Multiple sequence alignment - TraesCS3A01G244600

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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 TraesCS3A01G244600 chr3A 100.000 4997 0 0 1 4997 457665845 457660849 0.000000e+00 9228.0
1 TraesCS3A01G244600 chr3A 90.123 162 16 0 1244 1405 83728197 83728036 1.410000e-50 211.0
2 TraesCS3A01G244600 chr3D 93.487 2779 115 18 1661 4400 346060654 346063405 0.000000e+00 4069.0
3 TraesCS3A01G244600 chr3D 93.114 1249 49 14 438 1663 346059362 346060596 0.000000e+00 1796.0
4 TraesCS3A01G244600 chr3D 94.186 602 21 3 4392 4979 346064541 346065142 0.000000e+00 905.0
5 TraesCS3A01G244600 chr3D 88.554 332 19 6 1 330 346059047 346059361 7.850000e-103 385.0
6 TraesCS3A01G244600 chr3D 89.506 162 17 0 1244 1405 71499680 71499519 6.560000e-49 206.0
7 TraesCS3A01G244600 chr3D 80.247 162 30 2 228 388 25185591 25185751 2.440000e-23 121.0
8 TraesCS3A01G244600 chr3B 92.532 2812 134 32 1661 4457 445202800 445205550 0.000000e+00 3960.0
9 TraesCS3A01G244600 chr3B 87.382 1268 54 38 450 1663 445201527 445202742 0.000000e+00 1358.0
10 TraesCS3A01G244600 chr3B 88.942 208 20 2 87 294 445201322 445201526 2.310000e-63 254.0
11 TraesCS3A01G244600 chr3B 90.123 162 16 0 1244 1405 117556907 117556746 1.410000e-50 211.0
12 TraesCS3A01G244600 chr3B 95.506 89 3 1 1 88 445201130 445201218 1.880000e-29 141.0
13 TraesCS3A01G244600 chr3B 77.333 150 31 2 501 649 602351778 602351631 8.910000e-13 86.1
14 TraesCS3A01G244600 chr1A 85.278 360 43 8 1038 1395 539760006 539760357 3.680000e-96 363.0
15 TraesCS3A01G244600 chr1B 82.412 398 46 13 1001 1395 603298821 603299197 4.820000e-85 326.0
16 TraesCS3A01G244600 chr1B 77.519 129 27 1 501 629 614941508 614941382 5.360000e-10 76.8
17 TraesCS3A01G244600 chr1D 83.862 347 38 10 1049 1395 443821447 443821775 1.040000e-81 315.0
18 TraesCS3A01G244600 chr1D 97.297 37 1 0 352 388 445285517 445285553 4.180000e-06 63.9
19 TraesCS3A01G244600 chr5D 73.523 457 83 25 229 654 407783142 407783591 6.750000e-29 139.0
20 TraesCS3A01G244600 chr7B 78.082 219 35 10 394 602 624470840 624471055 5.250000e-25 126.0
21 TraesCS3A01G244600 chr7B 74.537 216 48 5 393 602 712675627 712675841 2.480000e-13 87.9
22 TraesCS3A01G244600 chr7D 77.576 165 34 3 227 388 7594768 7594932 4.120000e-16 97.1
23 TraesCS3A01G244600 chr2D 82.828 99 15 2 485 582 387224027 387223930 2.480000e-13 87.9
24 TraesCS3A01G244600 chr2D 75.796 157 34 3 501 655 122520038 122519884 5.360000e-10 76.8


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 TraesCS3A01G244600 chr3A 457660849 457665845 4996 True 9228.00 9228 100.00000 1 4997 1 chr3A.!!$R2 4996
1 TraesCS3A01G244600 chr3D 346059047 346065142 6095 False 1788.75 4069 92.33525 1 4979 4 chr3D.!!$F2 4978
2 TraesCS3A01G244600 chr3B 445201130 445205550 4420 False 1428.25 3960 91.09050 1 4457 4 chr3B.!!$F1 4456

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
389 514 0.027586 GTCGGTGTTTGTGTGTCTGC 59.972 55.0 0.00 0.00 0.00 4.26 F
395 520 0.028902 GTTTGTGTGTCTGCGGGTTC 59.971 55.0 0.00 0.00 0.00 3.62 F
396 521 0.107410 TTTGTGTGTCTGCGGGTTCT 60.107 50.0 0.00 0.00 0.00 3.01 F
2118 2381 0.108662 TGCACATACGACTGCAGAGG 60.109 55.0 23.35 13.87 38.49 3.69 F
2219 2489 0.593128 CACAGCTGGTGGCAAAGTAC 59.407 55.0 19.93 0.00 44.04 2.73 F
3797 4094 0.613260 CGAGTCATCTGGTTTGGGGA 59.387 55.0 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1989 0.031585 TCAACGGACGAGAACCACAG 59.968 55.0 0.00 0.00 0.00 3.66 R
1743 2002 0.110238 CACGGCAGAACATTCAACGG 60.110 55.0 0.00 0.00 0.00 4.44 R
2200 2465 0.593128 GTACTTTGCCACCAGCTGTG 59.407 55.0 13.81 10.81 44.23 3.66 R
2953 3223 0.036732 TGGTCAGCATGTTGGTCTCC 59.963 55.0 9.87 8.05 37.40 3.71 R
3939 4237 0.098376 GCTCAAATCTCTGCCTTGCG 59.902 55.0 0.00 0.00 0.00 4.85 R
4680 6125 0.319125 GCTGTCCGATCGAAGATCCC 60.319 60.0 18.66 0.00 45.12 3.85 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
121 228 9.716507 CCTAAAAATTGTATGTGAGATTTACGG 57.283 33.333 0.00 0.00 0.00 4.02
145 252 9.165035 CGGTTACAATTTTATAGGGTCAAACTA 57.835 33.333 0.00 0.00 0.00 2.24
195 302 7.671398 AGGAGAGTATGATTTTGTCCATTTTGT 59.329 33.333 0.00 0.00 0.00 2.83
196 303 8.306761 GGAGAGTATGATTTTGTCCATTTTGTT 58.693 33.333 0.00 0.00 0.00 2.83
197 304 9.696917 GAGAGTATGATTTTGTCCATTTTGTTT 57.303 29.630 0.00 0.00 0.00 2.83
198 305 9.480053 AGAGTATGATTTTGTCCATTTTGTTTG 57.520 29.630 0.00 0.00 0.00 2.93
199 306 9.474920 GAGTATGATTTTGTCCATTTTGTTTGA 57.525 29.630 0.00 0.00 0.00 2.69
200 307 9.260002 AGTATGATTTTGTCCATTTTGTTTGAC 57.740 29.630 0.00 0.00 0.00 3.18
201 308 6.917217 TGATTTTGTCCATTTTGTTTGACC 57.083 33.333 0.00 0.00 0.00 4.02
202 309 6.648192 TGATTTTGTCCATTTTGTTTGACCT 58.352 32.000 0.00 0.00 0.00 3.85
203 310 6.760770 TGATTTTGTCCATTTTGTTTGACCTC 59.239 34.615 0.00 0.00 0.00 3.85
204 311 5.667539 TTTGTCCATTTTGTTTGACCTCA 57.332 34.783 0.00 0.00 0.00 3.86
205 312 4.647424 TGTCCATTTTGTTTGACCTCAC 57.353 40.909 0.00 0.00 0.00 3.51
206 313 3.066064 TGTCCATTTTGTTTGACCTCACG 59.934 43.478 0.00 0.00 0.00 4.35
207 314 3.314080 GTCCATTTTGTTTGACCTCACGA 59.686 43.478 0.00 0.00 0.00 4.35
208 315 3.948473 TCCATTTTGTTTGACCTCACGAA 59.052 39.130 0.00 0.00 0.00 3.85
209 316 4.399618 TCCATTTTGTTTGACCTCACGAAA 59.600 37.500 0.00 0.00 32.10 3.46
210 317 4.502645 CCATTTTGTTTGACCTCACGAAAC 59.497 41.667 0.00 0.00 30.64 2.78
211 318 3.768468 TTTGTTTGACCTCACGAAACC 57.232 42.857 0.00 0.00 0.00 3.27
220 344 1.066358 CCTCACGAAACCTTCCCTACC 60.066 57.143 0.00 0.00 0.00 3.18
251 375 2.058595 GGTTCTCTCCGCCTAGCCA 61.059 63.158 0.00 0.00 0.00 4.75
259 383 4.176752 CGCCTAGCCACCTTCCCC 62.177 72.222 0.00 0.00 0.00 4.81
269 393 2.160646 ACCTTCCCCGTGGTGATTT 58.839 52.632 0.00 0.00 34.90 2.17
281 405 0.165944 GGTGATTTCAGCGTTGTCGG 59.834 55.000 0.00 0.00 37.56 4.79
330 455 3.710326 TCTTGAGGGATACGATCGTTG 57.290 47.619 27.88 5.93 37.60 4.10
331 456 3.021695 TCTTGAGGGATACGATCGTTGT 58.978 45.455 27.88 15.73 37.60 3.32
332 457 3.446161 TCTTGAGGGATACGATCGTTGTT 59.554 43.478 27.88 11.88 37.60 2.83
333 458 3.880047 TGAGGGATACGATCGTTGTTT 57.120 42.857 27.88 9.19 37.60 2.83
334 459 3.517602 TGAGGGATACGATCGTTGTTTG 58.482 45.455 27.88 0.00 37.60 2.93
335 460 3.056393 TGAGGGATACGATCGTTGTTTGT 60.056 43.478 27.88 7.24 37.60 2.83
336 461 3.518590 AGGGATACGATCGTTGTTTGTC 58.481 45.455 27.88 13.95 37.60 3.18
337 462 3.194968 AGGGATACGATCGTTGTTTGTCT 59.805 43.478 27.88 11.87 37.60 3.41
338 463 3.930848 GGGATACGATCGTTGTTTGTCTT 59.069 43.478 27.88 0.00 37.60 3.01
339 464 4.032558 GGGATACGATCGTTGTTTGTCTTC 59.967 45.833 27.88 9.14 37.60 2.87
340 465 4.259292 GGATACGATCGTTGTTTGTCTTCG 60.259 45.833 27.88 0.00 0.00 3.79
341 466 1.790623 ACGATCGTTGTTTGTCTTCGG 59.209 47.619 16.60 0.00 0.00 4.30
342 467 1.790623 CGATCGTTGTTTGTCTTCGGT 59.209 47.619 7.03 0.00 0.00 4.69
343 468 2.409752 CGATCGTTGTTTGTCTTCGGTG 60.410 50.000 7.03 0.00 0.00 4.94
344 469 1.292061 TCGTTGTTTGTCTTCGGTGG 58.708 50.000 0.00 0.00 0.00 4.61
345 470 1.134759 TCGTTGTTTGTCTTCGGTGGA 60.135 47.619 0.00 0.00 0.00 4.02
346 471 1.871039 CGTTGTTTGTCTTCGGTGGAT 59.129 47.619 0.00 0.00 0.00 3.41
347 472 2.096417 CGTTGTTTGTCTTCGGTGGATC 60.096 50.000 0.00 0.00 0.00 3.36
348 473 2.178912 TGTTTGTCTTCGGTGGATCC 57.821 50.000 4.20 4.20 0.00 3.36
349 474 1.418264 TGTTTGTCTTCGGTGGATCCA 59.582 47.619 11.44 11.44 35.57 3.41
350 475 1.804748 GTTTGTCTTCGGTGGATCCAC 59.195 52.381 33.14 33.14 45.49 4.02
363 488 1.606903 GATCCACGTAGATCCGGTCT 58.393 55.000 12.35 6.57 37.31 3.85
364 489 1.955080 GATCCACGTAGATCCGGTCTT 59.045 52.381 12.35 0.00 37.31 3.01
365 490 1.386533 TCCACGTAGATCCGGTCTTC 58.613 55.000 11.09 6.31 38.42 2.87
369 494 2.556534 CGTAGATCCGGTCTTCGTTT 57.443 50.000 18.13 0.00 41.23 3.60
370 495 2.182825 CGTAGATCCGGTCTTCGTTTG 58.817 52.381 18.13 0.00 41.23 2.93
371 496 2.415090 CGTAGATCCGGTCTTCGTTTGT 60.415 50.000 18.13 0.00 41.23 2.83
372 497 2.365408 AGATCCGGTCTTCGTTTGTC 57.635 50.000 0.00 0.00 37.11 3.18
373 498 0.989890 GATCCGGTCTTCGTTTGTCG 59.010 55.000 0.00 0.00 41.41 4.35
374 499 0.389426 ATCCGGTCTTCGTTTGTCGG 60.389 55.000 0.00 0.00 40.32 4.79
375 500 1.300388 CCGGTCTTCGTTTGTCGGT 60.300 57.895 0.00 0.00 40.32 4.69
376 501 1.554042 CCGGTCTTCGTTTGTCGGTG 61.554 60.000 0.00 0.00 40.32 4.94
377 502 0.872881 CGGTCTTCGTTTGTCGGTGT 60.873 55.000 0.00 0.00 40.32 4.16
378 503 1.292992 GGTCTTCGTTTGTCGGTGTT 58.707 50.000 0.00 0.00 40.32 3.32
379 504 1.667212 GGTCTTCGTTTGTCGGTGTTT 59.333 47.619 0.00 0.00 40.32 2.83
380 505 2.538132 GGTCTTCGTTTGTCGGTGTTTG 60.538 50.000 0.00 0.00 40.32 2.93
381 506 2.094734 GTCTTCGTTTGTCGGTGTTTGT 59.905 45.455 0.00 0.00 40.32 2.83
382 507 2.094575 TCTTCGTTTGTCGGTGTTTGTG 59.905 45.455 0.00 0.00 40.32 3.33
383 508 1.440708 TCGTTTGTCGGTGTTTGTGT 58.559 45.000 0.00 0.00 40.32 3.72
384 509 1.128878 TCGTTTGTCGGTGTTTGTGTG 59.871 47.619 0.00 0.00 40.32 3.82
385 510 1.135916 CGTTTGTCGGTGTTTGTGTGT 60.136 47.619 0.00 0.00 35.71 3.72
386 511 2.511879 GTTTGTCGGTGTTTGTGTGTC 58.488 47.619 0.00 0.00 0.00 3.67
387 512 2.102070 TTGTCGGTGTTTGTGTGTCT 57.898 45.000 0.00 0.00 0.00 3.41
388 513 1.364721 TGTCGGTGTTTGTGTGTCTG 58.635 50.000 0.00 0.00 0.00 3.51
389 514 0.027586 GTCGGTGTTTGTGTGTCTGC 59.972 55.000 0.00 0.00 0.00 4.26
390 515 1.011242 CGGTGTTTGTGTGTCTGCG 60.011 57.895 0.00 0.00 0.00 5.18
391 516 1.355210 GGTGTTTGTGTGTCTGCGG 59.645 57.895 0.00 0.00 0.00 5.69
392 517 1.355210 GTGTTTGTGTGTCTGCGGG 59.645 57.895 0.00 0.00 0.00 6.13
393 518 1.078072 TGTTTGTGTGTCTGCGGGT 60.078 52.632 0.00 0.00 0.00 5.28
394 519 0.678366 TGTTTGTGTGTCTGCGGGTT 60.678 50.000 0.00 0.00 0.00 4.11
395 520 0.028902 GTTTGTGTGTCTGCGGGTTC 59.971 55.000 0.00 0.00 0.00 3.62
396 521 0.107410 TTTGTGTGTCTGCGGGTTCT 60.107 50.000 0.00 0.00 0.00 3.01
397 522 0.107410 TTGTGTGTCTGCGGGTTCTT 60.107 50.000 0.00 0.00 0.00 2.52
398 523 0.107410 TGTGTGTCTGCGGGTTCTTT 60.107 50.000 0.00 0.00 0.00 2.52
399 524 1.021968 GTGTGTCTGCGGGTTCTTTT 58.978 50.000 0.00 0.00 0.00 2.27
400 525 1.002792 GTGTGTCTGCGGGTTCTTTTC 60.003 52.381 0.00 0.00 0.00 2.29
401 526 1.305201 GTGTCTGCGGGTTCTTTTCA 58.695 50.000 0.00 0.00 0.00 2.69
402 527 1.880027 GTGTCTGCGGGTTCTTTTCAT 59.120 47.619 0.00 0.00 0.00 2.57
403 528 2.095718 GTGTCTGCGGGTTCTTTTCATC 60.096 50.000 0.00 0.00 0.00 2.92
404 529 1.128692 GTCTGCGGGTTCTTTTCATCG 59.871 52.381 0.00 0.00 0.00 3.84
405 530 0.447801 CTGCGGGTTCTTTTCATCGG 59.552 55.000 0.00 0.00 0.00 4.18
406 531 1.136774 GCGGGTTCTTTTCATCGGC 59.863 57.895 0.00 0.00 0.00 5.54
407 532 1.423845 CGGGTTCTTTTCATCGGCG 59.576 57.895 0.00 0.00 0.00 6.46
408 533 1.800681 GGGTTCTTTTCATCGGCGG 59.199 57.895 7.21 0.00 0.00 6.13
409 534 1.136774 GGTTCTTTTCATCGGCGGC 59.863 57.895 7.21 0.00 0.00 6.53
410 535 1.305930 GGTTCTTTTCATCGGCGGCT 61.306 55.000 7.21 0.00 0.00 5.52
411 536 0.179189 GTTCTTTTCATCGGCGGCTG 60.179 55.000 7.21 1.35 0.00 4.85
412 537 0.605319 TTCTTTTCATCGGCGGCTGT 60.605 50.000 7.21 0.00 0.00 4.40
413 538 0.605319 TCTTTTCATCGGCGGCTGTT 60.605 50.000 7.21 0.00 0.00 3.16
414 539 0.454957 CTTTTCATCGGCGGCTGTTG 60.455 55.000 7.21 12.61 0.00 3.33
415 540 1.169661 TTTTCATCGGCGGCTGTTGT 61.170 50.000 17.01 0.00 0.00 3.32
416 541 1.169661 TTTCATCGGCGGCTGTTGTT 61.170 50.000 17.01 0.00 0.00 2.83
417 542 1.851021 TTCATCGGCGGCTGTTGTTG 61.851 55.000 17.01 8.14 0.00 3.33
418 543 2.281484 ATCGGCGGCTGTTGTTGT 60.281 55.556 7.21 0.00 0.00 3.32
419 544 1.896660 ATCGGCGGCTGTTGTTGTT 60.897 52.632 7.21 0.00 0.00 2.83
420 545 1.452145 ATCGGCGGCTGTTGTTGTTT 61.452 50.000 7.21 0.00 0.00 2.83
421 546 1.226831 CGGCGGCTGTTGTTGTTTT 60.227 52.632 7.61 0.00 0.00 2.43
422 547 0.804156 CGGCGGCTGTTGTTGTTTTT 60.804 50.000 7.61 0.00 0.00 1.94
423 548 0.649993 GGCGGCTGTTGTTGTTTTTG 59.350 50.000 0.00 0.00 0.00 2.44
424 549 1.355005 GCGGCTGTTGTTGTTTTTGT 58.645 45.000 0.00 0.00 0.00 2.83
425 550 1.060409 GCGGCTGTTGTTGTTTTTGTG 59.940 47.619 0.00 0.00 0.00 3.33
426 551 1.060409 CGGCTGTTGTTGTTTTTGTGC 59.940 47.619 0.00 0.00 0.00 4.57
427 552 1.060409 GGCTGTTGTTGTTTTTGTGCG 59.940 47.619 0.00 0.00 0.00 5.34
428 553 1.724082 GCTGTTGTTGTTTTTGTGCGT 59.276 42.857 0.00 0.00 0.00 5.24
429 554 2.156697 GCTGTTGTTGTTTTTGTGCGTT 59.843 40.909 0.00 0.00 0.00 4.84
430 555 3.719974 CTGTTGTTGTTTTTGTGCGTTG 58.280 40.909 0.00 0.00 0.00 4.10
431 556 2.476619 TGTTGTTGTTTTTGTGCGTTGG 59.523 40.909 0.00 0.00 0.00 3.77
432 557 2.440539 TGTTGTTTTTGTGCGTTGGT 57.559 40.000 0.00 0.00 0.00 3.67
433 558 2.329379 TGTTGTTTTTGTGCGTTGGTC 58.671 42.857 0.00 0.00 0.00 4.02
434 559 1.656594 GTTGTTTTTGTGCGTTGGTCC 59.343 47.619 0.00 0.00 0.00 4.46
435 560 1.178276 TGTTTTTGTGCGTTGGTCCT 58.822 45.000 0.00 0.00 0.00 3.85
436 561 1.135257 TGTTTTTGTGCGTTGGTCCTG 60.135 47.619 0.00 0.00 0.00 3.86
468 593 2.245942 CATGACGACTTCTCGACTGTG 58.754 52.381 0.00 0.00 43.06 3.66
481 606 4.569162 TCTCGACTGTGTTTGTTGGTTTAG 59.431 41.667 0.00 0.00 0.00 1.85
535 660 3.595819 GCCTTCGGCTTGCTTCAT 58.404 55.556 0.00 0.00 46.69 2.57
545 670 4.037690 CGGCTTGCTTCATTGTTTATAGC 58.962 43.478 0.00 0.00 0.00 2.97
552 677 5.007626 TGCTTCATTGTTTATAGCCATCGTC 59.992 40.000 0.00 0.00 0.00 4.20
584 709 9.667107 CTCTATGGACCTAAATGTAACTTTCAA 57.333 33.333 0.00 0.00 0.00 2.69
621 746 6.283544 TGTATACAACCTTGACCGTTGATA 57.716 37.500 2.20 0.04 42.63 2.15
631 756 9.793259 AACCTTGACCGTTGATAAATATATCAT 57.207 29.630 0.00 0.00 45.54 2.45
780 906 2.029828 ACTCTCCTCTATTTATGCGCGG 60.030 50.000 8.83 0.00 0.00 6.46
810 936 3.249917 CATAAACCATCCCAAAACACGC 58.750 45.455 0.00 0.00 0.00 5.34
812 938 1.801309 AACCATCCCAAAACACGCCG 61.801 55.000 0.00 0.00 0.00 6.46
900 1058 2.102420 TCTCGCTTCACCAAGAACAAGA 59.898 45.455 0.00 0.00 31.61 3.02
978 1152 2.548875 CATTTCCGCTCCAGAAGAGAG 58.451 52.381 0.00 0.00 46.50 3.20
1020 1194 1.079405 GGTGGCGATCGAGAACCAA 60.079 57.895 21.57 0.00 33.03 3.67
1386 1566 2.125106 GGCCGCATCGAGGAGTTT 60.125 61.111 0.00 0.00 0.00 2.66
1413 1593 3.848830 CGGGTACGTGCACATGCG 61.849 66.667 18.64 5.14 45.83 4.73
1414 1594 2.433491 GGGTACGTGCACATGCGA 60.433 61.111 18.64 0.00 45.83 5.10
1415 1595 2.030401 GGGTACGTGCACATGCGAA 61.030 57.895 18.64 0.00 45.83 4.70
1416 1596 1.131826 GGTACGTGCACATGCGAAC 59.868 57.895 18.64 4.80 45.83 3.95
1417 1597 1.131826 GTACGTGCACATGCGAACC 59.868 57.895 18.64 0.00 45.83 3.62
1418 1598 2.030401 TACGTGCACATGCGAACCC 61.030 57.895 18.64 0.00 45.83 4.11
1419 1599 2.717139 TACGTGCACATGCGAACCCA 62.717 55.000 18.64 0.00 45.83 4.51
1420 1600 2.689785 CGTGCACATGCGAACCCAT 61.690 57.895 18.64 0.00 45.83 4.00
1421 1601 1.365368 CGTGCACATGCGAACCCATA 61.365 55.000 18.64 0.00 45.83 2.74
1422 1602 0.808125 GTGCACATGCGAACCCATAA 59.192 50.000 13.17 0.00 45.83 1.90
1433 1613 3.631144 CGAACCCATAATAACGCGTCTA 58.369 45.455 14.44 7.96 0.00 2.59
1449 1634 6.689547 ACGCGTCTAAACAAAATAACTATCG 58.310 36.000 5.58 0.00 0.00 2.92
1469 1654 6.884280 ATCGAATTGTTTCTTCCTTTCAGT 57.116 33.333 0.00 0.00 0.00 3.41
1520 1715 2.634940 CTGGTCTCCTCTGTTTCTTGGA 59.365 50.000 0.00 0.00 0.00 3.53
1546 1741 4.749245 TTCTTTCTCGAACTGCCAAATC 57.251 40.909 0.00 0.00 0.00 2.17
1559 1754 4.276926 ACTGCCAAATCACTCTGTTTTCTC 59.723 41.667 0.00 0.00 0.00 2.87
1618 1813 7.692291 ACGAATGATTCAGTTATTTTTAGTGCG 59.308 33.333 5.95 0.00 0.00 5.34
1621 1816 6.908825 TGATTCAGTTATTTTTAGTGCGCTT 58.091 32.000 9.73 0.00 0.00 4.68
1627 1823 5.912955 AGTTATTTTTAGTGCGCTTGTGTTC 59.087 36.000 9.73 0.00 0.00 3.18
1631 1827 0.531090 TAGTGCGCTTGTGTTCGGTT 60.531 50.000 9.73 0.00 0.00 4.44
1633 1829 2.051345 GCGCTTGTGTTCGGTTGG 60.051 61.111 0.00 0.00 0.00 3.77
1641 1837 4.023536 GCTTGTGTTCGGTTGGATTTTAGA 60.024 41.667 0.00 0.00 0.00 2.10
1728 1987 4.261155 GCATGCAGCCGACTAATTTATTGA 60.261 41.667 14.21 0.00 37.23 2.57
1730 1989 5.229921 TGCAGCCGACTAATTTATTGAAC 57.770 39.130 0.00 0.00 0.00 3.18
1873 2132 5.640147 AGTCAATGAACTCCCATTTAACCA 58.360 37.500 0.00 0.00 34.77 3.67
1886 2145 9.696917 CTCCCATTTAACCAGAATTATTTATGC 57.303 33.333 0.00 0.00 0.00 3.14
1962 2225 2.798283 AGAAATGTGTGTTACGTGGACG 59.202 45.455 0.00 0.00 46.33 4.79
2028 2291 9.658799 CTCTTCCTTAGATTATTTCTTGTCACA 57.341 33.333 0.00 0.00 35.79 3.58
2111 2374 6.635030 TGATCTATAACTGCACATACGACT 57.365 37.500 0.00 0.00 0.00 4.18
2114 2377 2.734276 TAACTGCACATACGACTGCA 57.266 45.000 0.00 0.00 41.13 4.41
2118 2381 0.108662 TGCACATACGACTGCAGAGG 60.109 55.000 23.35 13.87 38.49 3.69
2171 2436 7.047460 AGCAATTGATTTGACTTGAGAAAGT 57.953 32.000 10.34 0.00 37.53 2.66
2179 2444 5.489792 TTGACTTGAGAAAGTAGGCAGAT 57.510 39.130 0.00 0.00 32.22 2.90
2197 2462 2.365293 AGATGACCAAGTTGGCAAAACC 59.635 45.455 22.25 6.65 42.67 3.27
2219 2489 0.593128 CACAGCTGGTGGCAAAGTAC 59.407 55.000 19.93 0.00 44.04 2.73
2225 2495 2.350102 GCTGGTGGCAAAGTACGTTTAC 60.350 50.000 0.00 0.00 41.35 2.01
2228 2498 3.312973 TGGTGGCAAAGTACGTTTACAAG 59.687 43.478 0.00 0.00 0.00 3.16
2245 2515 2.907042 ACAAGGAAGTAGCTTAGGCAGT 59.093 45.455 0.00 0.00 41.70 4.40
2246 2516 4.094476 ACAAGGAAGTAGCTTAGGCAGTA 58.906 43.478 0.00 0.00 41.70 2.74
2247 2517 4.717280 ACAAGGAAGTAGCTTAGGCAGTAT 59.283 41.667 0.00 0.00 41.70 2.12
2248 2518 4.946478 AGGAAGTAGCTTAGGCAGTATG 57.054 45.455 0.00 0.00 41.70 2.39
2271 2541 4.330250 CATCATGGTCCAACTCACTTTCT 58.670 43.478 0.00 0.00 0.00 2.52
2273 2543 5.762179 TCATGGTCCAACTCACTTTCTAT 57.238 39.130 0.00 0.00 0.00 1.98
2275 2545 3.674997 TGGTCCAACTCACTTTCTATGC 58.325 45.455 0.00 0.00 0.00 3.14
2289 2559 3.806949 TCTATGCCCCTTTGAAGTGTT 57.193 42.857 0.00 0.00 0.00 3.32
2317 2587 2.166254 GCTATAGCCAGAGGATGAGAGC 59.834 54.545 14.13 0.00 34.31 4.09
2450 2720 6.016276 GGAATGGAATACGGTTCATTGCTATT 60.016 38.462 5.38 0.00 35.84 1.73
2497 2767 9.190317 GTCCTTGGAAAATGATAGGAGTATTTT 57.810 33.333 0.00 0.00 35.77 1.82
2744 3014 2.224314 GTCAGGCTTACAACTCACAAGC 59.776 50.000 0.00 0.00 43.12 4.01
2760 3030 2.158623 ACAAGCATGGAACTGAACCTGA 60.159 45.455 0.00 0.00 0.00 3.86
2863 3133 1.826054 CCTGGAGGACGAGATCGCT 60.826 63.158 1.39 0.00 44.43 4.93
2953 3223 3.219281 TGGCAACATCATGATGGATGAG 58.781 45.455 33.31 20.38 46.00 2.90
2984 3254 2.703416 TGCTGACCATCATTGTGAGTC 58.297 47.619 0.00 0.00 0.00 3.36
3078 3374 1.880027 GGGATTCTCTTGCACGTTTGT 59.120 47.619 0.00 0.00 0.00 2.83
3174 3471 1.798813 GTGTCACGCCTCCACTAAAAG 59.201 52.381 0.00 0.00 0.00 2.27
3216 3513 1.133253 CGTGCAGCATGAAGAACCG 59.867 57.895 9.20 0.00 39.69 4.44
3295 3592 8.841300 ACAGTTTCTTAAGGAAATCTGAAGTTC 58.159 33.333 17.05 0.00 44.46 3.01
3307 3604 5.622346 ATCTGAAGTTCTATCCCACCTTC 57.378 43.478 4.17 0.00 33.74 3.46
3361 3658 7.232534 AGTTGGCAAGTTGGTTTGATCTTATTA 59.767 33.333 0.00 0.00 0.00 0.98
3363 3660 8.133024 TGGCAAGTTGGTTTGATCTTATTATT 57.867 30.769 4.75 0.00 0.00 1.40
3369 3666 6.478512 TGGTTTGATCTTATTATTTGCCCC 57.521 37.500 0.00 0.00 0.00 5.80
3390 3687 2.427453 CCTCGTGTGCTTACAGGACTAT 59.573 50.000 0.00 0.00 37.46 2.12
3531 3828 5.011943 TGCATTTCCCATTTAACTCTGCTTT 59.988 36.000 0.00 0.00 0.00 3.51
3554 3851 2.872858 GTTTTCGTTCAGCCTTCACTCT 59.127 45.455 0.00 0.00 0.00 3.24
3556 3853 3.299340 TTCGTTCAGCCTTCACTCTAC 57.701 47.619 0.00 0.00 0.00 2.59
3560 3857 3.330267 GTTCAGCCTTCACTCTACCTTG 58.670 50.000 0.00 0.00 0.00 3.61
3653 3950 3.059800 GCACTTCTCGTGAGTACAAAACC 60.060 47.826 0.00 0.00 46.81 3.27
3797 4094 0.613260 CGAGTCATCTGGTTTGGGGA 59.387 55.000 0.00 0.00 0.00 4.81
3852 4150 1.262417 TCGCCAACCTAGTCATCACA 58.738 50.000 0.00 0.00 0.00 3.58
3858 4156 5.186198 GCCAACCTAGTCATCACAGTAATT 58.814 41.667 0.00 0.00 0.00 1.40
3888 4186 6.644775 CGCTGCTATCTTCTAACTTTCATTC 58.355 40.000 0.00 0.00 0.00 2.67
3939 4237 3.624861 TCGACTTCGATTACCAGGAGTAC 59.375 47.826 0.00 0.00 44.22 2.73
3954 4252 2.622436 GAGTACGCAAGGCAGAGATTT 58.378 47.619 0.00 0.00 46.39 2.17
4112 4410 6.214208 TGGGATAATGACAGGAAGGATATGAG 59.786 42.308 0.00 0.00 0.00 2.90
4300 4599 6.478344 TGGAGTTGCATTTTGTATGTTGTTTC 59.522 34.615 0.00 0.00 0.00 2.78
4310 4609 4.720046 TGTATGTTGTTTCCCTAAGCACA 58.280 39.130 0.00 0.00 0.00 4.57
4459 5902 1.103803 TACTAGCTTGGAGACGGCAG 58.896 55.000 0.00 0.00 34.73 4.85
4622 6067 9.860898 GCTGAAGATTTAAATTGGTACATTCTT 57.139 29.630 1.43 0.00 39.30 2.52
4649 6094 2.759355 TCCAACGGATTCCACCTCTAT 58.241 47.619 3.09 0.00 0.00 1.98
4667 6112 6.267928 ACCTCTATTTATCGTGCTAAGTGGAT 59.732 38.462 0.00 0.00 0.00 3.41
4670 6115 7.145985 TCTATTTATCGTGCTAAGTGGATCAC 58.854 38.462 0.00 0.00 34.10 3.06
4680 6125 2.104132 TGGATCACGCATCGACGG 59.896 61.111 0.00 0.00 37.37 4.79
4681 6126 2.658593 GGATCACGCATCGACGGG 60.659 66.667 0.00 0.00 37.97 5.28
4702 6147 0.671251 ATCTTCGATCGGACAGCCTC 59.329 55.000 16.41 0.00 0.00 4.70
4703 6148 1.298713 CTTCGATCGGACAGCCTCG 60.299 63.158 16.41 0.00 0.00 4.63
4704 6149 1.994507 CTTCGATCGGACAGCCTCGT 61.995 60.000 16.41 0.00 33.10 4.18
4741 6195 0.898320 GTTAGCTCTCACCTGCTCCA 59.102 55.000 0.00 0.00 40.35 3.86
4834 6291 7.523052 GCATCAAGTATGTTTTAACTGGGTTGA 60.523 37.037 0.00 0.00 37.93 3.18
4865 6322 1.448540 CGTGTTCTGGCTGGCCTAG 60.449 63.158 13.05 8.58 36.94 3.02
4900 6357 2.672961 TCGATGCAAACCCTAGTCAG 57.327 50.000 0.00 0.00 0.00 3.51
4979 6436 7.539712 TGAAATTTAATTCGTCAGAGCCTAG 57.460 36.000 0.00 0.00 31.80 3.02
4980 6437 5.993106 AATTTAATTCGTCAGAGCCTAGC 57.007 39.130 0.00 0.00 0.00 3.42
4981 6438 4.465632 TTTAATTCGTCAGAGCCTAGCA 57.534 40.909 0.00 0.00 0.00 3.49
4982 6439 2.593346 AATTCGTCAGAGCCTAGCAG 57.407 50.000 0.00 0.00 0.00 4.24
4983 6440 1.479709 ATTCGTCAGAGCCTAGCAGT 58.520 50.000 0.00 0.00 0.00 4.40
4984 6441 1.257743 TTCGTCAGAGCCTAGCAGTT 58.742 50.000 0.00 0.00 0.00 3.16
4985 6442 0.811915 TCGTCAGAGCCTAGCAGTTC 59.188 55.000 0.00 0.00 0.00 3.01
4986 6443 0.528017 CGTCAGAGCCTAGCAGTTCA 59.472 55.000 0.00 0.00 0.00 3.18
4987 6444 1.135915 CGTCAGAGCCTAGCAGTTCAT 59.864 52.381 0.00 0.00 0.00 2.57
4988 6445 2.417924 CGTCAGAGCCTAGCAGTTCATT 60.418 50.000 0.00 0.00 0.00 2.57
4989 6446 3.604582 GTCAGAGCCTAGCAGTTCATTT 58.395 45.455 0.00 0.00 0.00 2.32
4990 6447 4.678044 CGTCAGAGCCTAGCAGTTCATTTA 60.678 45.833 0.00 0.00 0.00 1.40
4991 6448 4.808364 GTCAGAGCCTAGCAGTTCATTTAG 59.192 45.833 0.00 0.00 0.00 1.85
4992 6449 4.711846 TCAGAGCCTAGCAGTTCATTTAGA 59.288 41.667 0.00 0.00 0.00 2.10
4993 6450 4.808364 CAGAGCCTAGCAGTTCATTTAGAC 59.192 45.833 0.00 0.00 0.00 2.59
4994 6451 4.123506 GAGCCTAGCAGTTCATTTAGACC 58.876 47.826 0.00 0.00 0.00 3.85
4995 6452 3.777522 AGCCTAGCAGTTCATTTAGACCT 59.222 43.478 0.00 0.00 0.00 3.85
4996 6453 4.123506 GCCTAGCAGTTCATTTAGACCTC 58.876 47.826 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 208 8.780846 TGTAACCGTAAATCTCACATACAATT 57.219 30.769 0.00 0.00 0.00 2.32
164 271 5.068723 GGACAAAATCATACTCTCCTCCGTA 59.931 44.000 0.00 0.00 0.00 4.02
165 272 4.141914 GGACAAAATCATACTCTCCTCCGT 60.142 45.833 0.00 0.00 0.00 4.69
195 302 2.567985 GGAAGGTTTCGTGAGGTCAAA 58.432 47.619 0.00 0.00 0.00 2.69
196 303 1.202722 GGGAAGGTTTCGTGAGGTCAA 60.203 52.381 0.00 0.00 0.00 3.18
197 304 0.395312 GGGAAGGTTTCGTGAGGTCA 59.605 55.000 0.00 0.00 0.00 4.02
198 305 0.685660 AGGGAAGGTTTCGTGAGGTC 59.314 55.000 0.00 0.00 0.00 3.85
199 306 1.622312 GTAGGGAAGGTTTCGTGAGGT 59.378 52.381 0.00 0.00 0.00 3.85
200 307 1.066358 GGTAGGGAAGGTTTCGTGAGG 60.066 57.143 0.00 0.00 0.00 3.86
201 308 1.621814 TGGTAGGGAAGGTTTCGTGAG 59.378 52.381 0.00 0.00 0.00 3.51
202 309 1.719529 TGGTAGGGAAGGTTTCGTGA 58.280 50.000 0.00 0.00 0.00 4.35
203 310 2.423577 CTTGGTAGGGAAGGTTTCGTG 58.576 52.381 0.00 0.00 0.00 4.35
204 311 1.271217 GCTTGGTAGGGAAGGTTTCGT 60.271 52.381 0.00 0.00 0.00 3.85
205 312 1.271163 TGCTTGGTAGGGAAGGTTTCG 60.271 52.381 0.00 0.00 0.00 3.46
206 313 2.579410 TGCTTGGTAGGGAAGGTTTC 57.421 50.000 0.00 0.00 0.00 2.78
207 314 2.445525 TCTTGCTTGGTAGGGAAGGTTT 59.554 45.455 0.00 0.00 33.85 3.27
208 315 2.062636 TCTTGCTTGGTAGGGAAGGTT 58.937 47.619 0.00 0.00 33.85 3.50
209 316 1.742308 TCTTGCTTGGTAGGGAAGGT 58.258 50.000 0.00 0.00 33.85 3.50
210 317 2.879103 TTCTTGCTTGGTAGGGAAGG 57.121 50.000 0.00 0.00 33.85 3.46
211 318 4.884164 CCTTATTCTTGCTTGGTAGGGAAG 59.116 45.833 0.00 0.00 34.25 3.46
220 344 4.331168 CGGAGAGAACCTTATTCTTGCTTG 59.669 45.833 0.00 0.00 0.00 4.01
251 375 0.037734 GAAATCACCACGGGGAAGGT 59.962 55.000 12.96 0.00 39.10 3.50
259 383 0.586319 ACAACGCTGAAATCACCACG 59.414 50.000 0.00 0.00 0.00 4.94
269 393 4.373116 GCCCTCCGACAACGCTGA 62.373 66.667 0.00 0.00 38.29 4.26
298 422 0.382515 CCTCAAGATCCGACGGAGAC 59.617 60.000 22.99 17.70 34.05 3.36
299 423 0.752009 CCCTCAAGATCCGACGGAGA 60.752 60.000 22.99 12.66 34.05 3.71
300 424 0.752009 TCCCTCAAGATCCGACGGAG 60.752 60.000 22.99 8.65 34.05 4.63
330 455 1.804748 GTGGATCCACCGAAGACAAAC 59.195 52.381 31.37 4.21 42.61 2.93
331 456 1.606994 CGTGGATCCACCGAAGACAAA 60.607 52.381 34.05 0.00 43.49 2.83
332 457 0.037697 CGTGGATCCACCGAAGACAA 60.038 55.000 34.05 0.00 43.49 3.18
333 458 1.183030 ACGTGGATCCACCGAAGACA 61.183 55.000 34.05 0.00 43.49 3.41
334 459 0.813184 TACGTGGATCCACCGAAGAC 59.187 55.000 34.05 12.26 43.49 3.01
335 460 1.100510 CTACGTGGATCCACCGAAGA 58.899 55.000 34.05 16.47 43.49 2.87
336 461 1.100510 TCTACGTGGATCCACCGAAG 58.899 55.000 34.05 27.06 43.49 3.79
337 462 1.679680 GATCTACGTGGATCCACCGAA 59.320 52.381 34.05 20.41 43.49 4.30
338 463 1.315690 GATCTACGTGGATCCACCGA 58.684 55.000 34.05 27.09 43.49 4.69
339 464 3.867723 GATCTACGTGGATCCACCG 57.132 57.895 34.05 29.22 43.49 4.94
344 469 1.606903 AGACCGGATCTACGTGGATC 58.393 55.000 28.24 28.24 40.78 3.36
345 470 1.955080 GAAGACCGGATCTACGTGGAT 59.045 52.381 14.90 14.90 36.27 3.41
346 471 1.386533 GAAGACCGGATCTACGTGGA 58.613 55.000 9.46 3.36 36.27 4.02
347 472 0.029035 CGAAGACCGGATCTACGTGG 59.971 60.000 9.46 0.00 36.27 4.94
348 473 0.731417 ACGAAGACCGGATCTACGTG 59.269 55.000 9.46 1.39 43.93 4.49
349 474 1.457346 AACGAAGACCGGATCTACGT 58.543 50.000 9.46 10.51 43.93 3.57
350 475 2.182825 CAAACGAAGACCGGATCTACG 58.817 52.381 9.46 9.82 43.93 3.51
351 476 3.177487 GACAAACGAAGACCGGATCTAC 58.823 50.000 9.46 0.00 43.93 2.59
352 477 2.159476 CGACAAACGAAGACCGGATCTA 60.159 50.000 9.46 0.00 45.77 1.98
353 478 1.402456 CGACAAACGAAGACCGGATCT 60.402 52.381 9.46 4.30 45.77 2.75
354 479 0.989890 CGACAAACGAAGACCGGATC 59.010 55.000 9.46 1.42 45.77 3.36
355 480 0.389426 CCGACAAACGAAGACCGGAT 60.389 55.000 9.46 0.00 45.77 4.18
356 481 1.007038 CCGACAAACGAAGACCGGA 60.007 57.895 9.46 0.00 45.77 5.14
357 482 1.300388 ACCGACAAACGAAGACCGG 60.300 57.895 0.00 0.00 45.77 5.28
358 483 0.872881 ACACCGACAAACGAAGACCG 60.873 55.000 0.00 0.00 45.77 4.79
359 484 1.292992 AACACCGACAAACGAAGACC 58.707 50.000 0.00 0.00 45.77 3.85
360 485 2.094734 ACAAACACCGACAAACGAAGAC 59.905 45.455 0.00 0.00 45.77 3.01
361 486 2.094575 CACAAACACCGACAAACGAAGA 59.905 45.455 0.00 0.00 45.77 2.87
362 487 2.159626 ACACAAACACCGACAAACGAAG 60.160 45.455 0.00 0.00 45.77 3.79
363 488 1.805345 ACACAAACACCGACAAACGAA 59.195 42.857 0.00 0.00 45.77 3.85
364 489 1.128878 CACACAAACACCGACAAACGA 59.871 47.619 0.00 0.00 45.77 3.85
365 490 1.135916 ACACACAAACACCGACAAACG 60.136 47.619 0.00 0.00 42.18 3.60
366 491 2.160813 AGACACACAAACACCGACAAAC 59.839 45.455 0.00 0.00 0.00 2.93
367 492 2.160615 CAGACACACAAACACCGACAAA 59.839 45.455 0.00 0.00 0.00 2.83
368 493 1.735018 CAGACACACAAACACCGACAA 59.265 47.619 0.00 0.00 0.00 3.18
369 494 1.364721 CAGACACACAAACACCGACA 58.635 50.000 0.00 0.00 0.00 4.35
370 495 0.027586 GCAGACACACAAACACCGAC 59.972 55.000 0.00 0.00 0.00 4.79
371 496 1.425267 CGCAGACACACAAACACCGA 61.425 55.000 0.00 0.00 0.00 4.69
372 497 1.011242 CGCAGACACACAAACACCG 60.011 57.895 0.00 0.00 0.00 4.94
373 498 1.355210 CCGCAGACACACAAACACC 59.645 57.895 0.00 0.00 0.00 4.16
374 499 1.355210 CCCGCAGACACACAAACAC 59.645 57.895 0.00 0.00 0.00 3.32
375 500 0.678366 AACCCGCAGACACACAAACA 60.678 50.000 0.00 0.00 0.00 2.83
376 501 0.028902 GAACCCGCAGACACACAAAC 59.971 55.000 0.00 0.00 0.00 2.93
377 502 0.107410 AGAACCCGCAGACACACAAA 60.107 50.000 0.00 0.00 0.00 2.83
378 503 0.107410 AAGAACCCGCAGACACACAA 60.107 50.000 0.00 0.00 0.00 3.33
379 504 0.107410 AAAGAACCCGCAGACACACA 60.107 50.000 0.00 0.00 0.00 3.72
380 505 1.002792 GAAAAGAACCCGCAGACACAC 60.003 52.381 0.00 0.00 0.00 3.82
381 506 1.305201 GAAAAGAACCCGCAGACACA 58.695 50.000 0.00 0.00 0.00 3.72
382 507 1.305201 TGAAAAGAACCCGCAGACAC 58.695 50.000 0.00 0.00 0.00 3.67
383 508 2.151202 GATGAAAAGAACCCGCAGACA 58.849 47.619 0.00 0.00 0.00 3.41
384 509 1.128692 CGATGAAAAGAACCCGCAGAC 59.871 52.381 0.00 0.00 0.00 3.51
385 510 1.438651 CGATGAAAAGAACCCGCAGA 58.561 50.000 0.00 0.00 0.00 4.26
386 511 0.447801 CCGATGAAAAGAACCCGCAG 59.552 55.000 0.00 0.00 0.00 5.18
387 512 1.582610 GCCGATGAAAAGAACCCGCA 61.583 55.000 0.00 0.00 0.00 5.69
388 513 1.136774 GCCGATGAAAAGAACCCGC 59.863 57.895 0.00 0.00 0.00 6.13
389 514 1.423845 CGCCGATGAAAAGAACCCG 59.576 57.895 0.00 0.00 0.00 5.28
390 515 1.800681 CCGCCGATGAAAAGAACCC 59.199 57.895 0.00 0.00 0.00 4.11
391 516 1.136774 GCCGCCGATGAAAAGAACC 59.863 57.895 0.00 0.00 0.00 3.62
392 517 0.179189 CAGCCGCCGATGAAAAGAAC 60.179 55.000 0.00 0.00 0.00 3.01
393 518 0.605319 ACAGCCGCCGATGAAAAGAA 60.605 50.000 0.00 0.00 0.00 2.52
394 519 0.605319 AACAGCCGCCGATGAAAAGA 60.605 50.000 0.00 0.00 0.00 2.52
395 520 0.454957 CAACAGCCGCCGATGAAAAG 60.455 55.000 0.00 0.00 0.00 2.27
396 521 1.169661 ACAACAGCCGCCGATGAAAA 61.170 50.000 0.00 0.00 0.00 2.29
397 522 1.169661 AACAACAGCCGCCGATGAAA 61.170 50.000 0.00 0.00 0.00 2.69
398 523 1.599518 AACAACAGCCGCCGATGAA 60.600 52.632 0.00 0.00 0.00 2.57
399 524 2.031919 AACAACAGCCGCCGATGA 59.968 55.556 0.00 0.00 0.00 2.92
400 525 2.128853 AACAACAACAGCCGCCGATG 62.129 55.000 0.00 0.00 0.00 3.84
401 526 1.452145 AAACAACAACAGCCGCCGAT 61.452 50.000 0.00 0.00 0.00 4.18
402 527 1.658686 AAAACAACAACAGCCGCCGA 61.659 50.000 0.00 0.00 0.00 5.54
403 528 0.804156 AAAAACAACAACAGCCGCCG 60.804 50.000 0.00 0.00 0.00 6.46
404 529 0.649993 CAAAAACAACAACAGCCGCC 59.350 50.000 0.00 0.00 0.00 6.13
405 530 1.060409 CACAAAAACAACAACAGCCGC 59.940 47.619 0.00 0.00 0.00 6.53
406 531 1.060409 GCACAAAAACAACAACAGCCG 59.940 47.619 0.00 0.00 0.00 5.52
407 532 1.060409 CGCACAAAAACAACAACAGCC 59.940 47.619 0.00 0.00 0.00 4.85
408 533 1.724082 ACGCACAAAAACAACAACAGC 59.276 42.857 0.00 0.00 0.00 4.40
409 534 3.422862 CCAACGCACAAAAACAACAACAG 60.423 43.478 0.00 0.00 0.00 3.16
410 535 2.476619 CCAACGCACAAAAACAACAACA 59.523 40.909 0.00 0.00 0.00 3.33
411 536 2.476997 ACCAACGCACAAAAACAACAAC 59.523 40.909 0.00 0.00 0.00 3.32
412 537 2.731976 GACCAACGCACAAAAACAACAA 59.268 40.909 0.00 0.00 0.00 2.83
413 538 2.329379 GACCAACGCACAAAAACAACA 58.671 42.857 0.00 0.00 0.00 3.33
414 539 1.656594 GGACCAACGCACAAAAACAAC 59.343 47.619 0.00 0.00 0.00 3.32
415 540 1.546476 AGGACCAACGCACAAAAACAA 59.454 42.857 0.00 0.00 0.00 2.83
416 541 1.135257 CAGGACCAACGCACAAAAACA 60.135 47.619 0.00 0.00 0.00 2.83
417 542 1.135228 ACAGGACCAACGCACAAAAAC 60.135 47.619 0.00 0.00 0.00 2.43
418 543 1.178276 ACAGGACCAACGCACAAAAA 58.822 45.000 0.00 0.00 0.00 1.94
419 544 1.944024 CTACAGGACCAACGCACAAAA 59.056 47.619 0.00 0.00 0.00 2.44
420 545 1.588674 CTACAGGACCAACGCACAAA 58.411 50.000 0.00 0.00 0.00 2.83
421 546 0.250124 CCTACAGGACCAACGCACAA 60.250 55.000 0.00 0.00 37.39 3.33
422 547 1.369692 CCTACAGGACCAACGCACA 59.630 57.895 0.00 0.00 37.39 4.57
423 548 1.375523 CCCTACAGGACCAACGCAC 60.376 63.158 0.00 0.00 38.24 5.34
424 549 1.534476 TCCCTACAGGACCAACGCA 60.534 57.895 0.00 0.00 40.93 5.24
425 550 3.384348 TCCCTACAGGACCAACGC 58.616 61.111 0.00 0.00 40.93 4.84
432 557 3.031736 GTCATGCTAAGTCCCTACAGGA 58.968 50.000 0.00 0.00 44.91 3.86
433 558 2.223829 CGTCATGCTAAGTCCCTACAGG 60.224 54.545 0.00 0.00 0.00 4.00
434 559 2.688446 TCGTCATGCTAAGTCCCTACAG 59.312 50.000 0.00 0.00 0.00 2.74
435 560 2.426024 GTCGTCATGCTAAGTCCCTACA 59.574 50.000 0.00 0.00 0.00 2.74
436 561 2.688958 AGTCGTCATGCTAAGTCCCTAC 59.311 50.000 0.00 0.00 0.00 3.18
468 593 0.671796 AGCCGGCTAAACCAACAAAC 59.328 50.000 31.86 0.00 39.03 2.93
523 648 4.037690 GCTATAAACAATGAAGCAAGCCG 58.962 43.478 0.00 0.00 33.38 5.52
535 660 4.094294 GCACTTGACGATGGCTATAAACAA 59.906 41.667 0.00 0.00 0.00 2.83
545 670 2.101415 TCCATAGAGCACTTGACGATGG 59.899 50.000 4.09 4.09 37.86 3.51
552 677 5.431765 ACATTTAGGTCCATAGAGCACTTG 58.568 41.667 0.00 0.00 43.21 3.16
631 756 9.694137 TTTCTTTTCTTTTTCTGGAAAAACGTA 57.306 25.926 14.72 4.20 43.08 3.57
780 906 1.404035 GGATGGTTTATGTGGTTCGGC 59.596 52.381 0.00 0.00 0.00 5.54
810 936 0.955919 GGAGGTTTTGCTCTGTCCGG 60.956 60.000 0.00 0.00 0.00 5.14
812 938 0.402121 AGGGAGGTTTTGCTCTGTCC 59.598 55.000 0.00 0.00 0.00 4.02
978 1152 0.806102 TCGCTAATCACGCCTTCTGC 60.806 55.000 0.00 0.00 0.00 4.26
1386 1566 2.800053 CGTACCCGTGCGTGGATA 59.200 61.111 0.00 0.00 34.04 2.59
1410 1590 0.931702 CGCGTTATTATGGGTTCGCA 59.068 50.000 0.00 0.00 43.02 5.10
1411 1591 0.932399 ACGCGTTATTATGGGTTCGC 59.068 50.000 5.58 0.00 40.19 4.70
1412 1592 2.466846 AGACGCGTTATTATGGGTTCG 58.533 47.619 15.53 0.00 36.66 3.95
1413 1593 5.291614 TGTTTAGACGCGTTATTATGGGTTC 59.708 40.000 15.53 0.00 36.66 3.62
1414 1594 5.177326 TGTTTAGACGCGTTATTATGGGTT 58.823 37.500 15.53 0.00 36.66 4.11
1415 1595 4.757594 TGTTTAGACGCGTTATTATGGGT 58.242 39.130 15.53 0.00 38.96 4.51
1416 1596 5.721876 TTGTTTAGACGCGTTATTATGGG 57.278 39.130 15.53 0.00 0.00 4.00
1417 1597 9.705471 TTATTTTGTTTAGACGCGTTATTATGG 57.295 29.630 15.53 0.00 0.00 2.74
1546 1741 8.883731 TGAAAAACTCTTAGAGAAAACAGAGTG 58.116 33.333 16.95 0.00 44.25 3.51
1559 1754 6.507023 ACAAAGTGGCATGAAAAACTCTTAG 58.493 36.000 0.00 0.00 0.00 2.18
1618 1813 2.793278 AAATCCAACCGAACACAAGC 57.207 45.000 0.00 0.00 0.00 4.01
1621 1816 6.452494 TTTTCTAAAATCCAACCGAACACA 57.548 33.333 0.00 0.00 0.00 3.72
1627 1823 7.812669 AGCACTAAATTTTCTAAAATCCAACCG 59.187 33.333 0.00 0.00 37.62 4.44
1728 1987 0.462789 AACGGACGAGAACCACAGTT 59.537 50.000 0.00 0.00 39.54 3.16
1730 1989 0.031585 TCAACGGACGAGAACCACAG 59.968 55.000 0.00 0.00 0.00 3.66
1743 2002 0.110238 CACGGCAGAACATTCAACGG 60.110 55.000 0.00 0.00 0.00 4.44
1846 2105 8.749354 GGTTAAATGGGAGTTCATTGACTAATT 58.251 33.333 0.00 0.00 37.42 1.40
1873 2132 6.376248 AGTCACATGGGGCATAAATAATTCT 58.624 36.000 0.57 0.00 0.00 2.40
1886 2145 3.262420 CTTTCGACTAAGTCACATGGGG 58.738 50.000 0.00 0.00 32.09 4.96
2028 2291 6.429692 TGACTTCACACCACAAATTTATCGAT 59.570 34.615 2.16 2.16 0.00 3.59
2116 2379 5.435291 CATGGCTTTTCTAAGAGATGTCCT 58.565 41.667 0.00 0.00 32.92 3.85
2118 2381 4.036144 GCCATGGCTTTTCTAAGAGATGTC 59.964 45.833 29.98 0.00 38.26 3.06
2171 2436 1.340017 GCCAACTTGGTCATCTGCCTA 60.340 52.381 9.63 0.00 40.46 3.93
2179 2444 1.561643 TGGTTTTGCCAACTTGGTCA 58.438 45.000 9.63 5.41 45.94 4.02
2199 2464 1.172180 TACTTTGCCACCAGCTGTGC 61.172 55.000 13.81 12.67 44.01 4.57
2200 2465 0.593128 GTACTTTGCCACCAGCTGTG 59.407 55.000 13.81 10.81 44.23 3.66
2201 2466 0.884704 CGTACTTTGCCACCAGCTGT 60.885 55.000 13.81 0.00 44.23 4.40
2219 2489 4.329256 GCCTAAGCTACTTCCTTGTAAACG 59.671 45.833 0.00 0.00 35.50 3.60
2225 2495 3.618690 ACTGCCTAAGCTACTTCCTTG 57.381 47.619 0.00 0.00 40.80 3.61
2228 2498 3.181465 TGCATACTGCCTAAGCTACTTCC 60.181 47.826 0.00 0.00 44.23 3.46
2245 2515 3.200605 AGTGAGTTGGACCATGATGCATA 59.799 43.478 0.00 0.00 0.00 3.14
2246 2516 2.025605 AGTGAGTTGGACCATGATGCAT 60.026 45.455 0.00 0.00 0.00 3.96
2247 2517 1.352017 AGTGAGTTGGACCATGATGCA 59.648 47.619 0.00 0.00 0.00 3.96
2248 2518 2.119801 AGTGAGTTGGACCATGATGC 57.880 50.000 0.00 0.00 0.00 3.91
2249 2519 4.330250 AGAAAGTGAGTTGGACCATGATG 58.670 43.478 0.00 0.00 0.00 3.07
2271 2541 4.042311 TGACTAACACTTCAAAGGGGCATA 59.958 41.667 0.00 0.00 32.35 3.14
2273 2543 2.173782 TGACTAACACTTCAAAGGGGCA 59.826 45.455 0.00 0.00 32.35 5.36
2275 2545 3.191371 GCATGACTAACACTTCAAAGGGG 59.809 47.826 0.00 0.00 32.35 4.79
2289 2559 4.388577 TCCTCTGGCTATAGCATGACTA 57.611 45.455 25.53 8.76 44.36 2.59
2497 2767 1.145571 AGTTTGGCCACCTTGGTAGA 58.854 50.000 3.88 0.00 40.46 2.59
2744 3014 5.191426 AGATTCATCAGGTTCAGTTCCATG 58.809 41.667 0.00 0.00 0.00 3.66
2760 3030 8.037166 GCCAGTTCCTTCATTAAAAAGATTCAT 58.963 33.333 3.24 0.00 0.00 2.57
2953 3223 0.036732 TGGTCAGCATGTTGGTCTCC 59.963 55.000 9.87 8.05 37.40 3.71
2984 3254 6.570692 AGGAATTGCTTTTGAATGCATAGAG 58.429 36.000 0.00 0.00 38.61 2.43
3174 3471 4.888917 ACTCTCCAAGACTAAAACTCTGC 58.111 43.478 0.00 0.00 0.00 4.26
3216 3513 8.801913 GCATATACAACAAGAAAAGAAAGCATC 58.198 33.333 0.00 0.00 0.00 3.91
3295 3592 5.805728 ACAGTTTGTTAGAAGGTGGGATAG 58.194 41.667 0.00 0.00 0.00 2.08
3307 3604 7.962964 TTTAGGATGTCTGACAGTTTGTTAG 57.037 36.000 16.46 0.00 35.56 2.34
3361 3658 2.676471 GCACACGAGGGGGCAAAT 60.676 61.111 0.00 0.00 0.00 2.32
3363 3660 2.521451 TAAGCACACGAGGGGGCAA 61.521 57.895 1.24 0.00 0.00 4.52
3369 3666 0.603569 AGTCCTGTAAGCACACGAGG 59.396 55.000 0.00 0.00 0.00 4.63
3390 3687 2.224744 TGGGTTGAAGCTTGCATACTCA 60.225 45.455 2.10 6.68 0.00 3.41
3531 3828 3.013921 AGTGAAGGCTGAACGAAAACAA 58.986 40.909 0.00 0.00 0.00 2.83
3653 3950 5.504010 CGGACAATCGAACCAAGATAATTGG 60.504 44.000 5.10 5.10 44.91 3.16
3754 4051 0.456312 CGTGTACTTCTCCACGCTCC 60.456 60.000 0.00 0.00 46.45 4.70
3797 4094 4.489737 TCACCGATATTATTCCCCAGAGT 58.510 43.478 0.00 0.00 0.00 3.24
3852 4150 7.551585 AGAAGATAGCAGCGCATATAATTACT 58.448 34.615 11.47 0.00 0.00 2.24
3858 4156 6.516739 AGTTAGAAGATAGCAGCGCATATA 57.483 37.500 11.47 0.00 0.00 0.86
3888 4186 6.363473 GTTGACACGATCCTGTAAAGAAAAG 58.637 40.000 0.00 0.00 0.00 2.27
3939 4237 0.098376 GCTCAAATCTCTGCCTTGCG 59.902 55.000 0.00 0.00 0.00 4.85
3954 4252 1.632589 TCTTCTGCCAGTACTGCTCA 58.367 50.000 17.86 15.10 0.00 4.26
4112 4410 6.986817 TGCTTCCTTGTAATAGTATGCTTCTC 59.013 38.462 0.00 0.00 0.00 2.87
4300 4599 1.377725 CCACCAGCTGTGCTTAGGG 60.378 63.158 13.81 0.00 44.01 3.53
4310 4609 1.523711 CACACGAACACCACCAGCT 60.524 57.895 0.00 0.00 0.00 4.24
4459 5902 5.815740 TCTTATTATGGAGAACCGCAAAGAC 59.184 40.000 0.00 0.00 39.42 3.01
4503 5948 6.837312 TGATTTCTTAAGTTCAGGACCTGAA 58.163 36.000 29.45 29.45 46.50 3.02
4509 5954 7.054124 ACAGTGTTGATTTCTTAAGTTCAGGA 58.946 34.615 1.63 0.00 0.00 3.86
4622 6067 0.750850 GGAATCCGTTGGATCGAGGA 59.249 55.000 0.00 0.00 42.27 3.71
4649 6094 4.109766 CGTGATCCACTTAGCACGATAAA 58.890 43.478 8.80 0.00 31.34 1.40
4667 6112 3.133767 GATCCCCGTCGATGCGTGA 62.134 63.158 0.00 0.00 0.00 4.35
4670 6115 1.661821 GAAGATCCCCGTCGATGCG 60.662 63.158 0.00 0.00 0.00 4.73
4680 6125 0.319125 GCTGTCCGATCGAAGATCCC 60.319 60.000 18.66 0.00 45.12 3.85
4681 6126 0.319125 GGCTGTCCGATCGAAGATCC 60.319 60.000 18.66 8.24 45.12 3.36
4702 6147 2.431942 CCACCCGAGGACGAAACG 60.432 66.667 0.00 0.00 42.66 3.60
4703 6148 1.070275 AACCACCCGAGGACGAAAC 59.930 57.895 0.00 0.00 42.66 2.78
4704 6149 1.070105 CAACCACCCGAGGACGAAA 59.930 57.895 0.00 0.00 42.66 3.46
4773 6227 4.971924 AGGGTCTGAGGCTTTATAGTCATT 59.028 41.667 0.00 0.00 0.00 2.57
4834 6291 3.304525 CCAGAACACGACGTCTAGAGTTT 60.305 47.826 14.70 2.00 0.00 2.66
4865 6322 2.757686 TCGATCTCAGATGTGCGTAC 57.242 50.000 0.00 0.00 0.00 3.67
4900 6357 2.863401 AGCAAACTTGGGACGAAAAC 57.137 45.000 0.00 0.00 0.00 2.43
4959 6416 5.023533 TGCTAGGCTCTGACGAATTAAAT 57.976 39.130 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.