Multiple sequence alignment - TraesCS1D01G215400

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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 TraesCS1D01G215400 chr1D 100.000 3286 0 0 1 3286 300720324 300717039 0.000000e+00 6069.0
1 TraesCS1D01G215400 chr1D 84.571 350 43 5 1947 2287 300859818 300860165 1.460000e-88 337.0
2 TraesCS1D01G215400 chr1D 86.598 194 25 1 1498 1691 300326304 300326112 2.570000e-51 213.0
3 TraesCS1D01G215400 chr1D 82.692 208 31 5 1480 1686 300859085 300859288 2.610000e-41 180.0
4 TraesCS1D01G215400 chr1A 92.868 2608 95 31 610 3173 375114023 375111463 0.000000e+00 3701.0
5 TraesCS1D01G215400 chr1A 88.857 350 23 3 1 340 375114534 375114191 1.820000e-112 416.0
6 TraesCS1D01G215400 chr1A 85.714 350 39 5 1947 2287 375468969 375469316 3.120000e-95 359.0
7 TraesCS1D01G215400 chr1A 87.234 188 23 1 1498 1685 374690177 374689991 2.570000e-51 213.0
8 TraesCS1D01G215400 chr1B 95.312 1792 49 9 1404 3173 405906077 405904299 0.000000e+00 2811.0
9 TraesCS1D01G215400 chr1B 91.502 859 52 11 557 1404 405906970 405906122 0.000000e+00 1162.0
10 TraesCS1D01G215400 chr1B 90.050 402 21 6 1 399 405907348 405906963 1.360000e-138 503.0
11 TraesCS1D01G215400 chr1B 85.882 340 39 4 1957 2287 406037238 406037577 1.450000e-93 353.0
12 TraesCS1D01G215400 chr1B 87.113 194 24 1 1498 1691 405525543 405525351 5.520000e-53 219.0
13 TraesCS1D01G215400 chr4B 84.706 340 40 3 1957 2284 659329679 659329340 2.440000e-86 329.0
14 TraesCS1D01G215400 chr4B 80.000 180 31 5 2101 2278 659521548 659521724 9.570000e-26 128.0
15 TraesCS1D01G215400 chr5A 83.965 343 40 4 1957 2284 694760251 694760593 6.840000e-82 315.0
16 TraesCS1D01G215400 chr5A 81.564 179 30 3 2101 2278 693673605 693673429 9.500000e-31 145.0
17 TraesCS1D01G215400 chr5A 85.507 138 14 6 1262 1396 85165135 85165001 4.420000e-29 139.0
18 TraesCS1D01G215400 chr4D 82.521 349 40 7 1957 2284 508501905 508502253 1.490000e-73 287.0
19 TraesCS1D01G215400 chr4D 80.447 179 32 3 2101 2278 508431517 508431341 2.060000e-27 134.0
20 TraesCS1D01G215400 chrUn 86.932 176 23 0 1516 1691 76409314 76409489 7.190000e-47 198.0
21 TraesCS1D01G215400 chr6D 86.932 176 23 0 1516 1691 15551144 15550969 7.190000e-47 198.0
22 TraesCS1D01G215400 chr6A 86.932 176 23 0 1516 1691 16338192 16338367 7.190000e-47 198.0
23 TraesCS1D01G215400 chr5B 86.047 129 13 5 1273 1398 96765395 96765269 2.060000e-27 134.0
24 TraesCS1D01G215400 chr5D 84.058 138 16 6 1262 1396 91406626 91406492 9.570000e-26 128.0
25 TraesCS1D01G215400 chr3A 86.555 119 11 4 1275 1390 712572214 712572098 3.440000e-25 126.0
26 TraesCS1D01G215400 chr3D 85.345 116 13 3 1275 1388 577255581 577255468 2.070000e-22 117.0
27 TraesCS1D01G215400 chr3B 73.043 345 69 15 1958 2278 6118431 6118775 2.090000e-17 100.0
28 TraesCS1D01G215400 chr3B 91.111 45 4 0 1120 1164 769056161 769056117 9.850000e-06 62.1


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 TraesCS1D01G215400 chr1D 300717039 300720324 3285 True 6069.0 6069 100.0000 1 3286 1 chr1D.!!$R2 3285
1 TraesCS1D01G215400 chr1D 300859085 300860165 1080 False 258.5 337 83.6315 1480 2287 2 chr1D.!!$F1 807
2 TraesCS1D01G215400 chr1A 375111463 375114534 3071 True 2058.5 3701 90.8625 1 3173 2 chr1A.!!$R2 3172
3 TraesCS1D01G215400 chr1B 405904299 405907348 3049 True 1492.0 2811 92.2880 1 3173 3 chr1B.!!$R2 3172

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
460 475 0.032813 ATCATTTGCCCACCCCTGAG 60.033 55.0 0.0 0.0 0.00 3.35 F
496 511 0.038166 GGGGACACTTGCCATTGAGA 59.962 55.0 0.0 0.0 33.93 3.27 F
497 512 1.168714 GGGACACTTGCCATTGAGAC 58.831 55.0 0.0 0.0 32.04 3.36 F
1282 1421 1.252904 ATGTGCATTCAGGTGGTGCC 61.253 55.0 0.0 0.0 38.06 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1400 0.813184 CACCACCTGAATGCACATCC 59.187 55.0 0.00 0.00 0.0 3.51 R
1501 1685 0.930310 CGTTGGTGCATCGTATCTGG 59.070 55.0 0.00 0.00 0.0 3.86 R
1860 2394 1.710013 ATAAGTGTGAAGCGACGGTG 58.290 50.0 0.00 0.00 0.0 4.94 R
2656 3210 0.100503 AATTAATCCTTGGCGCGCAC 59.899 50.0 34.42 22.27 0.0 5.34 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
151 162 7.338710 TCCTGAAAGAGAATACGATTTTCCAT 58.661 34.615 0.00 0.00 34.07 3.41
159 173 8.915036 AGAGAATACGATTTTCCATAGTACTGT 58.085 33.333 5.39 0.00 0.00 3.55
160 174 8.873215 AGAATACGATTTTCCATAGTACTGTG 57.127 34.615 12.39 12.39 0.00 3.66
161 175 7.438459 AGAATACGATTTTCCATAGTACTGTGC 59.562 37.037 13.78 0.00 0.00 4.57
162 176 3.863424 ACGATTTTCCATAGTACTGTGCG 59.137 43.478 13.78 12.45 0.00 5.34
163 177 3.863424 CGATTTTCCATAGTACTGTGCGT 59.137 43.478 13.78 0.00 0.00 5.24
164 178 5.038683 CGATTTTCCATAGTACTGTGCGTA 58.961 41.667 13.78 0.00 0.00 4.42
237 251 0.995675 AGGGCAGGTAGGGATGCAAT 60.996 55.000 0.00 0.00 44.37 3.56
238 252 0.825010 GGGCAGGTAGGGATGCAATG 60.825 60.000 0.00 0.00 44.37 2.82
239 253 0.825010 GGCAGGTAGGGATGCAATGG 60.825 60.000 0.00 0.00 44.37 3.16
264 278 3.307108 TCCGCATGTCCACGACCA 61.307 61.111 0.00 0.00 0.00 4.02
267 281 1.447663 CGCATGTCCACGACCATCA 60.448 57.895 0.00 0.00 0.00 3.07
269 283 0.659427 GCATGTCCACGACCATCATG 59.341 55.000 0.00 0.00 38.87 3.07
285 300 6.400568 ACCATCATGGAAGCAAAAATTACAG 58.599 36.000 11.90 0.00 40.96 2.74
289 304 5.538053 TCATGGAAGCAAAAATTACAGGACA 59.462 36.000 0.00 0.00 26.84 4.02
313 328 1.080501 CGCATGTCCACGACTGTCT 60.081 57.895 6.21 0.00 33.15 3.41
339 354 4.410492 ACAGAAAAATGCAGACGATGTC 57.590 40.909 0.00 0.00 0.00 3.06
340 355 3.189287 ACAGAAAAATGCAGACGATGTCC 59.811 43.478 0.00 0.00 32.18 4.02
341 356 2.416547 AGAAAAATGCAGACGATGTCCG 59.583 45.455 0.00 0.00 45.44 4.79
342 357 0.447801 AAAATGCAGACGATGTCCGC 59.552 50.000 0.00 0.00 43.32 5.54
343 358 1.369091 AAATGCAGACGATGTCCGCC 61.369 55.000 2.97 0.00 43.32 6.13
344 359 2.244117 AATGCAGACGATGTCCGCCT 62.244 55.000 2.97 0.00 43.32 5.52
345 360 2.125512 GCAGACGATGTCCGCCTT 60.126 61.111 0.00 0.00 43.32 4.35
346 361 2.167861 GCAGACGATGTCCGCCTTC 61.168 63.158 0.00 0.00 43.32 3.46
347 362 1.215382 CAGACGATGTCCGCCTTCA 59.785 57.895 0.00 0.00 43.32 3.02
348 363 1.078759 CAGACGATGTCCGCCTTCAC 61.079 60.000 0.00 0.00 43.32 3.18
349 364 1.810030 GACGATGTCCGCCTTCACC 60.810 63.158 0.00 0.00 43.32 4.02
350 365 2.511600 CGATGTCCGCCTTCACCC 60.512 66.667 0.00 0.00 0.00 4.61
378 393 1.518929 CGAGCTTTGCTACATCTACGC 59.481 52.381 0.00 0.00 39.88 4.42
385 400 5.682943 TTTGCTACATCTACGCAAAAGTT 57.317 34.783 6.22 0.00 46.78 2.66
387 402 5.682943 TGCTACATCTACGCAAAAGTTTT 57.317 34.783 0.00 0.00 0.00 2.43
388 403 6.788684 TGCTACATCTACGCAAAAGTTTTA 57.211 33.333 0.00 0.00 0.00 1.52
390 405 7.240674 TGCTACATCTACGCAAAAGTTTTATG 58.759 34.615 0.00 3.08 0.00 1.90
391 406 7.118535 TGCTACATCTACGCAAAAGTTTTATGA 59.881 33.333 11.62 3.25 0.00 2.15
392 407 7.960738 GCTACATCTACGCAAAAGTTTTATGAA 59.039 33.333 11.62 0.00 0.00 2.57
393 408 9.820229 CTACATCTACGCAAAAGTTTTATGAAA 57.180 29.630 11.62 2.07 0.00 2.69
394 409 8.502161 ACATCTACGCAAAAGTTTTATGAAAC 57.498 30.769 11.62 4.99 44.35 2.78
451 466 7.961325 TTTTTCTAACTTTGATCATTTGCCC 57.039 32.000 0.00 0.00 0.00 5.36
452 467 6.662865 TTTCTAACTTTGATCATTTGCCCA 57.337 33.333 0.00 0.00 0.00 5.36
453 468 5.643379 TCTAACTTTGATCATTTGCCCAC 57.357 39.130 0.00 0.00 0.00 4.61
454 469 3.683365 AACTTTGATCATTTGCCCACC 57.317 42.857 0.00 0.00 0.00 4.61
455 470 1.901833 ACTTTGATCATTTGCCCACCC 59.098 47.619 0.00 0.00 0.00 4.61
456 471 1.207811 CTTTGATCATTTGCCCACCCC 59.792 52.381 0.00 0.00 0.00 4.95
457 472 0.413037 TTGATCATTTGCCCACCCCT 59.587 50.000 0.00 0.00 0.00 4.79
458 473 0.324552 TGATCATTTGCCCACCCCTG 60.325 55.000 0.00 0.00 0.00 4.45
459 474 0.033208 GATCATTTGCCCACCCCTGA 60.033 55.000 0.00 0.00 0.00 3.86
460 475 0.032813 ATCATTTGCCCACCCCTGAG 60.033 55.000 0.00 0.00 0.00 3.35
461 476 1.139498 TCATTTGCCCACCCCTGAGA 61.139 55.000 0.00 0.00 0.00 3.27
462 477 0.251742 CATTTGCCCACCCCTGAGAA 60.252 55.000 0.00 0.00 0.00 2.87
463 478 0.712380 ATTTGCCCACCCCTGAGAAT 59.288 50.000 0.00 0.00 0.00 2.40
464 479 0.486879 TTTGCCCACCCCTGAGAATT 59.513 50.000 0.00 0.00 0.00 2.17
465 480 1.377690 TTGCCCACCCCTGAGAATTA 58.622 50.000 0.00 0.00 0.00 1.40
466 481 0.623723 TGCCCACCCCTGAGAATTAC 59.376 55.000 0.00 0.00 0.00 1.89
467 482 0.623723 GCCCACCCCTGAGAATTACA 59.376 55.000 0.00 0.00 0.00 2.41
468 483 1.408822 GCCCACCCCTGAGAATTACAG 60.409 57.143 5.47 5.47 35.43 2.74
474 489 2.717639 CCTGAGAATTACAGGTGGGG 57.282 55.000 17.84 0.12 46.71 4.96
475 490 1.916181 CCTGAGAATTACAGGTGGGGT 59.084 52.381 17.84 0.00 46.71 4.95
476 491 2.092914 CCTGAGAATTACAGGTGGGGTC 60.093 54.545 17.84 0.00 46.71 4.46
477 492 1.553248 TGAGAATTACAGGTGGGGTCG 59.447 52.381 0.00 0.00 0.00 4.79
478 493 0.909623 AGAATTACAGGTGGGGTCGG 59.090 55.000 0.00 0.00 0.00 4.79
479 494 0.107361 GAATTACAGGTGGGGTCGGG 60.107 60.000 0.00 0.00 0.00 5.14
480 495 1.568118 AATTACAGGTGGGGTCGGGG 61.568 60.000 0.00 0.00 0.00 5.73
481 496 2.480255 ATTACAGGTGGGGTCGGGGA 62.480 60.000 0.00 0.00 0.00 4.81
482 497 3.910784 TACAGGTGGGGTCGGGGAC 62.911 68.421 0.00 0.00 0.00 4.46
486 501 3.246880 GTGGGGTCGGGGACACTT 61.247 66.667 0.00 0.00 36.06 3.16
487 502 3.246112 TGGGGTCGGGGACACTTG 61.246 66.667 0.00 0.00 36.06 3.16
488 503 4.717313 GGGGTCGGGGACACTTGC 62.717 72.222 0.00 0.00 36.06 4.01
489 504 4.717313 GGGTCGGGGACACTTGCC 62.717 72.222 0.00 0.00 32.50 4.52
490 505 3.948719 GGTCGGGGACACTTGCCA 61.949 66.667 0.00 0.00 33.93 4.92
491 506 2.351276 GTCGGGGACACTTGCCAT 59.649 61.111 0.00 0.00 33.93 4.40
492 507 1.303317 GTCGGGGACACTTGCCATT 60.303 57.895 0.00 0.00 33.93 3.16
493 508 1.303236 TCGGGGACACTTGCCATTG 60.303 57.895 0.00 0.00 33.93 2.82
494 509 1.303236 CGGGGACACTTGCCATTGA 60.303 57.895 0.00 0.00 33.93 2.57
495 510 1.308069 CGGGGACACTTGCCATTGAG 61.308 60.000 0.00 0.00 33.93 3.02
496 511 0.038166 GGGGACACTTGCCATTGAGA 59.962 55.000 0.00 0.00 33.93 3.27
497 512 1.168714 GGGACACTTGCCATTGAGAC 58.831 55.000 0.00 0.00 32.04 3.36
498 513 1.545428 GGGACACTTGCCATTGAGACA 60.545 52.381 0.00 0.00 32.04 3.41
499 514 2.229792 GGACACTTGCCATTGAGACAA 58.770 47.619 0.00 0.00 0.00 3.18
500 515 2.227388 GGACACTTGCCATTGAGACAAG 59.773 50.000 10.57 10.57 44.98 3.16
504 519 3.826236 CTTGCCATTGAGACAAGTCTG 57.174 47.619 7.57 0.00 40.61 3.51
505 520 2.189594 TGCCATTGAGACAAGTCTGG 57.810 50.000 7.57 4.76 40.61 3.86
506 521 1.699083 TGCCATTGAGACAAGTCTGGA 59.301 47.619 7.57 0.00 40.61 3.86
507 522 2.289882 TGCCATTGAGACAAGTCTGGAG 60.290 50.000 7.57 0.00 40.61 3.86
508 523 2.354259 CCATTGAGACAAGTCTGGAGC 58.646 52.381 7.57 0.00 40.61 4.70
509 524 2.289882 CCATTGAGACAAGTCTGGAGCA 60.290 50.000 7.57 0.00 40.61 4.26
510 525 3.405831 CATTGAGACAAGTCTGGAGCAA 58.594 45.455 7.57 6.05 40.61 3.91
511 526 3.558931 TTGAGACAAGTCTGGAGCAAA 57.441 42.857 7.57 0.00 40.61 3.68
512 527 3.777106 TGAGACAAGTCTGGAGCAAAT 57.223 42.857 7.57 0.00 40.61 2.32
513 528 4.090761 TGAGACAAGTCTGGAGCAAATT 57.909 40.909 7.57 0.00 40.61 1.82
514 529 5.227569 TGAGACAAGTCTGGAGCAAATTA 57.772 39.130 7.57 0.00 40.61 1.40
515 530 5.809001 TGAGACAAGTCTGGAGCAAATTAT 58.191 37.500 7.57 0.00 40.61 1.28
516 531 5.877012 TGAGACAAGTCTGGAGCAAATTATC 59.123 40.000 7.57 0.00 40.61 1.75
517 532 5.809001 AGACAAGTCTGGAGCAAATTATCA 58.191 37.500 1.20 0.00 38.75 2.15
518 533 6.240894 AGACAAGTCTGGAGCAAATTATCAA 58.759 36.000 1.20 0.00 38.75 2.57
519 534 6.716628 AGACAAGTCTGGAGCAAATTATCAAA 59.283 34.615 1.20 0.00 38.75 2.69
520 535 6.681777 ACAAGTCTGGAGCAAATTATCAAAC 58.318 36.000 0.00 0.00 0.00 2.93
521 536 5.904362 AGTCTGGAGCAAATTATCAAACC 57.096 39.130 0.00 0.00 0.00 3.27
522 537 4.706962 AGTCTGGAGCAAATTATCAAACCC 59.293 41.667 0.00 0.00 0.00 4.11
523 538 4.023291 TCTGGAGCAAATTATCAAACCCC 58.977 43.478 0.00 0.00 0.00 4.95
524 539 3.768757 CTGGAGCAAATTATCAAACCCCA 59.231 43.478 0.00 0.00 0.00 4.96
525 540 4.360889 TGGAGCAAATTATCAAACCCCAT 58.639 39.130 0.00 0.00 0.00 4.00
526 541 5.523588 TGGAGCAAATTATCAAACCCCATA 58.476 37.500 0.00 0.00 0.00 2.74
527 542 6.142498 TGGAGCAAATTATCAAACCCCATAT 58.858 36.000 0.00 0.00 0.00 1.78
528 543 7.301420 TGGAGCAAATTATCAAACCCCATATA 58.699 34.615 0.00 0.00 0.00 0.86
529 544 7.786943 TGGAGCAAATTATCAAACCCCATATAA 59.213 33.333 0.00 0.00 0.00 0.98
530 545 8.646900 GGAGCAAATTATCAAACCCCATATAAA 58.353 33.333 0.00 0.00 0.00 1.40
531 546 9.696917 GAGCAAATTATCAAACCCCATATAAAG 57.303 33.333 0.00 0.00 0.00 1.85
532 547 9.212593 AGCAAATTATCAAACCCCATATAAAGT 57.787 29.630 0.00 0.00 0.00 2.66
533 548 9.260002 GCAAATTATCAAACCCCATATAAAGTG 57.740 33.333 0.00 0.00 0.00 3.16
534 549 9.762933 CAAATTATCAAACCCCATATAAAGTGG 57.237 33.333 0.00 0.00 36.47 4.00
546 561 7.277174 CCATATAAAGTGGGACAAAAGATCC 57.723 40.000 0.00 0.00 44.16 3.36
547 562 6.833416 CCATATAAAGTGGGACAAAAGATCCA 59.167 38.462 0.00 0.00 44.16 3.41
548 563 7.341769 CCATATAAAGTGGGACAAAAGATCCAA 59.658 37.037 0.00 0.00 44.16 3.53
549 564 8.917088 CATATAAAGTGGGACAAAAGATCCAAT 58.083 33.333 0.00 0.00 44.16 3.16
550 565 5.728637 AAAGTGGGACAAAAGATCCAATC 57.271 39.130 0.00 0.00 44.16 2.67
551 566 3.701664 AGTGGGACAAAAGATCCAATCC 58.298 45.455 0.00 0.00 44.16 3.01
552 567 3.334881 AGTGGGACAAAAGATCCAATCCT 59.665 43.478 0.00 0.00 44.16 3.24
553 568 3.696548 GTGGGACAAAAGATCCAATCCTC 59.303 47.826 0.00 0.00 44.16 3.71
554 569 3.333381 TGGGACAAAAGATCCAATCCTCA 59.667 43.478 0.00 0.00 38.06 3.86
555 570 4.017222 TGGGACAAAAGATCCAATCCTCAT 60.017 41.667 0.00 0.00 38.06 2.90
592 710 6.237942 CGAGCTTACATAGTCTGATTTGGTTG 60.238 42.308 0.00 0.00 0.00 3.77
593 711 5.882557 AGCTTACATAGTCTGATTTGGTTGG 59.117 40.000 0.00 0.00 0.00 3.77
643 761 4.772100 TGAAATTCAAGGGGAAGGTGATTC 59.228 41.667 0.00 0.00 39.30 2.52
648 766 2.488153 CAAGGGGAAGGTGATTCGTTTC 59.512 50.000 0.00 0.00 38.95 2.78
667 786 5.572126 CGTTTCTAGAAAGGAAAGGTCGTAG 59.428 44.000 26.44 1.42 38.14 3.51
686 807 5.593095 TCGTAGCATCATGTAAGAGGTTACT 59.407 40.000 0.00 0.00 39.55 2.24
700 821 5.978814 AGAGGTTACTTAGGTGTAGCATTG 58.021 41.667 0.00 0.00 0.00 2.82
896 1024 5.630539 GCCTATAAATACCCCGGCAATATGA 60.631 44.000 0.00 0.00 37.48 2.15
921 1053 4.018960 ACTCCCAGAACATCAAAGCATAGT 60.019 41.667 0.00 0.00 0.00 2.12
923 1055 4.701651 TCCCAGAACATCAAAGCATAGTTG 59.298 41.667 0.00 0.00 0.00 3.16
1193 1332 4.429212 TACGTCTGCATGCGCCGT 62.429 61.111 25.28 25.28 37.34 5.68
1223 1362 3.816524 CGCCGCGGAGTTCTCTCT 61.817 66.667 33.48 0.00 40.29 3.10
1224 1363 2.103340 GCCGCGGAGTTCTCTCTC 59.897 66.667 33.48 2.06 40.29 3.20
1248 1387 8.735303 TCCATTAATTGAACGTTTGTGTAATG 57.265 30.769 18.88 18.88 0.00 1.90
1261 1400 2.677337 TGTGTAATGACATGCGGTGATG 59.323 45.455 0.00 0.00 38.04 3.07
1282 1421 1.252904 ATGTGCATTCAGGTGGTGCC 61.253 55.000 0.00 0.00 38.06 5.01
1501 1685 6.903883 TCTGATCGTTTACTATTGCCTTTC 57.096 37.500 0.00 0.00 0.00 2.62
1754 2074 3.119743 CCCTACGTGAACGATGAACAGTA 60.120 47.826 10.26 0.00 43.02 2.74
1802 2333 2.804647 CCCAACAAAACTTTCACGACC 58.195 47.619 0.00 0.00 0.00 4.79
1837 2368 1.843851 TGGGACCCAAATAGATTCGCT 59.156 47.619 12.05 0.00 0.00 4.93
1860 2394 7.012358 GCTGCGAATAATACTCTATTTTGAGC 58.988 38.462 0.00 0.00 37.58 4.26
1955 2489 0.815095 TTGCTGCTGCTGATGATTGG 59.185 50.000 17.00 0.00 40.48 3.16
2302 2845 1.534595 CTGAAGCTGCTGAACTGAACC 59.465 52.381 1.35 0.00 0.00 3.62
2303 2846 0.514691 GAAGCTGCTGAACTGAACCG 59.485 55.000 1.35 0.00 0.00 4.44
2304 2847 0.106708 AAGCTGCTGAACTGAACCGA 59.893 50.000 1.35 0.00 0.00 4.69
2305 2848 0.106708 AGCTGCTGAACTGAACCGAA 59.893 50.000 0.00 0.00 0.00 4.30
2306 2849 0.235926 GCTGCTGAACTGAACCGAAC 59.764 55.000 0.00 0.00 0.00 3.95
2656 3210 6.348540 GCCCTAGTACTTGTCAAACTTGATTG 60.349 42.308 0.00 0.00 39.73 2.67
2667 3221 1.798725 CTTGATTGTGCGCGCCAAG 60.799 57.895 30.77 27.37 0.00 3.61
2675 3229 0.100503 GTGCGCGCCAAGGATTAATT 59.899 50.000 30.77 0.00 0.00 1.40
2676 3230 0.100325 TGCGCGCCAAGGATTAATTG 59.900 50.000 30.77 0.00 0.00 2.32
2677 3231 1.208642 GCGCGCCAAGGATTAATTGC 61.209 55.000 23.24 0.00 0.00 3.56
2708 3262 5.232414 GGAATTCGATCCTGACTTTCTAACG 59.768 44.000 0.00 0.00 36.50 3.18
2764 3319 1.233019 TCCGGTAGATTCGACGATCC 58.767 55.000 0.00 0.00 0.00 3.36
3007 3564 7.911651 ACCTAATGATAGTGAATGATTCGGAT 58.088 34.615 0.18 0.00 31.18 4.18
3023 3580 5.520022 TTCGGATTAACTTTTACACGAGC 57.480 39.130 0.00 0.00 0.00 5.03
3027 3584 4.624452 GGATTAACTTTTACACGAGCGACT 59.376 41.667 0.00 0.00 0.00 4.18
3061 3619 2.930682 GCCGCCTAAAAGTTCACTCTAG 59.069 50.000 0.00 0.00 0.00 2.43
3080 3658 8.215132 CACTCTAGCTAAGAAAGTTGTTTAACG 58.785 37.037 9.14 0.00 36.44 3.18
3081 3659 8.139989 ACTCTAGCTAAGAAAGTTGTTTAACGA 58.860 33.333 9.14 0.00 36.44 3.85
3082 3660 8.290663 TCTAGCTAAGAAAGTTGTTTAACGAC 57.709 34.615 7.36 7.36 41.71 4.34
3137 3715 1.935199 GCCGTAAATACTGGCGCTAAA 59.065 47.619 7.64 0.00 36.63 1.85
3173 3751 3.614616 CGAGCTAGTCTTTGGTCATGTTC 59.385 47.826 0.00 0.00 0.00 3.18
3174 3752 4.619394 CGAGCTAGTCTTTGGTCATGTTCT 60.619 45.833 0.00 0.00 0.00 3.01
3175 3753 5.234466 AGCTAGTCTTTGGTCATGTTCTT 57.766 39.130 0.00 0.00 0.00 2.52
3176 3754 5.625150 AGCTAGTCTTTGGTCATGTTCTTT 58.375 37.500 0.00 0.00 0.00 2.52
3177 3755 6.064717 AGCTAGTCTTTGGTCATGTTCTTTT 58.935 36.000 0.00 0.00 0.00 2.27
3178 3756 7.224297 AGCTAGTCTTTGGTCATGTTCTTTTA 58.776 34.615 0.00 0.00 0.00 1.52
3179 3757 7.389053 AGCTAGTCTTTGGTCATGTTCTTTTAG 59.611 37.037 0.00 0.00 0.00 1.85
3180 3758 7.173390 GCTAGTCTTTGGTCATGTTCTTTTAGT 59.827 37.037 0.00 0.00 0.00 2.24
3181 3759 7.264373 AGTCTTTGGTCATGTTCTTTTAGTG 57.736 36.000 0.00 0.00 0.00 2.74
3182 3760 7.054124 AGTCTTTGGTCATGTTCTTTTAGTGA 58.946 34.615 0.00 0.00 0.00 3.41
3183 3761 7.556275 AGTCTTTGGTCATGTTCTTTTAGTGAA 59.444 33.333 0.00 0.00 0.00 3.18
3184 3762 8.188139 GTCTTTGGTCATGTTCTTTTAGTGAAA 58.812 33.333 0.00 0.00 0.00 2.69
3185 3763 8.912988 TCTTTGGTCATGTTCTTTTAGTGAAAT 58.087 29.630 0.00 0.00 0.00 2.17
3188 3766 9.959749 TTGGTCATGTTCTTTTAGTGAAATAAC 57.040 29.630 0.00 2.74 35.82 1.89
3189 3767 9.126151 TGGTCATGTTCTTTTAGTGAAATAACA 57.874 29.630 11.90 11.90 43.79 2.41
3190 3768 9.612620 GGTCATGTTCTTTTAGTGAAATAACAG 57.387 33.333 14.01 8.49 43.27 3.16
3191 3769 9.612620 GTCATGTTCTTTTAGTGAAATAACAGG 57.387 33.333 13.56 13.56 43.27 4.00
3192 3770 9.567776 TCATGTTCTTTTAGTGAAATAACAGGA 57.432 29.630 16.59 16.59 44.98 3.86
3193 3771 9.612620 CATGTTCTTTTAGTGAAATAACAGGAC 57.387 33.333 14.19 0.00 43.16 3.85
3194 3772 8.974060 TGTTCTTTTAGTGAAATAACAGGACT 57.026 30.769 7.10 0.00 38.58 3.85
3195 3773 9.052759 TGTTCTTTTAGTGAAATAACAGGACTC 57.947 33.333 7.10 0.00 38.58 3.36
3196 3774 9.274206 GTTCTTTTAGTGAAATAACAGGACTCT 57.726 33.333 4.41 0.00 35.53 3.24
3197 3775 8.833231 TCTTTTAGTGAAATAACAGGACTCTG 57.167 34.615 0.00 0.00 46.10 3.35
3198 3776 7.387948 TCTTTTAGTGAAATAACAGGACTCTGC 59.612 37.037 0.00 0.00 44.59 4.26
3199 3777 4.899352 AGTGAAATAACAGGACTCTGCT 57.101 40.909 0.00 0.00 44.59 4.24
3200 3778 4.826556 AGTGAAATAACAGGACTCTGCTC 58.173 43.478 0.00 0.00 44.59 4.26
3201 3779 3.935828 GTGAAATAACAGGACTCTGCTCC 59.064 47.826 0.00 0.00 44.59 4.70
3202 3780 2.969628 AATAACAGGACTCTGCTCCG 57.030 50.000 0.00 0.00 44.59 4.63
3203 3781 1.853963 ATAACAGGACTCTGCTCCGT 58.146 50.000 0.00 0.00 44.59 4.69
3204 3782 1.629043 TAACAGGACTCTGCTCCGTT 58.371 50.000 0.00 0.00 44.59 4.44
3205 3783 0.759346 AACAGGACTCTGCTCCGTTT 59.241 50.000 0.00 0.00 44.59 3.60
3206 3784 1.629043 ACAGGACTCTGCTCCGTTTA 58.371 50.000 0.00 0.00 44.59 2.01
3207 3785 1.546476 ACAGGACTCTGCTCCGTTTAG 59.454 52.381 0.00 0.00 44.59 1.85
3208 3786 1.546476 CAGGACTCTGCTCCGTTTAGT 59.454 52.381 0.00 0.00 35.20 2.24
3209 3787 1.819903 AGGACTCTGCTCCGTTTAGTC 59.180 52.381 0.00 0.00 35.20 2.59
3210 3788 1.819903 GGACTCTGCTCCGTTTAGTCT 59.180 52.381 0.00 0.00 37.36 3.24
3211 3789 2.231721 GGACTCTGCTCCGTTTAGTCTT 59.768 50.000 0.00 0.00 37.36 3.01
3212 3790 3.306156 GGACTCTGCTCCGTTTAGTCTTT 60.306 47.826 0.00 0.00 37.36 2.52
3213 3791 3.654414 ACTCTGCTCCGTTTAGTCTTTG 58.346 45.455 0.00 0.00 0.00 2.77
3214 3792 2.996621 CTCTGCTCCGTTTAGTCTTTGG 59.003 50.000 0.00 0.00 0.00 3.28
3215 3793 2.367567 TCTGCTCCGTTTAGTCTTTGGT 59.632 45.455 0.00 0.00 0.00 3.67
3216 3794 2.737252 CTGCTCCGTTTAGTCTTTGGTC 59.263 50.000 0.00 0.00 0.00 4.02
3217 3795 2.103432 TGCTCCGTTTAGTCTTTGGTCA 59.897 45.455 0.00 0.00 0.00 4.02
3218 3796 3.135994 GCTCCGTTTAGTCTTTGGTCAA 58.864 45.455 0.00 0.00 0.00 3.18
3219 3797 3.751698 GCTCCGTTTAGTCTTTGGTCAAT 59.248 43.478 0.00 0.00 0.00 2.57
3220 3798 4.378459 GCTCCGTTTAGTCTTTGGTCAATG 60.378 45.833 0.00 0.00 0.00 2.82
3221 3799 4.710324 TCCGTTTAGTCTTTGGTCAATGT 58.290 39.130 0.00 0.00 0.00 2.71
3222 3800 5.127491 TCCGTTTAGTCTTTGGTCAATGTT 58.873 37.500 0.00 0.00 0.00 2.71
3223 3801 5.237779 TCCGTTTAGTCTTTGGTCAATGTTC 59.762 40.000 0.00 0.00 0.00 3.18
3224 3802 5.238650 CCGTTTAGTCTTTGGTCAATGTTCT 59.761 40.000 0.00 0.00 0.00 3.01
3225 3803 6.363473 CGTTTAGTCTTTGGTCAATGTTCTC 58.637 40.000 0.00 0.00 0.00 2.87
3226 3804 6.018262 CGTTTAGTCTTTGGTCAATGTTCTCA 60.018 38.462 0.00 0.00 0.00 3.27
3227 3805 7.466725 CGTTTAGTCTTTGGTCAATGTTCTCAA 60.467 37.037 0.00 0.00 0.00 3.02
3228 3806 7.873719 TTAGTCTTTGGTCAATGTTCTCAAA 57.126 32.000 0.00 0.00 0.00 2.69
3229 3807 6.966534 AGTCTTTGGTCAATGTTCTCAAAT 57.033 33.333 0.00 0.00 0.00 2.32
3230 3808 7.352079 AGTCTTTGGTCAATGTTCTCAAATT 57.648 32.000 0.00 0.00 0.00 1.82
3231 3809 8.463930 AGTCTTTGGTCAATGTTCTCAAATTA 57.536 30.769 0.00 0.00 0.00 1.40
3232 3810 8.912988 AGTCTTTGGTCAATGTTCTCAAATTAA 58.087 29.630 0.00 0.00 0.00 1.40
3233 3811 9.528018 GTCTTTGGTCAATGTTCTCAAATTAAA 57.472 29.630 0.00 0.00 0.00 1.52
3234 3812 9.528018 TCTTTGGTCAATGTTCTCAAATTAAAC 57.472 29.630 0.00 0.00 0.00 2.01
3235 3813 9.533253 CTTTGGTCAATGTTCTCAAATTAAACT 57.467 29.630 0.00 0.00 0.00 2.66
3237 3815 9.959749 TTGGTCAATGTTCTCAAATTAAACTAC 57.040 29.630 0.00 0.00 0.00 2.73
3238 3816 9.349713 TGGTCAATGTTCTCAAATTAAACTACT 57.650 29.630 0.00 0.00 0.00 2.57
3239 3817 9.827411 GGTCAATGTTCTCAAATTAAACTACTC 57.173 33.333 0.00 0.00 0.00 2.59
3240 3818 9.827411 GTCAATGTTCTCAAATTAAACTACTCC 57.173 33.333 0.00 0.00 0.00 3.85
3241 3819 9.793259 TCAATGTTCTCAAATTAAACTACTCCT 57.207 29.630 0.00 0.00 0.00 3.69
3253 3831 9.802039 AATTAAACTACTCCTAAATGTGAACCA 57.198 29.630 0.00 0.00 0.00 3.67
3254 3832 9.802039 ATTAAACTACTCCTAAATGTGAACCAA 57.198 29.630 0.00 0.00 0.00 3.67
3255 3833 7.506328 AAACTACTCCTAAATGTGAACCAAC 57.494 36.000 0.00 0.00 0.00 3.77
3256 3834 5.557866 ACTACTCCTAAATGTGAACCAACC 58.442 41.667 0.00 0.00 0.00 3.77
3257 3835 4.724279 ACTCCTAAATGTGAACCAACCT 57.276 40.909 0.00 0.00 0.00 3.50
3258 3836 5.836024 ACTCCTAAATGTGAACCAACCTA 57.164 39.130 0.00 0.00 0.00 3.08
3259 3837 5.557866 ACTCCTAAATGTGAACCAACCTAC 58.442 41.667 0.00 0.00 0.00 3.18
3260 3838 5.072600 ACTCCTAAATGTGAACCAACCTACA 59.927 40.000 0.00 0.00 0.00 2.74
3261 3839 5.556915 TCCTAAATGTGAACCAACCTACAG 58.443 41.667 0.00 0.00 0.00 2.74
3262 3840 5.072600 TCCTAAATGTGAACCAACCTACAGT 59.927 40.000 0.00 0.00 0.00 3.55
3263 3841 5.768164 CCTAAATGTGAACCAACCTACAGTT 59.232 40.000 0.00 0.00 40.16 3.16
3274 3852 3.914426 ACCTACAGTTGGATGGCTAAG 57.086 47.619 8.17 0.00 0.00 2.18
3275 3853 3.450904 ACCTACAGTTGGATGGCTAAGA 58.549 45.455 8.17 0.00 0.00 2.10
3276 3854 3.452627 ACCTACAGTTGGATGGCTAAGAG 59.547 47.826 8.17 0.00 0.00 2.85
3277 3855 3.181461 CCTACAGTTGGATGGCTAAGAGG 60.181 52.174 0.00 0.00 0.00 3.69
3278 3856 2.551270 ACAGTTGGATGGCTAAGAGGA 58.449 47.619 0.00 0.00 0.00 3.71
3279 3857 2.237392 ACAGTTGGATGGCTAAGAGGAC 59.763 50.000 0.00 0.00 0.00 3.85
3280 3858 2.237143 CAGTTGGATGGCTAAGAGGACA 59.763 50.000 0.00 0.00 0.00 4.02
3281 3859 2.503356 AGTTGGATGGCTAAGAGGACAG 59.497 50.000 0.00 0.00 0.00 3.51
3282 3860 2.237392 GTTGGATGGCTAAGAGGACAGT 59.763 50.000 0.00 0.00 0.00 3.55
3283 3861 1.833630 TGGATGGCTAAGAGGACAGTG 59.166 52.381 0.00 0.00 0.00 3.66
3284 3862 1.834263 GGATGGCTAAGAGGACAGTGT 59.166 52.381 0.00 0.00 0.00 3.55
3285 3863 2.237392 GGATGGCTAAGAGGACAGTGTT 59.763 50.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 121 2.230508 TCAGGAACGTACAGCTAAGTGG 59.769 50.000 0.00 0.00 0.00 4.00
151 162 3.811497 AGATACGCATACGCACAGTACTA 59.189 43.478 0.00 0.00 45.53 1.82
159 173 3.710326 AGAAAGAGATACGCATACGCA 57.290 42.857 0.00 0.00 45.53 5.24
160 174 3.604627 GCTAGAAAGAGATACGCATACGC 59.395 47.826 0.00 0.00 45.53 4.42
161 175 6.784453 TTCTGCTAGAAAGAGATACGCATACG 60.784 42.308 0.00 0.00 36.93 3.06
162 176 6.003234 TCTGCTAGAAAGAGATACGCATAC 57.997 41.667 0.00 0.00 0.00 2.39
163 177 6.635030 TTCTGCTAGAAAGAGATACGCATA 57.365 37.500 0.00 0.00 29.99 3.14
164 178 5.521906 TTCTGCTAGAAAGAGATACGCAT 57.478 39.130 0.00 0.00 29.99 4.73
203 217 2.895865 CCTGCTCTGGCTGATGCG 60.896 66.667 0.00 0.00 40.82 4.73
264 278 6.211184 TGTCCTGTAATTTTTGCTTCCATGAT 59.789 34.615 0.00 0.00 0.00 2.45
267 281 5.567423 GCTGTCCTGTAATTTTTGCTTCCAT 60.567 40.000 0.00 0.00 0.00 3.41
269 283 4.237724 GCTGTCCTGTAATTTTTGCTTCC 58.762 43.478 0.00 0.00 0.00 3.46
313 328 3.625313 TCGTCTGCATTTTTCTGTTCACA 59.375 39.130 0.00 0.00 0.00 3.58
339 354 2.590092 CCTTAGGGGTGAAGGCGG 59.410 66.667 0.00 0.00 37.26 6.13
349 364 2.543067 AGCAAAGCTCGCCCTTAGGG 62.543 60.000 14.11 14.11 39.65 3.53
350 365 0.178068 TAGCAAAGCTCGCCCTTAGG 59.822 55.000 4.54 0.00 40.44 2.69
427 442 7.440856 GTGGGCAAATGATCAAAGTTAGAAAAA 59.559 33.333 0.00 0.00 0.00 1.94
428 443 6.928492 GTGGGCAAATGATCAAAGTTAGAAAA 59.072 34.615 0.00 0.00 0.00 2.29
429 444 6.454795 GTGGGCAAATGATCAAAGTTAGAAA 58.545 36.000 0.00 0.00 0.00 2.52
430 445 5.047377 GGTGGGCAAATGATCAAAGTTAGAA 60.047 40.000 0.00 0.00 0.00 2.10
431 446 4.462483 GGTGGGCAAATGATCAAAGTTAGA 59.538 41.667 0.00 0.00 0.00 2.10
432 447 4.381932 GGGTGGGCAAATGATCAAAGTTAG 60.382 45.833 0.00 0.00 0.00 2.34
433 448 3.513515 GGGTGGGCAAATGATCAAAGTTA 59.486 43.478 0.00 0.00 0.00 2.24
434 449 2.302733 GGGTGGGCAAATGATCAAAGTT 59.697 45.455 0.00 0.00 0.00 2.66
435 450 1.901833 GGGTGGGCAAATGATCAAAGT 59.098 47.619 0.00 0.00 0.00 2.66
436 451 1.207811 GGGGTGGGCAAATGATCAAAG 59.792 52.381 0.00 0.00 0.00 2.77
437 452 1.203288 AGGGGTGGGCAAATGATCAAA 60.203 47.619 0.00 0.00 0.00 2.69
438 453 0.413037 AGGGGTGGGCAAATGATCAA 59.587 50.000 0.00 0.00 0.00 2.57
439 454 0.324552 CAGGGGTGGGCAAATGATCA 60.325 55.000 0.00 0.00 0.00 2.92
440 455 0.033208 TCAGGGGTGGGCAAATGATC 60.033 55.000 0.00 0.00 0.00 2.92
441 456 0.032813 CTCAGGGGTGGGCAAATGAT 60.033 55.000 0.00 0.00 0.00 2.45
442 457 1.139498 TCTCAGGGGTGGGCAAATGA 61.139 55.000 0.00 0.00 0.00 2.57
443 458 0.251742 TTCTCAGGGGTGGGCAAATG 60.252 55.000 0.00 0.00 0.00 2.32
444 459 0.712380 ATTCTCAGGGGTGGGCAAAT 59.288 50.000 0.00 0.00 0.00 2.32
445 460 0.486879 AATTCTCAGGGGTGGGCAAA 59.513 50.000 0.00 0.00 0.00 3.68
446 461 1.005450 GTAATTCTCAGGGGTGGGCAA 59.995 52.381 0.00 0.00 0.00 4.52
447 462 0.623723 GTAATTCTCAGGGGTGGGCA 59.376 55.000 0.00 0.00 0.00 5.36
448 463 0.623723 TGTAATTCTCAGGGGTGGGC 59.376 55.000 0.00 0.00 0.00 5.36
449 464 1.212935 CCTGTAATTCTCAGGGGTGGG 59.787 57.143 17.05 0.00 46.03 4.61
450 465 2.717639 CCTGTAATTCTCAGGGGTGG 57.282 55.000 17.05 0.00 46.03 4.61
456 471 2.418746 CGACCCCACCTGTAATTCTCAG 60.419 54.545 4.25 4.25 0.00 3.35
457 472 1.553248 CGACCCCACCTGTAATTCTCA 59.447 52.381 0.00 0.00 0.00 3.27
458 473 1.134491 CCGACCCCACCTGTAATTCTC 60.134 57.143 0.00 0.00 0.00 2.87
459 474 0.909623 CCGACCCCACCTGTAATTCT 59.090 55.000 0.00 0.00 0.00 2.40
460 475 0.107361 CCCGACCCCACCTGTAATTC 60.107 60.000 0.00 0.00 0.00 2.17
461 476 1.568118 CCCCGACCCCACCTGTAATT 61.568 60.000 0.00 0.00 0.00 1.40
462 477 1.999002 CCCCGACCCCACCTGTAAT 60.999 63.158 0.00 0.00 0.00 1.89
463 478 2.608368 CCCCGACCCCACCTGTAA 60.608 66.667 0.00 0.00 0.00 2.41
464 479 3.603080 TCCCCGACCCCACCTGTA 61.603 66.667 0.00 0.00 0.00 2.74
469 484 3.246880 AAGTGTCCCCGACCCCAC 61.247 66.667 0.00 0.00 0.00 4.61
470 485 3.246112 CAAGTGTCCCCGACCCCA 61.246 66.667 0.00 0.00 0.00 4.96
471 486 4.717313 GCAAGTGTCCCCGACCCC 62.717 72.222 0.00 0.00 0.00 4.95
472 487 4.717313 GGCAAGTGTCCCCGACCC 62.717 72.222 0.00 0.00 0.00 4.46
473 488 2.764637 AATGGCAAGTGTCCCCGACC 62.765 60.000 0.00 0.00 0.00 4.79
474 489 1.303317 AATGGCAAGTGTCCCCGAC 60.303 57.895 0.00 0.00 0.00 4.79
475 490 1.303236 CAATGGCAAGTGTCCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
476 491 1.303236 TCAATGGCAAGTGTCCCCG 60.303 57.895 0.00 0.00 0.00 5.73
477 492 0.038166 TCTCAATGGCAAGTGTCCCC 59.962 55.000 0.00 0.00 0.00 4.81
478 493 1.168714 GTCTCAATGGCAAGTGTCCC 58.831 55.000 0.00 0.00 0.00 4.46
479 494 1.896220 TGTCTCAATGGCAAGTGTCC 58.104 50.000 0.00 0.00 0.00 4.02
485 500 2.106338 TCCAGACTTGTCTCAATGGCAA 59.894 45.455 0.00 0.00 38.03 4.52
486 501 1.699083 TCCAGACTTGTCTCAATGGCA 59.301 47.619 0.00 0.00 0.00 4.92
487 502 2.354259 CTCCAGACTTGTCTCAATGGC 58.646 52.381 0.00 0.00 0.00 4.40
488 503 2.289882 TGCTCCAGACTTGTCTCAATGG 60.290 50.000 0.00 0.83 0.00 3.16
489 504 3.049708 TGCTCCAGACTTGTCTCAATG 57.950 47.619 0.00 0.00 0.00 2.82
490 505 3.777106 TTGCTCCAGACTTGTCTCAAT 57.223 42.857 0.00 0.00 0.00 2.57
491 506 3.558931 TTTGCTCCAGACTTGTCTCAA 57.441 42.857 0.00 0.10 0.00 3.02
492 507 3.777106 ATTTGCTCCAGACTTGTCTCA 57.223 42.857 0.00 0.00 0.00 3.27
493 508 5.877012 TGATAATTTGCTCCAGACTTGTCTC 59.123 40.000 0.00 0.00 0.00 3.36
494 509 5.809001 TGATAATTTGCTCCAGACTTGTCT 58.191 37.500 0.00 0.00 0.00 3.41
495 510 6.500684 TTGATAATTTGCTCCAGACTTGTC 57.499 37.500 0.00 0.00 0.00 3.18
496 511 6.294731 GGTTTGATAATTTGCTCCAGACTTGT 60.295 38.462 0.00 0.00 0.00 3.16
497 512 6.095377 GGTTTGATAATTTGCTCCAGACTTG 58.905 40.000 0.00 0.00 0.00 3.16
498 513 5.185828 GGGTTTGATAATTTGCTCCAGACTT 59.814 40.000 0.00 0.00 0.00 3.01
499 514 4.706962 GGGTTTGATAATTTGCTCCAGACT 59.293 41.667 0.00 0.00 0.00 3.24
500 515 4.142160 GGGGTTTGATAATTTGCTCCAGAC 60.142 45.833 0.00 0.00 0.00 3.51
501 516 4.023291 GGGGTTTGATAATTTGCTCCAGA 58.977 43.478 0.00 0.00 0.00 3.86
502 517 3.768757 TGGGGTTTGATAATTTGCTCCAG 59.231 43.478 0.00 0.00 0.00 3.86
503 518 3.784178 TGGGGTTTGATAATTTGCTCCA 58.216 40.909 0.00 0.00 0.00 3.86
504 519 6.670695 ATATGGGGTTTGATAATTTGCTCC 57.329 37.500 0.00 0.00 0.00 4.70
505 520 9.696917 CTTTATATGGGGTTTGATAATTTGCTC 57.303 33.333 0.00 0.00 0.00 4.26
506 521 9.212593 ACTTTATATGGGGTTTGATAATTTGCT 57.787 29.630 0.00 0.00 0.00 3.91
507 522 9.260002 CACTTTATATGGGGTTTGATAATTTGC 57.740 33.333 0.00 0.00 0.00 3.68
508 523 9.762933 CCACTTTATATGGGGTTTGATAATTTG 57.237 33.333 0.00 0.00 33.18 2.32
522 537 6.833416 TGGATCTTTTGTCCCACTTTATATGG 59.167 38.462 0.00 0.00 34.76 2.74
523 538 7.880160 TGGATCTTTTGTCCCACTTTATATG 57.120 36.000 0.00 0.00 34.76 1.78
524 539 9.136323 GATTGGATCTTTTGTCCCACTTTATAT 57.864 33.333 0.00 0.00 34.76 0.86
525 540 7.559897 GGATTGGATCTTTTGTCCCACTTTATA 59.440 37.037 0.00 0.00 34.76 0.98
526 541 6.381133 GGATTGGATCTTTTGTCCCACTTTAT 59.619 38.462 0.00 0.00 34.76 1.40
527 542 5.714806 GGATTGGATCTTTTGTCCCACTTTA 59.285 40.000 0.00 0.00 34.76 1.85
528 543 4.528206 GGATTGGATCTTTTGTCCCACTTT 59.472 41.667 0.00 0.00 34.76 2.66
529 544 4.089361 GGATTGGATCTTTTGTCCCACTT 58.911 43.478 0.00 0.00 34.76 3.16
530 545 3.334881 AGGATTGGATCTTTTGTCCCACT 59.665 43.478 0.00 0.00 34.76 4.00
531 546 3.696548 GAGGATTGGATCTTTTGTCCCAC 59.303 47.826 0.00 0.00 34.76 4.61
532 547 3.333381 TGAGGATTGGATCTTTTGTCCCA 59.667 43.478 0.00 0.00 34.76 4.37
533 548 3.968265 TGAGGATTGGATCTTTTGTCCC 58.032 45.455 0.00 0.00 34.76 4.46
534 549 7.340487 AGTTTATGAGGATTGGATCTTTTGTCC 59.660 37.037 0.00 0.00 36.26 4.02
535 550 8.286191 AGTTTATGAGGATTGGATCTTTTGTC 57.714 34.615 0.00 0.00 0.00 3.18
536 551 8.655935 AAGTTTATGAGGATTGGATCTTTTGT 57.344 30.769 0.00 0.00 0.00 2.83
545 560 9.088512 GCTCGTATATAAGTTTATGAGGATTGG 57.911 37.037 5.02 0.00 33.79 3.16
546 561 9.862371 AGCTCGTATATAAGTTTATGAGGATTG 57.138 33.333 5.02 0.00 33.79 2.67
564 579 7.148641 CCAAATCAGACTATGTAAGCTCGTAT 58.851 38.462 0.00 0.00 0.00 3.06
567 582 5.352284 ACCAAATCAGACTATGTAAGCTCG 58.648 41.667 0.00 0.00 0.00 5.03
578 696 7.654022 TTTTTACTTCCAACCAAATCAGACT 57.346 32.000 0.00 0.00 0.00 3.24
608 726 0.034863 GAATTTCACGGGTGGGCCTA 60.035 55.000 4.53 0.00 34.45 3.93
643 761 4.304939 ACGACCTTTCCTTTCTAGAAACG 58.695 43.478 13.99 14.64 0.00 3.60
648 766 4.451629 TGCTACGACCTTTCCTTTCTAG 57.548 45.455 0.00 0.00 0.00 2.43
661 779 4.308899 ACCTCTTACATGATGCTACGAC 57.691 45.455 0.00 0.00 0.00 4.34
667 786 6.480320 CACCTAAGTAACCTCTTACATGATGC 59.520 42.308 0.00 0.00 35.56 3.91
700 821 1.298859 CGTACCTGCCCTTGAGCAAC 61.299 60.000 0.00 0.00 43.52 4.17
761 888 1.021390 CCTGCGAGAAATCACGGCTT 61.021 55.000 2.63 0.00 0.00 4.35
896 1024 4.574674 TGCTTTGATGTTCTGGGAGTAT 57.425 40.909 0.00 0.00 0.00 2.12
945 1077 0.038618 TAGTGTACCAGCGCACTGTG 60.039 55.000 11.47 2.76 44.59 3.66
946 1078 0.038526 GTAGTGTACCAGCGCACTGT 60.039 55.000 11.47 5.88 44.59 3.55
1043 1175 0.255318 GTAGGTGACGAGGAGGGAGA 59.745 60.000 0.00 0.00 0.00 3.71
1173 1308 2.813474 GCGCATGCAGACGTACCA 60.813 61.111 19.57 0.00 42.15 3.25
1214 1353 6.702329 ACGTTCAATTAATGGAGAGAGAACT 58.298 36.000 0.00 0.00 33.79 3.01
1215 1354 6.969828 ACGTTCAATTAATGGAGAGAGAAC 57.030 37.500 0.00 0.00 0.00 3.01
1219 1358 6.485313 ACACAAACGTTCAATTAATGGAGAGA 59.515 34.615 0.00 0.00 0.00 3.10
1221 1360 6.627395 ACACAAACGTTCAATTAATGGAGA 57.373 33.333 0.00 0.00 0.00 3.71
1222 1361 8.849490 CATTACACAAACGTTCAATTAATGGAG 58.151 33.333 17.01 6.15 0.00 3.86
1223 1362 8.568794 TCATTACACAAACGTTCAATTAATGGA 58.431 29.630 20.87 12.05 0.00 3.41
1224 1363 8.635124 GTCATTACACAAACGTTCAATTAATGG 58.365 33.333 20.87 10.78 0.00 3.16
1225 1364 9.175060 TGTCATTACACAAACGTTCAATTAATG 57.825 29.630 17.92 17.92 0.00 1.90
1226 1365 9.906660 ATGTCATTACACAAACGTTCAATTAAT 57.093 25.926 0.00 0.55 38.78 1.40
1235 1374 2.095969 CCGCATGTCATTACACAAACGT 60.096 45.455 0.00 0.00 38.78 3.99
1248 1387 0.659427 CACATCCATCACCGCATGTC 59.341 55.000 0.00 0.00 0.00 3.06
1261 1400 0.813184 CACCACCTGAATGCACATCC 59.187 55.000 0.00 0.00 0.00 3.51
1282 1421 0.817634 TGGTGTTCTTGAACCCGCAG 60.818 55.000 10.51 0.00 35.44 5.18
1501 1685 0.930310 CGTTGGTGCATCGTATCTGG 59.070 55.000 0.00 0.00 0.00 3.86
1802 2333 2.385091 CCCAGTTAAACCGGTCGCG 61.385 63.158 8.04 0.00 0.00 5.87
1837 2368 7.042051 GGTGCTCAAAATAGAGTATTATTCGCA 60.042 37.037 0.00 0.00 37.94 5.10
1860 2394 1.710013 ATAAGTGTGAAGCGACGGTG 58.290 50.000 0.00 0.00 0.00 4.94
1869 2403 2.477375 GACGACGGCAAATAAGTGTGAA 59.523 45.455 0.00 0.00 0.00 3.18
1901 2435 2.884012 TGCCATTGTAACTTGGTCTGTG 59.116 45.455 0.00 0.00 35.34 3.66
1908 2442 2.562298 ACCCATGTGCCATTGTAACTTG 59.438 45.455 0.00 0.00 0.00 3.16
2302 2845 4.974275 GCATGATTCCAAATGATGAGTTCG 59.026 41.667 0.00 0.00 0.00 3.95
2303 2846 5.898174 TGCATGATTCCAAATGATGAGTTC 58.102 37.500 0.00 0.00 0.00 3.01
2304 2847 5.925506 TGCATGATTCCAAATGATGAGTT 57.074 34.783 0.00 0.00 0.00 3.01
2305 2848 5.739070 GCATGCATGATTCCAAATGATGAGT 60.739 40.000 30.64 0.00 0.00 3.41
2306 2849 4.686091 GCATGCATGATTCCAAATGATGAG 59.314 41.667 30.64 0.00 0.00 2.90
2619 3173 4.021916 AGTACTAGGGCAATACGAACTGT 58.978 43.478 0.00 0.00 0.00 3.55
2656 3210 0.100503 AATTAATCCTTGGCGCGCAC 59.899 50.000 34.42 22.27 0.00 5.34
2667 3221 1.388547 TCCTGGCGTGCAATTAATCC 58.611 50.000 0.00 0.00 0.00 3.01
2675 3229 1.078497 ATCGAATTCCTGGCGTGCA 60.078 52.632 0.00 0.00 0.00 4.57
2676 3230 1.643832 GATCGAATTCCTGGCGTGC 59.356 57.895 0.00 0.00 0.00 5.34
2677 3231 0.179073 AGGATCGAATTCCTGGCGTG 60.179 55.000 6.78 0.00 44.63 5.34
2725 3279 4.576879 GGAACGGAGTAGAATTTCCACTT 58.423 43.478 0.00 0.00 45.00 3.16
2764 3319 0.599558 TGACGTACCGACCTTTCCAG 59.400 55.000 0.00 0.00 0.00 3.86
3007 3564 3.182972 GCAGTCGCTCGTGTAAAAGTTAA 59.817 43.478 0.00 0.00 34.30 2.01
3023 3580 3.853330 CGATGTTGCCGGCAGTCG 61.853 66.667 31.84 31.84 38.88 4.18
3061 3619 7.008278 GCTAGTCGTTAAACAACTTTCTTAGC 58.992 38.462 0.00 0.00 0.00 3.09
3137 3715 3.082579 GCTCGGCGATTGGGAGAGT 62.083 63.158 11.27 0.00 0.00 3.24
3173 3751 7.389053 AGCAGAGTCCTGTTATTTCACTAAAAG 59.611 37.037 0.00 0.00 42.35 2.27
3174 3752 7.224297 AGCAGAGTCCTGTTATTTCACTAAAA 58.776 34.615 0.00 0.00 42.35 1.52
3175 3753 6.769512 AGCAGAGTCCTGTTATTTCACTAAA 58.230 36.000 0.00 0.00 42.35 1.85
3176 3754 6.360370 AGCAGAGTCCTGTTATTTCACTAA 57.640 37.500 0.00 0.00 42.35 2.24
3177 3755 5.105310 GGAGCAGAGTCCTGTTATTTCACTA 60.105 44.000 0.00 0.00 42.35 2.74
3178 3756 4.323104 GGAGCAGAGTCCTGTTATTTCACT 60.323 45.833 0.00 0.00 42.35 3.41
3179 3757 3.935828 GGAGCAGAGTCCTGTTATTTCAC 59.064 47.826 0.00 0.00 42.35 3.18
3180 3758 3.368427 CGGAGCAGAGTCCTGTTATTTCA 60.368 47.826 0.00 0.00 42.35 2.69
3181 3759 3.190874 CGGAGCAGAGTCCTGTTATTTC 58.809 50.000 0.00 0.00 42.35 2.17
3182 3760 2.567615 ACGGAGCAGAGTCCTGTTATTT 59.432 45.455 0.00 0.00 42.35 1.40
3183 3761 2.180276 ACGGAGCAGAGTCCTGTTATT 58.820 47.619 0.00 0.00 42.35 1.40
3184 3762 1.853963 ACGGAGCAGAGTCCTGTTAT 58.146 50.000 0.00 0.00 42.35 1.89
3185 3763 1.629043 AACGGAGCAGAGTCCTGTTA 58.371 50.000 0.00 0.00 42.35 2.41
3186 3764 0.759346 AAACGGAGCAGAGTCCTGTT 59.241 50.000 0.00 0.00 42.35 3.16
3187 3765 1.546476 CTAAACGGAGCAGAGTCCTGT 59.454 52.381 0.00 0.00 42.35 4.00
3188 3766 1.546476 ACTAAACGGAGCAGAGTCCTG 59.454 52.381 0.00 0.00 43.22 3.86
3189 3767 1.819903 GACTAAACGGAGCAGAGTCCT 59.180 52.381 0.00 0.00 34.00 3.85
3190 3768 1.819903 AGACTAAACGGAGCAGAGTCC 59.180 52.381 0.00 0.00 37.79 3.85
3191 3769 3.579335 AAGACTAAACGGAGCAGAGTC 57.421 47.619 0.00 0.00 37.41 3.36
3192 3770 3.555168 CCAAAGACTAAACGGAGCAGAGT 60.555 47.826 0.00 0.00 0.00 3.24
3193 3771 2.996621 CCAAAGACTAAACGGAGCAGAG 59.003 50.000 0.00 0.00 0.00 3.35
3194 3772 2.367567 ACCAAAGACTAAACGGAGCAGA 59.632 45.455 0.00 0.00 0.00 4.26
3195 3773 2.737252 GACCAAAGACTAAACGGAGCAG 59.263 50.000 0.00 0.00 0.00 4.24
3196 3774 2.103432 TGACCAAAGACTAAACGGAGCA 59.897 45.455 0.00 0.00 0.00 4.26
3197 3775 2.762745 TGACCAAAGACTAAACGGAGC 58.237 47.619 0.00 0.00 0.00 4.70
3198 3776 4.755123 ACATTGACCAAAGACTAAACGGAG 59.245 41.667 0.00 0.00 0.00 4.63
3199 3777 4.710324 ACATTGACCAAAGACTAAACGGA 58.290 39.130 0.00 0.00 0.00 4.69
3200 3778 5.238650 AGAACATTGACCAAAGACTAAACGG 59.761 40.000 0.00 0.00 0.00 4.44
3201 3779 6.018262 TGAGAACATTGACCAAAGACTAAACG 60.018 38.462 0.00 0.00 0.00 3.60
3202 3780 7.259290 TGAGAACATTGACCAAAGACTAAAC 57.741 36.000 0.00 0.00 0.00 2.01
3203 3781 7.873719 TTGAGAACATTGACCAAAGACTAAA 57.126 32.000 0.00 0.00 0.00 1.85
3204 3782 7.873719 TTTGAGAACATTGACCAAAGACTAA 57.126 32.000 0.00 0.00 0.00 2.24
3205 3783 8.463930 AATTTGAGAACATTGACCAAAGACTA 57.536 30.769 0.00 0.00 31.42 2.59
3206 3784 6.966534 ATTTGAGAACATTGACCAAAGACT 57.033 33.333 0.00 0.00 31.42 3.24
3207 3785 9.528018 TTTAATTTGAGAACATTGACCAAAGAC 57.472 29.630 0.00 0.00 31.42 3.01
3208 3786 9.528018 GTTTAATTTGAGAACATTGACCAAAGA 57.472 29.630 0.00 0.00 31.42 2.52
3209 3787 9.533253 AGTTTAATTTGAGAACATTGACCAAAG 57.467 29.630 0.00 0.00 31.42 2.77
3211 3789 9.959749 GTAGTTTAATTTGAGAACATTGACCAA 57.040 29.630 0.00 0.00 0.00 3.67
3212 3790 9.349713 AGTAGTTTAATTTGAGAACATTGACCA 57.650 29.630 0.00 0.00 0.00 4.02
3213 3791 9.827411 GAGTAGTTTAATTTGAGAACATTGACC 57.173 33.333 0.00 0.00 0.00 4.02
3214 3792 9.827411 GGAGTAGTTTAATTTGAGAACATTGAC 57.173 33.333 0.00 0.00 0.00 3.18
3215 3793 9.793259 AGGAGTAGTTTAATTTGAGAACATTGA 57.207 29.630 0.00 0.00 0.00 2.57
3227 3805 9.802039 TGGTTCACATTTAGGAGTAGTTTAATT 57.198 29.630 0.00 0.00 0.00 1.40
3228 3806 9.802039 TTGGTTCACATTTAGGAGTAGTTTAAT 57.198 29.630 0.00 0.00 0.00 1.40
3229 3807 9.059260 GTTGGTTCACATTTAGGAGTAGTTTAA 57.941 33.333 0.00 0.00 0.00 1.52
3230 3808 7.662669 GGTTGGTTCACATTTAGGAGTAGTTTA 59.337 37.037 0.00 0.00 0.00 2.01
3231 3809 6.489022 GGTTGGTTCACATTTAGGAGTAGTTT 59.511 38.462 0.00 0.00 0.00 2.66
3232 3810 6.002082 GGTTGGTTCACATTTAGGAGTAGTT 58.998 40.000 0.00 0.00 0.00 2.24
3233 3811 5.309806 AGGTTGGTTCACATTTAGGAGTAGT 59.690 40.000 0.00 0.00 0.00 2.73
3234 3812 5.805728 AGGTTGGTTCACATTTAGGAGTAG 58.194 41.667 0.00 0.00 0.00 2.57
3235 3813 5.836024 AGGTTGGTTCACATTTAGGAGTA 57.164 39.130 0.00 0.00 0.00 2.59
3236 3814 4.724279 AGGTTGGTTCACATTTAGGAGT 57.276 40.909 0.00 0.00 0.00 3.85
3237 3815 5.556915 TGTAGGTTGGTTCACATTTAGGAG 58.443 41.667 0.00 0.00 0.00 3.69
3238 3816 5.072600 ACTGTAGGTTGGTTCACATTTAGGA 59.927 40.000 0.00 0.00 0.00 2.94
3239 3817 5.313712 ACTGTAGGTTGGTTCACATTTAGG 58.686 41.667 0.00 0.00 0.00 2.69
3240 3818 6.877611 AACTGTAGGTTGGTTCACATTTAG 57.122 37.500 0.00 0.00 36.70 1.85
3253 3831 3.844211 TCTTAGCCATCCAACTGTAGGTT 59.156 43.478 0.00 0.00 38.93 3.50
3254 3832 3.450904 TCTTAGCCATCCAACTGTAGGT 58.549 45.455 0.00 0.00 0.00 3.08
3255 3833 3.181461 CCTCTTAGCCATCCAACTGTAGG 60.181 52.174 0.00 0.00 0.00 3.18
3256 3834 3.706594 TCCTCTTAGCCATCCAACTGTAG 59.293 47.826 0.00 0.00 0.00 2.74
3257 3835 3.451178 GTCCTCTTAGCCATCCAACTGTA 59.549 47.826 0.00 0.00 0.00 2.74
3258 3836 2.237392 GTCCTCTTAGCCATCCAACTGT 59.763 50.000 0.00 0.00 0.00 3.55
3259 3837 2.237143 TGTCCTCTTAGCCATCCAACTG 59.763 50.000 0.00 0.00 0.00 3.16
3260 3838 2.503356 CTGTCCTCTTAGCCATCCAACT 59.497 50.000 0.00 0.00 0.00 3.16
3261 3839 2.237392 ACTGTCCTCTTAGCCATCCAAC 59.763 50.000 0.00 0.00 0.00 3.77
3262 3840 2.237143 CACTGTCCTCTTAGCCATCCAA 59.763 50.000 0.00 0.00 0.00 3.53
3263 3841 1.833630 CACTGTCCTCTTAGCCATCCA 59.166 52.381 0.00 0.00 0.00 3.41
3264 3842 1.834263 ACACTGTCCTCTTAGCCATCC 59.166 52.381 0.00 0.00 0.00 3.51
3265 3843 3.618690 AACACTGTCCTCTTAGCCATC 57.381 47.619 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.