Multiple sequence alignment - TraesCS1B01G315700

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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 TraesCS1B01G315700 chr1B 100.000 3506 0 0 1 3506 540153562 540157067 0.000000e+00 6475
1 TraesCS1B01G315700 chr1B 94.196 224 13 0 1 224 65537518 65537741 3.350000e-90 342
2 TraesCS1B01G315700 chr1B 87.166 187 16 8 188 369 445669790 445669973 4.590000e-49 206
3 TraesCS1B01G315700 chr1D 94.971 2247 71 20 785 3021 402294113 402296327 0.000000e+00 3485
4 TraesCS1B01G315700 chr1D 94.243 469 18 3 3047 3506 402296721 402297189 0.000000e+00 708
5 TraesCS1B01G315700 chr1D 89.035 456 18 11 364 799 402293652 402294095 1.430000e-148 536
6 TraesCS1B01G315700 chr1D 95.364 151 6 1 220 370 469043908 469043759 4.520000e-59 239
7 TraesCS1B01G315700 chr1D 70.668 1258 311 41 1170 2401 199277740 199276515 3.520000e-55 226
8 TraesCS1B01G315700 chr1A 92.711 2442 87 26 667 3043 497760372 497762787 0.000000e+00 3439
9 TraesCS1B01G315700 chr1A 90.941 287 13 4 3224 3506 497763237 497763514 1.190000e-99 374
10 TraesCS1B01G315700 chr1A 94.624 186 9 1 3047 3231 497762860 497763045 1.590000e-73 287
11 TraesCS1B01G315700 chr1A 94.444 72 0 2 599 670 497760139 497760206 1.330000e-19 108
12 TraesCS1B01G315700 chr3D 80.976 1393 211 33 1116 2493 8935849 8937202 0.000000e+00 1055
13 TraesCS1B01G315700 chr3D 78.632 819 145 23 1132 1929 8927422 8928231 1.870000e-142 516
14 TraesCS1B01G315700 chr3D 83.268 514 79 6 1989 2498 8913039 8913549 1.910000e-127 466
15 TraesCS1B01G315700 chr3D 84.058 207 24 3 3259 3465 8439531 8439334 1.280000e-44 191
16 TraesCS1B01G315700 chr3A 80.789 1395 216 31 1116 2496 11948758 11947402 0.000000e+00 1044
17 TraesCS1B01G315700 chr3A 80.015 1331 224 27 1179 2503 12039951 12038657 0.000000e+00 946
18 TraesCS1B01G315700 chr3A 79.422 831 136 25 1123 1929 11958696 11957877 3.950000e-154 555
19 TraesCS1B01G315700 chr3A 84.038 520 82 1 1979 2498 11957859 11957341 1.880000e-137 499
20 TraesCS1B01G315700 chr3A 87.383 214 14 13 160 369 382149027 382149231 2.100000e-57 233
21 TraesCS1B01G315700 chr3A 83.019 212 27 3 3254 3465 12443166 12442964 2.150000e-42 183
22 TraesCS1B01G315700 chr3B 80.573 1395 219 32 1116 2496 10963497 10962141 0.000000e+00 1027
23 TraesCS1B01G315700 chr3B 80.333 1383 215 42 1140 2499 11066856 11065508 0.000000e+00 994
24 TraesCS1B01G315700 chr3B 79.543 831 135 27 1123 1929 11009961 11009142 8.500000e-156 560
25 TraesCS1B01G315700 chr3B 77.886 823 147 25 1132 1929 10922114 10922926 2.450000e-131 479
26 TraesCS1B01G315700 chr3B 83.463 514 78 6 1989 2498 10922944 10923454 4.100000e-129 472
27 TraesCS1B01G315700 chr3B 94.924 197 9 1 408 604 46895591 46895396 1.220000e-79 307
28 TraesCS1B01G315700 chr4B 98.294 469 8 0 2476 2944 490347879 490348347 0.000000e+00 822
29 TraesCS1B01G315700 chr4B 98.571 210 3 0 2264 2473 490347878 490347669 4.270000e-99 372
30 TraesCS1B01G315700 chr4B 95.633 229 8 1 1 229 86056790 86056564 1.990000e-97 366
31 TraesCS1B01G315700 chr4B 93.750 224 14 0 1 224 585644916 585644693 1.560000e-88 337
32 TraesCS1B01G315700 chr4A 95.536 224 10 0 1 224 701267516 701267739 3.330000e-95 359
33 TraesCS1B01G315700 chr7B 94.643 224 12 0 1 224 12146294 12146071 7.200000e-92 348
34 TraesCS1B01G315700 chr7B 94.595 222 12 0 1 222 78061327 78061106 9.320000e-91 344
35 TraesCS1B01G315700 chr7B 91.983 237 18 1 1 236 110695485 110695249 7.250000e-87 331
36 TraesCS1B01G315700 chr7B 93.659 205 12 1 400 604 669827297 669827094 4.400000e-79 305
37 TraesCS1B01G315700 chr5B 94.643 224 12 0 1 224 417801743 417801520 7.200000e-92 348
38 TraesCS1B01G315700 chr5B 94.737 152 7 1 219 370 681821009 681820859 5.850000e-58 235
39 TraesCS1B01G315700 chr6B 94.196 224 13 0 1 224 638942870 638942647 3.350000e-90 342
40 TraesCS1B01G315700 chr6B 92.093 215 14 2 390 604 26081821 26081610 2.050000e-77 300
41 TraesCS1B01G315700 chr7A 94.118 204 11 1 401 604 545058233 545058435 3.400000e-80 309
42 TraesCS1B01G315700 chr7A 89.744 234 18 5 387 618 706669789 706669560 9.520000e-76 294
43 TraesCS1B01G315700 chr2B 92.857 210 13 2 396 604 575870997 575871205 1.580000e-78 303
44 TraesCS1B01G315700 chr2B 92.056 214 15 2 392 604 163230782 163230994 2.050000e-77 300
45 TraesCS1B01G315700 chr2B 86.538 208 17 11 159 363 155155113 155155312 5.890000e-53 219
46 TraesCS1B01G315700 chr5A 92.417 211 14 2 395 604 328805518 328805309 2.050000e-77 300
47 TraesCS1B01G315700 chr6D 94.040 151 8 1 220 370 368209252 368209103 9.790000e-56 228
48 TraesCS1B01G315700 chr5D 94.040 151 8 1 220 370 2621886 2622035 9.790000e-56 228
49 TraesCS1B01G315700 chr7D 94.000 150 7 2 220 369 83598745 83598598 3.520000e-55 226
50 TraesCS1B01G315700 chr7D 84.579 214 22 11 160 370 395325177 395324972 5.930000e-48 202


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 TraesCS1B01G315700 chr1B 540153562 540157067 3505 False 6475.000000 6475 100.000000 1 3506 1 chr1B.!!$F3 3505
1 TraesCS1B01G315700 chr1D 402293652 402297189 3537 False 1576.333333 3485 92.749667 364 3506 3 chr1D.!!$F1 3142
2 TraesCS1B01G315700 chr1D 199276515 199277740 1225 True 226.000000 226 70.668000 1170 2401 1 chr1D.!!$R1 1231
3 TraesCS1B01G315700 chr1A 497760139 497763514 3375 False 1052.000000 3439 93.180000 599 3506 4 chr1A.!!$F1 2907
4 TraesCS1B01G315700 chr3D 8935849 8937202 1353 False 1055.000000 1055 80.976000 1116 2493 1 chr3D.!!$F3 1377
5 TraesCS1B01G315700 chr3D 8927422 8928231 809 False 516.000000 516 78.632000 1132 1929 1 chr3D.!!$F2 797
6 TraesCS1B01G315700 chr3D 8913039 8913549 510 False 466.000000 466 83.268000 1989 2498 1 chr3D.!!$F1 509
7 TraesCS1B01G315700 chr3A 11947402 11948758 1356 True 1044.000000 1044 80.789000 1116 2496 1 chr3A.!!$R1 1380
8 TraesCS1B01G315700 chr3A 12038657 12039951 1294 True 946.000000 946 80.015000 1179 2503 1 chr3A.!!$R2 1324
9 TraesCS1B01G315700 chr3A 11957341 11958696 1355 True 527.000000 555 81.730000 1123 2498 2 chr3A.!!$R4 1375
10 TraesCS1B01G315700 chr3B 10962141 10963497 1356 True 1027.000000 1027 80.573000 1116 2496 1 chr3B.!!$R1 1380
11 TraesCS1B01G315700 chr3B 11065508 11066856 1348 True 994.000000 994 80.333000 1140 2499 1 chr3B.!!$R3 1359
12 TraesCS1B01G315700 chr3B 11009142 11009961 819 True 560.000000 560 79.543000 1123 1929 1 chr3B.!!$R2 806
13 TraesCS1B01G315700 chr3B 10922114 10923454 1340 False 475.500000 479 80.674500 1132 2498 2 chr3B.!!$F1 1366

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
275 276 0.032815 GTTTTTGGGCGCCTGCTAAA 59.967 50.000 28.56 18.69 42.25 1.85 F
393 394 0.108585 AGATGCGGTGACTGGTTTGT 59.891 50.000 0.00 0.00 0.00 2.83 F
977 1215 0.543277 TTTCCAGATCGCCTCAGCAT 59.457 50.000 0.00 0.00 39.83 3.79 F
2176 2458 1.229368 TCGGTGTTCATCCCCCAGA 60.229 57.895 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1638 0.322997 TCCGGGCGTGGAAAATCAAT 60.323 50.0 0.00 0.00 34.30 2.57 R
2202 2487 0.395724 TGCTCAGCACCTCCTCGATA 60.396 55.0 0.00 0.00 31.71 2.92 R
2469 2757 0.669318 GATCAAACTCGTGCGGACCA 60.669 55.0 0.00 0.00 0.00 4.02 R
2989 3324 1.481019 CGATCGCTGCAGAGCTTCAG 61.481 60.0 20.43 7.59 43.77 3.02 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
18 19 2.404083 GAGGAGAGGAGAGAGTGCG 58.596 63.158 0.00 0.00 0.00 5.34
19 20 0.107410 GAGGAGAGGAGAGAGTGCGA 60.107 60.000 0.00 0.00 0.00 5.10
20 21 0.393808 AGGAGAGGAGAGAGTGCGAC 60.394 60.000 0.00 0.00 0.00 5.19
21 22 1.711060 GGAGAGGAGAGAGTGCGACG 61.711 65.000 0.00 0.00 0.00 5.12
22 23 2.101380 GAGGAGAGAGTGCGACGC 59.899 66.667 14.19 14.19 0.00 5.19
23 24 3.726631 GAGGAGAGAGTGCGACGCG 62.727 68.421 16.14 3.53 0.00 6.01
24 25 3.800863 GGAGAGAGTGCGACGCGA 61.801 66.667 15.93 1.28 0.00 5.87
25 26 2.276994 GAGAGAGTGCGACGCGAG 60.277 66.667 15.93 7.68 0.00 5.03
26 27 4.468615 AGAGAGTGCGACGCGAGC 62.469 66.667 15.93 18.93 0.00 5.03
50 51 3.147294 GTGTGTCGCACGCTGTAG 58.853 61.111 13.79 0.00 41.09 2.74
51 52 2.733218 TGTGTCGCACGCTGTAGC 60.733 61.111 5.69 0.00 37.14 3.58
52 53 2.733218 GTGTCGCACGCTGTAGCA 60.733 61.111 4.59 0.00 42.21 3.49
53 54 2.430751 TGTCGCACGCTGTAGCAG 60.431 61.111 4.59 0.00 42.21 4.24
54 55 3.181967 GTCGCACGCTGTAGCAGG 61.182 66.667 4.59 0.00 42.21 4.85
68 69 3.312709 GCAGGCGCTCAAAATACAC 57.687 52.632 7.64 0.00 34.30 2.90
69 70 0.179163 GCAGGCGCTCAAAATACACC 60.179 55.000 7.64 0.00 34.30 4.16
70 71 0.096976 CAGGCGCTCAAAATACACCG 59.903 55.000 7.64 0.00 0.00 4.94
71 72 1.226295 GGCGCTCAAAATACACCGC 60.226 57.895 7.64 0.00 40.58 5.68
72 73 1.580132 GCGCTCAAAATACACCGCG 60.580 57.895 0.00 0.00 43.03 6.46
73 74 1.580132 CGCTCAAAATACACCGCGC 60.580 57.895 0.00 0.00 34.05 6.86
74 75 1.580132 GCTCAAAATACACCGCGCG 60.580 57.895 25.67 25.67 0.00 6.86
75 76 1.060308 CTCAAAATACACCGCGCGG 59.940 57.895 44.88 44.88 42.03 6.46
90 91 3.192922 CGGGATGGCGTTTCCGAC 61.193 66.667 14.59 0.00 44.69 4.79
108 109 4.367023 AGCGCGCCCAACTCGTTA 62.367 61.111 30.33 0.00 0.00 3.18
109 110 3.192922 GCGCGCCCAACTCGTTAT 61.193 61.111 23.24 0.00 0.00 1.89
110 111 1.879430 GCGCGCCCAACTCGTTATA 60.879 57.895 23.24 0.00 0.00 0.98
111 112 1.818221 GCGCGCCCAACTCGTTATAG 61.818 60.000 23.24 0.00 0.00 1.31
112 113 1.818221 CGCGCCCAACTCGTTATAGC 61.818 60.000 0.00 0.00 0.00 2.97
113 114 1.818221 GCGCCCAACTCGTTATAGCG 61.818 60.000 2.12 2.12 44.54 4.26
114 115 1.818221 CGCCCAACTCGTTATAGCGC 61.818 60.000 0.00 0.00 35.33 5.92
115 116 1.818221 GCCCAACTCGTTATAGCGCG 61.818 60.000 0.00 0.00 0.00 6.86
116 117 1.558383 CCAACTCGTTATAGCGCGC 59.442 57.895 26.66 26.66 0.00 6.86
117 118 1.195985 CAACTCGTTATAGCGCGCG 59.804 57.895 28.44 28.44 0.00 6.86
118 119 2.574222 AACTCGTTATAGCGCGCGC 61.574 57.895 45.10 45.10 42.33 6.86
177 178 3.475774 CGCGCGCTAAAACCGACT 61.476 61.111 30.48 0.00 0.00 4.18
178 179 2.153945 CGCGCGCTAAAACCGACTA 61.154 57.895 30.48 0.00 0.00 2.59
179 180 1.676438 CGCGCGCTAAAACCGACTAA 61.676 55.000 30.48 0.00 0.00 2.24
180 181 0.648958 GCGCGCTAAAACCGACTAAT 59.351 50.000 26.67 0.00 0.00 1.73
181 182 1.061566 GCGCGCTAAAACCGACTAATT 59.938 47.619 26.67 0.00 0.00 1.40
182 183 2.475022 GCGCGCTAAAACCGACTAATTT 60.475 45.455 26.67 0.00 0.00 1.82
183 184 3.088552 CGCGCTAAAACCGACTAATTTG 58.911 45.455 5.56 0.00 0.00 2.32
184 185 2.844223 GCGCTAAAACCGACTAATTTGC 59.156 45.455 0.00 0.00 0.00 3.68
185 186 3.088552 CGCTAAAACCGACTAATTTGCG 58.911 45.455 0.00 0.00 32.18 4.85
189 190 2.022762 CCGACTAATTTGCGGCGC 59.977 61.111 27.44 27.44 38.46 6.53
190 191 2.349648 CGACTAATTTGCGGCGCG 60.350 61.111 28.09 14.11 0.00 6.86
191 192 2.794355 CGACTAATTTGCGGCGCGA 61.794 57.895 28.09 24.12 0.00 5.87
192 193 1.296649 GACTAATTTGCGGCGCGAC 60.297 57.895 28.09 5.80 0.00 5.19
193 194 2.349648 CTAATTTGCGGCGCGACG 60.350 61.111 33.75 33.75 0.00 5.12
210 211 3.006706 GCTAGTTTAGCGCGGCTG 58.993 61.111 8.83 0.00 42.62 4.85
211 212 1.810030 GCTAGTTTAGCGCGGCTGT 60.810 57.895 8.83 0.00 42.62 4.40
212 213 1.359459 GCTAGTTTAGCGCGGCTGTT 61.359 55.000 8.83 0.00 42.62 3.16
213 214 0.370273 CTAGTTTAGCGCGGCTGTTG 59.630 55.000 8.83 0.00 40.10 3.33
214 215 1.017177 TAGTTTAGCGCGGCTGTTGG 61.017 55.000 8.83 0.00 40.10 3.77
215 216 2.031314 TTTAGCGCGGCTGTTGGA 59.969 55.556 8.83 0.00 40.10 3.53
216 217 2.032634 TTTAGCGCGGCTGTTGGAG 61.033 57.895 8.83 0.00 40.10 3.86
217 218 2.443260 TTTAGCGCGGCTGTTGGAGA 62.443 55.000 8.83 0.00 40.10 3.71
218 219 2.238847 TTAGCGCGGCTGTTGGAGAT 62.239 55.000 8.83 0.00 40.10 2.75
219 220 2.906182 TAGCGCGGCTGTTGGAGATG 62.906 60.000 8.83 0.00 40.10 2.90
220 221 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
221 222 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
222 223 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
223 224 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
224 225 0.809241 CGGCTGTTGGAGATGCTCTC 60.809 60.000 5.01 5.01 42.66 3.20
225 226 0.251354 GGCTGTTGGAGATGCTCTCA 59.749 55.000 13.06 0.00 45.12 3.27
226 227 1.367659 GCTGTTGGAGATGCTCTCAC 58.632 55.000 13.06 6.26 45.12 3.51
227 228 1.338484 GCTGTTGGAGATGCTCTCACA 60.338 52.381 13.06 9.43 45.12 3.58
228 229 2.873245 GCTGTTGGAGATGCTCTCACAA 60.873 50.000 13.06 11.47 45.12 3.33
229 230 3.607741 CTGTTGGAGATGCTCTCACAAT 58.392 45.455 13.06 0.00 45.12 2.71
230 231 4.008330 CTGTTGGAGATGCTCTCACAATT 58.992 43.478 13.06 0.00 45.12 2.32
231 232 4.401022 TGTTGGAGATGCTCTCACAATTT 58.599 39.130 13.06 0.00 45.12 1.82
232 233 4.216902 TGTTGGAGATGCTCTCACAATTTG 59.783 41.667 13.06 0.00 45.12 2.32
233 234 2.751259 TGGAGATGCTCTCACAATTTGC 59.249 45.455 13.06 0.00 45.12 3.68
234 235 2.751259 GGAGATGCTCTCACAATTTGCA 59.249 45.455 13.06 0.00 45.12 4.08
235 236 3.380637 GGAGATGCTCTCACAATTTGCAT 59.619 43.478 13.06 0.00 45.12 3.96
236 237 4.142227 GGAGATGCTCTCACAATTTGCATT 60.142 41.667 13.06 0.00 45.12 3.56
237 238 4.744570 AGATGCTCTCACAATTTGCATTG 58.255 39.130 0.00 0.00 43.28 2.82
252 253 1.421382 CATTGTCTGCTTTTTGGGCG 58.579 50.000 0.00 0.00 0.00 6.13
253 254 1.039856 ATTGTCTGCTTTTTGGGCGT 58.960 45.000 0.00 0.00 0.00 5.68
254 255 0.102120 TTGTCTGCTTTTTGGGCGTG 59.898 50.000 0.00 0.00 0.00 5.34
255 256 1.661509 GTCTGCTTTTTGGGCGTGC 60.662 57.895 0.00 0.00 0.00 5.34
256 257 2.730604 CTGCTTTTTGGGCGTGCG 60.731 61.111 0.00 0.00 0.00 5.34
257 258 3.483235 CTGCTTTTTGGGCGTGCGT 62.483 57.895 0.00 0.00 0.00 5.24
258 259 2.279186 GCTTTTTGGGCGTGCGTT 60.279 55.556 0.00 0.00 0.00 4.84
259 260 1.880796 GCTTTTTGGGCGTGCGTTT 60.881 52.632 0.00 0.00 0.00 3.60
260 261 1.425267 GCTTTTTGGGCGTGCGTTTT 61.425 50.000 0.00 0.00 0.00 2.43
261 262 1.003108 CTTTTTGGGCGTGCGTTTTT 58.997 45.000 0.00 0.00 0.00 1.94
262 263 0.721718 TTTTTGGGCGTGCGTTTTTG 59.278 45.000 0.00 0.00 0.00 2.44
263 264 1.084370 TTTTGGGCGTGCGTTTTTGG 61.084 50.000 0.00 0.00 0.00 3.28
264 265 2.907897 TTTGGGCGTGCGTTTTTGGG 62.908 55.000 0.00 0.00 0.00 4.12
272 273 3.977244 CGTTTTTGGGCGCCTGCT 61.977 61.111 28.56 0.00 42.25 4.24
273 274 2.622011 CGTTTTTGGGCGCCTGCTA 61.622 57.895 28.56 7.82 42.25 3.49
274 275 1.663173 GTTTTTGGGCGCCTGCTAA 59.337 52.632 28.56 13.76 42.25 3.09
275 276 0.032815 GTTTTTGGGCGCCTGCTAAA 59.967 50.000 28.56 18.69 42.25 1.85
276 277 0.316841 TTTTTGGGCGCCTGCTAAAG 59.683 50.000 28.56 0.00 42.25 1.85
277 278 2.153547 TTTTGGGCGCCTGCTAAAGC 62.154 55.000 28.56 7.32 42.25 3.51
289 290 2.724977 GCTAAAGCAAAGTTGGTCCC 57.275 50.000 0.00 0.00 41.59 4.46
290 291 1.068541 GCTAAAGCAAAGTTGGTCCCG 60.069 52.381 0.00 0.00 41.59 5.14
291 292 1.539827 CTAAAGCAAAGTTGGTCCCGG 59.460 52.381 0.00 0.00 38.04 5.73
292 293 1.744320 AAAGCAAAGTTGGTCCCGGC 61.744 55.000 0.00 0.00 38.04 6.13
293 294 2.909965 GCAAAGTTGGTCCCGGCA 60.910 61.111 0.00 0.00 0.00 5.69
294 295 3.039134 CAAAGTTGGTCCCGGCAC 58.961 61.111 0.00 0.00 0.00 5.01
295 296 1.826054 CAAAGTTGGTCCCGGCACA 60.826 57.895 0.00 0.00 0.00 4.57
296 297 1.152830 AAAGTTGGTCCCGGCACAT 59.847 52.632 0.00 0.00 0.00 3.21
297 298 0.469144 AAAGTTGGTCCCGGCACATT 60.469 50.000 0.00 0.00 0.00 2.71
298 299 0.402504 AAGTTGGTCCCGGCACATTA 59.597 50.000 0.00 0.00 0.00 1.90
299 300 0.402504 AGTTGGTCCCGGCACATTAA 59.597 50.000 0.00 0.00 0.00 1.40
300 301 1.202952 AGTTGGTCCCGGCACATTAAA 60.203 47.619 0.00 0.00 0.00 1.52
301 302 1.614413 GTTGGTCCCGGCACATTAAAA 59.386 47.619 0.00 0.00 0.00 1.52
302 303 1.540267 TGGTCCCGGCACATTAAAAG 58.460 50.000 0.00 0.00 0.00 2.27
303 304 1.202952 TGGTCCCGGCACATTAAAAGT 60.203 47.619 0.00 0.00 0.00 2.66
304 305 1.201414 GGTCCCGGCACATTAAAAGTG 59.799 52.381 0.00 6.97 39.92 3.16
314 315 4.475944 CACATTAAAAGTGCTACAGTGGC 58.524 43.478 0.99 0.99 0.00 5.01
315 316 3.188460 ACATTAAAAGTGCTACAGTGGCG 59.812 43.478 4.21 0.00 0.00 5.69
316 317 1.153353 TAAAAGTGCTACAGTGGCGC 58.847 50.000 14.31 14.31 40.08 6.53
317 318 1.841663 AAAAGTGCTACAGTGGCGCG 61.842 55.000 15.94 0.00 43.87 6.86
320 321 3.754530 TGCTACAGTGGCGCGCTA 61.755 61.111 32.29 24.64 0.00 4.26
321 322 2.279517 GCTACAGTGGCGCGCTAT 60.280 61.111 32.29 13.14 0.00 2.97
322 323 1.007734 GCTACAGTGGCGCGCTATA 60.008 57.895 32.29 13.63 0.00 1.31
323 324 0.596600 GCTACAGTGGCGCGCTATAA 60.597 55.000 32.29 11.71 0.00 0.98
324 325 1.129326 CTACAGTGGCGCGCTATAAC 58.871 55.000 32.29 22.40 0.00 1.89
325 326 0.593008 TACAGTGGCGCGCTATAACG 60.593 55.000 32.29 16.51 0.00 3.18
326 327 1.876714 CAGTGGCGCGCTATAACGT 60.877 57.895 32.29 5.71 34.88 3.99
327 328 1.153706 AGTGGCGCGCTATAACGTT 60.154 52.632 32.29 5.88 34.88 3.99
328 329 0.738412 AGTGGCGCGCTATAACGTTT 60.738 50.000 32.29 6.16 34.88 3.60
329 330 0.922717 GTGGCGCGCTATAACGTTTA 59.077 50.000 32.29 1.77 34.88 2.01
330 331 1.523934 GTGGCGCGCTATAACGTTTAT 59.476 47.619 32.29 0.73 34.88 1.40
331 332 2.033492 GTGGCGCGCTATAACGTTTATT 60.033 45.455 32.29 0.00 34.88 1.40
332 333 2.033577 TGGCGCGCTATAACGTTTATTG 60.034 45.455 32.29 0.86 34.88 1.90
333 334 2.556806 GCGCGCTATAACGTTTATTGG 58.443 47.619 26.67 0.00 34.88 3.16
334 335 2.660900 GCGCGCTATAACGTTTATTGGG 60.661 50.000 26.67 8.60 34.88 4.12
335 336 2.540931 CGCGCTATAACGTTTATTGGGT 59.459 45.455 5.91 0.00 34.88 4.51
336 337 3.602946 CGCGCTATAACGTTTATTGGGTG 60.603 47.826 5.91 9.94 34.88 4.61
337 338 3.847105 GCGCTATAACGTTTATTGGGTGC 60.847 47.826 5.91 6.18 34.88 5.01
338 339 3.310227 CGCTATAACGTTTATTGGGTGCA 59.690 43.478 5.91 0.00 0.00 4.57
339 340 4.551990 CGCTATAACGTTTATTGGGTGCAG 60.552 45.833 5.91 0.00 0.00 4.41
340 341 4.573201 GCTATAACGTTTATTGGGTGCAGA 59.427 41.667 5.91 0.00 0.00 4.26
341 342 5.065474 GCTATAACGTTTATTGGGTGCAGAA 59.935 40.000 5.91 0.00 0.00 3.02
342 343 6.238648 GCTATAACGTTTATTGGGTGCAGAAT 60.239 38.462 5.91 0.00 0.00 2.40
343 344 4.864704 AACGTTTATTGGGTGCAGAATT 57.135 36.364 0.00 0.00 0.00 2.17
344 345 4.864704 ACGTTTATTGGGTGCAGAATTT 57.135 36.364 0.00 0.00 0.00 1.82
345 346 5.208463 ACGTTTATTGGGTGCAGAATTTT 57.792 34.783 0.00 0.00 0.00 1.82
346 347 5.606505 ACGTTTATTGGGTGCAGAATTTTT 58.393 33.333 0.00 0.00 0.00 1.94
347 348 5.465056 ACGTTTATTGGGTGCAGAATTTTTG 59.535 36.000 0.00 0.00 0.00 2.44
348 349 5.465056 CGTTTATTGGGTGCAGAATTTTTGT 59.535 36.000 0.00 0.00 0.00 2.83
349 350 6.563753 CGTTTATTGGGTGCAGAATTTTTGTG 60.564 38.462 0.00 0.00 0.00 3.33
354 355 2.153039 GCAGAATTTTTGTGCGGCC 58.847 52.632 0.00 0.00 40.23 6.13
355 356 1.616872 GCAGAATTTTTGTGCGGCCG 61.617 55.000 24.05 24.05 40.23 6.13
356 357 0.318614 CAGAATTTTTGTGCGGCCGT 60.319 50.000 28.70 2.08 0.00 5.68
357 358 0.387565 AGAATTTTTGTGCGGCCGTT 59.612 45.000 28.70 10.38 0.00 4.44
358 359 0.506506 GAATTTTTGTGCGGCCGTTG 59.493 50.000 28.70 0.00 0.00 4.10
359 360 0.878086 AATTTTTGTGCGGCCGTTGG 60.878 50.000 28.70 0.00 0.00 3.77
360 361 1.739338 ATTTTTGTGCGGCCGTTGGA 61.739 50.000 28.70 8.23 0.00 3.53
361 362 2.343163 TTTTTGTGCGGCCGTTGGAG 62.343 55.000 28.70 0.00 0.00 3.86
362 363 3.758973 TTTGTGCGGCCGTTGGAGA 62.759 57.895 28.70 6.06 0.00 3.71
363 364 3.545124 TTGTGCGGCCGTTGGAGAT 62.545 57.895 28.70 0.00 0.00 2.75
364 365 3.499737 GTGCGGCCGTTGGAGATG 61.500 66.667 28.70 0.00 0.00 2.90
367 368 2.892425 CGGCCGTTGGAGATGCTC 60.892 66.667 19.50 0.00 0.00 4.26
368 369 2.586792 GGCCGTTGGAGATGCTCT 59.413 61.111 0.00 0.00 0.00 4.09
369 370 1.823295 GGCCGTTGGAGATGCTCTA 59.177 57.895 0.00 0.00 0.00 2.43
370 371 0.394565 GGCCGTTGGAGATGCTCTAT 59.605 55.000 0.00 0.00 0.00 1.98
393 394 0.108585 AGATGCGGTGACTGGTTTGT 59.891 50.000 0.00 0.00 0.00 2.83
445 446 7.718314 TGTATAAGTCATTCGCCTAGTTCTAGA 59.282 37.037 8.26 0.00 0.00 2.43
630 631 2.104170 GGACAGGACAGAGGGAGTAAG 58.896 57.143 0.00 0.00 0.00 2.34
631 632 2.557901 GGACAGGACAGAGGGAGTAAGT 60.558 54.545 0.00 0.00 0.00 2.24
721 901 2.871096 AACCTAATCACAGCCGGAAA 57.129 45.000 5.05 0.00 0.00 3.13
758 942 8.812513 ATAAATCAAGAGATTGTCCATCAACA 57.187 30.769 0.00 0.00 43.52 3.33
904 1142 4.021229 TGCTCTAATACTCCTCGGTTTGA 58.979 43.478 0.00 0.00 0.00 2.69
905 1143 4.142227 TGCTCTAATACTCCTCGGTTTGAC 60.142 45.833 0.00 0.00 0.00 3.18
906 1144 4.737055 GCTCTAATACTCCTCGGTTTGACC 60.737 50.000 0.00 0.00 34.05 4.02
907 1145 4.607239 TCTAATACTCCTCGGTTTGACCT 58.393 43.478 0.00 0.00 35.66 3.85
908 1146 5.021458 TCTAATACTCCTCGGTTTGACCTT 58.979 41.667 0.00 0.00 35.66 3.50
909 1147 3.611766 ATACTCCTCGGTTTGACCTTG 57.388 47.619 0.00 0.00 35.66 3.61
912 1150 2.143925 CTCCTCGGTTTGACCTTGTTC 58.856 52.381 0.00 0.00 35.66 3.18
913 1151 1.487142 TCCTCGGTTTGACCTTGTTCA 59.513 47.619 0.00 0.00 35.66 3.18
914 1152 2.092861 TCCTCGGTTTGACCTTGTTCAA 60.093 45.455 0.00 0.00 35.66 2.69
916 1154 4.069304 CCTCGGTTTGACCTTGTTCAATA 58.931 43.478 0.00 0.00 35.42 1.90
917 1155 4.700213 CCTCGGTTTGACCTTGTTCAATAT 59.300 41.667 0.00 0.00 35.42 1.28
918 1156 5.878116 CCTCGGTTTGACCTTGTTCAATATA 59.122 40.000 0.00 0.00 35.42 0.86
921 1159 6.370442 TCGGTTTGACCTTGTTCAATATACAG 59.630 38.462 0.00 0.00 35.42 2.74
950 1188 2.985282 TGCCCCGCTTGCTTCTTG 60.985 61.111 0.00 0.00 0.00 3.02
955 1193 1.493311 CCGCTTGCTTCTTGTCGTC 59.507 57.895 0.00 0.00 0.00 4.20
977 1215 0.543277 TTTCCAGATCGCCTCAGCAT 59.457 50.000 0.00 0.00 39.83 3.79
1055 1293 2.228914 GGACATTCTACGTCGCGGC 61.229 63.158 6.13 1.93 34.04 6.53
1736 2003 3.423154 GCAGGGCAACGACTTCGG 61.423 66.667 3.30 0.00 44.95 4.30
1935 2208 4.155950 TTGCTCGGCAAAGAAGCA 57.844 50.000 8.58 0.00 45.96 3.91
2176 2458 1.229368 TCGGTGTTCATCCCCCAGA 60.229 57.895 0.00 0.00 0.00 3.86
2262 2547 2.503061 CAGATGCGGGAGGAGGTG 59.497 66.667 0.00 0.00 0.00 4.00
2345 2630 3.103911 GTTCGACGTCGCAGTGGG 61.104 66.667 32.19 5.51 39.60 4.61
2469 2757 2.309755 TGAGGATGGCCAGACAGAAATT 59.690 45.455 13.05 0.00 36.29 1.82
2737 3053 4.890088 TGTAGATGCAAAAGTACTCCGTT 58.110 39.130 0.00 0.00 0.00 4.44
2771 3087 5.381174 AGTACGTACTGTGCTGACATTAA 57.619 39.130 26.87 0.00 42.42 1.40
2824 3144 9.765795 CTACCGTCTGAAATTAATTAAGGAGAT 57.234 33.333 0.01 0.00 0.00 2.75
2825 3145 8.664211 ACCGTCTGAAATTAATTAAGGAGATC 57.336 34.615 0.01 0.00 0.00 2.75
2826 3146 7.438459 ACCGTCTGAAATTAATTAAGGAGATCG 59.562 37.037 0.01 7.15 0.00 3.69
2827 3147 7.652105 CCGTCTGAAATTAATTAAGGAGATCGA 59.348 37.037 0.01 0.00 0.00 3.59
2925 3253 1.382522 CTAGGACGGCAAACATGCAT 58.617 50.000 0.00 0.00 36.33 3.96
2967 3302 6.260271 GGACTAGTTTTAGTTTGTTGCAGTCT 59.740 38.462 0.00 0.00 40.21 3.24
2987 3322 1.455383 GACAGGGGTGGCACAAACAG 61.455 60.000 20.82 8.01 44.16 3.16
2989 3324 3.615709 GGGGTGGCACAAACAGGC 61.616 66.667 20.82 0.00 44.16 4.85
3071 3782 8.347035 AGTACTAGCTCGCAAAAACAAAAATAA 58.653 29.630 0.00 0.00 0.00 1.40
3092 3803 1.327303 TTGGTGACCAATGGCTCAAC 58.673 50.000 14.05 11.31 38.75 3.18
3179 3891 7.483307 TCCTGAGAGAAACAAATGAACAAAAG 58.517 34.615 0.00 0.00 0.00 2.27
3215 3927 7.039270 TGTATGTGTACAACTGTGGATACATC 58.961 38.462 4.77 0.04 44.73 3.06
3301 4217 3.019003 GCCTCTTGGAGCACGGCTA 62.019 63.158 0.00 0.00 39.88 3.93
3333 4253 3.114065 GAGGTCGACGGTGATGTTAATC 58.886 50.000 9.92 0.00 0.00 1.75
3370 4290 2.045438 TGCCGCATGAACCCGAAT 60.045 55.556 0.00 0.00 0.00 3.34
3378 4298 3.541632 GCATGAACCCGAATCCTTTCTA 58.458 45.455 0.00 0.00 0.00 2.10
3478 4402 0.319383 GATCTCTGTGCGCGATCCAT 60.319 55.000 12.10 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107410 TCGCACTCTCTCCTCTCCTC 60.107 60.000 0.00 0.00 0.00 3.71
1 2 0.393808 GTCGCACTCTCTCCTCTCCT 60.394 60.000 0.00 0.00 0.00 3.69
3 4 1.719117 CGTCGCACTCTCTCCTCTC 59.281 63.158 0.00 0.00 0.00 3.20
8 9 2.276994 CTCGCGTCGCACTCTCTC 60.277 66.667 18.75 0.00 0.00 3.20
9 10 4.468615 GCTCGCGTCGCACTCTCT 62.469 66.667 18.75 0.00 0.00 3.10
21 22 4.702081 ACACACTCGACCGCTCGC 62.702 66.667 0.00 0.00 39.96 5.03
22 23 2.502080 GACACACTCGACCGCTCG 60.502 66.667 0.00 0.00 41.65 5.03
23 24 2.502080 CGACACACTCGACCGCTC 60.502 66.667 0.00 0.00 46.14 5.03
24 25 4.702081 GCGACACACTCGACCGCT 62.702 66.667 0.00 0.00 46.14 5.52
25 26 4.994201 TGCGACACACTCGACCGC 62.994 66.667 0.00 0.00 46.14 5.68
26 27 3.097728 GTGCGACACACTCGACCG 61.098 66.667 5.30 0.00 46.14 4.79
33 34 3.000080 GCTACAGCGTGCGACACAC 62.000 63.158 9.95 1.28 46.45 3.82
34 35 2.733218 GCTACAGCGTGCGACACA 60.733 61.111 9.95 0.00 33.40 3.72
35 36 2.720758 CTGCTACAGCGTGCGACAC 61.721 63.158 0.00 0.00 45.83 3.67
36 37 2.430751 CTGCTACAGCGTGCGACA 60.431 61.111 0.00 0.00 45.83 4.35
37 38 3.181967 CCTGCTACAGCGTGCGAC 61.182 66.667 0.00 0.00 45.83 5.19
50 51 0.179163 GGTGTATTTTGAGCGCCTGC 60.179 55.000 2.29 0.00 43.24 4.85
51 52 0.096976 CGGTGTATTTTGAGCGCCTG 59.903 55.000 2.29 0.00 0.00 4.85
52 53 2.466867 CGGTGTATTTTGAGCGCCT 58.533 52.632 2.29 0.00 0.00 5.52
55 56 4.643675 CGCGGTGTATTTTGAGCG 57.356 55.556 0.00 0.00 41.56 5.03
56 57 1.580132 CGCGCGGTGTATTTTGAGC 60.580 57.895 24.84 0.00 0.00 4.26
57 58 1.060308 CCGCGCGGTGTATTTTGAG 59.940 57.895 39.71 10.47 0.00 3.02
58 59 2.392181 CCCGCGCGGTGTATTTTGA 61.392 57.895 43.12 0.00 0.00 2.69
59 60 1.711060 ATCCCGCGCGGTGTATTTTG 61.711 55.000 43.12 26.97 0.00 2.44
60 61 1.450669 ATCCCGCGCGGTGTATTTT 60.451 52.632 43.12 18.98 0.00 1.82
61 62 2.177580 CATCCCGCGCGGTGTATTT 61.178 57.895 43.12 20.37 0.00 1.40
62 63 2.587753 CATCCCGCGCGGTGTATT 60.588 61.111 43.12 22.13 0.00 1.89
63 64 4.602259 CCATCCCGCGCGGTGTAT 62.602 66.667 43.12 30.48 0.00 2.29
91 92 2.287457 TATAACGAGTTGGGCGCGCT 62.287 55.000 32.29 10.98 44.20 5.92
92 93 1.818221 CTATAACGAGTTGGGCGCGC 61.818 60.000 25.94 25.94 44.20 6.86
93 94 1.818221 GCTATAACGAGTTGGGCGCG 61.818 60.000 0.00 0.00 45.80 6.86
94 95 1.818221 CGCTATAACGAGTTGGGCGC 61.818 60.000 0.00 0.00 35.13 6.53
95 96 1.818221 GCGCTATAACGAGTTGGGCG 61.818 60.000 19.09 19.09 43.21 6.13
96 97 1.818221 CGCGCTATAACGAGTTGGGC 61.818 60.000 5.56 1.85 34.06 5.36
97 98 1.818221 GCGCGCTATAACGAGTTGGG 61.818 60.000 26.67 0.00 35.14 4.12
98 99 1.558383 GCGCGCTATAACGAGTTGG 59.442 57.895 26.67 0.00 35.14 3.77
99 100 1.195985 CGCGCGCTATAACGAGTTG 59.804 57.895 30.48 4.48 35.14 3.16
100 101 2.574222 GCGCGCGCTATAACGAGTT 61.574 57.895 44.38 0.00 38.26 3.01
101 102 3.022914 GCGCGCGCTATAACGAGT 61.023 61.111 44.38 0.00 38.26 4.18
102 103 4.092062 CGCGCGCGCTATAACGAG 62.092 66.667 45.97 27.76 39.32 4.18
160 161 1.676438 TTAGTCGGTTTTAGCGCGCG 61.676 55.000 28.44 28.44 39.21 6.86
161 162 0.648958 ATTAGTCGGTTTTAGCGCGC 59.351 50.000 26.66 26.66 39.21 6.86
162 163 3.088552 CAAATTAGTCGGTTTTAGCGCG 58.911 45.455 0.00 0.00 39.21 6.86
163 164 2.844223 GCAAATTAGTCGGTTTTAGCGC 59.156 45.455 0.00 0.00 39.21 5.92
164 165 3.088552 CGCAAATTAGTCGGTTTTAGCG 58.911 45.455 0.00 0.00 40.97 4.26
165 166 3.422655 CCGCAAATTAGTCGGTTTTAGC 58.577 45.455 5.18 0.00 38.47 3.09
166 167 3.422655 GCCGCAAATTAGTCGGTTTTAG 58.577 45.455 12.51 0.00 44.58 1.85
167 168 2.159680 CGCCGCAAATTAGTCGGTTTTA 60.160 45.455 12.51 0.00 44.58 1.52
168 169 1.400500 CGCCGCAAATTAGTCGGTTTT 60.400 47.619 12.51 0.00 44.58 2.43
169 170 0.167251 CGCCGCAAATTAGTCGGTTT 59.833 50.000 12.51 0.00 44.58 3.27
170 171 1.791662 CGCCGCAAATTAGTCGGTT 59.208 52.632 12.51 0.00 44.58 4.44
171 172 2.746803 GCGCCGCAAATTAGTCGGT 61.747 57.895 3.15 0.00 44.58 4.69
172 173 2.022762 GCGCCGCAAATTAGTCGG 59.977 61.111 3.15 8.15 45.46 4.79
173 174 2.349648 CGCGCCGCAAATTAGTCG 60.350 61.111 10.75 0.00 0.00 4.18
174 175 1.296649 GTCGCGCCGCAAATTAGTC 60.297 57.895 10.75 0.00 0.00 2.59
175 176 2.782615 GTCGCGCCGCAAATTAGT 59.217 55.556 10.75 0.00 0.00 2.24
176 177 2.349648 CGTCGCGCCGCAAATTAG 60.350 61.111 10.75 0.00 0.00 1.73
194 195 0.370273 CAACAGCCGCGCTAAACTAG 59.630 55.000 5.56 0.00 36.40 2.57
195 196 1.017177 CCAACAGCCGCGCTAAACTA 61.017 55.000 5.56 0.00 36.40 2.24
196 197 2.325082 CCAACAGCCGCGCTAAACT 61.325 57.895 5.56 0.00 36.40 2.66
197 198 2.175811 CCAACAGCCGCGCTAAAC 59.824 61.111 5.56 0.00 36.40 2.01
198 199 2.031314 TCCAACAGCCGCGCTAAA 59.969 55.556 5.56 0.00 36.40 1.85
199 200 2.238847 ATCTCCAACAGCCGCGCTAA 62.239 55.000 5.56 0.00 36.40 3.09
200 201 2.721167 ATCTCCAACAGCCGCGCTA 61.721 57.895 5.56 0.00 36.40 4.26
201 202 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
202 203 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
203 204 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
204 205 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
205 206 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
213 214 8.505085 ACAATGCAAATTGTGAGAGCATCTCC 62.505 42.308 4.90 0.00 45.11 3.71
214 215 5.621555 ACAATGCAAATTGTGAGAGCATCTC 60.622 40.000 4.90 0.00 44.91 2.75
215 216 4.219944 ACAATGCAAATTGTGAGAGCATCT 59.780 37.500 4.90 0.00 44.40 2.90
216 217 4.491676 ACAATGCAAATTGTGAGAGCATC 58.508 39.130 4.90 0.00 44.40 3.91
217 218 4.219944 AGACAATGCAAATTGTGAGAGCAT 59.780 37.500 10.33 0.00 46.86 3.79
218 219 3.570975 AGACAATGCAAATTGTGAGAGCA 59.429 39.130 10.33 0.00 44.02 4.26
219 220 3.918591 CAGACAATGCAAATTGTGAGAGC 59.081 43.478 10.33 0.00 44.02 4.09
233 234 1.269726 ACGCCCAAAAAGCAGACAATG 60.270 47.619 0.00 0.00 0.00 2.82
234 235 1.039856 ACGCCCAAAAAGCAGACAAT 58.960 45.000 0.00 0.00 0.00 2.71
235 236 0.102120 CACGCCCAAAAAGCAGACAA 59.898 50.000 0.00 0.00 0.00 3.18
236 237 1.732917 CACGCCCAAAAAGCAGACA 59.267 52.632 0.00 0.00 0.00 3.41
237 238 1.661509 GCACGCCCAAAAAGCAGAC 60.662 57.895 0.00 0.00 0.00 3.51
238 239 2.727544 GCACGCCCAAAAAGCAGA 59.272 55.556 0.00 0.00 0.00 4.26
239 240 2.730604 CGCACGCCCAAAAAGCAG 60.731 61.111 0.00 0.00 0.00 4.24
240 241 2.564553 AAACGCACGCCCAAAAAGCA 62.565 50.000 0.00 0.00 0.00 3.91
241 242 1.425267 AAAACGCACGCCCAAAAAGC 61.425 50.000 0.00 0.00 0.00 3.51
242 243 1.003108 AAAAACGCACGCCCAAAAAG 58.997 45.000 0.00 0.00 0.00 2.27
243 244 0.721718 CAAAAACGCACGCCCAAAAA 59.278 45.000 0.00 0.00 0.00 1.94
244 245 1.084370 CCAAAAACGCACGCCCAAAA 61.084 50.000 0.00 0.00 0.00 2.44
245 246 1.519455 CCAAAAACGCACGCCCAAA 60.519 52.632 0.00 0.00 0.00 3.28
246 247 2.105128 CCAAAAACGCACGCCCAA 59.895 55.556 0.00 0.00 0.00 4.12
247 248 3.905678 CCCAAAAACGCACGCCCA 61.906 61.111 0.00 0.00 0.00 5.36
255 256 2.136196 TTAGCAGGCGCCCAAAAACG 62.136 55.000 26.15 4.00 39.83 3.60
256 257 0.032815 TTTAGCAGGCGCCCAAAAAC 59.967 50.000 26.15 6.31 39.83 2.43
257 258 0.316841 CTTTAGCAGGCGCCCAAAAA 59.683 50.000 26.15 17.21 39.83 1.94
258 259 1.963679 CTTTAGCAGGCGCCCAAAA 59.036 52.632 26.15 16.86 39.83 2.44
259 260 2.635443 GCTTTAGCAGGCGCCCAAA 61.635 57.895 26.15 16.90 41.59 3.28
260 261 3.061848 GCTTTAGCAGGCGCCCAA 61.062 61.111 26.15 9.72 41.59 4.12
270 271 1.068541 CGGGACCAACTTTGCTTTAGC 60.069 52.381 0.00 0.00 42.50 3.09
271 272 1.539827 CCGGGACCAACTTTGCTTTAG 59.460 52.381 0.00 0.00 0.00 1.85
272 273 1.611519 CCGGGACCAACTTTGCTTTA 58.388 50.000 0.00 0.00 0.00 1.85
273 274 1.744320 GCCGGGACCAACTTTGCTTT 61.744 55.000 2.18 0.00 0.00 3.51
274 275 2.200337 GCCGGGACCAACTTTGCTT 61.200 57.895 2.18 0.00 0.00 3.91
275 276 2.597510 GCCGGGACCAACTTTGCT 60.598 61.111 2.18 0.00 0.00 3.91
276 277 2.909965 TGCCGGGACCAACTTTGC 60.910 61.111 2.18 0.00 0.00 3.68
277 278 1.178534 ATGTGCCGGGACCAACTTTG 61.179 55.000 24.47 0.00 0.00 2.77
278 279 0.469144 AATGTGCCGGGACCAACTTT 60.469 50.000 24.47 6.58 0.00 2.66
279 280 0.402504 TAATGTGCCGGGACCAACTT 59.597 50.000 24.47 13.57 0.00 2.66
280 281 0.402504 TTAATGTGCCGGGACCAACT 59.597 50.000 24.47 7.56 0.00 3.16
281 282 1.249407 TTTAATGTGCCGGGACCAAC 58.751 50.000 24.47 0.00 0.00 3.77
282 283 1.889829 CTTTTAATGTGCCGGGACCAA 59.110 47.619 24.47 11.94 0.00 3.67
283 284 1.202952 ACTTTTAATGTGCCGGGACCA 60.203 47.619 24.47 12.06 0.00 4.02
284 285 1.201414 CACTTTTAATGTGCCGGGACC 59.799 52.381 24.47 6.11 0.00 4.46
285 286 2.629639 CACTTTTAATGTGCCGGGAC 57.370 50.000 20.69 20.69 0.00 4.46
292 293 4.475944 GCCACTGTAGCACTTTTAATGTG 58.524 43.478 6.61 6.61 38.36 3.21
293 294 3.188460 CGCCACTGTAGCACTTTTAATGT 59.812 43.478 0.00 0.00 0.00 2.71
294 295 3.747193 CGCCACTGTAGCACTTTTAATG 58.253 45.455 0.00 0.00 0.00 1.90
295 296 2.161609 GCGCCACTGTAGCACTTTTAAT 59.838 45.455 0.00 0.00 0.00 1.40
296 297 1.533731 GCGCCACTGTAGCACTTTTAA 59.466 47.619 0.00 0.00 0.00 1.52
297 298 1.153353 GCGCCACTGTAGCACTTTTA 58.847 50.000 0.00 0.00 0.00 1.52
298 299 1.841663 CGCGCCACTGTAGCACTTTT 61.842 55.000 0.00 0.00 0.00 2.27
299 300 2.317609 CGCGCCACTGTAGCACTTT 61.318 57.895 0.00 0.00 0.00 2.66
300 301 2.738521 CGCGCCACTGTAGCACTT 60.739 61.111 0.00 0.00 0.00 3.16
302 303 3.854618 TATAGCGCGCCACTGTAGCAC 62.855 57.143 30.33 0.00 0.00 4.40
303 304 1.730451 TATAGCGCGCCACTGTAGCA 61.730 55.000 30.33 2.34 0.00 3.49
304 305 0.596600 TTATAGCGCGCCACTGTAGC 60.597 55.000 30.33 0.00 0.00 3.58
305 306 1.129326 GTTATAGCGCGCCACTGTAG 58.871 55.000 30.33 0.00 0.00 2.74
306 307 0.593008 CGTTATAGCGCGCCACTGTA 60.593 55.000 30.33 14.06 0.00 2.74
307 308 1.876714 CGTTATAGCGCGCCACTGT 60.877 57.895 30.33 11.88 0.00 3.55
308 309 1.418342 AACGTTATAGCGCGCCACTG 61.418 55.000 30.33 15.61 34.88 3.66
309 310 0.738412 AAACGTTATAGCGCGCCACT 60.738 50.000 30.33 15.40 34.88 4.00
310 311 0.922717 TAAACGTTATAGCGCGCCAC 59.077 50.000 30.33 18.23 34.88 5.01
311 312 1.855513 ATAAACGTTATAGCGCGCCA 58.144 45.000 30.33 16.82 34.88 5.69
312 313 2.556806 CAATAAACGTTATAGCGCGCC 58.443 47.619 30.33 11.30 34.88 6.53
313 314 2.556806 CCAATAAACGTTATAGCGCGC 58.443 47.619 26.66 26.66 34.88 6.86
314 315 2.540931 ACCCAATAAACGTTATAGCGCG 59.459 45.455 9.05 0.00 34.88 6.86
315 316 3.847105 GCACCCAATAAACGTTATAGCGC 60.847 47.826 9.05 0.00 34.88 5.92
316 317 3.310227 TGCACCCAATAAACGTTATAGCG 59.690 43.478 7.49 7.49 37.94 4.26
317 318 4.573201 TCTGCACCCAATAAACGTTATAGC 59.427 41.667 0.00 0.00 0.00 2.97
318 319 6.671614 TTCTGCACCCAATAAACGTTATAG 57.328 37.500 0.00 0.00 0.00 1.31
319 320 7.633193 AATTCTGCACCCAATAAACGTTATA 57.367 32.000 0.00 0.00 0.00 0.98
320 321 6.524101 AATTCTGCACCCAATAAACGTTAT 57.476 33.333 0.00 0.00 0.00 1.89
321 322 5.968528 AATTCTGCACCCAATAAACGTTA 57.031 34.783 0.00 0.00 0.00 3.18
322 323 4.864704 AATTCTGCACCCAATAAACGTT 57.135 36.364 0.00 0.00 0.00 3.99
323 324 4.864704 AAATTCTGCACCCAATAAACGT 57.135 36.364 0.00 0.00 0.00 3.99
324 325 5.465056 ACAAAAATTCTGCACCCAATAAACG 59.535 36.000 0.00 0.00 0.00 3.60
325 326 6.657888 CACAAAAATTCTGCACCCAATAAAC 58.342 36.000 0.00 0.00 0.00 2.01
326 327 5.238214 GCACAAAAATTCTGCACCCAATAAA 59.762 36.000 0.00 0.00 0.00 1.40
327 328 4.754114 GCACAAAAATTCTGCACCCAATAA 59.246 37.500 0.00 0.00 0.00 1.40
328 329 4.314121 GCACAAAAATTCTGCACCCAATA 58.686 39.130 0.00 0.00 0.00 1.90
329 330 3.140623 GCACAAAAATTCTGCACCCAAT 58.859 40.909 0.00 0.00 0.00 3.16
330 331 2.559440 GCACAAAAATTCTGCACCCAA 58.441 42.857 0.00 0.00 0.00 4.12
331 332 1.537776 CGCACAAAAATTCTGCACCCA 60.538 47.619 0.00 0.00 0.00 4.51
332 333 1.139163 CGCACAAAAATTCTGCACCC 58.861 50.000 0.00 0.00 0.00 4.61
333 334 1.139163 CCGCACAAAAATTCTGCACC 58.861 50.000 0.00 0.00 0.00 5.01
334 335 0.508213 GCCGCACAAAAATTCTGCAC 59.492 50.000 0.00 0.00 0.00 4.57
335 336 0.599728 GGCCGCACAAAAATTCTGCA 60.600 50.000 0.00 0.00 0.00 4.41
336 337 1.616872 CGGCCGCACAAAAATTCTGC 61.617 55.000 14.67 0.00 0.00 4.26
337 338 0.318614 ACGGCCGCACAAAAATTCTG 60.319 50.000 28.58 0.00 0.00 3.02
338 339 0.387565 AACGGCCGCACAAAAATTCT 59.612 45.000 28.58 0.00 0.00 2.40
339 340 0.506506 CAACGGCCGCACAAAAATTC 59.493 50.000 28.58 0.00 0.00 2.17
340 341 0.878086 CCAACGGCCGCACAAAAATT 60.878 50.000 28.58 6.25 0.00 1.82
341 342 1.300542 CCAACGGCCGCACAAAAAT 60.301 52.632 28.58 0.00 0.00 1.82
342 343 2.105128 CCAACGGCCGCACAAAAA 59.895 55.556 28.58 0.00 0.00 1.94
343 344 2.829003 TCCAACGGCCGCACAAAA 60.829 55.556 28.58 2.77 0.00 2.44
344 345 3.283684 CTCCAACGGCCGCACAAA 61.284 61.111 28.58 6.34 0.00 2.83
345 346 3.545124 ATCTCCAACGGCCGCACAA 62.545 57.895 28.58 7.99 0.00 3.33
346 347 4.015406 ATCTCCAACGGCCGCACA 62.015 61.111 28.58 5.68 0.00 4.57
347 348 3.499737 CATCTCCAACGGCCGCAC 61.500 66.667 28.58 0.00 0.00 5.34
350 351 2.892425 GAGCATCTCCAACGGCCG 60.892 66.667 26.86 26.86 0.00 6.13
361 362 2.289320 ACCGCATCTCCAATAGAGCATC 60.289 50.000 0.00 0.00 42.90 3.91
362 363 1.696336 ACCGCATCTCCAATAGAGCAT 59.304 47.619 0.00 0.00 42.90 3.79
363 364 1.123077 ACCGCATCTCCAATAGAGCA 58.877 50.000 0.00 0.00 42.90 4.26
364 365 1.069204 TCACCGCATCTCCAATAGAGC 59.931 52.381 0.00 0.00 42.90 4.09
365 366 2.363680 AGTCACCGCATCTCCAATAGAG 59.636 50.000 0.00 0.00 44.75 2.43
366 367 2.101415 CAGTCACCGCATCTCCAATAGA 59.899 50.000 0.00 0.00 39.02 1.98
367 368 2.477825 CAGTCACCGCATCTCCAATAG 58.522 52.381 0.00 0.00 0.00 1.73
368 369 1.138859 CCAGTCACCGCATCTCCAATA 59.861 52.381 0.00 0.00 0.00 1.90
369 370 0.107508 CCAGTCACCGCATCTCCAAT 60.108 55.000 0.00 0.00 0.00 3.16
370 371 1.296392 CCAGTCACCGCATCTCCAA 59.704 57.895 0.00 0.00 0.00 3.53
412 413 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
605 606 1.079490 TCCCTCTGTCCTGTCCTGATT 59.921 52.381 0.00 0.00 0.00 2.57
721 901 6.493166 TCTCTTGATTTATTGGGTTGGATGT 58.507 36.000 0.00 0.00 0.00 3.06
909 1147 9.651718 GCAGCTAATTTGTACTGTATATTGAAC 57.348 33.333 0.00 0.00 32.65 3.18
912 1150 7.308589 GGGGCAGCTAATTTGTACTGTATATTG 60.309 40.741 0.00 0.00 32.65 1.90
913 1151 6.715264 GGGGCAGCTAATTTGTACTGTATATT 59.285 38.462 0.00 0.00 32.65 1.28
914 1152 6.238648 GGGGCAGCTAATTTGTACTGTATAT 58.761 40.000 0.00 0.00 32.65 0.86
916 1154 4.461198 GGGGCAGCTAATTTGTACTGTAT 58.539 43.478 0.00 0.00 32.65 2.29
917 1155 3.680475 CGGGGCAGCTAATTTGTACTGTA 60.680 47.826 0.00 0.00 32.65 2.74
918 1156 2.723273 GGGGCAGCTAATTTGTACTGT 58.277 47.619 0.00 0.00 32.65 3.55
921 1159 0.380733 GCGGGGCAGCTAATTTGTAC 59.619 55.000 0.00 0.00 0.00 2.90
950 1188 0.992802 GCGATCTGGAAACTGACGAC 59.007 55.000 0.00 0.00 41.39 4.34
955 1193 1.649664 CTGAGGCGATCTGGAAACTG 58.350 55.000 0.00 0.00 0.00 3.16
977 1215 3.068881 GCTACTGCTGGTGGGTGA 58.931 61.111 0.00 0.00 36.03 4.02
1055 1293 3.878519 GGACGACGGAGAGGAGCG 61.879 72.222 0.00 0.00 0.00 5.03
1380 1638 0.322997 TCCGGGCGTGGAAAATCAAT 60.323 50.000 0.00 0.00 34.30 2.57
1386 1644 2.267642 CTCATCCGGGCGTGGAAA 59.732 61.111 0.00 0.00 42.46 3.13
1818 2085 3.733344 GAAGCACCATAGCCGCCGA 62.733 63.158 0.00 0.00 34.23 5.54
1931 2204 1.073897 GGGCTCTTGGTCACTGCTT 59.926 57.895 0.00 0.00 0.00 3.91
1935 2208 3.322466 CCCGGGCTCTTGGTCACT 61.322 66.667 8.08 0.00 0.00 3.41
2202 2487 0.395724 TGCTCAGCACCTCCTCGATA 60.396 55.000 0.00 0.00 31.71 2.92
2340 2625 2.036731 TCGATGACCCGTCCCACT 59.963 61.111 0.00 0.00 0.00 4.00
2469 2757 0.669318 GATCAAACTCGTGCGGACCA 60.669 55.000 0.00 0.00 0.00 4.02
2737 3053 2.002586 GTACGTACTCGCTGGACTGTA 58.997 52.381 18.47 0.00 41.18 2.74
2824 3144 5.399013 CACATTATACCACGCTATCATCGA 58.601 41.667 0.00 0.00 0.00 3.59
2825 3145 4.031765 GCACATTATACCACGCTATCATCG 59.968 45.833 0.00 0.00 0.00 3.84
2826 3146 4.031765 CGCACATTATACCACGCTATCATC 59.968 45.833 0.00 0.00 0.00 2.92
2827 3147 3.926527 CGCACATTATACCACGCTATCAT 59.073 43.478 0.00 0.00 0.00 2.45
2868 3188 2.360852 CCCCTGCAGTTGGCTCAG 60.361 66.667 13.81 0.00 45.15 3.35
2878 3206 1.202927 CCTCTTGACTTTTCCCCTGCA 60.203 52.381 0.00 0.00 0.00 4.41
2925 3253 4.894252 AGTCCCTGATAGGTACCTAACA 57.106 45.455 25.44 25.44 31.93 2.41
2934 3262 7.621796 ACAAACTAAAACTAGTCCCTGATAGG 58.378 38.462 0.00 0.00 34.30 2.57
2967 3302 1.454847 GTTTGTGCCACCCCTGTCA 60.455 57.895 0.00 0.00 0.00 3.58
2989 3324 1.481019 CGATCGCTGCAGAGCTTCAG 61.481 60.000 20.43 7.59 43.77 3.02
3043 3685 6.847956 TTTGTTTTTGCGAGCTAGTACTAA 57.152 33.333 3.76 0.00 0.00 2.24
3044 3686 6.847956 TTTTGTTTTTGCGAGCTAGTACTA 57.152 33.333 1.89 1.89 0.00 1.82
3045 3687 5.744666 TTTTGTTTTTGCGAGCTAGTACT 57.255 34.783 0.00 0.00 0.00 2.73
3092 3803 3.667960 GCAGTTCAAGCACCGATTTGTAG 60.668 47.826 0.00 0.00 0.00 2.74
3123 3834 6.898912 TTGTTGAGATCTTCGATCATCTTG 57.101 37.500 0.00 0.00 29.01 3.02
3179 3891 9.973246 CAGTTGTACACATACATACTTCAATTC 57.027 33.333 0.00 0.00 41.02 2.17
3215 3927 5.487433 TGAACATACTGTCCAGTACAATGG 58.513 41.667 9.22 0.00 45.61 3.16
3288 4204 1.596934 CTTCCTAGCCGTGCTCCAA 59.403 57.895 1.46 0.00 40.44 3.53
3370 4290 2.097825 GCTCCACCGTACTAGAAAGGA 58.902 52.381 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.