Multiple sequence alignment - TraesCS3D01G365900

Loading Multiple Alignment...

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 TraesCS3D01G365900 chr3D 100.000 2597 0 0 1 2597 480148232 480150828 0.000000e+00 4796.0
1 TraesCS3D01G365900 chr3D 90.164 122 12 0 1138 1259 16887964 16888085 2.670000e-35 159.0
2 TraesCS3D01G365900 chr3D 100.000 33 0 0 1495 1527 480149073 480149041 7.760000e-06 62.1
3 TraesCS3D01G365900 chr3D 100.000 33 0 0 810 842 480149758 480149726 7.760000e-06 62.1
4 TraesCS3D01G365900 chr3B 94.130 1448 59 8 833 2276 640667292 640668717 0.000000e+00 2180.0
5 TraesCS3D01G365900 chr3B 91.615 322 25 2 2277 2597 640668779 640669099 6.590000e-121 444.0
6 TraesCS3D01G365900 chr3B 95.865 266 3 2 537 802 640667037 640667294 8.590000e-115 424.0
7 TraesCS3D01G365900 chr3B 94.531 128 7 0 1 128 640666920 640667047 5.670000e-47 198.0
8 TraesCS3D01G365900 chr3B 97.059 34 1 0 2241 2274 188438397 188438364 1.000000e-04 58.4
9 TraesCS3D01G365900 chr3B 100.000 30 0 0 813 842 640667981 640667952 3.610000e-04 56.5
10 TraesCS3D01G365900 chr3A 94.537 1080 49 7 840 1910 623223155 623224233 0.000000e+00 1659.0
11 TraesCS3D01G365900 chr3A 94.891 411 18 2 128 537 82104033 82104441 7.840000e-180 640.0
12 TraesCS3D01G365900 chr3A 98.872 266 2 1 537 802 623222888 623223152 8.410000e-130 473.0
13 TraesCS3D01G365900 chr3A 92.248 129 8 2 1 128 623222771 623222898 5.710000e-42 182.0
14 TraesCS3D01G365900 chr3A 89.683 126 12 1 1134 1259 19895847 19895723 2.670000e-35 159.0
15 TraesCS3D01G365900 chr3A 96.000 50 2 0 1973 2022 623224233 623224282 5.960000e-12 82.4
16 TraesCS3D01G365900 chr3A 100.000 30 0 0 813 842 623223846 623223817 3.610000e-04 56.5
17 TraesCS3D01G365900 chr2A 95.642 413 17 1 125 536 61475970 61475558 0.000000e+00 662.0
18 TraesCS3D01G365900 chr7A 95.192 416 17 3 128 540 625908186 625908601 0.000000e+00 654.0
19 TraesCS3D01G365900 chr7A 95.157 413 17 1 131 540 640497001 640496589 0.000000e+00 649.0
20 TraesCS3D01G365900 chr7D 95.146 412 16 4 127 536 63450292 63450701 0.000000e+00 647.0
21 TraesCS3D01G365900 chr5A 95.074 406 18 2 131 536 546707726 546708129 2.820000e-179 638.0
22 TraesCS3D01G365900 chr4D 94.660 412 18 2 125 536 495973754 495973347 1.010000e-178 636.0
23 TraesCS3D01G365900 chr4D 87.859 313 33 3 2285 2597 464079199 464078892 1.900000e-96 363.0
24 TraesCS3D01G365900 chr2D 94.245 417 17 5 121 536 600408201 600408611 4.720000e-177 630.0
25 TraesCS3D01G365900 chr2D 92.744 441 21 9 110 546 392527529 392527962 6.100000e-176 627.0
26 TraesCS3D01G365900 chr6B 82.812 320 49 2 2278 2597 706519782 706520095 5.470000e-72 281.0
27 TraesCS3D01G365900 chr6B 80.667 300 52 3 2278 2577 706349290 706349583 7.230000e-56 228.0
28 TraesCS3D01G365900 chr6B 80.667 300 52 3 2278 2577 706406276 706406569 7.230000e-56 228.0
29 TraesCS3D01G365900 chr6B 79.567 323 56 7 2278 2597 151292729 151293044 3.360000e-54 222.0
30 TraesCS3D01G365900 chr6B 100.000 33 0 0 2243 2275 39250303 39250271 7.760000e-06 62.1
31 TraesCS3D01G365900 chr4A 79.876 323 57 4 2277 2597 444159686 444159370 2.010000e-56 230.0
32 TraesCS3D01G365900 chr1B 80.333 300 55 1 2283 2582 494569468 494569173 9.350000e-55 224.0
33 TraesCS3D01G365900 chr4B 79.747 316 56 6 2284 2597 190164126 190164435 3.360000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G365900 chr3D 480148232 480150828 2596 False 4796.0 4796 100.00000 1 2597 1 chr3D.!!$F2 2596
1 TraesCS3D01G365900 chr3B 640666920 640669099 2179 False 811.5 2180 94.03525 1 2597 4 chr3B.!!$F1 2596
2 TraesCS3D01G365900 chr3A 623222771 623224282 1511 False 599.1 1659 95.41425 1 2022 4 chr3A.!!$F2 2021

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
990 992 0.109458 TACGTGTCACCTAGCAAGCG 60.109 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2351 0.313672 TTTGCACAAATGACTCGGCC 59.686 50.0 0.0 0.0 0.0 6.13 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
79 81 4.336889 TCTTCTTGGTTGGTACTGAGTG 57.663 45.455 0.00 0.00 0.00 3.51
113 115 4.384868 GGGAAAGGTGCAGGTAAGCTAATA 60.385 45.833 0.00 0.00 34.99 0.98
116 118 2.104963 AGGTGCAGGTAAGCTAATAGGC 59.895 50.000 0.00 0.00 34.99 3.93
128 130 2.865276 GCTAATAGGCCTTTCCGTACGG 60.865 54.545 28.66 28.66 40.77 4.02
129 131 1.488390 AATAGGCCTTTCCGTACGGA 58.512 50.000 32.61 32.61 43.52 4.69
142 144 3.995705 TCCGTACGGAAAATACACTTTGG 59.004 43.478 33.96 2.51 42.05 3.28
143 145 3.747529 CCGTACGGAAAATACACTTTGGT 59.252 43.478 30.64 0.00 37.50 3.67
144 146 4.213906 CCGTACGGAAAATACACTTTGGTT 59.786 41.667 30.64 0.00 37.50 3.67
145 147 5.376537 CGTACGGAAAATACACTTTGGTTC 58.623 41.667 7.57 0.00 0.00 3.62
146 148 4.841443 ACGGAAAATACACTTTGGTTCC 57.159 40.909 0.00 0.00 32.81 3.62
147 149 4.466827 ACGGAAAATACACTTTGGTTCCT 58.533 39.130 0.00 0.00 33.78 3.36
148 150 4.277423 ACGGAAAATACACTTTGGTTCCTG 59.723 41.667 0.00 0.00 33.78 3.86
149 151 4.320935 CGGAAAATACACTTTGGTTCCTGG 60.321 45.833 0.00 0.00 33.78 4.45
150 152 4.587262 GGAAAATACACTTTGGTTCCTGGT 59.413 41.667 0.00 0.00 33.28 4.00
151 153 5.069914 GGAAAATACACTTTGGTTCCTGGTT 59.930 40.000 0.00 0.00 33.28 3.67
152 154 5.529581 AAATACACTTTGGTTCCTGGTTG 57.470 39.130 0.00 0.00 0.00 3.77
153 155 2.525105 ACACTTTGGTTCCTGGTTGT 57.475 45.000 0.00 0.00 0.00 3.32
154 156 3.655615 ACACTTTGGTTCCTGGTTGTA 57.344 42.857 0.00 0.00 0.00 2.41
155 157 4.178956 ACACTTTGGTTCCTGGTTGTAT 57.821 40.909 0.00 0.00 0.00 2.29
156 158 5.313280 ACACTTTGGTTCCTGGTTGTATA 57.687 39.130 0.00 0.00 0.00 1.47
157 159 5.887754 ACACTTTGGTTCCTGGTTGTATAT 58.112 37.500 0.00 0.00 0.00 0.86
158 160 5.710099 ACACTTTGGTTCCTGGTTGTATATG 59.290 40.000 0.00 0.00 0.00 1.78
159 161 4.705023 ACTTTGGTTCCTGGTTGTATATGC 59.295 41.667 0.00 0.00 0.00 3.14
160 162 4.308526 TTGGTTCCTGGTTGTATATGCA 57.691 40.909 0.00 0.00 0.00 3.96
161 163 4.518278 TGGTTCCTGGTTGTATATGCAT 57.482 40.909 3.79 3.79 0.00 3.96
162 164 4.460263 TGGTTCCTGGTTGTATATGCATC 58.540 43.478 0.19 0.00 0.00 3.91
163 165 4.165950 TGGTTCCTGGTTGTATATGCATCT 59.834 41.667 0.19 0.00 0.00 2.90
164 166 5.133221 GGTTCCTGGTTGTATATGCATCTT 58.867 41.667 0.19 0.00 0.00 2.40
165 167 6.126623 TGGTTCCTGGTTGTATATGCATCTTA 60.127 38.462 0.19 0.00 0.00 2.10
166 168 6.942576 GGTTCCTGGTTGTATATGCATCTTAT 59.057 38.462 0.19 0.00 0.00 1.73
167 169 8.100791 GGTTCCTGGTTGTATATGCATCTTATA 58.899 37.037 0.19 0.00 0.00 0.98
168 170 9.672673 GTTCCTGGTTGTATATGCATCTTATAT 57.327 33.333 0.19 0.00 0.00 0.86
169 171 9.671279 TTCCTGGTTGTATATGCATCTTATATG 57.329 33.333 0.19 0.00 0.00 1.78
170 172 8.267183 TCCTGGTTGTATATGCATCTTATATGG 58.733 37.037 0.19 0.00 0.00 2.74
171 173 7.500227 CCTGGTTGTATATGCATCTTATATGGG 59.500 40.741 0.19 0.00 0.00 4.00
172 174 7.345691 TGGTTGTATATGCATCTTATATGGGG 58.654 38.462 0.19 0.00 0.00 4.96
173 175 7.183657 TGGTTGTATATGCATCTTATATGGGGA 59.816 37.037 0.19 0.00 0.00 4.81
174 176 8.220559 GGTTGTATATGCATCTTATATGGGGAT 58.779 37.037 0.19 0.00 0.00 3.85
175 177 9.632638 GTTGTATATGCATCTTATATGGGGATT 57.367 33.333 0.19 0.00 0.00 3.01
232 234 9.185680 AGGTAAGAACTATTTTGACAAAACACT 57.814 29.630 15.36 3.23 32.37 3.55
233 235 9.797556 GGTAAGAACTATTTTGACAAAACACTT 57.202 29.630 15.36 15.89 32.37 3.16
236 238 8.911247 AGAACTATTTTGACAAAACACTTGAC 57.089 30.769 15.36 5.14 32.37 3.18
237 239 8.739972 AGAACTATTTTGACAAAACACTTGACT 58.260 29.630 15.36 7.03 32.37 3.41
238 240 9.353999 GAACTATTTTGACAAAACACTTGACTT 57.646 29.630 15.36 0.00 32.37 3.01
240 242 9.783256 ACTATTTTGACAAAACACTTGACTTAC 57.217 29.630 15.36 0.00 32.37 2.34
243 245 9.705290 ATTTTGACAAAACACTTGACTTACTTT 57.295 25.926 15.36 0.00 32.37 2.66
244 246 9.535878 TTTTGACAAAACACTTGACTTACTTTT 57.464 25.926 9.30 0.00 0.00 2.27
245 247 8.514136 TTGACAAAACACTTGACTTACTTTTG 57.486 30.769 0.00 0.00 35.61 2.44
246 248 6.584563 TGACAAAACACTTGACTTACTTTTGC 59.415 34.615 0.00 0.00 33.72 3.68
247 249 6.451393 ACAAAACACTTGACTTACTTTTGCA 58.549 32.000 0.00 0.00 33.72 4.08
248 250 6.364976 ACAAAACACTTGACTTACTTTTGCAC 59.635 34.615 0.00 0.00 33.72 4.57
249 251 5.897377 AACACTTGACTTACTTTTGCACT 57.103 34.783 0.00 0.00 0.00 4.40
250 252 5.235305 ACACTTGACTTACTTTTGCACTG 57.765 39.130 0.00 0.00 0.00 3.66
251 253 4.941263 ACACTTGACTTACTTTTGCACTGA 59.059 37.500 0.00 0.00 0.00 3.41
252 254 5.590259 ACACTTGACTTACTTTTGCACTGAT 59.410 36.000 0.00 0.00 0.00 2.90
253 255 6.765989 ACACTTGACTTACTTTTGCACTGATA 59.234 34.615 0.00 0.00 0.00 2.15
254 256 7.445402 ACACTTGACTTACTTTTGCACTGATAT 59.555 33.333 0.00 0.00 0.00 1.63
255 257 8.935844 CACTTGACTTACTTTTGCACTGATATA 58.064 33.333 0.00 0.00 0.00 0.86
256 258 9.672673 ACTTGACTTACTTTTGCACTGATATAT 57.327 29.630 0.00 0.00 0.00 0.86
265 267 9.764363 ACTTTTGCACTGATATATAAATCTCGA 57.236 29.630 0.00 0.00 0.00 4.04
267 269 7.796958 TTGCACTGATATATAAATCTCGACG 57.203 36.000 0.00 0.00 0.00 5.12
268 270 7.141100 TGCACTGATATATAAATCTCGACGA 57.859 36.000 0.00 0.00 0.00 4.20
269 271 7.590279 TGCACTGATATATAAATCTCGACGAA 58.410 34.615 0.00 0.00 0.00 3.85
270 272 8.079809 TGCACTGATATATAAATCTCGACGAAA 58.920 33.333 0.00 0.00 0.00 3.46
271 273 8.912658 GCACTGATATATAAATCTCGACGAAAA 58.087 33.333 0.00 0.00 0.00 2.29
295 297 3.782889 AACAAAAGTTGACCTCACAGC 57.217 42.857 0.00 0.00 0.00 4.40
296 298 2.722094 ACAAAAGTTGACCTCACAGCA 58.278 42.857 0.00 0.00 0.00 4.41
297 299 3.088532 ACAAAAGTTGACCTCACAGCAA 58.911 40.909 0.00 0.00 0.00 3.91
298 300 3.509575 ACAAAAGTTGACCTCACAGCAAA 59.490 39.130 0.00 0.00 0.00 3.68
299 301 4.021544 ACAAAAGTTGACCTCACAGCAAAA 60.022 37.500 0.00 0.00 0.00 2.44
300 302 4.799564 AAAGTTGACCTCACAGCAAAAA 57.200 36.364 0.00 0.00 0.00 1.94
349 351 8.494016 AAGTCACTATTCACACTATTTTAGCC 57.506 34.615 0.00 0.00 0.00 3.93
350 352 7.620880 AGTCACTATTCACACTATTTTAGCCA 58.379 34.615 0.00 0.00 0.00 4.75
351 353 8.100791 AGTCACTATTCACACTATTTTAGCCAA 58.899 33.333 0.00 0.00 0.00 4.52
352 354 8.726988 GTCACTATTCACACTATTTTAGCCAAA 58.273 33.333 0.00 0.00 0.00 3.28
353 355 9.290988 TCACTATTCACACTATTTTAGCCAAAA 57.709 29.630 0.00 0.00 38.00 2.44
354 356 9.906660 CACTATTCACACTATTTTAGCCAAAAA 57.093 29.630 0.00 0.00 41.21 1.94
359 361 9.606631 TTCACACTATTTTAGCCAAAAATTTGT 57.393 25.926 11.38 11.68 43.75 2.83
360 362 9.255304 TCACACTATTTTAGCCAAAAATTTGTC 57.745 29.630 11.38 0.00 43.75 3.18
361 363 9.260002 CACACTATTTTAGCCAAAAATTTGTCT 57.740 29.630 11.38 0.28 43.75 3.41
362 364 9.260002 ACACTATTTTAGCCAAAAATTTGTCTG 57.740 29.630 11.38 0.00 43.75 3.51
363 365 9.260002 CACTATTTTAGCCAAAAATTTGTCTGT 57.740 29.630 11.38 2.33 43.75 3.41
364 366 9.830975 ACTATTTTAGCCAAAAATTTGTCTGTT 57.169 25.926 11.38 0.00 43.75 3.16
367 369 9.786105 ATTTTAGCCAAAAATTTGTCTGTTTTG 57.214 25.926 5.27 0.00 43.75 2.44
368 370 8.553459 TTTAGCCAAAAATTTGTCTGTTTTGA 57.447 26.923 9.13 0.00 42.28 2.69
369 371 8.553459 TTAGCCAAAAATTTGTCTGTTTTGAA 57.447 26.923 9.13 0.00 42.28 2.69
370 372 7.446001 AGCCAAAAATTTGTCTGTTTTGAAA 57.554 28.000 9.13 0.00 42.28 2.69
371 373 7.880105 AGCCAAAAATTTGTCTGTTTTGAAAA 58.120 26.923 9.13 0.00 42.28 2.29
372 374 8.022550 AGCCAAAAATTTGTCTGTTTTGAAAAG 58.977 29.630 9.13 0.00 42.28 2.27
373 375 8.020244 GCCAAAAATTTGTCTGTTTTGAAAAGA 58.980 29.630 9.13 0.00 42.28 2.52
374 376 9.890352 CCAAAAATTTGTCTGTTTTGAAAAGAA 57.110 25.926 9.13 0.00 42.28 2.52
378 380 9.487790 AAATTTGTCTGTTTTGAAAAGAAGACA 57.512 25.926 22.38 22.38 38.90 3.41
379 381 9.487790 AATTTGTCTGTTTTGAAAAGAAGACAA 57.512 25.926 27.74 27.74 43.12 3.18
380 382 8.879342 TTTGTCTGTTTTGAAAAGAAGACAAA 57.121 26.923 32.07 32.07 46.20 2.83
381 383 8.879342 TTGTCTGTTTTGAAAAGAAGACAAAA 57.121 26.923 28.53 17.48 42.57 2.44
382 384 8.519492 TGTCTGTTTTGAAAAGAAGACAAAAG 57.481 30.769 23.30 0.00 41.76 2.27
383 385 7.598493 TGTCTGTTTTGAAAAGAAGACAAAAGG 59.402 33.333 23.30 0.00 41.76 3.11
384 386 7.812669 GTCTGTTTTGAAAAGAAGACAAAAGGA 59.187 33.333 20.22 0.00 41.76 3.36
385 387 8.531146 TCTGTTTTGAAAAGAAGACAAAAGGAT 58.469 29.630 0.00 0.00 41.76 3.24
386 388 9.801873 CTGTTTTGAAAAGAAGACAAAAGGATA 57.198 29.630 0.00 0.00 41.76 2.59
416 418 8.795786 TTTTTGTGGATTTTATTTCTCACGAG 57.204 30.769 0.00 0.00 0.00 4.18
417 419 7.504924 TTTGTGGATTTTATTTCTCACGAGT 57.495 32.000 0.00 0.00 0.00 4.18
418 420 8.610248 TTTGTGGATTTTATTTCTCACGAGTA 57.390 30.769 0.00 0.00 0.00 2.59
419 421 7.591006 TGTGGATTTTATTTCTCACGAGTAC 57.409 36.000 0.00 0.00 0.00 2.73
420 422 7.156000 TGTGGATTTTATTTCTCACGAGTACA 58.844 34.615 0.00 0.00 0.00 2.90
421 423 7.658167 TGTGGATTTTATTTCTCACGAGTACAA 59.342 33.333 0.00 0.00 0.00 2.41
422 424 8.665685 GTGGATTTTATTTCTCACGAGTACAAT 58.334 33.333 0.00 0.00 0.00 2.71
423 425 9.878667 TGGATTTTATTTCTCACGAGTACAATA 57.121 29.630 0.00 0.00 0.00 1.90
428 430 9.582431 TTTATTTCTCACGAGTACAATAGAAGG 57.418 33.333 0.00 0.00 0.00 3.46
429 431 6.585695 TTTCTCACGAGTACAATAGAAGGT 57.414 37.500 0.00 0.00 0.00 3.50
430 432 5.814764 TCTCACGAGTACAATAGAAGGTC 57.185 43.478 0.00 0.00 0.00 3.85
431 433 5.250982 TCTCACGAGTACAATAGAAGGTCA 58.749 41.667 0.00 0.00 0.00 4.02
432 434 5.708697 TCTCACGAGTACAATAGAAGGTCAA 59.291 40.000 0.00 0.00 0.00 3.18
433 435 5.950883 TCACGAGTACAATAGAAGGTCAAG 58.049 41.667 0.00 0.00 0.00 3.02
434 436 5.475909 TCACGAGTACAATAGAAGGTCAAGT 59.524 40.000 0.00 0.00 0.00 3.16
435 437 6.015688 TCACGAGTACAATAGAAGGTCAAGTT 60.016 38.462 0.00 0.00 0.00 2.66
436 438 6.645415 CACGAGTACAATAGAAGGTCAAGTTT 59.355 38.462 0.00 0.00 0.00 2.66
437 439 7.811236 CACGAGTACAATAGAAGGTCAAGTTTA 59.189 37.037 0.00 0.00 0.00 2.01
438 440 8.529476 ACGAGTACAATAGAAGGTCAAGTTTAT 58.471 33.333 0.00 0.00 0.00 1.40
439 441 9.367444 CGAGTACAATAGAAGGTCAAGTTTATT 57.633 33.333 0.00 0.00 0.00 1.40
511 513 8.579850 TTTTTCCCATATAGGATGCATATGTC 57.420 34.615 0.00 0.00 41.22 3.06
512 514 5.894298 TCCCATATAGGATGCATATGTCC 57.106 43.478 0.00 4.42 41.22 4.02
513 515 4.660303 TCCCATATAGGATGCATATGTCCC 59.340 45.833 0.00 0.00 41.22 4.46
514 516 4.202503 CCCATATAGGATGCATATGTCCCC 60.203 50.000 0.00 0.00 41.22 4.81
515 517 4.413189 CCATATAGGATGCATATGTCCCCA 59.587 45.833 0.00 0.00 41.22 4.96
516 518 5.074102 CCATATAGGATGCATATGTCCCCAT 59.926 44.000 0.00 0.00 41.22 4.00
517 519 6.273026 CCATATAGGATGCATATGTCCCCATA 59.727 42.308 0.00 5.85 41.22 2.74
518 520 5.636903 ATAGGATGCATATGTCCCCATAC 57.363 43.478 0.00 0.03 36.40 2.39
519 521 3.259328 AGGATGCATATGTCCCCATACA 58.741 45.455 0.00 0.00 36.40 2.29
520 522 3.009473 AGGATGCATATGTCCCCATACAC 59.991 47.826 0.00 0.00 36.40 2.90
521 523 2.949177 TGCATATGTCCCCATACACC 57.051 50.000 4.29 0.00 36.40 4.16
522 524 2.131023 TGCATATGTCCCCATACACCA 58.869 47.619 4.29 0.00 36.40 4.17
523 525 2.511637 TGCATATGTCCCCATACACCAA 59.488 45.455 4.29 0.00 36.40 3.67
524 526 3.053320 TGCATATGTCCCCATACACCAAA 60.053 43.478 4.29 0.00 36.40 3.28
525 527 3.957497 GCATATGTCCCCATACACCAAAA 59.043 43.478 4.29 0.00 36.40 2.44
526 528 4.404073 GCATATGTCCCCATACACCAAAAA 59.596 41.667 4.29 0.00 36.40 1.94
527 529 5.070313 GCATATGTCCCCATACACCAAAAAT 59.930 40.000 4.29 0.00 36.40 1.82
528 530 6.407979 GCATATGTCCCCATACACCAAAAATT 60.408 38.462 4.29 0.00 36.40 1.82
529 531 5.675684 ATGTCCCCATACACCAAAAATTC 57.324 39.130 0.00 0.00 30.75 2.17
530 532 3.835395 TGTCCCCATACACCAAAAATTCC 59.165 43.478 0.00 0.00 0.00 3.01
531 533 3.196901 GTCCCCATACACCAAAAATTCCC 59.803 47.826 0.00 0.00 0.00 3.97
532 534 2.503765 CCCCATACACCAAAAATTCCCC 59.496 50.000 0.00 0.00 0.00 4.81
533 535 3.449918 CCCATACACCAAAAATTCCCCT 58.550 45.455 0.00 0.00 0.00 4.79
534 536 3.450817 CCCATACACCAAAAATTCCCCTC 59.549 47.826 0.00 0.00 0.00 4.30
535 537 3.450817 CCATACACCAAAAATTCCCCTCC 59.549 47.826 0.00 0.00 0.00 4.30
536 538 2.024176 ACACCAAAAATTCCCCTCCC 57.976 50.000 0.00 0.00 0.00 4.30
537 539 1.507742 ACACCAAAAATTCCCCTCCCT 59.492 47.619 0.00 0.00 0.00 4.20
538 540 2.090210 ACACCAAAAATTCCCCTCCCTT 60.090 45.455 0.00 0.00 0.00 3.95
539 541 2.978978 CACCAAAAATTCCCCTCCCTTT 59.021 45.455 0.00 0.00 0.00 3.11
540 542 3.007940 CACCAAAAATTCCCCTCCCTTTC 59.992 47.826 0.00 0.00 0.00 2.62
541 543 2.571653 CCAAAAATTCCCCTCCCTTTCC 59.428 50.000 0.00 0.00 0.00 3.13
542 544 2.231716 AAAATTCCCCTCCCTTTCCG 57.768 50.000 0.00 0.00 0.00 4.30
543 545 1.081481 AAATTCCCCTCCCTTTCCGT 58.919 50.000 0.00 0.00 0.00 4.69
544 546 1.975471 AATTCCCCTCCCTTTCCGTA 58.025 50.000 0.00 0.00 0.00 4.02
545 547 1.210538 ATTCCCCTCCCTTTCCGTAC 58.789 55.000 0.00 0.00 0.00 3.67
546 548 1.259840 TTCCCCTCCCTTTCCGTACG 61.260 60.000 8.69 8.69 0.00 3.67
547 549 1.986210 CCCCTCCCTTTCCGTACGT 60.986 63.158 15.21 0.00 0.00 3.57
548 550 1.514553 CCCTCCCTTTCCGTACGTC 59.485 63.158 15.21 0.00 0.00 4.34
549 551 1.514553 CCTCCCTTTCCGTACGTCC 59.485 63.158 15.21 0.00 0.00 4.79
550 552 0.969409 CCTCCCTTTCCGTACGTCCT 60.969 60.000 15.21 0.00 0.00 3.85
551 553 1.683011 CCTCCCTTTCCGTACGTCCTA 60.683 57.143 15.21 0.00 0.00 2.94
552 554 1.403323 CTCCCTTTCCGTACGTCCTAC 59.597 57.143 15.21 0.00 0.00 3.18
802 804 0.548510 ACCTCCAATCTTGCTAGGCC 59.451 55.000 0.00 0.00 34.80 5.19
803 805 0.533755 CCTCCAATCTTGCTAGGCCG 60.534 60.000 0.00 0.00 0.00 6.13
804 806 0.179000 CTCCAATCTTGCTAGGCCGT 59.821 55.000 0.00 0.00 0.00 5.68
805 807 0.618458 TCCAATCTTGCTAGGCCGTT 59.382 50.000 0.00 0.00 0.00 4.44
806 808 1.017387 CCAATCTTGCTAGGCCGTTC 58.983 55.000 0.00 0.00 0.00 3.95
807 809 1.407437 CCAATCTTGCTAGGCCGTTCT 60.407 52.381 0.00 0.00 0.00 3.01
808 810 2.158957 CCAATCTTGCTAGGCCGTTCTA 60.159 50.000 0.00 0.00 0.00 2.10
809 811 3.126831 CAATCTTGCTAGGCCGTTCTAG 58.873 50.000 0.00 0.00 39.64 2.43
810 812 1.848652 TCTTGCTAGGCCGTTCTAGT 58.151 50.000 0.00 0.00 39.05 2.57
811 813 3.008835 TCTTGCTAGGCCGTTCTAGTA 57.991 47.619 0.00 4.27 39.05 1.82
812 814 2.686915 TCTTGCTAGGCCGTTCTAGTAC 59.313 50.000 0.00 0.00 39.05 2.73
813 815 2.431954 TGCTAGGCCGTTCTAGTACT 57.568 50.000 0.00 0.00 39.05 2.73
814 816 2.022195 TGCTAGGCCGTTCTAGTACTG 58.978 52.381 5.39 0.00 39.05 2.74
815 817 2.022934 GCTAGGCCGTTCTAGTACTGT 58.977 52.381 5.39 0.00 39.05 3.55
816 818 2.033174 GCTAGGCCGTTCTAGTACTGTC 59.967 54.545 5.39 0.00 39.05 3.51
817 819 2.211250 AGGCCGTTCTAGTACTGTCA 57.789 50.000 5.39 0.00 0.00 3.58
818 820 2.736347 AGGCCGTTCTAGTACTGTCAT 58.264 47.619 5.39 0.00 0.00 3.06
819 821 2.688958 AGGCCGTTCTAGTACTGTCATC 59.311 50.000 5.39 0.00 0.00 2.92
820 822 2.223758 GGCCGTTCTAGTACTGTCATCC 60.224 54.545 5.39 0.00 0.00 3.51
821 823 2.541178 GCCGTTCTAGTACTGTCATCCG 60.541 54.545 5.39 0.37 0.00 4.18
822 824 2.541178 CCGTTCTAGTACTGTCATCCGC 60.541 54.545 5.39 0.00 0.00 5.54
823 825 2.355132 CGTTCTAGTACTGTCATCCGCT 59.645 50.000 5.39 0.00 0.00 5.52
824 826 3.696898 GTTCTAGTACTGTCATCCGCTG 58.303 50.000 5.39 0.00 0.00 5.18
825 827 2.298610 TCTAGTACTGTCATCCGCTGG 58.701 52.381 5.39 0.00 0.00 4.85
826 828 2.092592 TCTAGTACTGTCATCCGCTGGA 60.093 50.000 5.39 0.00 35.55 3.86
827 829 1.107114 AGTACTGTCATCCGCTGGAG 58.893 55.000 0.00 0.00 34.05 3.86
828 830 0.818296 GTACTGTCATCCGCTGGAGT 59.182 55.000 3.76 0.00 34.05 3.85
829 831 0.817654 TACTGTCATCCGCTGGAGTG 59.182 55.000 3.76 3.22 34.05 3.51
830 832 1.812922 CTGTCATCCGCTGGAGTGC 60.813 63.158 3.76 0.00 34.05 4.40
831 833 2.265739 GTCATCCGCTGGAGTGCA 59.734 61.111 3.76 0.00 34.05 4.57
832 834 1.812922 GTCATCCGCTGGAGTGCAG 60.813 63.158 7.39 7.39 34.05 4.41
833 835 2.513204 CATCCGCTGGAGTGCAGG 60.513 66.667 14.04 3.62 34.05 4.85
834 836 4.479993 ATCCGCTGGAGTGCAGGC 62.480 66.667 14.04 5.00 34.05 4.85
878 880 1.884464 CGTCCCATGCATGACTCCG 60.884 63.158 28.31 18.48 0.00 4.63
907 909 2.948720 GCAGGTGCGACTTCCCTCT 61.949 63.158 0.00 0.00 0.00 3.69
939 941 3.004839 GCGCTACATAATCTCTCACCTCA 59.995 47.826 0.00 0.00 0.00 3.86
962 964 1.784525 GTCGCTAACACTTGAGCACT 58.215 50.000 0.00 0.00 38.69 4.40
990 992 0.109458 TACGTGTCACCTAGCAAGCG 60.109 55.000 0.00 0.00 0.00 4.68
991 993 2.730672 CGTGTCACCTAGCAAGCGC 61.731 63.158 0.00 0.00 38.99 5.92
1524 1533 1.593787 CACTCCAGCGGATGACAGT 59.406 57.895 0.00 0.00 0.00 3.55
1607 1616 6.258160 CCACTTCATCGTGAAATTGGATAAC 58.742 40.000 15.57 0.00 39.91 1.89
1636 1645 6.413892 TCTTCACATGCATGAGTTAACCATA 58.586 36.000 32.75 3.76 0.00 2.74
1664 1673 1.002087 ACGAGTTGTCAAGTCCCATCC 59.998 52.381 13.65 0.00 0.00 3.51
1692 1701 3.624861 GGCTTATGACCATGTCACTTCTG 59.375 47.826 0.00 0.00 45.65 3.02
1693 1702 3.064545 GCTTATGACCATGTCACTTCTGC 59.935 47.826 0.00 0.00 45.65 4.26
1710 1719 0.690192 TGCCGTTCTCTTGGGAATCA 59.310 50.000 0.00 0.00 0.00 2.57
1715 1724 4.580580 GCCGTTCTCTTGGGAATCATATTT 59.419 41.667 0.00 0.00 0.00 1.40
1719 1728 6.203723 CGTTCTCTTGGGAATCATATTTCTCC 59.796 42.308 0.00 0.00 0.00 3.71
1722 1731 7.876371 TCTCTTGGGAATCATATTTCTCCTTT 58.124 34.615 0.00 0.00 0.00 3.11
1724 1733 8.899887 TCTTGGGAATCATATTTCTCCTTTTT 57.100 30.769 0.00 0.00 0.00 1.94
1890 1901 9.944663 TTGAATTAATCCATAAGTAAATCGTGC 57.055 29.630 0.00 0.00 0.00 5.34
1901 1912 5.034554 AGTAAATCGTGCTGACATTGTTG 57.965 39.130 0.00 0.00 0.00 3.33
1909 1920 5.181056 TCGTGCTGACATTGTTGACAATATT 59.819 36.000 8.88 0.29 44.10 1.28
2039 2050 4.790790 AGGAGGTTAGATTTCCCACTTCAT 59.209 41.667 0.00 0.00 0.00 2.57
2048 2059 7.923414 AGATTTCCCACTTCATTGTAACTAC 57.077 36.000 0.00 0.00 0.00 2.73
2049 2060 7.690256 AGATTTCCCACTTCATTGTAACTACT 58.310 34.615 0.00 0.00 0.00 2.57
2050 2061 7.607991 AGATTTCCCACTTCATTGTAACTACTG 59.392 37.037 0.00 0.00 0.00 2.74
2051 2062 6.428083 TTCCCACTTCATTGTAACTACTGA 57.572 37.500 0.00 0.00 0.00 3.41
2052 2063 6.428083 TCCCACTTCATTGTAACTACTGAA 57.572 37.500 0.00 0.00 0.00 3.02
2053 2064 6.833041 TCCCACTTCATTGTAACTACTGAAA 58.167 36.000 0.00 0.00 0.00 2.69
2054 2065 7.284074 TCCCACTTCATTGTAACTACTGAAAA 58.716 34.615 0.00 0.00 0.00 2.29
2055 2066 7.776030 TCCCACTTCATTGTAACTACTGAAAAA 59.224 33.333 0.00 0.00 0.00 1.94
2191 2202 0.677842 ACTAGTGGGTGTTGTCGTCC 59.322 55.000 0.00 0.00 0.00 4.79
2245 2256 2.765689 ACTGGATGGGTTGGTTTTCA 57.234 45.000 0.00 0.00 0.00 2.69
2256 2267 5.717654 TGGGTTGGTTTTCAAAGTAGACTTT 59.282 36.000 1.72 1.72 46.23 2.66
2279 2351 6.106648 TGAGAAGGCATATGATAAGGACAG 57.893 41.667 6.97 0.00 0.00 3.51
2281 2353 3.710209 AGGCATATGATAAGGACAGGC 57.290 47.619 6.97 0.00 0.00 4.85
2288 2360 1.112113 GATAAGGACAGGCCGAGTCA 58.888 55.000 25.94 11.53 43.43 3.41
2301 2373 2.472488 GCCGAGTCATTTGTGCAAAAAG 59.528 45.455 8.28 0.81 33.56 2.27
2305 2377 3.460103 AGTCATTTGTGCAAAAAGGCAG 58.540 40.909 9.16 0.00 45.96 4.85
2313 2385 1.524008 GCAAAAAGGCAGCGTAGGGT 61.524 55.000 0.00 0.00 0.00 4.34
2336 2408 6.308766 GGTTTAAAGTGAATGATGACACATGC 59.691 38.462 0.00 0.00 39.18 4.06
2350 2422 2.821969 ACACATGCCATTCTTTCCAGAC 59.178 45.455 0.00 0.00 0.00 3.51
2400 2472 5.410924 CGATGTCTCCTATCTTGTTCAACA 58.589 41.667 0.00 0.00 0.00 3.33
2407 2479 6.440647 TCTCCTATCTTGTTCAACATAGTGGT 59.559 38.462 0.00 0.00 0.00 4.16
2415 2487 8.758829 TCTTGTTCAACATAGTGGTAGATATGT 58.241 33.333 0.00 0.00 42.88 2.29
2447 2519 3.435682 TGGTAGGGCCAAAGAGGAT 57.564 52.632 6.18 0.00 45.94 3.24
2467 2539 4.112341 GCACGTAGGCGGACTCGT 62.112 66.667 3.08 3.08 43.45 4.18
2512 2585 2.249844 GGTGTCCATACCCCAATACG 57.750 55.000 0.00 0.00 34.56 3.06
2518 2591 1.140052 CCATACCCCAATACGCTGACA 59.860 52.381 0.00 0.00 0.00 3.58
2521 2594 0.672401 ACCCCAATACGCTGACAACG 60.672 55.000 0.00 0.00 0.00 4.10
2524 2597 1.136085 CCCAATACGCTGACAACGTTG 60.136 52.381 26.20 26.20 41.93 4.10
2564 2637 5.018809 TGATTTGGCAAAGGCTAGAGAAAT 58.981 37.500 18.61 0.00 40.87 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 2.034685 GCACCTTTCCCTTCTTGTCAAC 59.965 50.000 0.00 0.00 0.00 3.18
128 130 5.784578 ACCAGGAACCAAAGTGTATTTTC 57.215 39.130 0.00 0.00 0.00 2.29
129 131 5.423931 ACAACCAGGAACCAAAGTGTATTTT 59.576 36.000 0.00 0.00 0.00 1.82
130 132 4.959839 ACAACCAGGAACCAAAGTGTATTT 59.040 37.500 0.00 0.00 0.00 1.40
131 133 4.542697 ACAACCAGGAACCAAAGTGTATT 58.457 39.130 0.00 0.00 0.00 1.89
133 135 3.655615 ACAACCAGGAACCAAAGTGTA 57.344 42.857 0.00 0.00 0.00 2.90
134 136 2.525105 ACAACCAGGAACCAAAGTGT 57.475 45.000 0.00 0.00 0.00 3.55
135 137 5.393027 GCATATACAACCAGGAACCAAAGTG 60.393 44.000 0.00 0.00 0.00 3.16
136 138 4.705023 GCATATACAACCAGGAACCAAAGT 59.295 41.667 0.00 0.00 0.00 2.66
137 139 4.704540 TGCATATACAACCAGGAACCAAAG 59.295 41.667 0.00 0.00 0.00 2.77
138 140 4.667573 TGCATATACAACCAGGAACCAAA 58.332 39.130 0.00 0.00 0.00 3.28
139 141 4.308526 TGCATATACAACCAGGAACCAA 57.691 40.909 0.00 0.00 0.00 3.67
140 142 4.165950 AGATGCATATACAACCAGGAACCA 59.834 41.667 0.00 0.00 0.00 3.67
141 143 4.718961 AGATGCATATACAACCAGGAACC 58.281 43.478 0.00 0.00 0.00 3.62
142 144 7.986085 ATAAGATGCATATACAACCAGGAAC 57.014 36.000 0.00 0.00 0.00 3.62
143 145 9.671279 CATATAAGATGCATATACAACCAGGAA 57.329 33.333 0.00 0.00 0.00 3.36
144 146 8.267183 CCATATAAGATGCATATACAACCAGGA 58.733 37.037 0.00 0.00 0.00 3.86
145 147 7.500227 CCCATATAAGATGCATATACAACCAGG 59.500 40.741 0.00 0.00 0.00 4.45
146 148 7.500227 CCCCATATAAGATGCATATACAACCAG 59.500 40.741 0.00 0.00 0.00 4.00
147 149 7.183657 TCCCCATATAAGATGCATATACAACCA 59.816 37.037 0.00 0.00 0.00 3.67
148 150 7.573710 TCCCCATATAAGATGCATATACAACC 58.426 38.462 0.00 0.00 0.00 3.77
149 151 9.632638 AATCCCCATATAAGATGCATATACAAC 57.367 33.333 0.00 0.00 0.00 3.32
206 208 9.185680 AGTGTTTTGTCAAAATAGTTCTTACCT 57.814 29.630 13.65 0.34 32.22 3.08
207 209 9.797556 AAGTGTTTTGTCAAAATAGTTCTTACC 57.202 29.630 17.46 2.76 31.98 2.85
210 212 9.353999 GTCAAGTGTTTTGTCAAAATAGTTCTT 57.646 29.630 19.36 11.77 34.29 2.52
211 213 8.739972 AGTCAAGTGTTTTGTCAAAATAGTTCT 58.260 29.630 19.36 13.92 34.29 3.01
212 214 8.911247 AGTCAAGTGTTTTGTCAAAATAGTTC 57.089 30.769 19.36 12.43 34.29 3.01
214 216 9.783256 GTAAGTCAAGTGTTTTGTCAAAATAGT 57.217 29.630 13.65 11.04 32.22 2.12
217 219 9.705290 AAAGTAAGTCAAGTGTTTTGTCAAAAT 57.295 25.926 13.65 0.00 32.22 1.82
218 220 9.535878 AAAAGTAAGTCAAGTGTTTTGTCAAAA 57.464 25.926 6.65 6.65 0.00 2.44
219 221 8.973378 CAAAAGTAAGTCAAGTGTTTTGTCAAA 58.027 29.630 0.00 0.00 32.65 2.69
220 222 7.115663 GCAAAAGTAAGTCAAGTGTTTTGTCAA 59.884 33.333 0.00 0.00 37.26 3.18
221 223 6.584563 GCAAAAGTAAGTCAAGTGTTTTGTCA 59.415 34.615 0.00 0.00 37.26 3.58
222 224 6.584563 TGCAAAAGTAAGTCAAGTGTTTTGTC 59.415 34.615 0.00 0.00 37.26 3.18
223 225 6.364976 GTGCAAAAGTAAGTCAAGTGTTTTGT 59.635 34.615 0.00 0.00 37.26 2.83
224 226 6.586082 AGTGCAAAAGTAAGTCAAGTGTTTTG 59.414 34.615 0.00 0.00 37.74 2.44
225 227 6.586082 CAGTGCAAAAGTAAGTCAAGTGTTTT 59.414 34.615 0.00 0.00 0.00 2.43
226 228 6.072175 TCAGTGCAAAAGTAAGTCAAGTGTTT 60.072 34.615 0.00 0.00 0.00 2.83
227 229 5.414454 TCAGTGCAAAAGTAAGTCAAGTGTT 59.586 36.000 0.00 0.00 0.00 3.32
228 230 4.941263 TCAGTGCAAAAGTAAGTCAAGTGT 59.059 37.500 0.00 0.00 0.00 3.55
229 231 5.484173 TCAGTGCAAAAGTAAGTCAAGTG 57.516 39.130 0.00 0.00 0.00 3.16
230 232 7.986085 ATATCAGTGCAAAAGTAAGTCAAGT 57.014 32.000 0.00 0.00 0.00 3.16
239 241 9.764363 TCGAGATTTATATATCAGTGCAAAAGT 57.236 29.630 6.04 0.00 0.00 2.66
241 243 8.699749 CGTCGAGATTTATATATCAGTGCAAAA 58.300 33.333 6.04 0.00 0.00 2.44
242 244 8.079809 TCGTCGAGATTTATATATCAGTGCAAA 58.920 33.333 6.04 0.00 0.00 3.68
243 245 7.590279 TCGTCGAGATTTATATATCAGTGCAA 58.410 34.615 6.04 0.00 0.00 4.08
244 246 7.141100 TCGTCGAGATTTATATATCAGTGCA 57.859 36.000 6.04 0.00 0.00 4.57
245 247 8.449085 TTTCGTCGAGATTTATATATCAGTGC 57.551 34.615 6.04 0.00 0.00 4.40
272 274 4.929211 GCTGTGAGGTCAACTTTTGTTTTT 59.071 37.500 0.00 0.00 41.35 1.94
273 275 4.021544 TGCTGTGAGGTCAACTTTTGTTTT 60.022 37.500 0.00 0.00 41.35 2.43
274 276 3.509575 TGCTGTGAGGTCAACTTTTGTTT 59.490 39.130 0.00 0.00 41.35 2.83
275 277 3.088532 TGCTGTGAGGTCAACTTTTGTT 58.911 40.909 0.00 0.00 44.66 2.83
276 278 2.722094 TGCTGTGAGGTCAACTTTTGT 58.278 42.857 0.00 0.00 0.00 2.83
277 279 3.781079 TTGCTGTGAGGTCAACTTTTG 57.219 42.857 0.00 0.00 0.00 2.44
278 280 4.799564 TTTTGCTGTGAGGTCAACTTTT 57.200 36.364 0.00 0.00 0.00 2.27
279 281 4.799564 TTTTTGCTGTGAGGTCAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
323 325 9.595823 GGCTAAAATAGTGTGAATAGTGACTTA 57.404 33.333 0.00 0.00 0.00 2.24
324 326 8.100791 TGGCTAAAATAGTGTGAATAGTGACTT 58.899 33.333 0.00 0.00 0.00 3.01
325 327 7.620880 TGGCTAAAATAGTGTGAATAGTGACT 58.379 34.615 0.00 0.00 0.00 3.41
326 328 7.843490 TGGCTAAAATAGTGTGAATAGTGAC 57.157 36.000 0.00 0.00 0.00 3.67
327 329 8.856153 TTTGGCTAAAATAGTGTGAATAGTGA 57.144 30.769 0.00 0.00 0.00 3.41
328 330 9.906660 TTTTTGGCTAAAATAGTGTGAATAGTG 57.093 29.630 8.93 0.00 35.82 2.74
333 335 9.606631 ACAAATTTTTGGCTAAAATAGTGTGAA 57.393 25.926 22.86 0.00 43.84 3.18
334 336 9.255304 GACAAATTTTTGGCTAAAATAGTGTGA 57.745 29.630 25.81 0.92 43.84 3.58
347 349 8.020244 TCTTTTCAAAACAGACAAATTTTTGGC 58.980 29.630 7.85 4.44 46.60 4.52
348 350 9.890352 TTCTTTTCAAAACAGACAAATTTTTGG 57.110 25.926 7.85 0.00 42.34 3.28
352 354 9.487790 TGTCTTCTTTTCAAAACAGACAAATTT 57.512 25.926 14.20 0.00 35.62 1.82
353 355 9.487790 TTGTCTTCTTTTCAAAACAGACAAATT 57.512 25.926 21.01 0.00 40.47 1.82
354 356 9.487790 TTTGTCTTCTTTTCAAAACAGACAAAT 57.512 25.926 25.61 0.00 43.41 2.32
355 357 8.879342 TTTGTCTTCTTTTCAAAACAGACAAA 57.121 26.923 25.61 25.61 44.50 2.83
356 358 8.879342 TTTTGTCTTCTTTTCAAAACAGACAA 57.121 26.923 20.10 20.10 41.03 3.18
357 359 7.598493 CCTTTTGTCTTCTTTTCAAAACAGACA 59.402 33.333 13.12 13.12 36.55 3.41
358 360 7.812669 TCCTTTTGTCTTCTTTTCAAAACAGAC 59.187 33.333 9.34 9.34 36.55 3.51
359 361 7.891561 TCCTTTTGTCTTCTTTTCAAAACAGA 58.108 30.769 0.00 0.00 36.55 3.41
360 362 8.707938 ATCCTTTTGTCTTCTTTTCAAAACAG 57.292 30.769 0.00 0.00 36.55 3.16
391 393 8.410141 ACTCGTGAGAAATAAAATCCACAAAAA 58.590 29.630 3.44 0.00 41.32 1.94
392 394 7.936584 ACTCGTGAGAAATAAAATCCACAAAA 58.063 30.769 3.44 0.00 41.32 2.44
393 395 7.504924 ACTCGTGAGAAATAAAATCCACAAA 57.495 32.000 3.44 0.00 41.32 2.83
394 396 7.658167 TGTACTCGTGAGAAATAAAATCCACAA 59.342 33.333 3.44 0.00 41.32 3.33
395 397 7.156000 TGTACTCGTGAGAAATAAAATCCACA 58.844 34.615 3.44 0.00 41.32 4.17
396 398 7.591006 TGTACTCGTGAGAAATAAAATCCAC 57.409 36.000 3.44 0.00 41.32 4.02
397 399 8.786826 ATTGTACTCGTGAGAAATAAAATCCA 57.213 30.769 3.44 0.00 41.32 3.41
402 404 9.582431 CCTTCTATTGTACTCGTGAGAAATAAA 57.418 33.333 3.44 3.23 41.32 1.40
403 405 8.746530 ACCTTCTATTGTACTCGTGAGAAATAA 58.253 33.333 3.44 0.00 41.32 1.40
404 406 8.289939 ACCTTCTATTGTACTCGTGAGAAATA 57.710 34.615 3.44 4.58 41.32 1.40
405 407 7.093902 TGACCTTCTATTGTACTCGTGAGAAAT 60.094 37.037 3.44 3.72 41.32 2.17
406 408 6.208007 TGACCTTCTATTGTACTCGTGAGAAA 59.792 38.462 3.44 0.00 41.32 2.52
407 409 5.708697 TGACCTTCTATTGTACTCGTGAGAA 59.291 40.000 3.44 0.00 41.32 2.87
408 410 5.250982 TGACCTTCTATTGTACTCGTGAGA 58.749 41.667 3.44 0.00 39.12 3.27
409 411 5.562506 TGACCTTCTATTGTACTCGTGAG 57.437 43.478 0.00 0.00 0.00 3.51
410 412 5.475909 ACTTGACCTTCTATTGTACTCGTGA 59.524 40.000 0.00 0.00 0.00 4.35
411 413 5.710984 ACTTGACCTTCTATTGTACTCGTG 58.289 41.667 0.00 0.00 0.00 4.35
412 414 5.979288 ACTTGACCTTCTATTGTACTCGT 57.021 39.130 0.00 0.00 0.00 4.18
413 415 8.928270 ATAAACTTGACCTTCTATTGTACTCG 57.072 34.615 0.00 0.00 0.00 4.18
486 488 7.615365 GGACATATGCATCCTATATGGGAAAAA 59.385 37.037 12.36 0.88 40.92 1.94
487 489 7.118723 GGACATATGCATCCTATATGGGAAAA 58.881 38.462 12.36 1.24 40.92 2.29
488 490 6.353864 GGGACATATGCATCCTATATGGGAAA 60.354 42.308 12.36 1.61 40.92 3.13
489 491 5.132648 GGGACATATGCATCCTATATGGGAA 59.867 44.000 12.36 0.00 40.92 3.97
490 492 4.660303 GGGACATATGCATCCTATATGGGA 59.340 45.833 10.63 10.63 40.92 4.37
491 493 4.202503 GGGGACATATGCATCCTATATGGG 60.203 50.000 0.19 0.00 40.92 4.00
492 494 4.413189 TGGGGACATATGCATCCTATATGG 59.587 45.833 0.19 0.00 40.92 2.74
493 495 5.635278 TGGGGACATATGCATCCTATATG 57.365 43.478 0.19 3.34 41.85 1.78
509 511 3.196901 GGGAATTTTTGGTGTATGGGGAC 59.803 47.826 0.00 0.00 0.00 4.46
510 512 3.445987 GGGAATTTTTGGTGTATGGGGA 58.554 45.455 0.00 0.00 0.00 4.81
511 513 2.503765 GGGGAATTTTTGGTGTATGGGG 59.496 50.000 0.00 0.00 0.00 4.96
512 514 3.449918 AGGGGAATTTTTGGTGTATGGG 58.550 45.455 0.00 0.00 0.00 4.00
513 515 3.450817 GGAGGGGAATTTTTGGTGTATGG 59.549 47.826 0.00 0.00 0.00 2.74
514 516 3.450817 GGGAGGGGAATTTTTGGTGTATG 59.549 47.826 0.00 0.00 0.00 2.39
515 517 3.339742 AGGGAGGGGAATTTTTGGTGTAT 59.660 43.478 0.00 0.00 0.00 2.29
516 518 2.725227 AGGGAGGGGAATTTTTGGTGTA 59.275 45.455 0.00 0.00 0.00 2.90
517 519 1.507742 AGGGAGGGGAATTTTTGGTGT 59.492 47.619 0.00 0.00 0.00 4.16
518 520 2.325661 AGGGAGGGGAATTTTTGGTG 57.674 50.000 0.00 0.00 0.00 4.17
519 521 3.248024 GAAAGGGAGGGGAATTTTTGGT 58.752 45.455 0.00 0.00 0.00 3.67
520 522 2.571653 GGAAAGGGAGGGGAATTTTTGG 59.428 50.000 0.00 0.00 0.00 3.28
521 523 2.233676 CGGAAAGGGAGGGGAATTTTTG 59.766 50.000 0.00 0.00 0.00 2.44
522 524 2.158219 ACGGAAAGGGAGGGGAATTTTT 60.158 45.455 0.00 0.00 0.00 1.94
523 525 1.431633 ACGGAAAGGGAGGGGAATTTT 59.568 47.619 0.00 0.00 0.00 1.82
524 526 1.081481 ACGGAAAGGGAGGGGAATTT 58.919 50.000 0.00 0.00 0.00 1.82
525 527 1.562942 GTACGGAAAGGGAGGGGAATT 59.437 52.381 0.00 0.00 0.00 2.17
526 528 1.210538 GTACGGAAAGGGAGGGGAAT 58.789 55.000 0.00 0.00 0.00 3.01
527 529 1.259840 CGTACGGAAAGGGAGGGGAA 61.260 60.000 7.57 0.00 0.00 3.97
528 530 1.683365 CGTACGGAAAGGGAGGGGA 60.683 63.158 7.57 0.00 0.00 4.81
529 531 1.953231 GACGTACGGAAAGGGAGGGG 61.953 65.000 21.06 0.00 0.00 4.79
530 532 1.514553 GACGTACGGAAAGGGAGGG 59.485 63.158 21.06 0.00 0.00 4.30
531 533 0.969409 AGGACGTACGGAAAGGGAGG 60.969 60.000 21.06 0.00 0.00 4.30
532 534 1.403323 GTAGGACGTACGGAAAGGGAG 59.597 57.143 21.06 0.00 0.00 4.30
533 535 1.463674 GTAGGACGTACGGAAAGGGA 58.536 55.000 21.06 0.00 0.00 4.20
534 536 0.457443 GGTAGGACGTACGGAAAGGG 59.543 60.000 21.06 0.00 31.59 3.95
535 537 1.467920 AGGTAGGACGTACGGAAAGG 58.532 55.000 21.06 0.00 31.59 3.11
536 538 2.872370 CAAGGTAGGACGTACGGAAAG 58.128 52.381 21.06 0.00 31.59 2.62
537 539 1.067635 GCAAGGTAGGACGTACGGAAA 60.068 52.381 21.06 0.00 31.59 3.13
538 540 0.527565 GCAAGGTAGGACGTACGGAA 59.472 55.000 21.06 0.00 31.59 4.30
539 541 1.647545 CGCAAGGTAGGACGTACGGA 61.648 60.000 21.06 0.00 31.59 4.69
540 542 1.226491 CGCAAGGTAGGACGTACGG 60.226 63.158 21.06 1.43 31.59 4.02
541 543 1.870901 GCGCAAGGTAGGACGTACG 60.871 63.158 15.01 15.01 38.28 3.67
542 544 1.870901 CGCGCAAGGTAGGACGTAC 60.871 63.158 8.75 0.00 38.28 3.67
543 545 2.486504 CGCGCAAGGTAGGACGTA 59.513 61.111 8.75 0.00 38.28 3.57
544 546 4.430765 CCGCGCAAGGTAGGACGT 62.431 66.667 8.75 0.00 38.28 4.34
545 547 3.636313 TTCCGCGCAAGGTAGGACG 62.636 63.158 8.75 0.00 38.28 4.79
546 548 2.098831 GTTCCGCGCAAGGTAGGAC 61.099 63.158 8.75 0.00 38.28 3.85
547 549 2.221906 GAGTTCCGCGCAAGGTAGGA 62.222 60.000 8.75 0.82 38.28 2.94
548 550 1.810030 GAGTTCCGCGCAAGGTAGG 60.810 63.158 8.75 0.00 38.28 3.18
549 551 0.460284 ATGAGTTCCGCGCAAGGTAG 60.460 55.000 8.75 0.00 38.28 3.18
550 552 0.739462 CATGAGTTCCGCGCAAGGTA 60.739 55.000 8.75 0.00 38.28 3.08
551 553 2.034879 CATGAGTTCCGCGCAAGGT 61.035 57.895 8.75 0.00 38.28 3.50
552 554 2.753966 CCATGAGTTCCGCGCAAGG 61.754 63.158 8.75 0.38 38.28 3.61
802 804 2.355132 AGCGGATGACAGTACTAGAACG 59.645 50.000 0.00 0.00 0.00 3.95
803 805 3.489398 CCAGCGGATGACAGTACTAGAAC 60.489 52.174 0.00 0.00 0.00 3.01
804 806 2.688446 CCAGCGGATGACAGTACTAGAA 59.312 50.000 0.00 0.00 0.00 2.10
805 807 2.092592 TCCAGCGGATGACAGTACTAGA 60.093 50.000 0.00 0.00 0.00 2.43
806 808 2.292016 CTCCAGCGGATGACAGTACTAG 59.708 54.545 0.00 0.00 0.00 2.57
807 809 2.298610 CTCCAGCGGATGACAGTACTA 58.701 52.381 0.00 0.00 0.00 1.82
808 810 1.107114 CTCCAGCGGATGACAGTACT 58.893 55.000 0.00 0.00 0.00 2.73
809 811 0.818296 ACTCCAGCGGATGACAGTAC 59.182 55.000 0.00 0.00 0.00 2.73
810 812 0.817654 CACTCCAGCGGATGACAGTA 59.182 55.000 0.00 0.00 0.00 2.74
811 813 1.593787 CACTCCAGCGGATGACAGT 59.406 57.895 0.00 0.00 0.00 3.55
812 814 1.812922 GCACTCCAGCGGATGACAG 60.813 63.158 0.00 0.00 0.00 3.51
813 815 2.265739 GCACTCCAGCGGATGACA 59.734 61.111 0.00 0.00 0.00 3.58
814 816 1.812922 CTGCACTCCAGCGGATGAC 60.813 63.158 0.00 0.00 43.63 3.06
815 817 2.580815 CTGCACTCCAGCGGATGA 59.419 61.111 0.00 0.00 43.63 2.92
816 818 2.513204 CCTGCACTCCAGCGGATG 60.513 66.667 0.00 0.00 43.63 3.51
817 819 4.479993 GCCTGCACTCCAGCGGAT 62.480 66.667 0.00 0.00 43.63 4.18
821 823 4.687215 TCGTGCCTGCACTCCAGC 62.687 66.667 19.07 0.00 44.16 4.85
822 824 2.433838 CTCGTGCCTGCACTCCAG 60.434 66.667 19.07 9.00 44.16 3.86
823 825 4.687215 GCTCGTGCCTGCACTCCA 62.687 66.667 19.07 3.46 44.16 3.86
824 826 3.965539 ATGCTCGTGCCTGCACTCC 62.966 63.158 19.07 8.33 44.16 3.85
825 827 2.435586 ATGCTCGTGCCTGCACTC 60.436 61.111 19.07 9.27 44.16 3.51
826 828 2.745100 CATGCTCGTGCCTGCACT 60.745 61.111 19.07 0.00 44.16 4.40
827 829 3.031964 GACATGCTCGTGCCTGCAC 62.032 63.158 12.18 12.18 42.26 4.57
828 830 2.743538 GACATGCTCGTGCCTGCA 60.744 61.111 13.55 3.93 43.67 4.41
829 831 3.503363 GGACATGCTCGTGCCTGC 61.503 66.667 13.55 7.41 38.18 4.85
830 832 1.812922 GAGGACATGCTCGTGCCTG 60.813 63.158 12.30 12.30 40.03 4.85
831 833 2.581354 GAGGACATGCTCGTGCCT 59.419 61.111 7.05 0.00 38.71 4.75
832 834 2.512515 GGAGGACATGCTCGTGCC 60.513 66.667 7.05 0.00 38.71 5.01
833 835 2.635229 ATCGGAGGACATGCTCGTGC 62.635 60.000 1.71 1.71 40.20 5.34
834 836 0.179100 AATCGGAGGACATGCTCGTG 60.179 55.000 0.00 0.00 0.00 4.35
835 837 0.537188 AAATCGGAGGACATGCTCGT 59.463 50.000 0.00 0.00 0.00 4.18
836 838 1.202463 AGAAATCGGAGGACATGCTCG 60.202 52.381 0.00 0.00 0.00 5.03
837 839 2.611225 AGAAATCGGAGGACATGCTC 57.389 50.000 0.00 0.00 0.00 4.26
838 840 2.420687 GGAAGAAATCGGAGGACATGCT 60.421 50.000 0.00 0.00 0.00 3.79
878 880 1.282875 GCACCTGCACGGAGAAAAC 59.717 57.895 8.91 0.00 41.59 2.43
939 941 1.350193 CTCAAGTGTTAGCGACGCAT 58.650 50.000 23.70 9.74 41.29 4.73
990 992 4.916293 TCCGCCATGGATGAGCGC 62.916 66.667 18.40 0.00 43.74 5.92
1257 1263 2.105128 CTCATCCTGGCGTCGACC 59.895 66.667 10.58 2.55 0.00 4.79
1390 1396 1.679977 GCAGAGCATGGAAGGGCAA 60.680 57.895 0.00 0.00 0.00 4.52
1607 1616 3.542648 ACTCATGCATGTGAAGATGGAG 58.457 45.455 29.99 17.54 0.00 3.86
1614 1623 8.744568 TTATATGGTTAACTCATGCATGTGAA 57.255 30.769 29.99 16.99 0.00 3.18
1636 1645 5.873164 GGGACTTGACAACTCGTTACATTAT 59.127 40.000 0.00 0.00 0.00 1.28
1664 1673 3.209410 GACATGGTCATAAGCCTTGGAG 58.791 50.000 0.00 0.00 36.02 3.86
1692 1701 2.044123 ATGATTCCCAAGAGAACGGC 57.956 50.000 0.00 0.00 0.00 5.68
1693 1702 6.058183 AGAAATATGATTCCCAAGAGAACGG 58.942 40.000 0.00 0.00 0.00 4.44
1710 1719 9.189156 TCCGAATGAATGAAAAAGGAGAAATAT 57.811 29.630 0.00 0.00 0.00 1.28
1715 1724 5.560724 AGTCCGAATGAATGAAAAAGGAGA 58.439 37.500 0.00 0.00 0.00 3.71
1719 1728 7.411157 GCATGAAAGTCCGAATGAATGAAAAAG 60.411 37.037 0.00 0.00 0.00 2.27
1722 1731 5.401550 GCATGAAAGTCCGAATGAATGAAA 58.598 37.500 0.00 0.00 0.00 2.69
1724 1733 3.063861 CGCATGAAAGTCCGAATGAATGA 59.936 43.478 0.00 0.00 0.00 2.57
1890 1901 8.671028 TGAGATGAATATTGTCAACAATGTCAG 58.329 33.333 16.66 0.00 45.34 3.51
2026 2037 7.458397 TCAGTAGTTACAATGAAGTGGGAAAT 58.542 34.615 0.00 0.00 0.00 2.17
2054 2065 6.844097 TTGGTTTCAAGTCCAGTAGTTTTT 57.156 33.333 0.00 0.00 35.05 1.94
2055 2066 7.418337 AATTGGTTTCAAGTCCAGTAGTTTT 57.582 32.000 0.00 0.00 36.19 2.43
2056 2067 7.418337 AAATTGGTTTCAAGTCCAGTAGTTT 57.582 32.000 0.00 0.00 36.19 2.66
2057 2068 7.418337 AAAATTGGTTTCAAGTCCAGTAGTT 57.582 32.000 0.00 0.00 36.19 2.24
2058 2069 7.418337 AAAAATTGGTTTCAAGTCCAGTAGT 57.582 32.000 0.00 0.00 36.19 2.73
2084 2095 6.869913 CAGTCGGTTCATACCAACTTTAGTAA 59.130 38.462 0.00 0.00 38.58 2.24
2085 2096 6.209192 TCAGTCGGTTCATACCAACTTTAGTA 59.791 38.462 0.00 0.00 38.58 1.82
2089 2100 4.345859 TCAGTCGGTTCATACCAACTTT 57.654 40.909 0.00 0.00 38.58 2.66
2098 2109 2.941064 CAATCTGCATCAGTCGGTTCAT 59.059 45.455 0.00 0.00 32.61 2.57
2099 2110 2.349590 CAATCTGCATCAGTCGGTTCA 58.650 47.619 0.00 0.00 32.61 3.18
2191 2202 7.482743 GTGCATTTCATGTAGTGTTTCATGTAG 59.517 37.037 0.00 0.00 41.22 2.74
2245 2256 7.624549 TCATATGCCTTCTCAAAGTCTACTTT 58.375 34.615 2.24 2.24 46.23 2.66
2256 2267 5.012458 CCTGTCCTTATCATATGCCTTCTCA 59.988 44.000 0.00 0.00 0.00 3.27
2265 2276 3.511477 ACTCGGCCTGTCCTTATCATAT 58.489 45.455 0.00 0.00 0.00 1.78
2279 2351 0.313672 TTTGCACAAATGACTCGGCC 59.686 50.000 0.00 0.00 0.00 6.13
2281 2353 3.052036 CCTTTTTGCACAAATGACTCGG 58.948 45.455 0.00 0.00 0.00 4.63
2288 2360 1.219646 CGCTGCCTTTTTGCACAAAT 58.780 45.000 0.00 0.00 36.04 2.32
2301 2373 1.467342 CACTTTAAACCCTACGCTGCC 59.533 52.381 0.00 0.00 0.00 4.85
2305 2377 5.353123 TCATCATTCACTTTAAACCCTACGC 59.647 40.000 0.00 0.00 0.00 4.42
2313 2385 6.015603 TGGCATGTGTCATCATTCACTTTAAA 60.016 34.615 0.00 0.00 35.82 1.52
2336 2408 3.568538 CTTTTGCGTCTGGAAAGAATGG 58.431 45.455 0.00 0.00 36.73 3.16
2361 2433 2.963782 ACATCGGGTATCCCTGTCTTAC 59.036 50.000 3.25 0.00 42.67 2.34
2373 2445 4.180377 ACAAGATAGGAGACATCGGGTA 57.820 45.455 0.00 0.00 0.00 3.69
2377 2449 5.410924 TGTTGAACAAGATAGGAGACATCG 58.589 41.667 0.00 0.00 0.00 3.84
2383 2455 6.644347 ACCACTATGTTGAACAAGATAGGAG 58.356 40.000 24.76 19.63 44.36 3.69
2415 2487 5.445964 GGCCCTACCAATAAGAATTCTCAA 58.554 41.667 8.78 0.35 38.86 3.02
2496 2569 1.414919 TCAGCGTATTGGGGTATGGAC 59.585 52.381 0.00 0.00 0.00 4.02
2505 2578 1.529438 ACAACGTTGTCAGCGTATTGG 59.471 47.619 27.70 8.08 42.10 3.16
2512 2585 5.116983 CCATGAAAATAACAACGTTGTCAGC 59.883 40.000 32.36 18.53 41.31 4.26
2518 2591 7.429633 TCATGTTCCATGAAAATAACAACGTT 58.570 30.769 4.50 0.00 35.63 3.99
2522 2595 9.217278 CCAAATCATGTTCCATGAAAATAACAA 57.783 29.630 10.64 0.00 35.63 2.83
2524 2597 7.333921 TGCCAAATCATGTTCCATGAAAATAAC 59.666 33.333 10.64 1.66 0.00 1.89


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

AutoCloner maintained by Alex Coulton.