Multiple sequence alignment - TraesCS6B01G266600

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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 TraesCS6B01G266600 chr6B 100.000 2784 0 0 1 2784 479298658 479301441 0.000000e+00 5142
1 TraesCS6B01G266600 chr6D 93.203 1736 55 32 662 2357 341117842 341116130 0.000000e+00 2494
2 TraesCS6B01G266600 chr6D 94.082 490 26 3 2297 2784 341116129 341115641 0.000000e+00 741
3 TraesCS6B01G266600 chr6A 88.790 1579 61 45 662 2185 481083478 481081961 0.000000e+00 1829
4 TraesCS6B01G266600 chr6A 96.067 661 24 2 1 660 561235973 561236632 0.000000e+00 1075
5 TraesCS6B01G266600 chr6A 95.185 540 24 2 122 660 40741963 40741425 0.000000e+00 852
6 TraesCS6B01G266600 chr6A 95.185 540 25 1 122 660 58609187 58609726 0.000000e+00 852
7 TraesCS6B01G266600 chr6A 86.622 299 36 4 2432 2729 481080805 481080510 7.430000e-86 327
8 TraesCS6B01G266600 chr2B 96.526 662 22 1 1 661 175424373 175423712 0.000000e+00 1094
9 TraesCS6B01G266600 chr2B 78.159 641 93 30 1057 1676 590918855 590919469 5.670000e-97 364
10 TraesCS6B01G266600 chr2A 96.391 665 22 2 1 664 3767361 3766698 0.000000e+00 1094
11 TraesCS6B01G266600 chr2A 77.556 401 60 21 1047 1441 648341584 648341960 6.040000e-52 215
12 TraesCS6B01G266600 chr4A 95.764 661 26 2 1 660 16992631 16993290 0.000000e+00 1064
13 TraesCS6B01G266600 chr5D 94.242 660 26 2 1 659 26676735 26677383 0.000000e+00 998
14 TraesCS6B01G266600 chr1B 98.649 518 5 2 143 659 373111590 373111074 0.000000e+00 917
15 TraesCS6B01G266600 chr7A 89.561 661 58 7 1 658 456263676 456263024 0.000000e+00 828
16 TraesCS6B01G266600 chr2D 78.582 649 91 31 1054 1676 502929837 502930463 4.350000e-103 385


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 TraesCS6B01G266600 chr6B 479298658 479301441 2783 False 5142.0 5142 100.0000 1 2784 1 chr6B.!!$F1 2783
1 TraesCS6B01G266600 chr6D 341115641 341117842 2201 True 1617.5 2494 93.6425 662 2784 2 chr6D.!!$R1 2122
2 TraesCS6B01G266600 chr6A 481080510 481083478 2968 True 1078.0 1829 87.7060 662 2729 2 chr6A.!!$R2 2067
3 TraesCS6B01G266600 chr6A 561235973 561236632 659 False 1075.0 1075 96.0670 1 660 1 chr6A.!!$F2 659
4 TraesCS6B01G266600 chr6A 40741425 40741963 538 True 852.0 852 95.1850 122 660 1 chr6A.!!$R1 538
5 TraesCS6B01G266600 chr6A 58609187 58609726 539 False 852.0 852 95.1850 122 660 1 chr6A.!!$F1 538
6 TraesCS6B01G266600 chr2B 175423712 175424373 661 True 1094.0 1094 96.5260 1 661 1 chr2B.!!$R1 660
7 TraesCS6B01G266600 chr2B 590918855 590919469 614 False 364.0 364 78.1590 1057 1676 1 chr2B.!!$F1 619
8 TraesCS6B01G266600 chr2A 3766698 3767361 663 True 1094.0 1094 96.3910 1 664 1 chr2A.!!$R1 663
9 TraesCS6B01G266600 chr4A 16992631 16993290 659 False 1064.0 1064 95.7640 1 660 1 chr4A.!!$F1 659
10 TraesCS6B01G266600 chr5D 26676735 26677383 648 False 998.0 998 94.2420 1 659 1 chr5D.!!$F1 658
11 TraesCS6B01G266600 chr1B 373111074 373111590 516 True 917.0 917 98.6490 143 659 1 chr1B.!!$R1 516
12 TraesCS6B01G266600 chr7A 456263024 456263676 652 True 828.0 828 89.5610 1 658 1 chr7A.!!$R1 657
13 TraesCS6B01G266600 chr2D 502929837 502930463 626 False 385.0 385 78.5820 1054 1676 1 chr2D.!!$F1 622

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
622 626 1.076265 GGGCCCCTTATTGGTGTCC 60.076 63.158 12.23 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2392 0.604578 CTTTGTTCATGGGGGCACAG 59.395 55.0 0.0 0.0 0.0 3.66 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
48 49 5.132502 TGAGGTCAACAATGTCACAAGAAT 58.867 37.500 0.00 0.00 0.00 2.40
622 626 1.076265 GGGCCCCTTATTGGTGTCC 60.076 63.158 12.23 0.00 0.00 4.02
678 682 2.747855 CCCACTGCGAAAGAGGCC 60.748 66.667 0.00 0.00 35.41 5.19
713 719 1.458064 GCACGAAAGCAAAGCTACGTA 59.542 47.619 18.14 0.00 44.45 3.57
714 720 2.472397 GCACGAAAGCAAAGCTACGTAG 60.472 50.000 18.47 18.47 44.45 3.51
821 833 3.148084 CAGACCCACGTCCCAACT 58.852 61.111 0.00 0.00 40.12 3.16
915 946 2.930019 CCCCTGACTGGCTGACCA 60.930 66.667 0.00 0.00 46.51 4.02
938 970 5.248477 CAGCCTTTATATAAGAGCCCCACTA 59.752 44.000 12.66 0.00 0.00 2.74
1039 1081 4.608774 TGGACGGACGGACCACCT 62.609 66.667 8.34 0.00 38.90 4.00
1042 1084 4.608774 ACGGACGGACCACCTCCA 62.609 66.667 0.00 0.00 39.39 3.86
1868 1965 2.094700 TCGAAGCAACTTGTCGAGCTAT 60.095 45.455 1.43 0.00 38.78 2.97
1869 1966 2.028523 CGAAGCAACTTGTCGAGCTATG 59.971 50.000 0.00 0.00 36.07 2.23
1870 1967 3.254060 GAAGCAACTTGTCGAGCTATGA 58.746 45.455 0.00 0.00 36.07 2.15
1871 1968 3.533606 AGCAACTTGTCGAGCTATGAT 57.466 42.857 0.00 0.00 35.19 2.45
1872 1969 3.866651 AGCAACTTGTCGAGCTATGATT 58.133 40.909 0.00 0.00 35.19 2.57
1958 2067 3.873883 GCCACGATCTGCTGCAGC 61.874 66.667 31.89 31.89 42.50 5.25
2098 2208 5.919755 TGAATACAATATGTAGCCCGTCAA 58.080 37.500 0.00 0.00 36.14 3.18
2212 2354 3.311106 GCCGATCATTCGTAAACGGATA 58.689 45.455 0.00 0.00 43.97 2.59
2253 2395 2.415843 CACCGTGTCCGTGTCTGT 59.584 61.111 0.00 0.00 0.00 3.41
2277 2419 3.008266 CCCCCATGAACAAAGCAAGAAAT 59.992 43.478 0.00 0.00 0.00 2.17
2307 2450 0.912486 GCCTCCTTTCCTTCCTGCTA 59.088 55.000 0.00 0.00 0.00 3.49
2430 3534 1.070758 GGGATGGAAATGAGCGAGCTA 59.929 52.381 0.00 0.00 0.00 3.32
2437 3541 7.334421 GGATGGAAATGAGCGAGCTAATTATTA 59.666 37.037 8.02 0.00 0.00 0.98
2448 3552 2.798283 GCTAATTATTAGTCGCGGTGCA 59.202 45.455 6.13 0.00 35.66 4.57
2468 3572 1.814169 GCTCCGAATGAACCGGGTC 60.814 63.158 14.24 14.24 46.47 4.46
2474 3578 0.459759 GAATGAACCGGGTCGAGGAC 60.460 60.000 16.31 0.46 0.00 3.85
2552 3657 0.466555 TGGGACGTTGAGGTTTTGGG 60.467 55.000 0.00 0.00 0.00 4.12
2565 3670 1.872952 GTTTTGGGCCAACATGCTTTC 59.127 47.619 20.79 0.00 0.00 2.62
2652 3757 5.107375 CCGCATGATTTTGTTTTCTGAAAGG 60.107 40.000 0.00 0.00 0.00 3.11
2731 3836 6.540438 AAACGAAGGATGGATGTACTTCTA 57.460 37.500 8.51 3.16 37.71 2.10
2740 3845 6.294065 GGATGGATGTACTTCTAACCTCTACG 60.294 46.154 12.19 0.00 0.00 3.51
2752 3857 1.655654 CTCTACGAGATGCACGCGG 60.656 63.158 12.47 0.00 45.40 6.46
2760 3865 1.029408 AGATGCACGCGGCCAAATTA 61.029 50.000 12.47 0.00 43.89 1.40
2770 3875 5.341993 CACGCGGCCAAATTATATTTACATG 59.658 40.000 12.47 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.461312 ACATAAAGTAGCAAGACCATTTAATCA 57.539 29.630 0.00 0.00 0.00 2.57
664 668 4.394712 CCCGGCCTCTTTCGCAGT 62.395 66.667 0.00 0.00 0.00 4.40
670 674 4.016706 CGTCCACCCGGCCTCTTT 62.017 66.667 0.00 0.00 0.00 2.52
694 700 2.984471 TCTACGTAGCTTTGCTTTCGTG 59.016 45.455 18.00 15.48 43.18 4.35
713 719 2.280389 CACACTGTGGCGTGCTCT 60.280 61.111 13.09 0.00 38.45 4.09
806 818 0.683412 AGTTAGTTGGGACGTGGGTC 59.317 55.000 0.00 0.00 42.66 4.46
821 833 3.520862 CTCGGGCGGCGGTAGTTA 61.521 66.667 16.08 0.00 0.00 2.24
915 946 4.243643 AGTGGGGCTCTTATATAAAGGCT 58.756 43.478 20.20 0.00 35.99 4.58
938 970 2.504032 CGGGTGACACACAGTGGT 59.496 61.111 8.88 0.00 37.94 4.16
1039 1081 1.078214 CGATCTTGGCTGGCTTGGA 60.078 57.895 2.00 0.00 0.00 3.53
1042 1084 1.448540 CGTCGATCTTGGCTGGCTT 60.449 57.895 2.00 0.00 0.00 4.35
1441 1510 4.980805 GACGTGGCGGCAGTTGGA 62.981 66.667 13.91 0.00 33.63 3.53
1848 1943 1.698165 TAGCTCGACAAGTTGCTTCG 58.302 50.000 1.81 6.16 37.02 3.79
1852 1947 4.093408 TCAAATCATAGCTCGACAAGTTGC 59.907 41.667 1.81 0.00 0.00 4.17
1853 1948 5.784750 TCAAATCATAGCTCGACAAGTTG 57.215 39.130 0.00 0.00 0.00 3.16
1868 1965 5.398169 GTGGCAAACACGATATTCAAATCA 58.602 37.500 0.00 0.00 40.85 2.57
1869 1966 5.932021 GTGGCAAACACGATATTCAAATC 57.068 39.130 0.00 0.00 40.85 2.17
1914 2018 2.423517 GCTAGAAAGGGGAAGGAATGGG 60.424 54.545 0.00 0.00 0.00 4.00
1953 2062 2.110352 CCGCATCTCATGTGCTGCA 61.110 57.895 19.90 0.00 40.37 4.41
1954 2063 2.713770 CCGCATCTCATGTGCTGC 59.286 61.111 12.38 12.38 40.37 5.25
1955 2064 2.713770 GCCGCATCTCATGTGCTG 59.286 61.111 5.38 0.18 40.37 4.41
1956 2065 2.893895 CGCCGCATCTCATGTGCT 60.894 61.111 5.38 0.00 40.37 4.40
1958 2067 1.227060 TCTCGCCGCATCTCATGTG 60.227 57.895 0.00 0.00 40.37 3.21
1959 2068 1.227089 GTCTCGCCGCATCTCATGT 60.227 57.895 0.00 0.00 0.00 3.21
1960 2069 1.953138 GGTCTCGCCGCATCTCATG 60.953 63.158 0.00 0.00 0.00 3.07
1961 2070 1.960040 TTGGTCTCGCCGCATCTCAT 61.960 55.000 0.00 0.00 41.21 2.90
1962 2071 2.563050 CTTGGTCTCGCCGCATCTCA 62.563 60.000 0.00 0.00 41.21 3.27
1963 2072 1.880340 CTTGGTCTCGCCGCATCTC 60.880 63.158 0.00 0.00 41.21 2.75
1964 2073 1.888436 TTCTTGGTCTCGCCGCATCT 61.888 55.000 0.00 0.00 41.21 2.90
2098 2208 2.105128 GAGACCTACGCTGCGCAT 59.895 61.111 23.51 6.13 0.00 4.73
2109 2219 4.157849 TGATCTATCACTGTCGAGACCT 57.842 45.455 0.34 0.00 0.00 3.85
2212 2354 3.923017 GCTTTAACAATGAGCCACTGT 57.077 42.857 0.00 0.00 0.00 3.55
2250 2392 0.604578 CTTTGTTCATGGGGGCACAG 59.395 55.000 0.00 0.00 0.00 3.66
2253 2395 0.762082 TTGCTTTGTTCATGGGGGCA 60.762 50.000 0.00 0.00 0.00 5.36
2277 2419 0.773644 AAAGGAGGCAGCTTCCAGAA 59.226 50.000 24.76 0.00 37.18 3.02
2307 2450 1.583054 GTCTCGTGGAAAAGCAGTGT 58.417 50.000 0.00 0.00 0.00 3.55
2334 2546 1.358152 TGGCCTTGGCTGTTACTAGT 58.642 50.000 11.71 0.00 0.00 2.57
2430 3534 2.032030 GCATGCACCGCGACTAATAATT 60.032 45.455 14.21 0.00 0.00 1.40
2468 3572 4.796231 CCCGTTCGCCAGTCCTCG 62.796 72.222 0.00 0.00 0.00 4.63
2474 3578 0.744874 TCTCTATTCCCGTTCGCCAG 59.255 55.000 0.00 0.00 0.00 4.85
2552 3657 0.725784 CACGTCGAAAGCATGTTGGC 60.726 55.000 0.00 0.00 0.00 4.52
2740 3845 2.270297 AATTTGGCCGCGTGCATCTC 62.270 55.000 18.87 4.71 43.89 2.75


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

AutoCloner maintained by Alex Coulton.