Multiple sequence alignment - TraesCS2A01G004000

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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 TraesCS2A01G004000 chr2A 100.000 3458 0 0 1 3458 2358136 2361593 0.000000e+00 6386
1 TraesCS2A01G004000 chr2A 96.047 2707 66 11 1 2701 712852660 712849989 0.000000e+00 4368
2 TraesCS2A01G004000 chr2A 95.499 711 31 1 2749 3458 712849382 712848672 0.000000e+00 1134
3 TraesCS2A01G004000 chr2A 88.119 303 7 1 2655 2957 712849939 712849666 1.990000e-87 333
4 TraesCS2A01G004000 chr2A 95.062 162 8 0 2699 2860 712849827 712849666 4.430000e-64 255
5 TraesCS2A01G004000 chr2A 93.377 151 10 0 2699 2849 2361028 2361178 1.250000e-54 224
6 TraesCS2A01G004000 chr7D 95.690 2854 90 13 1 2827 95098781 95095934 0.000000e+00 4558
7 TraesCS2A01G004000 chr7D 96.317 2281 60 11 1 2257 590590577 590588297 0.000000e+00 3725
8 TraesCS2A01G004000 chr7D 96.125 2168 59 10 1 2167 362369441 362371584 0.000000e+00 3515
9 TraesCS2A01G004000 chr7D 91.818 1100 62 12 1942 3014 590588573 590587475 0.000000e+00 1507
10 TraesCS2A01G004000 chr7D 96.011 752 30 0 2705 3456 362372405 362373156 0.000000e+00 1223
11 TraesCS2A01G004000 chr7D 95.822 718 29 1 2742 3458 95095596 95094879 0.000000e+00 1158
12 TraesCS2A01G004000 chr7D 94.955 674 30 3 2786 3458 550680797 550681467 0.000000e+00 1053
13 TraesCS2A01G004000 chr5A 95.861 2706 78 7 1 2699 273996533 273993855 0.000000e+00 4346
14 TraesCS2A01G004000 chr5A 96.049 2025 61 7 194 2212 35060153 35062164 0.000000e+00 3278
15 TraesCS2A01G004000 chr5A 94.764 764 37 3 2697 3458 273992993 273992231 0.000000e+00 1186
16 TraesCS2A01G004000 chr5A 95.483 642 28 1 2817 3457 35083659 35084300 0.000000e+00 1024
17 TraesCS2A01G004000 chr4A 97.242 2212 48 1 1 2212 84937705 84939903 0.000000e+00 3735
18 TraesCS2A01G004000 chr4A 92.194 948 37 15 1993 2904 84939633 84940579 0.000000e+00 1306
19 TraesCS2A01G004000 chr4A 94.964 695 34 1 2765 3458 84940957 84941651 0.000000e+00 1088
20 TraesCS2A01G004000 chr6D 96.667 2190 58 6 1 2181 102250210 102248027 0.000000e+00 3626
21 TraesCS2A01G004000 chr1A 95.182 2221 90 8 1 2212 582350790 582353002 0.000000e+00 3493
22 TraesCS2A01G004000 chr1A 95.735 633 24 3 1993 2624 582352738 582353368 0.000000e+00 1016
23 TraesCS2A01G004000 chr4D 95.620 2169 66 15 1 2167 122724503 122722362 0.000000e+00 3452
24 TraesCS2A01G004000 chr4D 92.633 1018 56 10 2044 3043 122722581 122721565 0.000000e+00 1447
25 TraesCS2A01G004000 chr4D 96.058 761 28 2 2697 3456 122721815 122721056 0.000000e+00 1238
26 TraesCS2A01G004000 chrUn 97.526 2021 40 3 5 2016 108019641 108021660 0.000000e+00 3446
27 TraesCS2A01G004000 chr3D 97.692 1993 34 3 1 1984 53790511 53792500 0.000000e+00 3415
28 TraesCS2A01G004000 chr3D 91.864 971 54 12 1993 2939 5497427 5498396 0.000000e+00 1332
29 TraesCS2A01G004000 chr3D 91.106 832 51 12 2031 2839 53811380 53812211 0.000000e+00 1105
30 TraesCS2A01G004000 chr1D 85.559 1468 133 50 2044 3458 66574276 66572835 0.000000e+00 1463
31 TraesCS2A01G004000 chr1D 92.426 911 46 12 2044 2936 386771502 386770597 0.000000e+00 1279


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 TraesCS2A01G004000 chr2A 2358136 2361593 3457 False 3305.000000 6386 96.688500 1 3458 2 chr2A.!!$F1 3457
1 TraesCS2A01G004000 chr2A 712848672 712852660 3988 True 1522.500000 4368 93.681750 1 3458 4 chr2A.!!$R1 3457
2 TraesCS2A01G004000 chr7D 95094879 95098781 3902 True 2858.000000 4558 95.756000 1 3458 2 chr7D.!!$R1 3457
3 TraesCS2A01G004000 chr7D 590587475 590590577 3102 True 2616.000000 3725 94.067500 1 3014 2 chr7D.!!$R2 3013
4 TraesCS2A01G004000 chr7D 362369441 362373156 3715 False 2369.000000 3515 96.068000 1 3456 2 chr7D.!!$F2 3455
5 TraesCS2A01G004000 chr7D 550680797 550681467 670 False 1053.000000 1053 94.955000 2786 3458 1 chr7D.!!$F1 672
6 TraesCS2A01G004000 chr5A 35060153 35062164 2011 False 3278.000000 3278 96.049000 194 2212 1 chr5A.!!$F1 2018
7 TraesCS2A01G004000 chr5A 273992231 273996533 4302 True 2766.000000 4346 95.312500 1 3458 2 chr5A.!!$R1 3457
8 TraesCS2A01G004000 chr5A 35083659 35084300 641 False 1024.000000 1024 95.483000 2817 3457 1 chr5A.!!$F2 640
9 TraesCS2A01G004000 chr4A 84937705 84941651 3946 False 2043.000000 3735 94.800000 1 3458 3 chr4A.!!$F1 3457
10 TraesCS2A01G004000 chr6D 102248027 102250210 2183 True 3626.000000 3626 96.667000 1 2181 1 chr6D.!!$R1 2180
11 TraesCS2A01G004000 chr1A 582350790 582353368 2578 False 2254.500000 3493 95.458500 1 2624 2 chr1A.!!$F1 2623
12 TraesCS2A01G004000 chr4D 122721056 122724503 3447 True 2045.666667 3452 94.770333 1 3456 3 chr4D.!!$R1 3455
13 TraesCS2A01G004000 chrUn 108019641 108021660 2019 False 3446.000000 3446 97.526000 5 2016 1 chrUn.!!$F1 2011
14 TraesCS2A01G004000 chr3D 53790511 53792500 1989 False 3415.000000 3415 97.692000 1 1984 1 chr3D.!!$F2 1983
15 TraesCS2A01G004000 chr3D 5497427 5498396 969 False 1332.000000 1332 91.864000 1993 2939 1 chr3D.!!$F1 946
16 TraesCS2A01G004000 chr3D 53811380 53812211 831 False 1105.000000 1105 91.106000 2031 2839 1 chr3D.!!$F3 808
17 TraesCS2A01G004000 chr1D 66572835 66574276 1441 True 1463.000000 1463 85.559000 2044 3458 1 chr1D.!!$R1 1414
18 TraesCS2A01G004000 chr1D 386770597 386771502 905 True 1279.000000 1279 92.426000 2044 2936 1 chr1D.!!$R2 892

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
473 474 0.968405 GGGTTTCTCAATGGCTGCAA 59.032 50.0 0.5 0.0 0.00 4.08 F
2004 2061 0.036105 CTGCTACTGCACCATCACCA 60.036 55.0 0.0 0.0 45.31 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2728 0.031178 CCAGGTGTTGTTGCAGAAGC 59.969 55.000 0.0 0.00 42.57 3.86 R
2844 5048 1.603678 GGTTTTGTCGACGTCTAGCCA 60.604 52.381 14.7 1.69 0.00 4.75 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
329 330 6.936900 CAGTACACCAGGATTAGGGATTATTG 59.063 42.308 0.00 0.00 0.00 1.90
473 474 0.968405 GGGTTTCTCAATGGCTGCAA 59.032 50.000 0.50 0.00 0.00 4.08
692 693 6.017192 TGTTGATAAGGAGGACACTAACTCT 58.983 40.000 0.00 0.00 34.22 3.24
1052 1105 5.923204 ACATGGTTTTAAAACTGCAATGGA 58.077 33.333 25.89 5.45 38.89 3.41
1282 1335 7.652909 TCAAGTTCAATGCAAATAGAACAAAGG 59.347 33.333 19.26 9.97 42.01 3.11
1677 1734 1.352622 ACAAGGGAAGGGCACAGACA 61.353 55.000 0.00 0.00 0.00 3.41
1737 1794 0.329596 ACACCTCAAGAATGGCCTCC 59.670 55.000 3.32 0.00 0.00 4.30
1946 2003 2.290093 GCTCCTATGAACTTGATGCAGC 59.710 50.000 0.00 0.00 0.00 5.25
1947 2004 2.877168 CTCCTATGAACTTGATGCAGCC 59.123 50.000 0.00 0.00 0.00 4.85
1948 2005 2.239402 TCCTATGAACTTGATGCAGCCA 59.761 45.455 0.00 0.00 0.00 4.75
1949 2006 2.357009 CCTATGAACTTGATGCAGCCAC 59.643 50.000 0.00 0.00 0.00 5.01
1950 2007 1.913778 ATGAACTTGATGCAGCCACA 58.086 45.000 0.00 0.00 0.00 4.17
1951 2008 0.953727 TGAACTTGATGCAGCCACAC 59.046 50.000 0.00 0.00 0.00 3.82
1952 2009 0.242017 GAACTTGATGCAGCCACACC 59.758 55.000 0.00 0.00 0.00 4.16
1953 2010 0.467844 AACTTGATGCAGCCACACCA 60.468 50.000 0.00 0.00 0.00 4.17
1954 2011 0.892358 ACTTGATGCAGCCACACCAG 60.892 55.000 0.00 0.00 0.00 4.00
1955 2012 2.209064 CTTGATGCAGCCACACCAGC 62.209 60.000 0.00 0.00 0.00 4.85
1956 2013 2.674033 GATGCAGCCACACCAGCA 60.674 61.111 0.00 0.00 41.73 4.41
1957 2014 2.203523 ATGCAGCCACACCAGCAA 60.204 55.556 0.00 0.00 40.76 3.91
1958 2015 2.209064 GATGCAGCCACACCAGCAAG 62.209 60.000 0.00 0.00 40.76 4.01
1959 2016 3.677648 GCAGCCACACCAGCAAGG 61.678 66.667 0.00 0.00 45.67 3.61
1960 2017 2.113774 CAGCCACACCAGCAAGGA 59.886 61.111 1.83 0.00 41.22 3.36
1961 2018 1.970114 CAGCCACACCAGCAAGGAG 60.970 63.158 1.83 0.00 41.22 3.69
1962 2019 2.674380 GCCACACCAGCAAGGAGG 60.674 66.667 1.83 2.68 41.22 4.30
1963 2020 2.034687 CCACACCAGCAAGGAGGG 59.965 66.667 1.83 0.00 41.22 4.30
1964 2021 2.674380 CACACCAGCAAGGAGGGC 60.674 66.667 1.83 0.00 41.22 5.19
1965 2022 3.971702 ACACCAGCAAGGAGGGCC 61.972 66.667 0.00 0.00 41.22 5.80
1967 2024 3.334054 ACCAGCAAGGAGGGCCTC 61.334 66.667 25.80 25.80 46.28 4.70
1968 2025 3.013932 CCAGCAAGGAGGGCCTCT 61.014 66.667 31.39 15.75 46.28 3.69
1969 2026 2.610519 CCAGCAAGGAGGGCCTCTT 61.611 63.158 31.39 23.27 46.28 2.85
1970 2027 1.077858 CAGCAAGGAGGGCCTCTTC 60.078 63.158 31.39 16.97 46.28 2.87
1971 2028 1.229788 AGCAAGGAGGGCCTCTTCT 60.230 57.895 31.39 19.00 46.28 2.85
1972 2029 1.077858 GCAAGGAGGGCCTCTTCTG 60.078 63.158 31.39 24.41 46.28 3.02
1973 2030 1.077858 CAAGGAGGGCCTCTTCTGC 60.078 63.158 31.39 15.49 46.28 4.26
1974 2031 1.229788 AAGGAGGGCCTCTTCTGCT 60.230 57.895 31.39 17.53 46.28 4.24
1975 2032 1.560866 AAGGAGGGCCTCTTCTGCTG 61.561 60.000 31.39 0.00 46.28 4.41
1976 2033 2.124778 GAGGGCCTCTTCTGCTGC 60.125 66.667 26.44 0.00 0.00 5.25
1977 2034 2.610233 AGGGCCTCTTCTGCTGCT 60.610 61.111 0.00 0.00 0.00 4.24
1978 2035 2.438075 GGGCCTCTTCTGCTGCTG 60.438 66.667 0.84 0.00 0.00 4.41
1979 2036 2.438075 GGCCTCTTCTGCTGCTGG 60.438 66.667 6.69 0.00 0.00 4.85
1980 2037 2.350514 GCCTCTTCTGCTGCTGGT 59.649 61.111 6.69 0.00 0.00 4.00
1981 2038 2.039405 GCCTCTTCTGCTGCTGGTG 61.039 63.158 6.69 0.78 0.00 4.17
1982 2039 2.039405 CCTCTTCTGCTGCTGGTGC 61.039 63.158 6.69 0.00 40.20 5.01
1983 2040 1.003597 CTCTTCTGCTGCTGGTGCT 60.004 57.895 6.69 0.00 40.48 4.40
1984 2041 1.299562 CTCTTCTGCTGCTGGTGCTG 61.300 60.000 6.69 0.00 40.48 4.41
1990 2047 2.046604 CTGCTGGTGCTGCTGCTA 60.047 61.111 17.00 0.47 40.48 3.49
1991 2048 2.359107 TGCTGGTGCTGCTGCTAC 60.359 61.111 17.00 12.30 40.48 3.58
1992 2049 2.046507 GCTGGTGCTGCTGCTACT 60.047 61.111 17.00 0.00 40.48 2.57
1993 2050 2.396955 GCTGGTGCTGCTGCTACTG 61.397 63.158 17.00 13.17 40.48 2.74
1994 2051 2.359107 TGGTGCTGCTGCTACTGC 60.359 61.111 17.00 1.02 40.48 4.40
1997 2054 2.359107 TGCTGCTGCTACTGCACC 60.359 61.111 17.00 0.00 45.31 5.01
1998 2055 2.359107 GCTGCTGCTACTGCACCA 60.359 61.111 8.53 0.00 45.31 4.17
1999 2056 1.748122 GCTGCTGCTACTGCACCAT 60.748 57.895 8.53 0.00 45.31 3.55
2000 2057 1.712977 GCTGCTGCTACTGCACCATC 61.713 60.000 8.53 0.00 45.31 3.51
2001 2058 0.392060 CTGCTGCTACTGCACCATCA 60.392 55.000 0.00 0.00 45.31 3.07
2002 2059 0.674581 TGCTGCTACTGCACCATCAC 60.675 55.000 0.00 0.00 45.31 3.06
2003 2060 1.372087 GCTGCTACTGCACCATCACC 61.372 60.000 0.00 0.00 45.31 4.02
2004 2061 0.036105 CTGCTACTGCACCATCACCA 60.036 55.000 0.00 0.00 45.31 4.17
2005 2062 0.036105 TGCTACTGCACCATCACCAG 60.036 55.000 0.00 0.00 45.31 4.00
2006 2063 1.372087 GCTACTGCACCATCACCAGC 61.372 60.000 0.00 0.00 39.41 4.85
2007 2064 0.036105 CTACTGCACCATCACCAGCA 60.036 55.000 0.00 0.00 35.43 4.41
2008 2065 0.399833 TACTGCACCATCACCAGCAA 59.600 50.000 0.00 0.00 36.44 3.91
2009 2066 0.892358 ACTGCACCATCACCAGCAAG 60.892 55.000 0.00 0.00 36.44 4.01
2010 2067 1.592400 CTGCACCATCACCAGCAAGG 61.592 60.000 0.00 0.00 45.67 3.61
2011 2068 1.303561 GCACCATCACCAGCAAGGA 60.304 57.895 1.83 0.00 41.22 3.36
2012 2069 1.310933 GCACCATCACCAGCAAGGAG 61.311 60.000 1.83 0.00 41.22 3.69
2013 2070 0.679002 CACCATCACCAGCAAGGAGG 60.679 60.000 1.83 1.70 41.22 4.30
2014 2071 1.077212 CCATCACCAGCAAGGAGGG 60.077 63.158 1.83 0.00 41.22 4.30
2015 2072 1.751927 CATCACCAGCAAGGAGGGC 60.752 63.158 1.83 0.00 41.22 5.19
2016 2073 2.988839 ATCACCAGCAAGGAGGGCC 61.989 63.158 0.00 0.00 41.22 5.80
2018 2075 3.334054 ACCAGCAAGGAGGGCCTC 61.334 66.667 25.80 25.80 46.28 4.70
2019 2076 3.013932 CCAGCAAGGAGGGCCTCT 61.014 66.667 31.39 15.75 46.28 3.69
2020 2077 2.610519 CCAGCAAGGAGGGCCTCTT 61.611 63.158 31.39 23.27 46.28 2.85
2021 2078 1.077858 CAGCAAGGAGGGCCTCTTC 60.078 63.158 31.39 16.97 46.28 2.87
2022 2079 1.229788 AGCAAGGAGGGCCTCTTCT 60.230 57.895 31.39 19.00 46.28 2.85
2023 2080 1.077858 GCAAGGAGGGCCTCTTCTG 60.078 63.158 31.39 24.41 46.28 3.02
2024 2081 1.077858 CAAGGAGGGCCTCTTCTGC 60.078 63.158 31.39 15.49 46.28 4.26
2025 2082 1.229788 AAGGAGGGCCTCTTCTGCT 60.230 57.895 31.39 17.53 46.28 4.24
2026 2083 1.560866 AAGGAGGGCCTCTTCTGCTG 61.561 60.000 31.39 0.00 46.28 4.41
2027 2084 2.124778 GAGGGCCTCTTCTGCTGC 60.125 66.667 26.44 0.00 0.00 5.25
2028 2085 2.610233 AGGGCCTCTTCTGCTGCT 60.610 61.111 0.00 0.00 0.00 4.24
2029 2086 2.438075 GGGCCTCTTCTGCTGCTG 60.438 66.667 0.84 0.00 0.00 4.41
2085 2694 3.369892 GGGCATCTTCTTCTTCTGCTACA 60.370 47.826 0.00 0.00 33.43 2.74
2086 2695 3.870419 GGCATCTTCTTCTTCTGCTACAG 59.130 47.826 0.00 0.00 33.43 2.74
2098 2707 1.078848 GCTACAGCACCTGGACCAG 60.079 63.158 15.15 15.15 41.59 4.00
2099 2708 1.078848 CTACAGCACCTGGACCAGC 60.079 63.158 16.72 6.00 35.51 4.85
2100 2709 1.830587 CTACAGCACCTGGACCAGCA 61.831 60.000 16.72 0.00 35.51 4.41
2101 2710 1.414866 TACAGCACCTGGACCAGCAA 61.415 55.000 16.72 0.00 35.51 3.91
2102 2711 1.529010 CAGCACCTGGACCAGCAAA 60.529 57.895 16.72 0.00 0.00 3.68
2103 2712 1.228367 AGCACCTGGACCAGCAAAG 60.228 57.895 16.72 4.94 0.00 2.77
2104 2713 1.228245 GCACCTGGACCAGCAAAGA 60.228 57.895 16.72 0.00 0.00 2.52
2105 2714 0.823356 GCACCTGGACCAGCAAAGAA 60.823 55.000 16.72 0.00 0.00 2.52
2106 2715 1.242076 CACCTGGACCAGCAAAGAAG 58.758 55.000 16.72 3.04 0.00 2.85
2107 2716 1.140312 ACCTGGACCAGCAAAGAAGA 58.860 50.000 16.72 0.00 0.00 2.87
2108 2717 1.072965 ACCTGGACCAGCAAAGAAGAG 59.927 52.381 16.72 1.54 0.00 2.85
2109 2718 1.612726 CCTGGACCAGCAAAGAAGAGG 60.613 57.143 16.72 0.00 0.00 3.69
2110 2719 0.401738 TGGACCAGCAAAGAAGAGGG 59.598 55.000 0.00 0.00 0.00 4.30
2111 2720 0.962855 GGACCAGCAAAGAAGAGGGC 60.963 60.000 0.00 0.00 0.00 5.19
2112 2721 0.962855 GACCAGCAAAGAAGAGGGCC 60.963 60.000 0.00 0.00 0.00 5.80
2113 2722 1.381851 CCAGCAAAGAAGAGGGCCT 59.618 57.895 5.25 5.25 0.00 5.19
2114 2723 0.679321 CCAGCAAAGAAGAGGGCCTC 60.679 60.000 26.42 26.42 0.00 4.70
2115 2724 0.327591 CAGCAAAGAAGAGGGCCTCT 59.672 55.000 30.46 30.46 43.37 3.69
2121 2730 4.577320 AAGAGGGCCTCTTCTGCT 57.423 55.556 37.31 19.90 46.42 4.24
2122 2731 2.784371 AAGAGGGCCTCTTCTGCTT 58.216 52.632 37.31 19.16 46.42 3.91
2123 2732 0.617935 AAGAGGGCCTCTTCTGCTTC 59.382 55.000 37.31 9.24 46.42 3.86
2124 2733 0.252650 AGAGGGCCTCTTCTGCTTCT 60.253 55.000 30.46 5.18 37.60 2.85
2125 2734 0.107752 GAGGGCCTCTTCTGCTTCTG 60.108 60.000 26.44 0.00 0.00 3.02
2126 2735 1.748500 GGGCCTCTTCTGCTTCTGC 60.749 63.158 0.84 0.00 40.20 4.26
2297 3008 3.681034 GCTGCTGGTAGTTCATCATCTGT 60.681 47.826 0.00 0.00 0.00 3.41
2348 3059 1.303074 CAGCTGCTGCAAAGGGAGA 60.303 57.895 17.73 0.00 42.74 3.71
2511 3222 2.520069 TGGTCAGTTTGGTTGTGTGTT 58.480 42.857 0.00 0.00 0.00 3.32
2677 3548 7.430211 CGATGGTATTTTGTGATGATGAGTTTG 59.570 37.037 0.00 0.00 0.00 2.93
2755 3694 2.089600 ACCCTAGGTGATGGCTAGAC 57.910 55.000 8.29 0.00 32.98 2.59
2756 3695 1.291033 ACCCTAGGTGATGGCTAGACA 59.709 52.381 0.00 0.00 32.98 3.41
2852 5056 2.089600 ACCCTAGGTGATGGCTAGAC 57.910 55.000 8.29 0.00 32.98 2.59
2863 5365 1.774639 TGGCTAGACGTCGACAAAAC 58.225 50.000 17.16 3.39 0.00 2.43
2868 5370 1.415374 AGACGTCGACAAAACCATCG 58.585 50.000 17.16 0.08 39.72 3.84
2890 5392 4.941873 CGAAGATGCCTAAAAACCCTAGTT 59.058 41.667 0.00 0.00 38.03 2.24
2964 6129 2.735134 GCTAGACGTCGACAAAACCATT 59.265 45.455 17.16 0.00 0.00 3.16
3030 6293 3.535561 CATCGAAGATGGCTACAAACCT 58.464 45.455 2.29 0.00 45.12 3.50
3202 6465 5.922053 TCATAATCTCATTACAGCACAGCT 58.078 37.500 0.00 0.00 40.77 4.24
3226 6489 3.717913 ACCACACCCTACAAAAGGTAAGA 59.282 43.478 0.00 0.00 44.90 2.10
3258 6521 1.834263 GATAGTGCCCTCTTCCACAGT 59.166 52.381 0.00 0.00 34.48 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.124970 GACATTGCTCATCTATGCACTGA 58.875 43.478 11.20 0.00 40.67 3.41
288 289 1.301293 CTGGGCTTTCTGGTCTCCC 59.699 63.158 0.00 0.00 37.49 4.30
329 330 2.472695 TGTATCCAACACAGCCTGTC 57.527 50.000 0.00 0.00 31.43 3.51
1052 1105 5.298777 GCCTCACTCTCATTCTTTAATGCAT 59.701 40.000 0.00 0.00 41.96 3.96
1282 1335 3.895232 TTCCCATCTTACAGTCTCAGC 57.105 47.619 0.00 0.00 0.00 4.26
1677 1734 4.230502 TCATATTGGCCCTTTCTCCTCTTT 59.769 41.667 0.00 0.00 0.00 2.52
1737 1794 6.532657 CCTTTTTGCAATTAGAGCAGGTAATG 59.467 38.462 0.00 0.00 43.75 1.90
1946 2003 2.034687 CCCTCCTTGCTGGTGTGG 59.965 66.667 0.00 0.00 37.07 4.17
1947 2004 2.674380 GCCCTCCTTGCTGGTGTG 60.674 66.667 0.00 0.00 37.07 3.82
1948 2005 3.971702 GGCCCTCCTTGCTGGTGT 61.972 66.667 0.00 0.00 37.07 4.16
1949 2006 3.635268 GAGGCCCTCCTTGCTGGTG 62.635 68.421 0.00 0.00 44.46 4.17
1950 2007 3.334054 GAGGCCCTCCTTGCTGGT 61.334 66.667 0.00 0.00 44.46 4.00
1951 2008 2.549169 GAAGAGGCCCTCCTTGCTGG 62.549 65.000 7.26 0.00 44.46 4.85
1952 2009 1.077858 GAAGAGGCCCTCCTTGCTG 60.078 63.158 7.26 0.00 44.46 4.41
1953 2010 1.229788 AGAAGAGGCCCTCCTTGCT 60.230 57.895 7.26 0.00 44.46 3.91
1954 2011 1.077858 CAGAAGAGGCCCTCCTTGC 60.078 63.158 7.26 0.00 44.46 4.01
1955 2012 1.077858 GCAGAAGAGGCCCTCCTTG 60.078 63.158 7.26 4.78 44.46 3.61
1956 2013 1.229788 AGCAGAAGAGGCCCTCCTT 60.230 57.895 7.26 0.00 44.46 3.36
1958 2015 2.588989 CAGCAGAAGAGGCCCTCC 59.411 66.667 7.26 0.00 0.00 4.30
1959 2016 2.124778 GCAGCAGAAGAGGCCCTC 60.125 66.667 1.26 1.26 0.00 4.30
1960 2017 2.610233 AGCAGCAGAAGAGGCCCT 60.610 61.111 0.00 0.00 0.00 5.19
1961 2018 2.438075 CAGCAGCAGAAGAGGCCC 60.438 66.667 0.00 0.00 0.00 5.80
1962 2019 2.438075 CCAGCAGCAGAAGAGGCC 60.438 66.667 0.00 0.00 0.00 5.19
1963 2020 2.039405 CACCAGCAGCAGAAGAGGC 61.039 63.158 0.00 0.00 0.00 4.70
1964 2021 2.039405 GCACCAGCAGCAGAAGAGG 61.039 63.158 0.00 0.00 41.58 3.69
1965 2022 1.003597 AGCACCAGCAGCAGAAGAG 60.004 57.895 0.00 0.00 45.49 2.85
1966 2023 1.302271 CAGCACCAGCAGCAGAAGA 60.302 57.895 0.00 0.00 45.49 2.87
1967 2024 3.264947 CAGCACCAGCAGCAGAAG 58.735 61.111 0.00 0.00 45.49 2.85
1973 2030 2.046604 TAGCAGCAGCACCAGCAG 60.047 61.111 3.17 0.00 45.49 4.24
1974 2031 2.359107 GTAGCAGCAGCACCAGCA 60.359 61.111 3.17 0.00 45.49 4.41
1975 2032 2.046507 AGTAGCAGCAGCACCAGC 60.047 61.111 3.17 0.00 45.49 4.85
1976 2033 2.396955 GCAGTAGCAGCAGCACCAG 61.397 63.158 3.17 0.00 45.49 4.00
1977 2034 2.359107 GCAGTAGCAGCAGCACCA 60.359 61.111 3.17 0.00 45.49 4.17
1987 2044 1.372087 GCTGGTGATGGTGCAGTAGC 61.372 60.000 0.00 0.00 42.57 3.58
1988 2045 0.036105 TGCTGGTGATGGTGCAGTAG 60.036 55.000 0.00 0.00 0.00 2.57
1989 2046 0.399833 TTGCTGGTGATGGTGCAGTA 59.600 50.000 0.00 0.00 36.75 2.74
1990 2047 0.892358 CTTGCTGGTGATGGTGCAGT 60.892 55.000 0.00 0.00 36.75 4.40
1991 2048 1.592400 CCTTGCTGGTGATGGTGCAG 61.592 60.000 0.00 0.00 36.75 4.41
1992 2049 1.604308 CCTTGCTGGTGATGGTGCA 60.604 57.895 0.00 0.00 0.00 4.57
1993 2050 1.303561 TCCTTGCTGGTGATGGTGC 60.304 57.895 0.00 0.00 37.07 5.01
1994 2051 0.679002 CCTCCTTGCTGGTGATGGTG 60.679 60.000 0.00 0.00 37.07 4.17
1995 2052 1.687612 CCTCCTTGCTGGTGATGGT 59.312 57.895 0.00 0.00 37.07 3.55
1996 2053 1.077212 CCCTCCTTGCTGGTGATGG 60.077 63.158 0.00 0.00 37.07 3.51
1997 2054 1.751927 GCCCTCCTTGCTGGTGATG 60.752 63.158 0.00 0.00 37.07 3.07
1998 2055 2.679716 GCCCTCCTTGCTGGTGAT 59.320 61.111 0.00 0.00 37.07 3.06
1999 2056 3.650950 GGCCCTCCTTGCTGGTGA 61.651 66.667 0.00 0.00 37.07 4.02
2000 2057 3.635268 GAGGCCCTCCTTGCTGGTG 62.635 68.421 0.00 0.00 44.46 4.17
2001 2058 3.334054 GAGGCCCTCCTTGCTGGT 61.334 66.667 0.00 0.00 44.46 4.00
2002 2059 2.549169 GAAGAGGCCCTCCTTGCTGG 62.549 65.000 7.26 0.00 44.46 4.85
2003 2060 1.077858 GAAGAGGCCCTCCTTGCTG 60.078 63.158 7.26 0.00 44.46 4.41
2004 2061 1.229788 AGAAGAGGCCCTCCTTGCT 60.230 57.895 7.26 0.00 44.46 3.91
2005 2062 1.077858 CAGAAGAGGCCCTCCTTGC 60.078 63.158 7.26 0.00 44.46 4.01
2006 2063 1.077858 GCAGAAGAGGCCCTCCTTG 60.078 63.158 7.26 4.78 44.46 3.61
2007 2064 1.229788 AGCAGAAGAGGCCCTCCTT 60.230 57.895 7.26 0.00 44.46 3.36
2009 2066 2.588989 CAGCAGAAGAGGCCCTCC 59.411 66.667 7.26 0.00 0.00 4.30
2010 2067 2.124778 GCAGCAGAAGAGGCCCTC 60.125 66.667 1.26 1.26 0.00 4.30
2011 2068 2.610233 AGCAGCAGAAGAGGCCCT 60.610 61.111 0.00 0.00 0.00 5.19
2012 2069 2.438075 CAGCAGCAGAAGAGGCCC 60.438 66.667 0.00 0.00 0.00 5.80
2013 2070 2.438075 CCAGCAGCAGAAGAGGCC 60.438 66.667 0.00 0.00 0.00 5.19
2014 2071 2.039405 CACCAGCAGCAGAAGAGGC 61.039 63.158 0.00 0.00 0.00 4.70
2015 2072 2.039405 GCACCAGCAGCAGAAGAGG 61.039 63.158 0.00 0.00 41.58 3.69
2016 2073 1.003597 AGCACCAGCAGCAGAAGAG 60.004 57.895 0.00 0.00 45.49 2.85
2017 2074 1.302271 CAGCACCAGCAGCAGAAGA 60.302 57.895 0.00 0.00 45.49 2.87
2018 2075 3.264947 CAGCACCAGCAGCAGAAG 58.735 61.111 0.00 0.00 45.49 2.85
2024 2081 2.046604 TAGCAGCAGCACCAGCAG 60.047 61.111 3.17 0.00 45.49 4.24
2025 2082 2.359107 GTAGCAGCAGCACCAGCA 60.359 61.111 3.17 0.00 45.49 4.41
2026 2083 2.046507 AGTAGCAGCAGCACCAGC 60.047 61.111 3.17 0.00 45.49 4.85
2027 2084 2.396955 GCAGTAGCAGCAGCACCAG 61.397 63.158 3.17 0.00 45.49 4.00
2028 2085 2.359107 GCAGTAGCAGCAGCACCA 60.359 61.111 3.17 0.00 45.49 4.17
2085 2694 1.228367 CTTTGCTGGTCCAGGTGCT 60.228 57.895 20.72 0.00 31.21 4.40
2086 2695 0.823356 TTCTTTGCTGGTCCAGGTGC 60.823 55.000 20.72 7.82 31.21 5.01
2089 2698 1.612726 CCTCTTCTTTGCTGGTCCAGG 60.613 57.143 20.72 3.79 31.21 4.45
2091 2700 0.401738 CCCTCTTCTTTGCTGGTCCA 59.598 55.000 0.00 0.00 0.00 4.02
2092 2701 0.962855 GCCCTCTTCTTTGCTGGTCC 60.963 60.000 0.00 0.00 0.00 4.46
2093 2702 0.962855 GGCCCTCTTCTTTGCTGGTC 60.963 60.000 0.00 0.00 0.00 4.02
2098 2707 3.660343 AAGAGGCCCTCTTCTTTGC 57.340 52.632 20.53 0.00 46.42 3.68
2105 2714 0.252650 AGAAGCAGAAGAGGCCCTCT 60.253 55.000 7.68 7.68 43.37 3.69
2106 2715 0.107752 CAGAAGCAGAAGAGGCCCTC 60.108 60.000 1.26 1.26 0.00 4.30
2107 2716 1.989620 CAGAAGCAGAAGAGGCCCT 59.010 57.895 0.00 0.00 0.00 5.19
2108 2717 1.748500 GCAGAAGCAGAAGAGGCCC 60.749 63.158 0.00 0.00 41.58 5.80
2109 2718 3.902318 GCAGAAGCAGAAGAGGCC 58.098 61.111 0.00 0.00 41.58 5.19
2119 2728 0.031178 CCAGGTGTTGTTGCAGAAGC 59.969 55.000 0.00 0.00 42.57 3.86
2120 2729 1.334869 GTCCAGGTGTTGTTGCAGAAG 59.665 52.381 0.00 0.00 0.00 2.85
2121 2730 1.388547 GTCCAGGTGTTGTTGCAGAA 58.611 50.000 0.00 0.00 0.00 3.02
2122 2731 0.465460 GGTCCAGGTGTTGTTGCAGA 60.465 55.000 0.00 0.00 0.00 4.26
2123 2732 0.751277 TGGTCCAGGTGTTGTTGCAG 60.751 55.000 0.00 0.00 0.00 4.41
2124 2733 0.751277 CTGGTCCAGGTGTTGTTGCA 60.751 55.000 11.46 0.00 0.00 4.08
2125 2734 2.032981 CTGGTCCAGGTGTTGTTGC 58.967 57.895 11.46 0.00 0.00 4.17
2126 2735 0.751277 TGCTGGTCCAGGTGTTGTTG 60.751 55.000 20.72 0.00 31.21 3.33
2127 2736 0.033601 TTGCTGGTCCAGGTGTTGTT 60.034 50.000 20.72 0.00 31.21 2.83
2128 2737 0.033601 TTTGCTGGTCCAGGTGTTGT 60.034 50.000 20.72 0.00 31.21 3.32
2297 3008 2.763448 ACTGCTGTTTTACCCTTTGCAA 59.237 40.909 0.00 0.00 0.00 4.08
2677 3548 6.039047 AGCCTCATCATCACAAAATGTATGAC 59.961 38.462 0.00 0.00 29.79 3.06
2755 3694 4.581493 CATCTTCGATGGTTTTGTCGATG 58.419 43.478 0.00 1.88 45.13 3.84
2756 3695 3.063997 GCATCTTCGATGGTTTTGTCGAT 59.936 43.478 6.04 0.00 45.13 3.59
2774 4137 4.640647 CCTTCACTAGGGTTTTTAGGCATC 59.359 45.833 0.00 0.00 40.67 3.91
2844 5048 1.603678 GGTTTTGTCGACGTCTAGCCA 60.604 52.381 14.70 1.69 0.00 4.75
2852 5056 2.055838 TCTTCGATGGTTTTGTCGACG 58.944 47.619 11.62 0.00 45.43 5.12
2863 5365 3.066760 GGGTTTTTAGGCATCTTCGATGG 59.933 47.826 6.04 0.00 0.00 3.51
2868 5370 7.067129 CCTTAACTAGGGTTTTTAGGCATCTTC 59.933 40.741 0.00 0.00 40.67 2.87
2890 5392 4.020928 TGGTTTTGTCGACATCTAGCCTTA 60.021 41.667 20.80 0.00 0.00 2.69
2964 6129 5.013704 TCACTAGGGTTTTTAGGCATCTTCA 59.986 40.000 0.00 0.00 0.00 3.02
3179 6442 5.922053 AGCTGTGCTGTAATGAGATTATGA 58.078 37.500 0.00 0.00 37.57 2.15
3226 6489 3.776417 AGGGCACTATCATTTGGCATTTT 59.224 39.130 0.00 0.00 40.00 1.82
3258 6521 6.301486 CCATCCTAAATGAATGATCACCTGA 58.699 40.000 0.00 0.00 38.69 3.86


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

AutoCloner maintained by Alex Coulton.