Multiple sequence alignment - TraesCS1D01G020400

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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 TraesCS1D01G020400 chr1D 100.000 3711 0 0 1 3711 8796046 8799756 0.000000e+00 6854.0
1 TraesCS1D01G020400 chr1D 94.872 39 2 0 1963 2001 208823354 208823392 1.110000e-05 62.1
2 TraesCS1D01G020400 chr1D 97.222 36 1 0 1966 2001 228301470 228301435 1.110000e-05 62.1
3 TraesCS1D01G020400 chr1D 97.143 35 0 1 1961 1995 301636490 301636457 1.440000e-04 58.4
4 TraesCS1D01G020400 chr1D 70.695 331 80 14 2271 2591 481807504 481807827 1.440000e-04 58.4
5 TraesCS1D01G020400 chr1A 92.942 2111 112 22 945 3031 10126449 10128546 0.000000e+00 3038.0
6 TraesCS1D01G020400 chr1A 91.729 399 30 3 545 941 10125877 10126274 5.420000e-153 551.0
7 TraesCS1D01G020400 chr1A 87.037 378 21 7 14 389 10125534 10125885 5.770000e-108 401.0
8 TraesCS1D01G020400 chr1B 92.908 1114 54 14 1883 2980 11936950 11938054 0.000000e+00 1596.0
9 TraesCS1D01G020400 chr1B 95.536 896 40 0 945 1840 11935656 11936551 0.000000e+00 1434.0
10 TraesCS1D01G020400 chr1B 71.631 282 71 8 2255 2530 670413481 670413759 6.650000e-08 69.4
11 TraesCS1D01G020400 chr1B 97.222 36 1 0 1966 2001 327842105 327842070 1.110000e-05 62.1
12 TraesCS1D01G020400 chr3D 94.186 688 28 9 3032 3711 542074837 542074154 0.000000e+00 1038.0
13 TraesCS1D01G020400 chr3D 96.450 169 6 0 388 556 545912333 545912165 2.820000e-71 279.0
14 TraesCS1D01G020400 chr4A 90.988 688 47 9 3032 3711 615448713 615449393 0.000000e+00 913.0
15 TraesCS1D01G020400 chr4A 89.099 688 63 10 3029 3711 633698317 633698997 0.000000e+00 845.0
16 TraesCS1D01G020400 chr4A 100.000 29 0 0 2990 3018 24015104 24015076 2.000000e-03 54.7
17 TraesCS1D01G020400 chr5A 89.680 688 53 14 3032 3711 501557064 501556387 0.000000e+00 861.0
18 TraesCS1D01G020400 chr7A 89.535 688 55 13 3032 3711 101702051 101702729 0.000000e+00 856.0
19 TraesCS1D01G020400 chr7A 89.343 685 64 8 3031 3711 684300063 684300742 0.000000e+00 852.0
20 TraesCS1D01G020400 chr7A 97.024 168 5 0 388 555 643186890 643187057 2.180000e-72 283.0
21 TraesCS1D01G020400 chr7A 97.143 35 0 1 1961 1995 616747200 616747233 1.440000e-04 58.4
22 TraesCS1D01G020400 chr2A 89.436 691 54 17 3031 3711 665067203 665067884 0.000000e+00 854.0
23 TraesCS1D01G020400 chr2A 89.359 686 61 10 3030 3711 692152587 692151910 0.000000e+00 852.0
24 TraesCS1D01G020400 chr3A 89.343 685 61 9 3031 3711 705507244 705506568 0.000000e+00 850.0
25 TraesCS1D01G020400 chr3A 95.455 44 2 0 2990 3033 412832654 412832697 1.850000e-08 71.3
26 TraesCS1D01G020400 chr7D 97.605 167 4 0 388 554 312574292 312574126 1.690000e-73 287.0
27 TraesCS1D01G020400 chr7D 97.576 165 4 0 388 552 363148997 363148833 2.180000e-72 283.0
28 TraesCS1D01G020400 chr2B 97.041 169 5 0 388 556 519599025 519598857 6.070000e-73 285.0
29 TraesCS1D01G020400 chr6D 94.505 182 10 0 387 568 305359792 305359611 7.850000e-72 281.0
30 TraesCS1D01G020400 chr6A 97.006 167 5 0 387 553 458217709 458217875 7.850000e-72 281.0
31 TraesCS1D01G020400 chr6A 100.000 33 0 0 3001 3033 602239696 602239728 1.110000e-05 62.1
32 TraesCS1D01G020400 chr4D 95.930 172 7 0 385 556 93336681 93336852 2.820000e-71 279.0
33 TraesCS1D01G020400 chr7B 93.011 186 9 4 387 571 708478616 708478434 6.110000e-68 268.0
34 TraesCS1D01G020400 chr5D 95.556 45 2 0 2989 3033 520473118 520473074 5.140000e-09 73.1
35 TraesCS1D01G020400 chr6B 94.444 36 2 0 1965 2000 49827725 49827690 5.180000e-04 56.5
36 TraesCS1D01G020400 chr3B 94.595 37 1 1 2988 3024 773514806 773514771 5.180000e-04 56.5
37 TraesCS1D01G020400 chr3B 94.444 36 2 0 1965 2000 822536306 822536271 5.180000e-04 56.5


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 TraesCS1D01G020400 chr1D 8796046 8799756 3710 False 6854 6854 100.000000 1 3711 1 chr1D.!!$F1 3710
1 TraesCS1D01G020400 chr1A 10125534 10128546 3012 False 1330 3038 90.569333 14 3031 3 chr1A.!!$F1 3017
2 TraesCS1D01G020400 chr1B 11935656 11938054 2398 False 1515 1596 94.222000 945 2980 2 chr1B.!!$F2 2035
3 TraesCS1D01G020400 chr3D 542074154 542074837 683 True 1038 1038 94.186000 3032 3711 1 chr3D.!!$R1 679
4 TraesCS1D01G020400 chr4A 615448713 615449393 680 False 913 913 90.988000 3032 3711 1 chr4A.!!$F1 679
5 TraesCS1D01G020400 chr4A 633698317 633698997 680 False 845 845 89.099000 3029 3711 1 chr4A.!!$F2 682
6 TraesCS1D01G020400 chr5A 501556387 501557064 677 True 861 861 89.680000 3032 3711 1 chr5A.!!$R1 679
7 TraesCS1D01G020400 chr7A 101702051 101702729 678 False 856 856 89.535000 3032 3711 1 chr7A.!!$F1 679
8 TraesCS1D01G020400 chr7A 684300063 684300742 679 False 852 852 89.343000 3031 3711 1 chr7A.!!$F4 680
9 TraesCS1D01G020400 chr2A 665067203 665067884 681 False 854 854 89.436000 3031 3711 1 chr2A.!!$F1 680
10 TraesCS1D01G020400 chr2A 692151910 692152587 677 True 852 852 89.359000 3030 3711 1 chr2A.!!$R1 681
11 TraesCS1D01G020400 chr3A 705506568 705507244 676 True 850 850 89.343000 3031 3711 1 chr3A.!!$R1 680

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
404 407 0.115745 AGTACTCCCTCCGTTCCCAA 59.884 55.0 0.00 0.00 0.00 4.12 F
1237 1412 0.745486 CATGCTCCTCATGTTCGGCA 60.745 55.0 8.11 8.11 45.79 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1591 0.458197 CACTCAGCAGCTCGAGGAAG 60.458 60.0 15.58 9.93 33.36 3.46 R
2751 3309 0.683973 ACTGTGCTCTCACTCCCAAG 59.316 55.0 0.00 0.00 43.49 3.61 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
44 45 5.950549 TCTTCCACGTAAGAGATTAGTCCTT 59.049 40.000 0.00 0.00 43.62 3.36
51 52 5.966503 CGTAAGAGATTAGTCCTTCGAGTTG 59.033 44.000 0.00 0.00 43.02 3.16
87 90 2.011947 GTGCCTAACCGGTATCCAAAC 58.988 52.381 8.00 0.00 34.25 2.93
95 98 1.079875 CGGTATCCAAACCCACGACG 61.080 60.000 0.00 0.00 36.03 5.12
139 142 2.085677 GAGCTTTTCTCGCCTCAGC 58.914 57.895 0.00 0.00 31.20 4.26
140 143 1.365368 GAGCTTTTCTCGCCTCAGCC 61.365 60.000 0.00 0.00 34.57 4.85
141 144 2.744768 GCTTTTCTCGCCTCAGCCG 61.745 63.158 0.00 0.00 34.57 5.52
142 145 2.742372 TTTTCTCGCCTCAGCCGC 60.742 61.111 0.00 0.00 34.57 6.53
143 146 4.760047 TTTCTCGCCTCAGCCGCC 62.760 66.667 0.00 0.00 34.57 6.13
232 235 4.704833 CCTGGGAGTGCCACACCG 62.705 72.222 0.00 0.00 34.49 4.94
242 245 3.046087 CCACACCGCAGTCTGCTG 61.046 66.667 22.13 18.07 42.25 4.41
243 246 3.046087 CACACCGCAGTCTGCTGG 61.046 66.667 24.86 24.86 42.25 4.85
252 255 1.669779 GCAGTCTGCTGGTCATTCATC 59.330 52.381 17.89 0.00 42.78 2.92
261 264 2.165030 CTGGTCATTCATCAAGCCAACC 59.835 50.000 0.00 0.00 0.00 3.77
271 274 6.024552 TCATCAAGCCAACCTCAAAATAAC 57.975 37.500 0.00 0.00 0.00 1.89
272 275 4.864704 TCAAGCCAACCTCAAAATAACC 57.135 40.909 0.00 0.00 0.00 2.85
273 276 3.576550 TCAAGCCAACCTCAAAATAACCC 59.423 43.478 0.00 0.00 0.00 4.11
274 277 2.536066 AGCCAACCTCAAAATAACCCC 58.464 47.619 0.00 0.00 0.00 4.95
275 278 1.203758 GCCAACCTCAAAATAACCCCG 59.796 52.381 0.00 0.00 0.00 5.73
293 296 1.269051 CCGTCTGGTGGTTTTTGAAGC 60.269 52.381 0.00 0.00 0.00 3.86
307 310 2.203337 AAGCCGTTGAAGCAGCCA 60.203 55.556 0.00 0.00 0.00 4.75
326 329 3.694538 GCCGCCCTTGGTTGCATT 61.695 61.111 0.00 0.00 0.00 3.56
348 351 0.170339 TGTAGCCGACGACACTCATG 59.830 55.000 0.00 0.00 0.00 3.07
349 352 0.525668 GTAGCCGACGACACTCATGG 60.526 60.000 0.00 0.00 0.00 3.66
384 387 4.744631 GCGCAAATTCATTTGTTATAGGGG 59.255 41.667 0.30 0.00 46.63 4.79
385 388 5.451242 GCGCAAATTCATTTGTTATAGGGGA 60.451 40.000 0.30 0.00 46.63 4.81
386 389 6.208644 CGCAAATTCATTTGTTATAGGGGAG 58.791 40.000 12.71 0.00 46.63 4.30
387 390 6.183360 CGCAAATTCATTTGTTATAGGGGAGT 60.183 38.462 12.71 0.00 46.63 3.85
388 391 7.012894 CGCAAATTCATTTGTTATAGGGGAGTA 59.987 37.037 12.71 0.00 46.63 2.59
389 392 8.135529 GCAAATTCATTTGTTATAGGGGAGTAC 58.864 37.037 12.71 0.00 46.63 2.73
390 393 9.408648 CAAATTCATTTGTTATAGGGGAGTACT 57.591 33.333 0.00 0.00 41.58 2.73
391 394 9.628500 AAATTCATTTGTTATAGGGGAGTACTC 57.372 33.333 14.87 14.87 0.00 2.59
401 404 2.502633 GGAGTACTCCCTCCGTTCC 58.497 63.158 28.87 3.41 43.94 3.62
402 405 1.042003 GGAGTACTCCCTCCGTTCCC 61.042 65.000 28.87 2.34 43.94 3.97
403 406 0.324091 GAGTACTCCCTCCGTTCCCA 60.324 60.000 12.13 0.00 0.00 4.37
404 407 0.115745 AGTACTCCCTCCGTTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
405 408 0.978907 GTACTCCCTCCGTTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
406 409 1.558294 GTACTCCCTCCGTTCCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
407 410 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
408 411 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
409 412 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
410 413 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
411 414 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
412 415 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
413 416 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
414 417 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
415 418 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
416 419 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
417 420 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
418 421 7.122204 CCTCCGTTCCCAAATATAAGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
419 422 9.169592 CTCCGTTCCCAAATATAAGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
420 423 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
421 424 9.169592 CCGTTCCCAAATATAAGTCTTTTTAGA 57.830 33.333 0.00 0.00 0.00 2.10
434 437 8.753497 AAGTCTTTTTAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 0.00 3.16
435 438 8.159344 AGTCTTTTTAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 0.00 3.16
436 439 7.993183 AGTCTTTTTAGAGATTCCAACAAGTGA 59.007 33.333 0.00 0.00 0.00 3.41
437 440 8.070769 GTCTTTTTAGAGATTCCAACAAGTGAC 58.929 37.037 0.00 0.00 0.00 3.67
438 441 7.993183 TCTTTTTAGAGATTCCAACAAGTGACT 59.007 33.333 0.00 0.00 0.00 3.41
439 442 9.273016 CTTTTTAGAGATTCCAACAAGTGACTA 57.727 33.333 0.00 0.00 0.00 2.59
440 443 8.603242 TTTTAGAGATTCCAACAAGTGACTAC 57.397 34.615 0.00 0.00 0.00 2.73
441 444 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
442 445 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
443 446 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
444 447 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
445 448 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
446 449 4.182693 TCCAACAAGTGACTACATACGG 57.817 45.455 0.00 0.00 0.00 4.02
447 450 3.827876 TCCAACAAGTGACTACATACGGA 59.172 43.478 0.00 0.00 0.00 4.69
448 451 4.082408 TCCAACAAGTGACTACATACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
449 452 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
450 453 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
451 454 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
452 455 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
453 456 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
454 457 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
455 458 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
456 459 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
457 460 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
458 461 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
459 462 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
460 463 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
461 464 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
462 465 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
463 466 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
464 467 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
465 468 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
466 469 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
467 470 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
468 471 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
469 472 5.163713 GGAGCAAAATGAGTGAATCTACACC 60.164 44.000 0.00 0.00 41.12 4.16
470 473 4.702131 AGCAAAATGAGTGAATCTACACCC 59.298 41.667 0.00 0.00 41.12 4.61
471 474 4.702131 GCAAAATGAGTGAATCTACACCCT 59.298 41.667 0.00 0.00 41.12 4.34
472 475 5.880332 GCAAAATGAGTGAATCTACACCCTA 59.120 40.000 0.00 0.00 41.12 3.53
473 476 6.374333 GCAAAATGAGTGAATCTACACCCTAA 59.626 38.462 0.00 0.00 41.12 2.69
474 477 7.094377 GCAAAATGAGTGAATCTACACCCTAAA 60.094 37.037 0.00 0.00 41.12 1.85
475 478 8.792633 CAAAATGAGTGAATCTACACCCTAAAA 58.207 33.333 0.00 0.00 41.12 1.52
476 479 9.533831 AAAATGAGTGAATCTACACCCTAAAAT 57.466 29.630 0.00 0.00 41.12 1.82
479 482 9.784531 ATGAGTGAATCTACACCCTAAAATATG 57.215 33.333 0.00 0.00 41.12 1.78
480 483 8.768397 TGAGTGAATCTACACCCTAAAATATGT 58.232 33.333 0.00 0.00 41.12 2.29
481 484 9.262358 GAGTGAATCTACACCCTAAAATATGTC 57.738 37.037 0.00 0.00 41.12 3.06
482 485 8.993424 AGTGAATCTACACCCTAAAATATGTCT 58.007 33.333 0.00 0.00 41.12 3.41
491 494 9.998106 ACACCCTAAAATATGTCTACATACATC 57.002 33.333 4.98 0.00 41.15 3.06
492 495 9.436957 CACCCTAAAATATGTCTACATACATCC 57.563 37.037 4.98 0.00 41.15 3.51
493 496 8.311836 ACCCTAAAATATGTCTACATACATCCG 58.688 37.037 4.98 0.00 41.15 4.18
494 497 8.311836 CCCTAAAATATGTCTACATACATCCGT 58.688 37.037 4.98 0.00 41.15 4.69
505 508 4.715520 CATACATCCGTATGTTGCAGTC 57.284 45.455 0.00 0.00 46.70 3.51
506 509 2.024176 ACATCCGTATGTTGCAGTCC 57.976 50.000 0.00 0.00 44.07 3.85
507 510 1.277842 ACATCCGTATGTTGCAGTCCA 59.722 47.619 0.00 0.00 44.07 4.02
508 511 2.092968 ACATCCGTATGTTGCAGTCCAT 60.093 45.455 0.00 0.00 44.07 3.41
509 512 2.779755 TCCGTATGTTGCAGTCCATT 57.220 45.000 1.61 0.00 0.00 3.16
510 513 3.066291 TCCGTATGTTGCAGTCCATTT 57.934 42.857 1.61 0.00 0.00 2.32
511 514 2.746904 TCCGTATGTTGCAGTCCATTTG 59.253 45.455 1.61 0.00 0.00 2.32
512 515 2.746904 CCGTATGTTGCAGTCCATTTGA 59.253 45.455 1.61 0.00 0.00 2.69
513 516 3.190327 CCGTATGTTGCAGTCCATTTGAA 59.810 43.478 1.61 0.00 0.00 2.69
514 517 4.320861 CCGTATGTTGCAGTCCATTTGAAA 60.321 41.667 1.61 0.00 0.00 2.69
515 518 5.401550 CGTATGTTGCAGTCCATTTGAAAT 58.598 37.500 1.61 0.00 0.00 2.17
516 519 5.512788 CGTATGTTGCAGTCCATTTGAAATC 59.487 40.000 1.61 0.00 0.00 2.17
517 520 5.733620 ATGTTGCAGTCCATTTGAAATCT 57.266 34.783 0.00 0.00 0.00 2.40
518 521 5.125100 TGTTGCAGTCCATTTGAAATCTC 57.875 39.130 0.00 0.00 0.00 2.75
519 522 4.828939 TGTTGCAGTCCATTTGAAATCTCT 59.171 37.500 0.00 0.00 0.00 3.10
520 523 6.003326 TGTTGCAGTCCATTTGAAATCTCTA 58.997 36.000 0.00 0.00 0.00 2.43
521 524 6.489700 TGTTGCAGTCCATTTGAAATCTCTAA 59.510 34.615 0.00 0.00 0.00 2.10
522 525 7.014134 TGTTGCAGTCCATTTGAAATCTCTAAA 59.986 33.333 0.00 0.00 0.00 1.85
523 526 7.523293 TGCAGTCCATTTGAAATCTCTAAAA 57.477 32.000 0.00 0.00 0.00 1.52
524 527 7.950512 TGCAGTCCATTTGAAATCTCTAAAAA 58.049 30.769 0.00 0.00 0.00 1.94
525 528 8.084073 TGCAGTCCATTTGAAATCTCTAAAAAG 58.916 33.333 0.00 0.00 0.00 2.27
526 529 8.299570 GCAGTCCATTTGAAATCTCTAAAAAGA 58.700 33.333 0.00 0.00 0.00 2.52
527 530 9.617975 CAGTCCATTTGAAATCTCTAAAAAGAC 57.382 33.333 0.00 0.00 0.00 3.01
528 531 9.579932 AGTCCATTTGAAATCTCTAAAAAGACT 57.420 29.630 0.00 0.00 0.00 3.24
546 549 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
547 550 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
556 559 1.569548 AGGAACGGAGGGAGTAGATGA 59.430 52.381 0.00 0.00 0.00 2.92
568 571 4.037446 GGGAGTAGATGAGAGTAGCACTTG 59.963 50.000 0.00 0.00 0.00 3.16
580 583 5.663106 AGAGTAGCACTTGATAGATTCCCAA 59.337 40.000 0.00 0.00 0.00 4.12
620 623 9.981114 ATTCAATTGAAACTCGGAATTTTTAGT 57.019 25.926 23.91 0.00 37.61 2.24
712 715 3.221771 TGGTTCACAAGATGACCTTTGG 58.778 45.455 0.00 0.00 36.92 3.28
719 722 4.281688 CACAAGATGACCTTTGGTGGATTT 59.718 41.667 0.00 0.00 35.25 2.17
724 727 5.781818 AGATGACCTTTGGTGGATTTTCAAT 59.218 36.000 0.00 0.00 35.25 2.57
743 746 9.645059 TTTTCAATACAAGAACAATTCACACAA 57.355 25.926 0.00 0.00 0.00 3.33
785 788 7.040271 TGGGAGAGAAAAAGGTTTTAATTACCG 60.040 37.037 2.59 0.00 40.69 4.02
786 789 6.805271 GGAGAGAAAAAGGTTTTAATTACCGC 59.195 38.462 2.59 0.00 40.69 5.68
817 821 8.445275 AATTCAAAAGTTTATTGTTGGTTCCC 57.555 30.769 0.00 0.00 0.00 3.97
856 860 9.713713 AAAAACTTTTCCTAGTGCAAACTTTTA 57.286 25.926 0.00 0.00 0.00 1.52
857 861 9.713713 AAAACTTTTCCTAGTGCAAACTTTTAA 57.286 25.926 0.00 0.00 0.00 1.52
872 876 8.003784 GCAAACTTTTAAAATGTGACAGTATGC 58.996 33.333 0.09 0.00 42.53 3.14
877 881 2.647529 AATGTGACAGTATGCGTCGA 57.352 45.000 0.00 0.00 42.53 4.20
897 901 6.521821 CGTCGAACCAACCAAACATATTTAAG 59.478 38.462 0.00 0.00 0.00 1.85
919 923 7.563888 AAGAGAATCATGTCATGGTGTAATG 57.436 36.000 12.90 0.00 37.82 1.90
937 941 6.708054 GTGTAATGATCTGATAACAGGGAAGG 59.292 42.308 0.00 0.00 43.60 3.46
941 945 7.878621 ATGATCTGATAACAGGGAAGGATTA 57.121 36.000 0.00 0.00 43.60 1.75
943 947 6.846505 TGATCTGATAACAGGGAAGGATTACT 59.153 38.462 0.00 0.00 43.60 2.24
966 1141 8.233349 ACTGGAGGGAGTACTATATAAGATGA 57.767 38.462 0.00 0.00 0.00 2.92
969 1144 6.834969 GGAGGGAGTACTATATAAGATGACCC 59.165 46.154 0.00 0.00 33.09 4.46
1006 1181 1.889170 TCATAGCTAGCACGATGGAGG 59.111 52.381 18.83 0.00 0.00 4.30
1011 1186 1.604185 GCTAGCACGATGGAGGATGAC 60.604 57.143 10.63 0.00 0.00 3.06
1140 1315 1.452651 CCCATGGCAGCTACCTGTG 60.453 63.158 6.09 3.40 41.26 3.66
1237 1412 0.745486 CATGCTCCTCATGTTCGGCA 60.745 55.000 8.11 8.11 45.79 5.69
1270 1445 3.229156 ATCGTCGTTTCCACCGCCA 62.229 57.895 0.00 0.00 0.00 5.69
1398 1573 2.598099 TACGGTGACCACTGGCGA 60.598 61.111 12.96 0.00 41.89 5.54
1401 1576 2.110213 GGTGACCACTGGCGACAA 59.890 61.111 0.00 0.00 42.06 3.18
1464 1639 1.153647 CGCCACGTTCAGCTCCATA 60.154 57.895 0.00 0.00 0.00 2.74
1501 1676 1.069204 ACAGATTCATCCGGTCCATCG 59.931 52.381 0.00 0.00 0.00 3.84
1502 1677 1.069204 CAGATTCATCCGGTCCATCGT 59.931 52.381 0.00 0.00 0.00 3.73
1506 1681 3.080765 ATCCGGTCCATCGTGGCA 61.081 61.111 0.00 0.00 37.47 4.92
1537 1712 0.171455 GGTCGTGAATCTGAGCGAGT 59.829 55.000 0.00 0.00 33.90 4.18
1563 1738 1.663739 GGCGTACCTGACAGACACA 59.336 57.895 3.32 0.00 0.00 3.72
1605 1780 0.389166 GACAGTTCACGGAGCAGGAG 60.389 60.000 0.00 0.00 0.00 3.69
1716 1891 4.552365 AGCACCACACTGCGCAGT 62.552 61.111 36.44 36.44 42.42 4.40
1860 2035 3.334054 AGGGTGCAGGGAGAAGGC 61.334 66.667 0.00 0.00 0.00 4.35
1962 2514 8.928733 CCTAAATTTACAACTACTAGTTTGCGA 58.071 33.333 0.00 0.00 36.03 5.10
1963 2515 9.737025 CTAAATTTACAACTACTAGTTTGCGAC 57.263 33.333 0.00 0.00 36.03 5.19
1964 2516 5.811018 TTTACAACTACTAGTTTGCGACG 57.189 39.130 0.00 0.00 36.03 5.12
1977 2532 3.529634 TTGCGACGACACTTATTTTGG 57.470 42.857 0.00 0.00 0.00 3.28
1980 2535 2.676342 GCGACGACACTTATTTTGGGAT 59.324 45.455 0.00 0.00 0.00 3.85
2003 2558 3.003480 GAGGGAGTACAACTGAATGTGC 58.997 50.000 0.00 0.00 36.33 4.57
2007 2562 0.871722 GTACAACTGAATGTGCGCCA 59.128 50.000 4.18 2.31 34.75 5.69
2008 2563 0.871722 TACAACTGAATGTGCGCCAC 59.128 50.000 4.18 3.72 34.75 5.01
2014 2569 4.600692 ACTGAATGTGCGCCACTATATA 57.399 40.909 4.18 0.00 35.11 0.86
2015 2570 5.152623 ACTGAATGTGCGCCACTATATAT 57.847 39.130 4.18 0.00 35.11 0.86
2016 2571 4.931601 ACTGAATGTGCGCCACTATATATG 59.068 41.667 4.18 0.00 35.11 1.78
2017 2572 4.252878 TGAATGTGCGCCACTATATATGG 58.747 43.478 4.18 0.00 40.50 2.74
2177 2735 0.810648 GCGAAACCCAAGCATCATGA 59.189 50.000 0.00 0.00 0.00 3.07
2179 2737 1.133025 CGAAACCCAAGCATCATGACC 59.867 52.381 0.00 0.00 0.00 4.02
2237 2795 4.589908 ACAAAACAAGGTCACTGAAGAGT 58.410 39.130 0.00 0.00 0.00 3.24
2281 2839 2.034305 GCAATGCATCATCAAGGAGACC 59.966 50.000 0.00 0.00 0.00 3.85
2365 2923 1.290955 CTACGACGTGCCCAAAGGA 59.709 57.895 11.56 0.00 33.47 3.36
2504 3062 1.478916 TCGAGTTCATACCATTCGGCA 59.521 47.619 0.00 0.00 34.57 5.69
2533 3091 3.839353 GATCTGCCCCGGGATGCTG 62.839 68.421 26.32 21.50 0.00 4.41
2542 3100 1.978617 CGGGATGCTGTTTGGGCTT 60.979 57.895 0.00 0.00 0.00 4.35
2599 3157 4.934797 TCATTTTGATTGGAGTCTCCCT 57.065 40.909 16.60 3.54 35.03 4.20
2659 3217 2.666098 GGGAGTGGCGGCTAGGAAA 61.666 63.158 11.43 0.00 0.00 3.13
2751 3309 4.067896 TGCATCTGTTCTCTTTGGTTCTC 58.932 43.478 0.00 0.00 0.00 2.87
2752 3310 4.202398 TGCATCTGTTCTCTTTGGTTCTCT 60.202 41.667 0.00 0.00 0.00 3.10
2755 3313 4.708177 TCTGTTCTCTTTGGTTCTCTTGG 58.292 43.478 0.00 0.00 0.00 3.61
2756 3314 3.817647 CTGTTCTCTTTGGTTCTCTTGGG 59.182 47.826 0.00 0.00 0.00 4.12
2757 3315 3.458118 TGTTCTCTTTGGTTCTCTTGGGA 59.542 43.478 0.00 0.00 0.00 4.37
2758 3316 4.068599 GTTCTCTTTGGTTCTCTTGGGAG 58.931 47.826 0.00 0.00 40.73 4.30
2759 3317 3.318313 TCTCTTTGGTTCTCTTGGGAGT 58.682 45.455 0.00 0.00 40.29 3.85
2761 3319 3.045634 TCTTTGGTTCTCTTGGGAGTGA 58.954 45.455 0.00 0.00 40.29 3.41
2762 3320 3.071602 TCTTTGGTTCTCTTGGGAGTGAG 59.928 47.826 0.00 0.00 40.29 3.51
2792 3369 1.992834 TAGCCCGTGCAATCCTGGA 60.993 57.895 0.00 0.00 41.13 3.86
2803 3380 2.738314 GCAATCCTGGACATGTTTTTGC 59.262 45.455 11.75 11.75 0.00 3.68
2823 3400 3.446873 TGCCATTCTGTTCACAAGTTGTT 59.553 39.130 5.57 0.00 0.00 2.83
2964 3545 1.073397 ATCTCCATCCCTGACCCCC 60.073 63.158 0.00 0.00 0.00 5.40
2980 3561 1.322538 CCCCAAATTTCCTCCCGCAG 61.323 60.000 0.00 0.00 0.00 5.18
2982 3563 1.137404 CAAATTTCCTCCCGCAGCG 59.863 57.895 8.18 8.18 0.00 5.18
2985 3566 2.764637 AATTTCCTCCCGCAGCGGTT 62.765 55.000 31.68 15.10 46.80 4.44
2989 3570 3.726517 CTCCCGCAGCGGTTTGTG 61.727 66.667 31.68 16.48 46.80 3.33
3005 3586 3.770040 TGGACACGGATGCGGGAG 61.770 66.667 18.37 5.04 0.00 4.30
3017 3598 3.781307 CGGGAGCCGGTCATCCAA 61.781 66.667 19.84 0.00 44.15 3.53
3018 3599 2.919043 GGGAGCCGGTCATCCAAT 59.081 61.111 19.84 0.00 37.33 3.16
3024 3605 1.160137 GCCGGTCATCCAATGCTATC 58.840 55.000 1.90 0.00 0.00 2.08
3175 3758 2.162338 CTAAAGGCCGTCCACGTGGA 62.162 60.000 33.23 33.23 43.08 4.02
3334 3944 3.736094 TCTCTAATCACCACCCCTCATT 58.264 45.455 0.00 0.00 0.00 2.57
3335 3945 4.111577 TCTCTAATCACCACCCCTCATTT 58.888 43.478 0.00 0.00 0.00 2.32
3336 3946 5.285401 TCTCTAATCACCACCCCTCATTTA 58.715 41.667 0.00 0.00 0.00 1.40
3367 3988 5.557576 TCTCTAATCACCCCTCATCATTG 57.442 43.478 0.00 0.00 0.00 2.82
3426 4047 1.599606 CTACTCCAGCCTGAGCACGT 61.600 60.000 0.00 0.00 43.56 4.49
3435 4056 2.143925 GCCTGAGCACGTTTAACTTCT 58.856 47.619 0.00 0.00 39.53 2.85
3643 4264 4.023291 AGTTTGACCATTGTTTGACCACT 58.977 39.130 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.913821 ACGTGGAAGAACAAAAATACTCTTTTC 59.086 33.333 0.00 0.00 0.00 2.29
4 5 7.768240 ACGTGGAAGAACAAAAATACTCTTTT 58.232 30.769 0.00 0.00 0.00 2.27
6 7 6.937436 ACGTGGAAGAACAAAAATACTCTT 57.063 33.333 0.00 0.00 0.00 2.85
7 8 7.929785 TCTTACGTGGAAGAACAAAAATACTCT 59.070 33.333 0.00 0.00 32.46 3.24
8 9 8.080083 TCTTACGTGGAAGAACAAAAATACTC 57.920 34.615 0.00 0.00 32.46 2.59
9 10 7.929785 TCTCTTACGTGGAAGAACAAAAATACT 59.070 33.333 0.00 0.00 35.06 2.12
10 11 8.080083 TCTCTTACGTGGAAGAACAAAAATAC 57.920 34.615 0.00 0.00 35.06 1.89
11 12 8.842358 ATCTCTTACGTGGAAGAACAAAAATA 57.158 30.769 0.00 0.00 35.06 1.40
12 13 7.745620 ATCTCTTACGTGGAAGAACAAAAAT 57.254 32.000 0.00 0.00 35.06 1.82
13 14 7.562454 AATCTCTTACGTGGAAGAACAAAAA 57.438 32.000 0.00 0.00 35.06 1.94
14 15 7.929785 ACTAATCTCTTACGTGGAAGAACAAAA 59.070 33.333 0.00 0.00 35.06 2.44
15 16 7.439381 ACTAATCTCTTACGTGGAAGAACAAA 58.561 34.615 0.00 0.00 35.06 2.83
16 17 6.989659 ACTAATCTCTTACGTGGAAGAACAA 58.010 36.000 0.00 0.00 35.06 2.83
17 18 6.349944 GGACTAATCTCTTACGTGGAAGAACA 60.350 42.308 0.00 0.00 35.06 3.18
18 19 6.035217 GGACTAATCTCTTACGTGGAAGAAC 58.965 44.000 0.00 0.00 35.06 3.01
19 20 5.950549 AGGACTAATCTCTTACGTGGAAGAA 59.049 40.000 0.00 0.00 35.06 2.52
20 21 5.507637 AGGACTAATCTCTTACGTGGAAGA 58.492 41.667 0.00 0.00 34.30 2.87
44 45 7.960738 GCACTAATTAATTGCTAAACAACTCGA 59.039 33.333 11.05 0.00 42.27 4.04
102 105 0.454957 CGGCTTCCTTGCGTGATTTG 60.455 55.000 0.00 0.00 0.00 2.32
103 106 0.605319 TCGGCTTCCTTGCGTGATTT 60.605 50.000 0.00 0.00 0.00 2.17
139 142 4.394712 AAGGAGCAACGAGGGCGG 62.395 66.667 0.00 0.00 43.17 6.13
140 143 2.815647 GAAGGAGCAACGAGGGCG 60.816 66.667 0.00 0.00 44.79 6.13
141 144 2.035442 GTGAAGGAGCAACGAGGGC 61.035 63.158 0.00 0.00 0.00 5.19
142 145 1.376037 GGTGAAGGAGCAACGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
143 146 0.671781 CTGGTGAAGGAGCAACGAGG 60.672 60.000 0.00 0.00 0.00 4.63
144 147 0.318441 TCTGGTGAAGGAGCAACGAG 59.682 55.000 0.00 0.00 0.00 4.18
145 148 0.976641 ATCTGGTGAAGGAGCAACGA 59.023 50.000 0.00 0.00 0.00 3.85
146 149 1.081892 CATCTGGTGAAGGAGCAACG 58.918 55.000 0.00 0.00 0.00 4.10
147 150 1.457346 CCATCTGGTGAAGGAGCAAC 58.543 55.000 0.00 0.00 33.17 4.17
148 151 3.963733 CCATCTGGTGAAGGAGCAA 57.036 52.632 0.00 0.00 33.17 3.91
232 235 1.669779 GATGAATGACCAGCAGACTGC 59.330 52.381 20.12 20.12 45.46 4.40
234 237 3.607741 CTTGATGAATGACCAGCAGACT 58.392 45.455 0.00 0.00 33.72 3.24
242 245 2.424956 GAGGTTGGCTTGATGAATGACC 59.575 50.000 0.00 0.00 0.00 4.02
243 246 3.084039 TGAGGTTGGCTTGATGAATGAC 58.916 45.455 0.00 0.00 0.00 3.06
252 255 3.306710 GGGGTTATTTTGAGGTTGGCTTG 60.307 47.826 0.00 0.00 0.00 4.01
261 264 2.747446 CACCAGACGGGGTTATTTTGAG 59.253 50.000 0.00 0.00 39.79 3.02
271 274 0.466555 TCAAAAACCACCAGACGGGG 60.467 55.000 0.00 0.00 42.91 5.73
272 275 1.336755 CTTCAAAAACCACCAGACGGG 59.663 52.381 0.00 0.00 44.81 5.28
273 276 1.269051 GCTTCAAAAACCACCAGACGG 60.269 52.381 0.00 0.00 38.77 4.79
274 277 1.269051 GGCTTCAAAAACCACCAGACG 60.269 52.381 0.00 0.00 0.00 4.18
275 278 1.269051 CGGCTTCAAAAACCACCAGAC 60.269 52.381 0.00 0.00 0.00 3.51
293 296 4.389576 GCGTGGCTGCTTCAACGG 62.390 66.667 15.32 3.14 0.00 4.44
348 351 2.419057 TTTGCGCATGCTTCACCACC 62.419 55.000 12.75 0.00 43.34 4.61
349 352 0.388907 ATTTGCGCATGCTTCACCAC 60.389 50.000 12.75 0.00 43.34 4.16
384 387 0.324091 TGGGAACGGAGGGAGTACTC 60.324 60.000 14.87 14.87 36.76 2.59
385 388 0.115745 TTGGGAACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
386 389 0.978907 TTTGGGAACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
387 390 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
388 391 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
389 392 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
390 393 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
391 394 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
392 395 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
393 396 7.625828 AAAAGACTTATATTTGGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
394 397 9.169592 CTAAAAAGACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
395 398 9.169592 TCTAAAAAGACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
408 411 9.847224 ACTTGTTGGAATCTCTAAAAAGACTTA 57.153 29.630 9.03 0.00 35.06 2.24
409 412 8.624776 CACTTGTTGGAATCTCTAAAAAGACTT 58.375 33.333 9.03 0.00 35.06 3.01
410 413 7.993183 TCACTTGTTGGAATCTCTAAAAAGACT 59.007 33.333 9.03 0.00 35.06 3.24
411 414 8.070769 GTCACTTGTTGGAATCTCTAAAAAGAC 58.929 37.037 9.03 0.00 35.06 3.01
412 415 7.993183 AGTCACTTGTTGGAATCTCTAAAAAGA 59.007 33.333 9.03 0.00 35.06 2.52
413 416 8.159344 AGTCACTTGTTGGAATCTCTAAAAAG 57.841 34.615 2.17 2.17 37.94 2.27
414 417 9.052759 GTAGTCACTTGTTGGAATCTCTAAAAA 57.947 33.333 0.00 0.00 0.00 1.94
415 418 8.208224 TGTAGTCACTTGTTGGAATCTCTAAAA 58.792 33.333 0.00 0.00 0.00 1.52
416 419 7.732025 TGTAGTCACTTGTTGGAATCTCTAAA 58.268 34.615 0.00 0.00 0.00 1.85
417 420 7.297936 TGTAGTCACTTGTTGGAATCTCTAA 57.702 36.000 0.00 0.00 0.00 2.10
418 421 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
419 422 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
420 423 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
421 424 6.100004 CGTATGTAGTCACTTGTTGGAATCT 58.900 40.000 0.00 0.00 0.00 2.40
422 425 5.291128 CCGTATGTAGTCACTTGTTGGAATC 59.709 44.000 0.00 0.00 0.00 2.52
423 426 5.046878 TCCGTATGTAGTCACTTGTTGGAAT 60.047 40.000 0.00 0.00 0.00 3.01
424 427 4.281435 TCCGTATGTAGTCACTTGTTGGAA 59.719 41.667 0.00 0.00 0.00 3.53
425 428 3.827876 TCCGTATGTAGTCACTTGTTGGA 59.172 43.478 0.00 0.00 0.00 3.53
426 429 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
427 430 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
428 431 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
429 432 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
430 433 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
431 434 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
432 435 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
433 436 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
434 437 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
435 438 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
436 439 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
437 440 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
438 441 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
439 442 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
440 443 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
441 444 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
442 445 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
443 446 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
444 447 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
445 448 5.163713 GGTGTAGATTCACTCATTTTGCTCC 60.164 44.000 0.00 0.00 38.28 4.70
446 449 5.163713 GGGTGTAGATTCACTCATTTTGCTC 60.164 44.000 0.00 0.00 38.54 4.26
447 450 4.702131 GGGTGTAGATTCACTCATTTTGCT 59.298 41.667 0.00 0.00 38.54 3.91
448 451 4.702131 AGGGTGTAGATTCACTCATTTTGC 59.298 41.667 0.00 0.00 40.86 3.68
449 452 7.921786 TTAGGGTGTAGATTCACTCATTTTG 57.078 36.000 0.00 0.00 40.86 2.44
450 453 8.934023 TTTTAGGGTGTAGATTCACTCATTTT 57.066 30.769 0.00 0.00 40.86 1.82
453 456 9.784531 CATATTTTAGGGTGTAGATTCACTCAT 57.215 33.333 0.00 0.00 40.86 2.90
454 457 8.768397 ACATATTTTAGGGTGTAGATTCACTCA 58.232 33.333 0.00 0.00 40.86 3.41
455 458 9.262358 GACATATTTTAGGGTGTAGATTCACTC 57.738 37.037 0.00 0.00 38.92 3.51
456 459 8.993424 AGACATATTTTAGGGTGTAGATTCACT 58.007 33.333 0.00 0.00 38.28 3.41
465 468 9.998106 GATGTATGTAGACATATTTTAGGGTGT 57.002 33.333 5.69 0.00 40.18 4.16
466 469 9.436957 GGATGTATGTAGACATATTTTAGGGTG 57.563 37.037 5.69 0.00 40.18 4.61
467 470 8.311836 CGGATGTATGTAGACATATTTTAGGGT 58.688 37.037 5.69 0.00 40.18 4.34
468 471 8.311836 ACGGATGTATGTAGACATATTTTAGGG 58.688 37.037 5.69 0.00 40.18 3.53
485 488 3.133901 TGGACTGCAACATACGGATGTAT 59.866 43.478 15.10 1.45 45.93 2.29
486 489 2.498078 TGGACTGCAACATACGGATGTA 59.502 45.455 15.10 0.00 45.93 2.29
488 491 2.022764 TGGACTGCAACATACGGATG 57.977 50.000 5.94 5.94 39.16 3.51
489 492 3.281727 AATGGACTGCAACATACGGAT 57.718 42.857 0.00 0.00 0.00 4.18
490 493 2.746904 CAAATGGACTGCAACATACGGA 59.253 45.455 0.00 0.00 0.00 4.69
491 494 2.746904 TCAAATGGACTGCAACATACGG 59.253 45.455 0.00 0.00 0.00 4.02
492 495 4.418013 TTCAAATGGACTGCAACATACG 57.582 40.909 0.00 0.00 0.00 3.06
493 496 6.624423 AGATTTCAAATGGACTGCAACATAC 58.376 36.000 0.00 0.00 0.00 2.39
494 497 6.660521 AGAGATTTCAAATGGACTGCAACATA 59.339 34.615 0.00 0.00 0.00 2.29
495 498 5.479375 AGAGATTTCAAATGGACTGCAACAT 59.521 36.000 0.00 0.00 0.00 2.71
496 499 4.828939 AGAGATTTCAAATGGACTGCAACA 59.171 37.500 0.00 0.00 0.00 3.33
497 500 5.382618 AGAGATTTCAAATGGACTGCAAC 57.617 39.130 0.00 0.00 0.00 4.17
498 501 7.523293 TTTAGAGATTTCAAATGGACTGCAA 57.477 32.000 0.00 0.00 0.00 4.08
499 502 7.523293 TTTTAGAGATTTCAAATGGACTGCA 57.477 32.000 0.00 0.00 0.00 4.41
500 503 8.299570 TCTTTTTAGAGATTTCAAATGGACTGC 58.700 33.333 0.00 0.00 0.00 4.40
501 504 9.617975 GTCTTTTTAGAGATTTCAAATGGACTG 57.382 33.333 0.00 0.00 0.00 3.51
502 505 9.579932 AGTCTTTTTAGAGATTTCAAATGGACT 57.420 29.630 0.00 0.00 0.00 3.85
520 523 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
521 524 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
522 525 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
523 526 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
524 527 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
525 528 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
526 529 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
527 530 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
528 531 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
529 532 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
530 533 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
531 534 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
532 535 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
533 536 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
534 537 3.203710 TCATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
535 538 2.781757 TCATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
536 539 1.569548 TCATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
537 540 1.957877 CTCATCTACTCCCTCCGTTCC 59.042 57.143 0.00 0.00 0.00 3.62
538 541 2.882137 CTCTCATCTACTCCCTCCGTTC 59.118 54.545 0.00 0.00 0.00 3.95
539 542 2.242708 ACTCTCATCTACTCCCTCCGTT 59.757 50.000 0.00 0.00 0.00 4.44
540 543 1.847737 ACTCTCATCTACTCCCTCCGT 59.152 52.381 0.00 0.00 0.00 4.69
541 544 2.649531 ACTCTCATCTACTCCCTCCG 57.350 55.000 0.00 0.00 0.00 4.63
542 545 3.181438 TGCTACTCTCATCTACTCCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
543 546 3.818773 GTGCTACTCTCATCTACTCCCTC 59.181 52.174 0.00 0.00 0.00 4.30
544 547 3.461831 AGTGCTACTCTCATCTACTCCCT 59.538 47.826 0.00 0.00 0.00 4.20
545 548 3.827722 AGTGCTACTCTCATCTACTCCC 58.172 50.000 0.00 0.00 0.00 4.30
546 549 4.884744 TCAAGTGCTACTCTCATCTACTCC 59.115 45.833 0.00 0.00 0.00 3.85
547 550 6.633500 ATCAAGTGCTACTCTCATCTACTC 57.367 41.667 0.00 0.00 0.00 2.59
556 559 5.211973 TGGGAATCTATCAAGTGCTACTCT 58.788 41.667 0.00 0.00 0.00 3.24
594 597 9.981114 ACTAAAAATTCCGAGTTTCAATTGAAT 57.019 25.926 21.10 7.85 33.54 2.57
597 600 9.463443 AGAACTAAAAATTCCGAGTTTCAATTG 57.537 29.630 0.00 0.00 32.37 2.32
620 623 4.037923 CCCAAAGCTTTGACTTAGCAAGAA 59.962 41.667 35.25 0.00 41.11 2.52
636 639 5.052481 GCCAAATCTCATATTTCCCAAAGC 58.948 41.667 0.00 0.00 0.00 3.51
685 688 3.222603 GTCATCTTGTGAACCAACCCTT 58.777 45.455 0.00 0.00 38.90 3.95
712 715 9.474920 TGAATTGTTCTTGTATTGAAAATCCAC 57.525 29.630 0.00 0.00 0.00 4.02
719 722 8.681806 TCTTGTGTGAATTGTTCTTGTATTGAA 58.318 29.630 0.00 0.00 0.00 2.69
724 727 5.007234 CGGTCTTGTGTGAATTGTTCTTGTA 59.993 40.000 0.00 0.00 0.00 2.41
743 746 2.884639 CTCCCATTGTTTTGTTCGGTCT 59.115 45.455 0.00 0.00 0.00 3.85
831 835 9.713713 TTAAAAGTTTGCACTAGGAAAAGTTTT 57.286 25.926 21.52 21.52 43.53 2.43
836 840 9.660180 ACATTTTAAAAGTTTGCACTAGGAAAA 57.340 25.926 6.79 0.00 36.80 2.29
840 844 7.704472 TGTCACATTTTAAAAGTTTGCACTAGG 59.296 33.333 6.79 0.00 30.68 3.02
841 845 8.627487 TGTCACATTTTAAAAGTTTGCACTAG 57.373 30.769 6.79 0.00 30.68 2.57
846 850 8.003784 GCATACTGTCACATTTTAAAAGTTTGC 58.996 33.333 6.79 9.47 35.23 3.68
856 860 3.322369 TCGACGCATACTGTCACATTTT 58.678 40.909 0.00 0.00 36.11 1.82
857 861 2.954316 TCGACGCATACTGTCACATTT 58.046 42.857 0.00 0.00 36.11 2.32
872 876 4.413495 AATATGTTTGGTTGGTTCGACG 57.587 40.909 0.00 0.00 0.00 5.12
897 901 7.660617 AGATCATTACACCATGACATGATTCTC 59.339 37.037 17.24 1.89 35.97 2.87
919 923 7.158021 CAGTAATCCTTCCCTGTTATCAGATC 58.842 42.308 2.20 0.00 43.76 2.75
941 945 8.110908 GTCATCTTATATAGTACTCCCTCCAGT 58.889 40.741 0.00 0.00 0.00 4.00
943 947 7.411808 GGTCATCTTATATAGTACTCCCTCCA 58.588 42.308 0.00 0.00 0.00 3.86
964 1139 1.352017 TCTGTAGTGACTACCGGGTCA 59.648 52.381 19.17 8.08 42.96 4.02
966 1141 2.822707 ATCTGTAGTGACTACCGGGT 57.177 50.000 19.17 4.46 36.24 5.28
969 1144 5.239744 AGCTATGAATCTGTAGTGACTACCG 59.760 44.000 19.17 13.43 36.24 4.02
1006 1181 4.653806 GCATAAAGTAGGATGCGTCATC 57.346 45.455 8.47 10.26 39.15 2.92
1140 1315 0.249657 GATGGTGGAGACTGCCGATC 60.250 60.000 0.00 0.00 0.00 3.69
1270 1445 0.924823 ATCATCTCCTTGGCAGCCTT 59.075 50.000 14.15 0.00 0.00 4.35
1398 1573 3.708195 GCAGATCTTGCGCATTTGT 57.292 47.368 12.75 0.00 44.09 2.83
1416 1591 0.458197 CACTCAGCAGCTCGAGGAAG 60.458 60.000 15.58 9.93 33.36 3.46
1450 1625 0.541863 CCCCTTATGGAGCTGAACGT 59.458 55.000 0.00 0.00 35.39 3.99
1464 1639 1.000612 GTCCGTCTCCTCTCCCCTT 59.999 63.158 0.00 0.00 0.00 3.95
1501 1676 3.188786 CGGCTCTAGCGTTGCCAC 61.189 66.667 12.09 0.00 46.39 5.01
1502 1677 4.451150 CCGGCTCTAGCGTTGCCA 62.451 66.667 12.09 0.00 46.39 4.92
1506 1681 3.060615 ACGACCGGCTCTAGCGTT 61.061 61.111 0.00 0.00 43.26 4.84
1563 1738 1.097232 CCATGATCATGTGCACCGTT 58.903 50.000 29.23 0.11 37.11 4.44
1716 1891 2.599281 TCTCGGAACACCTCGGCA 60.599 61.111 0.00 0.00 0.00 5.69
1860 2035 1.303643 GAGGGGTGGCTCAAGGTTG 60.304 63.158 0.00 0.00 0.00 3.77
1962 2514 4.261801 CTCCATCCCAAAATAAGTGTCGT 58.738 43.478 0.00 0.00 0.00 4.34
1963 2515 3.627577 CCTCCATCCCAAAATAAGTGTCG 59.372 47.826 0.00 0.00 0.00 4.35
1964 2516 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
1977 2532 2.467880 TCAGTTGTACTCCCTCCATCC 58.532 52.381 0.00 0.00 0.00 3.51
1980 2535 3.007940 CACATTCAGTTGTACTCCCTCCA 59.992 47.826 0.00 0.00 0.00 3.86
2003 2558 6.753180 AGATAAGCATCCATATATAGTGGCG 58.247 40.000 2.73 0.00 36.66 5.69
2014 2569 9.060347 CATACTGTACAAAAGATAAGCATCCAT 57.940 33.333 0.00 0.00 0.00 3.41
2015 2570 8.046708 ACATACTGTACAAAAGATAAGCATCCA 58.953 33.333 0.00 0.00 0.00 3.41
2016 2571 8.438676 ACATACTGTACAAAAGATAAGCATCC 57.561 34.615 0.00 0.00 0.00 3.51
2177 2735 2.270205 CTCATCTTGCGCCCTGGT 59.730 61.111 4.18 0.00 0.00 4.00
2179 2737 1.817099 GACCTCATCTTGCGCCCTG 60.817 63.158 4.18 0.00 0.00 4.45
2237 2795 2.025793 AGTAGCTCAGCTCACCTAGACA 60.026 50.000 0.00 0.00 40.44 3.41
2305 2863 2.565834 TCTGCACTCCCTTGGTACTAAC 59.434 50.000 0.00 0.00 0.00 2.34
2332 2890 1.065102 TCGTAGCCGAGTATTCTGCAC 59.935 52.381 4.55 0.77 38.40 4.57
2365 2923 3.140325 ACATTGACGAGAATGGTGGTT 57.860 42.857 13.28 0.00 37.60 3.67
2518 3076 3.944250 AAACAGCATCCCGGGGCAG 62.944 63.158 23.50 16.65 0.00 4.85
2533 3091 3.181496 GCTCAATAGTAGCAAGCCCAAAC 60.181 47.826 0.00 0.00 39.83 2.93
2542 3100 4.500545 GCAAGAGCTAGCTCAATAGTAGCA 60.501 45.833 38.86 0.00 44.99 3.49
2599 3157 2.820178 TCACTAGGAAGAGTGCCATCA 58.180 47.619 0.00 0.00 45.44 3.07
2659 3217 1.109323 GCAACCACAGAGGCACCTTT 61.109 55.000 0.00 0.00 43.14 3.11
2751 3309 0.683973 ACTGTGCTCTCACTCCCAAG 59.316 55.000 0.00 0.00 43.49 3.61
2752 3310 1.618837 GTACTGTGCTCTCACTCCCAA 59.381 52.381 0.00 0.00 43.49 4.12
2755 3313 0.882474 ACGTACTGTGCTCTCACTCC 59.118 55.000 0.00 0.00 43.49 3.85
2756 3314 2.476519 GCTACGTACTGTGCTCTCACTC 60.477 54.545 0.00 0.00 43.49 3.51
2757 3315 1.469308 GCTACGTACTGTGCTCTCACT 59.531 52.381 0.00 0.00 43.49 3.41
2758 3316 1.467713 GGCTACGTACTGTGCTCTCAC 60.468 57.143 4.76 0.00 43.40 3.51
2759 3317 0.809385 GGCTACGTACTGTGCTCTCA 59.191 55.000 4.76 0.00 0.00 3.27
2761 3319 1.654954 CGGGCTACGTACTGTGCTCT 61.655 60.000 3.30 0.00 37.93 4.09
2762 3320 1.226603 CGGGCTACGTACTGTGCTC 60.227 63.158 4.76 0.00 37.93 4.26
2792 3369 4.810491 GTGAACAGAATGGCAAAAACATGT 59.190 37.500 0.00 0.00 43.62 3.21
2803 3380 6.966435 AAAAACAACTTGTGAACAGAATGG 57.034 33.333 0.00 0.00 43.62 3.16
2905 3482 5.889853 ACATTGCAGATCCATAACACAAGAT 59.110 36.000 0.00 0.00 0.00 2.40
2964 3545 1.137404 CGCTGCGGGAGGAAATTTG 59.863 57.895 15.40 0.00 0.00 2.32
2980 3561 1.964373 ATCCGTGTCCACAAACCGC 60.964 57.895 0.00 0.00 0.00 5.68
2982 3563 1.579429 GCATCCGTGTCCACAAACC 59.421 57.895 0.00 0.00 0.00 3.27
2985 3566 2.358125 CCGCATCCGTGTCCACAA 60.358 61.111 0.00 0.00 0.00 3.33
2988 3569 3.770040 CTCCCGCATCCGTGTCCA 61.770 66.667 0.00 0.00 0.00 4.02
3005 3586 1.160137 GATAGCATTGGATGACCGGC 58.840 55.000 0.00 0.00 39.42 6.13
3024 3605 4.369182 CCCTTTTCTACTAGTGTATGCGG 58.631 47.826 5.39 0.00 0.00 5.69
3334 3944 7.780822 AGGGGTGATTAGAGATTAGAGGATAA 58.219 38.462 0.00 0.00 0.00 1.75
3335 3945 7.019659 TGAGGGGTGATTAGAGATTAGAGGATA 59.980 40.741 0.00 0.00 0.00 2.59
3336 3946 6.183361 TGAGGGGTGATTAGAGATTAGAGGAT 60.183 42.308 0.00 0.00 0.00 3.24
3367 3988 3.312697 GTCCGGGAAGTTAGATGATTTGC 59.687 47.826 0.00 0.00 0.00 3.68
3426 4047 6.504279 AGGGAGAATAGAACCCAGAAGTTAAA 59.496 38.462 0.00 0.00 45.43 1.52
3435 4056 2.544844 ACGAGGGAGAATAGAACCCA 57.455 50.000 0.00 0.00 45.43 4.51
3502 4123 7.691993 AGCTAAATTCCTGAGGGTTAATAGA 57.308 36.000 0.00 0.00 0.00 1.98
3643 4264 2.752354 CTGGTCAAACTGTGGTCAAACA 59.248 45.455 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.