Multiple sequence alignment - TraesCS1B01G189300

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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 TraesCS1B01G189300 chr1B 100.000 2357 0 0 1 2357 339193558 339191202 0.000000e+00 4353
1 TraesCS1B01G189300 chr1B 93.833 2027 104 4 1 2019 368916894 368914881 0.000000e+00 3031
2 TraesCS1B01G189300 chr5A 93.160 1345 83 3 623 1960 547123887 547125229 0.000000e+00 1965
3 TraesCS1B01G189300 chr7D 93.070 1342 83 5 627 1960 485220897 485219558 0.000000e+00 1954
4 TraesCS1B01G189300 chr7D 95.980 398 12 3 1962 2357 505910154 505909759 0.000000e+00 643
5 TraesCS1B01G189300 chr7D 96.774 341 7 3 2019 2357 402672047 402671709 1.220000e-157 566
6 TraesCS1B01G189300 chr7D 95.349 86 4 0 1962 2047 310874179 310874094 1.140000e-28 137
7 TraesCS1B01G189300 chr4A 93.124 1338 82 4 630 1960 66588366 66589700 0.000000e+00 1953
8 TraesCS1B01G189300 chr4A 92.073 1312 93 6 637 1939 703773713 703772404 0.000000e+00 1836
9 TraesCS1B01G189300 chr4A 92.474 1249 86 3 627 1867 407213009 407211761 0.000000e+00 1779
10 TraesCS1B01G189300 chr3B 92.836 1340 87 5 628 1960 222272221 222273558 0.000000e+00 1934
11 TraesCS1B01G189300 chr3B 94.253 87 5 0 1962 2048 600141112 600141198 1.470000e-27 134
12 TraesCS1B01G189300 chr3A 93.018 1332 82 5 637 1960 660197247 660198575 0.000000e+00 1934
13 TraesCS1B01G189300 chr3A 92.692 1341 87 7 627 1959 186908146 186906809 0.000000e+00 1923
14 TraesCS1B01G189300 chrUn 96.019 628 23 2 1 626 18824504 18823877 0.000000e+00 1020
15 TraesCS1B01G189300 chrUn 96.774 341 9 2 2019 2357 479891755 479891415 3.400000e-158 568
16 TraesCS1B01G189300 chr4D 95.556 630 26 2 1 628 437483307 437483936 0.000000e+00 1007
17 TraesCS1B01G189300 chr4D 95.215 627 28 2 1 626 481814618 481815243 0.000000e+00 990
18 TraesCS1B01G189300 chr4D 95.763 354 8 6 2009 2357 488740871 488740520 4.400000e-157 564
19 TraesCS1B01G189300 chr3D 95.397 630 27 2 1 628 50673021 50672392 0.000000e+00 1002
20 TraesCS1B01G189300 chr3D 94.762 630 31 2 1 628 50723036 50723665 0.000000e+00 979
21 TraesCS1B01G189300 chr3D 95.226 398 14 4 1962 2357 365509411 365509017 1.990000e-175 625
22 TraesCS1B01G189300 chr3D 96.774 341 9 2 2019 2357 578843486 578843826 3.400000e-158 568
23 TraesCS1B01G189300 chr6D 95.231 629 29 1 1 628 26501794 26502422 0.000000e+00 994
24 TraesCS1B01G189300 chr6D 94.929 631 29 2 1 628 460678159 460677529 0.000000e+00 985
25 TraesCS1B01G189300 chr5D 94.896 627 30 2 1 626 354634693 354635318 0.000000e+00 979
26 TraesCS1B01G189300 chr1D 96.501 343 10 2 2017 2357 189392927 189393269 1.220000e-157 566
27 TraesCS1B01G189300 chr1D 96.491 342 10 2 2018 2357 495410077 495409736 4.400000e-157 564
28 TraesCS1B01G189300 chr1D 95.442 351 14 2 2009 2357 61782751 61782401 2.050000e-155 558
29 TraesCS1B01G189300 chr1D 94.318 88 4 1 1962 2048 27356126 27356039 1.470000e-27 134
30 TraesCS1B01G189300 chr6A 96.552 87 3 0 1962 2048 305755107 305755193 6.790000e-31 145
31 TraesCS1B01G189300 chr7A 94.253 87 5 0 1962 2048 144693455 144693541 1.470000e-27 134
32 TraesCS1B01G189300 chr2D 94.253 87 5 0 1962 2048 263416700 263416786 1.470000e-27 134
33 TraesCS1B01G189300 chr1A 94.253 87 5 0 1962 2048 522431595 522431681 1.470000e-27 134


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 TraesCS1B01G189300 chr1B 339191202 339193558 2356 True 4353 4353 100.000 1 2357 1 chr1B.!!$R1 2356
1 TraesCS1B01G189300 chr1B 368914881 368916894 2013 True 3031 3031 93.833 1 2019 1 chr1B.!!$R2 2018
2 TraesCS1B01G189300 chr5A 547123887 547125229 1342 False 1965 1965 93.160 623 1960 1 chr5A.!!$F1 1337
3 TraesCS1B01G189300 chr7D 485219558 485220897 1339 True 1954 1954 93.070 627 1960 1 chr7D.!!$R3 1333
4 TraesCS1B01G189300 chr4A 66588366 66589700 1334 False 1953 1953 93.124 630 1960 1 chr4A.!!$F1 1330
5 TraesCS1B01G189300 chr4A 703772404 703773713 1309 True 1836 1836 92.073 637 1939 1 chr4A.!!$R2 1302
6 TraesCS1B01G189300 chr4A 407211761 407213009 1248 True 1779 1779 92.474 627 1867 1 chr4A.!!$R1 1240
7 TraesCS1B01G189300 chr3B 222272221 222273558 1337 False 1934 1934 92.836 628 1960 1 chr3B.!!$F1 1332
8 TraesCS1B01G189300 chr3A 660197247 660198575 1328 False 1934 1934 93.018 637 1960 1 chr3A.!!$F1 1323
9 TraesCS1B01G189300 chr3A 186906809 186908146 1337 True 1923 1923 92.692 627 1959 1 chr3A.!!$R1 1332
10 TraesCS1B01G189300 chrUn 18823877 18824504 627 True 1020 1020 96.019 1 626 1 chrUn.!!$R1 625
11 TraesCS1B01G189300 chr4D 437483307 437483936 629 False 1007 1007 95.556 1 628 1 chr4D.!!$F1 627
12 TraesCS1B01G189300 chr4D 481814618 481815243 625 False 990 990 95.215 1 626 1 chr4D.!!$F2 625
13 TraesCS1B01G189300 chr3D 50672392 50673021 629 True 1002 1002 95.397 1 628 1 chr3D.!!$R1 627
14 TraesCS1B01G189300 chr3D 50723036 50723665 629 False 979 979 94.762 1 628 1 chr3D.!!$F1 627
15 TraesCS1B01G189300 chr6D 26501794 26502422 628 False 994 994 95.231 1 628 1 chr6D.!!$F1 627
16 TraesCS1B01G189300 chr6D 460677529 460678159 630 True 985 985 94.929 1 628 1 chr6D.!!$R1 627
17 TraesCS1B01G189300 chr5D 354634693 354635318 625 False 979 979 94.896 1 626 1 chr5D.!!$F1 625

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
804 811 2.290008 TGATGTAGTGGTGCCGAATGTT 60.29 45.455 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2042 0.036765 AACGCACGGGCATTCTTCTA 60.037 50.0 11.77 0.0 41.24 2.1 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
353 358 7.451566 AGGATGATTGTGGTAAACTAAAAAGCT 59.548 33.333 0.00 0.00 0.00 3.74
732 739 9.841295 AAAAGACCTTACAAAGTAGTACATCAA 57.159 29.630 2.52 0.00 0.00 2.57
738 745 9.601217 CCTTACAAAGTAGTACATCAATAAGCT 57.399 33.333 2.52 0.00 0.00 3.74
788 795 2.960104 GCTACTCCTACCCCCTTGATGT 60.960 54.545 0.00 0.00 0.00 3.06
804 811 2.290008 TGATGTAGTGGTGCCGAATGTT 60.290 45.455 0.00 0.00 0.00 2.71
829 836 5.123186 CGAGCCTAATACCAAACAAACATCA 59.877 40.000 0.00 0.00 0.00 3.07
939 946 4.697756 CGCCGCCTTCTTCCACCA 62.698 66.667 0.00 0.00 0.00 4.17
1114 1121 3.728076 ATGACGCGGTAGATACAACAT 57.272 42.857 12.47 0.00 0.00 2.71
1143 1150 2.352422 GCAGCCTCCACACCATCA 59.648 61.111 0.00 0.00 0.00 3.07
1161 1168 0.322975 CACCACTGCTGGAGCTACTT 59.677 55.000 0.00 0.00 40.55 2.24
1198 1206 0.252284 ACATCTCTCCCCCGAACAGT 60.252 55.000 0.00 0.00 0.00 3.55
1283 1291 6.983906 ATCCAGACTGAATTTTGGACTTTT 57.016 33.333 3.32 0.00 42.12 2.27
1437 1455 3.817787 CGTGTACTCCGGATCCGA 58.182 61.111 35.42 19.41 42.83 4.55
1478 1496 1.268437 GCGAAGATGAAAGAGCCATGC 60.268 52.381 0.00 0.00 0.00 4.06
1500 1518 1.272147 GCTCAACCCACCAGAAAGGAT 60.272 52.381 0.00 0.00 41.22 3.24
2033 2055 9.706691 TCTTTATTTATACTAGAAGAATGCCCG 57.293 33.333 0.00 0.00 0.00 6.13
2034 2056 9.490379 CTTTATTTATACTAGAAGAATGCCCGT 57.510 33.333 0.00 0.00 0.00 5.28
2035 2057 8.827177 TTATTTATACTAGAAGAATGCCCGTG 57.173 34.615 0.00 0.00 0.00 4.94
2036 2058 2.596904 TACTAGAAGAATGCCCGTGC 57.403 50.000 0.00 0.00 38.26 5.34
2037 2059 0.460284 ACTAGAAGAATGCCCGTGCG 60.460 55.000 0.00 0.00 41.78 5.34
2038 2060 0.460284 CTAGAAGAATGCCCGTGCGT 60.460 55.000 0.00 0.00 41.78 5.24
2040 2062 1.154225 GAAGAATGCCCGTGCGTTG 60.154 57.895 0.86 0.00 46.55 4.10
2041 2063 3.267597 AAGAATGCCCGTGCGTTGC 62.268 57.895 0.86 0.00 46.55 4.17
2042 2064 4.036804 GAATGCCCGTGCGTTGCA 62.037 61.111 0.86 8.11 46.55 4.08
2043 2065 3.550339 GAATGCCCGTGCGTTGCAA 62.550 57.895 0.86 0.00 46.55 4.08
2044 2066 3.839642 AATGCCCGTGCGTTGCAAC 62.840 57.895 19.89 19.89 44.90 4.17
2054 2076 3.302344 GTTGCAACGGGGCCACAT 61.302 61.111 14.90 0.00 30.39 3.21
2055 2077 2.522923 TTGCAACGGGGCCACATT 60.523 55.556 5.46 0.00 0.00 2.71
2056 2078 1.228583 TTGCAACGGGGCCACATTA 60.229 52.632 5.46 0.00 0.00 1.90
2057 2079 0.827925 TTGCAACGGGGCCACATTAA 60.828 50.000 5.46 0.00 0.00 1.40
2058 2080 1.214325 GCAACGGGGCCACATTAAC 59.786 57.895 5.46 0.00 0.00 2.01
2059 2081 1.248101 GCAACGGGGCCACATTAACT 61.248 55.000 5.46 0.00 0.00 2.24
2060 2082 1.253100 CAACGGGGCCACATTAACTT 58.747 50.000 5.46 0.00 0.00 2.66
2061 2083 1.616374 CAACGGGGCCACATTAACTTT 59.384 47.619 5.46 0.00 0.00 2.66
2062 2084 2.820787 CAACGGGGCCACATTAACTTTA 59.179 45.455 5.46 0.00 0.00 1.85
2063 2085 3.157750 ACGGGGCCACATTAACTTTAA 57.842 42.857 5.46 0.00 0.00 1.52
2064 2086 3.498334 ACGGGGCCACATTAACTTTAAA 58.502 40.909 5.46 0.00 0.00 1.52
2065 2087 3.896272 ACGGGGCCACATTAACTTTAAAA 59.104 39.130 5.46 0.00 0.00 1.52
2066 2088 4.021807 ACGGGGCCACATTAACTTTAAAAG 60.022 41.667 5.46 0.00 0.00 2.27
2067 2089 4.021807 CGGGGCCACATTAACTTTAAAAGT 60.022 41.667 5.46 0.00 45.46 2.66
2128 2150 9.463443 TCTCATACATATTAAGTGACATTGACG 57.537 33.333 0.00 0.00 0.00 4.35
2129 2151 9.463443 CTCATACATATTAAGTGACATTGACGA 57.537 33.333 0.00 0.00 0.00 4.20
2130 2152 9.244799 TCATACATATTAAGTGACATTGACGAC 57.755 33.333 0.00 0.00 0.00 4.34
2131 2153 6.903883 ACATATTAAGTGACATTGACGACC 57.096 37.500 0.00 0.00 0.00 4.79
2132 2154 6.640518 ACATATTAAGTGACATTGACGACCT 58.359 36.000 0.00 0.00 0.00 3.85
2133 2155 7.103641 ACATATTAAGTGACATTGACGACCTT 58.896 34.615 0.00 0.00 0.00 3.50
2134 2156 7.606456 ACATATTAAGTGACATTGACGACCTTT 59.394 33.333 0.00 0.00 0.00 3.11
2135 2157 6.877611 ATTAAGTGACATTGACGACCTTTT 57.122 33.333 0.00 0.00 0.00 2.27
2136 2158 6.687081 TTAAGTGACATTGACGACCTTTTT 57.313 33.333 0.00 0.00 0.00 1.94
2137 2159 7.789273 TTAAGTGACATTGACGACCTTTTTA 57.211 32.000 0.00 0.00 0.00 1.52
2138 2160 5.668558 AGTGACATTGACGACCTTTTTAC 57.331 39.130 0.00 0.00 0.00 2.01
2139 2161 4.514066 AGTGACATTGACGACCTTTTTACC 59.486 41.667 0.00 0.00 0.00 2.85
2140 2162 4.273969 GTGACATTGACGACCTTTTTACCA 59.726 41.667 0.00 0.00 0.00 3.25
2141 2163 5.048991 GTGACATTGACGACCTTTTTACCAT 60.049 40.000 0.00 0.00 0.00 3.55
2142 2164 5.180492 TGACATTGACGACCTTTTTACCATC 59.820 40.000 0.00 0.00 0.00 3.51
2143 2165 5.067273 ACATTGACGACCTTTTTACCATCA 58.933 37.500 0.00 0.00 0.00 3.07
2144 2166 5.533154 ACATTGACGACCTTTTTACCATCAA 59.467 36.000 0.00 0.00 0.00 2.57
2145 2167 6.039941 ACATTGACGACCTTTTTACCATCAAA 59.960 34.615 0.00 0.00 0.00 2.69
2146 2168 6.642707 TTGACGACCTTTTTACCATCAAAT 57.357 33.333 0.00 0.00 0.00 2.32
2147 2169 6.642707 TGACGACCTTTTTACCATCAAATT 57.357 33.333 0.00 0.00 0.00 1.82
2148 2170 6.674066 TGACGACCTTTTTACCATCAAATTC 58.326 36.000 0.00 0.00 0.00 2.17
2149 2171 6.488683 TGACGACCTTTTTACCATCAAATTCT 59.511 34.615 0.00 0.00 0.00 2.40
2150 2172 6.909909 ACGACCTTTTTACCATCAAATTCTC 58.090 36.000 0.00 0.00 0.00 2.87
2151 2173 6.488683 ACGACCTTTTTACCATCAAATTCTCA 59.511 34.615 0.00 0.00 0.00 3.27
2152 2174 6.801862 CGACCTTTTTACCATCAAATTCTCAC 59.198 38.462 0.00 0.00 0.00 3.51
2153 2175 7.521423 CGACCTTTTTACCATCAAATTCTCACA 60.521 37.037 0.00 0.00 0.00 3.58
2154 2176 7.433680 ACCTTTTTACCATCAAATTCTCACAC 58.566 34.615 0.00 0.00 0.00 3.82
2155 2177 7.069331 ACCTTTTTACCATCAAATTCTCACACA 59.931 33.333 0.00 0.00 0.00 3.72
2156 2178 7.382218 CCTTTTTACCATCAAATTCTCACACAC 59.618 37.037 0.00 0.00 0.00 3.82
2157 2179 6.951062 TTTACCATCAAATTCTCACACACA 57.049 33.333 0.00 0.00 0.00 3.72
2158 2180 4.836125 ACCATCAAATTCTCACACACAC 57.164 40.909 0.00 0.00 0.00 3.82
2159 2181 4.206375 ACCATCAAATTCTCACACACACA 58.794 39.130 0.00 0.00 0.00 3.72
2160 2182 4.036734 ACCATCAAATTCTCACACACACAC 59.963 41.667 0.00 0.00 0.00 3.82
2161 2183 4.036616 CCATCAAATTCTCACACACACACA 59.963 41.667 0.00 0.00 0.00 3.72
2162 2184 4.614555 TCAAATTCTCACACACACACAC 57.385 40.909 0.00 0.00 0.00 3.82
2163 2185 3.376859 TCAAATTCTCACACACACACACC 59.623 43.478 0.00 0.00 0.00 4.16
2164 2186 1.967319 ATTCTCACACACACACACCC 58.033 50.000 0.00 0.00 0.00 4.61
2165 2187 0.908910 TTCTCACACACACACACCCT 59.091 50.000 0.00 0.00 0.00 4.34
2166 2188 0.464036 TCTCACACACACACACCCTC 59.536 55.000 0.00 0.00 0.00 4.30
2167 2189 0.465705 CTCACACACACACACCCTCT 59.534 55.000 0.00 0.00 0.00 3.69
2168 2190 0.464036 TCACACACACACACCCTCTC 59.536 55.000 0.00 0.00 0.00 3.20
2169 2191 0.532862 CACACACACACACCCTCTCC 60.533 60.000 0.00 0.00 0.00 3.71
2170 2192 1.071471 CACACACACACCCTCTCCC 59.929 63.158 0.00 0.00 0.00 4.30
2171 2193 1.074471 ACACACACACCCTCTCCCT 60.074 57.895 0.00 0.00 0.00 4.20
2172 2194 1.122019 ACACACACACCCTCTCCCTC 61.122 60.000 0.00 0.00 0.00 4.30
2173 2195 1.536662 ACACACACCCTCTCCCTCC 60.537 63.158 0.00 0.00 0.00 4.30
2174 2196 2.122954 ACACACCCTCTCCCTCCC 59.877 66.667 0.00 0.00 0.00 4.30
2175 2197 2.452114 CACACCCTCTCCCTCCCT 59.548 66.667 0.00 0.00 0.00 4.20
2176 2198 1.687493 CACACCCTCTCCCTCCCTC 60.687 68.421 0.00 0.00 0.00 4.30
2177 2199 1.864559 ACACCCTCTCCCTCCCTCT 60.865 63.158 0.00 0.00 0.00 3.69
2178 2200 1.394151 CACCCTCTCCCTCCCTCTT 59.606 63.158 0.00 0.00 0.00 2.85
2179 2201 0.689412 CACCCTCTCCCTCCCTCTTC 60.689 65.000 0.00 0.00 0.00 2.87
2180 2202 1.074850 CCCTCTCCCTCCCTCTTCC 60.075 68.421 0.00 0.00 0.00 3.46
2181 2203 1.598856 CCCTCTCCCTCCCTCTTCCT 61.599 65.000 0.00 0.00 0.00 3.36
2182 2204 0.105709 CCTCTCCCTCCCTCTTCCTC 60.106 65.000 0.00 0.00 0.00 3.71
2183 2205 0.633921 CTCTCCCTCCCTCTTCCTCA 59.366 60.000 0.00 0.00 0.00 3.86
2184 2206 0.336737 TCTCCCTCCCTCTTCCTCAC 59.663 60.000 0.00 0.00 0.00 3.51
2185 2207 0.338120 CTCCCTCCCTCTTCCTCACT 59.662 60.000 0.00 0.00 0.00 3.41
2186 2208 0.336737 TCCCTCCCTCTTCCTCACTC 59.663 60.000 0.00 0.00 0.00 3.51
2187 2209 0.338120 CCCTCCCTCTTCCTCACTCT 59.662 60.000 0.00 0.00 0.00 3.24
2188 2210 1.687996 CCCTCCCTCTTCCTCACTCTC 60.688 61.905 0.00 0.00 0.00 3.20
2189 2211 1.287739 CCTCCCTCTTCCTCACTCTCT 59.712 57.143 0.00 0.00 0.00 3.10
2190 2212 2.654863 CTCCCTCTTCCTCACTCTCTC 58.345 57.143 0.00 0.00 0.00 3.20
2191 2213 2.242196 CTCCCTCTTCCTCACTCTCTCT 59.758 54.545 0.00 0.00 0.00 3.10
2192 2214 2.241176 TCCCTCTTCCTCACTCTCTCTC 59.759 54.545 0.00 0.00 0.00 3.20
2193 2215 2.654863 CCTCTTCCTCACTCTCTCTCC 58.345 57.143 0.00 0.00 0.00 3.71
2194 2216 2.654863 CTCTTCCTCACTCTCTCTCCC 58.345 57.143 0.00 0.00 0.00 4.30
2195 2217 1.286553 TCTTCCTCACTCTCTCTCCCC 59.713 57.143 0.00 0.00 0.00 4.81
2196 2218 0.336737 TTCCTCACTCTCTCTCCCCC 59.663 60.000 0.00 0.00 0.00 5.40
2197 2219 0.553862 TCCTCACTCTCTCTCCCCCT 60.554 60.000 0.00 0.00 0.00 4.79
2198 2220 0.106217 CCTCACTCTCTCTCCCCCTC 60.106 65.000 0.00 0.00 0.00 4.30
2199 2221 0.926293 CTCACTCTCTCTCCCCCTCT 59.074 60.000 0.00 0.00 0.00 3.69
2200 2222 0.923358 TCACTCTCTCTCCCCCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
2201 2223 0.106217 CACTCTCTCTCCCCCTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
2202 2224 1.293683 ACTCTCTCTCCCCCTCTCCC 61.294 65.000 0.00 0.00 0.00 4.30
2203 2225 0.998945 CTCTCTCTCCCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
2204 2226 0.996762 TCTCTCTCCCCCTCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
2205 2227 1.230650 TCTCTCCCCCTCTCCCTCA 60.231 63.158 0.00 0.00 0.00 3.86
2206 2228 1.075600 CTCTCCCCCTCTCCCTCAC 60.076 68.421 0.00 0.00 0.00 3.51
2207 2229 1.547755 TCTCCCCCTCTCCCTCACT 60.548 63.158 0.00 0.00 0.00 3.41
2208 2230 1.075600 CTCCCCCTCTCCCTCACTC 60.076 68.421 0.00 0.00 0.00 3.51
2209 2231 2.443016 CCCCCTCTCCCTCACTCG 60.443 72.222 0.00 0.00 0.00 4.18
2210 2232 2.443016 CCCCTCTCCCTCACTCGG 60.443 72.222 0.00 0.00 0.00 4.63
2211 2233 2.443016 CCCTCTCCCTCACTCGGG 60.443 72.222 0.00 0.00 46.13 5.14
2219 2241 2.037367 CTCACTCGGGAGGTGGGA 59.963 66.667 0.00 0.00 37.35 4.37
2220 2242 2.283676 TCACTCGGGAGGTGGGAC 60.284 66.667 0.00 0.00 35.61 4.46
2221 2243 2.603473 CACTCGGGAGGTGGGACA 60.603 66.667 0.00 0.00 0.00 4.02
2222 2244 2.203182 ACTCGGGAGGTGGGACAA 59.797 61.111 0.00 0.00 44.16 3.18
2223 2245 1.460689 ACTCGGGAGGTGGGACAAA 60.461 57.895 0.00 0.00 44.16 2.83
2224 2246 1.057851 ACTCGGGAGGTGGGACAAAA 61.058 55.000 0.00 0.00 44.16 2.44
2225 2247 0.109723 CTCGGGAGGTGGGACAAAAA 59.890 55.000 0.00 0.00 44.16 1.94
2226 2248 0.774908 TCGGGAGGTGGGACAAAAAT 59.225 50.000 0.00 0.00 44.16 1.82
2227 2249 1.986631 TCGGGAGGTGGGACAAAAATA 59.013 47.619 0.00 0.00 44.16 1.40
2228 2250 2.375845 TCGGGAGGTGGGACAAAAATAA 59.624 45.455 0.00 0.00 44.16 1.40
2229 2251 3.158676 CGGGAGGTGGGACAAAAATAAA 58.841 45.455 0.00 0.00 44.16 1.40
2230 2252 3.057104 CGGGAGGTGGGACAAAAATAAAC 60.057 47.826 0.00 0.00 44.16 2.01
2231 2253 3.259876 GGGAGGTGGGACAAAAATAAACC 59.740 47.826 0.00 0.00 44.16 3.27
2232 2254 3.259876 GGAGGTGGGACAAAAATAAACCC 59.740 47.826 0.00 0.00 44.16 4.11
2233 2255 2.894765 AGGTGGGACAAAAATAAACCCG 59.105 45.455 0.00 0.00 44.16 5.28
2234 2256 2.028839 GGTGGGACAAAAATAAACCCGG 60.029 50.000 0.00 0.00 44.16 5.73
2235 2257 2.892215 GTGGGACAAAAATAAACCCGGA 59.108 45.455 0.73 0.00 44.16 5.14
2236 2258 3.321396 GTGGGACAAAAATAAACCCGGAA 59.679 43.478 0.73 0.00 44.16 4.30
2237 2259 3.321396 TGGGACAAAAATAAACCCGGAAC 59.679 43.478 0.73 0.00 43.04 3.62
2238 2260 3.306225 GGGACAAAAATAAACCCGGAACC 60.306 47.826 0.73 0.00 0.00 3.62
2239 2261 3.567530 GACAAAAATAAACCCGGAACCG 58.432 45.455 0.73 6.25 39.44 4.44
2240 2262 3.220940 ACAAAAATAAACCCGGAACCGA 58.779 40.909 15.07 0.00 42.83 4.69
2241 2263 3.253921 ACAAAAATAAACCCGGAACCGAG 59.746 43.478 15.07 3.79 42.83 4.63
2242 2264 3.421919 AAAATAAACCCGGAACCGAGA 57.578 42.857 15.07 0.00 42.83 4.04
2243 2265 2.391616 AATAAACCCGGAACCGAGAC 57.608 50.000 15.07 0.00 42.83 3.36
2244 2266 1.565067 ATAAACCCGGAACCGAGACT 58.435 50.000 15.07 0.00 42.83 3.24
2245 2267 2.214376 TAAACCCGGAACCGAGACTA 57.786 50.000 15.07 0.00 42.83 2.59
2246 2268 0.605083 AAACCCGGAACCGAGACTAC 59.395 55.000 15.07 0.00 42.83 2.73
2247 2269 1.253593 AACCCGGAACCGAGACTACC 61.254 60.000 15.07 0.00 42.83 3.18
2248 2270 1.679977 CCCGGAACCGAGACTACCA 60.680 63.158 15.07 0.00 42.83 3.25
2249 2271 1.252904 CCCGGAACCGAGACTACCAA 61.253 60.000 15.07 0.00 42.83 3.67
2250 2272 0.108945 CCGGAACCGAGACTACCAAC 60.109 60.000 15.07 0.00 42.83 3.77
2251 2273 0.886563 CGGAACCGAGACTACCAACT 59.113 55.000 7.53 0.00 42.83 3.16
2252 2274 1.402456 CGGAACCGAGACTACCAACTG 60.402 57.143 7.53 0.00 42.83 3.16
2253 2275 1.891150 GGAACCGAGACTACCAACTGA 59.109 52.381 0.00 0.00 0.00 3.41
2254 2276 2.094649 GGAACCGAGACTACCAACTGAG 60.095 54.545 0.00 0.00 0.00 3.35
2255 2277 2.581216 ACCGAGACTACCAACTGAGA 57.419 50.000 0.00 0.00 0.00 3.27
2256 2278 2.161030 ACCGAGACTACCAACTGAGAC 58.839 52.381 0.00 0.00 0.00 3.36
2257 2279 2.160205 CCGAGACTACCAACTGAGACA 58.840 52.381 0.00 0.00 0.00 3.41
2258 2280 2.755655 CCGAGACTACCAACTGAGACAT 59.244 50.000 0.00 0.00 0.00 3.06
2259 2281 3.193691 CCGAGACTACCAACTGAGACATT 59.806 47.826 0.00 0.00 0.00 2.71
2260 2282 4.398358 CCGAGACTACCAACTGAGACATTA 59.602 45.833 0.00 0.00 0.00 1.90
2261 2283 5.449314 CCGAGACTACCAACTGAGACATTAG 60.449 48.000 0.00 0.00 0.00 1.73
2262 2284 5.449314 CGAGACTACCAACTGAGACATTAGG 60.449 48.000 0.00 0.00 0.00 2.69
2263 2285 5.580998 AGACTACCAACTGAGACATTAGGA 58.419 41.667 0.00 0.00 0.00 2.94
2264 2286 5.654650 AGACTACCAACTGAGACATTAGGAG 59.345 44.000 0.00 0.00 0.00 3.69
2265 2287 5.334421 ACTACCAACTGAGACATTAGGAGT 58.666 41.667 0.00 0.00 0.00 3.85
2266 2288 6.491383 ACTACCAACTGAGACATTAGGAGTA 58.509 40.000 0.00 0.00 0.00 2.59
2267 2289 5.923733 ACCAACTGAGACATTAGGAGTAG 57.076 43.478 0.00 0.00 0.00 2.57
2268 2290 5.580998 ACCAACTGAGACATTAGGAGTAGA 58.419 41.667 0.00 0.00 0.00 2.59
2269 2291 5.654650 ACCAACTGAGACATTAGGAGTAGAG 59.345 44.000 0.00 0.00 0.00 2.43
2270 2292 5.888724 CCAACTGAGACATTAGGAGTAGAGA 59.111 44.000 0.00 0.00 0.00 3.10
2271 2293 6.549364 CCAACTGAGACATTAGGAGTAGAGAT 59.451 42.308 0.00 0.00 0.00 2.75
2272 2294 7.255451 CCAACTGAGACATTAGGAGTAGAGATC 60.255 44.444 0.00 0.00 0.00 2.75
2273 2295 6.905736 ACTGAGACATTAGGAGTAGAGATCA 58.094 40.000 0.00 0.00 0.00 2.92
2274 2296 7.526041 ACTGAGACATTAGGAGTAGAGATCAT 58.474 38.462 0.00 0.00 0.00 2.45
2275 2297 8.004215 ACTGAGACATTAGGAGTAGAGATCATT 58.996 37.037 0.00 0.00 0.00 2.57
2276 2298 8.774546 TGAGACATTAGGAGTAGAGATCATTT 57.225 34.615 0.00 0.00 0.00 2.32
2277 2299 9.868160 TGAGACATTAGGAGTAGAGATCATTTA 57.132 33.333 0.00 0.00 0.00 1.40
2279 2301 9.875708 AGACATTAGGAGTAGAGATCATTTAGT 57.124 33.333 0.00 0.00 0.00 2.24
2319 2341 8.851960 AGAAAACGATGTTAAAAAGGAGAAAC 57.148 30.769 0.00 0.00 0.00 2.78
2320 2342 7.642586 AGAAAACGATGTTAAAAAGGAGAAACG 59.357 33.333 0.00 0.00 0.00 3.60
2321 2343 5.352643 ACGATGTTAAAAAGGAGAAACGG 57.647 39.130 0.00 0.00 0.00 4.44
2322 2344 5.058490 ACGATGTTAAAAAGGAGAAACGGA 58.942 37.500 0.00 0.00 0.00 4.69
2323 2345 5.704053 ACGATGTTAAAAAGGAGAAACGGAT 59.296 36.000 0.00 0.00 0.00 4.18
2324 2346 6.206048 ACGATGTTAAAAAGGAGAAACGGATT 59.794 34.615 0.00 0.00 0.00 3.01
2325 2347 7.388500 ACGATGTTAAAAAGGAGAAACGGATTA 59.612 33.333 0.00 0.00 0.00 1.75
2326 2348 7.903431 CGATGTTAAAAAGGAGAAACGGATTAG 59.097 37.037 0.00 0.00 0.00 1.73
2327 2349 8.857694 ATGTTAAAAAGGAGAAACGGATTAGA 57.142 30.769 0.00 0.00 0.00 2.10
2328 2350 8.680039 TGTTAAAAAGGAGAAACGGATTAGAA 57.320 30.769 0.00 0.00 0.00 2.10
2329 2351 9.292195 TGTTAAAAAGGAGAAACGGATTAGAAT 57.708 29.630 0.00 0.00 0.00 2.40
2335 2357 9.681062 AAAGGAGAAACGGATTAGAATAATTGA 57.319 29.630 0.00 0.00 0.00 2.57
2336 2358 9.681062 AAGGAGAAACGGATTAGAATAATTGAA 57.319 29.630 0.00 0.00 0.00 2.69
2337 2359 9.681062 AGGAGAAACGGATTAGAATAATTGAAA 57.319 29.630 0.00 0.00 0.00 2.69
2350 2372 8.587952 AGAATAATTGAAAAACCAAAAGGACG 57.412 30.769 0.00 0.00 0.00 4.79
2351 2373 8.417884 AGAATAATTGAAAAACCAAAAGGACGA 58.582 29.630 0.00 0.00 0.00 4.20
2352 2374 9.203421 GAATAATTGAAAAACCAAAAGGACGAT 57.797 29.630 0.00 0.00 0.00 3.73
2353 2375 6.843069 AATTGAAAAACCAAAAGGACGATG 57.157 33.333 0.00 0.00 0.00 3.84
2354 2376 4.993029 TGAAAAACCAAAAGGACGATGT 57.007 36.364 0.00 0.00 0.00 3.06
2355 2377 6.452494 TTGAAAAACCAAAAGGACGATGTA 57.548 33.333 0.00 0.00 0.00 2.29
2356 2378 6.452494 TGAAAAACCAAAAGGACGATGTAA 57.548 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 177 7.412672 CGGCAGTAGACTTGTTTTATAGAAACC 60.413 40.741 0.00 0.00 0.00 3.27
353 358 7.705325 GGAGCGTCTTGTATTATTTGAGTCTTA 59.295 37.037 0.00 0.00 0.00 2.10
466 473 2.135890 CAAAGCTTGGGGTTGCCTT 58.864 52.632 0.00 0.00 33.11 4.35
467 474 3.875390 CAAAGCTTGGGGTTGCCT 58.125 55.556 0.00 0.00 33.11 4.75
732 739 3.659183 AGATGGTGGCTTCAAGCTTAT 57.341 42.857 9.83 0.00 41.99 1.73
738 745 3.882131 GCCTAGATGGTGGCTTCAA 57.118 52.632 0.00 0.00 45.26 2.69
788 795 3.131326 CGAACATTCGGCACCACTA 57.869 52.632 6.11 0.00 46.30 2.74
804 811 4.643463 TGTTTGTTTGGTATTAGGCTCGA 58.357 39.130 0.00 0.00 0.00 4.04
829 836 5.594317 GGCATTAGATGTTAGGATTTGGTGT 59.406 40.000 0.00 0.00 0.00 4.16
939 946 1.890552 ACCTGCTCTGGAGATGGATT 58.109 50.000 13.27 0.00 0.00 3.01
1143 1150 0.322975 CAAGTAGCTCCAGCAGTGGT 59.677 55.000 0.48 0.00 45.28 4.16
1161 1168 2.159490 TTGTGGATGGTGGGCTCCA 61.159 57.895 4.67 4.67 42.01 3.86
1198 1206 2.890766 GCCGTCTTGGGAGGAACCA 61.891 63.158 0.00 0.00 41.20 3.67
1283 1291 2.606519 CCGAACCCCTCCTGGACA 60.607 66.667 0.00 0.00 35.39 4.02
1437 1455 0.953960 GGTTTCGGATCGTGGCTTGT 60.954 55.000 0.00 0.00 0.00 3.16
1478 1496 1.228124 TTTCTGGTGGGTTGAGCCG 60.228 57.895 0.00 0.00 38.44 5.52
1500 1518 6.918067 TCTACAAGGAGTTCTTCTTGATCA 57.082 37.500 22.85 9.78 41.94 2.92
1960 1982 5.897050 AGTGGTATTTTGTTTTCTTTCGCA 58.103 33.333 0.00 0.00 0.00 5.10
1961 1983 6.474102 TGAAGTGGTATTTTGTTTTCTTTCGC 59.526 34.615 0.00 0.00 0.00 4.70
1962 1984 7.979115 TGAAGTGGTATTTTGTTTTCTTTCG 57.021 32.000 0.00 0.00 0.00 3.46
1963 1985 8.817100 CCTTGAAGTGGTATTTTGTTTTCTTTC 58.183 33.333 0.00 0.00 0.00 2.62
1964 1986 8.318412 ACCTTGAAGTGGTATTTTGTTTTCTTT 58.682 29.630 0.00 0.00 35.80 2.52
2019 2041 0.460284 ACGCACGGGCATTCTTCTAG 60.460 55.000 11.77 0.00 41.24 2.43
2020 2042 0.036765 AACGCACGGGCATTCTTCTA 60.037 50.000 11.77 0.00 41.24 2.10
2021 2043 1.302511 AACGCACGGGCATTCTTCT 60.303 52.632 11.77 0.00 41.24 2.85
2022 2044 1.154225 CAACGCACGGGCATTCTTC 60.154 57.895 11.77 0.00 41.24 2.87
2023 2045 2.953821 CAACGCACGGGCATTCTT 59.046 55.556 11.77 0.00 41.24 2.52
2024 2046 3.737172 GCAACGCACGGGCATTCT 61.737 61.111 11.77 0.00 41.24 2.40
2025 2047 3.550339 TTGCAACGCACGGGCATTC 62.550 57.895 11.77 0.00 38.71 2.67
2026 2048 3.600694 TTGCAACGCACGGGCATT 61.601 55.556 11.77 0.00 38.71 3.56
2027 2049 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
2037 2059 1.528292 TAATGTGGCCCCGTTGCAAC 61.528 55.000 19.89 19.89 35.65 4.17
2038 2060 0.827925 TTAATGTGGCCCCGTTGCAA 60.828 50.000 0.00 0.00 0.00 4.08
2039 2061 1.228583 TTAATGTGGCCCCGTTGCA 60.229 52.632 0.00 0.00 0.00 4.08
2040 2062 1.214325 GTTAATGTGGCCCCGTTGC 59.786 57.895 0.00 0.00 0.00 4.17
2041 2063 1.253100 AAGTTAATGTGGCCCCGTTG 58.747 50.000 0.00 0.00 0.00 4.10
2042 2064 2.003937 AAAGTTAATGTGGCCCCGTT 57.996 45.000 0.00 0.00 0.00 4.44
2043 2065 2.883122 TAAAGTTAATGTGGCCCCGT 57.117 45.000 0.00 0.00 0.00 5.28
2044 2066 4.021807 ACTTTTAAAGTTAATGTGGCCCCG 60.022 41.667 4.30 0.00 39.04 5.73
2045 2067 5.477607 ACTTTTAAAGTTAATGTGGCCCC 57.522 39.130 4.30 0.00 39.04 5.80
2102 2124 9.463443 CGTCAATGTCACTTAATATGTATGAGA 57.537 33.333 0.00 0.00 0.00 3.27
2103 2125 9.463443 TCGTCAATGTCACTTAATATGTATGAG 57.537 33.333 0.00 0.00 0.00 2.90
2104 2126 9.244799 GTCGTCAATGTCACTTAATATGTATGA 57.755 33.333 0.00 0.00 0.00 2.15
2105 2127 8.487970 GGTCGTCAATGTCACTTAATATGTATG 58.512 37.037 0.00 0.00 0.00 2.39
2106 2128 8.421784 AGGTCGTCAATGTCACTTAATATGTAT 58.578 33.333 0.00 0.00 0.00 2.29
2107 2129 7.778083 AGGTCGTCAATGTCACTTAATATGTA 58.222 34.615 0.00 0.00 0.00 2.29
2108 2130 6.640518 AGGTCGTCAATGTCACTTAATATGT 58.359 36.000 0.00 0.00 0.00 2.29
2109 2131 7.539712 AAGGTCGTCAATGTCACTTAATATG 57.460 36.000 0.00 0.00 0.00 1.78
2110 2132 8.561738 AAAAGGTCGTCAATGTCACTTAATAT 57.438 30.769 0.00 0.00 0.00 1.28
2111 2133 7.972832 AAAAGGTCGTCAATGTCACTTAATA 57.027 32.000 0.00 0.00 0.00 0.98
2112 2134 6.877611 AAAAGGTCGTCAATGTCACTTAAT 57.122 33.333 0.00 0.00 0.00 1.40
2113 2135 6.687081 AAAAAGGTCGTCAATGTCACTTAA 57.313 33.333 0.00 0.00 0.00 1.85
2114 2136 6.203338 GGTAAAAAGGTCGTCAATGTCACTTA 59.797 38.462 0.00 0.00 0.00 2.24
2115 2137 5.008316 GGTAAAAAGGTCGTCAATGTCACTT 59.992 40.000 0.00 0.00 0.00 3.16
2116 2138 4.514066 GGTAAAAAGGTCGTCAATGTCACT 59.486 41.667 0.00 0.00 0.00 3.41
2117 2139 4.273969 TGGTAAAAAGGTCGTCAATGTCAC 59.726 41.667 0.00 0.00 0.00 3.67
2118 2140 4.452825 TGGTAAAAAGGTCGTCAATGTCA 58.547 39.130 0.00 0.00 0.00 3.58
2119 2141 5.180492 TGATGGTAAAAAGGTCGTCAATGTC 59.820 40.000 0.00 0.00 0.00 3.06
2120 2142 5.067273 TGATGGTAAAAAGGTCGTCAATGT 58.933 37.500 0.00 0.00 0.00 2.71
2121 2143 5.621197 TGATGGTAAAAAGGTCGTCAATG 57.379 39.130 0.00 0.00 0.00 2.82
2122 2144 6.642707 TTTGATGGTAAAAAGGTCGTCAAT 57.357 33.333 0.00 0.00 35.78 2.57
2123 2145 6.642707 ATTTGATGGTAAAAAGGTCGTCAA 57.357 33.333 0.00 0.00 34.54 3.18
2124 2146 6.488683 AGAATTTGATGGTAAAAAGGTCGTCA 59.511 34.615 0.00 0.00 0.00 4.35
2125 2147 6.909909 AGAATTTGATGGTAAAAAGGTCGTC 58.090 36.000 0.00 0.00 0.00 4.20
2126 2148 6.488683 TGAGAATTTGATGGTAAAAAGGTCGT 59.511 34.615 0.00 0.00 0.00 4.34
2127 2149 6.801862 GTGAGAATTTGATGGTAAAAAGGTCG 59.198 38.462 0.00 0.00 0.00 4.79
2128 2150 7.595130 GTGTGAGAATTTGATGGTAAAAAGGTC 59.405 37.037 0.00 0.00 0.00 3.85
2129 2151 7.069331 TGTGTGAGAATTTGATGGTAAAAAGGT 59.931 33.333 0.00 0.00 0.00 3.50
2130 2152 7.382218 GTGTGTGAGAATTTGATGGTAAAAAGG 59.618 37.037 0.00 0.00 0.00 3.11
2131 2153 7.920151 TGTGTGTGAGAATTTGATGGTAAAAAG 59.080 33.333 0.00 0.00 0.00 2.27
2132 2154 7.704472 GTGTGTGTGAGAATTTGATGGTAAAAA 59.296 33.333 0.00 0.00 0.00 1.94
2133 2155 7.148000 TGTGTGTGTGAGAATTTGATGGTAAAA 60.148 33.333 0.00 0.00 0.00 1.52
2134 2156 6.319911 TGTGTGTGTGAGAATTTGATGGTAAA 59.680 34.615 0.00 0.00 0.00 2.01
2135 2157 5.825151 TGTGTGTGTGAGAATTTGATGGTAA 59.175 36.000 0.00 0.00 0.00 2.85
2136 2158 5.238432 GTGTGTGTGTGAGAATTTGATGGTA 59.762 40.000 0.00 0.00 0.00 3.25
2137 2159 4.036734 GTGTGTGTGTGAGAATTTGATGGT 59.963 41.667 0.00 0.00 0.00 3.55
2138 2160 4.036616 TGTGTGTGTGTGAGAATTTGATGG 59.963 41.667 0.00 0.00 0.00 3.51
2139 2161 4.971830 GTGTGTGTGTGTGAGAATTTGATG 59.028 41.667 0.00 0.00 0.00 3.07
2140 2162 4.036734 GGTGTGTGTGTGTGAGAATTTGAT 59.963 41.667 0.00 0.00 0.00 2.57
2141 2163 3.376859 GGTGTGTGTGTGTGAGAATTTGA 59.623 43.478 0.00 0.00 0.00 2.69
2142 2164 3.489059 GGGTGTGTGTGTGTGAGAATTTG 60.489 47.826 0.00 0.00 0.00 2.32
2143 2165 2.687935 GGGTGTGTGTGTGTGAGAATTT 59.312 45.455 0.00 0.00 0.00 1.82
2144 2166 2.092429 AGGGTGTGTGTGTGTGAGAATT 60.092 45.455 0.00 0.00 0.00 2.17
2145 2167 1.490490 AGGGTGTGTGTGTGTGAGAAT 59.510 47.619 0.00 0.00 0.00 2.40
2146 2168 0.908910 AGGGTGTGTGTGTGTGAGAA 59.091 50.000 0.00 0.00 0.00 2.87
2147 2169 0.464036 GAGGGTGTGTGTGTGTGAGA 59.536 55.000 0.00 0.00 0.00 3.27
2148 2170 0.465705 AGAGGGTGTGTGTGTGTGAG 59.534 55.000 0.00 0.00 0.00 3.51
2149 2171 0.464036 GAGAGGGTGTGTGTGTGTGA 59.536 55.000 0.00 0.00 0.00 3.58
2150 2172 0.532862 GGAGAGGGTGTGTGTGTGTG 60.533 60.000 0.00 0.00 0.00 3.82
2151 2173 1.696097 GGGAGAGGGTGTGTGTGTGT 61.696 60.000 0.00 0.00 0.00 3.72
2152 2174 1.071471 GGGAGAGGGTGTGTGTGTG 59.929 63.158 0.00 0.00 0.00 3.82
2153 2175 1.074471 AGGGAGAGGGTGTGTGTGT 60.074 57.895 0.00 0.00 0.00 3.72
2154 2176 1.674057 GAGGGAGAGGGTGTGTGTG 59.326 63.158 0.00 0.00 0.00 3.82
2155 2177 1.536662 GGAGGGAGAGGGTGTGTGT 60.537 63.158 0.00 0.00 0.00 3.72
2156 2178 2.294078 GGGAGGGAGAGGGTGTGTG 61.294 68.421 0.00 0.00 0.00 3.82
2157 2179 2.122954 GGGAGGGAGAGGGTGTGT 59.877 66.667 0.00 0.00 0.00 3.72
2158 2180 1.687493 GAGGGAGGGAGAGGGTGTG 60.687 68.421 0.00 0.00 0.00 3.82
2159 2181 1.456518 AAGAGGGAGGGAGAGGGTGT 61.457 60.000 0.00 0.00 0.00 4.16
2160 2182 0.689412 GAAGAGGGAGGGAGAGGGTG 60.689 65.000 0.00 0.00 0.00 4.61
2161 2183 1.707200 GAAGAGGGAGGGAGAGGGT 59.293 63.158 0.00 0.00 0.00 4.34
2162 2184 1.074850 GGAAGAGGGAGGGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
2163 2185 0.105709 GAGGAAGAGGGAGGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
2164 2186 0.633921 TGAGGAAGAGGGAGGGAGAG 59.366 60.000 0.00 0.00 0.00 3.20
2165 2187 0.336737 GTGAGGAAGAGGGAGGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
2166 2188 0.338120 AGTGAGGAAGAGGGAGGGAG 59.662 60.000 0.00 0.00 0.00 4.30
2167 2189 0.336737 GAGTGAGGAAGAGGGAGGGA 59.663 60.000 0.00 0.00 0.00 4.20
2168 2190 0.338120 AGAGTGAGGAAGAGGGAGGG 59.662 60.000 0.00 0.00 0.00 4.30
2169 2191 1.287739 AGAGAGTGAGGAAGAGGGAGG 59.712 57.143 0.00 0.00 0.00 4.30
2170 2192 2.242196 AGAGAGAGTGAGGAAGAGGGAG 59.758 54.545 0.00 0.00 0.00 4.30
2171 2193 2.241176 GAGAGAGAGTGAGGAAGAGGGA 59.759 54.545 0.00 0.00 0.00 4.20
2172 2194 2.654863 GAGAGAGAGTGAGGAAGAGGG 58.345 57.143 0.00 0.00 0.00 4.30
2173 2195 2.654863 GGAGAGAGAGTGAGGAAGAGG 58.345 57.143 0.00 0.00 0.00 3.69
2174 2196 2.654863 GGGAGAGAGAGTGAGGAAGAG 58.345 57.143 0.00 0.00 0.00 2.85
2175 2197 1.286553 GGGGAGAGAGAGTGAGGAAGA 59.713 57.143 0.00 0.00 0.00 2.87
2176 2198 1.687996 GGGGGAGAGAGAGTGAGGAAG 60.688 61.905 0.00 0.00 0.00 3.46
2177 2199 0.336737 GGGGGAGAGAGAGTGAGGAA 59.663 60.000 0.00 0.00 0.00 3.36
2178 2200 0.553862 AGGGGGAGAGAGAGTGAGGA 60.554 60.000 0.00 0.00 0.00 3.71
2179 2201 0.106217 GAGGGGGAGAGAGAGTGAGG 60.106 65.000 0.00 0.00 0.00 3.86
2180 2202 0.926293 AGAGGGGGAGAGAGAGTGAG 59.074 60.000 0.00 0.00 0.00 3.51
2181 2203 0.923358 GAGAGGGGGAGAGAGAGTGA 59.077 60.000 0.00 0.00 0.00 3.41
2182 2204 0.106217 GGAGAGGGGGAGAGAGAGTG 60.106 65.000 0.00 0.00 0.00 3.51
2183 2205 1.293683 GGGAGAGGGGGAGAGAGAGT 61.294 65.000 0.00 0.00 0.00 3.24
2184 2206 0.998945 AGGGAGAGGGGGAGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
2185 2207 0.996762 GAGGGAGAGGGGGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
2186 2208 1.292941 TGAGGGAGAGGGGGAGAGAG 61.293 65.000 0.00 0.00 0.00 3.20
2187 2209 1.230650 TGAGGGAGAGGGGGAGAGA 60.231 63.158 0.00 0.00 0.00 3.10
2188 2210 1.075600 GTGAGGGAGAGGGGGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
2189 2211 1.547755 AGTGAGGGAGAGGGGGAGA 60.548 63.158 0.00 0.00 0.00 3.71
2190 2212 1.075600 GAGTGAGGGAGAGGGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
2191 2213 2.997584 CGAGTGAGGGAGAGGGGGA 61.998 68.421 0.00 0.00 0.00 4.81
2192 2214 2.443016 CGAGTGAGGGAGAGGGGG 60.443 72.222 0.00 0.00 0.00 5.40
2193 2215 2.443016 CCGAGTGAGGGAGAGGGG 60.443 72.222 0.00 0.00 0.00 4.79
2202 2224 2.037367 TCCCACCTCCCGAGTGAG 59.963 66.667 0.00 0.00 0.00 3.51
2203 2225 2.283676 GTCCCACCTCCCGAGTGA 60.284 66.667 0.00 0.00 0.00 3.41
2204 2226 1.764571 TTTGTCCCACCTCCCGAGTG 61.765 60.000 0.00 0.00 0.00 3.51
2205 2227 1.057851 TTTTGTCCCACCTCCCGAGT 61.058 55.000 0.00 0.00 0.00 4.18
2206 2228 0.109723 TTTTTGTCCCACCTCCCGAG 59.890 55.000 0.00 0.00 0.00 4.63
2207 2229 0.774908 ATTTTTGTCCCACCTCCCGA 59.225 50.000 0.00 0.00 0.00 5.14
2208 2230 2.500392 TATTTTTGTCCCACCTCCCG 57.500 50.000 0.00 0.00 0.00 5.14
2209 2231 3.259876 GGTTTATTTTTGTCCCACCTCCC 59.740 47.826 0.00 0.00 0.00 4.30
2210 2232 3.259876 GGGTTTATTTTTGTCCCACCTCC 59.740 47.826 0.00 0.00 38.15 4.30
2211 2233 3.057104 CGGGTTTATTTTTGTCCCACCTC 60.057 47.826 0.00 0.00 38.15 3.85
2212 2234 2.894765 CGGGTTTATTTTTGTCCCACCT 59.105 45.455 0.00 0.00 38.15 4.00
2213 2235 2.028839 CCGGGTTTATTTTTGTCCCACC 60.029 50.000 0.00 0.00 38.15 4.61
2214 2236 2.892215 TCCGGGTTTATTTTTGTCCCAC 59.108 45.455 0.00 0.00 38.15 4.61
2215 2237 3.240310 TCCGGGTTTATTTTTGTCCCA 57.760 42.857 0.00 0.00 38.15 4.37
2216 2238 3.306225 GGTTCCGGGTTTATTTTTGTCCC 60.306 47.826 0.00 0.00 35.22 4.46
2217 2239 3.612241 CGGTTCCGGGTTTATTTTTGTCC 60.612 47.826 0.00 0.00 0.00 4.02
2218 2240 3.252944 TCGGTTCCGGGTTTATTTTTGTC 59.747 43.478 11.37 0.00 0.00 3.18
2219 2241 3.220940 TCGGTTCCGGGTTTATTTTTGT 58.779 40.909 11.37 0.00 0.00 2.83
2220 2242 3.502979 TCTCGGTTCCGGGTTTATTTTTG 59.497 43.478 10.98 0.00 0.00 2.44
2221 2243 3.503363 GTCTCGGTTCCGGGTTTATTTTT 59.497 43.478 10.98 0.00 0.00 1.94
2222 2244 3.076621 GTCTCGGTTCCGGGTTTATTTT 58.923 45.455 10.98 0.00 0.00 1.82
2223 2245 2.303890 AGTCTCGGTTCCGGGTTTATTT 59.696 45.455 10.98 0.00 0.00 1.40
2224 2246 1.904537 AGTCTCGGTTCCGGGTTTATT 59.095 47.619 10.98 0.00 0.00 1.40
2225 2247 1.565067 AGTCTCGGTTCCGGGTTTAT 58.435 50.000 10.98 0.00 0.00 1.40
2226 2248 1.818674 GTAGTCTCGGTTCCGGGTTTA 59.181 52.381 10.98 2.71 0.00 2.01
2227 2249 0.605083 GTAGTCTCGGTTCCGGGTTT 59.395 55.000 10.98 3.61 0.00 3.27
2228 2250 1.253593 GGTAGTCTCGGTTCCGGGTT 61.254 60.000 10.98 3.94 0.00 4.11
2229 2251 1.680314 GGTAGTCTCGGTTCCGGGT 60.680 63.158 10.98 0.00 0.00 5.28
2230 2252 1.252904 TTGGTAGTCTCGGTTCCGGG 61.253 60.000 11.37 8.17 0.00 5.73
2231 2253 0.108945 GTTGGTAGTCTCGGTTCCGG 60.109 60.000 11.37 0.00 0.00 5.14
2232 2254 0.886563 AGTTGGTAGTCTCGGTTCCG 59.113 55.000 4.74 4.74 0.00 4.30
2233 2255 1.891150 TCAGTTGGTAGTCTCGGTTCC 59.109 52.381 0.00 0.00 0.00 3.62
2234 2256 2.818432 TCTCAGTTGGTAGTCTCGGTTC 59.182 50.000 0.00 0.00 0.00 3.62
2235 2257 2.557490 GTCTCAGTTGGTAGTCTCGGTT 59.443 50.000 0.00 0.00 0.00 4.44
2236 2258 2.161030 GTCTCAGTTGGTAGTCTCGGT 58.839 52.381 0.00 0.00 0.00 4.69
2237 2259 2.160205 TGTCTCAGTTGGTAGTCTCGG 58.840 52.381 0.00 0.00 0.00 4.63
2238 2260 4.442375 AATGTCTCAGTTGGTAGTCTCG 57.558 45.455 0.00 0.00 0.00 4.04
2239 2261 5.652891 TCCTAATGTCTCAGTTGGTAGTCTC 59.347 44.000 0.00 0.00 0.00 3.36
2240 2262 5.580998 TCCTAATGTCTCAGTTGGTAGTCT 58.419 41.667 0.00 0.00 0.00 3.24
2241 2263 5.419471 ACTCCTAATGTCTCAGTTGGTAGTC 59.581 44.000 0.00 0.00 0.00 2.59
2242 2264 5.334421 ACTCCTAATGTCTCAGTTGGTAGT 58.666 41.667 0.00 0.00 0.00 2.73
2243 2265 5.923733 ACTCCTAATGTCTCAGTTGGTAG 57.076 43.478 0.00 0.00 0.00 3.18
2244 2266 6.728411 TCTACTCCTAATGTCTCAGTTGGTA 58.272 40.000 0.00 0.00 0.00 3.25
2245 2267 5.580998 TCTACTCCTAATGTCTCAGTTGGT 58.419 41.667 0.00 0.00 0.00 3.67
2246 2268 5.888724 TCTCTACTCCTAATGTCTCAGTTGG 59.111 44.000 0.00 0.00 0.00 3.77
2247 2269 7.284261 TGATCTCTACTCCTAATGTCTCAGTTG 59.716 40.741 0.00 0.00 0.00 3.16
2248 2270 7.350382 TGATCTCTACTCCTAATGTCTCAGTT 58.650 38.462 0.00 0.00 0.00 3.16
2249 2271 6.905736 TGATCTCTACTCCTAATGTCTCAGT 58.094 40.000 0.00 0.00 0.00 3.41
2250 2272 8.408043 AATGATCTCTACTCCTAATGTCTCAG 57.592 38.462 0.00 0.00 0.00 3.35
2251 2273 8.774546 AAATGATCTCTACTCCTAATGTCTCA 57.225 34.615 0.00 0.00 0.00 3.27
2253 2275 9.875708 ACTAAATGATCTCTACTCCTAATGTCT 57.124 33.333 0.00 0.00 0.00 3.41
2293 2315 9.940166 GTTTCTCCTTTTTAACATCGTTTTCTA 57.060 29.630 0.00 0.00 0.00 2.10
2294 2316 7.642586 CGTTTCTCCTTTTTAACATCGTTTTCT 59.357 33.333 0.00 0.00 0.00 2.52
2295 2317 7.096763 CCGTTTCTCCTTTTTAACATCGTTTTC 60.097 37.037 0.00 0.00 0.00 2.29
2296 2318 6.693978 CCGTTTCTCCTTTTTAACATCGTTTT 59.306 34.615 0.00 0.00 0.00 2.43
2297 2319 6.038492 TCCGTTTCTCCTTTTTAACATCGTTT 59.962 34.615 0.00 0.00 0.00 3.60
2298 2320 5.528320 TCCGTTTCTCCTTTTTAACATCGTT 59.472 36.000 0.00 0.00 0.00 3.85
2299 2321 5.058490 TCCGTTTCTCCTTTTTAACATCGT 58.942 37.500 0.00 0.00 0.00 3.73
2300 2322 5.600908 TCCGTTTCTCCTTTTTAACATCG 57.399 39.130 0.00 0.00 0.00 3.84
2301 2323 8.943002 TCTAATCCGTTTCTCCTTTTTAACATC 58.057 33.333 0.00 0.00 0.00 3.06
2302 2324 8.857694 TCTAATCCGTTTCTCCTTTTTAACAT 57.142 30.769 0.00 0.00 0.00 2.71
2303 2325 8.680039 TTCTAATCCGTTTCTCCTTTTTAACA 57.320 30.769 0.00 0.00 0.00 2.41
2309 2331 9.681062 TCAATTATTCTAATCCGTTTCTCCTTT 57.319 29.630 0.00 0.00 0.00 3.11
2310 2332 9.681062 TTCAATTATTCTAATCCGTTTCTCCTT 57.319 29.630 0.00 0.00 0.00 3.36
2311 2333 9.681062 TTTCAATTATTCTAATCCGTTTCTCCT 57.319 29.630 0.00 0.00 0.00 3.69
2324 2346 9.685828 CGTCCTTTTGGTTTTTCAATTATTCTA 57.314 29.630 0.00 0.00 41.38 2.10
2325 2347 8.417884 TCGTCCTTTTGGTTTTTCAATTATTCT 58.582 29.630 0.00 0.00 41.38 2.40
2326 2348 8.582433 TCGTCCTTTTGGTTTTTCAATTATTC 57.418 30.769 0.00 0.00 41.38 1.75
2327 2349 8.987890 CATCGTCCTTTTGGTTTTTCAATTATT 58.012 29.630 0.00 0.00 41.38 1.40
2328 2350 8.147704 ACATCGTCCTTTTGGTTTTTCAATTAT 58.852 29.630 0.00 0.00 41.38 1.28
2329 2351 7.493367 ACATCGTCCTTTTGGTTTTTCAATTA 58.507 30.769 0.00 0.00 41.38 1.40
2330 2352 6.345298 ACATCGTCCTTTTGGTTTTTCAATT 58.655 32.000 0.00 0.00 41.38 2.32
2331 2353 5.912892 ACATCGTCCTTTTGGTTTTTCAAT 58.087 33.333 0.00 0.00 41.38 2.57
2332 2354 5.331876 ACATCGTCCTTTTGGTTTTTCAA 57.668 34.783 0.00 0.00 41.38 2.69
2333 2355 4.993029 ACATCGTCCTTTTGGTTTTTCA 57.007 36.364 0.00 0.00 41.38 2.69


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

AutoCloner maintained by Alex Coulton.