Multiple sequence alignment - TraesCS1D01G262800

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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 TraesCS1D01G262800 chr1D 100.000 4333 0 0 1 4333 356947858 356943526 0.000000e+00 8002.0
1 TraesCS1D01G262800 chr1D 85.222 203 22 5 402 600 303303781 303303979 7.350000e-48 202.0
2 TraesCS1D01G262800 chr1D 83.000 200 26 4 402 597 38280806 38281001 1.600000e-39 174.0
3 TraesCS1D01G262800 chr1A 92.999 3728 169 40 661 4333 458230386 458226696 0.000000e+00 5354.0
4 TraesCS1D01G262800 chr1B 93.950 1471 56 14 642 2091 480481342 480479884 0.000000e+00 2193.0
5 TraesCS1D01G262800 chr1B 96.686 1207 28 6 2199 3399 480479521 480478321 0.000000e+00 1997.0
6 TraesCS1D01G262800 chr1B 96.386 498 13 2 3841 4333 480477588 480477091 0.000000e+00 815.0
7 TraesCS1D01G262800 chr1B 92.292 480 12 4 3401 3856 480478080 480477602 0.000000e+00 658.0
8 TraesCS1D01G262800 chr1B 80.000 290 41 12 95 378 480481742 480481464 9.500000e-47 198.0
9 TraesCS1D01G262800 chr6D 79.602 402 50 22 1 383 419441464 419441076 4.300000e-65 259.0
10 TraesCS1D01G262800 chr5A 87.065 201 19 4 402 597 237602470 237602668 2.030000e-53 220.0
11 TraesCS1D01G262800 chr5A 83.168 202 22 7 402 597 708356325 708356130 1.600000e-39 174.0
12 TraesCS1D01G262800 chr4A 85.500 200 23 3 402 597 504667333 504667136 2.040000e-48 204.0
13 TraesCS1D01G262800 chr7A 85.000 200 21 6 402 597 450090935 450091129 1.230000e-45 195.0
14 TraesCS1D01G262800 chr7A 85.052 194 22 4 404 593 214782771 214782961 1.590000e-44 191.0
15 TraesCS1D01G262800 chr7A 77.446 368 51 18 40 380 245465718 245466080 1.590000e-44 191.0
16 TraesCS1D01G262800 chr7A 82.022 89 13 3 131 217 432969105 432969192 6.010000e-09 73.1
17 TraesCS1D01G262800 chr7D 83.173 208 24 8 402 603 216078806 216078604 3.440000e-41 180.0
18 TraesCS1D01G262800 chr7D 88.571 70 8 0 149 218 500220283 500220352 7.720000e-13 86.1
19 TraesCS1D01G262800 chr2A 83.500 200 25 4 402 597 703121260 703121455 3.440000e-41 180.0
20 TraesCS1D01G262800 chr2A 75.097 257 40 15 131 367 131698408 131698660 9.920000e-17 99.0
21 TraesCS1D01G262800 chr3B 74.696 411 63 24 1 380 482259447 482259047 1.260000e-30 145.0
22 TraesCS1D01G262800 chr6B 84.091 88 13 1 131 217 689982419 689982506 2.780000e-12 84.2
23 TraesCS1D01G262800 chr3A 83.333 78 12 1 136 212 453319758 453319835 2.160000e-08 71.3
24 TraesCS1D01G262800 chr4D 84.507 71 10 1 149 218 472497237 472497307 7.780000e-08 69.4


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 TraesCS1D01G262800 chr1D 356943526 356947858 4332 True 8002.0 8002 100.0000 1 4333 1 chr1D.!!$R1 4332
1 TraesCS1D01G262800 chr1A 458226696 458230386 3690 True 5354.0 5354 92.9990 661 4333 1 chr1A.!!$R1 3672
2 TraesCS1D01G262800 chr1B 480477091 480481742 4651 True 1172.2 2193 91.8628 95 4333 5 chr1B.!!$R1 4238

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
461 475 0.112412 ATCCCTTTTTGCGTGGGTCT 59.888 50.000 0.00 0.0 41.58 3.85 F
464 478 0.310854 CCTTTTTGCGTGGGTCTCAC 59.689 55.000 0.00 0.0 42.74 3.51 F
595 609 0.392706 CTTTGGAACCAAACAGGCCC 59.607 55.000 14.02 0.0 43.14 5.80 F
621 635 0.684535 TCGGTGCATGACTCTTTGGA 59.315 50.000 0.00 0.0 0.00 3.53 F
1134 1179 0.747255 GCTCGATCTGCTCTAACCCA 59.253 55.000 0.00 0.0 0.00 4.51 F
1548 1602 1.067915 TGCGTGCCAAAAATTAGAGCC 60.068 47.619 0.00 0.0 0.00 4.70 F
2942 3346 1.541310 TTCCTCCGACGATGGTTGCT 61.541 55.000 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2167 0.110486 CCCACTTAGGTTGCACCACT 59.890 55.000 7.86 0.00 41.95 4.00 R
2105 2176 2.795329 CAAGTTGCATCCCACTTAGGT 58.205 47.619 1.31 0.00 34.66 3.08 R
2365 2764 5.761726 TCAGACATGATGCTAATTGATCACC 59.238 40.000 0.00 0.00 31.47 4.02 R
2444 2843 6.596309 AGTGACTGAGTTACTGAATCATCA 57.404 37.500 9.38 0.00 31.25 3.07 R
2783 3182 0.105964 TGGACACACTACAGCGCTTT 59.894 50.000 7.50 3.33 0.00 3.51 R
3202 3608 1.899814 AGAATGACAACAGACCGGCTA 59.100 47.619 0.00 0.00 0.00 3.93 R
4116 4820 1.443194 CGTGCTGCAGATTTGGTGC 60.443 57.895 20.43 0.00 41.59 5.01 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
33 34 3.587933 GAGGAGGAGCGTCGCGAT 61.588 66.667 14.06 0.00 0.00 4.58
34 35 3.815569 GAGGAGGAGCGTCGCGATG 62.816 68.421 23.84 23.84 0.00 3.84
46 47 4.292178 GCGATGCGGAGGAGGAGG 62.292 72.222 0.00 0.00 0.00 4.30
47 48 2.519541 CGATGCGGAGGAGGAGGA 60.520 66.667 0.00 0.00 0.00 3.71
48 49 2.560119 CGATGCGGAGGAGGAGGAG 61.560 68.421 0.00 0.00 0.00 3.69
49 50 2.123077 ATGCGGAGGAGGAGGAGG 60.123 66.667 0.00 0.00 0.00 4.30
50 51 2.648613 GATGCGGAGGAGGAGGAGGA 62.649 65.000 0.00 0.00 0.00 3.71
51 52 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
52 53 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
53 54 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
54 55 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
55 56 1.152546 GAGGAGGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
56 57 2.520741 GGAGGAGGAGGAGGAGCG 60.521 72.222 0.00 0.00 0.00 5.03
57 58 3.223589 GAGGAGGAGGAGGAGCGC 61.224 72.222 0.00 0.00 0.00 5.92
58 59 4.851214 AGGAGGAGGAGGAGCGCC 62.851 72.222 2.29 0.00 0.00 6.53
126 127 1.384989 ATGACGTCGGTAGAGCCTGG 61.385 60.000 11.62 0.00 34.25 4.45
132 133 2.799371 GGTAGAGCCTGGTCGACG 59.201 66.667 9.92 0.00 0.00 5.12
134 135 2.045131 GTAGAGCCTGGTCGACGGT 61.045 63.158 9.92 0.88 0.00 4.83
177 179 2.278206 CGCTCATCGACCTCACCG 60.278 66.667 0.00 0.00 41.67 4.94
186 188 4.608774 ACCTCACCGGTCCCGACA 62.609 66.667 2.59 0.00 44.93 4.35
198 200 2.019951 CCCGACAACGACGACAAGG 61.020 63.158 0.00 0.00 42.66 3.61
204 206 2.853290 AACGACGACAAGGACGCCT 61.853 57.895 0.00 0.00 33.87 5.52
258 263 6.671190 AGTTAATGTAAAAGTAAACCCGTGC 58.329 36.000 0.00 0.00 0.00 5.34
263 268 1.601166 AAAGTAAACCCGTGCACTCC 58.399 50.000 16.19 0.00 0.00 3.85
264 269 0.763035 AAGTAAACCCGTGCACTCCT 59.237 50.000 16.19 0.00 0.00 3.69
283 297 0.538516 TGCGGGCCGGCATTAATATT 60.539 50.000 31.99 0.00 38.17 1.28
316 330 8.780482 ACGTTTTTATTTTTCAAAATGTTTGCG 58.220 25.926 7.63 8.73 38.42 4.85
317 331 8.249108 CGTTTTTATTTTTCAAAATGTTTGCGG 58.751 29.630 7.63 0.00 38.90 5.69
318 332 7.670894 TTTTATTTTTCAAAATGTTTGCGGC 57.329 28.000 7.63 0.00 38.90 6.53
319 333 4.889832 ATTTTTCAAAATGTTTGCGGCA 57.110 31.818 0.00 0.00 37.24 5.69
320 334 4.685169 TTTTTCAAAATGTTTGCGGCAA 57.315 31.818 12.11 12.11 0.00 4.52
321 335 4.889832 TTTTCAAAATGTTTGCGGCAAT 57.110 31.818 17.19 0.00 0.00 3.56
322 336 3.874400 TTCAAAATGTTTGCGGCAATG 57.126 38.095 17.19 10.62 0.00 2.82
361 375 2.267045 AAAAATGAGTCGGGCCAGC 58.733 52.632 4.39 0.00 0.00 4.85
378 392 2.278336 CATTGGATGCAAGCGCCG 60.278 61.111 2.29 0.00 37.32 6.46
380 394 2.475466 ATTGGATGCAAGCGCCGAG 61.475 57.895 2.29 0.00 37.32 4.63
399 413 4.457496 CGTGGAGAGCGCCATGGT 62.457 66.667 14.67 0.00 40.52 3.55
400 414 2.512515 GTGGAGAGCGCCATGGTC 60.513 66.667 14.67 2.83 45.59 4.02
406 420 3.386543 GAGCGCCATGGTCATAAGT 57.613 52.632 14.67 0.00 44.60 2.24
408 422 0.541392 AGCGCCATGGTCATAAGTCA 59.459 50.000 14.67 0.00 0.00 3.41
409 423 1.141657 AGCGCCATGGTCATAAGTCAT 59.858 47.619 14.67 0.00 0.00 3.06
410 424 2.368548 AGCGCCATGGTCATAAGTCATA 59.631 45.455 14.67 0.00 0.00 2.15
411 425 3.138304 GCGCCATGGTCATAAGTCATAA 58.862 45.455 14.67 0.00 0.00 1.90
412 426 3.187227 GCGCCATGGTCATAAGTCATAAG 59.813 47.826 14.67 0.00 0.00 1.73
414 428 4.816385 CGCCATGGTCATAAGTCATAAGTT 59.184 41.667 14.67 0.00 0.00 2.66
415 429 5.277490 CGCCATGGTCATAAGTCATAAGTTG 60.277 44.000 14.67 0.00 0.00 3.16
417 431 5.824624 CCATGGTCATAAGTCATAAGTTGCT 59.175 40.000 2.57 0.00 0.00 3.91
418 432 6.017605 CCATGGTCATAAGTCATAAGTTGCTC 60.018 42.308 2.57 0.00 0.00 4.26
419 433 5.428253 TGGTCATAAGTCATAAGTTGCTCC 58.572 41.667 0.00 0.00 0.00 4.70
422 436 5.294552 GTCATAAGTCATAAGTTGCTCCACC 59.705 44.000 0.00 0.00 0.00 4.61
423 437 2.789409 AGTCATAAGTTGCTCCACCC 57.211 50.000 0.00 0.00 0.00 4.61
424 438 1.282157 AGTCATAAGTTGCTCCACCCC 59.718 52.381 0.00 0.00 0.00 4.95
425 439 1.004277 GTCATAAGTTGCTCCACCCCA 59.996 52.381 0.00 0.00 0.00 4.96
426 440 1.707989 TCATAAGTTGCTCCACCCCAA 59.292 47.619 0.00 0.00 0.00 4.12
427 441 1.818674 CATAAGTTGCTCCACCCCAAC 59.181 52.381 0.00 0.00 41.13 3.77
428 442 3.674278 AGTTGCTCCACCCCAACT 58.326 55.556 0.56 0.56 44.86 3.16
429 443 1.930520 AGTTGCTCCACCCCAACTT 59.069 52.632 0.56 0.00 46.86 2.66
431 445 1.497286 AGTTGCTCCACCCCAACTTAA 59.503 47.619 0.56 0.00 46.86 1.85
432 446 1.611977 GTTGCTCCACCCCAACTTAAC 59.388 52.381 0.00 0.00 38.55 2.01
433 447 1.145571 TGCTCCACCCCAACTTAACT 58.854 50.000 0.00 0.00 0.00 2.24
436 450 3.079578 GCTCCACCCCAACTTAACTTAC 58.920 50.000 0.00 0.00 0.00 2.34
437 451 3.497227 GCTCCACCCCAACTTAACTTACA 60.497 47.826 0.00 0.00 0.00 2.41
438 452 4.721132 CTCCACCCCAACTTAACTTACAA 58.279 43.478 0.00 0.00 0.00 2.41
441 455 5.771165 TCCACCCCAACTTAACTTACAAATC 59.229 40.000 0.00 0.00 0.00 2.17
442 456 5.536916 CCACCCCAACTTAACTTACAAATCA 59.463 40.000 0.00 0.00 0.00 2.57
443 457 6.210584 CCACCCCAACTTAACTTACAAATCAT 59.789 38.462 0.00 0.00 0.00 2.45
444 458 7.312899 CACCCCAACTTAACTTACAAATCATC 58.687 38.462 0.00 0.00 0.00 2.92
445 459 6.436218 ACCCCAACTTAACTTACAAATCATCC 59.564 38.462 0.00 0.00 0.00 3.51
446 460 6.127451 CCCCAACTTAACTTACAAATCATCCC 60.127 42.308 0.00 0.00 0.00 3.85
447 461 6.663523 CCCAACTTAACTTACAAATCATCCCT 59.336 38.462 0.00 0.00 0.00 4.20
448 462 7.178451 CCCAACTTAACTTACAAATCATCCCTT 59.822 37.037 0.00 0.00 0.00 3.95
449 463 8.585018 CCAACTTAACTTACAAATCATCCCTTT 58.415 33.333 0.00 0.00 0.00 3.11
450 464 9.981114 CAACTTAACTTACAAATCATCCCTTTT 57.019 29.630 0.00 0.00 0.00 2.27
452 466 9.981114 ACTTAACTTACAAATCATCCCTTTTTG 57.019 29.630 0.00 0.00 36.62 2.44
453 467 8.825667 TTAACTTACAAATCATCCCTTTTTGC 57.174 30.769 0.00 0.00 34.47 3.68
454 468 5.469479 ACTTACAAATCATCCCTTTTTGCG 58.531 37.500 0.00 0.00 34.47 4.85
458 472 1.185315 ATCATCCCTTTTTGCGTGGG 58.815 50.000 0.00 0.00 42.20 4.61
459 473 0.178975 TCATCCCTTTTTGCGTGGGT 60.179 50.000 0.00 0.00 41.58 4.51
460 474 0.243636 CATCCCTTTTTGCGTGGGTC 59.756 55.000 0.00 0.00 41.58 4.46
461 475 0.112412 ATCCCTTTTTGCGTGGGTCT 59.888 50.000 0.00 0.00 41.58 3.85
462 476 0.536460 TCCCTTTTTGCGTGGGTCTC 60.536 55.000 0.00 0.00 41.58 3.36
463 477 0.821711 CCCTTTTTGCGTGGGTCTCA 60.822 55.000 0.00 0.00 36.32 3.27
464 478 0.310854 CCTTTTTGCGTGGGTCTCAC 59.689 55.000 0.00 0.00 42.74 3.51
465 479 0.310854 CTTTTTGCGTGGGTCTCACC 59.689 55.000 0.00 0.00 43.23 4.02
466 480 0.394488 TTTTTGCGTGGGTCTCACCA 60.394 50.000 0.00 0.00 43.23 4.17
478 492 6.894735 TGGGTCTCACCACCTTTATATTAA 57.105 37.500 0.00 0.00 41.02 1.40
479 493 7.273457 TGGGTCTCACCACCTTTATATTAAA 57.727 36.000 0.00 0.00 41.02 1.52
480 494 7.700846 TGGGTCTCACCACCTTTATATTAAAA 58.299 34.615 0.00 0.00 41.02 1.52
481 495 8.171400 TGGGTCTCACCACCTTTATATTAAAAA 58.829 33.333 0.00 0.00 41.02 1.94
502 516 6.824305 AAAACAAGATGAGAAGGTATGGTG 57.176 37.500 0.00 0.00 0.00 4.17
503 517 5.762179 AACAAGATGAGAAGGTATGGTGA 57.238 39.130 0.00 0.00 0.00 4.02
504 518 5.350504 ACAAGATGAGAAGGTATGGTGAG 57.649 43.478 0.00 0.00 0.00 3.51
505 519 4.163078 ACAAGATGAGAAGGTATGGTGAGG 59.837 45.833 0.00 0.00 0.00 3.86
506 520 4.000928 AGATGAGAAGGTATGGTGAGGT 57.999 45.455 0.00 0.00 0.00 3.85
507 521 3.708631 AGATGAGAAGGTATGGTGAGGTG 59.291 47.826 0.00 0.00 0.00 4.00
508 522 3.184382 TGAGAAGGTATGGTGAGGTGA 57.816 47.619 0.00 0.00 0.00 4.02
509 523 2.832129 TGAGAAGGTATGGTGAGGTGAC 59.168 50.000 0.00 0.00 0.00 3.67
511 525 3.515901 GAGAAGGTATGGTGAGGTGACTT 59.484 47.826 0.00 0.00 44.43 3.01
512 526 4.684724 AGAAGGTATGGTGAGGTGACTTA 58.315 43.478 0.00 0.00 44.43 2.24
513 527 5.281314 AGAAGGTATGGTGAGGTGACTTAT 58.719 41.667 0.00 0.00 44.43 1.73
514 528 6.441222 AGAAGGTATGGTGAGGTGACTTATA 58.559 40.000 0.00 0.00 44.43 0.98
515 529 6.324254 AGAAGGTATGGTGAGGTGACTTATAC 59.676 42.308 0.00 0.00 44.43 1.47
516 530 5.525484 AGGTATGGTGAGGTGACTTATACA 58.475 41.667 0.00 0.00 44.43 2.29
517 531 6.143915 AGGTATGGTGAGGTGACTTATACAT 58.856 40.000 0.00 0.00 44.43 2.29
518 532 6.267928 AGGTATGGTGAGGTGACTTATACATC 59.732 42.308 0.00 0.00 44.43 3.06
519 533 6.041637 GGTATGGTGAGGTGACTTATACATCA 59.958 42.308 0.00 0.00 44.43 3.07
520 534 5.598416 TGGTGAGGTGACTTATACATCAG 57.402 43.478 0.00 0.00 44.43 2.90
521 535 4.405680 TGGTGAGGTGACTTATACATCAGG 59.594 45.833 0.00 0.00 44.43 3.86
522 536 4.202264 GGTGAGGTGACTTATACATCAGGG 60.202 50.000 0.00 0.00 44.43 4.45
523 537 3.967326 TGAGGTGACTTATACATCAGGGG 59.033 47.826 0.00 0.00 44.43 4.79
524 538 4.223953 GAGGTGACTTATACATCAGGGGA 58.776 47.826 0.00 0.00 44.43 4.81
525 539 4.832492 AGGTGACTTATACATCAGGGGAT 58.168 43.478 0.00 0.00 37.44 3.85
526 540 5.977533 AGGTGACTTATACATCAGGGGATA 58.022 41.667 0.00 0.00 37.44 2.59
527 541 6.390504 AGGTGACTTATACATCAGGGGATAA 58.609 40.000 0.00 0.00 37.44 1.75
528 542 7.025620 AGGTGACTTATACATCAGGGGATAAT 58.974 38.462 0.00 0.00 37.44 1.28
529 543 7.181125 AGGTGACTTATACATCAGGGGATAATC 59.819 40.741 0.00 0.00 37.44 1.75
530 544 7.038302 GGTGACTTATACATCAGGGGATAATCA 60.038 40.741 0.00 0.00 30.87 2.57
531 545 8.375506 GTGACTTATACATCAGGGGATAATCAA 58.624 37.037 0.00 0.00 30.87 2.57
532 546 8.944138 TGACTTATACATCAGGGGATAATCAAA 58.056 33.333 0.00 0.00 30.87 2.69
533 547 9.442047 GACTTATACATCAGGGGATAATCAAAG 57.558 37.037 0.00 0.00 30.87 2.77
534 548 9.170890 ACTTATACATCAGGGGATAATCAAAGA 57.829 33.333 0.00 0.00 30.87 2.52
535 549 9.664332 CTTATACATCAGGGGATAATCAAAGAG 57.336 37.037 0.00 0.00 30.87 2.85
536 550 5.316158 ACATCAGGGGATAATCAAAGAGG 57.684 43.478 0.00 0.00 30.87 3.69
537 551 3.864789 TCAGGGGATAATCAAAGAGGC 57.135 47.619 0.00 0.00 0.00 4.70
538 552 2.443255 TCAGGGGATAATCAAAGAGGCC 59.557 50.000 0.00 0.00 0.00 5.19
539 553 2.444766 CAGGGGATAATCAAAGAGGCCT 59.555 50.000 3.86 3.86 0.00 5.19
540 554 2.444766 AGGGGATAATCAAAGAGGCCTG 59.555 50.000 12.00 0.00 0.00 4.85
541 555 2.443255 GGGGATAATCAAAGAGGCCTGA 59.557 50.000 12.00 1.10 0.00 3.86
542 556 3.481453 GGGATAATCAAAGAGGCCTGAC 58.519 50.000 12.00 0.00 0.00 3.51
543 557 3.137360 GGGATAATCAAAGAGGCCTGACT 59.863 47.826 12.00 0.00 0.00 3.41
544 558 4.385754 GGGATAATCAAAGAGGCCTGACTT 60.386 45.833 12.00 5.16 0.00 3.01
545 559 5.163195 GGGATAATCAAAGAGGCCTGACTTA 60.163 44.000 12.00 3.79 0.00 2.24
546 560 6.466470 GGGATAATCAAAGAGGCCTGACTTAT 60.466 42.308 12.00 8.29 0.00 1.73
547 561 7.256691 GGGATAATCAAAGAGGCCTGACTTATA 60.257 40.741 12.00 0.06 0.00 0.98
548 562 8.157476 GGATAATCAAAGAGGCCTGACTTATAA 58.843 37.037 12.00 0.00 0.00 0.98
549 563 9.213799 GATAATCAAAGAGGCCTGACTTATAAG 57.786 37.037 12.00 11.05 0.00 1.73
550 564 6.567602 ATCAAAGAGGCCTGACTTATAAGT 57.432 37.500 18.05 18.05 43.16 2.24
571 585 9.823647 ATAAGTCACACCTGATTTATAAGTCAG 57.176 33.333 24.08 24.08 37.48 3.51
586 600 2.341846 GTCAGGTGACTTTGGAACCA 57.658 50.000 2.72 0.00 41.65 3.67
587 601 2.650322 GTCAGGTGACTTTGGAACCAA 58.350 47.619 1.83 1.83 41.65 3.67
588 602 3.020984 GTCAGGTGACTTTGGAACCAAA 58.979 45.455 16.54 16.54 42.71 3.28
589 603 3.020984 TCAGGTGACTTTGGAACCAAAC 58.979 45.455 14.02 7.30 40.51 2.93
590 604 2.757868 CAGGTGACTTTGGAACCAAACA 59.242 45.455 14.02 9.54 40.51 2.83
591 605 3.023832 AGGTGACTTTGGAACCAAACAG 58.976 45.455 14.02 8.87 40.51 3.16
592 606 2.100749 GGTGACTTTGGAACCAAACAGG 59.899 50.000 14.02 8.31 40.51 4.00
593 607 1.754226 TGACTTTGGAACCAAACAGGC 59.246 47.619 14.02 9.10 43.14 4.85
594 608 1.068588 GACTTTGGAACCAAACAGGCC 59.931 52.381 14.02 0.00 43.14 5.19
595 609 0.392706 CTTTGGAACCAAACAGGCCC 59.607 55.000 14.02 0.00 43.14 5.80
598 612 0.854218 TGGAACCAAACAGGCCCTTA 59.146 50.000 0.00 0.00 43.14 2.69
599 613 1.431243 TGGAACCAAACAGGCCCTTAT 59.569 47.619 0.00 0.00 43.14 1.73
603 617 2.525368 ACCAAACAGGCCCTTATGTTC 58.475 47.619 8.41 0.00 43.14 3.18
604 618 1.472480 CCAAACAGGCCCTTATGTTCG 59.528 52.381 8.41 0.00 38.66 3.95
610 624 0.751643 GGCCCTTATGTTCGGTGCAT 60.752 55.000 0.00 0.00 0.00 3.96
616 630 3.525537 CTTATGTTCGGTGCATGACTCT 58.474 45.455 0.00 0.00 0.00 3.24
618 632 2.254546 TGTTCGGTGCATGACTCTTT 57.745 45.000 0.00 0.00 0.00 2.52
620 634 1.197721 GTTCGGTGCATGACTCTTTGG 59.802 52.381 0.00 0.00 0.00 3.28
621 635 0.684535 TCGGTGCATGACTCTTTGGA 59.315 50.000 0.00 0.00 0.00 3.53
622 636 1.278985 TCGGTGCATGACTCTTTGGAT 59.721 47.619 0.00 0.00 0.00 3.41
625 639 1.133790 GTGCATGACTCTTTGGATGCC 59.866 52.381 0.00 0.00 40.45 4.40
626 640 1.005097 TGCATGACTCTTTGGATGCCT 59.995 47.619 0.00 0.00 40.45 4.75
627 641 2.239402 TGCATGACTCTTTGGATGCCTA 59.761 45.455 0.00 0.00 40.45 3.93
628 642 2.877168 GCATGACTCTTTGGATGCCTAG 59.123 50.000 0.00 0.00 36.08 3.02
632 646 5.537300 TGACTCTTTGGATGCCTAGTATC 57.463 43.478 0.00 0.00 0.00 2.24
633 647 4.038042 TGACTCTTTGGATGCCTAGTATCG 59.962 45.833 0.00 0.00 0.00 2.92
634 648 4.215908 ACTCTTTGGATGCCTAGTATCGA 58.784 43.478 0.00 0.00 0.00 3.59
635 649 4.038162 ACTCTTTGGATGCCTAGTATCGAC 59.962 45.833 0.00 0.00 0.00 4.20
636 650 3.004419 TCTTTGGATGCCTAGTATCGACG 59.996 47.826 0.00 0.00 0.00 5.12
637 651 1.244816 TGGATGCCTAGTATCGACGG 58.755 55.000 0.00 0.00 0.00 4.79
640 654 0.882474 ATGCCTAGTATCGACGGCTC 59.118 55.000 11.22 0.00 42.90 4.70
659 673 3.614588 CTCGACGTTCCCAAACTTTTTC 58.385 45.455 0.00 0.00 32.95 2.29
674 692 8.606602 CCAAACTTTTTCTTTTCTTTGAGATGG 58.393 33.333 0.00 0.00 0.00 3.51
939 981 3.077556 TCTTGGCGGAGGAGGAGC 61.078 66.667 0.00 0.00 0.00 4.70
977 1022 3.494336 CGGTCGCCTCGTAGACGT 61.494 66.667 1.46 0.00 40.80 4.34
1134 1179 0.747255 GCTCGATCTGCTCTAACCCA 59.253 55.000 0.00 0.00 0.00 4.51
1149 1194 3.461773 CCACCGGGATCTGCGAGT 61.462 66.667 6.32 0.00 35.59 4.18
1153 1198 2.125326 CCGGGATCTGCGAGTGGTA 61.125 63.158 0.00 0.00 0.00 3.25
1177 1222 1.201429 AGATCTGGTTGAGGGGCGTT 61.201 55.000 0.00 0.00 0.00 4.84
1223 1268 1.227102 CCGCTGATTGGGGGATTCA 59.773 57.895 0.00 0.00 44.18 2.57
1231 1276 1.692534 TTGGGGGATTCAGGATTCCA 58.307 50.000 5.29 0.00 34.72 3.53
1383 1428 5.233689 CAGTTTAACCGTAAGATCCCGATTC 59.766 44.000 0.00 0.00 43.02 2.52
1423 1468 2.124570 CGCCTCAGGTGGATTGGG 60.125 66.667 0.00 0.00 0.00 4.12
1432 1477 1.640670 AGGTGGATTGGGTTGCTGTAT 59.359 47.619 0.00 0.00 0.00 2.29
1548 1602 1.067915 TGCGTGCCAAAAATTAGAGCC 60.068 47.619 0.00 0.00 0.00 4.70
1727 1782 2.478894 CACCACTTTATCGTTTGTCGCT 59.521 45.455 0.00 0.00 39.67 4.93
1728 1783 3.059188 CACCACTTTATCGTTTGTCGCTT 60.059 43.478 0.00 0.00 39.67 4.68
1786 1853 6.696583 TGAACTACATCACTGCATTGTTTTTG 59.303 34.615 3.77 1.69 0.00 2.44
1799 1866 7.020010 TGCATTGTTTTTGTTGCTTTTACAAG 58.980 30.769 0.00 0.00 36.89 3.16
1898 1966 8.621286 CCTTGATAAAGCGGAAGTTTAATACAT 58.379 33.333 0.00 0.00 32.85 2.29
1916 1986 9.647797 TTAATACATAATCATGTCATACGGGTC 57.352 33.333 0.00 0.00 44.42 4.46
2086 2157 7.445402 GCCTCTTGCTCTAAATCATAACCATTA 59.555 37.037 0.00 0.00 36.87 1.90
2090 2161 9.888878 CTTGCTCTAAATCATAACCATTACATG 57.111 33.333 0.00 0.00 0.00 3.21
2100 2171 7.995289 TCATAACCATTACATGCTTTTAGTGG 58.005 34.615 5.95 5.95 32.63 4.00
2105 2176 5.468592 CATTACATGCTTTTAGTGGTGCAA 58.531 37.500 0.00 0.00 38.96 4.08
2365 2764 6.484308 TCTGAACCAACATCATAGCATATGTG 59.516 38.462 4.29 0.00 36.47 3.21
2444 2843 7.604657 TGTAGGGTTTCCATTTAAACAACAT 57.395 32.000 0.00 0.00 40.42 2.71
2741 3140 4.202245 AGCAATAGCCGTAAAAGTGAGA 57.798 40.909 0.00 0.00 43.56 3.27
2742 3141 4.575885 AGCAATAGCCGTAAAAGTGAGAA 58.424 39.130 0.00 0.00 43.56 2.87
2857 3256 4.497507 GGAATTTTGCCGCTATGGTTAGAC 60.498 45.833 0.00 0.00 41.21 2.59
2894 3293 3.181329 TCCTGTGCCTCTCATTTCCTTA 58.819 45.455 0.00 0.00 0.00 2.69
2895 3294 3.587061 TCCTGTGCCTCTCATTTCCTTAA 59.413 43.478 0.00 0.00 0.00 1.85
2896 3295 3.691609 CCTGTGCCTCTCATTTCCTTAAC 59.308 47.826 0.00 0.00 0.00 2.01
2897 3296 3.686016 TGTGCCTCTCATTTCCTTAACC 58.314 45.455 0.00 0.00 0.00 2.85
2942 3346 1.541310 TTCCTCCGACGATGGTTGCT 61.541 55.000 0.00 0.00 0.00 3.91
3004 3410 6.399639 TGTTGTTCTATTTTTCAAGGTCCC 57.600 37.500 0.00 0.00 0.00 4.46
3737 4407 8.596380 GCTACACAAACTTCTTATGATGACTAC 58.404 37.037 0.00 0.00 0.00 2.73
3800 4470 8.291032 GCTCGTAGCCTCGTATTATCATATTAT 58.709 37.037 0.00 0.00 34.48 1.28
3998 4701 7.083062 TCTGTCATCCATCTAAAGGCATAAT 57.917 36.000 0.00 0.00 0.00 1.28
4275 4981 2.022934 CCGAGGAAGGTCTACTGTACC 58.977 57.143 0.00 0.00 37.27 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.587933 ATCGCGACGCTCCTCCTC 61.588 66.667 12.93 0.00 0.00 3.71
17 18 3.893763 CATCGCGACGCTCCTCCT 61.894 66.667 12.93 0.00 0.00 3.69
29 30 4.292178 CCTCCTCCTCCGCATCGC 62.292 72.222 0.00 0.00 0.00 4.58
30 31 2.519541 TCCTCCTCCTCCGCATCG 60.520 66.667 0.00 0.00 0.00 3.84
31 32 2.206536 CCTCCTCCTCCTCCGCATC 61.207 68.421 0.00 0.00 0.00 3.91
32 33 2.123077 CCTCCTCCTCCTCCGCAT 60.123 66.667 0.00 0.00 0.00 4.73
33 34 3.347590 TCCTCCTCCTCCTCCGCA 61.348 66.667 0.00 0.00 0.00 5.69
34 35 2.520741 CTCCTCCTCCTCCTCCGC 60.521 72.222 0.00 0.00 0.00 5.54
35 36 2.197324 CCTCCTCCTCCTCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
36 37 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
37 38 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
38 39 3.024217 GCTCCTCCTCCTCCTCCT 58.976 66.667 0.00 0.00 0.00 3.69
39 40 2.520741 CGCTCCTCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
40 41 3.223589 GCGCTCCTCCTCCTCCTC 61.224 72.222 0.00 0.00 0.00 3.71
41 42 4.851214 GGCGCTCCTCCTCCTCCT 62.851 72.222 7.64 0.00 0.00 3.69
42 43 4.851214 AGGCGCTCCTCCTCCTCC 62.851 72.222 7.64 0.00 38.72 4.30
43 44 2.762043 AAGGCGCTCCTCCTCCTC 60.762 66.667 7.64 0.00 43.40 3.71
44 45 3.080121 CAAGGCGCTCCTCCTCCT 61.080 66.667 7.64 0.00 43.40 3.69
45 46 4.847444 GCAAGGCGCTCCTCCTCC 62.847 72.222 7.64 0.00 43.40 4.30
46 47 4.847444 GGCAAGGCGCTCCTCCTC 62.847 72.222 7.64 0.00 43.40 3.71
100 101 3.405592 TACCGACGTCATCTGCCGC 62.406 63.158 17.16 0.00 0.00 6.53
101 102 1.298413 CTACCGACGTCATCTGCCG 60.298 63.158 17.16 0.00 0.00 5.69
102 103 0.029567 CTCTACCGACGTCATCTGCC 59.970 60.000 17.16 0.00 0.00 4.85
103 104 0.592754 GCTCTACCGACGTCATCTGC 60.593 60.000 17.16 7.83 0.00 4.26
104 105 0.029567 GGCTCTACCGACGTCATCTG 59.970 60.000 17.16 3.12 0.00 2.90
105 106 0.107116 AGGCTCTACCGACGTCATCT 60.107 55.000 17.16 0.00 46.52 2.90
106 107 0.029567 CAGGCTCTACCGACGTCATC 59.970 60.000 17.16 0.00 46.52 2.92
107 108 1.384989 CCAGGCTCTACCGACGTCAT 61.385 60.000 17.16 5.40 46.52 3.06
108 109 2.044555 CCAGGCTCTACCGACGTCA 61.045 63.158 17.16 0.00 46.52 4.35
116 117 2.045131 ACCGTCGACCAGGCTCTAC 61.045 63.158 10.58 0.00 0.00 2.59
126 127 1.068585 ACAAGGGAACACCGTCGAC 59.931 57.895 5.18 5.18 46.96 4.20
132 133 2.564721 GCCAGCACAAGGGAACACC 61.565 63.158 0.00 0.00 40.67 4.16
134 135 2.203480 GGCCAGCACAAGGGAACA 60.203 61.111 0.00 0.00 0.00 3.18
177 179 2.429739 GTCGTCGTTGTCGGGACC 60.430 66.667 0.00 0.00 36.08 4.46
179 181 1.008194 CTTGTCGTCGTTGTCGGGA 60.008 57.895 0.00 0.00 37.69 5.14
186 188 1.518056 TAGGCGTCCTTGTCGTCGTT 61.518 55.000 3.71 0.00 37.99 3.85
263 268 0.960364 ATATTAATGCCGGCCCGCAG 60.960 55.000 26.77 0.00 43.26 5.18
264 269 0.538516 AATATTAATGCCGGCCCGCA 60.539 50.000 26.77 21.20 44.35 5.69
267 272 6.528774 CGTTAATTAAATATTAATGCCGGCCC 59.471 38.462 26.77 0.00 0.00 5.80
296 310 6.363577 TGCCGCAAACATTTTGAAAAATAA 57.636 29.167 2.80 0.00 36.52 1.40
298 312 4.889832 TGCCGCAAACATTTTGAAAAAT 57.110 31.818 2.80 0.00 39.07 1.82
300 314 4.095483 ACATTGCCGCAAACATTTTGAAAA 59.905 33.333 10.42 0.00 0.00 2.29
302 316 3.201290 ACATTGCCGCAAACATTTTGAA 58.799 36.364 10.42 0.00 0.00 2.69
303 317 2.831333 ACATTGCCGCAAACATTTTGA 58.169 38.095 10.42 0.00 0.00 2.69
304 318 3.605743 AACATTGCCGCAAACATTTTG 57.394 38.095 10.42 5.26 0.00 2.44
306 320 4.629251 AAAAACATTGCCGCAAACATTT 57.371 31.818 10.42 8.14 0.00 2.32
345 359 0.323725 AATGCTGGCCCGACTCATTT 60.324 50.000 0.00 0.00 0.00 2.32
350 364 2.683465 ATCCAATGCTGGCCCGACT 61.683 57.895 0.00 0.00 43.17 4.18
361 375 2.278336 CGGCGCTTGCATCCAATG 60.278 61.111 7.64 0.00 41.71 2.82
383 397 2.512515 GACCATGGCGCTCTCCAC 60.513 66.667 13.04 0.00 39.25 4.02
384 398 1.048160 TATGACCATGGCGCTCTCCA 61.048 55.000 13.04 0.00 40.97 3.86
385 399 0.106708 TTATGACCATGGCGCTCTCC 59.893 55.000 13.04 0.00 0.00 3.71
386 400 1.202580 ACTTATGACCATGGCGCTCTC 60.203 52.381 13.04 1.41 0.00 3.20
387 401 0.833287 ACTTATGACCATGGCGCTCT 59.167 50.000 13.04 0.00 0.00 4.09
388 402 1.221414 GACTTATGACCATGGCGCTC 58.779 55.000 13.04 2.27 0.00 5.03
389 403 0.541392 TGACTTATGACCATGGCGCT 59.459 50.000 13.04 0.00 0.00 5.92
390 404 1.597742 ATGACTTATGACCATGGCGC 58.402 50.000 13.04 0.00 0.00 6.53
391 405 4.380531 ACTTATGACTTATGACCATGGCG 58.619 43.478 13.04 0.00 0.00 5.69
392 406 5.506317 GCAACTTATGACTTATGACCATGGC 60.506 44.000 13.04 5.35 0.00 4.40
393 407 5.824624 AGCAACTTATGACTTATGACCATGG 59.175 40.000 11.19 11.19 0.00 3.66
395 409 6.058183 GGAGCAACTTATGACTTATGACCAT 58.942 40.000 0.00 0.00 0.00 3.55
396 410 5.045942 TGGAGCAACTTATGACTTATGACCA 60.046 40.000 0.00 0.00 0.00 4.02
397 411 5.294552 GTGGAGCAACTTATGACTTATGACC 59.705 44.000 0.00 0.00 0.00 4.02
398 412 5.294552 GGTGGAGCAACTTATGACTTATGAC 59.705 44.000 0.00 0.00 0.00 3.06
399 413 5.428253 GGTGGAGCAACTTATGACTTATGA 58.572 41.667 0.00 0.00 0.00 2.15
400 414 4.576463 GGGTGGAGCAACTTATGACTTATG 59.424 45.833 0.00 0.00 0.00 1.90
401 415 4.385310 GGGGTGGAGCAACTTATGACTTAT 60.385 45.833 0.00 0.00 0.00 1.73
403 417 2.290960 GGGGTGGAGCAACTTATGACTT 60.291 50.000 0.00 0.00 0.00 3.01
404 418 1.282157 GGGGTGGAGCAACTTATGACT 59.718 52.381 0.00 0.00 0.00 3.41
405 419 1.004277 TGGGGTGGAGCAACTTATGAC 59.996 52.381 0.00 0.00 0.00 3.06
406 420 1.367346 TGGGGTGGAGCAACTTATGA 58.633 50.000 0.00 0.00 0.00 2.15
408 422 1.710809 AGTTGGGGTGGAGCAACTTAT 59.289 47.619 0.00 0.00 34.63 1.73
409 423 1.145571 AGTTGGGGTGGAGCAACTTA 58.854 50.000 0.00 0.00 34.63 2.24
410 424 0.261696 AAGTTGGGGTGGAGCAACTT 59.738 50.000 0.00 0.00 41.36 2.66
411 425 1.145571 TAAGTTGGGGTGGAGCAACT 58.854 50.000 0.00 0.00 39.27 3.16
412 426 1.611977 GTTAAGTTGGGGTGGAGCAAC 59.388 52.381 0.00 0.00 0.00 4.17
414 428 1.145571 AGTTAAGTTGGGGTGGAGCA 58.854 50.000 0.00 0.00 0.00 4.26
415 429 2.287977 AAGTTAAGTTGGGGTGGAGC 57.712 50.000 0.00 0.00 0.00 4.70
417 431 4.792513 TTGTAAGTTAAGTTGGGGTGGA 57.207 40.909 5.77 0.00 0.00 4.02
418 432 5.536916 TGATTTGTAAGTTAAGTTGGGGTGG 59.463 40.000 5.77 0.00 0.00 4.61
419 433 6.642707 TGATTTGTAAGTTAAGTTGGGGTG 57.357 37.500 5.77 0.00 0.00 4.61
422 436 6.663523 AGGGATGATTTGTAAGTTAAGTTGGG 59.336 38.462 5.77 0.00 0.00 4.12
423 437 7.703058 AGGGATGATTTGTAAGTTAAGTTGG 57.297 36.000 5.77 0.00 0.00 3.77
424 438 9.981114 AAAAGGGATGATTTGTAAGTTAAGTTG 57.019 29.630 5.77 0.00 0.00 3.16
426 440 9.981114 CAAAAAGGGATGATTTGTAAGTTAAGT 57.019 29.630 0.00 0.00 31.17 2.24
427 441 8.925700 GCAAAAAGGGATGATTTGTAAGTTAAG 58.074 33.333 0.00 0.00 36.63 1.85
428 442 7.596995 CGCAAAAAGGGATGATTTGTAAGTTAA 59.403 33.333 0.00 0.00 36.63 2.01
429 443 7.087639 CGCAAAAAGGGATGATTTGTAAGTTA 58.912 34.615 0.00 0.00 36.63 2.24
431 445 5.010617 ACGCAAAAAGGGATGATTTGTAAGT 59.989 36.000 0.00 0.00 36.63 2.24
432 446 5.345741 CACGCAAAAAGGGATGATTTGTAAG 59.654 40.000 0.00 0.00 36.63 2.34
433 447 5.226396 CACGCAAAAAGGGATGATTTGTAA 58.774 37.500 0.00 0.00 36.63 2.41
436 450 2.995258 CCACGCAAAAAGGGATGATTTG 59.005 45.455 0.00 0.00 37.17 2.32
437 451 2.028203 CCCACGCAAAAAGGGATGATTT 60.028 45.455 0.00 0.00 45.80 2.17
438 452 1.550072 CCCACGCAAAAAGGGATGATT 59.450 47.619 0.00 0.00 45.80 2.57
441 455 0.243636 GACCCACGCAAAAAGGGATG 59.756 55.000 3.32 0.00 45.80 3.51
442 456 0.112412 AGACCCACGCAAAAAGGGAT 59.888 50.000 3.32 0.00 45.80 3.85
443 457 0.536460 GAGACCCACGCAAAAAGGGA 60.536 55.000 3.32 0.00 45.80 4.20
445 459 0.310854 GTGAGACCCACGCAAAAAGG 59.689 55.000 0.00 0.00 35.86 3.11
446 460 0.310854 GGTGAGACCCACGCAAAAAG 59.689 55.000 0.00 0.00 46.62 2.27
447 461 0.394488 TGGTGAGACCCACGCAAAAA 60.394 50.000 0.00 0.00 46.62 1.94
448 462 1.098712 GTGGTGAGACCCACGCAAAA 61.099 55.000 0.00 0.00 45.03 2.44
449 463 1.525077 GTGGTGAGACCCACGCAAA 60.525 57.895 0.00 0.00 45.03 3.68
450 464 2.110213 GTGGTGAGACCCACGCAA 59.890 61.111 0.00 0.00 45.03 4.85
478 492 7.004086 TCACCATACCTTCTCATCTTGTTTTT 58.996 34.615 0.00 0.00 0.00 1.94
479 493 6.542821 TCACCATACCTTCTCATCTTGTTTT 58.457 36.000 0.00 0.00 0.00 2.43
480 494 6.126863 TCACCATACCTTCTCATCTTGTTT 57.873 37.500 0.00 0.00 0.00 2.83
481 495 5.338708 CCTCACCATACCTTCTCATCTTGTT 60.339 44.000 0.00 0.00 0.00 2.83
482 496 4.163078 CCTCACCATACCTTCTCATCTTGT 59.837 45.833 0.00 0.00 0.00 3.16
483 497 4.163078 ACCTCACCATACCTTCTCATCTTG 59.837 45.833 0.00 0.00 0.00 3.02
484 498 4.163078 CACCTCACCATACCTTCTCATCTT 59.837 45.833 0.00 0.00 0.00 2.40
485 499 3.708631 CACCTCACCATACCTTCTCATCT 59.291 47.826 0.00 0.00 0.00 2.90
486 500 3.706594 TCACCTCACCATACCTTCTCATC 59.293 47.826 0.00 0.00 0.00 2.92
487 501 3.452627 GTCACCTCACCATACCTTCTCAT 59.547 47.826 0.00 0.00 0.00 2.90
488 502 2.832129 GTCACCTCACCATACCTTCTCA 59.168 50.000 0.00 0.00 0.00 3.27
489 503 3.100671 AGTCACCTCACCATACCTTCTC 58.899 50.000 0.00 0.00 0.00 2.87
490 504 3.191888 AGTCACCTCACCATACCTTCT 57.808 47.619 0.00 0.00 0.00 2.85
491 505 3.983044 AAGTCACCTCACCATACCTTC 57.017 47.619 0.00 0.00 0.00 3.46
492 506 5.962031 TGTATAAGTCACCTCACCATACCTT 59.038 40.000 0.00 0.00 0.00 3.50
493 507 5.525484 TGTATAAGTCACCTCACCATACCT 58.475 41.667 0.00 0.00 0.00 3.08
494 508 5.864418 TGTATAAGTCACCTCACCATACC 57.136 43.478 0.00 0.00 0.00 2.73
495 509 7.050970 TGATGTATAAGTCACCTCACCATAC 57.949 40.000 0.00 0.00 0.00 2.39
496 510 6.267699 CCTGATGTATAAGTCACCTCACCATA 59.732 42.308 0.00 0.00 0.00 2.74
497 511 5.070981 CCTGATGTATAAGTCACCTCACCAT 59.929 44.000 0.00 0.00 0.00 3.55
498 512 4.405680 CCTGATGTATAAGTCACCTCACCA 59.594 45.833 0.00 0.00 0.00 4.17
499 513 4.202264 CCCTGATGTATAAGTCACCTCACC 60.202 50.000 0.00 0.00 0.00 4.02
500 514 4.202264 CCCCTGATGTATAAGTCACCTCAC 60.202 50.000 0.00 0.00 0.00 3.51
501 515 3.967326 CCCCTGATGTATAAGTCACCTCA 59.033 47.826 0.00 0.00 0.00 3.86
502 516 4.223953 TCCCCTGATGTATAAGTCACCTC 58.776 47.826 0.00 0.00 0.00 3.85
503 517 4.280789 TCCCCTGATGTATAAGTCACCT 57.719 45.455 0.00 0.00 0.00 4.00
504 518 6.681729 TTATCCCCTGATGTATAAGTCACC 57.318 41.667 0.00 0.00 32.18 4.02
505 519 7.907389 TGATTATCCCCTGATGTATAAGTCAC 58.093 38.462 0.00 0.00 32.18 3.67
506 520 8.504811 TTGATTATCCCCTGATGTATAAGTCA 57.495 34.615 0.00 0.00 32.18 3.41
507 521 9.442047 CTTTGATTATCCCCTGATGTATAAGTC 57.558 37.037 0.00 0.00 32.18 3.01
508 522 9.170890 TCTTTGATTATCCCCTGATGTATAAGT 57.829 33.333 0.00 0.00 32.18 2.24
509 523 9.664332 CTCTTTGATTATCCCCTGATGTATAAG 57.336 37.037 0.00 0.00 32.18 1.73
510 524 8.605947 CCTCTTTGATTATCCCCTGATGTATAA 58.394 37.037 0.00 0.00 32.18 0.98
511 525 7.311297 GCCTCTTTGATTATCCCCTGATGTATA 60.311 40.741 0.00 0.00 32.18 1.47
512 526 6.523150 GCCTCTTTGATTATCCCCTGATGTAT 60.523 42.308 0.00 0.00 32.18 2.29
513 527 5.221925 GCCTCTTTGATTATCCCCTGATGTA 60.222 44.000 0.00 0.00 32.18 2.29
514 528 4.446889 GCCTCTTTGATTATCCCCTGATGT 60.447 45.833 0.00 0.00 32.18 3.06
515 529 4.077822 GCCTCTTTGATTATCCCCTGATG 58.922 47.826 0.00 0.00 32.18 3.07
516 530 3.075134 GGCCTCTTTGATTATCCCCTGAT 59.925 47.826 0.00 0.00 34.87 2.90
517 531 2.443255 GGCCTCTTTGATTATCCCCTGA 59.557 50.000 0.00 0.00 0.00 3.86
518 532 2.444766 AGGCCTCTTTGATTATCCCCTG 59.555 50.000 0.00 0.00 0.00 4.45
519 533 2.444766 CAGGCCTCTTTGATTATCCCCT 59.555 50.000 0.00 0.00 0.00 4.79
520 534 2.443255 TCAGGCCTCTTTGATTATCCCC 59.557 50.000 0.00 0.00 0.00 4.81
521 535 3.137360 AGTCAGGCCTCTTTGATTATCCC 59.863 47.826 0.00 0.00 0.00 3.85
522 536 4.429854 AGTCAGGCCTCTTTGATTATCC 57.570 45.455 0.00 0.00 0.00 2.59
523 537 9.213799 CTTATAAGTCAGGCCTCTTTGATTATC 57.786 37.037 11.68 0.00 0.00 1.75
524 538 8.718656 ACTTATAAGTCAGGCCTCTTTGATTAT 58.281 33.333 12.50 8.99 32.86 1.28
525 539 8.090788 ACTTATAAGTCAGGCCTCTTTGATTA 57.909 34.615 12.50 2.57 32.86 1.75
526 540 6.963322 ACTTATAAGTCAGGCCTCTTTGATT 58.037 36.000 12.50 0.00 32.86 2.57
527 541 6.567602 ACTTATAAGTCAGGCCTCTTTGAT 57.432 37.500 12.50 3.87 32.86 2.57
545 559 9.823647 CTGACTTATAAATCAGGTGTGACTTAT 57.176 33.333 14.74 0.00 38.39 1.73
567 581 2.341846 TGGTTCCAAAGTCACCTGAC 57.658 50.000 0.00 0.00 45.08 3.51
568 582 3.020984 GTTTGGTTCCAAAGTCACCTGA 58.979 45.455 16.05 0.00 36.72 3.86
569 583 2.757868 TGTTTGGTTCCAAAGTCACCTG 59.242 45.455 16.05 0.00 36.72 4.00
570 584 3.023832 CTGTTTGGTTCCAAAGTCACCT 58.976 45.455 16.05 0.00 36.72 4.00
571 585 2.100749 CCTGTTTGGTTCCAAAGTCACC 59.899 50.000 16.05 6.18 36.72 4.02
572 586 2.481276 GCCTGTTTGGTTCCAAAGTCAC 60.481 50.000 16.05 7.12 36.72 3.67
573 587 1.754226 GCCTGTTTGGTTCCAAAGTCA 59.246 47.619 16.05 11.07 36.72 3.41
574 588 1.068588 GGCCTGTTTGGTTCCAAAGTC 59.931 52.381 16.05 7.44 36.72 3.01
575 589 1.119684 GGCCTGTTTGGTTCCAAAGT 58.880 50.000 16.05 0.00 36.72 2.66
576 590 0.392706 GGGCCTGTTTGGTTCCAAAG 59.607 55.000 16.05 6.75 36.72 2.77
577 591 0.031616 AGGGCCTGTTTGGTTCCAAA 60.032 50.000 4.50 12.29 38.35 3.28
578 592 0.031616 AAGGGCCTGTTTGGTTCCAA 60.032 50.000 6.92 0.00 38.35 3.53
579 593 0.854218 TAAGGGCCTGTTTGGTTCCA 59.146 50.000 6.92 0.00 38.35 3.53
580 594 1.824852 CATAAGGGCCTGTTTGGTTCC 59.175 52.381 6.92 0.00 38.35 3.62
581 595 2.525368 ACATAAGGGCCTGTTTGGTTC 58.475 47.619 6.92 0.00 38.35 3.62
582 596 2.694616 ACATAAGGGCCTGTTTGGTT 57.305 45.000 6.92 0.00 38.35 3.67
583 597 2.525368 GAACATAAGGGCCTGTTTGGT 58.475 47.619 6.92 3.38 35.80 3.67
584 598 1.472480 CGAACATAAGGGCCTGTTTGG 59.528 52.381 6.92 0.88 35.80 3.28
585 599 1.472480 CCGAACATAAGGGCCTGTTTG 59.528 52.381 6.92 12.03 35.80 2.93
586 600 1.074889 ACCGAACATAAGGGCCTGTTT 59.925 47.619 6.92 0.00 35.80 2.83
587 601 0.696501 ACCGAACATAAGGGCCTGTT 59.303 50.000 6.92 8.32 38.26 3.16
588 602 0.035439 CACCGAACATAAGGGCCTGT 60.035 55.000 6.92 0.00 0.00 4.00
589 603 1.376609 GCACCGAACATAAGGGCCTG 61.377 60.000 6.92 0.00 0.00 4.85
590 604 1.077716 GCACCGAACATAAGGGCCT 60.078 57.895 0.00 0.00 0.00 5.19
591 605 0.751643 ATGCACCGAACATAAGGGCC 60.752 55.000 0.00 0.00 0.00 5.80
592 606 0.381801 CATGCACCGAACATAAGGGC 59.618 55.000 0.00 0.00 0.00 5.19
593 607 1.670811 GTCATGCACCGAACATAAGGG 59.329 52.381 0.00 0.00 0.00 3.95
594 608 2.609459 GAGTCATGCACCGAACATAAGG 59.391 50.000 0.00 0.00 0.00 2.69
595 609 3.525537 AGAGTCATGCACCGAACATAAG 58.474 45.455 0.00 0.00 0.00 1.73
598 612 2.479566 AAGAGTCATGCACCGAACAT 57.520 45.000 0.00 0.00 0.00 2.71
599 613 1.872952 CAAAGAGTCATGCACCGAACA 59.127 47.619 0.00 0.00 0.00 3.18
603 617 1.399440 CATCCAAAGAGTCATGCACCG 59.601 52.381 0.00 0.00 0.00 4.94
604 618 1.133790 GCATCCAAAGAGTCATGCACC 59.866 52.381 7.34 0.00 41.16 5.01
610 624 4.038042 CGATACTAGGCATCCAAAGAGTCA 59.962 45.833 0.00 0.00 0.00 3.41
616 630 2.035449 CCGTCGATACTAGGCATCCAAA 59.965 50.000 0.00 0.00 0.00 3.28
618 632 1.244816 CCGTCGATACTAGGCATCCA 58.755 55.000 0.00 0.00 0.00 3.41
633 647 3.562779 TTGGGAACGTCGAGCCGTC 62.563 63.158 0.00 0.00 40.85 4.79
634 648 3.154584 TTTGGGAACGTCGAGCCGT 62.155 57.895 0.00 0.00 44.23 5.68
635 649 2.356553 TTTGGGAACGTCGAGCCG 60.357 61.111 0.00 0.00 0.00 5.52
636 650 0.883370 AAGTTTGGGAACGTCGAGCC 60.883 55.000 0.00 0.00 40.75 4.70
637 651 0.942252 AAAGTTTGGGAACGTCGAGC 59.058 50.000 0.00 0.00 40.75 5.03
640 654 3.685836 AGAAAAAGTTTGGGAACGTCG 57.314 42.857 0.00 0.00 40.75 5.12
648 662 8.606602 CCATCTCAAAGAAAAGAAAAAGTTTGG 58.393 33.333 0.00 0.00 0.00 3.28
659 673 5.106673 GGGAACGTACCATCTCAAAGAAAAG 60.107 44.000 4.45 0.00 0.00 2.27
674 692 3.250762 GGGTGTTTAGTTTGGGAACGTAC 59.749 47.826 0.00 0.00 40.75 3.67
968 1013 3.566853 CCGCGCCTACGTCTACGA 61.567 66.667 9.86 0.00 43.02 3.43
969 1014 4.602696 CCCGCGCCTACGTCTACG 62.603 72.222 0.00 0.04 46.33 3.51
977 1022 2.833582 CCTCTCTTCCCGCGCCTA 60.834 66.667 0.00 0.00 0.00 3.93
1134 1179 2.849096 TACCACTCGCAGATCCCGGT 62.849 60.000 0.00 0.00 33.89 5.28
1149 1194 3.455910 CCTCAACCAGATCTCCAATACCA 59.544 47.826 0.00 0.00 0.00 3.25
1153 1198 1.849039 CCCCTCAACCAGATCTCCAAT 59.151 52.381 0.00 0.00 0.00 3.16
1223 1268 6.428159 GCACTTGACGATAATAATGGAATCCT 59.572 38.462 0.00 0.00 0.00 3.24
1293 1338 1.432270 CGAGCTCTTCGGCCCAAATC 61.432 60.000 12.85 0.00 45.54 2.17
1314 1359 4.942761 GTGAAACTACCACGGGGATATA 57.057 45.455 12.96 0.00 38.05 0.86
1423 1468 2.092211 CCACGAGAAACGATACAGCAAC 59.908 50.000 0.00 0.00 45.77 4.17
1432 1477 0.946528 TCGACTTCCACGAGAAACGA 59.053 50.000 13.11 13.11 45.77 3.85
1548 1602 1.061131 CGCATCAAGCTGGAACTAACG 59.939 52.381 0.00 0.00 42.61 3.18
1574 1628 9.717942 ATGCTAATATTTATCAGAGTCTCCAAC 57.282 33.333 0.00 0.00 0.00 3.77
1604 1658 4.331968 TCAACAAGGACGGAAATAGCATT 58.668 39.130 0.00 0.00 0.00 3.56
1605 1659 3.941483 CTCAACAAGGACGGAAATAGCAT 59.059 43.478 0.00 0.00 0.00 3.79
1786 1853 7.016361 TGAAGAGAGTTCTTGTAAAAGCAAC 57.984 36.000 0.00 0.00 43.63 4.17
1799 1866 5.003804 TGGCTTTTACCATGAAGAGAGTTC 58.996 41.667 0.00 0.00 33.75 3.01
1898 1966 4.659111 AACGACCCGTATGACATGATTA 57.341 40.909 0.00 0.00 39.99 1.75
1911 1981 1.300697 GCTAGGCCATAACGACCCG 60.301 63.158 5.01 0.00 0.00 5.28
1916 1986 3.609644 CGAGTTAGAGCTAGGCCATAACG 60.610 52.174 5.01 0.00 36.07 3.18
1961 2031 7.692460 TCGTCATAACCTTTGTCTTAGTCTA 57.308 36.000 0.00 0.00 0.00 2.59
1970 2040 8.044908 ACCACTATATTTCGTCATAACCTTTGT 58.955 33.333 0.00 0.00 0.00 2.83
2038 2109 9.308318 GAGGCACTTAGTTTGTTTTTCAATTTA 57.692 29.630 0.00 0.00 41.55 1.40
2086 2157 2.035832 GGTTGCACCACTAAAAGCATGT 59.964 45.455 0.00 0.00 38.42 3.21
2090 2161 3.568430 ACTTAGGTTGCACCACTAAAAGC 59.432 43.478 7.86 0.00 41.95 3.51
2096 2167 0.110486 CCCACTTAGGTTGCACCACT 59.890 55.000 7.86 0.00 41.95 4.00
2105 2176 2.795329 CAAGTTGCATCCCACTTAGGT 58.205 47.619 1.31 0.00 34.66 3.08
2365 2764 5.761726 TCAGACATGATGCTAATTGATCACC 59.238 40.000 0.00 0.00 31.47 4.02
2444 2843 6.596309 AGTGACTGAGTTACTGAATCATCA 57.404 37.500 9.38 0.00 31.25 3.07
2742 3141 4.165779 CAGTTCTCAACAGCAACGTTTTT 58.834 39.130 0.00 0.00 0.00 1.94
2782 3181 1.226746 GGACACACTACAGCGCTTTT 58.773 50.000 7.50 0.00 0.00 2.27
2783 3182 0.105964 TGGACACACTACAGCGCTTT 59.894 50.000 7.50 3.33 0.00 3.51
2857 3256 2.878406 ACAGGAAACCGATCACACAAAG 59.122 45.455 0.00 0.00 0.00 2.77
2905 3309 4.050934 CCCTGCCCGCGTTTTTCC 62.051 66.667 4.92 0.00 0.00 3.13
3202 3608 1.899814 AGAATGACAACAGACCGGCTA 59.100 47.619 0.00 0.00 0.00 3.93
3605 4272 9.574458 GGCCTTTTTATCTTCAACTAGATTTTC 57.426 33.333 0.00 0.00 36.34 2.29
4116 4820 1.443194 CGTGCTGCAGATTTGGTGC 60.443 57.895 20.43 0.00 41.59 5.01


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

AutoCloner maintained by Alex Coulton.