Multiple sequence alignment - TraesCS4A01G049300

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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 TraesCS4A01G049300 chr4A 100.000 4459 0 0 1 4459 40254174 40249716 0.000000e+00 8235.0
1 TraesCS4A01G049300 chr4D 92.986 3892 170 47 636 4459 424465577 424469433 0.000000e+00 5579.0
2 TraesCS4A01G049300 chr4D 92.126 127 10 0 1 127 424463084 424463210 3.540000e-41 180.0
3 TraesCS4A01G049300 chr4B 92.633 3149 164 40 1333 4459 520396784 520399886 0.000000e+00 4468.0
4 TraesCS4A01G049300 chr4B 89.329 656 35 9 636 1287 520396144 520396768 0.000000e+00 791.0
5 TraesCS4A01G049300 chr4B 88.889 162 16 1 1 162 520394390 520394549 9.780000e-47 198.0
6 TraesCS4A01G049300 chr4B 88.350 103 10 2 360 461 520396046 520396147 6.060000e-24 122.0
7 TraesCS4A01G049300 chr4B 92.308 65 4 1 472 535 533485442 533485378 1.710000e-14 91.6
8 TraesCS4A01G049300 chr7B 87.213 610 57 11 1331 1937 407389890 407390481 0.000000e+00 675.0
9 TraesCS4A01G049300 chr1B 87.373 491 39 13 1383 1867 516975337 516974864 3.920000e-150 542.0
10 TraesCS4A01G049300 chr1B 87.169 491 40 13 1383 1867 117304837 117305310 1.830000e-148 536.0
11 TraesCS4A01G049300 chr1B 85.417 96 12 2 461 556 477515248 477515341 1.020000e-16 99.0
12 TraesCS4A01G049300 chr3A 85.519 366 42 3 1519 1874 486034922 486035286 5.450000e-99 372.0
13 TraesCS4A01G049300 chrUn 91.339 254 16 3 1620 1867 479459998 479460251 4.270000e-90 342.0
14 TraesCS4A01G049300 chr5A 84.821 112 17 0 453 564 504571201 504571312 3.650000e-21 113.0


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 TraesCS4A01G049300 chr4A 40249716 40254174 4458 True 8235.00 8235 100.00000 1 4459 1 chr4A.!!$R1 4458
1 TraesCS4A01G049300 chr4D 424463084 424469433 6349 False 2879.50 5579 92.55600 1 4459 2 chr4D.!!$F1 4458
2 TraesCS4A01G049300 chr4B 520394390 520399886 5496 False 1394.75 4468 89.80025 1 4459 4 chr4B.!!$F1 4458
3 TraesCS4A01G049300 chr7B 407389890 407390481 591 False 675.00 675 87.21300 1331 1937 1 chr7B.!!$F1 606

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 3982 0.035056 AAAAGCTGGGTGGAGGATCG 60.035 55.0 0.00 0.0 34.37 3.69 F
848 4252 0.107508 ACATGTCCGAGCCAAGGATG 60.108 55.0 0.00 0.0 40.30 3.51 F
1475 4941 0.024619 CTTACCGCGCGCTTAGAAAC 59.975 55.0 30.48 0.0 0.00 2.78 F
2741 6224 0.664767 GCGCCATCGACATCTACCTC 60.665 60.0 0.00 0.0 38.10 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 4910 0.158928 GCGCGGTAAGAATCGAATCG 59.841 55.000 8.83 0.0 0.00 3.34 R
2008 5486 1.134401 GCGATCATGACCCTCTGGAAA 60.134 52.381 0.00 0.0 34.81 3.13 R
2804 6287 1.410153 GCCCAAACCATCCATCACATC 59.590 52.381 0.00 0.0 0.00 3.06 R
3678 7177 0.818296 AGAAACGGGAGAGGATCGTG 59.182 55.000 0.00 0.0 42.67 4.35 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
34 35 5.022282 TGATTTCGTTGATGATAGCTCCA 57.978 39.130 0.00 0.00 0.00 3.86
111 112 7.718314 TGAAGATATAACGAAGTAGTGGAGCTA 59.282 37.037 0.00 0.00 45.00 3.32
117 118 6.770746 AACGAAGTAGTGGAGCTAAAGATA 57.229 37.500 0.00 0.00 45.00 1.98
127 1121 5.238214 GTGGAGCTAAAGATATTGAGCCAAG 59.762 44.000 5.77 0.00 35.45 3.61
154 1148 1.826385 CCTCCCGATATGAAATGGCC 58.174 55.000 0.00 0.00 0.00 5.36
252 1249 0.531090 AACGTGCACTAACAAGCCGA 60.531 50.000 16.19 0.00 0.00 5.54
298 1295 3.773974 CTTCAGCGAGACGGAAGC 58.226 61.111 0.00 0.00 42.42 3.86
302 1299 4.785512 AGCGAGACGGAAGCAGCG 62.786 66.667 0.00 0.00 0.00 5.18
306 1303 3.633094 GAGACGGAAGCAGCGCTGA 62.633 63.158 40.21 0.00 39.62 4.26
315 1312 2.667318 GCAGCGCTGACGTAAAGCA 61.667 57.895 40.21 0.00 40.86 3.91
335 2678 3.122250 GATGTAGTCGCCGCGGTCT 62.122 63.158 28.70 23.07 0.00 3.85
352 2696 0.611714 TCTCTGGGGCCGAGTTAAAC 59.388 55.000 15.63 0.00 0.00 2.01
384 2728 2.550208 GGGAATCAAGTCGTTGTGGTCT 60.550 50.000 0.00 0.00 34.98 3.85
388 2732 3.469008 TCAAGTCGTTGTGGTCTTGAT 57.531 42.857 0.00 0.00 40.46 2.57
450 3835 5.911335 CATACTTATATGGGCCTACTTCGGC 60.911 48.000 4.53 0.00 38.31 5.54
459 3844 0.459759 CCTACTTCGGCCGGAAACTC 60.460 60.000 27.83 0.00 33.34 3.01
460 3845 0.245539 CTACTTCGGCCGGAAACTCA 59.754 55.000 27.83 0.00 33.34 3.41
461 3846 0.245539 TACTTCGGCCGGAAACTCAG 59.754 55.000 27.83 5.83 33.34 3.35
462 3847 1.741770 CTTCGGCCGGAAACTCAGG 60.742 63.158 27.83 0.00 34.70 3.86
467 3852 2.668212 CCGGAAACTCAGGCGCAA 60.668 61.111 10.83 0.00 0.00 4.85
468 3853 2.040544 CCGGAAACTCAGGCGCAAT 61.041 57.895 10.83 0.00 0.00 3.56
469 3854 0.742990 CCGGAAACTCAGGCGCAATA 60.743 55.000 10.83 0.00 0.00 1.90
470 3855 0.373716 CGGAAACTCAGGCGCAATAC 59.626 55.000 10.83 0.00 0.00 1.89
471 3856 1.739067 GGAAACTCAGGCGCAATACT 58.261 50.000 10.83 0.00 0.00 2.12
472 3857 2.084546 GGAAACTCAGGCGCAATACTT 58.915 47.619 10.83 0.00 0.00 2.24
473 3858 2.488153 GGAAACTCAGGCGCAATACTTT 59.512 45.455 10.83 0.00 0.00 2.66
474 3859 3.057526 GGAAACTCAGGCGCAATACTTTT 60.058 43.478 10.83 0.27 0.00 2.27
475 3860 3.559238 AACTCAGGCGCAATACTTTTG 57.441 42.857 10.83 0.00 0.00 2.44
476 3861 2.778299 ACTCAGGCGCAATACTTTTGA 58.222 42.857 10.83 0.00 0.00 2.69
477 3862 2.484264 ACTCAGGCGCAATACTTTTGAC 59.516 45.455 10.83 0.00 0.00 3.18
478 3863 1.810151 TCAGGCGCAATACTTTTGACC 59.190 47.619 10.83 0.00 0.00 4.02
479 3864 0.802494 AGGCGCAATACTTTTGACCG 59.198 50.000 10.83 0.00 0.00 4.79
480 3865 0.800012 GGCGCAATACTTTTGACCGA 59.200 50.000 10.83 0.00 0.00 4.69
481 3866 1.400494 GGCGCAATACTTTTGACCGAT 59.600 47.619 10.83 0.00 0.00 4.18
482 3867 2.159435 GGCGCAATACTTTTGACCGATT 60.159 45.455 10.83 0.00 0.00 3.34
483 3868 3.098636 GCGCAATACTTTTGACCGATTC 58.901 45.455 0.30 0.00 0.00 2.52
484 3869 3.181510 GCGCAATACTTTTGACCGATTCT 60.182 43.478 0.30 0.00 0.00 2.40
485 3870 4.671766 GCGCAATACTTTTGACCGATTCTT 60.672 41.667 0.30 0.00 0.00 2.52
486 3871 5.022021 CGCAATACTTTTGACCGATTCTTC 58.978 41.667 0.00 0.00 0.00 2.87
487 3872 5.332707 GCAATACTTTTGACCGATTCTTCC 58.667 41.667 0.00 0.00 0.00 3.46
488 3873 5.106317 GCAATACTTTTGACCGATTCTTCCA 60.106 40.000 0.00 0.00 0.00 3.53
489 3874 6.546395 CAATACTTTTGACCGATTCTTCCAG 58.454 40.000 0.00 0.00 0.00 3.86
490 3875 4.351874 ACTTTTGACCGATTCTTCCAGA 57.648 40.909 0.00 0.00 0.00 3.86
491 3876 4.714632 ACTTTTGACCGATTCTTCCAGAA 58.285 39.130 0.00 0.00 38.78 3.02
492 3877 5.316987 ACTTTTGACCGATTCTTCCAGAAT 58.683 37.500 0.00 0.00 46.84 2.40
504 3889 5.921962 TCTTCCAGAATCTTGAGAATCGA 57.078 39.130 0.00 0.00 38.61 3.59
505 3890 5.655488 TCTTCCAGAATCTTGAGAATCGAC 58.345 41.667 0.00 0.00 38.61 4.20
506 3891 4.392921 TCCAGAATCTTGAGAATCGACC 57.607 45.455 0.00 0.00 38.61 4.79
507 3892 3.133003 TCCAGAATCTTGAGAATCGACCC 59.867 47.826 0.00 0.00 38.61 4.46
508 3893 3.133721 CCAGAATCTTGAGAATCGACCCT 59.866 47.826 0.00 0.00 38.61 4.34
509 3894 4.367450 CAGAATCTTGAGAATCGACCCTC 58.633 47.826 8.50 8.50 38.61 4.30
510 3895 3.386402 AGAATCTTGAGAATCGACCCTCC 59.614 47.826 11.86 0.00 38.61 4.30
511 3896 2.231716 TCTTGAGAATCGACCCTCCA 57.768 50.000 11.86 2.51 38.61 3.86
512 3897 2.752030 TCTTGAGAATCGACCCTCCAT 58.248 47.619 11.86 0.00 38.61 3.41
513 3898 2.695666 TCTTGAGAATCGACCCTCCATC 59.304 50.000 11.86 0.00 38.61 3.51
514 3899 1.414158 TGAGAATCGACCCTCCATCC 58.586 55.000 11.86 0.00 38.61 3.51
515 3900 1.342975 TGAGAATCGACCCTCCATCCA 60.343 52.381 11.86 0.00 38.61 3.41
516 3901 1.342819 GAGAATCGACCCTCCATCCAG 59.657 57.143 4.93 0.00 0.00 3.86
517 3902 0.250081 GAATCGACCCTCCATCCAGC 60.250 60.000 0.00 0.00 0.00 4.85
518 3903 0.692419 AATCGACCCTCCATCCAGCT 60.692 55.000 0.00 0.00 0.00 4.24
519 3904 0.692419 ATCGACCCTCCATCCAGCTT 60.692 55.000 0.00 0.00 0.00 3.74
520 3905 1.144936 CGACCCTCCATCCAGCTTC 59.855 63.158 0.00 0.00 0.00 3.86
521 3906 1.333636 CGACCCTCCATCCAGCTTCT 61.334 60.000 0.00 0.00 0.00 2.85
522 3907 0.915364 GACCCTCCATCCAGCTTCTT 59.085 55.000 0.00 0.00 0.00 2.52
523 3908 1.283321 GACCCTCCATCCAGCTTCTTT 59.717 52.381 0.00 0.00 0.00 2.52
524 3909 1.283321 ACCCTCCATCCAGCTTCTTTC 59.717 52.381 0.00 0.00 0.00 2.62
525 3910 1.283029 CCCTCCATCCAGCTTCTTTCA 59.717 52.381 0.00 0.00 0.00 2.69
526 3911 2.641305 CCTCCATCCAGCTTCTTTCAG 58.359 52.381 0.00 0.00 0.00 3.02
527 3912 2.238144 CCTCCATCCAGCTTCTTTCAGA 59.762 50.000 0.00 0.00 0.00 3.27
528 3913 3.307975 CCTCCATCCAGCTTCTTTCAGAA 60.308 47.826 0.00 0.00 32.50 3.02
529 3914 4.525024 CTCCATCCAGCTTCTTTCAGAAT 58.475 43.478 0.00 0.00 33.13 2.40
530 3915 4.521146 TCCATCCAGCTTCTTTCAGAATC 58.479 43.478 0.00 0.00 33.13 2.52
531 3916 4.226846 TCCATCCAGCTTCTTTCAGAATCT 59.773 41.667 0.00 0.00 33.13 2.40
532 3917 4.948621 CCATCCAGCTTCTTTCAGAATCTT 59.051 41.667 0.00 0.00 33.13 2.40
533 3918 5.163642 CCATCCAGCTTCTTTCAGAATCTTG 60.164 44.000 0.00 0.00 33.13 3.02
534 3919 4.978099 TCCAGCTTCTTTCAGAATCTTGT 58.022 39.130 0.00 0.00 33.13 3.16
535 3920 6.114187 TCCAGCTTCTTTCAGAATCTTGTA 57.886 37.500 0.00 0.00 33.13 2.41
536 3921 6.715280 TCCAGCTTCTTTCAGAATCTTGTAT 58.285 36.000 0.00 0.00 33.13 2.29
537 3922 6.820656 TCCAGCTTCTTTCAGAATCTTGTATC 59.179 38.462 0.00 0.00 33.13 2.24
538 3923 6.038050 CCAGCTTCTTTCAGAATCTTGTATCC 59.962 42.308 0.00 0.00 33.13 2.59
539 3924 6.596888 CAGCTTCTTTCAGAATCTTGTATCCA 59.403 38.462 0.00 0.00 33.13 3.41
540 3925 7.120285 CAGCTTCTTTCAGAATCTTGTATCCAA 59.880 37.037 0.00 0.00 33.13 3.53
541 3926 7.120432 AGCTTCTTTCAGAATCTTGTATCCAAC 59.880 37.037 0.00 0.00 33.13 3.77
542 3927 7.120432 GCTTCTTTCAGAATCTTGTATCCAACT 59.880 37.037 0.00 0.00 33.13 3.16
543 3928 8.924511 TTCTTTCAGAATCTTGTATCCAACTT 57.075 30.769 0.00 0.00 0.00 2.66
544 3929 8.924511 TCTTTCAGAATCTTGTATCCAACTTT 57.075 30.769 0.00 0.00 0.00 2.66
545 3930 9.354673 TCTTTCAGAATCTTGTATCCAACTTTT 57.645 29.630 0.00 0.00 0.00 2.27
546 3931 9.971922 CTTTCAGAATCTTGTATCCAACTTTTT 57.028 29.630 0.00 0.00 0.00 1.94
568 3953 6.642707 TTTTTACAATCCTAGTTGTGTGGG 57.357 37.500 8.58 0.00 42.02 4.61
569 3954 4.986054 TTACAATCCTAGTTGTGTGGGT 57.014 40.909 8.58 0.00 42.02 4.51
570 3955 3.876309 ACAATCCTAGTTGTGTGGGTT 57.124 42.857 0.00 0.00 40.60 4.11
571 3956 3.751518 ACAATCCTAGTTGTGTGGGTTC 58.248 45.455 0.00 0.00 40.60 3.62
572 3957 3.137544 ACAATCCTAGTTGTGTGGGTTCA 59.862 43.478 0.00 0.00 40.60 3.18
573 3958 4.141287 CAATCCTAGTTGTGTGGGTTCAA 58.859 43.478 0.00 0.00 0.00 2.69
574 3959 3.485463 TCCTAGTTGTGTGGGTTCAAG 57.515 47.619 0.00 0.00 0.00 3.02
575 3960 3.042682 TCCTAGTTGTGTGGGTTCAAGA 58.957 45.455 0.00 0.00 0.00 3.02
576 3961 3.071023 TCCTAGTTGTGTGGGTTCAAGAG 59.929 47.826 0.00 0.00 0.00 2.85
577 3962 3.071023 CCTAGTTGTGTGGGTTCAAGAGA 59.929 47.826 0.00 0.00 0.00 3.10
578 3963 3.644966 AGTTGTGTGGGTTCAAGAGAA 57.355 42.857 0.00 0.00 0.00 2.87
579 3964 3.963129 AGTTGTGTGGGTTCAAGAGAAA 58.037 40.909 0.00 0.00 35.08 2.52
580 3965 4.340617 AGTTGTGTGGGTTCAAGAGAAAA 58.659 39.130 0.00 0.00 35.08 2.29
581 3966 4.770010 AGTTGTGTGGGTTCAAGAGAAAAA 59.230 37.500 0.00 0.00 35.08 1.94
582 3967 4.981806 TGTGTGGGTTCAAGAGAAAAAG 57.018 40.909 0.00 0.00 35.08 2.27
583 3968 3.130340 TGTGTGGGTTCAAGAGAAAAAGC 59.870 43.478 0.00 0.00 35.08 3.51
584 3969 3.381590 GTGTGGGTTCAAGAGAAAAAGCT 59.618 43.478 0.00 0.00 35.08 3.74
585 3970 3.381272 TGTGGGTTCAAGAGAAAAAGCTG 59.619 43.478 0.00 0.00 35.08 4.24
586 3971 2.958355 TGGGTTCAAGAGAAAAAGCTGG 59.042 45.455 0.00 0.00 35.08 4.85
587 3972 2.297315 GGGTTCAAGAGAAAAAGCTGGG 59.703 50.000 0.00 0.00 35.08 4.45
588 3973 2.959030 GGTTCAAGAGAAAAAGCTGGGT 59.041 45.455 0.00 0.00 35.08 4.51
589 3974 3.243535 GGTTCAAGAGAAAAAGCTGGGTG 60.244 47.826 0.00 0.00 35.08 4.61
590 3975 2.586425 TCAAGAGAAAAAGCTGGGTGG 58.414 47.619 0.00 0.00 0.00 4.61
591 3976 2.174639 TCAAGAGAAAAAGCTGGGTGGA 59.825 45.455 0.00 0.00 0.00 4.02
592 3977 2.555757 CAAGAGAAAAAGCTGGGTGGAG 59.444 50.000 0.00 0.00 0.00 3.86
593 3978 1.074566 AGAGAAAAAGCTGGGTGGAGG 59.925 52.381 0.00 0.00 0.00 4.30
594 3979 1.073923 GAGAAAAAGCTGGGTGGAGGA 59.926 52.381 0.00 0.00 0.00 3.71
595 3980 1.713078 AGAAAAAGCTGGGTGGAGGAT 59.287 47.619 0.00 0.00 0.00 3.24
596 3981 2.095461 GAAAAAGCTGGGTGGAGGATC 58.905 52.381 0.00 0.00 0.00 3.36
597 3982 0.035056 AAAAGCTGGGTGGAGGATCG 60.035 55.000 0.00 0.00 34.37 3.69
598 3983 0.909610 AAAGCTGGGTGGAGGATCGA 60.910 55.000 0.00 0.00 34.37 3.59
599 3984 0.692419 AAGCTGGGTGGAGGATCGAT 60.692 55.000 0.00 0.00 34.37 3.59
600 3985 0.692419 AGCTGGGTGGAGGATCGATT 60.692 55.000 0.00 0.00 34.37 3.34
601 3986 0.181350 GCTGGGTGGAGGATCGATTT 59.819 55.000 0.00 0.00 34.37 2.17
602 3987 1.408822 GCTGGGTGGAGGATCGATTTT 60.409 52.381 0.00 0.00 34.37 1.82
603 3988 2.292267 CTGGGTGGAGGATCGATTTTG 58.708 52.381 0.00 0.00 34.37 2.44
604 3989 1.912731 TGGGTGGAGGATCGATTTTGA 59.087 47.619 0.00 0.00 34.37 2.69
605 3990 2.509548 TGGGTGGAGGATCGATTTTGAT 59.490 45.455 0.00 0.00 34.37 2.57
606 3991 3.053693 TGGGTGGAGGATCGATTTTGATT 60.054 43.478 0.00 0.00 34.37 2.57
607 3992 4.165180 TGGGTGGAGGATCGATTTTGATTA 59.835 41.667 0.00 0.00 34.37 1.75
608 3993 5.163099 TGGGTGGAGGATCGATTTTGATTAT 60.163 40.000 0.00 0.00 34.37 1.28
609 3994 5.182001 GGGTGGAGGATCGATTTTGATTATG 59.818 44.000 0.00 0.00 34.37 1.90
610 3995 5.997746 GGTGGAGGATCGATTTTGATTATGA 59.002 40.000 0.00 0.00 34.37 2.15
611 3996 6.486657 GGTGGAGGATCGATTTTGATTATGAA 59.513 38.462 0.00 0.00 34.37 2.57
612 3997 7.013274 GGTGGAGGATCGATTTTGATTATGAAA 59.987 37.037 0.00 0.00 34.37 2.69
613 3998 8.072567 GTGGAGGATCGATTTTGATTATGAAAG 58.927 37.037 0.00 0.00 34.37 2.62
614 3999 7.992608 TGGAGGATCGATTTTGATTATGAAAGA 59.007 33.333 0.00 0.00 34.37 2.52
615 4000 8.840321 GGAGGATCGATTTTGATTATGAAAGAA 58.160 33.333 0.00 0.00 34.37 2.52
618 4003 9.322776 GGATCGATTTTGATTATGAAAGAATCG 57.677 33.333 0.00 8.72 43.17 3.34
619 4004 9.322776 GATCGATTTTGATTATGAAAGAATCGG 57.677 33.333 13.42 0.00 42.49 4.18
620 4005 7.132213 TCGATTTTGATTATGAAAGAATCGGC 58.868 34.615 13.42 0.00 42.49 5.54
621 4006 6.360681 CGATTTTGATTATGAAAGAATCGGCC 59.639 38.462 0.00 0.00 40.10 6.13
622 4007 6.522625 TTTTGATTATGAAAGAATCGGCCA 57.477 33.333 2.24 0.00 36.30 5.36
623 4008 6.522625 TTTGATTATGAAAGAATCGGCCAA 57.477 33.333 2.24 0.00 36.30 4.52
624 4009 6.522625 TTGATTATGAAAGAATCGGCCAAA 57.477 33.333 2.24 0.00 36.30 3.28
625 4010 6.522625 TGATTATGAAAGAATCGGCCAAAA 57.477 33.333 2.24 0.00 36.30 2.44
626 4011 6.929625 TGATTATGAAAGAATCGGCCAAAAA 58.070 32.000 2.24 0.00 36.30 1.94
646 4031 0.684805 AACCGGGCCTCAAAAACACA 60.685 50.000 6.32 0.00 0.00 3.72
716 4101 6.981722 ACAAAGATTCCAGTGGTTAAATGAC 58.018 36.000 9.54 0.00 0.00 3.06
728 4113 4.088648 GGTTAAATGACGACAAGATTGCG 58.911 43.478 0.00 7.51 35.13 4.85
735 4120 3.367932 TGACGACAAGATTGCGAGATTTC 59.632 43.478 13.57 4.32 33.88 2.17
750 4135 1.466950 GATTTCCATCGCCGACACAAA 59.533 47.619 0.00 0.00 0.00 2.83
759 4144 1.596954 CGCCGACACAAACTTCCAAAG 60.597 52.381 0.00 0.00 0.00 2.77
760 4145 1.864029 GCCGACACAAACTTCCAAAGC 60.864 52.381 0.00 0.00 0.00 3.51
807 4192 1.133606 ACCAAAAAGGAAGGCCGAGAA 60.134 47.619 0.00 0.00 41.22 2.87
810 4195 2.623416 CAAAAAGGAAGGCCGAGAAAGT 59.377 45.455 0.00 0.00 39.96 2.66
844 4248 4.208632 GGACATGTCCGAGCCAAG 57.791 61.111 28.52 0.00 40.36 3.61
845 4249 1.450312 GGACATGTCCGAGCCAAGG 60.450 63.158 28.52 0.00 40.36 3.61
846 4250 1.596934 GACATGTCCGAGCCAAGGA 59.403 57.895 15.31 0.00 34.99 3.36
847 4251 0.179000 GACATGTCCGAGCCAAGGAT 59.821 55.000 15.31 0.00 40.30 3.24
848 4252 0.107508 ACATGTCCGAGCCAAGGATG 60.108 55.000 0.00 0.00 40.30 3.51
849 4253 0.178767 CATGTCCGAGCCAAGGATGA 59.821 55.000 0.00 0.00 40.30 2.92
850 4254 0.467384 ATGTCCGAGCCAAGGATGAG 59.533 55.000 0.00 0.00 40.30 2.90
851 4255 1.144936 GTCCGAGCCAAGGATGAGG 59.855 63.158 0.00 0.00 40.30 3.86
952 4394 1.005037 TCAATCCGCGAGTGTTGCT 60.005 52.632 8.23 0.00 0.00 3.91
1030 4476 3.446161 ACGTCGGGTGAGATAAAGATGAA 59.554 43.478 0.00 0.00 0.00 2.57
1031 4477 4.045104 CGTCGGGTGAGATAAAGATGAAG 58.955 47.826 0.00 0.00 0.00 3.02
1032 4478 4.202020 CGTCGGGTGAGATAAAGATGAAGA 60.202 45.833 0.00 0.00 0.00 2.87
1033 4479 5.508153 CGTCGGGTGAGATAAAGATGAAGAT 60.508 44.000 0.00 0.00 0.00 2.40
1034 4480 5.694006 GTCGGGTGAGATAAAGATGAAGATG 59.306 44.000 0.00 0.00 0.00 2.90
1035 4481 5.598417 TCGGGTGAGATAAAGATGAAGATGA 59.402 40.000 0.00 0.00 0.00 2.92
1036 4482 5.925397 CGGGTGAGATAAAGATGAAGATGAG 59.075 44.000 0.00 0.00 0.00 2.90
1065 4511 3.018423 AGAGAAGGGAGAAGAGAGAGC 57.982 52.381 0.00 0.00 0.00 4.09
1066 4512 1.676006 GAGAAGGGAGAAGAGAGAGCG 59.324 57.143 0.00 0.00 0.00 5.03
1068 4514 1.326951 AAGGGAGAAGAGAGAGCGGC 61.327 60.000 0.00 0.00 0.00 6.53
1112 4567 2.167662 TGCAGACCGATACTCAGTTCA 58.832 47.619 0.00 0.00 0.00 3.18
1114 4569 2.735762 GCAGACCGATACTCAGTTCACC 60.736 54.545 0.00 0.00 0.00 4.02
1156 4611 0.179153 GCGACTGGTACGTACCTTCC 60.179 60.000 37.37 25.68 46.58 3.46
1192 4647 2.621526 TGAATCTACGAGCTCGCCATTA 59.378 45.455 34.83 18.73 44.43 1.90
1197 4652 1.641577 ACGAGCTCGCCATTACTTTC 58.358 50.000 34.83 0.00 44.43 2.62
1243 4698 2.051882 GCAGCGTGCAGTGACAAC 60.052 61.111 0.00 0.00 44.26 3.32
1244 4699 2.633657 CAGCGTGCAGTGACAACC 59.366 61.111 0.00 0.00 0.00 3.77
1245 4700 2.591715 AGCGTGCAGTGACAACCC 60.592 61.111 0.00 0.00 0.00 4.11
1393 4855 3.921021 CGAGCGATATTACCATCCAAGTC 59.079 47.826 0.00 0.00 0.00 3.01
1444 4908 3.110031 AGCCAACCAACCCCACCT 61.110 61.111 0.00 0.00 0.00 4.00
1445 4909 2.123033 GCCAACCAACCCCACCTT 60.123 61.111 0.00 0.00 0.00 3.50
1446 4910 2.207229 GCCAACCAACCCCACCTTC 61.207 63.158 0.00 0.00 0.00 3.46
1447 4911 1.901464 CCAACCAACCCCACCTTCG 60.901 63.158 0.00 0.00 0.00 3.79
1448 4912 1.149627 CAACCAACCCCACCTTCGA 59.850 57.895 0.00 0.00 0.00 3.71
1451 4915 0.037734 ACCAACCCCACCTTCGATTC 59.962 55.000 0.00 0.00 0.00 2.52
1475 4941 0.024619 CTTACCGCGCGCTTAGAAAC 59.975 55.000 30.48 0.00 0.00 2.78
1485 4951 2.227865 GCGCTTAGAAACCACATGGAAA 59.772 45.455 4.53 0.00 38.94 3.13
1486 4952 3.305064 GCGCTTAGAAACCACATGGAAAA 60.305 43.478 4.53 0.00 38.94 2.29
1487 4953 4.794655 GCGCTTAGAAACCACATGGAAAAA 60.795 41.667 4.53 0.00 38.94 1.94
1490 4956 6.454795 GCTTAGAAACCACATGGAAAAATCA 58.545 36.000 4.53 0.00 38.94 2.57
1513 4979 4.461781 AGCAAAAATCCTGAGTTCTGATGG 59.538 41.667 0.00 0.00 0.00 3.51
1517 4983 3.726557 ATCCTGAGTTCTGATGGCAAA 57.273 42.857 0.00 0.00 0.00 3.68
1591 5068 4.754667 GCCAACGGGTCGAGGGTC 62.755 72.222 0.00 0.00 36.17 4.46
1607 5084 1.433879 GTCACCCACCTCGAGATCG 59.566 63.158 15.71 0.00 41.45 3.69
1609 5086 2.043852 ACCCACCTCGAGATCGCT 60.044 61.111 15.71 0.00 39.60 4.93
1890 5368 2.803155 ATTGGCAGGTGCATCGACGT 62.803 55.000 4.01 0.00 44.36 4.34
1894 5372 1.756375 GCAGGTGCATCGACGTCATC 61.756 60.000 17.16 0.00 41.59 2.92
1967 5445 1.813859 CCACCGAAGCCTGTCGATA 59.186 57.895 3.80 0.00 43.86 2.92
2005 5483 3.200887 GACGGCGCTGAGGATCGAT 62.201 63.158 25.98 0.00 38.61 3.59
2008 5486 1.857318 CGGCGCTGAGGATCGATACT 61.857 60.000 10.77 10.77 38.61 2.12
2172 5651 4.976224 TGCTATAGCTAACGTCTGACAA 57.024 40.909 24.61 0.00 42.66 3.18
2258 5741 2.738521 CACGAGAAGCGGGTGGTG 60.739 66.667 0.00 0.00 46.49 4.17
2261 5744 2.743928 GAGAAGCGGGTGGTGCTG 60.744 66.667 0.00 0.00 43.14 4.41
2675 6158 3.626924 AAGTTCACCGGCCTCGCT 61.627 61.111 0.00 0.00 34.56 4.93
2741 6224 0.664767 GCGCCATCGACATCTACCTC 60.665 60.000 0.00 0.00 38.10 3.85
2775 6258 9.944941 GTTCATTATAATCGATCTTCATTCGTC 57.055 33.333 0.00 0.00 37.82 4.20
2804 6287 6.573434 TGTTGTTATAGTGGATAGTGCTCAG 58.427 40.000 0.00 0.00 0.00 3.35
3075 6570 4.699522 AGCTTCAACGGGCGGGAC 62.700 66.667 0.00 0.00 0.00 4.46
3177 6672 3.760035 CTGAGGGACCCGTCGGTG 61.760 72.222 11.06 4.33 44.88 4.94
3405 6900 3.437049 GGCACTCCATTTCTTGACACTAC 59.563 47.826 0.00 0.00 0.00 2.73
3429 6924 4.917998 CGGATGGTGTAATCTAATCGTCAG 59.082 45.833 0.00 0.00 0.00 3.51
3448 6943 7.909267 TCGTCAGTTGAAGATAAATAAGCATG 58.091 34.615 0.00 0.00 0.00 4.06
3478 6973 2.404215 ACGTAGCACTGTACAGCTTTG 58.596 47.619 22.90 14.45 42.05 2.77
3594 7093 1.150536 TTCTGTTCCACTGGCCACC 59.849 57.895 0.00 0.00 0.00 4.61
3595 7094 1.352622 TTCTGTTCCACTGGCCACCT 61.353 55.000 0.00 0.00 0.00 4.00
3596 7095 1.601759 CTGTTCCACTGGCCACCTG 60.602 63.158 0.00 0.00 0.00 4.00
3597 7096 2.985847 GTTCCACTGGCCACCTGC 60.986 66.667 0.00 0.00 40.16 4.85
3606 7105 3.807538 GCCACCTGCTGCGATGTG 61.808 66.667 8.48 8.48 36.87 3.21
3627 7126 2.026734 CGATCGGATCACTGCGCT 59.973 61.111 17.53 0.00 35.99 5.92
3678 7177 3.316283 GAAGCATCTGATGTCGATCTCC 58.684 50.000 18.19 0.15 0.00 3.71
3698 7198 1.104630 ACGATCCTCTCCCGTTTCTC 58.895 55.000 0.00 0.00 32.03 2.87
3764 7264 0.232303 GCTCAGGACAAACGACAACG 59.768 55.000 0.00 0.00 45.75 4.10
3781 7289 4.057428 GAGCACCGAGACGTGGCT 62.057 66.667 0.00 0.00 37.13 4.75
3837 7345 1.875963 CACGGGACAATCCTTGCAC 59.124 57.895 0.00 0.00 36.57 4.57
3856 7364 2.035832 CACCAAACCAAGAGGCGAAAAT 59.964 45.455 0.00 0.00 39.06 1.82
3861 7369 4.664150 AACCAAGAGGCGAAAATGAAAA 57.336 36.364 0.00 0.00 39.06 2.29
3876 7384 7.695618 CGAAAATGAAAAGAGATCAGTGGATTC 59.304 37.037 0.00 0.00 32.67 2.52
3886 7394 1.486310 TCAGTGGATTCCCATTCTCCG 59.514 52.381 0.00 0.00 45.68 4.63
3889 7397 2.780010 AGTGGATTCCCATTCTCCGATT 59.220 45.455 0.00 0.00 45.68 3.34
3945 7453 0.324614 ATGGATCAGTCGGCAACACA 59.675 50.000 0.00 0.00 0.00 3.72
3946 7454 0.324614 TGGATCAGTCGGCAACACAT 59.675 50.000 0.00 0.00 0.00 3.21
3947 7455 0.729116 GGATCAGTCGGCAACACATG 59.271 55.000 0.00 0.00 0.00 3.21
3948 7456 1.442769 GATCAGTCGGCAACACATGT 58.557 50.000 0.00 0.00 0.00 3.21
3950 7458 0.392706 TCAGTCGGCAACACATGTCT 59.607 50.000 0.00 0.00 0.00 3.41
3951 7459 1.616374 TCAGTCGGCAACACATGTCTA 59.384 47.619 0.00 0.00 0.00 2.59
3962 7470 3.969553 ACACATGTCTAGTCTAGGCTCA 58.030 45.455 12.62 7.65 0.00 4.26
4024 7532 3.004734 CCAGTTTGGTTCAGGACATCAAC 59.995 47.826 0.00 0.00 31.35 3.18
4030 7538 2.225727 GGTTCAGGACATCAACCGTTTC 59.774 50.000 0.00 0.00 30.63 2.78
4074 7582 6.154706 TGGGTCAAAAGAATCCTAGTAGAGTC 59.845 42.308 0.00 0.00 0.00 3.36
4078 7586 6.154706 TCAAAAGAATCCTAGTAGAGTCCCAC 59.845 42.308 0.00 0.00 31.25 4.61
4268 7776 8.394121 CACAAAAAGTCAAGCTATATCTTCCTC 58.606 37.037 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.409484 AAGGCAACCAGGGTGCTTAT 59.591 50.000 29.03 12.73 37.17 1.73
111 112 5.221126 GCGATTTCCTTGGCTCAATATCTTT 60.221 40.000 0.00 0.00 0.00 2.52
117 118 1.106285 GGCGATTTCCTTGGCTCAAT 58.894 50.000 0.00 0.00 0.00 2.57
127 1121 1.275291 TCATATCGGGAGGCGATTTCC 59.725 52.381 0.00 0.00 0.00 3.13
143 1137 0.819259 GCGCTGGAGGCCATTTCATA 60.819 55.000 5.01 0.00 37.74 2.15
192 1186 0.170561 TACTTCCGTCTCGCTGAAGC 59.829 55.000 0.00 0.00 39.23 3.86
231 1228 1.753956 GGCTTGTTAGTGCACGTTTG 58.246 50.000 12.01 2.38 0.00 2.93
247 1244 1.134491 GTTGTAGCTATTGGGTCGGCT 60.134 52.381 0.00 0.00 38.62 5.52
252 1249 0.461339 CCGCGTTGTAGCTATTGGGT 60.461 55.000 4.92 0.00 34.40 4.51
297 1294 2.096594 GCTTTACGTCAGCGCTGC 59.903 61.111 32.44 24.35 42.83 5.25
298 1295 0.179240 CTTGCTTTACGTCAGCGCTG 60.179 55.000 31.53 31.53 40.45 5.18
302 1299 3.927142 ACTACATCTTGCTTTACGTCAGC 59.073 43.478 11.83 11.83 37.82 4.26
306 1303 2.921754 GCGACTACATCTTGCTTTACGT 59.078 45.455 0.00 0.00 0.00 3.57
315 1312 2.104331 CCGCGGCGACTACATCTT 59.896 61.111 25.92 0.00 0.00 2.40
335 2678 1.294138 CGTTTAACTCGGCCCCAGA 59.706 57.895 0.00 0.00 0.00 3.86
342 2685 3.304190 CCAAAAGAACCCGTTTAACTCGG 60.304 47.826 10.28 10.28 46.49 4.63
344 2687 3.884693 TCCCAAAAGAACCCGTTTAACTC 59.115 43.478 0.00 0.00 0.00 3.01
345 2688 3.900971 TCCCAAAAGAACCCGTTTAACT 58.099 40.909 0.00 0.00 0.00 2.24
352 2696 2.890945 ACTTGATTCCCAAAAGAACCCG 59.109 45.455 0.00 0.00 33.76 5.28
357 2701 4.036262 CACAACGACTTGATTCCCAAAAGA 59.964 41.667 0.00 0.00 33.76 2.52
361 2705 2.226330 CCACAACGACTTGATTCCCAA 58.774 47.619 0.00 0.00 0.00 4.12
411 3796 9.407380 CATATAAGTATGGGCCATTAGCAATTA 57.593 33.333 26.58 16.10 36.75 1.40
412 3797 8.297470 CATATAAGTATGGGCCATTAGCAATT 57.703 34.615 26.58 14.34 36.75 2.32
413 3798 7.886629 CATATAAGTATGGGCCATTAGCAAT 57.113 36.000 26.58 14.12 36.75 3.56
450 3835 0.742990 TATTGCGCCTGAGTTTCCGG 60.743 55.000 4.18 0.00 0.00 5.14
459 3844 1.465689 CGGTCAAAAGTATTGCGCCTG 60.466 52.381 4.18 0.00 0.00 4.85
460 3845 0.802494 CGGTCAAAAGTATTGCGCCT 59.198 50.000 4.18 0.00 0.00 5.52
461 3846 0.800012 TCGGTCAAAAGTATTGCGCC 59.200 50.000 4.18 0.00 0.00 6.53
462 3847 2.825086 ATCGGTCAAAAGTATTGCGC 57.175 45.000 0.00 0.00 0.00 6.09
463 3848 4.600012 AGAATCGGTCAAAAGTATTGCG 57.400 40.909 0.00 0.00 0.00 4.85
464 3849 5.106317 TGGAAGAATCGGTCAAAAGTATTGC 60.106 40.000 0.00 0.00 0.00 3.56
465 3850 6.371548 TCTGGAAGAATCGGTCAAAAGTATTG 59.628 38.462 0.00 0.00 42.31 1.90
466 3851 6.472887 TCTGGAAGAATCGGTCAAAAGTATT 58.527 36.000 0.00 0.00 42.31 1.89
467 3852 6.049955 TCTGGAAGAATCGGTCAAAAGTAT 57.950 37.500 0.00 0.00 42.31 2.12
468 3853 5.477607 TCTGGAAGAATCGGTCAAAAGTA 57.522 39.130 0.00 0.00 42.31 2.24
469 3854 4.351874 TCTGGAAGAATCGGTCAAAAGT 57.648 40.909 0.00 0.00 42.31 2.66
482 3867 5.394663 GGTCGATTCTCAAGATTCTGGAAGA 60.395 44.000 0.00 0.00 44.68 2.87
483 3868 4.808364 GGTCGATTCTCAAGATTCTGGAAG 59.192 45.833 0.00 0.00 0.00 3.46
484 3869 4.383118 GGGTCGATTCTCAAGATTCTGGAA 60.383 45.833 0.00 0.00 0.00 3.53
485 3870 3.133003 GGGTCGATTCTCAAGATTCTGGA 59.867 47.826 0.00 0.00 0.00 3.86
486 3871 3.133721 AGGGTCGATTCTCAAGATTCTGG 59.866 47.826 0.00 0.00 0.00 3.86
487 3872 4.367450 GAGGGTCGATTCTCAAGATTCTG 58.633 47.826 11.51 0.00 0.00 3.02
488 3873 3.386402 GGAGGGTCGATTCTCAAGATTCT 59.614 47.826 16.28 0.00 0.00 2.40
489 3874 3.133003 TGGAGGGTCGATTCTCAAGATTC 59.867 47.826 16.28 2.99 0.00 2.52
490 3875 3.107601 TGGAGGGTCGATTCTCAAGATT 58.892 45.455 16.28 0.00 0.00 2.40
491 3876 2.752030 TGGAGGGTCGATTCTCAAGAT 58.248 47.619 16.28 0.00 0.00 2.40
492 3877 2.231716 TGGAGGGTCGATTCTCAAGA 57.768 50.000 16.28 1.76 0.00 3.02
493 3878 2.224161 GGATGGAGGGTCGATTCTCAAG 60.224 54.545 16.28 0.00 0.00 3.02
494 3879 1.762957 GGATGGAGGGTCGATTCTCAA 59.237 52.381 16.28 8.40 0.00 3.02
495 3880 1.342975 TGGATGGAGGGTCGATTCTCA 60.343 52.381 16.28 6.49 0.00 3.27
496 3881 1.342819 CTGGATGGAGGGTCGATTCTC 59.657 57.143 8.82 8.82 0.00 2.87
497 3882 1.418334 CTGGATGGAGGGTCGATTCT 58.582 55.000 0.00 0.00 0.00 2.40
498 3883 0.250081 GCTGGATGGAGGGTCGATTC 60.250 60.000 0.00 0.00 0.00 2.52
499 3884 0.692419 AGCTGGATGGAGGGTCGATT 60.692 55.000 0.00 0.00 0.00 3.34
500 3885 0.692419 AAGCTGGATGGAGGGTCGAT 60.692 55.000 0.00 0.00 0.00 3.59
501 3886 1.306141 AAGCTGGATGGAGGGTCGA 60.306 57.895 0.00 0.00 0.00 4.20
502 3887 1.144936 GAAGCTGGATGGAGGGTCG 59.855 63.158 0.00 0.00 0.00 4.79
503 3888 0.915364 AAGAAGCTGGATGGAGGGTC 59.085 55.000 0.00 0.00 0.00 4.46
504 3889 1.283321 GAAAGAAGCTGGATGGAGGGT 59.717 52.381 0.00 0.00 0.00 4.34
505 3890 1.283029 TGAAAGAAGCTGGATGGAGGG 59.717 52.381 0.00 0.00 0.00 4.30
506 3891 2.238144 TCTGAAAGAAGCTGGATGGAGG 59.762 50.000 0.00 0.00 42.31 4.30
507 3892 3.623906 TCTGAAAGAAGCTGGATGGAG 57.376 47.619 0.00 0.00 42.31 3.86
545 3930 6.130569 ACCCACACAACTAGGATTGTAAAAA 58.869 36.000 0.00 0.00 40.89 1.94
546 3931 5.697067 ACCCACACAACTAGGATTGTAAAA 58.303 37.500 0.00 0.00 40.89 1.52
547 3932 5.313280 ACCCACACAACTAGGATTGTAAA 57.687 39.130 0.00 0.00 40.89 2.01
548 3933 4.986054 ACCCACACAACTAGGATTGTAA 57.014 40.909 0.00 0.00 40.89 2.41
549 3934 4.348461 TGAACCCACACAACTAGGATTGTA 59.652 41.667 0.00 0.00 40.89 2.41
550 3935 3.137544 TGAACCCACACAACTAGGATTGT 59.862 43.478 0.00 0.00 43.67 2.71
551 3936 3.750371 TGAACCCACACAACTAGGATTG 58.250 45.455 0.00 0.00 35.59 2.67
552 3937 4.104102 TCTTGAACCCACACAACTAGGATT 59.896 41.667 0.00 0.00 0.00 3.01
553 3938 3.650942 TCTTGAACCCACACAACTAGGAT 59.349 43.478 0.00 0.00 0.00 3.24
554 3939 3.042682 TCTTGAACCCACACAACTAGGA 58.957 45.455 0.00 0.00 0.00 2.94
555 3940 3.071023 TCTCTTGAACCCACACAACTAGG 59.929 47.826 0.00 0.00 0.00 3.02
556 3941 4.336889 TCTCTTGAACCCACACAACTAG 57.663 45.455 0.00 0.00 0.00 2.57
557 3942 4.764050 TTCTCTTGAACCCACACAACTA 57.236 40.909 0.00 0.00 0.00 2.24
558 3943 3.644966 TTCTCTTGAACCCACACAACT 57.355 42.857 0.00 0.00 0.00 3.16
559 3944 4.712122 TTTTCTCTTGAACCCACACAAC 57.288 40.909 0.00 0.00 31.02 3.32
560 3945 4.381505 GCTTTTTCTCTTGAACCCACACAA 60.382 41.667 0.00 0.00 31.02 3.33
561 3946 3.130340 GCTTTTTCTCTTGAACCCACACA 59.870 43.478 0.00 0.00 31.02 3.72
562 3947 3.381590 AGCTTTTTCTCTTGAACCCACAC 59.618 43.478 0.00 0.00 31.02 3.82
563 3948 3.381272 CAGCTTTTTCTCTTGAACCCACA 59.619 43.478 0.00 0.00 31.02 4.17
564 3949 3.243535 CCAGCTTTTTCTCTTGAACCCAC 60.244 47.826 0.00 0.00 31.02 4.61
565 3950 2.958355 CCAGCTTTTTCTCTTGAACCCA 59.042 45.455 0.00 0.00 31.02 4.51
566 3951 2.297315 CCCAGCTTTTTCTCTTGAACCC 59.703 50.000 0.00 0.00 31.02 4.11
567 3952 2.959030 ACCCAGCTTTTTCTCTTGAACC 59.041 45.455 0.00 0.00 31.02 3.62
568 3953 3.243535 CCACCCAGCTTTTTCTCTTGAAC 60.244 47.826 0.00 0.00 31.02 3.18
569 3954 2.958355 CCACCCAGCTTTTTCTCTTGAA 59.042 45.455 0.00 0.00 0.00 2.69
570 3955 2.174639 TCCACCCAGCTTTTTCTCTTGA 59.825 45.455 0.00 0.00 0.00 3.02
571 3956 2.555757 CTCCACCCAGCTTTTTCTCTTG 59.444 50.000 0.00 0.00 0.00 3.02
572 3957 2.489802 CCTCCACCCAGCTTTTTCTCTT 60.490 50.000 0.00 0.00 0.00 2.85
573 3958 1.074566 CCTCCACCCAGCTTTTTCTCT 59.925 52.381 0.00 0.00 0.00 3.10
574 3959 1.073923 TCCTCCACCCAGCTTTTTCTC 59.926 52.381 0.00 0.00 0.00 2.87
575 3960 1.149101 TCCTCCACCCAGCTTTTTCT 58.851 50.000 0.00 0.00 0.00 2.52
576 3961 2.095461 GATCCTCCACCCAGCTTTTTC 58.905 52.381 0.00 0.00 0.00 2.29
577 3962 1.614317 CGATCCTCCACCCAGCTTTTT 60.614 52.381 0.00 0.00 0.00 1.94
578 3963 0.035056 CGATCCTCCACCCAGCTTTT 60.035 55.000 0.00 0.00 0.00 2.27
579 3964 0.909610 TCGATCCTCCACCCAGCTTT 60.910 55.000 0.00 0.00 0.00 3.51
580 3965 0.692419 ATCGATCCTCCACCCAGCTT 60.692 55.000 0.00 0.00 0.00 3.74
581 3966 0.692419 AATCGATCCTCCACCCAGCT 60.692 55.000 0.00 0.00 0.00 4.24
582 3967 0.181350 AAATCGATCCTCCACCCAGC 59.819 55.000 0.00 0.00 0.00 4.85
583 3968 2.092968 TCAAAATCGATCCTCCACCCAG 60.093 50.000 0.00 0.00 0.00 4.45
584 3969 1.912731 TCAAAATCGATCCTCCACCCA 59.087 47.619 0.00 0.00 0.00 4.51
585 3970 2.710096 TCAAAATCGATCCTCCACCC 57.290 50.000 0.00 0.00 0.00 4.61
586 3971 5.997746 TCATAATCAAAATCGATCCTCCACC 59.002 40.000 0.00 0.00 0.00 4.61
587 3972 7.496529 TTCATAATCAAAATCGATCCTCCAC 57.503 36.000 0.00 0.00 0.00 4.02
588 3973 7.992608 TCTTTCATAATCAAAATCGATCCTCCA 59.007 33.333 0.00 0.00 0.00 3.86
589 3974 8.383318 TCTTTCATAATCAAAATCGATCCTCC 57.617 34.615 0.00 0.00 0.00 4.30
592 3977 9.322776 CGATTCTTTCATAATCAAAATCGATCC 57.677 33.333 0.00 0.00 43.90 3.36
593 3978 9.322776 CCGATTCTTTCATAATCAAAATCGATC 57.677 33.333 14.14 0.00 43.90 3.69
594 3979 7.805071 GCCGATTCTTTCATAATCAAAATCGAT 59.195 33.333 14.14 0.00 43.90 3.59
595 3980 7.132213 GCCGATTCTTTCATAATCAAAATCGA 58.868 34.615 14.14 0.00 43.90 3.59
596 3981 6.360681 GGCCGATTCTTTCATAATCAAAATCG 59.639 38.462 7.42 7.42 42.00 3.34
597 3982 7.202526 TGGCCGATTCTTTCATAATCAAAATC 58.797 34.615 0.00 0.00 33.75 2.17
598 3983 7.111247 TGGCCGATTCTTTCATAATCAAAAT 57.889 32.000 0.00 0.00 33.75 1.82
599 3984 6.522625 TGGCCGATTCTTTCATAATCAAAA 57.477 33.333 0.00 0.00 33.75 2.44
600 3985 6.522625 TTGGCCGATTCTTTCATAATCAAA 57.477 33.333 0.00 0.00 33.75 2.69
601 3986 6.522625 TTTGGCCGATTCTTTCATAATCAA 57.477 33.333 0.00 0.00 33.75 2.57
602 3987 6.522625 TTTTGGCCGATTCTTTCATAATCA 57.477 33.333 0.00 0.00 33.75 2.57
624 4009 1.555533 TGTTTTTGAGGCCCGGTTTTT 59.444 42.857 0.00 0.00 0.00 1.94
625 4010 1.134640 GTGTTTTTGAGGCCCGGTTTT 60.135 47.619 0.00 0.00 0.00 2.43
626 4011 0.462375 GTGTTTTTGAGGCCCGGTTT 59.538 50.000 0.00 0.00 0.00 3.27
627 4012 0.684805 TGTGTTTTTGAGGCCCGGTT 60.685 50.000 0.00 0.00 0.00 4.44
628 4013 1.076632 TGTGTTTTTGAGGCCCGGT 60.077 52.632 0.00 0.00 0.00 5.28
629 4014 0.821711 TCTGTGTTTTTGAGGCCCGG 60.822 55.000 0.00 0.00 0.00 5.73
630 4015 0.593128 CTCTGTGTTTTTGAGGCCCG 59.407 55.000 0.00 0.00 0.00 6.13
631 4016 1.609072 GTCTCTGTGTTTTTGAGGCCC 59.391 52.381 0.00 0.00 0.00 5.80
632 4017 2.291741 CAGTCTCTGTGTTTTTGAGGCC 59.708 50.000 0.00 0.00 33.37 5.19
633 4018 2.287248 GCAGTCTCTGTGTTTTTGAGGC 60.287 50.000 0.00 0.00 33.43 4.70
634 4019 2.945008 TGCAGTCTCTGTGTTTTTGAGG 59.055 45.455 0.00 0.00 33.43 3.86
635 4020 3.547613 GCTGCAGTCTCTGTGTTTTTGAG 60.548 47.826 16.64 0.00 33.43 3.02
636 4021 2.355756 GCTGCAGTCTCTGTGTTTTTGA 59.644 45.455 16.64 0.00 33.43 2.69
646 4031 0.694771 TTCATTGGGCTGCAGTCTCT 59.305 50.000 19.48 0.00 0.00 3.10
716 4101 2.672874 TGGAAATCTCGCAATCTTGTCG 59.327 45.455 0.00 0.00 0.00 4.35
728 4113 0.931005 GTGTCGGCGATGGAAATCTC 59.069 55.000 14.79 0.00 0.00 2.75
735 4120 0.165944 GAAGTTTGTGTCGGCGATGG 59.834 55.000 14.79 0.00 0.00 3.51
750 4135 1.074951 CCCTTCGGGCTTTGGAAGT 59.925 57.895 0.77 0.00 38.34 3.01
760 4145 1.379044 AAGCAAGATGCCCTTCGGG 60.379 57.895 0.00 0.00 46.52 5.14
807 4192 2.095161 CCTTGTCTTCTCTCGCGTACTT 60.095 50.000 5.77 0.00 0.00 2.24
810 4195 1.467734 GTCCTTGTCTTCTCTCGCGTA 59.532 52.381 5.77 0.00 0.00 4.42
840 4244 1.144936 GACTCGGCCTCATCCTTGG 59.855 63.158 0.00 0.00 0.00 3.61
841 4245 1.227089 CGACTCGGCCTCATCCTTG 60.227 63.158 0.00 0.00 0.00 3.61
842 4246 1.379977 TCGACTCGGCCTCATCCTT 60.380 57.895 0.00 0.00 0.00 3.36
843 4247 2.122167 GTCGACTCGGCCTCATCCT 61.122 63.158 8.70 0.00 0.00 3.24
844 4248 2.413765 GTCGACTCGGCCTCATCC 59.586 66.667 8.70 0.00 0.00 3.51
851 4255 3.444805 AGCTCTGGTCGACTCGGC 61.445 66.667 16.46 14.10 0.00 5.54
852 4256 2.259875 GACAGCTCTGGTCGACTCGG 62.260 65.000 16.46 10.74 34.19 4.63
853 4257 1.135731 GACAGCTCTGGTCGACTCG 59.864 63.158 16.46 6.90 34.19 4.18
952 4394 1.203287 CATCGAGTGAGTGAAGCAGGA 59.797 52.381 0.00 0.00 0.00 3.86
1030 4476 4.344679 CCCTTCTCTATGTTCTGCTCATCT 59.655 45.833 0.00 0.00 0.00 2.90
1031 4477 4.343526 TCCCTTCTCTATGTTCTGCTCATC 59.656 45.833 0.00 0.00 0.00 2.92
1032 4478 4.293494 TCCCTTCTCTATGTTCTGCTCAT 58.707 43.478 0.00 0.00 0.00 2.90
1033 4479 3.703556 CTCCCTTCTCTATGTTCTGCTCA 59.296 47.826 0.00 0.00 0.00 4.26
1034 4480 3.957497 TCTCCCTTCTCTATGTTCTGCTC 59.043 47.826 0.00 0.00 0.00 4.26
1035 4481 3.987745 TCTCCCTTCTCTATGTTCTGCT 58.012 45.455 0.00 0.00 0.00 4.24
1036 4482 4.404073 TCTTCTCCCTTCTCTATGTTCTGC 59.596 45.833 0.00 0.00 0.00 4.26
1066 4512 3.782244 CACTCACGCAAGCTCGCC 61.782 66.667 0.00 0.00 45.62 5.54
1068 4514 2.724708 GAGCACTCACGCAAGCTCG 61.725 63.158 0.00 0.00 43.27 5.03
1156 4611 1.471684 GATTCAAACAGGCAGCAGAGG 59.528 52.381 0.00 0.00 0.00 3.69
1192 4647 0.238289 CAGTTTCATGGCGCGAAAGT 59.762 50.000 12.10 9.39 36.65 2.66
1197 4652 1.052287 GAAAACAGTTTCATGGCGCG 58.948 50.000 0.00 0.00 42.40 6.86
1243 4698 8.073768 GTGATTGTTCCACATATAAAATACGGG 58.926 37.037 0.00 0.00 34.81 5.28
1244 4699 8.616942 TGTGATTGTTCCACATATAAAATACGG 58.383 33.333 0.00 0.00 39.36 4.02
1304 4766 2.550180 TCGGATCGAGCTCATGAACTAG 59.450 50.000 15.40 0.00 0.00 2.57
1308 4770 1.102978 TGTCGGATCGAGCTCATGAA 58.897 50.000 15.40 0.00 36.23 2.57
1393 4855 1.743252 GTTGAAGCTGCTCTCCCCG 60.743 63.158 1.00 0.00 0.00 5.73
1444 4908 2.114056 CGCGGTAAGAATCGAATCGAA 58.886 47.619 10.12 0.00 39.99 3.71
1445 4909 1.750351 CGCGGTAAGAATCGAATCGA 58.250 50.000 8.12 8.12 41.13 3.59
1446 4910 0.158928 GCGCGGTAAGAATCGAATCG 59.841 55.000 8.83 0.00 0.00 3.34
1447 4911 0.158928 CGCGCGGTAAGAATCGAATC 59.841 55.000 24.84 0.00 0.00 2.52
1448 4912 1.818221 GCGCGCGGTAAGAATCGAAT 61.818 55.000 33.06 0.00 0.00 3.34
1451 4915 1.204228 TAAGCGCGCGGTAAGAATCG 61.204 55.000 36.14 0.14 0.00 3.34
1475 4941 6.348704 GGATTTTTGCTGATTTTTCCATGTGG 60.349 38.462 0.00 0.00 0.00 4.17
1485 4951 6.266103 TCAGAACTCAGGATTTTTGCTGATTT 59.734 34.615 0.00 0.00 0.00 2.17
1486 4952 5.771666 TCAGAACTCAGGATTTTTGCTGATT 59.228 36.000 0.00 0.00 0.00 2.57
1487 4953 5.319453 TCAGAACTCAGGATTTTTGCTGAT 58.681 37.500 0.00 0.00 0.00 2.90
1490 4956 4.461781 CCATCAGAACTCAGGATTTTTGCT 59.538 41.667 0.00 0.00 0.00 3.91
1517 4983 1.302285 CCAGTGGGAGCTGCAGAAT 59.698 57.895 20.43 4.39 35.28 2.40
1537 5014 4.628074 TCCTTATGTAGCCGCATTTAGAC 58.372 43.478 0.00 0.00 0.00 2.59
1591 5068 2.105128 GCGATCTCGAGGTGGGTG 59.895 66.667 13.56 0.00 43.02 4.61
1890 5368 1.141665 CAGGTCATGGTCGCGATGA 59.858 57.895 14.06 9.84 0.00 2.92
1967 5445 4.003788 CTCGTCGGCCCACCAGTT 62.004 66.667 0.00 0.00 34.57 3.16
2005 5483 3.384789 CGATCATGACCCTCTGGAAAGTA 59.615 47.826 0.00 0.00 34.81 2.24
2008 5486 1.134401 GCGATCATGACCCTCTGGAAA 60.134 52.381 0.00 0.00 34.81 3.13
2038 5516 1.380380 GATGCCCTTGAACCCCCTG 60.380 63.158 0.00 0.00 0.00 4.45
2149 5628 4.669318 TGTCAGACGTTAGCTATAGCAAC 58.331 43.478 26.07 22.88 45.16 4.17
2172 5651 3.874543 TGCAACAAGTTACAAGTCGACAT 59.125 39.130 19.50 1.86 0.00 3.06
2258 5741 1.587613 GCTCACGATCGTCTCCAGC 60.588 63.158 19.84 18.31 0.00 4.85
2261 5744 1.357334 GAGGCTCACGATCGTCTCC 59.643 63.158 19.84 18.38 0.00 3.71
2594 6077 2.125552 TCCATGAGCTTGCCGACG 60.126 61.111 0.00 0.00 0.00 5.12
2618 6101 4.466133 GAGGAGATCTCGGCGAGA 57.534 61.111 38.07 38.07 43.20 4.04
2741 6224 6.868864 AGATCGATTATAATGAACGGACCTTG 59.131 38.462 1.78 0.00 0.00 3.61
2757 6240 7.704271 ACAAGTAGACGAATGAAGATCGATTA 58.296 34.615 0.00 0.00 42.76 1.75
2775 6258 8.198109 AGCACTATCCACTATAACAACAAGTAG 58.802 37.037 0.00 0.00 0.00 2.57
2804 6287 1.410153 GCCCAAACCATCCATCACATC 59.590 52.381 0.00 0.00 0.00 3.06
3405 6900 4.235360 GACGATTAGATTACACCATCCGG 58.765 47.826 0.00 0.00 38.77 5.14
3424 6919 7.688372 ACATGCTTATTTATCTTCAACTGACG 58.312 34.615 0.00 0.00 0.00 4.35
3429 6924 9.956720 ATGCTAACATGCTTATTTATCTTCAAC 57.043 29.630 0.00 0.00 34.35 3.18
3448 6943 1.927174 CAGTGCTACGTCCATGCTAAC 59.073 52.381 0.00 0.00 0.00 2.34
3549 7044 1.374758 CACTGACTGAACCCCGAGC 60.375 63.158 0.00 0.00 0.00 5.03
3597 7096 2.969238 GATCGGCCCACATCGCAG 60.969 66.667 0.00 0.00 0.00 5.18
3606 7105 2.029666 CAGTGATCCGATCGGCCC 59.970 66.667 29.62 21.65 34.68 5.80
3627 7126 4.478699 CAACGTTGTGGTAATCGTAGAGA 58.521 43.478 20.21 0.00 43.63 3.10
3678 7177 0.818296 AGAAACGGGAGAGGATCGTG 59.182 55.000 0.00 0.00 42.67 4.35
3764 7264 3.575351 AAGCCACGTCTCGGTGCTC 62.575 63.158 7.77 0.00 36.98 4.26
3781 7289 1.713647 TCTACCAGGGCCAAATTCCAA 59.286 47.619 6.18 0.00 0.00 3.53
3837 7345 2.295909 TCATTTTCGCCTCTTGGTTTGG 59.704 45.455 0.00 0.00 35.27 3.28
3856 7364 4.289410 TGGGAATCCACTGATCTCTTTTCA 59.711 41.667 0.09 0.00 38.32 2.69
3876 7384 6.349300 TCTTTTCTTAGAATCGGAGAATGGG 58.651 40.000 0.00 0.00 43.58 4.00
3913 7421 3.116590 ACTGATCCATGATGAGTAGGGGA 60.117 47.826 0.00 0.00 34.95 4.81
3945 7453 4.243793 ACAGTGAGCCTAGACTAGACAT 57.756 45.455 11.27 0.00 0.00 3.06
3946 7454 3.722908 ACAGTGAGCCTAGACTAGACA 57.277 47.619 11.27 5.65 0.00 3.41
3947 7455 4.023536 GCATACAGTGAGCCTAGACTAGAC 60.024 50.000 11.27 0.00 0.00 2.59
3948 7456 4.138290 GCATACAGTGAGCCTAGACTAGA 58.862 47.826 11.27 0.00 0.00 2.43
3950 7458 3.632604 GTGCATACAGTGAGCCTAGACTA 59.367 47.826 0.00 0.00 0.00 2.59
3951 7459 2.428890 GTGCATACAGTGAGCCTAGACT 59.571 50.000 0.00 0.00 0.00 3.24
4024 7532 2.280524 TCGTGCCCTGTGAAACGG 60.281 61.111 0.00 0.00 44.86 4.44
4074 7582 1.408340 TGAACATTGTGTTGCTGTGGG 59.592 47.619 0.00 0.00 41.28 4.61
4078 7586 4.422840 TGTCTTTGAACATTGTGTTGCTG 58.577 39.130 0.00 0.00 41.28 4.41
4139 7647 5.434408 TGGAGACACACACGTATCTAGTAT 58.566 41.667 0.00 0.00 33.40 2.12
4268 7776 1.803334 TCCCGATGAAAACAACGAGG 58.197 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.