Multiple sequence alignment - TraesCS2D01G281300

Loading Multiple Alignment...

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 TraesCS2D01G281300 chr2D 100.000 3028 0 0 1 3028 354377968 354380995 0.000000e+00 5592.0
1 TraesCS2D01G281300 chr2A 92.219 1645 50 18 667 2254 473600124 473601747 0.000000e+00 2257.0
2 TraesCS2D01G281300 chr2A 92.708 384 22 4 2255 2637 473601777 473602155 1.590000e-152 549.0
3 TraesCS2D01G281300 chr2A 90.176 397 36 3 1 395 473599728 473600123 5.790000e-142 514.0
4 TraesCS2D01G281300 chr2A 86.047 258 24 9 2640 2895 473604096 473604343 1.790000e-67 267.0
5 TraesCS2D01G281300 chr2B 91.637 1136 49 17 1157 2254 421247178 421248305 0.000000e+00 1530.0
6 TraesCS2D01G281300 chr2B 94.903 412 15 2 765 1173 421246744 421247152 9.150000e-180 640.0
7 TraesCS2D01G281300 chr2B 96.648 358 11 1 2255 2612 421248335 421248691 7.230000e-166 593.0
8 TraesCS2D01G281300 chr2B 94.690 113 5 1 2916 3028 421251087 421251198 1.120000e-39 174.0
9 TraesCS2D01G281300 chr2B 95.506 89 3 1 2609 2697 421250868 421250955 1.130000e-29 141.0
10 TraesCS2D01G281300 chr2B 100.000 33 0 0 2714 2746 421250948 421250980 9.060000e-06 62.1
11 TraesCS2D01G281300 chr7A 92.222 90 3 3 2940 3028 28471627 28471541 1.140000e-24 124.0
12 TraesCS2D01G281300 chr7A 82.178 101 16 1 175 273 507150296 507150196 5.380000e-13 86.1


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 TraesCS2D01G281300 chr2D 354377968 354380995 3027 False 5592.00 5592 100.0000 1 3028 1 chr2D.!!$F1 3027
1 TraesCS2D01G281300 chr2A 473599728 473604343 4615 False 896.75 2257 90.2875 1 2895 4 chr2A.!!$F1 2894
2 TraesCS2D01G281300 chr2B 421246744 421251198 4454 False 523.35 1530 95.5640 765 3028 6 chr2B.!!$F1 2263

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
597 599 0.036010 ACTCAATGCAGAAGTCGGGG 60.036 55.0 0.0 0.0 0.00 5.73 F
599 601 0.036388 TCAATGCAGAAGTCGGGGTC 60.036 55.0 0.0 0.0 0.00 4.46 F
1831 1891 0.176680 GTGTCGATCCAGGCATCTGT 59.823 55.0 0.0 0.0 39.31 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2013 0.394762 GCACTGGCTTGGGATGATGA 60.395 55.000 0.00 0.0 36.96 2.92 R
1961 2045 1.008079 GGGAACGTATAGCGGACGG 60.008 63.158 11.75 0.0 44.58 4.79 R
2696 6952 1.298859 GGTTTGGCACTGTAGCTCGG 61.299 60.000 0.00 0.0 34.17 4.63 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
18 19 3.745723 AATGTGGGGGTGTCAAGTC 57.254 52.632 0.00 0.00 0.00 3.01
27 28 1.279271 GGGTGTCAAGTCATACCTGCT 59.721 52.381 0.00 0.00 33.71 4.24
30 31 3.522553 GTGTCAAGTCATACCTGCTACC 58.477 50.000 0.00 0.00 0.00 3.18
48 49 2.202623 GACTGGTGCTACGCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
60 61 2.280457 GCTCGGTGGCTCCTATGC 60.280 66.667 3.83 1.78 0.00 3.14
75 76 5.276440 CTCCTATGCCCTATAGAGGTGATT 58.724 45.833 2.04 0.00 41.95 2.57
84 85 6.097129 GCCCTATAGAGGTGATTAGTCATACC 59.903 46.154 2.04 0.00 41.95 2.73
98 99 4.985538 AGTCATACCTGTTGTTGTTGGAT 58.014 39.130 0.00 0.00 0.00 3.41
114 115 1.691976 TGGATCGAAAGTGGTGTGACT 59.308 47.619 0.00 0.00 0.00 3.41
115 116 2.069273 GGATCGAAAGTGGTGTGACTG 58.931 52.381 0.00 0.00 0.00 3.51
119 120 1.593006 CGAAAGTGGTGTGACTGTGAC 59.407 52.381 0.00 0.00 0.00 3.67
124 125 1.006102 GGTGTGACTGTGACGGGAG 60.006 63.158 0.00 0.00 0.00 4.30
160 161 3.447586 TCTTTGTCTTCCGGTATCTCCTG 59.552 47.826 0.00 0.00 0.00 3.86
171 172 3.322254 CGGTATCTCCTGCAGAGGTAATT 59.678 47.826 17.39 0.00 39.97 1.40
177 178 2.103094 TCCTGCAGAGGTAATTGATCGG 59.897 50.000 17.39 0.00 40.76 4.18
179 180 1.140852 TGCAGAGGTAATTGATCGGGG 59.859 52.381 0.00 0.00 0.00 5.73
224 225 2.483877 TGTAAGATGCGGCTTCAACAAG 59.516 45.455 16.88 0.00 0.00 3.16
244 245 5.181245 ACAAGAAGTTTGTGTAATCCGATGG 59.819 40.000 0.00 0.00 0.00 3.51
270 271 3.758023 CACGAGATCTCTGATCAGGCTAT 59.242 47.826 22.42 12.97 0.00 2.97
280 281 1.196354 GATCAGGCTATGTTGATGCGC 59.804 52.381 0.00 0.00 34.33 6.09
281 282 0.107752 TCAGGCTATGTTGATGCGCA 60.108 50.000 14.96 14.96 0.00 6.09
283 284 1.097547 AGGCTATGTTGATGCGCACC 61.098 55.000 14.90 1.73 0.00 5.01
304 305 2.877691 GCCGTGCCCTTGCTAAAG 59.122 61.111 0.00 0.00 38.71 1.85
322 324 1.668151 GGTGGTGACCGAAGCTCAC 60.668 63.158 0.00 0.00 37.84 3.51
339 341 4.043435 AGCTCACTTTGGGGATAAAAGTCT 59.957 41.667 0.00 0.00 44.11 3.24
354 356 1.742768 GTCTCGGGACTGGCCTATG 59.257 63.158 8.58 0.00 39.24 2.23
365 367 0.907704 TGGCCTATGGTTGGACTCGT 60.908 55.000 3.32 0.00 32.71 4.18
375 377 1.471684 GTTGGACTCGTCACTATCGGT 59.528 52.381 0.00 0.00 0.00 4.69
413 415 4.569719 TTTCTTGAAGGCTTACCCTAGG 57.430 45.455 0.06 0.06 45.62 3.02
414 416 3.484953 TCTTGAAGGCTTACCCTAGGA 57.515 47.619 11.48 0.00 45.62 2.94
415 417 3.375699 TCTTGAAGGCTTACCCTAGGAG 58.624 50.000 11.48 0.10 45.62 3.69
416 418 3.012502 TCTTGAAGGCTTACCCTAGGAGA 59.987 47.826 11.48 0.00 45.62 3.71
417 419 3.708236 TGAAGGCTTACCCTAGGAGAT 57.292 47.619 11.48 0.00 45.62 2.75
418 420 4.827036 TGAAGGCTTACCCTAGGAGATA 57.173 45.455 11.48 0.00 45.62 1.98
419 421 5.355670 TGAAGGCTTACCCTAGGAGATAT 57.644 43.478 11.48 0.00 45.62 1.63
420 422 5.087323 TGAAGGCTTACCCTAGGAGATATG 58.913 45.833 11.48 3.58 45.62 1.78
421 423 4.768807 AGGCTTACCCTAGGAGATATGT 57.231 45.455 11.48 0.22 44.08 2.29
422 424 5.880279 AGGCTTACCCTAGGAGATATGTA 57.120 43.478 11.48 0.00 44.08 2.29
423 425 5.581975 AGGCTTACCCTAGGAGATATGTAC 58.418 45.833 11.48 0.00 44.08 2.90
424 426 4.398673 GGCTTACCCTAGGAGATATGTACG 59.601 50.000 11.48 1.68 0.00 3.67
425 427 5.251764 GCTTACCCTAGGAGATATGTACGA 58.748 45.833 11.48 0.00 0.00 3.43
426 428 5.354792 GCTTACCCTAGGAGATATGTACGAG 59.645 48.000 11.48 0.00 0.00 4.18
427 429 6.692849 TTACCCTAGGAGATATGTACGAGA 57.307 41.667 11.48 0.00 0.00 4.04
428 430 4.909001 ACCCTAGGAGATATGTACGAGAC 58.091 47.826 11.48 0.00 0.00 3.36
429 431 4.350225 ACCCTAGGAGATATGTACGAGACA 59.650 45.833 11.48 0.00 43.97 3.41
441 443 5.204409 TGTACGAGACATGTACTTTTGGT 57.796 39.130 0.00 0.00 42.09 3.67
442 444 5.603596 TGTACGAGACATGTACTTTTGGTT 58.396 37.500 0.00 0.00 42.09 3.67
443 445 6.050432 TGTACGAGACATGTACTTTTGGTTT 58.950 36.000 0.00 0.00 42.09 3.27
444 446 5.418310 ACGAGACATGTACTTTTGGTTTG 57.582 39.130 0.00 0.00 0.00 2.93
445 447 4.879545 ACGAGACATGTACTTTTGGTTTGT 59.120 37.500 0.00 0.00 0.00 2.83
446 448 5.355910 ACGAGACATGTACTTTTGGTTTGTT 59.644 36.000 0.00 0.00 0.00 2.83
447 449 6.127842 ACGAGACATGTACTTTTGGTTTGTTT 60.128 34.615 0.00 0.00 0.00 2.83
448 450 6.413818 CGAGACATGTACTTTTGGTTTGTTTC 59.586 38.462 0.00 0.00 0.00 2.78
449 451 6.262601 AGACATGTACTTTTGGTTTGTTTCG 58.737 36.000 0.00 0.00 0.00 3.46
450 452 5.344884 ACATGTACTTTTGGTTTGTTTCGG 58.655 37.500 0.00 0.00 0.00 4.30
451 453 5.105675 ACATGTACTTTTGGTTTGTTTCGGT 60.106 36.000 0.00 0.00 0.00 4.69
452 454 4.984205 TGTACTTTTGGTTTGTTTCGGTC 58.016 39.130 0.00 0.00 0.00 4.79
453 455 4.701171 TGTACTTTTGGTTTGTTTCGGTCT 59.299 37.500 0.00 0.00 0.00 3.85
454 456 5.879223 TGTACTTTTGGTTTGTTTCGGTCTA 59.121 36.000 0.00 0.00 0.00 2.59
455 457 6.543100 TGTACTTTTGGTTTGTTTCGGTCTAT 59.457 34.615 0.00 0.00 0.00 1.98
456 458 6.459670 ACTTTTGGTTTGTTTCGGTCTATT 57.540 33.333 0.00 0.00 0.00 1.73
457 459 7.571080 ACTTTTGGTTTGTTTCGGTCTATTA 57.429 32.000 0.00 0.00 0.00 0.98
458 460 7.998580 ACTTTTGGTTTGTTTCGGTCTATTAA 58.001 30.769 0.00 0.00 0.00 1.40
459 461 7.916977 ACTTTTGGTTTGTTTCGGTCTATTAAC 59.083 33.333 0.00 0.00 0.00 2.01
460 462 6.939132 TTGGTTTGTTTCGGTCTATTAACA 57.061 33.333 0.00 0.00 0.00 2.41
461 463 7.513371 TTGGTTTGTTTCGGTCTATTAACAT 57.487 32.000 0.00 0.00 31.30 2.71
462 464 8.618702 TTGGTTTGTTTCGGTCTATTAACATA 57.381 30.769 0.00 0.00 31.30 2.29
463 465 8.618702 TGGTTTGTTTCGGTCTATTAACATAA 57.381 30.769 0.00 0.00 31.30 1.90
464 466 8.723311 TGGTTTGTTTCGGTCTATTAACATAAG 58.277 33.333 0.00 0.00 31.30 1.73
465 467 8.179615 GGTTTGTTTCGGTCTATTAACATAAGG 58.820 37.037 0.00 0.00 31.30 2.69
466 468 8.724229 GTTTGTTTCGGTCTATTAACATAAGGT 58.276 33.333 0.00 0.00 31.30 3.50
467 469 8.851541 TTGTTTCGGTCTATTAACATAAGGTT 57.148 30.769 0.00 0.00 43.62 3.50
468 470 9.941325 TTGTTTCGGTCTATTAACATAAGGTTA 57.059 29.630 0.00 0.00 40.96 2.85
469 471 9.590451 TGTTTCGGTCTATTAACATAAGGTTAG 57.410 33.333 0.00 0.00 42.63 2.34
470 472 9.591792 GTTTCGGTCTATTAACATAAGGTTAGT 57.408 33.333 0.00 0.00 42.63 2.24
471 473 9.590451 TTTCGGTCTATTAACATAAGGTTAGTG 57.410 33.333 0.00 0.00 42.63 2.74
472 474 7.719483 TCGGTCTATTAACATAAGGTTAGTGG 58.281 38.462 0.00 0.00 42.63 4.00
473 475 7.342799 TCGGTCTATTAACATAAGGTTAGTGGT 59.657 37.037 0.00 0.00 42.63 4.16
474 476 7.983484 CGGTCTATTAACATAAGGTTAGTGGTT 59.017 37.037 0.00 0.00 42.63 3.67
481 483 9.850198 TTAACATAAGGTTAGTGGTTAACTTGT 57.150 29.630 5.42 0.00 42.63 3.16
482 484 7.739498 ACATAAGGTTAGTGGTTAACTTGTG 57.261 36.000 5.42 0.00 41.19 3.33
483 485 7.511268 ACATAAGGTTAGTGGTTAACTTGTGA 58.489 34.615 5.42 0.00 41.19 3.58
484 486 7.994334 ACATAAGGTTAGTGGTTAACTTGTGAA 59.006 33.333 5.42 0.00 41.19 3.18
485 487 6.937436 AAGGTTAGTGGTTAACTTGTGAAG 57.063 37.500 5.42 0.00 41.19 3.02
486 488 4.820173 AGGTTAGTGGTTAACTTGTGAAGC 59.180 41.667 5.42 4.19 41.19 3.86
487 489 4.820173 GGTTAGTGGTTAACTTGTGAAGCT 59.180 41.667 5.42 0.00 41.19 3.74
488 490 5.993441 GGTTAGTGGTTAACTTGTGAAGCTA 59.007 40.000 5.42 0.00 41.19 3.32
489 491 6.073385 GGTTAGTGGTTAACTTGTGAAGCTAC 60.073 42.308 5.42 0.00 41.19 3.58
490 492 5.291905 AGTGGTTAACTTGTGAAGCTACT 57.708 39.130 5.42 2.07 34.57 2.57
491 493 5.057149 AGTGGTTAACTTGTGAAGCTACTG 58.943 41.667 5.42 0.00 34.57 2.74
492 494 3.813166 TGGTTAACTTGTGAAGCTACTGC 59.187 43.478 5.42 0.00 40.05 4.40
493 495 3.188667 GGTTAACTTGTGAAGCTACTGCC 59.811 47.826 5.42 0.00 40.80 4.85
494 496 1.512926 AACTTGTGAAGCTACTGCCG 58.487 50.000 0.00 0.00 40.80 5.69
495 497 0.951040 ACTTGTGAAGCTACTGCCGC 60.951 55.000 0.00 0.00 40.80 6.53
496 498 1.959899 CTTGTGAAGCTACTGCCGCG 61.960 60.000 0.00 0.00 40.80 6.46
497 499 2.432628 GTGAAGCTACTGCCGCGT 60.433 61.111 4.92 0.00 40.80 6.01
498 500 2.432456 TGAAGCTACTGCCGCGTG 60.432 61.111 4.92 0.00 40.80 5.34
499 501 3.188786 GAAGCTACTGCCGCGTGG 61.189 66.667 11.67 11.67 40.80 4.94
510 512 3.049674 CGCGTGGCATGTGACCTT 61.050 61.111 15.01 0.00 0.00 3.50
511 513 2.870372 GCGTGGCATGTGACCTTC 59.130 61.111 8.75 0.00 0.00 3.46
512 514 3.027170 GCGTGGCATGTGACCTTCG 62.027 63.158 8.75 0.00 0.00 3.79
513 515 2.390599 CGTGGCATGTGACCTTCGG 61.391 63.158 0.00 0.00 0.00 4.30
514 516 2.040544 GTGGCATGTGACCTTCGGG 61.041 63.158 0.00 0.00 41.87 5.14
553 555 9.515020 TCGAATTTATTATGCTGTTGGATTTTC 57.485 29.630 0.00 0.00 0.00 2.29
554 556 9.520204 CGAATTTATTATGCTGTTGGATTTTCT 57.480 29.630 0.00 0.00 0.00 2.52
571 573 9.613428 TGGATTTTCTAATAATATATGGCTCCG 57.387 33.333 0.00 0.00 0.00 4.63
572 574 9.614792 GGATTTTCTAATAATATATGGCTCCGT 57.385 33.333 0.00 0.00 0.00 4.69
574 576 7.843490 TTTCTAATAATATATGGCTCCGTGC 57.157 36.000 0.00 0.00 41.94 5.34
575 577 6.538945 TCTAATAATATATGGCTCCGTGCA 57.461 37.500 0.30 0.00 45.15 4.57
576 578 7.124573 TCTAATAATATATGGCTCCGTGCAT 57.875 36.000 0.00 0.00 45.15 3.96
577 579 7.210174 TCTAATAATATATGGCTCCGTGCATC 58.790 38.462 0.00 0.00 45.15 3.91
578 580 3.701205 AATATATGGCTCCGTGCATCA 57.299 42.857 0.00 0.00 45.15 3.07
579 581 2.455674 TATATGGCTCCGTGCATCAC 57.544 50.000 0.00 0.00 45.15 3.06
580 582 0.761187 ATATGGCTCCGTGCATCACT 59.239 50.000 0.00 0.00 45.15 3.41
581 583 0.104855 TATGGCTCCGTGCATCACTC 59.895 55.000 0.00 0.00 45.15 3.51
582 584 1.902765 ATGGCTCCGTGCATCACTCA 61.903 55.000 0.00 0.00 45.15 3.41
583 585 1.375908 GGCTCCGTGCATCACTCAA 60.376 57.895 0.00 0.00 45.15 3.02
584 586 0.745845 GGCTCCGTGCATCACTCAAT 60.746 55.000 0.00 0.00 45.15 2.57
585 587 0.376152 GCTCCGTGCATCACTCAATG 59.624 55.000 0.00 0.00 42.31 2.82
594 596 3.653256 CATCACTCAATGCAGAAGTCG 57.347 47.619 0.00 0.00 0.00 4.18
595 597 2.084610 TCACTCAATGCAGAAGTCGG 57.915 50.000 0.00 0.00 0.00 4.79
596 598 1.081892 CACTCAATGCAGAAGTCGGG 58.918 55.000 0.00 0.00 0.00 5.14
597 599 0.036010 ACTCAATGCAGAAGTCGGGG 60.036 55.000 0.00 0.00 0.00 5.73
598 600 0.036010 CTCAATGCAGAAGTCGGGGT 60.036 55.000 0.00 0.00 0.00 4.95
599 601 0.036388 TCAATGCAGAAGTCGGGGTC 60.036 55.000 0.00 0.00 0.00 4.46
600 602 0.321564 CAATGCAGAAGTCGGGGTCA 60.322 55.000 0.00 0.00 0.00 4.02
601 603 0.620556 AATGCAGAAGTCGGGGTCAT 59.379 50.000 0.00 0.00 0.00 3.06
602 604 0.179000 ATGCAGAAGTCGGGGTCATC 59.821 55.000 0.00 0.00 0.00 2.92
603 605 1.153349 GCAGAAGTCGGGGTCATCC 60.153 63.158 0.00 0.00 0.00 3.51
604 606 1.617947 GCAGAAGTCGGGGTCATCCT 61.618 60.000 0.00 0.00 35.33 3.24
605 607 0.905357 CAGAAGTCGGGGTCATCCTT 59.095 55.000 0.00 0.00 35.33 3.36
606 608 1.134670 CAGAAGTCGGGGTCATCCTTC 60.135 57.143 0.00 0.00 35.33 3.46
607 609 1.196012 GAAGTCGGGGTCATCCTTCT 58.804 55.000 0.00 0.00 35.33 2.85
608 610 0.905357 AAGTCGGGGTCATCCTTCTG 59.095 55.000 0.00 0.00 35.33 3.02
609 611 0.252284 AGTCGGGGTCATCCTTCTGT 60.252 55.000 0.00 0.00 35.33 3.41
610 612 0.613777 GTCGGGGTCATCCTTCTGTT 59.386 55.000 0.00 0.00 35.33 3.16
611 613 1.003233 GTCGGGGTCATCCTTCTGTTT 59.997 52.381 0.00 0.00 35.33 2.83
612 614 1.003118 TCGGGGTCATCCTTCTGTTTG 59.997 52.381 0.00 0.00 35.33 2.93
613 615 1.003118 CGGGGTCATCCTTCTGTTTGA 59.997 52.381 0.00 0.00 35.33 2.69
614 616 2.552155 CGGGGTCATCCTTCTGTTTGAA 60.552 50.000 0.00 0.00 35.33 2.69
615 617 3.496331 GGGGTCATCCTTCTGTTTGAAA 58.504 45.455 0.00 0.00 33.79 2.69
616 618 3.895041 GGGGTCATCCTTCTGTTTGAAAA 59.105 43.478 0.00 0.00 33.79 2.29
617 619 4.343814 GGGGTCATCCTTCTGTTTGAAAAA 59.656 41.667 0.00 0.00 33.79 1.94
640 642 7.532682 AAAAACACTTTTAATCAACGCATGT 57.467 28.000 0.00 0.00 32.85 3.21
641 643 7.532682 AAAACACTTTTAATCAACGCATGTT 57.467 28.000 0.00 0.00 39.43 2.71
642 644 7.532682 AAACACTTTTAATCAACGCATGTTT 57.467 28.000 0.00 0.00 35.72 2.83
643 645 6.509317 ACACTTTTAATCAACGCATGTTTG 57.491 33.333 0.00 0.00 35.72 2.93
644 646 5.461737 ACACTTTTAATCAACGCATGTTTGG 59.538 36.000 8.73 0.00 35.72 3.28
645 647 4.447389 ACTTTTAATCAACGCATGTTTGGC 59.553 37.500 8.73 0.00 35.72 4.52
646 648 3.650070 TTAATCAACGCATGTTTGGCA 57.350 38.095 8.73 0.00 35.72 4.92
647 649 2.522836 AATCAACGCATGTTTGGCAA 57.477 40.000 0.00 0.00 35.72 4.52
648 650 2.522836 ATCAACGCATGTTTGGCAAA 57.477 40.000 8.93 8.93 35.72 3.68
649 651 2.299993 TCAACGCATGTTTGGCAAAA 57.700 40.000 15.29 5.80 35.72 2.44
650 652 2.831333 TCAACGCATGTTTGGCAAAAT 58.169 38.095 15.29 7.90 35.72 1.82
651 653 2.543012 TCAACGCATGTTTGGCAAAATG 59.457 40.909 15.29 18.95 35.72 2.32
652 654 2.522836 ACGCATGTTTGGCAAAATGA 57.477 40.000 25.51 12.34 0.00 2.57
653 655 2.831333 ACGCATGTTTGGCAAAATGAA 58.169 38.095 25.51 11.66 0.00 2.57
654 656 3.201290 ACGCATGTTTGGCAAAATGAAA 58.799 36.364 25.51 9.77 0.00 2.69
655 657 3.624861 ACGCATGTTTGGCAAAATGAAAA 59.375 34.783 25.51 8.43 0.00 2.29
656 658 4.275443 ACGCATGTTTGGCAAAATGAAAAT 59.725 33.333 25.51 9.86 0.00 1.82
657 659 5.468072 ACGCATGTTTGGCAAAATGAAAATA 59.532 32.000 25.51 2.97 0.00 1.40
658 660 5.789512 CGCATGTTTGGCAAAATGAAAATAC 59.210 36.000 25.51 10.99 0.00 1.89
659 661 6.565435 CGCATGTTTGGCAAAATGAAAATACA 60.565 34.615 25.51 15.12 0.00 2.29
660 662 7.137426 GCATGTTTGGCAAAATGAAAATACAA 58.863 30.769 25.51 0.00 0.00 2.41
661 663 7.808856 GCATGTTTGGCAAAATGAAAATACAAT 59.191 29.630 25.51 5.99 0.00 2.71
664 666 9.553064 TGTTTGGCAAAATGAAAATACAATACT 57.447 25.926 15.29 0.00 0.00 2.12
670 672 9.023967 GCAAAATGAAAATACAATACTAGGCAG 57.976 33.333 0.00 0.00 0.00 4.85
719 721 5.391312 ACTCACAATGTTGAAAATAGGCC 57.609 39.130 0.00 0.00 0.00 5.19
810 815 9.507198 ACGTAGCCGTCAACTTTAAAAAGTGTC 62.507 40.741 8.78 2.87 45.66 3.67
862 867 9.904198 TTGAGGAATAATGATGTGATTGTTAGA 57.096 29.630 0.00 0.00 0.00 2.10
915 920 1.534959 AGAGTGCAGACCAGCAGGA 60.535 57.895 0.35 0.00 46.69 3.86
1153 1158 1.794222 CTTCGTTCACCAATCGCCC 59.206 57.895 0.00 0.00 0.00 6.13
1166 1197 0.847373 ATCGCCCACCTCTCTCTCTA 59.153 55.000 0.00 0.00 0.00 2.43
1757 1817 3.046390 CTGAATATCTCGTGACTTCGGC 58.954 50.000 7.24 0.00 0.00 5.54
1772 1832 0.463654 TCGGCCGGATGAATTTCCAG 60.464 55.000 27.83 0.00 35.34 3.86
1807 1867 6.198216 GTGCTGAAAGAATTTTTACGAGCAAA 59.802 34.615 9.46 0.00 39.27 3.68
1808 1868 6.754209 TGCTGAAAGAATTTTTACGAGCAAAA 59.246 30.769 0.00 0.00 39.27 2.44
1831 1891 0.176680 GTGTCGATCCAGGCATCTGT 59.823 55.000 0.00 0.00 39.31 3.41
1833 1893 0.461548 GTCGATCCAGGCATCTGTCA 59.538 55.000 0.00 0.00 39.31 3.58
1837 1897 2.679059 CGATCCAGGCATCTGTCAAACT 60.679 50.000 0.00 0.00 39.31 2.66
1838 1898 2.957402 TCCAGGCATCTGTCAAACTT 57.043 45.000 0.00 0.00 39.31 2.66
1839 1899 2.507484 TCCAGGCATCTGTCAAACTTG 58.493 47.619 0.00 0.00 39.31 3.16
1841 1901 1.610038 CAGGCATCTGTCAAACTTGCA 59.390 47.619 0.00 0.00 36.30 4.08
1879 1944 5.702865 CTGCTAATGCTAAAACTTGCAGAA 58.297 37.500 0.00 0.00 46.40 3.02
1882 1947 6.026513 GCTAATGCTAAAACTTGCAGAAGAG 58.973 40.000 0.00 0.00 42.74 2.85
1883 1948 5.382618 AATGCTAAAACTTGCAGAAGAGG 57.617 39.130 0.00 0.00 42.74 3.69
1884 1949 4.085357 TGCTAAAACTTGCAGAAGAGGA 57.915 40.909 0.00 0.00 34.84 3.71
1895 1960 0.619832 AGAAGAGGATGAGCTGGGCA 60.620 55.000 0.00 0.00 0.00 5.36
1927 1998 4.065281 ACGCCTACACGCCAGACC 62.065 66.667 0.00 0.00 36.19 3.85
1928 1999 4.063967 CGCCTACACGCCAGACCA 62.064 66.667 0.00 0.00 0.00 4.02
1929 2000 2.125512 GCCTACACGCCAGACCAG 60.126 66.667 0.00 0.00 0.00 4.00
1930 2001 2.125512 CCTACACGCCAGACCAGC 60.126 66.667 0.00 0.00 0.00 4.85
1931 2002 2.656646 CTACACGCCAGACCAGCA 59.343 61.111 0.00 0.00 0.00 4.41
1932 2003 1.738099 CTACACGCCAGACCAGCAC 60.738 63.158 0.00 0.00 0.00 4.40
1933 2004 2.159819 CTACACGCCAGACCAGCACT 62.160 60.000 0.00 0.00 0.00 4.40
1934 2005 2.154798 TACACGCCAGACCAGCACTC 62.155 60.000 0.00 0.00 0.00 3.51
1935 2006 4.008933 ACGCCAGACCAGCACTCC 62.009 66.667 0.00 0.00 0.00 3.85
1937 2008 3.695606 GCCAGACCAGCACTCCGA 61.696 66.667 0.00 0.00 0.00 4.55
1938 2009 3.023949 GCCAGACCAGCACTCCGAT 62.024 63.158 0.00 0.00 0.00 4.18
1939 2010 1.142748 CCAGACCAGCACTCCGATC 59.857 63.158 0.00 0.00 0.00 3.69
1940 2011 1.607801 CCAGACCAGCACTCCGATCA 61.608 60.000 0.00 0.00 0.00 2.92
1941 2012 0.179116 CAGACCAGCACTCCGATCAG 60.179 60.000 0.00 0.00 0.00 2.90
1942 2013 0.613292 AGACCAGCACTCCGATCAGT 60.613 55.000 0.00 0.00 0.00 3.41
1961 2045 0.394762 TCATCATCCCAAGCCAGTGC 60.395 55.000 0.00 0.00 37.95 4.40
2086 2194 4.262277 CGTGCAAGTAGTACTAACGACATG 59.738 45.833 20.26 6.36 33.97 3.21
2094 2202 5.044428 AGTACTAACGACATGACAGACAC 57.956 43.478 0.00 0.00 0.00 3.67
2222 2330 2.126502 CAATTGCGCCCACGGTTC 60.127 61.111 4.18 0.00 40.57 3.62
2398 2536 1.238439 CACAAAGATGGGCGTTGAGT 58.762 50.000 0.00 0.00 38.08 3.41
2403 2541 3.418684 AAGATGGGCGTTGAGTTAAGT 57.581 42.857 0.00 0.00 0.00 2.24
2528 2666 6.539173 TGGGCTTAGTACATTTTCTTCTTCA 58.461 36.000 0.00 0.00 0.00 3.02
2602 2740 6.659242 TCTTTAGAGATTTTGACAATGACCCC 59.341 38.462 0.00 0.00 0.00 4.95
2619 4937 5.617252 TGACCCCGCTTCCTTATAAATTAG 58.383 41.667 0.00 0.00 0.00 1.73
2637 4955 6.566079 AATTAGATTCCAGTCTCATCACCA 57.434 37.500 0.00 0.00 0.00 4.17
2663 6919 1.969923 CCCAAATGAGAGGCCAAAACA 59.030 47.619 5.01 0.00 0.00 2.83
2696 6952 3.338275 TATTGCCCTCACCGGTGGC 62.338 63.158 33.40 28.38 45.56 5.01
2716 6972 1.626654 CGAGCTACAGTGCCAAACCG 61.627 60.000 0.00 0.00 0.00 4.44
2719 6975 1.674322 CTACAGTGCCAAACCGGGG 60.674 63.158 6.32 0.00 34.06 5.73
2783 7040 7.491048 GTGATCCAGTTTATTCTCAAGACTCTC 59.509 40.741 0.00 0.00 0.00 3.20
2792 7049 5.950758 TTCTCAAGACTCTCACTAGTCAC 57.049 43.478 6.76 0.00 46.89 3.67
2794 7051 5.626142 TCTCAAGACTCTCACTAGTCACTT 58.374 41.667 6.76 0.00 46.89 3.16
2795 7052 6.770542 TCTCAAGACTCTCACTAGTCACTTA 58.229 40.000 6.76 0.00 46.89 2.24
2796 7053 6.876789 TCTCAAGACTCTCACTAGTCACTTAG 59.123 42.308 6.76 0.00 46.89 2.18
2797 7054 6.535540 TCAAGACTCTCACTAGTCACTTAGT 58.464 40.000 6.76 0.00 46.89 2.24
2799 7056 6.116711 AGACTCTCACTAGTCACTTAGTCA 57.883 41.667 16.55 0.00 46.89 3.41
2800 7057 6.170506 AGACTCTCACTAGTCACTTAGTCAG 58.829 44.000 16.55 0.00 46.89 3.51
2801 7058 5.871834 ACTCTCACTAGTCACTTAGTCAGT 58.128 41.667 0.00 0.00 35.35 3.41
2802 7059 7.006865 ACTCTCACTAGTCACTTAGTCAGTA 57.993 40.000 0.00 0.00 32.76 2.74
2803 7060 6.875195 ACTCTCACTAGTCACTTAGTCAGTAC 59.125 42.308 0.00 0.00 32.76 2.73
2804 7061 6.171921 TCTCACTAGTCACTTAGTCAGTACC 58.828 44.000 0.00 0.00 32.76 3.34
2805 7062 5.251764 TCACTAGTCACTTAGTCAGTACCC 58.748 45.833 0.00 0.00 32.76 3.69
2806 7063 5.013913 TCACTAGTCACTTAGTCAGTACCCT 59.986 44.000 0.00 0.00 32.76 4.34
2807 7064 6.214208 TCACTAGTCACTTAGTCAGTACCCTA 59.786 42.308 0.00 0.00 32.76 3.53
2832 7089 1.745232 TTTGCCATGGGATGTACGAC 58.255 50.000 15.13 0.00 0.00 4.34
2884 7143 2.290960 GGCCCTCACTAACCATGACTTT 60.291 50.000 0.00 0.00 0.00 2.66
2905 7164 9.381033 GACTTTAAAATTACTACTCCCTCCTTC 57.619 37.037 0.00 0.00 0.00 3.46
2906 7165 8.327271 ACTTTAAAATTACTACTCCCTCCTTCC 58.673 37.037 0.00 0.00 0.00 3.46
2953 7230 1.164041 AGGCGTGCAGTTACAACCAC 61.164 55.000 0.00 0.00 0.00 4.16
2967 7244 0.739813 AACCACGCCAAGATCGCTAC 60.740 55.000 0.00 0.00 0.00 3.58
3013 7290 0.617820 GGTCTCTCCCCCTGTTAGCA 60.618 60.000 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.279271 AGCAGGTATGACTTGACACCC 59.721 52.381 0.00 0.00 0.00 4.61
10 11 2.165641 CGGTAGCAGGTATGACTTGACA 59.834 50.000 0.00 0.00 0.00 3.58
12 13 2.426024 GTCGGTAGCAGGTATGACTTGA 59.574 50.000 7.41 0.00 0.00 3.02
18 19 1.112113 ACCAGTCGGTAGCAGGTATG 58.888 55.000 0.00 0.00 46.71 2.39
43 44 2.280457 GCATAGGAGCCACCGAGC 60.280 66.667 0.00 0.00 44.74 5.03
75 76 5.554437 TCCAACAACAACAGGTATGACTA 57.446 39.130 0.00 0.00 0.00 2.59
84 85 4.282068 CACTTTCGATCCAACAACAACAG 58.718 43.478 0.00 0.00 0.00 3.16
98 99 1.478916 TCACAGTCACACCACTTTCGA 59.521 47.619 0.00 0.00 0.00 3.71
114 115 1.261938 CCATACCACCTCCCGTCACA 61.262 60.000 0.00 0.00 0.00 3.58
115 116 0.974010 TCCATACCACCTCCCGTCAC 60.974 60.000 0.00 0.00 0.00 3.67
119 120 1.410850 ATGCTCCATACCACCTCCCG 61.411 60.000 0.00 0.00 0.00 5.14
124 125 2.945668 GACAAAGATGCTCCATACCACC 59.054 50.000 0.00 0.00 0.00 4.61
160 161 1.884235 CCCCGATCAATTACCTCTGC 58.116 55.000 0.00 0.00 0.00 4.26
171 172 3.214123 CTACCGACGCCCCGATCA 61.214 66.667 0.00 0.00 0.00 2.92
191 192 3.560068 CGCATCTTACATTACCCTTGACC 59.440 47.826 0.00 0.00 0.00 4.02
224 225 5.873179 TTCCATCGGATTACACAAACTTC 57.127 39.130 0.00 0.00 0.00 3.01
232 233 3.193903 TCTCGTGTTTCCATCGGATTACA 59.806 43.478 0.00 0.00 0.00 2.41
244 245 4.358851 CCTGATCAGAGATCTCGTGTTTC 58.641 47.826 24.62 14.91 34.09 2.78
288 289 3.590824 CCTTTAGCAAGGGCACGG 58.409 61.111 0.00 0.00 45.63 4.94
301 302 0.250338 GAGCTTCGGTCACCACCTTT 60.250 55.000 0.00 0.00 41.17 3.11
304 305 2.741092 TGAGCTTCGGTCACCACC 59.259 61.111 0.00 0.00 35.04 4.61
317 319 4.336280 AGACTTTTATCCCCAAAGTGAGC 58.664 43.478 2.84 0.00 43.16 4.26
322 324 3.054655 TCCCGAGACTTTTATCCCCAAAG 60.055 47.826 0.00 0.00 37.29 2.77
339 341 1.306654 AACCATAGGCCAGTCCCGA 60.307 57.895 5.01 0.00 34.51 5.14
354 356 1.202268 CCGATAGTGACGAGTCCAACC 60.202 57.143 0.34 0.00 0.00 3.77
392 394 4.172807 TCCTAGGGTAAGCCTTCAAGAAA 58.827 43.478 9.46 0.00 34.45 2.52
395 397 3.375699 TCTCCTAGGGTAAGCCTTCAAG 58.624 50.000 9.46 0.00 34.45 3.02
396 398 3.484953 TCTCCTAGGGTAAGCCTTCAA 57.515 47.619 9.46 0.00 34.45 2.69
397 399 3.708236 ATCTCCTAGGGTAAGCCTTCA 57.292 47.619 9.46 0.00 34.45 3.02
398 400 5.088026 ACATATCTCCTAGGGTAAGCCTTC 58.912 45.833 9.46 0.00 34.45 3.46
399 401 5.094569 ACATATCTCCTAGGGTAAGCCTT 57.905 43.478 9.46 0.00 34.45 4.35
400 402 4.768807 ACATATCTCCTAGGGTAAGCCT 57.231 45.455 9.46 0.00 34.45 4.58
401 403 4.398673 CGTACATATCTCCTAGGGTAAGCC 59.601 50.000 9.46 0.00 0.00 4.35
402 404 5.251764 TCGTACATATCTCCTAGGGTAAGC 58.748 45.833 9.46 0.00 0.00 3.09
403 405 6.594937 GTCTCGTACATATCTCCTAGGGTAAG 59.405 46.154 9.46 4.72 0.00 2.34
404 406 6.043590 TGTCTCGTACATATCTCCTAGGGTAA 59.956 42.308 9.46 0.00 31.43 2.85
405 407 5.545335 TGTCTCGTACATATCTCCTAGGGTA 59.455 44.000 9.46 0.00 31.43 3.69
406 408 4.350225 TGTCTCGTACATATCTCCTAGGGT 59.650 45.833 9.46 0.00 31.43 4.34
407 409 4.907809 TGTCTCGTACATATCTCCTAGGG 58.092 47.826 9.46 0.00 31.43 3.53
419 421 5.204409 ACCAAAAGTACATGTCTCGTACA 57.796 39.130 0.00 0.00 41.40 2.90
420 422 6.018507 ACAAACCAAAAGTACATGTCTCGTAC 60.019 38.462 0.00 0.00 39.64 3.67
421 423 6.050432 ACAAACCAAAAGTACATGTCTCGTA 58.950 36.000 0.00 0.00 0.00 3.43
422 424 4.879545 ACAAACCAAAAGTACATGTCTCGT 59.120 37.500 0.00 0.00 0.00 4.18
423 425 5.418310 ACAAACCAAAAGTACATGTCTCG 57.582 39.130 0.00 0.00 0.00 4.04
424 426 6.413818 CGAAACAAACCAAAAGTACATGTCTC 59.586 38.462 0.00 0.00 0.00 3.36
425 427 6.262601 CGAAACAAACCAAAAGTACATGTCT 58.737 36.000 0.00 0.00 0.00 3.41
426 428 5.457473 CCGAAACAAACCAAAAGTACATGTC 59.543 40.000 0.00 0.00 0.00 3.06
427 429 5.105675 ACCGAAACAAACCAAAAGTACATGT 60.106 36.000 2.69 2.69 0.00 3.21
428 430 5.344884 ACCGAAACAAACCAAAAGTACATG 58.655 37.500 0.00 0.00 0.00 3.21
429 431 5.358725 AGACCGAAACAAACCAAAAGTACAT 59.641 36.000 0.00 0.00 0.00 2.29
430 432 4.701171 AGACCGAAACAAACCAAAAGTACA 59.299 37.500 0.00 0.00 0.00 2.90
431 433 5.239359 AGACCGAAACAAACCAAAAGTAC 57.761 39.130 0.00 0.00 0.00 2.73
432 434 7.571080 AATAGACCGAAACAAACCAAAAGTA 57.429 32.000 0.00 0.00 0.00 2.24
433 435 6.459670 AATAGACCGAAACAAACCAAAAGT 57.540 33.333 0.00 0.00 0.00 2.66
434 436 7.916450 TGTTAATAGACCGAAACAAACCAAAAG 59.084 33.333 0.00 0.00 0.00 2.27
435 437 7.769220 TGTTAATAGACCGAAACAAACCAAAA 58.231 30.769 0.00 0.00 0.00 2.44
436 438 7.330900 TGTTAATAGACCGAAACAAACCAAA 57.669 32.000 0.00 0.00 0.00 3.28
437 439 6.939132 TGTTAATAGACCGAAACAAACCAA 57.061 33.333 0.00 0.00 0.00 3.67
438 440 8.618702 TTATGTTAATAGACCGAAACAAACCA 57.381 30.769 0.00 0.00 35.63 3.67
439 441 8.179615 CCTTATGTTAATAGACCGAAACAAACC 58.820 37.037 0.00 0.00 35.63 3.27
440 442 8.724229 ACCTTATGTTAATAGACCGAAACAAAC 58.276 33.333 0.00 0.00 35.63 2.93
441 443 8.851541 ACCTTATGTTAATAGACCGAAACAAA 57.148 30.769 0.00 0.00 35.63 2.83
442 444 8.851541 AACCTTATGTTAATAGACCGAAACAA 57.148 30.769 0.00 0.00 35.63 2.83
443 445 9.590451 CTAACCTTATGTTAATAGACCGAAACA 57.410 33.333 0.00 0.00 38.91 2.83
444 446 9.591792 ACTAACCTTATGTTAATAGACCGAAAC 57.408 33.333 0.00 0.00 38.91 2.78
445 447 9.590451 CACTAACCTTATGTTAATAGACCGAAA 57.410 33.333 0.00 0.00 38.91 3.46
446 448 8.199449 CCACTAACCTTATGTTAATAGACCGAA 58.801 37.037 0.00 0.00 38.91 4.30
447 449 7.342799 ACCACTAACCTTATGTTAATAGACCGA 59.657 37.037 0.00 0.00 38.91 4.69
448 450 7.495055 ACCACTAACCTTATGTTAATAGACCG 58.505 38.462 0.00 0.00 38.91 4.79
455 457 9.850198 ACAAGTTAACCACTAACCTTATGTTAA 57.150 29.630 0.88 0.00 40.84 2.01
456 458 9.275398 CACAAGTTAACCACTAACCTTATGTTA 57.725 33.333 0.88 0.00 40.84 2.41
457 459 7.994334 TCACAAGTTAACCACTAACCTTATGTT 59.006 33.333 0.88 0.00 40.84 2.71
458 460 7.511268 TCACAAGTTAACCACTAACCTTATGT 58.489 34.615 0.88 0.00 40.84 2.29
459 461 7.972832 TCACAAGTTAACCACTAACCTTATG 57.027 36.000 0.88 0.00 40.84 1.90
460 462 7.174426 GCTTCACAAGTTAACCACTAACCTTAT 59.826 37.037 0.88 0.00 40.84 1.73
461 463 6.484308 GCTTCACAAGTTAACCACTAACCTTA 59.516 38.462 0.88 0.00 40.84 2.69
462 464 5.298527 GCTTCACAAGTTAACCACTAACCTT 59.701 40.000 0.88 0.00 40.84 3.50
463 465 4.820173 GCTTCACAAGTTAACCACTAACCT 59.180 41.667 0.88 0.00 40.84 3.50
464 466 4.820173 AGCTTCACAAGTTAACCACTAACC 59.180 41.667 0.88 0.00 40.84 2.85
465 467 6.704937 AGTAGCTTCACAAGTTAACCACTAAC 59.295 38.462 0.88 0.00 40.33 2.34
466 468 6.704493 CAGTAGCTTCACAAGTTAACCACTAA 59.296 38.462 0.88 0.00 32.94 2.24
467 469 6.220930 CAGTAGCTTCACAAGTTAACCACTA 58.779 40.000 0.88 0.00 32.94 2.74
468 470 5.057149 CAGTAGCTTCACAAGTTAACCACT 58.943 41.667 0.88 0.00 37.30 4.00
469 471 4.319549 GCAGTAGCTTCACAAGTTAACCAC 60.320 45.833 0.88 0.00 37.91 4.16
470 472 3.813166 GCAGTAGCTTCACAAGTTAACCA 59.187 43.478 0.88 0.00 37.91 3.67
471 473 3.188667 GGCAGTAGCTTCACAAGTTAACC 59.811 47.826 0.88 0.00 41.70 2.85
472 474 3.120649 CGGCAGTAGCTTCACAAGTTAAC 60.121 47.826 0.00 0.00 41.70 2.01
473 475 3.064207 CGGCAGTAGCTTCACAAGTTAA 58.936 45.455 0.00 0.00 41.70 2.01
474 476 2.683968 CGGCAGTAGCTTCACAAGTTA 58.316 47.619 0.00 0.00 41.70 2.24
475 477 1.512926 CGGCAGTAGCTTCACAAGTT 58.487 50.000 0.00 0.00 41.70 2.66
476 478 0.951040 GCGGCAGTAGCTTCACAAGT 60.951 55.000 0.00 0.00 41.70 3.16
477 479 1.790387 GCGGCAGTAGCTTCACAAG 59.210 57.895 0.00 0.00 41.70 3.16
478 480 2.027073 CGCGGCAGTAGCTTCACAA 61.027 57.895 0.00 0.00 41.70 3.33
479 481 2.432456 CGCGGCAGTAGCTTCACA 60.432 61.111 0.00 0.00 41.70 3.58
480 482 2.432628 ACGCGGCAGTAGCTTCAC 60.433 61.111 12.47 0.00 41.70 3.18
481 483 2.432456 CACGCGGCAGTAGCTTCA 60.432 61.111 12.47 0.00 41.70 3.02
482 484 3.188786 CCACGCGGCAGTAGCTTC 61.189 66.667 12.47 0.00 41.70 3.86
493 495 3.027170 GAAGGTCACATGCCACGCG 62.027 63.158 3.53 3.53 0.00 6.01
494 496 2.870372 GAAGGTCACATGCCACGC 59.130 61.111 0.00 0.00 0.00 5.34
495 497 3.168271 CGAAGGTCACATGCCACG 58.832 61.111 0.00 0.00 0.00 4.94
527 529 9.515020 GAAAATCCAACAGCATAATAAATTCGA 57.485 29.630 0.00 0.00 0.00 3.71
528 530 9.520204 AGAAAATCCAACAGCATAATAAATTCG 57.480 29.630 0.00 0.00 0.00 3.34
545 547 9.613428 CGGAGCCATATATTATTAGAAAATCCA 57.387 33.333 0.00 0.00 0.00 3.41
546 548 9.614792 ACGGAGCCATATATTATTAGAAAATCC 57.385 33.333 0.00 0.00 0.00 3.01
548 550 8.893727 GCACGGAGCCATATATTATTAGAAAAT 58.106 33.333 0.00 0.00 37.23 1.82
549 551 7.880713 TGCACGGAGCCATATATTATTAGAAAA 59.119 33.333 0.00 0.00 44.83 2.29
550 552 7.390823 TGCACGGAGCCATATATTATTAGAAA 58.609 34.615 0.00 0.00 44.83 2.52
551 553 6.941857 TGCACGGAGCCATATATTATTAGAA 58.058 36.000 0.00 0.00 44.83 2.10
552 554 6.538945 TGCACGGAGCCATATATTATTAGA 57.461 37.500 0.00 0.00 44.83 2.10
553 555 6.986231 TGATGCACGGAGCCATATATTATTAG 59.014 38.462 0.00 0.00 44.83 1.73
554 556 6.761242 GTGATGCACGGAGCCATATATTATTA 59.239 38.462 0.00 0.00 44.83 0.98
555 557 5.586243 GTGATGCACGGAGCCATATATTATT 59.414 40.000 0.00 0.00 44.83 1.40
556 558 5.104776 AGTGATGCACGGAGCCATATATTAT 60.105 40.000 0.00 0.00 44.83 1.28
557 559 4.222810 AGTGATGCACGGAGCCATATATTA 59.777 41.667 0.00 0.00 44.83 0.98
558 560 3.008375 AGTGATGCACGGAGCCATATATT 59.992 43.478 0.00 0.00 44.83 1.28
559 561 2.568956 AGTGATGCACGGAGCCATATAT 59.431 45.455 0.00 0.00 44.83 0.86
560 562 1.970640 AGTGATGCACGGAGCCATATA 59.029 47.619 0.00 0.00 44.83 0.86
561 563 0.761187 AGTGATGCACGGAGCCATAT 59.239 50.000 0.00 0.00 44.83 1.78
562 564 0.104855 GAGTGATGCACGGAGCCATA 59.895 55.000 0.00 0.00 44.83 2.74
563 565 1.153289 GAGTGATGCACGGAGCCAT 60.153 57.895 0.00 0.00 44.83 4.40
564 566 2.110757 TTGAGTGATGCACGGAGCCA 62.111 55.000 0.00 0.00 44.83 4.75
565 567 0.745845 ATTGAGTGATGCACGGAGCC 60.746 55.000 0.00 0.00 44.83 4.70
566 568 0.376152 CATTGAGTGATGCACGGAGC 59.624 55.000 0.00 0.00 45.96 4.70
574 576 2.350804 CCGACTTCTGCATTGAGTGATG 59.649 50.000 1.98 0.00 0.00 3.07
575 577 2.625737 CCGACTTCTGCATTGAGTGAT 58.374 47.619 1.98 0.00 0.00 3.06
576 578 1.338105 CCCGACTTCTGCATTGAGTGA 60.338 52.381 1.98 0.00 0.00 3.41
577 579 1.081892 CCCGACTTCTGCATTGAGTG 58.918 55.000 1.98 0.00 0.00 3.51
578 580 0.036010 CCCCGACTTCTGCATTGAGT 60.036 55.000 0.00 0.00 0.00 3.41
579 581 0.036010 ACCCCGACTTCTGCATTGAG 60.036 55.000 0.00 0.00 0.00 3.02
580 582 0.036388 GACCCCGACTTCTGCATTGA 60.036 55.000 0.00 0.00 0.00 2.57
581 583 0.321564 TGACCCCGACTTCTGCATTG 60.322 55.000 0.00 0.00 0.00 2.82
582 584 0.620556 ATGACCCCGACTTCTGCATT 59.379 50.000 0.00 0.00 0.00 3.56
583 585 0.179000 GATGACCCCGACTTCTGCAT 59.821 55.000 0.00 0.00 0.00 3.96
584 586 1.596934 GATGACCCCGACTTCTGCA 59.403 57.895 0.00 0.00 0.00 4.41
585 587 1.153349 GGATGACCCCGACTTCTGC 60.153 63.158 0.00 0.00 0.00 4.26
586 588 0.905357 AAGGATGACCCCGACTTCTG 59.095 55.000 0.00 0.00 36.73 3.02
587 589 1.196012 GAAGGATGACCCCGACTTCT 58.804 55.000 0.00 0.00 35.78 2.85
588 590 1.134670 CAGAAGGATGACCCCGACTTC 60.135 57.143 0.00 0.00 38.20 3.01
589 591 0.905357 CAGAAGGATGACCCCGACTT 59.095 55.000 0.00 0.00 36.73 3.01
590 592 0.252284 ACAGAAGGATGACCCCGACT 60.252 55.000 0.00 0.00 36.73 4.18
591 593 0.613777 AACAGAAGGATGACCCCGAC 59.386 55.000 0.00 0.00 36.73 4.79
592 594 1.003118 CAAACAGAAGGATGACCCCGA 59.997 52.381 0.00 0.00 36.73 5.14
593 595 1.003118 TCAAACAGAAGGATGACCCCG 59.997 52.381 0.00 0.00 36.73 5.73
594 596 2.879103 TCAAACAGAAGGATGACCCC 57.121 50.000 0.00 0.00 36.73 4.95
595 597 5.529581 TTTTTCAAACAGAAGGATGACCC 57.470 39.130 0.00 0.00 37.57 4.46
616 618 7.532682 ACATGCGTTGATTAAAAGTGTTTTT 57.467 28.000 0.00 0.00 39.69 1.94
617 619 7.532682 AACATGCGTTGATTAAAAGTGTTTT 57.467 28.000 0.00 0.00 32.81 2.43
618 620 7.397970 CAAACATGCGTTGATTAAAAGTGTTT 58.602 30.769 4.10 0.00 37.64 2.83
619 621 6.019156 CCAAACATGCGTTGATTAAAAGTGTT 60.019 34.615 10.53 0.00 34.86 3.32
620 622 5.461737 CCAAACATGCGTTGATTAAAAGTGT 59.538 36.000 10.53 0.00 34.86 3.55
621 623 5.612276 GCCAAACATGCGTTGATTAAAAGTG 60.612 40.000 10.53 0.00 34.86 3.16
622 624 4.447389 GCCAAACATGCGTTGATTAAAAGT 59.553 37.500 10.53 0.00 34.86 2.66
623 625 4.447054 TGCCAAACATGCGTTGATTAAAAG 59.553 37.500 10.53 0.00 34.86 2.27
624 626 4.371786 TGCCAAACATGCGTTGATTAAAA 58.628 34.783 10.53 0.00 34.86 1.52
625 627 3.982475 TGCCAAACATGCGTTGATTAAA 58.018 36.364 10.53 0.00 34.86 1.52
626 628 3.650070 TGCCAAACATGCGTTGATTAA 57.350 38.095 10.53 0.00 34.86 1.40
627 629 3.650070 TTGCCAAACATGCGTTGATTA 57.350 38.095 10.53 0.00 34.86 1.75
628 630 2.522836 TTGCCAAACATGCGTTGATT 57.477 40.000 10.53 0.00 34.86 2.57
629 631 2.522836 TTTGCCAAACATGCGTTGAT 57.477 40.000 10.53 0.00 34.86 2.57
630 632 2.299993 TTTTGCCAAACATGCGTTGA 57.700 40.000 10.53 0.00 34.86 3.18
631 633 2.543012 TCATTTTGCCAAACATGCGTTG 59.457 40.909 0.00 0.00 34.86 4.10
632 634 2.831333 TCATTTTGCCAAACATGCGTT 58.169 38.095 0.00 0.00 36.73 4.84
633 635 2.522836 TCATTTTGCCAAACATGCGT 57.477 40.000 0.00 0.00 0.00 5.24
634 636 3.874400 TTTCATTTTGCCAAACATGCG 57.126 38.095 0.00 0.00 0.00 4.73
635 637 6.666417 TGTATTTTCATTTTGCCAAACATGC 58.334 32.000 0.00 0.00 0.00 4.06
638 640 9.553064 AGTATTGTATTTTCATTTTGCCAAACA 57.447 25.926 0.00 0.00 0.00 2.83
641 643 9.868277 CCTAGTATTGTATTTTCATTTTGCCAA 57.132 29.630 0.00 0.00 0.00 4.52
642 644 7.978975 GCCTAGTATTGTATTTTCATTTTGCCA 59.021 33.333 0.00 0.00 0.00 4.92
643 645 7.978975 TGCCTAGTATTGTATTTTCATTTTGCC 59.021 33.333 0.00 0.00 0.00 4.52
644 646 8.925161 TGCCTAGTATTGTATTTTCATTTTGC 57.075 30.769 0.00 0.00 0.00 3.68
647 649 9.686683 AGACTGCCTAGTATTGTATTTTCATTT 57.313 29.630 0.00 0.00 37.25 2.32
649 651 9.765795 GTAGACTGCCTAGTATTGTATTTTCAT 57.234 33.333 0.00 0.00 37.25 2.57
650 652 8.755028 TGTAGACTGCCTAGTATTGTATTTTCA 58.245 33.333 0.00 0.00 37.25 2.69
651 653 9.765795 ATGTAGACTGCCTAGTATTGTATTTTC 57.234 33.333 0.00 0.00 37.25 2.29
654 656 9.765795 GAAATGTAGACTGCCTAGTATTGTATT 57.234 33.333 0.00 0.00 37.25 1.89
655 657 9.148879 AGAAATGTAGACTGCCTAGTATTGTAT 57.851 33.333 0.00 0.00 37.25 2.29
656 658 8.534954 AGAAATGTAGACTGCCTAGTATTGTA 57.465 34.615 0.00 0.00 37.25 2.41
657 659 7.124298 TGAGAAATGTAGACTGCCTAGTATTGT 59.876 37.037 0.00 0.00 37.25 2.71
658 660 7.492524 TGAGAAATGTAGACTGCCTAGTATTG 58.507 38.462 0.00 0.00 37.25 1.90
659 661 7.661536 TGAGAAATGTAGACTGCCTAGTATT 57.338 36.000 0.00 0.00 37.25 1.89
660 662 7.847711 ATGAGAAATGTAGACTGCCTAGTAT 57.152 36.000 0.00 0.00 37.25 2.12
661 663 7.661536 AATGAGAAATGTAGACTGCCTAGTA 57.338 36.000 0.00 0.00 37.25 1.82
662 664 6.552445 AATGAGAAATGTAGACTGCCTAGT 57.448 37.500 0.00 0.00 40.66 2.57
663 665 9.553064 AATTAATGAGAAATGTAGACTGCCTAG 57.447 33.333 0.00 0.00 0.00 3.02
719 721 4.930963 TGCAAATTGTACAAAGGTGACAG 58.069 39.130 13.23 0.00 0.00 3.51
792 797 5.505159 CGGAGGGACACTTTTTAAAGTTGAC 60.505 44.000 5.16 3.10 46.52 3.18
796 801 4.601765 CGCGGAGGGACACTTTTTAAAGT 61.602 47.826 0.00 2.10 46.70 2.66
810 815 2.755542 CTTGGATCGATCGCGGAGGG 62.756 65.000 18.81 1.79 44.04 4.30
862 867 3.138884 AGCATTTTGCCCGGAAATTTT 57.861 38.095 0.73 0.00 46.52 1.82
1082 1087 4.508763 GGGAGACCGAGATTTATAGAGGGA 60.509 50.000 0.00 0.00 43.64 4.20
1153 1158 3.323691 TCGGAGAGATAGAGAGAGAGGTG 59.676 52.174 0.00 0.00 0.00 4.00
1322 1369 4.953010 TTCTGCAGCAGCGGCCAA 62.953 61.111 18.43 3.30 46.95 4.52
1577 1624 1.606668 AGAAAACAAAATCGAGCCGCA 59.393 42.857 0.00 0.00 0.00 5.69
1579 1626 2.225491 TCCAGAAAACAAAATCGAGCCG 59.775 45.455 0.00 0.00 0.00 5.52
1580 1627 3.253432 ACTCCAGAAAACAAAATCGAGCC 59.747 43.478 0.00 0.00 0.00 4.70
1619 1666 9.448587 AACCCCTATTCTGTTCTATAACATACT 57.551 33.333 0.00 0.00 44.43 2.12
1658 1718 8.127327 CAGGAATCATTACTAATTCACTTGCAG 58.873 37.037 0.00 0.00 34.28 4.41
1659 1719 7.415541 GCAGGAATCATTACTAATTCACTTGCA 60.416 37.037 0.00 0.00 36.43 4.08
1757 1817 2.435372 TTCCCTGGAAATTCATCCGG 57.565 50.000 0.00 0.00 44.21 5.14
1772 1832 4.320608 TTCTTTCAGCACAACAATTCCC 57.679 40.909 0.00 0.00 0.00 3.97
1807 1867 2.198827 TGCCTGGATCGACACATTTT 57.801 45.000 0.00 0.00 0.00 1.82
1808 1868 2.092753 AGATGCCTGGATCGACACATTT 60.093 45.455 0.00 0.00 0.00 2.32
1817 1877 2.996631 AGTTTGACAGATGCCTGGATC 58.003 47.619 0.00 0.00 44.60 3.36
1862 1927 4.655963 TCCTCTTCTGCAAGTTTTAGCAT 58.344 39.130 0.00 0.00 40.42 3.79
1879 1944 3.644719 CTGCCCAGCTCATCCTCT 58.355 61.111 0.00 0.00 0.00 3.69
1895 1960 4.969196 CGTGTGTGTGGCTCGGCT 62.969 66.667 0.00 0.00 0.00 5.52
1927 1998 1.135721 TGATGACTGATCGGAGTGCTG 59.864 52.381 9.00 0.00 33.17 4.41
1928 1999 1.478631 TGATGACTGATCGGAGTGCT 58.521 50.000 9.00 0.00 33.17 4.40
1929 2000 2.402305 GATGATGACTGATCGGAGTGC 58.598 52.381 9.00 0.00 33.17 4.40
1930 2001 2.288702 GGGATGATGACTGATCGGAGTG 60.289 54.545 9.00 0.00 33.17 3.51
1931 2002 1.967066 GGGATGATGACTGATCGGAGT 59.033 52.381 9.00 0.00 33.17 3.85
1932 2003 1.966354 TGGGATGATGACTGATCGGAG 59.034 52.381 9.00 0.00 33.17 4.63
1933 2004 2.086610 TGGGATGATGACTGATCGGA 57.913 50.000 9.00 0.00 33.17 4.55
1934 2005 2.763933 CTTGGGATGATGACTGATCGG 58.236 52.381 0.00 0.00 33.17 4.18
1935 2006 2.141517 GCTTGGGATGATGACTGATCG 58.858 52.381 0.00 0.00 33.17 3.69
1936 2007 2.158711 TGGCTTGGGATGATGACTGATC 60.159 50.000 0.00 0.00 0.00 2.92
1937 2008 1.848388 TGGCTTGGGATGATGACTGAT 59.152 47.619 0.00 0.00 0.00 2.90
1938 2009 1.211212 CTGGCTTGGGATGATGACTGA 59.789 52.381 0.00 0.00 0.00 3.41
1939 2010 1.064906 ACTGGCTTGGGATGATGACTG 60.065 52.381 0.00 0.00 0.00 3.51
1940 2011 1.064906 CACTGGCTTGGGATGATGACT 60.065 52.381 0.00 0.00 0.00 3.41
1941 2012 1.386533 CACTGGCTTGGGATGATGAC 58.613 55.000 0.00 0.00 0.00 3.06
1942 2013 0.394762 GCACTGGCTTGGGATGATGA 60.395 55.000 0.00 0.00 36.96 2.92
1961 2045 1.008079 GGGAACGTATAGCGGACGG 60.008 63.158 11.75 0.00 44.58 4.79
2086 2194 2.479837 TCAAACATGTCCGTGTCTGTC 58.520 47.619 0.00 0.00 0.00 3.51
2094 2202 2.223249 CCGGCTAATTCAAACATGTCCG 60.223 50.000 0.00 4.21 0.00 4.79
2222 2330 2.731968 GCGGCAGACAATTGTGTTATGG 60.732 50.000 17.58 0.84 38.41 2.74
2403 2541 5.470437 TGCGTTTCATGTGTTCACCTAATAA 59.530 36.000 0.37 0.00 0.00 1.40
2602 2740 8.608844 ACTGGAATCTAATTTATAAGGAAGCG 57.391 34.615 0.00 0.00 0.00 4.68
2619 4937 6.429385 GGAATTATGGTGATGAGACTGGAATC 59.571 42.308 0.00 0.00 0.00 2.52
2637 4955 4.541250 TGGCCTCTCATTTGGGAATTAT 57.459 40.909 3.32 0.00 0.00 1.28
2696 6952 1.298859 GGTTTGGCACTGTAGCTCGG 61.299 60.000 0.00 0.00 34.17 4.63
2697 6953 1.626654 CGGTTTGGCACTGTAGCTCG 61.627 60.000 0.00 0.00 34.17 5.03
2716 6972 2.282603 TTTTGTACTGGCCGCCCC 60.283 61.111 7.03 0.00 0.00 5.80
2719 6975 2.034179 AGTTTTCTTTTGTACTGGCCGC 59.966 45.455 0.00 0.00 0.00 6.53
2752 7009 6.769134 TGAGAATAAACTGGATCACGAGTA 57.231 37.500 0.00 0.00 34.16 2.59
2757 7014 7.327214 AGAGTCTTGAGAATAAACTGGATCAC 58.673 38.462 0.00 0.00 0.00 3.06
2783 7040 5.254901 AGGGTACTGACTAAGTGACTAGTG 58.745 45.833 0.00 0.00 40.26 2.74
2792 7049 8.305317 GGCAAATATAGTAGGGTACTGACTAAG 58.695 40.741 0.00 0.00 39.81 2.18
2794 7051 7.299896 TGGCAAATATAGTAGGGTACTGACTA 58.700 38.462 0.00 0.00 39.81 2.59
2795 7052 6.141083 TGGCAAATATAGTAGGGTACTGACT 58.859 40.000 0.00 0.00 39.81 3.41
2796 7053 6.415206 TGGCAAATATAGTAGGGTACTGAC 57.585 41.667 0.00 0.00 39.81 3.51
2797 7054 6.013725 CCATGGCAAATATAGTAGGGTACTGA 60.014 42.308 0.00 0.00 39.81 3.41
2799 7056 5.250774 CCCATGGCAAATATAGTAGGGTACT 59.749 44.000 6.09 0.00 42.68 2.73
2800 7057 5.249852 TCCCATGGCAAATATAGTAGGGTAC 59.750 44.000 6.09 0.00 35.31 3.34
2801 7058 5.416858 TCCCATGGCAAATATAGTAGGGTA 58.583 41.667 6.09 0.00 35.31 3.69
2802 7059 4.247814 TCCCATGGCAAATATAGTAGGGT 58.752 43.478 6.09 0.00 35.31 4.34
2803 7060 4.927267 TCCCATGGCAAATATAGTAGGG 57.073 45.455 6.09 0.00 35.09 3.53
2804 7061 5.819991 ACATCCCATGGCAAATATAGTAGG 58.180 41.667 6.09 0.00 33.60 3.18
2805 7062 6.535150 CGTACATCCCATGGCAAATATAGTAG 59.465 42.308 6.09 0.00 33.60 2.57
2806 7063 6.211785 TCGTACATCCCATGGCAAATATAGTA 59.788 38.462 6.09 0.00 33.60 1.82
2807 7064 5.012664 TCGTACATCCCATGGCAAATATAGT 59.987 40.000 6.09 0.00 33.60 2.12
2816 7073 2.244651 GCGTCGTACATCCCATGGC 61.245 63.158 6.09 0.00 33.60 4.40
2832 7089 1.883275 TGTTACCAAAAGGGATGTGCG 59.117 47.619 0.00 0.00 41.15 5.34
2839 7096 2.774687 AGCTACGTGTTACCAAAAGGG 58.225 47.619 0.00 0.00 44.81 3.95
2876 7133 9.110502 GGAGGGAGTAGTAATTTTAAAGTCATG 57.889 37.037 0.00 0.00 0.00 3.07
2877 7134 9.059023 AGGAGGGAGTAGTAATTTTAAAGTCAT 57.941 33.333 0.00 0.00 0.00 3.06
2884 7143 6.273889 TGGGAAGGAGGGAGTAGTAATTTTA 58.726 40.000 0.00 0.00 0.00 1.52
2905 7164 4.305539 TGGGACTGCATGATATAATGGG 57.694 45.455 0.00 0.00 0.00 4.00
2906 7165 9.803507 ATATTATGGGACTGCATGATATAATGG 57.196 33.333 0.00 0.00 0.00 3.16
2953 7230 2.029728 CAGAAAAGTAGCGATCTTGGCG 59.970 50.000 0.00 0.00 35.00 5.69
2985 7262 3.148279 GGAGAGACCCGTCGCCAT 61.148 66.667 0.00 0.00 34.09 4.40


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

AutoCloner maintained by Alex Coulton.