Multiple sequence alignment - TraesCS5B01G529100

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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 TraesCS5B01G529100 chr5B 100.000 3768 0 0 1 3768 687744411 687748178 0.000000e+00 6959
1 TraesCS5B01G529100 chr5B 80.181 883 131 31 1525 2390 687739430 687738575 4.130000e-174 621
2 TraesCS5B01G529100 chr5B 79.210 481 63 25 701 1171 687740223 687739770 2.200000e-77 300
3 TraesCS5B01G529100 chr5D 93.575 3315 99 41 490 3768 545144937 545148173 0.000000e+00 4837
4 TraesCS5B01G529100 chr5D 79.772 1315 189 55 701 1979 545125043 545123770 0.000000e+00 883
5 TraesCS5B01G529100 chr5D 92.529 174 12 1 324 497 53583243 53583071 8.080000e-62 248
6 TraesCS5B01G529100 chr5D 79.300 343 42 19 1 337 545144626 545144945 2.950000e-51 213
7 TraesCS5B01G529100 chr1A 89.621 2428 136 52 654 3071 570155877 570153556 0.000000e+00 2981
8 TraesCS5B01G529100 chr1A 92.222 180 14 0 1800 1979 570160249 570160428 4.830000e-64 255
9 TraesCS5B01G529100 chr1A 94.000 100 5 1 3669 3768 570152481 570152383 2.340000e-32 150
10 TraesCS5B01G529100 chr4A 90.806 1327 49 28 2184 3491 624925814 624927086 0.000000e+00 1707
11 TraesCS5B01G529100 chr4A 82.979 705 83 23 654 1354 624925144 624925815 1.500000e-168 603
12 TraesCS5B01G529100 chr4A 80.510 549 78 25 1231 1751 624921456 624920909 9.810000e-106 394
13 TraesCS5B01G529100 chr4A 89.583 288 17 6 3490 3768 624927346 624927629 1.660000e-93 353
14 TraesCS5B01G529100 chr4A 91.667 180 15 0 1800 1979 624920768 624920589 2.250000e-62 250
15 TraesCS5B01G529100 chr2D 93.642 173 11 0 320 492 87407354 87407526 3.730000e-65 259
16 TraesCS5B01G529100 chr6B 95.092 163 8 0 330 492 119526809 119526971 1.340000e-64 257
17 TraesCS5B01G529100 chr6B 92.982 171 12 0 330 500 132353577 132353407 2.250000e-62 250
18 TraesCS5B01G529100 chr6B 91.667 180 13 2 316 494 314546973 314547151 8.080000e-62 248
19 TraesCS5B01G529100 chr3D 93.023 172 12 0 321 492 459077439 459077268 6.250000e-63 252
20 TraesCS5B01G529100 chr2B 78.571 420 62 22 1031 1429 160280829 160281241 6.250000e-63 252
21 TraesCS5B01G529100 chr1D 92.135 178 13 1 325 502 230842687 230842863 2.250000e-62 250
22 TraesCS5B01G529100 chr3A 90.811 185 11 5 315 497 648037460 648037280 3.760000e-60 243
23 TraesCS5B01G529100 chr1B 89.340 197 13 7 295 488 24349019 24349210 1.350000e-59 241


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 TraesCS5B01G529100 chr5B 687744411 687748178 3767 False 6959.000000 6959 100.000000 1 3768 1 chr5B.!!$F1 3767
1 TraesCS5B01G529100 chr5B 687738575 687740223 1648 True 460.500000 621 79.695500 701 2390 2 chr5B.!!$R1 1689
2 TraesCS5B01G529100 chr5D 545144626 545148173 3547 False 2525.000000 4837 86.437500 1 3768 2 chr5D.!!$F1 3767
3 TraesCS5B01G529100 chr5D 545123770 545125043 1273 True 883.000000 883 79.772000 701 1979 1 chr5D.!!$R2 1278
4 TraesCS5B01G529100 chr1A 570152383 570155877 3494 True 1565.500000 2981 91.810500 654 3768 2 chr1A.!!$R1 3114
5 TraesCS5B01G529100 chr4A 624925144 624927629 2485 False 887.666667 1707 87.789333 654 3768 3 chr4A.!!$F1 3114
6 TraesCS5B01G529100 chr4A 624920589 624921456 867 True 322.000000 394 86.088500 1231 1979 2 chr4A.!!$R1 748

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
279 283 0.321671 GCAGTGCAAGTCCTAGACCA 59.678 55.0 11.09 0.0 32.18 4.02 F
1418 1458 0.618968 AGTCGCCCAAGATCTTCCCT 60.619 55.0 4.57 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2182 0.957362 TGTGATTTGTGAATGCGGCA 59.043 45.0 4.58 4.58 0.0 5.69 R
2771 2971 0.886490 AGTTTGGTTCGAGCAGGCAG 60.886 55.0 0.53 0.00 0.0 4.85 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
62 63 7.772166 TCATACAGAGACAATACAGTTCGAAT 58.228 34.615 0.00 0.00 0.00 3.34
81 82 5.647658 TCGAATTCCTATGAGTGTGCATTTT 59.352 36.000 0.00 0.00 0.00 1.82
83 84 6.403527 CGAATTCCTATGAGTGTGCATTTTGA 60.404 38.462 0.00 0.00 0.00 2.69
106 107 0.976073 CCGGGTTCCCTAGAGCTTGA 60.976 60.000 6.31 0.00 0.00 3.02
108 109 1.278127 CGGGTTCCCTAGAGCTTGAAA 59.722 52.381 6.31 0.00 0.00 2.69
119 121 8.650490 TCCCTAGAGCTTGAAATTTCAAAAATT 58.350 29.630 28.49 18.61 45.61 1.82
174 176 9.871238 ATATACGTTTTGAACTGTATTGTCTCT 57.129 29.630 0.00 0.00 34.94 3.10
177 179 6.982141 ACGTTTTGAACTGTATTGTCTCTGTA 59.018 34.615 0.00 0.00 0.00 2.74
178 180 7.656137 ACGTTTTGAACTGTATTGTCTCTGTAT 59.344 33.333 0.00 0.00 0.00 2.29
179 181 8.162880 CGTTTTGAACTGTATTGTCTCTGTATC 58.837 37.037 0.00 0.00 0.00 2.24
180 182 8.988934 GTTTTGAACTGTATTGTCTCTGTATCA 58.011 33.333 0.00 0.00 0.00 2.15
181 183 9.725019 TTTTGAACTGTATTGTCTCTGTATCAT 57.275 29.630 0.00 0.00 0.00 2.45
191 193 7.930513 TTGTCTCTGTATCATATAAAGTGCG 57.069 36.000 0.00 0.00 0.00 5.34
192 194 7.039313 TGTCTCTGTATCATATAAAGTGCGT 57.961 36.000 0.00 0.00 0.00 5.24
193 195 6.918022 TGTCTCTGTATCATATAAAGTGCGTG 59.082 38.462 0.00 0.00 0.00 5.34
194 196 6.918569 GTCTCTGTATCATATAAAGTGCGTGT 59.081 38.462 0.00 0.00 0.00 4.49
195 197 7.435488 GTCTCTGTATCATATAAAGTGCGTGTT 59.565 37.037 0.00 0.00 0.00 3.32
196 198 7.979537 TCTCTGTATCATATAAAGTGCGTGTTT 59.020 33.333 0.00 0.00 0.00 2.83
197 199 7.905126 TCTGTATCATATAAAGTGCGTGTTTG 58.095 34.615 0.00 0.00 0.00 2.93
198 200 7.762159 TCTGTATCATATAAAGTGCGTGTTTGA 59.238 33.333 0.00 0.00 0.00 2.69
199 201 8.257830 TGTATCATATAAAGTGCGTGTTTGAA 57.742 30.769 0.00 0.00 0.00 2.69
200 202 8.722394 TGTATCATATAAAGTGCGTGTTTGAAA 58.278 29.630 0.00 0.00 0.00 2.69
201 203 9.549509 GTATCATATAAAGTGCGTGTTTGAAAA 57.450 29.630 0.00 0.00 0.00 2.29
203 205 9.638239 ATCATATAAAGTGCGTGTTTGAAAATT 57.362 25.926 0.00 0.00 0.00 1.82
204 206 9.469807 TCATATAAAGTGCGTGTTTGAAAATTT 57.530 25.926 0.00 0.00 0.00 1.82
205 207 9.514822 CATATAAAGTGCGTGTTTGAAAATTTG 57.485 29.630 0.00 0.00 0.00 2.32
206 208 3.923827 AGTGCGTGTTTGAAAATTTGC 57.076 38.095 0.00 0.00 0.00 3.68
207 209 3.257393 AGTGCGTGTTTGAAAATTTGCA 58.743 36.364 0.00 0.00 0.00 4.08
208 210 3.870419 AGTGCGTGTTTGAAAATTTGCAT 59.130 34.783 0.00 0.00 33.25 3.96
209 211 3.961240 GTGCGTGTTTGAAAATTTGCATG 59.039 39.130 0.00 0.00 33.25 4.06
212 214 5.291858 TGCGTGTTTGAAAATTTGCATGTTA 59.708 32.000 0.00 0.00 0.00 2.41
215 217 7.217070 GCGTGTTTGAAAATTTGCATGTTAAAA 59.783 29.630 0.00 0.00 0.00 1.52
228 230 8.581057 TTGCATGTTAAAATACGTTTTGATGT 57.419 26.923 0.00 0.00 38.01 3.06
229 231 8.001358 TGCATGTTAAAATACGTTTTGATGTG 57.999 30.769 0.00 0.00 38.01 3.21
236 238 2.748461 ACGTTTTGATGTGAACCACG 57.252 45.000 0.00 0.00 37.14 4.94
238 240 1.268285 CGTTTTGATGTGAACCACGCA 60.268 47.619 0.00 0.00 43.33 5.24
242 244 3.510388 TTGATGTGAACCACGCAAAAA 57.490 38.095 0.00 0.00 42.43 1.94
247 249 2.190161 GTGAACCACGCAAAAAGAACC 58.810 47.619 0.00 0.00 0.00 3.62
248 250 1.135333 TGAACCACGCAAAAAGAACCC 59.865 47.619 0.00 0.00 0.00 4.11
249 251 1.407618 GAACCACGCAAAAAGAACCCT 59.592 47.619 0.00 0.00 0.00 4.34
250 252 1.480789 ACCACGCAAAAAGAACCCTT 58.519 45.000 0.00 0.00 0.00 3.95
251 253 1.828595 ACCACGCAAAAAGAACCCTTT 59.171 42.857 0.00 0.00 44.00 3.11
271 275 5.163814 CCTTTTATAGTGAGCAGTGCAAGTC 60.164 44.000 19.20 6.91 0.00 3.01
279 283 0.321671 GCAGTGCAAGTCCTAGACCA 59.678 55.000 11.09 0.00 32.18 4.02
295 299 6.821665 TCCTAGACCATGATTTTCCTTAAACG 59.178 38.462 0.00 0.00 0.00 3.60
308 312 8.568676 TTTTCCTTAAACGTATTCCATCATGA 57.431 30.769 0.00 0.00 0.00 3.07
317 321 9.787532 AAACGTATTCCATCATGAAACTTTATG 57.212 29.630 0.00 0.00 0.00 1.90
336 340 8.220559 ACTTTATGAACATGCAATATACTCCCT 58.779 33.333 0.00 0.00 0.00 4.20
337 341 8.621532 TTTATGAACATGCAATATACTCCCTC 57.378 34.615 0.00 0.00 0.00 4.30
338 342 4.973168 TGAACATGCAATATACTCCCTCC 58.027 43.478 0.00 0.00 0.00 4.30
339 343 3.685139 ACATGCAATATACTCCCTCCG 57.315 47.619 0.00 0.00 0.00 4.63
342 346 3.746045 TGCAATATACTCCCTCCGTTC 57.254 47.619 0.00 0.00 0.00 3.95
344 348 2.633481 GCAATATACTCCCTCCGTTCCT 59.367 50.000 0.00 0.00 0.00 3.36
345 349 3.830755 GCAATATACTCCCTCCGTTCCTA 59.169 47.826 0.00 0.00 0.00 2.94
346 350 4.282703 GCAATATACTCCCTCCGTTCCTAA 59.717 45.833 0.00 0.00 0.00 2.69
347 351 5.221581 GCAATATACTCCCTCCGTTCCTAAA 60.222 44.000 0.00 0.00 0.00 1.85
348 352 6.520231 GCAATATACTCCCTCCGTTCCTAAAT 60.520 42.308 0.00 0.00 0.00 1.40
349 353 7.310237 GCAATATACTCCCTCCGTTCCTAAATA 60.310 40.741 0.00 0.00 0.00 1.40
350 354 8.759782 CAATATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
353 357 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
354 358 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
355 359 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
356 360 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
357 361 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
358 362 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
359 363 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
390 394 9.425577 GATTTCACTATTAACTACATAGGGAGC 57.574 37.037 0.00 0.00 37.82 4.70
391 395 7.907841 TTCACTATTAACTACATAGGGAGCA 57.092 36.000 0.00 0.00 37.82 4.26
392 396 7.907841 TCACTATTAACTACATAGGGAGCAA 57.092 36.000 0.00 0.00 32.62 3.91
393 397 8.313944 TCACTATTAACTACATAGGGAGCAAA 57.686 34.615 0.00 0.00 32.62 3.68
394 398 8.764558 TCACTATTAACTACATAGGGAGCAAAA 58.235 33.333 0.00 0.00 32.62 2.44
395 399 9.561069 CACTATTAACTACATAGGGAGCAAAAT 57.439 33.333 0.00 0.00 30.09 1.82
396 400 9.561069 ACTATTAACTACATAGGGAGCAAAATG 57.439 33.333 0.00 0.00 0.00 2.32
397 401 9.778741 CTATTAACTACATAGGGAGCAAAATGA 57.221 33.333 0.00 0.00 0.00 2.57
398 402 8.682936 ATTAACTACATAGGGAGCAAAATGAG 57.317 34.615 0.00 0.00 0.00 2.90
399 403 5.700402 ACTACATAGGGAGCAAAATGAGT 57.300 39.130 0.00 0.00 0.00 3.41
400 404 5.431765 ACTACATAGGGAGCAAAATGAGTG 58.568 41.667 0.00 0.00 0.00 3.51
401 405 4.574674 ACATAGGGAGCAAAATGAGTGA 57.425 40.909 0.00 0.00 0.00 3.41
402 406 4.922206 ACATAGGGAGCAAAATGAGTGAA 58.078 39.130 0.00 0.00 0.00 3.18
403 407 5.513233 ACATAGGGAGCAAAATGAGTGAAT 58.487 37.500 0.00 0.00 0.00 2.57
404 408 5.591877 ACATAGGGAGCAAAATGAGTGAATC 59.408 40.000 0.00 0.00 0.00 2.52
405 409 4.313020 AGGGAGCAAAATGAGTGAATCT 57.687 40.909 0.00 0.00 0.00 2.40
406 410 5.441718 AGGGAGCAAAATGAGTGAATCTA 57.558 39.130 0.00 0.00 0.00 1.98
407 411 5.189180 AGGGAGCAAAATGAGTGAATCTAC 58.811 41.667 0.00 0.00 0.00 2.59
408 412 4.943705 GGGAGCAAAATGAGTGAATCTACA 59.056 41.667 0.00 0.00 0.00 2.74
409 413 5.163713 GGGAGCAAAATGAGTGAATCTACAC 60.164 44.000 0.00 0.00 40.60 2.90
452 456 7.432148 ACATCCATATGTAGTTTGTAGTGGA 57.568 36.000 1.24 0.00 44.66 4.02
453 457 7.857456 ACATCCATATGTAGTTTGTAGTGGAA 58.143 34.615 1.24 0.00 44.66 3.53
454 458 8.494433 ACATCCATATGTAGTTTGTAGTGGAAT 58.506 33.333 1.24 0.00 44.66 3.01
455 459 8.993121 CATCCATATGTAGTTTGTAGTGGAATC 58.007 37.037 1.24 0.00 37.96 2.52
456 460 8.319057 TCCATATGTAGTTTGTAGTGGAATCT 57.681 34.615 1.24 0.00 32.02 2.40
457 461 8.768397 TCCATATGTAGTTTGTAGTGGAATCTT 58.232 33.333 1.24 0.00 32.02 2.40
458 462 9.396022 CCATATGTAGTTTGTAGTGGAATCTTT 57.604 33.333 1.24 0.00 0.00 2.52
461 465 8.918202 ATGTAGTTTGTAGTGGAATCTTTCAA 57.082 30.769 0.00 0.00 0.00 2.69
462 466 8.740123 TGTAGTTTGTAGTGGAATCTTTCAAA 57.260 30.769 0.00 0.00 0.00 2.69
463 467 9.179909 TGTAGTTTGTAGTGGAATCTTTCAAAA 57.820 29.630 0.00 0.00 0.00 2.44
464 468 9.665264 GTAGTTTGTAGTGGAATCTTTCAAAAG 57.335 33.333 0.00 0.00 37.36 2.27
466 470 8.406297 AGTTTGTAGTGGAATCTTTCAAAAGAC 58.594 33.333 7.32 0.00 46.80 3.01
467 471 8.406297 GTTTGTAGTGGAATCTTTCAAAAGACT 58.594 33.333 7.32 0.00 46.80 3.24
468 472 8.519799 TTGTAGTGGAATCTTTCAAAAGACTT 57.480 30.769 7.32 4.22 46.80 3.01
469 473 9.621629 TTGTAGTGGAATCTTTCAAAAGACTTA 57.378 29.630 7.32 0.00 46.80 2.24
470 474 9.793259 TGTAGTGGAATCTTTCAAAAGACTTAT 57.207 29.630 7.32 0.00 46.80 1.73
483 487 9.947433 TTCAAAAGACTTATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
484 488 9.595823 TCAAAAGACTTATATTTAGGAACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
485 489 8.827677 CAAAAGACTTATATTTAGGAACGGAGG 58.172 37.037 0.00 0.00 0.00 4.30
486 490 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
487 491 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
488 492 6.267242 AGACTTATATTTAGGAACGGAGGGAC 59.733 42.308 0.00 0.00 0.00 4.46
490 494 7.300658 ACTTATATTTAGGAACGGAGGGACTA 58.699 38.462 0.00 0.00 41.55 2.59
491 495 7.232330 ACTTATATTTAGGAACGGAGGGACTAC 59.768 40.741 0.00 0.00 41.55 2.73
492 496 2.905415 TTAGGAACGGAGGGACTACA 57.095 50.000 0.00 0.00 41.36 2.74
493 497 3.393426 TTAGGAACGGAGGGACTACAT 57.607 47.619 0.00 0.00 41.36 2.29
494 498 1.777941 AGGAACGGAGGGACTACATC 58.222 55.000 0.00 0.00 41.36 3.06
495 499 1.006758 AGGAACGGAGGGACTACATCA 59.993 52.381 0.00 0.00 41.36 3.07
496 500 1.136500 GGAACGGAGGGACTACATCAC 59.864 57.143 0.00 0.00 41.36 3.06
498 502 3.285484 GAACGGAGGGACTACATCACTA 58.715 50.000 0.00 0.00 43.11 2.74
499 503 3.596940 ACGGAGGGACTACATCACTAT 57.403 47.619 0.00 0.00 43.11 2.12
500 504 4.719026 ACGGAGGGACTACATCACTATA 57.281 45.455 0.00 0.00 43.11 1.31
501 505 5.258216 ACGGAGGGACTACATCACTATAT 57.742 43.478 0.00 0.00 43.11 0.86
502 506 6.384342 ACGGAGGGACTACATCACTATATA 57.616 41.667 0.00 0.00 43.11 0.86
503 507 6.179040 ACGGAGGGACTACATCACTATATAC 58.821 44.000 0.00 0.00 43.11 1.47
504 508 6.178324 CGGAGGGACTACATCACTATATACA 58.822 44.000 0.00 0.00 43.11 2.29
505 509 6.829298 CGGAGGGACTACATCACTATATACAT 59.171 42.308 0.00 0.00 43.11 2.29
506 510 7.201741 CGGAGGGACTACATCACTATATACATG 60.202 44.444 0.00 0.00 43.11 3.21
507 511 7.411486 AGGGACTACATCACTATATACATGC 57.589 40.000 0.00 0.00 40.32 4.06
508 512 6.954102 AGGGACTACATCACTATATACATGCA 59.046 38.462 0.00 0.00 40.32 3.96
509 513 7.621285 AGGGACTACATCACTATATACATGCAT 59.379 37.037 0.00 0.00 40.32 3.96
563 567 9.971922 ATCGAAATCTGATTTTTGAGTTTTTCT 57.028 25.926 16.14 0.50 33.58 2.52
638 643 5.043903 CCTCTAACTACATCCATGTTCACG 58.956 45.833 0.00 0.00 41.97 4.35
647 652 4.635765 ACATCCATGTTCACGACAATAAGG 59.364 41.667 0.00 0.00 42.62 2.69
670 675 1.069978 TGCCGACATGTCTTCAACTCA 59.930 47.619 22.95 7.61 0.00 3.41
708 717 3.550820 TCGGAGAGAGAAAGGATCTGAG 58.449 50.000 0.00 0.00 38.96 3.35
756 769 6.313324 AGGAACTAGTGGGGTCATATACTAC 58.687 44.000 0.00 0.00 36.02 2.73
812 829 4.211374 CCCTTTTGACGTCTGACTTTGTAG 59.789 45.833 17.92 1.62 0.00 2.74
1005 1028 1.337167 GCAAACTCCAAACTGATGGCC 60.337 52.381 0.00 0.00 40.46 5.36
1135 1161 3.677424 CGAAAAGGAGCTCCAGGTAAGAG 60.677 52.174 33.90 13.31 38.89 2.85
1227 1260 8.688151 GTGAATGGAGTATAGGAGTATATCACC 58.312 40.741 0.00 0.00 0.00 4.02
1418 1458 0.618968 AGTCGCCCAAGATCTTCCCT 60.619 55.000 4.57 0.00 0.00 4.20
1622 1692 2.125552 CCATTCGCTGCTCCGTCA 60.126 61.111 0.00 0.00 0.00 4.35
1793 1965 8.705048 AGTAGTTAAGTAATTGACTAAGCTGC 57.295 34.615 8.87 0.00 37.44 5.25
1794 1966 8.532819 AGTAGTTAAGTAATTGACTAAGCTGCT 58.467 33.333 8.87 0.00 37.44 4.24
1992 2168 5.999600 ACAACCCTGTATGTTACCAACTAAC 59.000 40.000 0.00 0.00 33.35 2.34
1993 2169 6.183361 ACAACCCTGTATGTTACCAACTAACT 60.183 38.462 0.00 0.00 33.66 2.24
1994 2170 7.016465 ACAACCCTGTATGTTACCAACTAACTA 59.984 37.037 0.00 0.00 33.66 2.24
2006 2182 4.020485 ACCAACTAACTAATTGACCTCGCT 60.020 41.667 0.00 0.00 0.00 4.93
2020 2196 2.186350 CTCGCTGCCGCATTCACAAA 62.186 55.000 0.00 0.00 35.30 2.83
2065 2241 3.708121 TCTCACTCATGGACTGCATATGT 59.292 43.478 4.29 0.00 0.00 2.29
2066 2242 4.895297 TCTCACTCATGGACTGCATATGTA 59.105 41.667 4.29 0.00 0.00 2.29
2067 2243 5.541484 TCTCACTCATGGACTGCATATGTAT 59.459 40.000 4.29 0.00 0.00 2.29
2068 2244 5.544650 TCACTCATGGACTGCATATGTATG 58.455 41.667 4.29 0.00 36.78 2.39
2391 2573 3.118371 GCTTGCACACCTACCCTATTACT 60.118 47.826 0.00 0.00 0.00 2.24
2395 2577 6.169557 TGCACACCTACCCTATTACTATTG 57.830 41.667 0.00 0.00 0.00 1.90
2399 2581 7.525029 GCACACCTACCCTATTACTATTGGTAG 60.525 44.444 6.98 6.98 45.25 3.18
2401 2583 8.736675 ACACCTACCCTATTACTATTGGTAGTA 58.263 37.037 11.78 0.00 44.54 1.82
2508 2706 8.598924 CATCATCTGTTGTAGTAATGACTCAAC 58.401 37.037 14.14 14.14 40.44 3.18
2509 2707 7.097192 TCATCTGTTGTAGTAATGACTCAACC 58.903 38.462 16.57 5.98 39.92 3.77
2510 2708 5.466819 TCTGTTGTAGTAATGACTCAACCG 58.533 41.667 16.57 12.79 39.92 4.44
2511 2709 5.242171 TCTGTTGTAGTAATGACTCAACCGA 59.758 40.000 16.57 14.18 39.92 4.69
2512 2710 6.032956 TGTTGTAGTAATGACTCAACCGAT 57.967 37.500 16.57 0.00 39.92 4.18
2513 2711 5.867174 TGTTGTAGTAATGACTCAACCGATG 59.133 40.000 16.57 0.00 39.92 3.84
2514 2712 5.907866 TGTAGTAATGACTCAACCGATGA 57.092 39.130 0.00 0.00 37.10 2.92
2515 2713 5.647589 TGTAGTAATGACTCAACCGATGAC 58.352 41.667 0.00 0.00 37.10 3.06
2516 2714 5.417894 TGTAGTAATGACTCAACCGATGACT 59.582 40.000 0.00 0.00 37.10 3.41
2517 2715 5.000012 AGTAATGACTCAACCGATGACTC 58.000 43.478 0.00 0.00 33.47 3.36
2518 2716 3.961480 AATGACTCAACCGATGACTCA 57.039 42.857 0.00 0.00 35.98 3.41
2519 2717 3.961480 ATGACTCAACCGATGACTCAA 57.039 42.857 5.24 0.00 35.42 3.02
2771 2971 4.211389 CAGACGCCGCAACAATTAATATC 58.789 43.478 0.00 0.00 0.00 1.63
2839 3039 7.745594 TGTGTGTTTAAGTTCACTTTTACGTTC 59.254 33.333 0.00 0.00 37.40 3.95
2858 3058 4.994852 CGTTCAGTTTGGGAGTTCAATCTA 59.005 41.667 0.00 0.00 0.00 1.98
2875 3075 9.358123 GTTCAATCTATTTGATTTATGTCGTCG 57.642 33.333 0.00 0.00 43.73 5.12
2876 3076 8.642908 TCAATCTATTTGATTTATGTCGTCGT 57.357 30.769 0.00 0.00 43.00 4.34
2877 3077 9.093970 TCAATCTATTTGATTTATGTCGTCGTT 57.906 29.630 0.00 0.00 43.00 3.85
2878 3078 9.702726 CAATCTATTTGATTTATGTCGTCGTTT 57.297 29.630 0.00 0.00 43.00 3.60
2985 3185 8.559536 GTTTATGTGACGTGGAAATGATATCAT 58.440 33.333 12.62 12.62 38.41 2.45
2986 3186 5.989551 TGTGACGTGGAAATGATATCATG 57.010 39.130 18.85 7.81 36.56 3.07
2987 3187 5.427378 TGTGACGTGGAAATGATATCATGT 58.573 37.500 18.85 13.72 36.56 3.21
2988 3188 5.879777 TGTGACGTGGAAATGATATCATGTT 59.120 36.000 18.85 14.10 36.56 2.71
2989 3189 7.044798 TGTGACGTGGAAATGATATCATGTTA 58.955 34.615 18.85 5.61 36.56 2.41
2990 3190 7.550906 TGTGACGTGGAAATGATATCATGTTAA 59.449 33.333 18.85 3.43 36.56 2.01
2991 3191 7.850982 GTGACGTGGAAATGATATCATGTTAAC 59.149 37.037 18.85 13.57 36.56 2.01
2992 3192 7.768582 TGACGTGGAAATGATATCATGTTAACT 59.231 33.333 18.85 0.00 36.56 2.24
2993 3193 9.256477 GACGTGGAAATGATATCATGTTAACTA 57.744 33.333 18.85 4.80 36.56 2.24
2994 3194 9.778741 ACGTGGAAATGATATCATGTTAACTAT 57.221 29.630 18.85 0.00 36.56 2.12
2999 3199 9.831737 GAAATGATATCATGTTAACTATGGTGC 57.168 33.333 18.85 0.00 36.56 5.01
3000 3200 9.578576 AAATGATATCATGTTAACTATGGTGCT 57.421 29.630 18.85 0.00 36.56 4.40
3001 3201 7.967890 TGATATCATGTTAACTATGGTGCTG 57.032 36.000 7.22 0.00 0.00 4.41
3002 3202 7.508687 TGATATCATGTTAACTATGGTGCTGT 58.491 34.615 7.22 0.00 0.00 4.40
3003 3203 7.992608 TGATATCATGTTAACTATGGTGCTGTT 59.007 33.333 7.22 0.00 0.00 3.16
3004 3204 5.878332 TCATGTTAACTATGGTGCTGTTG 57.122 39.130 7.22 0.00 0.00 3.33
3005 3205 5.312895 TCATGTTAACTATGGTGCTGTTGT 58.687 37.500 7.22 0.00 0.00 3.32
3006 3206 6.468543 TCATGTTAACTATGGTGCTGTTGTA 58.531 36.000 7.22 0.00 0.00 2.41
3007 3207 6.937465 TCATGTTAACTATGGTGCTGTTGTAA 59.063 34.615 7.22 0.00 0.00 2.41
3111 3329 5.634020 GGCCATTGTTAGAGTCGTATATCAC 59.366 44.000 0.00 0.00 0.00 3.06
3245 3463 5.897377 ATACACTGCATGGTTTTTCCTAC 57.103 39.130 0.00 0.00 37.07 3.18
3258 3476 2.307496 TTCCTACCTTGGACACGGTA 57.693 50.000 7.38 7.38 35.58 4.02
3286 3504 0.606401 CAACCCTCAACACCGATGCT 60.606 55.000 0.00 0.00 0.00 3.79
3287 3505 0.981183 AACCCTCAACACCGATGCTA 59.019 50.000 0.00 0.00 0.00 3.49
3290 3508 0.462047 CCTCAACACCGATGCTACCC 60.462 60.000 0.00 0.00 0.00 3.69
3314 3532 5.387444 CGTGCACATAATTCACGCTCTATAC 60.387 44.000 18.64 0.00 45.22 1.47
3358 3576 5.629079 ACTTGCCTTTTATGCACTAGTTC 57.371 39.130 0.00 0.00 38.72 3.01
3395 3613 6.706055 TGATCATTCACTTTTGAGTCGTAC 57.294 37.500 0.00 0.00 31.71 3.67
3413 3631 3.894288 CGTACGTATCGGTGTATGTAACG 59.106 47.826 7.22 0.00 30.24 3.18
3443 3661 2.147958 TGGTTTGTATGGTTGCGACTC 58.852 47.619 3.59 0.00 0.00 3.36
3516 3995 8.978874 TGTTATAACAGCATACCATGAGAATT 57.021 30.769 14.35 0.00 34.30 2.17
3590 4069 3.234386 GCGTTAGCAAAATTGACAGTCC 58.766 45.455 0.00 0.00 44.35 3.85
3591 4070 3.304391 GCGTTAGCAAAATTGACAGTCCA 60.304 43.478 0.00 0.00 44.35 4.02
3607 4086 6.982141 TGACAGTCCACGGATGTATTATAAAC 59.018 38.462 0.00 0.00 0.00 2.01
3634 4116 2.543777 AGAGCAACTTGTAAGCCGAA 57.456 45.000 0.00 0.00 0.00 4.30
3671 5134 6.563422 TGACATAAGCAAGGATAATGTTTGC 58.437 36.000 0.46 0.46 45.64 3.68
3725 5192 6.810676 CCACATCGATCTTCATACTATTCCAG 59.189 42.308 0.00 0.00 0.00 3.86
3728 5195 6.018589 TCGATCTTCATACTATTCCAGCTG 57.981 41.667 6.78 6.78 0.00 4.24
3760 5227 2.866762 GGAGAGGAATCAATACGTGCAC 59.133 50.000 6.82 6.82 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.509855 GAACTGTATTGTCTCTGTATGAACTAG 57.490 37.037 0.00 0.00 0.00 2.57
51 52 6.330278 CACACTCATAGGAATTCGAACTGTA 58.670 40.000 0.00 0.00 0.00 2.74
62 63 5.316167 AGTCAAAATGCACACTCATAGGAA 58.684 37.500 0.00 0.00 0.00 3.36
149 151 9.135843 CAGAGACAATACAGTTCAAAACGTATA 57.864 33.333 0.00 0.00 33.77 1.47
153 155 6.287107 ACAGAGACAATACAGTTCAAAACG 57.713 37.500 0.00 0.00 36.23 3.60
155 157 9.725019 ATGATACAGAGACAATACAGTTCAAAA 57.275 29.630 0.00 0.00 0.00 2.44
165 167 9.626045 CGCACTTTATATGATACAGAGACAATA 57.374 33.333 0.00 0.00 0.00 1.90
166 168 8.144478 ACGCACTTTATATGATACAGAGACAAT 58.856 33.333 0.00 0.00 0.00 2.71
167 169 7.435192 CACGCACTTTATATGATACAGAGACAA 59.565 37.037 0.00 0.00 0.00 3.18
168 170 6.918022 CACGCACTTTATATGATACAGAGACA 59.082 38.462 0.00 0.00 0.00 3.41
169 171 6.918569 ACACGCACTTTATATGATACAGAGAC 59.081 38.462 0.00 0.00 0.00 3.36
170 172 7.039313 ACACGCACTTTATATGATACAGAGA 57.961 36.000 0.00 0.00 0.00 3.10
171 173 7.700322 AACACGCACTTTATATGATACAGAG 57.300 36.000 0.00 0.00 0.00 3.35
172 174 7.762159 TCAAACACGCACTTTATATGATACAGA 59.238 33.333 0.00 0.00 0.00 3.41
174 176 7.835634 TCAAACACGCACTTTATATGATACA 57.164 32.000 0.00 0.00 0.00 2.29
177 179 9.638239 AATTTTCAAACACGCACTTTATATGAT 57.362 25.926 0.00 0.00 0.00 2.45
178 180 9.469807 AAATTTTCAAACACGCACTTTATATGA 57.530 25.926 0.00 0.00 0.00 2.15
179 181 9.514822 CAAATTTTCAAACACGCACTTTATATG 57.485 29.630 0.00 0.00 0.00 1.78
180 182 8.220434 GCAAATTTTCAAACACGCACTTTATAT 58.780 29.630 0.00 0.00 0.00 0.86
181 183 7.222805 TGCAAATTTTCAAACACGCACTTTATA 59.777 29.630 0.00 0.00 0.00 0.98
182 184 6.036517 TGCAAATTTTCAAACACGCACTTTAT 59.963 30.769 0.00 0.00 0.00 1.40
184 186 4.153117 TGCAAATTTTCAAACACGCACTTT 59.847 33.333 0.00 0.00 0.00 2.66
185 187 3.681897 TGCAAATTTTCAAACACGCACTT 59.318 34.783 0.00 0.00 0.00 3.16
186 188 3.257393 TGCAAATTTTCAAACACGCACT 58.743 36.364 0.00 0.00 0.00 4.40
187 189 3.648179 TGCAAATTTTCAAACACGCAC 57.352 38.095 0.00 0.00 0.00 5.34
188 190 3.620374 ACATGCAAATTTTCAAACACGCA 59.380 34.783 0.00 0.00 0.00 5.24
189 191 4.194381 ACATGCAAATTTTCAAACACGC 57.806 36.364 0.00 0.00 0.00 5.34
190 192 8.593057 TTTTAACATGCAAATTTTCAAACACG 57.407 26.923 0.00 0.00 0.00 4.49
202 204 9.035607 ACATCAAAACGTATTTTAACATGCAAA 57.964 25.926 0.00 0.00 35.79 3.68
203 205 8.483218 CACATCAAAACGTATTTTAACATGCAA 58.517 29.630 0.00 0.00 35.79 4.08
204 206 7.862873 TCACATCAAAACGTATTTTAACATGCA 59.137 29.630 0.00 0.00 35.79 3.96
205 207 8.221801 TCACATCAAAACGTATTTTAACATGC 57.778 30.769 0.00 0.00 35.79 4.06
206 208 9.987901 GTTCACATCAAAACGTATTTTAACATG 57.012 29.630 0.00 0.00 35.79 3.21
207 209 9.187455 GGTTCACATCAAAACGTATTTTAACAT 57.813 29.630 0.00 0.00 35.79 2.71
208 210 8.188799 TGGTTCACATCAAAACGTATTTTAACA 58.811 29.630 0.00 0.00 35.79 2.41
209 211 8.473796 GTGGTTCACATCAAAACGTATTTTAAC 58.526 33.333 0.00 0.00 33.83 2.01
212 214 5.683743 CGTGGTTCACATCAAAACGTATTTT 59.316 36.000 0.00 0.00 34.68 1.82
215 217 3.364565 GCGTGGTTCACATCAAAACGTAT 60.365 43.478 0.00 0.00 33.40 3.06
217 219 1.268335 GCGTGGTTCACATCAAAACGT 60.268 47.619 0.00 0.00 33.40 3.99
218 220 1.268285 TGCGTGGTTCACATCAAAACG 60.268 47.619 0.00 0.00 33.40 3.60
228 230 1.135333 GGGTTCTTTTTGCGTGGTTCA 59.865 47.619 0.00 0.00 0.00 3.18
229 231 1.407618 AGGGTTCTTTTTGCGTGGTTC 59.592 47.619 0.00 0.00 0.00 3.62
242 244 5.491982 CACTGCTCACTATAAAAGGGTTCT 58.508 41.667 0.00 0.00 0.00 3.01
247 249 4.697352 ACTTGCACTGCTCACTATAAAAGG 59.303 41.667 1.98 0.00 0.00 3.11
248 250 5.163814 GGACTTGCACTGCTCACTATAAAAG 60.164 44.000 1.98 0.00 0.00 2.27
249 251 4.695455 GGACTTGCACTGCTCACTATAAAA 59.305 41.667 1.98 0.00 0.00 1.52
250 252 4.020218 AGGACTTGCACTGCTCACTATAAA 60.020 41.667 1.98 0.00 0.00 1.40
251 253 3.515502 AGGACTTGCACTGCTCACTATAA 59.484 43.478 1.98 0.00 0.00 0.98
252 254 3.099905 AGGACTTGCACTGCTCACTATA 58.900 45.455 1.98 0.00 0.00 1.31
253 255 1.905215 AGGACTTGCACTGCTCACTAT 59.095 47.619 1.98 0.00 0.00 2.12
255 257 1.274728 CTAGGACTTGCACTGCTCACT 59.725 52.381 1.98 0.00 0.00 3.41
271 275 6.598064 ACGTTTAAGGAAAATCATGGTCTAGG 59.402 38.462 0.00 0.00 0.00 3.02
279 283 9.184523 TGATGGAATACGTTTAAGGAAAATCAT 57.815 29.630 0.00 0.00 0.00 2.45
316 320 4.503123 CGGAGGGAGTATATTGCATGTTCA 60.503 45.833 0.00 0.00 0.00 3.18
317 321 3.997021 CGGAGGGAGTATATTGCATGTTC 59.003 47.826 0.00 0.00 0.00 3.18
332 336 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
333 337 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
364 368 9.425577 GCTCCCTATGTAGTTAATAGTGAAATC 57.574 37.037 0.00 0.00 0.00 2.17
365 369 8.934697 TGCTCCCTATGTAGTTAATAGTGAAAT 58.065 33.333 0.00 0.00 0.00 2.17
366 370 8.313944 TGCTCCCTATGTAGTTAATAGTGAAA 57.686 34.615 0.00 0.00 0.00 2.69
367 371 7.907841 TGCTCCCTATGTAGTTAATAGTGAA 57.092 36.000 0.00 0.00 0.00 3.18
368 372 7.907841 TTGCTCCCTATGTAGTTAATAGTGA 57.092 36.000 0.00 0.00 0.00 3.41
369 373 8.958119 TTTTGCTCCCTATGTAGTTAATAGTG 57.042 34.615 0.00 0.00 0.00 2.74
370 374 9.561069 CATTTTGCTCCCTATGTAGTTAATAGT 57.439 33.333 0.00 0.00 0.00 2.12
371 375 9.778741 TCATTTTGCTCCCTATGTAGTTAATAG 57.221 33.333 0.00 0.00 0.00 1.73
372 376 9.778741 CTCATTTTGCTCCCTATGTAGTTAATA 57.221 33.333 0.00 0.00 0.00 0.98
373 377 8.275040 ACTCATTTTGCTCCCTATGTAGTTAAT 58.725 33.333 0.00 0.00 0.00 1.40
374 378 7.552687 CACTCATTTTGCTCCCTATGTAGTTAA 59.447 37.037 0.00 0.00 0.00 2.01
375 379 7.047891 CACTCATTTTGCTCCCTATGTAGTTA 58.952 38.462 0.00 0.00 0.00 2.24
376 380 5.882557 CACTCATTTTGCTCCCTATGTAGTT 59.117 40.000 0.00 0.00 0.00 2.24
377 381 5.189736 TCACTCATTTTGCTCCCTATGTAGT 59.810 40.000 0.00 0.00 0.00 2.73
378 382 5.674525 TCACTCATTTTGCTCCCTATGTAG 58.325 41.667 0.00 0.00 0.00 2.74
379 383 5.692115 TCACTCATTTTGCTCCCTATGTA 57.308 39.130 0.00 0.00 0.00 2.29
380 384 4.574674 TCACTCATTTTGCTCCCTATGT 57.425 40.909 0.00 0.00 0.00 2.29
381 385 5.826737 AGATTCACTCATTTTGCTCCCTATG 59.173 40.000 0.00 0.00 0.00 2.23
382 386 6.011122 AGATTCACTCATTTTGCTCCCTAT 57.989 37.500 0.00 0.00 0.00 2.57
383 387 5.441718 AGATTCACTCATTTTGCTCCCTA 57.558 39.130 0.00 0.00 0.00 3.53
384 388 4.313020 AGATTCACTCATTTTGCTCCCT 57.687 40.909 0.00 0.00 0.00 4.20
385 389 4.943705 TGTAGATTCACTCATTTTGCTCCC 59.056 41.667 0.00 0.00 0.00 4.30
386 390 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
387 391 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
426 430 9.154632 TCCACTACAAACTACATATGGATGTAT 57.845 33.333 7.80 0.00 45.42 2.29
427 431 8.541899 TCCACTACAAACTACATATGGATGTA 57.458 34.615 7.80 3.84 44.77 2.29
429 433 8.908786 ATTCCACTACAAACTACATATGGATG 57.091 34.615 7.80 0.00 35.03 3.51
430 434 8.938883 AGATTCCACTACAAACTACATATGGAT 58.061 33.333 7.80 0.00 35.03 3.41
431 435 8.319057 AGATTCCACTACAAACTACATATGGA 57.681 34.615 7.80 0.00 33.21 3.41
432 436 8.964476 AAGATTCCACTACAAACTACATATGG 57.036 34.615 7.80 0.00 0.00 2.74
436 440 8.918202 TTGAAAGATTCCACTACAAACTACAT 57.082 30.769 0.00 0.00 0.00 2.29
437 441 8.740123 TTTGAAAGATTCCACTACAAACTACA 57.260 30.769 0.00 0.00 0.00 2.74
438 442 9.665264 CTTTTGAAAGATTCCACTACAAACTAC 57.335 33.333 0.00 0.00 38.28 2.73
439 443 9.621629 TCTTTTGAAAGATTCCACTACAAACTA 57.378 29.630 2.16 0.00 39.95 2.24
440 444 8.406297 GTCTTTTGAAAGATTCCACTACAAACT 58.594 33.333 9.20 0.00 45.83 2.66
441 445 8.406297 AGTCTTTTGAAAGATTCCACTACAAAC 58.594 33.333 9.20 0.00 45.83 2.93
442 446 8.519799 AGTCTTTTGAAAGATTCCACTACAAA 57.480 30.769 9.20 0.00 45.83 2.83
443 447 8.519799 AAGTCTTTTGAAAGATTCCACTACAA 57.480 30.769 9.20 0.00 45.83 2.41
444 448 9.793259 ATAAGTCTTTTGAAAGATTCCACTACA 57.207 29.630 9.20 0.00 45.83 2.74
457 461 9.947433 TCCGTTCCTAAATATAAGTCTTTTGAA 57.053 29.630 0.00 0.00 0.00 2.69
458 462 9.595823 CTCCGTTCCTAAATATAAGTCTTTTGA 57.404 33.333 0.00 0.00 0.00 2.69
459 463 8.827677 CCTCCGTTCCTAAATATAAGTCTTTTG 58.172 37.037 0.00 0.00 0.00 2.44
460 464 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
461 465 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
462 466 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
463 467 6.267242 GTCCCTCCGTTCCTAAATATAAGTCT 59.733 42.308 0.00 0.00 0.00 3.24
464 468 6.267242 AGTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
465 469 6.141790 AGTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
466 470 6.667558 AGTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
467 471 7.068702 TGTAGTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
468 472 6.613699 TGTAGTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
469 473 5.461327 TGTAGTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
470 474 4.870636 TGTAGTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
471 475 3.716431 TGTAGTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
472 476 3.173953 TGTAGTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
473 477 2.905415 TGTAGTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
474 478 2.242965 TGATGTAGTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
475 479 1.006758 TGATGTAGTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
476 480 1.136500 GTGATGTAGTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
477 481 2.100989 AGTGATGTAGTCCCTCCGTTC 58.899 52.381 0.00 0.00 0.00 3.95
478 482 2.233305 AGTGATGTAGTCCCTCCGTT 57.767 50.000 0.00 0.00 0.00 4.44
479 483 3.596940 ATAGTGATGTAGTCCCTCCGT 57.403 47.619 0.00 0.00 0.00 4.69
480 484 6.178324 TGTATATAGTGATGTAGTCCCTCCG 58.822 44.000 0.00 0.00 0.00 4.63
481 485 7.416890 GCATGTATATAGTGATGTAGTCCCTCC 60.417 44.444 0.00 0.00 0.00 4.30
482 486 7.122799 TGCATGTATATAGTGATGTAGTCCCTC 59.877 40.741 0.00 0.00 0.00 4.30
483 487 6.954102 TGCATGTATATAGTGATGTAGTCCCT 59.046 38.462 0.00 0.00 0.00 4.20
484 488 7.170393 TGCATGTATATAGTGATGTAGTCCC 57.830 40.000 0.00 0.00 0.00 4.46
485 489 8.253810 ACATGCATGTATATAGTGATGTAGTCC 58.746 37.037 30.50 0.00 39.68 3.85
486 490 9.080915 CACATGCATGTATATAGTGATGTAGTC 57.919 37.037 30.92 0.00 39.39 2.59
487 491 8.588472 ACACATGCATGTATATAGTGATGTAGT 58.412 33.333 30.92 16.42 39.39 2.73
488 492 8.866956 CACACATGCATGTATATAGTGATGTAG 58.133 37.037 29.54 17.60 39.39 2.74
489 493 8.761575 CACACATGCATGTATATAGTGATGTA 57.238 34.615 29.54 0.00 39.39 2.29
490 494 7.662604 CACACATGCATGTATATAGTGATGT 57.337 36.000 29.54 19.08 39.39 3.06
505 509 9.725565 AGAAAATTCTGAAAAGGCACACATGCA 62.726 37.037 1.18 0.00 44.47 3.96
506 510 7.452046 AGAAAATTCTGAAAAGGCACACATGC 61.452 38.462 0.00 0.00 43.04 4.06
507 511 5.987347 AGAAAATTCTGAAAAGGCACACATG 59.013 36.000 0.00 0.00 35.89 3.21
508 512 6.165700 AGAAAATTCTGAAAAGGCACACAT 57.834 33.333 0.00 0.00 35.89 3.21
509 513 5.596836 AGAAAATTCTGAAAAGGCACACA 57.403 34.783 0.00 0.00 35.89 3.72
563 567 0.181114 CTCCATGGAGCCCGAATTCA 59.819 55.000 28.45 0.00 35.31 2.57
584 589 3.246301 TGGAAATTGCTTTTGGATCCCA 58.754 40.909 9.90 0.00 0.00 4.37
638 643 3.627577 ACATGTCGGCAATCCTTATTGTC 59.372 43.478 0.00 0.00 43.75 3.18
647 652 2.744202 AGTTGAAGACATGTCGGCAATC 59.256 45.455 27.34 21.97 33.00 2.67
670 675 9.331282 CTCTCTCCGATCCTTTTTAATACAATT 57.669 33.333 0.00 0.00 0.00 2.32
708 717 8.487176 CCTTGTGCACAAAAGAATATTACAAAC 58.513 33.333 30.62 0.00 35.15 2.93
756 769 8.944029 CCAGCTAATCCAGAATTCATAATAGTG 58.056 37.037 8.44 0.00 0.00 2.74
812 829 1.534729 CCTCAACTGCAGGGGTTAAC 58.465 55.000 19.93 0.00 0.00 2.01
877 895 2.883574 AGACAACGTCTGAAACAACGA 58.116 42.857 1.52 0.00 41.76 3.85
878 896 3.548668 TGTAGACAACGTCTGAAACAACG 59.451 43.478 6.90 0.00 43.30 4.10
922 940 4.723309 AGGTGGCAGAGAATATGGATTTC 58.277 43.478 0.00 0.00 0.00 2.17
1005 1028 1.005037 TGCAGCAGAACTACCACCG 60.005 57.895 0.00 0.00 0.00 4.94
1227 1260 3.494626 AGTTTCTACACACAACTCATGCG 59.505 43.478 0.00 0.00 0.00 4.73
1310 1350 1.811266 CATCACCGTCAAGAGGCCG 60.811 63.158 0.00 0.00 0.00 6.13
1418 1458 5.201713 CTCAGTTGGTGAGTTACTTCTGA 57.798 43.478 0.00 0.00 46.89 3.27
1792 1964 3.119602 ACTGATCAATCATGCACACAAGC 60.120 43.478 0.00 0.00 36.02 4.01
1793 1965 4.696899 ACTGATCAATCATGCACACAAG 57.303 40.909 0.00 0.00 36.02 3.16
1794 1966 4.321378 CCAACTGATCAATCATGCACACAA 60.321 41.667 0.00 0.00 36.02 3.33
1992 2168 1.766143 GCGGCAGCGAGGTCAATTAG 61.766 60.000 0.00 0.00 0.00 1.73
1993 2169 1.813753 GCGGCAGCGAGGTCAATTA 60.814 57.895 0.00 0.00 0.00 1.40
1994 2170 3.127533 GCGGCAGCGAGGTCAATT 61.128 61.111 0.00 0.00 0.00 2.32
2006 2182 0.957362 TGTGATTTGTGAATGCGGCA 59.043 45.000 4.58 4.58 0.00 5.69
2065 2241 5.787380 CCAATAGAGTCTGCAGCATACATA 58.213 41.667 9.47 6.11 0.00 2.29
2066 2242 4.639334 CCAATAGAGTCTGCAGCATACAT 58.361 43.478 9.47 4.19 0.00 2.29
2067 2243 3.742327 GCCAATAGAGTCTGCAGCATACA 60.742 47.826 9.47 0.00 0.00 2.29
2068 2244 2.805099 GCCAATAGAGTCTGCAGCATAC 59.195 50.000 9.47 1.80 0.00 2.39
2514 2712 9.494766 GCACTTGCATACAATGGATCATTGAGT 62.495 40.741 22.52 13.33 45.45 3.41
2515 2713 7.223487 GCACTTGCATACAATGGATCATTGAG 61.223 42.308 22.52 12.83 45.45 3.02
2516 2714 5.450826 GCACTTGCATACAATGGATCATTGA 60.451 40.000 22.52 10.09 45.45 2.57
2517 2715 4.743151 GCACTTGCATACAATGGATCATTG 59.257 41.667 16.29 16.29 46.55 2.82
2518 2716 4.940463 GCACTTGCATACAATGGATCATT 58.060 39.130 0.00 0.00 41.59 2.57
2519 2717 4.579454 GCACTTGCATACAATGGATCAT 57.421 40.909 0.00 0.00 41.59 2.45
2771 2971 0.886490 AGTTTGGTTCGAGCAGGCAG 60.886 55.000 0.53 0.00 0.00 4.85
2839 3039 7.452880 TCAAATAGATTGAACTCCCAAACTG 57.547 36.000 0.00 0.00 44.94 3.16
2858 3058 9.834628 ATTTACAAACGACGACATAAATCAAAT 57.165 25.926 0.00 0.00 0.00 2.32
2874 3074 5.938322 ACAGCACCATAGAATTTACAAACG 58.062 37.500 0.00 0.00 0.00 3.60
2875 3075 7.145323 ACAACAGCACCATAGAATTTACAAAC 58.855 34.615 0.00 0.00 0.00 2.93
2876 3076 7.283625 ACAACAGCACCATAGAATTTACAAA 57.716 32.000 0.00 0.00 0.00 2.83
2877 3077 6.892658 ACAACAGCACCATAGAATTTACAA 57.107 33.333 0.00 0.00 0.00 2.41
2878 3078 7.987750 TTACAACAGCACCATAGAATTTACA 57.012 32.000 0.00 0.00 0.00 2.41
2985 3185 8.315482 TCTATTACAACAGCACCATAGTTAACA 58.685 33.333 8.61 0.00 0.00 2.41
2986 3186 8.712285 TCTATTACAACAGCACCATAGTTAAC 57.288 34.615 0.00 0.00 0.00 2.01
2987 3187 9.899661 AATCTATTACAACAGCACCATAGTTAA 57.100 29.630 0.00 0.00 0.00 2.01
2988 3188 9.899661 AAATCTATTACAACAGCACCATAGTTA 57.100 29.630 0.00 0.00 0.00 2.24
2989 3189 8.677300 CAAATCTATTACAACAGCACCATAGTT 58.323 33.333 0.00 0.00 0.00 2.24
2990 3190 7.829211 ACAAATCTATTACAACAGCACCATAGT 59.171 33.333 0.00 0.00 0.00 2.12
2991 3191 8.213518 ACAAATCTATTACAACAGCACCATAG 57.786 34.615 0.00 0.00 0.00 2.23
2992 3192 8.574251 AACAAATCTATTACAACAGCACCATA 57.426 30.769 0.00 0.00 0.00 2.74
2993 3193 7.466746 AACAAATCTATTACAACAGCACCAT 57.533 32.000 0.00 0.00 0.00 3.55
2994 3194 6.892658 AACAAATCTATTACAACAGCACCA 57.107 33.333 0.00 0.00 0.00 4.17
2995 3195 7.865385 TGAAAACAAATCTATTACAACAGCACC 59.135 33.333 0.00 0.00 0.00 5.01
2996 3196 8.795786 TGAAAACAAATCTATTACAACAGCAC 57.204 30.769 0.00 0.00 0.00 4.40
2997 3197 9.809096 TTTGAAAACAAATCTATTACAACAGCA 57.191 25.926 0.00 0.00 0.00 4.41
3111 3329 5.817816 AGGTAGAAATAGCATTTCTGGTTCG 59.182 40.000 23.19 0.00 38.98 3.95
3212 3430 3.548745 TGCAGTGTATTAGAGCAGCAT 57.451 42.857 0.00 0.00 0.00 3.79
3245 3463 0.902531 ACCTCATACCGTGTCCAAGG 59.097 55.000 0.00 0.00 35.99 3.61
3395 3613 4.201208 AGACGTTACATACACCGATACG 57.799 45.455 0.00 0.00 0.00 3.06
3413 3631 3.000727 CCATACAAACCAGAACGGAGAC 58.999 50.000 0.00 0.00 38.63 3.36
3443 3661 5.651172 TTGACAATTTATGGATACTCGCG 57.349 39.130 0.00 0.00 37.61 5.87
3570 4049 4.219033 GTGGACTGTCAATTTTGCTAACG 58.781 43.478 10.38 0.00 0.00 3.18
3581 4060 3.973206 AATACATCCGTGGACTGTCAA 57.027 42.857 10.38 0.00 0.00 3.18
3582 4061 6.718522 TTATAATACATCCGTGGACTGTCA 57.281 37.500 10.38 0.00 0.00 3.58
3583 4062 6.982141 TGTTTATAATACATCCGTGGACTGTC 59.018 38.462 0.00 0.00 0.00 3.51
3584 4063 6.880484 TGTTTATAATACATCCGTGGACTGT 58.120 36.000 0.00 0.33 0.00 3.55
3586 4065 6.099269 ACCTGTTTATAATACATCCGTGGACT 59.901 38.462 0.00 0.00 0.00 3.85
3587 4066 6.202188 CACCTGTTTATAATACATCCGTGGAC 59.798 42.308 0.00 0.00 0.00 4.02
3589 4068 6.285224 TCACCTGTTTATAATACATCCGTGG 58.715 40.000 14.25 9.53 0.00 4.94
3590 4069 7.780008 TTCACCTGTTTATAATACATCCGTG 57.220 36.000 0.00 2.61 0.00 4.94
3591 4070 8.262227 TCTTTCACCTGTTTATAATACATCCGT 58.738 33.333 0.00 0.00 0.00 4.69
3607 4086 4.555511 GCTTACAAGTTGCTCTTTCACCTG 60.556 45.833 1.81 0.00 33.63 4.00
3634 4116 3.686691 GCTTATGTCATTGGGAAGCCTCT 60.687 47.826 6.75 0.00 37.20 3.69
3671 5134 1.381928 GCATGTGTCCCTCTGGCATG 61.382 60.000 0.00 0.00 39.68 4.06
3672 5135 1.077212 GCATGTGTCCCTCTGGCAT 60.077 57.895 0.00 0.00 0.00 4.40
3674 5137 0.471617 ATAGCATGTGTCCCTCTGGC 59.528 55.000 0.00 0.00 0.00 4.85
3675 5138 1.071385 GGATAGCATGTGTCCCTCTGG 59.929 57.143 0.00 0.00 0.00 3.86
3725 5192 1.137872 CCTCTCCAGGACATGTACAGC 59.862 57.143 11.55 0.00 43.65 4.40


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

AutoCloner maintained by Alex Coulton.