Multiple sequence alignment - TraesCS4B01G087100

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 TraesCS4B01G087100 chr4B 100.000 3815 0 0 1 3815 87411502 87415316 0.000000e+00 7046.0
1 TraesCS4B01G087100 chr4D 95.346 2385 71 17 906 3261 58144607 58146980 0.000000e+00 3753.0
2 TraesCS4B01G087100 chr4D 89.141 396 25 9 3436 3815 58147250 58147643 9.590000e-131 477.0
3 TraesCS4B01G087100 chr4D 94.326 282 7 3 3174 3452 58146959 58147234 1.270000e-114 424.0
4 TraesCS4B01G087100 chr4D 84.464 457 37 17 365 812 58143843 58144274 1.640000e-113 420.0
5 TraesCS4B01G087100 chr4A 93.301 2284 88 14 607 2856 537600254 537598002 0.000000e+00 3310.0
6 TraesCS4B01G087100 chr4A 88.077 931 61 19 613 1529 537602253 537601359 0.000000e+00 1059.0
7 TraesCS4B01G087100 chr4A 94.686 414 10 4 2853 3258 537597922 537597513 1.930000e-177 632.0
8 TraesCS4B01G087100 chr4A 90.780 282 7 3 3174 3452 537597467 537597202 3.620000e-95 359.0
9 TraesCS4B01G087100 chr4A 92.373 236 10 4 373 606 537600805 537600576 2.840000e-86 329.0
10 TraesCS4B01G087100 chr4A 90.955 199 10 4 409 606 537602560 537602369 1.050000e-65 261.0
11 TraesCS4B01G087100 chr4A 89.394 198 13 4 409 605 537600556 537600366 3.810000e-60 243.0
12 TraesCS4B01G087100 chr4A 79.894 189 24 12 374 557 720376079 720375900 4.000000e-25 126.0
13 TraesCS4B01G087100 chr4A 91.011 89 3 4 3174 3261 537597530 537597446 8.660000e-22 115.0
14 TraesCS4B01G087100 chr6B 98.356 365 6 0 1 365 151604162 151604526 3.210000e-180 641.0
15 TraesCS4B01G087100 chr6B 98.347 363 6 0 1 363 711659185 711658823 4.160000e-179 638.0
16 TraesCS4B01G087100 chr6B 96.721 366 8 2 2 363 405865971 405865606 1.170000e-169 606.0
17 TraesCS4B01G087100 chr3A 97.796 363 8 0 1 363 391891339 391890977 9.000000e-176 627.0
18 TraesCS4B01G087100 chr3A 95.276 381 12 4 2 377 606520352 606519973 1.960000e-167 599.0
19 TraesCS4B01G087100 chr7B 96.970 363 11 0 1 363 745009107 745009469 9.060000e-171 610.0
20 TraesCS4B01G087100 chr7B 77.895 190 34 7 371 559 740955029 740954847 1.120000e-20 111.0
21 TraesCS4B01G087100 chr5B 96.721 366 8 2 2 363 649539186 649539551 1.170000e-169 606.0
22 TraesCS4B01G087100 chr5A 96.467 368 7 2 2 363 495091358 495090991 1.520000e-168 603.0
23 TraesCS4B01G087100 chr1B 96.448 366 9 2 2 363 614567468 614567833 5.450000e-168 601.0
24 TraesCS4B01G087100 chr5D 81.152 191 27 9 371 559 66974055 66973872 1.100000e-30 145.0
25 TraesCS4B01G087100 chr2B 79.532 171 24 7 390 557 762448184 762448022 1.120000e-20 111.0
26 TraesCS4B01G087100 chr7D 84.694 98 10 5 381 475 480994498 480994403 4.060000e-15 93.5
27 TraesCS4B01G087100 chr7D 85.106 94 9 5 375 465 34846319 34846410 1.460000e-14 91.6
28 TraesCS4B01G087100 chr3D 82.653 98 13 4 391 486 4173786 4173881 2.440000e-12 84.2


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 TraesCS4B01G087100 chr4B 87411502 87415316 3814 False 7046.0 7046 100.000000 1 3815 1 chr4B.!!$F1 3814
1 TraesCS4B01G087100 chr4D 58143843 58147643 3800 False 1268.5 3753 90.819250 365 3815 4 chr4D.!!$F1 3450
2 TraesCS4B01G087100 chr4A 537597202 537602560 5358 True 788.5 3310 91.322125 373 3452 8 chr4A.!!$R2 3079

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
966 2924 0.029163 TAGCCCCATTCCATCCTCCA 60.029 55.0 0.0 0.0 0.00 3.86 F
1874 3878 0.394899 CCATTCTGGCAACTCTCCCC 60.395 60.0 0.0 0.0 37.61 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 3984 0.034896 TCCTCTGCACCGGAAGAAAC 59.965 55.0 9.46 0.00 0.00 2.78 R
3035 5135 0.321122 CTGTGAGCTCACTGGGTTCC 60.321 60.0 38.81 17.32 46.55 3.62 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
38 39 4.773117 GACGTCGACCCGAGCCAC 62.773 72.222 10.58 0.00 36.23 5.01
41 42 4.131088 GTCGACCCGAGCCACCTC 62.131 72.222 3.51 0.00 36.23 3.85
49 50 4.719369 GAGCCACCTCGTTCGCGT 62.719 66.667 5.77 0.00 42.11 6.01
50 51 3.332493 GAGCCACCTCGTTCGCGTA 62.332 63.158 5.77 0.00 42.11 4.42
51 52 2.202703 GCCACCTCGTTCGCGTAT 60.203 61.111 5.77 0.00 42.11 3.06
54 55 0.179145 CCACCTCGTTCGCGTATTCT 60.179 55.000 5.77 0.00 42.11 2.40
55 56 1.625616 CACCTCGTTCGCGTATTCTT 58.374 50.000 5.77 0.00 42.11 2.52
56 57 1.320555 CACCTCGTTCGCGTATTCTTG 59.679 52.381 5.77 0.00 42.11 3.02
57 58 0.921347 CCTCGTTCGCGTATTCTTGG 59.079 55.000 5.77 0.00 42.11 3.61
58 59 1.468565 CCTCGTTCGCGTATTCTTGGA 60.469 52.381 5.77 0.00 42.11 3.53
61 62 1.641577 GTTCGCGTATTCTTGGAGCT 58.358 50.000 5.77 0.00 0.00 4.09
62 63 1.324736 GTTCGCGTATTCTTGGAGCTG 59.675 52.381 5.77 0.00 0.00 4.24
63 64 0.530744 TCGCGTATTCTTGGAGCTGT 59.469 50.000 5.77 0.00 0.00 4.40
64 65 0.647410 CGCGTATTCTTGGAGCTGTG 59.353 55.000 0.00 0.00 0.00 3.66
65 66 1.009829 GCGTATTCTTGGAGCTGTGG 58.990 55.000 0.00 0.00 0.00 4.17
66 67 1.009829 CGTATTCTTGGAGCTGTGGC 58.990 55.000 0.00 0.00 39.06 5.01
78 79 0.727398 GCTGTGGCTGGTCGATTTAC 59.273 55.000 0.00 0.00 35.22 2.01
79 80 1.943968 GCTGTGGCTGGTCGATTTACA 60.944 52.381 0.00 0.00 35.22 2.41
80 81 2.632377 CTGTGGCTGGTCGATTTACAT 58.368 47.619 0.00 0.00 0.00 2.29
81 82 2.352651 CTGTGGCTGGTCGATTTACATG 59.647 50.000 0.00 0.00 0.00 3.21
82 83 2.027653 TGTGGCTGGTCGATTTACATGA 60.028 45.455 0.00 0.00 0.00 3.07
84 85 3.438781 GTGGCTGGTCGATTTACATGAAA 59.561 43.478 0.00 0.00 0.00 2.69
85 86 4.096382 GTGGCTGGTCGATTTACATGAAAT 59.904 41.667 0.00 1.08 40.62 2.17
87 88 5.883115 TGGCTGGTCGATTTACATGAAATTA 59.117 36.000 0.00 0.00 37.90 1.40
88 89 6.375736 TGGCTGGTCGATTTACATGAAATTAA 59.624 34.615 0.00 0.00 37.90 1.40
89 90 7.068103 TGGCTGGTCGATTTACATGAAATTAAT 59.932 33.333 0.00 0.00 37.90 1.40
92 93 9.450807 CTGGTCGATTTACATGAAATTAATTCC 57.549 33.333 0.00 0.00 37.90 3.01
93 94 8.410141 TGGTCGATTTACATGAAATTAATTCCC 58.590 33.333 0.00 0.00 37.90 3.97
94 95 8.630037 GGTCGATTTACATGAAATTAATTCCCT 58.370 33.333 0.00 0.00 37.90 4.20
95 96 9.665264 GTCGATTTACATGAAATTAATTCCCTC 57.335 33.333 0.00 0.00 37.90 4.30
96 97 9.402320 TCGATTTACATGAAATTAATTCCCTCA 57.598 29.630 0.00 2.43 37.90 3.86
97 98 9.669353 CGATTTACATGAAATTAATTCCCTCAG 57.331 33.333 0.00 0.23 37.90 3.35
102 103 8.059798 ACATGAAATTAATTCCCTCAGTTCTG 57.940 34.615 0.00 0.70 37.22 3.02
103 104 7.123247 ACATGAAATTAATTCCCTCAGTTCTGG 59.877 37.037 0.00 0.00 37.22 3.86
104 105 6.552008 TGAAATTAATTCCCTCAGTTCTGGT 58.448 36.000 0.10 0.00 37.22 4.00
105 106 6.434028 TGAAATTAATTCCCTCAGTTCTGGTG 59.566 38.462 0.10 0.00 37.22 4.17
106 107 2.887151 AATTCCCTCAGTTCTGGTGG 57.113 50.000 0.00 3.54 0.00 4.61
107 108 0.329596 ATTCCCTCAGTTCTGGTGGC 59.670 55.000 0.00 0.00 0.00 5.01
108 109 1.059584 TTCCCTCAGTTCTGGTGGCA 61.060 55.000 0.00 0.00 0.00 4.92
109 110 1.059584 TCCCTCAGTTCTGGTGGCAA 61.060 55.000 0.00 0.00 0.00 4.52
110 111 0.178992 CCCTCAGTTCTGGTGGCAAA 60.179 55.000 0.00 0.00 0.00 3.68
114 115 4.385199 CCCTCAGTTCTGGTGGCAAATATA 60.385 45.833 0.00 0.00 0.00 0.86
116 117 5.829924 CCTCAGTTCTGGTGGCAAATATAAT 59.170 40.000 0.00 0.00 0.00 1.28
117 118 6.998074 CCTCAGTTCTGGTGGCAAATATAATA 59.002 38.462 0.00 0.00 0.00 0.98
118 119 7.041098 CCTCAGTTCTGGTGGCAAATATAATAC 60.041 40.741 0.00 0.00 0.00 1.89
119 120 7.342581 TCAGTTCTGGTGGCAAATATAATACA 58.657 34.615 0.00 0.00 0.00 2.29
120 121 7.282224 TCAGTTCTGGTGGCAAATATAATACAC 59.718 37.037 0.00 0.00 0.00 2.90
122 123 7.779798 AGTTCTGGTGGCAAATATAATACACAT 59.220 33.333 0.00 0.00 0.00 3.21
123 124 9.062524 GTTCTGGTGGCAAATATAATACACATA 57.937 33.333 0.00 0.00 0.00 2.29
146 147 9.481800 CATAATTCATATTGTTATGCACTAGCG 57.518 33.333 0.00 0.00 46.23 4.26
147 148 7.496529 AATTCATATTGTTATGCACTAGCGT 57.503 32.000 0.00 0.00 46.23 5.07
148 149 5.905480 TCATATTGTTATGCACTAGCGTG 57.095 39.130 0.00 0.00 46.23 5.34
149 150 5.356426 TCATATTGTTATGCACTAGCGTGT 58.644 37.500 0.00 0.00 46.23 4.49
150 151 6.508777 TCATATTGTTATGCACTAGCGTGTA 58.491 36.000 0.00 0.00 46.23 2.90
151 152 7.151976 TCATATTGTTATGCACTAGCGTGTAT 58.848 34.615 0.00 1.46 46.23 2.29
152 153 5.657470 ATTGTTATGCACTAGCGTGTATG 57.343 39.130 5.76 0.00 44.57 2.39
154 155 3.862845 TGTTATGCACTAGCGTGTATGTG 59.137 43.478 5.76 0.00 44.57 3.21
156 157 1.708822 TGCACTAGCGTGTATGTGTG 58.291 50.000 0.00 0.00 46.23 3.82
158 159 2.288518 TGCACTAGCGTGTATGTGTGAA 60.289 45.455 0.00 0.00 46.23 3.18
159 160 2.734606 GCACTAGCGTGTATGTGTGAAA 59.265 45.455 0.00 0.00 43.16 2.69
162 163 5.276395 GCACTAGCGTGTATGTGTGAAATAG 60.276 44.000 0.00 0.00 43.16 1.73
165 166 5.973651 AGCGTGTATGTGTGAAATAGATG 57.026 39.130 0.00 0.00 0.00 2.90
166 167 4.811024 AGCGTGTATGTGTGAAATAGATGG 59.189 41.667 0.00 0.00 0.00 3.51
167 168 4.808895 GCGTGTATGTGTGAAATAGATGGA 59.191 41.667 0.00 0.00 0.00 3.41
169 170 6.017934 GCGTGTATGTGTGAAATAGATGGATT 60.018 38.462 0.00 0.00 0.00 3.01
170 171 7.170828 GCGTGTATGTGTGAAATAGATGGATTA 59.829 37.037 0.00 0.00 0.00 1.75
171 172 9.208022 CGTGTATGTGTGAAATAGATGGATTAT 57.792 33.333 0.00 0.00 0.00 1.28
173 174 9.506018 TGTATGTGTGAAATAGATGGATTATGG 57.494 33.333 0.00 0.00 0.00 2.74
176 177 6.998074 TGTGTGAAATAGATGGATTATGGTCC 59.002 38.462 0.00 0.00 38.81 4.46
177 178 6.431234 GTGTGAAATAGATGGATTATGGTCCC 59.569 42.308 0.00 0.00 37.48 4.46
178 179 5.643777 GTGAAATAGATGGATTATGGTCCCG 59.356 44.000 0.00 0.00 37.48 5.14
179 180 5.309543 TGAAATAGATGGATTATGGTCCCGT 59.690 40.000 0.00 0.00 37.48 5.28
181 182 5.934402 ATAGATGGATTATGGTCCCGTAC 57.066 43.478 0.00 0.00 37.48 3.67
192 193 3.121738 GGTCCCGTACCCAATAAGATG 57.878 52.381 0.00 0.00 43.16 2.90
193 194 2.224450 GGTCCCGTACCCAATAAGATGG 60.224 54.545 0.00 0.00 43.16 3.51
194 195 2.701951 GTCCCGTACCCAATAAGATGGA 59.298 50.000 0.00 0.00 43.54 3.41
195 196 3.326880 GTCCCGTACCCAATAAGATGGAT 59.673 47.826 0.00 0.00 43.54 3.41
196 197 4.529377 GTCCCGTACCCAATAAGATGGATA 59.471 45.833 0.00 0.00 43.54 2.59
198 199 5.188948 TCCCGTACCCAATAAGATGGATATG 59.811 44.000 0.00 0.00 43.54 1.78
201 202 6.464222 CGTACCCAATAAGATGGATATGTGT 58.536 40.000 0.00 0.00 43.54 3.72
202 203 6.368791 CGTACCCAATAAGATGGATATGTGTG 59.631 42.308 0.00 0.00 43.54 3.82
203 204 6.266131 ACCCAATAAGATGGATATGTGTGT 57.734 37.500 0.00 0.00 43.54 3.72
204 205 6.064060 ACCCAATAAGATGGATATGTGTGTG 58.936 40.000 0.00 0.00 43.54 3.82
205 206 6.064060 CCCAATAAGATGGATATGTGTGTGT 58.936 40.000 0.00 0.00 43.54 3.72
206 207 6.016860 CCCAATAAGATGGATATGTGTGTGTG 60.017 42.308 0.00 0.00 43.54 3.82
207 208 6.543465 CCAATAAGATGGATATGTGTGTGTGT 59.457 38.462 0.00 0.00 43.54 3.72
208 209 7.067372 CCAATAAGATGGATATGTGTGTGTGTT 59.933 37.037 0.00 0.00 43.54 3.32
209 210 9.108284 CAATAAGATGGATATGTGTGTGTGTTA 57.892 33.333 0.00 0.00 0.00 2.41
210 211 8.893219 ATAAGATGGATATGTGTGTGTGTTAG 57.107 34.615 0.00 0.00 0.00 2.34
211 212 6.544928 AGATGGATATGTGTGTGTGTTAGA 57.455 37.500 0.00 0.00 0.00 2.10
213 214 5.993748 TGGATATGTGTGTGTGTTAGAGA 57.006 39.130 0.00 0.00 0.00 3.10
214 215 5.965922 TGGATATGTGTGTGTGTTAGAGAG 58.034 41.667 0.00 0.00 0.00 3.20
215 216 5.714806 TGGATATGTGTGTGTGTTAGAGAGA 59.285 40.000 0.00 0.00 0.00 3.10
216 217 6.127619 TGGATATGTGTGTGTGTTAGAGAGAG 60.128 42.308 0.00 0.00 0.00 3.20
217 218 6.095580 GGATATGTGTGTGTGTTAGAGAGAGA 59.904 42.308 0.00 0.00 0.00 3.10
218 219 4.837896 TGTGTGTGTGTTAGAGAGAGAG 57.162 45.455 0.00 0.00 0.00 3.20
219 220 3.570125 TGTGTGTGTGTTAGAGAGAGAGG 59.430 47.826 0.00 0.00 0.00 3.69
220 221 3.057174 GTGTGTGTGTTAGAGAGAGAGGG 60.057 52.174 0.00 0.00 0.00 4.30
222 223 3.442273 GTGTGTGTTAGAGAGAGAGGGAG 59.558 52.174 0.00 0.00 0.00 4.30
223 224 3.330998 TGTGTGTTAGAGAGAGAGGGAGA 59.669 47.826 0.00 0.00 0.00 3.71
224 225 3.945285 GTGTGTTAGAGAGAGAGGGAGAG 59.055 52.174 0.00 0.00 0.00 3.20
225 226 3.053991 TGTGTTAGAGAGAGAGGGAGAGG 60.054 52.174 0.00 0.00 0.00 3.69
226 227 2.512056 TGTTAGAGAGAGAGGGAGAGGG 59.488 54.545 0.00 0.00 0.00 4.30
227 228 1.827792 TAGAGAGAGAGGGAGAGGGG 58.172 60.000 0.00 0.00 0.00 4.79
228 229 0.998945 AGAGAGAGAGGGAGAGGGGG 60.999 65.000 0.00 0.00 0.00 5.40
231 232 1.059364 AGAGAGAGGGAGAGGGGGATA 60.059 57.143 0.00 0.00 0.00 2.59
232 233 1.357761 GAGAGAGGGAGAGGGGGATAG 59.642 61.905 0.00 0.00 0.00 2.08
235 236 1.059364 AGAGGGAGAGGGGGATAGAGA 60.059 57.143 0.00 0.00 0.00 3.10
236 237 1.357761 GAGGGAGAGGGGGATAGAGAG 59.642 61.905 0.00 0.00 0.00 3.20
237 238 1.163408 GGGAGAGGGGGATAGAGAGT 58.837 60.000 0.00 0.00 0.00 3.24
238 239 1.203125 GGGAGAGGGGGATAGAGAGTG 60.203 61.905 0.00 0.00 0.00 3.51
239 240 1.203125 GGAGAGGGGGATAGAGAGTGG 60.203 61.905 0.00 0.00 0.00 4.00
240 241 0.863956 AGAGGGGGATAGAGAGTGGG 59.136 60.000 0.00 0.00 0.00 4.61
242 243 0.633835 AGGGGGATAGAGAGTGGGGA 60.634 60.000 0.00 0.00 0.00 4.81
243 244 0.267960 GGGGGATAGAGAGTGGGGAA 59.732 60.000 0.00 0.00 0.00 3.97
244 245 1.723288 GGGGATAGAGAGTGGGGAAG 58.277 60.000 0.00 0.00 0.00 3.46
245 246 1.220750 GGGGATAGAGAGTGGGGAAGA 59.779 57.143 0.00 0.00 0.00 2.87
246 247 2.604139 GGGATAGAGAGTGGGGAAGAG 58.396 57.143 0.00 0.00 0.00 2.85
248 249 2.604139 GATAGAGAGTGGGGAAGAGGG 58.396 57.143 0.00 0.00 0.00 4.30
249 250 1.695065 TAGAGAGTGGGGAAGAGGGA 58.305 55.000 0.00 0.00 0.00 4.20
250 251 0.338120 AGAGAGTGGGGAAGAGGGAG 59.662 60.000 0.00 0.00 0.00 4.30
251 252 0.689412 GAGAGTGGGGAAGAGGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
252 253 1.690985 GAGTGGGGAAGAGGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
253 254 2.182858 GAGTGGGGAAGAGGGAGGGA 62.183 65.000 0.00 0.00 0.00 4.20
254 255 1.690985 GTGGGGAAGAGGGAGGGAG 60.691 68.421 0.00 0.00 0.00 4.30
255 256 1.866997 TGGGGAAGAGGGAGGGAGA 60.867 63.158 0.00 0.00 0.00 3.71
256 257 1.074850 GGGGAAGAGGGAGGGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
258 259 0.689412 GGGAAGAGGGAGGGAGAGTG 60.689 65.000 0.00 0.00 0.00 3.51
259 260 0.041982 GGAAGAGGGAGGGAGAGTGT 59.958 60.000 0.00 0.00 0.00 3.55
260 261 1.190643 GAAGAGGGAGGGAGAGTGTG 58.809 60.000 0.00 0.00 0.00 3.82
262 263 0.252012 AGAGGGAGGGAGAGTGTGTG 60.252 60.000 0.00 0.00 0.00 3.82
265 266 1.122019 GGGAGGGAGAGTGTGTGTGT 61.122 60.000 0.00 0.00 0.00 3.72
267 268 0.601311 GAGGGAGAGTGTGTGTGTGC 60.601 60.000 0.00 0.00 0.00 4.57
269 270 1.227263 GGAGAGTGTGTGTGTGCGT 60.227 57.895 0.00 0.00 0.00 5.24
270 271 1.490693 GGAGAGTGTGTGTGTGCGTG 61.491 60.000 0.00 0.00 0.00 5.34
272 273 0.528466 AGAGTGTGTGTGTGCGTGAG 60.528 55.000 0.00 0.00 0.00 3.51
274 275 1.520564 GTGTGTGTGTGCGTGAGGA 60.521 57.895 0.00 0.00 0.00 3.71
276 277 0.179059 TGTGTGTGTGCGTGAGGATT 60.179 50.000 0.00 0.00 0.00 3.01
277 278 0.944386 GTGTGTGTGCGTGAGGATTT 59.056 50.000 0.00 0.00 0.00 2.17
278 279 0.943673 TGTGTGTGCGTGAGGATTTG 59.056 50.000 0.00 0.00 0.00 2.32
279 280 1.225855 GTGTGTGCGTGAGGATTTGA 58.774 50.000 0.00 0.00 0.00 2.69
280 281 1.806542 GTGTGTGCGTGAGGATTTGAT 59.193 47.619 0.00 0.00 0.00 2.57
281 282 1.805943 TGTGTGCGTGAGGATTTGATG 59.194 47.619 0.00 0.00 0.00 3.07
282 283 1.131126 GTGTGCGTGAGGATTTGATGG 59.869 52.381 0.00 0.00 0.00 3.51
283 284 1.271325 TGTGCGTGAGGATTTGATGGT 60.271 47.619 0.00 0.00 0.00 3.55
285 286 3.006940 GTGCGTGAGGATTTGATGGTAA 58.993 45.455 0.00 0.00 0.00 2.85
286 287 3.438781 GTGCGTGAGGATTTGATGGTAAA 59.561 43.478 0.00 0.00 0.00 2.01
287 288 4.075682 TGCGTGAGGATTTGATGGTAAAA 58.924 39.130 0.00 0.00 0.00 1.52
288 289 4.520874 TGCGTGAGGATTTGATGGTAAAAA 59.479 37.500 0.00 0.00 0.00 1.94
307 308 5.934935 AAAAAGGTCGTCAATGTCGTAAT 57.065 34.783 0.00 0.00 0.00 1.89
310 311 7.605410 AAAAGGTCGTCAATGTCGTAATATT 57.395 32.000 0.00 0.00 0.00 1.28
311 312 6.583912 AAGGTCGTCAATGTCGTAATATTG 57.416 37.500 0.00 0.00 35.84 1.90
312 313 5.898174 AGGTCGTCAATGTCGTAATATTGA 58.102 37.500 0.00 0.00 39.73 2.57
313 314 6.334989 AGGTCGTCAATGTCGTAATATTGAA 58.665 36.000 0.00 0.00 42.44 2.69
314 315 6.255020 AGGTCGTCAATGTCGTAATATTGAAC 59.745 38.462 0.00 0.00 42.44 3.18
316 317 7.328112 GTCGTCAATGTCGTAATATTGAACTC 58.672 38.462 0.00 0.00 42.44 3.01
318 319 7.758076 TCGTCAATGTCGTAATATTGAACTCTT 59.242 33.333 0.00 0.00 42.44 2.85
319 320 9.016623 CGTCAATGTCGTAATATTGAACTCTTA 57.983 33.333 0.00 0.00 42.44 2.10
334 335 5.977489 AACTCTTAAAGTTAATGTGGCCC 57.023 39.130 0.00 0.00 46.55 5.80
335 336 4.341487 ACTCTTAAAGTTAATGTGGCCCC 58.659 43.478 0.00 0.00 33.03 5.80
337 338 2.883122 TAAAGTTAATGTGGCCCCGT 57.117 45.000 0.00 0.00 0.00 5.28
339 340 1.253100 AAGTTAATGTGGCCCCGTTG 58.747 50.000 0.00 0.00 0.00 4.10
340 341 1.214325 GTTAATGTGGCCCCGTTGC 59.786 57.895 0.00 0.00 0.00 4.17
341 342 1.228583 TTAATGTGGCCCCGTTGCA 60.229 52.632 0.00 0.00 0.00 4.08
342 343 0.827925 TTAATGTGGCCCCGTTGCAA 60.828 50.000 0.00 0.00 0.00 4.08
343 344 1.528292 TAATGTGGCCCCGTTGCAAC 61.528 55.000 19.89 19.89 35.65 4.17
367 368 1.689813 TGGGCGTTCTTCTAGTGTGAA 59.310 47.619 0.00 0.00 0.00 3.18
376 377 7.218583 GCGTTCTTCTAGTGTGAAGTTAGATAC 59.781 40.741 0.00 0.00 42.76 2.24
386 1770 6.311690 GTGTGAAGTTAGATACTCTCTTTGGC 59.688 42.308 0.00 0.00 35.54 4.52
606 1995 7.974501 AGTACACATCTGTAAAGAAATACTCCG 59.025 37.037 0.00 0.00 34.53 4.63
608 1997 7.833786 ACACATCTGTAAAGAAATACTCCGTA 58.166 34.615 0.00 0.00 0.00 4.02
609 1998 8.475639 ACACATCTGTAAAGAAATACTCCGTAT 58.524 33.333 0.00 0.00 0.00 3.06
611 2000 8.692710 ACATCTGTAAAGAAATACTCCGTATGA 58.307 33.333 0.00 0.00 0.00 2.15
613 2002 8.515695 TCTGTAAAGAAATACTCCGTATGAGA 57.484 34.615 0.00 0.00 44.42 3.27
614 2003 9.132923 TCTGTAAAGAAATACTCCGTATGAGAT 57.867 33.333 0.00 0.00 44.42 2.75
615 2004 9.751542 CTGTAAAGAAATACTCCGTATGAGATT 57.248 33.333 0.00 0.00 44.42 2.40
824 2539 1.153449 GTCGTCATCGGCCCAATCA 60.153 57.895 0.00 0.00 35.48 2.57
845 2565 3.919804 CACCGTTACAGCAAATTGAATGG 59.080 43.478 0.00 0.00 33.25 3.16
879 2599 0.376152 TTACGGACGCAGATCTCGAC 59.624 55.000 17.60 12.61 0.00 4.20
885 2606 2.418910 CGCAGATCTCGACACCCCT 61.419 63.158 8.35 0.00 0.00 4.79
887 2608 1.040339 GCAGATCTCGACACCCCTCT 61.040 60.000 0.00 0.00 0.00 3.69
890 2611 0.106419 GATCTCGACACCCCTCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
909 2867 0.681564 TCTCTCCTCCAACGGCTCTC 60.682 60.000 0.00 0.00 0.00 3.20
910 2868 0.682855 CTCTCCTCCAACGGCTCTCT 60.683 60.000 0.00 0.00 0.00 3.10
911 2869 0.681564 TCTCCTCCAACGGCTCTCTC 60.682 60.000 0.00 0.00 0.00 3.20
949 2907 1.432514 CGATGACATCGCCCCATTAG 58.567 55.000 23.70 0.00 46.55 1.73
966 2924 0.029163 TAGCCCCATTCCATCCTCCA 60.029 55.000 0.00 0.00 0.00 3.86
1019 2993 1.762522 ATGCCGAGGCCATACTCCAG 61.763 60.000 12.05 0.00 41.09 3.86
1206 3180 1.380515 CTTCCTCCTCTCCTCCGCA 60.381 63.158 0.00 0.00 0.00 5.69
1321 3295 1.880340 CGTCTGCCGGATCAAGAGC 60.880 63.158 5.05 0.00 0.00 4.09
1874 3878 0.394899 CCATTCTGGCAACTCTCCCC 60.395 60.000 0.00 0.00 37.61 4.81
1875 3879 0.745845 CATTCTGGCAACTCTCCCCG 60.746 60.000 0.00 0.00 37.61 5.73
1876 3880 1.915078 ATTCTGGCAACTCTCCCCGG 61.915 60.000 0.00 0.00 37.61 5.73
1877 3881 3.003173 CTGGCAACTCTCCCCGGA 61.003 66.667 0.73 0.00 37.61 5.14
1878 3882 3.316573 CTGGCAACTCTCCCCGGAC 62.317 68.421 0.73 0.00 37.61 4.79
1879 3883 3.003763 GGCAACTCTCCCCGGACT 61.004 66.667 0.73 0.00 0.00 3.85
1880 3884 2.266055 GCAACTCTCCCCGGACTG 59.734 66.667 0.73 0.00 0.00 3.51
1881 3885 2.266055 CAACTCTCCCCGGACTGC 59.734 66.667 0.73 0.00 0.00 4.40
1882 3886 2.203788 AACTCTCCCCGGACTGCA 60.204 61.111 0.73 0.00 0.00 4.41
1920 3933 1.599576 GGTCCTTGGAGGTCTGCTC 59.400 63.158 0.00 0.00 36.53 4.26
1992 4005 2.125912 CTTCCGGTGCAGAGGACG 60.126 66.667 9.42 4.74 36.06 4.79
2039 4052 4.253685 CCCTTCTCGCTTATTGTGAAGAA 58.746 43.478 0.00 0.00 37.03 2.52
2160 4173 3.476552 TGGTGAGTCATGGTCTGAAAAC 58.523 45.455 0.00 0.00 35.07 2.43
2178 4191 2.908940 GGCAGCACAGGCAAGTGT 60.909 61.111 11.00 0.00 44.61 3.55
2268 4281 1.360393 TGAGTTTGTCCCCAAGGCCT 61.360 55.000 0.00 0.00 0.00 5.19
2358 4371 1.082756 GTTTGCTGGTGCTTCGACG 60.083 57.895 0.00 0.00 40.48 5.12
2532 4545 2.228545 TGGATTGCTGCCAATGGTTA 57.771 45.000 0.00 0.00 41.60 2.85
2591 4604 2.125269 GGCGTTGCCCGATACAGT 60.125 61.111 0.00 0.00 44.06 3.55
2640 4653 2.502295 CAGGAGGATAGCAAGCAATCC 58.498 52.381 0.00 0.00 41.77 3.01
2700 4716 7.502561 GGTGGATTAAATTATGACAGTAAGGCT 59.497 37.037 0.00 0.00 0.00 4.58
2721 4737 4.504340 GCTACTCCAAACCCTGTTCAAGTA 60.504 45.833 0.00 0.00 0.00 2.24
2932 5031 7.420913 CCCTCCCAGCCTTGTATACTTATTTTA 60.421 40.741 4.17 0.00 0.00 1.52
3035 5135 9.956720 GAATATAATCACTCCTGGTTCATTTTG 57.043 33.333 0.00 0.00 0.00 2.44
3064 5164 3.570559 GTGAGCTCACAGTTCAGAGTAC 58.429 50.000 36.23 9.03 45.75 2.73
3131 5239 4.992381 ATTCTTCTGAACAAGTACGCAC 57.008 40.909 0.00 0.00 34.71 5.34
3132 5240 2.390938 TCTTCTGAACAAGTACGCACG 58.609 47.619 0.00 0.00 0.00 5.34
3305 5540 1.952296 GACAGACATGCATTGGGATCC 59.048 52.381 1.92 1.92 0.00 3.36
3306 5541 0.949397 CAGACATGCATTGGGATCCG 59.051 55.000 5.45 0.00 0.00 4.18
3307 5542 0.179009 AGACATGCATTGGGATCCGG 60.179 55.000 5.45 0.00 0.00 5.14
3308 5543 1.152694 ACATGCATTGGGATCCGGG 60.153 57.895 5.45 0.00 0.00 5.73
3309 5544 1.151221 CATGCATTGGGATCCGGGA 59.849 57.895 5.45 0.00 0.00 5.14
3310 5545 0.892358 CATGCATTGGGATCCGGGAG 60.892 60.000 5.45 0.00 0.00 4.30
3341 5576 1.003233 AGGCGCCTTGAGGTTTCTC 60.003 57.895 27.08 0.00 40.36 2.87
3476 5747 4.094739 TGATGATGTGCAGAAATTGTACGG 59.905 41.667 0.00 0.00 44.39 4.02
3479 5750 1.876799 TGTGCAGAAATTGTACGGTGG 59.123 47.619 0.00 0.00 44.39 4.61
3491 5762 0.398696 TACGGTGGTTTGCATCAGGT 59.601 50.000 0.00 0.00 0.00 4.00
3532 5804 4.316205 ACGGACAAATTTGACCCTTTTC 57.684 40.909 26.80 12.51 39.36 2.29
3575 5847 5.844301 AATCAAATCCGCACAAAATTCAC 57.156 34.783 0.00 0.00 0.00 3.18
3586 5858 4.815846 GCACAAAATTCACAAAATGACCCT 59.184 37.500 0.00 0.00 36.92 4.34
3589 5861 7.628153 GCACAAAATTCACAAAATGACCCTTTT 60.628 33.333 0.00 0.00 36.92 2.27
3592 5864 9.108284 CAAAATTCACAAAATGACCCTTTTACT 57.892 29.630 0.00 0.00 36.92 2.24
3595 5867 5.369833 TCACAAAATGACCCTTTTACTCGA 58.630 37.500 0.00 0.00 29.99 4.04
3600 5872 0.738762 GACCCTTTTACTCGACGCCC 60.739 60.000 0.00 0.00 0.00 6.13
3632 5918 2.285969 ATGCTCCTGGCCTGAGGT 60.286 61.111 20.12 0.00 40.92 3.85
3633 5919 2.677289 ATGCTCCTGGCCTGAGGTG 61.677 63.158 20.12 13.95 40.92 4.00
3634 5920 3.325753 GCTCCTGGCCTGAGGTGT 61.326 66.667 20.12 0.00 34.36 4.16
3685 5971 1.959042 AAGGGCGTCAATGCTATCTG 58.041 50.000 0.00 0.00 34.52 2.90
3689 5975 0.305922 GCGTCAATGCTATCTGGCAC 59.694 55.000 0.00 0.00 45.36 5.01
3799 6085 5.551233 AGATCAAATCTGTCCGTTTTCTCA 58.449 37.500 0.00 0.00 38.44 3.27
3805 6091 3.601435 TCTGTCCGTTTTCTCACACAAA 58.399 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.773117 GTGGCTCGGGTCGACGTC 62.773 72.222 9.92 5.18 34.94 4.34
24 25 4.131088 GAGGTGGCTCGGGTCGAC 62.131 72.222 7.13 7.13 0.00 4.20
32 33 2.609183 ATACGCGAACGAGGTGGCTC 62.609 60.000 15.93 0.00 43.93 4.70
33 34 2.221906 AATACGCGAACGAGGTGGCT 62.222 55.000 15.93 0.00 43.93 4.75
34 35 1.749609 GAATACGCGAACGAGGTGGC 61.750 60.000 15.93 0.00 43.93 5.01
35 36 0.179145 AGAATACGCGAACGAGGTGG 60.179 55.000 15.93 0.00 43.93 4.61
36 37 1.320555 CAAGAATACGCGAACGAGGTG 59.679 52.381 15.93 0.00 43.93 4.00
37 38 1.625616 CAAGAATACGCGAACGAGGT 58.374 50.000 15.93 0.00 43.93 3.85
38 39 0.921347 CCAAGAATACGCGAACGAGG 59.079 55.000 15.93 1.32 43.93 4.63
39 40 1.846782 CTCCAAGAATACGCGAACGAG 59.153 52.381 15.93 1.74 43.93 4.18
42 43 1.324736 CAGCTCCAAGAATACGCGAAC 59.675 52.381 15.93 0.24 0.00 3.95
43 44 1.067142 ACAGCTCCAAGAATACGCGAA 60.067 47.619 15.93 0.00 0.00 4.70
44 45 0.530744 ACAGCTCCAAGAATACGCGA 59.469 50.000 15.93 0.00 0.00 5.87
45 46 0.647410 CACAGCTCCAAGAATACGCG 59.353 55.000 3.53 3.53 0.00 6.01
46 47 1.009829 CCACAGCTCCAAGAATACGC 58.990 55.000 0.00 0.00 0.00 4.42
47 48 1.009829 GCCACAGCTCCAAGAATACG 58.990 55.000 0.00 0.00 35.50 3.06
61 62 2.027653 TCATGTAAATCGACCAGCCACA 60.028 45.455 0.00 0.00 0.00 4.17
62 63 2.627945 TCATGTAAATCGACCAGCCAC 58.372 47.619 0.00 0.00 0.00 5.01
63 64 3.342377 TTCATGTAAATCGACCAGCCA 57.658 42.857 0.00 0.00 0.00 4.75
64 65 4.900635 ATTTCATGTAAATCGACCAGCC 57.099 40.909 0.00 0.00 32.00 4.85
65 66 8.856490 AATTAATTTCATGTAAATCGACCAGC 57.144 30.769 0.00 0.00 36.76 4.85
66 67 9.450807 GGAATTAATTTCATGTAAATCGACCAG 57.549 33.333 1.43 0.00 36.76 4.00
67 68 8.410141 GGGAATTAATTTCATGTAAATCGACCA 58.590 33.333 8.74 0.00 36.76 4.02
68 69 8.630037 AGGGAATTAATTTCATGTAAATCGACC 58.370 33.333 8.74 0.00 36.76 4.79
70 71 9.402320 TGAGGGAATTAATTTCATGTAAATCGA 57.598 29.630 8.74 0.00 36.76 3.59
71 72 9.669353 CTGAGGGAATTAATTTCATGTAAATCG 57.331 33.333 8.74 0.00 36.76 3.34
75 76 9.753674 AGAACTGAGGGAATTAATTTCATGTAA 57.246 29.630 8.74 0.00 35.94 2.41
78 79 7.123247 ACCAGAACTGAGGGAATTAATTTCATG 59.877 37.037 8.74 1.95 35.94 3.07
79 80 7.123247 CACCAGAACTGAGGGAATTAATTTCAT 59.877 37.037 8.74 0.56 35.94 2.57
80 81 6.434028 CACCAGAACTGAGGGAATTAATTTCA 59.566 38.462 8.74 5.07 35.94 2.69
81 82 6.127619 CCACCAGAACTGAGGGAATTAATTTC 60.128 42.308 1.43 0.00 0.00 2.17
82 83 5.716703 CCACCAGAACTGAGGGAATTAATTT 59.283 40.000 1.43 0.00 0.00 1.82
84 85 4.860022 CCACCAGAACTGAGGGAATTAAT 58.140 43.478 3.19 0.00 0.00 1.40
85 86 3.561313 GCCACCAGAACTGAGGGAATTAA 60.561 47.826 13.11 0.00 0.00 1.40
87 88 1.272147 GCCACCAGAACTGAGGGAATT 60.272 52.381 13.11 0.00 0.00 2.17
88 89 0.329596 GCCACCAGAACTGAGGGAAT 59.670 55.000 13.11 0.00 0.00 3.01
89 90 1.059584 TGCCACCAGAACTGAGGGAA 61.060 55.000 13.11 3.14 0.00 3.97
92 93 1.915141 ATTTGCCACCAGAACTGAGG 58.085 50.000 3.19 6.21 0.00 3.86
93 94 6.949352 ATTATATTTGCCACCAGAACTGAG 57.051 37.500 3.19 0.00 0.00 3.35
94 95 7.282224 GTGTATTATATTTGCCACCAGAACTGA 59.718 37.037 3.19 0.00 0.00 3.41
95 96 7.066887 TGTGTATTATATTTGCCACCAGAACTG 59.933 37.037 0.00 0.00 0.00 3.16
96 97 7.116075 TGTGTATTATATTTGCCACCAGAACT 58.884 34.615 0.00 0.00 0.00 3.01
97 98 7.328277 TGTGTATTATATTTGCCACCAGAAC 57.672 36.000 0.00 0.00 0.00 3.01
98 99 9.634021 TTATGTGTATTATATTTGCCACCAGAA 57.366 29.630 0.00 0.00 0.00 3.02
99 100 9.806448 ATTATGTGTATTATATTTGCCACCAGA 57.194 29.630 0.00 0.00 0.00 3.86
120 121 9.481800 CGCTAGTGCATAACAATATGAATTATG 57.518 33.333 0.00 8.50 41.25 1.90
122 123 8.495148 CACGCTAGTGCATAACAATATGAATTA 58.505 33.333 2.40 0.00 41.94 1.40
123 124 7.355017 CACGCTAGTGCATAACAATATGAATT 58.645 34.615 2.40 0.00 41.94 2.17
126 127 5.905480 CACGCTAGTGCATAACAATATGA 57.095 39.130 2.40 0.00 41.94 2.15
140 141 6.203808 TCTATTTCACACATACACGCTAGT 57.796 37.500 0.00 0.00 0.00 2.57
141 142 6.144563 CCATCTATTTCACACATACACGCTAG 59.855 42.308 0.00 0.00 0.00 3.42
142 143 5.983118 CCATCTATTTCACACATACACGCTA 59.017 40.000 0.00 0.00 0.00 4.26
143 144 4.811024 CCATCTATTTCACACATACACGCT 59.189 41.667 0.00 0.00 0.00 5.07
144 145 4.808895 TCCATCTATTTCACACATACACGC 59.191 41.667 0.00 0.00 0.00 5.34
145 146 7.482654 AATCCATCTATTTCACACATACACG 57.517 36.000 0.00 0.00 0.00 4.49
147 148 9.506018 CCATAATCCATCTATTTCACACATACA 57.494 33.333 0.00 0.00 0.00 2.29
148 149 9.507329 ACCATAATCCATCTATTTCACACATAC 57.493 33.333 0.00 0.00 0.00 2.39
149 150 9.725019 GACCATAATCCATCTATTTCACACATA 57.275 33.333 0.00 0.00 0.00 2.29
150 151 7.667219 GGACCATAATCCATCTATTTCACACAT 59.333 37.037 0.00 0.00 38.77 3.21
151 152 6.998074 GGACCATAATCCATCTATTTCACACA 59.002 38.462 0.00 0.00 38.77 3.72
152 153 6.431234 GGGACCATAATCCATCTATTTCACAC 59.569 42.308 0.00 0.00 40.96 3.82
154 155 5.643777 CGGGACCATAATCCATCTATTTCAC 59.356 44.000 0.00 0.00 40.96 3.18
156 157 5.805728 ACGGGACCATAATCCATCTATTTC 58.194 41.667 0.00 0.00 40.96 2.17
158 159 6.295719 GTACGGGACCATAATCCATCTATT 57.704 41.667 0.00 0.00 40.96 1.73
159 160 5.934402 GTACGGGACCATAATCCATCTAT 57.066 43.478 0.00 0.00 40.96 1.98
173 174 2.701951 TCCATCTTATTGGGTACGGGAC 59.298 50.000 0.00 0.00 37.37 4.46
176 177 5.874810 CACATATCCATCTTATTGGGTACGG 59.125 44.000 0.00 0.00 35.20 4.02
177 178 6.368791 CACACATATCCATCTTATTGGGTACG 59.631 42.308 0.00 0.00 35.20 3.67
178 179 7.173218 CACACACATATCCATCTTATTGGGTAC 59.827 40.741 0.00 0.00 35.20 3.34
179 180 7.147391 ACACACACATATCCATCTTATTGGGTA 60.147 37.037 0.00 0.00 36.79 3.69
181 182 6.016860 CACACACACATATCCATCTTATTGGG 60.017 42.308 0.00 0.00 37.37 4.12
182 183 6.543465 ACACACACACATATCCATCTTATTGG 59.457 38.462 0.00 0.00 38.18 3.16
183 184 7.558161 ACACACACACATATCCATCTTATTG 57.442 36.000 0.00 0.00 0.00 1.90
188 189 6.381133 TCTCTAACACACACACATATCCATCT 59.619 38.462 0.00 0.00 0.00 2.90
189 190 6.573434 TCTCTAACACACACACATATCCATC 58.427 40.000 0.00 0.00 0.00 3.51
190 191 6.381133 TCTCTCTAACACACACACATATCCAT 59.619 38.462 0.00 0.00 0.00 3.41
191 192 5.714806 TCTCTCTAACACACACACATATCCA 59.285 40.000 0.00 0.00 0.00 3.41
192 193 6.095580 TCTCTCTCTAACACACACACATATCC 59.904 42.308 0.00 0.00 0.00 2.59
193 194 7.089770 TCTCTCTCTAACACACACACATATC 57.910 40.000 0.00 0.00 0.00 1.63
194 195 6.096141 CCTCTCTCTCTAACACACACACATAT 59.904 42.308 0.00 0.00 0.00 1.78
195 196 5.416013 CCTCTCTCTCTAACACACACACATA 59.584 44.000 0.00 0.00 0.00 2.29
196 197 4.219507 CCTCTCTCTCTAACACACACACAT 59.780 45.833 0.00 0.00 0.00 3.21
198 199 3.057174 CCCTCTCTCTCTAACACACACAC 60.057 52.174 0.00 0.00 0.00 3.82
201 202 3.330998 TCTCCCTCTCTCTCTAACACACA 59.669 47.826 0.00 0.00 0.00 3.72
202 203 3.945285 CTCTCCCTCTCTCTCTAACACAC 59.055 52.174 0.00 0.00 0.00 3.82
203 204 3.053991 CCTCTCCCTCTCTCTCTAACACA 60.054 52.174 0.00 0.00 0.00 3.72
204 205 3.551846 CCTCTCCCTCTCTCTCTAACAC 58.448 54.545 0.00 0.00 0.00 3.32
205 206 2.512056 CCCTCTCCCTCTCTCTCTAACA 59.488 54.545 0.00 0.00 0.00 2.41
206 207 2.158519 CCCCTCTCCCTCTCTCTCTAAC 60.159 59.091 0.00 0.00 0.00 2.34
207 208 2.140224 CCCCTCTCCCTCTCTCTCTAA 58.860 57.143 0.00 0.00 0.00 2.10
208 209 1.700907 CCCCCTCTCCCTCTCTCTCTA 60.701 61.905 0.00 0.00 0.00 2.43
209 210 0.998945 CCCCCTCTCCCTCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
210 211 0.996762 TCCCCCTCTCCCTCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
211 212 0.330431 ATCCCCCTCTCCCTCTCTCT 60.330 60.000 0.00 0.00 0.00 3.10
213 214 1.059364 TCTATCCCCCTCTCCCTCTCT 60.059 57.143 0.00 0.00 0.00 3.10
214 215 1.357761 CTCTATCCCCCTCTCCCTCTC 59.642 61.905 0.00 0.00 0.00 3.20
215 216 1.059364 TCTCTATCCCCCTCTCCCTCT 60.059 57.143 0.00 0.00 0.00 3.69
216 217 1.357761 CTCTCTATCCCCCTCTCCCTC 59.642 61.905 0.00 0.00 0.00 4.30
217 218 1.348160 ACTCTCTATCCCCCTCTCCCT 60.348 57.143 0.00 0.00 0.00 4.20
218 219 1.163408 ACTCTCTATCCCCCTCTCCC 58.837 60.000 0.00 0.00 0.00 4.30
219 220 1.203125 CCACTCTCTATCCCCCTCTCC 60.203 61.905 0.00 0.00 0.00 3.71
220 221 1.203125 CCCACTCTCTATCCCCCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
222 223 0.178918 CCCCACTCTCTATCCCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
223 224 0.633835 TCCCCACTCTCTATCCCCCT 60.634 60.000 0.00 0.00 0.00 4.79
224 225 0.267960 TTCCCCACTCTCTATCCCCC 59.732 60.000 0.00 0.00 0.00 5.40
225 226 1.220750 TCTTCCCCACTCTCTATCCCC 59.779 57.143 0.00 0.00 0.00 4.81
226 227 2.604139 CTCTTCCCCACTCTCTATCCC 58.396 57.143 0.00 0.00 0.00 3.85
227 228 2.604139 CCTCTTCCCCACTCTCTATCC 58.396 57.143 0.00 0.00 0.00 2.59
228 229 2.178106 TCCCTCTTCCCCACTCTCTATC 59.822 54.545 0.00 0.00 0.00 2.08
231 232 0.338120 CTCCCTCTTCCCCACTCTCT 59.662 60.000 0.00 0.00 0.00 3.10
232 233 0.689412 CCTCCCTCTTCCCCACTCTC 60.689 65.000 0.00 0.00 0.00 3.20
235 236 2.184631 TCCCTCCCTCTTCCCCACT 61.185 63.158 0.00 0.00 0.00 4.00
236 237 1.690985 CTCCCTCCCTCTTCCCCAC 60.691 68.421 0.00 0.00 0.00 4.61
237 238 1.866997 TCTCCCTCCCTCTTCCCCA 60.867 63.158 0.00 0.00 0.00 4.96
238 239 1.074850 CTCTCCCTCCCTCTTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
239 240 0.689412 CACTCTCCCTCCCTCTTCCC 60.689 65.000 0.00 0.00 0.00 3.97
240 241 0.041982 ACACTCTCCCTCCCTCTTCC 59.958 60.000 0.00 0.00 0.00 3.46
242 243 0.489567 ACACACTCTCCCTCCCTCTT 59.510 55.000 0.00 0.00 0.00 2.85
243 244 0.252012 CACACACTCTCCCTCCCTCT 60.252 60.000 0.00 0.00 0.00 3.69
244 245 0.543174 ACACACACTCTCCCTCCCTC 60.543 60.000 0.00 0.00 0.00 4.30
245 246 0.833834 CACACACACTCTCCCTCCCT 60.834 60.000 0.00 0.00 0.00 4.20
246 247 1.122019 ACACACACACTCTCCCTCCC 61.122 60.000 0.00 0.00 0.00 4.30
248 249 0.601311 GCACACACACACTCTCCCTC 60.601 60.000 0.00 0.00 0.00 4.30
249 250 1.447643 GCACACACACACTCTCCCT 59.552 57.895 0.00 0.00 0.00 4.20
250 251 1.956170 CGCACACACACACTCTCCC 60.956 63.158 0.00 0.00 0.00 4.30
251 252 1.227263 ACGCACACACACACTCTCC 60.227 57.895 0.00 0.00 0.00 3.71
252 253 0.527600 TCACGCACACACACACTCTC 60.528 55.000 0.00 0.00 0.00 3.20
253 254 0.528466 CTCACGCACACACACACTCT 60.528 55.000 0.00 0.00 0.00 3.24
254 255 1.490693 CCTCACGCACACACACACTC 61.491 60.000 0.00 0.00 0.00 3.51
255 256 1.521457 CCTCACGCACACACACACT 60.521 57.895 0.00 0.00 0.00 3.55
256 257 0.880278 ATCCTCACGCACACACACAC 60.880 55.000 0.00 0.00 0.00 3.82
258 259 0.944386 AAATCCTCACGCACACACAC 59.056 50.000 0.00 0.00 0.00 3.82
259 260 0.943673 CAAATCCTCACGCACACACA 59.056 50.000 0.00 0.00 0.00 3.72
260 261 1.225855 TCAAATCCTCACGCACACAC 58.774 50.000 0.00 0.00 0.00 3.82
262 263 1.131126 CCATCAAATCCTCACGCACAC 59.869 52.381 0.00 0.00 0.00 3.82
265 266 3.342377 TTACCATCAAATCCTCACGCA 57.658 42.857 0.00 0.00 0.00 5.24
285 286 5.934935 ATTACGACATTGACGACCTTTTT 57.065 34.783 15.06 0.00 34.70 1.94
286 287 7.332430 TCAATATTACGACATTGACGACCTTTT 59.668 33.333 15.06 1.42 36.49 2.27
287 288 6.814644 TCAATATTACGACATTGACGACCTTT 59.185 34.615 15.06 0.00 36.49 3.11
288 289 6.334989 TCAATATTACGACATTGACGACCTT 58.665 36.000 15.06 0.00 36.49 3.50
289 290 5.898174 TCAATATTACGACATTGACGACCT 58.102 37.500 15.06 2.07 36.49 3.85
290 291 6.255020 AGTTCAATATTACGACATTGACGACC 59.745 38.462 15.06 0.00 40.06 4.79
291 292 7.218145 AGTTCAATATTACGACATTGACGAC 57.782 36.000 15.06 0.19 40.06 4.34
292 293 7.255569 AGAGTTCAATATTACGACATTGACGA 58.744 34.615 15.06 0.00 40.06 4.20
293 294 7.451281 AGAGTTCAATATTACGACATTGACG 57.549 36.000 6.97 6.97 40.06 4.35
307 308 8.736244 GGCCACATTAACTTTAAGAGTTCAATA 58.264 33.333 0.00 0.00 45.40 1.90
310 311 5.475564 GGGCCACATTAACTTTAAGAGTTCA 59.524 40.000 4.39 0.00 45.40 3.18
311 312 5.105877 GGGGCCACATTAACTTTAAGAGTTC 60.106 44.000 4.39 0.00 45.40 3.01
313 314 4.341487 GGGGCCACATTAACTTTAAGAGT 58.659 43.478 4.39 0.00 41.47 3.24
314 315 3.377172 CGGGGCCACATTAACTTTAAGAG 59.623 47.826 5.46 0.00 0.00 2.85
316 317 3.086282 ACGGGGCCACATTAACTTTAAG 58.914 45.455 5.46 0.00 0.00 1.85
318 319 2.820787 CAACGGGGCCACATTAACTTTA 59.179 45.455 5.46 0.00 0.00 1.85
319 320 1.616374 CAACGGGGCCACATTAACTTT 59.384 47.619 5.46 0.00 0.00 2.66
321 322 1.248101 GCAACGGGGCCACATTAACT 61.248 55.000 5.46 0.00 0.00 2.24
322 323 1.214325 GCAACGGGGCCACATTAAC 59.786 57.895 5.46 0.00 0.00 2.01
323 324 0.827925 TTGCAACGGGGCCACATTAA 60.828 50.000 5.46 0.00 0.00 1.40
325 326 2.522923 TTGCAACGGGGCCACATT 60.523 55.556 5.46 0.00 0.00 2.71
345 346 2.002586 CACACTAGAAGAACGCCCATG 58.997 52.381 0.00 0.00 0.00 3.66
348 349 2.288886 ACTTCACACTAGAAGAACGCCC 60.289 50.000 10.37 0.00 46.18 6.13
349 350 3.027974 ACTTCACACTAGAAGAACGCC 57.972 47.619 10.37 0.00 46.18 5.68
350 351 5.458891 TCTAACTTCACACTAGAAGAACGC 58.541 41.667 10.37 0.00 46.18 4.84
351 352 8.452534 AGTATCTAACTTCACACTAGAAGAACG 58.547 37.037 10.37 0.00 46.18 3.95
352 353 9.777575 GAGTATCTAACTTCACACTAGAAGAAC 57.222 37.037 10.37 0.48 46.18 3.01
376 377 3.348119 GGAGTAAAAGGGCCAAAGAGAG 58.652 50.000 6.18 0.00 0.00 3.20
386 1770 4.336889 TCTCATATGCGGAGTAAAAGGG 57.663 45.455 0.00 0.00 34.04 3.95
448 1834 9.683069 GTATTGAGAATGTTGATGTTTTTGTCT 57.317 29.630 0.00 0.00 0.00 3.41
451 1837 9.681692 TCTGTATTGAGAATGTTGATGTTTTTG 57.318 29.630 0.00 0.00 0.00 2.44
798 2513 1.631072 CCGATGACGACGCATTGAC 59.369 57.895 16.34 2.08 42.66 3.18
824 2539 3.572255 ACCATTCAATTTGCTGTAACGGT 59.428 39.130 0.00 0.00 0.00 4.83
845 2565 1.347320 CGTAAACTGAGCCCTCGAAC 58.653 55.000 0.00 0.00 0.00 3.95
879 2599 0.106217 GAGGAGAGAGGAGAGGGGTG 60.106 65.000 0.00 0.00 0.00 4.61
885 2606 0.033991 CCGTTGGAGGAGAGAGGAGA 60.034 60.000 0.00 0.00 0.00 3.71
887 2608 1.682684 GCCGTTGGAGGAGAGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
890 2611 0.681564 GAGAGCCGTTGGAGGAGAGA 60.682 60.000 0.00 0.00 0.00 3.10
909 2867 0.615850 GGTTTGGACAGGAGGAGGAG 59.384 60.000 0.00 0.00 0.00 3.69
910 2868 0.840722 GGGTTTGGACAGGAGGAGGA 60.841 60.000 0.00 0.00 0.00 3.71
911 2869 1.685820 GGGTTTGGACAGGAGGAGG 59.314 63.158 0.00 0.00 0.00 4.30
949 2907 0.251519 GATGGAGGATGGAATGGGGC 60.252 60.000 0.00 0.00 0.00 5.80
1005 2979 0.466124 GTGTCCTGGAGTATGGCCTC 59.534 60.000 3.32 0.00 0.00 4.70
1441 3415 3.432588 GTGCTCCTGCTGCTGCTG 61.433 66.667 17.00 15.58 40.48 4.41
1442 3416 4.719106 GGTGCTCCTGCTGCTGCT 62.719 66.667 17.00 0.00 40.48 4.24
1725 3729 2.125793 GAACACGTACCGGCCTCC 60.126 66.667 0.00 0.00 0.00 4.30
1875 3879 4.643387 AACAGCCCCGTGCAGTCC 62.643 66.667 0.00 0.00 44.83 3.85
1876 3880 3.357079 CAACAGCCCCGTGCAGTC 61.357 66.667 0.00 0.00 44.83 3.51
1877 3881 4.954970 CCAACAGCCCCGTGCAGT 62.955 66.667 0.00 0.00 44.83 4.40
1920 3933 2.202298 GCCGGCGTGTCAAAATCG 60.202 61.111 12.58 0.00 0.00 3.34
1971 3984 0.034896 TCCTCTGCACCGGAAGAAAC 59.965 55.000 9.46 0.00 0.00 2.78
1992 4005 2.740055 CTGTCACCAGTGCTCGGC 60.740 66.667 0.00 0.00 33.80 5.54
2039 4052 0.763652 AGAGGAATGCGATGATGCCT 59.236 50.000 0.00 0.00 0.00 4.75
2160 4173 4.034258 CACTTGCCTGTGCTGCCG 62.034 66.667 0.00 0.00 38.71 5.69
2178 4191 1.829222 CTAACCCTCGCTAACCCTGAA 59.171 52.381 0.00 0.00 0.00 3.02
2235 4248 2.593346 AACTCATCATCTCGAGGCAC 57.407 50.000 13.56 0.00 33.36 5.01
2268 4281 4.727792 TTGATCATAATCAGCATCCCCA 57.272 40.909 0.00 0.00 42.72 4.96
2358 4371 3.389329 TCAAGTCTATGGATTCCAGAGGC 59.611 47.826 21.62 21.62 46.48 4.70
2532 4545 4.659368 AGTGGTCCATCTTCATCATCAGAT 59.341 41.667 0.00 0.00 33.87 2.90
2591 4604 2.625823 GCGCTACCTGGCTGCAAAA 61.626 57.895 0.00 0.00 34.10 2.44
2640 4653 4.116328 TCGACAGAGCCGAAGCCG 62.116 66.667 0.00 0.00 41.25 5.52
2652 4665 1.013596 CACTGCAACCAAACTCGACA 58.986 50.000 0.00 0.00 0.00 4.35
2700 4716 4.504340 GCTACTTGAACAGGGTTTGGAGTA 60.504 45.833 0.00 0.00 0.00 2.59
2721 4737 3.295585 TCTGCTCTCATAGACTCTGCT 57.704 47.619 0.00 0.00 0.00 4.24
3035 5135 0.321122 CTGTGAGCTCACTGGGTTCC 60.321 60.000 38.81 17.32 46.55 3.62
3131 5239 4.116747 ACTCCAGATTACTGCTTTCTCG 57.883 45.455 0.00 0.00 42.25 4.04
3132 5240 6.035112 CGTAAACTCCAGATTACTGCTTTCTC 59.965 42.308 5.51 0.00 42.25 2.87
3306 5541 4.779733 TCAGGACCTCCCGCTCCC 62.780 72.222 0.00 0.00 40.87 4.30
3307 5542 3.151022 CTCAGGACCTCCCGCTCC 61.151 72.222 0.00 0.00 40.87 4.70
3308 5543 3.151022 CCTCAGGACCTCCCGCTC 61.151 72.222 0.00 0.00 40.87 5.03
3341 5576 4.584325 TCTTTCAGAAATGAAACCAGTGGG 59.416 41.667 15.21 0.00 41.29 4.61
3491 5762 4.441634 CCGTTTCACCAAATTTGTTGGGTA 60.442 41.667 14.84 0.05 43.71 3.69
3512 5783 4.584327 AGAAAAGGGTCAAATTTGTCCG 57.416 40.909 22.67 0.00 37.27 4.79
3551 5823 6.925718 TGTGAATTTTGTGCGGATTTGATTTA 59.074 30.769 0.00 0.00 0.00 1.40
3562 5834 4.318689 GGGTCATTTTGTGAATTTTGTGCG 60.319 41.667 0.00 0.00 38.90 5.34
3575 5847 4.708601 CGTCGAGTAAAAGGGTCATTTTG 58.291 43.478 3.95 0.00 34.35 2.44
3586 5858 2.262292 CCGGGGCGTCGAGTAAAA 59.738 61.111 0.00 0.00 0.00 1.52
3605 5877 3.267233 AGGAGCATGGCACCCCAA 61.267 61.111 0.95 0.00 46.14 4.12
3632 5918 2.752939 CGCGCCATCAAGCATGACA 61.753 57.895 0.00 0.00 38.69 3.58
3633 5919 2.023741 CGCGCCATCAAGCATGAC 59.976 61.111 0.00 0.00 38.69 3.06
3634 5920 3.204119 CCGCGCCATCAAGCATGA 61.204 61.111 0.00 0.00 40.57 3.07
3653 5939 1.449778 GCCCTTTGTCGAGGTAGCC 60.450 63.158 0.00 0.00 34.88 3.93
3685 5971 1.197721 CTGAACCTGAAATGTCGTGCC 59.802 52.381 0.00 0.00 0.00 5.01
3689 5975 0.443869 CGCCTGAACCTGAAATGTCG 59.556 55.000 0.00 0.00 0.00 4.35
3735 6021 8.971073 AGAATGAACCGGATCTGAAAATATTTT 58.029 29.630 9.46 13.24 0.00 1.82
3776 6062 5.409826 GTGAGAAAACGGACAGATTTGATCT 59.590 40.000 0.00 0.00 41.15 2.75


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

AutoCloner maintained by Alex Coulton.