Multiple sequence alignment - TraesCS1B01G253600

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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 TraesCS1B01G253600 chr1B 100.000 2989 0 0 1 2989 447175044 447172056 0.000000e+00 5520.0
1 TraesCS1B01G253600 chr1D 93.563 1942 107 13 290 2220 332413191 332411257 0.000000e+00 2878.0
2 TraesCS1B01G253600 chr1D 92.127 724 48 6 2274 2989 332410886 332410164 0.000000e+00 1013.0
3 TraesCS1B01G253600 chr1D 78.347 1621 271 54 369 1937 427039110 427040702 0.000000e+00 976.0
4 TraesCS1B01G253600 chr1A 91.198 1511 107 14 1320 2812 430188956 430187454 0.000000e+00 2030.0
5 TraesCS1B01G253600 chr1A 93.087 1027 60 5 295 1317 430190054 430189035 0.000000e+00 1493.0
6 TraesCS1B01G253600 chr1A 79.684 950 145 25 369 1280 522189658 522190597 2.510000e-180 641.0
7 TraesCS1B01G253600 chr1A 78.261 943 158 28 369 1280 521989815 521990741 2.010000e-156 562.0
8 TraesCS1B01G253600 chr1A 80.668 569 94 13 1377 1937 522190718 522191278 7.660000e-116 427.0
9 TraesCS1B01G253600 chr1A 95.000 140 7 0 2850 2989 430187451 430187312 1.390000e-53 220.0
10 TraesCS1B01G253600 chr3B 90.583 223 18 3 44 264 656737007 656737228 2.910000e-75 292.0
11 TraesCS1B01G253600 chr5B 100.000 28 0 0 2294 2321 386644162 386644135 5.000000e-03 52.8


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 TraesCS1B01G253600 chr1B 447172056 447175044 2988 True 5520.000000 5520 100.000 1 2989 1 chr1B.!!$R1 2988
1 TraesCS1B01G253600 chr1D 332410164 332413191 3027 True 1945.500000 2878 92.845 290 2989 2 chr1D.!!$R1 2699
2 TraesCS1B01G253600 chr1D 427039110 427040702 1592 False 976.000000 976 78.347 369 1937 1 chr1D.!!$F1 1568
3 TraesCS1B01G253600 chr1A 430187312 430190054 2742 True 1247.666667 2030 93.095 295 2989 3 chr1A.!!$R1 2694
4 TraesCS1B01G253600 chr1A 521989815 521990741 926 False 562.000000 562 78.261 369 1280 1 chr1A.!!$F1 911
5 TraesCS1B01G253600 chr1A 522189658 522191278 1620 False 534.000000 641 80.176 369 1937 2 chr1A.!!$F2 1568

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
26 27 0.043310 CAATTAAGTAGCCGACGCGC 60.043 55.0 5.73 0.00 41.18 6.86 F
27 28 0.179119 AATTAAGTAGCCGACGCGCT 60.179 50.0 5.73 13.94 43.09 5.92 F
287 288 0.181350 AATGGCAGAGGATCCGGTTC 59.819 55.0 5.98 1.67 33.66 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1134 0.460311 CCGCTGTCCGACTTATCCTT 59.54 55.000 0.00 0.0 40.02 3.36 R
1957 2109 0.960364 TGCGACAAGGATCAAAGGGC 60.96 55.000 0.00 0.0 0.00 5.19 R
2161 2322 1.619669 CCCCTAGGGCTCCAACCTT 60.62 63.158 23.84 0.0 39.54 3.50 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
21 22 4.119442 GACTGGACAATTAAGTAGCCGA 57.881 45.455 0.00 0.00 0.00 5.54
22 23 3.858247 ACTGGACAATTAAGTAGCCGAC 58.142 45.455 0.00 0.00 0.00 4.79
23 24 2.858344 CTGGACAATTAAGTAGCCGACG 59.142 50.000 0.00 0.00 0.00 5.12
24 25 1.591619 GGACAATTAAGTAGCCGACGC 59.408 52.381 0.00 0.00 0.00 5.19
25 26 1.254570 GACAATTAAGTAGCCGACGCG 59.745 52.381 3.53 3.53 41.18 6.01
26 27 0.043310 CAATTAAGTAGCCGACGCGC 60.043 55.000 5.73 0.00 41.18 6.86
27 28 0.179119 AATTAAGTAGCCGACGCGCT 60.179 50.000 5.73 13.94 43.09 5.92
28 29 0.594284 ATTAAGTAGCCGACGCGCTC 60.594 55.000 5.73 1.80 40.39 5.03
29 30 2.908088 TTAAGTAGCCGACGCGCTCG 62.908 60.000 19.47 19.47 40.39 5.03
39 40 3.390017 CGCGCTCGTCCGATGATG 61.390 66.667 5.56 0.00 0.00 3.07
40 41 3.032609 GCGCTCGTCCGATGATGG 61.033 66.667 0.00 0.00 0.00 3.51
41 42 3.032609 CGCTCGTCCGATGATGGC 61.033 66.667 0.00 0.00 0.00 4.40
42 43 2.419198 GCTCGTCCGATGATGGCT 59.581 61.111 0.00 0.00 0.00 4.75
43 44 1.953138 GCTCGTCCGATGATGGCTG 60.953 63.158 0.00 0.00 0.00 4.85
44 45 1.735973 CTCGTCCGATGATGGCTGA 59.264 57.895 0.00 0.00 0.00 4.26
45 46 0.318529 CTCGTCCGATGATGGCTGAG 60.319 60.000 0.00 0.00 0.00 3.35
46 47 0.751643 TCGTCCGATGATGGCTGAGA 60.752 55.000 0.00 0.00 0.00 3.27
47 48 0.318529 CGTCCGATGATGGCTGAGAG 60.319 60.000 0.00 0.00 0.00 3.20
48 49 1.035923 GTCCGATGATGGCTGAGAGA 58.964 55.000 0.00 0.00 0.00 3.10
49 50 1.410517 GTCCGATGATGGCTGAGAGAA 59.589 52.381 0.00 0.00 0.00 2.87
50 51 1.685517 TCCGATGATGGCTGAGAGAAG 59.314 52.381 0.00 0.00 0.00 2.85
51 52 1.411977 CCGATGATGGCTGAGAGAAGT 59.588 52.381 0.00 0.00 0.00 3.01
52 53 2.158986 CCGATGATGGCTGAGAGAAGTT 60.159 50.000 0.00 0.00 0.00 2.66
53 54 3.529533 CGATGATGGCTGAGAGAAGTTT 58.470 45.455 0.00 0.00 0.00 2.66
54 55 3.937706 CGATGATGGCTGAGAGAAGTTTT 59.062 43.478 0.00 0.00 0.00 2.43
55 56 4.394300 CGATGATGGCTGAGAGAAGTTTTT 59.606 41.667 0.00 0.00 0.00 1.94
87 88 6.630203 TTTTATTTCCTAGGTGCCTAGTCA 57.370 37.500 20.27 7.15 43.22 3.41
88 89 5.871396 TTATTTCCTAGGTGCCTAGTCAG 57.129 43.478 20.27 8.53 43.22 3.51
89 90 1.486211 TTCCTAGGTGCCTAGTCAGC 58.514 55.000 20.27 0.00 43.22 4.26
90 91 0.335019 TCCTAGGTGCCTAGTCAGCA 59.665 55.000 20.27 0.00 43.22 4.41
91 92 0.749649 CCTAGGTGCCTAGTCAGCAG 59.250 60.000 20.27 1.28 43.22 4.24
92 93 1.479709 CTAGGTGCCTAGTCAGCAGT 58.520 55.000 15.33 0.00 41.87 4.40
93 94 1.407258 CTAGGTGCCTAGTCAGCAGTC 59.593 57.143 15.33 0.00 41.87 3.51
94 95 1.219393 GGTGCCTAGTCAGCAGTCC 59.781 63.158 0.00 0.00 41.87 3.85
95 96 1.219393 GTGCCTAGTCAGCAGTCCC 59.781 63.158 0.00 0.00 41.87 4.46
96 97 2.351244 TGCCTAGTCAGCAGTCCCG 61.351 63.158 0.00 0.00 34.69 5.14
97 98 2.352032 GCCTAGTCAGCAGTCCCGT 61.352 63.158 0.00 0.00 0.00 5.28
98 99 1.810532 CCTAGTCAGCAGTCCCGTC 59.189 63.158 0.00 0.00 0.00 4.79
99 100 1.429825 CTAGTCAGCAGTCCCGTCG 59.570 63.158 0.00 0.00 0.00 5.12
100 101 1.994507 CTAGTCAGCAGTCCCGTCGG 61.995 65.000 3.60 3.60 0.00 4.79
101 102 2.759641 TAGTCAGCAGTCCCGTCGGT 62.760 60.000 11.06 0.00 0.00 4.69
102 103 3.680786 TCAGCAGTCCCGTCGGTG 61.681 66.667 11.06 3.07 0.00 4.94
103 104 3.991051 CAGCAGTCCCGTCGGTGT 61.991 66.667 11.06 0.00 0.00 4.16
104 105 3.231736 AGCAGTCCCGTCGGTGTT 61.232 61.111 11.06 0.00 0.00 3.32
105 106 3.041940 GCAGTCCCGTCGGTGTTG 61.042 66.667 11.06 6.18 0.00 3.33
106 107 2.732016 CAGTCCCGTCGGTGTTGA 59.268 61.111 11.06 0.00 0.00 3.18
107 108 1.663702 CAGTCCCGTCGGTGTTGAC 60.664 63.158 11.06 10.21 35.49 3.18
108 109 1.831286 AGTCCCGTCGGTGTTGACT 60.831 57.895 11.06 12.38 36.71 3.41
109 110 1.068585 GTCCCGTCGGTGTTGACTT 59.931 57.895 11.06 0.00 36.71 3.01
110 111 0.531311 GTCCCGTCGGTGTTGACTTT 60.531 55.000 11.06 0.00 36.71 2.66
111 112 0.531090 TCCCGTCGGTGTTGACTTTG 60.531 55.000 11.06 0.00 36.71 2.77
112 113 1.503818 CCCGTCGGTGTTGACTTTGG 61.504 60.000 11.06 0.00 36.71 3.28
113 114 0.812412 CCGTCGGTGTTGACTTTGGT 60.812 55.000 2.08 0.00 36.71 3.67
114 115 0.580104 CGTCGGTGTTGACTTTGGTC 59.420 55.000 0.00 0.00 42.42 4.02
130 131 1.670791 GGTCAAAACCACTTCACGGA 58.329 50.000 0.00 0.00 45.68 4.69
131 132 2.227194 GGTCAAAACCACTTCACGGAT 58.773 47.619 0.00 0.00 45.68 4.18
132 133 3.404899 GGTCAAAACCACTTCACGGATA 58.595 45.455 0.00 0.00 45.68 2.59
133 134 3.187842 GGTCAAAACCACTTCACGGATAC 59.812 47.826 0.00 0.00 45.68 2.24
134 135 3.810941 GTCAAAACCACTTCACGGATACA 59.189 43.478 0.00 0.00 0.00 2.29
135 136 4.273969 GTCAAAACCACTTCACGGATACAA 59.726 41.667 0.00 0.00 0.00 2.41
136 137 4.882427 TCAAAACCACTTCACGGATACAAA 59.118 37.500 0.00 0.00 0.00 2.83
137 138 5.357314 TCAAAACCACTTCACGGATACAAAA 59.643 36.000 0.00 0.00 0.00 2.44
138 139 4.823790 AACCACTTCACGGATACAAAAC 57.176 40.909 0.00 0.00 0.00 2.43
139 140 3.143728 ACCACTTCACGGATACAAAACC 58.856 45.455 0.00 0.00 0.00 3.27
149 150 4.402056 GGATACAAAACCGAGATCAGGA 57.598 45.455 13.34 0.00 0.00 3.86
150 151 4.962155 GGATACAAAACCGAGATCAGGAT 58.038 43.478 13.34 0.00 0.00 3.24
151 152 5.368989 GGATACAAAACCGAGATCAGGATT 58.631 41.667 13.34 5.72 0.00 3.01
152 153 5.237344 GGATACAAAACCGAGATCAGGATTG 59.763 44.000 13.34 16.66 36.21 2.67
153 154 4.286297 ACAAAACCGAGATCAGGATTGA 57.714 40.909 23.01 0.00 37.81 2.57
154 155 4.256920 ACAAAACCGAGATCAGGATTGAG 58.743 43.478 23.01 13.97 36.61 3.02
155 156 4.256920 CAAAACCGAGATCAGGATTGAGT 58.743 43.478 13.34 0.00 36.61 3.41
156 157 4.559862 AAACCGAGATCAGGATTGAGTT 57.440 40.909 13.34 0.00 36.61 3.01
157 158 4.559862 AACCGAGATCAGGATTGAGTTT 57.440 40.909 13.34 0.00 36.61 2.66
158 159 4.559862 ACCGAGATCAGGATTGAGTTTT 57.440 40.909 13.34 0.00 36.61 2.43
159 160 4.256920 ACCGAGATCAGGATTGAGTTTTG 58.743 43.478 13.34 0.00 36.61 2.44
160 161 3.624861 CCGAGATCAGGATTGAGTTTTGG 59.375 47.826 1.35 0.00 36.61 3.28
161 162 4.507710 CGAGATCAGGATTGAGTTTTGGA 58.492 43.478 0.00 0.00 36.61 3.53
162 163 4.331168 CGAGATCAGGATTGAGTTTTGGAC 59.669 45.833 0.00 0.00 36.61 4.02
163 164 4.593956 AGATCAGGATTGAGTTTTGGACC 58.406 43.478 0.00 0.00 36.61 4.46
164 165 4.290722 AGATCAGGATTGAGTTTTGGACCT 59.709 41.667 0.00 0.00 36.61 3.85
165 166 4.021102 TCAGGATTGAGTTTTGGACCTC 57.979 45.455 0.00 0.00 0.00 3.85
166 167 2.744202 CAGGATTGAGTTTTGGACCTCG 59.256 50.000 0.00 0.00 0.00 4.63
167 168 2.372172 AGGATTGAGTTTTGGACCTCGT 59.628 45.455 0.00 0.00 0.00 4.18
168 169 3.581332 AGGATTGAGTTTTGGACCTCGTA 59.419 43.478 0.00 0.00 0.00 3.43
169 170 3.933332 GGATTGAGTTTTGGACCTCGTAG 59.067 47.826 0.00 0.00 0.00 3.51
170 171 4.562963 GGATTGAGTTTTGGACCTCGTAGT 60.563 45.833 0.00 0.00 0.00 2.73
171 172 4.411256 TTGAGTTTTGGACCTCGTAGTT 57.589 40.909 0.00 0.00 0.00 2.24
172 173 5.534207 TTGAGTTTTGGACCTCGTAGTTA 57.466 39.130 0.00 0.00 0.00 2.24
173 174 5.130292 TGAGTTTTGGACCTCGTAGTTAG 57.870 43.478 0.00 0.00 0.00 2.34
174 175 4.586001 TGAGTTTTGGACCTCGTAGTTAGT 59.414 41.667 0.00 0.00 0.00 2.24
175 176 5.069516 TGAGTTTTGGACCTCGTAGTTAGTT 59.930 40.000 0.00 0.00 0.00 2.24
176 177 5.536260 AGTTTTGGACCTCGTAGTTAGTTC 58.464 41.667 0.00 0.00 0.00 3.01
177 178 5.069516 AGTTTTGGACCTCGTAGTTAGTTCA 59.930 40.000 0.00 0.00 0.00 3.18
178 179 5.534207 TTTGGACCTCGTAGTTAGTTCAA 57.466 39.130 0.00 0.00 0.00 2.69
179 180 4.778534 TGGACCTCGTAGTTAGTTCAAG 57.221 45.455 0.00 0.00 0.00 3.02
180 181 3.508793 TGGACCTCGTAGTTAGTTCAAGG 59.491 47.826 0.00 0.00 0.00 3.61
181 182 3.509184 GGACCTCGTAGTTAGTTCAAGGT 59.491 47.826 0.00 0.00 38.33 3.50
182 183 4.483311 GACCTCGTAGTTAGTTCAAGGTG 58.517 47.826 0.00 0.00 35.84 4.00
183 184 3.893813 ACCTCGTAGTTAGTTCAAGGTGT 59.106 43.478 0.00 0.00 34.46 4.16
184 185 5.072741 ACCTCGTAGTTAGTTCAAGGTGTA 58.927 41.667 0.00 0.00 34.46 2.90
185 186 5.713861 ACCTCGTAGTTAGTTCAAGGTGTAT 59.286 40.000 0.00 0.00 34.46 2.29
186 187 6.210185 ACCTCGTAGTTAGTTCAAGGTGTATT 59.790 38.462 0.00 0.00 34.46 1.89
187 188 7.095270 CCTCGTAGTTAGTTCAAGGTGTATTT 58.905 38.462 0.00 0.00 0.00 1.40
188 189 7.275123 CCTCGTAGTTAGTTCAAGGTGTATTTC 59.725 40.741 0.00 0.00 0.00 2.17
189 190 7.660112 TCGTAGTTAGTTCAAGGTGTATTTCA 58.340 34.615 0.00 0.00 0.00 2.69
190 191 8.143193 TCGTAGTTAGTTCAAGGTGTATTTCAA 58.857 33.333 0.00 0.00 0.00 2.69
191 192 8.219105 CGTAGTTAGTTCAAGGTGTATTTCAAC 58.781 37.037 0.00 0.00 0.00 3.18
192 193 7.506328 AGTTAGTTCAAGGTGTATTTCAACC 57.494 36.000 0.00 0.00 33.55 3.77
193 194 6.204108 AGTTAGTTCAAGGTGTATTTCAACCG 59.796 38.462 0.00 0.00 33.55 4.44
194 195 3.818773 AGTTCAAGGTGTATTTCAACCGG 59.181 43.478 0.00 0.00 33.55 5.28
195 196 3.495434 TCAAGGTGTATTTCAACCGGT 57.505 42.857 0.00 0.00 33.55 5.28
196 197 3.822940 TCAAGGTGTATTTCAACCGGTT 58.177 40.909 15.86 15.86 33.55 4.44
197 198 4.208746 TCAAGGTGTATTTCAACCGGTTT 58.791 39.130 19.55 5.68 33.55 3.27
198 199 4.276431 TCAAGGTGTATTTCAACCGGTTTC 59.724 41.667 19.55 4.90 33.55 2.78
199 200 2.809696 AGGTGTATTTCAACCGGTTTCG 59.190 45.455 19.55 7.84 33.55 3.46
200 201 2.549329 GGTGTATTTCAACCGGTTTCGT 59.451 45.455 19.55 6.80 33.95 3.85
201 202 3.745458 GGTGTATTTCAACCGGTTTCGTA 59.255 43.478 19.55 5.75 33.95 3.43
202 203 4.143052 GGTGTATTTCAACCGGTTTCGTAG 60.143 45.833 19.55 6.14 33.95 3.51
203 204 4.448732 GTGTATTTCAACCGGTTTCGTAGT 59.551 41.667 19.55 4.54 33.95 2.73
204 205 5.050159 GTGTATTTCAACCGGTTTCGTAGTT 60.050 40.000 19.55 1.62 33.95 2.24
205 206 5.526846 TGTATTTCAACCGGTTTCGTAGTTT 59.473 36.000 19.55 0.00 33.95 2.66
206 207 6.703607 TGTATTTCAACCGGTTTCGTAGTTTA 59.296 34.615 19.55 0.00 33.95 2.01
207 208 5.655893 TTTCAACCGGTTTCGTAGTTTAG 57.344 39.130 19.55 1.96 33.95 1.85
208 209 3.652274 TCAACCGGTTTCGTAGTTTAGG 58.348 45.455 19.55 1.38 33.95 2.69
209 210 2.738314 CAACCGGTTTCGTAGTTTAGGG 59.262 50.000 19.55 0.00 33.95 3.53
210 211 1.970640 ACCGGTTTCGTAGTTTAGGGT 59.029 47.619 0.00 0.00 33.95 4.34
211 212 2.368548 ACCGGTTTCGTAGTTTAGGGTT 59.631 45.455 0.00 0.00 33.95 4.11
212 213 2.738314 CCGGTTTCGTAGTTTAGGGTTG 59.262 50.000 0.00 0.00 33.95 3.77
213 214 3.392882 CGGTTTCGTAGTTTAGGGTTGT 58.607 45.455 0.00 0.00 0.00 3.32
214 215 4.555262 CGGTTTCGTAGTTTAGGGTTGTA 58.445 43.478 0.00 0.00 0.00 2.41
215 216 4.987912 CGGTTTCGTAGTTTAGGGTTGTAA 59.012 41.667 0.00 0.00 0.00 2.41
216 217 5.465056 CGGTTTCGTAGTTTAGGGTTGTAAA 59.535 40.000 0.00 0.00 0.00 2.01
217 218 6.147656 CGGTTTCGTAGTTTAGGGTTGTAAAT 59.852 38.462 0.00 0.00 0.00 1.40
218 219 7.307930 CGGTTTCGTAGTTTAGGGTTGTAAATT 60.308 37.037 0.00 0.00 0.00 1.82
219 220 8.998377 GGTTTCGTAGTTTAGGGTTGTAAATTA 58.002 33.333 0.00 0.00 0.00 1.40
223 224 8.998377 TCGTAGTTTAGGGTTGTAAATTAAACC 58.002 33.333 8.45 8.45 44.31 3.27
224 225 8.782144 CGTAGTTTAGGGTTGTAAATTAAACCA 58.218 33.333 15.63 0.00 46.41 3.67
227 228 9.204337 AGTTTAGGGTTGTAAATTAAACCAAGT 57.796 29.630 15.63 5.77 46.41 3.16
228 229 9.251792 GTTTAGGGTTGTAAATTAAACCAAGTG 57.748 33.333 15.63 0.00 46.41 3.16
229 230 6.413783 AGGGTTGTAAATTAAACCAAGTGG 57.586 37.500 15.63 0.00 46.41 4.00
240 241 3.834732 CCAAGTGGTTAGTCCGAGG 57.165 57.895 0.00 0.00 39.52 4.63
241 242 0.974383 CCAAGTGGTTAGTCCGAGGT 59.026 55.000 0.00 0.00 39.52 3.85
242 243 1.346722 CCAAGTGGTTAGTCCGAGGTT 59.653 52.381 0.00 0.00 39.52 3.50
243 244 2.413837 CAAGTGGTTAGTCCGAGGTTG 58.586 52.381 0.00 0.00 39.52 3.77
244 245 2.005370 AGTGGTTAGTCCGAGGTTGA 57.995 50.000 0.00 0.00 39.52 3.18
245 246 2.322658 AGTGGTTAGTCCGAGGTTGAA 58.677 47.619 0.00 0.00 39.52 2.69
246 247 2.701951 AGTGGTTAGTCCGAGGTTGAAA 59.298 45.455 0.00 0.00 39.52 2.69
247 248 3.326880 AGTGGTTAGTCCGAGGTTGAAAT 59.673 43.478 0.00 0.00 39.52 2.17
248 249 3.435671 GTGGTTAGTCCGAGGTTGAAATG 59.564 47.826 0.00 0.00 39.52 2.32
249 250 3.071892 TGGTTAGTCCGAGGTTGAAATGT 59.928 43.478 0.00 0.00 39.52 2.71
250 251 3.435671 GGTTAGTCCGAGGTTGAAATGTG 59.564 47.826 0.00 0.00 0.00 3.21
251 252 2.185004 AGTCCGAGGTTGAAATGTGG 57.815 50.000 0.00 0.00 0.00 4.17
252 253 1.697432 AGTCCGAGGTTGAAATGTGGA 59.303 47.619 0.00 0.00 0.00 4.02
253 254 1.804748 GTCCGAGGTTGAAATGTGGAC 59.195 52.381 0.00 0.00 37.81 4.02
254 255 1.697432 TCCGAGGTTGAAATGTGGACT 59.303 47.619 0.00 0.00 0.00 3.85
255 256 2.105821 TCCGAGGTTGAAATGTGGACTT 59.894 45.455 0.00 0.00 0.00 3.01
256 257 2.484264 CCGAGGTTGAAATGTGGACTTC 59.516 50.000 0.00 0.00 0.00 3.01
257 258 3.403038 CGAGGTTGAAATGTGGACTTCT 58.597 45.455 0.00 0.00 0.00 2.85
258 259 3.433615 CGAGGTTGAAATGTGGACTTCTC 59.566 47.826 0.00 0.00 0.00 2.87
259 260 4.646572 GAGGTTGAAATGTGGACTTCTCT 58.353 43.478 0.00 0.00 0.00 3.10
260 261 4.646572 AGGTTGAAATGTGGACTTCTCTC 58.353 43.478 0.00 0.00 0.00 3.20
261 262 4.349342 AGGTTGAAATGTGGACTTCTCTCT 59.651 41.667 0.00 0.00 0.00 3.10
262 263 5.066593 GGTTGAAATGTGGACTTCTCTCTT 58.933 41.667 0.00 0.00 0.00 2.85
263 264 5.180304 GGTTGAAATGTGGACTTCTCTCTTC 59.820 44.000 0.00 0.00 0.00 2.87
264 265 5.815233 TGAAATGTGGACTTCTCTCTTCT 57.185 39.130 0.00 0.00 0.00 2.85
265 266 6.179906 TGAAATGTGGACTTCTCTCTTCTT 57.820 37.500 0.00 0.00 0.00 2.52
266 267 7.303182 TGAAATGTGGACTTCTCTCTTCTTA 57.697 36.000 0.00 0.00 0.00 2.10
267 268 7.735917 TGAAATGTGGACTTCTCTCTTCTTAA 58.264 34.615 0.00 0.00 0.00 1.85
268 269 8.210946 TGAAATGTGGACTTCTCTCTTCTTAAA 58.789 33.333 0.00 0.00 0.00 1.52
269 270 8.980481 AAATGTGGACTTCTCTCTTCTTAAAA 57.020 30.769 0.00 0.00 0.00 1.52
270 271 9.579932 AAATGTGGACTTCTCTCTTCTTAAAAT 57.420 29.630 0.00 0.00 0.00 1.82
271 272 7.969536 TGTGGACTTCTCTCTTCTTAAAATG 57.030 36.000 0.00 0.00 0.00 2.32
272 273 6.936900 TGTGGACTTCTCTCTTCTTAAAATGG 59.063 38.462 0.00 0.00 0.00 3.16
273 274 5.940470 TGGACTTCTCTCTTCTTAAAATGGC 59.060 40.000 0.00 0.00 0.00 4.40
274 275 5.940470 GGACTTCTCTCTTCTTAAAATGGCA 59.060 40.000 0.00 0.00 0.00 4.92
275 276 6.093357 GGACTTCTCTCTTCTTAAAATGGCAG 59.907 42.308 0.00 0.00 0.00 4.85
276 277 6.773638 ACTTCTCTCTTCTTAAAATGGCAGA 58.226 36.000 0.00 0.00 0.00 4.26
277 278 6.878389 ACTTCTCTCTTCTTAAAATGGCAGAG 59.122 38.462 0.00 0.00 0.00 3.35
278 279 5.738909 TCTCTCTTCTTAAAATGGCAGAGG 58.261 41.667 0.00 0.00 0.00 3.69
279 280 5.485353 TCTCTCTTCTTAAAATGGCAGAGGA 59.515 40.000 0.00 0.00 0.00 3.71
280 281 6.157645 TCTCTCTTCTTAAAATGGCAGAGGAT 59.842 38.462 0.00 0.00 0.00 3.24
281 282 6.352516 TCTCTTCTTAAAATGGCAGAGGATC 58.647 40.000 0.00 0.00 0.00 3.36
282 283 5.440610 TCTTCTTAAAATGGCAGAGGATCC 58.559 41.667 2.48 2.48 33.66 3.36
283 284 3.808728 TCTTAAAATGGCAGAGGATCCG 58.191 45.455 5.98 0.00 33.66 4.18
284 285 2.638480 TAAAATGGCAGAGGATCCGG 57.362 50.000 5.98 0.00 33.66 5.14
285 286 0.625849 AAAATGGCAGAGGATCCGGT 59.374 50.000 5.98 0.00 33.66 5.28
286 287 0.625849 AAATGGCAGAGGATCCGGTT 59.374 50.000 5.98 0.00 33.66 4.44
287 288 0.181350 AATGGCAGAGGATCCGGTTC 59.819 55.000 5.98 1.67 33.66 3.62
288 289 1.700042 ATGGCAGAGGATCCGGTTCC 61.700 60.000 22.05 22.05 33.66 3.62
320 321 2.269172 GTACGCCTTAAGTTCAGCTCC 58.731 52.381 0.97 0.00 0.00 4.70
359 360 1.577468 CACACACGTGCTCCAACTTA 58.423 50.000 17.22 0.00 36.06 2.24
360 361 2.143122 CACACACGTGCTCCAACTTAT 58.857 47.619 17.22 0.00 36.06 1.73
367 369 4.025396 CACGTGCTCCAACTTATGATGATC 60.025 45.833 0.82 0.00 0.00 2.92
425 427 0.968393 AGTCCTCTGCCTCGTCTTCC 60.968 60.000 0.00 0.00 0.00 3.46
430 432 2.096248 CTCTGCCTCGTCTTCCTAGTT 58.904 52.381 0.00 0.00 0.00 2.24
729 743 3.006756 GCACTCTCTACGGCTGCCA 62.007 63.158 20.29 0.00 0.00 4.92
835 849 3.724914 CTCTTTCCGCTCCCTCCGC 62.725 68.421 0.00 0.00 0.00 5.54
1101 1140 1.721664 CGGGACTCGACGCAAGGATA 61.722 60.000 0.00 0.00 46.39 2.59
1110 1149 0.892755 ACGCAAGGATAAGTCGGACA 59.107 50.000 11.27 0.00 46.39 4.02
1184 1226 1.300697 GAGCAAACGACGGTGAGGT 60.301 57.895 0.00 0.00 0.00 3.85
1243 1288 2.352561 TGGTGATCAGGGGTTTAGGA 57.647 50.000 0.00 0.00 0.00 2.94
1338 1486 4.043608 ACTGTAACCTAGCACCAGTAGA 57.956 45.455 0.00 0.00 34.77 2.59
1374 1523 2.476873 ACACGATCGATCCTTCTTCG 57.523 50.000 24.34 10.17 37.94 3.79
1683 1835 2.497138 GGATCATGATCAACGCATGGA 58.503 47.619 31.49 0.00 42.53 3.41
1715 1867 2.752238 AGCGAGTCGTGGGAGGAG 60.752 66.667 15.08 0.00 0.00 3.69
1922 2074 1.003233 GACCCGGAGTCATTTGAGGTT 59.997 52.381 0.73 0.00 45.55 3.50
1998 2150 5.811613 GCAAAACCTTTATAAGCATGCATCA 59.188 36.000 21.98 4.23 0.00 3.07
2003 2155 5.242393 ACCTTTATAAGCATGCATCATGTCC 59.758 40.000 21.98 0.00 43.10 4.02
2005 2157 6.071560 CCTTTATAAGCATGCATCATGTCCAT 60.072 38.462 21.98 0.00 43.10 3.41
2020 2172 6.834107 TCATGTCCATGATGAATGTATCACT 58.166 36.000 5.88 0.00 42.42 3.41
2033 2185 8.470657 TGAATGTATCACTGATCTTACTAGCT 57.529 34.615 0.00 0.00 31.50 3.32
2034 2186 9.574516 TGAATGTATCACTGATCTTACTAGCTA 57.425 33.333 0.00 0.00 31.50 3.32
2084 2237 1.742768 CGAAGGCTCTAGGGCGAAT 59.257 57.895 8.90 0.00 45.89 3.34
2135 2288 3.948196 ATAGCGAGTCACGTAGAAGTC 57.052 47.619 0.00 0.00 44.60 3.01
2136 2289 0.803740 AGCGAGTCACGTAGAAGTCC 59.196 55.000 0.00 0.00 44.60 3.85
2137 2290 0.520404 GCGAGTCACGTAGAAGTCCA 59.480 55.000 0.00 0.00 44.60 4.02
2138 2291 1.132643 GCGAGTCACGTAGAAGTCCAT 59.867 52.381 0.00 0.00 44.60 3.41
2161 2322 2.015726 GGGAGGGAGAGGGAGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
2174 2335 0.912006 GAGAGGAAGGTTGGAGCCCT 60.912 60.000 0.00 0.00 0.00 5.19
2210 2371 5.541845 TGGAGACTATGAAGACACAAGTTG 58.458 41.667 0.00 0.00 0.00 3.16
2211 2372 4.390297 GGAGACTATGAAGACACAAGTTGC 59.610 45.833 1.81 0.00 0.00 4.17
2213 2374 3.412386 ACTATGAAGACACAAGTTGCCC 58.588 45.455 1.81 0.00 0.00 5.36
2214 2375 2.363306 ATGAAGACACAAGTTGCCCA 57.637 45.000 1.81 0.00 0.00 5.36
2217 2378 2.024414 GAAGACACAAGTTGCCCAAGT 58.976 47.619 1.81 0.00 0.00 3.16
2219 2380 3.290948 AGACACAAGTTGCCCAAGTTA 57.709 42.857 1.81 0.00 33.03 2.24
2224 2387 1.000843 CAAGTTGCCCAAGTTAAGCCC 59.999 52.381 1.11 0.00 33.03 5.19
2256 2419 1.563879 CCAATGGGTGATGGACCTACA 59.436 52.381 0.00 0.00 45.33 2.74
2272 2751 8.275187 TGGACCTACATCCTATTATTCATGTT 57.725 34.615 0.00 0.00 39.75 2.71
2334 2813 5.063880 ACAAGCTAGGTTTCAAGGTGTTAG 58.936 41.667 3.96 0.00 0.00 2.34
2351 2830 4.278419 GTGTTAGGTCTTCACAAATGGCTT 59.722 41.667 0.00 0.00 33.04 4.35
2361 2840 4.206375 TCACAAATGGCTTGAGTCTTTGA 58.794 39.130 7.14 0.00 38.50 2.69
2364 2843 4.402155 ACAAATGGCTTGAGTCTTTGACAA 59.598 37.500 7.14 0.00 38.50 3.18
2370 2849 3.808728 CTTGAGTCTTTGACAAGGGACA 58.191 45.455 18.81 6.89 37.80 4.02
2402 2881 7.946655 CTCATGTAGAGGCATTTTATTCGTA 57.053 36.000 0.00 0.00 40.84 3.43
2403 2882 8.365399 CTCATGTAGAGGCATTTTATTCGTAA 57.635 34.615 0.00 0.00 40.84 3.18
2411 2890 7.494952 AGAGGCATTTTATTCGTAAGTAAGTCC 59.505 37.037 0.00 0.00 39.48 3.85
2466 2945 1.958205 CTCCTGGAATCATCGCGGC 60.958 63.158 6.13 0.00 0.00 6.53
2496 2978 1.678635 CCAAATGCAAGCCTCGGGA 60.679 57.895 0.00 0.00 0.00 5.14
2512 2994 2.687425 TCGGGAAACATATGCACCAATG 59.313 45.455 1.58 0.00 0.00 2.82
2559 3041 6.935208 CCCAGATGGTATACCTTTTTAGTAGC 59.065 42.308 22.41 2.73 36.82 3.58
2662 3146 2.264455 AGTCTGCCACCTTTCAGATCT 58.736 47.619 0.00 0.00 40.89 2.75
2684 3170 1.003118 CCCGACAAGATCCTTGGTCAA 59.997 52.381 10.91 0.00 0.00 3.18
2698 3184 4.214332 CCTTGGTCAAGTTTCTAGAAGCAC 59.786 45.833 19.87 10.19 36.72 4.40
2705 3191 1.464997 GTTTCTAGAAGCACTTGGGCG 59.535 52.381 13.85 0.00 39.27 6.13
2789 3275 6.007076 TGCTCTGAGTAAGATATCCCTAGTG 58.993 44.000 6.53 0.00 33.29 2.74
2816 3302 2.224523 TGTGAAACATCCCACACTCCTC 60.225 50.000 0.00 0.00 45.67 3.71
2819 3305 1.553690 AACATCCCACACTCCTCGGG 61.554 60.000 0.00 0.00 41.76 5.14
2844 3330 4.021544 GGTAATGGACTCACAAATTGGCAA 60.022 41.667 0.68 0.68 0.00 4.52
2892 3378 1.814394 CACTGTCATTGTGGATGGTGG 59.186 52.381 0.00 0.00 36.37 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.864003 GTCGGCTACTTAATTGTCCAGTC 59.136 47.826 0.00 0.00 0.00 3.51
1 2 3.675228 CGTCGGCTACTTAATTGTCCAGT 60.675 47.826 0.00 0.00 0.00 4.00
2 3 2.858344 CGTCGGCTACTTAATTGTCCAG 59.142 50.000 0.00 0.00 0.00 3.86
3 4 2.883574 CGTCGGCTACTTAATTGTCCA 58.116 47.619 0.00 0.00 0.00 4.02
4 5 1.591619 GCGTCGGCTACTTAATTGTCC 59.408 52.381 0.00 0.00 35.83 4.02
5 6 1.254570 CGCGTCGGCTACTTAATTGTC 59.745 52.381 0.00 0.00 36.88 3.18
6 7 1.274596 CGCGTCGGCTACTTAATTGT 58.725 50.000 0.00 0.00 36.88 2.71
7 8 0.043310 GCGCGTCGGCTACTTAATTG 60.043 55.000 8.43 0.00 36.88 2.32
8 9 0.179119 AGCGCGTCGGCTACTTAATT 60.179 50.000 8.43 0.00 42.62 1.40
9 10 0.594284 GAGCGCGTCGGCTACTTAAT 60.594 55.000 8.43 0.00 44.93 1.40
10 11 1.226491 GAGCGCGTCGGCTACTTAA 60.226 57.895 8.43 0.00 44.93 1.85
11 12 2.406401 GAGCGCGTCGGCTACTTA 59.594 61.111 8.43 0.00 44.93 2.24
12 13 4.831307 CGAGCGCGTCGGCTACTT 62.831 66.667 18.91 0.00 44.93 2.24
22 23 3.390017 CATCATCGGACGAGCGCG 61.390 66.667 8.75 8.75 44.79 6.86
23 24 3.032609 CCATCATCGGACGAGCGC 61.033 66.667 0.00 0.00 0.00 5.92
24 25 3.032609 GCCATCATCGGACGAGCG 61.033 66.667 0.00 0.00 0.00 5.03
25 26 1.953138 CAGCCATCATCGGACGAGC 60.953 63.158 0.00 0.00 0.00 5.03
26 27 0.318529 CTCAGCCATCATCGGACGAG 60.319 60.000 0.00 0.00 0.00 4.18
27 28 0.751643 TCTCAGCCATCATCGGACGA 60.752 55.000 0.00 0.00 0.00 4.20
28 29 0.318529 CTCTCAGCCATCATCGGACG 60.319 60.000 0.00 0.00 0.00 4.79
29 30 1.035923 TCTCTCAGCCATCATCGGAC 58.964 55.000 0.00 0.00 0.00 4.79
30 31 1.685517 CTTCTCTCAGCCATCATCGGA 59.314 52.381 0.00 0.00 0.00 4.55
31 32 1.411977 ACTTCTCTCAGCCATCATCGG 59.588 52.381 0.00 0.00 0.00 4.18
32 33 2.886862 ACTTCTCTCAGCCATCATCG 57.113 50.000 0.00 0.00 0.00 3.84
33 34 5.893897 AAAAACTTCTCTCAGCCATCATC 57.106 39.130 0.00 0.00 0.00 2.92
74 75 1.475403 GACTGCTGACTAGGCACCTA 58.525 55.000 0.00 0.00 35.71 3.08
75 76 1.261238 GGACTGCTGACTAGGCACCT 61.261 60.000 0.00 0.00 35.71 4.00
76 77 1.219393 GGACTGCTGACTAGGCACC 59.781 63.158 0.00 0.00 35.71 5.01
77 78 1.219393 GGGACTGCTGACTAGGCAC 59.781 63.158 0.00 0.00 35.71 5.01
78 79 2.351244 CGGGACTGCTGACTAGGCA 61.351 63.158 0.00 0.00 38.10 4.75
79 80 2.286127 GACGGGACTGCTGACTAGGC 62.286 65.000 0.00 0.00 0.00 3.93
80 81 1.810532 GACGGGACTGCTGACTAGG 59.189 63.158 0.00 0.00 0.00 3.02
81 82 1.429825 CGACGGGACTGCTGACTAG 59.570 63.158 0.00 0.00 0.00 2.57
82 83 2.044555 CCGACGGGACTGCTGACTA 61.045 63.158 5.81 0.00 34.06 2.59
83 84 3.374402 CCGACGGGACTGCTGACT 61.374 66.667 5.81 0.00 34.06 3.41
84 85 3.681835 ACCGACGGGACTGCTGAC 61.682 66.667 20.00 0.00 36.97 3.51
85 86 3.680786 CACCGACGGGACTGCTGA 61.681 66.667 20.00 0.00 36.97 4.26
86 87 3.515316 AACACCGACGGGACTGCTG 62.515 63.158 20.00 8.63 36.97 4.41
87 88 3.231736 AACACCGACGGGACTGCT 61.232 61.111 20.00 0.00 36.97 4.24
88 89 3.041940 CAACACCGACGGGACTGC 61.042 66.667 20.00 0.00 36.97 4.40
89 90 1.663702 GTCAACACCGACGGGACTG 60.664 63.158 20.00 10.20 36.97 3.51
90 91 1.397390 AAGTCAACACCGACGGGACT 61.397 55.000 20.00 17.24 40.98 3.85
91 92 0.531311 AAAGTCAACACCGACGGGAC 60.531 55.000 20.00 15.21 40.98 4.46
92 93 0.531090 CAAAGTCAACACCGACGGGA 60.531 55.000 20.00 2.25 40.98 5.14
93 94 1.503818 CCAAAGTCAACACCGACGGG 61.504 60.000 20.00 9.81 40.98 5.28
94 95 0.812412 ACCAAAGTCAACACCGACGG 60.812 55.000 13.61 13.61 40.98 4.79
95 96 0.580104 GACCAAAGTCAACACCGACG 59.420 55.000 0.00 0.00 42.99 5.12
105 106 4.421058 GTGAAGTGGTTTTGACCAAAGTC 58.579 43.478 0.00 0.00 42.10 3.01
106 107 3.119637 CGTGAAGTGGTTTTGACCAAAGT 60.120 43.478 0.00 0.00 42.10 2.66
107 108 3.434637 CGTGAAGTGGTTTTGACCAAAG 58.565 45.455 0.00 0.00 42.10 2.77
108 109 2.164624 CCGTGAAGTGGTTTTGACCAAA 59.835 45.455 0.00 0.00 42.10 3.28
109 110 1.746220 CCGTGAAGTGGTTTTGACCAA 59.254 47.619 0.00 0.00 42.10 3.67
110 111 1.065345 TCCGTGAAGTGGTTTTGACCA 60.065 47.619 0.00 0.00 37.46 4.02
111 112 1.670791 TCCGTGAAGTGGTTTTGACC 58.329 50.000 0.00 0.00 0.00 4.02
112 113 3.810941 TGTATCCGTGAAGTGGTTTTGAC 59.189 43.478 0.00 0.00 0.00 3.18
113 114 4.074627 TGTATCCGTGAAGTGGTTTTGA 57.925 40.909 0.00 0.00 0.00 2.69
114 115 4.822036 TTGTATCCGTGAAGTGGTTTTG 57.178 40.909 0.00 0.00 0.00 2.44
115 116 5.450826 GGTTTTGTATCCGTGAAGTGGTTTT 60.451 40.000 0.00 0.00 0.00 2.43
116 117 4.037089 GGTTTTGTATCCGTGAAGTGGTTT 59.963 41.667 0.00 0.00 0.00 3.27
117 118 3.566742 GGTTTTGTATCCGTGAAGTGGTT 59.433 43.478 0.00 0.00 0.00 3.67
118 119 3.143728 GGTTTTGTATCCGTGAAGTGGT 58.856 45.455 0.00 0.00 0.00 4.16
119 120 2.158841 CGGTTTTGTATCCGTGAAGTGG 59.841 50.000 0.00 0.00 41.58 4.00
120 121 3.061322 TCGGTTTTGTATCCGTGAAGTG 58.939 45.455 3.64 0.00 45.88 3.16
121 122 3.006110 TCTCGGTTTTGTATCCGTGAAGT 59.994 43.478 6.02 0.00 43.38 3.01
122 123 3.581755 TCTCGGTTTTGTATCCGTGAAG 58.418 45.455 6.02 0.00 43.38 3.02
123 124 3.663995 TCTCGGTTTTGTATCCGTGAA 57.336 42.857 6.02 0.00 43.38 3.18
125 126 3.517602 TGATCTCGGTTTTGTATCCGTG 58.482 45.455 3.64 1.88 45.88 4.94
126 127 3.430374 CCTGATCTCGGTTTTGTATCCGT 60.430 47.826 3.64 0.00 45.88 4.69
127 128 3.123804 CCTGATCTCGGTTTTGTATCCG 58.876 50.000 0.00 0.00 46.93 4.18
128 129 4.402056 TCCTGATCTCGGTTTTGTATCC 57.598 45.455 0.00 0.00 0.00 2.59
129 130 6.049149 TCAATCCTGATCTCGGTTTTGTATC 58.951 40.000 0.00 0.00 0.00 2.24
130 131 5.989477 TCAATCCTGATCTCGGTTTTGTAT 58.011 37.500 0.00 0.00 0.00 2.29
131 132 5.046591 ACTCAATCCTGATCTCGGTTTTGTA 60.047 40.000 0.00 0.00 0.00 2.41
132 133 4.256920 CTCAATCCTGATCTCGGTTTTGT 58.743 43.478 0.00 0.00 0.00 2.83
133 134 4.256920 ACTCAATCCTGATCTCGGTTTTG 58.743 43.478 0.00 4.51 0.00 2.44
134 135 4.559862 ACTCAATCCTGATCTCGGTTTT 57.440 40.909 0.00 0.00 0.00 2.43
135 136 4.559862 AACTCAATCCTGATCTCGGTTT 57.440 40.909 0.00 0.00 0.00 3.27
136 137 4.559862 AAACTCAATCCTGATCTCGGTT 57.440 40.909 0.00 0.00 0.00 4.44
137 138 4.256920 CAAAACTCAATCCTGATCTCGGT 58.743 43.478 0.00 0.00 0.00 4.69
138 139 3.624861 CCAAAACTCAATCCTGATCTCGG 59.375 47.826 0.00 0.00 0.00 4.63
139 140 4.331168 GTCCAAAACTCAATCCTGATCTCG 59.669 45.833 0.00 0.00 0.00 4.04
140 141 4.637977 GGTCCAAAACTCAATCCTGATCTC 59.362 45.833 0.00 0.00 0.00 2.75
141 142 4.290722 AGGTCCAAAACTCAATCCTGATCT 59.709 41.667 0.00 0.00 0.00 2.75
142 143 4.593956 AGGTCCAAAACTCAATCCTGATC 58.406 43.478 0.00 0.00 0.00 2.92
143 144 4.593956 GAGGTCCAAAACTCAATCCTGAT 58.406 43.478 0.00 0.00 33.95 2.90
144 145 3.557054 CGAGGTCCAAAACTCAATCCTGA 60.557 47.826 0.00 0.00 33.36 3.86
145 146 2.744202 CGAGGTCCAAAACTCAATCCTG 59.256 50.000 0.00 0.00 33.36 3.86
146 147 2.372172 ACGAGGTCCAAAACTCAATCCT 59.628 45.455 0.00 0.00 33.36 3.24
147 148 2.779506 ACGAGGTCCAAAACTCAATCC 58.220 47.619 0.00 0.00 33.36 3.01
148 149 4.566987 ACTACGAGGTCCAAAACTCAATC 58.433 43.478 0.00 0.00 33.36 2.67
149 150 4.618920 ACTACGAGGTCCAAAACTCAAT 57.381 40.909 0.00 0.00 33.36 2.57
150 151 4.411256 AACTACGAGGTCCAAAACTCAA 57.589 40.909 0.00 0.00 33.36 3.02
151 152 4.586001 ACTAACTACGAGGTCCAAAACTCA 59.414 41.667 0.00 0.00 33.36 3.41
152 153 5.131594 ACTAACTACGAGGTCCAAAACTC 57.868 43.478 0.00 0.00 0.00 3.01
153 154 5.069516 TGAACTAACTACGAGGTCCAAAACT 59.930 40.000 0.00 0.00 28.82 2.66
154 155 5.291971 TGAACTAACTACGAGGTCCAAAAC 58.708 41.667 0.00 0.00 28.82 2.43
155 156 5.534207 TGAACTAACTACGAGGTCCAAAA 57.466 39.130 0.00 0.00 28.82 2.44
156 157 5.510179 CCTTGAACTAACTACGAGGTCCAAA 60.510 44.000 0.00 0.00 32.31 3.28
157 158 4.021719 CCTTGAACTAACTACGAGGTCCAA 60.022 45.833 0.00 0.00 32.31 3.53
158 159 3.508793 CCTTGAACTAACTACGAGGTCCA 59.491 47.826 0.00 0.00 32.31 4.02
159 160 3.509184 ACCTTGAACTAACTACGAGGTCC 59.491 47.826 0.00 0.00 42.65 4.46
160 161 4.022503 ACACCTTGAACTAACTACGAGGTC 60.023 45.833 0.00 0.00 43.90 3.85
161 162 3.893813 ACACCTTGAACTAACTACGAGGT 59.106 43.478 0.00 0.00 45.83 3.85
162 163 4.516365 ACACCTTGAACTAACTACGAGG 57.484 45.455 0.00 0.00 40.09 4.63
163 164 7.811236 TGAAATACACCTTGAACTAACTACGAG 59.189 37.037 0.00 0.00 0.00 4.18
164 165 7.660112 TGAAATACACCTTGAACTAACTACGA 58.340 34.615 0.00 0.00 0.00 3.43
165 166 7.878477 TGAAATACACCTTGAACTAACTACG 57.122 36.000 0.00 0.00 0.00 3.51
166 167 8.501580 GGTTGAAATACACCTTGAACTAACTAC 58.498 37.037 0.00 0.00 0.00 2.73
167 168 7.385752 CGGTTGAAATACACCTTGAACTAACTA 59.614 37.037 0.00 0.00 0.00 2.24
168 169 6.204108 CGGTTGAAATACACCTTGAACTAACT 59.796 38.462 0.00 0.00 0.00 2.24
169 170 6.368213 CGGTTGAAATACACCTTGAACTAAC 58.632 40.000 0.00 0.00 0.00 2.34
170 171 5.470777 CCGGTTGAAATACACCTTGAACTAA 59.529 40.000 0.00 0.00 0.00 2.24
171 172 4.998672 CCGGTTGAAATACACCTTGAACTA 59.001 41.667 0.00 0.00 0.00 2.24
172 173 3.818773 CCGGTTGAAATACACCTTGAACT 59.181 43.478 0.00 0.00 0.00 3.01
173 174 3.566742 ACCGGTTGAAATACACCTTGAAC 59.433 43.478 0.00 0.00 0.00 3.18
174 175 3.822940 ACCGGTTGAAATACACCTTGAA 58.177 40.909 0.00 0.00 0.00 2.69
175 176 3.495434 ACCGGTTGAAATACACCTTGA 57.505 42.857 0.00 0.00 0.00 3.02
176 177 4.542735 GAAACCGGTTGAAATACACCTTG 58.457 43.478 23.08 0.00 0.00 3.61
177 178 3.251487 CGAAACCGGTTGAAATACACCTT 59.749 43.478 23.08 0.00 0.00 3.50
178 179 2.809696 CGAAACCGGTTGAAATACACCT 59.190 45.455 23.08 0.00 0.00 4.00
179 180 2.549329 ACGAAACCGGTTGAAATACACC 59.451 45.455 23.08 1.22 0.00 4.16
180 181 3.883631 ACGAAACCGGTTGAAATACAC 57.116 42.857 23.08 4.54 0.00 2.90
181 182 4.630111 ACTACGAAACCGGTTGAAATACA 58.370 39.130 23.08 1.88 0.00 2.29
182 183 5.596268 AACTACGAAACCGGTTGAAATAC 57.404 39.130 23.08 7.60 0.00 1.89
183 184 6.368516 CCTAAACTACGAAACCGGTTGAAATA 59.631 38.462 23.08 10.33 0.00 1.40
184 185 5.179929 CCTAAACTACGAAACCGGTTGAAAT 59.820 40.000 23.08 4.37 0.00 2.17
185 186 4.511082 CCTAAACTACGAAACCGGTTGAAA 59.489 41.667 23.08 6.17 0.00 2.69
186 187 4.057432 CCTAAACTACGAAACCGGTTGAA 58.943 43.478 23.08 5.80 0.00 2.69
187 188 3.554752 CCCTAAACTACGAAACCGGTTGA 60.555 47.826 23.08 5.95 0.00 3.18
188 189 2.738314 CCCTAAACTACGAAACCGGTTG 59.262 50.000 23.08 12.19 0.00 3.77
189 190 2.368548 ACCCTAAACTACGAAACCGGTT 59.631 45.455 15.86 15.86 0.00 4.44
190 191 1.970640 ACCCTAAACTACGAAACCGGT 59.029 47.619 0.00 0.00 0.00 5.28
191 192 2.738314 CAACCCTAAACTACGAAACCGG 59.262 50.000 0.00 0.00 0.00 5.28
192 193 3.392882 ACAACCCTAAACTACGAAACCG 58.607 45.455 0.00 0.00 0.00 4.44
193 194 6.859420 TTTACAACCCTAAACTACGAAACC 57.141 37.500 0.00 0.00 0.00 3.27
197 198 8.998377 GGTTTAATTTACAACCCTAAACTACGA 58.002 33.333 0.00 0.00 37.11 3.43
198 199 8.782144 TGGTTTAATTTACAACCCTAAACTACG 58.218 33.333 10.03 0.00 41.73 3.51
201 202 9.204337 ACTTGGTTTAATTTACAACCCTAAACT 57.796 29.630 10.03 0.00 41.73 2.66
202 203 9.251792 CACTTGGTTTAATTTACAACCCTAAAC 57.748 33.333 10.03 0.00 41.73 2.01
203 204 8.422566 CCACTTGGTTTAATTTACAACCCTAAA 58.577 33.333 10.03 0.84 41.73 1.85
204 205 7.953752 CCACTTGGTTTAATTTACAACCCTAA 58.046 34.615 10.03 1.35 41.73 2.69
205 206 7.527568 CCACTTGGTTTAATTTACAACCCTA 57.472 36.000 10.03 1.10 41.73 3.53
206 207 6.413783 CCACTTGGTTTAATTTACAACCCT 57.586 37.500 10.03 0.00 41.73 4.34
222 223 0.974383 ACCTCGGACTAACCACTTGG 59.026 55.000 0.00 0.00 38.90 3.61
223 224 2.036733 TCAACCTCGGACTAACCACTTG 59.963 50.000 0.00 0.00 38.90 3.16
224 225 2.322658 TCAACCTCGGACTAACCACTT 58.677 47.619 0.00 0.00 38.90 3.16
225 226 2.005370 TCAACCTCGGACTAACCACT 57.995 50.000 0.00 0.00 38.90 4.00
226 227 2.825861 TTCAACCTCGGACTAACCAC 57.174 50.000 0.00 0.00 38.90 4.16
227 228 3.071892 ACATTTCAACCTCGGACTAACCA 59.928 43.478 0.00 0.00 38.90 3.67
228 229 3.435671 CACATTTCAACCTCGGACTAACC 59.564 47.826 0.00 0.00 0.00 2.85
229 230 3.435671 CCACATTTCAACCTCGGACTAAC 59.564 47.826 0.00 0.00 0.00 2.34
230 231 3.325425 TCCACATTTCAACCTCGGACTAA 59.675 43.478 0.00 0.00 0.00 2.24
231 232 2.901192 TCCACATTTCAACCTCGGACTA 59.099 45.455 0.00 0.00 0.00 2.59
232 233 1.697432 TCCACATTTCAACCTCGGACT 59.303 47.619 0.00 0.00 0.00 3.85
233 234 1.804748 GTCCACATTTCAACCTCGGAC 59.195 52.381 0.00 0.00 35.13 4.79
234 235 1.697432 AGTCCACATTTCAACCTCGGA 59.303 47.619 0.00 0.00 0.00 4.55
235 236 2.185004 AGTCCACATTTCAACCTCGG 57.815 50.000 0.00 0.00 0.00 4.63
236 237 3.403038 AGAAGTCCACATTTCAACCTCG 58.597 45.455 0.00 0.00 0.00 4.63
237 238 4.646572 AGAGAAGTCCACATTTCAACCTC 58.353 43.478 0.00 0.00 0.00 3.85
238 239 4.349342 AGAGAGAAGTCCACATTTCAACCT 59.651 41.667 0.00 0.00 0.00 3.50
239 240 4.646572 AGAGAGAAGTCCACATTTCAACC 58.353 43.478 0.00 0.00 0.00 3.77
240 241 5.994668 AGAAGAGAGAAGTCCACATTTCAAC 59.005 40.000 0.00 0.00 0.00 3.18
241 242 6.179906 AGAAGAGAGAAGTCCACATTTCAA 57.820 37.500 0.00 0.00 0.00 2.69
242 243 5.815233 AGAAGAGAGAAGTCCACATTTCA 57.185 39.130 0.00 0.00 0.00 2.69
243 244 8.608844 TTTAAGAAGAGAGAAGTCCACATTTC 57.391 34.615 0.00 0.00 0.00 2.17
244 245 8.980481 TTTTAAGAAGAGAGAAGTCCACATTT 57.020 30.769 0.00 0.00 0.00 2.32
245 246 9.007901 CATTTTAAGAAGAGAGAAGTCCACATT 57.992 33.333 0.00 0.00 0.00 2.71
246 247 7.609532 CCATTTTAAGAAGAGAGAAGTCCACAT 59.390 37.037 0.00 0.00 0.00 3.21
247 248 6.936900 CCATTTTAAGAAGAGAGAAGTCCACA 59.063 38.462 0.00 0.00 0.00 4.17
248 249 6.128145 GCCATTTTAAGAAGAGAGAAGTCCAC 60.128 42.308 0.00 0.00 0.00 4.02
249 250 5.940470 GCCATTTTAAGAAGAGAGAAGTCCA 59.060 40.000 0.00 0.00 0.00 4.02
250 251 5.940470 TGCCATTTTAAGAAGAGAGAAGTCC 59.060 40.000 0.00 0.00 0.00 3.85
251 252 6.876257 TCTGCCATTTTAAGAAGAGAGAAGTC 59.124 38.462 0.00 0.00 0.00 3.01
252 253 6.773638 TCTGCCATTTTAAGAAGAGAGAAGT 58.226 36.000 0.00 0.00 0.00 3.01
253 254 6.315891 CCTCTGCCATTTTAAGAAGAGAGAAG 59.684 42.308 0.00 0.00 34.40 2.85
254 255 6.013379 TCCTCTGCCATTTTAAGAAGAGAGAA 60.013 38.462 0.00 0.00 34.40 2.87
255 256 5.485353 TCCTCTGCCATTTTAAGAAGAGAGA 59.515 40.000 0.00 0.00 34.40 3.10
256 257 5.738909 TCCTCTGCCATTTTAAGAAGAGAG 58.261 41.667 0.01 0.00 34.40 3.20
257 258 5.762179 TCCTCTGCCATTTTAAGAAGAGA 57.238 39.130 0.01 0.00 34.40 3.10
258 259 5.530543 GGATCCTCTGCCATTTTAAGAAGAG 59.469 44.000 3.84 0.00 0.00 2.85
259 260 5.440610 GGATCCTCTGCCATTTTAAGAAGA 58.559 41.667 3.84 0.00 0.00 2.87
260 261 4.274459 CGGATCCTCTGCCATTTTAAGAAG 59.726 45.833 10.75 0.00 0.00 2.85
261 262 4.199310 CGGATCCTCTGCCATTTTAAGAA 58.801 43.478 10.75 0.00 0.00 2.52
262 263 3.433598 CCGGATCCTCTGCCATTTTAAGA 60.434 47.826 10.75 0.00 0.00 2.10
263 264 2.880890 CCGGATCCTCTGCCATTTTAAG 59.119 50.000 10.75 0.00 0.00 1.85
264 265 2.241176 ACCGGATCCTCTGCCATTTTAA 59.759 45.455 9.46 0.00 0.00 1.52
265 266 1.843851 ACCGGATCCTCTGCCATTTTA 59.156 47.619 9.46 0.00 0.00 1.52
266 267 0.625849 ACCGGATCCTCTGCCATTTT 59.374 50.000 9.46 0.00 0.00 1.82
267 268 0.625849 AACCGGATCCTCTGCCATTT 59.374 50.000 9.46 0.00 0.00 2.32
268 269 0.181350 GAACCGGATCCTCTGCCATT 59.819 55.000 9.46 0.00 0.00 3.16
269 270 1.700042 GGAACCGGATCCTCTGCCAT 61.700 60.000 22.87 0.00 36.50 4.40
270 271 2.367202 GGAACCGGATCCTCTGCCA 61.367 63.158 22.87 0.00 36.50 4.92
271 272 2.367202 TGGAACCGGATCCTCTGCC 61.367 63.158 28.84 4.86 40.35 4.85
272 273 1.153349 GTGGAACCGGATCCTCTGC 60.153 63.158 28.84 14.06 40.35 4.26
273 274 1.141881 CGTGGAACCGGATCCTCTG 59.858 63.158 28.84 17.80 40.35 3.35
274 275 3.617368 CGTGGAACCGGATCCTCT 58.383 61.111 28.84 0.00 40.35 3.69
282 283 3.107661 GTACGTGCCGTGGAACCG 61.108 66.667 10.01 0.00 41.39 4.44
283 284 2.470801 TACGTACGTGCCGTGGAACC 62.471 60.000 30.25 0.00 41.39 3.62
284 285 1.081509 TACGTACGTGCCGTGGAAC 60.082 57.895 30.25 0.00 41.39 3.62
285 286 1.081509 GTACGTACGTGCCGTGGAA 60.082 57.895 30.25 5.06 41.39 3.53
286 287 2.560861 GTACGTACGTGCCGTGGA 59.439 61.111 30.25 5.88 41.39 4.02
287 288 2.871080 CGTACGTACGTGCCGTGG 60.871 66.667 33.95 12.49 44.13 4.94
297 298 2.489329 AGCTGAACTTAAGGCGTACGTA 59.511 45.455 17.90 0.00 0.00 3.57
320 321 2.213499 GGAATGGCCACGTAGAAGATG 58.787 52.381 8.16 0.00 36.34 2.90
359 360 1.296755 GCCATGAGCGCGATCATCAT 61.297 55.000 34.74 20.99 37.84 2.45
360 361 1.957695 GCCATGAGCGCGATCATCA 60.958 57.895 34.74 19.73 37.84 3.07
367 369 3.729965 AAGAGAGGCCATGAGCGCG 62.730 63.158 5.01 0.00 45.17 6.86
425 427 4.499183 ACGAGGAAGATGCAAGAAACTAG 58.501 43.478 0.00 0.00 0.00 2.57
430 432 1.806542 GCAACGAGGAAGATGCAAGAA 59.193 47.619 0.00 0.00 39.33 2.52
708 722 2.361357 AGCCGTAGAGAGTGCCGT 60.361 61.111 0.00 0.00 0.00 5.68
715 729 2.360726 TCGTGGCAGCCGTAGAGA 60.361 61.111 7.03 0.00 0.00 3.10
835 849 1.379044 GCCCATGACCTCCTGTTGG 60.379 63.158 0.00 0.00 0.00 3.77
838 852 1.903877 CGAAGCCCATGACCTCCTGT 61.904 60.000 0.00 0.00 0.00 4.00
1064 1100 4.954118 TCGCCCAGTCCACCCACT 62.954 66.667 0.00 0.00 0.00 4.00
1086 1125 2.563471 GACTTATCCTTGCGTCGAGT 57.437 50.000 0.00 0.00 0.00 4.18
1095 1134 0.460311 CCGCTGTCCGACTTATCCTT 59.540 55.000 0.00 0.00 40.02 3.36
1101 1140 3.288308 CTCAGCCGCTGTCCGACTT 62.288 63.158 19.77 0.00 40.02 3.01
1110 1149 4.127040 CTGTCGAGCTCAGCCGCT 62.127 66.667 15.40 0.00 44.33 5.52
1184 1226 1.899437 GCCGTCCAGGAGGTCATGAA 61.899 60.000 8.37 0.00 45.00 2.57
1243 1288 2.421952 CCTTGACATCAATCCGGTCCAT 60.422 50.000 0.00 0.00 35.02 3.41
1374 1523 2.953466 ATGAACATGTCCTGCAATGC 57.047 45.000 0.00 0.00 0.00 3.56
1683 1835 2.893398 GCTGTCCCTTCCGATCGT 59.107 61.111 15.09 0.00 0.00 3.73
1922 2074 1.006571 GAAGCCGTTGGACTCGACA 60.007 57.895 0.00 0.00 0.00 4.35
1952 2104 2.489722 GACAAGGATCAAAGGGCACTTC 59.510 50.000 0.00 0.00 35.41 3.01
1957 2109 0.960364 TGCGACAAGGATCAAAGGGC 60.960 55.000 0.00 0.00 0.00 5.19
1998 2150 6.834107 TCAGTGATACATTCATCATGGACAT 58.166 36.000 0.00 0.00 37.28 3.06
2003 2155 9.708092 AGTAAGATCAGTGATACATTCATCATG 57.292 33.333 5.38 0.00 37.28 3.07
2031 2183 9.490663 GCCAAAACAACGATAATATATGATAGC 57.509 33.333 0.00 0.00 0.00 2.97
2084 2237 2.237143 CACCCCAAGAAGTGCTCTATCA 59.763 50.000 0.00 0.00 32.46 2.15
2161 2322 1.619669 CCCCTAGGGCTCCAACCTT 60.620 63.158 23.84 0.00 39.54 3.50
2181 2342 5.716703 TGTGTCTTCATAGTCTCCAATGAGA 59.283 40.000 0.00 0.00 45.39 3.27
2285 2764 7.411808 AGGTCCAATCTAGTTCTTGTACTCTA 58.588 38.462 0.00 0.00 0.00 2.43
2297 2776 4.896482 CCTAGCTTGTAGGTCCAATCTAGT 59.104 45.833 0.00 0.00 38.55 2.57
2325 2804 4.827284 CCATTTGTGAAGACCTAACACCTT 59.173 41.667 0.00 0.00 34.18 3.50
2334 2813 2.887152 ACTCAAGCCATTTGTGAAGACC 59.113 45.455 0.00 0.00 38.01 3.85
2351 2830 4.136796 CAATGTCCCTTGTCAAAGACTCA 58.863 43.478 13.69 0.00 35.19 3.41
2361 2840 2.344592 TGAGTACCCAATGTCCCTTGT 58.655 47.619 0.00 0.00 0.00 3.16
2364 2843 2.562296 ACATGAGTACCCAATGTCCCT 58.438 47.619 0.00 0.00 0.00 4.20
2370 2849 3.384168 TGCCTCTACATGAGTACCCAAT 58.616 45.455 0.00 0.00 41.11 3.16
2402 2881 2.290197 ACGAGAGACCGAGGACTTACTT 60.290 50.000 0.00 0.00 0.00 2.24
2403 2882 1.278699 ACGAGAGACCGAGGACTTACT 59.721 52.381 0.00 0.00 0.00 2.24
2411 2890 1.132453 TGTATTGCACGAGAGACCGAG 59.868 52.381 0.00 0.00 0.00 4.63
2466 2945 4.201990 GCTTGCATTTGGAGATAAGGACAG 60.202 45.833 0.00 0.00 0.00 3.51
2512 2994 3.192633 GTGTGGATGGATTGTACCAAACC 59.807 47.826 0.00 0.00 43.47 3.27
2518 3000 2.238646 TCTGGGTGTGGATGGATTGTAC 59.761 50.000 0.00 0.00 0.00 2.90
2522 3004 2.742428 CATCTGGGTGTGGATGGATT 57.258 50.000 0.00 0.00 36.60 3.01
2553 3035 2.835156 TGGGTGTAGTGCATTGCTACTA 59.165 45.455 10.49 12.32 39.47 1.82
2558 3040 0.958091 TTGTGGGTGTAGTGCATTGC 59.042 50.000 0.46 0.46 0.00 3.56
2559 3041 1.068333 GCTTGTGGGTGTAGTGCATTG 60.068 52.381 0.00 0.00 0.00 2.82
2646 3130 1.004745 GGGAAGATCTGAAAGGTGGCA 59.995 52.381 0.00 0.00 0.00 4.92
2662 3146 1.278127 GACCAAGGATCTTGTCGGGAA 59.722 52.381 6.86 0.00 0.00 3.97
2684 3170 2.784347 GCCCAAGTGCTTCTAGAAACT 58.216 47.619 6.63 5.34 0.00 2.66
2698 3184 1.017387 GCCTGACTAAATCGCCCAAG 58.983 55.000 0.00 0.00 0.00 3.61
2705 3191 1.473434 CCCCGTGAGCCTGACTAAATC 60.473 57.143 0.00 0.00 0.00 2.17
2789 3275 2.557924 TGTGGGATGTTTCACATTCTGC 59.442 45.455 0.00 0.00 39.27 4.26
2819 3305 3.447229 CCAATTTGTGAGTCCATTACCCC 59.553 47.826 0.00 0.00 0.00 4.95
2886 3372 4.037446 GTGTGTATGTTTTGTCACCACCAT 59.963 41.667 0.00 0.00 0.00 3.55
2892 3378 5.238650 AGCTAAGGTGTGTATGTTTTGTCAC 59.761 40.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.