Multiple sequence alignment - TraesCS4A01G088200

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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 TraesCS4A01G088200 chr4A 100.000 3198 0 0 1 3198 93688102 93684905 0.000000e+00 5906
1 TraesCS4A01G088200 chr4D 92.043 2300 113 43 561 2836 370692945 370690692 0.000000e+00 3169
2 TraesCS4A01G088200 chr4D 94.510 255 6 5 2945 3198 370690388 370690141 1.390000e-103 387
3 TraesCS4A01G088200 chr4D 89.320 309 24 2 1 300 370693251 370692943 2.330000e-101 379
4 TraesCS4A01G088200 chr4B 92.809 1933 62 34 1092 2996 455910354 455908471 0.000000e+00 2728
5 TraesCS4A01G088200 chr4B 91.021 568 16 15 561 1101 455911159 455910600 0.000000e+00 734
6 TraesCS4A01G088200 chr4B 89.644 309 21 4 1 300 455911463 455911157 1.800000e-102 383
7 TraesCS4A01G088200 chr4B 91.852 270 18 4 298 566 213995634 213995900 1.080000e-99 374
8 TraesCS4A01G088200 chr4B 93.868 212 11 2 2988 3198 455908443 455908233 5.150000e-83 318
9 TraesCS4A01G088200 chr2D 92.509 267 18 2 298 564 459018061 459018325 6.470000e-102 381
10 TraesCS4A01G088200 chr1D 91.071 280 23 2 294 573 57541163 57541440 8.370000e-101 377
11 TraesCS4A01G088200 chr7D 92.135 267 19 2 298 564 58401398 58401662 3.010000e-100 375
12 TraesCS4A01G088200 chr7D 92.164 268 15 4 299 566 358981356 358981095 1.080000e-99 374
13 TraesCS4A01G088200 chr2B 92.135 267 19 2 298 564 726596530 726596794 3.010000e-100 375
14 TraesCS4A01G088200 chr7A 91.513 271 19 3 291 560 732188198 732188465 1.400000e-98 370
15 TraesCS4A01G088200 chr7B 90.426 282 22 4 293 573 740431330 740431053 1.810000e-97 366
16 TraesCS4A01G088200 chr3B 90.391 281 23 4 294 573 502556930 502556653 1.810000e-97 366


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 TraesCS4A01G088200 chr4A 93684905 93688102 3197 True 5906.000000 5906 100.000000 1 3198 1 chr4A.!!$R1 3197
1 TraesCS4A01G088200 chr4D 370690141 370693251 3110 True 1311.666667 3169 91.957667 1 3198 3 chr4D.!!$R1 3197
2 TraesCS4A01G088200 chr4B 455908233 455911463 3230 True 1040.750000 2728 91.835500 1 3198 4 chr4B.!!$R1 3197

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
940 982 0.178885 TTTCCCCTCTTCCTTCCGGA 60.179 55.0 0.0 0.0 37.6 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2866 0.037605 ACGCTCCAAGGAAGTAACCG 60.038 55.0 0.0 0.0 34.73 4.44 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
64 65 2.972505 GCGCCATACCACCATCCG 60.973 66.667 0.00 0.00 0.00 4.18
97 106 2.159476 CCGATGAAGTGCCAATGTTGAG 60.159 50.000 0.00 0.00 0.00 3.02
125 135 1.522806 GCTGACGACCACCACAACA 60.523 57.895 0.00 0.00 0.00 3.33
133 143 1.034838 ACCACCACAACATTGCACGT 61.035 50.000 0.00 0.00 0.00 4.49
136 146 0.380378 ACCACAACATTGCACGTGAC 59.620 50.000 22.23 11.46 0.00 3.67
174 184 1.613630 ATGAGCCGAAGACACCCCT 60.614 57.895 0.00 0.00 0.00 4.79
181 191 3.901797 GAAGACACCCCTGCCACCG 62.902 68.421 0.00 0.00 0.00 4.94
232 242 1.040893 TCTAATGGCGGCGAGAAGGA 61.041 55.000 12.98 0.00 0.00 3.36
254 264 0.548510 GAAAGGATGGAGAGGGTGGG 59.451 60.000 0.00 0.00 0.00 4.61
280 290 4.083862 GGGTCTGACCACTCGCCC 62.084 72.222 26.94 5.34 41.02 6.13
300 310 1.201921 CGTGCCGCTCAAGTTTGATAC 60.202 52.381 0.00 0.00 36.46 2.24
301 311 2.076863 GTGCCGCTCAAGTTTGATACT 58.923 47.619 0.00 0.00 39.32 2.12
302 312 2.094417 GTGCCGCTCAAGTTTGATACTC 59.906 50.000 0.00 0.00 35.54 2.59
303 313 1.666189 GCCGCTCAAGTTTGATACTCC 59.334 52.381 0.00 0.00 35.54 3.85
304 314 2.280628 CCGCTCAAGTTTGATACTCCC 58.719 52.381 0.00 0.00 35.54 4.30
305 315 2.093447 CCGCTCAAGTTTGATACTCCCT 60.093 50.000 0.00 0.00 35.54 4.20
306 316 3.190874 CGCTCAAGTTTGATACTCCCTC 58.809 50.000 0.00 0.00 35.54 4.30
307 317 3.536570 GCTCAAGTTTGATACTCCCTCC 58.463 50.000 0.00 0.00 35.54 4.30
308 318 3.786635 CTCAAGTTTGATACTCCCTCCG 58.213 50.000 0.00 0.00 35.54 4.63
309 319 3.170717 TCAAGTTTGATACTCCCTCCGT 58.829 45.455 0.00 0.00 35.54 4.69
310 320 3.581332 TCAAGTTTGATACTCCCTCCGTT 59.419 43.478 0.00 0.00 35.54 4.44
311 321 3.889520 AGTTTGATACTCCCTCCGTTC 57.110 47.619 0.00 0.00 28.23 3.95
312 322 2.500504 AGTTTGATACTCCCTCCGTTCC 59.499 50.000 0.00 0.00 28.23 3.62
313 323 2.500504 GTTTGATACTCCCTCCGTTCCT 59.499 50.000 0.00 0.00 0.00 3.36
314 324 3.675348 TTGATACTCCCTCCGTTCCTA 57.325 47.619 0.00 0.00 0.00 2.94
315 325 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
316 326 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
317 327 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
318 328 5.708544 TGATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
319 329 6.320518 TGATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
320 330 7.472741 TGATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
321 331 7.614583 TGATACTCCCTCCGTTCCTAAATATAG 59.385 40.741 0.00 0.00 0.00 1.31
340 350 8.459911 AATATAGGGTGTATAGTTTTTGGCAC 57.540 34.615 0.00 0.00 0.00 5.01
341 351 3.078837 AGGGTGTATAGTTTTTGGCACG 58.921 45.455 0.00 0.00 0.00 5.34
342 352 2.162809 GGGTGTATAGTTTTTGGCACGG 59.837 50.000 0.00 0.00 0.00 4.94
343 353 3.075884 GGTGTATAGTTTTTGGCACGGA 58.924 45.455 0.00 0.00 0.00 4.69
344 354 3.502979 GGTGTATAGTTTTTGGCACGGAA 59.497 43.478 0.00 0.00 0.00 4.30
345 355 4.023021 GGTGTATAGTTTTTGGCACGGAAA 60.023 41.667 0.00 0.00 0.00 3.13
346 356 5.336134 GGTGTATAGTTTTTGGCACGGAAAT 60.336 40.000 0.00 0.00 0.00 2.17
347 357 6.153756 GTGTATAGTTTTTGGCACGGAAATT 58.846 36.000 0.00 0.00 0.00 1.82
348 358 7.306953 GTGTATAGTTTTTGGCACGGAAATTA 58.693 34.615 0.00 0.00 0.00 1.40
349 359 7.808856 GTGTATAGTTTTTGGCACGGAAATTAA 59.191 33.333 0.00 0.00 0.00 1.40
350 360 8.358148 TGTATAGTTTTTGGCACGGAAATTAAA 58.642 29.630 0.00 0.00 0.00 1.52
351 361 7.883229 ATAGTTTTTGGCACGGAAATTAAAG 57.117 32.000 0.00 0.00 0.00 1.85
352 362 5.908341 AGTTTTTGGCACGGAAATTAAAGA 58.092 33.333 0.00 0.00 0.00 2.52
353 363 6.342111 AGTTTTTGGCACGGAAATTAAAGAA 58.658 32.000 0.00 0.00 0.00 2.52
354 364 6.819146 AGTTTTTGGCACGGAAATTAAAGAAA 59.181 30.769 0.00 0.00 0.00 2.52
355 365 6.591313 TTTTGGCACGGAAATTAAAGAAAC 57.409 33.333 0.00 0.00 0.00 2.78
356 366 4.920640 TGGCACGGAAATTAAAGAAACA 57.079 36.364 0.00 0.00 0.00 2.83
357 367 4.612943 TGGCACGGAAATTAAAGAAACAC 58.387 39.130 0.00 0.00 0.00 3.32
358 368 4.098044 TGGCACGGAAATTAAAGAAACACA 59.902 37.500 0.00 0.00 0.00 3.72
359 369 5.221342 TGGCACGGAAATTAAAGAAACACAT 60.221 36.000 0.00 0.00 0.00 3.21
360 370 5.118510 GGCACGGAAATTAAAGAAACACATG 59.881 40.000 0.00 0.00 0.00 3.21
361 371 5.689961 GCACGGAAATTAAAGAAACACATGT 59.310 36.000 0.00 0.00 0.00 3.21
362 372 6.345723 GCACGGAAATTAAAGAAACACATGTG 60.346 38.462 24.25 24.25 0.00 3.21
363 373 6.143758 CACGGAAATTAAAGAAACACATGTGG 59.856 38.462 28.64 11.73 34.19 4.17
364 374 6.039941 ACGGAAATTAAAGAAACACATGTGGA 59.960 34.615 28.64 5.53 34.19 4.02
365 375 7.090173 CGGAAATTAAAGAAACACATGTGGAT 58.910 34.615 28.64 17.14 34.19 3.41
366 376 7.062138 CGGAAATTAAAGAAACACATGTGGATG 59.938 37.037 28.64 5.10 35.49 3.51
367 377 7.331687 GGAAATTAAAGAAACACATGTGGATGG 59.668 37.037 28.64 4.63 33.39 3.51
368 378 7.537596 AATTAAAGAAACACATGTGGATGGA 57.462 32.000 28.64 8.08 33.39 3.41
369 379 6.968263 TTAAAGAAACACATGTGGATGGAA 57.032 33.333 28.64 11.35 33.39 3.53
370 380 5.867903 AAAGAAACACATGTGGATGGAAA 57.132 34.783 28.64 0.00 33.39 3.13
371 381 5.867903 AAGAAACACATGTGGATGGAAAA 57.132 34.783 28.64 0.00 33.39 2.29
372 382 6.423776 AAGAAACACATGTGGATGGAAAAT 57.576 33.333 28.64 2.30 33.39 1.82
373 383 6.423776 AGAAACACATGTGGATGGAAAATT 57.576 33.333 28.64 8.61 33.39 1.82
374 384 6.829849 AGAAACACATGTGGATGGAAAATTT 58.170 32.000 28.64 16.18 33.39 1.82
375 385 6.930722 AGAAACACATGTGGATGGAAAATTTC 59.069 34.615 28.64 22.37 33.39 2.17
376 386 5.804944 ACACATGTGGATGGAAAATTTCA 57.195 34.783 28.64 0.00 33.39 2.69
377 387 5.540911 ACACATGTGGATGGAAAATTTCAC 58.459 37.500 28.64 0.00 33.39 3.18
378 388 5.070180 ACACATGTGGATGGAAAATTTCACA 59.930 36.000 28.64 9.69 39.07 3.58
379 389 5.990386 CACATGTGGATGGAAAATTTCACAA 59.010 36.000 18.51 0.00 38.39 3.33
380 390 6.146510 CACATGTGGATGGAAAATTTCACAAG 59.853 38.462 18.51 9.55 38.39 3.16
381 391 5.867903 TGTGGATGGAAAATTTCACAAGT 57.132 34.783 8.09 0.00 33.05 3.16
382 392 6.232581 TGTGGATGGAAAATTTCACAAGTT 57.767 33.333 8.09 0.00 33.05 2.66
383 393 6.648192 TGTGGATGGAAAATTTCACAAGTTT 58.352 32.000 8.09 0.00 32.91 2.66
384 394 7.108847 TGTGGATGGAAAATTTCACAAGTTTT 58.891 30.769 8.09 0.00 30.39 2.43
385 395 7.065563 TGTGGATGGAAAATTTCACAAGTTTTG 59.934 33.333 8.09 0.00 30.39 2.44
386 396 6.541641 TGGATGGAAAATTTCACAAGTTTTGG 59.458 34.615 8.09 0.00 30.39 3.28
387 397 6.017192 GGATGGAAAATTTCACAAGTTTTGGG 60.017 38.462 8.09 0.00 30.39 4.12
388 398 4.637977 TGGAAAATTTCACAAGTTTTGGGC 59.362 37.500 8.09 0.00 30.39 5.36
389 399 4.637977 GGAAAATTTCACAAGTTTTGGGCA 59.362 37.500 8.09 0.00 30.39 5.36
390 400 5.124617 GGAAAATTTCACAAGTTTTGGGCAA 59.875 36.000 8.09 0.00 30.39 4.52
391 401 5.816449 AAATTTCACAAGTTTTGGGCAAG 57.184 34.783 0.00 0.00 32.92 4.01
392 402 4.751767 ATTTCACAAGTTTTGGGCAAGA 57.248 36.364 0.00 0.00 32.92 3.02
393 403 4.751767 TTTCACAAGTTTTGGGCAAGAT 57.248 36.364 0.00 0.00 32.92 2.40
394 404 4.751767 TTCACAAGTTTTGGGCAAGATT 57.248 36.364 0.00 0.00 32.92 2.40
395 405 5.860941 TTCACAAGTTTTGGGCAAGATTA 57.139 34.783 0.00 0.00 32.92 1.75
396 406 5.195001 TCACAAGTTTTGGGCAAGATTAC 57.805 39.130 0.00 0.00 32.92 1.89
397 407 4.646945 TCACAAGTTTTGGGCAAGATTACA 59.353 37.500 0.00 0.00 32.92 2.41
398 408 4.744631 CACAAGTTTTGGGCAAGATTACAC 59.255 41.667 0.00 0.00 34.12 2.90
399 409 4.202212 ACAAGTTTTGGGCAAGATTACACC 60.202 41.667 0.00 0.00 34.12 4.16
400 410 3.844640 AGTTTTGGGCAAGATTACACCT 58.155 40.909 0.00 0.00 0.00 4.00
401 411 3.573967 AGTTTTGGGCAAGATTACACCTG 59.426 43.478 0.00 0.00 0.00 4.00
402 412 3.517296 TTTGGGCAAGATTACACCTGA 57.483 42.857 0.00 0.00 0.00 3.86
403 413 2.489938 TGGGCAAGATTACACCTGAC 57.510 50.000 0.00 0.00 0.00 3.51
404 414 1.985159 TGGGCAAGATTACACCTGACT 59.015 47.619 0.00 0.00 0.00 3.41
405 415 3.178046 TGGGCAAGATTACACCTGACTA 58.822 45.455 0.00 0.00 0.00 2.59
406 416 3.585289 TGGGCAAGATTACACCTGACTAA 59.415 43.478 0.00 0.00 0.00 2.24
407 417 4.227300 TGGGCAAGATTACACCTGACTAAT 59.773 41.667 0.00 0.00 0.00 1.73
408 418 5.193679 GGGCAAGATTACACCTGACTAATT 58.806 41.667 0.00 0.00 0.00 1.40
409 419 5.066505 GGGCAAGATTACACCTGACTAATTG 59.933 44.000 0.00 0.00 0.00 2.32
410 420 5.880332 GGCAAGATTACACCTGACTAATTGA 59.120 40.000 0.00 0.00 0.00 2.57
411 421 6.183360 GGCAAGATTACACCTGACTAATTGAC 60.183 42.308 0.00 0.00 0.00 3.18
412 422 6.371548 GCAAGATTACACCTGACTAATTGACA 59.628 38.462 0.00 0.00 0.00 3.58
413 423 7.066284 GCAAGATTACACCTGACTAATTGACAT 59.934 37.037 0.00 0.00 0.00 3.06
414 424 8.393366 CAAGATTACACCTGACTAATTGACATG 58.607 37.037 0.00 0.00 0.00 3.21
415 425 7.851228 AGATTACACCTGACTAATTGACATGA 58.149 34.615 0.00 0.00 0.00 3.07
416 426 8.321353 AGATTACACCTGACTAATTGACATGAA 58.679 33.333 0.00 0.00 0.00 2.57
417 427 8.862325 ATTACACCTGACTAATTGACATGAAA 57.138 30.769 0.00 0.00 0.00 2.69
418 428 8.684386 TTACACCTGACTAATTGACATGAAAA 57.316 30.769 0.00 0.00 0.00 2.29
419 429 7.581213 ACACCTGACTAATTGACATGAAAAA 57.419 32.000 0.00 0.00 0.00 1.94
436 446 3.746792 AAAAATAGAGGAGCTTGCCCT 57.253 42.857 0.00 0.00 36.57 5.19
437 447 4.862641 AAAAATAGAGGAGCTTGCCCTA 57.137 40.909 0.00 0.00 33.36 3.53
438 448 5.394562 AAAAATAGAGGAGCTTGCCCTAT 57.605 39.130 0.00 0.00 33.36 2.57
439 449 6.515512 AAAAATAGAGGAGCTTGCCCTATA 57.484 37.500 0.00 0.00 33.36 1.31
440 450 6.710499 AAAATAGAGGAGCTTGCCCTATAT 57.290 37.500 2.09 2.09 39.22 0.86
441 451 7.814693 AAAATAGAGGAGCTTGCCCTATATA 57.185 36.000 7.35 0.00 37.26 0.86
442 452 7.814693 AAATAGAGGAGCTTGCCCTATATAA 57.185 36.000 7.35 0.00 37.26 0.98
443 453 7.430760 AATAGAGGAGCTTGCCCTATATAAG 57.569 40.000 7.35 0.00 37.26 1.73
444 454 4.100373 AGAGGAGCTTGCCCTATATAAGG 58.900 47.826 0.00 0.00 46.09 2.69
484 494 8.574196 ACCTTCAAAAATTATTCAAACGAGTG 57.426 30.769 0.00 0.00 0.00 3.51
485 495 7.651704 ACCTTCAAAAATTATTCAAACGAGTGG 59.348 33.333 0.00 0.00 0.00 4.00
486 496 7.651704 CCTTCAAAAATTATTCAAACGAGTGGT 59.348 33.333 0.00 0.00 0.00 4.16
487 497 7.922505 TCAAAAATTATTCAAACGAGTGGTG 57.077 32.000 0.00 0.00 0.00 4.17
488 498 7.708051 TCAAAAATTATTCAAACGAGTGGTGA 58.292 30.769 0.00 0.00 0.00 4.02
489 499 8.191446 TCAAAAATTATTCAAACGAGTGGTGAA 58.809 29.630 0.00 5.46 35.83 3.18
490 500 8.812329 CAAAAATTATTCAAACGAGTGGTGAAA 58.188 29.630 0.00 0.00 35.07 2.69
491 501 9.541143 AAAAATTATTCAAACGAGTGGTGAAAT 57.459 25.926 0.00 0.00 35.07 2.17
492 502 8.519492 AAATTATTCAAACGAGTGGTGAAATG 57.481 30.769 0.00 0.00 35.07 2.32
493 503 3.347958 TTCAAACGAGTGGTGAAATGC 57.652 42.857 0.00 0.00 0.00 3.56
494 504 2.293170 TCAAACGAGTGGTGAAATGCA 58.707 42.857 0.00 0.00 0.00 3.96
495 505 2.685388 TCAAACGAGTGGTGAAATGCAA 59.315 40.909 0.00 0.00 0.00 4.08
496 506 3.317711 TCAAACGAGTGGTGAAATGCAAT 59.682 39.130 0.00 0.00 0.00 3.56
497 507 2.995466 ACGAGTGGTGAAATGCAATG 57.005 45.000 0.00 0.00 0.00 2.82
498 508 1.068333 ACGAGTGGTGAAATGCAATGC 60.068 47.619 0.00 0.00 0.00 3.56
499 509 1.068402 CGAGTGGTGAAATGCAATGCA 60.068 47.619 11.44 11.44 44.86 3.96
500 510 2.331194 GAGTGGTGAAATGCAATGCAC 58.669 47.619 11.23 4.07 43.04 4.57
501 511 1.001181 AGTGGTGAAATGCAATGCACC 59.999 47.619 23.39 23.39 46.74 5.01
502 512 0.321021 TGGTGAAATGCAATGCACCC 59.679 50.000 26.36 11.12 46.30 4.61
503 513 0.609662 GGTGAAATGCAATGCACCCT 59.390 50.000 20.11 0.00 43.12 4.34
504 514 1.824230 GGTGAAATGCAATGCACCCTA 59.176 47.619 20.11 0.00 43.12 3.53
505 515 2.431782 GGTGAAATGCAATGCACCCTAT 59.568 45.455 20.11 0.00 43.12 2.57
506 516 3.636300 GGTGAAATGCAATGCACCCTATA 59.364 43.478 20.11 0.00 43.12 1.31
507 517 4.281688 GGTGAAATGCAATGCACCCTATAT 59.718 41.667 20.11 0.00 43.12 0.86
508 518 5.221501 GGTGAAATGCAATGCACCCTATATT 60.222 40.000 20.11 0.00 43.12 1.28
509 519 6.282930 GTGAAATGCAATGCACCCTATATTT 58.717 36.000 11.23 5.14 43.04 1.40
510 520 6.762661 GTGAAATGCAATGCACCCTATATTTT 59.237 34.615 11.23 4.31 43.04 1.82
511 521 6.762187 TGAAATGCAATGCACCCTATATTTTG 59.238 34.615 11.23 0.00 43.04 2.44
512 522 4.669206 TGCAATGCACCCTATATTTTGG 57.331 40.909 2.72 0.00 31.71 3.28
513 523 4.285020 TGCAATGCACCCTATATTTTGGA 58.715 39.130 2.72 0.00 31.71 3.53
514 524 4.099266 TGCAATGCACCCTATATTTTGGAC 59.901 41.667 2.72 0.00 31.71 4.02
515 525 4.342092 GCAATGCACCCTATATTTTGGACT 59.658 41.667 0.00 0.00 0.00 3.85
516 526 5.163416 GCAATGCACCCTATATTTTGGACTT 60.163 40.000 0.00 0.00 0.00 3.01
517 527 6.630188 GCAATGCACCCTATATTTTGGACTTT 60.630 38.462 0.00 0.00 0.00 2.66
518 528 7.330262 CAATGCACCCTATATTTTGGACTTTT 58.670 34.615 0.00 0.00 0.00 2.27
519 529 6.926630 TGCACCCTATATTTTGGACTTTTT 57.073 33.333 0.00 0.00 0.00 1.94
520 530 6.930731 TGCACCCTATATTTTGGACTTTTTC 58.069 36.000 0.00 0.00 0.00 2.29
521 531 6.723977 TGCACCCTATATTTTGGACTTTTTCT 59.276 34.615 0.00 0.00 0.00 2.52
522 532 7.891183 TGCACCCTATATTTTGGACTTTTTCTA 59.109 33.333 0.00 0.00 0.00 2.10
523 533 8.745590 GCACCCTATATTTTGGACTTTTTCTAA 58.254 33.333 0.00 0.00 0.00 2.10
550 560 9.661563 AAAAATCTATACACGTTGTATCAAGGA 57.338 29.630 12.06 8.52 42.16 3.36
551 561 9.661563 AAAATCTATACACGTTGTATCAAGGAA 57.338 29.630 12.06 0.00 42.16 3.36
552 562 8.644318 AATCTATACACGTTGTATCAAGGAAC 57.356 34.615 12.06 0.00 42.16 3.62
553 563 6.260377 TCTATACACGTTGTATCAAGGAACG 58.740 40.000 12.06 0.00 42.16 3.95
554 564 2.409975 ACACGTTGTATCAAGGAACGG 58.590 47.619 0.00 0.00 45.22 4.44
555 565 2.036217 ACACGTTGTATCAAGGAACGGA 59.964 45.455 0.00 0.00 45.22 4.69
556 566 2.666508 CACGTTGTATCAAGGAACGGAG 59.333 50.000 0.00 0.00 45.22 4.63
557 567 2.268298 CGTTGTATCAAGGAACGGAGG 58.732 52.381 0.00 0.00 38.99 4.30
558 568 2.629051 GTTGTATCAAGGAACGGAGGG 58.371 52.381 0.00 0.00 0.00 4.30
559 569 2.235402 GTTGTATCAAGGAACGGAGGGA 59.765 50.000 0.00 0.00 0.00 4.20
560 570 2.542550 TGTATCAAGGAACGGAGGGAA 58.457 47.619 0.00 0.00 0.00 3.97
561 571 3.112263 TGTATCAAGGAACGGAGGGAAT 58.888 45.455 0.00 0.00 0.00 3.01
562 572 4.291792 TGTATCAAGGAACGGAGGGAATA 58.708 43.478 0.00 0.00 0.00 1.75
568 578 3.863086 AGGAACGGAGGGAATATGAGAT 58.137 45.455 0.00 0.00 0.00 2.75
591 602 8.718734 AGATTTGGACAGAGATTTAAAACGTAC 58.281 33.333 0.00 0.00 0.00 3.67
635 649 5.187687 GGGACACCCGATTAATAAAAGACA 58.812 41.667 0.00 0.00 32.13 3.41
675 689 0.255318 CTCTCTTGGCCCTGCTTCAT 59.745 55.000 0.00 0.00 0.00 2.57
676 690 0.254178 TCTCTTGGCCCTGCTTCATC 59.746 55.000 0.00 0.00 0.00 2.92
682 696 1.895131 TGGCCCTGCTTCATCTTTTTC 59.105 47.619 0.00 0.00 0.00 2.29
735 749 0.746923 GAAATTAGGTTCGGCGCCCT 60.747 55.000 23.46 14.86 34.74 5.19
815 830 0.179234 TGCAAATCCCGAGCCGAATA 59.821 50.000 0.00 0.00 0.00 1.75
891 933 1.604593 CCCCACCACTTCTGCCAAG 60.605 63.158 0.00 0.00 0.00 3.61
892 934 2.270986 CCCACCACTTCTGCCAAGC 61.271 63.158 0.00 0.00 0.00 4.01
895 937 2.437897 CCACTTCTGCCAAGCCCT 59.562 61.111 0.00 0.00 0.00 5.19
938 980 0.984995 ACTTTCCCCTCTTCCTTCCG 59.015 55.000 0.00 0.00 0.00 4.30
939 981 0.253327 CTTTCCCCTCTTCCTTCCGG 59.747 60.000 0.00 0.00 0.00 5.14
940 982 0.178885 TTTCCCCTCTTCCTTCCGGA 60.179 55.000 0.00 0.00 37.60 5.14
942 984 1.306226 CCCCTCTTCCTTCCGGACT 60.306 63.158 1.83 0.00 39.60 3.85
943 985 0.910088 CCCCTCTTCCTTCCGGACTT 60.910 60.000 1.83 0.00 39.60 3.01
945 987 0.537653 CCTCTTCCTTCCGGACTTCC 59.462 60.000 1.83 0.00 39.60 3.46
1347 1643 1.654954 CCGTCCAGTACCTCCTCGTG 61.655 65.000 0.00 0.00 0.00 4.35
1732 2028 2.518834 TCCCCCAAAGTCCAGGTAAAAA 59.481 45.455 0.00 0.00 0.00 1.94
1734 2030 3.513912 CCCCCAAAGTCCAGGTAAAAATC 59.486 47.826 0.00 0.00 0.00 2.17
1789 2092 3.605749 TTCCCTTCCTCCGCAAGCG 62.606 63.158 7.60 7.60 39.44 4.68
1811 2114 0.179070 GGGCTGATCGAAAGGGACTC 60.179 60.000 0.00 0.00 38.49 3.36
1812 2115 0.179070 GGCTGATCGAAAGGGACTCC 60.179 60.000 0.00 0.00 38.49 3.85
1813 2116 0.528684 GCTGATCGAAAGGGACTCCG 60.529 60.000 0.00 0.00 38.49 4.63
1814 2117 0.818296 CTGATCGAAAGGGACTCCGT 59.182 55.000 0.00 0.00 38.49 4.69
1901 2204 0.589729 CATACAAGCAATGCGGCGTC 60.590 55.000 9.37 0.91 39.27 5.19
1999 2305 7.232941 GGAAGCTACTGGTATTAATCTAGTGGA 59.767 40.741 14.08 0.00 29.44 4.02
2094 2400 0.615261 TGGGGGCCGGGTAAATTTTC 60.615 55.000 2.18 0.00 0.00 2.29
2095 2401 0.324923 GGGGGCCGGGTAAATTTTCT 60.325 55.000 2.18 0.00 0.00 2.52
2096 2402 1.108776 GGGGCCGGGTAAATTTTCTC 58.891 55.000 2.18 0.00 0.00 2.87
2097 2403 1.617533 GGGGCCGGGTAAATTTTCTCA 60.618 52.381 2.18 0.00 0.00 3.27
2098 2404 1.475280 GGGCCGGGTAAATTTTCTCAC 59.525 52.381 2.18 0.00 0.00 3.51
2112 2418 0.482887 TCTCACCTCACCTCACCTCA 59.517 55.000 0.00 0.00 0.00 3.86
2119 2425 1.827969 CTCACCTCACCTCACCTTAGG 59.172 57.143 0.00 0.00 42.82 2.69
2134 2440 2.308690 CTTAGGAGGAGGAGGTTACCG 58.691 57.143 0.00 0.00 34.73 4.02
2198 2507 6.769512 AGTATATAAATCAGTCGCCATGGTT 58.230 36.000 14.67 0.00 0.00 3.67
2199 2508 6.874134 AGTATATAAATCAGTCGCCATGGTTC 59.126 38.462 14.67 4.26 0.00 3.62
2200 2509 2.496899 AAATCAGTCGCCATGGTTCT 57.503 45.000 14.67 6.63 0.00 3.01
2243 2552 2.597510 AAAGGGAAGTGGTGCGGC 60.598 61.111 0.00 0.00 0.00 6.53
2276 2585 1.519455 GCGAGTGGAATCTGACCGG 60.519 63.158 0.00 0.00 0.00 5.28
2335 2653 0.879090 GAATGGTTTCCCTTCGCGTT 59.121 50.000 5.77 0.00 0.00 4.84
2348 2666 4.656117 GCGTTTTTGGGTGGGCCG 62.656 66.667 0.00 0.00 34.97 6.13
2548 2866 1.671054 TCAAAGGCAGCTGTACGGC 60.671 57.895 19.39 19.39 38.96 5.68
2549 2867 2.742372 AAAGGCAGCTGTACGGCG 60.742 61.111 20.70 16.00 40.85 6.46
2550 2868 4.760047 AAGGCAGCTGTACGGCGG 62.760 66.667 20.93 20.93 40.85 6.13
2604 2922 2.599612 GCATTGCGTGGAAAAAGTTTGC 60.600 45.455 0.00 0.00 0.00 3.68
2606 2924 2.202295 TGCGTGGAAAAAGTTTGCTC 57.798 45.000 0.00 0.00 0.00 4.26
2607 2925 1.202359 TGCGTGGAAAAAGTTTGCTCC 60.202 47.619 9.22 9.22 0.00 4.70
2629 2947 4.502645 CCAAGTTGAAATTTGACGTTCCAC 59.497 41.667 3.87 0.00 0.00 4.02
2668 2987 5.233225 TCGACAGACGATAGGAATATACGT 58.767 41.667 0.00 0.00 46.45 3.57
2766 3086 5.105997 GGATGAAGATGGGTTTTTCTGACAG 60.106 44.000 0.00 0.00 0.00 3.51
2767 3087 5.047566 TGAAGATGGGTTTTTCTGACAGA 57.952 39.130 0.00 0.00 0.00 3.41
2853 3179 2.223548 TGTGTTGATGCACAAGCTTGTC 60.224 45.455 28.97 21.92 45.17 3.18
2869 3195 0.673333 TGTCGTGCCATCGAATTGCT 60.673 50.000 0.00 0.00 41.47 3.91
2871 3197 0.726827 TCGTGCCATCGAATTGCTTC 59.273 50.000 0.00 0.00 36.89 3.86
2872 3198 0.729116 CGTGCCATCGAATTGCTTCT 59.271 50.000 0.00 0.00 0.00 2.85
2907 3233 2.325484 GTGGTTGGGGAAAAGGATTGT 58.675 47.619 0.00 0.00 0.00 2.71
2934 3260 9.763465 CCTACATTCGTTCGTGTATTAAATTTT 57.237 29.630 0.00 0.00 31.06 1.82
2964 3485 6.315144 TCACGTCTTCAAGTTTCATCAAAAGA 59.685 34.615 0.00 0.00 0.00 2.52
2966 3487 7.112565 CACGTCTTCAAGTTTCATCAAAAGATG 59.887 37.037 0.00 0.00 35.45 2.90
2967 3488 7.134815 CGTCTTCAAGTTTCATCAAAAGATGT 58.865 34.615 5.48 0.00 34.39 3.06
2968 3489 8.282592 CGTCTTCAAGTTTCATCAAAAGATGTA 58.717 33.333 5.48 0.00 34.39 2.29
2969 3490 9.604626 GTCTTCAAGTTTCATCAAAAGATGTAG 57.395 33.333 5.48 0.00 34.39 2.74
2970 3491 8.786898 TCTTCAAGTTTCATCAAAAGATGTAGG 58.213 33.333 5.48 0.00 34.39 3.18
2971 3492 8.690203 TTCAAGTTTCATCAAAAGATGTAGGA 57.310 30.769 5.48 0.00 34.39 2.94
3090 3649 4.861210 ACGATTAAGCCACTAGATCGAAG 58.139 43.478 12.92 0.00 41.37 3.79
3092 3651 4.557695 CGATTAAGCCACTAGATCGAAGCT 60.558 45.833 0.00 0.00 41.37 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 158 0.737367 TCTTCGGCTCATCGCAACAG 60.737 55.000 0.00 0.00 41.67 3.16
149 159 1.014044 GTCTTCGGCTCATCGCAACA 61.014 55.000 0.00 0.00 41.67 3.33
232 242 2.476199 CACCCTCTCCATCCTTTCTCT 58.524 52.381 0.00 0.00 0.00 3.10
254 264 3.851128 GTCAGACCCTAGCCGCCC 61.851 72.222 0.00 0.00 0.00 6.13
280 290 3.329231 TCAAACTTGAGCGGCACG 58.671 55.556 1.45 0.00 44.10 5.34
314 324 8.909923 GTGCCAAAAACTATACACCCTATATTT 58.090 33.333 0.00 0.00 0.00 1.40
315 325 7.227910 CGTGCCAAAAACTATACACCCTATATT 59.772 37.037 0.00 0.00 0.00 1.28
316 326 6.708949 CGTGCCAAAAACTATACACCCTATAT 59.291 38.462 0.00 0.00 0.00 0.86
317 327 6.050432 CGTGCCAAAAACTATACACCCTATA 58.950 40.000 0.00 0.00 0.00 1.31
318 328 4.879545 CGTGCCAAAAACTATACACCCTAT 59.120 41.667 0.00 0.00 0.00 2.57
319 329 4.255301 CGTGCCAAAAACTATACACCCTA 58.745 43.478 0.00 0.00 0.00 3.53
320 330 3.078837 CGTGCCAAAAACTATACACCCT 58.921 45.455 0.00 0.00 0.00 4.34
321 331 2.162809 CCGTGCCAAAAACTATACACCC 59.837 50.000 0.00 0.00 0.00 4.61
322 332 3.075884 TCCGTGCCAAAAACTATACACC 58.924 45.455 0.00 0.00 0.00 4.16
323 333 4.752661 TTCCGTGCCAAAAACTATACAC 57.247 40.909 0.00 0.00 0.00 2.90
324 334 5.968528 ATTTCCGTGCCAAAAACTATACA 57.031 34.783 0.00 0.00 0.00 2.29
325 335 8.745464 TTTAATTTCCGTGCCAAAAACTATAC 57.255 30.769 0.00 0.00 0.00 1.47
326 336 8.794553 TCTTTAATTTCCGTGCCAAAAACTATA 58.205 29.630 0.00 0.00 0.00 1.31
327 337 7.662897 TCTTTAATTTCCGTGCCAAAAACTAT 58.337 30.769 0.00 0.00 0.00 2.12
328 338 7.040473 TCTTTAATTTCCGTGCCAAAAACTA 57.960 32.000 0.00 0.00 0.00 2.24
329 339 5.908341 TCTTTAATTTCCGTGCCAAAAACT 58.092 33.333 0.00 0.00 0.00 2.66
330 340 6.591313 TTCTTTAATTTCCGTGCCAAAAAC 57.409 33.333 0.00 0.00 0.00 2.43
331 341 6.594159 TGTTTCTTTAATTTCCGTGCCAAAAA 59.406 30.769 0.00 0.00 0.00 1.94
332 342 6.036191 GTGTTTCTTTAATTTCCGTGCCAAAA 59.964 34.615 0.00 0.00 0.00 2.44
333 343 5.520649 GTGTTTCTTTAATTTCCGTGCCAAA 59.479 36.000 0.00 0.00 0.00 3.28
334 344 5.044558 GTGTTTCTTTAATTTCCGTGCCAA 58.955 37.500 0.00 0.00 0.00 4.52
335 345 4.098044 TGTGTTTCTTTAATTTCCGTGCCA 59.902 37.500 0.00 0.00 0.00 4.92
336 346 4.612943 TGTGTTTCTTTAATTTCCGTGCC 58.387 39.130 0.00 0.00 0.00 5.01
337 347 5.689961 ACATGTGTTTCTTTAATTTCCGTGC 59.310 36.000 0.00 0.00 0.00 5.34
338 348 6.143758 CCACATGTGTTTCTTTAATTTCCGTG 59.856 38.462 23.79 0.00 0.00 4.94
339 349 6.039941 TCCACATGTGTTTCTTTAATTTCCGT 59.960 34.615 23.79 0.00 0.00 4.69
340 350 6.442952 TCCACATGTGTTTCTTTAATTTCCG 58.557 36.000 23.79 3.43 0.00 4.30
341 351 7.331687 CCATCCACATGTGTTTCTTTAATTTCC 59.668 37.037 23.79 0.00 0.00 3.13
342 352 8.087750 TCCATCCACATGTGTTTCTTTAATTTC 58.912 33.333 23.79 0.00 0.00 2.17
343 353 7.961351 TCCATCCACATGTGTTTCTTTAATTT 58.039 30.769 23.79 0.00 0.00 1.82
344 354 7.537596 TCCATCCACATGTGTTTCTTTAATT 57.462 32.000 23.79 0.00 0.00 1.40
345 355 7.537596 TTCCATCCACATGTGTTTCTTTAAT 57.462 32.000 23.79 2.51 0.00 1.40
346 356 6.968263 TTCCATCCACATGTGTTTCTTTAA 57.032 33.333 23.79 7.06 0.00 1.52
347 357 6.968263 TTTCCATCCACATGTGTTTCTTTA 57.032 33.333 23.79 2.53 0.00 1.85
348 358 5.867903 TTTCCATCCACATGTGTTTCTTT 57.132 34.783 23.79 0.00 0.00 2.52
349 359 5.867903 TTTTCCATCCACATGTGTTTCTT 57.132 34.783 23.79 1.63 0.00 2.52
350 360 6.423776 AATTTTCCATCCACATGTGTTTCT 57.576 33.333 23.79 3.22 0.00 2.52
351 361 6.705381 TGAAATTTTCCATCCACATGTGTTTC 59.295 34.615 23.79 20.62 0.00 2.78
352 362 6.482973 GTGAAATTTTCCATCCACATGTGTTT 59.517 34.615 23.79 13.83 0.00 2.83
353 363 5.990996 GTGAAATTTTCCATCCACATGTGTT 59.009 36.000 23.79 8.80 0.00 3.32
354 364 5.070180 TGTGAAATTTTCCATCCACATGTGT 59.930 36.000 23.79 3.99 30.67 3.72
355 365 5.539979 TGTGAAATTTTCCATCCACATGTG 58.460 37.500 19.31 19.31 30.67 3.21
356 366 5.804944 TGTGAAATTTTCCATCCACATGT 57.195 34.783 6.68 0.00 30.67 3.21
357 367 6.225318 ACTTGTGAAATTTTCCATCCACATG 58.775 36.000 14.52 14.52 34.95 3.21
358 368 6.423776 ACTTGTGAAATTTTCCATCCACAT 57.576 33.333 6.68 0.00 34.95 3.21
359 369 5.867903 ACTTGTGAAATTTTCCATCCACA 57.132 34.783 6.68 4.52 33.38 4.17
360 370 7.408910 CAAAACTTGTGAAATTTTCCATCCAC 58.591 34.615 6.68 0.00 0.00 4.02
361 371 6.541641 CCAAAACTTGTGAAATTTTCCATCCA 59.458 34.615 6.68 0.00 0.00 3.41
362 372 6.017192 CCCAAAACTTGTGAAATTTTCCATCC 60.017 38.462 6.68 0.00 0.00 3.51
363 373 6.513230 GCCCAAAACTTGTGAAATTTTCCATC 60.513 38.462 6.68 0.00 0.00 3.51
364 374 5.299028 GCCCAAAACTTGTGAAATTTTCCAT 59.701 36.000 6.68 0.00 0.00 3.41
365 375 4.637977 GCCCAAAACTTGTGAAATTTTCCA 59.362 37.500 6.68 2.14 0.00 3.53
366 376 4.637977 TGCCCAAAACTTGTGAAATTTTCC 59.362 37.500 6.68 0.00 0.00 3.13
367 377 5.809719 TGCCCAAAACTTGTGAAATTTTC 57.190 34.783 2.05 2.05 0.00 2.29
368 378 5.942826 TCTTGCCCAAAACTTGTGAAATTTT 59.057 32.000 0.00 0.00 0.00 1.82
369 379 5.495640 TCTTGCCCAAAACTTGTGAAATTT 58.504 33.333 0.00 0.00 0.00 1.82
370 380 5.096443 TCTTGCCCAAAACTTGTGAAATT 57.904 34.783 0.00 0.00 0.00 1.82
371 381 4.751767 TCTTGCCCAAAACTTGTGAAAT 57.248 36.364 0.00 0.00 0.00 2.17
372 382 4.751767 ATCTTGCCCAAAACTTGTGAAA 57.248 36.364 0.00 0.00 0.00 2.69
373 383 4.751767 AATCTTGCCCAAAACTTGTGAA 57.248 36.364 0.00 0.00 0.00 3.18
374 384 4.646945 TGTAATCTTGCCCAAAACTTGTGA 59.353 37.500 0.00 0.00 0.00 3.58
375 385 4.744631 GTGTAATCTTGCCCAAAACTTGTG 59.255 41.667 0.00 0.00 0.00 3.33
376 386 4.202212 GGTGTAATCTTGCCCAAAACTTGT 60.202 41.667 0.00 0.00 0.00 3.16
377 387 4.039124 AGGTGTAATCTTGCCCAAAACTTG 59.961 41.667 0.00 0.00 0.00 3.16
378 388 4.039124 CAGGTGTAATCTTGCCCAAAACTT 59.961 41.667 0.00 0.00 0.00 2.66
379 389 3.573967 CAGGTGTAATCTTGCCCAAAACT 59.426 43.478 0.00 0.00 0.00 2.66
380 390 3.572255 TCAGGTGTAATCTTGCCCAAAAC 59.428 43.478 0.00 0.00 0.00 2.43
381 391 3.572255 GTCAGGTGTAATCTTGCCCAAAA 59.428 43.478 0.00 0.00 0.00 2.44
382 392 3.153919 GTCAGGTGTAATCTTGCCCAAA 58.846 45.455 0.00 0.00 0.00 3.28
383 393 2.375174 AGTCAGGTGTAATCTTGCCCAA 59.625 45.455 0.00 0.00 0.00 4.12
384 394 1.985159 AGTCAGGTGTAATCTTGCCCA 59.015 47.619 0.00 0.00 0.00 5.36
385 395 2.789409 AGTCAGGTGTAATCTTGCCC 57.211 50.000 0.00 0.00 0.00 5.36
386 396 5.880332 TCAATTAGTCAGGTGTAATCTTGCC 59.120 40.000 0.00 0.00 0.00 4.52
387 397 6.371548 TGTCAATTAGTCAGGTGTAATCTTGC 59.628 38.462 0.00 0.00 0.00 4.01
388 398 7.905604 TGTCAATTAGTCAGGTGTAATCTTG 57.094 36.000 0.00 0.00 0.00 3.02
389 399 8.321353 TCATGTCAATTAGTCAGGTGTAATCTT 58.679 33.333 0.00 0.00 0.00 2.40
390 400 7.851228 TCATGTCAATTAGTCAGGTGTAATCT 58.149 34.615 0.00 0.00 0.00 2.40
391 401 8.492673 TTCATGTCAATTAGTCAGGTGTAATC 57.507 34.615 0.00 0.00 0.00 1.75
392 402 8.862325 TTTCATGTCAATTAGTCAGGTGTAAT 57.138 30.769 0.00 0.00 0.00 1.89
393 403 8.684386 TTTTCATGTCAATTAGTCAGGTGTAA 57.316 30.769 0.00 0.00 0.00 2.41
394 404 8.684386 TTTTTCATGTCAATTAGTCAGGTGTA 57.316 30.769 0.00 0.00 0.00 2.90
395 405 7.581213 TTTTTCATGTCAATTAGTCAGGTGT 57.419 32.000 0.00 0.00 0.00 4.16
416 426 3.746792 AGGGCAAGCTCCTCTATTTTT 57.253 42.857 0.00 0.00 0.00 1.94
417 427 6.710499 ATATAGGGCAAGCTCCTCTATTTT 57.290 37.500 10.88 0.08 35.92 1.82
418 428 7.092668 CCTTATATAGGGCAAGCTCCTCTATTT 60.093 40.741 10.88 7.07 40.67 1.40
419 429 6.385467 CCTTATATAGGGCAAGCTCCTCTATT 59.615 42.308 10.88 4.22 40.67 1.73
420 430 5.902431 CCTTATATAGGGCAAGCTCCTCTAT 59.098 44.000 10.55 10.55 40.67 1.98
421 431 5.016352 TCCTTATATAGGGCAAGCTCCTCTA 59.984 44.000 6.02 0.00 44.86 2.43
422 432 4.100373 CCTTATATAGGGCAAGCTCCTCT 58.900 47.826 0.00 0.00 40.67 3.69
423 433 4.097418 TCCTTATATAGGGCAAGCTCCTC 58.903 47.826 6.02 0.00 44.86 3.71
424 434 4.147667 TCCTTATATAGGGCAAGCTCCT 57.852 45.455 6.02 7.16 44.86 3.69
425 435 4.910458 TTCCTTATATAGGGCAAGCTCC 57.090 45.455 6.02 0.00 44.86 4.70
426 436 6.241645 ACATTTCCTTATATAGGGCAAGCTC 58.758 40.000 6.02 0.00 44.86 4.09
427 437 6.206180 ACATTTCCTTATATAGGGCAAGCT 57.794 37.500 6.02 0.00 44.86 3.74
428 438 7.996098 TTACATTTCCTTATATAGGGCAAGC 57.004 36.000 6.02 0.00 44.86 4.01
429 439 9.739276 TGATTACATTTCCTTATATAGGGCAAG 57.261 33.333 6.02 0.07 44.86 4.01
458 468 9.672086 CACTCGTTTGAATAATTTTTGAAGGTA 57.328 29.630 0.00 0.00 0.00 3.08
459 469 7.651704 CCACTCGTTTGAATAATTTTTGAAGGT 59.348 33.333 0.00 0.00 0.00 3.50
460 470 7.651704 ACCACTCGTTTGAATAATTTTTGAAGG 59.348 33.333 0.00 0.00 0.00 3.46
461 471 8.479280 CACCACTCGTTTGAATAATTTTTGAAG 58.521 33.333 0.00 0.00 0.00 3.02
462 472 8.191446 TCACCACTCGTTTGAATAATTTTTGAA 58.809 29.630 0.00 0.00 0.00 2.69
463 473 7.708051 TCACCACTCGTTTGAATAATTTTTGA 58.292 30.769 0.00 0.00 0.00 2.69
464 474 7.922505 TCACCACTCGTTTGAATAATTTTTG 57.077 32.000 0.00 0.00 0.00 2.44
465 475 8.934507 TTTCACCACTCGTTTGAATAATTTTT 57.065 26.923 0.00 0.00 0.00 1.94
466 476 8.977505 CATTTCACCACTCGTTTGAATAATTTT 58.022 29.630 0.00 0.00 0.00 1.82
467 477 7.116233 GCATTTCACCACTCGTTTGAATAATTT 59.884 33.333 0.00 0.00 0.00 1.82
468 478 6.586082 GCATTTCACCACTCGTTTGAATAATT 59.414 34.615 0.00 0.00 0.00 1.40
469 479 6.092748 GCATTTCACCACTCGTTTGAATAAT 58.907 36.000 0.00 0.00 0.00 1.28
470 480 5.009110 TGCATTTCACCACTCGTTTGAATAA 59.991 36.000 0.00 0.00 0.00 1.40
471 481 4.517075 TGCATTTCACCACTCGTTTGAATA 59.483 37.500 0.00 0.00 0.00 1.75
472 482 3.317711 TGCATTTCACCACTCGTTTGAAT 59.682 39.130 0.00 0.00 0.00 2.57
473 483 2.685388 TGCATTTCACCACTCGTTTGAA 59.315 40.909 0.00 0.00 0.00 2.69
474 484 2.293170 TGCATTTCACCACTCGTTTGA 58.707 42.857 0.00 0.00 0.00 2.69
475 485 2.772568 TGCATTTCACCACTCGTTTG 57.227 45.000 0.00 0.00 0.00 2.93
476 486 3.641648 CATTGCATTTCACCACTCGTTT 58.358 40.909 0.00 0.00 0.00 3.60
477 487 2.607771 GCATTGCATTTCACCACTCGTT 60.608 45.455 3.15 0.00 0.00 3.85
478 488 1.068333 GCATTGCATTTCACCACTCGT 60.068 47.619 3.15 0.00 0.00 4.18
479 489 1.068402 TGCATTGCATTTCACCACTCG 60.068 47.619 7.38 0.00 31.71 4.18
480 490 2.331194 GTGCATTGCATTTCACCACTC 58.669 47.619 15.49 0.00 41.91 3.51
481 491 1.001181 GGTGCATTGCATTTCACCACT 59.999 47.619 20.82 0.00 46.09 4.00
482 492 1.431496 GGTGCATTGCATTTCACCAC 58.569 50.000 20.82 8.22 46.09 4.16
483 493 3.910817 GGTGCATTGCATTTCACCA 57.089 47.368 20.82 0.00 46.09 4.17
484 494 0.609662 AGGGTGCATTGCATTTCACC 59.390 50.000 18.49 18.49 46.10 4.02
485 495 3.806625 ATAGGGTGCATTGCATTTCAC 57.193 42.857 15.49 3.06 41.91 3.18
486 496 6.482898 AAATATAGGGTGCATTGCATTTCA 57.517 33.333 15.49 1.65 41.91 2.69
487 497 6.203338 CCAAAATATAGGGTGCATTGCATTTC 59.797 38.462 15.49 7.72 41.91 2.17
488 498 6.056884 CCAAAATATAGGGTGCATTGCATTT 58.943 36.000 15.49 6.47 41.91 2.32
489 499 5.366186 TCCAAAATATAGGGTGCATTGCATT 59.634 36.000 15.49 6.56 41.91 3.56
490 500 4.900652 TCCAAAATATAGGGTGCATTGCAT 59.099 37.500 15.49 1.17 41.91 3.96
491 501 4.099266 GTCCAAAATATAGGGTGCATTGCA 59.901 41.667 7.38 7.38 35.60 4.08
492 502 4.342092 AGTCCAAAATATAGGGTGCATTGC 59.658 41.667 0.46 0.46 0.00 3.56
493 503 6.469782 AAGTCCAAAATATAGGGTGCATTG 57.530 37.500 0.00 0.00 0.00 2.82
494 504 7.494922 AAAAGTCCAAAATATAGGGTGCATT 57.505 32.000 0.00 0.00 0.00 3.56
495 505 7.400052 AGAAAAAGTCCAAAATATAGGGTGCAT 59.600 33.333 0.00 0.00 0.00 3.96
496 506 6.723977 AGAAAAAGTCCAAAATATAGGGTGCA 59.276 34.615 0.00 0.00 0.00 4.57
497 507 7.170393 AGAAAAAGTCCAAAATATAGGGTGC 57.830 36.000 0.00 0.00 0.00 5.01
524 534 9.661563 TCCTTGATACAACGTGTATAGATTTTT 57.338 29.630 9.61 0.00 43.08 1.94
525 535 9.661563 TTCCTTGATACAACGTGTATAGATTTT 57.338 29.630 9.61 0.00 43.08 1.82
526 536 9.095065 GTTCCTTGATACAACGTGTATAGATTT 57.905 33.333 9.61 0.00 43.08 2.17
527 537 7.434307 CGTTCCTTGATACAACGTGTATAGATT 59.566 37.037 9.61 0.00 43.08 2.40
528 538 6.916387 CGTTCCTTGATACAACGTGTATAGAT 59.084 38.462 9.61 0.00 43.08 1.98
529 539 6.260377 CGTTCCTTGATACAACGTGTATAGA 58.740 40.000 9.61 4.31 43.08 1.98
530 540 5.457799 CCGTTCCTTGATACAACGTGTATAG 59.542 44.000 9.61 6.06 43.08 1.31
531 541 5.125257 TCCGTTCCTTGATACAACGTGTATA 59.875 40.000 9.61 0.00 43.08 1.47
532 542 4.082081 TCCGTTCCTTGATACAACGTGTAT 60.082 41.667 9.46 9.46 45.48 2.29
533 543 3.255395 TCCGTTCCTTGATACAACGTGTA 59.745 43.478 0.00 0.00 41.03 2.90
534 544 2.036217 TCCGTTCCTTGATACAACGTGT 59.964 45.455 0.00 0.00 41.03 4.49
535 545 2.666508 CTCCGTTCCTTGATACAACGTG 59.333 50.000 0.00 0.00 41.03 4.49
536 546 2.353406 CCTCCGTTCCTTGATACAACGT 60.353 50.000 3.08 0.00 41.03 3.99
537 547 2.268298 CCTCCGTTCCTTGATACAACG 58.732 52.381 0.00 0.00 42.02 4.10
538 548 2.235402 TCCCTCCGTTCCTTGATACAAC 59.765 50.000 0.00 0.00 0.00 3.32
539 549 2.542550 TCCCTCCGTTCCTTGATACAA 58.457 47.619 0.00 0.00 0.00 2.41
540 550 2.241281 TCCCTCCGTTCCTTGATACA 57.759 50.000 0.00 0.00 0.00 2.29
541 551 3.840124 ATTCCCTCCGTTCCTTGATAC 57.160 47.619 0.00 0.00 0.00 2.24
542 552 5.152193 TCATATTCCCTCCGTTCCTTGATA 58.848 41.667 0.00 0.00 0.00 2.15
543 553 3.973973 TCATATTCCCTCCGTTCCTTGAT 59.026 43.478 0.00 0.00 0.00 2.57
544 554 3.380393 TCATATTCCCTCCGTTCCTTGA 58.620 45.455 0.00 0.00 0.00 3.02
545 555 3.388024 TCTCATATTCCCTCCGTTCCTTG 59.612 47.826 0.00 0.00 0.00 3.61
546 556 3.654273 TCTCATATTCCCTCCGTTCCTT 58.346 45.455 0.00 0.00 0.00 3.36
547 557 3.330126 TCTCATATTCCCTCCGTTCCT 57.670 47.619 0.00 0.00 0.00 3.36
548 558 4.625607 AATCTCATATTCCCTCCGTTCC 57.374 45.455 0.00 0.00 0.00 3.62
549 559 4.757149 CCAAATCTCATATTCCCTCCGTTC 59.243 45.833 0.00 0.00 0.00 3.95
550 560 4.412199 TCCAAATCTCATATTCCCTCCGTT 59.588 41.667 0.00 0.00 0.00 4.44
551 561 3.973973 TCCAAATCTCATATTCCCTCCGT 59.026 43.478 0.00 0.00 0.00 4.69
552 562 4.202357 TGTCCAAATCTCATATTCCCTCCG 60.202 45.833 0.00 0.00 0.00 4.63
553 563 5.072329 TCTGTCCAAATCTCATATTCCCTCC 59.928 44.000 0.00 0.00 0.00 4.30
554 564 6.042552 TCTCTGTCCAAATCTCATATTCCCTC 59.957 42.308 0.00 0.00 0.00 4.30
555 565 5.907662 TCTCTGTCCAAATCTCATATTCCCT 59.092 40.000 0.00 0.00 0.00 4.20
556 566 6.179906 TCTCTGTCCAAATCTCATATTCCC 57.820 41.667 0.00 0.00 0.00 3.97
557 567 8.688747 AAATCTCTGTCCAAATCTCATATTCC 57.311 34.615 0.00 0.00 0.00 3.01
562 572 8.454106 CGTTTTAAATCTCTGTCCAAATCTCAT 58.546 33.333 0.00 0.00 0.00 2.90
568 578 7.789273 TGTACGTTTTAAATCTCTGTCCAAA 57.211 32.000 0.00 0.00 0.00 3.28
591 602 5.414454 TCCCGTGTTTTCTAAATCTTGGATG 59.586 40.000 0.00 0.00 0.00 3.51
645 659 4.907875 AGGGCCAAGAGAGCAAAGTATATA 59.092 41.667 6.18 0.00 0.00 0.86
646 660 3.718956 AGGGCCAAGAGAGCAAAGTATAT 59.281 43.478 6.18 0.00 0.00 0.86
675 689 5.011738 AGGATCTGTTGTACTCCGAAAAAGA 59.988 40.000 0.00 0.00 32.87 2.52
676 690 5.120830 CAGGATCTGTTGTACTCCGAAAAAG 59.879 44.000 0.00 0.00 32.87 2.27
682 696 1.478510 AGCAGGATCTGTTGTACTCCG 59.521 52.381 0.00 0.00 33.43 4.63
735 749 5.393678 CCGAACCTGTTTCTTTTTCTTTGGA 60.394 40.000 0.00 0.00 31.20 3.53
815 830 0.391597 TTCTCTCGTGCTCCGGTTTT 59.608 50.000 0.00 0.00 37.11 2.43
891 933 3.805207 AGGTGATTACGATTTACAGGGC 58.195 45.455 0.00 0.00 0.00 5.19
892 934 4.377897 GGAGGTGATTACGATTTACAGGG 58.622 47.826 0.00 0.00 0.00 4.45
895 937 6.040166 GTCTAGGGAGGTGATTACGATTTACA 59.960 42.308 0.00 0.00 0.00 2.41
938 980 1.134438 AGTGGGGTGGAAGGAAGTCC 61.134 60.000 0.00 0.00 38.27 3.85
939 981 0.325272 GAGTGGGGTGGAAGGAAGTC 59.675 60.000 0.00 0.00 0.00 3.01
940 982 1.481056 CGAGTGGGGTGGAAGGAAGT 61.481 60.000 0.00 0.00 0.00 3.01
942 984 2.890766 GCGAGTGGGGTGGAAGGAA 61.891 63.158 0.00 0.00 0.00 3.36
943 985 3.319198 GCGAGTGGGGTGGAAGGA 61.319 66.667 0.00 0.00 0.00 3.36
945 987 2.358737 GTGCGAGTGGGGTGGAAG 60.359 66.667 0.00 0.00 0.00 3.46
1305 1601 0.951040 CCTGGTTGAGGTCGAACTGC 60.951 60.000 8.28 0.00 37.02 4.40
1494 1790 2.124860 GGCACCCCGTGGTACATC 60.125 66.667 0.00 0.00 45.57 3.06
1732 2028 1.235112 CCGGGGGTGGTAGGTAGAT 59.765 63.158 0.00 0.00 0.00 1.98
1734 2030 1.002017 TTCCGGGGGTGGTAGGTAG 59.998 63.158 0.00 0.00 0.00 3.18
1739 2035 2.122054 TTGGTTCCGGGGGTGGTA 60.122 61.111 0.00 0.00 0.00 3.25
1740 2036 3.893399 GTTGGTTCCGGGGGTGGT 61.893 66.667 0.00 0.00 0.00 4.16
1742 2038 2.650226 AAAGGTTGGTTCCGGGGGTG 62.650 60.000 0.00 0.00 0.00 4.61
1743 2039 1.951923 AAAAGGTTGGTTCCGGGGGT 61.952 55.000 0.00 0.00 0.00 4.95
1744 2040 0.761323 AAAAAGGTTGGTTCCGGGGG 60.761 55.000 0.00 0.00 0.00 5.40
1745 2041 2.829094 AAAAAGGTTGGTTCCGGGG 58.171 52.632 0.00 0.00 0.00 5.73
1789 2092 2.897350 CCTTTCGATCAGCCCGGC 60.897 66.667 0.00 0.00 0.00 6.13
1791 2094 1.521681 GTCCCTTTCGATCAGCCCG 60.522 63.158 0.00 0.00 0.00 6.13
1811 2114 0.316689 GCAGGTTTTGTTCACGACGG 60.317 55.000 0.00 0.00 0.00 4.79
1812 2115 0.375454 TGCAGGTTTTGTTCACGACG 59.625 50.000 0.00 0.00 0.00 5.12
1813 2116 1.268539 CCTGCAGGTTTTGTTCACGAC 60.269 52.381 25.53 0.00 0.00 4.34
1814 2117 1.021202 CCTGCAGGTTTTGTTCACGA 58.979 50.000 25.53 0.00 0.00 4.35
1901 2204 1.585521 CTACACGCTTAGCCCGTCG 60.586 63.158 0.00 0.00 36.69 5.12
1999 2305 9.156940 CAGATTCCCATCCACATATATCTATCT 57.843 37.037 0.00 0.00 0.00 1.98
2094 2400 0.605589 GTGAGGTGAGGTGAGGTGAG 59.394 60.000 0.00 0.00 0.00 3.51
2095 2401 0.832135 GGTGAGGTGAGGTGAGGTGA 60.832 60.000 0.00 0.00 0.00 4.02
2096 2402 0.833834 AGGTGAGGTGAGGTGAGGTG 60.834 60.000 0.00 0.00 0.00 4.00
2097 2403 0.104934 AAGGTGAGGTGAGGTGAGGT 60.105 55.000 0.00 0.00 0.00 3.85
2098 2404 1.827969 CTAAGGTGAGGTGAGGTGAGG 59.172 57.143 0.00 0.00 0.00 3.86
2112 2418 2.023210 GGTAACCTCCTCCTCCTAAGGT 60.023 54.545 0.00 0.00 43.96 3.50
2119 2425 0.683504 TCAGCGGTAACCTCCTCCTC 60.684 60.000 0.00 0.00 0.00 3.71
2123 2429 1.867363 AGAATCAGCGGTAACCTCCT 58.133 50.000 0.00 0.00 0.00 3.69
2124 2430 2.280628 CAAGAATCAGCGGTAACCTCC 58.719 52.381 0.00 0.00 0.00 4.30
2134 2440 5.747197 CCAGCAATAATTCACAAGAATCAGC 59.253 40.000 0.00 0.00 43.52 4.26
2198 2507 0.960364 GCAACGGCCATGGAAGAAGA 60.960 55.000 18.40 0.00 0.00 2.87
2199 2508 0.962356 AGCAACGGCCATGGAAGAAG 60.962 55.000 18.40 2.48 42.56 2.85
2200 2509 0.539438 AAGCAACGGCCATGGAAGAA 60.539 50.000 18.40 0.00 42.56 2.52
2231 2540 2.240612 CTTTAGCGCCGCACCACTTC 62.241 60.000 13.36 0.00 0.00 3.01
2257 2566 1.519455 CGGTCAGATTCCACTCGCC 60.519 63.158 0.00 0.00 0.00 5.54
2335 2653 4.924187 CCCACGGCCCACCCAAAA 62.924 66.667 0.00 0.00 0.00 2.44
2348 2666 4.016706 CACCGACTCCCACCCCAC 62.017 72.222 0.00 0.00 0.00 4.61
2480 2798 1.237285 CCGTGGAAGCAGGAAACCAG 61.237 60.000 0.00 0.00 32.89 4.00
2504 2822 2.667199 CCCCCACCACGACGAAAC 60.667 66.667 0.00 0.00 0.00 2.78
2548 2866 0.037605 ACGCTCCAAGGAAGTAACCG 60.038 55.000 0.00 0.00 34.73 4.44
2549 2867 1.439679 CACGCTCCAAGGAAGTAACC 58.560 55.000 0.00 0.00 0.00 2.85
2550 2868 1.439679 CCACGCTCCAAGGAAGTAAC 58.560 55.000 0.00 0.00 0.00 2.50
2604 2922 4.976116 GGAACGTCAAATTTCAACTTGGAG 59.024 41.667 0.00 0.00 0.00 3.86
2606 2924 4.502645 GTGGAACGTCAAATTTCAACTTGG 59.497 41.667 0.00 0.00 0.00 3.61
2607 2925 5.339990 AGTGGAACGTCAAATTTCAACTTG 58.660 37.500 0.00 0.00 45.86 3.16
2629 2947 3.470567 GACAAGCGTCGCACGGAG 61.471 66.667 21.09 6.43 42.82 4.63
2684 3003 8.893563 TGTAGATCCCACCATTTTCTAATTTT 57.106 30.769 0.00 0.00 0.00 1.82
2685 3004 7.068716 GCTGTAGATCCCACCATTTTCTAATTT 59.931 37.037 0.00 0.00 0.00 1.82
2687 3006 6.064717 GCTGTAGATCCCACCATTTTCTAAT 58.935 40.000 0.00 0.00 0.00 1.73
2766 3086 3.427233 GCCATGTGCAAACTGAGATTCTC 60.427 47.826 6.73 6.73 40.77 2.87
2767 3087 2.490903 GCCATGTGCAAACTGAGATTCT 59.509 45.455 0.00 0.00 40.77 2.40
2802 3128 2.037121 TGGAAGTCTCGCACAGATTCAA 59.963 45.455 0.00 0.00 32.08 2.69
2853 3179 0.729116 AGAAGCAATTCGATGGCACG 59.271 50.000 0.00 0.00 0.00 5.34
2893 3219 3.732048 TGTAGGACAATCCTTTTCCCC 57.268 47.619 1.99 0.00 46.91 4.81
2907 3233 8.706492 AATTTAATACACGAACGAATGTAGGA 57.294 30.769 0.14 0.00 34.88 2.94
2914 3240 8.838452 ACAACAAAATTTAATACACGAACGAA 57.162 26.923 0.14 0.00 0.00 3.85
2915 3241 8.121086 TGACAACAAAATTTAATACACGAACGA 58.879 29.630 0.14 0.00 0.00 3.85
2916 3242 8.196241 GTGACAACAAAATTTAATACACGAACG 58.804 33.333 0.00 0.00 0.00 3.95
2917 3243 8.196241 CGTGACAACAAAATTTAATACACGAAC 58.804 33.333 20.06 3.11 46.10 3.95
2934 3260 3.997681 TGAAACTTGAAGACGTGACAACA 59.002 39.130 0.00 0.00 0.00 3.33
2964 3485 9.015367 CACAGTGCTATTATAGTACTCCTACAT 57.985 37.037 17.81 0.00 46.70 2.29
2966 3487 8.291032 CACACAGTGCTATTATAGTACTCCTAC 58.709 40.741 17.81 0.00 46.70 3.18
2967 3488 8.392372 CACACAGTGCTATTATAGTACTCCTA 57.608 38.462 17.81 0.00 46.70 2.94
2968 3489 7.278461 CACACAGTGCTATTATAGTACTCCT 57.722 40.000 17.81 5.87 46.70 3.69
3090 3649 0.514691 CTGGTCAAGCGAAGTGAAGC 59.485 55.000 0.00 0.00 0.00 3.86
3092 3651 1.540363 GGTCTGGTCAAGCGAAGTGAA 60.540 52.381 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.