Multiple sequence alignment - TraesCS5A01G184600

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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 TraesCS5A01G184600 chr5A 100.000 3056 0 0 1 3056 384214795 384211740 0.000000e+00 5644
1 TraesCS5A01G184600 chr5A 97.448 431 11 0 2626 3056 384197302 384197732 0.000000e+00 736
2 TraesCS5A01G184600 chr5A 94.737 114 4 2 2504 2617 384200045 384200156 3.130000e-40 176
3 TraesCS5A01G184600 chr5B 94.680 2049 88 10 1 2048 332436962 332434934 0.000000e+00 3160
4 TraesCS5A01G184600 chr5B 95.128 431 21 0 2626 3056 669172275 669171845 0.000000e+00 680
5 TraesCS5A01G184600 chr5D 92.812 2059 111 18 1 2051 291886275 291884246 0.000000e+00 2948
6 TraesCS5A01G184600 chr4B 95.592 431 19 0 2626 3056 285571457 285571027 0.000000e+00 691
7 TraesCS5A01G184600 chr4B 96.758 401 12 1 2116 2515 300037069 300036669 0.000000e+00 667
8 TraesCS5A01G184600 chr4B 96.517 402 11 3 2115 2515 45136112 45136511 0.000000e+00 662
9 TraesCS5A01G184600 chr3A 95.370 432 20 0 2625 3056 187268998 187269429 0.000000e+00 688
10 TraesCS5A01G184600 chr3A 95.360 431 20 0 2626 3056 102384750 102385180 0.000000e+00 686
11 TraesCS5A01G184600 chr6B 95.360 431 20 0 2626 3056 245970727 245970297 0.000000e+00 686
12 TraesCS5A01G184600 chr6B 96.517 402 13 1 2115 2515 491632354 491632755 0.000000e+00 664
13 TraesCS5A01G184600 chr6B 86.957 115 15 0 2503 2617 645568819 645568705 2.470000e-26 130
14 TraesCS5A01G184600 chr2B 95.360 431 20 0 2626 3056 106425824 106426254 0.000000e+00 686
15 TraesCS5A01G184600 chr2B 95.128 431 21 0 2626 3056 260643467 260643897 0.000000e+00 680
16 TraesCS5A01G184600 chr2B 95.128 431 21 0 2626 3056 581794625 581795055 0.000000e+00 680
17 TraesCS5A01G184600 chr2B 86.441 118 14 2 2502 2617 429246820 429246703 8.890000e-26 128
18 TraesCS5A01G184600 chr1B 97.943 389 8 0 2115 2503 340349642 340349254 0.000000e+00 675
19 TraesCS5A01G184600 chr1B 96.766 402 12 1 2115 2515 29549788 29549387 0.000000e+00 669
20 TraesCS5A01G184600 chr1B 96.269 402 14 1 2115 2515 591222656 591222255 0.000000e+00 658
21 TraesCS5A01G184600 chr3B 96.766 402 12 1 2115 2515 375453801 375454202 0.000000e+00 669
22 TraesCS5A01G184600 chr3B 86.290 124 8 5 2503 2617 661761588 661761711 3.200000e-25 126
23 TraesCS5A01G184600 chr3B 85.246 122 11 3 2503 2617 661728899 661729020 5.350000e-23 119
24 TraesCS5A01G184600 chr7B 94.952 416 19 2 2102 2515 605570640 605570225 0.000000e+00 651
25 TraesCS5A01G184600 chr7B 95.025 402 19 1 2115 2515 115497872 115498273 5.560000e-177 630
26 TraesCS5A01G184600 chr7B 86.087 115 14 2 2503 2617 76897890 76898002 4.140000e-24 122
27 TraesCS5A01G184600 chr4A 85.470 117 15 2 2503 2617 623343666 623343782 1.490000e-23 121
28 TraesCS5A01G184600 chr6A 87.500 96 12 0 2522 2617 455782622 455782527 8.960000e-21 111


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 TraesCS5A01G184600 chr5A 384211740 384214795 3055 True 5644 5644 100.0000 1 3056 1 chr5A.!!$R1 3055
1 TraesCS5A01G184600 chr5A 384197302 384200156 2854 False 456 736 96.0925 2504 3056 2 chr5A.!!$F1 552
2 TraesCS5A01G184600 chr5B 332434934 332436962 2028 True 3160 3160 94.6800 1 2048 1 chr5B.!!$R1 2047
3 TraesCS5A01G184600 chr5D 291884246 291886275 2029 True 2948 2948 92.8120 1 2051 1 chr5D.!!$R1 2050

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
278 279 1.606885 AAGCAATGGGGATGCCAACG 61.607 55.0 5.3 0.0 44.91 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2078 0.035439 TGAGCCGGTTCCCTCAAATC 60.035 55.0 16.38 0.0 35.32 2.17 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
25 26 2.487775 TGCTGGAAAATAGAGCCCCTA 58.512 47.619 0.00 0.00 31.31 3.53
142 143 6.547141 CCATTACCTTGGATCAGCTTATTGAA 59.453 38.462 0.00 0.00 39.25 2.69
278 279 1.606885 AAGCAATGGGGATGCCAACG 61.607 55.000 5.30 0.00 44.91 4.10
399 400 5.501156 ACATGGAAGTTCCCTTAGATTGAC 58.499 41.667 19.42 0.00 35.03 3.18
400 401 5.014123 ACATGGAAGTTCCCTTAGATTGACA 59.986 40.000 19.42 0.00 35.03 3.58
423 424 4.141390 ACAAGACAATAGGGGCAGGATAAG 60.141 45.833 0.00 0.00 0.00 1.73
685 691 4.077108 TGAAGTTGCTTGATCTTCATGCT 58.923 39.130 14.12 0.00 44.77 3.79
706 712 3.490759 CGTGCTTGGCGTGCCTAG 61.491 66.667 16.52 16.52 40.94 3.02
749 762 9.377312 ATTTTAACAAAATTACAGTGTTGCTGT 57.623 25.926 0.00 5.21 44.35 4.40
825 838 4.657504 AGATGAACCAGATGCCAATCTCTA 59.342 41.667 0.00 0.00 41.43 2.43
907 921 5.480422 GGAAAGCCTCCAATTCCTTTCTTTA 59.520 40.000 10.59 0.00 44.67 1.85
1011 1025 2.124570 GCAGCCATGTCCGACCAT 60.125 61.111 0.00 0.00 0.00 3.55
1161 1175 4.295199 GGTCCACCCCCACCAACC 62.295 72.222 0.00 0.00 32.33 3.77
1631 1645 2.639286 CGTGCCACTGCCAAGAAC 59.361 61.111 0.00 0.00 36.33 3.01
1633 1647 2.594303 TGCCACTGCCAAGAACCG 60.594 61.111 0.00 0.00 36.33 4.44
1771 1785 1.565156 GCGCGTGGACATCAAGAACA 61.565 55.000 8.43 0.00 0.00 3.18
1837 1851 1.545706 GGAGAAGCCAGAGGAACCGT 61.546 60.000 0.00 0.00 36.34 4.83
2048 2063 2.509561 GAGGAAGGCGCGGAAGAC 60.510 66.667 8.83 0.00 0.00 3.01
2051 2066 2.048127 GAAGGCGCGGAAGACAGT 60.048 61.111 8.83 0.00 0.00 3.55
2052 2067 2.357517 AAGGCGCGGAAGACAGTG 60.358 61.111 8.83 0.00 0.00 3.66
2053 2068 3.165160 AAGGCGCGGAAGACAGTGT 62.165 57.895 8.83 0.00 0.00 3.55
2054 2069 1.812686 AAGGCGCGGAAGACAGTGTA 61.813 55.000 8.83 0.00 0.00 2.90
2055 2070 1.805945 GGCGCGGAAGACAGTGTAG 60.806 63.158 8.83 0.00 0.00 2.74
2056 2071 1.805945 GCGCGGAAGACAGTGTAGG 60.806 63.158 8.83 0.00 0.00 3.18
2057 2072 1.880894 CGCGGAAGACAGTGTAGGA 59.119 57.895 0.00 0.00 0.00 2.94
2058 2073 0.456312 CGCGGAAGACAGTGTAGGAC 60.456 60.000 0.00 0.00 0.00 3.85
2059 2074 0.601558 GCGGAAGACAGTGTAGGACA 59.398 55.000 0.00 0.00 0.00 4.02
2060 2075 1.000506 GCGGAAGACAGTGTAGGACAA 59.999 52.381 0.00 0.00 0.00 3.18
2061 2076 2.353803 GCGGAAGACAGTGTAGGACAAT 60.354 50.000 0.00 0.00 0.00 2.71
2062 2077 3.119245 GCGGAAGACAGTGTAGGACAATA 60.119 47.826 0.00 0.00 0.00 1.90
2063 2078 4.673441 CGGAAGACAGTGTAGGACAATAG 58.327 47.826 0.00 0.00 0.00 1.73
2064 2079 4.398358 CGGAAGACAGTGTAGGACAATAGA 59.602 45.833 0.00 0.00 0.00 1.98
2065 2080 5.067936 CGGAAGACAGTGTAGGACAATAGAT 59.932 44.000 0.00 0.00 0.00 1.98
2066 2081 6.405953 CGGAAGACAGTGTAGGACAATAGATT 60.406 42.308 0.00 0.00 0.00 2.40
2067 2082 7.331791 GGAAGACAGTGTAGGACAATAGATTT 58.668 38.462 0.00 0.00 0.00 2.17
2068 2083 7.278868 GGAAGACAGTGTAGGACAATAGATTTG 59.721 40.741 0.00 0.00 0.00 2.32
2069 2084 7.482169 AGACAGTGTAGGACAATAGATTTGA 57.518 36.000 0.00 0.00 0.00 2.69
2070 2085 7.551585 AGACAGTGTAGGACAATAGATTTGAG 58.448 38.462 0.00 0.00 0.00 3.02
2071 2086 6.644347 ACAGTGTAGGACAATAGATTTGAGG 58.356 40.000 0.00 0.00 0.00 3.86
2072 2087 6.051717 CAGTGTAGGACAATAGATTTGAGGG 58.948 44.000 0.00 0.00 0.00 4.30
2073 2088 5.964477 AGTGTAGGACAATAGATTTGAGGGA 59.036 40.000 0.00 0.00 0.00 4.20
2074 2089 6.443849 AGTGTAGGACAATAGATTTGAGGGAA 59.556 38.462 0.00 0.00 0.00 3.97
2075 2090 6.539103 GTGTAGGACAATAGATTTGAGGGAAC 59.461 42.308 0.00 0.00 0.00 3.62
2087 2102 3.069778 GGGAACCGGCTCAACTCT 58.930 61.111 7.26 0.00 40.86 3.24
2088 2103 1.375326 GGGAACCGGCTCAACTCTT 59.625 57.895 7.26 0.00 40.86 2.85
2089 2104 0.250770 GGGAACCGGCTCAACTCTTT 60.251 55.000 7.26 0.00 40.86 2.52
2090 2105 1.002773 GGGAACCGGCTCAACTCTTTA 59.997 52.381 7.26 0.00 40.86 1.85
2091 2106 2.347731 GGAACCGGCTCAACTCTTTAG 58.652 52.381 7.26 0.00 0.00 1.85
2092 2107 2.347731 GAACCGGCTCAACTCTTTAGG 58.652 52.381 0.00 0.00 0.00 2.69
2093 2108 1.640917 ACCGGCTCAACTCTTTAGGA 58.359 50.000 0.00 0.00 0.00 2.94
2094 2109 1.550976 ACCGGCTCAACTCTTTAGGAG 59.449 52.381 0.00 0.00 46.87 3.69
2095 2110 1.134670 CCGGCTCAACTCTTTAGGAGG 60.135 57.143 0.00 0.00 45.83 4.30
2096 2111 1.740718 CGGCTCAACTCTTTAGGAGGC 60.741 57.143 0.00 0.00 45.83 4.70
2097 2112 1.407575 GGCTCAACTCTTTAGGAGGCC 60.408 57.143 0.00 0.00 45.83 5.19
2098 2113 1.557371 GCTCAACTCTTTAGGAGGCCT 59.443 52.381 3.86 3.86 45.83 5.19
2099 2114 2.766828 GCTCAACTCTTTAGGAGGCCTA 59.233 50.000 4.42 0.00 45.83 3.93
2100 2115 3.389656 GCTCAACTCTTTAGGAGGCCTAT 59.610 47.826 4.42 0.00 45.83 2.57
2101 2116 4.502431 GCTCAACTCTTTAGGAGGCCTATC 60.502 50.000 4.42 0.15 45.83 2.08
2102 2117 4.620723 TCAACTCTTTAGGAGGCCTATCA 58.379 43.478 4.42 0.00 45.83 2.15
2103 2118 4.406003 TCAACTCTTTAGGAGGCCTATCAC 59.594 45.833 4.42 0.00 45.83 3.06
2104 2119 3.995636 ACTCTTTAGGAGGCCTATCACA 58.004 45.455 4.42 0.00 45.83 3.58
2105 2120 3.707102 ACTCTTTAGGAGGCCTATCACAC 59.293 47.826 4.42 0.00 45.83 3.82
2106 2121 3.706594 CTCTTTAGGAGGCCTATCACACA 59.293 47.826 4.42 0.00 35.87 3.72
2107 2122 3.451178 TCTTTAGGAGGCCTATCACACAC 59.549 47.826 4.42 0.00 35.87 3.82
2108 2123 2.543037 TAGGAGGCCTATCACACACA 57.457 50.000 4.42 0.00 34.61 3.72
2109 2124 0.905357 AGGAGGCCTATCACACACAC 59.095 55.000 4.42 0.00 28.47 3.82
2110 2125 0.613260 GGAGGCCTATCACACACACA 59.387 55.000 4.42 0.00 0.00 3.72
2111 2126 1.676014 GGAGGCCTATCACACACACAC 60.676 57.143 4.42 0.00 0.00 3.82
2112 2127 1.001974 GAGGCCTATCACACACACACA 59.998 52.381 4.42 0.00 0.00 3.72
2113 2128 1.156736 GGCCTATCACACACACACAC 58.843 55.000 0.00 0.00 0.00 3.82
2114 2129 1.542328 GGCCTATCACACACACACACA 60.542 52.381 0.00 0.00 0.00 3.72
2115 2130 2.426522 GCCTATCACACACACACACAT 58.573 47.619 0.00 0.00 0.00 3.21
2116 2131 3.595173 GCCTATCACACACACACACATA 58.405 45.455 0.00 0.00 0.00 2.29
2117 2132 4.191544 GCCTATCACACACACACACATAT 58.808 43.478 0.00 0.00 0.00 1.78
2118 2133 5.356426 GCCTATCACACACACACACATATA 58.644 41.667 0.00 0.00 0.00 0.86
2119 2134 5.991606 GCCTATCACACACACACACATATAT 59.008 40.000 0.00 0.00 0.00 0.86
2120 2135 7.151976 GCCTATCACACACACACACATATATA 58.848 38.462 0.00 0.00 0.00 0.86
2121 2136 7.819415 GCCTATCACACACACACACATATATAT 59.181 37.037 0.00 0.00 0.00 0.86
2127 2142 9.586435 CACACACACACACATATATATATAGGG 57.414 37.037 16.54 9.92 0.00 3.53
2128 2143 9.541884 ACACACACACACATATATATATAGGGA 57.458 33.333 16.54 0.00 0.00 4.20
2144 2159 3.953542 AGGGAAAATCCATCCTACCAC 57.046 47.619 0.00 0.00 38.64 4.16
2145 2160 2.514160 AGGGAAAATCCATCCTACCACC 59.486 50.000 0.00 0.00 38.64 4.61
2146 2161 2.424379 GGGAAAATCCATCCTACCACCC 60.424 54.545 0.00 0.00 38.64 4.61
2147 2162 2.572290 GAAAATCCATCCTACCACCCG 58.428 52.381 0.00 0.00 0.00 5.28
2148 2163 0.843984 AAATCCATCCTACCACCCGG 59.156 55.000 0.00 0.00 38.77 5.73
2160 2175 1.598517 CACCCGGTGGTAGTTACCC 59.401 63.158 9.99 0.00 45.57 3.69
2161 2176 1.613332 ACCCGGTGGTAGTTACCCC 60.613 63.158 0.00 5.97 45.45 4.95
2162 2177 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
2169 2184 2.910544 TGGTAGTTACCCCACATGTCT 58.089 47.619 0.00 0.00 45.87 3.41
2170 2185 2.835764 TGGTAGTTACCCCACATGTCTC 59.164 50.000 0.00 0.00 45.87 3.36
2171 2186 2.835764 GGTAGTTACCCCACATGTCTCA 59.164 50.000 0.00 0.00 40.53 3.27
2172 2187 3.454812 GGTAGTTACCCCACATGTCTCAT 59.545 47.826 0.00 0.00 40.53 2.90
2173 2188 4.652421 GGTAGTTACCCCACATGTCTCATA 59.348 45.833 0.00 0.00 40.53 2.15
2174 2189 5.307196 GGTAGTTACCCCACATGTCTCATAT 59.693 44.000 0.00 0.00 40.53 1.78
2175 2190 6.495872 GGTAGTTACCCCACATGTCTCATATA 59.504 42.308 0.00 0.00 40.53 0.86
2176 2191 6.420913 AGTTACCCCACATGTCTCATATAC 57.579 41.667 0.00 0.00 0.00 1.47
2177 2192 6.143915 AGTTACCCCACATGTCTCATATACT 58.856 40.000 0.00 0.00 0.00 2.12
2178 2193 7.302948 AGTTACCCCACATGTCTCATATACTA 58.697 38.462 0.00 0.00 0.00 1.82
2179 2194 7.451877 AGTTACCCCACATGTCTCATATACTAG 59.548 40.741 0.00 0.00 0.00 2.57
2180 2195 4.528596 ACCCCACATGTCTCATATACTAGC 59.471 45.833 0.00 0.00 0.00 3.42
2181 2196 4.528206 CCCCACATGTCTCATATACTAGCA 59.472 45.833 0.00 0.00 0.00 3.49
2182 2197 5.188555 CCCCACATGTCTCATATACTAGCAT 59.811 44.000 0.00 0.00 0.00 3.79
2183 2198 6.104665 CCCACATGTCTCATATACTAGCATG 58.895 44.000 0.00 0.00 38.41 4.06
2184 2199 6.295518 CCCACATGTCTCATATACTAGCATGT 60.296 42.308 0.00 14.02 43.91 3.21
2186 2201 6.695429 ACATGTCTCATATACTAGCATGTGG 58.305 40.000 16.56 0.00 42.26 4.17
2187 2202 6.268617 ACATGTCTCATATACTAGCATGTGGT 59.731 38.462 16.56 0.00 42.26 4.16
2188 2203 7.451566 ACATGTCTCATATACTAGCATGTGGTA 59.548 37.037 16.56 0.00 42.26 3.25
2189 2204 7.215719 TGTCTCATATACTAGCATGTGGTAC 57.784 40.000 0.34 0.79 0.00 3.34
2190 2205 7.004691 TGTCTCATATACTAGCATGTGGTACT 58.995 38.462 0.34 0.00 0.00 2.73
2191 2206 8.161425 TGTCTCATATACTAGCATGTGGTACTA 58.839 37.037 0.34 0.00 0.00 1.82
2192 2207 9.179909 GTCTCATATACTAGCATGTGGTACTAT 57.820 37.037 0.34 0.00 0.00 2.12
2201 2216 9.647918 ACTAGCATGTGGTACTATATATGCTAT 57.352 33.333 23.11 15.82 46.65 2.97
2424 2439 9.655769 ACTACATACTACACGTACATATTTTCG 57.344 33.333 0.00 0.00 0.00 3.46
2425 2440 7.919313 ACATACTACACGTACATATTTTCGG 57.081 36.000 0.00 0.00 0.00 4.30
2426 2441 7.483307 ACATACTACACGTACATATTTTCGGT 58.517 34.615 0.00 0.00 0.00 4.69
2427 2442 7.975616 ACATACTACACGTACATATTTTCGGTT 59.024 33.333 0.00 0.00 0.00 4.44
2428 2443 8.810427 CATACTACACGTACATATTTTCGGTTT 58.190 33.333 0.00 0.00 0.00 3.27
2429 2444 7.281991 ACTACACGTACATATTTTCGGTTTC 57.718 36.000 0.00 0.00 0.00 2.78
2430 2445 5.194199 ACACGTACATATTTTCGGTTTCG 57.806 39.130 0.00 0.00 37.82 3.46
2431 2446 4.922692 ACACGTACATATTTTCGGTTTCGA 59.077 37.500 0.00 0.00 44.44 3.71
2432 2447 5.164061 ACACGTACATATTTTCGGTTTCGAC 60.164 40.000 0.00 0.00 45.92 4.20
2433 2448 4.922692 ACGTACATATTTTCGGTTTCGACA 59.077 37.500 0.00 0.00 45.92 4.35
2434 2449 5.061311 ACGTACATATTTTCGGTTTCGACAG 59.939 40.000 0.00 0.00 45.92 3.51
2435 2450 5.286797 CGTACATATTTTCGGTTTCGACAGA 59.713 40.000 0.00 0.00 45.92 3.41
2436 2451 6.020121 CGTACATATTTTCGGTTTCGACAGAT 60.020 38.462 0.00 0.00 45.92 2.90
2437 2452 7.166307 CGTACATATTTTCGGTTTCGACAGATA 59.834 37.037 0.00 0.00 45.92 1.98
2438 2453 7.230466 ACATATTTTCGGTTTCGACAGATAC 57.770 36.000 0.00 0.00 45.92 2.24
2439 2454 7.039882 ACATATTTTCGGTTTCGACAGATACT 58.960 34.615 0.00 0.00 45.92 2.12
2440 2455 8.192774 ACATATTTTCGGTTTCGACAGATACTA 58.807 33.333 0.00 0.00 45.92 1.82
2441 2456 6.882458 ATTTTCGGTTTCGACAGATACTAC 57.118 37.500 0.00 0.00 45.92 2.73
2442 2457 5.375417 TTTCGGTTTCGACAGATACTACA 57.625 39.130 0.00 0.00 45.92 2.74
2443 2458 5.571784 TTCGGTTTCGACAGATACTACAT 57.428 39.130 0.00 0.00 45.92 2.29
2444 2459 6.682423 TTCGGTTTCGACAGATACTACATA 57.318 37.500 0.00 0.00 45.92 2.29
2445 2460 6.052840 TCGGTTTCGACAGATACTACATAC 57.947 41.667 0.00 0.00 40.88 2.39
2446 2461 5.585844 TCGGTTTCGACAGATACTACATACA 59.414 40.000 0.00 0.00 40.88 2.29
2447 2462 6.093909 TCGGTTTCGACAGATACTACATACAA 59.906 38.462 0.00 0.00 40.88 2.41
2448 2463 6.195983 CGGTTTCGACAGATACTACATACAAC 59.804 42.308 0.00 0.00 39.00 3.32
2449 2464 7.031372 GGTTTCGACAGATACTACATACAACA 58.969 38.462 0.00 0.00 0.00 3.33
2450 2465 7.705325 GGTTTCGACAGATACTACATACAACAT 59.295 37.037 0.00 0.00 0.00 2.71
2451 2466 9.726232 GTTTCGACAGATACTACATACAACATA 57.274 33.333 0.00 0.00 0.00 2.29
2452 2467 9.726232 TTTCGACAGATACTACATACAACATAC 57.274 33.333 0.00 0.00 0.00 2.39
2453 2468 8.441312 TCGACAGATACTACATACAACATACA 57.559 34.615 0.00 0.00 0.00 2.29
2454 2469 8.895737 TCGACAGATACTACATACAACATACAA 58.104 33.333 0.00 0.00 0.00 2.41
2455 2470 9.511144 CGACAGATACTACATACAACATACAAA 57.489 33.333 0.00 0.00 0.00 2.83
2459 2474 8.814235 AGATACTACATACAACATACAAAACGC 58.186 33.333 0.00 0.00 0.00 4.84
2460 2475 6.788684 ACTACATACAACATACAAAACGCA 57.211 33.333 0.00 0.00 0.00 5.24
2461 2476 7.192148 ACTACATACAACATACAAAACGCAA 57.808 32.000 0.00 0.00 0.00 4.85
2476 2491 1.435577 CGCAAGTGGTGGTAACTACC 58.564 55.000 0.00 0.00 46.62 3.18
2488 2503 3.858247 GGTAACTACCACTGCTTGTAGG 58.142 50.000 0.80 0.00 45.73 3.18
2489 2504 3.512724 GGTAACTACCACTGCTTGTAGGA 59.487 47.826 0.80 0.00 45.73 2.94
2490 2505 4.020839 GGTAACTACCACTGCTTGTAGGAA 60.021 45.833 0.80 0.00 45.73 3.36
2491 2506 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
2492 2507 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
2493 2508 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
2494 2509 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
2495 2510 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
2496 2511 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
2497 2512 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
2498 2513 4.037923 CCACTGCTTGTAGGAAACATTTGT 59.962 41.667 0.00 0.00 38.10 2.83
2499 2514 5.215160 CACTGCTTGTAGGAAACATTTGTC 58.785 41.667 0.00 0.00 38.10 3.18
2500 2515 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
2501 2516 4.469657 TGCTTGTAGGAAACATTTGTCCT 58.530 39.130 0.00 0.00 46.29 3.85
2502 2517 5.626142 TGCTTGTAGGAAACATTTGTCCTA 58.374 37.500 0.00 0.00 42.68 2.94
2503 2518 6.245408 TGCTTGTAGGAAACATTTGTCCTAT 58.755 36.000 1.00 0.00 45.89 2.57
2504 2519 7.398829 TGCTTGTAGGAAACATTTGTCCTATA 58.601 34.615 1.00 0.00 45.89 1.31
2505 2520 8.052748 TGCTTGTAGGAAACATTTGTCCTATAT 58.947 33.333 1.00 0.00 45.89 0.86
2506 2521 9.555727 GCTTGTAGGAAACATTTGTCCTATATA 57.444 33.333 1.00 0.00 45.89 0.86
2537 2552 9.959721 ATATGAAGGGGTATACAATGTTACATC 57.040 33.333 5.01 0.00 0.00 3.06
2538 2553 7.201702 TGAAGGGGTATACAATGTTACATCA 57.798 36.000 5.01 0.00 0.00 3.07
2539 2554 7.811282 TGAAGGGGTATACAATGTTACATCAT 58.189 34.615 5.01 0.00 0.00 2.45
2540 2555 8.939932 TGAAGGGGTATACAATGTTACATCATA 58.060 33.333 5.01 0.00 0.00 2.15
2541 2556 9.959721 GAAGGGGTATACAATGTTACATCATAT 57.040 33.333 5.01 2.81 0.00 1.78
2542 2557 9.739276 AAGGGGTATACAATGTTACATCATATG 57.261 33.333 5.01 0.00 0.00 1.78
2543 2558 8.890472 AGGGGTATACAATGTTACATCATATGT 58.110 33.333 5.01 2.00 46.92 2.29
2575 2590 6.210287 ACAGAAGCTATACAGTCTAACACC 57.790 41.667 0.00 0.00 0.00 4.16
2576 2591 5.952947 ACAGAAGCTATACAGTCTAACACCT 59.047 40.000 0.00 0.00 0.00 4.00
2577 2592 6.437793 ACAGAAGCTATACAGTCTAACACCTT 59.562 38.462 0.00 0.00 0.00 3.50
2578 2593 6.975772 CAGAAGCTATACAGTCTAACACCTTC 59.024 42.308 0.00 0.00 0.00 3.46
2579 2594 5.855740 AGCTATACAGTCTAACACCTTCC 57.144 43.478 0.00 0.00 0.00 3.46
2580 2595 4.650131 AGCTATACAGTCTAACACCTTCCC 59.350 45.833 0.00 0.00 0.00 3.97
2581 2596 4.650131 GCTATACAGTCTAACACCTTCCCT 59.350 45.833 0.00 0.00 0.00 4.20
2582 2597 5.128991 GCTATACAGTCTAACACCTTCCCTT 59.871 44.000 0.00 0.00 0.00 3.95
2583 2598 6.323225 GCTATACAGTCTAACACCTTCCCTTA 59.677 42.308 0.00 0.00 0.00 2.69
2584 2599 7.147776 GCTATACAGTCTAACACCTTCCCTTAA 60.148 40.741 0.00 0.00 0.00 1.85
2585 2600 7.750947 ATACAGTCTAACACCTTCCCTTAAT 57.249 36.000 0.00 0.00 0.00 1.40
2586 2601 6.051179 ACAGTCTAACACCTTCCCTTAATC 57.949 41.667 0.00 0.00 0.00 1.75
2587 2602 5.785940 ACAGTCTAACACCTTCCCTTAATCT 59.214 40.000 0.00 0.00 0.00 2.40
2588 2603 6.272558 ACAGTCTAACACCTTCCCTTAATCTT 59.727 38.462 0.00 0.00 0.00 2.40
2589 2604 7.456902 ACAGTCTAACACCTTCCCTTAATCTTA 59.543 37.037 0.00 0.00 0.00 2.10
2590 2605 7.982354 CAGTCTAACACCTTCCCTTAATCTTAG 59.018 40.741 0.00 0.00 0.00 2.18
2591 2606 6.762187 GTCTAACACCTTCCCTTAATCTTAGC 59.238 42.308 0.00 0.00 0.00 3.09
2592 2607 4.505324 ACACCTTCCCTTAATCTTAGCC 57.495 45.455 0.00 0.00 0.00 3.93
2593 2608 3.850173 ACACCTTCCCTTAATCTTAGCCA 59.150 43.478 0.00 0.00 0.00 4.75
2594 2609 4.200092 CACCTTCCCTTAATCTTAGCCAC 58.800 47.826 0.00 0.00 0.00 5.01
2595 2610 4.080299 CACCTTCCCTTAATCTTAGCCACT 60.080 45.833 0.00 0.00 0.00 4.00
2596 2611 4.540502 ACCTTCCCTTAATCTTAGCCACTT 59.459 41.667 0.00 0.00 0.00 3.16
2597 2612 5.015284 ACCTTCCCTTAATCTTAGCCACTTT 59.985 40.000 0.00 0.00 0.00 2.66
2598 2613 5.590663 CCTTCCCTTAATCTTAGCCACTTTC 59.409 44.000 0.00 0.00 0.00 2.62
2599 2614 6.388619 TTCCCTTAATCTTAGCCACTTTCT 57.611 37.500 0.00 0.00 0.00 2.52
2600 2615 7.365652 CCTTCCCTTAATCTTAGCCACTTTCTA 60.366 40.741 0.00 0.00 0.00 2.10
2601 2616 7.504926 TCCCTTAATCTTAGCCACTTTCTAA 57.495 36.000 0.00 0.00 0.00 2.10
2602 2617 7.924541 TCCCTTAATCTTAGCCACTTTCTAAA 58.075 34.615 0.00 0.00 0.00 1.85
2603 2618 8.047310 TCCCTTAATCTTAGCCACTTTCTAAAG 58.953 37.037 0.90 0.90 41.73 1.85
2604 2619 8.047310 CCCTTAATCTTAGCCACTTTCTAAAGA 58.953 37.037 9.37 0.00 39.31 2.52
2605 2620 9.449719 CCTTAATCTTAGCCACTTTCTAAAGAA 57.550 33.333 9.37 0.00 39.31 2.52
2611 2626 9.256228 TCTTAGCCACTTTCTAAAGAATCTAGA 57.744 33.333 9.37 0.00 39.31 2.43
2612 2627 9.877178 CTTAGCCACTTTCTAAAGAATCTAGAA 57.123 33.333 9.37 0.00 39.31 2.10
2613 2628 9.877178 TTAGCCACTTTCTAAAGAATCTAGAAG 57.123 33.333 9.37 0.00 36.87 2.85
2614 2629 7.334858 AGCCACTTTCTAAAGAATCTAGAAGG 58.665 38.462 9.37 4.09 36.87 3.46
2615 2630 6.540551 GCCACTTTCTAAAGAATCTAGAAGGG 59.459 42.308 9.37 7.43 37.00 3.95
2616 2631 7.625469 CCACTTTCTAAAGAATCTAGAAGGGT 58.375 38.462 9.37 4.67 37.00 4.34
2617 2632 8.103935 CCACTTTCTAAAGAATCTAGAAGGGTT 58.896 37.037 9.37 0.00 37.00 4.11
2618 2633 8.940952 CACTTTCTAAAGAATCTAGAAGGGTTG 58.059 37.037 9.37 0.00 37.00 3.77
2619 2634 8.881262 ACTTTCTAAAGAATCTAGAAGGGTTGA 58.119 33.333 9.37 0.00 37.00 3.18
2620 2635 9.377312 CTTTCTAAAGAATCTAGAAGGGTTGAG 57.623 37.037 0.00 0.00 36.87 3.02
2621 2636 6.879400 TCTAAAGAATCTAGAAGGGTTGAGC 58.121 40.000 0.00 0.00 0.00 4.26
2622 2637 4.495690 AAGAATCTAGAAGGGTTGAGCC 57.504 45.455 0.00 0.00 0.00 4.70
2623 2638 2.432510 AGAATCTAGAAGGGTTGAGCCG 59.567 50.000 0.00 0.00 38.44 5.52
2624 2639 1.123928 ATCTAGAAGGGTTGAGCCGG 58.876 55.000 0.00 0.00 38.44 6.13
2625 2640 0.252103 TCTAGAAGGGTTGAGCCGGT 60.252 55.000 1.90 0.00 38.44 5.28
2626 2641 0.613777 CTAGAAGGGTTGAGCCGGTT 59.386 55.000 1.90 0.00 38.44 4.44
2627 2642 0.611714 TAGAAGGGTTGAGCCGGTTC 59.388 55.000 11.99 11.99 38.44 3.62
2628 2643 1.128188 AGAAGGGTTGAGCCGGTTCT 61.128 55.000 19.73 6.86 36.77 3.01
2629 2644 0.250770 GAAGGGTTGAGCCGGTTCTT 60.251 55.000 19.73 4.61 38.44 2.52
2647 2662 6.055588 GGTTCTTACTAGGCATGCAAATAGA 58.944 40.000 21.36 10.75 0.00 1.98
2660 2675 6.618811 CATGCAAATAGAAGTCTTCAGCTTT 58.381 36.000 14.97 7.97 0.00 3.51
2661 2676 7.627088 GCATGCAAATAGAAGTCTTCAGCTTTA 60.627 37.037 14.21 0.00 0.00 1.85
2682 2697 7.931948 GCTTTATAATGTGCTTAGAGTTCCCTA 59.068 37.037 0.84 0.00 0.00 3.53
2798 2813 2.093658 GGCACGAGGGACATTCTTCTTA 60.094 50.000 0.00 0.00 0.00 2.10
2848 2863 4.842292 GAGCATCCTGATGTCGCA 57.158 55.556 8.79 0.00 40.80 5.10
2849 2864 3.302375 GAGCATCCTGATGTCGCAT 57.698 52.632 8.79 0.00 40.80 4.73
2903 2918 1.375908 TGGCATGCTCGTCTTGGTC 60.376 57.895 18.92 0.00 0.00 4.02
2937 2952 3.124466 CCTATCGTTCGTCATGTTTTGCA 59.876 43.478 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.555586 GGCATGCTTCCTTGTCAACAAAT 60.556 43.478 18.92 0.00 35.15 2.32
142 143 3.971702 GGGGGCAACAGAGCAGGT 61.972 66.667 0.00 0.00 39.74 4.00
278 279 6.036517 ACATCACGATTTTCTTCAGTATGCTC 59.963 38.462 0.00 0.00 34.76 4.26
399 400 1.281867 TCCTGCCCCTATTGTCTTGTG 59.718 52.381 0.00 0.00 0.00 3.33
400 401 1.668826 TCCTGCCCCTATTGTCTTGT 58.331 50.000 0.00 0.00 0.00 3.16
749 762 3.055675 TCACATGAGCTCACATCATCACA 60.056 43.478 20.97 0.00 35.20 3.58
799 812 0.394762 TGGCATCTGGTTCATCTGGC 60.395 55.000 0.00 0.00 0.00 4.85
825 838 1.209261 CCACAAGTTTTGGCCAGGTTT 59.791 47.619 5.11 0.00 34.12 3.27
847 860 5.620738 TTGGAGAAGGATGGATGAACTAG 57.379 43.478 0.00 0.00 0.00 2.57
848 861 6.388100 AGATTTGGAGAAGGATGGATGAACTA 59.612 38.462 0.00 0.00 0.00 2.24
1050 1064 0.036875 AAGGAAGCCAGAACCGGAAG 59.963 55.000 9.46 0.00 0.00 3.46
1212 1226 1.150081 GTCAGCCTGGATGGGGATG 59.850 63.158 12.67 0.00 41.11 3.51
1219 1233 2.418910 CGGACGAGTCAGCCTGGAT 61.419 63.158 0.00 0.00 0.00 3.41
1392 1406 2.184322 GAGATCTTGGCGCCGTCA 59.816 61.111 23.90 7.84 0.00 4.35
1616 1630 2.410322 ATCGGTTCTTGGCAGTGGCA 62.410 55.000 16.56 16.56 43.71 4.92
1664 1678 2.407428 TTCACGTTTGCGGCAACCA 61.407 52.632 16.15 0.00 43.45 3.67
1668 1682 2.712539 CTGTTCACGTTTGCGGCA 59.287 55.556 0.00 0.00 43.45 5.69
1674 1688 0.522495 GCACGTTGCTGTTCACGTTT 60.522 50.000 0.00 0.00 40.96 3.60
1698 1712 1.416049 CATCGCCGAGTTGTTCACG 59.584 57.895 0.00 0.00 0.00 4.35
2048 2063 6.051717 CCCTCAAATCTATTGTCCTACACTG 58.948 44.000 0.00 0.00 0.00 3.66
2051 2066 6.352737 GGTTCCCTCAAATCTATTGTCCTACA 60.353 42.308 0.00 0.00 0.00 2.74
2052 2067 6.056236 GGTTCCCTCAAATCTATTGTCCTAC 58.944 44.000 0.00 0.00 0.00 3.18
2053 2068 5.163343 CGGTTCCCTCAAATCTATTGTCCTA 60.163 44.000 0.00 0.00 0.00 2.94
2054 2069 4.384208 CGGTTCCCTCAAATCTATTGTCCT 60.384 45.833 0.00 0.00 0.00 3.85
2055 2070 3.877508 CGGTTCCCTCAAATCTATTGTCC 59.122 47.826 0.00 0.00 0.00 4.02
2056 2071 3.877508 CCGGTTCCCTCAAATCTATTGTC 59.122 47.826 0.00 0.00 0.00 3.18
2057 2072 3.886123 CCGGTTCCCTCAAATCTATTGT 58.114 45.455 0.00 0.00 0.00 2.71
2058 2073 2.618709 GCCGGTTCCCTCAAATCTATTG 59.381 50.000 1.90 0.00 0.00 1.90
2059 2074 2.509964 AGCCGGTTCCCTCAAATCTATT 59.490 45.455 1.90 0.00 0.00 1.73
2060 2075 2.104963 GAGCCGGTTCCCTCAAATCTAT 59.895 50.000 7.13 0.00 0.00 1.98
2061 2076 1.485066 GAGCCGGTTCCCTCAAATCTA 59.515 52.381 7.13 0.00 0.00 1.98
2062 2077 0.253327 GAGCCGGTTCCCTCAAATCT 59.747 55.000 7.13 0.00 0.00 2.40
2063 2078 0.035439 TGAGCCGGTTCCCTCAAATC 60.035 55.000 16.38 0.00 35.32 2.17
2064 2079 0.404040 TTGAGCCGGTTCCCTCAAAT 59.596 50.000 16.38 0.00 43.06 2.32
2065 2080 0.536460 GTTGAGCCGGTTCCCTCAAA 60.536 55.000 19.74 4.17 46.22 2.69
2066 2081 1.072505 GTTGAGCCGGTTCCCTCAA 59.927 57.895 16.38 15.97 43.60 3.02
2067 2082 1.827399 GAGTTGAGCCGGTTCCCTCA 61.827 60.000 22.16 15.23 36.38 3.86
2068 2083 1.079057 GAGTTGAGCCGGTTCCCTC 60.079 63.158 16.38 16.06 0.00 4.30
2069 2084 1.128188 AAGAGTTGAGCCGGTTCCCT 61.128 55.000 16.38 11.37 0.00 4.20
2070 2085 0.250770 AAAGAGTTGAGCCGGTTCCC 60.251 55.000 16.38 6.41 0.00 3.97
2071 2086 2.347731 CTAAAGAGTTGAGCCGGTTCC 58.652 52.381 16.38 0.80 0.00 3.62
2072 2087 2.028385 TCCTAAAGAGTTGAGCCGGTTC 60.028 50.000 11.99 11.99 0.00 3.62
2073 2088 1.975680 TCCTAAAGAGTTGAGCCGGTT 59.024 47.619 1.90 0.00 0.00 4.44
2074 2089 1.550976 CTCCTAAAGAGTTGAGCCGGT 59.449 52.381 1.90 0.00 37.87 5.28
2075 2090 1.134670 CCTCCTAAAGAGTTGAGCCGG 60.135 57.143 0.00 0.00 41.47 6.13
2076 2091 1.740718 GCCTCCTAAAGAGTTGAGCCG 60.741 57.143 0.00 0.00 41.47 5.52
2077 2092 1.407575 GGCCTCCTAAAGAGTTGAGCC 60.408 57.143 0.00 0.00 41.47 4.70
2078 2093 1.557371 AGGCCTCCTAAAGAGTTGAGC 59.443 52.381 0.00 0.00 41.47 4.26
2079 2094 4.651503 TGATAGGCCTCCTAAAGAGTTGAG 59.348 45.833 9.68 0.00 39.77 3.02
2080 2095 4.406003 GTGATAGGCCTCCTAAAGAGTTGA 59.594 45.833 9.68 0.00 39.77 3.18
2081 2096 4.162320 TGTGATAGGCCTCCTAAAGAGTTG 59.838 45.833 9.68 0.00 39.77 3.16
2082 2097 4.162509 GTGTGATAGGCCTCCTAAAGAGTT 59.837 45.833 9.68 0.00 39.77 3.01
2083 2098 3.707102 GTGTGATAGGCCTCCTAAAGAGT 59.293 47.826 9.68 0.00 39.77 3.24
2084 2099 3.706594 TGTGTGATAGGCCTCCTAAAGAG 59.293 47.826 9.68 0.00 39.77 2.85
2085 2100 3.451178 GTGTGTGATAGGCCTCCTAAAGA 59.549 47.826 9.68 0.00 39.77 2.52
2086 2101 3.197766 TGTGTGTGATAGGCCTCCTAAAG 59.802 47.826 9.68 0.00 39.77 1.85
2087 2102 3.055385 GTGTGTGTGATAGGCCTCCTAAA 60.055 47.826 9.68 0.00 39.77 1.85
2088 2103 2.500098 GTGTGTGTGATAGGCCTCCTAA 59.500 50.000 9.68 0.00 39.77 2.69
2089 2104 2.108168 GTGTGTGTGATAGGCCTCCTA 58.892 52.381 9.68 0.00 40.71 2.94
2090 2105 0.905357 GTGTGTGTGATAGGCCTCCT 59.095 55.000 9.68 0.00 37.71 3.69
2091 2106 0.613260 TGTGTGTGTGATAGGCCTCC 59.387 55.000 9.68 2.65 0.00 4.30
2092 2107 1.001974 TGTGTGTGTGTGATAGGCCTC 59.998 52.381 9.68 0.00 0.00 4.70
2093 2108 1.055849 TGTGTGTGTGTGATAGGCCT 58.944 50.000 11.78 11.78 0.00 5.19
2094 2109 1.156736 GTGTGTGTGTGTGATAGGCC 58.843 55.000 0.00 0.00 0.00 5.19
2095 2110 1.877637 TGTGTGTGTGTGTGATAGGC 58.122 50.000 0.00 0.00 0.00 3.93
2101 2116 9.586435 CCCTATATATATATGTGTGTGTGTGTG 57.414 37.037 14.42 0.00 0.00 3.82
2102 2117 9.541884 TCCCTATATATATATGTGTGTGTGTGT 57.458 33.333 14.42 0.00 0.00 3.72
2118 2133 9.004231 GTGGTAGGATGGATTTTCCCTATATAT 57.996 37.037 0.00 0.00 35.03 0.86
2119 2134 7.404980 GGTGGTAGGATGGATTTTCCCTATATA 59.595 40.741 0.00 0.00 35.03 0.86
2120 2135 6.217693 GGTGGTAGGATGGATTTTCCCTATAT 59.782 42.308 0.00 0.00 35.03 0.86
2121 2136 5.550403 GGTGGTAGGATGGATTTTCCCTATA 59.450 44.000 0.00 0.00 35.03 1.31
2122 2137 4.354087 GGTGGTAGGATGGATTTTCCCTAT 59.646 45.833 0.00 0.00 35.03 2.57
2123 2138 3.720002 GGTGGTAGGATGGATTTTCCCTA 59.280 47.826 0.00 0.00 35.03 3.53
2124 2139 2.514160 GGTGGTAGGATGGATTTTCCCT 59.486 50.000 0.00 0.00 35.03 4.20
2125 2140 2.424379 GGGTGGTAGGATGGATTTTCCC 60.424 54.545 0.00 0.00 35.03 3.97
2126 2141 2.748465 CGGGTGGTAGGATGGATTTTCC 60.748 54.545 0.00 0.00 36.96 3.13
2127 2142 2.572290 CGGGTGGTAGGATGGATTTTC 58.428 52.381 0.00 0.00 0.00 2.29
2128 2143 1.214424 CCGGGTGGTAGGATGGATTTT 59.786 52.381 0.00 0.00 0.00 1.82
2129 2144 0.843984 CCGGGTGGTAGGATGGATTT 59.156 55.000 0.00 0.00 0.00 2.17
2130 2145 2.539983 CCGGGTGGTAGGATGGATT 58.460 57.895 0.00 0.00 0.00 3.01
2131 2146 4.313523 CCGGGTGGTAGGATGGAT 57.686 61.111 0.00 0.00 0.00 3.41
2150 2165 2.835764 TGAGACATGTGGGGTAACTACC 59.164 50.000 1.15 0.00 45.71 3.18
2151 2166 4.755266 ATGAGACATGTGGGGTAACTAC 57.245 45.455 1.15 0.00 0.00 2.73
2152 2167 7.302948 AGTATATGAGACATGTGGGGTAACTA 58.697 38.462 1.15 0.00 0.00 2.24
2153 2168 6.143915 AGTATATGAGACATGTGGGGTAACT 58.856 40.000 1.15 0.00 0.00 2.24
2154 2169 6.420913 AGTATATGAGACATGTGGGGTAAC 57.579 41.667 1.15 0.00 0.00 2.50
2155 2170 6.210784 GCTAGTATATGAGACATGTGGGGTAA 59.789 42.308 1.15 0.00 0.00 2.85
2156 2171 5.715279 GCTAGTATATGAGACATGTGGGGTA 59.285 44.000 1.15 0.00 0.00 3.69
2157 2172 4.528596 GCTAGTATATGAGACATGTGGGGT 59.471 45.833 1.15 0.00 0.00 4.95
2158 2173 4.528206 TGCTAGTATATGAGACATGTGGGG 59.472 45.833 1.15 0.00 0.00 4.96
2159 2174 5.728637 TGCTAGTATATGAGACATGTGGG 57.271 43.478 1.15 0.00 0.00 4.61
2160 2175 6.695429 ACATGCTAGTATATGAGACATGTGG 58.305 40.000 1.15 0.00 43.50 4.17
2162 2177 6.268617 ACCACATGCTAGTATATGAGACATGT 59.731 38.462 0.00 0.00 45.39 3.21
2163 2178 6.695429 ACCACATGCTAGTATATGAGACATG 58.305 40.000 0.06 0.74 39.38 3.21
2164 2179 6.924913 ACCACATGCTAGTATATGAGACAT 57.075 37.500 0.06 0.00 0.00 3.06
2165 2180 7.004691 AGTACCACATGCTAGTATATGAGACA 58.995 38.462 0.06 0.00 0.00 3.41
2166 2181 7.455641 AGTACCACATGCTAGTATATGAGAC 57.544 40.000 0.06 0.00 0.00 3.36
2173 2188 9.647918 AGCATATATAGTACCACATGCTAGTAT 57.352 33.333 13.30 0.00 45.30 2.12
2175 2190 7.962995 AGCATATATAGTACCACATGCTAGT 57.037 36.000 13.30 0.00 45.30 2.57
2398 2413 9.655769 CGAAAATATGTACGTGTAGTATGTAGT 57.344 33.333 0.00 0.00 37.69 2.73
2399 2414 9.110617 CCGAAAATATGTACGTGTAGTATGTAG 57.889 37.037 0.00 0.00 37.69 2.74
2400 2415 8.620416 ACCGAAAATATGTACGTGTAGTATGTA 58.380 33.333 0.00 0.00 37.69 2.29
2401 2416 7.483307 ACCGAAAATATGTACGTGTAGTATGT 58.517 34.615 0.00 0.00 37.69 2.29
2402 2417 7.919313 ACCGAAAATATGTACGTGTAGTATG 57.081 36.000 0.00 0.00 37.69 2.39
2403 2418 8.931385 AAACCGAAAATATGTACGTGTAGTAT 57.069 30.769 0.00 0.00 37.69 2.12
2404 2419 7.218014 CGAAACCGAAAATATGTACGTGTAGTA 59.782 37.037 0.00 0.00 0.00 1.82
2405 2420 6.033831 CGAAACCGAAAATATGTACGTGTAGT 59.966 38.462 0.00 0.00 0.00 2.73
2406 2421 6.251163 TCGAAACCGAAAATATGTACGTGTAG 59.749 38.462 0.00 0.00 32.51 2.74
2407 2422 6.033407 GTCGAAACCGAAAATATGTACGTGTA 59.967 38.462 0.00 0.00 37.85 2.90
2408 2423 4.922692 TCGAAACCGAAAATATGTACGTGT 59.077 37.500 0.00 0.00 32.51 4.49
2409 2424 5.164070 TGTCGAAACCGAAAATATGTACGTG 60.164 40.000 0.00 0.00 37.85 4.49
2410 2425 4.922692 TGTCGAAACCGAAAATATGTACGT 59.077 37.500 0.00 0.00 37.85 3.57
2411 2426 5.286797 TCTGTCGAAACCGAAAATATGTACG 59.713 40.000 0.00 0.00 37.85 3.67
2412 2427 6.636666 TCTGTCGAAACCGAAAATATGTAC 57.363 37.500 0.00 0.00 37.85 2.90
2413 2428 8.192774 AGTATCTGTCGAAACCGAAAATATGTA 58.807 33.333 0.00 0.00 37.85 2.29
2414 2429 7.039882 AGTATCTGTCGAAACCGAAAATATGT 58.960 34.615 0.00 0.00 37.85 2.29
2415 2430 7.464830 AGTATCTGTCGAAACCGAAAATATG 57.535 36.000 0.00 0.00 37.85 1.78
2416 2431 8.192774 TGTAGTATCTGTCGAAACCGAAAATAT 58.807 33.333 0.00 0.00 37.85 1.28
2417 2432 7.537715 TGTAGTATCTGTCGAAACCGAAAATA 58.462 34.615 0.00 0.00 37.85 1.40
2418 2433 6.392354 TGTAGTATCTGTCGAAACCGAAAAT 58.608 36.000 0.00 0.00 37.85 1.82
2419 2434 5.771469 TGTAGTATCTGTCGAAACCGAAAA 58.229 37.500 0.00 0.00 37.85 2.29
2420 2435 5.375417 TGTAGTATCTGTCGAAACCGAAA 57.625 39.130 0.00 0.00 37.85 3.46
2421 2436 5.571784 ATGTAGTATCTGTCGAAACCGAA 57.428 39.130 0.00 0.00 37.85 4.30
2422 2437 5.585844 TGTATGTAGTATCTGTCGAAACCGA 59.414 40.000 0.00 0.00 0.00 4.69
2423 2438 5.813717 TGTATGTAGTATCTGTCGAAACCG 58.186 41.667 0.00 0.00 0.00 4.44
2424 2439 7.031372 TGTTGTATGTAGTATCTGTCGAAACC 58.969 38.462 0.00 0.00 0.00 3.27
2425 2440 8.630278 ATGTTGTATGTAGTATCTGTCGAAAC 57.370 34.615 0.00 0.00 0.00 2.78
2426 2441 9.726232 GTATGTTGTATGTAGTATCTGTCGAAA 57.274 33.333 0.00 0.00 0.00 3.46
2427 2442 8.895737 TGTATGTTGTATGTAGTATCTGTCGAA 58.104 33.333 0.00 0.00 0.00 3.71
2428 2443 8.441312 TGTATGTTGTATGTAGTATCTGTCGA 57.559 34.615 0.00 0.00 0.00 4.20
2429 2444 9.511144 TTTGTATGTTGTATGTAGTATCTGTCG 57.489 33.333 0.00 0.00 0.00 4.35
2433 2448 8.814235 GCGTTTTGTATGTTGTATGTAGTATCT 58.186 33.333 0.00 0.00 0.00 1.98
2434 2449 8.597227 TGCGTTTTGTATGTTGTATGTAGTATC 58.403 33.333 0.00 0.00 0.00 2.24
2435 2450 8.481974 TGCGTTTTGTATGTTGTATGTAGTAT 57.518 30.769 0.00 0.00 0.00 2.12
2436 2451 7.886405 TGCGTTTTGTATGTTGTATGTAGTA 57.114 32.000 0.00 0.00 0.00 1.82
2437 2452 6.788684 TGCGTTTTGTATGTTGTATGTAGT 57.211 33.333 0.00 0.00 0.00 2.73
2438 2453 7.268235 CACTTGCGTTTTGTATGTTGTATGTAG 59.732 37.037 0.00 0.00 0.00 2.74
2439 2454 7.072647 CACTTGCGTTTTGTATGTTGTATGTA 58.927 34.615 0.00 0.00 0.00 2.29
2440 2455 5.912396 CACTTGCGTTTTGTATGTTGTATGT 59.088 36.000 0.00 0.00 0.00 2.29
2441 2456 5.341993 CCACTTGCGTTTTGTATGTTGTATG 59.658 40.000 0.00 0.00 0.00 2.39
2442 2457 5.009210 ACCACTTGCGTTTTGTATGTTGTAT 59.991 36.000 0.00 0.00 0.00 2.29
2443 2458 4.335874 ACCACTTGCGTTTTGTATGTTGTA 59.664 37.500 0.00 0.00 0.00 2.41
2444 2459 3.129638 ACCACTTGCGTTTTGTATGTTGT 59.870 39.130 0.00 0.00 0.00 3.32
2445 2460 3.485378 CACCACTTGCGTTTTGTATGTTG 59.515 43.478 0.00 0.00 0.00 3.33
2446 2461 3.490078 CCACCACTTGCGTTTTGTATGTT 60.490 43.478 0.00 0.00 0.00 2.71
2447 2462 2.034053 CCACCACTTGCGTTTTGTATGT 59.966 45.455 0.00 0.00 0.00 2.29
2448 2463 2.034053 ACCACCACTTGCGTTTTGTATG 59.966 45.455 0.00 0.00 0.00 2.39
2449 2464 2.303175 ACCACCACTTGCGTTTTGTAT 58.697 42.857 0.00 0.00 0.00 2.29
2450 2465 1.752683 ACCACCACTTGCGTTTTGTA 58.247 45.000 0.00 0.00 0.00 2.41
2451 2466 1.752683 TACCACCACTTGCGTTTTGT 58.247 45.000 0.00 0.00 0.00 2.83
2452 2467 2.098443 AGTTACCACCACTTGCGTTTTG 59.902 45.455 0.00 0.00 0.00 2.44
2453 2468 2.371306 AGTTACCACCACTTGCGTTTT 58.629 42.857 0.00 0.00 0.00 2.43
2454 2469 2.047002 AGTTACCACCACTTGCGTTT 57.953 45.000 0.00 0.00 0.00 3.60
2455 2470 2.486918 GTAGTTACCACCACTTGCGTT 58.513 47.619 0.00 0.00 0.00 4.84
2456 2471 1.270465 GGTAGTTACCACCACTTGCGT 60.270 52.381 3.45 0.00 45.73 5.24
2457 2472 1.435577 GGTAGTTACCACCACTTGCG 58.564 55.000 3.45 0.00 45.73 4.85
2467 2482 3.512724 TCCTACAAGCAGTGGTAGTTACC 59.487 47.826 0.00 1.25 46.62 2.85
2468 2483 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
2469 2484 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
2470 2485 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
2471 2486 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
2472 2487 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
2473 2488 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
2474 2489 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
2475 2490 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
2476 2491 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
2477 2492 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
2478 2493 4.520492 AGGACAAATGTTTCCTACAAGCAG 59.480 41.667 0.00 0.00 40.70 4.24
2479 2494 4.469657 AGGACAAATGTTTCCTACAAGCA 58.530 39.130 0.00 0.00 40.70 3.91
2480 2495 6.759497 ATAGGACAAATGTTTCCTACAAGC 57.241 37.500 0.00 0.00 45.37 4.01
2511 2526 9.959721 GATGTAACATTGTATACCCCTTCATAT 57.040 33.333 0.00 0.00 0.00 1.78
2512 2527 8.939932 TGATGTAACATTGTATACCCCTTCATA 58.060 33.333 0.00 0.00 0.00 2.15
2513 2528 7.811282 TGATGTAACATTGTATACCCCTTCAT 58.189 34.615 0.00 0.00 0.00 2.57
2514 2529 7.201702 TGATGTAACATTGTATACCCCTTCA 57.798 36.000 0.00 0.00 0.00 3.02
2515 2530 9.959721 ATATGATGTAACATTGTATACCCCTTC 57.040 33.333 0.00 0.00 0.00 3.46
2516 2531 9.739276 CATATGATGTAACATTGTATACCCCTT 57.261 33.333 0.00 0.00 0.00 3.95
2517 2532 8.890472 ACATATGATGTAACATTGTATACCCCT 58.110 33.333 10.38 0.00 42.78 4.79
2549 2564 9.064706 GGTGTTAGACTGTATAGCTTCTGTATA 57.935 37.037 0.00 0.00 0.00 1.47
2550 2565 7.780745 AGGTGTTAGACTGTATAGCTTCTGTAT 59.219 37.037 0.00 0.00 0.00 2.29
2551 2566 7.117397 AGGTGTTAGACTGTATAGCTTCTGTA 58.883 38.462 0.00 0.00 0.00 2.74
2552 2567 5.952947 AGGTGTTAGACTGTATAGCTTCTGT 59.047 40.000 0.00 0.00 0.00 3.41
2553 2568 6.458232 AGGTGTTAGACTGTATAGCTTCTG 57.542 41.667 0.00 0.00 0.00 3.02
2554 2569 6.097129 GGAAGGTGTTAGACTGTATAGCTTCT 59.903 42.308 18.44 0.00 40.52 2.85
2555 2570 6.274579 GGAAGGTGTTAGACTGTATAGCTTC 58.725 44.000 14.29 14.29 40.17 3.86
2556 2571 5.128991 GGGAAGGTGTTAGACTGTATAGCTT 59.871 44.000 0.00 0.00 0.00 3.74
2557 2572 4.650131 GGGAAGGTGTTAGACTGTATAGCT 59.350 45.833 0.00 0.00 0.00 3.32
2558 2573 4.650131 AGGGAAGGTGTTAGACTGTATAGC 59.350 45.833 0.00 0.00 0.00 2.97
2559 2574 6.793505 AAGGGAAGGTGTTAGACTGTATAG 57.206 41.667 0.00 0.00 0.00 1.31
2560 2575 8.849543 ATTAAGGGAAGGTGTTAGACTGTATA 57.150 34.615 0.00 0.00 0.00 1.47
2561 2576 7.624077 AGATTAAGGGAAGGTGTTAGACTGTAT 59.376 37.037 0.00 0.00 0.00 2.29
2562 2577 6.958192 AGATTAAGGGAAGGTGTTAGACTGTA 59.042 38.462 0.00 0.00 0.00 2.74
2563 2578 5.785940 AGATTAAGGGAAGGTGTTAGACTGT 59.214 40.000 0.00 0.00 0.00 3.55
2564 2579 6.301169 AGATTAAGGGAAGGTGTTAGACTG 57.699 41.667 0.00 0.00 0.00 3.51
2565 2580 6.954352 AAGATTAAGGGAAGGTGTTAGACT 57.046 37.500 0.00 0.00 0.00 3.24
2566 2581 6.762187 GCTAAGATTAAGGGAAGGTGTTAGAC 59.238 42.308 0.00 0.00 0.00 2.59
2567 2582 6.126854 GGCTAAGATTAAGGGAAGGTGTTAGA 60.127 42.308 0.00 0.00 0.00 2.10
2568 2583 6.056236 GGCTAAGATTAAGGGAAGGTGTTAG 58.944 44.000 0.00 0.00 0.00 2.34
2569 2584 5.489637 TGGCTAAGATTAAGGGAAGGTGTTA 59.510 40.000 0.00 0.00 0.00 2.41
2570 2585 4.291249 TGGCTAAGATTAAGGGAAGGTGTT 59.709 41.667 0.00 0.00 0.00 3.32
2571 2586 3.850173 TGGCTAAGATTAAGGGAAGGTGT 59.150 43.478 0.00 0.00 0.00 4.16
2572 2587 4.080299 AGTGGCTAAGATTAAGGGAAGGTG 60.080 45.833 0.00 0.00 0.00 4.00
2573 2588 4.112331 AGTGGCTAAGATTAAGGGAAGGT 58.888 43.478 0.00 0.00 0.00 3.50
2574 2589 4.779993 AGTGGCTAAGATTAAGGGAAGG 57.220 45.455 0.00 0.00 0.00 3.46
2575 2590 6.418946 AGAAAGTGGCTAAGATTAAGGGAAG 58.581 40.000 0.00 0.00 0.00 3.46
2576 2591 6.388619 AGAAAGTGGCTAAGATTAAGGGAA 57.611 37.500 0.00 0.00 0.00 3.97
2577 2592 7.504926 TTAGAAAGTGGCTAAGATTAAGGGA 57.495 36.000 0.00 0.00 0.00 4.20
2578 2593 8.047310 TCTTTAGAAAGTGGCTAAGATTAAGGG 58.953 37.037 2.10 0.00 37.31 3.95
2579 2594 9.449719 TTCTTTAGAAAGTGGCTAAGATTAAGG 57.550 33.333 2.10 0.00 37.31 2.69
2585 2600 9.256228 TCTAGATTCTTTAGAAAGTGGCTAAGA 57.744 33.333 2.10 0.00 37.61 2.10
2586 2601 9.877178 TTCTAGATTCTTTAGAAAGTGGCTAAG 57.123 33.333 0.00 0.00 37.61 2.18
2587 2602 9.877178 CTTCTAGATTCTTTAGAAAGTGGCTAA 57.123 33.333 0.00 0.00 36.87 3.09
2588 2603 8.478877 CCTTCTAGATTCTTTAGAAAGTGGCTA 58.521 37.037 0.00 2.54 36.87 3.93
2589 2604 7.334858 CCTTCTAGATTCTTTAGAAAGTGGCT 58.665 38.462 0.00 1.64 36.87 4.75
2590 2605 6.540551 CCCTTCTAGATTCTTTAGAAAGTGGC 59.459 42.308 0.00 0.00 36.87 5.01
2591 2606 7.625469 ACCCTTCTAGATTCTTTAGAAAGTGG 58.375 38.462 0.00 0.70 36.87 4.00
2592 2607 8.940952 CAACCCTTCTAGATTCTTTAGAAAGTG 58.059 37.037 0.00 0.00 36.87 3.16
2593 2608 8.881262 TCAACCCTTCTAGATTCTTTAGAAAGT 58.119 33.333 0.00 0.00 36.87 2.66
2594 2609 9.377312 CTCAACCCTTCTAGATTCTTTAGAAAG 57.623 37.037 0.00 0.00 36.87 2.62
2595 2610 7.824779 GCTCAACCCTTCTAGATTCTTTAGAAA 59.175 37.037 0.00 0.00 36.87 2.52
2596 2611 7.331791 GCTCAACCCTTCTAGATTCTTTAGAA 58.668 38.462 0.00 0.00 36.15 2.10
2597 2612 6.127026 GGCTCAACCCTTCTAGATTCTTTAGA 60.127 42.308 0.00 0.00 0.00 2.10
2598 2613 6.052360 GGCTCAACCCTTCTAGATTCTTTAG 58.948 44.000 0.00 0.00 0.00 1.85
2599 2614 5.395324 CGGCTCAACCCTTCTAGATTCTTTA 60.395 44.000 0.00 0.00 33.26 1.85
2600 2615 4.624125 CGGCTCAACCCTTCTAGATTCTTT 60.624 45.833 0.00 0.00 33.26 2.52
2601 2616 3.118592 CGGCTCAACCCTTCTAGATTCTT 60.119 47.826 0.00 0.00 33.26 2.52
2602 2617 2.432510 CGGCTCAACCCTTCTAGATTCT 59.567 50.000 0.00 0.00 33.26 2.40
2603 2618 2.483889 CCGGCTCAACCCTTCTAGATTC 60.484 54.545 0.00 0.00 33.26 2.52
2604 2619 1.486726 CCGGCTCAACCCTTCTAGATT 59.513 52.381 0.00 0.00 33.26 2.40
2605 2620 1.123928 CCGGCTCAACCCTTCTAGAT 58.876 55.000 0.00 0.00 33.26 1.98
2606 2621 0.252103 ACCGGCTCAACCCTTCTAGA 60.252 55.000 0.00 0.00 33.26 2.43
2607 2622 0.613777 AACCGGCTCAACCCTTCTAG 59.386 55.000 0.00 0.00 33.26 2.43
2608 2623 0.611714 GAACCGGCTCAACCCTTCTA 59.388 55.000 0.00 0.00 33.26 2.10
2609 2624 1.128188 AGAACCGGCTCAACCCTTCT 61.128 55.000 7.76 0.51 33.26 2.85
2610 2625 0.250770 AAGAACCGGCTCAACCCTTC 60.251 55.000 7.76 0.00 33.26 3.46
2611 2626 1.061546 TAAGAACCGGCTCAACCCTT 58.938 50.000 7.76 0.79 33.26 3.95
2612 2627 0.323957 GTAAGAACCGGCTCAACCCT 59.676 55.000 7.76 0.00 33.26 4.34
2613 2628 0.323957 AGTAAGAACCGGCTCAACCC 59.676 55.000 7.76 0.00 33.26 4.11
2614 2629 2.418334 CCTAGTAAGAACCGGCTCAACC 60.418 54.545 7.76 0.00 0.00 3.77
2615 2630 2.889852 CCTAGTAAGAACCGGCTCAAC 58.110 52.381 7.76 5.00 0.00 3.18
2616 2631 1.206371 GCCTAGTAAGAACCGGCTCAA 59.794 52.381 7.76 0.00 38.82 3.02
2617 2632 0.822164 GCCTAGTAAGAACCGGCTCA 59.178 55.000 7.76 0.00 38.82 4.26
2618 2633 0.822164 TGCCTAGTAAGAACCGGCTC 59.178 55.000 0.00 0.00 41.15 4.70
2619 2634 1.139058 CATGCCTAGTAAGAACCGGCT 59.861 52.381 0.00 0.00 41.15 5.52
2620 2635 1.583054 CATGCCTAGTAAGAACCGGC 58.417 55.000 0.00 0.00 41.02 6.13
2621 2636 1.134521 TGCATGCCTAGTAAGAACCGG 60.135 52.381 16.68 0.00 0.00 5.28
2622 2637 2.309528 TGCATGCCTAGTAAGAACCG 57.690 50.000 16.68 0.00 0.00 4.44
2623 2638 6.055588 TCTATTTGCATGCCTAGTAAGAACC 58.944 40.000 16.68 0.00 0.00 3.62
2624 2639 7.281100 ACTTCTATTTGCATGCCTAGTAAGAAC 59.719 37.037 16.68 0.00 0.00 3.01
2625 2640 7.338710 ACTTCTATTTGCATGCCTAGTAAGAA 58.661 34.615 16.68 14.48 0.00 2.52
2626 2641 6.889198 ACTTCTATTTGCATGCCTAGTAAGA 58.111 36.000 16.68 7.78 0.00 2.10
2627 2642 6.989169 AGACTTCTATTTGCATGCCTAGTAAG 59.011 38.462 16.68 17.28 0.00 2.34
2628 2643 6.889198 AGACTTCTATTTGCATGCCTAGTAA 58.111 36.000 16.68 0.00 0.00 2.24
2629 2644 6.485830 AGACTTCTATTTGCATGCCTAGTA 57.514 37.500 16.68 6.70 0.00 1.82
2647 2662 7.693969 AAGCACATTATAAAGCTGAAGACTT 57.306 32.000 10.11 0.00 37.41 3.01
2660 2675 8.367911 CACATAGGGAACTCTAAGCACATTATA 58.632 37.037 0.00 0.00 43.67 0.98
2661 2676 7.071196 TCACATAGGGAACTCTAAGCACATTAT 59.929 37.037 0.00 0.00 43.67 1.28
2665 2680 4.081642 GTCACATAGGGAACTCTAAGCACA 60.082 45.833 0.00 0.00 43.67 4.57
2682 2697 3.814842 TGAAAGAAGATTGCGTGTCACAT 59.185 39.130 3.42 0.00 0.00 3.21
2840 2855 0.247419 CTGAACACGCATGCGACATC 60.247 55.000 43.72 32.82 42.83 3.06
2848 2863 1.512926 GAACTCCACTGAACACGCAT 58.487 50.000 0.00 0.00 0.00 4.73
2849 2864 0.874175 CGAACTCCACTGAACACGCA 60.874 55.000 0.00 0.00 0.00 5.24
2903 2918 1.153369 CGATAGGTGTGGCTGGGTG 60.153 63.158 0.00 0.00 0.00 4.61
2937 2952 2.810439 GCTAGGAAGCTCATGACGAT 57.190 50.000 0.00 0.00 45.85 3.73


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

AutoCloner maintained by Alex Coulton.