Multiple sequence alignment - TraesCS3A01G188500

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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 TraesCS3A01G188500 chr3A 100.000 3710 0 0 1 3710 227924393 227920684 0.000000e+00 6852.0
1 TraesCS3A01G188500 chr3D 97.194 2566 64 3 737 3302 181103577 181106134 0.000000e+00 4333.0
2 TraesCS3A01G188500 chr3D 96.000 450 17 1 294 743 181103082 181103530 0.000000e+00 730.0
3 TraesCS3A01G188500 chr3D 92.874 421 19 1 3301 3710 181106168 181106588 5.300000e-168 601.0
4 TraesCS3A01G188500 chr3B 94.000 2500 135 8 737 3232 259370383 259372871 0.000000e+00 3771.0
5 TraesCS3A01G188500 chr3B 96.018 452 15 2 294 743 259369886 259370336 0.000000e+00 732.0
6 TraesCS3A01G188500 chr3B 90.351 228 21 1 3481 3707 259372873 259373100 7.790000e-77 298.0
7 TraesCS3A01G188500 chr7D 90.197 2132 193 11 736 2864 576333027 576335145 0.000000e+00 2765.0
8 TraesCS3A01G188500 chr7D 87.288 118 8 6 3515 3631 576335442 576335553 1.080000e-25 128.0
9 TraesCS3A01G188500 chr7D 93.056 72 5 0 417 488 576332565 576332636 5.070000e-19 106.0
10 TraesCS3A01G188500 chr7B 90.166 1993 189 4 735 2727 639083166 639085151 0.000000e+00 2588.0
11 TraesCS3A01G188500 chr7B 87.778 90 7 2 2754 2841 639085150 639085237 6.560000e-18 102.0
12 TraesCS3A01G188500 chr7B 82.692 104 6 7 3528 3631 704092969 704092878 8.540000e-12 82.4
13 TraesCS3A01G188500 chr7B 81.731 104 7 6 3528 3631 704158036 704157945 3.970000e-10 76.8
14 TraesCS3A01G188500 chr7B 93.617 47 3 0 442 488 639082740 639082786 1.850000e-08 71.3
15 TraesCS3A01G188500 chr7A 90.080 1865 178 3 1093 2955 667475057 667476916 0.000000e+00 2412.0
16 TraesCS3A01G188500 chr7A 96.259 294 9 2 1 293 558145839 558146131 7.210000e-132 481.0
17 TraesCS3A01G188500 chr7A 94.237 295 14 2 1 293 558156614 558156907 7.310000e-122 448.0
18 TraesCS3A01G188500 chr7A 87.212 391 45 3 736 1126 667474678 667475063 1.220000e-119 440.0
19 TraesCS3A01G188500 chr7A 84.000 125 11 7 3508 3631 667477143 667477259 1.090000e-20 111.0
20 TraesCS3A01G188500 chr7A 100.000 30 0 0 3602 3631 705142176 705142147 5.180000e-04 56.5
21 TraesCS3A01G188500 chr5A 96.246 293 10 1 1 292 458188391 458188099 2.590000e-131 479.0
22 TraesCS3A01G188500 chr1D 92.491 293 20 2 1 292 62870845 62871136 5.730000e-113 418.0
23 TraesCS3A01G188500 chr1D 91.753 291 20 4 1 288 365711784 365711495 5.770000e-108 401.0
24 TraesCS3A01G188500 chr1A 94.224 277 8 2 16 292 526581397 526581665 2.060000e-112 416.0
25 TraesCS3A01G188500 chr6D 94.872 39 2 0 3442 3480 90193078 90193040 1.110000e-05 62.1


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 TraesCS3A01G188500 chr3A 227920684 227924393 3709 True 6852.000000 6852 100.000000 1 3710 1 chr3A.!!$R1 3709
1 TraesCS3A01G188500 chr3D 181103082 181106588 3506 False 1888.000000 4333 95.356000 294 3710 3 chr3D.!!$F1 3416
2 TraesCS3A01G188500 chr3B 259369886 259373100 3214 False 1600.333333 3771 93.456333 294 3707 3 chr3B.!!$F1 3413
3 TraesCS3A01G188500 chr7D 576332565 576335553 2988 False 999.666667 2765 90.180333 417 3631 3 chr7D.!!$F1 3214
4 TraesCS3A01G188500 chr7B 639082740 639085237 2497 False 920.433333 2588 90.520333 442 2841 3 chr7B.!!$F1 2399
5 TraesCS3A01G188500 chr7A 667474678 667477259 2581 False 987.666667 2412 87.097333 736 3631 3 chr7A.!!$F3 2895

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
107 108 0.106268 TTGGGCTGCCAGTTCAAAGA 60.106 50.0 22.05 0.0 0.00 2.52 F
139 140 0.108585 ATGAAACACAGGACGCCACT 59.891 50.0 0.00 0.0 0.00 4.00 F
197 198 0.179092 GGCCGTACCTGAACGCTATT 60.179 55.0 0.00 0.0 41.51 1.73 F
762 927 0.180406 AACCGTGCCTTCTCTGTTGT 59.820 50.0 0.00 0.0 0.00 3.32 F
859 1028 0.461961 GTATGCTGGAGGAGACGCTT 59.538 55.0 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2207 1.321474 CAGGTCCTTGCACACAATGT 58.679 50.000 0.0 0.0 34.61 2.71 R
2305 2506 0.755327 GGGGGCATGGACATTGTACC 60.755 60.000 0.0 0.0 0.00 3.34 R
2318 2519 0.334335 TATGACTGCATTTGGGGGCA 59.666 50.000 0.0 0.0 38.52 5.36 R
2495 2696 4.102838 CCTCCTTCATCATCATCCTCACTT 59.897 45.833 0.0 0.0 0.00 3.16 R
2922 3155 6.355397 AGACTACATCGAGCATCAAAATTG 57.645 37.500 0.0 0.0 33.17 2.32 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
20 21 3.876309 TCTAACAAAGAGCAAAGGGGT 57.124 42.857 0.00 0.00 0.00 4.95
21 22 3.486383 TCTAACAAAGAGCAAAGGGGTG 58.514 45.455 0.00 0.00 0.00 4.61
22 23 0.752658 AACAAAGAGCAAAGGGGTGC 59.247 50.000 0.00 0.00 45.28 5.01
28 29 2.653115 GCAAAGGGGTGCAGAAGC 59.347 61.111 0.00 0.00 44.29 3.86
39 40 2.098293 GCAGAAGCACCATTACCGG 58.902 57.895 0.00 0.00 41.58 5.28
40 41 0.676782 GCAGAAGCACCATTACCGGT 60.677 55.000 13.98 13.98 41.07 5.28
46 47 2.674754 ACCATTACCGGTGGCTGG 59.325 61.111 19.93 21.91 40.49 4.85
47 48 1.921346 ACCATTACCGGTGGCTGGA 60.921 57.895 28.42 3.75 40.49 3.86
48 49 1.279025 ACCATTACCGGTGGCTGGAT 61.279 55.000 28.42 15.48 40.49 3.41
49 50 0.762418 CCATTACCGGTGGCTGGATA 59.238 55.000 19.93 0.00 33.36 2.59
50 51 1.270839 CCATTACCGGTGGCTGGATAG 60.271 57.143 19.93 0.00 33.36 2.08
78 79 4.162690 GAGGTGCGCGAGGGGAAT 62.163 66.667 12.10 0.00 0.00 3.01
79 80 2.762459 AGGTGCGCGAGGGGAATA 60.762 61.111 12.10 0.00 0.00 1.75
80 81 2.188469 GGTGCGCGAGGGGAATAA 59.812 61.111 12.10 0.00 0.00 1.40
81 82 2.178235 GGTGCGCGAGGGGAATAAC 61.178 63.158 12.10 0.00 0.00 1.89
82 83 1.448893 GTGCGCGAGGGGAATAACA 60.449 57.895 12.10 0.00 0.00 2.41
83 84 1.153449 TGCGCGAGGGGAATAACAG 60.153 57.895 12.10 0.00 0.00 3.16
84 85 1.143183 GCGCGAGGGGAATAACAGA 59.857 57.895 12.10 0.00 0.00 3.41
85 86 0.876342 GCGCGAGGGGAATAACAGAG 60.876 60.000 12.10 0.00 0.00 3.35
86 87 0.876342 CGCGAGGGGAATAACAGAGC 60.876 60.000 0.00 0.00 0.00 4.09
87 88 0.178068 GCGAGGGGAATAACAGAGCA 59.822 55.000 0.00 0.00 0.00 4.26
88 89 1.202698 GCGAGGGGAATAACAGAGCAT 60.203 52.381 0.00 0.00 0.00 3.79
89 90 2.746472 GCGAGGGGAATAACAGAGCATT 60.746 50.000 0.00 0.00 0.00 3.56
90 91 2.874701 CGAGGGGAATAACAGAGCATTG 59.125 50.000 0.00 0.00 0.00 2.82
91 92 3.217626 GAGGGGAATAACAGAGCATTGG 58.782 50.000 0.00 0.00 0.00 3.16
92 93 2.091665 AGGGGAATAACAGAGCATTGGG 60.092 50.000 0.00 0.00 0.00 4.12
93 94 1.683385 GGGAATAACAGAGCATTGGGC 59.317 52.381 0.00 0.00 45.30 5.36
102 103 2.575461 GCATTGGGCTGCCAGTTC 59.425 61.111 22.05 3.09 40.25 3.01
103 104 2.277591 GCATTGGGCTGCCAGTTCA 61.278 57.895 22.05 6.10 40.25 3.18
104 105 1.818959 GCATTGGGCTGCCAGTTCAA 61.819 55.000 22.05 15.25 40.25 2.69
105 106 0.680618 CATTGGGCTGCCAGTTCAAA 59.319 50.000 22.05 4.93 0.00 2.69
106 107 0.971386 ATTGGGCTGCCAGTTCAAAG 59.029 50.000 22.05 0.00 0.00 2.77
107 108 0.106268 TTGGGCTGCCAGTTCAAAGA 60.106 50.000 22.05 0.00 0.00 2.52
108 109 0.106268 TGGGCTGCCAGTTCAAAGAA 60.106 50.000 22.05 0.00 0.00 2.52
109 110 1.260544 GGGCTGCCAGTTCAAAGAAT 58.739 50.000 22.05 0.00 0.00 2.40
110 111 1.620323 GGGCTGCCAGTTCAAAGAATT 59.380 47.619 22.05 0.00 0.00 2.17
111 112 2.037641 GGGCTGCCAGTTCAAAGAATTT 59.962 45.455 22.05 0.00 40.26 1.82
127 128 6.642707 AAGAATTTGGGTCGTAATGAAACA 57.357 33.333 0.00 0.00 0.00 2.83
128 129 6.009115 AGAATTTGGGTCGTAATGAAACAC 57.991 37.500 0.00 0.00 0.00 3.32
129 130 5.533154 AGAATTTGGGTCGTAATGAAACACA 59.467 36.000 0.00 0.00 0.00 3.72
130 131 4.822036 TTTGGGTCGTAATGAAACACAG 57.178 40.909 0.00 0.00 0.00 3.66
131 132 2.773487 TGGGTCGTAATGAAACACAGG 58.227 47.619 0.00 0.00 0.00 4.00
132 133 2.369203 TGGGTCGTAATGAAACACAGGA 59.631 45.455 0.00 0.00 0.00 3.86
133 134 2.740447 GGGTCGTAATGAAACACAGGAC 59.260 50.000 0.00 0.00 0.00 3.85
134 135 2.410730 GGTCGTAATGAAACACAGGACG 59.589 50.000 0.00 0.00 39.93 4.79
135 136 2.063266 TCGTAATGAAACACAGGACGC 58.937 47.619 0.00 0.00 39.08 5.19
136 137 1.127951 CGTAATGAAACACAGGACGCC 59.872 52.381 0.00 0.00 35.13 5.68
137 138 2.147958 GTAATGAAACACAGGACGCCA 58.852 47.619 0.00 0.00 0.00 5.69
138 139 0.951558 AATGAAACACAGGACGCCAC 59.048 50.000 0.00 0.00 0.00 5.01
139 140 0.108585 ATGAAACACAGGACGCCACT 59.891 50.000 0.00 0.00 0.00 4.00
140 141 0.753867 TGAAACACAGGACGCCACTA 59.246 50.000 0.00 0.00 0.00 2.74
141 142 1.139256 TGAAACACAGGACGCCACTAA 59.861 47.619 0.00 0.00 0.00 2.24
142 143 1.529865 GAAACACAGGACGCCACTAAC 59.470 52.381 0.00 0.00 0.00 2.34
143 144 0.466543 AACACAGGACGCCACTAACA 59.533 50.000 0.00 0.00 0.00 2.41
144 145 0.466543 ACACAGGACGCCACTAACAA 59.533 50.000 0.00 0.00 0.00 2.83
145 146 0.865769 CACAGGACGCCACTAACAAC 59.134 55.000 0.00 0.00 0.00 3.32
146 147 0.466543 ACAGGACGCCACTAACAACA 59.533 50.000 0.00 0.00 0.00 3.33
147 148 1.148310 CAGGACGCCACTAACAACAG 58.852 55.000 0.00 0.00 0.00 3.16
148 149 0.602905 AGGACGCCACTAACAACAGC 60.603 55.000 0.00 0.00 0.00 4.40
150 151 3.637714 CGCCACTAACAACAGCGT 58.362 55.556 0.00 0.00 41.78 5.07
151 152 1.491563 CGCCACTAACAACAGCGTC 59.508 57.895 0.00 0.00 41.78 5.19
152 153 1.866925 GCCACTAACAACAGCGTCC 59.133 57.895 0.00 0.00 0.00 4.79
153 154 0.882927 GCCACTAACAACAGCGTCCA 60.883 55.000 0.00 0.00 0.00 4.02
154 155 0.865769 CCACTAACAACAGCGTCCAC 59.134 55.000 0.00 0.00 0.00 4.02
155 156 0.506932 CACTAACAACAGCGTCCACG 59.493 55.000 0.00 0.00 43.27 4.94
168 169 4.657824 CCACGCCTGGACGTCGTT 62.658 66.667 9.92 0.00 46.34 3.85
169 170 2.256158 CACGCCTGGACGTCGTTA 59.744 61.111 9.92 0.00 46.34 3.18
170 171 1.800315 CACGCCTGGACGTCGTTAG 60.800 63.158 9.92 7.73 46.34 2.34
171 172 2.879462 CGCCTGGACGTCGTTAGC 60.879 66.667 9.92 8.80 0.00 3.09
172 173 2.260434 GCCTGGACGTCGTTAGCA 59.740 61.111 9.92 0.03 0.00 3.49
173 174 1.373748 GCCTGGACGTCGTTAGCAA 60.374 57.895 9.92 0.00 0.00 3.91
174 175 1.623973 GCCTGGACGTCGTTAGCAAC 61.624 60.000 9.92 0.00 0.00 4.17
175 176 0.319211 CCTGGACGTCGTTAGCAACA 60.319 55.000 9.92 0.00 0.00 3.33
176 177 1.060713 CTGGACGTCGTTAGCAACAG 58.939 55.000 9.92 4.68 0.00 3.16
177 178 0.942410 TGGACGTCGTTAGCAACAGC 60.942 55.000 9.92 0.00 0.00 4.40
178 179 1.411089 GACGTCGTTAGCAACAGCG 59.589 57.895 0.00 0.00 35.35 5.18
179 180 1.941476 GACGTCGTTAGCAACAGCGG 61.941 60.000 0.00 0.00 34.13 5.52
180 181 2.474712 GTCGTTAGCAACAGCGGC 59.525 61.111 0.00 0.00 0.00 6.53
181 182 2.740826 TCGTTAGCAACAGCGGCC 60.741 61.111 0.00 0.00 0.00 6.13
182 183 4.147322 CGTTAGCAACAGCGGCCG 62.147 66.667 24.05 24.05 0.00 6.13
183 184 3.047877 GTTAGCAACAGCGGCCGT 61.048 61.111 28.70 11.01 0.00 5.68
184 185 1.738830 GTTAGCAACAGCGGCCGTA 60.739 57.895 28.70 6.10 0.00 4.02
185 186 1.738830 TTAGCAACAGCGGCCGTAC 60.739 57.895 28.70 11.34 0.00 3.67
186 187 3.652539 TAGCAACAGCGGCCGTACC 62.653 63.158 28.70 10.48 0.00 3.34
188 189 3.118454 CAACAGCGGCCGTACCTG 61.118 66.667 28.70 26.08 35.61 4.00
189 190 3.307906 AACAGCGGCCGTACCTGA 61.308 61.111 30.16 0.00 35.61 3.86
190 191 2.874664 AACAGCGGCCGTACCTGAA 61.875 57.895 30.16 0.00 35.61 3.02
191 192 2.813908 CAGCGGCCGTACCTGAAC 60.814 66.667 28.70 7.06 35.61 3.18
192 193 4.430765 AGCGGCCGTACCTGAACG 62.431 66.667 28.70 0.00 42.49 3.95
194 195 4.430765 CGGCCGTACCTGAACGCT 62.431 66.667 19.50 0.00 41.51 5.07
195 196 2.887360 GGCCGTACCTGAACGCTA 59.113 61.111 0.00 0.00 41.51 4.26
196 197 1.440476 GGCCGTACCTGAACGCTAT 59.560 57.895 0.00 0.00 41.51 2.97
197 198 0.179092 GGCCGTACCTGAACGCTATT 60.179 55.000 0.00 0.00 41.51 1.73
198 199 1.067516 GGCCGTACCTGAACGCTATTA 59.932 52.381 0.00 0.00 41.51 0.98
199 200 2.481795 GGCCGTACCTGAACGCTATTAA 60.482 50.000 0.00 0.00 41.51 1.40
200 201 3.387397 GCCGTACCTGAACGCTATTAAT 58.613 45.455 0.00 0.00 41.51 1.40
201 202 3.427863 GCCGTACCTGAACGCTATTAATC 59.572 47.826 0.00 0.00 41.51 1.75
202 203 4.613944 CCGTACCTGAACGCTATTAATCA 58.386 43.478 0.00 0.00 41.51 2.57
203 204 4.443394 CCGTACCTGAACGCTATTAATCAC 59.557 45.833 0.00 0.00 41.51 3.06
204 205 5.038683 CGTACCTGAACGCTATTAATCACA 58.961 41.667 0.00 0.00 35.87 3.58
205 206 5.173312 CGTACCTGAACGCTATTAATCACAG 59.827 44.000 0.00 0.00 35.87 3.66
206 207 3.871594 ACCTGAACGCTATTAATCACAGC 59.128 43.478 0.00 0.00 0.00 4.40
213 214 4.717188 GCTATTAATCACAGCGTCCTTC 57.283 45.455 0.00 0.00 0.00 3.46
214 215 3.495001 GCTATTAATCACAGCGTCCTTCC 59.505 47.826 0.00 0.00 0.00 3.46
215 216 3.914426 ATTAATCACAGCGTCCTTCCT 57.086 42.857 0.00 0.00 0.00 3.36
216 217 5.509163 GCTATTAATCACAGCGTCCTTCCTA 60.509 44.000 0.00 0.00 0.00 2.94
217 218 2.674796 AATCACAGCGTCCTTCCTAC 57.325 50.000 0.00 0.00 0.00 3.18
218 219 1.853963 ATCACAGCGTCCTTCCTACT 58.146 50.000 0.00 0.00 0.00 2.57
219 220 1.629043 TCACAGCGTCCTTCCTACTT 58.371 50.000 0.00 0.00 0.00 2.24
220 221 2.799017 TCACAGCGTCCTTCCTACTTA 58.201 47.619 0.00 0.00 0.00 2.24
221 222 2.490903 TCACAGCGTCCTTCCTACTTAC 59.509 50.000 0.00 0.00 0.00 2.34
222 223 2.230508 CACAGCGTCCTTCCTACTTACA 59.769 50.000 0.00 0.00 0.00 2.41
223 224 2.230750 ACAGCGTCCTTCCTACTTACAC 59.769 50.000 0.00 0.00 0.00 2.90
224 225 2.230508 CAGCGTCCTTCCTACTTACACA 59.769 50.000 0.00 0.00 0.00 3.72
225 226 2.895404 AGCGTCCTTCCTACTTACACAA 59.105 45.455 0.00 0.00 0.00 3.33
226 227 3.514309 AGCGTCCTTCCTACTTACACAAT 59.486 43.478 0.00 0.00 0.00 2.71
227 228 4.020485 AGCGTCCTTCCTACTTACACAATT 60.020 41.667 0.00 0.00 0.00 2.32
228 229 4.694037 GCGTCCTTCCTACTTACACAATTT 59.306 41.667 0.00 0.00 0.00 1.82
229 230 5.163884 GCGTCCTTCCTACTTACACAATTTC 60.164 44.000 0.00 0.00 0.00 2.17
230 231 5.350640 CGTCCTTCCTACTTACACAATTTCC 59.649 44.000 0.00 0.00 0.00 3.13
231 232 6.235664 GTCCTTCCTACTTACACAATTTCCA 58.764 40.000 0.00 0.00 0.00 3.53
232 233 6.371825 GTCCTTCCTACTTACACAATTTCCAG 59.628 42.308 0.00 0.00 0.00 3.86
233 234 6.043938 TCCTTCCTACTTACACAATTTCCAGT 59.956 38.462 0.00 0.00 0.00 4.00
234 235 6.715264 CCTTCCTACTTACACAATTTCCAGTT 59.285 38.462 0.00 0.00 0.00 3.16
235 236 7.308589 CCTTCCTACTTACACAATTTCCAGTTG 60.309 40.741 0.00 0.00 0.00 3.16
236 237 5.472137 TCCTACTTACACAATTTCCAGTTGC 59.528 40.000 0.00 0.00 0.00 4.17
237 238 4.584327 ACTTACACAATTTCCAGTTGCC 57.416 40.909 0.00 0.00 0.00 4.52
238 239 3.320826 ACTTACACAATTTCCAGTTGCCC 59.679 43.478 0.00 0.00 0.00 5.36
239 240 2.086610 ACACAATTTCCAGTTGCCCT 57.913 45.000 0.00 0.00 0.00 5.19
240 241 2.397597 ACACAATTTCCAGTTGCCCTT 58.602 42.857 0.00 0.00 0.00 3.95
241 242 2.771372 ACACAATTTCCAGTTGCCCTTT 59.229 40.909 0.00 0.00 0.00 3.11
242 243 3.964031 ACACAATTTCCAGTTGCCCTTTA 59.036 39.130 0.00 0.00 0.00 1.85
243 244 4.202212 ACACAATTTCCAGTTGCCCTTTAC 60.202 41.667 0.00 0.00 0.00 2.01
244 245 3.323691 ACAATTTCCAGTTGCCCTTTACC 59.676 43.478 0.00 0.00 0.00 2.85
245 246 2.757894 TTTCCAGTTGCCCTTTACCA 57.242 45.000 0.00 0.00 0.00 3.25
246 247 2.286365 TTCCAGTTGCCCTTTACCAG 57.714 50.000 0.00 0.00 0.00 4.00
247 248 1.145571 TCCAGTTGCCCTTTACCAGT 58.854 50.000 0.00 0.00 0.00 4.00
248 249 1.497286 TCCAGTTGCCCTTTACCAGTT 59.503 47.619 0.00 0.00 0.00 3.16
249 250 1.886542 CCAGTTGCCCTTTACCAGTTC 59.113 52.381 0.00 0.00 0.00 3.01
250 251 1.886542 CAGTTGCCCTTTACCAGTTCC 59.113 52.381 0.00 0.00 0.00 3.62
251 252 0.879090 GTTGCCCTTTACCAGTTCCG 59.121 55.000 0.00 0.00 0.00 4.30
252 253 0.475044 TTGCCCTTTACCAGTTCCGT 59.525 50.000 0.00 0.00 0.00 4.69
253 254 1.350071 TGCCCTTTACCAGTTCCGTA 58.650 50.000 0.00 0.00 0.00 4.02
254 255 1.698532 TGCCCTTTACCAGTTCCGTAA 59.301 47.619 0.00 0.00 0.00 3.18
255 256 2.306512 TGCCCTTTACCAGTTCCGTAAT 59.693 45.455 0.00 0.00 0.00 1.89
256 257 3.244981 TGCCCTTTACCAGTTCCGTAATT 60.245 43.478 0.00 0.00 0.00 1.40
257 258 4.019501 TGCCCTTTACCAGTTCCGTAATTA 60.020 41.667 0.00 0.00 0.00 1.40
258 259 4.573607 GCCCTTTACCAGTTCCGTAATTAG 59.426 45.833 0.00 0.00 0.00 1.73
259 260 5.627503 GCCCTTTACCAGTTCCGTAATTAGA 60.628 44.000 0.00 0.00 0.00 2.10
260 261 6.589135 CCCTTTACCAGTTCCGTAATTAGAT 58.411 40.000 0.00 0.00 0.00 1.98
261 262 7.687592 GCCCTTTACCAGTTCCGTAATTAGATA 60.688 40.741 0.00 0.00 0.00 1.98
262 263 8.206189 CCCTTTACCAGTTCCGTAATTAGATAA 58.794 37.037 0.00 0.00 0.00 1.75
263 264 9.774413 CCTTTACCAGTTCCGTAATTAGATAAT 57.226 33.333 0.00 0.00 0.00 1.28
588 595 2.542020 TGGTGCTCGAATTGAACAGA 57.458 45.000 0.00 0.00 0.00 3.41
598 605 5.152097 TCGAATTGAACAGAAGACGTAGAC 58.848 41.667 0.00 0.00 0.00 2.59
607 614 5.753713 CAGAAGACGTAGACATTCTGTTG 57.246 43.478 14.12 0.00 42.28 3.33
672 692 9.831737 AGAAATTGTCAAATAGAAGATGAAACG 57.168 29.630 0.00 0.00 0.00 3.60
681 701 3.347216 AGAAGATGAAACGGACCATTGG 58.653 45.455 0.00 0.00 0.00 3.16
762 927 0.180406 AACCGTGCCTTCTCTGTTGT 59.820 50.000 0.00 0.00 0.00 3.32
841 1010 2.288666 AGTTGATGTTCGTGTGCAAGT 58.711 42.857 0.00 0.00 0.00 3.16
859 1028 0.461961 GTATGCTGGAGGAGACGCTT 59.538 55.000 0.00 0.00 0.00 4.68
895 1064 4.224715 CAGCCACAATCTGCTTATGATG 57.775 45.455 0.00 0.00 35.12 3.07
908 1078 4.276678 TGCTTATGATGTGCATAAAGCTCC 59.723 41.667 15.69 0.00 45.99 4.70
964 1135 7.847096 TGATAAGCATAACTAACTCAAGACCA 58.153 34.615 0.00 0.00 0.00 4.02
1169 1370 2.032799 GTCTGTGTGTGGCGAATTTTGA 59.967 45.455 0.00 0.00 0.00 2.69
1327 1528 7.283580 TCAATGATTGTATGCATGACATCTTGA 59.716 33.333 10.16 13.85 40.38 3.02
1386 1587 4.891566 CGGTTCGCTAGCTCAAGT 57.108 55.556 13.93 0.00 0.00 3.16
1517 1718 5.426833 AGTTGCATAGGAGAGGAATAAGTGT 59.573 40.000 0.00 0.00 0.00 3.55
1528 1729 8.402472 GGAGAGGAATAAGTGTCGATATATCTG 58.598 40.741 10.93 4.96 0.00 2.90
1735 1936 2.754946 AAATACCGTGTCGTGGACAT 57.245 45.000 1.36 0.00 44.63 3.06
1803 2004 5.396101 CCTCAAGGTATTTCAGCTGATGAGA 60.396 44.000 29.76 14.40 40.05 3.27
1852 2053 6.048732 TCACATTTGCCACTATCTTCAGTA 57.951 37.500 0.00 0.00 0.00 2.74
1863 2064 7.041721 CCACTATCTTCAGTATGTGCACTAAA 58.958 38.462 19.41 0.00 37.40 1.85
1993 2194 4.148838 CGGGAATATAATTGAGGCCCAAA 58.851 43.478 10.21 0.48 38.43 3.28
2006 2207 5.083122 TGAGGCCCAAACAATATTTGAGAA 58.917 37.500 0.00 0.00 0.00 2.87
2305 2506 1.368641 TGAAGCGTGGGATTTGATCG 58.631 50.000 0.00 0.00 0.00 3.69
2318 2519 4.821805 GGATTTGATCGGTACAATGTCCAT 59.178 41.667 0.00 0.00 35.00 3.41
2495 2696 1.303561 GCTGGAGTGATGTGGCCAA 60.304 57.895 7.24 0.00 0.00 4.52
2631 2832 5.184864 CCAAATAAACAATGTCCTGGCTGTA 59.815 40.000 0.00 0.00 0.00 2.74
2855 3088 6.160576 TGTGATATGATTCGTCTGATTCCA 57.839 37.500 0.00 0.00 0.00 3.53
2878 3111 8.739039 TCCAACCTCAAAGTATTCAATATTGTG 58.261 33.333 14.97 4.70 0.00 3.33
2922 3155 3.634397 TCCCACCTGACATCTGATTTC 57.366 47.619 0.00 0.00 0.00 2.17
2936 3169 6.750501 ACATCTGATTTCAATTTTGATGCTCG 59.249 34.615 0.00 0.00 37.00 5.03
3037 3270 7.595819 AGTGTGAATCATTTGGGAACTTTAA 57.404 32.000 0.00 0.00 0.00 1.52
3170 3410 8.849168 ACATCATAATTTCAGTTTGACACTTGA 58.151 29.630 0.00 0.00 30.92 3.02
3312 3587 7.932134 TGGCTTTGACCATCAATATATATCCT 58.068 34.615 0.00 0.00 36.11 3.24
3314 3589 9.905713 GGCTTTGACCATCAATATATATCCTAA 57.094 33.333 0.00 0.00 36.11 2.69
3422 3708 7.094805 TGGTAGACATGCAATAAAGTCAAAGTC 60.095 37.037 0.00 0.00 33.56 3.01
3431 3717 5.862924 ATAAAGTCAAAGTCGTGTGATGG 57.137 39.130 0.00 0.00 0.00 3.51
3473 3759 4.568152 CGCCTTATATTTTGTGAAGGGG 57.432 45.455 2.66 2.66 43.11 4.79
3512 3798 7.613801 AGTTGCATTCTTGTGGGTATGTTTATA 59.386 33.333 0.00 0.00 0.00 0.98
3524 3811 9.850628 GTGGGTATGTTTATAGTTTTTCCTTTC 57.149 33.333 0.00 0.00 0.00 2.62
3647 3934 2.365408 AAGGCTTCGTTCGGTTAGAG 57.635 50.000 0.00 0.00 0.00 2.43
3656 3943 3.006728 CGGTTAGAGCCCACCCCA 61.007 66.667 0.00 0.00 0.00 4.96
3696 3983 0.034574 CATGGTTTCATCCCACCCGA 60.035 55.000 0.00 0.00 34.07 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.486383 CACCCCTTTGCTCTTTGTTAGA 58.514 45.455 0.00 0.00 0.00 2.10
1 2 2.029918 GCACCCCTTTGCTCTTTGTTAG 60.030 50.000 0.00 0.00 39.59 2.34
2 3 1.960689 GCACCCCTTTGCTCTTTGTTA 59.039 47.619 0.00 0.00 39.59 2.41
3 4 0.752658 GCACCCCTTTGCTCTTTGTT 59.247 50.000 0.00 0.00 39.59 2.83
4 5 0.396974 TGCACCCCTTTGCTCTTTGT 60.397 50.000 0.00 0.00 43.41 2.83
5 6 0.316204 CTGCACCCCTTTGCTCTTTG 59.684 55.000 0.00 0.00 43.41 2.77
6 7 0.185901 TCTGCACCCCTTTGCTCTTT 59.814 50.000 0.00 0.00 43.41 2.52
7 8 0.185901 TTCTGCACCCCTTTGCTCTT 59.814 50.000 0.00 0.00 43.41 2.85
8 9 0.251077 CTTCTGCACCCCTTTGCTCT 60.251 55.000 0.00 0.00 43.41 4.09
9 10 1.871126 GCTTCTGCACCCCTTTGCTC 61.871 60.000 0.00 0.00 43.41 4.26
10 11 1.905354 GCTTCTGCACCCCTTTGCT 60.905 57.895 0.00 0.00 43.41 3.91
11 12 2.202395 TGCTTCTGCACCCCTTTGC 61.202 57.895 0.00 0.00 45.31 3.68
12 13 4.179361 TGCTTCTGCACCCCTTTG 57.821 55.556 0.00 0.00 45.31 2.77
21 22 0.676782 ACCGGTAATGGTGCTTCTGC 60.677 55.000 4.49 0.00 41.85 4.26
22 23 3.551259 ACCGGTAATGGTGCTTCTG 57.449 52.632 4.49 0.00 41.85 3.02
29 30 1.279025 ATCCAGCCACCGGTAATGGT 61.279 55.000 23.81 12.70 45.21 3.55
30 31 0.762418 TATCCAGCCACCGGTAATGG 59.238 55.000 20.62 20.62 40.50 3.16
31 32 1.878102 GCTATCCAGCCACCGGTAATG 60.878 57.143 6.87 6.31 42.37 1.90
32 33 0.396811 GCTATCCAGCCACCGGTAAT 59.603 55.000 6.87 0.00 42.37 1.89
33 34 1.827394 GCTATCCAGCCACCGGTAA 59.173 57.895 6.87 0.00 42.37 2.85
34 35 2.495409 CGCTATCCAGCCACCGGTA 61.495 63.158 6.87 0.00 45.64 4.02
35 36 3.849951 CGCTATCCAGCCACCGGT 61.850 66.667 0.00 0.00 45.64 5.28
36 37 4.609018 CCGCTATCCAGCCACCGG 62.609 72.222 0.00 0.00 45.64 5.28
38 39 4.175337 TGCCGCTATCCAGCCACC 62.175 66.667 0.00 0.00 45.64 4.61
39 40 2.590007 CTGCCGCTATCCAGCCAC 60.590 66.667 0.00 0.00 45.64 5.01
40 41 4.552365 GCTGCCGCTATCCAGCCA 62.552 66.667 1.38 0.00 46.59 4.75
43 44 2.355599 CTCGCTGCCGCTATCCAG 60.356 66.667 0.00 0.00 0.00 3.86
44 45 3.916544 CCTCGCTGCCGCTATCCA 61.917 66.667 0.00 0.00 0.00 3.41
45 46 3.565910 CTCCTCGCTGCCGCTATCC 62.566 68.421 0.00 0.00 0.00 2.59
46 47 2.049618 CTCCTCGCTGCCGCTATC 60.050 66.667 0.00 0.00 0.00 2.08
47 48 3.610669 CCTCCTCGCTGCCGCTAT 61.611 66.667 0.00 0.00 0.00 2.97
61 62 2.306255 TTATTCCCCTCGCGCACCTC 62.306 60.000 8.75 0.00 0.00 3.85
62 63 2.363975 TTATTCCCCTCGCGCACCT 61.364 57.895 8.75 0.00 0.00 4.00
63 64 2.178235 GTTATTCCCCTCGCGCACC 61.178 63.158 8.75 0.00 0.00 5.01
64 65 1.429148 CTGTTATTCCCCTCGCGCAC 61.429 60.000 8.75 0.00 0.00 5.34
65 66 1.153449 CTGTTATTCCCCTCGCGCA 60.153 57.895 8.75 0.00 0.00 6.09
66 67 0.876342 CTCTGTTATTCCCCTCGCGC 60.876 60.000 0.00 0.00 0.00 6.86
67 68 0.876342 GCTCTGTTATTCCCCTCGCG 60.876 60.000 0.00 0.00 0.00 5.87
68 69 0.178068 TGCTCTGTTATTCCCCTCGC 59.822 55.000 0.00 0.00 0.00 5.03
69 70 2.874701 CAATGCTCTGTTATTCCCCTCG 59.125 50.000 0.00 0.00 0.00 4.63
70 71 3.217626 CCAATGCTCTGTTATTCCCCTC 58.782 50.000 0.00 0.00 0.00 4.30
71 72 2.091665 CCCAATGCTCTGTTATTCCCCT 60.092 50.000 0.00 0.00 0.00 4.79
72 73 2.310538 CCCAATGCTCTGTTATTCCCC 58.689 52.381 0.00 0.00 0.00 4.81
73 74 1.683385 GCCCAATGCTCTGTTATTCCC 59.317 52.381 0.00 0.00 36.87 3.97
85 86 1.818959 TTGAACTGGCAGCCCAATGC 61.819 55.000 15.89 0.00 45.74 3.56
86 87 0.680618 TTTGAACTGGCAGCCCAATG 59.319 50.000 15.89 0.00 41.58 2.82
87 88 0.971386 CTTTGAACTGGCAGCCCAAT 59.029 50.000 15.89 0.00 41.58 3.16
88 89 0.106268 TCTTTGAACTGGCAGCCCAA 60.106 50.000 15.89 15.56 41.58 4.12
89 90 0.106268 TTCTTTGAACTGGCAGCCCA 60.106 50.000 15.89 9.94 39.32 5.36
90 91 1.260544 ATTCTTTGAACTGGCAGCCC 58.739 50.000 15.89 7.11 0.00 5.19
91 92 3.062042 CAAATTCTTTGAACTGGCAGCC 58.938 45.455 15.89 3.66 43.26 4.85
92 93 3.062042 CCAAATTCTTTGAACTGGCAGC 58.938 45.455 15.89 0.00 43.26 5.25
93 94 3.070015 ACCCAAATTCTTTGAACTGGCAG 59.930 43.478 14.16 14.16 43.26 4.85
94 95 3.037549 ACCCAAATTCTTTGAACTGGCA 58.962 40.909 1.28 0.00 43.26 4.92
95 96 3.653344 GACCCAAATTCTTTGAACTGGC 58.347 45.455 1.28 0.00 43.26 4.85
96 97 3.317993 ACGACCCAAATTCTTTGAACTGG 59.682 43.478 1.28 0.00 43.26 4.00
97 98 4.568152 ACGACCCAAATTCTTTGAACTG 57.432 40.909 1.28 0.00 43.26 3.16
98 99 6.488683 TCATTACGACCCAAATTCTTTGAACT 59.511 34.615 1.28 0.00 43.26 3.01
99 100 6.674066 TCATTACGACCCAAATTCTTTGAAC 58.326 36.000 1.28 0.00 43.26 3.18
100 101 6.885952 TCATTACGACCCAAATTCTTTGAA 57.114 33.333 1.28 0.00 43.26 2.69
101 102 6.885952 TTCATTACGACCCAAATTCTTTGA 57.114 33.333 1.28 0.00 43.26 2.69
102 103 6.920758 TGTTTCATTACGACCCAAATTCTTTG 59.079 34.615 0.00 0.00 40.32 2.77
103 104 6.921307 GTGTTTCATTACGACCCAAATTCTTT 59.079 34.615 0.00 0.00 0.00 2.52
104 105 6.039941 TGTGTTTCATTACGACCCAAATTCTT 59.960 34.615 0.00 0.00 0.00 2.52
105 106 5.533154 TGTGTTTCATTACGACCCAAATTCT 59.467 36.000 0.00 0.00 0.00 2.40
106 107 5.764131 TGTGTTTCATTACGACCCAAATTC 58.236 37.500 0.00 0.00 0.00 2.17
107 108 5.278758 CCTGTGTTTCATTACGACCCAAATT 60.279 40.000 0.00 0.00 0.00 1.82
108 109 4.217550 CCTGTGTTTCATTACGACCCAAAT 59.782 41.667 0.00 0.00 0.00 2.32
109 110 3.566322 CCTGTGTTTCATTACGACCCAAA 59.434 43.478 0.00 0.00 0.00 3.28
110 111 3.142951 CCTGTGTTTCATTACGACCCAA 58.857 45.455 0.00 0.00 0.00 4.12
111 112 2.369203 TCCTGTGTTTCATTACGACCCA 59.631 45.455 0.00 0.00 0.00 4.51
112 113 2.740447 GTCCTGTGTTTCATTACGACCC 59.260 50.000 0.00 0.00 0.00 4.46
113 114 2.410730 CGTCCTGTGTTTCATTACGACC 59.589 50.000 0.00 0.00 36.70 4.79
114 115 2.159881 GCGTCCTGTGTTTCATTACGAC 60.160 50.000 0.00 0.00 36.70 4.34
115 116 2.063266 GCGTCCTGTGTTTCATTACGA 58.937 47.619 0.00 0.00 36.70 3.43
116 117 1.127951 GGCGTCCTGTGTTTCATTACG 59.872 52.381 0.00 0.00 37.23 3.18
117 118 2.095919 GTGGCGTCCTGTGTTTCATTAC 60.096 50.000 0.00 0.00 0.00 1.89
118 119 2.147958 GTGGCGTCCTGTGTTTCATTA 58.852 47.619 0.00 0.00 0.00 1.90
119 120 0.951558 GTGGCGTCCTGTGTTTCATT 59.048 50.000 0.00 0.00 0.00 2.57
120 121 0.108585 AGTGGCGTCCTGTGTTTCAT 59.891 50.000 0.00 0.00 0.00 2.57
121 122 0.753867 TAGTGGCGTCCTGTGTTTCA 59.246 50.000 0.00 0.00 0.00 2.69
122 123 1.529865 GTTAGTGGCGTCCTGTGTTTC 59.470 52.381 0.00 0.00 0.00 2.78
123 124 1.134340 TGTTAGTGGCGTCCTGTGTTT 60.134 47.619 0.00 0.00 0.00 2.83
124 125 0.466543 TGTTAGTGGCGTCCTGTGTT 59.533 50.000 0.00 0.00 0.00 3.32
125 126 0.466543 TTGTTAGTGGCGTCCTGTGT 59.533 50.000 0.00 0.00 0.00 3.72
126 127 0.865769 GTTGTTAGTGGCGTCCTGTG 59.134 55.000 0.00 0.00 0.00 3.66
127 128 0.466543 TGTTGTTAGTGGCGTCCTGT 59.533 50.000 0.00 0.00 0.00 4.00
128 129 1.148310 CTGTTGTTAGTGGCGTCCTG 58.852 55.000 0.00 0.00 0.00 3.86
129 130 0.602905 GCTGTTGTTAGTGGCGTCCT 60.603 55.000 0.00 0.00 0.00 3.85
130 131 1.866925 GCTGTTGTTAGTGGCGTCC 59.133 57.895 0.00 0.00 0.00 4.79
131 132 1.491563 CGCTGTTGTTAGTGGCGTC 59.508 57.895 0.00 0.00 40.78 5.19
132 133 3.637714 CGCTGTTGTTAGTGGCGT 58.362 55.556 0.00 0.00 40.78 5.68
134 135 0.882927 TGGACGCTGTTGTTAGTGGC 60.883 55.000 0.00 0.00 35.44 5.01
135 136 0.865769 GTGGACGCTGTTGTTAGTGG 59.134 55.000 0.00 0.00 32.56 4.00
136 137 0.506932 CGTGGACGCTGTTGTTAGTG 59.493 55.000 0.00 0.00 0.00 2.74
137 138 2.895039 CGTGGACGCTGTTGTTAGT 58.105 52.632 0.00 0.00 0.00 2.24
155 156 1.373748 TTGCTAACGACGTCCAGGC 60.374 57.895 10.58 9.91 0.00 4.85
156 157 0.319211 TGTTGCTAACGACGTCCAGG 60.319 55.000 10.58 0.00 32.23 4.45
157 158 1.060713 CTGTTGCTAACGACGTCCAG 58.939 55.000 10.58 4.91 32.23 3.86
158 159 0.942410 GCTGTTGCTAACGACGTCCA 60.942 55.000 10.58 0.00 36.03 4.02
159 160 1.779683 GCTGTTGCTAACGACGTCC 59.220 57.895 10.58 0.00 36.03 4.79
160 161 1.411089 CGCTGTTGCTAACGACGTC 59.589 57.895 5.18 5.18 36.97 4.34
161 162 2.019951 CCGCTGTTGCTAACGACGT 61.020 57.895 0.00 0.00 36.97 4.34
162 163 2.769617 CCGCTGTTGCTAACGACG 59.230 61.111 0.00 0.00 36.97 5.12
163 164 2.474712 GCCGCTGTTGCTAACGAC 59.525 61.111 0.00 0.00 36.97 4.34
164 165 2.740826 GGCCGCTGTTGCTAACGA 60.741 61.111 0.00 0.00 36.97 3.85
165 166 4.147322 CGGCCGCTGTTGCTAACG 62.147 66.667 14.67 0.00 36.97 3.18
166 167 1.738830 TACGGCCGCTGTTGCTAAC 60.739 57.895 28.58 0.00 36.97 2.34
167 168 1.738830 GTACGGCCGCTGTTGCTAA 60.739 57.895 28.58 0.00 36.97 3.09
168 169 2.125832 GTACGGCCGCTGTTGCTA 60.126 61.111 28.58 4.93 36.97 3.49
171 172 3.118454 CAGGTACGGCCGCTGTTG 61.118 66.667 28.58 15.48 43.70 3.33
172 173 2.874664 TTCAGGTACGGCCGCTGTT 61.875 57.895 28.58 8.43 43.70 3.16
173 174 3.307906 TTCAGGTACGGCCGCTGT 61.308 61.111 28.58 8.89 43.70 4.40
174 175 2.813908 GTTCAGGTACGGCCGCTG 60.814 66.667 28.58 24.13 43.70 5.18
175 176 4.430765 CGTTCAGGTACGGCCGCT 62.431 66.667 28.58 12.20 43.70 5.52
177 178 2.345880 ATAGCGTTCAGGTACGGCCG 62.346 60.000 26.86 26.86 43.70 6.13
178 179 0.179092 AATAGCGTTCAGGTACGGCC 60.179 55.000 0.00 0.00 41.65 6.13
179 180 2.497107 TAATAGCGTTCAGGTACGGC 57.503 50.000 0.00 0.00 41.65 5.68
180 181 4.443394 GTGATTAATAGCGTTCAGGTACGG 59.557 45.833 0.00 0.00 41.65 4.02
181 182 5.038683 TGTGATTAATAGCGTTCAGGTACG 58.961 41.667 0.00 0.00 44.09 3.67
182 183 5.050972 GCTGTGATTAATAGCGTTCAGGTAC 60.051 44.000 0.00 0.00 35.43 3.34
183 184 5.047847 GCTGTGATTAATAGCGTTCAGGTA 58.952 41.667 0.00 0.00 37.22 3.08
184 185 3.871594 GCTGTGATTAATAGCGTTCAGGT 59.128 43.478 0.00 0.00 0.00 4.00
185 186 4.458951 GCTGTGATTAATAGCGTTCAGG 57.541 45.455 0.00 0.00 0.00 3.86
192 193 3.495001 GGAAGGACGCTGTGATTAATAGC 59.505 47.826 0.00 0.00 0.00 2.97
193 194 4.950050 AGGAAGGACGCTGTGATTAATAG 58.050 43.478 0.00 0.00 0.00 1.73
194 195 5.597182 AGTAGGAAGGACGCTGTGATTAATA 59.403 40.000 0.00 0.00 0.00 0.98
195 196 3.914426 AGGAAGGACGCTGTGATTAAT 57.086 42.857 0.00 0.00 0.00 1.40
196 197 3.767673 AGTAGGAAGGACGCTGTGATTAA 59.232 43.478 0.00 0.00 0.00 1.40
197 198 3.362706 AGTAGGAAGGACGCTGTGATTA 58.637 45.455 0.00 0.00 0.00 1.75
198 199 2.180276 AGTAGGAAGGACGCTGTGATT 58.820 47.619 0.00 0.00 0.00 2.57
199 200 1.853963 AGTAGGAAGGACGCTGTGAT 58.146 50.000 0.00 0.00 0.00 3.06
200 201 1.629043 AAGTAGGAAGGACGCTGTGA 58.371 50.000 0.00 0.00 0.00 3.58
201 202 2.230508 TGTAAGTAGGAAGGACGCTGTG 59.769 50.000 0.00 0.00 0.00 3.66
202 203 2.230750 GTGTAAGTAGGAAGGACGCTGT 59.769 50.000 0.00 0.00 0.00 4.40
203 204 2.230508 TGTGTAAGTAGGAAGGACGCTG 59.769 50.000 0.00 0.00 0.00 5.18
204 205 2.522185 TGTGTAAGTAGGAAGGACGCT 58.478 47.619 0.00 0.00 0.00 5.07
205 206 3.308438 TTGTGTAAGTAGGAAGGACGC 57.692 47.619 0.00 0.00 0.00 5.19
206 207 5.350640 GGAAATTGTGTAAGTAGGAAGGACG 59.649 44.000 0.00 0.00 0.00 4.79
207 208 6.235664 TGGAAATTGTGTAAGTAGGAAGGAC 58.764 40.000 0.00 0.00 0.00 3.85
208 209 6.043938 ACTGGAAATTGTGTAAGTAGGAAGGA 59.956 38.462 0.00 0.00 0.00 3.36
209 210 6.238648 ACTGGAAATTGTGTAAGTAGGAAGG 58.761 40.000 0.00 0.00 0.00 3.46
210 211 7.584987 CAACTGGAAATTGTGTAAGTAGGAAG 58.415 38.462 0.00 0.00 0.00 3.46
211 212 6.016610 GCAACTGGAAATTGTGTAAGTAGGAA 60.017 38.462 0.00 0.00 0.00 3.36
212 213 5.472137 GCAACTGGAAATTGTGTAAGTAGGA 59.528 40.000 0.00 0.00 0.00 2.94
213 214 5.335661 GGCAACTGGAAATTGTGTAAGTAGG 60.336 44.000 0.00 0.00 0.00 3.18
214 215 5.335661 GGGCAACTGGAAATTGTGTAAGTAG 60.336 44.000 0.00 0.00 0.00 2.57
215 216 4.521256 GGGCAACTGGAAATTGTGTAAGTA 59.479 41.667 0.00 0.00 0.00 2.24
216 217 3.320826 GGGCAACTGGAAATTGTGTAAGT 59.679 43.478 0.00 0.00 0.00 2.24
217 218 3.573967 AGGGCAACTGGAAATTGTGTAAG 59.426 43.478 0.00 0.00 0.00 2.34
218 219 3.571590 AGGGCAACTGGAAATTGTGTAA 58.428 40.909 0.00 0.00 0.00 2.41
219 220 3.237268 AGGGCAACTGGAAATTGTGTA 57.763 42.857 0.00 0.00 0.00 2.90
220 221 2.086610 AGGGCAACTGGAAATTGTGT 57.913 45.000 0.00 0.00 0.00 3.72
221 222 3.473923 AAAGGGCAACTGGAAATTGTG 57.526 42.857 0.00 0.00 0.00 3.33
222 223 3.323691 GGTAAAGGGCAACTGGAAATTGT 59.676 43.478 0.00 0.00 0.00 2.71
223 224 3.323403 TGGTAAAGGGCAACTGGAAATTG 59.677 43.478 0.00 0.00 0.00 2.32
224 225 3.578282 CTGGTAAAGGGCAACTGGAAATT 59.422 43.478 0.00 0.00 0.00 1.82
225 226 3.165071 CTGGTAAAGGGCAACTGGAAAT 58.835 45.455 0.00 0.00 0.00 2.17
226 227 2.091555 ACTGGTAAAGGGCAACTGGAAA 60.092 45.455 0.00 0.00 0.00 3.13
227 228 1.497286 ACTGGTAAAGGGCAACTGGAA 59.503 47.619 0.00 0.00 0.00 3.53
228 229 1.145571 ACTGGTAAAGGGCAACTGGA 58.854 50.000 0.00 0.00 0.00 3.86
229 230 1.886542 GAACTGGTAAAGGGCAACTGG 59.113 52.381 0.00 0.00 0.00 4.00
230 231 1.886542 GGAACTGGTAAAGGGCAACTG 59.113 52.381 0.00 0.00 0.00 3.16
231 232 1.544759 CGGAACTGGTAAAGGGCAACT 60.545 52.381 0.00 0.00 0.00 3.16
232 233 0.879090 CGGAACTGGTAAAGGGCAAC 59.121 55.000 0.00 0.00 0.00 4.17
233 234 0.475044 ACGGAACTGGTAAAGGGCAA 59.525 50.000 0.00 0.00 0.00 4.52
234 235 1.350071 TACGGAACTGGTAAAGGGCA 58.650 50.000 0.00 0.00 0.00 5.36
235 236 2.477845 TTACGGAACTGGTAAAGGGC 57.522 50.000 0.00 0.00 0.00 5.19
236 237 5.981174 TCTAATTACGGAACTGGTAAAGGG 58.019 41.667 0.00 0.00 33.92 3.95
237 238 9.774413 ATTATCTAATTACGGAACTGGTAAAGG 57.226 33.333 0.00 0.00 33.92 3.11
283 284 1.081708 GTGCGTTCGCCCGATTTTT 60.082 52.632 14.44 0.00 0.00 1.94
284 285 2.559330 GTGCGTTCGCCCGATTTT 59.441 55.556 14.44 0.00 0.00 1.82
285 286 3.784412 CGTGCGTTCGCCCGATTT 61.784 61.111 15.71 0.00 34.15 2.17
322 323 4.541648 AGGCGGGGATAGGCGAGT 62.542 66.667 0.00 0.00 39.33 4.18
550 557 2.224018 CCAAAACATGACACACTTGGGG 60.224 50.000 0.00 0.00 31.59 4.96
598 605 2.975193 CACAATCACGCACAACAGAATG 59.025 45.455 0.00 0.00 46.00 2.67
607 614 1.207593 GTCCTGCACAATCACGCAC 59.792 57.895 0.00 0.00 33.75 5.34
681 701 3.117046 GAGATGCTCGCTAGTACCAAAC 58.883 50.000 0.00 0.00 0.00 2.93
694 714 6.090628 GCTAGTAATGCAATACAGAGATGCTC 59.909 42.308 14.21 0.00 40.66 4.26
728 748 6.278363 AGGCACGGTTAGTAATACAATACAG 58.722 40.000 0.00 0.00 0.00 2.74
762 927 5.741011 CCAATAGCTTAACTGTCCCTACAA 58.259 41.667 0.00 0.00 34.49 2.41
841 1010 0.747255 GAAGCGTCTCCTCCAGCATA 59.253 55.000 0.00 0.00 0.00 3.14
859 1028 1.912731 TGGCTGCATTACTAACCCTGA 59.087 47.619 0.50 0.00 0.00 3.86
895 1064 1.291132 GGACTCGGAGCTTTATGCAC 58.709 55.000 4.58 0.00 45.94 4.57
908 1078 6.150396 AGATTTACTAATCCACTGGACTCG 57.850 41.667 0.00 0.00 40.91 4.18
1169 1370 4.667573 TCTCTCAGATGGTAAGTGACTGT 58.332 43.478 0.00 0.00 0.00 3.55
1227 1428 1.940613 ACGAGGTGCAAAACTCTCAAC 59.059 47.619 11.19 0.00 0.00 3.18
1272 1473 2.828520 GTGATGAGACAGACCTTCCTCA 59.171 50.000 0.00 0.00 39.60 3.86
1327 1528 6.380079 ACCATGATTTCCTAACTGAACTCT 57.620 37.500 0.00 0.00 0.00 3.24
1386 1587 9.290988 TCAGGTAAAATTTGCTCTGTGTTATTA 57.709 29.630 11.90 0.00 0.00 0.98
1517 1718 6.813649 GGCAGATGCTAAAACAGATATATCGA 59.186 38.462 7.08 0.00 41.70 3.59
1528 1729 2.686915 AGCTCATGGCAGATGCTAAAAC 59.313 45.455 4.59 0.00 44.79 2.43
1735 1936 6.212589 TCCTGTACATAACCAGAAATGAGTGA 59.787 38.462 0.00 0.00 0.00 3.41
1803 2004 4.996434 GGCCTGCACGCTGACTGT 62.996 66.667 7.62 0.00 0.00 3.55
1887 2088 3.644884 AGTTCTAGACCGTGAACACTG 57.355 47.619 8.28 0.00 43.38 3.66
2006 2207 1.321474 CAGGTCCTTGCACACAATGT 58.679 50.000 0.00 0.00 34.61 2.71
2305 2506 0.755327 GGGGGCATGGACATTGTACC 60.755 60.000 0.00 0.00 0.00 3.34
2318 2519 0.334335 TATGACTGCATTTGGGGGCA 59.666 50.000 0.00 0.00 38.52 5.36
2495 2696 4.102838 CCTCCTTCATCATCATCCTCACTT 59.897 45.833 0.00 0.00 0.00 3.16
2798 3031 7.168219 AGGTGTGAGTCATGCTTTTTCTATAA 58.832 34.615 0.00 0.00 0.00 0.98
2799 3032 6.711277 AGGTGTGAGTCATGCTTTTTCTATA 58.289 36.000 0.00 0.00 0.00 1.31
2855 3088 8.246180 CAGCACAATATTGAATACTTTGAGGTT 58.754 33.333 22.16 0.00 0.00 3.50
2922 3155 6.355397 AGACTACATCGAGCATCAAAATTG 57.645 37.500 0.00 0.00 33.17 2.32
2936 3169 7.701078 TCAAGTGCGTATAAGAAAGACTACATC 59.299 37.037 0.00 0.00 0.00 3.06
3106 3340 5.296283 CAGACCAATCCAAAATAGCAGAGAG 59.704 44.000 0.00 0.00 0.00 3.20
3450 3736 3.380004 CCCTTCACAAAATATAAGGCGCA 59.620 43.478 10.83 0.00 37.71 6.09
3473 3759 6.168270 AGAATGCAACTAAGAGATACTCCC 57.832 41.667 0.00 0.00 0.00 4.30
3477 3763 6.037610 CCCACAAGAATGCAACTAAGAGATAC 59.962 42.308 0.00 0.00 0.00 2.24
3512 3798 8.129496 TCTAAAAACCACTGAAAGGAAAAACT 57.871 30.769 0.00 0.00 39.30 2.66
3656 3943 2.938798 TTTGGCCCCGATCCCAGT 60.939 61.111 0.00 0.00 31.73 4.00


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

AutoCloner maintained by Alex Coulton.