Multiple sequence alignment - TraesCS7B01G376100

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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 TraesCS7B01G376100 chr7B 100.000 1984 0 0 1 1984 641147902 641145919 0.000000e+00 3664
1 TraesCS7B01G376100 chr7B 81.542 493 86 4 986 1477 640946192 640945704 3.780000e-108 401
2 TraesCS7B01G376100 chr7B 100.000 197 0 0 1 197 489548971 489549167 4.960000e-97 364
3 TraesCS7B01G376100 chr7B 100.000 196 0 0 1 196 436824518 436824713 1.780000e-96 363
4 TraesCS7B01G376100 chr7B 85.448 268 31 5 1204 1469 641094953 641094692 3.090000e-69 272
5 TraesCS7B01G376100 chr7B 85.477 241 35 0 1096 1336 641029492 641029252 4.030000e-63 252
6 TraesCS7B01G376100 chr7B 100.000 128 0 0 2314 2441 641145589 641145462 1.130000e-58 237
7 TraesCS7B01G376100 chr7B 72.917 720 133 36 248 933 641092344 641091653 2.480000e-45 193
8 TraesCS7B01G376100 chr7A 88.457 1828 103 47 196 1984 669777831 669776073 0.000000e+00 2108
9 TraesCS7B01G376100 chr7A 99.010 202 2 0 1 202 317176170 317175969 1.780000e-96 363
10 TraesCS7B01G376100 chr7A 81.593 364 56 7 1082 1441 669774470 669774114 8.540000e-75 291
11 TraesCS7B01G376100 chr7A 96.875 128 3 1 2314 2441 669776036 669775910 1.900000e-51 213
12 TraesCS7B01G376100 chr7D 82.996 494 82 2 950 1442 577706740 577706248 1.720000e-121 446
13 TraesCS7B01G376100 chr7D 77.326 688 109 30 989 1647 577621032 577620363 1.780000e-96 363
14 TraesCS7B01G376100 chr4B 100.000 197 0 0 1 197 128541020 128541216 4.960000e-97 364
15 TraesCS7B01G376100 chr4B 100.000 196 0 0 1 196 4887575 4887380 1.780000e-96 363
16 TraesCS7B01G376100 chr4B 99.000 200 1 1 1 200 370705729 370705927 8.300000e-95 357
17 TraesCS7B01G376100 chr1A 100.000 195 0 0 1 195 29811203 29811009 6.420000e-96 361
18 TraesCS7B01G376100 chr1A 100.000 195 0 0 1 195 341181261 341181455 6.420000e-96 361
19 TraesCS7B01G376100 chr5A 98.039 204 2 1 1 204 602451831 602451630 1.070000e-93 353


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 TraesCS7B01G376100 chr7B 641145462 641147902 2440 True 1950.500000 3664 100.0000 1 2441 2 chr7B.!!$R4 2440
1 TraesCS7B01G376100 chr7B 641091653 641094953 3300 True 232.500000 272 79.1825 248 1469 2 chr7B.!!$R3 1221
2 TraesCS7B01G376100 chr7A 669774114 669777831 3717 True 870.666667 2108 88.9750 196 2441 3 chr7A.!!$R2 2245
3 TraesCS7B01G376100 chr7D 577620363 577621032 669 True 363.000000 363 77.3260 989 1647 1 chr7D.!!$R1 658

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
731 748 0.027194 CACGCGATGCTGAAATGAGG 59.973 55.0 15.93 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2399 1.080025 GGAACCGCGTAGAACTGCT 60.08 57.895 4.92 0.0 0.0 4.24 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
26 27 8.807948 AATATGTATTAGCTCTCTCTCTCCTC 57.192 38.462 0.00 0.00 0.00 3.71
27 28 5.638530 TGTATTAGCTCTCTCTCTCCTCA 57.361 43.478 0.00 0.00 0.00 3.86
28 29 6.199557 TGTATTAGCTCTCTCTCTCCTCAT 57.800 41.667 0.00 0.00 0.00 2.90
29 30 6.609876 TGTATTAGCTCTCTCTCTCCTCATT 58.390 40.000 0.00 0.00 0.00 2.57
30 31 7.066142 TGTATTAGCTCTCTCTCTCCTCATTT 58.934 38.462 0.00 0.00 0.00 2.32
31 32 8.221251 TGTATTAGCTCTCTCTCTCCTCATTTA 58.779 37.037 0.00 0.00 0.00 1.40
32 33 9.073475 GTATTAGCTCTCTCTCTCCTCATTTAA 57.927 37.037 0.00 0.00 0.00 1.52
33 34 8.725606 ATTAGCTCTCTCTCTCCTCATTTAAT 57.274 34.615 0.00 0.00 0.00 1.40
34 35 8.546083 TTAGCTCTCTCTCTCCTCATTTAATT 57.454 34.615 0.00 0.00 0.00 1.40
35 36 7.054491 AGCTCTCTCTCTCCTCATTTAATTC 57.946 40.000 0.00 0.00 0.00 2.17
36 37 6.041979 AGCTCTCTCTCTCCTCATTTAATTCC 59.958 42.308 0.00 0.00 0.00 3.01
37 38 6.041979 GCTCTCTCTCTCCTCATTTAATTCCT 59.958 42.308 0.00 0.00 0.00 3.36
38 39 7.595819 TCTCTCTCTCCTCATTTAATTCCTC 57.404 40.000 0.00 0.00 0.00 3.71
39 40 7.361438 TCTCTCTCTCCTCATTTAATTCCTCT 58.639 38.462 0.00 0.00 0.00 3.69
40 41 7.505585 TCTCTCTCTCCTCATTTAATTCCTCTC 59.494 40.741 0.00 0.00 0.00 3.20
41 42 6.553100 TCTCTCTCCTCATTTAATTCCTCTCC 59.447 42.308 0.00 0.00 0.00 3.71
42 43 6.448202 TCTCTCCTCATTTAATTCCTCTCCT 58.552 40.000 0.00 0.00 0.00 3.69
43 44 6.905776 TCTCTCCTCATTTAATTCCTCTCCTT 59.094 38.462 0.00 0.00 0.00 3.36
44 45 8.068110 TCTCTCCTCATTTAATTCCTCTCCTTA 58.932 37.037 0.00 0.00 0.00 2.69
45 46 8.256356 TCTCCTCATTTAATTCCTCTCCTTAG 57.744 38.462 0.00 0.00 0.00 2.18
46 47 7.846823 TCTCCTCATTTAATTCCTCTCCTTAGT 59.153 37.037 0.00 0.00 0.00 2.24
47 48 8.393959 TCCTCATTTAATTCCTCTCCTTAGTT 57.606 34.615 0.00 0.00 0.00 2.24
48 49 8.487028 TCCTCATTTAATTCCTCTCCTTAGTTC 58.513 37.037 0.00 0.00 0.00 3.01
49 50 8.490311 CCTCATTTAATTCCTCTCCTTAGTTCT 58.510 37.037 0.00 0.00 0.00 3.01
50 51 9.323985 CTCATTTAATTCCTCTCCTTAGTTCTG 57.676 37.037 0.00 0.00 0.00 3.02
51 52 8.267894 TCATTTAATTCCTCTCCTTAGTTCTGG 58.732 37.037 0.00 0.00 0.00 3.86
52 53 7.808279 TTTAATTCCTCTCCTTAGTTCTGGA 57.192 36.000 0.00 0.00 0.00 3.86
53 54 7.996758 TTAATTCCTCTCCTTAGTTCTGGAT 57.003 36.000 0.00 0.00 0.00 3.41
54 55 6.899892 AATTCCTCTCCTTAGTTCTGGATT 57.100 37.500 0.00 0.00 0.00 3.01
55 56 5.683876 TTCCTCTCCTTAGTTCTGGATTG 57.316 43.478 0.00 0.00 0.00 2.67
56 57 4.033709 TCCTCTCCTTAGTTCTGGATTGG 58.966 47.826 0.00 0.00 0.00 3.16
57 58 4.033709 CCTCTCCTTAGTTCTGGATTGGA 58.966 47.826 0.00 0.00 31.05 3.53
58 59 4.100808 CCTCTCCTTAGTTCTGGATTGGAG 59.899 50.000 0.00 0.00 40.47 3.86
59 60 4.033709 TCTCCTTAGTTCTGGATTGGAGG 58.966 47.826 0.00 0.00 39.80 4.30
60 61 3.115390 TCCTTAGTTCTGGATTGGAGGG 58.885 50.000 0.00 0.00 0.00 4.30
61 62 2.846827 CCTTAGTTCTGGATTGGAGGGT 59.153 50.000 0.00 0.00 0.00 4.34
62 63 3.267031 CCTTAGTTCTGGATTGGAGGGTT 59.733 47.826 0.00 0.00 0.00 4.11
63 64 4.263949 CCTTAGTTCTGGATTGGAGGGTTT 60.264 45.833 0.00 0.00 0.00 3.27
64 65 3.160679 AGTTCTGGATTGGAGGGTTTG 57.839 47.619 0.00 0.00 0.00 2.93
65 66 2.171003 GTTCTGGATTGGAGGGTTTGG 58.829 52.381 0.00 0.00 0.00 3.28
66 67 1.753903 TCTGGATTGGAGGGTTTGGA 58.246 50.000 0.00 0.00 0.00 3.53
67 68 1.635487 TCTGGATTGGAGGGTTTGGAG 59.365 52.381 0.00 0.00 0.00 3.86
68 69 0.704076 TGGATTGGAGGGTTTGGAGG 59.296 55.000 0.00 0.00 0.00 4.30
69 70 0.999712 GGATTGGAGGGTTTGGAGGA 59.000 55.000 0.00 0.00 0.00 3.71
70 71 1.570979 GGATTGGAGGGTTTGGAGGAT 59.429 52.381 0.00 0.00 0.00 3.24
71 72 2.783510 GGATTGGAGGGTTTGGAGGATA 59.216 50.000 0.00 0.00 0.00 2.59
72 73 3.204382 GGATTGGAGGGTTTGGAGGATAA 59.796 47.826 0.00 0.00 0.00 1.75
73 74 4.140924 GGATTGGAGGGTTTGGAGGATAAT 60.141 45.833 0.00 0.00 0.00 1.28
74 75 5.074515 GGATTGGAGGGTTTGGAGGATAATA 59.925 44.000 0.00 0.00 0.00 0.98
75 76 6.411554 GGATTGGAGGGTTTGGAGGATAATAA 60.412 42.308 0.00 0.00 0.00 1.40
76 77 6.410222 TTGGAGGGTTTGGAGGATAATAAA 57.590 37.500 0.00 0.00 0.00 1.40
77 78 6.606241 TGGAGGGTTTGGAGGATAATAAAT 57.394 37.500 0.00 0.00 0.00 1.40
78 79 6.372931 TGGAGGGTTTGGAGGATAATAAATG 58.627 40.000 0.00 0.00 0.00 2.32
79 80 5.243954 GGAGGGTTTGGAGGATAATAAATGC 59.756 44.000 0.00 0.00 0.00 3.56
80 81 6.030727 AGGGTTTGGAGGATAATAAATGCT 57.969 37.500 0.00 0.00 0.00 3.79
81 82 6.071320 AGGGTTTGGAGGATAATAAATGCTC 58.929 40.000 0.00 0.00 36.02 4.26
82 83 5.833131 GGGTTTGGAGGATAATAAATGCTCA 59.167 40.000 8.48 0.00 38.10 4.26
83 84 6.323739 GGGTTTGGAGGATAATAAATGCTCAA 59.676 38.462 8.48 0.00 38.10 3.02
84 85 7.015584 GGGTTTGGAGGATAATAAATGCTCAAT 59.984 37.037 8.48 0.00 38.10 2.57
85 86 9.077885 GGTTTGGAGGATAATAAATGCTCAATA 57.922 33.333 8.48 0.00 38.10 1.90
88 89 9.866655 TTGGAGGATAATAAATGCTCAATAACT 57.133 29.630 8.48 0.00 38.10 2.24
121 122 7.051000 AGTCTCTTTAGTATTTGGATCCAAGC 58.949 38.462 25.69 19.18 37.24 4.01
122 123 6.823689 GTCTCTTTAGTATTTGGATCCAAGCA 59.176 38.462 25.69 14.00 37.24 3.91
123 124 7.500559 GTCTCTTTAGTATTTGGATCCAAGCAT 59.499 37.037 25.69 19.69 37.24 3.79
124 125 7.500227 TCTCTTTAGTATTTGGATCCAAGCATG 59.500 37.037 25.69 12.43 37.24 4.06
135 136 2.322355 CCAAGCATGGGTGAGACTAG 57.678 55.000 0.00 0.00 43.51 2.57
136 137 1.661341 CAAGCATGGGTGAGACTAGC 58.339 55.000 0.00 0.00 0.00 3.42
137 138 1.065926 CAAGCATGGGTGAGACTAGCA 60.066 52.381 0.00 0.00 0.00 3.49
138 139 1.279496 AGCATGGGTGAGACTAGCAA 58.721 50.000 0.00 0.00 0.00 3.91
139 140 1.209019 AGCATGGGTGAGACTAGCAAG 59.791 52.381 0.00 0.00 0.00 4.01
140 141 1.065854 GCATGGGTGAGACTAGCAAGT 60.066 52.381 0.00 0.00 39.21 3.16
141 142 2.616510 GCATGGGTGAGACTAGCAAGTT 60.617 50.000 0.00 0.00 35.56 2.66
142 143 3.679389 CATGGGTGAGACTAGCAAGTTT 58.321 45.455 0.00 0.00 35.56 2.66
143 144 3.857157 TGGGTGAGACTAGCAAGTTTT 57.143 42.857 0.00 0.00 35.56 2.43
144 145 4.967084 TGGGTGAGACTAGCAAGTTTTA 57.033 40.909 0.00 0.00 35.56 1.52
145 146 4.894784 TGGGTGAGACTAGCAAGTTTTAG 58.105 43.478 0.00 0.00 35.56 1.85
146 147 4.347000 TGGGTGAGACTAGCAAGTTTTAGT 59.653 41.667 0.00 0.00 35.56 2.24
147 148 4.930405 GGGTGAGACTAGCAAGTTTTAGTC 59.070 45.833 13.08 13.08 43.83 2.59
148 149 4.930405 GGTGAGACTAGCAAGTTTTAGTCC 59.070 45.833 15.72 10.59 44.32 3.85
149 150 4.930405 GTGAGACTAGCAAGTTTTAGTCCC 59.070 45.833 15.72 8.76 44.32 4.46
150 151 4.591498 TGAGACTAGCAAGTTTTAGTCCCA 59.409 41.667 15.72 10.61 44.32 4.37
151 152 4.895961 AGACTAGCAAGTTTTAGTCCCAC 58.104 43.478 15.72 0.00 44.32 4.61
152 153 4.593634 AGACTAGCAAGTTTTAGTCCCACT 59.406 41.667 15.72 1.62 44.32 4.00
153 154 5.778750 AGACTAGCAAGTTTTAGTCCCACTA 59.221 40.000 15.72 0.00 44.32 2.74
154 155 5.791666 ACTAGCAAGTTTTAGTCCCACTAC 58.208 41.667 0.00 0.00 27.15 2.73
155 156 4.976540 AGCAAGTTTTAGTCCCACTACT 57.023 40.909 0.00 0.00 28.93 2.57
156 157 5.306114 AGCAAGTTTTAGTCCCACTACTT 57.694 39.130 0.00 0.00 28.93 2.24
157 158 5.691896 AGCAAGTTTTAGTCCCACTACTTT 58.308 37.500 0.00 0.00 28.93 2.66
158 159 6.127101 AGCAAGTTTTAGTCCCACTACTTTT 58.873 36.000 0.00 0.00 28.93 2.27
159 160 7.284820 AGCAAGTTTTAGTCCCACTACTTTTA 58.715 34.615 0.00 0.00 28.93 1.52
160 161 7.444487 AGCAAGTTTTAGTCCCACTACTTTTAG 59.556 37.037 0.00 0.00 28.93 1.85
161 162 7.228108 GCAAGTTTTAGTCCCACTACTTTTAGT 59.772 37.037 0.00 0.00 39.30 2.24
162 163 8.771766 CAAGTTTTAGTCCCACTACTTTTAGTC 58.228 37.037 0.00 0.00 36.31 2.59
163 164 8.026396 AGTTTTAGTCCCACTACTTTTAGTCA 57.974 34.615 0.00 0.00 36.31 3.41
164 165 8.657712 AGTTTTAGTCCCACTACTTTTAGTCAT 58.342 33.333 0.00 0.00 36.31 3.06
165 166 8.718734 GTTTTAGTCCCACTACTTTTAGTCATG 58.281 37.037 0.00 0.00 36.31 3.07
166 167 5.422214 AGTCCCACTACTTTTAGTCATGG 57.578 43.478 0.00 0.00 36.31 3.66
167 168 4.225267 AGTCCCACTACTTTTAGTCATGGG 59.775 45.833 16.70 16.70 46.94 4.00
182 183 4.761975 GTCATGGGACTAAAACGTATCCA 58.238 43.478 0.00 0.00 40.99 3.41
183 184 5.180271 GTCATGGGACTAAAACGTATCCAA 58.820 41.667 0.00 0.00 40.99 3.53
184 185 5.293569 GTCATGGGACTAAAACGTATCCAAG 59.706 44.000 0.00 0.00 40.99 3.61
185 186 3.602483 TGGGACTAAAACGTATCCAAGC 58.398 45.455 0.00 0.00 32.45 4.01
186 187 3.008157 TGGGACTAAAACGTATCCAAGCA 59.992 43.478 0.00 0.00 32.45 3.91
187 188 4.196971 GGGACTAAAACGTATCCAAGCAT 58.803 43.478 0.00 0.00 32.45 3.79
188 189 4.035208 GGGACTAAAACGTATCCAAGCATG 59.965 45.833 0.00 0.00 32.45 4.06
189 190 4.495844 GGACTAAAACGTATCCAAGCATGC 60.496 45.833 10.51 10.51 0.00 4.06
190 191 4.261801 ACTAAAACGTATCCAAGCATGCT 58.738 39.130 16.30 16.30 0.00 3.79
191 192 3.764885 AAAACGTATCCAAGCATGCTC 57.235 42.857 22.93 6.18 0.00 4.26
192 193 2.698855 AACGTATCCAAGCATGCTCT 57.301 45.000 22.93 8.65 0.00 4.09
193 194 2.698855 ACGTATCCAAGCATGCTCTT 57.301 45.000 22.93 2.64 0.00 2.85
194 195 3.819564 ACGTATCCAAGCATGCTCTTA 57.180 42.857 22.93 9.53 0.00 2.10
218 219 1.768275 CTTTTCCCCAGCAAACCCTTT 59.232 47.619 0.00 0.00 0.00 3.11
219 220 1.127343 TTTCCCCAGCAAACCCTTTG 58.873 50.000 0.00 0.00 43.44 2.77
234 235 2.091665 CCCTTTGGGTTCATATCCTGCT 60.092 50.000 0.00 0.00 38.25 4.24
303 304 2.283676 TCCACCCGAGGAGTCACC 60.284 66.667 0.00 0.00 39.35 4.02
304 305 2.603473 CCACCCGAGGAGTCACCA 60.603 66.667 0.00 0.00 42.04 4.17
313 314 1.122019 AGGAGTCACCACACCACCTC 61.122 60.000 0.00 0.00 42.04 3.85
324 325 0.517316 CACCACCTCGCTGCTTTTAC 59.483 55.000 0.00 0.00 0.00 2.01
328 329 0.875059 ACCTCGCTGCTTTTACTTGC 59.125 50.000 0.00 0.00 0.00 4.01
329 330 0.874390 CCTCGCTGCTTTTACTTGCA 59.126 50.000 0.00 0.00 37.63 4.08
330 331 1.266718 CCTCGCTGCTTTTACTTGCAA 59.733 47.619 0.00 0.00 38.81 4.08
331 332 2.310577 CTCGCTGCTTTTACTTGCAAC 58.689 47.619 0.00 0.00 38.81 4.17
359 360 2.954318 CTGCTGTATAAATTGCCCTGCT 59.046 45.455 0.00 0.00 0.00 4.24
361 362 2.294512 GCTGTATAAATTGCCCTGCTCC 59.705 50.000 0.00 0.00 0.00 4.70
362 363 2.549754 CTGTATAAATTGCCCTGCTCCG 59.450 50.000 0.00 0.00 0.00 4.63
363 364 2.171659 TGTATAAATTGCCCTGCTCCGA 59.828 45.455 0.00 0.00 0.00 4.55
364 365 1.680338 ATAAATTGCCCTGCTCCGAC 58.320 50.000 0.00 0.00 0.00 4.79
365 366 0.618458 TAAATTGCCCTGCTCCGACT 59.382 50.000 0.00 0.00 0.00 4.18
367 368 0.678048 AATTGCCCTGCTCCGACTTC 60.678 55.000 0.00 0.00 0.00 3.01
370 374 2.035442 GCCCTGCTCCGACTTCAAC 61.035 63.158 0.00 0.00 0.00 3.18
397 401 2.185310 CTTCTCACCCCCAACCTCCG 62.185 65.000 0.00 0.00 0.00 4.63
402 406 4.426313 CCCCCAACCTCCGCTTCC 62.426 72.222 0.00 0.00 0.00 3.46
403 407 4.778143 CCCCAACCTCCGCTTCCG 62.778 72.222 0.00 0.00 0.00 4.30
415 419 1.446966 GCTTCCGCTGTCTCTCCAC 60.447 63.158 0.00 0.00 0.00 4.02
417 421 1.533033 TTCCGCTGTCTCTCCACCA 60.533 57.895 0.00 0.00 0.00 4.17
445 449 2.652095 CCAACAGCCTTGGCCATGG 61.652 63.158 29.23 29.23 32.18 3.66
452 456 2.983791 CTTGGCCATGGCAAAGGG 59.016 61.111 37.21 20.17 46.84 3.95
468 472 4.509737 GGCCTCACGTCGGGTAGC 62.510 72.222 0.00 0.00 0.00 3.58
469 473 4.849329 GCCTCACGTCGGGTAGCG 62.849 72.222 0.00 0.00 0.00 4.26
470 474 3.437795 CCTCACGTCGGGTAGCGT 61.438 66.667 0.00 0.00 42.45 5.07
476 480 4.729856 GTCGGGTAGCGTGCGGTT 62.730 66.667 0.68 0.00 0.00 4.44
477 481 4.728102 TCGGGTAGCGTGCGGTTG 62.728 66.667 0.68 0.00 0.00 3.77
479 483 2.667199 GGGTAGCGTGCGGTTGTT 60.667 61.111 0.68 0.00 0.00 2.83
480 484 2.554272 GGTAGCGTGCGGTTGTTG 59.446 61.111 0.68 0.00 0.00 3.33
481 485 2.127383 GTAGCGTGCGGTTGTTGC 60.127 61.111 0.68 0.00 0.00 4.17
482 486 3.707700 TAGCGTGCGGTTGTTGCG 61.708 61.111 0.68 0.00 34.24 4.85
572 589 1.417890 GTGGGACTTCGATGGATCCAT 59.582 52.381 27.66 27.66 39.69 3.41
584 601 1.160137 GGATCCATTGCTATCCACGC 58.840 55.000 6.95 0.00 41.21 5.34
590 607 1.867233 CATTGCTATCCACGCTGGTAC 59.133 52.381 4.33 0.00 39.03 3.34
605 622 4.759516 CTGGTACGGCAATAGTTTTGTT 57.240 40.909 0.00 0.00 0.00 2.83
610 627 4.911514 ACGGCAATAGTTTTGTTGAGTT 57.088 36.364 0.00 0.00 0.00 3.01
640 657 0.846427 TTCCTCAGTGAAGCCCCCAT 60.846 55.000 0.00 0.00 0.00 4.00
641 658 1.077212 CCTCAGTGAAGCCCCCATG 60.077 63.158 0.00 0.00 0.00 3.66
642 659 1.687612 CTCAGTGAAGCCCCCATGT 59.312 57.895 0.00 0.00 0.00 3.21
688 705 4.394712 CCTGGTGCACCCGGAGAC 62.395 72.222 35.97 10.18 42.35 3.36
707 724 1.411394 CGTCGTCGTACCAAATGTGT 58.589 50.000 0.00 0.00 0.00 3.72
709 726 2.129607 GTCGTCGTACCAAATGTGTGT 58.870 47.619 0.00 0.00 0.00 3.72
710 727 3.307674 GTCGTCGTACCAAATGTGTGTA 58.692 45.455 0.00 0.00 0.00 2.90
711 728 3.922240 GTCGTCGTACCAAATGTGTGTAT 59.078 43.478 0.00 0.00 0.00 2.29
712 729 4.030977 GTCGTCGTACCAAATGTGTGTATC 59.969 45.833 0.00 0.00 0.00 2.24
713 730 3.921630 CGTCGTACCAAATGTGTGTATCA 59.078 43.478 0.00 0.00 0.00 2.15
714 731 4.201551 CGTCGTACCAAATGTGTGTATCAC 60.202 45.833 0.00 0.00 46.31 3.06
722 739 2.665777 GTGTGTATCACGCGATGCT 58.334 52.632 15.93 1.27 37.14 3.79
731 748 0.027194 CACGCGATGCTGAAATGAGG 59.973 55.000 15.93 0.00 0.00 3.86
737 754 2.715046 GATGCTGAAATGAGGGTGTCA 58.285 47.619 0.00 0.00 40.38 3.58
746 763 4.853924 AATGAGGGTGTCACATGTTTTC 57.146 40.909 5.12 0.00 38.28 2.29
770 787 2.328099 CCACAAAGACTGCTCCGGC 61.328 63.158 0.00 0.00 39.26 6.13
791 808 1.433534 GAGTCCTGCTCGTCAAAAGG 58.566 55.000 0.00 0.00 34.13 3.11
806 823 0.323957 AAAGGTCACTTCTACGGCCC 59.676 55.000 0.00 0.00 35.41 5.80
877 894 7.225538 CACAGTTATGAAGGAACAGATGGATAC 59.774 40.741 0.00 0.00 0.00 2.24
878 895 6.422100 CAGTTATGAAGGAACAGATGGATACG 59.578 42.308 0.00 0.00 42.51 3.06
886 903 4.451900 GAACAGATGGATACGGAAACCAT 58.548 43.478 9.10 9.10 45.50 3.55
934 951 1.004044 CAAGCACCTTGGTGATCTCCT 59.996 52.381 22.52 7.41 37.77 3.69
948 965 2.498644 TCTCCTCAAGAGCGAGAAGA 57.501 50.000 12.73 0.00 42.90 2.87
1012 1057 0.684535 TGTTCTCATGGCCGAGTTCA 59.315 50.000 7.44 5.76 34.46 3.18
1025 1070 1.293924 GAGTTCATCGGGCACATGAG 58.706 55.000 0.00 0.00 31.84 2.90
1031 1076 1.690219 ATCGGGCACATGAGGGAGAC 61.690 60.000 0.00 0.00 0.00 3.36
1036 1081 1.226802 CACATGAGGGAGACGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
1038 1083 2.441164 ATGAGGGAGACGAGCGCT 60.441 61.111 11.27 11.27 0.00 5.92
1039 1084 2.485795 ATGAGGGAGACGAGCGCTC 61.486 63.158 27.64 27.64 43.32 5.03
1040 1085 3.134792 GAGGGAGACGAGCGCTCA 61.135 66.667 34.69 0.00 42.76 4.26
1104 1149 3.059393 CCATGCTGCACTTCATATACACG 60.059 47.826 3.57 0.00 0.00 4.49
1109 1154 3.517602 TGCACTTCATATACACGGACAC 58.482 45.455 0.00 0.00 0.00 3.67
1110 1155 2.864343 GCACTTCATATACACGGACACC 59.136 50.000 0.00 0.00 0.00 4.16
1126 1171 3.609853 GACACCATGCCTGAACTTGATA 58.390 45.455 0.00 0.00 0.00 2.15
1143 1188 1.984288 ATAAGGAACTGGAGGCCGCC 61.984 60.000 20.28 20.28 40.86 6.13
1173 1218 1.093159 CTCAGCATCTTCTTGTGGCC 58.907 55.000 0.00 0.00 0.00 5.36
1420 1479 4.616953 GCTTACTAGCATTGTCCTCTCTC 58.383 47.826 0.00 0.00 46.95 3.20
1460 1524 1.797025 AAACGAAGCTGTAGGTGCTC 58.203 50.000 0.00 0.00 40.22 4.26
1466 1530 3.614150 CGAAGCTGTAGGTGCTCAAGTTA 60.614 47.826 0.00 0.00 40.22 2.24
1477 1541 9.542462 GTAGGTGCTCAAGTTACAATATATTCA 57.458 33.333 0.00 0.00 0.00 2.57
1480 1544 8.552034 GGTGCTCAAGTTACAATATATTCAGTC 58.448 37.037 0.00 0.00 0.00 3.51
1481 1545 8.269424 GTGCTCAAGTTACAATATATTCAGTCG 58.731 37.037 0.00 0.00 0.00 4.18
1482 1546 8.194769 TGCTCAAGTTACAATATATTCAGTCGA 58.805 33.333 0.00 0.00 0.00 4.20
1483 1547 8.480853 GCTCAAGTTACAATATATTCAGTCGAC 58.519 37.037 7.70 7.70 0.00 4.20
1486 1560 5.624081 AGTTACAATATATTCAGTCGACGCG 59.376 40.000 10.46 3.53 0.00 6.01
1503 1577 2.162809 ACGCGTTTTGTCACTTCCTTTT 59.837 40.909 5.58 0.00 0.00 2.27
1551 1634 8.588290 AATTATGTGTACTTTTGCCTAATGGA 57.412 30.769 0.00 0.00 34.57 3.41
1553 1636 3.756434 TGTGTACTTTTGCCTAATGGAGC 59.244 43.478 0.00 0.00 34.57 4.70
1572 1655 5.954752 TGGAGCCATCTATCCTACTTCTATG 59.045 44.000 0.00 0.00 36.50 2.23
1589 1672 7.148641 ACTTCTATGTATATTCCGAGCAACTG 58.851 38.462 0.00 0.00 0.00 3.16
1595 1678 0.322816 ATTCCGAGCAACTGCCATGT 60.323 50.000 0.00 0.00 43.38 3.21
1671 1754 5.648178 TGTGTGCAAAATCATCTAATGCT 57.352 34.783 0.00 0.00 37.86 3.79
1700 1783 5.314529 TGTTTTGTTATCCCCGTGAATGTA 58.685 37.500 0.00 0.00 0.00 2.29
1709 1792 1.087771 CCGTGAATGTACCCCTTCGC 61.088 60.000 0.00 0.00 0.00 4.70
1779 2206 3.551846 ACTTGGTGAGAACGGTTTCATT 58.448 40.909 0.00 0.00 33.72 2.57
1782 2209 2.616376 TGGTGAGAACGGTTTCATTGTG 59.384 45.455 0.00 0.00 33.72 3.33
1783 2210 2.604614 GGTGAGAACGGTTTCATTGTGC 60.605 50.000 0.00 0.00 33.72 4.57
1785 2212 1.263217 GAGAACGGTTTCATTGTGCGT 59.737 47.619 0.00 0.00 33.72 5.24
1882 2381 9.696917 AAGTTAGAAAAATGATTGATGACCAAC 57.303 29.630 0.00 0.00 37.63 3.77
1900 2399 3.953612 CCAACCTATTCCAAATGCAGCTA 59.046 43.478 0.00 0.00 0.00 3.32
1912 2411 2.292803 GCAGCTAGCAGTTCTACGC 58.707 57.895 18.83 2.30 44.79 4.42
2342 2841 8.479313 TGCTTGTATATTCAGAGTGTAAACTG 57.521 34.615 0.00 0.00 35.72 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.390143 TGAGGAGAGAGAGAGCTAATACATATT 58.610 37.037 0.00 0.00 0.00 1.28
2 3 7.927788 TGAGGAGAGAGAGAGCTAATACATAT 58.072 38.462 0.00 0.00 0.00 1.78
3 4 7.323052 TGAGGAGAGAGAGAGCTAATACATA 57.677 40.000 0.00 0.00 0.00 2.29
4 5 6.199557 TGAGGAGAGAGAGAGCTAATACAT 57.800 41.667 0.00 0.00 0.00 2.29
5 6 5.638530 TGAGGAGAGAGAGAGCTAATACA 57.361 43.478 0.00 0.00 0.00 2.29
6 7 7.524717 AAATGAGGAGAGAGAGAGCTAATAC 57.475 40.000 0.00 0.00 0.00 1.89
7 8 9.821240 ATTAAATGAGGAGAGAGAGAGCTAATA 57.179 33.333 0.00 0.00 0.00 0.98
8 9 8.725606 ATTAAATGAGGAGAGAGAGAGCTAAT 57.274 34.615 0.00 0.00 0.00 1.73
9 10 8.546083 AATTAAATGAGGAGAGAGAGAGCTAA 57.454 34.615 0.00 0.00 0.00 3.09
10 11 7.232534 GGAATTAAATGAGGAGAGAGAGAGCTA 59.767 40.741 0.00 0.00 0.00 3.32
11 12 6.041979 GGAATTAAATGAGGAGAGAGAGAGCT 59.958 42.308 0.00 0.00 0.00 4.09
12 13 6.041979 AGGAATTAAATGAGGAGAGAGAGAGC 59.958 42.308 0.00 0.00 0.00 4.09
13 14 7.506938 AGAGGAATTAAATGAGGAGAGAGAGAG 59.493 40.741 0.00 0.00 0.00 3.20
14 15 7.361438 AGAGGAATTAAATGAGGAGAGAGAGA 58.639 38.462 0.00 0.00 0.00 3.10
15 16 7.255942 GGAGAGGAATTAAATGAGGAGAGAGAG 60.256 44.444 0.00 0.00 0.00 3.20
16 17 6.553100 GGAGAGGAATTAAATGAGGAGAGAGA 59.447 42.308 0.00 0.00 0.00 3.10
17 18 6.554605 AGGAGAGGAATTAAATGAGGAGAGAG 59.445 42.308 0.00 0.00 0.00 3.20
18 19 6.448202 AGGAGAGGAATTAAATGAGGAGAGA 58.552 40.000 0.00 0.00 0.00 3.10
19 20 6.745794 AGGAGAGGAATTAAATGAGGAGAG 57.254 41.667 0.00 0.00 0.00 3.20
20 21 7.846823 ACTAAGGAGAGGAATTAAATGAGGAGA 59.153 37.037 0.00 0.00 0.00 3.71
21 22 8.028652 ACTAAGGAGAGGAATTAAATGAGGAG 57.971 38.462 0.00 0.00 0.00 3.69
22 23 7.996758 ACTAAGGAGAGGAATTAAATGAGGA 57.003 36.000 0.00 0.00 0.00 3.71
23 24 8.490311 AGAACTAAGGAGAGGAATTAAATGAGG 58.510 37.037 0.00 0.00 0.00 3.86
24 25 9.323985 CAGAACTAAGGAGAGGAATTAAATGAG 57.676 37.037 0.00 0.00 0.00 2.90
25 26 8.267894 CCAGAACTAAGGAGAGGAATTAAATGA 58.732 37.037 0.00 0.00 0.00 2.57
26 27 8.267894 TCCAGAACTAAGGAGAGGAATTAAATG 58.732 37.037 0.00 0.00 0.00 2.32
27 28 8.393959 TCCAGAACTAAGGAGAGGAATTAAAT 57.606 34.615 0.00 0.00 0.00 1.40
28 29 7.808279 TCCAGAACTAAGGAGAGGAATTAAA 57.192 36.000 0.00 0.00 0.00 1.52
29 30 7.996758 ATCCAGAACTAAGGAGAGGAATTAA 57.003 36.000 0.00 0.00 37.34 1.40
30 31 7.147479 CCAATCCAGAACTAAGGAGAGGAATTA 60.147 40.741 0.00 0.00 37.34 1.40
31 32 6.353429 CCAATCCAGAACTAAGGAGAGGAATT 60.353 42.308 0.00 0.00 37.34 2.17
32 33 5.131809 CCAATCCAGAACTAAGGAGAGGAAT 59.868 44.000 0.00 0.00 37.34 3.01
33 34 4.471386 CCAATCCAGAACTAAGGAGAGGAA 59.529 45.833 0.00 0.00 37.34 3.36
34 35 4.033709 CCAATCCAGAACTAAGGAGAGGA 58.966 47.826 0.00 0.00 37.34 3.71
35 36 4.033709 TCCAATCCAGAACTAAGGAGAGG 58.966 47.826 0.00 0.00 37.34 3.69
36 37 4.100808 CCTCCAATCCAGAACTAAGGAGAG 59.899 50.000 7.12 0.00 42.87 3.20
37 38 4.033709 CCTCCAATCCAGAACTAAGGAGA 58.966 47.826 7.12 0.00 42.87 3.71
38 39 3.135530 CCCTCCAATCCAGAACTAAGGAG 59.864 52.174 0.00 0.00 40.58 3.69
39 40 3.115390 CCCTCCAATCCAGAACTAAGGA 58.885 50.000 0.00 0.00 38.50 3.36
40 41 2.846827 ACCCTCCAATCCAGAACTAAGG 59.153 50.000 0.00 0.00 0.00 2.69
41 42 4.576330 AACCCTCCAATCCAGAACTAAG 57.424 45.455 0.00 0.00 0.00 2.18
42 43 4.508405 CCAAACCCTCCAATCCAGAACTAA 60.508 45.833 0.00 0.00 0.00 2.24
43 44 3.010138 CCAAACCCTCCAATCCAGAACTA 59.990 47.826 0.00 0.00 0.00 2.24
44 45 2.225117 CCAAACCCTCCAATCCAGAACT 60.225 50.000 0.00 0.00 0.00 3.01
45 46 2.171003 CCAAACCCTCCAATCCAGAAC 58.829 52.381 0.00 0.00 0.00 3.01
46 47 2.041620 CTCCAAACCCTCCAATCCAGAA 59.958 50.000 0.00 0.00 0.00 3.02
47 48 1.635487 CTCCAAACCCTCCAATCCAGA 59.365 52.381 0.00 0.00 0.00 3.86
48 49 1.341383 CCTCCAAACCCTCCAATCCAG 60.341 57.143 0.00 0.00 0.00 3.86
49 50 0.704076 CCTCCAAACCCTCCAATCCA 59.296 55.000 0.00 0.00 0.00 3.41
50 51 0.999712 TCCTCCAAACCCTCCAATCC 59.000 55.000 0.00 0.00 0.00 3.01
51 52 4.519906 TTATCCTCCAAACCCTCCAATC 57.480 45.455 0.00 0.00 0.00 2.67
52 53 6.606241 TTATTATCCTCCAAACCCTCCAAT 57.394 37.500 0.00 0.00 0.00 3.16
53 54 6.410222 TTTATTATCCTCCAAACCCTCCAA 57.590 37.500 0.00 0.00 0.00 3.53
54 55 6.372931 CATTTATTATCCTCCAAACCCTCCA 58.627 40.000 0.00 0.00 0.00 3.86
55 56 5.243954 GCATTTATTATCCTCCAAACCCTCC 59.756 44.000 0.00 0.00 0.00 4.30
56 57 6.071320 AGCATTTATTATCCTCCAAACCCTC 58.929 40.000 0.00 0.00 0.00 4.30
57 58 6.030727 AGCATTTATTATCCTCCAAACCCT 57.969 37.500 0.00 0.00 0.00 4.34
58 59 5.833131 TGAGCATTTATTATCCTCCAAACCC 59.167 40.000 0.00 0.00 0.00 4.11
59 60 6.959639 TGAGCATTTATTATCCTCCAAACC 57.040 37.500 0.00 0.00 0.00 3.27
62 63 9.866655 AGTTATTGAGCATTTATTATCCTCCAA 57.133 29.630 0.00 0.00 0.00 3.53
95 96 8.204836 GCTTGGATCCAAATACTAAAGAGACTA 58.795 37.037 26.87 0.00 35.33 2.59
96 97 7.051000 GCTTGGATCCAAATACTAAAGAGACT 58.949 38.462 26.87 0.00 35.33 3.24
97 98 6.823689 TGCTTGGATCCAAATACTAAAGAGAC 59.176 38.462 26.87 8.83 35.33 3.36
98 99 6.957631 TGCTTGGATCCAAATACTAAAGAGA 58.042 36.000 26.87 1.15 35.33 3.10
99 100 7.255381 CCATGCTTGGATCCAAATACTAAAGAG 60.255 40.741 26.87 12.80 46.92 2.85
100 101 6.547141 CCATGCTTGGATCCAAATACTAAAGA 59.453 38.462 26.87 1.90 46.92 2.52
101 102 6.239120 CCCATGCTTGGATCCAAATACTAAAG 60.239 42.308 26.87 14.21 46.92 1.85
102 103 5.598005 CCCATGCTTGGATCCAAATACTAAA 59.402 40.000 26.87 8.81 46.92 1.85
103 104 5.139727 CCCATGCTTGGATCCAAATACTAA 58.860 41.667 26.87 10.11 46.92 2.24
104 105 4.167892 ACCCATGCTTGGATCCAAATACTA 59.832 41.667 26.87 12.31 46.92 1.82
105 106 3.052642 ACCCATGCTTGGATCCAAATACT 60.053 43.478 26.87 10.16 46.92 2.12
106 107 3.068590 CACCCATGCTTGGATCCAAATAC 59.931 47.826 26.87 19.00 46.92 1.89
107 108 3.053019 TCACCCATGCTTGGATCCAAATA 60.053 43.478 26.87 18.63 46.92 1.40
108 109 2.112998 CACCCATGCTTGGATCCAAAT 58.887 47.619 26.87 16.27 46.92 2.32
109 110 1.076841 TCACCCATGCTTGGATCCAAA 59.923 47.619 26.87 14.63 46.92 3.28
110 111 0.703488 TCACCCATGCTTGGATCCAA 59.297 50.000 25.53 25.53 46.92 3.53
111 112 0.256752 CTCACCCATGCTTGGATCCA 59.743 55.000 19.85 11.44 46.92 3.41
112 113 0.548031 TCTCACCCATGCTTGGATCC 59.452 55.000 19.85 4.20 46.92 3.36
113 114 1.211457 AGTCTCACCCATGCTTGGATC 59.789 52.381 19.85 3.99 46.92 3.36
114 115 1.293062 AGTCTCACCCATGCTTGGAT 58.707 50.000 19.85 0.00 46.92 3.41
115 116 1.833630 CTAGTCTCACCCATGCTTGGA 59.166 52.381 19.85 0.00 46.92 3.53
116 117 1.745141 GCTAGTCTCACCCATGCTTGG 60.745 57.143 11.68 11.68 43.23 3.61
117 118 1.065926 TGCTAGTCTCACCCATGCTTG 60.066 52.381 0.00 0.00 0.00 4.01
118 119 1.279496 TGCTAGTCTCACCCATGCTT 58.721 50.000 0.00 0.00 0.00 3.91
119 120 1.209019 CTTGCTAGTCTCACCCATGCT 59.791 52.381 0.00 0.00 0.00 3.79
120 121 1.065854 ACTTGCTAGTCTCACCCATGC 60.066 52.381 0.00 0.00 0.00 4.06
121 122 3.340814 AACTTGCTAGTCTCACCCATG 57.659 47.619 0.07 0.00 31.99 3.66
122 123 4.373156 AAAACTTGCTAGTCTCACCCAT 57.627 40.909 0.07 0.00 31.99 4.00
123 124 3.857157 AAAACTTGCTAGTCTCACCCA 57.143 42.857 0.07 0.00 31.99 4.51
124 125 4.895961 ACTAAAACTTGCTAGTCTCACCC 58.104 43.478 0.07 0.00 31.99 4.61
125 126 4.930405 GGACTAAAACTTGCTAGTCTCACC 59.070 45.833 0.07 0.00 42.42 4.02
126 127 4.930405 GGGACTAAAACTTGCTAGTCTCAC 59.070 45.833 0.07 0.00 42.76 3.51
127 128 5.148651 GGGACTAAAACTTGCTAGTCTCA 57.851 43.478 0.07 0.00 42.76 3.27
128 129 4.930405 GTGGGACTAAAACTTGCTAGTCTC 59.070 45.833 0.07 1.39 43.29 3.36
129 130 4.593634 AGTGGGACTAAAACTTGCTAGTCT 59.406 41.667 0.07 0.00 42.42 3.24
130 131 4.895961 AGTGGGACTAAAACTTGCTAGTC 58.104 43.478 0.07 0.62 42.17 2.59
131 132 4.976540 AGTGGGACTAAAACTTGCTAGT 57.023 40.909 0.00 0.00 35.68 2.57
132 133 6.038997 AGTAGTGGGACTAAAACTTGCTAG 57.961 41.667 0.00 0.00 31.62 3.42
133 134 6.429521 AAGTAGTGGGACTAAAACTTGCTA 57.570 37.500 0.00 0.00 31.62 3.49
134 135 4.976540 AGTAGTGGGACTAAAACTTGCT 57.023 40.909 0.00 0.00 31.62 3.91
135 136 6.387041 AAAAGTAGTGGGACTAAAACTTGC 57.613 37.500 0.00 0.00 31.62 4.01
136 137 8.672823 ACTAAAAGTAGTGGGACTAAAACTTG 57.327 34.615 0.00 0.00 39.20 3.16
137 138 8.488668 TGACTAAAAGTAGTGGGACTAAAACTT 58.511 33.333 0.00 0.00 40.82 2.66
138 139 8.026396 TGACTAAAAGTAGTGGGACTAAAACT 57.974 34.615 0.00 0.00 40.82 2.66
139 140 8.718734 CATGACTAAAAGTAGTGGGACTAAAAC 58.281 37.037 0.00 0.00 40.82 2.43
140 141 7.881232 CCATGACTAAAAGTAGTGGGACTAAAA 59.119 37.037 0.00 0.00 40.82 1.52
141 142 7.391620 CCATGACTAAAAGTAGTGGGACTAAA 58.608 38.462 0.00 0.00 40.82 1.85
142 143 6.942976 CCATGACTAAAAGTAGTGGGACTAA 58.057 40.000 0.00 0.00 40.82 2.24
143 144 6.540438 CCATGACTAAAAGTAGTGGGACTA 57.460 41.667 0.00 0.00 40.82 2.59
144 145 5.422214 CCATGACTAAAAGTAGTGGGACT 57.578 43.478 0.00 0.00 40.82 3.85
147 148 4.514401 GTCCCATGACTAAAAGTAGTGGG 58.486 47.826 17.22 17.22 46.41 4.61
158 159 5.657745 TGGATACGTTTTAGTCCCATGACTA 59.342 40.000 0.00 0.00 45.97 2.59
160 161 4.761975 TGGATACGTTTTAGTCCCATGAC 58.238 43.478 0.00 0.00 40.25 3.06
161 162 5.423704 TTGGATACGTTTTAGTCCCATGA 57.576 39.130 0.00 0.00 42.51 3.07
162 163 4.035208 GCTTGGATACGTTTTAGTCCCATG 59.965 45.833 0.00 0.00 42.51 3.66
163 164 4.196971 GCTTGGATACGTTTTAGTCCCAT 58.803 43.478 0.00 0.00 42.51 4.00
164 165 3.008157 TGCTTGGATACGTTTTAGTCCCA 59.992 43.478 0.00 0.00 42.51 4.37
165 166 3.602483 TGCTTGGATACGTTTTAGTCCC 58.398 45.455 0.00 0.00 42.51 4.46
166 167 4.495844 GCATGCTTGGATACGTTTTAGTCC 60.496 45.833 11.37 0.00 42.51 3.85
167 168 4.332819 AGCATGCTTGGATACGTTTTAGTC 59.667 41.667 16.30 0.00 42.51 2.59
168 169 4.261801 AGCATGCTTGGATACGTTTTAGT 58.738 39.130 16.30 0.00 42.51 2.24
169 170 4.572389 AGAGCATGCTTGGATACGTTTTAG 59.428 41.667 23.61 0.00 42.51 1.85
170 171 4.513442 AGAGCATGCTTGGATACGTTTTA 58.487 39.130 23.61 0.00 42.51 1.52
171 172 3.347216 AGAGCATGCTTGGATACGTTTT 58.653 40.909 23.61 0.00 42.51 2.43
172 173 2.991250 AGAGCATGCTTGGATACGTTT 58.009 42.857 23.61 0.00 42.51 3.60
173 174 2.698855 AGAGCATGCTTGGATACGTT 57.301 45.000 23.61 0.00 42.51 3.99
174 175 2.698855 AAGAGCATGCTTGGATACGT 57.301 45.000 23.61 2.80 42.51 3.57
175 176 3.492383 CACTAAGAGCATGCTTGGATACG 59.508 47.826 23.61 9.36 42.51 3.06
176 177 3.249559 GCACTAAGAGCATGCTTGGATAC 59.750 47.826 23.61 7.76 36.40 2.24
177 178 3.470709 GCACTAAGAGCATGCTTGGATA 58.529 45.455 23.61 11.43 36.40 2.59
178 179 2.295885 GCACTAAGAGCATGCTTGGAT 58.704 47.619 23.61 10.87 36.40 3.41
179 180 1.742761 GCACTAAGAGCATGCTTGGA 58.257 50.000 23.61 8.88 36.40 3.53
184 185 2.159324 GGGAAAAGCACTAAGAGCATGC 60.159 50.000 10.51 10.51 39.74 4.06
185 186 2.424956 GGGGAAAAGCACTAAGAGCATG 59.575 50.000 0.00 0.00 0.00 4.06
186 187 2.041620 TGGGGAAAAGCACTAAGAGCAT 59.958 45.455 0.00 0.00 0.00 3.79
187 188 1.423541 TGGGGAAAAGCACTAAGAGCA 59.576 47.619 0.00 0.00 0.00 4.26
188 189 2.087646 CTGGGGAAAAGCACTAAGAGC 58.912 52.381 0.00 0.00 0.00 4.09
189 190 2.087646 GCTGGGGAAAAGCACTAAGAG 58.912 52.381 0.00 0.00 40.52 2.85
190 191 1.423541 TGCTGGGGAAAAGCACTAAGA 59.576 47.619 0.00 0.00 45.50 2.10
191 192 1.909700 TGCTGGGGAAAAGCACTAAG 58.090 50.000 0.00 0.00 45.50 2.18
218 219 4.524802 ATCAAAGCAGGATATGAACCCA 57.475 40.909 0.00 0.00 0.00 4.51
219 220 4.889409 TCAATCAAAGCAGGATATGAACCC 59.111 41.667 0.00 0.00 0.00 4.11
300 301 2.666190 CAGCGAGGTGGTGTGGTG 60.666 66.667 0.00 0.00 41.21 4.17
313 314 1.268999 TGGTTGCAAGTAAAAGCAGCG 60.269 47.619 0.00 0.00 42.00 5.18
324 325 1.833934 AGCAGGGGTTGGTTGCAAG 60.834 57.895 0.00 0.00 40.22 4.01
328 329 2.799126 TATACAGCAGGGGTTGGTTG 57.201 50.000 0.00 0.00 34.69 3.77
329 330 3.818295 TTTATACAGCAGGGGTTGGTT 57.182 42.857 0.00 0.00 34.69 3.67
330 331 4.023291 CAATTTATACAGCAGGGGTTGGT 58.977 43.478 0.00 0.00 38.24 3.67
331 332 3.181476 GCAATTTATACAGCAGGGGTTGG 60.181 47.826 0.00 0.00 0.00 3.77
359 360 2.187958 AGATGATGGGTTGAAGTCGGA 58.812 47.619 0.00 0.00 0.00 4.55
361 362 3.866651 AGAAGATGATGGGTTGAAGTCG 58.133 45.455 0.00 0.00 0.00 4.18
362 363 4.633565 GTGAGAAGATGATGGGTTGAAGTC 59.366 45.833 0.00 0.00 0.00 3.01
363 364 4.566488 GGTGAGAAGATGATGGGTTGAAGT 60.566 45.833 0.00 0.00 0.00 3.01
364 365 3.944015 GGTGAGAAGATGATGGGTTGAAG 59.056 47.826 0.00 0.00 0.00 3.02
365 366 3.308402 GGGTGAGAAGATGATGGGTTGAA 60.308 47.826 0.00 0.00 0.00 2.69
367 368 2.648059 GGGTGAGAAGATGATGGGTTG 58.352 52.381 0.00 0.00 0.00 3.77
370 374 0.475906 GGGGGTGAGAAGATGATGGG 59.524 60.000 0.00 0.00 0.00 4.00
402 406 1.142748 GGATGGTGGAGAGACAGCG 59.857 63.158 0.00 0.00 41.54 5.18
403 407 0.107945 GTGGATGGTGGAGAGACAGC 60.108 60.000 0.00 0.00 39.22 4.40
404 408 1.566211 AGTGGATGGTGGAGAGACAG 58.434 55.000 0.00 0.00 0.00 3.51
415 419 0.967380 GCTGTTGGGGAAGTGGATGG 60.967 60.000 0.00 0.00 0.00 3.51
417 421 1.142688 AGGCTGTTGGGGAAGTGGAT 61.143 55.000 0.00 0.00 0.00 3.41
445 449 3.423154 CGACGTGAGGCCCTTTGC 61.423 66.667 0.00 0.00 33.32 3.68
452 456 4.849329 CGCTACCCGACGTGAGGC 62.849 72.222 0.00 0.00 40.02 4.70
469 473 4.025401 CTCCCGCAACAACCGCAC 62.025 66.667 0.00 0.00 0.00 5.34
470 474 4.555709 ACTCCCGCAACAACCGCA 62.556 61.111 0.00 0.00 0.00 5.69
471 475 3.249973 GAACTCCCGCAACAACCGC 62.250 63.158 0.00 0.00 0.00 5.68
472 476 1.841663 CTGAACTCCCGCAACAACCG 61.842 60.000 0.00 0.00 0.00 4.44
473 477 1.515521 CCTGAACTCCCGCAACAACC 61.516 60.000 0.00 0.00 0.00 3.77
474 478 0.534203 TCCTGAACTCCCGCAACAAC 60.534 55.000 0.00 0.00 0.00 3.32
475 479 0.400213 ATCCTGAACTCCCGCAACAA 59.600 50.000 0.00 0.00 0.00 2.83
476 480 0.036388 GATCCTGAACTCCCGCAACA 60.036 55.000 0.00 0.00 0.00 3.33
477 481 0.036388 TGATCCTGAACTCCCGCAAC 60.036 55.000 0.00 0.00 0.00 4.17
478 482 0.690192 TTGATCCTGAACTCCCGCAA 59.310 50.000 0.00 0.00 0.00 4.85
479 483 0.911769 ATTGATCCTGAACTCCCGCA 59.088 50.000 0.00 0.00 0.00 5.69
480 484 1.134401 TCATTGATCCTGAACTCCCGC 60.134 52.381 0.00 0.00 0.00 6.13
481 485 2.988010 TCATTGATCCTGAACTCCCG 57.012 50.000 0.00 0.00 0.00 5.14
482 486 5.195940 TGAAATCATTGATCCTGAACTCCC 58.804 41.667 0.00 0.00 0.00 4.30
483 487 5.221009 GCTGAAATCATTGATCCTGAACTCC 60.221 44.000 0.00 0.00 0.00 3.85
572 589 0.179121 CGTACCAGCGTGGATAGCAA 60.179 55.000 10.46 0.00 40.96 3.91
584 601 4.214545 TCAACAAAACTATTGCCGTACCAG 59.785 41.667 0.00 0.00 0.00 4.00
590 607 4.854399 TGAACTCAACAAAACTATTGCCG 58.146 39.130 0.00 0.00 0.00 5.69
605 622 3.582647 TGAGGAACATAAGCCTGAACTCA 59.417 43.478 0.00 0.00 33.84 3.41
610 627 3.173151 TCACTGAGGAACATAAGCCTGA 58.827 45.455 0.00 0.00 33.84 3.86
688 705 1.123576 CACACATTTGGTACGACGACG 59.876 52.381 5.58 5.58 45.75 5.12
689 706 2.129607 ACACACATTTGGTACGACGAC 58.870 47.619 0.00 0.00 0.00 4.34
690 707 2.512485 ACACACATTTGGTACGACGA 57.488 45.000 0.00 0.00 0.00 4.20
691 708 3.921630 TGATACACACATTTGGTACGACG 59.078 43.478 0.00 0.00 0.00 5.12
704 721 0.298707 CAGCATCGCGTGATACACAC 59.701 55.000 11.84 0.00 45.11 3.82
705 722 0.172352 TCAGCATCGCGTGATACACA 59.828 50.000 11.84 0.00 33.40 3.72
706 723 1.277326 TTCAGCATCGCGTGATACAC 58.723 50.000 11.84 4.49 32.18 2.90
707 724 2.003196 TTTCAGCATCGCGTGATACA 57.997 45.000 11.84 0.00 32.18 2.29
709 726 2.796593 CTCATTTCAGCATCGCGTGATA 59.203 45.455 11.84 0.00 32.18 2.15
710 727 1.596260 CTCATTTCAGCATCGCGTGAT 59.404 47.619 5.43 5.43 34.28 3.06
711 728 1.001624 CTCATTTCAGCATCGCGTGA 58.998 50.000 5.77 0.00 0.00 4.35
712 729 0.027194 CCTCATTTCAGCATCGCGTG 59.973 55.000 5.77 5.06 0.00 5.34
713 730 1.091771 CCCTCATTTCAGCATCGCGT 61.092 55.000 5.77 0.00 0.00 6.01
714 731 1.091771 ACCCTCATTTCAGCATCGCG 61.092 55.000 0.00 0.00 0.00 5.87
715 732 0.379669 CACCCTCATTTCAGCATCGC 59.620 55.000 0.00 0.00 0.00 4.58
716 733 1.667724 GACACCCTCATTTCAGCATCG 59.332 52.381 0.00 0.00 0.00 3.84
717 734 2.421424 GTGACACCCTCATTTCAGCATC 59.579 50.000 0.00 0.00 0.00 3.91
718 735 2.224843 TGTGACACCCTCATTTCAGCAT 60.225 45.455 2.45 0.00 0.00 3.79
719 736 1.142667 TGTGACACCCTCATTTCAGCA 59.857 47.619 2.45 0.00 0.00 4.41
720 737 1.896220 TGTGACACCCTCATTTCAGC 58.104 50.000 2.45 0.00 0.00 4.26
721 738 3.415212 ACATGTGACACCCTCATTTCAG 58.585 45.455 0.00 0.00 0.00 3.02
722 739 3.507162 ACATGTGACACCCTCATTTCA 57.493 42.857 0.00 0.00 0.00 2.69
731 748 3.115554 GCACTTGAAAACATGTGACACC 58.884 45.455 16.41 0.00 33.64 4.16
737 754 3.883830 TTGTGGCACTTGAAAACATGT 57.116 38.095 19.83 0.00 0.00 3.21
746 763 1.002033 GAGCAGTCTTTGTGGCACTTG 60.002 52.381 19.83 8.80 0.00 3.16
770 787 0.319555 TTTTGACGAGCAGGACTCCG 60.320 55.000 0.00 0.00 43.01 4.63
791 808 2.582978 GGGGGCCGTAGAAGTGAC 59.417 66.667 0.00 0.00 0.00 3.67
934 951 2.088423 GGACTCTCTTCTCGCTCTTGA 58.912 52.381 0.00 0.00 0.00 3.02
948 965 1.722034 TGTGAGCAAGGAAGGACTCT 58.278 50.000 0.00 0.00 0.00 3.24
1012 1057 1.383109 TCTCCCTCATGTGCCCGAT 60.383 57.895 0.00 0.00 0.00 4.18
1025 1070 2.507324 GTTGAGCGCTCGTCTCCC 60.507 66.667 30.75 11.74 0.00 4.30
1036 1081 2.730090 CCTCAATCACAATGCGTTGAGC 60.730 50.000 25.13 0.00 43.75 4.26
1038 1083 2.483877 GTCCTCAATCACAATGCGTTGA 59.516 45.455 25.13 4.02 38.71 3.18
1039 1084 2.226200 TGTCCTCAATCACAATGCGTTG 59.774 45.455 17.16 17.16 41.20 4.10
1040 1085 2.503331 TGTCCTCAATCACAATGCGTT 58.497 42.857 0.00 0.00 0.00 4.84
1104 1149 0.883833 CAAGTTCAGGCATGGTGTCC 59.116 55.000 0.00 0.00 0.00 4.02
1109 1154 3.889815 TCCTTATCAAGTTCAGGCATGG 58.110 45.455 0.00 0.00 0.00 3.66
1110 1155 4.946157 AGTTCCTTATCAAGTTCAGGCATG 59.054 41.667 0.00 0.00 0.00 4.06
1126 1171 4.035102 GGCGGCCTCCAGTTCCTT 62.035 66.667 12.87 0.00 0.00 3.36
1143 1188 2.370824 GATGCTGAGCCATCGTTGCG 62.371 60.000 0.23 0.00 33.06 4.85
1173 1218 1.522355 CAGCCCATACCTGTCAGCG 60.522 63.158 0.00 0.00 0.00 5.18
1202 1247 2.895680 TGCCCTCGCAGATCACTC 59.104 61.111 0.00 0.00 41.12 3.51
1420 1479 2.743928 GTGGCTTCTCCCACGCAG 60.744 66.667 0.00 0.00 45.13 5.18
1460 1524 7.274367 GCGTCGACTGAATATATTGTAACTTG 58.726 38.462 14.70 0.00 0.00 3.16
1466 1530 3.961182 ACGCGTCGACTGAATATATTGT 58.039 40.909 14.70 0.00 0.00 2.71
1477 1541 0.526954 AGTGACAAAACGCGTCGACT 60.527 50.000 14.44 5.58 36.11 4.18
1480 1544 0.382636 GGAAGTGACAAAACGCGTCG 60.383 55.000 14.44 7.01 36.11 5.12
1481 1545 0.935196 AGGAAGTGACAAAACGCGTC 59.065 50.000 14.44 0.00 0.00 5.19
1482 1546 1.375551 AAGGAAGTGACAAAACGCGT 58.624 45.000 5.58 5.58 0.00 6.01
1483 1547 2.468532 AAAGGAAGTGACAAAACGCG 57.531 45.000 3.53 3.53 0.00 6.01
1486 1560 5.108517 TGCATCAAAAGGAAGTGACAAAAC 58.891 37.500 0.00 0.00 0.00 2.43
1544 1627 6.667414 AGAAGTAGGATAGATGGCTCCATTAG 59.333 42.308 2.53 0.00 36.70 1.73
1572 1655 2.833794 TGGCAGTTGCTCGGAATATAC 58.166 47.619 3.88 0.00 41.70 1.47
1589 1672 2.104253 GCAAATGCAGGCACATGGC 61.104 57.895 0.00 0.00 41.59 4.40
1595 1678 2.148446 ATAAGGAGCAAATGCAGGCA 57.852 45.000 8.28 0.00 45.16 4.75
1671 1754 3.244981 ACGGGGATAACAAAACAAGCCTA 60.245 43.478 0.00 0.00 0.00 3.93
1700 1783 2.143876 ATATGCAAAAGCGAAGGGGT 57.856 45.000 0.00 0.00 0.00 4.95
1882 2381 3.911661 GCTAGCTGCATTTGGAATAGG 57.088 47.619 7.70 0.00 42.31 2.57
1900 2399 1.080025 GGAACCGCGTAGAACTGCT 60.080 57.895 4.92 0.00 0.00 4.24
1907 2406 3.121279 CGAATATGAATGGAACCGCGTAG 59.879 47.826 4.92 0.00 0.00 3.51
1911 2410 4.378459 GGATTCGAATATGAATGGAACCGC 60.378 45.833 11.38 0.00 38.65 5.68
1912 2411 4.154195 GGGATTCGAATATGAATGGAACCG 59.846 45.833 11.38 0.00 38.65 4.44


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

AutoCloner maintained by Alex Coulton.