Multiple sequence alignment - TraesCS1A01G231200

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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 TraesCS1A01G231200 chr1A 100.000 2673 0 0 1 2673 403832202 403829530 0.000000e+00 4937
1 TraesCS1A01G231200 chr1B 92.458 769 42 8 338 1094 432116047 432116811 0.000000e+00 1085
2 TraesCS1A01G231200 chr1B 87.892 892 64 23 1114 1975 432116901 432117778 0.000000e+00 1009
3 TraesCS1A01G231200 chr1B 87.965 457 35 11 2232 2673 432118160 432118611 3.050000e-144 521
4 TraesCS1A01G231200 chr1D 88.395 922 63 15 1114 2028 319429699 319430583 0.000000e+00 1070
5 TraesCS1A01G231200 chr1D 92.327 391 17 7 707 1094 319429229 319429609 6.510000e-151 544
6 TraesCS1A01G231200 chr1D 93.567 342 13 3 338 672 319428814 319429153 3.970000e-138 501
7 TraesCS1A01G231200 chr1D 89.971 339 20 6 2237 2572 319433297 319433624 2.460000e-115 425
8 TraesCS1A01G231200 chr1D 93.269 104 4 3 2569 2670 319433885 319433987 1.660000e-32 150
9 TraesCS1A01G231200 chr1D 80.090 221 22 10 2046 2264 319432801 319433001 7.710000e-31 145
10 TraesCS1A01G231200 chr7D 88.791 339 32 5 1 336 572316425 572316090 6.890000e-111 411
11 TraesCS1A01G231200 chr7D 86.744 347 38 8 1 342 450261071 450260728 1.940000e-101 379
12 TraesCS1A01G231200 chr7D 86.217 341 39 8 1 338 383276008 383275673 1.960000e-96 363
13 TraesCS1A01G231200 chr3D 87.059 340 37 6 1 338 275640983 275641317 6.990000e-101 377
14 TraesCS1A01G231200 chr3D 86.337 344 37 9 3 344 577192930 577193265 1.510000e-97 366
15 TraesCS1A01G231200 chr3D 86.176 340 41 6 1 339 107040004 107039670 1.960000e-96 363
16 TraesCS1A01G231200 chr3D 86.350 337 39 6 3 336 511423359 511423691 7.030000e-96 361
17 TraesCS1A01G231200 chr4D 86.607 336 39 6 1 334 378284204 378283873 1.510000e-97 366
18 TraesCS1A01G231200 chr5D 86.377 345 34 9 1 338 509376977 509377315 5.440000e-97 364
19 TraesCS1A01G231200 chr3A 80.255 157 23 6 1290 1442 573112567 573112719 7.820000e-21 111


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 TraesCS1A01G231200 chr1A 403829530 403832202 2672 True 4937.000000 4937 100.000000 1 2673 1 chr1A.!!$R1 2672
1 TraesCS1A01G231200 chr1B 432116047 432118611 2564 False 871.666667 1085 89.438333 338 2673 3 chr1B.!!$F1 2335
2 TraesCS1A01G231200 chr1D 319428814 319433987 5173 False 472.500000 1070 89.603167 338 2670 6 chr1D.!!$F1 2332

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
279 280 0.033228 CAAACCCATTGCCGCTCAAA 59.967 50.0 0.0 0.0 38.34 2.69 F
333 334 0.179081 GGTCGGATGGTGGAGTTAGC 60.179 60.0 0.0 0.0 0.00 3.09 F
357 358 0.250338 AAAGACACAAGAGTCGGGGC 60.250 55.0 0.0 0.0 43.24 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1354 0.036294 CGGTTTCTCCTTCACCTCCC 60.036 60.0 0.0 0.0 0.0 4.30 R
1531 1658 0.179070 GAAGGGGAGACGAAGATGCC 60.179 60.0 0.0 0.0 0.0 4.40 R
1963 2111 0.301687 GATTGCCGTAGATGTGCGTG 59.698 55.0 0.0 0.0 0.0 5.34 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
53 54 7.457024 TTTTAGGTTACTTATGAAACTGGGC 57.543 36.000 0.00 0.00 0.00 5.36
54 55 3.964411 AGGTTACTTATGAAACTGGGCC 58.036 45.455 0.00 0.00 0.00 5.80
55 56 2.681344 GGTTACTTATGAAACTGGGCCG 59.319 50.000 0.00 0.00 0.00 6.13
56 57 3.340928 GTTACTTATGAAACTGGGCCGT 58.659 45.455 0.00 0.00 0.00 5.68
57 58 2.579410 ACTTATGAAACTGGGCCGTT 57.421 45.000 0.00 3.25 0.00 4.44
58 59 2.871453 ACTTATGAAACTGGGCCGTTT 58.129 42.857 20.89 20.89 39.63 3.60
59 60 4.023726 ACTTATGAAACTGGGCCGTTTA 57.976 40.909 20.82 12.67 37.24 2.01
60 61 4.400120 ACTTATGAAACTGGGCCGTTTAA 58.600 39.130 20.82 16.31 37.24 1.52
61 62 4.457949 ACTTATGAAACTGGGCCGTTTAAG 59.542 41.667 20.82 20.72 37.24 1.85
62 63 2.351706 TGAAACTGGGCCGTTTAAGT 57.648 45.000 20.82 7.01 37.24 2.24
63 64 1.950909 TGAAACTGGGCCGTTTAAGTG 59.049 47.619 20.82 0.00 37.24 3.16
64 65 1.268625 GAAACTGGGCCGTTTAAGTGG 59.731 52.381 20.82 0.00 37.24 4.00
65 66 0.475044 AACTGGGCCGTTTAAGTGGA 59.525 50.000 0.00 0.00 0.00 4.02
66 67 0.250597 ACTGGGCCGTTTAAGTGGAC 60.251 55.000 0.00 0.00 0.00 4.02
67 68 0.036306 CTGGGCCGTTTAAGTGGACT 59.964 55.000 0.00 0.00 32.17 3.85
68 69 0.250553 TGGGCCGTTTAAGTGGACTG 60.251 55.000 0.00 0.00 32.17 3.51
69 70 0.035739 GGGCCGTTTAAGTGGACTGA 59.964 55.000 0.00 0.00 32.17 3.41
70 71 1.439679 GGCCGTTTAAGTGGACTGAG 58.560 55.000 0.00 0.00 0.00 3.35
71 72 1.001633 GGCCGTTTAAGTGGACTGAGA 59.998 52.381 0.00 0.00 0.00 3.27
72 73 2.549349 GGCCGTTTAAGTGGACTGAGAA 60.549 50.000 0.00 0.00 0.00 2.87
73 74 3.135994 GCCGTTTAAGTGGACTGAGAAA 58.864 45.455 0.00 0.00 0.00 2.52
74 75 3.059120 GCCGTTTAAGTGGACTGAGAAAC 60.059 47.826 0.00 0.00 0.00 2.78
75 76 4.377897 CCGTTTAAGTGGACTGAGAAACT 58.622 43.478 0.00 0.00 0.00 2.66
76 77 5.535333 CCGTTTAAGTGGACTGAGAAACTA 58.465 41.667 0.00 0.00 0.00 2.24
77 78 5.634020 CCGTTTAAGTGGACTGAGAAACTAG 59.366 44.000 0.00 0.00 0.00 2.57
78 79 5.634020 CGTTTAAGTGGACTGAGAAACTAGG 59.366 44.000 0.00 0.00 0.00 3.02
79 80 3.686916 AAGTGGACTGAGAAACTAGGC 57.313 47.619 0.00 0.00 0.00 3.93
80 81 1.903183 AGTGGACTGAGAAACTAGGCC 59.097 52.381 0.00 0.00 42.74 5.19
81 82 0.895530 TGGACTGAGAAACTAGGCCG 59.104 55.000 0.00 0.00 45.52 6.13
82 83 0.896226 GGACTGAGAAACTAGGCCGT 59.104 55.000 0.00 0.00 31.20 5.68
83 84 1.275573 GGACTGAGAAACTAGGCCGTT 59.724 52.381 0.00 0.00 31.20 4.44
84 85 2.289506 GGACTGAGAAACTAGGCCGTTT 60.290 50.000 8.33 8.33 39.63 3.60
85 86 3.400255 GACTGAGAAACTAGGCCGTTTT 58.600 45.455 9.74 4.79 37.24 2.43
86 87 3.813724 GACTGAGAAACTAGGCCGTTTTT 59.186 43.478 9.74 4.85 37.24 1.94
87 88 3.564225 ACTGAGAAACTAGGCCGTTTTTG 59.436 43.478 9.74 4.52 37.24 2.44
88 89 3.547746 TGAGAAACTAGGCCGTTTTTGT 58.452 40.909 9.74 3.25 37.24 2.83
89 90 3.314080 TGAGAAACTAGGCCGTTTTTGTG 59.686 43.478 9.74 0.00 37.24 3.33
90 91 2.621526 AGAAACTAGGCCGTTTTTGTGG 59.378 45.455 9.74 0.00 37.24 4.17
95 96 2.656973 GCCGTTTTTGTGGCCGTG 60.657 61.111 0.00 0.00 45.73 4.94
96 97 3.111939 CCGTTTTTGTGGCCGTGA 58.888 55.556 0.00 0.00 0.00 4.35
97 98 1.298788 CCGTTTTTGTGGCCGTGAC 60.299 57.895 0.00 0.00 0.00 3.67
98 99 1.298788 CGTTTTTGTGGCCGTGACC 60.299 57.895 0.00 0.00 0.00 4.02
99 100 1.066752 GTTTTTGTGGCCGTGACCC 59.933 57.895 0.00 0.00 0.00 4.46
100 101 1.379977 TTTTTGTGGCCGTGACCCA 60.380 52.632 0.00 0.00 0.00 4.51
101 102 0.757188 TTTTTGTGGCCGTGACCCAT 60.757 50.000 0.00 0.00 34.34 4.00
102 103 0.110678 TTTTGTGGCCGTGACCCATA 59.889 50.000 0.00 0.00 34.34 2.74
103 104 0.329931 TTTGTGGCCGTGACCCATAT 59.670 50.000 0.00 0.00 34.34 1.78
104 105 1.205055 TTGTGGCCGTGACCCATATA 58.795 50.000 0.00 0.00 34.34 0.86
105 106 1.429930 TGTGGCCGTGACCCATATAT 58.570 50.000 0.00 0.00 34.34 0.86
106 107 2.610873 TGTGGCCGTGACCCATATATA 58.389 47.619 0.00 0.00 34.34 0.86
107 108 3.178046 TGTGGCCGTGACCCATATATAT 58.822 45.455 0.00 0.00 34.34 0.86
108 109 3.055458 TGTGGCCGTGACCCATATATATG 60.055 47.826 14.78 14.78 34.34 1.78
109 110 3.055385 GTGGCCGTGACCCATATATATGT 60.055 47.826 19.11 4.05 34.34 2.29
110 111 3.585289 TGGCCGTGACCCATATATATGTT 59.415 43.478 19.11 7.68 31.82 2.71
111 112 4.042311 TGGCCGTGACCCATATATATGTTT 59.958 41.667 19.11 7.36 31.82 2.83
112 113 5.007682 GGCCGTGACCCATATATATGTTTT 58.992 41.667 19.11 5.12 31.82 2.43
113 114 6.174760 GGCCGTGACCCATATATATGTTTTA 58.825 40.000 19.11 2.47 31.82 1.52
114 115 6.826741 GGCCGTGACCCATATATATGTTTTAT 59.173 38.462 19.11 2.48 31.82 1.40
115 116 7.201696 GGCCGTGACCCATATATATGTTTTATG 60.202 40.741 19.11 8.98 31.82 1.90
116 117 7.335924 GCCGTGACCCATATATATGTTTTATGT 59.664 37.037 19.11 7.99 31.82 2.29
117 118 9.226606 CCGTGACCCATATATATGTTTTATGTT 57.773 33.333 19.11 0.00 31.82 2.71
190 191 8.842280 TCATATATTTTTCATTTACGTCCACCC 58.158 33.333 0.00 0.00 0.00 4.61
191 192 4.794278 ATTTTTCATTTACGTCCACCCC 57.206 40.909 0.00 0.00 0.00 4.95
192 193 1.810959 TTTCATTTACGTCCACCCCG 58.189 50.000 0.00 0.00 0.00 5.73
193 194 0.036199 TTCATTTACGTCCACCCCGG 60.036 55.000 0.00 0.00 0.00 5.73
194 195 0.903924 TCATTTACGTCCACCCCGGA 60.904 55.000 0.73 0.00 43.61 5.14
201 202 2.448931 TCCACCCCGGACTGGTTT 60.449 61.111 0.73 0.00 39.64 3.27
202 203 2.079911 TCCACCCCGGACTGGTTTT 61.080 57.895 0.73 0.00 39.64 2.43
203 204 1.901464 CCACCCCGGACTGGTTTTG 60.901 63.158 0.73 0.00 36.56 2.44
204 205 1.149627 CACCCCGGACTGGTTTTGA 59.850 57.895 0.73 0.00 32.46 2.69
205 206 0.889186 CACCCCGGACTGGTTTTGAG 60.889 60.000 0.73 0.00 32.46 3.02
206 207 1.303317 CCCCGGACTGGTTTTGAGG 60.303 63.158 0.73 0.00 35.15 3.86
207 208 1.454539 CCCGGACTGGTTTTGAGGT 59.545 57.895 0.73 0.00 35.15 3.85
208 209 0.889186 CCCGGACTGGTTTTGAGGTG 60.889 60.000 0.73 0.00 35.15 4.00
209 210 1.515521 CCGGACTGGTTTTGAGGTGC 61.516 60.000 0.00 0.00 0.00 5.01
210 211 1.841663 CGGACTGGTTTTGAGGTGCG 61.842 60.000 0.00 0.00 37.21 5.34
211 212 1.515521 GGACTGGTTTTGAGGTGCGG 61.516 60.000 0.00 0.00 0.00 5.69
212 213 2.130073 GACTGGTTTTGAGGTGCGGC 62.130 60.000 0.00 0.00 0.00 6.53
213 214 2.909965 TGGTTTTGAGGTGCGGCC 60.910 61.111 0.00 0.00 37.58 6.13
214 215 4.038080 GGTTTTGAGGTGCGGCCG 62.038 66.667 24.05 24.05 43.70 6.13
215 216 4.700365 GTTTTGAGGTGCGGCCGC 62.700 66.667 42.35 42.35 43.70 6.53
233 234 2.023741 GCATTGAGCGCATCCACG 59.976 61.111 11.47 0.00 0.00 4.94
234 235 2.463620 GCATTGAGCGCATCCACGA 61.464 57.895 11.47 0.00 34.06 4.35
235 236 1.349627 CATTGAGCGCATCCACGAC 59.650 57.895 11.47 0.00 34.06 4.34
236 237 1.815421 ATTGAGCGCATCCACGACC 60.815 57.895 11.47 0.00 34.06 4.79
237 238 3.950794 TTGAGCGCATCCACGACCC 62.951 63.158 11.47 0.00 34.06 4.46
238 239 4.451150 GAGCGCATCCACGACCCA 62.451 66.667 11.47 0.00 34.06 4.51
239 240 3.740128 GAGCGCATCCACGACCCAT 62.740 63.158 11.47 0.00 34.06 4.00
240 241 3.272334 GCGCATCCACGACCCATC 61.272 66.667 0.30 0.00 34.06 3.51
250 251 1.721487 CGACCCATCGGACAAATGC 59.279 57.895 0.00 0.00 44.99 3.56
251 252 1.024046 CGACCCATCGGACAAATGCA 61.024 55.000 0.00 0.00 44.99 3.96
252 253 0.734889 GACCCATCGGACAAATGCAG 59.265 55.000 0.00 0.00 0.00 4.41
253 254 0.327924 ACCCATCGGACAAATGCAGA 59.672 50.000 0.00 0.00 0.00 4.26
254 255 0.734889 CCCATCGGACAAATGCAGAC 59.265 55.000 0.00 0.00 0.00 3.51
255 256 1.452110 CCATCGGACAAATGCAGACA 58.548 50.000 0.00 0.00 0.00 3.41
256 257 2.019249 CCATCGGACAAATGCAGACAT 58.981 47.619 0.00 0.00 38.49 3.06
257 258 2.223409 CCATCGGACAAATGCAGACATG 60.223 50.000 0.00 0.00 36.36 3.21
258 259 2.470983 TCGGACAAATGCAGACATGA 57.529 45.000 0.00 0.00 36.36 3.07
259 260 2.349590 TCGGACAAATGCAGACATGAG 58.650 47.619 0.00 0.00 36.36 2.90
260 261 1.202110 CGGACAAATGCAGACATGAGC 60.202 52.381 0.00 0.68 36.36 4.26
261 262 1.814394 GGACAAATGCAGACATGAGCA 59.186 47.619 12.92 12.92 45.92 4.26
262 263 2.229543 GGACAAATGCAGACATGAGCAA 59.770 45.455 14.14 1.86 44.88 3.91
263 264 3.305539 GGACAAATGCAGACATGAGCAAA 60.306 43.478 14.14 0.00 44.88 3.68
264 265 3.645884 ACAAATGCAGACATGAGCAAAC 58.354 40.909 14.14 0.00 44.88 2.93
265 266 2.991190 CAAATGCAGACATGAGCAAACC 59.009 45.455 14.14 0.00 44.88 3.27
266 267 1.180029 ATGCAGACATGAGCAAACCC 58.820 50.000 14.14 0.00 44.88 4.11
267 268 0.178995 TGCAGACATGAGCAAACCCA 60.179 50.000 0.00 0.00 37.90 4.51
268 269 1.180029 GCAGACATGAGCAAACCCAT 58.820 50.000 0.00 0.00 0.00 4.00
269 270 1.547372 GCAGACATGAGCAAACCCATT 59.453 47.619 0.00 0.00 0.00 3.16
270 271 2.673043 GCAGACATGAGCAAACCCATTG 60.673 50.000 0.00 0.00 42.21 2.82
277 278 3.364442 CAAACCCATTGCCGCTCA 58.636 55.556 0.00 0.00 31.00 4.26
278 279 1.664873 CAAACCCATTGCCGCTCAA 59.335 52.632 0.00 0.00 39.32 3.02
279 280 0.033228 CAAACCCATTGCCGCTCAAA 59.967 50.000 0.00 0.00 38.34 2.69
280 281 0.755686 AAACCCATTGCCGCTCAAAA 59.244 45.000 0.00 0.00 38.34 2.44
281 282 0.755686 AACCCATTGCCGCTCAAAAA 59.244 45.000 0.00 0.00 38.34 1.94
299 300 4.624336 AAAAACAAAATTCGGCCAAACC 57.376 36.364 2.24 0.00 0.00 3.27
308 309 4.089105 GGCCAAACCGAACATCCA 57.911 55.556 0.00 0.00 0.00 3.41
309 310 2.578683 GGCCAAACCGAACATCCAT 58.421 52.632 0.00 0.00 0.00 3.41
310 311 0.894835 GGCCAAACCGAACATCCATT 59.105 50.000 0.00 0.00 0.00 3.16
311 312 1.275010 GGCCAAACCGAACATCCATTT 59.725 47.619 0.00 0.00 0.00 2.32
312 313 2.336667 GCCAAACCGAACATCCATTTG 58.663 47.619 0.00 0.00 0.00 2.32
313 314 2.029470 GCCAAACCGAACATCCATTTGA 60.029 45.455 0.00 0.00 33.08 2.69
314 315 3.836949 CCAAACCGAACATCCATTTGAG 58.163 45.455 0.00 0.00 33.08 3.02
315 316 3.367292 CCAAACCGAACATCCATTTGAGG 60.367 47.826 0.00 0.00 33.08 3.86
316 317 2.879103 ACCGAACATCCATTTGAGGT 57.121 45.000 0.00 0.00 40.33 3.85
317 318 2.711542 ACCGAACATCCATTTGAGGTC 58.288 47.619 0.00 0.00 36.89 3.85
318 319 1.665679 CCGAACATCCATTTGAGGTCG 59.334 52.381 0.00 0.00 36.89 4.79
319 320 1.665679 CGAACATCCATTTGAGGTCGG 59.334 52.381 0.00 0.00 36.89 4.79
320 321 2.676750 CGAACATCCATTTGAGGTCGGA 60.677 50.000 0.00 0.00 36.89 4.55
321 322 3.545703 GAACATCCATTTGAGGTCGGAT 58.454 45.455 0.00 0.00 36.89 4.18
323 324 2.645838 ATCCATTTGAGGTCGGATGG 57.354 50.000 0.00 5.48 36.88 3.51
324 325 1.285280 TCCATTTGAGGTCGGATGGT 58.715 50.000 9.84 0.00 39.95 3.55
325 326 1.065491 TCCATTTGAGGTCGGATGGTG 60.065 52.381 9.84 0.00 39.95 4.17
326 327 1.382522 CATTTGAGGTCGGATGGTGG 58.617 55.000 0.00 0.00 0.00 4.61
327 328 1.065491 CATTTGAGGTCGGATGGTGGA 60.065 52.381 0.00 0.00 0.00 4.02
328 329 0.613260 TTTGAGGTCGGATGGTGGAG 59.387 55.000 0.00 0.00 0.00 3.86
329 330 0.544357 TTGAGGTCGGATGGTGGAGT 60.544 55.000 0.00 0.00 0.00 3.85
330 331 0.544357 TGAGGTCGGATGGTGGAGTT 60.544 55.000 0.00 0.00 0.00 3.01
331 332 1.272816 TGAGGTCGGATGGTGGAGTTA 60.273 52.381 0.00 0.00 0.00 2.24
332 333 1.409427 GAGGTCGGATGGTGGAGTTAG 59.591 57.143 0.00 0.00 0.00 2.34
333 334 0.179081 GGTCGGATGGTGGAGTTAGC 60.179 60.000 0.00 0.00 0.00 3.09
334 335 0.179081 GTCGGATGGTGGAGTTAGCC 60.179 60.000 0.00 0.00 0.00 3.93
335 336 0.325296 TCGGATGGTGGAGTTAGCCT 60.325 55.000 0.00 0.00 0.00 4.58
336 337 1.063492 TCGGATGGTGGAGTTAGCCTA 60.063 52.381 0.00 0.00 0.00 3.93
350 351 6.147985 GGAGTTAGCCTAAAAAGACACAAGAG 59.852 42.308 0.00 0.00 0.00 2.85
357 358 0.250338 AAAGACACAAGAGTCGGGGC 60.250 55.000 0.00 0.00 43.24 5.80
413 420 3.737172 CTTCAGCAAACCGGGGCG 61.737 66.667 6.32 3.65 34.54 6.13
586 594 4.561731 GTGACTCAGCGAGACACC 57.438 61.111 20.86 10.09 44.77 4.16
658 666 2.743718 CTCCACGTCTTGCCACCT 59.256 61.111 0.00 0.00 0.00 4.00
709 747 4.619227 CACGCACCCACCGACCTT 62.619 66.667 0.00 0.00 0.00 3.50
712 750 2.430367 GCACCCACCGACCTTTCT 59.570 61.111 0.00 0.00 0.00 2.52
713 751 1.671379 GCACCCACCGACCTTTCTC 60.671 63.158 0.00 0.00 0.00 2.87
714 752 1.374252 CACCCACCGACCTTTCTCG 60.374 63.158 0.00 0.00 0.00 4.04
791 840 0.935366 GCATACAGTCGTCGGCTAGC 60.935 60.000 6.04 6.04 0.00 3.42
843 892 1.151668 CGGTTTCTTGGACTCTGCTG 58.848 55.000 0.00 0.00 0.00 4.41
861 912 2.569404 GCTGGCTATATAGAGCAAGGGT 59.431 50.000 22.31 0.00 42.91 4.34
881 932 3.365265 GGGGTTGCAGTTGAGGCG 61.365 66.667 0.00 0.00 0.00 5.52
885 936 2.979676 TTGCAGTTGAGGCGCAGG 60.980 61.111 10.83 0.00 36.91 4.85
898 949 1.872197 GCGCAGGCCACATAAAACCA 61.872 55.000 5.01 0.00 0.00 3.67
1104 1161 2.175878 TCCTCGCCGGTAGATACTAC 57.824 55.000 1.90 0.00 0.00 2.73
1105 1162 1.696336 TCCTCGCCGGTAGATACTACT 59.304 52.381 1.90 0.00 0.00 2.57
1106 1163 2.899900 TCCTCGCCGGTAGATACTACTA 59.100 50.000 1.90 0.00 0.00 1.82
1108 1165 2.672381 CTCGCCGGTAGATACTACTAGC 59.328 54.545 1.90 9.89 37.46 3.42
1118 1239 7.046652 GGTAGATACTACTAGCGGACATGATA 58.953 42.308 0.00 0.00 32.60 2.15
1123 1244 5.131067 ACTACTAGCGGACATGATAGACAA 58.869 41.667 0.00 0.00 32.33 3.18
1125 1246 5.339008 ACTAGCGGACATGATAGACAAAA 57.661 39.130 0.00 0.00 32.33 2.44
1126 1247 5.109903 ACTAGCGGACATGATAGACAAAAC 58.890 41.667 0.00 0.00 32.33 2.43
1127 1248 3.937814 AGCGGACATGATAGACAAAACA 58.062 40.909 0.00 0.00 0.00 2.83
1159 1286 5.529791 TGTAGCTAGCGTTTTCCATATCTC 58.470 41.667 9.55 0.00 0.00 2.75
1169 1296 6.510799 GCGTTTTCCATATCTCTGATTGACAG 60.511 42.308 0.00 0.00 46.97 3.51
1199 1326 5.491070 TGCATGCTAATCTGTTCTGTACTT 58.509 37.500 20.33 0.00 0.00 2.24
1207 1334 7.530861 GCTAATCTGTTCTGTACTTTTCGTTTG 59.469 37.037 0.00 0.00 0.00 2.93
1227 1354 5.828299 TTGTGTTTCTCTTTGTAAGGTGG 57.172 39.130 0.00 0.00 0.00 4.61
1236 1363 1.822425 TTGTAAGGTGGGGAGGTGAA 58.178 50.000 0.00 0.00 0.00 3.18
1248 1375 0.321996 GAGGTGAAGGAGAAACCGCT 59.678 55.000 0.00 0.00 44.74 5.52
1329 1456 3.162154 GGAGATCCGGGACCCCAC 61.162 72.222 4.46 0.00 35.37 4.61
1509 1636 3.423154 GCCCAAGAAGCGTCGGTG 61.423 66.667 0.00 0.00 0.00 4.94
1528 1655 3.444805 GTCGCTGCCGAGGAGAGT 61.445 66.667 0.00 0.00 45.38 3.24
1531 1658 2.202676 GCTGCCGAGGAGAGTTCG 60.203 66.667 0.00 0.00 37.78 3.95
1539 1666 1.535015 CGAGGAGAGTTCGGCATCTTC 60.535 57.143 0.00 0.00 34.56 2.87
1546 1673 0.806492 GTTCGGCATCTTCGTCTCCC 60.806 60.000 0.00 0.00 0.00 4.30
1554 1681 1.982938 CTTCGTCTCCCCTTCCGGT 60.983 63.158 0.00 0.00 0.00 5.28
1558 1685 1.911766 GTCTCCCCTTCCGGTCACA 60.912 63.158 0.00 0.00 0.00 3.58
1562 1689 2.046892 CCCTTCCGGTCACAGCTG 60.047 66.667 13.48 13.48 0.00 4.24
1669 1805 1.000283 GCCGTCGATCTCATCTTGGAT 60.000 52.381 0.00 0.00 0.00 3.41
1714 1861 1.134037 GGCGTCCATGGGGTACATTTA 60.134 52.381 13.02 0.00 37.84 1.40
1760 1907 6.460781 TGGTCGAAGTCTTTTGATTAGCTAA 58.539 36.000 8.99 8.99 0.00 3.09
1768 1915 9.871238 AAGTCTTTTGATTAGCTAAAGTATCGA 57.129 29.630 10.85 0.36 39.39 3.59
1787 1934 1.625315 GATTGGCTTTCCTGGGCTTTT 59.375 47.619 0.00 0.00 0.00 2.27
1816 1964 1.358152 TCCAGGTCCTTTGTAGTGGG 58.642 55.000 0.00 0.00 0.00 4.61
1848 1996 2.939460 TCGAGCATGACGATCAGAAA 57.061 45.000 10.48 0.00 34.85 2.52
1884 2032 0.746659 ACTTGCACCAACTTTCCTGC 59.253 50.000 0.00 0.00 0.00 4.85
1885 2033 1.035139 CTTGCACCAACTTTCCTGCT 58.965 50.000 0.00 0.00 0.00 4.24
1888 2036 3.712016 TGCACCAACTTTCCTGCTATA 57.288 42.857 0.00 0.00 0.00 1.31
1915 2063 9.827411 AAAATAGAACTTTTCACGCTCTAATTC 57.173 29.630 0.00 0.00 0.00 2.17
1952 2100 5.052633 CGAAAAAGTTCATGTCCGTGTTTTC 60.053 40.000 0.00 2.99 32.89 2.29
1953 2101 4.974368 AAAGTTCATGTCCGTGTTTTCA 57.026 36.364 0.00 0.00 0.00 2.69
1954 2102 3.963383 AGTTCATGTCCGTGTTTTCAC 57.037 42.857 0.00 0.00 46.33 3.18
2037 2541 9.561270 GTCTATATTTTCCTTCTCTTTTTGTGC 57.439 33.333 0.00 0.00 0.00 4.57
2038 2542 8.450964 TCTATATTTTCCTTCTCTTTTTGTGCG 58.549 33.333 0.00 0.00 0.00 5.34
2041 2545 1.864711 TCCTTCTCTTTTTGTGCGTCG 59.135 47.619 0.00 0.00 0.00 5.12
2043 2547 2.348591 CCTTCTCTTTTTGTGCGTCGAC 60.349 50.000 5.18 5.18 0.00 4.20
2052 3779 1.154073 GTGCGTCGACCAGTAGACC 60.154 63.158 10.58 0.58 32.60 3.85
2084 4539 1.021968 AAACAACGGGTCTGCTTCAC 58.978 50.000 0.00 0.00 0.00 3.18
2107 4562 6.663523 CACTACACCCCCTCTCAAAAATAAAT 59.336 38.462 0.00 0.00 0.00 1.40
2109 4564 8.395605 ACTACACCCCCTCTCAAAAATAAATAA 58.604 33.333 0.00 0.00 0.00 1.40
2135 4590 2.694213 TGTAGCTATGTTTGCTTCGCA 58.306 42.857 0.00 0.00 41.46 5.10
2147 4602 1.401552 TGCTTCGCAAGGAATGTATGC 59.598 47.619 0.00 0.00 34.76 3.14
2148 4612 1.401552 GCTTCGCAAGGAATGTATGCA 59.598 47.619 0.00 0.00 40.04 3.96
2165 4629 8.976986 ATGTATGCACATTCTTTCTTTTTCTC 57.023 30.769 0.00 0.00 42.98 2.87
2166 4630 7.077605 TGTATGCACATTCTTTCTTTTTCTCG 58.922 34.615 0.00 0.00 0.00 4.04
2168 4632 6.130298 TGCACATTCTTTCTTTTTCTCGAA 57.870 33.333 0.00 0.00 0.00 3.71
2169 4633 6.738114 TGCACATTCTTTCTTTTTCTCGAAT 58.262 32.000 0.00 0.00 0.00 3.34
2170 4634 7.202526 TGCACATTCTTTCTTTTTCTCGAATT 58.797 30.769 0.00 0.00 0.00 2.17
2171 4635 8.349245 TGCACATTCTTTCTTTTTCTCGAATTA 58.651 29.630 0.00 0.00 0.00 1.40
2172 4636 9.346725 GCACATTCTTTCTTTTTCTCGAATTAT 57.653 29.630 0.00 0.00 0.00 1.28
2190 4654 7.921745 TCGAATTATTGATGTACGTACATTCCA 59.078 33.333 34.92 27.23 46.20 3.53
2200 4664 2.093658 ACGTACATTCCATCTGTCCCAC 60.094 50.000 0.00 0.00 0.00 4.61
2203 4667 4.499865 CGTACATTCCATCTGTCCCACTAG 60.500 50.000 0.00 0.00 0.00 2.57
2204 4668 2.774234 ACATTCCATCTGTCCCACTAGG 59.226 50.000 0.00 0.00 0.00 3.02
2205 4669 1.204146 TTCCATCTGTCCCACTAGGC 58.796 55.000 0.00 0.00 34.51 3.93
2206 4670 0.042581 TCCATCTGTCCCACTAGGCA 59.957 55.000 0.00 0.00 34.51 4.75
2207 4671 0.179000 CCATCTGTCCCACTAGGCAC 59.821 60.000 0.00 0.00 34.51 5.01
2208 4672 1.198713 CATCTGTCCCACTAGGCACT 58.801 55.000 0.00 0.00 46.37 4.40
2209 4673 2.388735 CATCTGTCCCACTAGGCACTA 58.611 52.381 0.00 0.00 41.75 2.74
2260 4724 8.918658 CATCAAATCAAAGTGTACCAAATTCAG 58.081 33.333 0.00 0.00 0.00 3.02
2264 4728 5.197451 TCAAAGTGTACCAAATTCAGGTGT 58.803 37.500 11.67 0.00 40.26 4.16
2275 5060 7.602753 ACCAAATTCAGGTGTATTTTTCTAGC 58.397 34.615 1.98 0.00 38.13 3.42
2281 5066 6.252995 TCAGGTGTATTTTTCTAGCCCATTT 58.747 36.000 0.00 0.00 0.00 2.32
2291 5078 4.222124 TCTAGCCCATTTTTGTCCTCTC 57.778 45.455 0.00 0.00 0.00 3.20
2296 5083 4.952335 AGCCCATTTTTGTCCTCTCTATTG 59.048 41.667 0.00 0.00 0.00 1.90
2314 5101 3.823281 TTGTCCCTCAAAACTGACGTA 57.177 42.857 0.00 0.00 32.64 3.57
2317 5104 4.062293 TGTCCCTCAAAACTGACGTATTG 58.938 43.478 0.00 0.00 0.00 1.90
2329 5116 2.094442 TGACGTATTGAGAATCGTGCCA 60.094 45.455 0.00 0.00 38.61 4.92
2330 5117 2.927477 GACGTATTGAGAATCGTGCCAA 59.073 45.455 0.00 0.00 38.61 4.52
2331 5118 3.531538 ACGTATTGAGAATCGTGCCAAT 58.468 40.909 0.00 0.00 38.61 3.16
2332 5119 3.938963 ACGTATTGAGAATCGTGCCAATT 59.061 39.130 0.00 0.00 38.61 2.32
2333 5120 5.113383 ACGTATTGAGAATCGTGCCAATTA 58.887 37.500 0.00 0.00 38.61 1.40
2334 5121 5.583061 ACGTATTGAGAATCGTGCCAATTAA 59.417 36.000 0.00 0.00 38.61 1.40
2335 5122 6.092944 ACGTATTGAGAATCGTGCCAATTAAA 59.907 34.615 0.00 0.00 38.61 1.52
2353 5140 9.048446 CCAATTAAAATGATTAAATGCCTCTGG 57.952 33.333 0.00 0.00 0.00 3.86
2374 5167 1.228154 AACCACTTTGCCGGTCTCC 60.228 57.895 1.90 0.00 33.17 3.71
2397 5197 3.642848 GGGATCGTACCAAACCCTATACA 59.357 47.826 0.00 0.00 37.75 2.29
2412 5212 9.502035 AAACCCTATACATATATAGCTAGGCAA 57.498 33.333 0.00 0.00 39.29 4.52
2428 5228 3.276846 AACGGTCGCCTGCACAAC 61.277 61.111 0.00 0.00 0.00 3.32
2636 5703 3.126343 GGTCCGTACGCTCATTCATTTTT 59.874 43.478 10.49 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.039574 GGCCCAGTTTCATAAGTAACCTAAAAA 60.040 37.037 0.00 0.00 0.00 1.94
29 30 6.434965 GGCCCAGTTTCATAAGTAACCTAAAA 59.565 38.462 0.00 0.00 0.00 1.52
30 31 5.947566 GGCCCAGTTTCATAAGTAACCTAAA 59.052 40.000 0.00 0.00 0.00 1.85
31 32 5.503002 GGCCCAGTTTCATAAGTAACCTAA 58.497 41.667 0.00 0.00 0.00 2.69
32 33 4.383335 CGGCCCAGTTTCATAAGTAACCTA 60.383 45.833 0.00 0.00 0.00 3.08
33 34 3.621461 CGGCCCAGTTTCATAAGTAACCT 60.621 47.826 0.00 0.00 0.00 3.50
34 35 2.681344 CGGCCCAGTTTCATAAGTAACC 59.319 50.000 0.00 0.00 0.00 2.85
35 36 3.340928 ACGGCCCAGTTTCATAAGTAAC 58.659 45.455 0.00 0.00 0.00 2.50
36 37 3.706600 ACGGCCCAGTTTCATAAGTAA 57.293 42.857 0.00 0.00 0.00 2.24
37 38 3.706600 AACGGCCCAGTTTCATAAGTA 57.293 42.857 0.00 0.00 0.00 2.24
38 39 2.579410 AACGGCCCAGTTTCATAAGT 57.421 45.000 0.00 0.00 0.00 2.24
39 40 4.457949 ACTTAAACGGCCCAGTTTCATAAG 59.542 41.667 11.49 11.92 42.63 1.73
40 41 4.216687 CACTTAAACGGCCCAGTTTCATAA 59.783 41.667 11.49 1.96 42.63 1.90
41 42 3.754323 CACTTAAACGGCCCAGTTTCATA 59.246 43.478 11.49 0.41 42.63 2.15
42 43 2.556622 CACTTAAACGGCCCAGTTTCAT 59.443 45.455 11.49 0.00 42.63 2.57
43 44 1.950909 CACTTAAACGGCCCAGTTTCA 59.049 47.619 11.49 1.69 42.63 2.69
44 45 1.268625 CCACTTAAACGGCCCAGTTTC 59.731 52.381 11.49 0.00 42.63 2.78
45 46 1.133730 TCCACTTAAACGGCCCAGTTT 60.134 47.619 12.58 12.58 45.22 2.66
46 47 0.475044 TCCACTTAAACGGCCCAGTT 59.525 50.000 0.00 0.00 35.59 3.16
47 48 0.250597 GTCCACTTAAACGGCCCAGT 60.251 55.000 0.00 0.00 0.00 4.00
48 49 0.036306 AGTCCACTTAAACGGCCCAG 59.964 55.000 0.00 0.00 0.00 4.45
49 50 0.250553 CAGTCCACTTAAACGGCCCA 60.251 55.000 0.00 0.00 0.00 5.36
50 51 0.035739 TCAGTCCACTTAAACGGCCC 59.964 55.000 0.00 0.00 0.00 5.80
51 52 1.001633 TCTCAGTCCACTTAAACGGCC 59.998 52.381 0.00 0.00 0.00 6.13
52 53 2.450609 TCTCAGTCCACTTAAACGGC 57.549 50.000 0.00 0.00 0.00 5.68
53 54 4.377897 AGTTTCTCAGTCCACTTAAACGG 58.622 43.478 0.00 0.00 33.27 4.44
54 55 5.634020 CCTAGTTTCTCAGTCCACTTAAACG 59.366 44.000 0.00 0.00 33.27 3.60
55 56 5.408909 GCCTAGTTTCTCAGTCCACTTAAAC 59.591 44.000 0.00 0.00 0.00 2.01
56 57 5.512576 GGCCTAGTTTCTCAGTCCACTTAAA 60.513 44.000 0.00 0.00 0.00 1.52
57 58 4.020485 GGCCTAGTTTCTCAGTCCACTTAA 60.020 45.833 0.00 0.00 0.00 1.85
58 59 3.514309 GGCCTAGTTTCTCAGTCCACTTA 59.486 47.826 0.00 0.00 0.00 2.24
59 60 2.303311 GGCCTAGTTTCTCAGTCCACTT 59.697 50.000 0.00 0.00 0.00 3.16
60 61 1.903183 GGCCTAGTTTCTCAGTCCACT 59.097 52.381 0.00 0.00 0.00 4.00
61 62 1.404315 CGGCCTAGTTTCTCAGTCCAC 60.404 57.143 0.00 0.00 0.00 4.02
62 63 0.895530 CGGCCTAGTTTCTCAGTCCA 59.104 55.000 0.00 0.00 0.00 4.02
63 64 0.896226 ACGGCCTAGTTTCTCAGTCC 59.104 55.000 0.00 0.00 0.00 3.85
64 65 2.745515 AACGGCCTAGTTTCTCAGTC 57.254 50.000 0.00 0.00 0.00 3.51
65 66 3.487120 AAAACGGCCTAGTTTCTCAGT 57.513 42.857 8.93 0.00 42.81 3.41
66 67 3.564225 ACAAAAACGGCCTAGTTTCTCAG 59.436 43.478 8.93 3.50 42.81 3.35
67 68 3.314080 CACAAAAACGGCCTAGTTTCTCA 59.686 43.478 8.93 0.00 42.81 3.27
68 69 3.304458 CCACAAAAACGGCCTAGTTTCTC 60.304 47.826 8.93 0.00 42.81 2.87
69 70 2.621526 CCACAAAAACGGCCTAGTTTCT 59.378 45.455 8.93 0.00 42.81 2.52
70 71 2.860971 GCCACAAAAACGGCCTAGTTTC 60.861 50.000 8.93 0.00 42.81 2.78
71 72 1.067974 GCCACAAAAACGGCCTAGTTT 59.932 47.619 0.00 1.42 45.21 2.66
72 73 0.671796 GCCACAAAAACGGCCTAGTT 59.328 50.000 0.00 0.00 42.82 2.24
73 74 2.337361 GCCACAAAAACGGCCTAGT 58.663 52.632 0.00 0.00 42.82 2.57
79 80 1.298788 GTCACGGCCACAAAAACGG 60.299 57.895 2.24 0.00 0.00 4.44
80 81 1.298788 GGTCACGGCCACAAAAACG 60.299 57.895 2.24 0.00 0.00 3.60
81 82 1.066752 GGGTCACGGCCACAAAAAC 59.933 57.895 2.24 0.00 0.00 2.43
82 83 0.757188 ATGGGTCACGGCCACAAAAA 60.757 50.000 2.24 0.00 0.00 1.94
83 84 0.110678 TATGGGTCACGGCCACAAAA 59.889 50.000 2.24 0.00 0.00 2.44
84 85 0.329931 ATATGGGTCACGGCCACAAA 59.670 50.000 2.24 0.00 0.00 2.83
85 86 1.205055 TATATGGGTCACGGCCACAA 58.795 50.000 2.24 0.00 0.00 3.33
86 87 1.429930 ATATATGGGTCACGGCCACA 58.570 50.000 2.24 0.00 0.00 4.17
87 88 3.055385 ACATATATATGGGTCACGGCCAC 60.055 47.826 23.44 0.00 38.00 5.01
88 89 3.178046 ACATATATATGGGTCACGGCCA 58.822 45.455 23.44 0.00 38.00 5.36
89 90 3.906720 ACATATATATGGGTCACGGCC 57.093 47.619 23.44 0.00 38.00 6.13
90 91 7.335924 ACATAAAACATATATATGGGTCACGGC 59.664 37.037 23.44 0.00 38.00 5.68
91 92 8.786826 ACATAAAACATATATATGGGTCACGG 57.213 34.615 23.44 11.47 38.00 4.94
164 165 8.842280 GGGTGGACGTAAATGAAAAATATATGA 58.158 33.333 0.00 0.00 0.00 2.15
165 166 8.079809 GGGGTGGACGTAAATGAAAAATATATG 58.920 37.037 0.00 0.00 0.00 1.78
166 167 7.040961 CGGGGTGGACGTAAATGAAAAATATAT 60.041 37.037 0.00 0.00 0.00 0.86
167 168 6.260493 CGGGGTGGACGTAAATGAAAAATATA 59.740 38.462 0.00 0.00 0.00 0.86
168 169 5.066764 CGGGGTGGACGTAAATGAAAAATAT 59.933 40.000 0.00 0.00 0.00 1.28
169 170 4.395542 CGGGGTGGACGTAAATGAAAAATA 59.604 41.667 0.00 0.00 0.00 1.40
170 171 3.191791 CGGGGTGGACGTAAATGAAAAAT 59.808 43.478 0.00 0.00 0.00 1.82
171 172 2.553172 CGGGGTGGACGTAAATGAAAAA 59.447 45.455 0.00 0.00 0.00 1.94
172 173 2.152830 CGGGGTGGACGTAAATGAAAA 58.847 47.619 0.00 0.00 0.00 2.29
173 174 1.611148 CCGGGGTGGACGTAAATGAAA 60.611 52.381 0.00 0.00 42.00 2.69
174 175 0.036199 CCGGGGTGGACGTAAATGAA 60.036 55.000 0.00 0.00 42.00 2.57
175 176 0.903924 TCCGGGGTGGACGTAAATGA 60.904 55.000 0.00 0.00 43.74 2.57
176 177 1.597989 TCCGGGGTGGACGTAAATG 59.402 57.895 0.00 0.00 43.74 2.32
177 178 4.133612 TCCGGGGTGGACGTAAAT 57.866 55.556 0.00 0.00 43.74 1.40
185 186 1.901464 CAAAACCAGTCCGGGGTGG 60.901 63.158 18.55 18.55 39.01 4.61
186 187 0.889186 CTCAAAACCAGTCCGGGGTG 60.889 60.000 0.00 0.00 39.01 4.61
187 188 1.454539 CTCAAAACCAGTCCGGGGT 59.545 57.895 0.00 0.00 41.41 4.95
188 189 1.303317 CCTCAAAACCAGTCCGGGG 60.303 63.158 0.00 0.00 40.22 5.73
189 190 0.889186 CACCTCAAAACCAGTCCGGG 60.889 60.000 0.00 0.00 40.22 5.73
190 191 1.515521 GCACCTCAAAACCAGTCCGG 61.516 60.000 0.00 0.00 42.50 5.14
191 192 1.841663 CGCACCTCAAAACCAGTCCG 61.842 60.000 0.00 0.00 0.00 4.79
192 193 1.515521 CCGCACCTCAAAACCAGTCC 61.516 60.000 0.00 0.00 0.00 3.85
193 194 1.949257 CCGCACCTCAAAACCAGTC 59.051 57.895 0.00 0.00 0.00 3.51
194 195 2.193536 GCCGCACCTCAAAACCAGT 61.194 57.895 0.00 0.00 0.00 4.00
195 196 2.644992 GCCGCACCTCAAAACCAG 59.355 61.111 0.00 0.00 0.00 4.00
196 197 2.909965 GGCCGCACCTCAAAACCA 60.910 61.111 0.00 0.00 34.51 3.67
197 198 4.038080 CGGCCGCACCTCAAAACC 62.038 66.667 14.67 0.00 35.61 3.27
198 199 4.700365 GCGGCCGCACCTCAAAAC 62.700 66.667 43.55 11.09 41.49 2.43
216 217 2.023741 CGTGGATGCGCTCAATGC 59.976 61.111 9.73 0.00 38.57 3.56
217 218 1.349627 GTCGTGGATGCGCTCAATG 59.650 57.895 9.73 2.99 0.00 2.82
218 219 1.815421 GGTCGTGGATGCGCTCAAT 60.815 57.895 9.73 0.00 0.00 2.57
219 220 2.434185 GGTCGTGGATGCGCTCAA 60.434 61.111 9.73 0.00 0.00 3.02
220 221 4.451150 GGGTCGTGGATGCGCTCA 62.451 66.667 9.73 1.22 0.00 4.26
221 222 3.740128 ATGGGTCGTGGATGCGCTC 62.740 63.158 9.73 3.37 0.00 5.03
222 223 3.740128 GATGGGTCGTGGATGCGCT 62.740 63.158 9.73 0.00 0.00 5.92
223 224 3.272334 GATGGGTCGTGGATGCGC 61.272 66.667 0.00 0.00 0.00 6.09
224 225 2.961721 CGATGGGTCGTGGATGCG 60.962 66.667 0.00 0.00 42.78 4.73
225 226 2.588877 CCGATGGGTCGTGGATGC 60.589 66.667 0.00 0.00 46.25 3.91
226 227 1.227263 GTCCGATGGGTCGTGGATG 60.227 63.158 0.00 0.00 46.25 3.51
227 228 1.261938 TTGTCCGATGGGTCGTGGAT 61.262 55.000 0.00 0.00 46.25 3.41
228 229 1.473497 TTTGTCCGATGGGTCGTGGA 61.473 55.000 0.00 0.00 46.25 4.02
229 230 0.392461 ATTTGTCCGATGGGTCGTGG 60.392 55.000 0.00 0.00 46.25 4.94
230 231 0.726827 CATTTGTCCGATGGGTCGTG 59.273 55.000 0.00 0.00 46.25 4.35
231 232 1.024579 GCATTTGTCCGATGGGTCGT 61.025 55.000 0.00 0.00 46.25 4.34
233 234 0.734889 CTGCATTTGTCCGATGGGTC 59.265 55.000 0.00 0.00 33.83 4.46
234 235 0.327924 TCTGCATTTGTCCGATGGGT 59.672 50.000 0.00 0.00 33.83 4.51
235 236 0.734889 GTCTGCATTTGTCCGATGGG 59.265 55.000 0.00 0.00 0.00 4.00
236 237 1.452110 TGTCTGCATTTGTCCGATGG 58.548 50.000 0.00 0.00 0.00 3.51
237 238 2.679336 TCATGTCTGCATTTGTCCGATG 59.321 45.455 0.00 0.00 31.99 3.84
238 239 2.941064 CTCATGTCTGCATTTGTCCGAT 59.059 45.455 0.00 0.00 31.99 4.18
239 240 2.349590 CTCATGTCTGCATTTGTCCGA 58.650 47.619 0.00 0.00 31.99 4.55
240 241 1.202110 GCTCATGTCTGCATTTGTCCG 60.202 52.381 0.00 0.00 31.99 4.79
241 242 1.814394 TGCTCATGTCTGCATTTGTCC 59.186 47.619 6.68 0.00 33.94 4.02
242 243 3.564235 TTGCTCATGTCTGCATTTGTC 57.436 42.857 10.43 0.00 39.07 3.18
243 244 3.553508 GGTTTGCTCATGTCTGCATTTGT 60.554 43.478 10.43 0.00 39.07 2.83
244 245 2.991190 GGTTTGCTCATGTCTGCATTTG 59.009 45.455 10.43 0.00 39.07 2.32
245 246 2.028748 GGGTTTGCTCATGTCTGCATTT 60.029 45.455 10.43 0.00 39.07 2.32
246 247 1.547372 GGGTTTGCTCATGTCTGCATT 59.453 47.619 10.43 0.00 39.07 3.56
247 248 1.180029 GGGTTTGCTCATGTCTGCAT 58.820 50.000 10.43 0.00 39.07 3.96
248 249 0.178995 TGGGTTTGCTCATGTCTGCA 60.179 50.000 6.68 6.68 37.42 4.41
249 250 1.180029 ATGGGTTTGCTCATGTCTGC 58.820 50.000 0.00 0.00 33.84 4.26
250 251 3.226346 CAATGGGTTTGCTCATGTCTG 57.774 47.619 0.00 0.00 35.65 3.51
260 261 0.033228 TTTGAGCGGCAATGGGTTTG 59.967 50.000 1.45 0.00 36.15 2.93
261 262 0.755686 TTTTGAGCGGCAATGGGTTT 59.244 45.000 1.45 0.00 36.15 3.27
262 263 0.755686 TTTTTGAGCGGCAATGGGTT 59.244 45.000 1.45 0.00 36.15 4.11
263 264 2.435418 TTTTTGAGCGGCAATGGGT 58.565 47.368 1.45 0.00 36.15 4.51
278 279 4.624336 GGTTTGGCCGAATTTTGTTTTT 57.376 36.364 9.15 0.00 0.00 1.94
291 292 0.894835 AATGGATGTTCGGTTTGGCC 59.105 50.000 0.00 0.00 0.00 5.36
292 293 2.029470 TCAAATGGATGTTCGGTTTGGC 60.029 45.455 0.00 0.00 32.26 4.52
293 294 3.367292 CCTCAAATGGATGTTCGGTTTGG 60.367 47.826 0.00 0.00 32.26 3.28
294 295 3.255642 ACCTCAAATGGATGTTCGGTTTG 59.744 43.478 0.00 0.00 0.00 2.93
295 296 3.496331 ACCTCAAATGGATGTTCGGTTT 58.504 40.909 0.00 0.00 0.00 3.27
296 297 3.081804 GACCTCAAATGGATGTTCGGTT 58.918 45.455 0.00 0.00 0.00 4.44
297 298 2.711542 GACCTCAAATGGATGTTCGGT 58.288 47.619 0.00 0.00 0.00 4.69
298 299 1.665679 CGACCTCAAATGGATGTTCGG 59.334 52.381 0.00 0.00 0.00 4.30
299 300 1.665679 CCGACCTCAAATGGATGTTCG 59.334 52.381 0.00 0.00 0.00 3.95
300 301 2.985896 TCCGACCTCAAATGGATGTTC 58.014 47.619 0.00 0.00 0.00 3.18
301 302 3.652057 ATCCGACCTCAAATGGATGTT 57.348 42.857 0.00 0.00 39.69 2.71
304 305 1.846439 ACCATCCGACCTCAAATGGAT 59.154 47.619 7.21 0.00 40.98 3.41
305 306 1.065491 CACCATCCGACCTCAAATGGA 60.065 52.381 7.21 0.00 40.98 3.41
306 307 1.382522 CACCATCCGACCTCAAATGG 58.617 55.000 0.00 0.00 43.52 3.16
307 308 1.065491 TCCACCATCCGACCTCAAATG 60.065 52.381 0.00 0.00 0.00 2.32
308 309 1.210478 CTCCACCATCCGACCTCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
309 310 0.613260 CTCCACCATCCGACCTCAAA 59.387 55.000 0.00 0.00 0.00 2.69
310 311 0.544357 ACTCCACCATCCGACCTCAA 60.544 55.000 0.00 0.00 0.00 3.02
311 312 0.544357 AACTCCACCATCCGACCTCA 60.544 55.000 0.00 0.00 0.00 3.86
312 313 1.409427 CTAACTCCACCATCCGACCTC 59.591 57.143 0.00 0.00 0.00 3.85
313 314 1.486211 CTAACTCCACCATCCGACCT 58.514 55.000 0.00 0.00 0.00 3.85
314 315 0.179081 GCTAACTCCACCATCCGACC 60.179 60.000 0.00 0.00 0.00 4.79
315 316 0.179081 GGCTAACTCCACCATCCGAC 60.179 60.000 0.00 0.00 0.00 4.79
316 317 0.325296 AGGCTAACTCCACCATCCGA 60.325 55.000 0.00 0.00 0.00 4.55
317 318 1.410004 TAGGCTAACTCCACCATCCG 58.590 55.000 0.00 0.00 0.00 4.18
318 319 3.926058 TTTAGGCTAACTCCACCATCC 57.074 47.619 6.43 0.00 0.00 3.51
319 320 5.354513 GTCTTTTTAGGCTAACTCCACCATC 59.645 44.000 6.43 0.00 0.00 3.51
320 321 5.222048 TGTCTTTTTAGGCTAACTCCACCAT 60.222 40.000 6.43 0.00 0.00 3.55
321 322 4.103469 TGTCTTTTTAGGCTAACTCCACCA 59.897 41.667 6.43 0.00 0.00 4.17
322 323 4.454847 GTGTCTTTTTAGGCTAACTCCACC 59.545 45.833 6.43 0.00 0.00 4.61
323 324 5.061179 TGTGTCTTTTTAGGCTAACTCCAC 58.939 41.667 6.43 9.88 0.00 4.02
324 325 5.298989 TGTGTCTTTTTAGGCTAACTCCA 57.701 39.130 6.43 0.00 0.00 3.86
325 326 5.995897 TCTTGTGTCTTTTTAGGCTAACTCC 59.004 40.000 6.43 0.00 0.00 3.85
326 327 6.706716 ACTCTTGTGTCTTTTTAGGCTAACTC 59.293 38.462 6.43 0.00 0.00 3.01
327 328 6.592870 ACTCTTGTGTCTTTTTAGGCTAACT 58.407 36.000 6.43 0.00 0.00 2.24
328 329 6.346678 CGACTCTTGTGTCTTTTTAGGCTAAC 60.347 42.308 6.43 0.00 35.00 2.34
329 330 5.694910 CGACTCTTGTGTCTTTTTAGGCTAA 59.305 40.000 2.04 2.04 35.00 3.09
330 331 5.227908 CGACTCTTGTGTCTTTTTAGGCTA 58.772 41.667 0.00 0.00 35.00 3.93
331 332 4.058817 CGACTCTTGTGTCTTTTTAGGCT 58.941 43.478 0.00 0.00 35.00 4.58
332 333 3.186613 CCGACTCTTGTGTCTTTTTAGGC 59.813 47.826 0.00 0.00 35.00 3.93
333 334 3.746492 CCCGACTCTTGTGTCTTTTTAGG 59.254 47.826 0.00 0.00 35.00 2.69
334 335 3.746492 CCCCGACTCTTGTGTCTTTTTAG 59.254 47.826 0.00 0.00 35.00 1.85
335 336 3.735591 CCCCGACTCTTGTGTCTTTTTA 58.264 45.455 0.00 0.00 35.00 1.52
336 337 2.572290 CCCCGACTCTTGTGTCTTTTT 58.428 47.619 0.00 0.00 35.00 1.94
479 486 2.430332 TGAAAAGGCAGGGTGAAAAGTG 59.570 45.455 0.00 0.00 0.00 3.16
554 562 1.832608 TCACTGTGGACTGCCGACT 60.833 57.895 8.11 0.00 36.79 4.18
634 642 4.021925 AAGACGTGGAGGCCAGGC 62.022 66.667 5.01 1.26 42.42 4.85
642 650 2.425592 CAGGTGGCAAGACGTGGA 59.574 61.111 0.00 0.00 0.00 4.02
705 743 1.671379 GAAAGCGGCCGAGAAAGGT 60.671 57.895 33.48 5.34 0.00 3.50
709 747 1.745115 CATGGAAAGCGGCCGAGAA 60.745 57.895 33.48 7.67 0.00 2.87
764 813 2.897350 GACTGTATGCAGCCCGGC 60.897 66.667 11.09 0.00 46.30 6.13
767 816 1.878522 CGACGACTGTATGCAGCCC 60.879 63.158 11.09 2.37 46.30 5.19
799 848 1.738099 CACAGTGGCAGAGGTACGC 60.738 63.158 0.00 0.00 0.00 4.42
843 892 2.237392 CCCACCCTTGCTCTATATAGCC 59.763 54.545 7.58 0.00 42.05 3.93
881 932 2.612721 CCTTTGGTTTTATGTGGCCTGC 60.613 50.000 3.32 0.00 0.00 4.85
885 936 4.864704 TCTTCCTTTGGTTTTATGTGGC 57.135 40.909 0.00 0.00 0.00 5.01
893 944 4.524053 ACGTTCTCTTCTTCCTTTGGTTT 58.476 39.130 0.00 0.00 0.00 3.27
895 946 3.388350 AGACGTTCTCTTCTTCCTTTGGT 59.612 43.478 0.00 0.00 0.00 3.67
898 949 4.099573 TGACAGACGTTCTCTTCTTCCTTT 59.900 41.667 0.00 0.00 0.00 3.11
1085 1136 1.696336 AGTAGTATCTACCGGCGAGGA 59.304 52.381 9.30 3.41 45.00 3.71
1090 1141 1.736681 CCGCTAGTAGTATCTACCGGC 59.263 57.143 0.00 9.38 34.08 6.13
1104 1161 5.109210 TGTTTTGTCTATCATGTCCGCTAG 58.891 41.667 0.00 0.00 0.00 3.42
1105 1162 5.079689 TGTTTTGTCTATCATGTCCGCTA 57.920 39.130 0.00 0.00 0.00 4.26
1106 1163 3.937814 TGTTTTGTCTATCATGTCCGCT 58.062 40.909 0.00 0.00 0.00 5.52
1108 1165 7.496704 CAAAATGTTTTGTCTATCATGTCCG 57.503 36.000 9.48 0.00 41.87 4.79
1126 1247 7.218204 GGAAAACGCTAGCTACATTACAAAATG 59.782 37.037 13.93 0.00 46.66 2.32
1127 1248 7.094549 TGGAAAACGCTAGCTACATTACAAAAT 60.095 33.333 13.93 0.00 0.00 1.82
1148 1275 7.186570 TCACTGTCAATCAGAGATATGGAAA 57.813 36.000 1.79 0.00 46.27 3.13
1169 1296 2.681848 ACAGATTAGCATGCAAGCTCAC 59.318 45.455 21.34 12.54 45.26 3.51
1199 1326 7.024768 CCTTACAAAGAGAAACACAAACGAAA 58.975 34.615 0.00 0.00 0.00 3.46
1207 1334 3.568430 CCCCACCTTACAAAGAGAAACAC 59.432 47.826 0.00 0.00 0.00 3.32
1227 1354 0.036294 CGGTTTCTCCTTCACCTCCC 60.036 60.000 0.00 0.00 0.00 4.30
1519 1646 0.457851 AAGATGCCGAACTCTCCTCG 59.542 55.000 0.00 0.00 36.06 4.63
1528 1655 1.515954 GGGAGACGAAGATGCCGAA 59.484 57.895 0.00 0.00 0.00 4.30
1531 1658 0.179070 GAAGGGGAGACGAAGATGCC 60.179 60.000 0.00 0.00 0.00 4.40
1534 1661 2.506065 CGGAAGGGGAGACGAAGAT 58.494 57.895 0.00 0.00 0.00 2.40
1647 1783 0.598680 CAAGATGAGATCGACGGCCC 60.599 60.000 0.00 0.00 0.00 5.80
1714 1861 8.691661 ACCAATCTGCTTATTTATTTATCGGT 57.308 30.769 0.00 0.00 0.00 4.69
1719 1866 9.391006 ACTTCGACCAATCTGCTTATTTATTTA 57.609 29.630 0.00 0.00 0.00 1.40
1720 1867 8.281212 ACTTCGACCAATCTGCTTATTTATTT 57.719 30.769 0.00 0.00 0.00 1.40
1721 1868 7.770897 AGACTTCGACCAATCTGCTTATTTATT 59.229 33.333 0.00 0.00 0.00 1.40
1760 1907 3.545703 CCAGGAAAGCCAATCGATACTT 58.454 45.455 0.00 0.00 36.29 2.24
1768 1915 1.348696 CAAAAGCCCAGGAAAGCCAAT 59.651 47.619 0.00 0.00 36.29 3.16
1770 1917 1.757423 GCAAAAGCCCAGGAAAGCCA 61.757 55.000 0.00 0.00 36.29 4.75
1787 1934 0.695462 AGGACCTGGATATGCTGGCA 60.695 55.000 18.29 0.00 0.00 4.92
1848 1996 3.243401 GCAAGTTCTCGGAACCACATTTT 60.243 43.478 11.61 0.00 0.00 1.82
1857 2005 1.134220 AGTTGGTGCAAGTTCTCGGAA 60.134 47.619 0.00 0.00 0.00 4.30
1858 2006 0.468226 AGTTGGTGCAAGTTCTCGGA 59.532 50.000 0.00 0.00 0.00 4.55
1859 2007 1.308998 AAGTTGGTGCAAGTTCTCGG 58.691 50.000 0.00 0.00 32.31 4.63
1860 2008 2.287009 GGAAAGTTGGTGCAAGTTCTCG 60.287 50.000 0.00 0.00 36.18 4.04
1861 2009 2.952310 AGGAAAGTTGGTGCAAGTTCTC 59.048 45.455 0.00 0.00 36.18 2.87
1933 2081 3.066203 GGTGAAAACACGGACATGAACTT 59.934 43.478 0.00 0.00 0.00 2.66
1963 2111 0.301687 GATTGCCGTAGATGTGCGTG 59.698 55.000 0.00 0.00 0.00 5.34
1975 2123 6.064846 ACTTATGCATTCTAAAGATTGCCG 57.935 37.500 18.97 10.49 45.60 5.69
2016 2273 6.385649 ACGCACAAAAAGAGAAGGAAAATA 57.614 33.333 0.00 0.00 0.00 1.40
2037 2541 2.941064 TCTATTGGTCTACTGGTCGACG 59.059 50.000 9.92 0.00 0.00 5.12
2038 2542 3.066481 GGTCTATTGGTCTACTGGTCGAC 59.934 52.174 7.13 7.13 0.00 4.20
2041 2545 4.024670 AGTGGTCTATTGGTCTACTGGTC 58.975 47.826 0.00 0.00 0.00 4.02
2043 2547 6.540438 TTTAGTGGTCTATTGGTCTACTGG 57.460 41.667 0.00 0.00 0.00 4.00
2052 3779 4.758165 ACCCGTTGTTTTAGTGGTCTATTG 59.242 41.667 0.00 0.00 0.00 1.90
2084 4539 8.817092 TTATTTATTTTTGAGAGGGGGTGTAG 57.183 34.615 0.00 0.00 0.00 2.74
2107 4562 8.175069 CGAAGCAAACATAGCTACATTTTCTTA 58.825 33.333 13.06 0.00 42.53 2.10
2109 4564 6.546395 CGAAGCAAACATAGCTACATTTTCT 58.454 36.000 0.00 0.00 42.53 2.52
2161 4625 9.524106 AATGTACGTACATCAATAATTCGAGAA 57.476 29.630 34.66 7.22 45.55 2.87
2162 4626 9.177304 GAATGTACGTACATCAATAATTCGAGA 57.823 33.333 34.66 7.58 45.55 4.04
2163 4627 8.425491 GGAATGTACGTACATCAATAATTCGAG 58.575 37.037 34.66 0.00 45.55 4.04
2164 4628 7.921745 TGGAATGTACGTACATCAATAATTCGA 59.078 33.333 34.66 23.02 45.55 3.71
2165 4629 8.067780 TGGAATGTACGTACATCAATAATTCG 57.932 34.615 34.66 0.00 45.55 3.34
2168 4632 9.208022 CAGATGGAATGTACGTACATCAATAAT 57.792 33.333 34.66 24.05 45.55 1.28
2169 4633 8.201464 ACAGATGGAATGTACGTACATCAATAA 58.799 33.333 34.66 21.22 45.55 1.40
2170 4634 7.722363 ACAGATGGAATGTACGTACATCAATA 58.278 34.615 34.66 23.01 45.55 1.90
2171 4635 6.582636 ACAGATGGAATGTACGTACATCAAT 58.417 36.000 34.66 27.17 45.55 2.57
2172 4636 5.972935 ACAGATGGAATGTACGTACATCAA 58.027 37.500 34.66 24.46 45.55 2.57
2173 4637 5.451381 GGACAGATGGAATGTACGTACATCA 60.451 44.000 34.66 28.96 45.55 3.07
2174 4638 4.982916 GGACAGATGGAATGTACGTACATC 59.017 45.833 34.66 26.67 45.55 3.06
2180 4644 2.168521 AGTGGGACAGATGGAATGTACG 59.831 50.000 0.00 0.00 41.80 3.67
2200 4664 7.865706 AACAAATGTAAATCCTAGTGCCTAG 57.134 36.000 3.06 3.06 34.16 3.02
2203 4667 6.919721 TCAAACAAATGTAAATCCTAGTGCC 58.080 36.000 0.00 0.00 0.00 5.01
2204 4668 8.986477 ATTCAAACAAATGTAAATCCTAGTGC 57.014 30.769 0.00 0.00 0.00 4.40
2260 4724 7.158697 ACAAAAATGGGCTAGAAAAATACACC 58.841 34.615 0.00 0.00 0.00 4.16
2264 4728 7.673926 AGAGGACAAAAATGGGCTAGAAAAATA 59.326 33.333 0.00 0.00 0.00 1.40
2275 5060 5.358160 GGACAATAGAGAGGACAAAAATGGG 59.642 44.000 0.00 0.00 0.00 4.00
2281 5066 4.425772 TGAGGGACAATAGAGAGGACAAA 58.574 43.478 0.00 0.00 0.00 2.83
2291 5078 4.315803 ACGTCAGTTTTGAGGGACAATAG 58.684 43.478 2.82 0.00 42.15 1.73
2296 5083 4.312443 TCAATACGTCAGTTTTGAGGGAC 58.688 43.478 0.00 0.00 41.23 4.46
2314 5101 7.546358 TCATTTTAATTGGCACGATTCTCAAT 58.454 30.769 0.00 0.00 0.00 2.57
2317 5104 7.992180 AATCATTTTAATTGGCACGATTCTC 57.008 32.000 0.00 0.00 0.00 2.87
2355 5148 1.515521 GGAGACCGGCAAAGTGGTTG 61.516 60.000 0.00 0.00 38.99 3.77
2374 5167 1.113788 TAGGGTTTGGTACGATCCCG 58.886 55.000 11.09 0.00 42.57 5.14
2376 5169 4.942761 TGTATAGGGTTTGGTACGATCC 57.057 45.455 0.00 0.00 0.00 3.36
2397 5197 3.181489 GCGACCGTTGCCTAGCTATATAT 60.181 47.826 0.00 0.00 0.00 0.86
2431 5231 0.179163 GCAAGTGATTAAGGCGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
2439 5240 6.691754 TGTCAAAAGAGTGCAAGTGATTAA 57.308 33.333 0.00 0.00 0.00 1.40
2522 5323 2.106683 GTTTCGGTGGATGCGGAGG 61.107 63.158 0.00 0.00 0.00 4.30
2646 5713 0.955428 GCAGAGATGACCGTGGCAAA 60.955 55.000 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.