Multiple sequence alignment - TraesCS5A01G393300

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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 TraesCS5A01G393300 chr5A 100.000 4711 0 0 1 4711 589223431 589218721 0.000000e+00 8700.0
1 TraesCS5A01G393300 chr5A 93.333 285 13 2 72 354 1838640 1838920 2.620000e-112 416.0
2 TraesCS5A01G393300 chr5A 78.108 370 47 18 4329 4677 603528509 603528153 2.220000e-48 204.0
3 TraesCS5A01G393300 chr5B 89.666 3290 191 65 1468 4707 575782042 575778852 0.000000e+00 4054.0
4 TraesCS5A01G393300 chr5B 87.328 1089 78 24 370 1446 575783078 575782038 0.000000e+00 1192.0
5 TraesCS5A01G393300 chr5B 79.518 415 63 12 1931 2332 697244993 697244588 4.640000e-70 276.0
6 TraesCS5A01G393300 chr5B 75.584 385 67 15 1957 2332 697568292 697567926 1.050000e-36 165.0
7 TraesCS5A01G393300 chr5B 75.134 374 69 15 1931 2291 697186860 697186498 2.270000e-33 154.0
8 TraesCS5A01G393300 chr5B 73.123 413 70 21 1932 2327 697610427 697610039 4.980000e-20 110.0
9 TraesCS5A01G393300 chr5B 95.833 48 2 0 1 48 575783168 575783121 1.410000e-10 78.7
10 TraesCS5A01G393300 chr5D 88.255 2086 137 49 370 2401 469061995 469059964 0.000000e+00 2396.0
11 TraesCS5A01G393300 chr5D 93.830 1491 74 9 2444 3925 469059956 469058475 0.000000e+00 2228.0
12 TraesCS5A01G393300 chr5D 91.088 763 41 16 3959 4711 469058471 469057726 0.000000e+00 1007.0
13 TraesCS5A01G393300 chr5D 75.645 349 67 12 1931 2270 553506846 553507185 1.750000e-34 158.0
14 TraesCS5A01G393300 chr5D 75.692 325 68 6 1949 2262 553483689 553484013 8.170000e-33 152.0
15 TraesCS5A01G393300 chr2A 92.105 304 18 2 68 369 30311635 30311934 1.570000e-114 424.0
16 TraesCS5A01G393300 chr2A 93.950 281 11 3 76 354 306176196 306176472 2.030000e-113 420.0
17 TraesCS5A01G393300 chr2A 81.786 280 34 7 4409 4676 104867696 104867970 7.940000e-53 219.0
18 TraesCS5A01G393300 chr1A 93.684 285 12 3 72 354 354954298 354954578 5.640000e-114 422.0
19 TraesCS5A01G393300 chr1A 79.054 296 51 10 4346 4638 578755989 578755702 4.810000e-45 193.0
20 TraesCS5A01G393300 chr7A 93.380 287 13 2 70 354 215187667 215187949 2.030000e-113 420.0
21 TraesCS5A01G393300 chr2B 93.333 285 12 5 73 354 78102621 78102341 9.430000e-112 414.0
22 TraesCS5A01G393300 chr6A 92.982 285 14 2 72 354 208378592 208378312 1.220000e-110 411.0
23 TraesCS5A01G393300 chr6A 91.611 298 17 4 75 369 613972769 613972477 5.680000e-109 405.0
24 TraesCS5A01G393300 chr3B 91.089 303 21 2 69 369 145960291 145959993 5.680000e-109 405.0
25 TraesCS5A01G393300 chr3B 77.451 408 64 19 4312 4698 145310693 145311093 7.940000e-53 219.0
26 TraesCS5A01G393300 chr4D 78.788 396 44 24 4313 4696 37521131 37520764 3.670000e-56 230.0
27 TraesCS5A01G393300 chr4D 79.193 322 49 14 4386 4696 44758852 44758538 1.720000e-49 207.0
28 TraesCS5A01G393300 chr7B 77.262 409 64 16 4311 4701 84488898 84488501 3.690000e-51 213.0
29 TraesCS5A01G393300 chr6D 79.705 271 42 10 4398 4656 409339589 409339320 2.900000e-42 183.0
30 TraesCS5A01G393300 chr1D 77.160 324 55 14 4332 4650 481929564 481929255 2.250000e-38 171.0
31 TraesCS5A01G393300 chr6B 76.491 285 46 12 4429 4693 614304730 614304447 8.220000e-28 135.0


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 TraesCS5A01G393300 chr5A 589218721 589223431 4710 True 8700.0 8700 100.000000 1 4711 1 chr5A.!!$R1 4710
1 TraesCS5A01G393300 chr5B 575778852 575783168 4316 True 1774.9 4054 90.942333 1 4707 3 chr5B.!!$R5 4706
2 TraesCS5A01G393300 chr5D 469057726 469061995 4269 True 1877.0 2396 91.057667 370 4711 3 chr5D.!!$R1 4341

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
870 920 0.109226 CACCGACGTCTCTTCCTTCC 60.109 60.0 14.70 0.0 0.00 3.46 F
1380 1431 0.035739 TTACCGTTCCCAACTCTGGC 59.964 55.0 0.00 0.0 41.99 4.85 F
1913 2004 0.251165 TGGCCTGGTTGCTAGTTTCC 60.251 55.0 3.32 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2217 0.391130 GCCACGCCTGTCAGTCAATA 60.391 55.0 0.0 0.0 0.0 1.90 R
3290 3413 0.442699 GAAGTGGAAGGTAAAGCGCG 59.557 55.0 0.0 0.0 0.0 6.86 R
3798 3927 0.372679 GACAGCGTCTCGTCGTGATA 59.627 55.0 0.0 0.0 0.0 2.15 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
52 71 5.335661 GGAGTACACTTTTGCATAGGTTTGG 60.336 44.000 0.00 0.00 0.00 3.28
56 75 6.909550 ACACTTTTGCATAGGTTTGGATAA 57.090 33.333 0.00 0.00 0.00 1.75
62 81 4.839121 TGCATAGGTTTGGATAAACGTCT 58.161 39.130 0.00 0.00 45.60 4.18
64 83 4.035208 GCATAGGTTTGGATAAACGTCTGG 59.965 45.833 0.00 2.30 45.60 3.86
66 85 3.671716 AGGTTTGGATAAACGTCTGGTC 58.328 45.455 0.00 0.00 45.60 4.02
72 91 2.354805 GGATAAACGTCTGGTCCAAGCT 60.355 50.000 0.00 0.00 0.00 3.74
73 92 2.922740 TAAACGTCTGGTCCAAGCTT 57.077 45.000 0.00 0.00 0.00 3.74
74 93 2.922740 AAACGTCTGGTCCAAGCTTA 57.077 45.000 0.00 0.00 0.00 3.09
75 94 2.457366 AACGTCTGGTCCAAGCTTAG 57.543 50.000 0.00 0.00 0.00 2.18
76 95 0.608640 ACGTCTGGTCCAAGCTTAGG 59.391 55.000 0.00 3.44 0.00 2.69
77 96 0.741221 CGTCTGGTCCAAGCTTAGGC 60.741 60.000 0.00 0.00 39.06 3.93
78 97 0.393132 GTCTGGTCCAAGCTTAGGCC 60.393 60.000 8.76 8.76 39.73 5.19
79 98 0.547712 TCTGGTCCAAGCTTAGGCCT 60.548 55.000 16.64 11.78 39.73 5.19
80 99 0.329596 CTGGTCCAAGCTTAGGCCTT 59.670 55.000 16.64 0.00 39.73 4.35
81 100 0.777446 TGGTCCAAGCTTAGGCCTTT 59.223 50.000 16.64 0.00 39.73 3.11
82 101 1.146982 TGGTCCAAGCTTAGGCCTTTT 59.853 47.619 16.64 0.00 39.73 2.27
83 102 2.248248 GGTCCAAGCTTAGGCCTTTTT 58.752 47.619 12.58 0.00 39.73 1.94
110 129 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
111 130 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
134 153 9.413734 AGGAATAGGAATTTTGTAGGAAATGAG 57.586 33.333 0.00 0.00 30.06 2.90
135 154 9.408648 GGAATAGGAATTTTGTAGGAAATGAGA 57.591 33.333 0.00 0.00 30.06 3.27
138 157 7.651027 AGGAATTTTGTAGGAAATGAGATGG 57.349 36.000 0.00 0.00 30.06 3.51
139 158 6.097412 AGGAATTTTGTAGGAAATGAGATGGC 59.903 38.462 0.00 0.00 30.06 4.40
140 159 6.127366 GGAATTTTGTAGGAAATGAGATGGCA 60.127 38.462 0.00 0.00 30.06 4.92
141 160 7.418254 GGAATTTTGTAGGAAATGAGATGGCAT 60.418 37.037 0.00 0.00 30.06 4.40
142 161 5.840243 TTTGTAGGAAATGAGATGGCATG 57.160 39.130 3.81 0.00 0.00 4.06
143 162 4.508551 TGTAGGAAATGAGATGGCATGT 57.491 40.909 3.81 0.00 0.00 3.21
144 163 5.628797 TGTAGGAAATGAGATGGCATGTA 57.371 39.130 3.81 0.00 0.00 2.29
145 164 6.191657 TGTAGGAAATGAGATGGCATGTAT 57.808 37.500 3.81 0.00 0.00 2.29
146 165 6.233434 TGTAGGAAATGAGATGGCATGTATC 58.767 40.000 3.81 0.45 0.00 2.24
147 166 5.579753 AGGAAATGAGATGGCATGTATCT 57.420 39.130 3.81 12.53 37.59 1.98
148 167 5.558818 AGGAAATGAGATGGCATGTATCTC 58.441 41.667 23.83 23.83 46.82 2.75
157 176 8.789825 GAGATGGCATGTATCTCAAATCTTAT 57.210 34.615 24.83 2.03 46.22 1.73
158 177 8.563123 AGATGGCATGTATCTCAAATCTTATG 57.437 34.615 3.81 0.00 29.05 1.90
159 178 7.610692 AGATGGCATGTATCTCAAATCTTATGG 59.389 37.037 3.81 0.00 29.05 2.74
160 179 6.005823 TGGCATGTATCTCAAATCTTATGGG 58.994 40.000 0.00 0.00 0.00 4.00
161 180 5.105997 GGCATGTATCTCAAATCTTATGGGC 60.106 44.000 0.00 0.00 0.00 5.36
162 181 5.474532 GCATGTATCTCAAATCTTATGGGCA 59.525 40.000 0.00 0.00 0.00 5.36
163 182 6.349115 GCATGTATCTCAAATCTTATGGGCAG 60.349 42.308 0.00 0.00 0.00 4.85
164 183 5.624159 TGTATCTCAAATCTTATGGGCAGG 58.376 41.667 0.00 0.00 0.00 4.85
165 184 5.369404 TGTATCTCAAATCTTATGGGCAGGA 59.631 40.000 0.00 0.00 0.00 3.86
166 185 4.860802 TCTCAAATCTTATGGGCAGGAA 57.139 40.909 0.00 0.00 0.00 3.36
167 186 5.393068 TCTCAAATCTTATGGGCAGGAAT 57.607 39.130 0.00 0.00 0.00 3.01
168 187 6.514012 TCTCAAATCTTATGGGCAGGAATA 57.486 37.500 0.00 0.00 0.00 1.75
169 188 6.537355 TCTCAAATCTTATGGGCAGGAATAG 58.463 40.000 0.00 0.00 0.00 1.73
170 189 6.329986 TCTCAAATCTTATGGGCAGGAATAGA 59.670 38.462 0.00 0.00 0.00 1.98
171 190 6.910191 TCAAATCTTATGGGCAGGAATAGAA 58.090 36.000 0.00 0.00 0.00 2.10
172 191 7.353525 TCAAATCTTATGGGCAGGAATAGAAA 58.646 34.615 0.00 0.00 0.00 2.52
173 192 7.838696 TCAAATCTTATGGGCAGGAATAGAAAA 59.161 33.333 0.00 0.00 0.00 2.29
174 193 8.477256 CAAATCTTATGGGCAGGAATAGAAAAA 58.523 33.333 0.00 0.00 0.00 1.94
175 194 7.830099 ATCTTATGGGCAGGAATAGAAAAAG 57.170 36.000 0.00 0.00 0.00 2.27
176 195 6.969043 TCTTATGGGCAGGAATAGAAAAAGA 58.031 36.000 0.00 0.00 0.00 2.52
177 196 7.056635 TCTTATGGGCAGGAATAGAAAAAGAG 58.943 38.462 0.00 0.00 0.00 2.85
178 197 4.927267 TGGGCAGGAATAGAAAAAGAGA 57.073 40.909 0.00 0.00 0.00 3.10
179 198 5.456921 TGGGCAGGAATAGAAAAAGAGAT 57.543 39.130 0.00 0.00 0.00 2.75
180 199 5.195940 TGGGCAGGAATAGAAAAAGAGATG 58.804 41.667 0.00 0.00 0.00 2.90
181 200 5.196695 GGGCAGGAATAGAAAAAGAGATGT 58.803 41.667 0.00 0.00 0.00 3.06
182 201 5.298026 GGGCAGGAATAGAAAAAGAGATGTC 59.702 44.000 0.00 0.00 0.00 3.06
183 202 5.882557 GGCAGGAATAGAAAAAGAGATGTCA 59.117 40.000 0.00 0.00 0.00 3.58
184 203 6.545298 GGCAGGAATAGAAAAAGAGATGTCAT 59.455 38.462 0.00 0.00 0.00 3.06
185 204 7.067981 GGCAGGAATAGAAAAAGAGATGTCATT 59.932 37.037 0.00 0.00 0.00 2.57
186 205 8.465201 GCAGGAATAGAAAAAGAGATGTCATTT 58.535 33.333 0.00 0.00 0.00 2.32
187 206 9.784680 CAGGAATAGAAAAAGAGATGTCATTTG 57.215 33.333 0.00 0.00 0.00 2.32
188 207 8.964772 AGGAATAGAAAAAGAGATGTCATTTGG 58.035 33.333 0.00 0.00 0.00 3.28
189 208 8.743714 GGAATAGAAAAAGAGATGTCATTTGGT 58.256 33.333 0.00 0.00 0.00 3.67
191 210 9.918630 AATAGAAAAAGAGATGTCATTTGGTTG 57.081 29.630 0.00 0.00 0.00 3.77
192 211 7.587037 AGAAAAAGAGATGTCATTTGGTTGA 57.413 32.000 0.00 0.00 0.00 3.18
193 212 7.428826 AGAAAAAGAGATGTCATTTGGTTGAC 58.571 34.615 0.00 0.00 45.05 3.18
254 273 7.896383 TTATTTTCCTATGAAATGTGGAGGG 57.104 36.000 0.00 0.00 40.08 4.30
255 274 5.528600 TTTTCCTATGAAATGTGGAGGGA 57.471 39.130 0.00 0.00 40.08 4.20
256 275 4.778213 TTCCTATGAAATGTGGAGGGAG 57.222 45.455 0.00 0.00 33.16 4.30
257 276 3.048600 TCCTATGAAATGTGGAGGGAGG 58.951 50.000 0.00 0.00 0.00 4.30
258 277 3.048600 CCTATGAAATGTGGAGGGAGGA 58.951 50.000 0.00 0.00 0.00 3.71
259 278 3.654806 CCTATGAAATGTGGAGGGAGGAT 59.345 47.826 0.00 0.00 0.00 3.24
260 279 4.846367 CCTATGAAATGTGGAGGGAGGATA 59.154 45.833 0.00 0.00 0.00 2.59
261 280 4.989875 ATGAAATGTGGAGGGAGGATAG 57.010 45.455 0.00 0.00 0.00 2.08
262 281 3.048600 TGAAATGTGGAGGGAGGATAGG 58.951 50.000 0.00 0.00 0.00 2.57
263 282 3.311327 TGAAATGTGGAGGGAGGATAGGA 60.311 47.826 0.00 0.00 0.00 2.94
264 283 3.438131 AATGTGGAGGGAGGATAGGAA 57.562 47.619 0.00 0.00 0.00 3.36
265 284 2.176247 TGTGGAGGGAGGATAGGAAC 57.824 55.000 0.00 0.00 0.00 3.62
266 285 1.344087 TGTGGAGGGAGGATAGGAACC 60.344 57.143 0.00 0.00 0.00 3.62
267 286 1.023719 TGGAGGGAGGATAGGAACCA 58.976 55.000 0.00 0.00 0.00 3.67
268 287 1.368203 TGGAGGGAGGATAGGAACCAA 59.632 52.381 0.00 0.00 0.00 3.67
269 288 2.021042 TGGAGGGAGGATAGGAACCAAT 60.021 50.000 0.00 0.00 0.00 3.16
270 289 2.640332 GGAGGGAGGATAGGAACCAATC 59.360 54.545 0.00 0.00 0.00 2.67
308 327 6.442513 GAATCTATTCCTGTGAACCAAAGG 57.557 41.667 0.00 0.00 40.12 3.11
309 328 4.301072 TCTATTCCTGTGAACCAAAGGG 57.699 45.455 3.53 0.00 39.27 3.95
310 329 1.632589 ATTCCTGTGAACCAAAGGGC 58.367 50.000 3.53 0.00 39.27 5.19
311 330 0.555769 TTCCTGTGAACCAAAGGGCT 59.444 50.000 3.53 0.00 39.27 5.19
312 331 1.440618 TCCTGTGAACCAAAGGGCTA 58.559 50.000 3.53 0.00 39.27 3.93
313 332 1.777878 TCCTGTGAACCAAAGGGCTAA 59.222 47.619 3.53 0.00 39.27 3.09
314 333 2.175931 TCCTGTGAACCAAAGGGCTAAA 59.824 45.455 3.53 0.00 39.27 1.85
315 334 2.558359 CCTGTGAACCAAAGGGCTAAAG 59.442 50.000 0.00 0.00 35.31 1.85
316 335 2.558359 CTGTGAACCAAAGGGCTAAAGG 59.442 50.000 0.00 0.00 37.90 3.11
317 336 2.175931 TGTGAACCAAAGGGCTAAAGGA 59.824 45.455 0.00 0.00 37.90 3.36
318 337 3.227614 GTGAACCAAAGGGCTAAAGGAA 58.772 45.455 0.00 0.00 37.90 3.36
319 338 3.639561 GTGAACCAAAGGGCTAAAGGAAA 59.360 43.478 0.00 0.00 37.90 3.13
320 339 4.100344 GTGAACCAAAGGGCTAAAGGAAAA 59.900 41.667 0.00 0.00 37.90 2.29
321 340 4.717280 TGAACCAAAGGGCTAAAGGAAAAA 59.283 37.500 0.00 0.00 37.90 1.94
359 378 9.462606 TTCCTATCCTCTAAAATTCCTTCAAAC 57.537 33.333 0.00 0.00 0.00 2.93
360 379 8.053355 TCCTATCCTCTAAAATTCCTTCAAACC 58.947 37.037 0.00 0.00 0.00 3.27
361 380 7.834181 CCTATCCTCTAAAATTCCTTCAAACCA 59.166 37.037 0.00 0.00 0.00 3.67
362 381 9.243105 CTATCCTCTAAAATTCCTTCAAACCAA 57.757 33.333 0.00 0.00 0.00 3.67
363 382 7.906199 TCCTCTAAAATTCCTTCAAACCAAA 57.094 32.000 0.00 0.00 0.00 3.28
364 383 7.951591 TCCTCTAAAATTCCTTCAAACCAAAG 58.048 34.615 0.00 0.00 0.00 2.77
365 384 7.015195 TCCTCTAAAATTCCTTCAAACCAAAGG 59.985 37.037 0.00 0.00 43.94 3.11
436 455 2.051345 GCAACGTGTCCCAAAGCG 60.051 61.111 0.00 0.00 0.00 4.68
477 497 8.580720 TGATTCCGTTCCTTGAAAATGAAATAA 58.419 29.630 0.00 0.00 32.31 1.40
478 498 9.418045 GATTCCGTTCCTTGAAAATGAAATAAA 57.582 29.630 0.00 0.00 32.31 1.40
606 627 1.601419 CCCCCACAAAGCATGAGCAG 61.601 60.000 0.00 0.00 45.49 4.24
799 846 3.792053 GATCGGTTCGCATCGGGCT 62.792 63.158 0.00 0.00 41.67 5.19
805 852 3.664025 TTCGCATCGGGCTGTCCAG 62.664 63.158 0.00 0.00 41.67 3.86
870 920 0.109226 CACCGACGTCTCTTCCTTCC 60.109 60.000 14.70 0.00 0.00 3.46
871 921 0.251253 ACCGACGTCTCTTCCTTCCT 60.251 55.000 14.70 0.00 0.00 3.36
872 922 0.889306 CCGACGTCTCTTCCTTCCTT 59.111 55.000 14.70 0.00 0.00 3.36
873 923 2.089980 CCGACGTCTCTTCCTTCCTTA 58.910 52.381 14.70 0.00 0.00 2.69
890 940 2.553466 CCTTACGATCGATCCCCTCTCT 60.553 54.545 24.34 0.00 0.00 3.10
914 964 0.338814 TCCTACTCCTCCCCCACTTC 59.661 60.000 0.00 0.00 0.00 3.01
997 1047 3.096357 CCCCACCCCAAACCCTAG 58.904 66.667 0.00 0.00 0.00 3.02
998 1048 2.359011 CCCACCCCAAACCCTAGC 59.641 66.667 0.00 0.00 0.00 3.42
999 1049 2.359011 CCACCCCAAACCCTAGCC 59.641 66.667 0.00 0.00 0.00 3.93
1000 1050 2.359011 CACCCCAAACCCTAGCCC 59.641 66.667 0.00 0.00 0.00 5.19
1150 1200 4.218686 GCCCCTGTGGTGGGTGTT 62.219 66.667 0.00 0.00 45.70 3.32
1220 1270 3.952628 CTTCGTCGGGTTCCTGGCC 62.953 68.421 0.00 0.00 0.00 5.36
1380 1431 0.035739 TTACCGTTCCCAACTCTGGC 59.964 55.000 0.00 0.00 41.99 4.85
1388 1439 1.195115 CCCAACTCTGGCTGCTAGTA 58.805 55.000 12.90 0.00 41.99 1.82
1389 1440 1.137872 CCCAACTCTGGCTGCTAGTAG 59.862 57.143 12.90 10.98 41.99 2.57
1391 1442 2.417924 CCAACTCTGGCTGCTAGTAGTG 60.418 54.545 12.90 8.77 35.39 2.74
1433 1485 6.925610 TGCATAAATGATGTGGAGTAACTC 57.074 37.500 0.00 0.00 37.90 3.01
1441 1493 2.511659 TGTGGAGTAACTCGTGCTAGT 58.488 47.619 0.00 0.00 0.00 2.57
1442 1494 2.889045 TGTGGAGTAACTCGTGCTAGTT 59.111 45.455 5.29 5.29 42.31 2.24
1443 1495 3.319972 TGTGGAGTAACTCGTGCTAGTTT 59.680 43.478 5.26 0.00 40.20 2.66
1444 1496 4.202182 TGTGGAGTAACTCGTGCTAGTTTT 60.202 41.667 5.26 0.00 40.20 2.43
1445 1497 4.748600 GTGGAGTAACTCGTGCTAGTTTTT 59.251 41.667 5.26 0.00 40.20 1.94
1498 1550 6.116806 TGACTTCTTCTACTAGAGGCTAGTG 58.883 44.000 15.40 7.30 0.00 2.74
1520 1572 6.028987 GTGAAGTAGGTAGACGAGTTCAATC 58.971 44.000 0.00 0.00 42.98 2.67
1530 1582 8.350722 GGTAGACGAGTTCAATCAGTTATCATA 58.649 37.037 0.00 0.00 0.00 2.15
1549 1601 0.981183 AACGTTGGGTAGGATCAGCA 59.019 50.000 0.00 0.00 0.00 4.41
1555 1645 0.833287 GGGTAGGATCAGCAGCAAGA 59.167 55.000 0.00 0.00 0.00 3.02
1569 1659 3.691609 GCAGCAAGAAAGGTTACAGCTAT 59.308 43.478 0.00 0.00 0.00 2.97
1572 1662 4.019321 AGCAAGAAAGGTTACAGCTATGGA 60.019 41.667 0.00 0.00 0.00 3.41
1578 1668 0.928229 GTTACAGCTATGGAACCGCG 59.072 55.000 0.00 0.00 43.48 6.46
1582 1672 0.317160 CAGCTATGGAACCGCGGATA 59.683 55.000 35.90 18.03 0.00 2.59
1588 1678 2.163818 TGGAACCGCGGATATGAATC 57.836 50.000 35.90 16.37 0.00 2.52
1600 1690 5.461526 CGGATATGAATCTGCGTTCTTAGA 58.538 41.667 0.00 0.00 31.81 2.10
1605 1695 8.804688 ATATGAATCTGCGTTCTTAGACTTAC 57.195 34.615 0.00 0.00 0.00 2.34
1618 1708 8.756864 GTTCTTAGACTTACTGAACAGTTCAAG 58.243 37.037 16.85 13.46 42.54 3.02
1632 1722 5.043248 ACAGTTCAAGTTTTGTATGCTTGC 58.957 37.500 0.00 0.00 39.36 4.01
1669 1759 5.193679 AGGAGCAGAATAATTGGGTACAAC 58.806 41.667 0.00 0.00 39.87 3.32
1670 1760 4.338400 GGAGCAGAATAATTGGGTACAACC 59.662 45.833 0.00 0.00 39.87 3.77
1671 1761 3.945285 AGCAGAATAATTGGGTACAACCG 59.055 43.478 0.00 0.00 39.83 4.44
1672 1762 3.692593 GCAGAATAATTGGGTACAACCGT 59.307 43.478 0.00 0.00 39.83 4.83
1673 1763 4.877251 GCAGAATAATTGGGTACAACCGTA 59.123 41.667 0.00 0.00 39.83 4.02
1674 1764 5.220719 GCAGAATAATTGGGTACAACCGTAC 60.221 44.000 0.00 0.00 46.18 3.67
1736 1827 8.915036 TGTGTACATATGGTTTACCTTTTGTTT 58.085 29.630 7.80 0.00 36.92 2.83
1799 1890 2.234661 CACAGAAGCAGATGAGTGGGTA 59.765 50.000 0.00 0.00 0.00 3.69
1844 1935 5.943706 AATTAATGATGAGCTAGCAGCAG 57.056 39.130 18.83 0.00 45.56 4.24
1861 1952 2.846827 AGCAGGCTTCTGGTAGGTATTT 59.153 45.455 0.00 0.00 46.15 1.40
1904 1995 2.513753 TGAGTACAATTGGCCTGGTTG 58.486 47.619 10.83 8.99 0.00 3.77
1913 2004 0.251165 TGGCCTGGTTGCTAGTTTCC 60.251 55.000 3.32 0.00 0.00 3.13
1924 2015 2.084546 GCTAGTTTCCGGTTGCTTGAT 58.915 47.619 0.00 0.00 0.00 2.57
2001 2100 3.632145 CCACTGTTCTATGGGGTAATTGC 59.368 47.826 0.00 0.00 31.83 3.56
2035 2134 5.047847 GCTGCTCATATGCATGTGATTTTT 58.952 37.500 24.18 0.00 42.48 1.94
2041 2140 6.566141 TCATATGCATGTGATTTTTGACCTG 58.434 36.000 20.85 0.00 33.57 4.00
2051 2150 7.202526 TGTGATTTTTGACCTGTTTCATCTTC 58.797 34.615 0.00 0.00 0.00 2.87
2063 2162 4.814234 TGTTTCATCTTCAGTAACGTTGCT 59.186 37.500 13.53 13.53 0.00 3.91
2124 2223 8.850454 TCTTGTTTAACAGCAGTTTTATTGAC 57.150 30.769 0.00 0.00 39.15 3.18
2127 2226 7.990917 TGTTTAACAGCAGTTTTATTGACTGA 58.009 30.769 0.00 0.00 45.72 3.41
2301 2400 4.720649 TGTTATCTCTGGTGCTGTAGTC 57.279 45.455 0.00 0.00 0.00 2.59
2402 2503 1.816224 TGGGCCAGATTTTTCGTAAGC 59.184 47.619 0.00 0.00 37.18 3.09
2442 2557 7.093024 TGGTTTTAGTTCAAGGAGGGAGTATAG 60.093 40.741 0.00 0.00 0.00 1.31
2453 2568 7.304054 AGGAGGGAGTATAGGATATCATTGA 57.696 40.000 4.83 0.00 0.00 2.57
2515 2630 7.200434 ACTATTTATCAGGTTCACCATGTCT 57.800 36.000 0.00 0.00 38.89 3.41
2524 2639 8.877864 TCAGGTTCACCATGTCTTTTTATTAT 57.122 30.769 0.00 0.00 38.89 1.28
2581 2697 6.631016 TGGAGTGTGTATTCAAGTCTGTATC 58.369 40.000 0.00 0.00 0.00 2.24
2584 2700 6.634805 AGTGTGTATTCAAGTCTGTATCTGG 58.365 40.000 0.00 0.00 0.00 3.86
2672 2788 2.739379 GGCTGCTACAGAGAGAAAACAC 59.261 50.000 0.00 0.00 32.44 3.32
2811 2929 1.283321 GCCTCACATTTCCTCCCTCTT 59.717 52.381 0.00 0.00 0.00 2.85
2829 2947 8.742125 TCCCTCTTCAGACCATATATGTATTT 57.258 34.615 11.73 0.00 0.00 1.40
2832 2950 7.335422 CCTCTTCAGACCATATATGTATTTGGC 59.665 40.741 11.73 0.00 38.04 4.52
2922 3040 4.037923 CACAAATTGGTGCTTACAGGAGTT 59.962 41.667 0.00 0.00 31.10 3.01
2952 3070 4.725359 TGATTGTTTTCATGCATCACTCG 58.275 39.130 0.00 0.00 0.00 4.18
3052 3171 9.835389 TTGATGATCATCATTGTGTACTCAATA 57.165 29.630 33.23 14.43 46.12 1.90
3270 3393 5.104941 TGTCTATTGTGCAGGCTGTATAACT 60.105 40.000 16.18 8.91 0.00 2.24
3290 3413 5.197682 ACTTCACTACTGTCTGTTACCAC 57.802 43.478 0.00 0.00 0.00 4.16
3393 3516 5.127491 ACCTCTCTTTCTGTACTCCTATCG 58.873 45.833 0.00 0.00 0.00 2.92
3430 3553 4.037923 CACTGGAGTGTTTTATGTGCCTTT 59.962 41.667 0.00 0.00 40.96 3.11
3450 3573 6.438763 CCTTTTTGTTCCTGTAGTGATTGTC 58.561 40.000 0.00 0.00 0.00 3.18
3457 3580 6.437477 TGTTCCTGTAGTGATTGTCTATGTCT 59.563 38.462 0.00 0.00 0.00 3.41
3469 3592 4.460263 TGTCTATGTCTTTGCCTGTTTGT 58.540 39.130 0.00 0.00 0.00 2.83
3536 3659 1.178276 ACTCCGAGATGAAAGACGCT 58.822 50.000 1.33 0.00 0.00 5.07
3548 3671 1.594331 AAGACGCTGGGTTCTTTGAC 58.406 50.000 0.00 0.00 0.00 3.18
3574 3697 0.679640 TGGGATTAAACCTGCCTGCG 60.680 55.000 1.37 0.00 0.00 5.18
3577 3700 1.017387 GATTAAACCTGCCTGCGGAG 58.983 55.000 0.00 0.00 0.00 4.63
3627 3751 1.075542 TGAATTTGCACGGAGTAGCG 58.924 50.000 0.00 0.00 41.61 4.26
3742 3868 1.537202 GCACACCTGATTTGTGTCCTC 59.463 52.381 4.53 0.00 44.77 3.71
3748 3874 3.070018 CCTGATTTGTGTCCTCTGTCAC 58.930 50.000 0.00 0.00 35.43 3.67
3757 3883 2.705658 TGTCCTCTGTCACCATCTGTTT 59.294 45.455 0.00 0.00 0.00 2.83
3788 3917 5.828747 CAAGAATTGCCATACCTCAGATTG 58.171 41.667 0.00 0.00 40.39 2.67
3797 3926 5.380043 CCATACCTCAGATTGCCAATTACT 58.620 41.667 0.00 0.00 0.00 2.24
3798 3927 5.829924 CCATACCTCAGATTGCCAATTACTT 59.170 40.000 0.00 0.00 0.00 2.24
3817 3946 0.372679 TATCACGACGAGACGCTGTC 59.627 55.000 0.00 1.15 36.70 3.51
3832 3961 1.333619 GCTGTCGAAACTTGAAAGCCA 59.666 47.619 0.00 0.00 40.20 4.75
3855 3984 3.627395 ACTGGTGGTACATGTATGTGG 57.373 47.619 9.18 1.10 44.52 4.17
3895 4024 1.888215 TTTGTTCTGGCAGCTCTCTG 58.112 50.000 10.34 0.00 43.16 3.35
3902 4031 1.209990 CTGGCAGCTCTCTGGAATCTT 59.790 52.381 0.00 0.00 40.65 2.40
3909 4039 3.449018 AGCTCTCTGGAATCTTTTCGCTA 59.551 43.478 0.00 0.00 32.28 4.26
3922 4052 9.733219 GAATCTTTTCGCTACTAGTGTTACTAT 57.267 33.333 5.39 0.00 29.08 2.12
3925 4055 9.994432 TCTTTTCGCTACTAGTGTTACTATTAC 57.006 33.333 5.39 0.00 29.08 1.89
3929 4059 9.823647 TTCGCTACTAGTGTTACTATTACTACT 57.176 33.333 5.39 0.00 29.08 2.57
3930 4060 9.823647 TCGCTACTAGTGTTACTATTACTACTT 57.176 33.333 5.39 0.00 29.08 2.24
3931 4061 9.861138 CGCTACTAGTGTTACTATTACTACTTG 57.139 37.037 5.39 0.00 29.08 3.16
4026 4156 4.415881 TGTGTCATTTCTGTGTACTGGT 57.584 40.909 0.00 0.00 0.00 4.00
4055 4185 3.642377 TGTTGGATTGGATATGGCATTGG 59.358 43.478 4.78 0.00 0.00 3.16
4065 4195 3.078836 GGCATTGGCATGGGCAGT 61.079 61.111 5.17 0.00 43.71 4.40
4071 4201 3.446570 GGCATGGGCAGTGACAGC 61.447 66.667 0.00 0.00 43.71 4.40
4081 4211 3.375299 GGGCAGTGACAGCAGTTATTTAG 59.625 47.826 1.64 0.00 0.00 1.85
4082 4212 4.253685 GGCAGTGACAGCAGTTATTTAGA 58.746 43.478 1.64 0.00 0.00 2.10
4083 4213 4.331168 GGCAGTGACAGCAGTTATTTAGAG 59.669 45.833 1.64 0.00 0.00 2.43
4084 4214 4.932200 GCAGTGACAGCAGTTATTTAGAGT 59.068 41.667 0.00 0.00 0.00 3.24
4085 4215 6.100004 GCAGTGACAGCAGTTATTTAGAGTA 58.900 40.000 0.00 0.00 0.00 2.59
4086 4216 6.758886 GCAGTGACAGCAGTTATTTAGAGTAT 59.241 38.462 0.00 0.00 0.00 2.12
4087 4217 7.278868 GCAGTGACAGCAGTTATTTAGAGTATT 59.721 37.037 0.00 0.00 0.00 1.89
4088 4218 9.803315 CAGTGACAGCAGTTATTTAGAGTATTA 57.197 33.333 0.00 0.00 0.00 0.98
4105 4235 6.789959 AGAGTATTAGTTATGGCTTGGAGGAT 59.210 38.462 0.00 0.00 0.00 3.24
4178 4310 0.596082 TGAGTTCATGACGCGACAGA 59.404 50.000 15.93 9.85 0.00 3.41
4193 4325 3.044305 AGACAGCGCTTCAACGGC 61.044 61.111 7.50 0.00 0.00 5.68
4212 4348 2.205022 CCTGAAACAGAGGCCATTGA 57.795 50.000 5.01 0.00 32.44 2.57
4225 4361 5.960202 AGAGGCCATTGATTTTGATTTAGGT 59.040 36.000 5.01 0.00 0.00 3.08
4329 4465 0.460284 CGGACATGGAGTTTCTCGGG 60.460 60.000 0.00 0.00 0.00 5.14
4361 4501 3.071479 GCCCAGATGAACAGTAAAACGA 58.929 45.455 0.00 0.00 0.00 3.85
4470 4617 6.017109 AGCTTGAAATCACATTCGTGTAAGTT 60.017 34.615 0.00 0.00 44.02 2.66
4530 4683 5.759506 TTGAAAGTATTTTGGAGCGTTGA 57.240 34.783 0.00 0.00 39.27 3.18
4679 4835 1.271656 GCCAAGAGCATTTGAGCTTGT 59.728 47.619 0.00 0.00 46.75 3.16
4708 4864 5.873179 ATTAGGATTTTTCGCTTCGACAA 57.127 34.783 0.00 0.00 34.89 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.856894 GTGTACTCCAAGACGAGTAAGATATTC 59.143 40.741 0.23 0.00 44.79 1.75
12 13 7.055378 AGTGTACTCCAAGACGAGTAAGATAT 58.945 38.462 0.23 0.00 44.79 1.63
52 71 2.973945 AGCTTGGACCAGACGTTTATC 58.026 47.619 0.00 0.00 0.00 1.75
56 75 1.002087 CCTAAGCTTGGACCAGACGTT 59.998 52.381 11.99 0.00 0.00 3.99
62 81 0.777446 AAAGGCCTAAGCTTGGACCA 59.223 50.000 17.24 0.00 39.73 4.02
84 103 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
85 104 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
108 127 9.413734 CTCATTTCCTACAAAATTCCTATTCCT 57.586 33.333 0.00 0.00 0.00 3.36
109 128 9.408648 TCTCATTTCCTACAAAATTCCTATTCC 57.591 33.333 0.00 0.00 0.00 3.01
112 131 9.359653 CCATCTCATTTCCTACAAAATTCCTAT 57.640 33.333 0.00 0.00 0.00 2.57
113 132 7.285401 GCCATCTCATTTCCTACAAAATTCCTA 59.715 37.037 0.00 0.00 0.00 2.94
114 133 6.097412 GCCATCTCATTTCCTACAAAATTCCT 59.903 38.462 0.00 0.00 0.00 3.36
115 134 6.127366 TGCCATCTCATTTCCTACAAAATTCC 60.127 38.462 0.00 0.00 0.00 3.01
116 135 6.866480 TGCCATCTCATTTCCTACAAAATTC 58.134 36.000 0.00 0.00 0.00 2.17
117 136 6.855763 TGCCATCTCATTTCCTACAAAATT 57.144 33.333 0.00 0.00 0.00 1.82
118 137 6.381994 ACATGCCATCTCATTTCCTACAAAAT 59.618 34.615 0.00 0.00 0.00 1.82
119 138 5.716228 ACATGCCATCTCATTTCCTACAAAA 59.284 36.000 0.00 0.00 0.00 2.44
120 139 5.263599 ACATGCCATCTCATTTCCTACAAA 58.736 37.500 0.00 0.00 0.00 2.83
121 140 4.858850 ACATGCCATCTCATTTCCTACAA 58.141 39.130 0.00 0.00 0.00 2.41
122 141 4.508551 ACATGCCATCTCATTTCCTACA 57.491 40.909 0.00 0.00 0.00 2.74
123 142 6.471146 AGATACATGCCATCTCATTTCCTAC 58.529 40.000 4.89 0.00 0.00 3.18
124 143 6.692849 AGATACATGCCATCTCATTTCCTA 57.307 37.500 4.89 0.00 0.00 2.94
125 144 5.558818 GAGATACATGCCATCTCATTTCCT 58.441 41.667 23.49 0.00 45.17 3.36
126 145 5.876612 GAGATACATGCCATCTCATTTCC 57.123 43.478 23.49 5.23 45.17 3.13
132 151 8.666573 CATAAGATTTGAGATACATGCCATCTC 58.333 37.037 22.40 22.40 45.76 2.75
133 152 7.610692 CCATAAGATTTGAGATACATGCCATCT 59.389 37.037 9.57 9.57 35.43 2.90
134 153 7.148120 CCCATAAGATTTGAGATACATGCCATC 60.148 40.741 0.00 0.00 0.00 3.51
135 154 6.662234 CCCATAAGATTTGAGATACATGCCAT 59.338 38.462 0.00 0.00 0.00 4.40
136 155 6.005823 CCCATAAGATTTGAGATACATGCCA 58.994 40.000 0.00 0.00 0.00 4.92
137 156 5.105997 GCCCATAAGATTTGAGATACATGCC 60.106 44.000 0.00 0.00 0.00 4.40
138 157 5.474532 TGCCCATAAGATTTGAGATACATGC 59.525 40.000 0.00 0.00 0.00 4.06
139 158 6.150641 CCTGCCCATAAGATTTGAGATACATG 59.849 42.308 0.00 0.00 0.00 3.21
140 159 6.044754 TCCTGCCCATAAGATTTGAGATACAT 59.955 38.462 0.00 0.00 0.00 2.29
141 160 5.369404 TCCTGCCCATAAGATTTGAGATACA 59.631 40.000 0.00 0.00 0.00 2.29
142 161 5.869579 TCCTGCCCATAAGATTTGAGATAC 58.130 41.667 0.00 0.00 0.00 2.24
143 162 6.514012 TTCCTGCCCATAAGATTTGAGATA 57.486 37.500 0.00 0.00 0.00 1.98
144 163 5.393068 TTCCTGCCCATAAGATTTGAGAT 57.607 39.130 0.00 0.00 0.00 2.75
145 164 4.860802 TTCCTGCCCATAAGATTTGAGA 57.139 40.909 0.00 0.00 0.00 3.27
146 165 6.537355 TCTATTCCTGCCCATAAGATTTGAG 58.463 40.000 0.00 0.00 0.00 3.02
147 166 6.514012 TCTATTCCTGCCCATAAGATTTGA 57.486 37.500 0.00 0.00 0.00 2.69
148 167 7.587037 TTTCTATTCCTGCCCATAAGATTTG 57.413 36.000 0.00 0.00 0.00 2.32
149 168 8.608185 TTTTTCTATTCCTGCCCATAAGATTT 57.392 30.769 0.00 0.00 0.00 2.17
150 169 8.061304 TCTTTTTCTATTCCTGCCCATAAGATT 58.939 33.333 0.00 0.00 0.00 2.40
151 170 7.586349 TCTTTTTCTATTCCTGCCCATAAGAT 58.414 34.615 0.00 0.00 0.00 2.40
152 171 6.969043 TCTTTTTCTATTCCTGCCCATAAGA 58.031 36.000 0.00 0.00 0.00 2.10
153 172 7.056635 TCTCTTTTTCTATTCCTGCCCATAAG 58.943 38.462 0.00 0.00 0.00 1.73
154 173 6.969043 TCTCTTTTTCTATTCCTGCCCATAA 58.031 36.000 0.00 0.00 0.00 1.90
155 174 6.575244 TCTCTTTTTCTATTCCTGCCCATA 57.425 37.500 0.00 0.00 0.00 2.74
156 175 5.456921 TCTCTTTTTCTATTCCTGCCCAT 57.543 39.130 0.00 0.00 0.00 4.00
157 176 4.927267 TCTCTTTTTCTATTCCTGCCCA 57.073 40.909 0.00 0.00 0.00 5.36
158 177 5.196695 ACATCTCTTTTTCTATTCCTGCCC 58.803 41.667 0.00 0.00 0.00 5.36
159 178 5.882557 TGACATCTCTTTTTCTATTCCTGCC 59.117 40.000 0.00 0.00 0.00 4.85
160 179 6.992063 TGACATCTCTTTTTCTATTCCTGC 57.008 37.500 0.00 0.00 0.00 4.85
161 180 9.784680 CAAATGACATCTCTTTTTCTATTCCTG 57.215 33.333 0.00 0.00 0.00 3.86
162 181 8.964772 CCAAATGACATCTCTTTTTCTATTCCT 58.035 33.333 0.00 0.00 0.00 3.36
163 182 8.743714 ACCAAATGACATCTCTTTTTCTATTCC 58.256 33.333 0.00 0.00 0.00 3.01
165 184 9.918630 CAACCAAATGACATCTCTTTTTCTATT 57.081 29.630 0.00 0.00 0.00 1.73
166 185 9.300681 TCAACCAAATGACATCTCTTTTTCTAT 57.699 29.630 0.00 0.00 0.00 1.98
167 186 8.690203 TCAACCAAATGACATCTCTTTTTCTA 57.310 30.769 0.00 0.00 0.00 2.10
168 187 7.587037 TCAACCAAATGACATCTCTTTTTCT 57.413 32.000 0.00 0.00 0.00 2.52
228 247 8.757877 CCCTCCACATTTCATAGGAAAATAAAA 58.242 33.333 6.65 0.00 45.52 1.52
229 248 8.119246 TCCCTCCACATTTCATAGGAAAATAAA 58.881 33.333 6.65 0.00 45.52 1.40
230 249 7.647827 TCCCTCCACATTTCATAGGAAAATAA 58.352 34.615 6.65 0.00 45.52 1.40
231 250 7.219601 TCCCTCCACATTTCATAGGAAAATA 57.780 36.000 6.65 0.00 45.52 1.40
232 251 6.091076 TCCCTCCACATTTCATAGGAAAAT 57.909 37.500 6.65 0.00 45.52 1.82
233 252 5.509498 CTCCCTCCACATTTCATAGGAAAA 58.491 41.667 6.65 0.00 45.52 2.29
234 253 4.079787 CCTCCCTCCACATTTCATAGGAAA 60.080 45.833 4.85 4.85 46.36 3.13
235 254 3.459598 CCTCCCTCCACATTTCATAGGAA 59.540 47.826 0.00 0.00 0.00 3.36
236 255 3.048600 CCTCCCTCCACATTTCATAGGA 58.951 50.000 0.00 0.00 0.00 2.94
237 256 3.048600 TCCTCCCTCCACATTTCATAGG 58.951 50.000 0.00 0.00 0.00 2.57
238 257 4.989875 ATCCTCCCTCCACATTTCATAG 57.010 45.455 0.00 0.00 0.00 2.23
239 258 4.846367 CCTATCCTCCCTCCACATTTCATA 59.154 45.833 0.00 0.00 0.00 2.15
240 259 3.654806 CCTATCCTCCCTCCACATTTCAT 59.345 47.826 0.00 0.00 0.00 2.57
241 260 3.048600 CCTATCCTCCCTCCACATTTCA 58.951 50.000 0.00 0.00 0.00 2.69
242 261 3.318313 TCCTATCCTCCCTCCACATTTC 58.682 50.000 0.00 0.00 0.00 2.17
243 262 3.438131 TCCTATCCTCCCTCCACATTT 57.562 47.619 0.00 0.00 0.00 2.32
244 263 3.049344 GTTCCTATCCTCCCTCCACATT 58.951 50.000 0.00 0.00 0.00 2.71
245 264 2.695585 GTTCCTATCCTCCCTCCACAT 58.304 52.381 0.00 0.00 0.00 3.21
246 265 1.344087 GGTTCCTATCCTCCCTCCACA 60.344 57.143 0.00 0.00 0.00 4.17
247 266 1.344087 TGGTTCCTATCCTCCCTCCAC 60.344 57.143 0.00 0.00 0.00 4.02
248 267 1.023719 TGGTTCCTATCCTCCCTCCA 58.976 55.000 0.00 0.00 0.00 3.86
249 268 2.191981 TTGGTTCCTATCCTCCCTCC 57.808 55.000 0.00 0.00 0.00 4.30
250 269 2.640332 GGATTGGTTCCTATCCTCCCTC 59.360 54.545 19.71 0.00 41.78 4.30
251 270 2.707554 GGATTGGTTCCTATCCTCCCT 58.292 52.381 19.71 0.00 41.78 4.20
285 304 5.358160 CCCTTTGGTTCACAGGAATAGATTC 59.642 44.000 1.99 0.00 33.52 2.52
286 305 5.264395 CCCTTTGGTTCACAGGAATAGATT 58.736 41.667 1.99 0.00 33.52 2.40
287 306 4.860022 CCCTTTGGTTCACAGGAATAGAT 58.140 43.478 1.99 0.00 33.52 1.98
288 307 3.561313 GCCCTTTGGTTCACAGGAATAGA 60.561 47.826 1.99 0.00 33.52 1.98
289 308 2.755103 GCCCTTTGGTTCACAGGAATAG 59.245 50.000 1.99 0.00 33.52 1.73
290 309 2.378547 AGCCCTTTGGTTCACAGGAATA 59.621 45.455 1.99 0.00 33.52 1.75
291 310 1.147817 AGCCCTTTGGTTCACAGGAAT 59.852 47.619 1.99 0.00 33.52 3.01
292 311 0.555769 AGCCCTTTGGTTCACAGGAA 59.444 50.000 1.99 0.00 33.52 3.36
293 312 1.440618 TAGCCCTTTGGTTCACAGGA 58.559 50.000 1.99 0.00 33.52 3.86
294 313 2.286365 TTAGCCCTTTGGTTCACAGG 57.714 50.000 0.00 0.00 31.67 4.00
295 314 2.558359 CCTTTAGCCCTTTGGTTCACAG 59.442 50.000 0.00 0.00 0.00 3.66
296 315 2.175931 TCCTTTAGCCCTTTGGTTCACA 59.824 45.455 0.00 0.00 0.00 3.58
297 316 2.871453 TCCTTTAGCCCTTTGGTTCAC 58.129 47.619 0.00 0.00 0.00 3.18
298 317 3.603965 TTCCTTTAGCCCTTTGGTTCA 57.396 42.857 0.00 0.00 0.00 3.18
299 318 4.948341 TTTTCCTTTAGCCCTTTGGTTC 57.052 40.909 0.00 0.00 0.00 3.62
333 352 9.462606 GTTTGAAGGAATTTTAGAGGATAGGAA 57.537 33.333 0.00 0.00 0.00 3.36
334 353 8.053355 GGTTTGAAGGAATTTTAGAGGATAGGA 58.947 37.037 0.00 0.00 0.00 2.94
335 354 7.834181 TGGTTTGAAGGAATTTTAGAGGATAGG 59.166 37.037 0.00 0.00 0.00 2.57
336 355 8.807948 TGGTTTGAAGGAATTTTAGAGGATAG 57.192 34.615 0.00 0.00 0.00 2.08
337 356 9.594936 TTTGGTTTGAAGGAATTTTAGAGGATA 57.405 29.630 0.00 0.00 0.00 2.59
338 357 8.491045 TTTGGTTTGAAGGAATTTTAGAGGAT 57.509 30.769 0.00 0.00 0.00 3.24
339 358 7.015195 CCTTTGGTTTGAAGGAATTTTAGAGGA 59.985 37.037 0.00 0.00 45.25 3.71
340 359 7.154656 CCTTTGGTTTGAAGGAATTTTAGAGG 58.845 38.462 0.00 0.00 45.25 3.69
358 377 5.221641 GCCAAGAAAAATAACCTCCTTTGGT 60.222 40.000 0.00 0.00 43.11 3.67
359 378 5.221621 TGCCAAGAAAAATAACCTCCTTTGG 60.222 40.000 0.00 0.00 0.00 3.28
360 379 5.696270 GTGCCAAGAAAAATAACCTCCTTTG 59.304 40.000 0.00 0.00 0.00 2.77
361 380 5.508994 CGTGCCAAGAAAAATAACCTCCTTT 60.509 40.000 0.00 0.00 0.00 3.11
362 381 4.022329 CGTGCCAAGAAAAATAACCTCCTT 60.022 41.667 0.00 0.00 0.00 3.36
363 382 3.506067 CGTGCCAAGAAAAATAACCTCCT 59.494 43.478 0.00 0.00 0.00 3.69
364 383 3.366985 CCGTGCCAAGAAAAATAACCTCC 60.367 47.826 0.00 0.00 0.00 4.30
365 384 3.833442 CCGTGCCAAGAAAAATAACCTC 58.167 45.455 0.00 0.00 0.00 3.85
366 385 2.029380 GCCGTGCCAAGAAAAATAACCT 60.029 45.455 0.00 0.00 0.00 3.50
367 386 2.333926 GCCGTGCCAAGAAAAATAACC 58.666 47.619 0.00 0.00 0.00 2.85
436 455 3.003068 CGGAATCATGGATGAAAGCAGAC 59.997 47.826 0.00 0.00 40.69 3.51
477 497 5.462398 GTCACTACGCGGATATCATCTTTTT 59.538 40.000 12.47 0.00 0.00 1.94
478 498 4.982916 GTCACTACGCGGATATCATCTTTT 59.017 41.667 12.47 0.00 0.00 2.27
503 523 0.525761 TGTACCCCTAACGTACGTGC 59.474 55.000 23.57 0.96 39.16 5.34
511 531 5.829391 TGGAAAAGAAAGTTGTACCCCTAAC 59.171 40.000 0.00 0.00 0.00 2.34
514 534 4.529716 TGGAAAAGAAAGTTGTACCCCT 57.470 40.909 0.00 0.00 0.00 4.79
515 535 4.082949 CGATGGAAAAGAAAGTTGTACCCC 60.083 45.833 0.00 0.00 0.00 4.95
587 608 1.601419 CTGCTCATGCTTTGTGGGGG 61.601 60.000 0.00 0.00 40.48 5.40
744 786 5.630661 TCTTTGTGTTCGTTCCTCAAAAA 57.369 34.783 0.00 0.00 0.00 1.94
746 788 3.064820 GCTCTTTGTGTTCGTTCCTCAAA 59.935 43.478 0.00 0.00 0.00 2.69
747 789 2.612212 GCTCTTTGTGTTCGTTCCTCAA 59.388 45.455 0.00 0.00 0.00 3.02
748 790 2.210116 GCTCTTTGTGTTCGTTCCTCA 58.790 47.619 0.00 0.00 0.00 3.86
749 791 2.210116 TGCTCTTTGTGTTCGTTCCTC 58.790 47.619 0.00 0.00 0.00 3.71
752 794 2.612212 TCCTTGCTCTTTGTGTTCGTTC 59.388 45.455 0.00 0.00 0.00 3.95
755 797 2.614057 ACTTCCTTGCTCTTTGTGTTCG 59.386 45.455 0.00 0.00 0.00 3.95
756 798 4.319839 GCTACTTCCTTGCTCTTTGTGTTC 60.320 45.833 0.00 0.00 0.00 3.18
799 846 1.483595 CCTGTTGGGAGCTCTGGACA 61.484 60.000 14.64 13.78 37.23 4.02
870 920 2.785562 AGAGAGGGGATCGATCGTAAG 58.214 52.381 18.81 0.00 0.00 2.34
871 921 2.953284 AGAGAGGGGATCGATCGTAA 57.047 50.000 18.81 0.00 0.00 3.18
872 922 2.953284 AAGAGAGGGGATCGATCGTA 57.047 50.000 18.81 2.15 0.00 3.43
873 923 1.957877 GAAAGAGAGGGGATCGATCGT 59.042 52.381 18.81 6.30 0.00 3.73
890 940 1.368203 TGGGGGAGGAGTAGGATGAAA 59.632 52.381 0.00 0.00 0.00 2.69
914 964 0.248843 GAACTCTGGAGCTGGGTCAG 59.751 60.000 0.00 0.00 34.12 3.51
1280 1330 2.439701 AGGAGCGCGTAGTAGGCA 60.440 61.111 14.71 0.00 0.00 4.75
1366 1417 0.324943 TAGCAGCCAGAGTTGGGAAC 59.675 55.000 0.00 0.00 45.16 3.62
1397 1449 7.068962 ACATCATTTATGCATCAGAATTCACCA 59.931 33.333 0.19 0.00 39.39 4.17
1473 1525 6.600032 CACTAGCCTCTAGTAGAAGAAGTCAA 59.400 42.308 6.23 0.00 0.00 3.18
1486 1538 5.993441 GTCTACCTACTTCACTAGCCTCTAG 59.007 48.000 0.00 0.00 0.00 2.43
1498 1550 6.127952 ACTGATTGAACTCGTCTACCTACTTC 60.128 42.308 0.00 0.00 0.00 3.01
1520 1572 5.909477 TCCTACCCAACGTTATGATAACTG 58.091 41.667 12.94 9.06 0.00 3.16
1530 1582 0.981183 TGCTGATCCTACCCAACGTT 59.019 50.000 0.00 0.00 0.00 3.99
1549 1601 4.019321 TCCATAGCTGTAACCTTTCTTGCT 60.019 41.667 0.00 0.00 0.00 3.91
1555 1645 3.606687 CGGTTCCATAGCTGTAACCTTT 58.393 45.455 11.91 0.00 39.39 3.11
1569 1659 1.691976 AGATTCATATCCGCGGTTCCA 59.308 47.619 27.15 5.72 0.00 3.53
1572 1662 1.512926 GCAGATTCATATCCGCGGTT 58.487 50.000 27.15 20.39 0.00 4.44
1578 1668 6.451393 AGTCTAAGAACGCAGATTCATATCC 58.549 40.000 0.00 0.00 0.00 2.59
1582 1672 6.754209 CAGTAAGTCTAAGAACGCAGATTCAT 59.246 38.462 0.00 0.00 0.00 2.57
1588 1678 5.220381 TGTTCAGTAAGTCTAAGAACGCAG 58.780 41.667 0.00 0.00 40.95 5.18
1600 1690 7.448748 ACAAAACTTGAACTGTTCAGTAAGT 57.551 32.000 21.13 18.67 41.38 2.24
1605 1695 6.498304 AGCATACAAAACTTGAACTGTTCAG 58.502 36.000 21.13 17.25 41.38 3.02
1618 1708 5.290643 TCAAACACAAGCAAGCATACAAAAC 59.709 36.000 0.00 0.00 0.00 2.43
1632 1722 3.817084 TCTGCTCCTCAATCAAACACAAG 59.183 43.478 0.00 0.00 0.00 3.16
1669 1759 6.449698 TGAAAAGTCTACCTAACTTGTACGG 58.550 40.000 0.00 0.00 37.06 4.02
1670 1760 8.530269 AATGAAAAGTCTACCTAACTTGTACG 57.470 34.615 0.00 0.00 37.06 3.67
1673 1763 9.708092 GTCTAATGAAAAGTCTACCTAACTTGT 57.292 33.333 0.00 0.00 37.06 3.16
1674 1764 9.706691 TGTCTAATGAAAAGTCTACCTAACTTG 57.293 33.333 0.00 0.00 37.06 3.16
1676 1766 9.930693 CTTGTCTAATGAAAAGTCTACCTAACT 57.069 33.333 0.00 0.00 33.83 2.24
1736 1827 7.255173 CCATTCATTCAATTGCCAAGTTGAAAA 60.255 33.333 3.87 0.00 44.62 2.29
1752 1843 4.039004 CACAACCCAACTTCCATTCATTCA 59.961 41.667 0.00 0.00 0.00 2.57
1799 1890 3.856206 ACCAGACCAAAACCTACCCATAT 59.144 43.478 0.00 0.00 0.00 1.78
1844 1935 4.489306 ACAGAAATACCTACCAGAAGCC 57.511 45.455 0.00 0.00 0.00 4.35
1847 1938 7.016268 AGTCTTGAACAGAAATACCTACCAGAA 59.984 37.037 0.00 0.00 31.28 3.02
1861 1952 6.876789 TCAAGTTGTTTGTAGTCTTGAACAGA 59.123 34.615 2.11 0.00 40.55 3.41
1904 1995 1.519408 TCAAGCAACCGGAAACTAGC 58.481 50.000 9.46 2.14 0.00 3.42
1913 2004 3.500982 CCAATGTGTAATCAAGCAACCG 58.499 45.455 0.00 0.00 0.00 4.44
1924 2015 3.799432 AGTAACCAGGCCAATGTGTAA 57.201 42.857 5.01 0.00 0.00 2.41
2035 2134 4.988540 CGTTACTGAAGATGAAACAGGTCA 59.011 41.667 0.00 0.00 36.17 4.02
2041 2140 5.050363 TGAGCAACGTTACTGAAGATGAAAC 60.050 40.000 5.58 0.00 0.00 2.78
2051 2150 4.629634 TGGAACATATGAGCAACGTTACTG 59.370 41.667 10.38 0.00 0.00 2.74
2118 2217 0.391130 GCCACGCCTGTCAGTCAATA 60.391 55.000 0.00 0.00 0.00 1.90
2124 2223 2.434658 TACACTGCCACGCCTGTCAG 62.435 60.000 0.00 0.00 0.00 3.51
2127 2226 1.375908 CATACACTGCCACGCCTGT 60.376 57.895 0.00 0.00 0.00 4.00
2301 2400 3.064958 CCTTGAGCAATACATCAGCACTG 59.935 47.826 0.00 0.00 0.00 3.66
2402 2503 5.183228 ACTAAAACCAGATCACGGGTAATG 58.817 41.667 6.19 1.03 43.29 1.90
2410 2511 5.412904 CCTCCTTGAACTAAAACCAGATCAC 59.587 44.000 0.00 0.00 28.23 3.06
2411 2512 5.514834 CCCTCCTTGAACTAAAACCAGATCA 60.515 44.000 0.00 0.00 0.00 2.92
2413 2514 4.601857 TCCCTCCTTGAACTAAAACCAGAT 59.398 41.667 0.00 0.00 0.00 2.90
2415 2516 4.202472 ACTCCCTCCTTGAACTAAAACCAG 60.202 45.833 0.00 0.00 0.00 4.00
2581 2697 6.506500 AGATTTAGCATCAACAGAAACCAG 57.493 37.500 0.00 0.00 0.00 4.00
2584 2700 5.024555 GCGAGATTTAGCATCAACAGAAAC 58.975 41.667 0.00 0.00 0.00 2.78
2672 2788 7.607250 AGAGTGAAGAGTTAAACTATGGAGTG 58.393 38.462 0.00 0.00 35.52 3.51
2761 2877 6.295916 GGCAACATACAGTTCCCTAGCTATAT 60.296 42.308 0.00 0.00 38.74 0.86
2811 2929 7.448161 CCAAAGCCAAATACATATATGGTCTGA 59.552 37.037 16.96 0.00 35.34 3.27
2829 2947 1.859302 ACAAAGGAACACCAAAGCCA 58.141 45.000 0.00 0.00 0.00 4.75
2832 2950 6.067263 TCGATAAACAAAGGAACACCAAAG 57.933 37.500 0.00 0.00 0.00 2.77
2922 3040 5.791666 TGCATGAAAACAATCAAGCCATAA 58.208 33.333 0.00 0.00 41.92 1.90
2952 3070 1.066071 GGTAGCCTGTCTTTCCACCTC 60.066 57.143 0.00 0.00 0.00 3.85
3004 3122 9.814899 ATCAAACAACAGATTTGAAACATACAA 57.185 25.926 4.43 0.00 46.26 2.41
3008 3126 9.199982 GATCATCAAACAACAGATTTGAAACAT 57.800 29.630 4.43 0.00 46.26 2.71
3052 3171 7.230849 TGCTGTCATAAAAAGGTGAAATGAT 57.769 32.000 0.00 0.00 0.00 2.45
3290 3413 0.442699 GAAGTGGAAGGTAAAGCGCG 59.557 55.000 0.00 0.00 0.00 6.86
3393 3516 3.243907 ACTCCAGTGTACAAGCTGAAGAC 60.244 47.826 13.58 0.00 34.87 3.01
3430 3553 7.450074 ACATAGACAATCACTACAGGAACAAA 58.550 34.615 0.00 0.00 0.00 2.83
3450 3573 5.459762 CACAAACAAACAGGCAAAGACATAG 59.540 40.000 0.00 0.00 0.00 2.23
3457 3580 3.667497 TCACACAAACAAACAGGCAAA 57.333 38.095 0.00 0.00 0.00 3.68
3469 3592 4.698201 TCCTCCTACAACATCACACAAA 57.302 40.909 0.00 0.00 0.00 2.83
3536 3659 0.468226 AGTCAGCGTCAAAGAACCCA 59.532 50.000 0.00 0.00 0.00 4.51
3548 3671 2.009774 CAGGTTTAATCCCAGTCAGCG 58.990 52.381 0.00 0.00 0.00 5.18
3574 3697 2.159099 TCATACAGCGTGAATGGACTCC 60.159 50.000 0.00 0.00 0.00 3.85
3577 3700 2.893637 AGTCATACAGCGTGAATGGAC 58.106 47.619 0.00 0.00 0.00 4.02
3581 3704 6.985188 ACAAATAAGTCATACAGCGTGAAT 57.015 33.333 0.00 0.00 0.00 2.57
3627 3751 5.884792 AGATTCATTCAGTTTCCAGGATGAC 59.115 40.000 0.00 0.00 39.69 3.06
3748 3874 1.542915 CTTGAGGTGCCAAACAGATGG 59.457 52.381 0.00 0.00 43.70 3.51
3787 3916 4.109766 CTCGTCGTGATAAGTAATTGGCA 58.890 43.478 0.00 0.00 0.00 4.92
3788 3917 4.206609 GTCTCGTCGTGATAAGTAATTGGC 59.793 45.833 0.00 0.00 0.00 4.52
3797 3926 0.800631 ACAGCGTCTCGTCGTGATAA 59.199 50.000 0.00 0.00 0.00 1.75
3798 3927 0.372679 GACAGCGTCTCGTCGTGATA 59.627 55.000 0.00 0.00 0.00 2.15
3817 3946 4.475944 CCAGTTATGGCTTTCAAGTTTCG 58.524 43.478 0.00 0.00 40.52 3.46
3832 3961 5.427157 TCCACATACATGTACCACCAGTTAT 59.573 40.000 7.96 0.00 39.39 1.89
3895 4024 7.034397 AGTAACACTAGTAGCGAAAAGATTCC 58.966 38.462 0.00 0.00 31.52 3.01
3922 4052 5.870978 GCAACTCGAAATACCCAAGTAGTAA 59.129 40.000 0.00 0.00 0.00 2.24
3925 4055 3.621715 GGCAACTCGAAATACCCAAGTAG 59.378 47.826 0.00 0.00 0.00 2.57
3926 4056 3.008157 TGGCAACTCGAAATACCCAAGTA 59.992 43.478 0.00 0.00 37.61 2.24
3927 4057 2.224670 TGGCAACTCGAAATACCCAAGT 60.225 45.455 0.00 0.00 37.61 3.16
3928 4058 2.420022 CTGGCAACTCGAAATACCCAAG 59.580 50.000 0.00 0.00 37.61 3.61
3929 4059 2.224670 ACTGGCAACTCGAAATACCCAA 60.225 45.455 0.00 0.00 37.61 4.12
3930 4060 1.349688 ACTGGCAACTCGAAATACCCA 59.650 47.619 0.00 0.00 37.61 4.51
3931 4061 1.737793 CACTGGCAACTCGAAATACCC 59.262 52.381 0.00 0.00 37.61 3.69
3933 4063 2.527442 GCACTGGCAACTCGAAATAC 57.473 50.000 0.00 0.00 40.72 1.89
3956 4086 3.056536 TCGAATCTCACTCCAACTTCCTG 60.057 47.826 0.00 0.00 0.00 3.86
3957 4087 3.165875 TCGAATCTCACTCCAACTTCCT 58.834 45.455 0.00 0.00 0.00 3.36
3958 4088 3.516615 CTCGAATCTCACTCCAACTTCC 58.483 50.000 0.00 0.00 0.00 3.46
4026 4156 4.878971 CCATATCCAATCCAACAACGTACA 59.121 41.667 0.00 0.00 0.00 2.90
4055 4185 2.674033 TGCTGTCACTGCCCATGC 60.674 61.111 3.95 0.00 38.26 4.06
4081 4211 6.420913 TCCTCCAAGCCATAACTAATACTC 57.579 41.667 0.00 0.00 0.00 2.59
4082 4212 6.240002 CCATCCTCCAAGCCATAACTAATACT 60.240 42.308 0.00 0.00 0.00 2.12
4083 4213 5.940470 CCATCCTCCAAGCCATAACTAATAC 59.060 44.000 0.00 0.00 0.00 1.89
4084 4214 5.849475 TCCATCCTCCAAGCCATAACTAATA 59.151 40.000 0.00 0.00 0.00 0.98
4085 4215 4.665009 TCCATCCTCCAAGCCATAACTAAT 59.335 41.667 0.00 0.00 0.00 1.73
4086 4216 4.044308 TCCATCCTCCAAGCCATAACTAA 58.956 43.478 0.00 0.00 0.00 2.24
4087 4217 3.648067 CTCCATCCTCCAAGCCATAACTA 59.352 47.826 0.00 0.00 0.00 2.24
4088 4218 2.441001 CTCCATCCTCCAAGCCATAACT 59.559 50.000 0.00 0.00 0.00 2.24
4089 4219 2.487986 CCTCCATCCTCCAAGCCATAAC 60.488 54.545 0.00 0.00 0.00 1.89
4093 4223 2.002977 CCCTCCATCCTCCAAGCCA 61.003 63.158 0.00 0.00 0.00 4.75
4138 4268 0.244178 GTCACCTTCGTCCAGTCTCC 59.756 60.000 0.00 0.00 0.00 3.71
4145 4275 2.288825 TGAACTCATGTCACCTTCGTCC 60.289 50.000 0.00 0.00 0.00 4.79
4178 4310 4.626081 AGGCCGTTGAAGCGCTGT 62.626 61.111 12.58 0.03 0.00 4.40
4193 4325 2.205022 TCAATGGCCTCTGTTTCAGG 57.795 50.000 3.32 0.00 31.51 3.86
4212 4348 6.252995 TGGCCTCTAACACCTAAATCAAAAT 58.747 36.000 3.32 0.00 0.00 1.82
4225 4361 2.576191 AGCTAACCAATGGCCTCTAACA 59.424 45.455 3.32 0.00 35.85 2.41
4278 4414 1.096416 TTTGTGGGTGTCCGTTTGAC 58.904 50.000 0.00 0.00 44.72 3.18
4289 4425 1.133513 TGTCCAAGAGCATTTGTGGGT 60.134 47.619 0.00 0.00 0.00 4.51
4489 4640 4.897224 TCAAAAATAGCATCTTCGAAGCG 58.103 39.130 20.56 14.28 31.18 4.68
4505 4656 7.036220 TCAACGCTCCAAAATACTTTCAAAAA 58.964 30.769 0.00 0.00 0.00 1.94
4509 4660 5.957842 ATCAACGCTCCAAAATACTTTCA 57.042 34.783 0.00 0.00 0.00 2.69
4679 4835 6.292865 CGAAGCGAAAAATCCTAATATGAGCA 60.293 38.462 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.