0.00 0.00 0.00 4.79
1997 2409 4.762289 GACCTGGTCCTCATCAATAACT 57.238 45.455 16.14 0.00 0.00 2.24
2075 2492 3.866910 CGCTGCTAAATTTTGCATCCATT 59.133 39.130 24.07 0.00 38.19 3.16
2076 2493 3.450578 CGCTGCTAAATTTTGCATCCAT 58.549 40.909 24.07 0.00 38.19 3.41
2094 2511 2.228822 CCACTGAAATTTAACCAGCGCT 59.771 45.455 2.64 2.64 0.00 5.92
2095 2512 2.227865 TCCACTGAAATTTAACCAGCGC 59.772 45.455 0.00 0.00 0.00 5.92
2098 2515 4.520492 AGCAGTCCACTGAAATTTAACCAG 59.480 41.667 11.04 4.31 46.59 4.00
2150 2567 3.557898 GCTGCTCCTGCTATAATGGCTTA 60.558 47.826 0.00 0.00 40.48 3.09
2151 2568 2.813354 GCTGCTCCTGCTATAATGGCTT 60.813 50.000 0.00 0.00 40.48 4.35
2154 2571 2.149578 GTGCTGCTCCTGCTATAATGG 58.850 52.381 0.00 0.00 40.48 3.16
2194 2611 3.141398 ACTCGATCATTGCTGTTGTGTT 58.859 40.909 0.00 0.00 0.00 3.32
2220 2637 4.713824 TTATGTCCTCCACTACTTCACG 57.286 45.455 0.00 0.00 0.00 4.35
2237 2654 3.028850 TGGGACGGAGGAGTACTTTATG 58.971 50.000 0.00 0.00 0.00 1.90
2243 2660 6.888632 TCTTATATTATGGGACGGAGGAGTAC 59.111 42.308 0.00 0.00 0.00 2.73
2253 2670 7.254227 TGCAAAACGTCTTATATTATGGGAC 57.746 36.000 0.00 0.00 0.00 4.46
2254 2671 7.468084 GCTTGCAAAACGTCTTATATTATGGGA 60.468 37.037 0.00 0.00 0.00 4.37
2257 2674 9.929722 TTAGCTTGCAAAACGTCTTATATTATG 57.070 29.630 0.00 0.00 0.00 1.90
2259 2676 8.937884 TGTTAGCTTGCAAAACGTCTTATATTA 58.062 29.630 0.00 0.00 0.00 0.98
2261 2678 7.372451 TGTTAGCTTGCAAAACGTCTTATAT 57.628 32.000 0.00 0.00 0.00 0.86
2262 2679 6.788684 TGTTAGCTTGCAAAACGTCTTATA 57.211 33.333 0.00 0.00 0.00 0.98
2263 2680 5.682943 TGTTAGCTTGCAAAACGTCTTAT 57.317 34.783 0.00 0.00 0.00 1.73
2264 2681 5.682943 ATGTTAGCTTGCAAAACGTCTTA 57.317 34.783 0.00 0.00 0.00 2.10
2265 2682 4.568152 ATGTTAGCTTGCAAAACGTCTT 57.432 36.364 0.00 0.00 0.00 3.01
2266 2683 5.283060 CTATGTTAGCTTGCAAAACGTCT 57.717 39.130 9.84 1.49 0.00 4.18
2304 2721 7.307989 CGCCTAAAACTTATAGCAGCACAATAT 60.308 37.037 0.00 0.00 0.00 1.28
2305 2722 6.018262 CGCCTAAAACTTATAGCAGCACAATA 60.018 38.462 0.00 0.00 0.00 1.90
2306 2723 5.220854 CGCCTAAAACTTATAGCAGCACAAT 60.221 40.000 0.00 0.00 0.00 2.71
2307 2724 4.094294 CGCCTAAAACTTATAGCAGCACAA 59.906 41.667 0.00 0.00 0.00 3.33
2309 2726 3.621715 ACGCCTAAAACTTATAGCAGCAC 59.378 43.478 0.00 0.00 0.00 4.40
2310 2727 3.869065 ACGCCTAAAACTTATAGCAGCA 58.131 40.909 0.00 0.00 0.00 4.41
2311 2728 3.060473 CGACGCCTAAAACTTATAGCAGC 60.060 47.826 0.00 0.00 0.00 5.25
2312 2729 4.110482 ACGACGCCTAAAACTTATAGCAG 58.890 43.478 0.00 0.00 0.00 4.24
2313 2730 4.114058 ACGACGCCTAAAACTTATAGCA 57.886 40.909 0.00 0.00 0.00 3.49
2315 2732 6.581542 CCTGATACGACGCCTAAAACTTATAG 59.418 42.308 0.00 0.00 0.00 1.31
2316 2733 6.039717 ACCTGATACGACGCCTAAAACTTATA 59.960 38.462 0.00 0.00 0.00 0.98
2318 2735 4.158394 ACCTGATACGACGCCTAAAACTTA 59.842 41.667 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.