Multiple sequence alignment - TraesCS4B01G398700

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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 TraesCS4B01G398700 chr4B 100.000 4479 0 0 1 4479 672940227 672935749 0.000000e+00 8272.0
1 TraesCS4B01G398700 chrUn 94.270 1850 49 17 1995 3817 99396910 99398729 0.000000e+00 2776.0
2 TraesCS4B01G398700 chrUn 97.521 726 18 0 817 1542 99395409 99396134 0.000000e+00 1242.0
3 TraesCS4B01G398700 chrUn 89.744 663 56 10 3822 4479 99426761 99427416 0.000000e+00 837.0
4 TraesCS4B01G398700 chrUn 96.833 442 8 3 1557 1997 99396092 99396528 0.000000e+00 734.0
5 TraesCS4B01G398700 chrUn 88.000 275 23 5 322 586 99395133 99395407 2.600000e-82 316.0
6 TraesCS4B01G398700 chrUn 98.802 167 1 1 1 166 99394971 99395137 3.390000e-76 296.0
7 TraesCS4B01G398700 chr5A 94.359 1294 42 13 1578 2868 707266724 707267989 0.000000e+00 1956.0
8 TraesCS4B01G398700 chr5A 97.211 753 21 0 769 1521 707265993 707266745 0.000000e+00 1275.0
9 TraesCS4B01G398700 chr5A 97.024 672 14 2 2894 3565 707267984 707268649 0.000000e+00 1125.0
10 TraesCS4B01G398700 chr5A 96.000 200 8 0 322 521 707265610 707265809 4.320000e-85 326.0
11 TraesCS4B01G398700 chr5A 91.071 224 15 3 4256 4479 707457116 707457334 9.420000e-77 298.0
12 TraesCS4B01G398700 chr5A 98.193 166 3 0 1 166 707265449 707265614 1.580000e-74 291.0
13 TraesCS4B01G398700 chr5A 96.241 133 4 1 3686 3817 707268664 707268796 2.710000e-52 217.0
14 TraesCS4B01G398700 chr5A 88.889 90 9 1 597 686 676375884 676375796 4.740000e-20 110.0
15 TraesCS4B01G398700 chr2B 95.858 169 7 0 163 331 659017214 659017046 1.590000e-69 274.0
16 TraesCS4B01G398700 chr2B 96.319 163 6 0 164 326 755622444 755622282 7.390000e-68 268.0
17 TraesCS4B01G398700 chr2B 91.848 184 11 3 160 340 519180656 519180838 2.070000e-63 254.0
18 TraesCS4B01G398700 chr2B 90.625 192 14 4 158 348 278161980 278161792 7.440000e-63 252.0
19 TraesCS4B01G398700 chr3D 95.294 170 8 0 158 327 238999582 238999413 2.050000e-68 270.0
20 TraesCS4B01G398700 chr3D 94.152 171 10 0 157 327 507038750 507038580 1.240000e-65 261.0
21 TraesCS4B01G398700 chr2D 95.181 166 8 0 165 330 445733671 445733836 3.440000e-66 263.0
22 TraesCS4B01G398700 chr7A 93.714 175 10 1 157 330 105168366 105168192 1.240000e-65 261.0
23 TraesCS4B01G398700 chr7A 89.773 88 9 0 597 684 626606771 626606858 3.660000e-21 113.0
24 TraesCS4B01G398700 chr7A 89.535 86 9 0 598 683 222506231 222506316 4.740000e-20 110.0
25 TraesCS4B01G398700 chr6B 94.152 171 10 0 161 331 708822397 708822567 1.240000e-65 261.0
26 TraesCS4B01G398700 chr2A 76.667 300 64 6 3998 4293 12244310 12244607 1.290000e-35 161.0
27 TraesCS4B01G398700 chr1D 93.103 87 6 0 597 683 231021121 231021207 1.310000e-25 128.0
28 TraesCS4B01G398700 chr5D 92.771 83 6 0 597 679 480858516 480858434 2.190000e-23 121.0
29 TraesCS4B01G398700 chr1B 92.771 83 6 0 597 679 668967865 668967783 2.190000e-23 121.0
30 TraesCS4B01G398700 chr7B 90.909 88 8 0 597 684 588243654 588243741 7.870000e-23 119.0
31 TraesCS4B01G398700 chr7B 90.909 88 8 0 597 684 588256208 588256295 7.870000e-23 119.0
32 TraesCS4B01G398700 chr3B 92.500 80 6 0 597 676 85338046 85338125 1.020000e-21 115.0
33 TraesCS4B01G398700 chr1A 91.837 49 4 0 4234 4282 35104839 35104887 8.040000e-08 69.4


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 TraesCS4B01G398700 chr4B 672935749 672940227 4478 True 8272.0 8272 100.000000 1 4479 1 chr4B.!!$R1 4478
1 TraesCS4B01G398700 chrUn 99394971 99398729 3758 False 1072.8 2776 95.085200 1 3817 5 chrUn.!!$F2 3816
2 TraesCS4B01G398700 chrUn 99426761 99427416 655 False 837.0 837 89.744000 3822 4479 1 chrUn.!!$F1 657
3 TraesCS4B01G398700 chr5A 707265449 707268796 3347 False 865.0 1956 96.504667 1 3817 6 chr5A.!!$F2 3816

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
753 803 0.107017 AATATGTGCTTGCCCTCGCT 60.107 50.0 0.00 0.0 35.36 4.93 F
1116 1166 0.178964 CAAGGCCAGAAAAGGGGTCA 60.179 55.0 5.01 0.0 0.00 4.02 F
1928 1979 0.892755 CACATGCCCTGCACATTTCT 59.107 50.0 0.00 0.0 43.04 2.52 F
2809 3251 0.956633 CGAAATGCATGGAGGATGGG 59.043 55.0 0.00 0.0 31.99 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2548 1.187567 GGTGCCTTGGTTTGATGGCT 61.188 55.000 0.00 0.0 45.11 4.75 R
2519 2961 1.415659 GAGCATGAGTACCTCTGCCAT 59.584 52.381 0.00 0.0 36.25 4.40 R
3140 3588 1.270147 GGTAGCTACGGTATGCCCTTG 60.270 57.143 17.48 0.0 0.00 3.61 R
4093 4568 0.458370 GATTTCCAACACCGCATGCC 60.458 55.000 13.15 0.0 0.00 4.40 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
166 168 6.081693 CCACGCCATTTTAGTTAACAACTAC 58.918 40.000 8.61 0.00 43.30 2.73
167 169 6.072893 CCACGCCATTTTAGTTAACAACTACT 60.073 38.462 8.61 0.00 43.30 2.57
168 170 7.013529 CACGCCATTTTAGTTAACAACTACTC 58.986 38.462 8.61 0.00 43.30 2.59
169 171 6.148315 ACGCCATTTTAGTTAACAACTACTCC 59.852 38.462 8.61 0.00 43.30 3.85
170 172 6.402875 CGCCATTTTAGTTAACAACTACTCCC 60.403 42.308 8.61 0.00 43.30 4.30
171 173 6.657966 GCCATTTTAGTTAACAACTACTCCCT 59.342 38.462 8.61 0.00 43.30 4.20
172 174 7.148289 GCCATTTTAGTTAACAACTACTCCCTC 60.148 40.741 8.61 0.00 43.30 4.30
173 175 7.336176 CCATTTTAGTTAACAACTACTCCCTCC 59.664 40.741 8.61 0.00 43.30 4.30
174 176 5.649782 TTAGTTAACAACTACTCCCTCCG 57.350 43.478 8.61 0.00 43.30 4.63
175 177 3.504375 AGTTAACAACTACTCCCTCCGT 58.496 45.455 8.61 0.00 40.69 4.69
176 178 3.899980 AGTTAACAACTACTCCCTCCGTT 59.100 43.478 8.61 0.00 40.69 4.44
177 179 4.021632 AGTTAACAACTACTCCCTCCGTTC 60.022 45.833 8.61 0.00 40.69 3.95
178 180 1.264295 ACAACTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
179 181 1.203149 ACAACTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
180 182 2.042162 ACAACTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
181 183 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
182 184 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
183 185 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
184 186 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
185 187 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
186 188 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
187 189 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
188 190 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
189 191 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
190 192 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
191 193 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
192 194 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
193 195 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
194 196 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
195 197 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
196 198 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
197 199 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
198 200 8.202137 CCGTTCCTAAATATAAGTCTTTGGAGA 58.798 37.037 0.00 0.00 0.00 3.71
199 201 9.250624 CGTTCCTAAATATAAGTCTTTGGAGAG 57.749 37.037 0.00 0.00 31.07 3.20
223 225 3.989056 TCCACTATGGACCACATACAGA 58.011 45.455 0.00 0.00 42.67 3.41
224 226 3.960755 TCCACTATGGACCACATACAGAG 59.039 47.826 0.00 0.00 42.67 3.35
225 227 3.493350 CCACTATGGACCACATACAGAGC 60.493 52.174 0.00 0.00 40.96 4.09
226 228 3.132824 CACTATGGACCACATACAGAGCA 59.867 47.826 0.00 0.00 41.03 4.26
227 229 3.774766 ACTATGGACCACATACAGAGCAA 59.225 43.478 0.00 0.00 41.03 3.91
228 230 3.719268 ATGGACCACATACAGAGCAAA 57.281 42.857 0.00 0.00 38.26 3.68
229 231 3.500448 TGGACCACATACAGAGCAAAA 57.500 42.857 0.00 0.00 0.00 2.44
230 232 4.032960 TGGACCACATACAGAGCAAAAT 57.967 40.909 0.00 0.00 0.00 1.82
231 233 3.758023 TGGACCACATACAGAGCAAAATG 59.242 43.478 0.00 0.00 0.00 2.32
232 234 4.009675 GGACCACATACAGAGCAAAATGA 58.990 43.478 0.00 0.00 0.00 2.57
233 235 4.095483 GGACCACATACAGAGCAAAATGAG 59.905 45.833 0.00 0.00 0.00 2.90
234 236 4.655963 ACCACATACAGAGCAAAATGAGT 58.344 39.130 0.00 0.00 0.00 3.41
235 237 4.456911 ACCACATACAGAGCAAAATGAGTG 59.543 41.667 0.00 0.00 0.00 3.51
236 238 4.696877 CCACATACAGAGCAAAATGAGTGA 59.303 41.667 0.00 0.00 0.00 3.41
237 239 5.181811 CCACATACAGAGCAAAATGAGTGAA 59.818 40.000 0.00 0.00 0.00 3.18
238 240 6.082338 CACATACAGAGCAAAATGAGTGAAC 58.918 40.000 0.00 0.00 0.00 3.18
239 241 5.182001 ACATACAGAGCAAAATGAGTGAACC 59.818 40.000 0.00 0.00 0.00 3.62
240 242 3.825328 ACAGAGCAAAATGAGTGAACCT 58.175 40.909 0.00 0.00 0.00 3.50
241 243 4.973168 ACAGAGCAAAATGAGTGAACCTA 58.027 39.130 0.00 0.00 0.00 3.08
242 244 4.757149 ACAGAGCAAAATGAGTGAACCTAC 59.243 41.667 0.00 0.00 0.00 3.18
243 245 4.756642 CAGAGCAAAATGAGTGAACCTACA 59.243 41.667 0.00 0.00 0.00 2.74
244 246 4.757149 AGAGCAAAATGAGTGAACCTACAC 59.243 41.667 0.00 0.00 40.60 2.90
255 257 5.865085 AGTGAACCTACACTCTAAAATGCA 58.135 37.500 0.00 0.00 46.36 3.96
256 258 6.476378 AGTGAACCTACACTCTAAAATGCAT 58.524 36.000 0.00 0.00 46.36 3.96
257 259 6.942576 AGTGAACCTACACTCTAAAATGCATT 59.057 34.615 5.99 5.99 46.36 3.56
258 260 7.448469 AGTGAACCTACACTCTAAAATGCATTT 59.552 33.333 18.99 18.99 46.36 2.32
259 261 8.726988 GTGAACCTACACTCTAAAATGCATTTA 58.273 33.333 24.35 8.89 37.73 1.40
260 262 9.461312 TGAACCTACACTCTAAAATGCATTTAT 57.539 29.630 24.35 16.18 33.15 1.40
276 278 7.841915 TGCATTTATATACATCCGTATGTGG 57.158 36.000 3.56 0.00 45.99 4.17
277 279 7.390823 TGCATTTATATACATCCGTATGTGGT 58.609 34.615 3.56 0.00 45.99 4.16
278 280 7.880713 TGCATTTATATACATCCGTATGTGGTT 59.119 33.333 3.56 0.00 45.99 3.67
279 281 8.388103 GCATTTATATACATCCGTATGTGGTTC 58.612 37.037 3.56 0.00 45.99 3.62
280 282 9.430623 CATTTATATACATCCGTATGTGGTTCA 57.569 33.333 3.56 0.00 45.99 3.18
284 286 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
285 287 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
286 288 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
287 289 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
288 290 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
289 291 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
290 292 6.046593 TCCGTATGTGGTTCATAGTGAAATC 58.953 40.000 0.00 0.00 38.22 2.17
291 293 6.049149 CCGTATGTGGTTCATAGTGAAATCT 58.951 40.000 0.00 0.00 38.22 2.40
292 294 6.201044 CCGTATGTGGTTCATAGTGAAATCTC 59.799 42.308 0.00 0.00 38.22 2.75
293 295 6.980978 CGTATGTGGTTCATAGTGAAATCTCT 59.019 38.462 0.00 0.00 38.22 3.10
294 296 8.135529 CGTATGTGGTTCATAGTGAAATCTCTA 58.864 37.037 0.00 0.00 38.22 2.43
295 297 9.250624 GTATGTGGTTCATAGTGAAATCTCTAC 57.749 37.037 0.00 0.00 38.22 2.59
296 298 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
297 299 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
298 300 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
299 301 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
300 302 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
301 303 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
302 304 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
319 321 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
320 322 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
321 323 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
322 324 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
323 325 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
324 326 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
325 327 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
403 407 3.372954 ACTATGTGCTACTTTCGATCGC 58.627 45.455 11.09 0.00 0.00 4.58
408 412 4.368315 TGTGCTACTTTCGATCGCAATAT 58.632 39.130 11.09 0.00 31.77 1.28
517 555 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
521 559 4.403752 TCTCTCTCTCTCTCTCTCTGTCTG 59.596 50.000 0.00 0.00 0.00 3.51
522 560 4.096681 TCTCTCTCTCTCTCTCTGTCTGT 58.903 47.826 0.00 0.00 0.00 3.41
523 561 4.081476 TCTCTCTCTCTCTCTCTGTCTGTG 60.081 50.000 0.00 0.00 0.00 3.66
524 562 3.582647 TCTCTCTCTCTCTCTGTCTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
525 563 3.673902 TCTCTCTCTCTCTGTCTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
526 564 3.072330 TCTCTCTCTCTCTGTCTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
527 565 3.145286 TCTCTCTCTCTGTCTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
528 566 2.884012 CTCTCTCTCTGTCTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
529 567 2.620585 TCTCTCTCTGTCTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
530 568 2.360483 CTCTCTCTGTCTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
531 569 2.099756 TCTCTCTGTCTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
532 570 0.933097 CTCTGTCTGTGTGTGTGTGC 59.067 55.000 0.00 0.00 0.00 4.57
533 571 0.805711 TCTGTCTGTGTGTGTGTGCG 60.806 55.000 0.00 0.00 0.00 5.34
534 572 2.324477 GTCTGTGTGTGTGTGCGC 59.676 61.111 0.00 0.00 0.00 6.09
535 573 3.261216 TCTGTGTGTGTGTGCGCG 61.261 61.111 0.00 0.00 0.00 6.86
536 574 4.943591 CTGTGTGTGTGTGCGCGC 62.944 66.667 27.26 27.26 36.27 6.86
643 693 6.437477 TCTTAGCTTCTTACCTCTCATGTGAA 59.563 38.462 0.00 0.00 0.00 3.18
652 702 2.996631 CTCTCATGTGAAAAGAGGGGG 58.003 52.381 0.00 0.00 34.24 5.40
653 703 2.307098 CTCTCATGTGAAAAGAGGGGGT 59.693 50.000 0.00 0.00 34.24 4.95
654 704 3.519510 CTCTCATGTGAAAAGAGGGGGTA 59.480 47.826 0.00 0.00 34.24 3.69
655 705 3.913799 TCTCATGTGAAAAGAGGGGGTAA 59.086 43.478 0.00 0.00 0.00 2.85
656 706 4.019321 TCTCATGTGAAAAGAGGGGGTAAG 60.019 45.833 0.00 0.00 0.00 2.34
657 707 3.913799 TCATGTGAAAAGAGGGGGTAAGA 59.086 43.478 0.00 0.00 0.00 2.10
658 708 4.019321 TCATGTGAAAAGAGGGGGTAAGAG 60.019 45.833 0.00 0.00 0.00 2.85
659 709 2.642807 TGTGAAAAGAGGGGGTAAGAGG 59.357 50.000 0.00 0.00 0.00 3.69
660 710 2.026169 GTGAAAAGAGGGGGTAAGAGGG 60.026 54.545 0.00 0.00 0.00 4.30
661 711 2.157911 TGAAAAGAGGGGGTAAGAGGGA 60.158 50.000 0.00 0.00 0.00 4.20
690 740 8.887264 TGTTAAAATTACTCCTCTCTCTCTCT 57.113 34.615 0.00 0.00 0.00 3.10
691 741 8.962679 TGTTAAAATTACTCCTCTCTCTCTCTC 58.037 37.037 0.00 0.00 0.00 3.20
692 742 8.410912 GTTAAAATTACTCCTCTCTCTCTCTCC 58.589 40.741 0.00 0.00 0.00 3.71
693 743 4.724279 ATTACTCCTCTCTCTCTCTCCC 57.276 50.000 0.00 0.00 0.00 4.30
694 744 2.286935 ACTCCTCTCTCTCTCTCCCT 57.713 55.000 0.00 0.00 0.00 4.20
695 745 2.127708 ACTCCTCTCTCTCTCTCCCTC 58.872 57.143 0.00 0.00 0.00 4.30
696 746 2.293856 ACTCCTCTCTCTCTCTCCCTCT 60.294 54.545 0.00 0.00 0.00 3.69
697 747 2.370189 CTCCTCTCTCTCTCTCCCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
698 748 2.022035 TCCTCTCTCTCTCTCCCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
709 759 5.876357 TCTCTCCCTCTCTAGCTAATCTTC 58.124 45.833 0.00 0.00 0.00 2.87
711 761 3.150767 TCCCTCTCTAGCTAATCTTCGC 58.849 50.000 0.00 0.00 0.00 4.70
712 762 2.887783 CCCTCTCTAGCTAATCTTCGCA 59.112 50.000 0.00 0.00 0.00 5.10
751 801 3.508744 AAAAATATGTGCTTGCCCTCG 57.491 42.857 0.00 0.00 0.00 4.63
752 802 0.740737 AAATATGTGCTTGCCCTCGC 59.259 50.000 0.00 0.00 0.00 5.03
753 803 0.107017 AATATGTGCTTGCCCTCGCT 60.107 50.000 0.00 0.00 35.36 4.93
754 804 0.533755 ATATGTGCTTGCCCTCGCTC 60.534 55.000 0.00 0.00 35.36 5.03
755 805 2.593468 TATGTGCTTGCCCTCGCTCC 62.593 60.000 0.00 0.00 35.36 4.70
756 806 4.400961 GTGCTTGCCCTCGCTCCT 62.401 66.667 0.00 0.00 35.36 3.69
757 807 3.640407 TGCTTGCCCTCGCTCCTT 61.640 61.111 0.00 0.00 35.36 3.36
758 808 2.290287 TGCTTGCCCTCGCTCCTTA 61.290 57.895 0.00 0.00 35.36 2.69
759 809 1.522580 GCTTGCCCTCGCTCCTTAG 60.523 63.158 0.00 0.00 35.36 2.18
760 810 1.961180 GCTTGCCCTCGCTCCTTAGA 61.961 60.000 0.00 0.00 35.36 2.10
761 811 0.537188 CTTGCCCTCGCTCCTTAGAA 59.463 55.000 0.00 0.00 35.36 2.10
762 812 1.139853 CTTGCCCTCGCTCCTTAGAAT 59.860 52.381 0.00 0.00 35.36 2.40
763 813 0.465705 TGCCCTCGCTCCTTAGAATG 59.534 55.000 0.00 0.00 35.36 2.67
764 814 0.466124 GCCCTCGCTCCTTAGAATGT 59.534 55.000 0.00 0.00 0.00 2.71
765 815 1.687123 GCCCTCGCTCCTTAGAATGTA 59.313 52.381 0.00 0.00 0.00 2.29
766 816 2.300437 GCCCTCGCTCCTTAGAATGTAT 59.700 50.000 0.00 0.00 0.00 2.29
767 817 3.615351 GCCCTCGCTCCTTAGAATGTATC 60.615 52.174 0.00 0.00 0.00 2.24
768 818 3.574396 CCCTCGCTCCTTAGAATGTATCA 59.426 47.826 0.00 0.00 0.00 2.15
769 819 4.039245 CCCTCGCTCCTTAGAATGTATCAA 59.961 45.833 0.00 0.00 0.00 2.57
775 825 6.925718 CGCTCCTTAGAATGTATCAATTGAGA 59.074 38.462 14.54 6.47 0.00 3.27
966 1016 6.128035 CGTCCATCATTGTTTGTTCATTAGGA 60.128 38.462 0.00 0.00 0.00 2.94
992 1042 4.024809 GTCTGCTCCACAACACTAAGTTTC 60.025 45.833 0.00 0.00 38.74 2.78
1028 1078 2.740826 ATTTCGTCCGGGTGCGTG 60.741 61.111 0.00 0.00 0.00 5.34
1031 1081 2.360949 TTTCGTCCGGGTGCGTGTTA 62.361 55.000 0.00 0.00 0.00 2.41
1058 1108 3.831715 AGCAGTTATTTTTCTCACCGC 57.168 42.857 0.00 0.00 0.00 5.68
1116 1166 0.178964 CAAGGCCAGAAAAGGGGTCA 60.179 55.000 5.01 0.00 0.00 4.02
1142 1192 1.909700 CCACCTATTGCAAGTGGTGT 58.090 50.000 32.94 14.96 46.02 4.16
1167 1217 2.038426 TCTTGTAGCTGCTTTGCCTACA 59.962 45.455 7.79 1.41 0.00 2.74
1368 1418 1.470051 TCCCTATTTTCGGCAAAGGC 58.530 50.000 0.00 0.00 40.13 4.35
1413 1463 6.148315 TCGAAACTAGAAACAGACAGATACGA 59.852 38.462 0.00 0.00 0.00 3.43
1820 1871 9.691362 TTAATTTGCTGGAATAAACTTCTTCAC 57.309 29.630 0.00 0.00 0.00 3.18
1828 1879 4.766404 ATAAACTTCTTCACCAAAGCCG 57.234 40.909 0.00 0.00 34.76 5.52
1928 1979 0.892755 CACATGCCCTGCACATTTCT 59.107 50.000 0.00 0.00 43.04 2.52
1931 1982 1.135199 CATGCCCTGCACATTTCTGAC 60.135 52.381 0.00 0.00 43.04 3.51
2018 2453 2.041620 AGGATGCCTGCTCAAAACCTAA 59.958 45.455 0.00 0.00 29.57 2.69
2103 2539 4.575885 ACCAGTAGTTTGTATGCGAACAT 58.424 39.130 15.34 4.43 40.59 2.71
2112 2548 8.432110 AGTTTGTATGCGAACATATCACATAA 57.568 30.769 15.34 0.00 40.79 1.90
2115 2551 5.408299 TGTATGCGAACATATCACATAAGCC 59.592 40.000 0.00 0.00 40.79 4.35
2116 2552 3.802866 TGCGAACATATCACATAAGCCA 58.197 40.909 0.00 0.00 0.00 4.75
2117 2553 4.388485 TGCGAACATATCACATAAGCCAT 58.612 39.130 0.00 0.00 0.00 4.40
2118 2554 4.452114 TGCGAACATATCACATAAGCCATC 59.548 41.667 0.00 0.00 0.00 3.51
2119 2555 4.452114 GCGAACATATCACATAAGCCATCA 59.548 41.667 0.00 0.00 0.00 3.07
2130 2566 4.994744 GCCATCAAACCAAGGCAC 57.005 55.556 0.00 0.00 46.26 5.01
2181 2621 6.823689 GCTATGAGACTATCCAAACCTTTTCA 59.176 38.462 0.00 0.00 0.00 2.69
2184 2624 7.452880 TGAGACTATCCAAACCTTTTCATTG 57.547 36.000 0.00 0.00 0.00 2.82
2185 2625 7.004086 TGAGACTATCCAAACCTTTTCATTGT 58.996 34.615 0.00 0.00 0.00 2.71
2186 2626 8.160765 TGAGACTATCCAAACCTTTTCATTGTA 58.839 33.333 0.00 0.00 0.00 2.41
2187 2627 8.934023 AGACTATCCAAACCTTTTCATTGTAA 57.066 30.769 0.00 0.00 0.00 2.41
2234 2674 1.005037 TCCGAAAGCGTGACTGCAT 60.005 52.632 0.00 0.00 37.31 3.96
2262 2702 5.386924 TCCTTAGCAGGTAACCTCTAGATC 58.613 45.833 0.00 0.00 41.69 2.75
2271 2711 1.153989 CCTCTAGATCGCCTCCCCA 59.846 63.158 0.00 0.00 0.00 4.96
2284 2724 3.447229 CGCCTCCCCAAAATTCATAAACT 59.553 43.478 0.00 0.00 0.00 2.66
2285 2725 4.081697 CGCCTCCCCAAAATTCATAAACTT 60.082 41.667 0.00 0.00 0.00 2.66
2286 2726 5.126384 CGCCTCCCCAAAATTCATAAACTTA 59.874 40.000 0.00 0.00 0.00 2.24
2287 2727 6.350612 CGCCTCCCCAAAATTCATAAACTTAA 60.351 38.462 0.00 0.00 0.00 1.85
2288 2728 7.390823 GCCTCCCCAAAATTCATAAACTTAAA 58.609 34.615 0.00 0.00 0.00 1.52
2289 2729 7.333423 GCCTCCCCAAAATTCATAAACTTAAAC 59.667 37.037 0.00 0.00 0.00 2.01
2458 2900 6.483974 GCTCATTTCTCATGATGTTCATCTCT 59.516 38.462 12.94 0.00 34.28 3.10
2488 2930 5.428184 AGGACTACTTCTCAAAATGGGAG 57.572 43.478 0.00 0.00 0.00 4.30
2519 2961 6.432162 GGGCATAATTGATCTAAAGCATGAGA 59.568 38.462 0.00 0.00 0.00 3.27
2711 3153 4.451150 CGCGTGCTAGGCTGGGAA 62.451 66.667 0.00 0.00 0.00 3.97
2755 3197 2.972625 TCACGTAAAATCTCAGGCCAG 58.027 47.619 5.01 0.00 0.00 4.85
2785 3227 8.353423 AGGATGATGTGCTACAAAAACTTATT 57.647 30.769 0.00 0.00 0.00 1.40
2809 3251 0.956633 CGAAATGCATGGAGGATGGG 59.043 55.000 0.00 0.00 31.99 4.00
2986 3434 4.074627 TGGAAAACACGGACAAGATGTA 57.925 40.909 0.00 0.00 0.00 2.29
2987 3435 4.062293 TGGAAAACACGGACAAGATGTAG 58.938 43.478 0.00 0.00 0.00 2.74
2988 3436 4.062991 GGAAAACACGGACAAGATGTAGT 58.937 43.478 0.00 0.00 0.00 2.73
2989 3437 5.221481 TGGAAAACACGGACAAGATGTAGTA 60.221 40.000 0.00 0.00 0.00 1.82
2990 3438 5.347907 GGAAAACACGGACAAGATGTAGTAG 59.652 44.000 0.00 0.00 0.00 2.57
2991 3439 5.464030 AAACACGGACAAGATGTAGTAGT 57.536 39.130 0.00 0.00 0.00 2.73
3096 3544 1.376543 ATGCGCCATGTGAAGAAGAG 58.623 50.000 4.18 0.00 0.00 2.85
3112 3560 5.283457 AGAAGAGCTTCACTGTACAAACT 57.717 39.130 12.32 0.00 41.84 2.66
3140 3588 4.455606 AGGCTACAGCTATGAAATTCCAC 58.544 43.478 0.54 0.00 41.70 4.02
3193 3641 0.383231 GCAACCAGCTGCCACATATC 59.617 55.000 8.66 0.00 41.15 1.63
3319 3767 1.954927 CTTGCTTCGGGGAGGAATAC 58.045 55.000 0.00 0.00 0.00 1.89
3478 3926 3.057033 GGCGACTTCTTGTCAGTACCTAA 60.057 47.826 0.00 0.00 45.60 2.69
3480 3928 4.483311 CGACTTCTTGTCAGTACCTAACC 58.517 47.826 0.00 0.00 45.60 2.85
3482 3930 5.211174 ACTTCTTGTCAGTACCTAACCAC 57.789 43.478 0.00 0.00 0.00 4.16
3483 3931 4.900054 ACTTCTTGTCAGTACCTAACCACT 59.100 41.667 0.00 0.00 0.00 4.00
3529 3977 6.487668 GGGTGGTTGTAATAAGTTTGTACTGT 59.512 38.462 0.00 0.00 34.01 3.55
3530 3978 7.013559 GGGTGGTTGTAATAAGTTTGTACTGTT 59.986 37.037 0.00 0.00 34.01 3.16
3531 3979 9.054922 GGTGGTTGTAATAAGTTTGTACTGTTA 57.945 33.333 0.00 0.00 34.01 2.41
3565 4017 6.893554 TGTCTACTTATGTAAGCAGTCCCTTA 59.106 38.462 0.00 0.00 36.79 2.69
3654 4127 2.100631 GTGACATGTCGCCCTTCCG 61.101 63.158 25.74 0.00 34.22 4.30
3656 4129 3.665675 GACATGTCGCCCTTCCGCT 62.666 63.158 10.69 0.00 0.00 5.52
3657 4130 2.292794 GACATGTCGCCCTTCCGCTA 62.293 60.000 10.69 0.00 0.00 4.26
3658 4131 1.069765 CATGTCGCCCTTCCGCTAT 59.930 57.895 0.00 0.00 0.00 2.97
3659 4132 0.532862 CATGTCGCCCTTCCGCTATT 60.533 55.000 0.00 0.00 0.00 1.73
3660 4133 1.045407 ATGTCGCCCTTCCGCTATTA 58.955 50.000 0.00 0.00 0.00 0.98
3670 4143 6.116126 GCCCTTCCGCTATTATATTTGAGAT 58.884 40.000 0.00 0.00 0.00 2.75
3690 4163 8.365060 TGAGATCATATCACCAAAAATGGTTT 57.635 30.769 0.00 0.00 40.85 3.27
3726 4199 0.326264 GTGGTGGATGGCTGAGAGTT 59.674 55.000 0.00 0.00 0.00 3.01
3739 4212 2.937149 CTGAGAGTTGGATGATGTGCTG 59.063 50.000 0.00 0.00 0.00 4.41
3813 4286 3.348647 TTCCCATGTCACGATTGATGT 57.651 42.857 0.00 0.00 33.11 3.06
3816 4289 3.439825 TCCCATGTCACGATTGATGTTTG 59.560 43.478 0.00 0.00 33.11 2.93
3818 4291 2.987413 TGTCACGATTGATGTTTGGC 57.013 45.000 0.00 0.00 33.11 4.52
3819 4292 1.539388 TGTCACGATTGATGTTTGGCC 59.461 47.619 0.00 0.00 33.11 5.36
3820 4293 0.801872 TCACGATTGATGTTTGGCCG 59.198 50.000 0.00 0.00 0.00 6.13
3821 4294 0.521291 CACGATTGATGTTTGGCCGT 59.479 50.000 0.00 0.00 0.00 5.68
3822 4295 1.068610 CACGATTGATGTTTGGCCGTT 60.069 47.619 0.00 0.00 0.00 4.44
3823 4296 1.611491 ACGATTGATGTTTGGCCGTTT 59.389 42.857 0.00 0.00 0.00 3.60
3824 4297 2.035321 ACGATTGATGTTTGGCCGTTTT 59.965 40.909 0.00 0.00 0.00 2.43
3825 4298 3.056304 CGATTGATGTTTGGCCGTTTTT 58.944 40.909 0.00 0.00 0.00 1.94
3826 4299 3.121113 CGATTGATGTTTGGCCGTTTTTC 59.879 43.478 0.00 0.00 0.00 2.29
3830 4303 3.131223 TGATGTTTGGCCGTTTTTCTTCA 59.869 39.130 0.00 0.00 0.00 3.02
3831 4304 3.157932 TGTTTGGCCGTTTTTCTTCAG 57.842 42.857 0.00 0.00 0.00 3.02
3836 4309 4.195225 TGGCCGTTTTTCTTCAGTTTTT 57.805 36.364 0.00 0.00 0.00 1.94
3910 4383 6.872670 TTCGCACACTTTTTAAAATTCGTT 57.127 29.167 0.55 0.00 0.00 3.85
3983 4457 9.847224 ACTCATAACCTTTTTCTAGTTCTGAAA 57.153 29.630 0.00 0.00 29.62 2.69
4016 4490 2.865551 CACACCATGCCAAGTTGTTTTC 59.134 45.455 1.45 0.00 0.00 2.29
4028 4502 6.346999 GCCAAGTTGTTTTCGTTTTCAAGAAA 60.347 34.615 1.45 0.00 34.91 2.52
4056 4530 6.154445 TGTATTTTCTAGAGTGTTGTCGGTC 58.846 40.000 0.00 0.00 0.00 4.79
4081 4556 6.505044 AAAAAGGTGGATAAATGGTCGTAC 57.495 37.500 0.00 0.00 0.00 3.67
4093 4568 1.602877 GGTCGTACGTGTCGCAACTG 61.603 60.000 16.05 0.00 0.00 3.16
4098 4573 1.288419 TACGTGTCGCAACTGGCATG 61.288 55.000 0.00 0.00 45.17 4.06
4120 4595 3.855524 GCGGTGTTGGAAATCGTTCAAAT 60.856 43.478 0.00 0.00 35.25 2.32
4121 4596 4.295051 CGGTGTTGGAAATCGTTCAAATT 58.705 39.130 0.00 0.00 35.25 1.82
4133 4608 6.773976 ATCGTTCAAATTTGGTATGGATGT 57.226 33.333 17.90 0.00 0.00 3.06
4134 4609 6.582677 TCGTTCAAATTTGGTATGGATGTT 57.417 33.333 17.90 0.00 0.00 2.71
4190 4665 6.773976 TGGGGTTATTTCAAGAATGATCAC 57.226 37.500 0.00 0.00 34.96 3.06
4193 4668 7.399765 TGGGGTTATTTCAAGAATGATCACAAT 59.600 33.333 0.00 0.00 34.96 2.71
4208 4683 6.623486 TGATCACAATTGGATCATGTTCAAC 58.377 36.000 24.15 7.18 44.51 3.18
4209 4684 6.434965 TGATCACAATTGGATCATGTTCAACT 59.565 34.615 24.15 0.00 44.51 3.16
4225 4700 5.012354 TGTTCAACTAAGGGTGTTAGGGTAG 59.988 44.000 0.00 0.00 0.00 3.18
4231 4707 1.632965 GGGTGTTAGGGTAGGCCAGG 61.633 65.000 5.01 0.00 36.17 4.45
4261 4737 3.320626 TCTGAGAGCACATTGTTTCTCG 58.679 45.455 17.05 13.48 39.08 4.04
4266 4742 4.067896 AGAGCACATTGTTTCTCGACATT 58.932 39.130 9.09 0.00 0.00 2.71
4276 4752 4.035091 TGTTTCTCGACATTGTTGAACTGG 59.965 41.667 8.09 0.00 0.00 4.00
4277 4753 2.143122 TCTCGACATTGTTGAACTGGC 58.857 47.619 8.09 0.00 0.00 4.85
4281 4757 0.105760 ACATTGTTGAACTGGCCCCA 60.106 50.000 0.00 0.00 0.00 4.96
4332 4808 0.324645 ATTTGGTGGTGGGAGGCATC 60.325 55.000 0.00 0.00 0.00 3.91
4334 4810 3.017581 GGTGGTGGGAGGCATCCT 61.018 66.667 18.35 0.00 45.85 3.24
4364 4840 4.985409 GGAGAGGAATATGCTTACACGAAG 59.015 45.833 0.00 0.00 38.30 3.79
4383 4859 7.336931 ACACGAAGAATAAAGCAATATGGAGTT 59.663 33.333 0.00 0.00 0.00 3.01
4394 4870 5.300286 AGCAATATGGAGTTGTTTCCTATGC 59.700 40.000 0.00 0.00 38.12 3.14
4426 4902 9.635404 TGAGTTAAAAATTACTTCTCCTTTCCA 57.365 29.630 0.00 0.00 0.00 3.53
4461 4937 7.969690 TTTGATAAAATCATTTCCAGCCCTA 57.030 32.000 0.00 0.00 39.39 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 168 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
167 169 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
168 170 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
169 171 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
170 172 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
171 173 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
172 174 8.202137 TCTCCAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
173 175 9.250624 CTCTCCAAAGACTTATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
202 204 3.960755 CTCTGTATGTGGTCCATAGTGGA 59.039 47.826 0.00 0.00 45.98 4.02
203 205 3.493350 GCTCTGTATGTGGTCCATAGTGG 60.493 52.174 0.00 0.00 36.71 4.00
204 206 3.132824 TGCTCTGTATGTGGTCCATAGTG 59.867 47.826 0.00 0.00 36.71 2.74
205 207 3.374764 TGCTCTGTATGTGGTCCATAGT 58.625 45.455 0.00 0.00 36.71 2.12
206 208 4.406648 TTGCTCTGTATGTGGTCCATAG 57.593 45.455 0.00 0.00 36.71 2.23
207 209 4.835284 TTTGCTCTGTATGTGGTCCATA 57.165 40.909 0.00 0.00 34.86 2.74
208 210 3.719268 TTTGCTCTGTATGTGGTCCAT 57.281 42.857 0.00 0.00 37.58 3.41
209 211 3.500448 TTTTGCTCTGTATGTGGTCCA 57.500 42.857 0.00 0.00 0.00 4.02
210 212 4.009675 TCATTTTGCTCTGTATGTGGTCC 58.990 43.478 0.00 0.00 0.00 4.46
211 213 4.697352 ACTCATTTTGCTCTGTATGTGGTC 59.303 41.667 0.00 0.00 0.00 4.02
212 214 4.456911 CACTCATTTTGCTCTGTATGTGGT 59.543 41.667 0.00 0.00 0.00 4.16
213 215 4.696877 TCACTCATTTTGCTCTGTATGTGG 59.303 41.667 0.00 0.00 0.00 4.17
214 216 5.868043 TCACTCATTTTGCTCTGTATGTG 57.132 39.130 0.00 0.00 0.00 3.21
215 217 5.182001 GGTTCACTCATTTTGCTCTGTATGT 59.818 40.000 0.00 0.00 0.00 2.29
216 218 5.413833 AGGTTCACTCATTTTGCTCTGTATG 59.586 40.000 0.00 0.00 0.00 2.39
217 219 5.564550 AGGTTCACTCATTTTGCTCTGTAT 58.435 37.500 0.00 0.00 0.00 2.29
218 220 4.973168 AGGTTCACTCATTTTGCTCTGTA 58.027 39.130 0.00 0.00 0.00 2.74
219 221 3.825328 AGGTTCACTCATTTTGCTCTGT 58.175 40.909 0.00 0.00 0.00 3.41
220 222 4.756642 TGTAGGTTCACTCATTTTGCTCTG 59.243 41.667 0.00 0.00 0.00 3.35
221 223 4.757149 GTGTAGGTTCACTCATTTTGCTCT 59.243 41.667 0.00 0.00 35.68 4.09
222 224 4.757149 AGTGTAGGTTCACTCATTTTGCTC 59.243 41.667 0.00 0.00 44.07 4.26
223 225 4.718961 AGTGTAGGTTCACTCATTTTGCT 58.281 39.130 0.00 0.00 44.07 3.91
233 235 6.743575 ATGCATTTTAGAGTGTAGGTTCAC 57.256 37.500 0.00 0.00 38.46 3.18
234 236 7.759489 AAATGCATTTTAGAGTGTAGGTTCA 57.241 32.000 18.99 0.00 0.00 3.18
250 252 8.892723 CCACATACGGATGTATATAAATGCATT 58.107 33.333 14.23 5.99 44.82 3.56
251 253 8.046708 ACCACATACGGATGTATATAAATGCAT 58.953 33.333 14.23 0.00 44.82 3.96
252 254 7.390823 ACCACATACGGATGTATATAAATGCA 58.609 34.615 14.23 0.00 44.82 3.96
253 255 7.843490 ACCACATACGGATGTATATAAATGC 57.157 36.000 14.23 0.00 44.82 3.56
254 256 9.430623 TGAACCACATACGGATGTATATAAATG 57.569 33.333 14.23 0.00 44.82 2.32
258 260 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
259 261 8.251026 CACTATGAACCACATACGGATGTATAT 58.749 37.037 14.23 1.68 44.82 0.86
260 262 7.449086 TCACTATGAACCACATACGGATGTATA 59.551 37.037 14.23 6.48 44.82 1.47
261 263 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
262 264 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
263 265 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
264 266 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
265 267 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
266 268 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
267 269 6.049149 AGATTTCACTATGAACCACATACGG 58.951 40.000 0.00 0.00 35.89 4.02
268 270 6.980978 AGAGATTTCACTATGAACCACATACG 59.019 38.462 0.00 0.00 35.89 3.06
269 271 9.250624 GTAGAGATTTCACTATGAACCACATAC 57.749 37.037 0.00 0.00 35.89 2.39
270 272 8.977412 TGTAGAGATTTCACTATGAACCACATA 58.023 33.333 0.00 0.00 35.89 2.29
271 273 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
272 274 7.239763 TGTAGAGATTTCACTATGAACCACA 57.760 36.000 0.00 0.00 35.89 4.17
273 275 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
274 276 8.593679 TCTTTGTAGAGATTTCACTATGAACCA 58.406 33.333 0.00 0.00 35.89 3.67
275 277 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
276 278 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
294 296 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
295 297 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
296 298 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
297 299 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
298 300 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
299 301 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
300 302 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
303 305 9.991906 CAAATACTTCCTCCGTTCCTAAATATA 57.008 33.333 0.00 0.00 0.00 0.86
304 306 8.491958 ACAAATACTTCCTCCGTTCCTAAATAT 58.508 33.333 0.00 0.00 0.00 1.28
305 307 7.854337 ACAAATACTTCCTCCGTTCCTAAATA 58.146 34.615 0.00 0.00 0.00 1.40
306 308 6.718294 ACAAATACTTCCTCCGTTCCTAAAT 58.282 36.000 0.00 0.00 0.00 1.40
307 309 6.117975 ACAAATACTTCCTCCGTTCCTAAA 57.882 37.500 0.00 0.00 0.00 1.85
308 310 5.246656 TGACAAATACTTCCTCCGTTCCTAA 59.753 40.000 0.00 0.00 0.00 2.69
309 311 4.773674 TGACAAATACTTCCTCCGTTCCTA 59.226 41.667 0.00 0.00 0.00 2.94
310 312 3.581332 TGACAAATACTTCCTCCGTTCCT 59.419 43.478 0.00 0.00 0.00 3.36
311 313 3.934068 TGACAAATACTTCCTCCGTTCC 58.066 45.455 0.00 0.00 0.00 3.62
312 314 4.995487 ACTTGACAAATACTTCCTCCGTTC 59.005 41.667 0.00 0.00 0.00 3.95
313 315 4.969484 ACTTGACAAATACTTCCTCCGTT 58.031 39.130 0.00 0.00 0.00 4.44
314 316 4.039973 TGACTTGACAAATACTTCCTCCGT 59.960 41.667 0.00 0.00 0.00 4.69
315 317 4.566004 TGACTTGACAAATACTTCCTCCG 58.434 43.478 0.00 0.00 0.00 4.63
316 318 5.181433 GGTTGACTTGACAAATACTTCCTCC 59.819 44.000 0.00 0.00 0.00 4.30
317 319 5.998363 AGGTTGACTTGACAAATACTTCCTC 59.002 40.000 0.00 0.00 0.00 3.71
318 320 5.941788 AGGTTGACTTGACAAATACTTCCT 58.058 37.500 0.00 0.00 0.00 3.36
319 321 5.763204 TGAGGTTGACTTGACAAATACTTCC 59.237 40.000 0.00 0.00 0.00 3.46
320 322 6.260050 TGTGAGGTTGACTTGACAAATACTTC 59.740 38.462 0.00 0.00 0.00 3.01
321 323 6.119536 TGTGAGGTTGACTTGACAAATACTT 58.880 36.000 0.00 0.00 0.00 2.24
322 324 5.680619 TGTGAGGTTGACTTGACAAATACT 58.319 37.500 0.00 0.00 0.00 2.12
323 325 6.371809 TTGTGAGGTTGACTTGACAAATAC 57.628 37.500 0.00 0.00 32.22 1.89
324 326 7.397892 TTTTGTGAGGTTGACTTGACAAATA 57.602 32.000 10.65 2.29 39.52 1.40
325 327 5.913137 TTTGTGAGGTTGACTTGACAAAT 57.087 34.783 6.86 0.00 37.13 2.32
403 407 8.834465 GCAATGTGCTATCTTATAGGGATATTG 58.166 37.037 0.00 0.00 40.96 1.90
489 493 6.019656 AGAGAGAGAGAGAGAGAGAGAGTA 57.980 45.833 0.00 0.00 0.00 2.59
490 494 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
517 555 2.324477 GCGCACACACACACAGAC 59.676 61.111 0.30 0.00 0.00 3.51
540 578 2.602474 CTAAAATTTGCGCGCGCG 59.398 55.556 45.73 45.73 45.51 6.86
541 579 1.741947 ATGCTAAAATTTGCGCGCGC 61.742 50.000 45.02 45.02 42.35 6.86
542 580 0.639756 AATGCTAAAATTTGCGCGCG 59.360 45.000 28.44 28.44 0.00 6.86
543 581 1.919918 AGAATGCTAAAATTTGCGCGC 59.080 42.857 27.26 27.26 0.00 6.86
544 582 3.429085 AGAGAATGCTAAAATTTGCGCG 58.571 40.909 0.00 0.00 0.00 6.86
545 583 3.793492 GGAGAGAATGCTAAAATTTGCGC 59.207 43.478 0.00 0.00 0.00 6.09
546 584 4.354587 GGGAGAGAATGCTAAAATTTGCG 58.645 43.478 0.00 0.00 0.00 4.85
611 661 9.036980 TGAGAGGTAAGAAGCTAAGAGTTAATT 57.963 33.333 0.00 0.00 32.30 1.40
623 673 5.934625 TCTTTTCACATGAGAGGTAAGAAGC 59.065 40.000 0.00 0.00 0.00 3.86
643 693 1.906692 GCTCCCTCTTACCCCCTCTTT 60.907 57.143 0.00 0.00 0.00 2.52
652 702 8.507524 AGTAATTTTAACATGCTCCCTCTTAC 57.492 34.615 0.00 0.00 0.00 2.34
653 703 7.773690 GGAGTAATTTTAACATGCTCCCTCTTA 59.226 37.037 11.54 0.00 36.09 2.10
654 704 6.603599 GGAGTAATTTTAACATGCTCCCTCTT 59.396 38.462 11.54 0.00 36.09 2.85
655 705 6.069381 AGGAGTAATTTTAACATGCTCCCTCT 60.069 38.462 15.99 2.89 41.23 3.69
656 706 6.122964 AGGAGTAATTTTAACATGCTCCCTC 58.877 40.000 15.99 0.00 41.23 4.30
657 707 6.069381 AGAGGAGTAATTTTAACATGCTCCCT 60.069 38.462 15.99 12.10 41.23 4.20
658 708 6.122964 AGAGGAGTAATTTTAACATGCTCCC 58.877 40.000 15.99 10.78 41.23 4.30
659 709 7.051000 AGAGAGGAGTAATTTTAACATGCTCC 58.949 38.462 13.49 13.49 40.78 4.70
660 710 7.984617 AGAGAGAGGAGTAATTTTAACATGCTC 59.015 37.037 0.00 0.00 0.00 4.26
661 711 7.856415 AGAGAGAGGAGTAATTTTAACATGCT 58.144 34.615 0.00 0.00 0.00 3.79
690 740 3.150767 GCGAAGATTAGCTAGAGAGGGA 58.849 50.000 0.00 0.00 0.00 4.20
691 741 2.887783 TGCGAAGATTAGCTAGAGAGGG 59.112 50.000 0.00 0.00 0.00 4.30
692 742 3.568007 ACTGCGAAGATTAGCTAGAGAGG 59.432 47.826 0.00 0.00 0.00 3.69
693 743 4.829064 ACTGCGAAGATTAGCTAGAGAG 57.171 45.455 0.00 0.00 0.00 3.20
694 744 5.584253 AAACTGCGAAGATTAGCTAGAGA 57.416 39.130 0.00 0.00 0.00 3.10
695 745 6.654793 AAAAACTGCGAAGATTAGCTAGAG 57.345 37.500 0.00 0.00 0.00 2.43
736 786 1.153369 GAGCGAGGGCAAGCACATA 60.153 57.895 0.00 0.00 43.41 2.29
737 787 2.437359 GAGCGAGGGCAAGCACAT 60.437 61.111 0.00 0.00 43.41 3.21
738 788 4.704833 GGAGCGAGGGCAAGCACA 62.705 66.667 0.00 0.00 43.41 4.57
739 789 2.521958 TAAGGAGCGAGGGCAAGCAC 62.522 60.000 0.00 0.00 43.41 4.40
740 790 2.244117 CTAAGGAGCGAGGGCAAGCA 62.244 60.000 0.00 0.00 43.41 3.91
741 791 1.522580 CTAAGGAGCGAGGGCAAGC 60.523 63.158 0.00 0.00 43.41 4.01
742 792 0.537188 TTCTAAGGAGCGAGGGCAAG 59.463 55.000 0.00 0.00 43.41 4.01
743 793 1.134401 CATTCTAAGGAGCGAGGGCAA 60.134 52.381 0.00 0.00 43.41 4.52
744 794 0.465705 CATTCTAAGGAGCGAGGGCA 59.534 55.000 0.00 0.00 43.41 5.36
745 795 0.466124 ACATTCTAAGGAGCGAGGGC 59.534 55.000 0.00 0.00 40.37 5.19
746 796 3.574396 TGATACATTCTAAGGAGCGAGGG 59.426 47.826 0.00 0.00 0.00 4.30
747 797 4.855715 TGATACATTCTAAGGAGCGAGG 57.144 45.455 0.00 0.00 0.00 4.63
748 798 6.925718 TCAATTGATACATTCTAAGGAGCGAG 59.074 38.462 3.38 0.00 0.00 5.03
749 799 6.816136 TCAATTGATACATTCTAAGGAGCGA 58.184 36.000 3.38 0.00 0.00 4.93
750 800 6.925718 TCTCAATTGATACATTCTAAGGAGCG 59.074 38.462 8.96 0.00 0.00 5.03
751 801 8.845413 ATCTCAATTGATACATTCTAAGGAGC 57.155 34.615 8.96 0.00 0.00 4.70
752 802 9.993454 TGATCTCAATTGATACATTCTAAGGAG 57.007 33.333 8.96 0.00 0.00 3.69
850 900 7.037438 GTGTCATGCAAATCTCCACATAAATT 58.963 34.615 0.00 0.00 0.00 1.82
966 1016 0.833287 AGTGTTGTGGAGCAGACAGT 59.167 50.000 0.00 0.00 0.00 3.55
992 1042 9.878599 GACGAAATGTTATATCCATTTTGGTAG 57.121 33.333 21.06 11.73 43.42 3.18
1016 1066 2.025418 CTGTAACACGCACCCGGAC 61.025 63.158 0.73 0.00 39.22 4.79
1031 1081 7.277981 CGGTGAGAAAAATAACTGCTATACTGT 59.722 37.037 0.00 0.00 0.00 3.55
1116 1166 2.224867 ACTTGCAATAGGTGGCTGAAGT 60.225 45.455 0.00 0.00 0.00 3.01
1142 1192 2.554032 GGCAAAGCAGCTACAAGAGAAA 59.446 45.455 0.00 0.00 34.17 2.52
1251 1301 6.040504 GTCCAACCAATAAAGTCACCTTCTTT 59.959 38.462 0.00 0.00 38.45 2.52
1368 1418 7.789341 TTCGAAATCCACATCAAAAATAACG 57.211 32.000 0.00 0.00 0.00 3.18
1793 1844 9.691362 TGAAGAAGTTTATTCCAGCAAATTAAC 57.309 29.630 0.00 0.00 31.53 2.01
1820 1871 2.644992 GTCACCTTGCGGCTTTGG 59.355 61.111 0.00 3.27 0.00 3.28
1893 1944 4.211164 GGCATGTGCTTGTTTTAGGAAAAC 59.789 41.667 4.84 7.68 44.48 2.43
1928 1979 7.984422 ACTATGATCAAAGTCATTTGTGTCA 57.016 32.000 0.00 11.13 45.06 3.58
2103 2539 5.593909 CCTTGGTTTGATGGCTTATGTGATA 59.406 40.000 0.00 0.00 0.00 2.15
2112 2548 1.187567 GGTGCCTTGGTTTGATGGCT 61.188 55.000 0.00 0.00 45.11 4.75
2115 2551 1.529226 TACGGTGCCTTGGTTTGATG 58.471 50.000 0.00 0.00 0.00 3.07
2116 2552 2.507407 ATACGGTGCCTTGGTTTGAT 57.493 45.000 0.00 0.00 0.00 2.57
2117 2553 3.275143 CATATACGGTGCCTTGGTTTGA 58.725 45.455 0.00 0.00 0.00 2.69
2118 2554 3.013921 ACATATACGGTGCCTTGGTTTG 58.986 45.455 0.00 0.00 0.00 2.93
2119 2555 3.359695 ACATATACGGTGCCTTGGTTT 57.640 42.857 0.00 0.00 0.00 3.27
2128 2564 4.411327 CAAAACTGCCAACATATACGGTG 58.589 43.478 0.00 0.00 0.00 4.94
2130 2566 3.128589 AGCAAAACTGCCAACATATACGG 59.871 43.478 0.00 0.00 34.90 4.02
2187 2627 9.386122 AGGATGTTCTCATCTATATTTGGTACT 57.614 33.333 7.89 0.00 46.74 2.73
2214 2654 1.664965 GCAGTCACGCTTTCGGACT 60.665 57.895 0.00 0.00 42.60 3.85
2262 2702 3.447229 AGTTTATGAATTTTGGGGAGGCG 59.553 43.478 0.00 0.00 0.00 5.52
2419 2861 5.169295 AGAAATGAGCCACTCGTTAGTTAC 58.831 41.667 2.65 0.00 38.58 2.50
2420 2862 5.047590 TGAGAAATGAGCCACTCGTTAGTTA 60.048 40.000 2.65 0.00 38.58 2.24
2488 2930 6.639632 TTTAGATCAATTATGCCCTCTTGC 57.360 37.500 0.00 0.00 0.00 4.01
2519 2961 1.415659 GAGCATGAGTACCTCTGCCAT 59.584 52.381 0.00 0.00 36.25 4.40
2703 3145 5.819991 TCTCATGGAATATATTTCCCAGCC 58.180 41.667 10.65 2.80 37.79 4.85
2755 3197 3.266510 TGTAGCACATCATCCTCAACC 57.733 47.619 0.00 0.00 0.00 3.77
2785 3227 1.554617 TCCTCCATGCATTTCGAGTCA 59.445 47.619 0.00 0.00 0.00 3.41
3096 3544 5.635700 CCTTCTCTAGTTTGTACAGTGAAGC 59.364 44.000 13.99 0.00 38.04 3.86
3112 3560 6.985653 ATTTCATAGCTGTAGCCTTCTCTA 57.014 37.500 0.00 0.00 43.38 2.43
3140 3588 1.270147 GGTAGCTACGGTATGCCCTTG 60.270 57.143 17.48 0.00 0.00 3.61
3184 3632 6.360370 TGAGGGTCTTTATAGATATGTGGC 57.640 41.667 0.00 0.00 31.86 5.01
3193 3641 8.478877 GGGTCATATACATGAGGGTCTTTATAG 58.521 40.741 0.00 0.00 41.87 1.31
3478 3926 6.716934 AATTACGATCTCATCAGTAGTGGT 57.283 37.500 0.00 0.00 0.00 4.16
3480 3928 7.810282 CCCTTAATTACGATCTCATCAGTAGTG 59.190 40.741 0.00 0.00 0.00 2.74
3482 3930 7.810282 CACCCTTAATTACGATCTCATCAGTAG 59.190 40.741 0.00 0.00 0.00 2.57
3483 3931 7.255836 CCACCCTTAATTACGATCTCATCAGTA 60.256 40.741 0.00 0.00 0.00 2.74
3565 4017 4.515191 ACATGTACTTTCATTGCAACTCGT 59.485 37.500 0.00 0.00 0.00 4.18
3690 4163 3.820467 CACCACAGAAAAACATAGAGCCA 59.180 43.478 0.00 0.00 0.00 4.75
3726 4199 2.568509 TGAGTTCTCAGCACATCATCCA 59.431 45.455 0.00 0.00 0.00 3.41
3739 4212 3.124976 GCAACTCTGCAAGATGAGTTCTC 59.875 47.826 14.29 7.51 46.70 2.87
3813 4286 3.878160 AACTGAAGAAAAACGGCCAAA 57.122 38.095 2.24 0.00 0.00 3.28
3871 4344 9.744468 AAGTGTGCGAATTAAGAAAATAAAAGT 57.256 25.926 0.00 0.00 0.00 2.66
3890 4363 9.961266 AAAGTTAACGAATTTTAAAAAGTGTGC 57.039 25.926 4.44 1.25 0.00 4.57
3953 4426 9.067986 AGAACTAGAAAAAGGTTATGAGTTTGG 57.932 33.333 0.00 0.00 0.00 3.28
3990 4464 3.134442 ACAACTTGGCATGGTGTGAATTT 59.866 39.130 21.66 0.00 0.00 1.82
4028 4502 8.504005 CCGACAACACTCTAGAAAATACAAAAT 58.496 33.333 0.00 0.00 0.00 1.82
4065 4540 3.731565 CGACACGTACGACCATTTATCCA 60.732 47.826 24.41 0.00 0.00 3.41
4079 4554 1.005512 ATGCCAGTTGCGACACGTA 60.006 52.632 6.90 0.00 45.60 3.57
4081 4556 2.174107 CATGCCAGTTGCGACACG 59.826 61.111 6.90 0.00 45.60 4.49
4093 4568 0.458370 GATTTCCAACACCGCATGCC 60.458 55.000 13.15 0.00 0.00 4.40
4098 4573 0.589223 TGAACGATTTCCAACACCGC 59.411 50.000 0.00 0.00 0.00 5.68
4154 4629 6.659242 TGAAATAACCCCAACTTTTGCAAAAA 59.341 30.769 23.92 7.73 0.00 1.94
4190 4665 6.153340 ACCCTTAGTTGAACATGATCCAATTG 59.847 38.462 0.00 0.00 0.00 2.32
4193 4668 5.009631 CACCCTTAGTTGAACATGATCCAA 58.990 41.667 0.00 0.00 0.00 3.53
4208 4683 1.767088 GGCCTACCCTAACACCCTTAG 59.233 57.143 0.00 0.00 0.00 2.18
4209 4684 1.080835 TGGCCTACCCTAACACCCTTA 59.919 52.381 3.32 0.00 33.59 2.69
4248 4724 5.509771 TCAACAATGTCGAGAAACAATGTG 58.490 37.500 0.00 0.00 41.28 3.21
4251 4727 6.201517 CAGTTCAACAATGTCGAGAAACAAT 58.798 36.000 0.00 0.00 31.81 2.71
4261 4737 0.603065 GGGGCCAGTTCAACAATGTC 59.397 55.000 4.39 0.00 0.00 3.06
4266 4742 1.799933 AAAATGGGGCCAGTTCAACA 58.200 45.000 4.39 0.00 32.85 3.33
4307 4783 2.560981 CCTCCCACCACCAAATGTAAAC 59.439 50.000 0.00 0.00 0.00 2.01
4332 4808 3.474600 CATATTCCTCTCCAGTGCAAGG 58.525 50.000 0.00 0.00 0.00 3.61
4334 4810 2.507058 AGCATATTCCTCTCCAGTGCAA 59.493 45.455 0.00 0.00 33.80 4.08
4364 4840 8.470002 AGGAAACAACTCCATATTGCTTTATTC 58.530 33.333 0.00 0.00 38.02 1.75
4383 4859 7.575414 TTAACTCAAAGTTGCATAGGAAACA 57.425 32.000 0.25 0.00 39.11 2.83
4438 4914 7.969690 TTAGGGCTGGAAATGATTTTATCAA 57.030 32.000 0.00 0.00 43.50 2.57


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

AutoCloner maintained by Alex Coulton.