Multiple sequence alignment - TraesCS3D01G309400

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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 TraesCS3D01G309400 chr3D 100.000 2480 0 0 1 2480 423391061 423388582 0.000000e+00 4580
1 TraesCS3D01G309400 chr3A 93.600 2250 111 15 257 2480 565463590 565465832 0.000000e+00 3326
2 TraesCS3D01G309400 chr3B 93.275 2156 90 24 372 2480 553569941 553572088 0.000000e+00 3127
3 TraesCS3D01G309400 chr3B 83.455 411 44 15 1 387 553185705 553185295 6.520000e-96 361
4 TraesCS3D01G309400 chr1D 83.626 342 40 13 1153 1481 419994500 419994838 8.620000e-80 307
5 TraesCS3D01G309400 chr1B 82.507 343 46 12 1148 1481 566981228 566981565 3.120000e-74 289
6 TraesCS3D01G309400 chr1A 82.456 342 41 17 1153 1481 516586570 516586905 5.220000e-72 281


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 TraesCS3D01G309400 chr3D 423388582 423391061 2479 True 4580 4580 100.000 1 2480 1 chr3D.!!$R1 2479
1 TraesCS3D01G309400 chr3A 565463590 565465832 2242 False 3326 3326 93.600 257 2480 1 chr3A.!!$F1 2223
2 TraesCS3D01G309400 chr3B 553569941 553572088 2147 False 3127 3127 93.275 372 2480 1 chr3B.!!$F1 2108

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
29 30 0.034670 GCCTTGATGCTTGGGAGACT 60.035 55.0 0.0 0.0 0.00 3.24 F
191 192 0.036875 GTTTAGCTGGGTGGCTGAGT 59.963 55.0 0.0 0.0 43.01 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 1184 0.027979 CTGCACGGTTAATCGGCATG 59.972 55.0 19.78 8.42 36.4 4.06 R
1668 1727 1.044725 CTGTGCGTGCGTGAAATTTC 58.955 50.0 11.41 11.41 0.0 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
17 18 2.998097 TTGCTAGCGGGCCTTGAT 59.002 55.556 10.77 0.00 0.00 2.57
18 19 1.451927 TTGCTAGCGGGCCTTGATG 60.452 57.895 10.77 0.00 0.00 3.07
19 20 3.282920 GCTAGCGGGCCTTGATGC 61.283 66.667 0.84 0.00 0.00 3.91
20 21 2.507944 CTAGCGGGCCTTGATGCT 59.492 61.111 0.84 4.87 41.32 3.79
21 22 1.153086 CTAGCGGGCCTTGATGCTT 60.153 57.895 8.18 0.00 38.82 3.91
22 23 1.442526 CTAGCGGGCCTTGATGCTTG 61.443 60.000 8.18 3.04 38.82 4.01
23 24 2.891941 TAGCGGGCCTTGATGCTTGG 62.892 60.000 8.18 0.00 38.82 3.61
24 25 3.142838 CGGGCCTTGATGCTTGGG 61.143 66.667 0.84 0.00 0.00 4.12
25 26 2.360191 GGGCCTTGATGCTTGGGA 59.640 61.111 0.84 0.00 0.00 4.37
26 27 1.755783 GGGCCTTGATGCTTGGGAG 60.756 63.158 0.84 0.00 0.00 4.30
27 28 1.304282 GGCCTTGATGCTTGGGAGA 59.696 57.895 0.00 0.00 0.00 3.71
28 29 1.034292 GGCCTTGATGCTTGGGAGAC 61.034 60.000 0.00 0.00 0.00 3.36
29 30 0.034670 GCCTTGATGCTTGGGAGACT 60.035 55.000 0.00 0.00 0.00 3.24
30 31 2.016096 GCCTTGATGCTTGGGAGACTC 61.016 57.143 0.00 0.00 0.00 3.36
31 32 1.280133 CCTTGATGCTTGGGAGACTCA 59.720 52.381 4.53 0.00 0.00 3.41
32 33 2.354259 CTTGATGCTTGGGAGACTCAC 58.646 52.381 4.53 0.07 0.00 3.51
33 34 0.615331 TGATGCTTGGGAGACTCACC 59.385 55.000 1.29 2.71 0.00 4.02
34 35 0.615331 GATGCTTGGGAGACTCACCA 59.385 55.000 1.29 5.45 34.29 4.17
35 36 1.003580 GATGCTTGGGAGACTCACCAA 59.996 52.381 18.69 18.69 44.04 3.67
36 37 0.843309 TGCTTGGGAGACTCACCAAA 59.157 50.000 19.67 8.86 45.39 3.28
37 38 1.202806 TGCTTGGGAGACTCACCAAAG 60.203 52.381 19.67 11.80 45.39 2.77
38 39 1.528129 CTTGGGAGACTCACCAAAGC 58.472 55.000 19.67 0.00 45.39 3.51
39 40 0.110486 TTGGGAGACTCACCAAAGCC 59.890 55.000 17.94 4.37 43.35 4.35
40 41 1.059584 TGGGAGACTCACCAAAGCCA 61.060 55.000 1.29 0.00 32.89 4.75
41 42 0.329596 GGGAGACTCACCAAAGCCAT 59.670 55.000 4.53 0.00 0.00 4.40
42 43 1.680249 GGGAGACTCACCAAAGCCATC 60.680 57.143 4.53 0.00 0.00 3.51
43 44 1.680249 GGAGACTCACCAAAGCCATCC 60.680 57.143 4.53 0.00 0.00 3.51
44 45 1.280421 GAGACTCACCAAAGCCATCCT 59.720 52.381 0.00 0.00 0.00 3.24
45 46 1.707427 AGACTCACCAAAGCCATCCTT 59.293 47.619 0.00 0.00 34.51 3.36
46 47 2.108952 AGACTCACCAAAGCCATCCTTT 59.891 45.455 0.00 0.00 44.45 3.11
55 56 3.733443 AAGCCATCCTTTGTGTTTGAC 57.267 42.857 0.00 0.00 0.00 3.18
56 57 1.608590 AGCCATCCTTTGTGTTTGACG 59.391 47.619 0.00 0.00 0.00 4.35
57 58 1.606668 GCCATCCTTTGTGTTTGACGA 59.393 47.619 0.00 0.00 0.00 4.20
58 59 2.228822 GCCATCCTTTGTGTTTGACGAT 59.771 45.455 0.00 0.00 0.00 3.73
59 60 3.825308 CCATCCTTTGTGTTTGACGATG 58.175 45.455 0.00 0.00 0.00 3.84
60 61 3.253188 CCATCCTTTGTGTTTGACGATGT 59.747 43.478 0.00 0.00 0.00 3.06
61 62 4.454161 CCATCCTTTGTGTTTGACGATGTA 59.546 41.667 0.00 0.00 0.00 2.29
62 63 5.382303 CATCCTTTGTGTTTGACGATGTAC 58.618 41.667 0.00 0.00 0.00 2.90
63 64 3.810941 TCCTTTGTGTTTGACGATGTACC 59.189 43.478 0.00 0.00 0.00 3.34
64 65 3.813166 CCTTTGTGTTTGACGATGTACCT 59.187 43.478 0.00 0.00 0.00 3.08
65 66 4.084013 CCTTTGTGTTTGACGATGTACCTC 60.084 45.833 0.00 0.00 0.00 3.85
66 67 2.668250 TGTGTTTGACGATGTACCTCG 58.332 47.619 17.51 17.51 44.14 4.63
73 74 2.593376 CGATGTACCTCGTGGCATG 58.407 57.895 11.85 0.00 36.63 4.06
74 75 0.875908 CGATGTACCTCGTGGCATGG 60.876 60.000 11.85 4.78 36.63 3.66
75 76 1.153168 ATGTACCTCGTGGCATGGC 60.153 57.895 13.29 13.29 36.63 4.40
85 86 4.573950 GGCATGGCCGCCGATTTG 62.574 66.667 8.35 1.14 43.52 2.32
86 87 4.573950 GCATGGCCGCCGATTTGG 62.574 66.667 4.58 0.00 42.50 3.28
87 88 3.140141 CATGGCCGCCGATTTGGT 61.140 61.111 4.58 0.00 41.21 3.67
88 89 2.362375 ATGGCCGCCGATTTGGTT 60.362 55.556 4.58 0.00 41.21 3.67
89 90 1.077357 ATGGCCGCCGATTTGGTTA 60.077 52.632 4.58 0.00 41.21 2.85
90 91 0.681564 ATGGCCGCCGATTTGGTTAA 60.682 50.000 4.58 0.00 41.21 2.01
91 92 0.894184 TGGCCGCCGATTTGGTTAAA 60.894 50.000 4.58 0.00 41.21 1.52
92 93 0.458260 GGCCGCCGATTTGGTTAAAT 59.542 50.000 0.00 0.00 41.21 1.40
93 94 1.134936 GGCCGCCGATTTGGTTAAATT 60.135 47.619 0.00 0.00 41.21 1.82
94 95 2.190161 GCCGCCGATTTGGTTAAATTC 58.810 47.619 0.00 0.00 41.21 2.17
95 96 2.416162 GCCGCCGATTTGGTTAAATTCA 60.416 45.455 0.00 0.00 41.21 2.57
96 97 3.736740 GCCGCCGATTTGGTTAAATTCAT 60.737 43.478 0.00 0.00 41.21 2.57
97 98 4.429108 CCGCCGATTTGGTTAAATTCATT 58.571 39.130 0.00 0.00 41.21 2.57
98 99 4.867608 CCGCCGATTTGGTTAAATTCATTT 59.132 37.500 0.00 0.00 41.21 2.32
99 100 5.220378 CCGCCGATTTGGTTAAATTCATTTG 60.220 40.000 0.00 0.00 41.21 2.32
100 101 5.347364 CGCCGATTTGGTTAAATTCATTTGT 59.653 36.000 0.00 0.00 41.21 2.83
101 102 6.453659 CGCCGATTTGGTTAAATTCATTTGTC 60.454 38.462 0.00 0.00 41.21 3.18
102 103 6.589907 GCCGATTTGGTTAAATTCATTTGTCT 59.410 34.615 0.00 0.00 41.21 3.41
103 104 7.757624 GCCGATTTGGTTAAATTCATTTGTCTA 59.242 33.333 0.00 0.00 41.21 2.59
104 105 9.632807 CCGATTTGGTTAAATTCATTTGTCTAA 57.367 29.630 0.00 0.00 36.66 2.10
115 116 9.675464 AAATTCATTTGTCTAATGGAATGCAAT 57.325 25.926 7.09 0.00 43.19 3.56
116 117 8.657074 ATTCATTTGTCTAATGGAATGCAATG 57.343 30.769 7.09 0.00 43.19 2.82
117 118 7.172868 TCATTTGTCTAATGGAATGCAATGT 57.827 32.000 7.09 0.00 43.19 2.71
118 119 7.036829 TCATTTGTCTAATGGAATGCAATGTG 58.963 34.615 7.09 0.00 43.19 3.21
119 120 5.981088 TTGTCTAATGGAATGCAATGTGT 57.019 34.783 0.00 0.00 0.00 3.72
120 121 5.981088 TGTCTAATGGAATGCAATGTGTT 57.019 34.783 0.00 0.00 0.00 3.32
121 122 5.953183 TGTCTAATGGAATGCAATGTGTTC 58.047 37.500 0.00 0.00 0.00 3.18
122 123 5.105797 TGTCTAATGGAATGCAATGTGTTCC 60.106 40.000 8.78 8.78 41.37 3.62
123 124 3.615224 AATGGAATGCAATGTGTTCCC 57.385 42.857 12.40 0.00 40.51 3.97
124 125 0.887247 TGGAATGCAATGTGTTCCCG 59.113 50.000 12.40 0.00 40.51 5.14
125 126 0.887933 GGAATGCAATGTGTTCCCGT 59.112 50.000 4.91 0.00 36.29 5.28
126 127 1.272212 GGAATGCAATGTGTTCCCGTT 59.728 47.619 4.91 0.00 36.29 4.44
127 128 2.490115 GGAATGCAATGTGTTCCCGTTA 59.510 45.455 4.91 0.00 36.29 3.18
128 129 3.057174 GGAATGCAATGTGTTCCCGTTAA 60.057 43.478 4.91 0.00 36.29 2.01
129 130 4.551388 GAATGCAATGTGTTCCCGTTAAA 58.449 39.130 0.00 0.00 0.00 1.52
130 131 4.592485 ATGCAATGTGTTCCCGTTAAAA 57.408 36.364 0.00 0.00 0.00 1.52
131 132 4.386867 TGCAATGTGTTCCCGTTAAAAA 57.613 36.364 0.00 0.00 0.00 1.94
132 133 4.363999 TGCAATGTGTTCCCGTTAAAAAG 58.636 39.130 0.00 0.00 0.00 2.27
133 134 4.098044 TGCAATGTGTTCCCGTTAAAAAGA 59.902 37.500 0.00 0.00 0.00 2.52
134 135 4.443063 GCAATGTGTTCCCGTTAAAAAGAC 59.557 41.667 0.00 0.00 0.00 3.01
135 136 5.583495 CAATGTGTTCCCGTTAAAAAGACA 58.417 37.500 0.00 0.00 31.79 3.41
136 137 4.886247 TGTGTTCCCGTTAAAAAGACAG 57.114 40.909 0.00 0.00 0.00 3.51
137 138 4.515361 TGTGTTCCCGTTAAAAAGACAGA 58.485 39.130 0.00 0.00 0.00 3.41
138 139 5.127491 TGTGTTCCCGTTAAAAAGACAGAT 58.873 37.500 0.00 0.00 0.00 2.90
139 140 6.289834 TGTGTTCCCGTTAAAAAGACAGATA 58.710 36.000 0.00 0.00 0.00 1.98
140 141 6.938030 TGTGTTCCCGTTAAAAAGACAGATAT 59.062 34.615 0.00 0.00 0.00 1.63
141 142 8.095792 TGTGTTCCCGTTAAAAAGACAGATATA 58.904 33.333 0.00 0.00 0.00 0.86
142 143 8.938906 GTGTTCCCGTTAAAAAGACAGATATAA 58.061 33.333 0.00 0.00 0.00 0.98
143 144 9.504708 TGTTCCCGTTAAAAAGACAGATATAAA 57.495 29.630 0.00 0.00 0.00 1.40
144 145 9.764870 GTTCCCGTTAAAAAGACAGATATAAAC 57.235 33.333 0.00 0.00 0.00 2.01
145 146 8.188531 TCCCGTTAAAAAGACAGATATAAACG 57.811 34.615 0.00 0.00 37.51 3.60
146 147 8.034215 TCCCGTTAAAAAGACAGATATAAACGA 58.966 33.333 5.45 0.00 39.45 3.85
147 148 8.325997 CCCGTTAAAAAGACAGATATAAACGAG 58.674 37.037 5.45 0.00 39.45 4.18
148 149 8.866956 CCGTTAAAAAGACAGATATAAACGAGT 58.133 33.333 5.45 0.00 39.45 4.18
156 157 9.570488 AAGACAGATATAAACGAGTTTAGTGAC 57.430 33.333 13.00 8.55 38.30 3.67
157 158 8.189460 AGACAGATATAAACGAGTTTAGTGACC 58.811 37.037 13.00 2.88 38.30 4.02
158 159 7.263496 ACAGATATAAACGAGTTTAGTGACCC 58.737 38.462 13.00 1.80 38.30 4.46
159 160 7.093640 ACAGATATAAACGAGTTTAGTGACCCA 60.094 37.037 13.00 0.00 38.30 4.51
160 161 7.762615 CAGATATAAACGAGTTTAGTGACCCAA 59.237 37.037 13.00 0.00 38.30 4.12
161 162 8.316214 AGATATAAACGAGTTTAGTGACCCAAA 58.684 33.333 13.00 0.00 38.30 3.28
162 163 9.106070 GATATAAACGAGTTTAGTGACCCAAAT 57.894 33.333 13.00 0.00 38.30 2.32
167 168 9.457436 AAACGAGTTTAGTGACCCAAATATATT 57.543 29.630 0.00 0.00 0.00 1.28
169 170 9.760077 ACGAGTTTAGTGACCCAAATATATTAG 57.240 33.333 0.00 0.00 0.00 1.73
170 171 9.204570 CGAGTTTAGTGACCCAAATATATTAGG 57.795 37.037 11.27 11.27 0.00 2.69
178 179 9.000486 GTGACCCAAATATATTAGGAGTTTAGC 58.000 37.037 17.35 0.00 0.00 3.09
179 180 8.945193 TGACCCAAATATATTAGGAGTTTAGCT 58.055 33.333 17.35 0.00 0.00 3.32
180 181 9.220767 GACCCAAATATATTAGGAGTTTAGCTG 57.779 37.037 17.35 1.30 0.00 4.24
181 182 8.164070 ACCCAAATATATTAGGAGTTTAGCTGG 58.836 37.037 17.35 8.71 0.00 4.85
182 183 7.611855 CCCAAATATATTAGGAGTTTAGCTGGG 59.388 40.741 8.22 8.30 0.00 4.45
183 184 8.164070 CCAAATATATTAGGAGTTTAGCTGGGT 58.836 37.037 0.00 0.00 0.00 4.51
184 185 9.003658 CAAATATATTAGGAGTTTAGCTGGGTG 57.996 37.037 0.00 0.00 0.00 4.61
185 186 3.933861 ATTAGGAGTTTAGCTGGGTGG 57.066 47.619 0.00 0.00 0.00 4.61
186 187 0.909623 TAGGAGTTTAGCTGGGTGGC 59.090 55.000 0.00 0.00 0.00 5.01
187 188 0.842467 AGGAGTTTAGCTGGGTGGCT 60.842 55.000 0.00 0.00 45.29 4.75
188 189 0.678048 GGAGTTTAGCTGGGTGGCTG 60.678 60.000 0.00 0.00 43.01 4.85
189 190 0.324943 GAGTTTAGCTGGGTGGCTGA 59.675 55.000 0.00 0.00 43.01 4.26
190 191 0.326264 AGTTTAGCTGGGTGGCTGAG 59.674 55.000 0.00 0.00 43.01 3.35
191 192 0.036875 GTTTAGCTGGGTGGCTGAGT 59.963 55.000 0.00 0.00 43.01 3.41
192 193 0.771127 TTTAGCTGGGTGGCTGAGTT 59.229 50.000 0.00 0.00 43.01 3.01
193 194 1.651737 TTAGCTGGGTGGCTGAGTTA 58.348 50.000 0.00 0.00 43.01 2.24
194 195 1.651737 TAGCTGGGTGGCTGAGTTAA 58.348 50.000 0.00 0.00 43.01 2.01
195 196 0.771127 AGCTGGGTGGCTGAGTTAAA 59.229 50.000 0.00 0.00 41.43 1.52
196 197 0.881796 GCTGGGTGGCTGAGTTAAAC 59.118 55.000 0.00 0.00 0.00 2.01
197 198 1.817740 GCTGGGTGGCTGAGTTAAACA 60.818 52.381 0.00 0.00 0.00 2.83
198 199 2.582052 CTGGGTGGCTGAGTTAAACAA 58.418 47.619 0.00 0.00 0.00 2.83
199 200 2.554032 CTGGGTGGCTGAGTTAAACAAG 59.446 50.000 0.00 0.00 0.00 3.16
200 201 2.092103 TGGGTGGCTGAGTTAAACAAGT 60.092 45.455 0.00 0.00 0.00 3.16
201 202 2.956333 GGGTGGCTGAGTTAAACAAGTT 59.044 45.455 0.00 0.00 0.00 2.66
202 203 3.383505 GGGTGGCTGAGTTAAACAAGTTT 59.616 43.478 3.47 3.47 36.63 2.66
203 204 4.581409 GGGTGGCTGAGTTAAACAAGTTTA 59.419 41.667 1.46 1.46 34.23 2.01
204 205 5.278315 GGGTGGCTGAGTTAAACAAGTTTAG 60.278 44.000 5.64 0.00 36.52 1.85
205 206 5.298527 GGTGGCTGAGTTAAACAAGTTTAGT 59.701 40.000 5.64 0.00 36.52 2.24
206 207 6.484308 GGTGGCTGAGTTAAACAAGTTTAGTA 59.516 38.462 5.64 0.00 36.52 1.82
207 208 7.012610 GGTGGCTGAGTTAAACAAGTTTAGTAA 59.987 37.037 5.64 0.00 36.52 2.24
208 209 8.400186 GTGGCTGAGTTAAACAAGTTTAGTAAA 58.600 33.333 5.64 0.00 36.52 2.01
209 210 9.127277 TGGCTGAGTTAAACAAGTTTAGTAAAT 57.873 29.630 0.00 0.00 36.52 1.40
210 211 9.961265 GGCTGAGTTAAACAAGTTTAGTAAATT 57.039 29.630 0.00 0.00 36.52 1.82
220 221 8.575649 ACAAGTTTAGTAAATTAGGATGTGGG 57.424 34.615 0.00 0.00 0.00 4.61
221 222 7.614192 ACAAGTTTAGTAAATTAGGATGTGGGG 59.386 37.037 0.00 0.00 0.00 4.96
222 223 6.669631 AGTTTAGTAAATTAGGATGTGGGGG 58.330 40.000 0.00 0.00 0.00 5.40
223 224 6.218938 AGTTTAGTAAATTAGGATGTGGGGGT 59.781 38.462 0.00 0.00 0.00 4.95
224 225 4.790718 AGTAAATTAGGATGTGGGGGTC 57.209 45.455 0.00 0.00 0.00 4.46
225 226 2.729028 AAATTAGGATGTGGGGGTCG 57.271 50.000 0.00 0.00 0.00 4.79
226 227 1.591768 AATTAGGATGTGGGGGTCGT 58.408 50.000 0.00 0.00 0.00 4.34
227 228 1.591768 ATTAGGATGTGGGGGTCGTT 58.408 50.000 0.00 0.00 0.00 3.85
228 229 1.364269 TTAGGATGTGGGGGTCGTTT 58.636 50.000 0.00 0.00 0.00 3.60
229 230 0.906775 TAGGATGTGGGGGTCGTTTC 59.093 55.000 0.00 0.00 0.00 2.78
230 231 1.743995 GGATGTGGGGGTCGTTTCG 60.744 63.158 0.00 0.00 0.00 3.46
231 232 1.004200 GATGTGGGGGTCGTTTCGT 60.004 57.895 0.00 0.00 0.00 3.85
232 233 0.604511 GATGTGGGGGTCGTTTCGTT 60.605 55.000 0.00 0.00 0.00 3.85
233 234 0.179012 ATGTGGGGGTCGTTTCGTTT 60.179 50.000 0.00 0.00 0.00 3.60
234 235 1.096386 TGTGGGGGTCGTTTCGTTTG 61.096 55.000 0.00 0.00 0.00 2.93
235 236 0.814812 GTGGGGGTCGTTTCGTTTGA 60.815 55.000 0.00 0.00 0.00 2.69
236 237 0.108963 TGGGGGTCGTTTCGTTTGAT 59.891 50.000 0.00 0.00 0.00 2.57
237 238 1.241165 GGGGGTCGTTTCGTTTGATT 58.759 50.000 0.00 0.00 0.00 2.57
238 239 1.198408 GGGGGTCGTTTCGTTTGATTC 59.802 52.381 0.00 0.00 0.00 2.52
239 240 1.198408 GGGGTCGTTTCGTTTGATTCC 59.802 52.381 0.00 0.00 0.00 3.01
240 241 2.148768 GGGTCGTTTCGTTTGATTCCT 58.851 47.619 0.00 0.00 0.00 3.36
241 242 3.328505 GGGTCGTTTCGTTTGATTCCTA 58.671 45.455 0.00 0.00 0.00 2.94
242 243 3.370061 GGGTCGTTTCGTTTGATTCCTAG 59.630 47.826 0.00 0.00 0.00 3.02
243 244 3.181523 GGTCGTTTCGTTTGATTCCTAGC 60.182 47.826 0.00 0.00 0.00 3.42
244 245 2.997986 TCGTTTCGTTTGATTCCTAGCC 59.002 45.455 0.00 0.00 0.00 3.93
245 246 2.739913 CGTTTCGTTTGATTCCTAGCCA 59.260 45.455 0.00 0.00 0.00 4.75
246 247 3.374058 CGTTTCGTTTGATTCCTAGCCAT 59.626 43.478 0.00 0.00 0.00 4.40
247 248 4.569162 CGTTTCGTTTGATTCCTAGCCATA 59.431 41.667 0.00 0.00 0.00 2.74
248 249 5.501897 CGTTTCGTTTGATTCCTAGCCATAC 60.502 44.000 0.00 0.00 0.00 2.39
249 250 5.353394 TTCGTTTGATTCCTAGCCATACT 57.647 39.130 0.00 0.00 0.00 2.12
250 251 5.353394 TCGTTTGATTCCTAGCCATACTT 57.647 39.130 0.00 0.00 0.00 2.24
251 252 5.741011 TCGTTTGATTCCTAGCCATACTTT 58.259 37.500 0.00 0.00 0.00 2.66
252 253 5.584649 TCGTTTGATTCCTAGCCATACTTTG 59.415 40.000 0.00 0.00 0.00 2.77
253 254 5.354234 CGTTTGATTCCTAGCCATACTTTGT 59.646 40.000 0.00 0.00 0.00 2.83
254 255 6.456988 CGTTTGATTCCTAGCCATACTTTGTC 60.457 42.308 0.00 0.00 0.00 3.18
255 256 4.693283 TGATTCCTAGCCATACTTTGTCG 58.307 43.478 0.00 0.00 0.00 4.35
256 257 2.596904 TCCTAGCCATACTTTGTCGC 57.403 50.000 0.00 0.00 0.00 5.19
257 258 1.828595 TCCTAGCCATACTTTGTCGCA 59.171 47.619 0.00 0.00 0.00 5.10
258 259 2.434336 TCCTAGCCATACTTTGTCGCAT 59.566 45.455 0.00 0.00 0.00 4.73
259 260 3.639561 TCCTAGCCATACTTTGTCGCATA 59.360 43.478 0.00 0.00 0.00 3.14
260 261 4.283467 TCCTAGCCATACTTTGTCGCATAT 59.717 41.667 0.00 0.00 0.00 1.78
261 262 4.997395 CCTAGCCATACTTTGTCGCATATT 59.003 41.667 0.00 0.00 0.00 1.28
262 263 4.818534 AGCCATACTTTGTCGCATATTG 57.181 40.909 0.00 0.00 0.00 1.90
263 264 4.450976 AGCCATACTTTGTCGCATATTGA 58.549 39.130 0.00 0.00 0.00 2.57
264 265 4.881273 AGCCATACTTTGTCGCATATTGAA 59.119 37.500 0.00 0.00 0.00 2.69
265 266 5.532406 AGCCATACTTTGTCGCATATTGAAT 59.468 36.000 0.00 0.00 0.00 2.57
266 267 6.710295 AGCCATACTTTGTCGCATATTGAATA 59.290 34.615 0.00 0.00 0.00 1.75
267 268 7.017645 GCCATACTTTGTCGCATATTGAATAG 58.982 38.462 0.00 0.00 0.00 1.73
268 269 7.521529 CCATACTTTGTCGCATATTGAATAGG 58.478 38.462 0.00 0.00 0.00 2.57
282 283 6.976934 ATTGAATAGGTGTTTGGTTCAAGT 57.023 33.333 0.00 0.00 40.72 3.16
287 288 3.631250 AGGTGTTTGGTTCAAGTCACAT 58.369 40.909 14.49 8.62 34.47 3.21
288 289 4.787551 AGGTGTTTGGTTCAAGTCACATA 58.212 39.130 14.49 0.00 34.47 2.29
289 290 5.385198 AGGTGTTTGGTTCAAGTCACATAT 58.615 37.500 14.49 0.00 34.47 1.78
294 295 8.730680 GTGTTTGGTTCAAGTCACATATTAGAT 58.269 33.333 10.58 0.00 33.72 1.98
330 332 1.270907 AAAATAAACCCGGCATGCCA 58.729 45.000 34.93 16.13 35.37 4.92
333 335 2.603075 ATAAACCCGGCATGCCATAT 57.397 45.000 34.93 20.27 35.37 1.78
348 350 2.916716 GCCATATGCACAAAAACGTGAG 59.083 45.455 0.00 0.00 39.34 3.51
368 370 7.012421 ACGTGAGAATATTTTCTTAGGCAATCC 59.988 37.037 7.44 0.00 42.34 3.01
370 372 7.012421 GTGAGAATATTTTCTTAGGCAATCCGT 59.988 37.037 7.44 0.00 42.34 4.69
379 381 2.112815 GGCAATCCGTAGTGTGGCC 61.113 63.158 0.00 0.00 0.00 5.36
407 409 8.211629 AGAGTTTGTGAACCTAAAGTTAGACAT 58.788 33.333 0.00 0.00 39.40 3.06
409 411 7.990886 AGTTTGTGAACCTAAAGTTAGACATGA 59.009 33.333 0.00 0.00 39.40 3.07
449 453 5.480073 TGGCAAACTATGTCAAAATTAGCCT 59.520 36.000 0.00 0.00 41.69 4.58
450 454 6.036470 GGCAAACTATGTCAAAATTAGCCTC 58.964 40.000 0.00 0.00 34.59 4.70
469 473 1.033574 CAAACCAAACAGGCCCGTAA 58.966 50.000 0.00 0.00 43.14 3.18
642 669 3.938963 GAGAATTAGCATCGGGACAACAA 59.061 43.478 0.00 0.00 0.00 2.83
739 766 0.244994 AACTAGAGTCGCTGTGCAGG 59.755 55.000 0.00 0.00 0.00 4.85
753 780 1.539827 GTGCAGGCGTCCACTTATTTT 59.460 47.619 0.00 0.00 0.00 1.82
769 796 6.259608 CACTTATTTTCATCGGAGAATCTGCT 59.740 38.462 0.00 0.00 43.58 4.24
883 918 6.311690 TCGCTTATTGTCGATATTTTCACACA 59.688 34.615 0.00 0.00 0.00 3.72
1097 1135 4.735132 GCCGCTACGTGCCACTGA 62.735 66.667 0.00 0.00 38.78 3.41
1128 1175 2.992689 CCATGTGCAGCCCAAGCA 60.993 61.111 0.00 0.00 43.56 3.91
1488 1541 2.227865 CCTCTCGCTCTAAGCCATAGTC 59.772 54.545 0.00 0.00 38.18 2.59
1490 1543 3.556999 TCTCGCTCTAAGCCATAGTCTT 58.443 45.455 0.00 0.00 38.18 3.01
1613 1667 2.324330 CGCCGTCAGATGGTTTGCA 61.324 57.895 10.58 0.00 0.00 4.08
1693 1752 2.509336 ACGCACGCACAGATAGGC 60.509 61.111 0.00 0.00 0.00 3.93
1696 1755 2.586079 CACGCACAGATAGGCCCG 60.586 66.667 0.00 0.00 0.00 6.13
1809 1868 9.499479 CAGCTATTTGATCAGAACCATATAACT 57.501 33.333 0.00 0.00 0.00 2.24
1909 1969 2.427506 GTGCTCCAAGTTAGGTGGAAG 58.572 52.381 0.00 0.00 44.55 3.46
1957 2017 8.526978 TCAGCTGGTACTATCTTCAATATGATC 58.473 37.037 15.13 0.00 0.00 2.92
1967 2027 6.907853 TCTTCAATATGATCGTCCTGAGAT 57.092 37.500 0.00 0.00 0.00 2.75
2016 2076 4.284490 TCTGTTCAGAGATGCTTAAGGTGT 59.716 41.667 4.29 0.00 0.00 4.16
2018 2078 4.284490 TGTTCAGAGATGCTTAAGGTGTCT 59.716 41.667 4.29 0.00 0.00 3.41
2093 2153 2.042464 TCTATTGGCTCAGAATCGCCT 58.958 47.619 0.00 0.00 46.42 5.52
2129 2189 3.558931 TCAAGGTGTTGAGCTCTTGAA 57.441 42.857 16.19 0.00 41.48 2.69
2147 2207 2.357637 TGAACTGGTTTTCAAAGGCTCG 59.642 45.455 0.00 0.00 32.42 5.03
2153 2213 2.218603 GTTTTCAAAGGCTCGTCAGGA 58.781 47.619 0.00 0.00 0.00 3.86
2272 2332 5.592054 TCTAGAATTCTGCGTGTTATCCTG 58.408 41.667 18.47 0.00 0.00 3.86
2277 2337 1.271379 TCTGCGTGTTATCCTGTTCGT 59.729 47.619 0.00 0.00 0.00 3.85
2342 2402 4.583073 GGACAAACTCCCTAGCAAAAAGAA 59.417 41.667 0.00 0.00 31.83 2.52
2343 2403 5.068591 GGACAAACTCCCTAGCAAAAAGAAA 59.931 40.000 0.00 0.00 31.83 2.52
2347 2407 8.870116 ACAAACTCCCTAGCAAAAAGAAATATT 58.130 29.630 0.00 0.00 0.00 1.28
2356 2416 5.850931 GCAAAAAGAAATATTGCAGTCAGC 58.149 37.500 4.96 0.00 46.57 4.26
2389 2449 3.367910 GCACCTTCAACTTCAAACCAACA 60.368 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.451927 CATCAAGGCCCGCTAGCAA 60.452 57.895 16.45 0.00 0.00 3.91
1 2 2.190313 CATCAAGGCCCGCTAGCA 59.810 61.111 16.45 0.00 0.00 3.49
2 3 3.282920 GCATCAAGGCCCGCTAGC 61.283 66.667 4.06 4.06 0.00 3.42
3 4 1.153086 AAGCATCAAGGCCCGCTAG 60.153 57.895 0.00 0.00 33.45 3.42
5 6 2.753043 CAAGCATCAAGGCCCGCT 60.753 61.111 0.00 0.00 35.90 5.52
7 8 3.142838 CCCAAGCATCAAGGCCCG 61.143 66.667 0.00 0.00 0.00 6.13
8 9 1.755783 CTCCCAAGCATCAAGGCCC 60.756 63.158 0.00 0.00 0.00 5.80
9 10 1.034292 GTCTCCCAAGCATCAAGGCC 61.034 60.000 0.00 0.00 0.00 5.19
11 12 1.280133 TGAGTCTCCCAAGCATCAAGG 59.720 52.381 0.00 0.00 0.00 3.61
12 13 2.354259 GTGAGTCTCCCAAGCATCAAG 58.646 52.381 0.00 0.00 0.00 3.02
13 14 1.003580 GGTGAGTCTCCCAAGCATCAA 59.996 52.381 0.00 0.00 0.00 2.57
14 15 0.615331 GGTGAGTCTCCCAAGCATCA 59.385 55.000 0.00 0.00 0.00 3.07
15 16 0.615331 TGGTGAGTCTCCCAAGCATC 59.385 55.000 8.74 0.00 0.00 3.91
16 17 1.067295 TTGGTGAGTCTCCCAAGCAT 58.933 50.000 15.13 0.00 35.84 3.79
17 18 0.843309 TTTGGTGAGTCTCCCAAGCA 59.157 50.000 17.22 5.10 41.51 3.91
18 19 1.528129 CTTTGGTGAGTCTCCCAAGC 58.472 55.000 17.22 2.89 41.51 4.01
19 20 1.528129 GCTTTGGTGAGTCTCCCAAG 58.472 55.000 16.87 16.87 41.51 3.61
20 21 0.110486 GGCTTTGGTGAGTCTCCCAA 59.890 55.000 15.13 15.13 38.92 4.12
21 22 1.059584 TGGCTTTGGTGAGTCTCCCA 61.060 55.000 8.74 3.55 0.00 4.37
22 23 0.329596 ATGGCTTTGGTGAGTCTCCC 59.670 55.000 8.74 0.84 0.00 4.30
23 24 1.680249 GGATGGCTTTGGTGAGTCTCC 60.680 57.143 4.18 4.18 0.00 3.71
24 25 1.280421 AGGATGGCTTTGGTGAGTCTC 59.720 52.381 0.00 0.00 0.00 3.36
25 26 1.366319 AGGATGGCTTTGGTGAGTCT 58.634 50.000 0.00 0.00 0.00 3.24
26 27 2.206576 AAGGATGGCTTTGGTGAGTC 57.793 50.000 0.00 0.00 0.00 3.36
27 28 2.242043 CAAAGGATGGCTTTGGTGAGT 58.758 47.619 0.00 0.00 37.94 3.41
28 29 2.029649 CACAAAGGATGGCTTTGGTGAG 60.030 50.000 1.40 0.00 43.73 3.51
29 30 1.962807 CACAAAGGATGGCTTTGGTGA 59.037 47.619 1.40 0.00 43.73 4.02
30 31 1.688197 ACACAAAGGATGGCTTTGGTG 59.312 47.619 1.40 0.49 43.73 4.17
31 32 2.086610 ACACAAAGGATGGCTTTGGT 57.913 45.000 1.40 0.00 43.73 3.67
32 33 3.132925 CAAACACAAAGGATGGCTTTGG 58.867 45.455 1.40 0.00 43.73 3.28
33 34 3.803778 GTCAAACACAAAGGATGGCTTTG 59.196 43.478 0.00 0.00 44.64 2.77
34 35 3.490761 CGTCAAACACAAAGGATGGCTTT 60.491 43.478 0.00 0.00 0.00 3.51
35 36 2.034558 CGTCAAACACAAAGGATGGCTT 59.965 45.455 0.00 0.00 0.00 4.35
36 37 1.608590 CGTCAAACACAAAGGATGGCT 59.391 47.619 0.00 0.00 0.00 4.75
37 38 1.606668 TCGTCAAACACAAAGGATGGC 59.393 47.619 0.00 0.00 0.00 4.40
38 39 3.253188 ACATCGTCAAACACAAAGGATGG 59.747 43.478 8.56 0.00 38.80 3.51
39 40 4.488126 ACATCGTCAAACACAAAGGATG 57.512 40.909 0.00 0.00 39.79 3.51
40 41 4.454504 GGTACATCGTCAAACACAAAGGAT 59.545 41.667 0.00 0.00 0.00 3.24
41 42 3.810941 GGTACATCGTCAAACACAAAGGA 59.189 43.478 0.00 0.00 0.00 3.36
42 43 3.813166 AGGTACATCGTCAAACACAAAGG 59.187 43.478 0.00 0.00 0.00 3.11
43 44 4.376008 CGAGGTACATCGTCAAACACAAAG 60.376 45.833 21.02 0.00 37.91 2.77
44 45 3.491639 CGAGGTACATCGTCAAACACAAA 59.508 43.478 21.02 0.00 37.91 2.83
45 46 3.054166 CGAGGTACATCGTCAAACACAA 58.946 45.455 21.02 0.00 37.91 3.33
46 47 2.668250 CGAGGTACATCGTCAAACACA 58.332 47.619 21.02 0.00 37.91 3.72
56 57 1.160329 GCCATGCCACGAGGTACATC 61.160 60.000 0.00 0.00 37.19 3.06
57 58 1.153168 GCCATGCCACGAGGTACAT 60.153 57.895 0.00 0.00 37.19 2.29
58 59 2.267642 GCCATGCCACGAGGTACA 59.732 61.111 0.00 0.00 37.19 2.90
69 70 4.573950 CCAAATCGGCGGCCATGC 62.574 66.667 20.71 0.00 0.00 4.06
70 71 1.380403 TAACCAAATCGGCGGCCATG 61.380 55.000 20.71 11.50 39.03 3.66
71 72 0.681564 TTAACCAAATCGGCGGCCAT 60.682 50.000 20.71 8.91 39.03 4.40
72 73 0.894184 TTTAACCAAATCGGCGGCCA 60.894 50.000 20.71 6.72 39.03 5.36
73 74 0.458260 ATTTAACCAAATCGGCGGCC 59.542 50.000 9.54 9.54 39.03 6.13
74 75 2.190161 GAATTTAACCAAATCGGCGGC 58.810 47.619 7.21 0.00 39.03 6.53
75 76 3.495670 TGAATTTAACCAAATCGGCGG 57.504 42.857 7.21 0.00 39.03 6.13
76 77 5.347364 ACAAATGAATTTAACCAAATCGGCG 59.653 36.000 0.00 0.00 39.03 6.46
77 78 6.589907 AGACAAATGAATTTAACCAAATCGGC 59.410 34.615 0.00 0.00 39.03 5.54
78 79 9.632807 TTAGACAAATGAATTTAACCAAATCGG 57.367 29.630 0.00 0.00 42.50 4.18
89 90 9.675464 ATTGCATTCCATTAGACAAATGAATTT 57.325 25.926 0.00 0.00 46.81 1.82
90 91 9.104965 CATTGCATTCCATTAGACAAATGAATT 57.895 29.630 0.00 0.00 46.81 2.17
91 92 8.262227 ACATTGCATTCCATTAGACAAATGAAT 58.738 29.630 0.00 0.00 46.81 2.57
92 93 7.546316 CACATTGCATTCCATTAGACAAATGAA 59.454 33.333 0.00 0.00 46.81 2.57
93 94 7.036829 CACATTGCATTCCATTAGACAAATGA 58.963 34.615 0.00 0.00 46.81 2.57
94 95 6.814644 ACACATTGCATTCCATTAGACAAATG 59.185 34.615 0.00 0.00 43.99 2.32
95 96 6.938507 ACACATTGCATTCCATTAGACAAAT 58.061 32.000 0.00 0.00 0.00 2.32
96 97 6.343716 ACACATTGCATTCCATTAGACAAA 57.656 33.333 0.00 0.00 0.00 2.83
97 98 5.981088 ACACATTGCATTCCATTAGACAA 57.019 34.783 0.00 0.00 0.00 3.18
98 99 5.105797 GGAACACATTGCATTCCATTAGACA 60.106 40.000 10.52 0.00 41.40 3.41
99 100 5.343249 GGAACACATTGCATTCCATTAGAC 58.657 41.667 10.52 0.00 41.40 2.59
100 101 4.402155 GGGAACACATTGCATTCCATTAGA 59.598 41.667 15.98 0.00 43.21 2.10
101 102 4.685924 GGGAACACATTGCATTCCATTAG 58.314 43.478 15.98 0.00 43.21 1.73
102 103 3.130164 CGGGAACACATTGCATTCCATTA 59.870 43.478 15.98 0.00 43.21 1.90
103 104 2.094078 CGGGAACACATTGCATTCCATT 60.094 45.455 15.98 0.00 43.21 3.16
104 105 1.477700 CGGGAACACATTGCATTCCAT 59.522 47.619 15.98 0.00 43.21 3.41
105 106 0.887247 CGGGAACACATTGCATTCCA 59.113 50.000 15.98 0.00 43.21 3.53
106 107 0.887933 ACGGGAACACATTGCATTCC 59.112 50.000 7.39 7.39 41.09 3.01
107 108 2.723124 AACGGGAACACATTGCATTC 57.277 45.000 0.00 0.00 0.00 2.67
108 109 4.592485 TTTAACGGGAACACATTGCATT 57.408 36.364 0.00 0.00 0.00 3.56
109 110 4.592485 TTTTAACGGGAACACATTGCAT 57.408 36.364 0.00 0.00 0.00 3.96
110 111 4.098044 TCTTTTTAACGGGAACACATTGCA 59.902 37.500 0.00 0.00 0.00 4.08
111 112 4.443063 GTCTTTTTAACGGGAACACATTGC 59.557 41.667 0.00 0.00 0.00 3.56
112 113 5.583495 TGTCTTTTTAACGGGAACACATTG 58.417 37.500 0.00 0.00 0.00 2.82
113 114 5.591067 TCTGTCTTTTTAACGGGAACACATT 59.409 36.000 0.00 0.00 0.00 2.71
114 115 5.127491 TCTGTCTTTTTAACGGGAACACAT 58.873 37.500 0.00 0.00 0.00 3.21
115 116 4.515361 TCTGTCTTTTTAACGGGAACACA 58.485 39.130 0.00 0.00 0.00 3.72
116 117 5.684550 ATCTGTCTTTTTAACGGGAACAC 57.315 39.130 0.00 0.00 0.00 3.32
117 118 9.504708 TTTATATCTGTCTTTTTAACGGGAACA 57.495 29.630 0.00 0.00 0.00 3.18
118 119 9.764870 GTTTATATCTGTCTTTTTAACGGGAAC 57.235 33.333 0.00 0.00 0.00 3.62
119 120 8.658609 CGTTTATATCTGTCTTTTTAACGGGAA 58.341 33.333 0.00 0.00 34.08 3.97
120 121 8.034215 TCGTTTATATCTGTCTTTTTAACGGGA 58.966 33.333 0.00 0.00 37.16 5.14
121 122 8.188531 TCGTTTATATCTGTCTTTTTAACGGG 57.811 34.615 0.00 0.00 37.16 5.28
122 123 8.866956 ACTCGTTTATATCTGTCTTTTTAACGG 58.133 33.333 0.00 0.00 37.16 4.44
130 131 9.570488 GTCACTAAACTCGTTTATATCTGTCTT 57.430 33.333 3.01 0.00 34.86 3.01
131 132 8.189460 GGTCACTAAACTCGTTTATATCTGTCT 58.811 37.037 3.01 0.00 34.86 3.41
132 133 7.434602 GGGTCACTAAACTCGTTTATATCTGTC 59.565 40.741 3.01 0.00 34.86 3.51
133 134 7.093640 TGGGTCACTAAACTCGTTTATATCTGT 60.094 37.037 3.01 0.00 34.86 3.41
134 135 7.262772 TGGGTCACTAAACTCGTTTATATCTG 58.737 38.462 3.01 0.00 34.86 2.90
135 136 7.414222 TGGGTCACTAAACTCGTTTATATCT 57.586 36.000 3.01 0.00 34.86 1.98
136 137 8.483307 TTTGGGTCACTAAACTCGTTTATATC 57.517 34.615 3.01 0.00 34.86 1.63
141 142 9.457436 AATATATTTGGGTCACTAAACTCGTTT 57.543 29.630 0.35 0.35 36.63 3.60
143 144 9.760077 CTAATATATTTGGGTCACTAAACTCGT 57.240 33.333 2.68 0.00 29.45 4.18
144 145 9.204570 CCTAATATATTTGGGTCACTAAACTCG 57.795 37.037 15.78 0.00 29.45 4.18
152 153 9.000486 GCTAAACTCCTAATATATTTGGGTCAC 58.000 37.037 21.17 6.02 34.16 3.67
153 154 8.945193 AGCTAAACTCCTAATATATTTGGGTCA 58.055 33.333 21.17 6.04 34.16 4.02
154 155 9.220767 CAGCTAAACTCCTAATATATTTGGGTC 57.779 37.037 21.17 9.44 34.16 4.46
155 156 8.164070 CCAGCTAAACTCCTAATATATTTGGGT 58.836 37.037 21.17 15.93 34.16 4.51
156 157 7.611855 CCCAGCTAAACTCCTAATATATTTGGG 59.388 40.741 21.17 14.67 34.16 4.12
157 158 8.164070 ACCCAGCTAAACTCCTAATATATTTGG 58.836 37.037 17.06 17.06 34.59 3.28
158 159 9.003658 CACCCAGCTAAACTCCTAATATATTTG 57.996 37.037 2.68 1.43 0.00 2.32
159 160 8.164070 CCACCCAGCTAAACTCCTAATATATTT 58.836 37.037 2.68 0.00 0.00 1.40
160 161 7.690256 CCACCCAGCTAAACTCCTAATATATT 58.310 38.462 2.97 2.97 0.00 1.28
161 162 6.296489 GCCACCCAGCTAAACTCCTAATATAT 60.296 42.308 0.00 0.00 0.00 0.86
162 163 5.012768 GCCACCCAGCTAAACTCCTAATATA 59.987 44.000 0.00 0.00 0.00 0.86
163 164 4.202472 GCCACCCAGCTAAACTCCTAATAT 60.202 45.833 0.00 0.00 0.00 1.28
164 165 3.135895 GCCACCCAGCTAAACTCCTAATA 59.864 47.826 0.00 0.00 0.00 0.98
165 166 2.092375 GCCACCCAGCTAAACTCCTAAT 60.092 50.000 0.00 0.00 0.00 1.73
166 167 1.280998 GCCACCCAGCTAAACTCCTAA 59.719 52.381 0.00 0.00 0.00 2.69
167 168 0.909623 GCCACCCAGCTAAACTCCTA 59.090 55.000 0.00 0.00 0.00 2.94
168 169 0.842467 AGCCACCCAGCTAAACTCCT 60.842 55.000 0.00 0.00 42.70 3.69
169 170 0.678048 CAGCCACCCAGCTAAACTCC 60.678 60.000 0.00 0.00 42.61 3.85
170 171 0.324943 TCAGCCACCCAGCTAAACTC 59.675 55.000 0.00 0.00 42.61 3.01
171 172 0.326264 CTCAGCCACCCAGCTAAACT 59.674 55.000 0.00 0.00 42.61 2.66
172 173 0.036875 ACTCAGCCACCCAGCTAAAC 59.963 55.000 0.00 0.00 42.61 2.01
173 174 0.771127 AACTCAGCCACCCAGCTAAA 59.229 50.000 0.00 0.00 42.61 1.85
174 175 1.651737 TAACTCAGCCACCCAGCTAA 58.348 50.000 0.00 0.00 42.61 3.09
175 176 1.651737 TTAACTCAGCCACCCAGCTA 58.348 50.000 0.00 0.00 42.61 3.32
176 177 0.771127 TTTAACTCAGCCACCCAGCT 59.229 50.000 0.00 0.00 46.45 4.24
177 178 0.881796 GTTTAACTCAGCCACCCAGC 59.118 55.000 0.00 0.00 0.00 4.85
178 179 2.270352 TGTTTAACTCAGCCACCCAG 57.730 50.000 0.00 0.00 0.00 4.45
179 180 2.092103 ACTTGTTTAACTCAGCCACCCA 60.092 45.455 0.00 0.00 0.00 4.51
180 181 2.583143 ACTTGTTTAACTCAGCCACCC 58.417 47.619 0.00 0.00 0.00 4.61
181 182 4.649088 AAACTTGTTTAACTCAGCCACC 57.351 40.909 0.00 0.00 0.00 4.61
182 183 6.373186 ACTAAACTTGTTTAACTCAGCCAC 57.627 37.500 7.28 0.00 0.00 5.01
183 184 8.508883 TTTACTAAACTTGTTTAACTCAGCCA 57.491 30.769 7.28 0.00 0.00 4.75
184 185 9.961265 AATTTACTAAACTTGTTTAACTCAGCC 57.039 29.630 7.28 0.00 0.00 4.85
194 195 9.020731 CCCACATCCTAATTTACTAAACTTGTT 57.979 33.333 0.00 0.00 0.00 2.83
195 196 7.614192 CCCCACATCCTAATTTACTAAACTTGT 59.386 37.037 0.00 0.00 0.00 3.16
196 197 7.068226 CCCCCACATCCTAATTTACTAAACTTG 59.932 40.741 0.00 0.00 0.00 3.16
197 198 7.123383 CCCCCACATCCTAATTTACTAAACTT 58.877 38.462 0.00 0.00 0.00 2.66
198 199 6.218938 ACCCCCACATCCTAATTTACTAAACT 59.781 38.462 0.00 0.00 0.00 2.66
199 200 6.429151 ACCCCCACATCCTAATTTACTAAAC 58.571 40.000 0.00 0.00 0.00 2.01
200 201 6.633127 CGACCCCCACATCCTAATTTACTAAA 60.633 42.308 0.00 0.00 0.00 1.85
201 202 5.163280 CGACCCCCACATCCTAATTTACTAA 60.163 44.000 0.00 0.00 0.00 2.24
202 203 4.345837 CGACCCCCACATCCTAATTTACTA 59.654 45.833 0.00 0.00 0.00 1.82
203 204 3.135895 CGACCCCCACATCCTAATTTACT 59.864 47.826 0.00 0.00 0.00 2.24
204 205 3.118149 ACGACCCCCACATCCTAATTTAC 60.118 47.826 0.00 0.00 0.00 2.01
205 206 3.116959 ACGACCCCCACATCCTAATTTA 58.883 45.455 0.00 0.00 0.00 1.40
206 207 1.920351 ACGACCCCCACATCCTAATTT 59.080 47.619 0.00 0.00 0.00 1.82
207 208 1.591768 ACGACCCCCACATCCTAATT 58.408 50.000 0.00 0.00 0.00 1.40
208 209 1.591768 AACGACCCCCACATCCTAAT 58.408 50.000 0.00 0.00 0.00 1.73
209 210 1.279846 GAAACGACCCCCACATCCTAA 59.720 52.381 0.00 0.00 0.00 2.69
210 211 0.906775 GAAACGACCCCCACATCCTA 59.093 55.000 0.00 0.00 0.00 2.94
211 212 1.683441 GAAACGACCCCCACATCCT 59.317 57.895 0.00 0.00 0.00 3.24
212 213 1.743995 CGAAACGACCCCCACATCC 60.744 63.158 0.00 0.00 0.00 3.51
213 214 0.604511 AACGAAACGACCCCCACATC 60.605 55.000 0.00 0.00 0.00 3.06
214 215 0.179012 AAACGAAACGACCCCCACAT 60.179 50.000 0.00 0.00 0.00 3.21
215 216 1.096386 CAAACGAAACGACCCCCACA 61.096 55.000 0.00 0.00 0.00 4.17
216 217 0.814812 TCAAACGAAACGACCCCCAC 60.815 55.000 0.00 0.00 0.00 4.61
217 218 0.108963 ATCAAACGAAACGACCCCCA 59.891 50.000 0.00 0.00 0.00 4.96
218 219 1.198408 GAATCAAACGAAACGACCCCC 59.802 52.381 0.00 0.00 0.00 5.40
219 220 1.198408 GGAATCAAACGAAACGACCCC 59.802 52.381 0.00 0.00 0.00 4.95
220 221 2.148768 AGGAATCAAACGAAACGACCC 58.851 47.619 0.00 0.00 0.00 4.46
221 222 3.181523 GCTAGGAATCAAACGAAACGACC 60.182 47.826 0.00 0.00 0.00 4.79
222 223 3.181523 GGCTAGGAATCAAACGAAACGAC 60.182 47.826 0.00 0.00 0.00 4.34
223 224 2.997986 GGCTAGGAATCAAACGAAACGA 59.002 45.455 0.00 0.00 0.00 3.85
224 225 2.739913 TGGCTAGGAATCAAACGAAACG 59.260 45.455 0.00 0.00 0.00 3.60
225 226 4.965119 ATGGCTAGGAATCAAACGAAAC 57.035 40.909 0.00 0.00 0.00 2.78
226 227 5.741011 AGTATGGCTAGGAATCAAACGAAA 58.259 37.500 0.00 0.00 0.00 3.46
227 228 5.353394 AGTATGGCTAGGAATCAAACGAA 57.647 39.130 0.00 0.00 0.00 3.85
228 229 5.353394 AAGTATGGCTAGGAATCAAACGA 57.647 39.130 0.00 0.00 0.00 3.85
229 230 5.354234 ACAAAGTATGGCTAGGAATCAAACG 59.646 40.000 0.00 0.00 0.00 3.60
230 231 6.456988 CGACAAAGTATGGCTAGGAATCAAAC 60.457 42.308 0.00 0.00 33.51 2.93
231 232 5.584649 CGACAAAGTATGGCTAGGAATCAAA 59.415 40.000 0.00 0.00 33.51 2.69
232 233 5.116180 CGACAAAGTATGGCTAGGAATCAA 58.884 41.667 0.00 0.00 33.51 2.57
233 234 4.693283 CGACAAAGTATGGCTAGGAATCA 58.307 43.478 0.00 0.00 33.51 2.57
234 235 3.495001 GCGACAAAGTATGGCTAGGAATC 59.505 47.826 0.00 0.00 33.51 2.52
235 236 3.118408 TGCGACAAAGTATGGCTAGGAAT 60.118 43.478 0.00 0.00 33.51 3.01
236 237 2.235155 TGCGACAAAGTATGGCTAGGAA 59.765 45.455 0.00 0.00 33.51 3.36
237 238 1.828595 TGCGACAAAGTATGGCTAGGA 59.171 47.619 0.00 0.00 33.51 2.94
238 239 2.309528 TGCGACAAAGTATGGCTAGG 57.690 50.000 0.00 0.00 33.51 3.02
239 240 5.696270 TCAATATGCGACAAAGTATGGCTAG 59.304 40.000 0.00 0.00 33.51 3.42
240 241 5.606505 TCAATATGCGACAAAGTATGGCTA 58.393 37.500 0.00 0.00 33.51 3.93
241 242 4.450976 TCAATATGCGACAAAGTATGGCT 58.549 39.130 0.00 0.00 33.51 4.75
242 243 4.811555 TCAATATGCGACAAAGTATGGC 57.188 40.909 0.00 0.00 0.00 4.40
243 244 7.173218 ACCTATTCAATATGCGACAAAGTATGG 59.827 37.037 0.00 0.00 0.00 2.74
244 245 8.011673 CACCTATTCAATATGCGACAAAGTATG 58.988 37.037 0.00 0.00 0.00 2.39
245 246 7.715249 ACACCTATTCAATATGCGACAAAGTAT 59.285 33.333 0.00 0.00 0.00 2.12
246 247 7.045416 ACACCTATTCAATATGCGACAAAGTA 58.955 34.615 0.00 0.00 0.00 2.24
247 248 5.880332 ACACCTATTCAATATGCGACAAAGT 59.120 36.000 0.00 0.00 0.00 2.66
248 249 6.363577 ACACCTATTCAATATGCGACAAAG 57.636 37.500 0.00 0.00 0.00 2.77
249 250 6.751514 AACACCTATTCAATATGCGACAAA 57.248 33.333 0.00 0.00 0.00 2.83
250 251 6.404184 CCAAACACCTATTCAATATGCGACAA 60.404 38.462 0.00 0.00 0.00 3.18
251 252 5.065859 CCAAACACCTATTCAATATGCGACA 59.934 40.000 0.00 0.00 0.00 4.35
252 253 5.065988 ACCAAACACCTATTCAATATGCGAC 59.934 40.000 0.00 0.00 0.00 5.19
253 254 5.189928 ACCAAACACCTATTCAATATGCGA 58.810 37.500 0.00 0.00 0.00 5.10
254 255 5.499139 ACCAAACACCTATTCAATATGCG 57.501 39.130 0.00 0.00 0.00 4.73
255 256 6.862209 TGAACCAAACACCTATTCAATATGC 58.138 36.000 0.00 0.00 0.00 3.14
256 257 8.522830 ACTTGAACCAAACACCTATTCAATATG 58.477 33.333 0.00 0.00 38.30 1.78
257 258 8.650143 ACTTGAACCAAACACCTATTCAATAT 57.350 30.769 0.00 0.00 38.30 1.28
258 259 7.721842 TGACTTGAACCAAACACCTATTCAATA 59.278 33.333 0.00 0.00 38.30 1.90
259 260 6.549364 TGACTTGAACCAAACACCTATTCAAT 59.451 34.615 0.00 0.00 38.30 2.57
260 261 5.888724 TGACTTGAACCAAACACCTATTCAA 59.111 36.000 0.00 0.00 37.03 2.69
261 262 5.298276 GTGACTTGAACCAAACACCTATTCA 59.702 40.000 0.00 0.00 30.62 2.57
262 263 5.298276 TGTGACTTGAACCAAACACCTATTC 59.702 40.000 0.00 0.00 33.40 1.75
263 264 5.197451 TGTGACTTGAACCAAACACCTATT 58.803 37.500 0.00 0.00 33.40 1.73
264 265 4.787551 TGTGACTTGAACCAAACACCTAT 58.212 39.130 0.00 0.00 33.40 2.57
265 266 4.223556 TGTGACTTGAACCAAACACCTA 57.776 40.909 0.00 0.00 33.40 3.08
266 267 3.080300 TGTGACTTGAACCAAACACCT 57.920 42.857 0.00 0.00 33.40 4.00
267 268 5.705609 ATATGTGACTTGAACCAAACACC 57.294 39.130 0.00 0.00 33.40 4.16
268 269 8.094798 TCTAATATGTGACTTGAACCAAACAC 57.905 34.615 0.00 0.00 34.21 3.32
302 303 5.183228 TGCCGGGTTTATTTTTCACAAAAA 58.817 33.333 2.18 0.00 43.76 1.94
330 332 9.638239 AAAATATTCTCACGTTTTTGTGCATAT 57.362 25.926 0.00 0.00 39.73 1.78
333 335 7.199766 AGAAAATATTCTCACGTTTTTGTGCA 58.800 30.769 0.00 0.00 42.26 4.57
343 345 7.355778 GGATTGCCTAAGAAAATATTCTCACG 58.644 38.462 0.00 0.00 45.19 4.35
348 350 8.283291 CACTACGGATTGCCTAAGAAAATATTC 58.717 37.037 0.00 0.00 35.70 1.75
368 370 1.531149 CAAACTCTTGGCCACACTACG 59.469 52.381 3.88 0.00 0.00 3.51
370 372 2.171659 TCACAAACTCTTGGCCACACTA 59.828 45.455 3.88 0.00 36.82 2.74
379 381 8.336080 GTCTAACTTTAGGTTCACAAACTCTTG 58.664 37.037 0.00 0.00 39.17 3.02
407 409 5.465532 TGCCACTCAAATTTTGCTAATCA 57.534 34.783 4.19 0.00 0.00 2.57
409 411 6.290605 AGTTTGCCACTCAAATTTTGCTAAT 58.709 32.000 4.19 0.00 45.43 1.73
437 439 6.227298 TGTTTGGTTTGAGGCTAATTTTGA 57.773 33.333 0.00 0.00 0.00 2.69
449 453 0.183014 TACGGGCCTGTTTGGTTTGA 59.817 50.000 25.37 0.00 38.35 2.69
450 454 1.033574 TTACGGGCCTGTTTGGTTTG 58.966 50.000 25.37 0.00 38.35 2.93
469 473 8.842358 TTTAGACGGTCATTGAACTCTTAAAT 57.158 30.769 11.27 0.00 0.00 1.40
574 601 3.836949 CCCCACTTGTTTCATTTCGATG 58.163 45.455 0.00 0.00 0.00 3.84
575 602 2.231235 GCCCCACTTGTTTCATTTCGAT 59.769 45.455 0.00 0.00 0.00 3.59
642 669 9.979578 TTTTGCCATATTGATTAATTAATCGCT 57.020 25.926 25.73 19.40 43.80 4.93
739 766 2.933906 TCCGATGAAAATAAGTGGACGC 59.066 45.455 0.00 0.00 0.00 5.19
753 780 1.410517 GACCAGCAGATTCTCCGATGA 59.589 52.381 0.00 0.00 0.00 2.92
996 1033 0.029834 CGCTGATGGTAGCCATTTGC 59.970 55.000 1.88 8.65 45.26 3.68
1093 1131 0.810031 GGAACACACACACGCTCAGT 60.810 55.000 0.00 0.00 0.00 3.41
1128 1175 2.874701 GTTAATCGGCATGTCAGCTCAT 59.125 45.455 0.00 0.00 34.17 2.90
1137 1184 0.027979 CTGCACGGTTAATCGGCATG 59.972 55.000 19.78 8.42 36.40 4.06
1138 1185 1.095228 CCTGCACGGTTAATCGGCAT 61.095 55.000 19.78 0.00 36.40 4.40
1488 1541 4.283678 GGATTACATGAGACGACGAGAAG 58.716 47.826 0.00 0.00 0.00 2.85
1490 1543 2.287103 CGGATTACATGAGACGACGAGA 59.713 50.000 0.00 0.00 0.00 4.04
1668 1727 1.044725 CTGTGCGTGCGTGAAATTTC 58.955 50.000 11.41 11.41 0.00 2.17
1693 1752 4.003648 AGCAATTTTACTGAGAACTCGGG 58.996 43.478 14.04 4.78 40.22 5.14
1696 1755 7.118971 ACAGATCAGCAATTTTACTGAGAACTC 59.881 37.037 0.00 0.00 45.55 3.01
1749 1808 2.861147 ACACTAGAAGCAAAGGACCC 57.139 50.000 0.00 0.00 0.00 4.46
1751 1810 7.097834 AGTTATGTACACTAGAAGCAAAGGAC 58.902 38.462 0.00 0.00 0.00 3.85
1809 1868 5.467035 TGCAGTGATCCGATATATGTTCA 57.533 39.130 0.00 0.00 0.00 3.18
1826 1885 7.759489 TCAAAAAGGTATATTCTGTTGCAGT 57.241 32.000 0.00 0.00 32.61 4.40
1909 1969 3.197983 ACCATTAGAGTAGGCACCAGTTC 59.802 47.826 0.00 0.00 0.00 3.01
1967 2027 4.277515 AGTTACTGCTGAAGAGATTGCA 57.722 40.909 0.00 0.00 0.00 4.08
2129 2189 1.947456 GACGAGCCTTTGAAAACCAGT 59.053 47.619 0.00 0.00 0.00 4.00
2147 2207 2.360475 GCCACAAGCCCTCCTGAC 60.360 66.667 0.00 0.00 34.35 3.51
2153 2213 2.207501 CTCATCCAGCCACAAGCCCT 62.208 60.000 0.00 0.00 45.47 5.19
2220 2280 1.537202 GCACCCCGATGAATCTTATGC 59.463 52.381 0.00 0.00 0.00 3.14
2272 2332 4.314961 TGGCATATCATACCATGACGAAC 58.685 43.478 0.00 0.00 43.01 3.95
2277 2337 6.487668 CAGAAACTTGGCATATCATACCATGA 59.512 38.462 0.00 0.00 44.55 3.07
2342 2402 5.627499 TTTTCTTCGCTGACTGCAATATT 57.373 34.783 5.11 0.00 43.06 1.28
2343 2403 5.393962 GTTTTTCTTCGCTGACTGCAATAT 58.606 37.500 5.11 0.00 43.06 1.28
2347 2407 1.003972 CGTTTTTCTTCGCTGACTGCA 60.004 47.619 5.11 0.00 43.06 4.41
2356 2416 2.748461 TGAAGGTGCGTTTTTCTTCG 57.252 45.000 0.00 0.00 38.63 3.79
2357 2417 4.028852 AGTTGAAGGTGCGTTTTTCTTC 57.971 40.909 0.00 0.00 36.93 2.87
2389 2449 9.737427 CTTTTGTCACTTCGATCTAGTATACAT 57.263 33.333 5.50 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.