Multiple sequence alignment - TraesCS2A01G118000

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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 TraesCS2A01G118000 chr2A 100.000 2912 0 0 1 2912 68503852 68506763 0.000000e+00 5378.0
1 TraesCS2A01G118000 chr2A 82.526 2003 293 35 1 1972 68811413 68813389 0.000000e+00 1707.0
2 TraesCS2A01G118000 chr2D 94.430 1975 105 4 1 1972 66462814 66460842 0.000000e+00 3033.0
3 TraesCS2A01G118000 chr2D 83.608 2001 273 26 3 1972 65719028 65717052 0.000000e+00 1827.0
4 TraesCS2A01G118000 chr2D 89.130 230 17 2 2252 2481 66460789 66460568 2.210000e-71 279.0
5 TraesCS2A01G118000 chr2D 89.506 162 12 3 2752 2912 66460582 66460425 1.770000e-47 200.0
6 TraesCS2A01G118000 chr2D 94.118 51 1 2 2128 2178 66460831 66460783 3.110000e-10 76.8
7 TraesCS2A01G118000 chr2B 91.439 1974 143 11 1 1972 104894275 104896224 0.000000e+00 2686.0
8 TraesCS2A01G118000 chr2B 82.943 2005 282 29 1 1971 105372513 105374491 0.000000e+00 1753.0
9 TraesCS2A01G118000 chr2B 88.131 396 25 4 2108 2481 104896490 104896885 4.430000e-123 451.0
10 TraesCS2A01G118000 chr2B 80.251 319 50 11 552 862 104947680 104947993 8.120000e-56 228.0
11 TraesCS2A01G118000 chr2B 95.161 124 6 0 1986 2109 104896208 104896331 2.290000e-46 196.0
12 TraesCS2A01G118000 chr2B 86.420 162 13 4 2752 2912 104896871 104897024 4.990000e-38 169.0
13 TraesCS2A01G118000 chr1D 94.077 287 16 1 2481 2766 17231832 17232118 4.460000e-118 435.0
14 TraesCS2A01G118000 chr3A 96.538 260 8 1 2508 2766 737950103 737950362 2.070000e-116 429.0
15 TraesCS2A01G118000 chr3A 92.308 286 22 0 2481 2766 675461856 675461571 9.720000e-110 407.0
16 TraesCS2A01G118000 chrUn 93.031 287 20 0 2479 2765 316391785 316392071 1.250000e-113 420.0
17 TraesCS2A01G118000 chrUn 91.986 287 23 0 2479 2765 316393684 316393970 1.260000e-108 403.0
18 TraesCS2A01G118000 chr4D 93.080 289 17 3 2480 2765 474303698 474303410 1.250000e-113 420.0
19 TraesCS2A01G118000 chr4D 91.362 301 22 4 2468 2765 183800840 183801139 2.700000e-110 409.0
20 TraesCS2A01G118000 chr1A 92.388 289 20 2 2479 2765 265880869 265881157 7.510000e-111 411.0
21 TraesCS2A01G118000 chr6A 92.334 287 20 1 2480 2764 591481591 591481305 9.720000e-110 407.0


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 TraesCS2A01G118000 chr2A 68503852 68506763 2911 False 5378.0 5378 100.00000 1 2912 1 chr2A.!!$F1 2911
1 TraesCS2A01G118000 chr2A 68811413 68813389 1976 False 1707.0 1707 82.52600 1 1972 1 chr2A.!!$F2 1971
2 TraesCS2A01G118000 chr2D 65717052 65719028 1976 True 1827.0 1827 83.60800 3 1972 1 chr2D.!!$R1 1969
3 TraesCS2A01G118000 chr2D 66460425 66462814 2389 True 897.2 3033 91.79600 1 2912 4 chr2D.!!$R2 2911
4 TraesCS2A01G118000 chr2B 105372513 105374491 1978 False 1753.0 1753 82.94300 1 1971 1 chr2B.!!$F2 1970
5 TraesCS2A01G118000 chr2B 104894275 104897024 2749 False 875.5 2686 90.28775 1 2912 4 chr2B.!!$F3 2911
6 TraesCS2A01G118000 chrUn 316391785 316393970 2185 False 411.5 420 92.50850 2479 2765 2 chrUn.!!$F1 286

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
513 534 0.03831 CAAGGGGAGGAAGGGTCAAC 59.962 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2115 0.031857 CATGCACACGGCTTTTTGGA 59.968 50.0 0.0 0.0 45.15 3.53 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
40 41 1.144298 GGGAGGGGCCGTATTTTATGT 59.856 52.381 0.00 0.00 37.63 2.29
102 103 5.565259 GTCGTTTGCAAATTGATGTAGTCAG 59.435 40.000 16.21 0.00 38.29 3.51
138 139 5.470437 TCACCAACAATACGAACAAATAGCA 59.530 36.000 0.00 0.00 0.00 3.49
175 178 8.031277 ACGACAAATAAGTCTTAGTTAACCGAT 58.969 33.333 18.58 7.82 36.38 4.18
205 208 4.394729 GAGACAATGGTGGGTTTCTACAA 58.605 43.478 0.00 0.00 0.00 2.41
207 210 5.393866 AGACAATGGTGGGTTTCTACAATT 58.606 37.500 0.00 0.00 29.40 2.32
211 214 2.158385 TGGTGGGTTTCTACAATTGGCT 60.158 45.455 10.83 0.00 0.00 4.75
232 235 2.157834 ACCGAGTTTACGCAACATGA 57.842 45.000 0.00 0.00 37.93 3.07
247 250 4.034279 GCAACATGAAATTGTGCACTTTGT 59.966 37.500 19.41 7.99 0.00 2.83
267 270 3.513119 TGTAGCACTTGAGCTCATCTCTT 59.487 43.478 19.04 6.52 45.26 2.85
287 290 1.155624 GGGGACGGCTAGGGAGTAT 59.844 63.158 0.00 0.00 0.00 2.12
433 437 5.822519 GCACAACCCATCTTATCACATTAGA 59.177 40.000 0.00 0.00 0.00 2.10
440 458 6.214208 CCCATCTTATCACATTAGATCCTCCA 59.786 42.308 0.00 0.00 0.00 3.86
513 534 0.038310 CAAGGGGAGGAAGGGTCAAC 59.962 60.000 0.00 0.00 0.00 3.18
517 538 1.077169 GGGGAGGAAGGGTCAACAATT 59.923 52.381 0.00 0.00 0.00 2.32
526 547 5.926542 GGAAGGGTCAACAATTTAGCTTTTC 59.073 40.000 0.00 0.00 0.00 2.29
529 550 4.679654 GGGTCAACAATTTAGCTTTTCGTG 59.320 41.667 0.00 0.00 0.00 4.35
544 565 1.699730 TCGTGAGGGAGTCTTGTTGA 58.300 50.000 0.00 0.00 0.00 3.18
672 694 3.977312 AGAGCTATATATACCCACGGCA 58.023 45.455 0.00 0.00 0.00 5.69
673 695 4.350245 AGAGCTATATATACCCACGGCAA 58.650 43.478 0.00 0.00 0.00 4.52
674 696 4.159879 AGAGCTATATATACCCACGGCAAC 59.840 45.833 0.00 0.00 0.00 4.17
726 748 5.538433 ACCTTAACAATGCATGGTTTGTAGT 59.462 36.000 24.17 13.69 35.09 2.73
728 750 7.027161 CCTTAACAATGCATGGTTTGTAGTAC 58.973 38.462 24.17 0.00 35.09 2.73
819 844 7.937700 TTTAGTCTAAATCATCCCATCCTCT 57.062 36.000 0.65 0.00 0.00 3.69
821 846 9.621239 TTTAGTCTAAATCATCCCATCCTCTAT 57.379 33.333 0.65 0.00 0.00 1.98
833 858 4.993584 CCCATCCTCTATCATTCTTTCACG 59.006 45.833 0.00 0.00 0.00 4.35
922 948 2.300956 TTCAAAACCATGGCCTAGCA 57.699 45.000 13.04 0.00 0.00 3.49
929 955 0.742505 CCATGGCCTAGCAACACATG 59.257 55.000 3.32 0.00 38.82 3.21
953 979 6.655003 TGATGTCCATGAGTTCCTAGTTTTTC 59.345 38.462 0.00 0.00 0.00 2.29
989 1017 2.682856 TCTGTTGGAGAGTTTGTTGTGC 59.317 45.455 0.00 0.00 0.00 4.57
1114 1151 4.129737 CGCACGAGGGACACCGAT 62.130 66.667 0.00 0.00 43.47 4.18
1264 1301 1.630148 GCGTCGCTTCAACTACATCT 58.370 50.000 10.68 0.00 0.00 2.90
1582 1619 1.925455 CCACCCCACATCCTCCAGT 60.925 63.158 0.00 0.00 0.00 4.00
1590 1627 2.364842 ATCCTCCAGTGCGCTCCT 60.365 61.111 9.73 0.76 0.00 3.69
1591 1628 1.075970 ATCCTCCAGTGCGCTCCTA 60.076 57.895 9.73 0.00 0.00 2.94
1645 1682 1.299850 CCACAGCTGTTCGACGACA 60.300 57.895 18.94 0.00 0.00 4.35
1849 1889 1.112113 ATCCGTCCACTATGCGAACT 58.888 50.000 0.00 0.00 0.00 3.01
1946 1986 8.160106 GGTATGACAAGGAATAAATCTCTGGAT 58.840 37.037 0.00 0.00 0.00 3.41
1972 2012 1.964552 CCATGTCAATCCTGGAGCTC 58.035 55.000 4.71 4.71 34.42 4.09
1973 2013 1.211212 CCATGTCAATCCTGGAGCTCA 59.789 52.381 17.19 0.61 34.42 4.26
1974 2014 2.286872 CATGTCAATCCTGGAGCTCAC 58.713 52.381 17.19 5.63 0.00 3.51
1975 2015 0.615331 TGTCAATCCTGGAGCTCACC 59.385 55.000 17.19 0.00 0.00 4.02
1976 2016 0.908198 GTCAATCCTGGAGCTCACCT 59.092 55.000 17.19 0.00 0.00 4.00
1977 2017 0.907486 TCAATCCTGGAGCTCACCTG 59.093 55.000 17.19 3.62 0.00 4.00
1978 2018 0.747283 CAATCCTGGAGCTCACCTGC 60.747 60.000 17.19 0.00 0.00 4.85
1979 2019 1.203441 AATCCTGGAGCTCACCTGCA 61.203 55.000 17.19 2.54 39.82 4.41
1980 2020 1.203441 ATCCTGGAGCTCACCTGCAA 61.203 55.000 17.19 0.00 41.66 4.08
1981 2021 1.073722 CCTGGAGCTCACCTGCAAA 59.926 57.895 17.19 0.00 41.66 3.68
1982 2022 0.538057 CCTGGAGCTCACCTGCAAAA 60.538 55.000 17.19 0.00 41.66 2.44
1983 2023 1.321474 CTGGAGCTCACCTGCAAAAA 58.679 50.000 17.19 0.00 41.66 1.94
2012 2052 5.658634 TCAATCCTAGAGCTAGTGTCATTGT 59.341 40.000 4.02 0.00 0.00 2.71
2013 2053 4.991153 TCCTAGAGCTAGTGTCATTGTG 57.009 45.455 4.02 0.00 0.00 3.33
2014 2054 3.131223 TCCTAGAGCTAGTGTCATTGTGC 59.869 47.826 4.02 0.00 0.00 4.57
2015 2055 2.001812 AGAGCTAGTGTCATTGTGCG 57.998 50.000 0.00 0.00 0.00 5.34
2016 2056 0.371645 GAGCTAGTGTCATTGTGCGC 59.628 55.000 0.00 0.00 0.00 6.09
2017 2057 0.320683 AGCTAGTGTCATTGTGCGCA 60.321 50.000 5.66 5.66 0.00 6.09
2018 2058 0.729116 GCTAGTGTCATTGTGCGCAT 59.271 50.000 15.91 0.00 0.00 4.73
2019 2059 1.530441 GCTAGTGTCATTGTGCGCATG 60.530 52.381 15.91 8.55 0.00 4.06
2020 2060 2.001872 CTAGTGTCATTGTGCGCATGA 58.998 47.619 15.91 11.34 0.00 3.07
2021 2061 0.518636 AGTGTCATTGTGCGCATGAC 59.481 50.000 27.62 27.62 43.50 3.06
2022 2062 0.790495 GTGTCATTGTGCGCATGACG 60.790 55.000 28.03 13.87 45.47 4.35
2023 2063 1.226101 GTCATTGTGCGCATGACGG 60.226 57.895 22.61 9.28 43.93 4.79
2024 2064 2.577644 CATTGTGCGCATGACGGC 60.578 61.111 15.91 0.00 43.93 5.68
2025 2065 2.747460 ATTGTGCGCATGACGGCT 60.747 55.556 15.91 0.00 43.93 5.52
2026 2066 3.042842 ATTGTGCGCATGACGGCTG 62.043 57.895 15.91 0.00 43.93 4.85
2032 2072 3.857854 GCATGACGGCTGCGACAG 61.858 66.667 0.00 2.92 34.12 3.51
2051 2091 3.716006 GCGTGCATGCGTGTCTGT 61.716 61.111 16.43 0.00 0.00 3.41
2052 2092 2.938253 CGTGCATGCGTGTCTGTT 59.062 55.556 14.09 0.00 0.00 3.16
2053 2093 1.439201 CGTGCATGCGTGTCTGTTG 60.439 57.895 14.09 0.00 0.00 3.33
2054 2094 1.648720 GTGCATGCGTGTCTGTTGT 59.351 52.632 14.09 0.00 0.00 3.32
2055 2095 0.658244 GTGCATGCGTGTCTGTTGTG 60.658 55.000 14.09 0.00 0.00 3.33
2056 2096 1.094650 TGCATGCGTGTCTGTTGTGT 61.095 50.000 14.09 0.00 0.00 3.72
2057 2097 0.384725 GCATGCGTGTCTGTTGTGTC 60.385 55.000 0.00 0.00 0.00 3.67
2058 2098 0.235665 CATGCGTGTCTGTTGTGTCC 59.764 55.000 0.00 0.00 0.00 4.02
2059 2099 1.221466 ATGCGTGTCTGTTGTGTCCG 61.221 55.000 0.00 0.00 0.00 4.79
2060 2100 2.928361 CGTGTCTGTTGTGTCCGC 59.072 61.111 0.00 0.00 0.00 5.54
2061 2101 2.927618 CGTGTCTGTTGTGTCCGCG 61.928 63.158 0.00 0.00 0.00 6.46
2062 2102 1.881252 GTGTCTGTTGTGTCCGCGT 60.881 57.895 4.92 0.00 0.00 6.01
2063 2103 1.153529 TGTCTGTTGTGTCCGCGTT 60.154 52.632 4.92 0.00 0.00 4.84
2064 2104 1.149361 TGTCTGTTGTGTCCGCGTTC 61.149 55.000 4.92 0.00 0.00 3.95
2065 2105 1.142097 TCTGTTGTGTCCGCGTTCA 59.858 52.632 4.92 0.03 0.00 3.18
2066 2106 0.460459 TCTGTTGTGTCCGCGTTCAA 60.460 50.000 4.92 1.83 0.00 2.69
2067 2107 0.042188 CTGTTGTGTCCGCGTTCAAG 60.042 55.000 4.92 0.00 0.00 3.02
2068 2108 1.368850 GTTGTGTCCGCGTTCAAGC 60.369 57.895 4.92 0.00 0.00 4.01
2069 2109 1.815840 TTGTGTCCGCGTTCAAGCA 60.816 52.632 4.92 0.00 36.85 3.91
2070 2110 1.771073 TTGTGTCCGCGTTCAAGCAG 61.771 55.000 4.92 0.00 36.85 4.24
2071 2111 2.108157 TGTCCGCGTTCAAGCAGT 59.892 55.556 4.92 0.00 36.85 4.40
2072 2112 2.243957 TGTCCGCGTTCAAGCAGTG 61.244 57.895 4.92 0.00 36.85 3.66
2073 2113 2.664851 TCCGCGTTCAAGCAGTGG 60.665 61.111 4.92 0.00 36.85 4.00
2074 2114 3.726517 CCGCGTTCAAGCAGTGGG 61.727 66.667 4.92 0.00 36.85 4.61
2075 2115 2.972505 CGCGTTCAAGCAGTGGGT 60.973 61.111 0.00 0.00 36.85 4.51
2076 2116 2.946762 GCGTTCAAGCAGTGGGTC 59.053 61.111 0.00 0.00 37.05 4.46
2077 2117 2.617274 GCGTTCAAGCAGTGGGTCC 61.617 63.158 0.00 0.00 37.05 4.46
2078 2118 1.227823 CGTTCAAGCAGTGGGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
2079 2119 0.817634 CGTTCAAGCAGTGGGTCCAA 60.818 55.000 0.00 0.00 0.00 3.53
2080 2120 1.398692 GTTCAAGCAGTGGGTCCAAA 58.601 50.000 0.00 0.00 0.00 3.28
2081 2121 1.754226 GTTCAAGCAGTGGGTCCAAAA 59.246 47.619 0.00 0.00 0.00 2.44
2082 2122 2.151502 TCAAGCAGTGGGTCCAAAAA 57.848 45.000 0.00 0.00 0.00 1.94
2083 2123 2.031120 TCAAGCAGTGGGTCCAAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
2084 2124 0.752658 AAGCAGTGGGTCCAAAAAGC 59.247 50.000 0.00 0.00 0.00 3.51
2085 2125 1.115326 AGCAGTGGGTCCAAAAAGCC 61.115 55.000 0.00 0.00 37.32 4.35
2086 2126 1.659794 CAGTGGGTCCAAAAAGCCG 59.340 57.895 0.00 0.00 39.76 5.52
2087 2127 1.106944 CAGTGGGTCCAAAAAGCCGT 61.107 55.000 0.00 0.00 39.76 5.68
2088 2128 1.106944 AGTGGGTCCAAAAAGCCGTG 61.107 55.000 0.00 0.00 39.76 4.94
2089 2129 1.076632 TGGGTCCAAAAAGCCGTGT 60.077 52.632 0.00 0.00 39.76 4.49
2090 2130 1.362355 GGGTCCAAAAAGCCGTGTG 59.638 57.895 0.00 0.00 0.00 3.82
2091 2131 1.299850 GGTCCAAAAAGCCGTGTGC 60.300 57.895 0.00 0.00 41.71 4.57
2092 2132 1.435515 GTCCAAAAAGCCGTGTGCA 59.564 52.632 0.00 0.00 44.83 4.57
2093 2133 0.031994 GTCCAAAAAGCCGTGTGCAT 59.968 50.000 0.00 0.00 44.83 3.96
2094 2134 0.031857 TCCAAAAAGCCGTGTGCATG 59.968 50.000 0.00 0.00 44.83 4.06
2095 2135 0.945265 CCAAAAAGCCGTGTGCATGG 60.945 55.000 6.09 6.09 44.83 3.66
2096 2136 0.249405 CAAAAAGCCGTGTGCATGGT 60.249 50.000 11.59 0.00 44.83 3.55
2097 2137 0.463620 AAAAAGCCGTGTGCATGGTT 59.536 45.000 11.59 3.30 44.83 3.67
2098 2138 0.031994 AAAAGCCGTGTGCATGGTTC 59.968 50.000 11.59 0.00 44.83 3.62
2099 2139 0.823356 AAAGCCGTGTGCATGGTTCT 60.823 50.000 11.59 0.00 44.83 3.01
2100 2140 0.823356 AAGCCGTGTGCATGGTTCTT 60.823 50.000 11.59 5.21 44.83 2.52
2101 2141 0.036164 AGCCGTGTGCATGGTTCTTA 59.964 50.000 11.59 0.00 44.83 2.10
2102 2142 1.094785 GCCGTGTGCATGGTTCTTAT 58.905 50.000 11.59 0.00 39.68 1.73
2103 2143 1.472480 GCCGTGTGCATGGTTCTTATT 59.528 47.619 11.59 0.00 39.68 1.40
2104 2144 2.680841 GCCGTGTGCATGGTTCTTATTA 59.319 45.455 11.59 0.00 39.68 0.98
2105 2145 3.486875 GCCGTGTGCATGGTTCTTATTAC 60.487 47.826 11.59 0.00 39.68 1.89
2106 2146 3.687212 CCGTGTGCATGGTTCTTATTACA 59.313 43.478 2.37 0.00 32.81 2.41
2107 2147 4.335315 CCGTGTGCATGGTTCTTATTACAT 59.665 41.667 2.37 0.00 32.81 2.29
2108 2148 5.525745 CCGTGTGCATGGTTCTTATTACATA 59.474 40.000 2.37 0.00 32.81 2.29
2109 2149 6.204688 CCGTGTGCATGGTTCTTATTACATAT 59.795 38.462 2.37 0.00 32.81 1.78
2110 2150 7.255104 CCGTGTGCATGGTTCTTATTACATATT 60.255 37.037 2.37 0.00 32.81 1.28
2111 2151 8.128582 CGTGTGCATGGTTCTTATTACATATTT 58.871 33.333 0.00 0.00 0.00 1.40
2158 2473 4.139234 GTGGCGGTAGTCGGTCCC 62.139 72.222 0.00 0.00 39.69 4.46
2159 2474 4.371417 TGGCGGTAGTCGGTCCCT 62.371 66.667 0.00 0.00 39.69 4.20
2171 2486 1.001376 GGTCCCTAGGAACGTCCCT 59.999 63.158 11.48 0.00 37.19 4.20
2188 2503 6.118170 ACGTCCCTATATGTGTATAGCGTAT 58.882 40.000 0.00 0.00 38.87 3.06
2189 2504 7.275183 ACGTCCCTATATGTGTATAGCGTATA 58.725 38.462 0.00 0.00 38.87 1.47
2242 2557 8.952278 GTGGAGATATATATATCCGATGGAGAC 58.048 40.741 24.61 14.93 44.90 3.36
2294 2609 9.221933 AGTGTTATGTTATTGTTTTATCCGTCA 57.778 29.630 0.00 0.00 0.00 4.35
2325 2640 6.535540 TGTGTAATGTTTCCCTAAGCACTTA 58.464 36.000 0.00 0.00 0.00 2.24
2328 2643 9.169592 GTGTAATGTTTCCCTAAGCACTTATTA 57.830 33.333 0.00 0.00 0.00 0.98
2404 2741 9.654663 AGTTTGTCTGATAACTAAGGTGTATTC 57.345 33.333 6.41 0.00 33.06 1.75
2412 2749 9.982651 TGATAACTAAGGTGTATTCTTATCTGC 57.017 33.333 0.00 0.00 0.00 4.26
2467 2804 2.542907 CGTGCCGCTTTGTCTGGTT 61.543 57.895 0.00 0.00 0.00 3.67
2494 2831 6.542370 TGTTATGAGATACTAGCAAAAAGGCC 59.458 38.462 0.00 0.00 0.00 5.19
2495 2832 3.886123 TGAGATACTAGCAAAAAGGCCC 58.114 45.455 0.00 0.00 0.00 5.80
2504 2841 3.783478 AAAAAGGCCCGTGCGTTGC 62.783 57.895 0.00 0.00 44.30 4.17
2588 2925 2.000447 GTTGGCAGGTTATGACTCGAC 59.000 52.381 0.00 0.00 38.04 4.20
2646 2983 3.209410 GTCATATGGGCTTCCTCTGTTG 58.791 50.000 2.13 0.00 0.00 3.33
2649 2986 1.142688 ATGGGCTTCCTCTGTTGGGT 61.143 55.000 0.00 0.00 0.00 4.51
2675 3012 0.594602 GGGTGGCAAGTAACGAAACC 59.405 55.000 0.00 0.00 0.00 3.27
2676 3013 1.310904 GGTGGCAAGTAACGAAACCA 58.689 50.000 0.00 0.00 0.00 3.67
2686 3023 6.522165 GCAAGTAACGAAACCAAATAGCTTAC 59.478 38.462 0.00 0.00 0.00 2.34
2713 3050 8.708742 GTGAAATTAATTAAAGCAGGACCAAAC 58.291 33.333 1.21 0.00 0.00 2.93
2717 3054 5.523438 AATTAAAGCAGGACCAAACGAAA 57.477 34.783 0.00 0.00 0.00 3.46
2724 3061 0.814812 GGACCAAACGAAACGGGACA 60.815 55.000 0.00 0.00 0.00 4.02
2728 3065 2.186891 CCAAACGAAACGGGACAAAAC 58.813 47.619 0.00 0.00 0.00 2.43
2821 3689 2.265424 GCAAAATGCCGGCATGGT 59.735 55.556 41.00 28.75 41.21 3.55
2826 3694 0.817013 AAATGCCGGCATGGTTGTAG 59.183 50.000 41.00 0.00 41.21 2.74
2844 3985 6.428771 GGTTGTAGCCACAATAAGTAAAGACA 59.571 38.462 0.00 0.00 46.03 3.41
2889 4444 5.897250 TGTTAGTGGATATACAGCTTGGAGA 59.103 40.000 0.00 0.00 0.00 3.71
2893 4448 5.011533 AGTGGATATACAGCTTGGAGATCAC 59.988 44.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.616842 CACACATAAAATACGGCCCCTC 59.383 50.000 0.00 0.00 0.00 4.30
40 41 1.822371 TGCGCTAGTCATAACTCCACA 59.178 47.619 9.73 0.00 36.92 4.17
85 86 3.419915 CACGCTGACTACATCAATTTGC 58.580 45.455 0.00 0.00 36.69 3.68
102 103 2.560119 TTGGTGATTGTGGCCACGC 61.560 57.895 30.07 21.48 34.30 5.34
138 139 1.064825 ATTTGTCGTCCCCTGTCCTT 58.935 50.000 0.00 0.00 0.00 3.36
175 178 2.626950 CCCACCATTGTCTCCTCTCCTA 60.627 54.545 0.00 0.00 0.00 2.94
205 208 2.004733 GCGTAAACTCGGTAAGCCAAT 58.995 47.619 0.00 0.00 34.09 3.16
207 210 0.317799 TGCGTAAACTCGGTAAGCCA 59.682 50.000 0.00 0.00 34.09 4.75
211 214 3.651206 TCATGTTGCGTAAACTCGGTAA 58.349 40.909 0.00 0.00 39.70 2.85
247 250 3.118847 CCAAGAGATGAGCTCAAGTGCTA 60.119 47.826 22.50 0.00 46.45 3.49
267 270 4.475444 CTCCCTAGCCGTCCCCCA 62.475 72.222 0.00 0.00 0.00 4.96
287 290 4.892934 ACATCTTTTGGCTAGGTTCAACAA 59.107 37.500 0.00 0.00 0.00 2.83
433 437 0.409092 TTTGTGGTGGCATGGAGGAT 59.591 50.000 0.00 0.00 0.00 3.24
440 458 1.541147 CATCTCGTTTTGTGGTGGCAT 59.459 47.619 0.00 0.00 0.00 4.40
513 534 4.455877 ACTCCCTCACGAAAAGCTAAATTG 59.544 41.667 0.00 0.00 0.00 2.32
517 538 2.897969 AGACTCCCTCACGAAAAGCTAA 59.102 45.455 0.00 0.00 0.00 3.09
526 547 2.035961 TCTTCAACAAGACTCCCTCACG 59.964 50.000 0.00 0.00 33.38 4.35
544 565 5.014123 TCTGGGTATTTGGACATTGAGTCTT 59.986 40.000 0.00 0.00 46.72 3.01
672 694 2.013400 TGTGTGATCTGTGTTTGCGTT 58.987 42.857 0.00 0.00 0.00 4.84
673 695 1.662517 TGTGTGATCTGTGTTTGCGT 58.337 45.000 0.00 0.00 0.00 5.24
674 696 2.481568 AGATGTGTGATCTGTGTTTGCG 59.518 45.455 0.00 0.00 0.00 4.85
681 703 4.141846 GGTGTATGGAGATGTGTGATCTGT 60.142 45.833 0.00 0.00 0.00 3.41
726 748 4.320398 TGAGGATGGGGGAATATTTGGTA 58.680 43.478 0.00 0.00 0.00 3.25
728 750 3.897505 GTTGAGGATGGGGGAATATTTGG 59.102 47.826 0.00 0.00 0.00 3.28
819 844 2.618241 GCATGGCCGTGAAAGAATGATA 59.382 45.455 29.54 0.00 0.00 2.15
821 846 0.810648 GCATGGCCGTGAAAGAATGA 59.189 50.000 29.54 0.00 0.00 2.57
929 955 6.655003 TGAAAAACTAGGAACTCATGGACATC 59.345 38.462 0.00 0.00 41.75 3.06
953 979 6.820152 TCTCCAACAGATGAACAATACTGATG 59.180 38.462 0.00 0.00 34.54 3.07
989 1017 5.887598 TCCATGGTTGTCATCCTTAATCAAG 59.112 40.000 12.58 0.00 32.92 3.02
1107 1144 2.358247 GACGCCCACAATCGGTGT 60.358 61.111 0.00 0.00 46.44 4.16
1179 1216 1.511305 CGTCCAGTCGTGGCTGTAT 59.489 57.895 0.26 0.00 44.60 2.29
1380 1417 1.153647 CCACAGCTCGAATACGCCA 60.154 57.895 0.00 0.00 39.58 5.69
1582 1619 2.571757 CGAAGTGGTAGGAGCGCA 59.428 61.111 11.47 0.00 0.00 6.09
1645 1682 2.937689 AGTGGCCTGCAGGGTGAT 60.938 61.111 33.46 0.96 37.43 3.06
1765 1802 4.388499 GGTCGGCATGGTGGTCGT 62.388 66.667 0.00 0.00 37.15 4.34
1807 1844 1.308326 CGTCCTCCTCCTCCTCCTT 59.692 63.158 0.00 0.00 0.00 3.36
1849 1889 1.544691 GTTCAGCAGGGAGTCTTCGTA 59.455 52.381 0.00 0.00 0.00 3.43
1956 1996 0.615331 GGTGAGCTCCAGGATTGACA 59.385 55.000 12.15 0.00 0.00 3.58
1960 2000 1.203441 TGCAGGTGAGCTCCAGGATT 61.203 55.000 12.15 0.00 34.99 3.01
1980 2020 7.038658 ACACTAGCTCTAGGATTGACTCTTTTT 60.039 37.037 8.60 0.00 37.49 1.94
1981 2021 6.439058 ACACTAGCTCTAGGATTGACTCTTTT 59.561 38.462 8.60 0.00 37.49 2.27
1982 2022 5.955355 ACACTAGCTCTAGGATTGACTCTTT 59.045 40.000 8.60 0.00 37.49 2.52
1983 2023 5.515106 ACACTAGCTCTAGGATTGACTCTT 58.485 41.667 8.60 0.00 37.49 2.85
1984 2024 5.124036 ACACTAGCTCTAGGATTGACTCT 57.876 43.478 8.60 0.00 37.49 3.24
1985 2025 4.884744 TGACACTAGCTCTAGGATTGACTC 59.115 45.833 8.60 0.00 37.49 3.36
1986 2026 4.861196 TGACACTAGCTCTAGGATTGACT 58.139 43.478 8.60 0.00 37.49 3.41
1987 2027 5.782893 ATGACACTAGCTCTAGGATTGAC 57.217 43.478 8.60 0.41 37.49 3.18
1988 2028 5.658634 ACAATGACACTAGCTCTAGGATTGA 59.341 40.000 17.44 0.00 37.49 2.57
1989 2029 5.752472 CACAATGACACTAGCTCTAGGATTG 59.248 44.000 8.60 11.38 37.49 2.67
1990 2030 5.683509 GCACAATGACACTAGCTCTAGGATT 60.684 44.000 8.60 0.00 37.49 3.01
1991 2031 4.202202 GCACAATGACACTAGCTCTAGGAT 60.202 45.833 8.60 0.00 37.49 3.24
1992 2032 3.131223 GCACAATGACACTAGCTCTAGGA 59.869 47.826 8.60 0.00 37.49 2.94
1993 2033 3.452474 GCACAATGACACTAGCTCTAGG 58.548 50.000 8.60 1.13 37.49 3.02
1994 2034 3.111838 CGCACAATGACACTAGCTCTAG 58.888 50.000 0.00 2.55 39.04 2.43
1995 2035 2.735444 GCGCACAATGACACTAGCTCTA 60.735 50.000 0.30 0.00 0.00 2.43
1996 2036 2.001812 CGCACAATGACACTAGCTCT 57.998 50.000 0.00 0.00 0.00 4.09
1997 2037 0.371645 GCGCACAATGACACTAGCTC 59.628 55.000 0.30 0.00 0.00 4.09
1998 2038 0.320683 TGCGCACAATGACACTAGCT 60.321 50.000 5.66 0.00 0.00 3.32
1999 2039 0.729116 ATGCGCACAATGACACTAGC 59.271 50.000 14.90 0.00 0.00 3.42
2000 2040 2.001872 TCATGCGCACAATGACACTAG 58.998 47.619 14.90 0.00 0.00 2.57
2001 2041 1.731709 GTCATGCGCACAATGACACTA 59.268 47.619 28.75 1.41 42.93 2.74
2015 2055 3.857854 CTGTCGCAGCCGTCATGC 61.858 66.667 0.00 0.00 40.35 4.06
2034 2074 3.240606 AACAGACACGCATGCACGC 62.241 57.895 19.57 0.00 36.19 5.34
2035 2075 1.439201 CAACAGACACGCATGCACG 60.439 57.895 19.57 10.25 39.50 5.34
2036 2076 0.658244 CACAACAGACACGCATGCAC 60.658 55.000 19.57 5.81 0.00 4.57
2037 2077 1.094650 ACACAACAGACACGCATGCA 61.095 50.000 19.57 0.00 0.00 3.96
2038 2078 0.384725 GACACAACAGACACGCATGC 60.385 55.000 7.91 7.91 0.00 4.06
2039 2079 0.235665 GGACACAACAGACACGCATG 59.764 55.000 0.00 0.00 0.00 4.06
2040 2080 1.221466 CGGACACAACAGACACGCAT 61.221 55.000 0.00 0.00 0.00 4.73
2041 2081 1.880796 CGGACACAACAGACACGCA 60.881 57.895 0.00 0.00 0.00 5.24
2042 2082 2.928361 CGGACACAACAGACACGC 59.072 61.111 0.00 0.00 0.00 5.34
2043 2083 2.927618 CGCGGACACAACAGACACG 61.928 63.158 0.00 0.00 0.00 4.49
2044 2084 1.426041 AACGCGGACACAACAGACAC 61.426 55.000 12.47 0.00 0.00 3.67
2045 2085 1.149361 GAACGCGGACACAACAGACA 61.149 55.000 12.47 0.00 0.00 3.41
2046 2086 1.149361 TGAACGCGGACACAACAGAC 61.149 55.000 12.47 0.00 0.00 3.51
2047 2087 0.460459 TTGAACGCGGACACAACAGA 60.460 50.000 12.47 0.00 0.00 3.41
2048 2088 0.042188 CTTGAACGCGGACACAACAG 60.042 55.000 12.47 0.53 0.00 3.16
2049 2089 2.010670 CTTGAACGCGGACACAACA 58.989 52.632 12.47 0.00 0.00 3.33
2050 2090 1.368850 GCTTGAACGCGGACACAAC 60.369 57.895 12.47 0.00 0.00 3.32
2051 2091 1.771073 CTGCTTGAACGCGGACACAA 61.771 55.000 12.47 9.95 38.57 3.33
2052 2092 2.202946 TGCTTGAACGCGGACACA 60.203 55.556 12.47 1.49 0.00 3.72
2053 2093 2.244651 ACTGCTTGAACGCGGACAC 61.245 57.895 12.47 0.00 39.56 3.67
2054 2094 2.108157 ACTGCTTGAACGCGGACA 59.892 55.556 12.47 7.29 39.56 4.02
2055 2095 2.551270 CACTGCTTGAACGCGGAC 59.449 61.111 12.47 4.20 39.56 4.79
2056 2096 2.664851 CCACTGCTTGAACGCGGA 60.665 61.111 12.47 0.00 39.56 5.54
2057 2097 3.726517 CCCACTGCTTGAACGCGG 61.727 66.667 12.47 0.00 42.00 6.46
2058 2098 2.954753 GACCCACTGCTTGAACGCG 61.955 63.158 3.53 3.53 0.00 6.01
2059 2099 2.617274 GGACCCACTGCTTGAACGC 61.617 63.158 0.00 0.00 0.00 4.84
2060 2100 0.817634 TTGGACCCACTGCTTGAACG 60.818 55.000 0.00 0.00 0.00 3.95
2061 2101 1.398692 TTTGGACCCACTGCTTGAAC 58.601 50.000 0.00 0.00 0.00 3.18
2062 2102 2.151502 TTTTGGACCCACTGCTTGAA 57.848 45.000 0.00 0.00 0.00 2.69
2063 2103 2.031120 CTTTTTGGACCCACTGCTTGA 58.969 47.619 0.00 0.00 0.00 3.02
2064 2104 1.538849 GCTTTTTGGACCCACTGCTTG 60.539 52.381 0.00 0.00 0.00 4.01
2065 2105 0.752658 GCTTTTTGGACCCACTGCTT 59.247 50.000 0.00 0.00 0.00 3.91
2066 2106 1.115326 GGCTTTTTGGACCCACTGCT 61.115 55.000 0.00 0.00 0.00 4.24
2067 2107 1.367471 GGCTTTTTGGACCCACTGC 59.633 57.895 0.00 0.00 0.00 4.40
2068 2108 1.106944 ACGGCTTTTTGGACCCACTG 61.107 55.000 0.00 0.00 0.00 3.66
2069 2109 1.106944 CACGGCTTTTTGGACCCACT 61.107 55.000 0.00 0.00 0.00 4.00
2070 2110 1.362355 CACGGCTTTTTGGACCCAC 59.638 57.895 0.00 0.00 0.00 4.61
2071 2111 1.076632 ACACGGCTTTTTGGACCCA 60.077 52.632 0.00 0.00 0.00 4.51
2072 2112 1.362355 CACACGGCTTTTTGGACCC 59.638 57.895 0.00 0.00 0.00 4.46
2073 2113 1.299850 GCACACGGCTTTTTGGACC 60.300 57.895 0.00 0.00 40.25 4.46
2074 2114 0.031994 ATGCACACGGCTTTTTGGAC 59.968 50.000 0.00 0.00 45.15 4.02
2075 2115 0.031857 CATGCACACGGCTTTTTGGA 59.968 50.000 0.00 0.00 45.15 3.53
2076 2116 0.945265 CCATGCACACGGCTTTTTGG 60.945 55.000 0.00 0.00 45.15 3.28
2077 2117 0.249405 ACCATGCACACGGCTTTTTG 60.249 50.000 0.00 0.00 45.15 2.44
2078 2118 0.463620 AACCATGCACACGGCTTTTT 59.536 45.000 0.00 0.00 45.15 1.94
2079 2119 0.031994 GAACCATGCACACGGCTTTT 59.968 50.000 0.00 0.00 45.15 2.27
2080 2120 0.823356 AGAACCATGCACACGGCTTT 60.823 50.000 0.00 0.00 45.15 3.51
2081 2121 0.823356 AAGAACCATGCACACGGCTT 60.823 50.000 0.00 0.00 45.15 4.35
2082 2122 0.036164 TAAGAACCATGCACACGGCT 59.964 50.000 0.00 0.00 45.15 5.52
2083 2123 1.094785 ATAAGAACCATGCACACGGC 58.905 50.000 0.00 0.00 45.13 5.68
2084 2124 3.687212 TGTAATAAGAACCATGCACACGG 59.313 43.478 0.00 0.00 0.00 4.94
2085 2125 4.937696 TGTAATAAGAACCATGCACACG 57.062 40.909 0.00 0.00 0.00 4.49
2121 2161 3.221389 GGCGCCCATGCATGACAT 61.221 61.111 28.31 0.00 40.66 3.06
2122 2162 4.737177 TGGCGCCCATGCATGACA 62.737 61.111 28.31 14.61 37.32 3.58
2123 2163 3.420214 CTTGGCGCCCATGCATGAC 62.420 63.158 28.31 17.64 37.32 3.06
2124 2164 3.142162 CTTGGCGCCCATGCATGA 61.142 61.111 28.31 3.60 37.32 3.07
2125 2165 3.454573 ACTTGGCGCCCATGCATG 61.455 61.111 26.77 20.19 37.32 4.06
2126 2166 3.454573 CACTTGGCGCCCATGCAT 61.455 61.111 26.77 0.00 37.32 3.96
2158 2473 7.201714 GCTATACACATATAGGGACGTTCCTAG 60.202 44.444 26.49 16.07 42.11 3.02
2159 2474 6.600822 GCTATACACATATAGGGACGTTCCTA 59.399 42.308 25.01 25.01 40.48 2.94
2188 2503 6.169557 AGACGGCACTTATTTATGACCATA 57.830 37.500 0.00 0.00 0.00 2.74
2189 2504 5.036117 AGACGGCACTTATTTATGACCAT 57.964 39.130 0.00 0.00 0.00 3.55
2269 2584 9.485591 CTGACGGATAAAACAATAACATAACAC 57.514 33.333 0.00 0.00 0.00 3.32
2294 2609 4.159557 AGGGAAACATTACACATTTGCCT 58.840 39.130 3.45 3.45 45.95 4.75
2356 2693 0.618968 AAGGAACCGAGGAGGCATCT 60.619 55.000 0.00 0.00 46.52 2.90
2357 2694 0.253327 AAAGGAACCGAGGAGGCATC 59.747 55.000 0.00 0.00 46.52 3.91
2467 2804 7.065803 GCCTTTTTGCTAGTATCTCATAACACA 59.934 37.037 0.00 0.00 0.00 3.72
2588 2925 5.576774 GCCAGGTCGGAGAAAAATAAAATTG 59.423 40.000 0.00 0.00 39.69 2.32
2603 2940 4.704833 CACTGTGGGCCAGGTCGG 62.705 72.222 6.40 2.54 46.06 4.79
2626 2963 2.173356 CCAACAGAGGAAGCCCATATGA 59.827 50.000 3.65 0.00 33.88 2.15
2629 2966 0.918983 CCCAACAGAGGAAGCCCATA 59.081 55.000 0.00 0.00 33.88 2.74
2646 2983 2.082629 CTTGCCACCCGTTTTGACCC 62.083 60.000 0.00 0.00 0.00 4.46
2649 2986 1.677052 GTTACTTGCCACCCGTTTTGA 59.323 47.619 0.00 0.00 0.00 2.69
2686 3023 6.616947 TGGTCCTGCTTTAATTAATTTCACG 58.383 36.000 5.91 0.00 0.00 4.35
2699 3036 1.064952 CGTTTCGTTTGGTCCTGCTTT 59.935 47.619 0.00 0.00 0.00 3.51
2713 3050 2.563471 TTTGGTTTTGTCCCGTTTCG 57.437 45.000 0.00 0.00 0.00 3.46
2717 3054 5.510009 GGTGATATTTTTGGTTTTGTCCCGT 60.510 40.000 0.00 0.00 0.00 5.28
2765 3102 6.418101 ACACTTGAACATATACATGCTCCTT 58.582 36.000 0.00 0.00 35.39 3.36
2770 3599 9.225201 CATAACAACACTTGAACATATACATGC 57.775 33.333 0.00 0.00 35.39 4.06
2783 3651 9.469807 TTTTGCCTATTAACATAACAACACTTG 57.530 29.630 0.00 0.00 0.00 3.16
2826 3694 8.135529 ACTTCTTTTGTCTTTACTTATTGTGGC 58.864 33.333 0.00 0.00 0.00 5.01
2863 4418 6.953101 TCCAAGCTGTATATCCACTAACAAA 58.047 36.000 0.00 0.00 0.00 2.83
2864 4419 6.382859 TCTCCAAGCTGTATATCCACTAACAA 59.617 38.462 0.00 0.00 0.00 2.83
2865 4420 5.897250 TCTCCAAGCTGTATATCCACTAACA 59.103 40.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.