Multiple sequence alignment - TraesCS6D01G242700

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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 TraesCS6D01G242700 chr6D 100.000 2458 0 0 1 2458 344703747 344701290 0.000000e+00 4540
1 TraesCS6D01G242700 chr6A 93.844 1397 55 17 642 2024 485157982 485156603 0.000000e+00 2074
2 TraesCS6D01G242700 chr6A 91.852 540 40 4 1 538 485160506 485159969 0.000000e+00 750
3 TraesCS6D01G242700 chr6A 94.400 375 18 2 2087 2458 485156601 485156227 7.620000e-160 573
4 TraesCS6D01G242700 chr6B 90.273 1501 82 30 553 2009 520547207 520545727 0.000000e+00 1905
5 TraesCS6D01G242700 chr6B 87.281 228 22 5 335 560 520547605 520547383 1.130000e-63 254
6 TraesCS6D01G242700 chr6B 89.565 115 11 1 129 242 520548063 520547949 7.080000e-31 145
7 TraesCS6D01G242700 chr6B 92.857 98 7 0 244 341 520547768 520547671 2.550000e-30 143


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 TraesCS6D01G242700 chr6D 344701290 344703747 2457 True 4540.000000 4540 100.000000 1 2458 1 chr6D.!!$R1 2457
1 TraesCS6D01G242700 chr6A 485156227 485160506 4279 True 1132.333333 2074 93.365333 1 2458 3 chr6A.!!$R1 2457
2 TraesCS6D01G242700 chr6B 520545727 520548063 2336 True 611.750000 1905 89.994000 129 2009 4 chr6B.!!$R1 1880

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
893 3085 0.112218 TGCCATGCGCCCCTTTATAT 59.888 50.0 4.18 0.0 36.24 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 4579 0.107165 GCCCCGGTCTTGCTTCTAAT 60.107 55.0 0.0 0.0 0.0 1.73 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
49 50 4.610605 TCACTCAATTCCTCGGTAACAA 57.389 40.909 0.00 0.00 0.00 2.83
54 55 5.174037 TCAATTCCTCGGTAACAAGGATT 57.826 39.130 0.00 0.00 0.00 3.01
67 68 3.343617 ACAAGGATTCCACATTGTACCG 58.656 45.455 5.29 0.00 41.72 4.02
70 71 2.092429 AGGATTCCACATTGTACCGCAT 60.092 45.455 5.29 0.00 0.00 4.73
72 73 1.364721 TTCCACATTGTACCGCATCG 58.635 50.000 0.00 0.00 0.00 3.84
91 92 0.965866 GTGCTAAAGGCTTGGGTCCC 60.966 60.000 0.00 0.00 42.39 4.46
93 94 1.749258 CTAAAGGCTTGGGTCCCGC 60.749 63.158 0.00 0.73 0.00 6.13
95 96 2.478335 TAAAGGCTTGGGTCCCGCTG 62.478 60.000 0.00 0.00 0.00 5.18
122 123 2.592102 TTTTGCTTGGCTCCTCATCT 57.408 45.000 0.00 0.00 0.00 2.90
123 124 3.719268 TTTTGCTTGGCTCCTCATCTA 57.281 42.857 0.00 0.00 0.00 1.98
244 245 2.222678 GCCATAACTCGATGCACATCTG 59.777 50.000 8.87 4.47 35.72 2.90
256 436 2.718062 TGCACATCTGGGGAATATGGAT 59.282 45.455 0.00 0.00 0.00 3.41
266 446 2.884639 GGGAATATGGATGAACGGGTTG 59.115 50.000 0.00 0.00 0.00 3.77
304 484 1.148273 TGTGAGGAACCCACACTGC 59.852 57.895 13.19 0.00 39.33 4.40
305 485 1.600916 GTGAGGAACCCACACTGCC 60.601 63.158 6.36 0.00 40.91 4.85
365 617 6.543831 GTGAGCCATTAGTGATCTATTTGGTT 59.456 38.462 0.00 0.00 34.76 3.67
366 618 6.543465 TGAGCCATTAGTGATCTATTTGGTTG 59.457 38.462 0.00 0.00 34.76 3.77
367 619 5.300286 AGCCATTAGTGATCTATTTGGTTGC 59.700 40.000 0.00 0.00 34.76 4.17
402 654 6.009589 TCTTGGTAGATTTTGGAATGAAGCA 58.990 36.000 0.00 0.00 0.00 3.91
461 713 3.194755 GGGTGCCGTTGGAGAAAATTAAT 59.805 43.478 0.00 0.00 0.00 1.40
499 753 9.627395 TCTTTGAACGTTAAAAGAAATCAAACA 57.373 25.926 30.35 11.12 38.98 2.83
506 760 8.113675 ACGTTAAAAGAAATCAAACAACAATGC 58.886 29.630 0.00 0.00 0.00 3.56
567 1004 9.722056 CTATTCACATATGTTTAAGAAAGGCAC 57.278 33.333 5.37 0.00 0.00 5.01
570 1007 6.488344 TCACATATGTTTAAGAAAGGCACACA 59.512 34.615 5.37 0.00 0.00 3.72
580 1017 5.633830 AGAAAGGCACACATAGAATGTTG 57.366 39.130 0.00 0.00 42.70 3.33
671 2841 9.545105 TTTCATGCTTTTATGTTTTTCATCAGT 57.455 25.926 0.00 0.00 37.91 3.41
672 2842 9.545105 TTCATGCTTTTATGTTTTTCATCAGTT 57.455 25.926 0.00 0.00 37.91 3.16
673 2843 9.545105 TCATGCTTTTATGTTTTTCATCAGTTT 57.455 25.926 0.00 0.00 37.91 2.66
717 2887 4.559906 GCATGTGCATGGCATGTAATGTAT 60.560 41.667 26.94 13.04 43.53 2.29
729 2899 4.415881 TGTAATGTATTGTCTCCGCCAT 57.584 40.909 0.00 0.00 0.00 4.40
733 2903 1.691976 TGTATTGTCTCCGCCATAGGG 59.308 52.381 0.00 0.00 37.18 3.53
803 2995 0.391661 ACTCCAACTATGCAGCCGTG 60.392 55.000 0.00 0.00 0.00 4.94
893 3085 0.112218 TGCCATGCGCCCCTTTATAT 59.888 50.000 4.18 0.00 36.24 0.86
937 3133 1.229658 CCACCACCTCCTCCTTCCT 60.230 63.158 0.00 0.00 0.00 3.36
938 3134 1.268283 CCACCACCTCCTCCTTCCTC 61.268 65.000 0.00 0.00 0.00 3.71
939 3135 1.081277 ACCACCTCCTCCTTCCTCC 59.919 63.158 0.00 0.00 0.00 4.30
940 3136 1.690985 CCACCTCCTCCTTCCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
941 3137 1.081092 CACCTCCTCCTTCCTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
942 3138 0.547712 CACCTCCTCCTTCCTCCCAA 60.548 60.000 0.00 0.00 0.00 4.12
943 3139 0.252927 ACCTCCTCCTTCCTCCCAAG 60.253 60.000 0.00 0.00 0.00 3.61
951 3147 0.321653 CTTCCTCCCAAGTCCCAACG 60.322 60.000 0.00 0.00 0.00 4.10
955 3151 0.396811 CTCCCAAGTCCCAACGAACT 59.603 55.000 0.00 0.00 0.00 3.01
980 3176 0.331954 ACAAGGAGGGAGCTAGACGA 59.668 55.000 0.00 0.00 0.00 4.20
1247 3444 0.175760 ACATCTTACGCCGTCATGCT 59.824 50.000 0.00 0.00 0.00 3.79
1276 3474 1.246056 ACTGTGATGGTGGCATGTGC 61.246 55.000 0.00 0.00 41.14 4.57
1374 3572 3.418744 GAGGCGGCGGAGAAGAGAC 62.419 68.421 9.78 0.00 0.00 3.36
1514 3714 0.387878 GCTCGATGCTACTCCATCCG 60.388 60.000 0.00 0.00 38.68 4.18
1555 3755 1.870901 GTATGCGGACCGACGTGAC 60.871 63.158 20.50 3.55 35.98 3.67
1622 3822 4.522022 AGTTCTTGGAGGCAAAAGAAGATG 59.478 41.667 8.84 0.00 41.72 2.90
1691 3892 0.107897 TGTGTGCGATCCCCATGTAC 60.108 55.000 0.00 0.00 0.00 2.90
1731 3932 4.442706 GAAGAAATAAGATCACCGAGGCA 58.557 43.478 0.00 0.00 0.00 4.75
1732 3933 4.487714 AGAAATAAGATCACCGAGGCAA 57.512 40.909 0.00 0.00 0.00 4.52
1760 3961 2.258591 CGACTGTGTCCGGTCTGG 59.741 66.667 0.00 0.00 43.59 3.86
1766 3967 1.597027 GTGTCCGGTCTGGTGTTGG 60.597 63.158 0.00 0.00 39.52 3.77
1776 3978 5.163385 CCGGTCTGGTGTTGGAATACTATTA 60.163 44.000 0.00 0.00 0.00 0.98
1815 4018 1.065926 AGTCCGTGTCACATGCATGAT 60.066 47.619 32.75 14.29 0.00 2.45
1858 4063 2.101082 TGCAACGAGTAACTGTACCACA 59.899 45.455 0.00 0.00 0.00 4.17
1859 4064 2.473984 GCAACGAGTAACTGTACCACAC 59.526 50.000 0.00 0.00 0.00 3.82
1860 4065 3.054878 CAACGAGTAACTGTACCACACC 58.945 50.000 0.00 0.00 0.00 4.16
1862 4067 2.694628 ACGAGTAACTGTACCACACCAA 59.305 45.455 0.00 0.00 0.00 3.67
1863 4068 3.243636 ACGAGTAACTGTACCACACCAAG 60.244 47.826 0.00 0.00 0.00 3.61
1865 4070 4.700700 GAGTAACTGTACCACACCAAGTT 58.299 43.478 0.00 0.00 0.00 2.66
1927 4132 2.455674 TCCAGACTGGATTTCGTGTG 57.544 50.000 20.74 0.00 42.67 3.82
2024 4230 9.563898 CCGTATTATTCGCATTATTCTACACTA 57.436 33.333 0.00 0.00 0.00 2.74
2241 4450 9.546909 CAAAAGAATACATACATGTCACTTCAC 57.453 33.333 0.00 0.00 41.97 3.18
2242 4451 8.846943 AAAGAATACATACATGTCACTTCACA 57.153 30.769 0.00 0.00 41.97 3.58
2243 4452 9.453572 AAAGAATACATACATGTCACTTCACAT 57.546 29.630 0.00 0.00 41.97 3.21
2269 4478 7.012894 TGTTCCACGAGTTCAATTGAAAATACT 59.987 33.333 22.07 15.50 35.58 2.12
2282 4491 9.655769 CAATTGAAAATACTTCGTATCAGGATG 57.344 33.333 0.00 0.00 37.54 3.51
2284 4493 6.582636 TGAAAATACTTCGTATCAGGATGCT 58.417 36.000 0.00 0.00 34.76 3.79
2325 4534 7.062605 GCACATAATTTCTCAACAACAATCCAG 59.937 37.037 0.00 0.00 0.00 3.86
2331 4540 2.620115 CTCAACAACAATCCAGCACTGT 59.380 45.455 0.00 0.00 0.00 3.55
2370 4579 1.003118 CCTTTGATTGGACTGGACGGA 59.997 52.381 0.00 0.00 0.00 4.69
2405 4614 1.665442 GGCAAAGCCCGTGTGATTT 59.335 52.632 0.00 0.00 44.06 2.17
2428 4637 2.756400 GAGGGCACACCACCATCA 59.244 61.111 0.00 0.00 43.89 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.280710 TGCGGTACAATGTGGAATCCT 59.719 47.619 0.00 0.00 0.00 3.24
54 55 0.248012 ACGATGCGGTACAATGTGGA 59.752 50.000 0.00 0.00 0.00 4.02
91 92 3.121778 GCCAAGCAAAATTACTTTCAGCG 59.878 43.478 0.00 0.00 33.17 5.18
93 94 4.925646 GGAGCCAAGCAAAATTACTTTCAG 59.074 41.667 0.00 0.00 0.00 3.02
95 96 5.139435 AGGAGCCAAGCAAAATTACTTTC 57.861 39.130 0.00 0.00 0.00 2.62
122 123 9.043548 GCTATCAACCTTTATACCCCTCTTATA 57.956 37.037 0.00 0.00 0.00 0.98
123 124 7.037514 GGCTATCAACCTTTATACCCCTCTTAT 60.038 40.741 0.00 0.00 0.00 1.73
137 138 1.282157 GACACCTGGGCTATCAACCTT 59.718 52.381 0.00 0.00 0.00 3.50
138 139 0.912486 GACACCTGGGCTATCAACCT 59.088 55.000 0.00 0.00 0.00 3.50
244 245 1.423921 ACCCGTTCATCCATATTCCCC 59.576 52.381 0.00 0.00 0.00 4.81
256 436 1.149627 CAAGACCCCAACCCGTTCA 59.850 57.895 0.00 0.00 0.00 3.18
266 446 1.652947 TGGTAGGAGTTCAAGACCCC 58.347 55.000 0.00 0.00 0.00 4.95
304 484 3.670627 GCTAACTGCCAATTTTCTCACGG 60.671 47.826 0.00 0.00 35.15 4.94
305 485 3.492313 GCTAACTGCCAATTTTCTCACG 58.508 45.455 0.00 0.00 35.15 4.35
345 597 5.593909 TGGCAACCAAATAGATCACTAATGG 59.406 40.000 0.00 0.00 41.39 3.16
365 617 2.584835 ACCAAGAAACTAGCATGGCA 57.415 45.000 0.00 0.00 34.45 4.92
366 618 3.873910 TCTACCAAGAAACTAGCATGGC 58.126 45.455 0.00 0.00 34.45 4.40
367 619 7.253422 CAAAATCTACCAAGAAACTAGCATGG 58.747 38.462 0.00 0.00 34.73 3.66
445 697 8.223769 CCATCTCGATATTAATTTTCTCCAACG 58.776 37.037 0.00 0.00 0.00 4.10
461 713 5.068234 ACGTTCAAAGAACCATCTCGATA 57.932 39.130 4.47 0.00 33.77 2.92
499 753 1.006813 TGGAGTATGGGGGCATTGTT 58.993 50.000 0.00 0.00 0.00 2.83
631 1078 8.659925 AAAAGCATGAAATCATTTGTAACACA 57.340 26.923 0.00 0.00 33.61 3.72
674 2844 9.571810 CACATGCACATAATTTAGTGTGTTTAT 57.428 29.630 15.32 8.39 45.66 1.40
729 2899 0.752743 ATGCACGTACGCCTACCCTA 60.753 55.000 16.72 0.00 0.00 3.53
733 2903 1.334779 CCTAGATGCACGTACGCCTAC 60.335 57.143 16.72 2.69 0.00 3.18
779 2971 3.610911 GGCTGCATAGTTGGAGTAGTTT 58.389 45.455 0.50 0.00 42.83 2.66
803 2995 1.156645 GCGTGATCCTGACATCCTGC 61.157 60.000 0.00 0.00 0.00 4.85
937 3133 0.395312 GAGTTCGTTGGGACTTGGGA 59.605 55.000 0.00 0.00 0.00 4.37
938 3134 0.107831 TGAGTTCGTTGGGACTTGGG 59.892 55.000 0.00 0.00 0.00 4.12
939 3135 1.512926 CTGAGTTCGTTGGGACTTGG 58.487 55.000 0.00 0.00 0.00 3.61
940 3136 0.868406 GCTGAGTTCGTTGGGACTTG 59.132 55.000 0.00 0.00 0.00 3.16
941 3137 0.468226 TGCTGAGTTCGTTGGGACTT 59.532 50.000 0.00 0.00 0.00 3.01
942 3138 0.468226 TTGCTGAGTTCGTTGGGACT 59.532 50.000 0.00 0.00 0.00 3.85
943 3139 0.586802 GTTGCTGAGTTCGTTGGGAC 59.413 55.000 0.00 0.00 0.00 4.46
951 3147 1.072331 TCCCTCCTTGTTGCTGAGTTC 59.928 52.381 0.00 0.00 0.00 3.01
955 3151 1.130054 AGCTCCCTCCTTGTTGCTGA 61.130 55.000 0.00 0.00 0.00 4.26
980 3176 1.990160 TTCCTGGCTCGGTTGGTGTT 61.990 55.000 0.00 0.00 0.00 3.32
1247 3444 1.774254 ACCATCACAGTCAAACCCAGA 59.226 47.619 0.00 0.00 0.00 3.86
1276 3474 2.053627 GCCAGCAAAGAATCACGTTTG 58.946 47.619 0.00 0.00 36.84 2.93
1443 3641 0.687757 TGCTTCTACCGAGCCCAGAT 60.688 55.000 0.00 0.00 39.38 2.90
1514 3714 7.865706 ACATCCACAATCCTGAAGTTTATAC 57.134 36.000 0.00 0.00 0.00 1.47
1555 3755 1.096386 GCTCCCTCAAGCTGCTCATG 61.096 60.000 1.00 0.00 39.27 3.07
1746 3947 0.880278 CAACACCAGACCGGACACAG 60.880 60.000 9.46 0.00 38.63 3.66
1815 4018 4.993705 AACCTGTCTCCCTGTAAATTCA 57.006 40.909 0.00 0.00 0.00 2.57
1858 4063 6.493189 AATGGTTGGATTTTGTAACTTGGT 57.507 33.333 0.00 0.00 0.00 3.67
1859 4064 9.150348 GAATAATGGTTGGATTTTGTAACTTGG 57.850 33.333 0.00 0.00 0.00 3.61
1860 4065 9.150348 GGAATAATGGTTGGATTTTGTAACTTG 57.850 33.333 0.00 0.00 0.00 3.16
1862 4067 7.678171 AGGGAATAATGGTTGGATTTTGTAACT 59.322 33.333 0.00 0.00 0.00 2.24
1863 4068 7.847096 AGGGAATAATGGTTGGATTTTGTAAC 58.153 34.615 0.00 0.00 0.00 2.50
1865 4070 7.418378 AGAGGGAATAATGGTTGGATTTTGTA 58.582 34.615 0.00 0.00 0.00 2.41
2085 4291 9.555727 GTGGGCATGAATAATACGGTTATATAT 57.444 33.333 0.00 0.00 0.00 0.86
2140 4346 5.526115 ACACTGCAATGATTCACAAGAAAG 58.474 37.500 0.26 0.00 37.29 2.62
2144 4350 6.129009 GCTTAAACACTGCAATGATTCACAAG 60.129 38.462 0.26 0.00 0.00 3.16
2148 4354 5.710513 AGCTTAAACACTGCAATGATTCA 57.289 34.783 0.26 0.00 0.00 2.57
2241 4450 5.518812 TTTCAATTGAACTCGTGGAACATG 58.481 37.500 20.35 0.00 39.25 3.21
2242 4451 5.766150 TTTCAATTGAACTCGTGGAACAT 57.234 34.783 20.35 0.00 35.20 2.71
2243 4452 5.568685 TTTTCAATTGAACTCGTGGAACA 57.431 34.783 20.35 0.00 31.98 3.18
2282 4491 2.189342 GTGCTATTCTCACTCGTCAGC 58.811 52.381 0.00 0.00 0.00 4.26
2284 4493 5.576447 TTATGTGCTATTCTCACTCGTCA 57.424 39.130 0.00 0.00 35.58 4.35
2314 4523 2.346766 TCACAGTGCTGGATTGTTGT 57.653 45.000 4.11 0.00 34.19 3.32
2325 4534 5.113502 ACTTTTCAGCTAAATCACAGTGC 57.886 39.130 0.00 0.00 0.00 4.40
2331 4540 7.001674 TCAAAGGGTACTTTTCAGCTAAATCA 58.998 34.615 0.00 0.00 44.26 2.57
2370 4579 0.107165 GCCCCGGTCTTGCTTCTAAT 60.107 55.000 0.00 0.00 0.00 1.73
2405 4614 2.524640 TGGTGTGCCCTCCGTACA 60.525 61.111 0.00 0.00 34.34 2.90


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

AutoCloner maintained by Alex Coulton.