Multiple sequence alignment - TraesCS3B01G368200

Loading Multiple Alignment...

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 TraesCS3B01G368200 chr3B 100.000 3050 0 0 1 3050 580354001 580350952 0.000000e+00 5633
1 TraesCS3B01G368200 chr3D 89.234 2805 167 48 294 3011 442809448 442806692 0.000000e+00 3382
2 TraesCS3B01G368200 chr3A 90.782 2506 156 37 607 3050 584011521 584009029 0.000000e+00 3278
3 TraesCS3B01G368200 chr6D 88.757 169 17 2 206 374 90135051 90134885 3.990000e-49 206
4 TraesCS3B01G368200 chr6D 86.188 181 22 3 195 374 147691308 147691130 3.100000e-45 193
5 TraesCS3B01G368200 chr6A 88.757 169 17 2 206 374 108924033 108924199 3.990000e-49 206
6 TraesCS3B01G368200 chr2A 89.873 158 15 1 212 369 249754614 249754458 5.160000e-48 202
7 TraesCS3B01G368200 chr2D 90.260 154 14 1 217 370 560153898 560154050 1.850000e-47 200
8 TraesCS3B01G368200 chr2D 88.024 167 18 2 205 370 305517900 305517735 2.400000e-46 196
9 TraesCS3B01G368200 chr4A 88.889 162 17 1 206 367 75320421 75320581 6.670000e-47 198
10 TraesCS3B01G368200 chr7B 87.500 168 19 2 205 372 48281314 48281149 3.100000e-45 193
11 TraesCS3B01G368200 chr4B 87.500 168 19 2 202 368 517751225 517751059 3.100000e-45 193
12 TraesCS3B01G368200 chr5A 79.856 139 25 3 27 164 518024907 518024771 6.960000e-17 99


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 TraesCS3B01G368200 chr3B 580350952 580354001 3049 True 5633 5633 100.000 1 3050 1 chr3B.!!$R1 3049
1 TraesCS3B01G368200 chr3D 442806692 442809448 2756 True 3382 3382 89.234 294 3011 1 chr3D.!!$R1 2717
2 TraesCS3B01G368200 chr3A 584009029 584011521 2492 True 3278 3278 90.782 607 3050 1 chr3A.!!$R1 2443

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 0.033366 GCATGTTGTCAAACCCCACC 59.967 55.0 0.0 0.0 35.25 4.61 F
34 35 0.041238 TTGTCAAACCCCACCAACCA 59.959 50.0 0.0 0.0 0.00 3.67 F
51 52 0.106335 CCACCATGCAAGCAACCAAA 59.894 50.0 0.0 0.0 0.00 3.28 F
549 557 0.108804 TTCATCCCGACTCGCTTGTC 60.109 55.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 1941 0.179240 CAACGAAGTGCGATCACAGC 60.179 55.000 0.00 0.0 45.00 4.40 R
1920 1991 2.203195 AGCCTTGCGAGCAACACA 60.203 55.556 6.39 0.0 0.00 3.72 R
2036 2107 3.146104 ACCCAAATCACTTGTCCTCAG 57.854 47.619 0.00 0.0 32.65 3.35 R
2523 2620 2.485426 TGTAACCTGTCGAACTAGTCCG 59.515 50.000 0.00 0.0 0.00 4.79 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
18 19 2.334307 GTGTGAGCCTGCATGTTGT 58.666 52.632 0.00 0.00 0.00 3.32
19 20 0.239347 GTGTGAGCCTGCATGTTGTC 59.761 55.000 0.00 0.00 0.00 3.18
20 21 0.179023 TGTGAGCCTGCATGTTGTCA 60.179 50.000 0.00 0.00 0.00 3.58
21 22 0.953727 GTGAGCCTGCATGTTGTCAA 59.046 50.000 0.00 0.00 0.00 3.18
22 23 1.337703 GTGAGCCTGCATGTTGTCAAA 59.662 47.619 0.00 0.00 0.00 2.69
23 24 1.337703 TGAGCCTGCATGTTGTCAAAC 59.662 47.619 0.00 0.00 36.78 2.93
24 25 0.675633 AGCCTGCATGTTGTCAAACC 59.324 50.000 0.00 0.00 35.25 3.27
25 26 0.319813 GCCTGCATGTTGTCAAACCC 60.320 55.000 0.00 0.00 35.25 4.11
26 27 0.318120 CCTGCATGTTGTCAAACCCC 59.682 55.000 0.00 0.00 35.25 4.95
27 28 1.039068 CTGCATGTTGTCAAACCCCA 58.961 50.000 0.00 0.00 35.25 4.96
28 29 0.749649 TGCATGTTGTCAAACCCCAC 59.250 50.000 0.00 0.00 35.25 4.61
29 30 0.033366 GCATGTTGTCAAACCCCACC 59.967 55.000 0.00 0.00 35.25 4.61
30 31 1.407936 CATGTTGTCAAACCCCACCA 58.592 50.000 0.00 0.00 35.25 4.17
31 32 1.759445 CATGTTGTCAAACCCCACCAA 59.241 47.619 0.00 0.00 35.25 3.67
32 33 1.187087 TGTTGTCAAACCCCACCAAC 58.813 50.000 0.00 0.00 35.25 3.77
33 34 0.462375 GTTGTCAAACCCCACCAACC 59.538 55.000 0.00 0.00 31.50 3.77
34 35 0.041238 TTGTCAAACCCCACCAACCA 59.959 50.000 0.00 0.00 0.00 3.67
35 36 0.684805 TGTCAAACCCCACCAACCAC 60.685 55.000 0.00 0.00 0.00 4.16
36 37 1.075896 TCAAACCCCACCAACCACC 60.076 57.895 0.00 0.00 0.00 4.61
37 38 1.381872 CAAACCCCACCAACCACCA 60.382 57.895 0.00 0.00 0.00 4.17
38 39 0.762461 CAAACCCCACCAACCACCAT 60.762 55.000 0.00 0.00 0.00 3.55
39 40 0.762461 AAACCCCACCAACCACCATG 60.762 55.000 0.00 0.00 0.00 3.66
40 41 2.996734 CCCCACCAACCACCATGC 60.997 66.667 0.00 0.00 0.00 4.06
41 42 2.203611 CCCACCAACCACCATGCA 60.204 61.111 0.00 0.00 0.00 3.96
42 43 1.836158 CCCACCAACCACCATGCAA 60.836 57.895 0.00 0.00 0.00 4.08
43 44 1.667151 CCACCAACCACCATGCAAG 59.333 57.895 0.00 0.00 0.00 4.01
44 45 1.005867 CACCAACCACCATGCAAGC 60.006 57.895 0.00 0.00 0.00 4.01
45 46 1.457267 ACCAACCACCATGCAAGCA 60.457 52.632 0.00 0.00 0.00 3.91
46 47 1.047596 ACCAACCACCATGCAAGCAA 61.048 50.000 0.00 0.00 0.00 3.91
47 48 0.600782 CCAACCACCATGCAAGCAAC 60.601 55.000 0.00 0.00 0.00 4.17
48 49 0.600782 CAACCACCATGCAAGCAACC 60.601 55.000 0.00 0.00 0.00 3.77
49 50 1.047596 AACCACCATGCAAGCAACCA 61.048 50.000 0.00 0.00 0.00 3.67
50 51 1.047596 ACCACCATGCAAGCAACCAA 61.048 50.000 0.00 0.00 0.00 3.67
51 52 0.106335 CCACCATGCAAGCAACCAAA 59.894 50.000 0.00 0.00 0.00 3.28
52 53 1.219646 CACCATGCAAGCAACCAAAC 58.780 50.000 0.00 0.00 0.00 2.93
53 54 0.829333 ACCATGCAAGCAACCAAACA 59.171 45.000 0.00 0.00 0.00 2.83
54 55 1.209019 ACCATGCAAGCAACCAAACAA 59.791 42.857 0.00 0.00 0.00 2.83
55 56 1.598601 CCATGCAAGCAACCAAACAAC 59.401 47.619 0.00 0.00 0.00 3.32
56 57 2.277969 CATGCAAGCAACCAAACAACA 58.722 42.857 0.00 0.00 0.00 3.33
57 58 2.462456 TGCAAGCAACCAAACAACAA 57.538 40.000 0.00 0.00 0.00 2.83
58 59 2.344950 TGCAAGCAACCAAACAACAAG 58.655 42.857 0.00 0.00 0.00 3.16
59 60 2.028658 TGCAAGCAACCAAACAACAAGA 60.029 40.909 0.00 0.00 0.00 3.02
60 61 2.348362 GCAAGCAACCAAACAACAAGAC 59.652 45.455 0.00 0.00 0.00 3.01
61 62 3.848726 CAAGCAACCAAACAACAAGACT 58.151 40.909 0.00 0.00 0.00 3.24
62 63 4.676723 GCAAGCAACCAAACAACAAGACTA 60.677 41.667 0.00 0.00 0.00 2.59
63 64 4.632538 AGCAACCAAACAACAAGACTAC 57.367 40.909 0.00 0.00 0.00 2.73
64 65 4.013728 AGCAACCAAACAACAAGACTACA 58.986 39.130 0.00 0.00 0.00 2.74
65 66 4.644685 AGCAACCAAACAACAAGACTACAT 59.355 37.500 0.00 0.00 0.00 2.29
66 67 4.976116 GCAACCAAACAACAAGACTACATC 59.024 41.667 0.00 0.00 0.00 3.06
67 68 5.449862 GCAACCAAACAACAAGACTACATCA 60.450 40.000 0.00 0.00 0.00 3.07
68 69 6.735694 GCAACCAAACAACAAGACTACATCAT 60.736 38.462 0.00 0.00 0.00 2.45
69 70 6.959639 ACCAAACAACAAGACTACATCATT 57.040 33.333 0.00 0.00 0.00 2.57
70 71 7.346751 ACCAAACAACAAGACTACATCATTT 57.653 32.000 0.00 0.00 0.00 2.32
71 72 7.781056 ACCAAACAACAAGACTACATCATTTT 58.219 30.769 0.00 0.00 0.00 1.82
72 73 8.257306 ACCAAACAACAAGACTACATCATTTTT 58.743 29.630 0.00 0.00 0.00 1.94
95 96 8.925161 TTTTGTACTGTTTTTCTTCAATCTGG 57.075 30.769 0.00 0.00 0.00 3.86
96 97 6.072112 TGTACTGTTTTTCTTCAATCTGGC 57.928 37.500 0.00 0.00 0.00 4.85
97 98 5.827797 TGTACTGTTTTTCTTCAATCTGGCT 59.172 36.000 0.00 0.00 0.00 4.75
98 99 5.444663 ACTGTTTTTCTTCAATCTGGCTC 57.555 39.130 0.00 0.00 0.00 4.70
99 100 5.136105 ACTGTTTTTCTTCAATCTGGCTCT 58.864 37.500 0.00 0.00 0.00 4.09
100 101 5.009410 ACTGTTTTTCTTCAATCTGGCTCTG 59.991 40.000 0.00 0.00 0.00 3.35
101 102 4.233005 GTTTTTCTTCAATCTGGCTCTGC 58.767 43.478 0.00 0.00 0.00 4.26
102 103 2.865119 TTCTTCAATCTGGCTCTGCA 57.135 45.000 0.00 0.00 0.00 4.41
103 104 2.105006 TCTTCAATCTGGCTCTGCAC 57.895 50.000 0.00 0.00 0.00 4.57
104 105 1.348696 TCTTCAATCTGGCTCTGCACA 59.651 47.619 0.00 0.00 0.00 4.57
105 106 1.738350 CTTCAATCTGGCTCTGCACAG 59.262 52.381 0.00 0.00 36.07 3.66
106 107 0.675837 TCAATCTGGCTCTGCACAGC 60.676 55.000 5.25 5.25 38.84 4.40
112 113 2.346739 GCTCTGCACAGCCTGACT 59.653 61.111 1.98 0.00 32.76 3.41
113 114 1.302351 GCTCTGCACAGCCTGACTT 60.302 57.895 1.98 0.00 32.76 3.01
114 115 0.888285 GCTCTGCACAGCCTGACTTT 60.888 55.000 1.98 0.00 32.76 2.66
115 116 1.602311 CTCTGCACAGCCTGACTTTT 58.398 50.000 0.00 0.00 0.00 2.27
116 117 1.952296 CTCTGCACAGCCTGACTTTTT 59.048 47.619 0.00 0.00 0.00 1.94
133 134 2.922740 TTTTTCTCGTACAGCCTGGT 57.077 45.000 0.00 0.00 0.00 4.00
134 135 2.450609 TTTTCTCGTACAGCCTGGTC 57.549 50.000 0.00 0.00 0.00 4.02
135 136 0.606604 TTTCTCGTACAGCCTGGTCC 59.393 55.000 0.00 0.00 0.00 4.46
136 137 0.541063 TTCTCGTACAGCCTGGTCCA 60.541 55.000 0.00 0.00 0.00 4.02
137 138 0.541063 TCTCGTACAGCCTGGTCCAA 60.541 55.000 0.00 0.00 0.00 3.53
138 139 0.537188 CTCGTACAGCCTGGTCCAAT 59.463 55.000 0.00 0.00 0.00 3.16
139 140 0.249120 TCGTACAGCCTGGTCCAATG 59.751 55.000 0.00 0.00 0.00 2.82
140 141 0.744414 CGTACAGCCTGGTCCAATGG 60.744 60.000 0.00 0.00 0.00 3.16
141 142 1.032114 GTACAGCCTGGTCCAATGGC 61.032 60.000 13.23 13.23 46.42 4.40
146 147 2.191128 GCCTGGTCCAATGGCTATAG 57.809 55.000 13.72 0.00 43.05 1.31
147 148 1.271597 GCCTGGTCCAATGGCTATAGG 60.272 57.143 13.72 0.90 43.05 2.57
148 149 1.271597 CCTGGTCCAATGGCTATAGGC 60.272 57.143 19.02 19.02 41.50 3.93
159 160 1.400494 GGCTATAGGCAACCAAACACG 59.600 52.381 20.73 0.00 44.01 4.49
160 161 2.081462 GCTATAGGCAACCAAACACGT 58.919 47.619 1.04 0.00 41.35 4.49
161 162 2.095372 GCTATAGGCAACCAAACACGTC 59.905 50.000 1.04 0.00 41.35 4.34
162 163 1.530323 ATAGGCAACCAAACACGTCC 58.470 50.000 0.00 0.00 37.17 4.79
163 164 0.470766 TAGGCAACCAAACACGTCCT 59.529 50.000 0.00 0.00 37.17 3.85
164 165 0.395173 AGGCAACCAAACACGTCCTT 60.395 50.000 0.00 0.00 37.17 3.36
165 166 0.248866 GGCAACCAAACACGTCCTTG 60.249 55.000 0.00 0.00 0.00 3.61
166 167 0.736053 GCAACCAAACACGTCCTTGA 59.264 50.000 7.55 0.00 0.00 3.02
167 168 1.336755 GCAACCAAACACGTCCTTGAT 59.663 47.619 7.55 0.00 0.00 2.57
168 169 2.858260 GCAACCAAACACGTCCTTGATG 60.858 50.000 7.55 7.33 0.00 3.07
169 170 0.951558 ACCAAACACGTCCTTGATGC 59.048 50.000 7.55 0.00 0.00 3.91
170 171 1.238439 CCAAACACGTCCTTGATGCT 58.762 50.000 7.55 0.00 0.00 3.79
171 172 1.608590 CCAAACACGTCCTTGATGCTT 59.391 47.619 7.55 0.00 0.00 3.91
172 173 2.034558 CCAAACACGTCCTTGATGCTTT 59.965 45.455 7.55 0.00 0.00 3.51
173 174 3.300009 CAAACACGTCCTTGATGCTTTC 58.700 45.455 0.68 0.00 0.00 2.62
174 175 2.550830 ACACGTCCTTGATGCTTTCT 57.449 45.000 0.00 0.00 0.00 2.52
175 176 2.851195 ACACGTCCTTGATGCTTTCTT 58.149 42.857 0.00 0.00 0.00 2.52
176 177 3.214328 ACACGTCCTTGATGCTTTCTTT 58.786 40.909 0.00 0.00 0.00 2.52
177 178 3.003689 ACACGTCCTTGATGCTTTCTTTG 59.996 43.478 0.00 0.00 0.00 2.77
178 179 2.030805 ACGTCCTTGATGCTTTCTTTGC 60.031 45.455 0.00 0.00 0.00 3.68
179 180 2.589014 GTCCTTGATGCTTTCTTTGCG 58.411 47.619 0.00 0.00 0.00 4.85
180 181 1.068333 TCCTTGATGCTTTCTTTGCGC 60.068 47.619 0.00 0.00 0.00 6.09
181 182 1.336148 CCTTGATGCTTTCTTTGCGCA 60.336 47.619 5.66 5.66 38.14 6.09
182 183 2.396601 CTTGATGCTTTCTTTGCGCAA 58.603 42.857 21.02 21.02 37.20 4.85
183 184 1.769733 TGATGCTTTCTTTGCGCAAC 58.230 45.000 24.99 10.96 37.20 4.17
184 185 0.704551 GATGCTTTCTTTGCGCAACG 59.295 50.000 24.99 22.06 37.20 4.10
204 205 3.259207 GCTTTGTGCGAATATAGCCAG 57.741 47.619 0.00 0.00 0.00 4.85
205 206 2.614057 GCTTTGTGCGAATATAGCCAGT 59.386 45.455 0.00 0.00 0.00 4.00
206 207 3.807622 GCTTTGTGCGAATATAGCCAGTA 59.192 43.478 0.00 0.00 0.00 2.74
207 208 4.272504 GCTTTGTGCGAATATAGCCAGTAA 59.727 41.667 0.00 0.00 0.00 2.24
208 209 5.049405 GCTTTGTGCGAATATAGCCAGTAAT 60.049 40.000 0.00 0.00 0.00 1.89
209 210 6.539649 TTTGTGCGAATATAGCCAGTAATC 57.460 37.500 0.00 0.00 0.00 1.75
210 211 5.208463 TGTGCGAATATAGCCAGTAATCA 57.792 39.130 0.00 0.00 0.00 2.57
211 212 4.988540 TGTGCGAATATAGCCAGTAATCAC 59.011 41.667 0.00 0.00 0.00 3.06
212 213 5.221441 TGTGCGAATATAGCCAGTAATCACT 60.221 40.000 0.00 0.00 34.42 3.41
213 214 5.346281 GTGCGAATATAGCCAGTAATCACTC 59.654 44.000 0.00 0.00 30.46 3.51
214 215 5.010617 TGCGAATATAGCCAGTAATCACTCA 59.989 40.000 0.00 0.00 30.46 3.41
215 216 5.574830 GCGAATATAGCCAGTAATCACTCAG 59.425 44.000 0.00 0.00 30.46 3.35
216 217 6.682746 CGAATATAGCCAGTAATCACTCAGT 58.317 40.000 0.00 0.00 30.46 3.41
217 218 7.148641 CGAATATAGCCAGTAATCACTCAGTT 58.851 38.462 0.00 0.00 30.46 3.16
218 219 7.327275 CGAATATAGCCAGTAATCACTCAGTTC 59.673 40.741 0.00 0.00 30.46 3.01
219 220 3.618690 AGCCAGTAATCACTCAGTTCC 57.381 47.619 0.00 0.00 30.46 3.62
220 221 3.177228 AGCCAGTAATCACTCAGTTCCT 58.823 45.455 0.00 0.00 30.46 3.36
221 222 4.353777 AGCCAGTAATCACTCAGTTCCTA 58.646 43.478 0.00 0.00 30.46 2.94
222 223 4.777896 AGCCAGTAATCACTCAGTTCCTAA 59.222 41.667 0.00 0.00 30.46 2.69
223 224 5.248477 AGCCAGTAATCACTCAGTTCCTAAA 59.752 40.000 0.00 0.00 30.46 1.85
224 225 6.069963 AGCCAGTAATCACTCAGTTCCTAAAT 60.070 38.462 0.00 0.00 30.46 1.40
225 226 7.125811 AGCCAGTAATCACTCAGTTCCTAAATA 59.874 37.037 0.00 0.00 30.46 1.40
226 227 7.934120 GCCAGTAATCACTCAGTTCCTAAATAT 59.066 37.037 0.00 0.00 30.46 1.28
263 264 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
264 265 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
265 266 8.647796 AGATTTCAATATGGACTACATACGGAA 58.352 33.333 0.00 0.00 44.41 4.30
266 267 9.436957 GATTTCAATATGGACTACATACGGAAT 57.563 33.333 0.00 0.00 44.41 3.01
274 275 8.833231 ATGGACTACATACGGAATAAAATGAG 57.167 34.615 0.00 0.00 38.26 2.90
275 276 7.788026 TGGACTACATACGGAATAAAATGAGT 58.212 34.615 0.00 0.00 0.00 3.41
276 277 7.709182 TGGACTACATACGGAATAAAATGAGTG 59.291 37.037 0.00 0.00 0.00 3.51
277 278 7.924412 GGACTACATACGGAATAAAATGAGTGA 59.076 37.037 0.00 0.00 0.00 3.41
278 279 9.309516 GACTACATACGGAATAAAATGAGTGAA 57.690 33.333 0.00 0.00 0.00 3.18
279 280 9.832445 ACTACATACGGAATAAAATGAGTGAAT 57.168 29.630 0.00 0.00 0.00 2.57
281 282 8.964476 ACATACGGAATAAAATGAGTGAATCT 57.036 30.769 0.00 0.00 0.00 2.40
285 286 8.197988 ACGGAATAAAATGAGTGAATCTACAC 57.802 34.615 0.00 0.00 40.60 2.90
374 375 8.887264 TTAGAAATCAGAGAGAGTAGTTCCTT 57.113 34.615 0.00 0.00 0.00 3.36
386 387 6.851318 AGAGTAGTTCCTTATAGGGTAGGAC 58.149 44.000 0.11 0.00 40.19 3.85
402 403 1.048601 GGACTGGAGTGGAGTTGTGA 58.951 55.000 0.00 0.00 0.00 3.58
405 406 3.496870 GGACTGGAGTGGAGTTGTGATTT 60.497 47.826 0.00 0.00 0.00 2.17
417 418 8.299570 GTGGAGTTGTGATTTCTTGTAATCATT 58.700 33.333 6.08 0.00 44.01 2.57
419 420 8.514594 GGAGTTGTGATTTCTTGTAATCATTCA 58.485 33.333 6.08 0.00 44.01 2.57
444 452 1.945580 AAACTTGTTTGGTGGTGGGT 58.054 45.000 0.00 0.00 0.00 4.51
450 458 1.550976 TGTTTGGTGGTGGGTTTGTTC 59.449 47.619 0.00 0.00 0.00 3.18
452 460 2.235155 GTTTGGTGGTGGGTTTGTTCTT 59.765 45.455 0.00 0.00 0.00 2.52
453 461 1.770294 TGGTGGTGGGTTTGTTCTTC 58.230 50.000 0.00 0.00 0.00 2.87
455 463 1.686741 GGTGGTGGGTTTGTTCTTCCA 60.687 52.381 0.00 0.00 0.00 3.53
482 490 5.892160 TCTCTAATATTACATCCGTCCCG 57.108 43.478 0.00 0.00 0.00 5.14
489 497 4.950205 ATTACATCCGTCCCGAATTACT 57.050 40.909 0.00 0.00 0.00 2.24
497 505 6.076981 TCCGTCCCGAATTACTTATCTTAC 57.923 41.667 0.00 0.00 0.00 2.34
532 540 6.837992 ACATGGATGTATTTACACACGTTTC 58.162 36.000 0.00 0.00 39.68 2.78
533 541 6.428465 ACATGGATGTATTTACACACGTTTCA 59.572 34.615 0.00 0.00 39.68 2.69
540 548 2.068837 TACACACGTTTCATCCCGAC 57.931 50.000 0.00 0.00 0.00 4.79
543 551 0.388134 ACACGTTTCATCCCGACTCG 60.388 55.000 0.00 0.00 0.00 4.18
544 552 1.445582 ACGTTTCATCCCGACTCGC 60.446 57.895 0.00 0.00 0.00 5.03
545 553 1.153823 CGTTTCATCCCGACTCGCT 60.154 57.895 0.00 0.00 0.00 4.93
549 557 0.108804 TTCATCCCGACTCGCTTGTC 60.109 55.000 0.00 0.00 0.00 3.18
555 563 1.405821 CCCGACTCGCTTGTCTTAGAT 59.594 52.381 0.00 0.00 35.00 1.98
568 576 8.841822 CGCTTGTCTTAGATTTGTATAGATACG 58.158 37.037 0.00 0.00 36.06 3.06
569 577 8.640291 GCTTGTCTTAGATTTGTATAGATACGC 58.360 37.037 0.00 0.00 36.06 4.42
588 601 2.877168 CGCTAGACACGTAGGGAAGTAT 59.123 50.000 0.00 0.00 35.48 2.12
610 629 1.340465 CGTGCGAGTGTGCGTATTC 59.660 57.895 0.00 0.00 37.81 1.75
664 683 2.942376 ACGCAAGAGTGTGAATCAAACA 59.058 40.909 6.31 0.00 38.69 2.83
668 687 5.052172 CGCAAGAGTGTGAATCAAACAAAAG 60.052 40.000 6.31 0.00 37.45 2.27
670 689 4.936891 AGAGTGTGAATCAAACAAAAGCC 58.063 39.130 6.31 0.00 0.00 4.35
683 702 4.429854 ACAAAAGCCCAGGCAAAATTTA 57.570 36.364 12.03 0.00 44.88 1.40
684 703 4.984295 ACAAAAGCCCAGGCAAAATTTAT 58.016 34.783 12.03 0.00 44.88 1.40
685 704 5.384336 ACAAAAGCCCAGGCAAAATTTATT 58.616 33.333 12.03 0.00 44.88 1.40
686 705 5.832595 ACAAAAGCCCAGGCAAAATTTATTT 59.167 32.000 12.03 0.00 44.88 1.40
732 754 5.659440 TTTTCAGAGGAAGCAAACAAAGT 57.341 34.783 0.00 0.00 33.82 2.66
742 764 7.781056 AGGAAGCAAACAAAGTGAAATTCTTA 58.219 30.769 0.00 0.00 0.00 2.10
743 765 8.424133 AGGAAGCAAACAAAGTGAAATTCTTAT 58.576 29.630 0.00 0.00 0.00 1.73
947 993 4.959596 GCATCTCGCGCCTCTCCC 62.960 72.222 0.00 0.00 0.00 4.30
988 1034 3.063084 GACACCGAGCGTCTCCCT 61.063 66.667 2.00 0.00 0.00 4.20
1047 1094 4.698625 AGGTTCCTCCCGTCCGCT 62.699 66.667 0.00 0.00 36.75 5.52
1113 1160 0.737715 CCTCAAACCTCGCCTTCTCG 60.738 60.000 0.00 0.00 0.00 4.04
1587 1658 0.974010 TGTTCGAGCCGGGTCCTTAT 60.974 55.000 27.11 0.00 0.00 1.73
1629 1700 3.131850 CCTTTTGTCCAAGGGCACT 57.868 52.632 0.00 0.00 39.95 4.40
1696 1767 2.225791 CTCCAACGGTCTCATCGCCA 62.226 60.000 0.00 0.00 0.00 5.69
1743 1814 4.218686 ACCCCAAACAAGGCGCCT 62.219 61.111 27.08 27.08 0.00 5.52
1857 1928 1.305129 CAATGTCATGCCACCCCCA 60.305 57.895 0.00 0.00 0.00 4.96
1870 1941 1.380302 CCCCCAGTCTTCAAGGTGG 59.620 63.158 0.64 0.64 0.00 4.61
1884 1955 1.672356 GGTGGCTGTGATCGCACTT 60.672 57.895 4.45 0.00 45.36 3.16
1920 1991 0.482446 TGCTTGGTGGGATGTCCTTT 59.518 50.000 0.00 0.00 36.20 3.11
2121 2192 1.270839 GCATCGCCCTAGCCTCATTTA 60.271 52.381 0.00 0.00 34.57 1.40
2213 2284 7.169140 GCTTGAAATATTTTGTTCAGTCGGTTT 59.831 33.333 1.43 0.00 35.29 3.27
2224 2295 2.894765 TCAGTCGGTTTGTGGTGATCTA 59.105 45.455 0.00 0.00 0.00 1.98
2257 2328 6.835174 AGATGGCTTGCTTAGATGATCTTAA 58.165 36.000 0.00 0.00 0.00 1.85
2302 2373 4.794762 CGTGTGCTCATTTGGTCAATTATG 59.205 41.667 0.00 0.00 0.00 1.90
2325 2414 4.210120 GCATCTGCAGTCTTTACCTATTCG 59.790 45.833 14.67 0.00 41.59 3.34
2351 2440 5.798132 AGTTCATGTTGATCTGTCTGCTTA 58.202 37.500 0.00 0.00 0.00 3.09
2445 2534 6.944557 GTTGGGTAAACTTATTGATGCAAC 57.055 37.500 0.00 0.00 35.75 4.17
2446 2535 6.451393 GTTGGGTAAACTTATTGATGCAACA 58.549 36.000 0.00 0.00 35.75 3.33
2457 2554 1.275856 TGATGCAACAAGGCCAAATCC 59.724 47.619 5.01 0.00 0.00 3.01
2485 2582 1.134877 ACAGTGTGCCGAGATGATCTG 60.135 52.381 0.00 0.00 0.00 2.90
2502 2599 9.962783 AGATGATCTGCTAAATTAAATTTCTGC 57.037 29.630 0.00 0.00 34.57 4.26
2523 2620 5.041287 TGCATATGCTAGTGTCGTAACTTC 58.959 41.667 27.13 0.00 42.66 3.01
2532 2629 3.817647 AGTGTCGTAACTTCGGACTAGTT 59.182 43.478 0.00 1.16 39.13 2.24
2556 2653 7.400599 TCGACAGGTTACATTGTACTATCTT 57.599 36.000 0.00 0.00 0.00 2.40
2601 2698 5.123979 GCATTTCTCTTGGTAATCGAAAGGT 59.876 40.000 0.00 0.00 30.68 3.50
2622 2719 4.513442 GTTGTATCAGTCTGGTGGCAATA 58.487 43.478 0.00 0.00 0.00 1.90
2624 2721 6.288294 GTTGTATCAGTCTGGTGGCAATATA 58.712 40.000 0.00 0.00 0.00 0.86
2647 2744 5.828299 TTTGGAAGTTATAATTCCCTGCG 57.172 39.130 17.12 0.00 44.76 5.18
2689 2788 9.075678 AGAATGATTGTCTTGATCTGAAGTTTT 57.924 29.630 0.00 0.00 0.00 2.43
2721 2820 1.244816 CTGGGGAGTATATGCGTCGA 58.755 55.000 0.00 0.00 0.00 4.20
2726 2825 2.034305 GGGAGTATATGCGTCGACACTT 59.966 50.000 17.16 6.79 0.00 3.16
2750 2849 3.303351 ACTGGCTCATAATTTCCCCAG 57.697 47.619 0.00 0.00 44.09 4.45
2758 2857 5.185828 GCTCATAATTTCCCCAGAAGTTGTT 59.814 40.000 0.00 0.00 34.20 2.83
2803 2904 4.023622 CACATTGACATTCCACGGTTGTAA 60.024 41.667 0.00 0.00 0.00 2.41
2812 2913 6.487331 ACATTCCACGGTTGTAATTTTAGTCA 59.513 34.615 0.00 0.00 0.00 3.41
2822 2923 8.349983 GGTTGTAATTTTAGTCATTGTGTCTGT 58.650 33.333 0.00 0.00 0.00 3.41
2823 2924 9.382244 GTTGTAATTTTAGTCATTGTGTCTGTC 57.618 33.333 0.00 0.00 0.00 3.51
2825 2926 5.862924 ATTTTAGTCATTGTGTCTGTCCG 57.137 39.130 0.00 0.00 0.00 4.79
2830 2931 0.249120 CATTGTGTCTGTCCGGGCTA 59.751 55.000 7.97 0.00 0.00 3.93
2831 2932 1.134401 CATTGTGTCTGTCCGGGCTAT 60.134 52.381 7.97 0.00 0.00 2.97
2832 2933 1.855295 TTGTGTCTGTCCGGGCTATA 58.145 50.000 7.97 0.00 0.00 1.31
2842 2957 0.768622 CCGGGCTATATGTTTGGGGA 59.231 55.000 0.00 0.00 0.00 4.81
2885 3000 5.531287 GGTGGTGACTAGTGTTTCAGATTTT 59.469 40.000 0.00 0.00 0.00 1.82
2896 3011 8.691661 AGTGTTTCAGATTTTAGAAGGCTAAA 57.308 30.769 0.00 0.00 43.06 1.85
2911 3026 4.006319 AGGCTAAACTTTCTGCTGACATC 58.994 43.478 0.00 0.00 0.00 3.06
2912 3027 3.127721 GGCTAAACTTTCTGCTGACATCC 59.872 47.826 0.00 0.00 0.00 3.51
2916 3031 4.363991 AACTTTCTGCTGACATCCTTCT 57.636 40.909 0.00 0.00 0.00 2.85
2951 3066 7.721286 ATATCAATAGTTTGTACTGCTGCTC 57.279 36.000 0.00 0.00 35.78 4.26
2974 3089 1.507713 CGATGCTGTCGTTGTTGCG 60.508 57.895 4.26 0.00 45.19 4.85
2977 3101 3.995669 GCTGTCGTTGTTGCGCGA 61.996 61.111 12.10 0.00 34.54 5.87
2993 3117 1.448985 GCGAAAGTATTGGCTGGTCA 58.551 50.000 0.00 0.00 37.31 4.02
3005 3129 1.373570 GCTGGTCATGCCTCTTGTAC 58.626 55.000 7.54 0.00 38.35 2.90
3011 3135 2.098117 GTCATGCCTCTTGTACATTGCC 59.902 50.000 0.00 0.00 0.00 4.52
3012 3136 2.093890 CATGCCTCTTGTACATTGCCA 58.906 47.619 0.00 0.00 0.00 4.92
3013 3137 2.512692 TGCCTCTTGTACATTGCCAT 57.487 45.000 0.00 0.00 0.00 4.40
3030 3162 0.448990 CATGTGGATGCACGAACAGG 59.551 55.000 13.03 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.239347 GACAACATGCAGGCTCACAC 59.761 55.000 0.00 0.00 0.00 3.82
1 2 0.179023 TGACAACATGCAGGCTCACA 60.179 50.000 0.00 0.00 0.00 3.58
2 3 0.953727 TTGACAACATGCAGGCTCAC 59.046 50.000 0.00 0.00 0.00 3.51
4 5 1.336240 GGTTTGACAACATGCAGGCTC 60.336 52.381 0.00 0.00 34.15 4.70
6 7 0.319813 GGGTTTGACAACATGCAGGC 60.320 55.000 0.00 0.00 34.15 4.85
7 8 0.318120 GGGGTTTGACAACATGCAGG 59.682 55.000 0.00 0.00 34.15 4.85
8 9 1.039068 TGGGGTTTGACAACATGCAG 58.961 50.000 0.00 0.00 34.15 4.41
9 10 0.749649 GTGGGGTTTGACAACATGCA 59.250 50.000 0.00 0.00 34.15 3.96
10 11 0.033366 GGTGGGGTTTGACAACATGC 59.967 55.000 0.00 0.00 34.15 4.06
11 12 1.407936 TGGTGGGGTTTGACAACATG 58.592 50.000 0.00 0.00 34.15 3.21
12 13 1.760029 GTTGGTGGGGTTTGACAACAT 59.240 47.619 0.00 0.00 40.66 2.71
13 14 1.187087 GTTGGTGGGGTTTGACAACA 58.813 50.000 0.00 0.00 40.66 3.33
14 15 0.462375 GGTTGGTGGGGTTTGACAAC 59.538 55.000 0.00 0.00 40.35 3.32
15 16 0.041238 TGGTTGGTGGGGTTTGACAA 59.959 50.000 0.00 0.00 0.00 3.18
16 17 0.684805 GTGGTTGGTGGGGTTTGACA 60.685 55.000 0.00 0.00 0.00 3.58
17 18 1.396607 GGTGGTTGGTGGGGTTTGAC 61.397 60.000 0.00 0.00 0.00 3.18
18 19 1.075896 GGTGGTTGGTGGGGTTTGA 60.076 57.895 0.00 0.00 0.00 2.69
19 20 0.762461 ATGGTGGTTGGTGGGGTTTG 60.762 55.000 0.00 0.00 0.00 2.93
20 21 0.762461 CATGGTGGTTGGTGGGGTTT 60.762 55.000 0.00 0.00 0.00 3.27
21 22 1.152355 CATGGTGGTTGGTGGGGTT 60.152 57.895 0.00 0.00 0.00 4.11
22 23 2.525592 CATGGTGGTTGGTGGGGT 59.474 61.111 0.00 0.00 0.00 4.95
23 24 2.996734 GCATGGTGGTTGGTGGGG 60.997 66.667 0.00 0.00 0.00 4.96
24 25 1.818959 CTTGCATGGTGGTTGGTGGG 61.819 60.000 0.00 0.00 0.00 4.61
25 26 1.667151 CTTGCATGGTGGTTGGTGG 59.333 57.895 0.00 0.00 0.00 4.61
26 27 1.005867 GCTTGCATGGTGGTTGGTG 60.006 57.895 1.34 0.00 0.00 4.17
27 28 1.047596 TTGCTTGCATGGTGGTTGGT 61.048 50.000 1.34 0.00 0.00 3.67
28 29 0.600782 GTTGCTTGCATGGTGGTTGG 60.601 55.000 1.34 0.00 0.00 3.77
29 30 0.600782 GGTTGCTTGCATGGTGGTTG 60.601 55.000 1.34 0.00 0.00 3.77
30 31 1.047596 TGGTTGCTTGCATGGTGGTT 61.048 50.000 1.34 0.00 0.00 3.67
31 32 1.047596 TTGGTTGCTTGCATGGTGGT 61.048 50.000 1.34 0.00 0.00 4.16
32 33 0.106335 TTTGGTTGCTTGCATGGTGG 59.894 50.000 1.34 0.00 0.00 4.61
33 34 1.219646 GTTTGGTTGCTTGCATGGTG 58.780 50.000 1.34 0.00 0.00 4.17
34 35 0.829333 TGTTTGGTTGCTTGCATGGT 59.171 45.000 1.34 0.00 0.00 3.55
35 36 1.598601 GTTGTTTGGTTGCTTGCATGG 59.401 47.619 1.34 0.00 0.00 3.66
36 37 2.277969 TGTTGTTTGGTTGCTTGCATG 58.722 42.857 0.00 0.00 0.00 4.06
37 38 2.687700 TGTTGTTTGGTTGCTTGCAT 57.312 40.000 0.00 0.00 0.00 3.96
38 39 2.028658 TCTTGTTGTTTGGTTGCTTGCA 60.029 40.909 0.00 0.00 0.00 4.08
39 40 2.348362 GTCTTGTTGTTTGGTTGCTTGC 59.652 45.455 0.00 0.00 0.00 4.01
40 41 3.848726 AGTCTTGTTGTTTGGTTGCTTG 58.151 40.909 0.00 0.00 0.00 4.01
41 42 4.461081 TGTAGTCTTGTTGTTTGGTTGCTT 59.539 37.500 0.00 0.00 0.00 3.91
42 43 4.013728 TGTAGTCTTGTTGTTTGGTTGCT 58.986 39.130 0.00 0.00 0.00 3.91
43 44 4.364415 TGTAGTCTTGTTGTTTGGTTGC 57.636 40.909 0.00 0.00 0.00 4.17
44 45 6.130298 TGATGTAGTCTTGTTGTTTGGTTG 57.870 37.500 0.00 0.00 0.00 3.77
45 46 6.959639 ATGATGTAGTCTTGTTGTTTGGTT 57.040 33.333 0.00 0.00 0.00 3.67
46 47 6.959639 AATGATGTAGTCTTGTTGTTTGGT 57.040 33.333 0.00 0.00 0.00 3.67
47 48 8.647143 AAAAATGATGTAGTCTTGTTGTTTGG 57.353 30.769 0.00 0.00 0.00 3.28
69 70 9.364989 CCAGATTGAAGAAAAACAGTACAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
70 71 7.491048 GCCAGATTGAAGAAAAACAGTACAAAA 59.509 33.333 0.00 0.00 0.00 2.44
71 72 6.978080 GCCAGATTGAAGAAAAACAGTACAAA 59.022 34.615 0.00 0.00 0.00 2.83
72 73 6.321181 AGCCAGATTGAAGAAAAACAGTACAA 59.679 34.615 0.00 0.00 0.00 2.41
73 74 5.827797 AGCCAGATTGAAGAAAAACAGTACA 59.172 36.000 0.00 0.00 0.00 2.90
74 75 6.205658 AGAGCCAGATTGAAGAAAAACAGTAC 59.794 38.462 0.00 0.00 0.00 2.73
75 76 6.205464 CAGAGCCAGATTGAAGAAAAACAGTA 59.795 38.462 0.00 0.00 0.00 2.74
76 77 5.009410 CAGAGCCAGATTGAAGAAAAACAGT 59.991 40.000 0.00 0.00 0.00 3.55
77 78 5.458891 CAGAGCCAGATTGAAGAAAAACAG 58.541 41.667 0.00 0.00 0.00 3.16
78 79 4.261741 GCAGAGCCAGATTGAAGAAAAACA 60.262 41.667 0.00 0.00 0.00 2.83
79 80 4.233005 GCAGAGCCAGATTGAAGAAAAAC 58.767 43.478 0.00 0.00 0.00 2.43
80 81 3.890756 TGCAGAGCCAGATTGAAGAAAAA 59.109 39.130 0.00 0.00 0.00 1.94
81 82 3.254166 GTGCAGAGCCAGATTGAAGAAAA 59.746 43.478 0.00 0.00 0.00 2.29
82 83 2.816087 GTGCAGAGCCAGATTGAAGAAA 59.184 45.455 0.00 0.00 0.00 2.52
83 84 2.224597 TGTGCAGAGCCAGATTGAAGAA 60.225 45.455 0.00 0.00 0.00 2.52
84 85 1.348696 TGTGCAGAGCCAGATTGAAGA 59.651 47.619 0.00 0.00 0.00 2.87
85 86 1.738350 CTGTGCAGAGCCAGATTGAAG 59.262 52.381 0.00 0.00 31.74 3.02
86 87 1.817357 CTGTGCAGAGCCAGATTGAA 58.183 50.000 0.00 0.00 31.74 2.69
87 88 0.675837 GCTGTGCAGAGCCAGATTGA 60.676 55.000 24.66 0.00 31.74 2.57
88 89 1.801332 GCTGTGCAGAGCCAGATTG 59.199 57.895 24.66 0.00 31.74 2.67
89 90 4.315588 GCTGTGCAGAGCCAGATT 57.684 55.556 24.66 0.00 31.74 2.40
95 96 0.888285 AAAGTCAGGCTGTGCAGAGC 60.888 55.000 26.78 26.78 38.34 4.09
96 97 1.602311 AAAAGTCAGGCTGTGCAGAG 58.398 50.000 15.27 6.48 0.00 3.35
97 98 2.057137 AAAAAGTCAGGCTGTGCAGA 57.943 45.000 15.27 0.00 0.00 4.26
114 115 2.549349 GGACCAGGCTGTACGAGAAAAA 60.549 50.000 14.43 0.00 0.00 1.94
115 116 1.001633 GGACCAGGCTGTACGAGAAAA 59.998 52.381 14.43 0.00 0.00 2.29
116 117 0.606604 GGACCAGGCTGTACGAGAAA 59.393 55.000 14.43 0.00 0.00 2.52
117 118 0.541063 TGGACCAGGCTGTACGAGAA 60.541 55.000 14.43 0.00 0.00 2.87
118 119 0.541063 TTGGACCAGGCTGTACGAGA 60.541 55.000 14.43 0.00 0.00 4.04
119 120 0.537188 ATTGGACCAGGCTGTACGAG 59.463 55.000 14.43 0.00 0.00 4.18
120 121 0.249120 CATTGGACCAGGCTGTACGA 59.751 55.000 14.43 2.81 0.00 3.43
121 122 0.744414 CCATTGGACCAGGCTGTACG 60.744 60.000 14.43 0.23 0.00 3.67
122 123 1.032114 GCCATTGGACCAGGCTGTAC 61.032 60.000 15.88 6.69 44.92 2.90
123 124 1.302949 GCCATTGGACCAGGCTGTA 59.697 57.895 15.88 0.00 44.92 2.74
124 125 2.036256 GCCATTGGACCAGGCTGT 59.964 61.111 15.88 1.17 44.92 4.40
128 129 1.271597 GCCTATAGCCATTGGACCAGG 60.272 57.143 6.95 7.68 34.35 4.45
129 130 1.421268 TGCCTATAGCCATTGGACCAG 59.579 52.381 6.95 0.00 42.71 4.00
130 131 1.517238 TGCCTATAGCCATTGGACCA 58.483 50.000 6.95 0.00 42.71 4.02
131 132 2.230660 GTTGCCTATAGCCATTGGACC 58.769 52.381 6.95 0.00 42.71 4.46
132 133 2.230660 GGTTGCCTATAGCCATTGGAC 58.769 52.381 6.95 0.00 42.71 4.02
133 134 1.849692 TGGTTGCCTATAGCCATTGGA 59.150 47.619 6.95 0.00 42.71 3.53
134 135 2.363306 TGGTTGCCTATAGCCATTGG 57.637 50.000 0.00 0.00 42.71 3.16
135 136 3.446873 TGTTTGGTTGCCTATAGCCATTG 59.553 43.478 0.00 0.00 42.71 2.82
136 137 3.447229 GTGTTTGGTTGCCTATAGCCATT 59.553 43.478 0.00 0.00 42.71 3.16
137 138 3.023832 GTGTTTGGTTGCCTATAGCCAT 58.976 45.455 0.00 0.00 42.71 4.40
138 139 2.442413 GTGTTTGGTTGCCTATAGCCA 58.558 47.619 0.00 0.00 42.71 4.75
139 140 1.400494 CGTGTTTGGTTGCCTATAGCC 59.600 52.381 0.00 0.00 42.71 3.93
140 141 2.081462 ACGTGTTTGGTTGCCTATAGC 58.919 47.619 0.00 0.00 44.14 2.97
141 142 2.676342 GGACGTGTTTGGTTGCCTATAG 59.324 50.000 0.00 0.00 0.00 1.31
142 143 2.303600 AGGACGTGTTTGGTTGCCTATA 59.696 45.455 0.00 0.00 0.00 1.31
143 144 1.073284 AGGACGTGTTTGGTTGCCTAT 59.927 47.619 0.00 0.00 0.00 2.57
144 145 0.470766 AGGACGTGTTTGGTTGCCTA 59.529 50.000 0.00 0.00 0.00 3.93
145 146 0.395173 AAGGACGTGTTTGGTTGCCT 60.395 50.000 0.00 0.00 0.00 4.75
146 147 0.248866 CAAGGACGTGTTTGGTTGCC 60.249 55.000 0.00 0.00 0.00 4.52
147 148 0.736053 TCAAGGACGTGTTTGGTTGC 59.264 50.000 0.00 0.00 0.00 4.17
148 149 2.858260 GCATCAAGGACGTGTTTGGTTG 60.858 50.000 0.00 0.93 0.00 3.77
149 150 1.336755 GCATCAAGGACGTGTTTGGTT 59.663 47.619 0.00 0.00 0.00 3.67
150 151 0.951558 GCATCAAGGACGTGTTTGGT 59.048 50.000 0.00 0.00 0.00 3.67
151 152 1.238439 AGCATCAAGGACGTGTTTGG 58.762 50.000 0.00 0.00 0.00 3.28
152 153 3.003689 AGAAAGCATCAAGGACGTGTTTG 59.996 43.478 0.00 0.00 0.00 2.93
153 154 3.214328 AGAAAGCATCAAGGACGTGTTT 58.786 40.909 0.00 0.00 0.00 2.83
154 155 2.851195 AGAAAGCATCAAGGACGTGTT 58.149 42.857 0.00 0.00 0.00 3.32
155 156 2.550830 AGAAAGCATCAAGGACGTGT 57.449 45.000 0.00 0.00 0.00 4.49
156 157 3.558505 CAAAGAAAGCATCAAGGACGTG 58.441 45.455 0.00 0.00 0.00 4.49
157 158 2.030805 GCAAAGAAAGCATCAAGGACGT 60.031 45.455 0.00 0.00 0.00 4.34
158 159 2.589014 GCAAAGAAAGCATCAAGGACG 58.411 47.619 0.00 0.00 0.00 4.79
159 160 2.589014 CGCAAAGAAAGCATCAAGGAC 58.411 47.619 0.00 0.00 0.00 3.85
160 161 1.068333 GCGCAAAGAAAGCATCAAGGA 60.068 47.619 0.30 0.00 0.00 3.36
161 162 1.336148 TGCGCAAAGAAAGCATCAAGG 60.336 47.619 8.16 0.00 35.81 3.61
162 163 2.054687 TGCGCAAAGAAAGCATCAAG 57.945 45.000 8.16 0.00 35.81 3.02
163 164 2.126467 GTTGCGCAAAGAAAGCATCAA 58.874 42.857 26.87 0.00 40.83 2.57
164 165 1.769733 GTTGCGCAAAGAAAGCATCA 58.230 45.000 26.87 0.00 40.83 3.07
165 166 0.704551 CGTTGCGCAAAGAAAGCATC 59.295 50.000 28.69 10.62 40.83 3.91
166 167 2.800096 CGTTGCGCAAAGAAAGCAT 58.200 47.368 28.69 0.00 40.83 3.79
167 168 4.300457 CGTTGCGCAAAGAAAGCA 57.700 50.000 28.69 0.00 39.33 3.91
184 185 2.614057 ACTGGCTATATTCGCACAAAGC 59.386 45.455 0.00 0.00 40.87 3.51
185 186 5.984233 TTACTGGCTATATTCGCACAAAG 57.016 39.130 0.00 0.00 0.00 2.77
186 187 6.018262 GTGATTACTGGCTATATTCGCACAAA 60.018 38.462 0.00 0.00 0.00 2.83
187 188 5.465390 GTGATTACTGGCTATATTCGCACAA 59.535 40.000 0.00 0.00 0.00 3.33
188 189 4.988540 GTGATTACTGGCTATATTCGCACA 59.011 41.667 0.00 0.00 0.00 4.57
189 190 5.230942 AGTGATTACTGGCTATATTCGCAC 58.769 41.667 0.00 0.00 35.34 5.34
190 191 5.010617 TGAGTGATTACTGGCTATATTCGCA 59.989 40.000 0.00 0.00 37.25 5.10
191 192 5.470368 TGAGTGATTACTGGCTATATTCGC 58.530 41.667 0.00 0.00 37.25 4.70
192 193 6.682746 ACTGAGTGATTACTGGCTATATTCG 58.317 40.000 0.00 0.00 37.25 3.34
193 194 7.600752 GGAACTGAGTGATTACTGGCTATATTC 59.399 40.741 0.00 0.00 37.25 1.75
194 195 7.291182 AGGAACTGAGTGATTACTGGCTATATT 59.709 37.037 0.00 0.00 37.18 1.28
195 196 6.784969 AGGAACTGAGTGATTACTGGCTATAT 59.215 38.462 0.00 0.00 37.18 0.86
196 197 6.136857 AGGAACTGAGTGATTACTGGCTATA 58.863 40.000 0.00 0.00 37.18 1.31
197 198 4.965532 AGGAACTGAGTGATTACTGGCTAT 59.034 41.667 0.00 0.00 37.18 2.97
198 199 4.353777 AGGAACTGAGTGATTACTGGCTA 58.646 43.478 0.00 0.00 37.18 3.93
199 200 3.177228 AGGAACTGAGTGATTACTGGCT 58.823 45.455 0.00 0.00 37.18 4.75
200 201 3.618690 AGGAACTGAGTGATTACTGGC 57.381 47.619 0.00 0.00 37.18 4.85
237 238 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
238 239 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
239 240 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
240 241 8.827177 TTCCGTATGTAGTCCATATTGAAATC 57.173 34.615 0.00 0.00 38.29 2.17
248 249 9.923143 CTCATTTTATTCCGTATGTAGTCCATA 57.077 33.333 0.00 0.00 34.86 2.74
249 250 8.429641 ACTCATTTTATTCCGTATGTAGTCCAT 58.570 33.333 0.00 0.00 37.58 3.41
250 251 7.709182 CACTCATTTTATTCCGTATGTAGTCCA 59.291 37.037 0.00 0.00 0.00 4.02
251 252 7.924412 TCACTCATTTTATTCCGTATGTAGTCC 59.076 37.037 0.00 0.00 0.00 3.85
252 253 8.867112 TCACTCATTTTATTCCGTATGTAGTC 57.133 34.615 0.00 0.00 0.00 2.59
253 254 9.832445 ATTCACTCATTTTATTCCGTATGTAGT 57.168 29.630 0.00 0.00 0.00 2.73
256 257 8.964476 AGATTCACTCATTTTATTCCGTATGT 57.036 30.769 0.00 0.00 0.00 2.29
259 260 9.309516 GTGTAGATTCACTCATTTTATTCCGTA 57.690 33.333 0.00 0.00 35.68 4.02
260 261 8.041323 AGTGTAGATTCACTCATTTTATTCCGT 58.959 33.333 0.00 0.00 44.07 4.69
261 262 8.425577 AGTGTAGATTCACTCATTTTATTCCG 57.574 34.615 0.00 0.00 44.07 4.30
347 348 9.487442 AGGAACTACTCTCTCTGATTTCTAAAT 57.513 33.333 0.00 0.00 36.02 1.40
358 359 6.851965 ACCCTATAAGGAACTACTCTCTCT 57.148 41.667 0.00 0.00 38.49 3.10
362 363 6.624860 AGTCCTACCCTATAAGGAACTACTCT 59.375 42.308 0.00 0.00 43.44 3.24
374 375 3.398292 CTCCACTCCAGTCCTACCCTATA 59.602 52.174 0.00 0.00 0.00 1.31
386 387 4.013267 AGAAATCACAACTCCACTCCAG 57.987 45.455 0.00 0.00 0.00 3.86
417 418 6.102663 CACCACCAAACAAGTTTTACATTGA 58.897 36.000 0.00 0.00 0.00 2.57
419 420 5.423886 CCACCACCAAACAAGTTTTACATT 58.576 37.500 0.00 0.00 0.00 2.71
452 460 9.090103 ACGGATGTAATATTAGAGAAGAATGGA 57.910 33.333 0.00 0.00 0.00 3.41
453 461 9.360093 GACGGATGTAATATTAGAGAAGAATGG 57.640 37.037 0.00 0.00 0.00 3.16
455 463 8.532819 GGGACGGATGTAATATTAGAGAAGAAT 58.467 37.037 0.00 0.00 0.00 2.40
507 515 6.417191 AACGTGTGTAAATACATCCATGTC 57.583 37.500 8.58 0.00 41.97 3.06
509 517 6.836953 TGAAACGTGTGTAAATACATCCATG 58.163 36.000 0.00 0.21 38.63 3.66
511 519 6.092944 GGATGAAACGTGTGTAAATACATCCA 59.907 38.462 13.01 0.00 45.72 3.41
523 531 1.068474 GAGTCGGGATGAAACGTGTG 58.932 55.000 0.00 0.00 0.00 3.82
525 533 1.683790 GCGAGTCGGGATGAAACGTG 61.684 60.000 15.52 0.00 32.49 4.49
532 540 0.108615 AAGACAAGCGAGTCGGGATG 60.109 55.000 15.52 0.00 43.24 3.51
533 541 1.405821 CTAAGACAAGCGAGTCGGGAT 59.594 52.381 15.52 0.00 43.24 3.85
543 551 8.640291 GCGTATCTATACAAATCTAAGACAAGC 58.360 37.037 1.37 0.00 32.87 4.01
544 552 9.900710 AGCGTATCTATACAAATCTAAGACAAG 57.099 33.333 1.37 0.00 32.87 3.16
555 563 6.609237 ACGTGTCTAGCGTATCTATACAAA 57.391 37.500 0.00 0.00 41.06 2.83
568 576 6.183360 CGTATATACTTCCCTACGTGTCTAGC 60.183 46.154 11.05 0.00 33.96 3.42
569 577 6.870965 ACGTATATACTTCCCTACGTGTCTAG 59.129 42.308 11.05 0.00 45.85 2.43
571 584 5.615289 ACGTATATACTTCCCTACGTGTCT 58.385 41.667 11.05 0.00 45.85 3.41
576 589 3.433274 TCGCACGTATATACTTCCCTACG 59.567 47.826 11.05 0.33 41.89 3.51
577 590 4.453819 ACTCGCACGTATATACTTCCCTAC 59.546 45.833 11.05 0.00 0.00 3.18
581 594 3.973135 CACACTCGCACGTATATACTTCC 59.027 47.826 11.05 0.00 0.00 3.46
588 601 0.726256 TACGCACACTCGCACGTATA 59.274 50.000 0.00 0.00 39.78 1.47
595 614 0.522705 TCTCGAATACGCACACTCGC 60.523 55.000 0.00 0.00 39.58 5.03
664 683 6.548993 TGAAAATAAATTTTGCCTGGGCTTTT 59.451 30.769 13.05 8.12 39.86 2.27
668 687 5.244755 TCTGAAAATAAATTTTGCCTGGGC 58.755 37.500 5.44 4.43 39.86 5.36
670 689 6.168389 AGCTCTGAAAATAAATTTTGCCTGG 58.832 36.000 5.44 0.00 39.86 4.45
706 728 5.850557 TGTTTGCTTCCTCTGAAAATTCA 57.149 34.783 0.00 0.00 35.57 2.57
732 754 8.950210 CCTCAGCTTGAACTAATAAGAATTTCA 58.050 33.333 0.00 0.00 0.00 2.69
742 764 2.678190 GCGGACCTCAGCTTGAACTAAT 60.678 50.000 0.00 0.00 34.22 1.73
743 765 1.337823 GCGGACCTCAGCTTGAACTAA 60.338 52.381 0.00 0.00 34.22 2.24
745 767 1.004440 GCGGACCTCAGCTTGAACT 60.004 57.895 0.00 0.00 34.22 3.01
747 769 1.004560 CTGCGGACCTCAGCTTGAA 60.005 57.895 0.00 0.00 37.92 2.69
748 770 2.659016 CTGCGGACCTCAGCTTGA 59.341 61.111 0.00 0.00 37.92 3.02
894 931 1.106351 TTGGTGTGATGTGGTGGTGC 61.106 55.000 0.00 0.00 0.00 5.01
895 932 0.667993 GTTGGTGTGATGTGGTGGTG 59.332 55.000 0.00 0.00 0.00 4.17
896 933 0.467290 GGTTGGTGTGATGTGGTGGT 60.467 55.000 0.00 0.00 0.00 4.16
897 934 1.178534 GGGTTGGTGTGATGTGGTGG 61.179 60.000 0.00 0.00 0.00 4.61
898 935 1.178534 GGGGTTGGTGTGATGTGGTG 61.179 60.000 0.00 0.00 0.00 4.17
899 936 1.152830 GGGGTTGGTGTGATGTGGT 59.847 57.895 0.00 0.00 0.00 4.16
900 937 1.606313 GGGGGTTGGTGTGATGTGG 60.606 63.158 0.00 0.00 0.00 4.17
901 938 0.468958 TTGGGGGTTGGTGTGATGTG 60.469 55.000 0.00 0.00 0.00 3.21
981 1027 4.593864 GCGATCGGGCAGGGAGAC 62.594 72.222 18.30 0.00 0.00 3.36
1041 1088 2.486042 GAGTCGAGGTGAGCGGAC 59.514 66.667 0.00 1.57 0.00 4.79
1047 1094 2.750637 GCGGAGGAGTCGAGGTGA 60.751 66.667 0.00 0.00 0.00 4.02
1098 1145 2.047179 GGCGAGAAGGCGAGGTTT 60.047 61.111 0.00 0.00 35.04 3.27
1233 1292 4.521062 GCTGCGTCGCCAGATCCT 62.521 66.667 15.88 0.00 34.77 3.24
1302 1361 2.727392 CCACCCGGCGAGGAACATA 61.727 63.158 19.10 0.00 45.00 2.29
1603 1674 1.407258 CTTGGACAAAAGGGTCGCAAA 59.593 47.619 0.00 0.00 38.70 3.68
1605 1676 0.821711 CCTTGGACAAAAGGGTCGCA 60.822 55.000 0.00 0.00 42.68 5.10
1614 1685 0.470766 ACGTAGTGCCCTTGGACAAA 59.529 50.000 0.00 0.00 42.51 2.83
1615 1686 0.470766 AACGTAGTGCCCTTGGACAA 59.529 50.000 0.00 0.00 45.00 3.18
1629 1700 4.360964 CCCACCACCGCGAACGTA 62.361 66.667 8.23 0.00 37.70 3.57
1696 1767 1.153086 GGTCCATGCGCTTCCTCAT 60.153 57.895 9.73 0.00 0.00 2.90
1857 1928 1.131638 TCACAGCCACCTTGAAGACT 58.868 50.000 0.00 0.00 0.00 3.24
1870 1941 0.179240 CAACGAAGTGCGATCACAGC 60.179 55.000 0.00 0.00 45.00 4.40
1920 1991 2.203195 AGCCTTGCGAGCAACACA 60.203 55.556 6.39 0.00 0.00 3.72
2036 2107 3.146104 ACCCAAATCACTTGTCCTCAG 57.854 47.619 0.00 0.00 32.65 3.35
2213 2284 6.183360 CCATCTCATAACACTAGATCACCACA 60.183 42.308 0.00 0.00 0.00 4.17
2224 2295 3.641434 AGCAAGCCATCTCATAACACT 57.359 42.857 0.00 0.00 0.00 3.55
2257 2328 9.020731 ACACGGGAGAATGATAAAACTTTATTT 57.979 29.630 0.00 0.00 33.72 1.40
2302 2373 4.210120 CGAATAGGTAAAGACTGCAGATGC 59.790 45.833 23.35 9.30 42.50 3.91
2318 2407 6.422100 CAGATCAACATGAACTACCGAATAGG 59.578 42.308 0.00 0.00 35.06 2.57
2319 2408 6.980978 ACAGATCAACATGAACTACCGAATAG 59.019 38.462 0.00 0.00 36.89 1.73
2325 2414 4.331168 GCAGACAGATCAACATGAACTACC 59.669 45.833 0.00 0.00 27.94 3.18
2502 2599 4.675565 CCGAAGTTACGACACTAGCATATG 59.324 45.833 0.00 0.00 35.09 1.78
2523 2620 2.485426 TGTAACCTGTCGAACTAGTCCG 59.515 50.000 0.00 0.00 0.00 4.79
2532 2629 7.400599 AAGATAGTACAATGTAACCTGTCGA 57.599 36.000 0.00 0.00 0.00 4.20
2601 2698 3.719268 ATTGCCACCAGACTGATACAA 57.281 42.857 3.32 3.55 0.00 2.41
2622 2719 7.724061 ACGCAGGGAATTATAACTTCCAAATAT 59.276 33.333 19.57 7.18 43.34 1.28
2624 2721 5.891551 ACGCAGGGAATTATAACTTCCAAAT 59.108 36.000 19.57 9.02 43.34 2.32
2641 2738 1.912417 AGTATCCTAGCTACGCAGGG 58.088 55.000 0.35 0.00 31.29 4.45
2647 2744 8.364142 ACAATCATTCTCAAGTATCCTAGCTAC 58.636 37.037 0.00 0.00 0.00 3.58
2721 2820 6.151144 GGAAATTATGAGCCAGTACAAAGTGT 59.849 38.462 0.00 0.00 0.00 3.55
2726 2825 4.017958 TGGGGAAATTATGAGCCAGTACAA 60.018 41.667 0.00 0.00 0.00 2.41
2750 2849 2.424956 GGAGGCCATGATGAACAACTTC 59.575 50.000 5.01 0.00 0.00 3.01
2758 2857 0.030195 TACCTGGGAGGCCATGATGA 60.030 55.000 5.01 0.00 39.63 2.92
2803 2904 4.695455 CCGGACAGACACAATGACTAAAAT 59.305 41.667 0.00 0.00 0.00 1.82
2812 2913 1.204146 ATAGCCCGGACAGACACAAT 58.796 50.000 0.73 0.00 0.00 2.71
2822 2923 0.768622 CCCCAAACATATAGCCCGGA 59.231 55.000 0.73 0.00 0.00 5.14
2823 2924 0.768622 TCCCCAAACATATAGCCCGG 59.231 55.000 0.00 0.00 0.00 5.73
2825 2926 2.963101 GGTTTCCCCAAACATATAGCCC 59.037 50.000 0.38 0.00 43.41 5.19
2846 2961 5.242393 AGTCACCACCAAAGATCAAGATTTG 59.758 40.000 0.00 0.00 36.40 2.32
2860 2975 3.035363 TCTGAAACACTAGTCACCACCA 58.965 45.455 0.00 0.00 0.00 4.17
2861 2976 3.746045 TCTGAAACACTAGTCACCACC 57.254 47.619 0.00 0.00 0.00 4.61
2862 2977 6.619801 AAAATCTGAAACACTAGTCACCAC 57.380 37.500 0.00 0.00 0.00 4.16
2885 3000 5.221641 TGTCAGCAGAAAGTTTAGCCTTCTA 60.222 40.000 8.46 0.00 0.00 2.10
2896 3011 5.489792 TTAGAAGGATGTCAGCAGAAAGT 57.510 39.130 0.00 0.00 0.00 2.66
2941 3056 2.002586 GCATCGAAAAGAGCAGCAGTA 58.997 47.619 0.00 0.00 0.00 2.74
2974 3089 1.448985 TGACCAGCCAATACTTTCGC 58.551 50.000 0.00 0.00 0.00 4.70
2993 3117 2.512692 TGGCAATGTACAAGAGGCAT 57.487 45.000 14.80 0.00 0.00 4.40
3005 3129 0.526739 CGTGCATCCACATGGCAATG 60.527 55.000 0.00 0.00 42.17 2.82
3011 3135 0.448990 CCTGTTCGTGCATCCACATG 59.551 55.000 0.00 0.00 42.17 3.21
3012 3136 1.308069 GCCTGTTCGTGCATCCACAT 61.308 55.000 0.00 0.00 42.17 3.21
3013 3137 1.965930 GCCTGTTCGTGCATCCACA 60.966 57.895 0.00 0.00 42.17 4.17
3030 3162 0.033781 TTGCTGCAACTTTCCCATGC 59.966 50.000 11.69 0.00 40.45 4.06


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

AutoCloner maintained by Alex Coulton.