Multiple sequence alignment - TraesCS4D01G046800

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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 TraesCS4D01G046800 chr4D 100.000 5494 0 0 1 5494 22033672 22039165 0.000000e+00 10146
1 TraesCS4D01G046800 chr4D 89.446 379 17 8 132 487 452805840 452806218 1.800000e-124 457
2 TraesCS4D01G046800 chr4B 92.892 5065 221 51 486 5492 34051024 34056007 0.000000e+00 7230
3 TraesCS4D01G046800 chr4B 91.919 99 5 3 34 131 34050926 34051022 9.600000e-28 135
4 TraesCS4D01G046800 chr4A 96.998 3598 81 10 1553 5130 579850956 579847366 0.000000e+00 6021
5 TraesCS4D01G046800 chr4A 92.118 1053 56 10 486 1524 579851992 579850953 0.000000e+00 1459
6 TraesCS4D01G046800 chr4A 94.578 166 9 0 5138 5303 579847277 579847112 1.960000e-64 257
7 TraesCS4D01G046800 chr4A 92.593 135 6 2 1 131 579852128 579851994 2.020000e-44 191
8 TraesCS4D01G046800 chr4A 92.683 123 4 1 5377 5494 579847113 579846991 7.320000e-39 172
9 TraesCS4D01G046800 chr6B 85.570 596 44 18 656 1241 542942404 542942967 2.200000e-163 586
10 TraesCS4D01G046800 chr6A 84.992 593 52 17 656 1241 265784605 265784043 7.990000e-158 568
11 TraesCS4D01G046800 chr7D 82.019 723 53 37 532 1241 20342471 20343129 1.350000e-150 544
12 TraesCS4D01G046800 chr7D 88.770 374 17 11 131 487 18920332 18920697 8.450000e-118 435
13 TraesCS4D01G046800 chr7D 88.564 376 18 13 131 482 136187315 136187689 3.040000e-117 433
14 TraesCS4D01G046800 chr7D 87.328 363 39 7 132 487 95128861 95128499 5.120000e-110 409
15 TraesCS4D01G046800 chr7D 89.524 315 6 9 200 487 13078269 13077955 1.870000e-99 374
16 TraesCS4D01G046800 chr5D 75.515 1164 250 26 3346 4489 355204086 355205234 6.260000e-149 538
17 TraesCS4D01G046800 chr5D 93.243 370 12 7 131 487 422434790 422435159 2.910000e-147 532
18 TraesCS4D01G046800 chr5B 75.872 1090 226 26 3346 4418 419998889 419999958 6.310000e-144 521
19 TraesCS4D01G046800 chr5A 75.780 1090 233 23 3346 4418 457436268 457437343 6.310000e-144 521
20 TraesCS4D01G046800 chr5A 86.667 375 29 12 132 487 311157556 311157184 3.990000e-106 396
21 TraesCS4D01G046800 chr5A 87.838 148 14 4 1098 1241 162034292 162034145 2.630000e-38 171
22 TraesCS4D01G046800 chr5A 85.484 124 10 2 733 854 162034409 162034292 7.470000e-24 122
23 TraesCS4D01G046800 chr3D 90.789 380 11 11 132 487 48279113 48278734 2.300000e-133 486
24 TraesCS4D01G046800 chr3D 88.281 384 17 7 132 487 143138779 143138396 8.450000e-118 435
25 TraesCS4D01G046800 chr3D 85.786 401 12 9 132 487 299540598 299540198 3.110000e-102 383
26 TraesCS4D01G046800 chr1D 87.918 389 13 10 132 487 332409009 332408622 1.410000e-115 427
27 TraesCS4D01G046800 chr1D 85.749 407 8 9 131 487 42814751 42814345 8.630000e-103 385
28 TraesCS4D01G046800 chr7A 85.360 403 15 12 129 487 690024288 690023886 1.440000e-100 377
29 TraesCS4D01G046800 chr2B 81.500 400 27 14 132 487 28373901 28373505 9.010000e-73 285
30 TraesCS4D01G046800 chr3A 87.310 197 17 5 656 850 427382136 427381946 9.270000e-53 219
31 TraesCS4D01G046800 chr3A 88.889 153 11 3 1095 1241 427381946 427381794 3.380000e-42 183


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 TraesCS4D01G046800 chr4D 22033672 22039165 5493 False 10146.0 10146 100.0000 1 5494 1 chr4D.!!$F1 5493
1 TraesCS4D01G046800 chr4B 34050926 34056007 5081 False 3682.5 7230 92.4055 34 5492 2 chr4B.!!$F1 5458
2 TraesCS4D01G046800 chr4A 579846991 579852128 5137 True 1620.0 6021 93.7940 1 5494 5 chr4A.!!$R1 5493
3 TraesCS4D01G046800 chr6B 542942404 542942967 563 False 586.0 586 85.5700 656 1241 1 chr6B.!!$F1 585
4 TraesCS4D01G046800 chr6A 265784043 265784605 562 True 568.0 568 84.9920 656 1241 1 chr6A.!!$R1 585
5 TraesCS4D01G046800 chr7D 20342471 20343129 658 False 544.0 544 82.0190 532 1241 1 chr7D.!!$F2 709
6 TraesCS4D01G046800 chr5D 355204086 355205234 1148 False 538.0 538 75.5150 3346 4489 1 chr5D.!!$F1 1143
7 TraesCS4D01G046800 chr5B 419998889 419999958 1069 False 521.0 521 75.8720 3346 4418 1 chr5B.!!$F1 1072
8 TraesCS4D01G046800 chr5A 457436268 457437343 1075 False 521.0 521 75.7800 3346 4418 1 chr5A.!!$F1 1072

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
482 488 0.036732 ATTTGAGCTCGGGTGCAGAA 59.963 50.0 9.64 0.0 34.99 3.02 F
483 489 0.179032 TTTGAGCTCGGGTGCAGAAA 60.179 50.0 9.64 0.0 34.99 2.52 F
1711 1765 0.336048 AATGATGGTCAGGTTGGGGG 59.664 55.0 0.00 0.0 0.00 5.40 F
1726 1780 1.049289 GGGGGCTCGTCTTATCCAGT 61.049 60.0 0.00 0.0 0.00 4.00 F
3764 3837 0.613853 CCTTCCCCCAGTACGAGACA 60.614 60.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1633 1.211743 GAAAGCAAACCAGCAGCAAC 58.788 50.000 0.00 0.00 36.85 4.17 R
2187 2248 1.276622 AACATACTGTCCTTCCCGCT 58.723 50.000 0.00 0.00 0.00 5.52 R
3315 3385 3.176552 ACTGAAGCGATTCTCATCCAG 57.823 47.619 15.31 5.51 0.00 3.86 R
3795 3868 6.629128 CCATACATGTTTGTAGGCAATTGAA 58.371 36.000 10.34 0.00 41.49 2.69 R
5235 5423 1.281867 TGGGCCATCTACAAGAACAGG 59.718 52.381 0.00 0.00 0.00 4.00 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
83 89 0.037975 GCAATGGGCCAGTTCAGTTG 60.038 55.000 13.78 11.69 36.11 3.16
98 104 2.041620 TCAGTTGAGGCCCAGCTAAAAT 59.958 45.455 0.00 0.00 34.39 1.82
131 137 0.674534 ACAAGTGGAGTGGACTCGTC 59.325 55.000 0.74 0.00 43.76 4.20
132 138 0.387367 CAAGTGGAGTGGACTCGTCG 60.387 60.000 0.74 0.00 43.76 5.12
133 139 0.536687 AAGTGGAGTGGACTCGTCGA 60.537 55.000 0.00 0.00 43.76 4.20
134 140 0.536687 AGTGGAGTGGACTCGTCGAA 60.537 55.000 0.00 0.00 43.76 3.71
135 141 0.313043 GTGGAGTGGACTCGTCGAAA 59.687 55.000 0.00 0.00 43.76 3.46
136 142 0.596577 TGGAGTGGACTCGTCGAAAG 59.403 55.000 0.00 0.00 43.76 2.62
137 143 0.597072 GGAGTGGACTCGTCGAAAGT 59.403 55.000 1.53 1.53 43.76 2.66
138 144 1.666311 GGAGTGGACTCGTCGAAAGTG 60.666 57.143 6.45 0.00 43.76 3.16
139 145 0.318784 AGTGGACTCGTCGAAAGTGC 60.319 55.000 12.15 12.15 35.82 4.40
140 146 1.006571 TGGACTCGTCGAAAGTGCC 60.007 57.895 15.21 11.85 34.50 5.01
141 147 1.289380 GGACTCGTCGAAAGTGCCT 59.711 57.895 6.45 0.00 0.00 4.75
142 148 0.319641 GGACTCGTCGAAAGTGCCTT 60.320 55.000 6.45 0.00 0.00 4.35
143 149 1.499049 GACTCGTCGAAAGTGCCTTT 58.501 50.000 6.45 0.46 36.29 3.11
144 150 1.456165 GACTCGTCGAAAGTGCCTTTC 59.544 52.381 14.28 14.28 44.29 2.62
145 151 1.068741 ACTCGTCGAAAGTGCCTTTCT 59.931 47.619 19.11 3.80 45.19 2.52
146 152 1.457303 CTCGTCGAAAGTGCCTTTCTG 59.543 52.381 19.11 14.44 45.19 3.02
147 153 0.110644 CGTCGAAAGTGCCTTTCTGC 60.111 55.000 19.11 12.98 45.19 4.26
148 154 1.230324 GTCGAAAGTGCCTTTCTGCT 58.770 50.000 19.11 0.00 45.19 4.24
149 155 1.195674 GTCGAAAGTGCCTTTCTGCTC 59.804 52.381 19.11 8.24 45.19 4.26
150 156 0.519077 CGAAAGTGCCTTTCTGCTCC 59.481 55.000 19.11 1.19 45.19 4.70
151 157 0.884514 GAAAGTGCCTTTCTGCTCCC 59.115 55.000 16.08 0.00 44.33 4.30
152 158 0.890996 AAAGTGCCTTTCTGCTCCCG 60.891 55.000 0.00 0.00 0.00 5.14
153 159 1.768684 AAGTGCCTTTCTGCTCCCGA 61.769 55.000 0.00 0.00 0.00 5.14
154 160 1.743252 GTGCCTTTCTGCTCCCGAG 60.743 63.158 0.00 0.00 0.00 4.63
175 181 2.416747 CTCATTTGAGCTCGGTGAACA 58.583 47.619 9.64 0.00 35.13 3.18
176 182 2.414481 CTCATTTGAGCTCGGTGAACAG 59.586 50.000 9.64 0.00 35.13 3.16
177 183 2.146342 CATTTGAGCTCGGTGAACAGT 58.854 47.619 9.64 0.00 0.00 3.55
178 184 3.006430 TCATTTGAGCTCGGTGAACAGTA 59.994 43.478 9.64 0.00 0.00 2.74
179 185 3.462483 TTTGAGCTCGGTGAACAGTAA 57.538 42.857 9.64 0.00 0.00 2.24
180 186 3.462483 TTGAGCTCGGTGAACAGTAAA 57.538 42.857 9.64 0.00 0.00 2.01
181 187 3.462483 TGAGCTCGGTGAACAGTAAAA 57.538 42.857 9.64 0.00 0.00 1.52
182 188 4.002906 TGAGCTCGGTGAACAGTAAAAT 57.997 40.909 9.64 0.00 0.00 1.82
183 189 3.994392 TGAGCTCGGTGAACAGTAAAATC 59.006 43.478 9.64 0.00 0.00 2.17
184 190 2.993899 AGCTCGGTGAACAGTAAAATCG 59.006 45.455 0.00 0.00 0.00 3.34
185 191 2.991190 GCTCGGTGAACAGTAAAATCGA 59.009 45.455 0.00 0.00 0.00 3.59
186 192 3.430895 GCTCGGTGAACAGTAAAATCGAA 59.569 43.478 0.00 0.00 0.00 3.71
187 193 4.084223 GCTCGGTGAACAGTAAAATCGAAA 60.084 41.667 0.00 0.00 0.00 3.46
188 194 5.559417 GCTCGGTGAACAGTAAAATCGAAAA 60.559 40.000 0.00 0.00 0.00 2.29
189 195 6.360844 TCGGTGAACAGTAAAATCGAAAAA 57.639 33.333 0.00 0.00 0.00 1.94
225 231 9.487790 TTTTTGAGAGAAACATTGACAAAAGTT 57.512 25.926 0.00 0.00 37.18 2.66
226 232 9.487790 TTTTGAGAGAAACATTGACAAAAGTTT 57.512 25.926 17.09 17.09 39.28 2.66
227 233 9.487790 TTTGAGAGAAACATTGACAAAAGTTTT 57.512 25.926 17.76 0.00 37.33 2.43
233 239 8.655970 AGAAACATTGACAAAAGTTTTAAGTGC 58.344 29.630 17.76 8.51 37.33 4.40
234 240 6.902224 ACATTGACAAAAGTTTTAAGTGCC 57.098 33.333 0.00 0.00 0.00 5.01
235 241 6.639563 ACATTGACAAAAGTTTTAAGTGCCT 58.360 32.000 0.00 0.00 0.00 4.75
236 242 6.534793 ACATTGACAAAAGTTTTAAGTGCCTG 59.465 34.615 0.00 0.00 0.00 4.85
237 243 5.652994 TGACAAAAGTTTTAAGTGCCTGT 57.347 34.783 0.00 0.00 0.00 4.00
238 244 6.761099 TGACAAAAGTTTTAAGTGCCTGTA 57.239 33.333 0.00 0.00 0.00 2.74
239 245 7.159322 TGACAAAAGTTTTAAGTGCCTGTAA 57.841 32.000 0.00 0.00 0.00 2.41
240 246 7.603651 TGACAAAAGTTTTAAGTGCCTGTAAA 58.396 30.769 0.00 0.00 0.00 2.01
241 247 8.088981 TGACAAAAGTTTTAAGTGCCTGTAAAA 58.911 29.630 0.00 0.00 0.00 1.52
242 248 8.834749 ACAAAAGTTTTAAGTGCCTGTAAAAA 57.165 26.923 0.00 0.00 32.52 1.94
243 249 9.443323 ACAAAAGTTTTAAGTGCCTGTAAAAAT 57.557 25.926 0.00 0.00 32.52 1.82
246 252 9.660180 AAAGTTTTAAGTGCCTGTAAAAATTCA 57.340 25.926 8.18 0.00 36.82 2.57
247 253 9.830975 AAGTTTTAAGTGCCTGTAAAAATTCAT 57.169 25.926 0.00 0.00 34.26 2.57
248 254 9.476202 AGTTTTAAGTGCCTGTAAAAATTCATC 57.524 29.630 0.00 0.00 32.52 2.92
249 255 9.255304 GTTTTAAGTGCCTGTAAAAATTCATCA 57.745 29.630 0.00 0.00 32.52 3.07
250 256 9.995003 TTTTAAGTGCCTGTAAAAATTCATCAT 57.005 25.926 0.00 0.00 0.00 2.45
251 257 8.984891 TTAAGTGCCTGTAAAAATTCATCATG 57.015 30.769 0.00 0.00 0.00 3.07
252 258 6.839124 AGTGCCTGTAAAAATTCATCATGA 57.161 33.333 0.00 0.00 0.00 3.07
253 259 7.230849 AGTGCCTGTAAAAATTCATCATGAA 57.769 32.000 1.59 1.59 41.09 2.57
254 260 7.669427 AGTGCCTGTAAAAATTCATCATGAAA 58.331 30.769 3.63 0.00 40.12 2.69
255 261 8.316214 AGTGCCTGTAAAAATTCATCATGAAAT 58.684 29.630 3.63 0.00 40.12 2.17
256 262 8.598075 GTGCCTGTAAAAATTCATCATGAAATC 58.402 33.333 3.63 0.00 40.12 2.17
257 263 8.312564 TGCCTGTAAAAATTCATCATGAAATCA 58.687 29.630 3.63 0.00 40.12 2.57
258 264 8.598075 GCCTGTAAAAATTCATCATGAAATCAC 58.402 33.333 3.63 0.00 40.12 3.06
259 265 8.800972 CCTGTAAAAATTCATCATGAAATCACG 58.199 33.333 3.63 0.00 40.12 4.35
260 266 9.345517 CTGTAAAAATTCATCATGAAATCACGT 57.654 29.630 3.63 0.00 40.12 4.49
261 267 9.689976 TGTAAAAATTCATCATGAAATCACGTT 57.310 25.926 3.63 0.00 40.12 3.99
263 269 7.816945 AAAATTCATCATGAAATCACGTTCC 57.183 32.000 3.63 0.00 40.12 3.62
264 270 6.764308 AATTCATCATGAAATCACGTTCCT 57.236 33.333 3.63 0.00 40.12 3.36
265 271 5.550232 TTCATCATGAAATCACGTTCCTG 57.450 39.130 0.00 0.00 32.71 3.86
266 272 4.578871 TCATCATGAAATCACGTTCCTGT 58.421 39.130 0.00 0.00 0.00 4.00
267 273 5.729510 TCATCATGAAATCACGTTCCTGTA 58.270 37.500 0.00 0.00 0.00 2.74
268 274 6.169800 TCATCATGAAATCACGTTCCTGTAA 58.830 36.000 0.00 0.00 0.00 2.41
269 275 6.313658 TCATCATGAAATCACGTTCCTGTAAG 59.686 38.462 0.00 0.00 0.00 2.34
270 276 5.789521 TCATGAAATCACGTTCCTGTAAGA 58.210 37.500 0.00 0.00 34.07 2.10
271 277 5.637810 TCATGAAATCACGTTCCTGTAAGAC 59.362 40.000 0.00 0.00 34.07 3.01
272 278 3.985279 TGAAATCACGTTCCTGTAAGACG 59.015 43.478 0.00 0.00 42.13 4.18
275 281 3.879912 ACGTTCCTGTAAGACGTGG 57.120 52.632 0.00 0.00 46.86 4.94
276 282 0.319297 ACGTTCCTGTAAGACGTGGC 60.319 55.000 0.00 0.00 46.86 5.01
277 283 0.319211 CGTTCCTGTAAGACGTGGCA 60.319 55.000 0.00 0.00 34.07 4.92
278 284 1.870580 CGTTCCTGTAAGACGTGGCAA 60.871 52.381 0.00 0.00 34.07 4.52
279 285 2.215196 GTTCCTGTAAGACGTGGCAAA 58.785 47.619 0.00 0.00 34.07 3.68
280 286 2.614983 GTTCCTGTAAGACGTGGCAAAA 59.385 45.455 0.00 0.00 34.07 2.44
281 287 2.920524 TCCTGTAAGACGTGGCAAAAA 58.079 42.857 0.00 0.00 34.07 1.94
305 311 8.898983 AAAAACAAATTCAGTGCTTCAAAATG 57.101 26.923 0.00 0.00 0.00 2.32
306 312 5.662211 ACAAATTCAGTGCTTCAAAATGC 57.338 34.783 0.00 0.00 0.00 3.56
307 313 5.362263 ACAAATTCAGTGCTTCAAAATGCT 58.638 33.333 0.00 0.00 0.00 3.79
308 314 5.818857 ACAAATTCAGTGCTTCAAAATGCTT 59.181 32.000 0.00 0.00 0.00 3.91
309 315 6.316890 ACAAATTCAGTGCTTCAAAATGCTTT 59.683 30.769 0.00 0.00 0.00 3.51
310 316 6.930667 AATTCAGTGCTTCAAAATGCTTTT 57.069 29.167 0.00 0.00 0.00 2.27
326 332 8.491331 AAATGCTTTTGAAAGTAGCTTTTTCA 57.509 26.923 17.30 17.30 41.40 2.69
327 333 7.704789 ATGCTTTTGAAAGTAGCTTTTTCAG 57.295 32.000 19.21 12.77 43.22 3.02
328 334 6.862209 TGCTTTTGAAAGTAGCTTTTTCAGA 58.138 32.000 19.21 15.01 43.22 3.27
329 335 6.974622 TGCTTTTGAAAGTAGCTTTTTCAGAG 59.025 34.615 19.21 19.75 43.22 3.35
330 336 6.975197 GCTTTTGAAAGTAGCTTTTTCAGAGT 59.025 34.615 19.21 0.00 43.22 3.24
331 337 8.129211 GCTTTTGAAAGTAGCTTTTTCAGAGTA 58.871 33.333 19.21 8.08 43.22 2.59
332 338 9.439537 CTTTTGAAAGTAGCTTTTTCAGAGTAC 57.560 33.333 19.21 0.00 43.22 2.73
333 339 8.732746 TTTGAAAGTAGCTTTTTCAGAGTACT 57.267 30.769 19.21 0.00 43.22 2.73
334 340 7.715265 TGAAAGTAGCTTTTTCAGAGTACTG 57.285 36.000 17.30 0.00 39.05 2.74
335 341 7.272978 TGAAAGTAGCTTTTTCAGAGTACTGT 58.727 34.615 17.30 0.00 39.05 3.55
336 342 7.769044 TGAAAGTAGCTTTTTCAGAGTACTGTT 59.231 33.333 17.30 0.00 39.05 3.16
337 343 8.507524 AAAGTAGCTTTTTCAGAGTACTGTTT 57.492 30.769 0.00 0.00 36.62 2.83
338 344 8.507524 AAGTAGCTTTTTCAGAGTACTGTTTT 57.492 30.769 0.00 0.00 43.81 2.43
339 345 8.507524 AGTAGCTTTTTCAGAGTACTGTTTTT 57.492 30.769 0.00 0.00 43.81 1.94
340 346 8.398665 AGTAGCTTTTTCAGAGTACTGTTTTTG 58.601 33.333 0.00 0.00 43.81 2.44
341 347 7.158099 AGCTTTTTCAGAGTACTGTTTTTGT 57.842 32.000 0.00 0.00 43.81 2.83
342 348 7.602753 AGCTTTTTCAGAGTACTGTTTTTGTT 58.397 30.769 0.00 0.00 43.81 2.83
343 349 8.088365 AGCTTTTTCAGAGTACTGTTTTTGTTT 58.912 29.630 0.00 0.00 43.81 2.83
344 350 8.708742 GCTTTTTCAGAGTACTGTTTTTGTTTT 58.291 29.630 0.00 0.00 43.81 2.43
364 370 4.620589 TTTTTGCCATGTGGAATGTGAT 57.379 36.364 2.55 0.00 37.39 3.06
365 371 4.620589 TTTTGCCATGTGGAATGTGATT 57.379 36.364 2.55 0.00 37.39 2.57
366 372 4.620589 TTTGCCATGTGGAATGTGATTT 57.379 36.364 2.55 0.00 37.39 2.17
367 373 3.872511 TGCCATGTGGAATGTGATTTC 57.127 42.857 2.55 0.00 37.39 2.17
368 374 3.163467 TGCCATGTGGAATGTGATTTCA 58.837 40.909 2.55 0.00 37.39 2.69
369 375 3.770388 TGCCATGTGGAATGTGATTTCAT 59.230 39.130 2.55 0.00 37.39 2.57
370 376 4.116961 GCCATGTGGAATGTGATTTCATG 58.883 43.478 2.55 0.00 37.39 3.07
371 377 4.142116 GCCATGTGGAATGTGATTTCATGA 60.142 41.667 2.55 0.00 37.39 3.07
372 378 5.345702 CCATGTGGAATGTGATTTCATGAC 58.654 41.667 0.00 0.00 37.39 3.06
373 379 4.683501 TGTGGAATGTGATTTCATGACG 57.316 40.909 0.00 0.00 28.88 4.35
374 380 4.322567 TGTGGAATGTGATTTCATGACGA 58.677 39.130 0.00 0.00 28.88 4.20
375 381 4.759183 TGTGGAATGTGATTTCATGACGAA 59.241 37.500 0.00 0.00 28.88 3.85
376 382 5.415389 TGTGGAATGTGATTTCATGACGAAT 59.585 36.000 0.00 0.00 32.32 3.34
377 383 6.072008 TGTGGAATGTGATTTCATGACGAATT 60.072 34.615 0.00 0.00 32.32 2.17
378 384 6.808212 GTGGAATGTGATTTCATGACGAATTT 59.192 34.615 0.00 0.00 32.32 1.82
379 385 7.329226 GTGGAATGTGATTTCATGACGAATTTT 59.671 33.333 0.00 0.00 32.32 1.82
380 386 7.871973 TGGAATGTGATTTCATGACGAATTTTT 59.128 29.630 0.00 0.00 32.32 1.94
381 387 8.164153 GGAATGTGATTTCATGACGAATTTTTG 58.836 33.333 0.00 0.00 32.32 2.44
382 388 6.450845 TGTGATTTCATGACGAATTTTTGC 57.549 33.333 0.00 0.00 32.32 3.68
383 389 5.981915 TGTGATTTCATGACGAATTTTTGCA 59.018 32.000 0.00 0.00 32.32 4.08
384 390 6.478016 TGTGATTTCATGACGAATTTTTGCAA 59.522 30.769 0.00 0.00 32.32 4.08
385 391 7.005380 GTGATTTCATGACGAATTTTTGCAAG 58.995 34.615 0.00 0.00 32.32 4.01
386 392 4.970472 TTCATGACGAATTTTTGCAAGC 57.030 36.364 0.00 0.00 0.00 4.01
387 393 3.974912 TCATGACGAATTTTTGCAAGCA 58.025 36.364 0.00 0.00 0.00 3.91
388 394 3.735240 TCATGACGAATTTTTGCAAGCAC 59.265 39.130 0.00 0.00 0.00 4.40
389 395 3.435105 TGACGAATTTTTGCAAGCACT 57.565 38.095 0.00 0.00 0.00 4.40
390 396 3.779759 TGACGAATTTTTGCAAGCACTT 58.220 36.364 0.00 0.00 0.00 3.16
391 397 4.926244 TGACGAATTTTTGCAAGCACTTA 58.074 34.783 0.00 0.00 0.00 2.24
392 398 5.344066 TGACGAATTTTTGCAAGCACTTAA 58.656 33.333 0.00 0.00 0.00 1.85
393 399 5.807520 TGACGAATTTTTGCAAGCACTTAAA 59.192 32.000 0.00 0.00 0.00 1.52
394 400 6.311445 TGACGAATTTTTGCAAGCACTTAAAA 59.689 30.769 0.00 0.00 0.00 1.52
395 401 6.474364 ACGAATTTTTGCAAGCACTTAAAAC 58.526 32.000 0.00 0.00 0.00 2.43
396 402 6.312672 ACGAATTTTTGCAAGCACTTAAAACT 59.687 30.769 0.00 0.00 0.00 2.66
397 403 7.148490 ACGAATTTTTGCAAGCACTTAAAACTT 60.148 29.630 0.00 0.47 0.00 2.66
398 404 7.691877 CGAATTTTTGCAAGCACTTAAAACTTT 59.308 29.630 0.00 0.00 0.00 2.66
399 405 9.340695 GAATTTTTGCAAGCACTTAAAACTTTT 57.659 25.926 0.00 0.00 0.00 2.27
400 406 8.672214 ATTTTTGCAAGCACTTAAAACTTTTG 57.328 26.923 0.00 0.00 0.00 2.44
401 407 6.793492 TTTGCAAGCACTTAAAACTTTTGT 57.207 29.167 0.00 0.00 0.00 2.83
402 408 6.401955 TTGCAAGCACTTAAAACTTTTGTC 57.598 33.333 0.00 0.00 0.00 3.18
403 409 5.473931 TGCAAGCACTTAAAACTTTTGTCA 58.526 33.333 0.00 0.00 0.00 3.58
404 410 5.928839 TGCAAGCACTTAAAACTTTTGTCAA 59.071 32.000 0.00 0.00 0.00 3.18
405 411 6.593382 TGCAAGCACTTAAAACTTTTGTCAAT 59.407 30.769 0.00 0.00 0.00 2.57
406 412 6.901357 GCAAGCACTTAAAACTTTTGTCAATG 59.099 34.615 0.00 0.00 0.00 2.82
407 413 7.412891 GCAAGCACTTAAAACTTTTGTCAATGT 60.413 33.333 0.00 0.00 0.00 2.71
408 414 8.442384 CAAGCACTTAAAACTTTTGTCAATGTT 58.558 29.630 0.00 0.00 32.90 2.71
409 415 8.546597 AGCACTTAAAACTTTTGTCAATGTTT 57.453 26.923 9.87 9.87 40.32 2.83
410 416 8.655970 AGCACTTAAAACTTTTGTCAATGTTTC 58.344 29.630 13.86 5.09 38.61 2.78
411 417 8.655970 GCACTTAAAACTTTTGTCAATGTTTCT 58.344 29.630 13.86 9.23 38.61 2.52
458 464 6.452494 TTTTTGATTTTACTGTTCACCCGA 57.548 33.333 0.00 0.00 0.00 5.14
459 465 5.682943 TTTGATTTTACTGTTCACCCGAG 57.317 39.130 0.00 0.00 0.00 4.63
460 466 3.071479 TGATTTTACTGTTCACCCGAGC 58.929 45.455 0.00 0.00 0.00 5.03
461 467 2.922740 TTTTACTGTTCACCCGAGCT 57.077 45.000 0.00 0.00 0.00 4.09
462 468 2.450609 TTTACTGTTCACCCGAGCTC 57.549 50.000 2.73 2.73 0.00 4.09
463 469 1.334160 TTACTGTTCACCCGAGCTCA 58.666 50.000 15.40 0.00 0.00 4.26
464 470 1.557099 TACTGTTCACCCGAGCTCAT 58.443 50.000 15.40 0.00 0.00 2.90
465 471 0.687354 ACTGTTCACCCGAGCTCATT 59.313 50.000 15.40 0.00 0.00 2.57
466 472 1.072331 ACTGTTCACCCGAGCTCATTT 59.928 47.619 15.40 0.00 0.00 2.32
467 473 1.466167 CTGTTCACCCGAGCTCATTTG 59.534 52.381 15.40 6.81 0.00 2.32
468 474 1.071542 TGTTCACCCGAGCTCATTTGA 59.928 47.619 15.40 9.18 0.00 2.69
469 475 1.734465 GTTCACCCGAGCTCATTTGAG 59.266 52.381 15.40 3.13 44.75 3.02
478 484 2.093216 CTCATTTGAGCTCGGGTGC 58.907 57.895 9.64 0.00 35.13 5.01
479 485 0.674581 CTCATTTGAGCTCGGGTGCA 60.675 55.000 9.64 0.00 35.13 4.57
480 486 0.674581 TCATTTGAGCTCGGGTGCAG 60.675 55.000 9.64 0.00 34.99 4.41
481 487 0.674581 CATTTGAGCTCGGGTGCAGA 60.675 55.000 9.64 0.00 34.99 4.26
482 488 0.036732 ATTTGAGCTCGGGTGCAGAA 59.963 50.000 9.64 0.00 34.99 3.02
483 489 0.179032 TTTGAGCTCGGGTGCAGAAA 60.179 50.000 9.64 0.00 34.99 2.52
484 490 0.884704 TTGAGCTCGGGTGCAGAAAC 60.885 55.000 9.64 0.00 34.99 2.78
803 830 2.358195 GCTTCCTCCCTTCTCTCTCTCT 60.358 54.545 0.00 0.00 0.00 3.10
804 831 3.555966 CTTCCTCCCTTCTCTCTCTCTC 58.444 54.545 0.00 0.00 0.00 3.20
805 832 2.858644 TCCTCCCTTCTCTCTCTCTCT 58.141 52.381 0.00 0.00 0.00 3.10
806 833 2.777692 TCCTCCCTTCTCTCTCTCTCTC 59.222 54.545 0.00 0.00 0.00 3.20
820 847 2.033602 TCTCTCGTGGCCGTCTGA 59.966 61.111 0.00 0.00 35.01 3.27
926 953 6.466812 CCCTAAAATTGAATGCCTTTTCTGT 58.533 36.000 0.00 0.00 0.00 3.41
949 976 1.081092 CAGGGACTCAGGGAGGGAA 59.919 63.158 0.00 0.00 34.60 3.97
1015 1042 2.156098 GAACAATGGCGGTGGTAAAGA 58.844 47.619 0.00 0.00 0.00 2.52
1030 1057 3.309265 GGTAAAGACCTCCTCTCCTCTCA 60.309 52.174 0.00 0.00 43.16 3.27
1040 1067 2.819608 CCTCTCCTCTCATCGATTCCTC 59.180 54.545 0.00 0.00 0.00 3.71
1067 1094 5.451908 TGTTCTGCATGAAACGATTCTTTC 58.548 37.500 6.98 0.00 36.30 2.62
1093 1120 2.103340 GCCGAGAAGAGACCGAGC 59.897 66.667 0.00 0.00 0.00 5.03
1284 1331 1.369625 CTACATGCCGAGGTTTCCAC 58.630 55.000 0.00 0.00 0.00 4.02
1327 1375 8.352942 CACTTAGCAGTCTTTAATTTGAAACCT 58.647 33.333 0.00 0.00 0.00 3.50
1350 1400 2.032549 GTGACGATGCATGCTATGGTTC 60.033 50.000 20.33 8.26 0.00 3.62
1399 1449 1.069227 GTTTTGACATCTGTGGGACGC 60.069 52.381 0.00 0.00 40.62 5.19
1450 1504 5.803461 GGCAGTTTTCTTTCTGTTTAAACGT 59.197 36.000 13.45 0.00 34.72 3.99
1532 1586 0.523072 GATGTCGCATGGCTGTTGTT 59.477 50.000 0.00 0.00 0.00 2.83
1534 1588 1.730547 GTCGCATGGCTGTTGTTGC 60.731 57.895 0.00 0.00 0.00 4.17
1565 1619 2.183300 GTGTCATGCCCTCGCGTA 59.817 61.111 5.77 0.00 38.08 4.42
1579 1633 2.784380 CTCGCGTAATTTCTCTTCTCCG 59.216 50.000 5.77 0.00 0.00 4.63
1586 1640 1.512926 TTTCTCTTCTCCGTTGCTGC 58.487 50.000 0.00 0.00 0.00 5.25
1646 1700 4.389992 GTGGTGTCACTCATGTTACAGATG 59.610 45.833 2.35 0.00 40.58 2.90
1711 1765 0.336048 AATGATGGTCAGGTTGGGGG 59.664 55.000 0.00 0.00 0.00 5.40
1726 1780 1.049289 GGGGGCTCGTCTTATCCAGT 61.049 60.000 0.00 0.00 0.00 4.00
1729 1783 1.404843 GGCTCGTCTTATCCAGTCCT 58.595 55.000 0.00 0.00 0.00 3.85
1777 1831 1.741770 CGCTGGTGAGGCAGGTAAC 60.742 63.158 0.00 0.00 0.00 2.50
1899 1957 4.219944 TGTTACTGATCTAAAGGACGCTGT 59.780 41.667 0.00 0.00 0.00 4.40
2071 2132 4.431809 TGATGTTTTGCACCTTCAGTTTG 58.568 39.130 0.00 0.00 0.00 2.93
2187 2248 4.528206 TCTGAGTTGACCTCTTGCTTCATA 59.472 41.667 0.00 0.00 41.11 2.15
2437 2501 3.492337 TCAGCTTGGTAACCGGAATTTT 58.508 40.909 9.46 0.00 0.00 1.82
2870 2936 7.220683 GCATCATGTTGTACAATTACATTCACC 59.779 37.037 12.26 0.00 38.05 4.02
3764 3837 0.613853 CCTTCCCCCAGTACGAGACA 60.614 60.000 0.00 0.00 0.00 3.41
3795 3868 0.178990 GTGGGACCAAAGAAGGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
3998 4071 2.678336 GGAGTTTCTGCTTGGTTATCCG 59.322 50.000 0.00 0.00 36.30 4.18
4010 4083 2.090943 TGGTTATCCGAGGGACCATACT 60.091 50.000 8.23 0.00 37.26 2.12
4033 4106 3.074538 AGGGGAGCTAGCAAGAAAAAGAA 59.925 43.478 18.83 0.00 0.00 2.52
4349 4422 3.626930 ACAACTTGGTGGCTTTGACTTA 58.373 40.909 0.00 0.00 0.00 2.24
4466 4539 8.994429 ACTATGTTAGAATCTTGAACTCTGTG 57.006 34.615 0.00 0.00 0.00 3.66
4514 4589 6.288941 TGATGATTGCATTCCATGTTCTTT 57.711 33.333 6.16 0.00 34.11 2.52
4570 4645 4.278419 AGGTTTGGAACATCAAGTAACTGC 59.722 41.667 0.00 0.00 39.30 4.40
4715 4790 8.466086 AGAAACTTGTTTTGATCTTTGTGAAC 57.534 30.769 0.06 0.00 0.00 3.18
4724 4799 8.534778 GTTTTGATCTTTGTGAACACTGAATTC 58.465 33.333 0.00 0.00 0.00 2.17
4735 4810 6.361748 GTGAACACTGAATTCATTGCTTTCTC 59.638 38.462 21.86 15.97 38.31 2.87
4915 5018 4.029520 ACTCATGTGCTTCAGATAGAGGT 58.970 43.478 0.00 0.00 0.00 3.85
4922 5025 5.300539 TGTGCTTCAGATAGAGGTTAGCTAG 59.699 44.000 0.00 0.00 0.00 3.42
4925 5028 5.300792 GCTTCAGATAGAGGTTAGCTAGTGT 59.699 44.000 0.00 0.00 0.00 3.55
5015 5118 5.304357 CCCTTGGTTAAAGTCCATTTCTTGT 59.696 40.000 0.00 0.00 34.75 3.16
5028 5131 8.383175 AGTCCATTTCTTGTATTTGTTCTCCTA 58.617 33.333 0.00 0.00 0.00 2.94
5031 5134 7.414098 CCATTTCTTGTATTTGTTCTCCTACCG 60.414 40.741 0.00 0.00 0.00 4.02
5032 5135 5.733620 TCTTGTATTTGTTCTCCTACCGT 57.266 39.130 0.00 0.00 0.00 4.83
5130 5235 4.002906 ACAAGCTTTCGTGGAAGACATA 57.997 40.909 0.00 0.00 0.00 2.29
5131 5236 4.579869 ACAAGCTTTCGTGGAAGACATAT 58.420 39.130 0.00 0.00 0.00 1.78
5181 5369 1.545582 TGCTTAGGTGCAGATTTTGGC 59.454 47.619 0.00 0.00 38.12 4.52
5204 5392 6.636850 GGCGCTATTTTCTTACCATTTATGTG 59.363 38.462 7.64 0.00 0.00 3.21
5235 5423 3.971150 ACATCGATGTCTGCTTACTAGC 58.029 45.455 25.18 0.00 41.70 3.42
5268 5456 3.983410 AGATGGCCCAGTAACCTATCATT 59.017 43.478 0.00 0.00 0.00 2.57
5421 5614 5.415389 TCATACACCTGTCAATCAAATGTGG 59.585 40.000 0.00 0.00 0.00 4.17
5437 5630 6.430925 TCAAATGTGGTAGAAGGACAAATGAG 59.569 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.113462 AGGCCACTCCAGTCTTTTTATTTATTA 58.887 33.333 5.01 0.00 37.29 0.98
83 89 2.576615 CTGGTATTTTAGCTGGGCCTC 58.423 52.381 4.53 0.00 0.00 4.70
98 104 2.549992 CCACTTGTTGTAGCAGCTGGTA 60.550 50.000 21.35 21.35 0.00 3.25
136 142 1.743252 CTCGGGAGCAGAAAGGCAC 60.743 63.158 0.00 0.00 35.83 5.01
137 143 2.665000 CTCGGGAGCAGAAAGGCA 59.335 61.111 0.00 0.00 35.83 4.75
155 161 2.414481 CTGTTCACCGAGCTCAAATGAG 59.586 50.000 15.40 6.05 44.75 2.90
156 162 2.224281 ACTGTTCACCGAGCTCAAATGA 60.224 45.455 15.40 10.78 0.00 2.57
157 163 2.146342 ACTGTTCACCGAGCTCAAATG 58.854 47.619 15.40 8.47 0.00 2.32
158 164 2.550830 ACTGTTCACCGAGCTCAAAT 57.449 45.000 15.40 0.00 0.00 2.32
159 165 3.462483 TTACTGTTCACCGAGCTCAAA 57.538 42.857 15.40 0.00 0.00 2.69
160 166 3.462483 TTTACTGTTCACCGAGCTCAA 57.538 42.857 15.40 0.00 0.00 3.02
161 167 3.462483 TTTTACTGTTCACCGAGCTCA 57.538 42.857 15.40 0.00 0.00 4.26
162 168 3.060895 CGATTTTACTGTTCACCGAGCTC 59.939 47.826 2.73 2.73 0.00 4.09
163 169 2.993899 CGATTTTACTGTTCACCGAGCT 59.006 45.455 0.00 0.00 0.00 4.09
164 170 2.991190 TCGATTTTACTGTTCACCGAGC 59.009 45.455 0.00 0.00 0.00 5.03
165 171 5.585500 TTTCGATTTTACTGTTCACCGAG 57.415 39.130 0.00 0.00 0.00 4.63
166 172 5.987777 TTTTCGATTTTACTGTTCACCGA 57.012 34.783 0.00 0.00 0.00 4.69
199 205 9.487790 AACTTTTGTCAATGTTTCTCTCAAAAA 57.512 25.926 0.00 0.00 34.51 1.94
200 206 9.487790 AAACTTTTGTCAATGTTTCTCTCAAAA 57.512 25.926 9.87 0.00 36.13 2.44
201 207 9.487790 AAAACTTTTGTCAATGTTTCTCTCAAA 57.512 25.926 13.86 0.00 38.61 2.69
207 213 8.655970 GCACTTAAAACTTTTGTCAATGTTTCT 58.344 29.630 13.86 9.23 38.61 2.52
208 214 7.902917 GGCACTTAAAACTTTTGTCAATGTTTC 59.097 33.333 13.86 4.96 38.61 2.78
209 215 7.606073 AGGCACTTAAAACTTTTGTCAATGTTT 59.394 29.630 9.87 9.87 37.32 2.83
210 216 7.064490 CAGGCACTTAAAACTTTTGTCAATGTT 59.936 33.333 0.00 0.00 34.60 2.71
211 217 6.534793 CAGGCACTTAAAACTTTTGTCAATGT 59.465 34.615 0.00 0.00 34.60 2.71
212 218 6.534793 ACAGGCACTTAAAACTTTTGTCAATG 59.465 34.615 0.00 0.00 34.60 2.82
213 219 6.639563 ACAGGCACTTAAAACTTTTGTCAAT 58.360 32.000 0.00 0.00 34.60 2.57
214 220 6.031751 ACAGGCACTTAAAACTTTTGTCAA 57.968 33.333 0.00 0.00 34.60 3.18
215 221 5.652994 ACAGGCACTTAAAACTTTTGTCA 57.347 34.783 0.00 0.00 34.60 3.58
216 222 8.468720 TTTTACAGGCACTTAAAACTTTTGTC 57.531 30.769 0.00 0.00 34.60 3.18
217 223 8.834749 TTTTTACAGGCACTTAAAACTTTTGT 57.165 26.923 0.00 0.00 34.60 2.83
220 226 9.660180 TGAATTTTTACAGGCACTTAAAACTTT 57.340 25.926 0.00 0.00 34.60 2.66
221 227 9.830975 ATGAATTTTTACAGGCACTTAAAACTT 57.169 25.926 0.00 0.00 34.60 2.66
222 228 9.476202 GATGAATTTTTACAGGCACTTAAAACT 57.524 29.630 0.00 0.00 34.60 2.66
223 229 9.255304 TGATGAATTTTTACAGGCACTTAAAAC 57.745 29.630 0.00 0.00 34.60 2.43
224 230 9.995003 ATGATGAATTTTTACAGGCACTTAAAA 57.005 25.926 0.00 0.00 34.60 1.52
225 231 9.421806 CATGATGAATTTTTACAGGCACTTAAA 57.578 29.630 0.00 0.00 34.60 1.52
226 232 8.801299 TCATGATGAATTTTTACAGGCACTTAA 58.199 29.630 0.00 0.00 34.60 1.85
227 233 8.347004 TCATGATGAATTTTTACAGGCACTTA 57.653 30.769 0.00 0.00 34.60 2.24
228 234 7.230849 TCATGATGAATTTTTACAGGCACTT 57.769 32.000 0.00 0.00 34.60 3.16
229 235 6.839124 TCATGATGAATTTTTACAGGCACT 57.161 33.333 0.00 0.00 43.88 4.40
230 236 7.887996 TTTCATGATGAATTTTTACAGGCAC 57.112 32.000 8.90 0.00 36.11 5.01
231 237 8.312564 TGATTTCATGATGAATTTTTACAGGCA 58.687 29.630 8.90 0.00 36.11 4.75
232 238 8.598075 GTGATTTCATGATGAATTTTTACAGGC 58.402 33.333 8.90 0.00 36.11 4.85
233 239 8.800972 CGTGATTTCATGATGAATTTTTACAGG 58.199 33.333 8.90 2.65 36.11 4.00
234 240 9.345517 ACGTGATTTCATGATGAATTTTTACAG 57.654 29.630 8.90 4.46 36.11 2.74
235 241 9.689976 AACGTGATTTCATGATGAATTTTTACA 57.310 25.926 8.90 0.00 36.11 2.41
237 243 9.352784 GGAACGTGATTTCATGATGAATTTTTA 57.647 29.630 8.90 0.00 36.11 1.52
238 244 8.090214 AGGAACGTGATTTCATGATGAATTTTT 58.910 29.630 8.90 0.00 36.11 1.94
239 245 7.543172 CAGGAACGTGATTTCATGATGAATTTT 59.457 33.333 8.90 0.00 39.17 1.82
240 246 7.031372 CAGGAACGTGATTTCATGATGAATTT 58.969 34.615 8.90 0.00 39.17 1.82
241 247 6.151648 ACAGGAACGTGATTTCATGATGAATT 59.848 34.615 8.90 5.47 39.17 2.17
242 248 5.649395 ACAGGAACGTGATTTCATGATGAAT 59.351 36.000 8.90 0.00 39.17 2.57
243 249 5.003160 ACAGGAACGTGATTTCATGATGAA 58.997 37.500 3.29 3.29 39.17 2.57
244 250 4.578871 ACAGGAACGTGATTTCATGATGA 58.421 39.130 6.63 0.00 39.17 2.92
245 251 4.952262 ACAGGAACGTGATTTCATGATG 57.048 40.909 6.63 0.00 39.17 3.07
246 252 6.313905 GTCTTACAGGAACGTGATTTCATGAT 59.686 38.462 6.63 0.00 39.17 2.45
247 253 5.637810 GTCTTACAGGAACGTGATTTCATGA 59.362 40.000 6.63 0.00 39.17 3.07
248 254 5.444613 CGTCTTACAGGAACGTGATTTCATG 60.445 44.000 0.00 0.00 41.88 3.07
249 255 4.625742 CGTCTTACAGGAACGTGATTTCAT 59.374 41.667 0.00 0.00 0.00 2.57
250 256 3.985279 CGTCTTACAGGAACGTGATTTCA 59.015 43.478 0.00 0.00 0.00 2.69
251 257 3.985925 ACGTCTTACAGGAACGTGATTTC 59.014 43.478 0.00 0.00 35.63 2.17
252 258 3.986277 ACGTCTTACAGGAACGTGATTT 58.014 40.909 0.00 0.00 35.63 2.17
253 259 3.655276 ACGTCTTACAGGAACGTGATT 57.345 42.857 0.00 0.00 35.63 2.57
257 263 0.319297 GCCACGTCTTACAGGAACGT 60.319 55.000 0.00 0.00 37.53 3.99
258 264 0.319211 TGCCACGTCTTACAGGAACG 60.319 55.000 0.00 0.00 0.00 3.95
259 265 1.873698 TTGCCACGTCTTACAGGAAC 58.126 50.000 0.00 0.00 0.00 3.62
260 266 2.623878 TTTGCCACGTCTTACAGGAA 57.376 45.000 0.00 0.00 0.00 3.36
261 267 2.623878 TTTTGCCACGTCTTACAGGA 57.376 45.000 0.00 0.00 0.00 3.86
280 286 7.485595 GCATTTTGAAGCACTGAATTTGTTTTT 59.514 29.630 0.00 0.00 0.00 1.94
281 287 6.968335 GCATTTTGAAGCACTGAATTTGTTTT 59.032 30.769 0.00 0.00 0.00 2.43
282 288 6.316890 AGCATTTTGAAGCACTGAATTTGTTT 59.683 30.769 0.00 0.00 0.00 2.83
283 289 5.818857 AGCATTTTGAAGCACTGAATTTGTT 59.181 32.000 0.00 0.00 0.00 2.83
284 290 5.362263 AGCATTTTGAAGCACTGAATTTGT 58.638 33.333 0.00 0.00 0.00 2.83
285 291 5.917541 AGCATTTTGAAGCACTGAATTTG 57.082 34.783 0.00 0.00 0.00 2.32
286 292 6.930667 AAAGCATTTTGAAGCACTGAATTT 57.069 29.167 0.00 0.00 31.62 1.82
300 306 8.945057 TGAAAAAGCTACTTTCAAAAGCATTTT 58.055 25.926 17.31 8.72 44.86 1.82
301 307 8.491331 TGAAAAAGCTACTTTCAAAAGCATTT 57.509 26.923 17.31 0.00 39.28 2.32
302 308 7.981225 TCTGAAAAAGCTACTTTCAAAAGCATT 59.019 29.630 19.14 0.00 41.10 3.56
303 309 7.491682 TCTGAAAAAGCTACTTTCAAAAGCAT 58.508 30.769 19.14 0.00 41.10 3.79
304 310 6.862209 TCTGAAAAAGCTACTTTCAAAAGCA 58.138 32.000 19.14 3.07 41.10 3.91
305 311 6.975197 ACTCTGAAAAAGCTACTTTCAAAAGC 59.025 34.615 19.14 0.00 41.10 3.51
306 312 9.439537 GTACTCTGAAAAAGCTACTTTCAAAAG 57.560 33.333 19.14 19.31 41.10 2.27
307 313 9.174166 AGTACTCTGAAAAAGCTACTTTCAAAA 57.826 29.630 19.14 12.25 41.10 2.44
308 314 8.612619 CAGTACTCTGAAAAAGCTACTTTCAAA 58.387 33.333 19.14 9.92 41.10 2.69
309 315 7.769044 ACAGTACTCTGAAAAAGCTACTTTCAA 59.231 33.333 19.14 12.10 41.10 2.69
310 316 7.272978 ACAGTACTCTGAAAAAGCTACTTTCA 58.727 34.615 18.13 18.13 43.76 2.69
311 317 7.716768 ACAGTACTCTGAAAAAGCTACTTTC 57.283 36.000 12.26 12.26 43.76 2.62
312 318 8.507524 AAACAGTACTCTGAAAAAGCTACTTT 57.492 30.769 0.00 0.00 43.76 2.66
313 319 8.507524 AAAACAGTACTCTGAAAAAGCTACTT 57.492 30.769 0.00 0.00 43.76 2.24
314 320 8.398665 CAAAAACAGTACTCTGAAAAAGCTACT 58.601 33.333 0.00 0.00 43.76 2.57
315 321 8.182227 ACAAAAACAGTACTCTGAAAAAGCTAC 58.818 33.333 0.00 0.00 43.76 3.58
316 322 8.276252 ACAAAAACAGTACTCTGAAAAAGCTA 57.724 30.769 0.00 0.00 43.76 3.32
317 323 7.158099 ACAAAAACAGTACTCTGAAAAAGCT 57.842 32.000 0.00 0.00 43.76 3.74
318 324 7.812309 AACAAAAACAGTACTCTGAAAAAGC 57.188 32.000 0.00 0.00 43.76 3.51
343 349 4.620589 ATCACATTCCACATGGCAAAAA 57.379 36.364 0.00 0.00 34.44 1.94
344 350 4.620589 AATCACATTCCACATGGCAAAA 57.379 36.364 0.00 0.00 34.44 2.44
345 351 4.040095 TGAAATCACATTCCACATGGCAAA 59.960 37.500 0.00 0.00 34.44 3.68
346 352 3.577415 TGAAATCACATTCCACATGGCAA 59.423 39.130 0.00 0.00 34.44 4.52
347 353 3.163467 TGAAATCACATTCCACATGGCA 58.837 40.909 0.00 0.00 34.44 4.92
348 354 3.872511 TGAAATCACATTCCACATGGC 57.127 42.857 0.00 0.00 34.44 4.40
349 355 5.345702 GTCATGAAATCACATTCCACATGG 58.654 41.667 0.00 0.00 35.74 3.66
350 356 5.032220 CGTCATGAAATCACATTCCACATG 58.968 41.667 0.00 0.00 36.17 3.21
351 357 4.943093 TCGTCATGAAATCACATTCCACAT 59.057 37.500 0.00 0.00 0.00 3.21
352 358 4.322567 TCGTCATGAAATCACATTCCACA 58.677 39.130 0.00 0.00 0.00 4.17
353 359 4.944962 TCGTCATGAAATCACATTCCAC 57.055 40.909 0.00 0.00 0.00 4.02
354 360 6.513806 AATTCGTCATGAAATCACATTCCA 57.486 33.333 0.00 0.00 40.71 3.53
355 361 7.816945 AAAATTCGTCATGAAATCACATTCC 57.183 32.000 0.00 0.00 40.71 3.01
356 362 7.685304 GCAAAAATTCGTCATGAAATCACATTC 59.315 33.333 0.00 0.00 40.71 2.67
357 363 7.171167 TGCAAAAATTCGTCATGAAATCACATT 59.829 29.630 0.00 0.00 40.71 2.71
358 364 6.645827 TGCAAAAATTCGTCATGAAATCACAT 59.354 30.769 0.00 0.00 40.71 3.21
359 365 5.981915 TGCAAAAATTCGTCATGAAATCACA 59.018 32.000 0.00 0.00 40.71 3.58
360 366 6.450845 TGCAAAAATTCGTCATGAAATCAC 57.549 33.333 0.00 0.00 40.71 3.06
361 367 6.346758 GCTTGCAAAAATTCGTCATGAAATCA 60.347 34.615 0.00 0.00 40.71 2.57
362 368 6.011277 GCTTGCAAAAATTCGTCATGAAATC 58.989 36.000 0.00 0.00 40.71 2.17
363 369 5.466058 TGCTTGCAAAAATTCGTCATGAAAT 59.534 32.000 0.00 0.00 40.71 2.17
364 370 4.807834 TGCTTGCAAAAATTCGTCATGAAA 59.192 33.333 0.00 0.00 40.71 2.69
365 371 4.208873 GTGCTTGCAAAAATTCGTCATGAA 59.791 37.500 0.00 0.00 41.81 2.57
366 372 3.735240 GTGCTTGCAAAAATTCGTCATGA 59.265 39.130 0.00 0.00 0.00 3.07
367 373 3.737266 AGTGCTTGCAAAAATTCGTCATG 59.263 39.130 0.00 0.00 0.00 3.07
368 374 3.981211 AGTGCTTGCAAAAATTCGTCAT 58.019 36.364 0.00 0.00 0.00 3.06
369 375 3.435105 AGTGCTTGCAAAAATTCGTCA 57.565 38.095 0.00 0.00 0.00 4.35
370 376 5.881637 TTAAGTGCTTGCAAAAATTCGTC 57.118 34.783 0.00 0.00 0.00 4.20
371 377 6.312672 AGTTTTAAGTGCTTGCAAAAATTCGT 59.687 30.769 0.00 0.00 0.00 3.85
372 378 6.704819 AGTTTTAAGTGCTTGCAAAAATTCG 58.295 32.000 0.00 0.00 0.00 3.34
373 379 8.894409 AAAGTTTTAAGTGCTTGCAAAAATTC 57.106 26.923 0.00 0.00 29.83 2.17
374 380 9.127006 CAAAAGTTTTAAGTGCTTGCAAAAATT 57.873 25.926 0.00 0.00 31.70 1.82
375 381 8.296000 ACAAAAGTTTTAAGTGCTTGCAAAAAT 58.704 25.926 0.00 0.00 0.00 1.82
376 382 7.643579 ACAAAAGTTTTAAGTGCTTGCAAAAA 58.356 26.923 0.00 0.00 0.00 1.94
377 383 7.041780 TGACAAAAGTTTTAAGTGCTTGCAAAA 60.042 29.630 0.00 0.00 0.00 2.44
378 384 6.425114 TGACAAAAGTTTTAAGTGCTTGCAAA 59.575 30.769 0.00 0.00 0.00 3.68
379 385 5.928839 TGACAAAAGTTTTAAGTGCTTGCAA 59.071 32.000 0.00 0.00 0.00 4.08
380 386 5.473931 TGACAAAAGTTTTAAGTGCTTGCA 58.526 33.333 0.00 0.00 0.00 4.08
381 387 6.401955 TTGACAAAAGTTTTAAGTGCTTGC 57.598 33.333 0.00 0.00 0.00 4.01
382 388 7.962917 ACATTGACAAAAGTTTTAAGTGCTTG 58.037 30.769 0.00 0.00 0.00 4.01
383 389 8.546597 AACATTGACAAAAGTTTTAAGTGCTT 57.453 26.923 0.00 0.00 0.00 3.91
384 390 8.546597 AAACATTGACAAAAGTTTTAAGTGCT 57.453 26.923 13.35 0.00 34.43 4.40
385 391 8.655970 AGAAACATTGACAAAAGTTTTAAGTGC 58.344 29.630 17.76 8.51 37.33 4.40
435 441 6.452494 TCGGGTGAACAGTAAAATCAAAAA 57.548 33.333 0.00 0.00 0.00 1.94
436 442 5.506649 GCTCGGGTGAACAGTAAAATCAAAA 60.507 40.000 0.00 0.00 0.00 2.44
437 443 4.023536 GCTCGGGTGAACAGTAAAATCAAA 60.024 41.667 0.00 0.00 0.00 2.69
438 444 3.500680 GCTCGGGTGAACAGTAAAATCAA 59.499 43.478 0.00 0.00 0.00 2.57
439 445 3.071479 GCTCGGGTGAACAGTAAAATCA 58.929 45.455 0.00 0.00 0.00 2.57
440 446 3.335579 AGCTCGGGTGAACAGTAAAATC 58.664 45.455 0.00 0.00 0.00 2.17
441 447 3.244422 TGAGCTCGGGTGAACAGTAAAAT 60.244 43.478 9.64 0.00 0.00 1.82
442 448 2.103432 TGAGCTCGGGTGAACAGTAAAA 59.897 45.455 9.64 0.00 0.00 1.52
443 449 1.689813 TGAGCTCGGGTGAACAGTAAA 59.310 47.619 9.64 0.00 0.00 2.01
444 450 1.334160 TGAGCTCGGGTGAACAGTAA 58.666 50.000 9.64 0.00 0.00 2.24
445 451 1.557099 ATGAGCTCGGGTGAACAGTA 58.443 50.000 9.64 0.00 0.00 2.74
446 452 0.687354 AATGAGCTCGGGTGAACAGT 59.313 50.000 9.64 0.00 0.00 3.55
447 453 1.466167 CAAATGAGCTCGGGTGAACAG 59.534 52.381 9.64 0.00 0.00 3.16
448 454 1.071542 TCAAATGAGCTCGGGTGAACA 59.928 47.619 9.64 0.00 0.00 3.18
449 455 1.734465 CTCAAATGAGCTCGGGTGAAC 59.266 52.381 9.64 0.00 35.13 3.18
450 456 2.099141 CTCAAATGAGCTCGGGTGAA 57.901 50.000 9.64 0.00 35.13 3.18
451 457 3.840831 CTCAAATGAGCTCGGGTGA 57.159 52.632 9.64 10.63 35.13 4.02
460 466 0.674581 TGCACCCGAGCTCAAATGAG 60.675 55.000 15.40 6.05 44.75 2.90
461 467 0.674581 CTGCACCCGAGCTCAAATGA 60.675 55.000 15.40 0.00 34.99 2.57
462 468 0.674581 TCTGCACCCGAGCTCAAATG 60.675 55.000 15.40 9.02 34.99 2.32
463 469 0.036732 TTCTGCACCCGAGCTCAAAT 59.963 50.000 15.40 0.00 34.99 2.32
464 470 0.179032 TTTCTGCACCCGAGCTCAAA 60.179 50.000 15.40 0.86 34.99 2.69
465 471 0.884704 GTTTCTGCACCCGAGCTCAA 60.885 55.000 15.40 0.00 34.99 3.02
466 472 1.301716 GTTTCTGCACCCGAGCTCA 60.302 57.895 15.40 0.00 34.99 4.26
467 473 1.004440 AGTTTCTGCACCCGAGCTC 60.004 57.895 2.73 2.73 34.99 4.09
468 474 1.004440 GAGTTTCTGCACCCGAGCT 60.004 57.895 0.00 0.00 34.99 4.09
469 475 2.383527 CGAGTTTCTGCACCCGAGC 61.384 63.158 0.00 0.00 0.00 5.03
470 476 1.006102 ACGAGTTTCTGCACCCGAG 60.006 57.895 0.00 0.00 0.00 4.63
471 477 1.006571 GACGAGTTTCTGCACCCGA 60.007 57.895 0.00 0.00 0.00 5.14
472 478 2.372690 CGACGAGTTTCTGCACCCG 61.373 63.158 0.00 0.00 0.00 5.28
473 479 2.668280 GCGACGAGTTTCTGCACCC 61.668 63.158 0.00 0.00 0.00 4.61
474 480 1.618640 GAGCGACGAGTTTCTGCACC 61.619 60.000 0.00 0.00 0.00 5.01
475 481 1.618640 GGAGCGACGAGTTTCTGCAC 61.619 60.000 0.00 0.00 0.00 4.57
476 482 1.372997 GGAGCGACGAGTTTCTGCA 60.373 57.895 0.00 0.00 0.00 4.41
477 483 1.347817 CTGGAGCGACGAGTTTCTGC 61.348 60.000 0.00 0.00 0.00 4.26
478 484 0.039074 ACTGGAGCGACGAGTTTCTG 60.039 55.000 0.00 0.00 33.96 3.02
479 485 0.241481 GACTGGAGCGACGAGTTTCT 59.759 55.000 0.00 0.00 37.67 2.52
480 486 0.733223 GGACTGGAGCGACGAGTTTC 60.733 60.000 0.00 0.00 37.67 2.78
481 487 1.179814 AGGACTGGAGCGACGAGTTT 61.180 55.000 0.00 0.00 37.67 2.66
482 488 1.587933 GAGGACTGGAGCGACGAGTT 61.588 60.000 0.00 0.00 37.67 3.01
483 489 2.034376 AGGACTGGAGCGACGAGT 59.966 61.111 0.00 0.00 40.12 4.18
484 490 1.309499 AAGAGGACTGGAGCGACGAG 61.309 60.000 0.00 0.00 0.00 4.18
542 554 2.363925 GGAGGTGGCGGAGTAGGT 60.364 66.667 0.00 0.00 0.00 3.08
581 593 4.933064 CTCGTCGATGGCCCTCGC 62.933 72.222 23.86 17.44 38.52 5.03
803 830 1.378646 ATCAGACGGCCACGAGAGA 60.379 57.895 2.24 0.00 44.60 3.10
804 831 1.226802 CATCAGACGGCCACGAGAG 60.227 63.158 2.24 0.00 44.60 3.20
805 832 2.710902 CCATCAGACGGCCACGAGA 61.711 63.158 2.24 0.63 44.60 4.04
806 833 2.202797 CCATCAGACGGCCACGAG 60.203 66.667 2.24 0.00 44.60 4.18
820 847 1.527370 GAGCGAAACCCTAGCCCAT 59.473 57.895 0.00 0.00 0.00 4.00
871 898 3.360340 GACGGACGGACGGACACT 61.360 66.667 6.00 0.00 38.39 3.55
926 953 1.535444 TCCCTGAGTCCCTGCGAAA 60.535 57.895 0.00 0.00 0.00 3.46
949 976 1.258445 CCGGCCAAGTCCTAGACAGT 61.258 60.000 2.24 0.00 34.60 3.55
1015 1042 1.217916 TCGATGAGAGGAGAGGAGGT 58.782 55.000 0.00 0.00 0.00 3.85
1040 1067 4.611310 ATCGTTTCATGCAGAACATCTG 57.389 40.909 3.00 3.00 46.90 2.90
1093 1120 8.026607 TGAAGAAAAAGAAACCAACTAAGTGTG 58.973 33.333 0.00 0.00 0.00 3.82
1211 1257 5.473504 GTCCAGGATCACATTTTACAACTGT 59.526 40.000 0.00 0.00 0.00 3.55
1212 1258 5.473162 TGTCCAGGATCACATTTTACAACTG 59.527 40.000 0.00 0.00 0.00 3.16
1230 1276 0.971386 AATTTGCTGCCCTTGTCCAG 59.029 50.000 0.00 0.00 0.00 3.86
1284 1331 3.784701 AGTGCTAACCATCACTAGACG 57.215 47.619 0.00 0.00 41.32 4.18
1327 1375 1.490621 CATAGCATGCATCGTCACGA 58.509 50.000 21.98 0.28 41.13 4.35
1350 1400 1.660052 CGGTTTATCGCATGCAATCGG 60.660 52.381 19.57 0.14 0.00 4.18
1399 1449 1.732941 TCGATCCAACCGACCATTTG 58.267 50.000 0.00 0.00 0.00 2.32
1475 1529 3.221771 ACAAGAAATTAGCACAGCCACA 58.778 40.909 0.00 0.00 0.00 4.17
1524 1578 2.736531 CCCCAAGGCAACAACAGC 59.263 61.111 0.00 0.00 41.41 4.40
1534 1588 1.302832 GACACACTGAGCCCCAAGG 60.303 63.158 0.00 0.00 0.00 3.61
1539 1593 2.042831 GGCATGACACACTGAGCCC 61.043 63.158 0.00 0.00 36.17 5.19
1545 1599 2.046892 GCGAGGGCATGACACACT 60.047 61.111 0.00 0.00 39.62 3.55
1565 1619 2.485814 GCAGCAACGGAGAAGAGAAATT 59.514 45.455 0.00 0.00 0.00 1.82
1579 1633 1.211743 GAAAGCAAACCAGCAGCAAC 58.788 50.000 0.00 0.00 36.85 4.17
1646 1700 2.973694 TATCGCTAACCAAGTCCACC 57.026 50.000 0.00 0.00 0.00 4.61
1711 1765 2.025155 TCAGGACTGGATAAGACGAGC 58.975 52.381 0.00 0.00 0.00 5.03
1726 1780 3.143675 GCATCAGCGTTTCTCAGGA 57.856 52.632 0.00 0.00 0.00 3.86
1777 1831 5.582665 GCTTAAAGACACCCACTTCTATCAG 59.417 44.000 0.00 0.00 0.00 2.90
1863 1921 9.856488 TTAGATCAGTAACAAACATCAGACTAC 57.144 33.333 0.00 0.00 0.00 2.73
2071 2132 5.293324 CCCTGAAAGCAAAACAAAAGGTTAC 59.707 40.000 0.00 0.00 39.29 2.50
2187 2248 1.276622 AACATACTGTCCTTCCCGCT 58.723 50.000 0.00 0.00 0.00 5.52
3315 3385 3.176552 ACTGAAGCGATTCTCATCCAG 57.823 47.619 15.31 5.51 0.00 3.86
3795 3868 6.629128 CCATACATGTTTGTAGGCAATTGAA 58.371 36.000 10.34 0.00 41.49 2.69
3998 4071 1.828050 GCTCCCCTAGTATGGTCCCTC 60.828 61.905 0.00 0.00 0.00 4.30
4010 4083 3.844211 TCTTTTTCTTGCTAGCTCCCCTA 59.156 43.478 17.23 0.00 0.00 3.53
4033 4106 5.549742 TGAATTTCCAAGGCATTTGTCTT 57.450 34.783 0.00 0.00 41.26 3.01
4349 4422 3.090532 GGGCTTCCCCCGATCACT 61.091 66.667 0.00 0.00 45.91 3.41
4466 4539 4.386049 CCTACATTCGCCATAATCGACTTC 59.614 45.833 0.00 0.00 35.51 3.01
4535 4610 8.160765 TGATGTTCCAAACCTAAATGAAGTAGA 58.839 33.333 0.00 0.00 0.00 2.59
4570 4645 7.797123 GTCTGTCTACAAAATAAACTTTCACCG 59.203 37.037 0.00 0.00 0.00 4.94
4679 4754 6.094048 TCAAAACAAGTTTCTTCTCTGTCAGG 59.906 38.462 0.00 0.00 31.45 3.86
4715 4790 6.866770 ACAATGAGAAAGCAATGAATTCAGTG 59.133 34.615 27.15 27.15 43.96 3.66
4735 4810 9.345517 CCACAAGTGTAGAATGAAAATACAATG 57.654 33.333 0.00 0.00 31.61 2.82
4904 4983 9.504708 GTAATACACTAGCTAACCTCTATCTGA 57.495 37.037 0.00 0.00 0.00 3.27
4915 5018 7.484993 TGTTTCCAGGTAATACACTAGCTAA 57.515 36.000 0.00 0.00 0.00 3.09
4922 5025 9.567848 CACATAATTTGTTTCCAGGTAATACAC 57.432 33.333 0.00 0.00 36.00 2.90
4925 5028 8.465999 CAGCACATAATTTGTTTCCAGGTAATA 58.534 33.333 0.00 0.00 36.00 0.98
5015 5118 4.546829 AAGCACGGTAGGAGAACAAATA 57.453 40.909 0.00 0.00 0.00 1.40
5053 5158 5.238432 ACACAACATTTCTAACGCATCTCAA 59.762 36.000 0.00 0.00 0.00 3.02
5131 5236 9.373603 ACGTGCACATAAAAATATCTAGTAACA 57.626 29.630 18.64 0.00 0.00 2.41
5204 5392 6.448006 AGCAGACATCGATGTACCTTATAAC 58.552 40.000 30.04 14.53 41.95 1.89
5235 5423 1.281867 TGGGCCATCTACAAGAACAGG 59.718 52.381 0.00 0.00 0.00 4.00
5268 5456 4.400529 TTCCAGCATCGAAGTATAAGCA 57.599 40.909 0.00 0.00 0.00 3.91
5421 5614 5.869888 CAGTGGTACTCATTTGTCCTTCTAC 59.130 44.000 0.00 0.00 0.00 2.59
5437 5630 6.535274 AACTTTGTCGAAATACAGTGGTAC 57.465 37.500 0.00 0.00 30.94 3.34


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

AutoCloner maintained by Alex Coulton.