Multiple sequence alignment - TraesCS4D01G177000

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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 TraesCS4D01G177000 chr4D 100.000 3956 0 0 1 3956 308372691 308368736 0.000000e+00 7306
1 TraesCS4D01G177000 chr4D 94.178 292 16 1 3666 3956 212158427 212158136 1.010000e-120 444
2 TraesCS4D01G177000 chr4A 94.334 3424 98 42 1 3374 168791088 168794465 0.000000e+00 5160
3 TraesCS4D01G177000 chr4A 90.120 334 23 8 3339 3664 168794466 168794797 3.650000e-115 425
4 TraesCS4D01G177000 chr4B 95.531 2797 81 25 889 3664 384293097 384290324 0.000000e+00 4433
5 TraesCS4D01G177000 chr4B 89.396 943 40 20 1 893 384294054 384293122 0.000000e+00 1133
6 TraesCS4D01G177000 chr2D 83.051 826 120 16 1201 2010 51192947 51192126 0.000000e+00 732
7 TraesCS4D01G177000 chr2A 81.290 930 146 23 1201 2113 52665880 52664962 0.000000e+00 728
8 TraesCS4D01G177000 chr2B 81.882 861 127 25 1202 2043 80122435 80121585 0.000000e+00 699
9 TraesCS4D01G177000 chr1D 95.946 296 11 1 3661 3956 109826454 109826160 2.770000e-131 479
10 TraesCS4D01G177000 chr1D 93.603 297 19 0 3660 3956 329438 329734 1.010000e-120 444
11 TraesCS4D01G177000 chr7D 95.890 292 11 1 3666 3956 494517106 494516815 4.630000e-129 472
12 TraesCS4D01G177000 chr3B 89.420 293 30 1 3664 3955 746105368 746105660 6.250000e-98 368
13 TraesCS4D01G177000 chr1B 88.776 294 32 1 3662 3955 113501382 113501090 3.760000e-95 359
14 TraesCS4D01G177000 chr1B 88.435 294 33 1 3662 3955 113216477 113216185 1.750000e-93 353
15 TraesCS4D01G177000 chr1B 88.435 294 33 1 3662 3955 113411371 113411079 1.750000e-93 353
16 TraesCS4D01G177000 chr5B 88.396 293 33 1 3664 3955 650127532 650127824 6.290000e-93 351


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 TraesCS4D01G177000 chr4D 308368736 308372691 3955 True 7306.0 7306 100.0000 1 3956 1 chr4D.!!$R2 3955
1 TraesCS4D01G177000 chr4A 168791088 168794797 3709 False 2792.5 5160 92.2270 1 3664 2 chr4A.!!$F1 3663
2 TraesCS4D01G177000 chr4B 384290324 384294054 3730 True 2783.0 4433 92.4635 1 3664 2 chr4B.!!$R1 3663
3 TraesCS4D01G177000 chr2D 51192126 51192947 821 True 732.0 732 83.0510 1201 2010 1 chr2D.!!$R1 809
4 TraesCS4D01G177000 chr2A 52664962 52665880 918 True 728.0 728 81.2900 1201 2113 1 chr2A.!!$R1 912
5 TraesCS4D01G177000 chr2B 80121585 80122435 850 True 699.0 699 81.8820 1202 2043 1 chr2B.!!$R1 841

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
997 1101 0.689623 AGGGAGAGTTGCTTGAGTGG 59.310 55.000 0.0 0.0 0.0 4.00 F
2340 2459 2.590575 AACAACGTCCAGTGCCCG 60.591 61.111 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2658 2777 0.250513 AGAAACCCTCGTCCATCTGC 59.749 55.0 0.0 0.0 0.0 4.26 R
3933 4141 0.105039 GGAGGCGGATTGTGTAGAGG 59.895 60.0 0.0 0.0 0.0 3.69 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
92 120 6.402118 CCAACTGTCGATACCTGTTTTACATG 60.402 42.308 0.00 0.00 0.00 3.21
181 209 3.379372 AGTGATTGGATCAAAGCAATCCG 59.621 43.478 1.46 0.00 44.81 4.18
182 210 3.378112 GTGATTGGATCAAAGCAATCCGA 59.622 43.478 1.46 0.00 44.81 4.55
183 211 4.037208 GTGATTGGATCAAAGCAATCCGAT 59.963 41.667 1.46 4.84 46.03 4.18
184 212 4.843220 ATTGGATCAAAGCAATCCGATC 57.157 40.909 0.00 0.00 41.65 3.69
186 214 3.889815 TGGATCAAAGCAATCCGATCTT 58.110 40.909 0.00 0.00 44.81 2.40
187 215 4.272489 TGGATCAAAGCAATCCGATCTTT 58.728 39.130 0.00 0.00 44.81 2.52
188 216 4.336433 TGGATCAAAGCAATCCGATCTTTC 59.664 41.667 0.00 0.00 44.81 2.62
189 217 4.336433 GGATCAAAGCAATCCGATCTTTCA 59.664 41.667 0.00 0.00 35.62 2.69
190 218 5.009410 GGATCAAAGCAATCCGATCTTTCAT 59.991 40.000 0.00 0.00 35.62 2.57
206 234 8.699749 CGATCTTTCATACGCTTAAACATGATA 58.300 33.333 0.00 0.00 0.00 2.15
211 239 9.929722 TTTCATACGCTTAAACATGATACAATC 57.070 29.630 0.00 0.00 0.00 2.67
299 334 5.916883 CAGATGTGTTAAGTTTTCTGCCTTG 59.083 40.000 0.00 0.00 0.00 3.61
305 340 6.811665 GTGTTAAGTTTTCTGCCTTGTTCTTT 59.188 34.615 0.00 0.00 0.00 2.52
317 352 7.665559 TCTGCCTTGTTCTTTCATTAGTGTATT 59.334 33.333 0.00 0.00 0.00 1.89
318 353 8.177119 TGCCTTGTTCTTTCATTAGTGTATTT 57.823 30.769 0.00 0.00 0.00 1.40
319 354 8.296713 TGCCTTGTTCTTTCATTAGTGTATTTC 58.703 33.333 0.00 0.00 0.00 2.17
320 355 7.481798 GCCTTGTTCTTTCATTAGTGTATTTCG 59.518 37.037 0.00 0.00 0.00 3.46
347 391 6.043127 ACTCCTATATGGTCATGCATAACACA 59.957 38.462 1.58 0.00 37.07 3.72
348 392 6.230472 TCCTATATGGTCATGCATAACACAC 58.770 40.000 1.58 0.00 37.07 3.82
349 393 5.412594 CCTATATGGTCATGCATAACACACC 59.587 44.000 1.58 3.50 35.78 4.16
350 394 2.877097 TGGTCATGCATAACACACCT 57.123 45.000 1.58 0.00 36.09 4.00
656 711 7.390440 TCTGGGATGTTTTGTGAACTAATACTG 59.610 37.037 0.00 0.00 0.00 2.74
657 712 6.432783 TGGGATGTTTTGTGAACTAATACTGG 59.567 38.462 0.00 0.00 0.00 4.00
679 737 4.023107 GGTCCAGCTGTTTTCTTTAAGGAC 60.023 45.833 13.81 7.89 41.63 3.85
966 1070 6.468543 ACAAGTAGAGGAAGTGGAATTTCTC 58.531 40.000 0.00 0.00 32.53 2.87
967 1071 6.271159 ACAAGTAGAGGAAGTGGAATTTCTCT 59.729 38.462 3.29 3.29 32.53 3.10
974 1078 4.827284 GGAAGTGGAATTTCTCTTGTGGAA 59.173 41.667 5.78 0.00 32.53 3.53
997 1101 0.689623 AGGGAGAGTTGCTTGAGTGG 59.310 55.000 0.00 0.00 0.00 4.00
1020 1124 3.412624 GATGGGAGGTGGGCTGCTC 62.413 68.421 0.00 0.00 0.00 4.26
2214 2333 3.693085 CCATCCTGAATGACAAGTTCCTG 59.307 47.826 0.00 0.00 37.59 3.86
2271 2390 3.637769 GGAGTATGTCCAGAAGAGGAGT 58.362 50.000 0.00 0.00 46.10 3.85
2340 2459 2.590575 AACAACGTCCAGTGCCCG 60.591 61.111 0.00 0.00 0.00 6.13
2654 2773 2.834505 CAATGCCATCACCCCGGG 60.835 66.667 15.80 15.80 0.00 5.73
2656 2775 3.060614 AATGCCATCACCCCGGGAG 62.061 63.158 26.32 15.37 0.00 4.30
2747 2872 3.056588 TGTCAGTAACATGATGCAGCA 57.943 42.857 7.31 7.31 31.20 4.41
2748 2873 3.004862 TGTCAGTAACATGATGCAGCAG 58.995 45.455 11.66 5.32 31.20 4.24
2749 2874 2.011947 TCAGTAACATGATGCAGCAGC 58.988 47.619 11.66 2.87 42.57 5.25
2971 3120 9.021863 GGTACTACTGAATGAAGAATAAACTCG 57.978 37.037 0.00 0.00 0.00 4.18
2997 3146 7.170393 AGGGTCATCATAAGCTTTTAAAACC 57.830 36.000 3.20 6.19 0.00 3.27
3240 3401 2.681976 GCTGTTCATATGACTGGCTGGT 60.682 50.000 4.48 0.00 0.00 4.00
3251 3412 2.362077 GACTGGCTGGTTGTCAAATTGT 59.638 45.455 0.00 0.00 0.00 2.71
3326 3487 5.764686 TGCTCTCTTATGTGATCTCTCTCTC 59.235 44.000 0.00 0.00 0.00 3.20
3327 3488 6.000219 GCTCTCTTATGTGATCTCTCTCTCT 59.000 44.000 0.00 0.00 0.00 3.10
3328 3489 6.488006 GCTCTCTTATGTGATCTCTCTCTCTT 59.512 42.308 0.00 0.00 0.00 2.85
3329 3490 7.308229 GCTCTCTTATGTGATCTCTCTCTCTTC 60.308 44.444 0.00 0.00 0.00 2.87
3330 3491 6.998074 TCTCTTATGTGATCTCTCTCTCTTCC 59.002 42.308 0.00 0.00 0.00 3.46
3379 3582 0.749649 TTGCAAAACTTCCATGCCGT 59.250 45.000 0.00 0.00 39.31 5.68
3394 3597 4.310769 CATGCCGTGGAATTTTGGTAAAA 58.689 39.130 0.00 0.00 34.41 1.52
3408 3614 6.956299 TTTGGTAAAATAGACAGCTACGTC 57.044 37.500 0.00 0.00 36.08 4.34
3415 3621 4.785511 ATAGACAGCTACGTCTGTTTGT 57.214 40.909 15.19 2.02 46.40 2.83
3422 3628 2.755650 CTACGTCTGTTTGTCAGGCTT 58.244 47.619 0.00 0.00 45.61 4.35
3462 3669 0.321653 AGGTTCACTTGGATGTCGGC 60.322 55.000 0.00 0.00 0.00 5.54
3485 3692 2.504367 AGAAACGGACCAACCAAGATG 58.496 47.619 0.00 0.00 38.90 2.90
3548 3756 2.226437 CCGCTGAGCTGCTTCTTTTTAA 59.774 45.455 2.53 0.00 0.00 1.52
3551 3759 4.471373 GCTGAGCTGCTTCTTTTTAAGTC 58.529 43.478 2.53 0.00 0.00 3.01
3664 3872 5.515797 AGTGGCAAACCTAAGAAAAGTTC 57.484 39.130 0.00 0.00 36.63 3.01
3665 3873 5.201243 AGTGGCAAACCTAAGAAAAGTTCT 58.799 37.500 0.00 0.00 38.17 3.01
3693 3901 8.943594 TTTTAAACTTGGGCCTCTTTATTAGA 57.056 30.769 4.53 0.00 0.00 2.10
3694 3902 9.541884 TTTTAAACTTGGGCCTCTTTATTAGAT 57.458 29.630 4.53 0.00 30.92 1.98
3695 3903 8.747538 TTAAACTTGGGCCTCTTTATTAGATC 57.252 34.615 4.53 0.00 30.92 2.75
3696 3904 5.975988 ACTTGGGCCTCTTTATTAGATCA 57.024 39.130 4.53 0.00 30.92 2.92
3697 3905 6.327386 ACTTGGGCCTCTTTATTAGATCAA 57.673 37.500 4.53 0.00 30.92 2.57
3698 3906 6.731467 ACTTGGGCCTCTTTATTAGATCAAA 58.269 36.000 4.53 0.00 30.92 2.69
3699 3907 6.603599 ACTTGGGCCTCTTTATTAGATCAAAC 59.396 38.462 4.53 0.00 30.92 2.93
3700 3908 6.073447 TGGGCCTCTTTATTAGATCAAACA 57.927 37.500 4.53 0.00 30.92 2.83
3701 3909 6.489603 TGGGCCTCTTTATTAGATCAAACAA 58.510 36.000 4.53 0.00 30.92 2.83
3702 3910 6.377146 TGGGCCTCTTTATTAGATCAAACAAC 59.623 38.462 4.53 0.00 30.92 3.32
3703 3911 6.183360 GGGCCTCTTTATTAGATCAAACAACC 60.183 42.308 0.84 0.00 30.92 3.77
3704 3912 6.458342 GGCCTCTTTATTAGATCAAACAACCG 60.458 42.308 0.00 0.00 30.92 4.44
3705 3913 6.093633 GCCTCTTTATTAGATCAAACAACCGT 59.906 38.462 0.00 0.00 30.92 4.83
3706 3914 7.361799 GCCTCTTTATTAGATCAAACAACCGTT 60.362 37.037 0.00 0.00 31.84 4.44
3707 3915 9.158233 CCTCTTTATTAGATCAAACAACCGTTA 57.842 33.333 0.00 0.00 30.84 3.18
3708 3916 9.968743 CTCTTTATTAGATCAAACAACCGTTAC 57.031 33.333 0.00 0.00 30.84 2.50
3709 3917 9.491675 TCTTTATTAGATCAAACAACCGTTACA 57.508 29.630 0.00 0.00 33.99 2.41
3712 3920 7.915293 ATTAGATCAAACAACCGTTACATCA 57.085 32.000 0.00 0.00 33.99 3.07
3713 3921 7.915293 TTAGATCAAACAACCGTTACATCAT 57.085 32.000 0.00 0.00 33.99 2.45
3714 3922 6.422776 AGATCAAACAACCGTTACATCATC 57.577 37.500 0.00 0.00 33.99 2.92
3715 3923 5.354234 AGATCAAACAACCGTTACATCATCC 59.646 40.000 0.00 0.00 33.99 3.51
3716 3924 4.390264 TCAAACAACCGTTACATCATCCA 58.610 39.130 0.00 0.00 33.99 3.41
3717 3925 4.214545 TCAAACAACCGTTACATCATCCAC 59.785 41.667 0.00 0.00 33.99 4.02
3718 3926 2.706890 ACAACCGTTACATCATCCACC 58.293 47.619 0.00 0.00 0.00 4.61
3719 3927 2.039216 ACAACCGTTACATCATCCACCA 59.961 45.455 0.00 0.00 0.00 4.17
3720 3928 2.677836 CAACCGTTACATCATCCACCAG 59.322 50.000 0.00 0.00 0.00 4.00
3721 3929 1.299541 CCGTTACATCATCCACCAGC 58.700 55.000 0.00 0.00 0.00 4.85
3722 3930 1.299541 CGTTACATCATCCACCAGCC 58.700 55.000 0.00 0.00 0.00 4.85
3723 3931 1.406751 CGTTACATCATCCACCAGCCA 60.407 52.381 0.00 0.00 0.00 4.75
3724 3932 2.746142 CGTTACATCATCCACCAGCCAT 60.746 50.000 0.00 0.00 0.00 4.40
3725 3933 2.880890 GTTACATCATCCACCAGCCATC 59.119 50.000 0.00 0.00 0.00 3.51
3726 3934 1.219773 ACATCATCCACCAGCCATCT 58.780 50.000 0.00 0.00 0.00 2.90
3727 3935 1.142465 ACATCATCCACCAGCCATCTC 59.858 52.381 0.00 0.00 0.00 2.75
3728 3936 1.142262 CATCATCCACCAGCCATCTCA 59.858 52.381 0.00 0.00 0.00 3.27
3729 3937 0.543277 TCATCCACCAGCCATCTCAC 59.457 55.000 0.00 0.00 0.00 3.51
3730 3938 0.253894 CATCCACCAGCCATCTCACA 59.746 55.000 0.00 0.00 0.00 3.58
3731 3939 0.994247 ATCCACCAGCCATCTCACAA 59.006 50.000 0.00 0.00 0.00 3.33
3732 3940 0.994247 TCCACCAGCCATCTCACAAT 59.006 50.000 0.00 0.00 0.00 2.71
3733 3941 2.195727 TCCACCAGCCATCTCACAATA 58.804 47.619 0.00 0.00 0.00 1.90
3734 3942 2.171237 TCCACCAGCCATCTCACAATAG 59.829 50.000 0.00 0.00 0.00 1.73
3735 3943 2.171237 CCACCAGCCATCTCACAATAGA 59.829 50.000 0.00 0.00 0.00 1.98
3736 3944 3.181447 CCACCAGCCATCTCACAATAGAT 60.181 47.826 0.00 0.00 36.64 1.98
3742 3950 3.117491 CATCTCACAATAGATGCCGGT 57.883 47.619 1.90 0.00 44.63 5.28
3743 3951 2.602257 TCTCACAATAGATGCCGGTG 57.398 50.000 1.90 0.00 0.00 4.94
3744 3952 1.138859 TCTCACAATAGATGCCGGTGG 59.861 52.381 1.90 0.00 0.00 4.61
3745 3953 0.908910 TCACAATAGATGCCGGTGGT 59.091 50.000 1.90 0.00 0.00 4.16
3746 3954 1.280710 TCACAATAGATGCCGGTGGTT 59.719 47.619 1.90 0.00 0.00 3.67
3747 3955 1.670811 CACAATAGATGCCGGTGGTTC 59.329 52.381 1.90 0.00 0.00 3.62
3748 3956 1.308998 CAATAGATGCCGGTGGTTCC 58.691 55.000 1.90 0.00 0.00 3.62
3749 3957 1.134098 CAATAGATGCCGGTGGTTCCT 60.134 52.381 1.90 0.00 0.00 3.36
3750 3958 0.759346 ATAGATGCCGGTGGTTCCTC 59.241 55.000 1.90 0.00 0.00 3.71
3751 3959 1.672854 TAGATGCCGGTGGTTCCTCG 61.673 60.000 1.90 0.00 0.00 4.63
3752 3960 3.000819 ATGCCGGTGGTTCCTCGA 61.001 61.111 1.90 0.00 0.00 4.04
3753 3961 3.310860 ATGCCGGTGGTTCCTCGAC 62.311 63.158 1.90 0.00 0.00 4.20
3754 3962 4.754667 GCCGGTGGTTCCTCGACC 62.755 72.222 1.90 0.00 40.77 4.79
3755 3963 4.078516 CCGGTGGTTCCTCGACCC 62.079 72.222 0.00 0.00 41.04 4.46
3756 3964 3.307906 CGGTGGTTCCTCGACCCA 61.308 66.667 0.00 0.00 41.04 4.51
3757 3965 2.346365 GGTGGTTCCTCGACCCAC 59.654 66.667 9.30 9.30 46.35 4.61
3758 3966 3.144285 GTGGTTCCTCGACCCACA 58.856 61.111 11.82 0.00 46.33 4.17
3759 3967 1.448497 GTGGTTCCTCGACCCACAA 59.552 57.895 11.82 0.00 46.33 3.33
3760 3968 0.036306 GTGGTTCCTCGACCCACAAT 59.964 55.000 11.82 0.00 46.33 2.71
3761 3969 0.323629 TGGTTCCTCGACCCACAATC 59.676 55.000 0.00 0.00 39.01 2.67
3762 3970 0.392595 GGTTCCTCGACCCACAATCC 60.393 60.000 0.00 0.00 33.41 3.01
3763 3971 0.739813 GTTCCTCGACCCACAATCCG 60.740 60.000 0.00 0.00 0.00 4.18
3764 3972 1.895020 TTCCTCGACCCACAATCCGG 61.895 60.000 0.00 0.00 0.00 5.14
3779 3987 1.823797 TCCGGGTGGATTAAAAACCG 58.176 50.000 0.00 5.84 40.17 4.44
3780 3988 0.171679 CCGGGTGGATTAAAAACCGC 59.828 55.000 7.03 4.88 39.96 5.68
3784 3992 1.990799 GTGGATTAAAAACCGCCAGC 58.009 50.000 0.00 0.00 0.00 4.85
3785 3993 0.892063 TGGATTAAAAACCGCCAGCC 59.108 50.000 0.00 0.00 0.00 4.85
3786 3994 1.182667 GGATTAAAAACCGCCAGCCT 58.817 50.000 0.00 0.00 0.00 4.58
3787 3995 2.291024 TGGATTAAAAACCGCCAGCCTA 60.291 45.455 0.00 0.00 0.00 3.93
3788 3996 2.357952 GGATTAAAAACCGCCAGCCTAG 59.642 50.000 0.00 0.00 0.00 3.02
3789 3997 1.170442 TTAAAAACCGCCAGCCTAGC 58.830 50.000 0.00 0.00 0.00 3.42
3790 3998 0.326927 TAAAAACCGCCAGCCTAGCT 59.673 50.000 0.00 0.00 40.77 3.32
3791 3999 0.326927 AAAAACCGCCAGCCTAGCTA 59.673 50.000 0.00 0.00 36.40 3.32
3792 4000 0.107654 AAAACCGCCAGCCTAGCTAG 60.108 55.000 14.20 14.20 36.40 3.42
3793 4001 2.595009 AAACCGCCAGCCTAGCTAGC 62.595 60.000 15.74 6.62 39.72 3.42
3794 4002 3.230245 CCGCCAGCCTAGCTAGCT 61.230 66.667 23.12 23.12 40.85 3.32
3795 4003 2.338257 CGCCAGCCTAGCTAGCTC 59.662 66.667 23.26 7.22 40.85 4.09
3796 4004 2.493651 CGCCAGCCTAGCTAGCTCA 61.494 63.158 23.26 7.11 40.85 4.26
3797 4005 1.814772 CGCCAGCCTAGCTAGCTCAT 61.815 60.000 23.26 0.00 40.85 2.90
3798 4006 0.320596 GCCAGCCTAGCTAGCTCATG 60.321 60.000 23.26 14.98 39.96 3.07
3799 4007 1.336131 CCAGCCTAGCTAGCTCATGA 58.664 55.000 23.26 1.96 38.95 3.07
3800 4008 1.273048 CCAGCCTAGCTAGCTCATGAG 59.727 57.143 23.26 18.84 38.95 2.90
3801 4009 2.237643 CAGCCTAGCTAGCTCATGAGA 58.762 52.381 27.04 5.37 38.95 3.27
3802 4010 2.229543 CAGCCTAGCTAGCTCATGAGAG 59.770 54.545 27.04 16.20 40.12 3.20
3803 4011 2.108075 AGCCTAGCTAGCTCATGAGAGA 59.892 50.000 27.04 11.55 39.89 3.10
3804 4012 2.228822 GCCTAGCTAGCTCATGAGAGAC 59.771 54.545 27.04 11.60 44.98 3.36
3805 4013 3.485394 CCTAGCTAGCTCATGAGAGACA 58.515 50.000 27.04 6.38 44.98 3.41
3806 4014 3.253188 CCTAGCTAGCTCATGAGAGACAC 59.747 52.174 27.04 8.03 44.98 3.67
3807 4015 2.732763 AGCTAGCTCATGAGAGACACA 58.267 47.619 27.04 2.91 44.98 3.72
3808 4016 3.095332 AGCTAGCTCATGAGAGACACAA 58.905 45.455 27.04 1.89 44.98 3.33
3809 4017 3.705579 AGCTAGCTCATGAGAGACACAAT 59.294 43.478 27.04 0.86 44.98 2.71
3810 4018 4.161942 AGCTAGCTCATGAGAGACACAATT 59.838 41.667 27.04 0.00 44.98 2.32
3811 4019 4.874966 GCTAGCTCATGAGAGACACAATTT 59.125 41.667 27.04 0.88 44.98 1.82
3812 4020 5.220624 GCTAGCTCATGAGAGACACAATTTG 60.221 44.000 27.04 0.00 44.98 2.32
3813 4021 3.439476 AGCTCATGAGAGACACAATTTGC 59.561 43.478 27.04 6.76 44.98 3.68
3814 4022 3.427233 GCTCATGAGAGACACAATTTGCC 60.427 47.826 27.04 0.00 44.98 4.52
3815 4023 4.008330 CTCATGAGAGACACAATTTGCCT 58.992 43.478 18.34 0.00 44.98 4.75
3816 4024 4.005650 TCATGAGAGACACAATTTGCCTC 58.994 43.478 0.00 1.69 0.00 4.70
3817 4025 3.777106 TGAGAGACACAATTTGCCTCT 57.223 42.857 13.15 13.15 36.97 3.69
3818 4026 3.668447 TGAGAGACACAATTTGCCTCTC 58.332 45.455 23.26 23.26 46.00 3.20
3819 4027 2.670414 GAGAGACACAATTTGCCTCTCG 59.330 50.000 19.26 0.00 40.00 4.04
3820 4028 2.300152 AGAGACACAATTTGCCTCTCGA 59.700 45.455 14.01 0.00 31.81 4.04
3821 4029 2.670414 GAGACACAATTTGCCTCTCGAG 59.330 50.000 5.93 5.93 0.00 4.04
3830 4038 3.700109 CCTCTCGAGGGCAGTGAA 58.300 61.111 13.56 0.00 44.87 3.18
3831 4039 1.975327 CCTCTCGAGGGCAGTGAAA 59.025 57.895 13.56 0.00 44.87 2.69
3832 4040 0.108424 CCTCTCGAGGGCAGTGAAAG 60.108 60.000 13.56 0.00 44.87 2.62
3833 4041 0.891373 CTCTCGAGGGCAGTGAAAGA 59.109 55.000 13.56 0.00 0.00 2.52
3834 4042 1.273606 CTCTCGAGGGCAGTGAAAGAA 59.726 52.381 13.56 0.00 0.00 2.52
3835 4043 1.691976 TCTCGAGGGCAGTGAAAGAAA 59.308 47.619 13.56 0.00 0.00 2.52
3836 4044 2.072298 CTCGAGGGCAGTGAAAGAAAG 58.928 52.381 3.91 0.00 0.00 2.62
3837 4045 1.691976 TCGAGGGCAGTGAAAGAAAGA 59.308 47.619 0.00 0.00 0.00 2.52
3838 4046 1.801178 CGAGGGCAGTGAAAGAAAGAC 59.199 52.381 0.00 0.00 0.00 3.01
3839 4047 2.806745 CGAGGGCAGTGAAAGAAAGACA 60.807 50.000 0.00 0.00 0.00 3.41
3840 4048 3.416156 GAGGGCAGTGAAAGAAAGACAT 58.584 45.455 0.00 0.00 0.00 3.06
3841 4049 3.416156 AGGGCAGTGAAAGAAAGACATC 58.584 45.455 0.00 0.00 0.00 3.06
3842 4050 2.160417 GGGCAGTGAAAGAAAGACATCG 59.840 50.000 0.00 0.00 0.00 3.84
3843 4051 3.067106 GGCAGTGAAAGAAAGACATCGA 58.933 45.455 0.00 0.00 0.00 3.59
3844 4052 3.498397 GGCAGTGAAAGAAAGACATCGAA 59.502 43.478 0.00 0.00 0.00 3.71
3845 4053 4.377841 GGCAGTGAAAGAAAGACATCGAAG 60.378 45.833 0.00 0.00 0.00 3.79
3846 4054 4.212214 GCAGTGAAAGAAAGACATCGAAGT 59.788 41.667 0.00 0.00 0.00 3.01
3847 4055 5.405571 GCAGTGAAAGAAAGACATCGAAGTA 59.594 40.000 0.00 0.00 0.00 2.24
3848 4056 6.091441 GCAGTGAAAGAAAGACATCGAAGTAT 59.909 38.462 0.00 0.00 0.00 2.12
3849 4057 7.275779 GCAGTGAAAGAAAGACATCGAAGTATA 59.724 37.037 0.00 0.00 0.00 1.47
3850 4058 8.802856 CAGTGAAAGAAAGACATCGAAGTATAG 58.197 37.037 0.00 0.00 0.00 1.31
3851 4059 8.524487 AGTGAAAGAAAGACATCGAAGTATAGT 58.476 33.333 0.00 0.00 0.00 2.12
3852 4060 8.800031 GTGAAAGAAAGACATCGAAGTATAGTC 58.200 37.037 0.00 0.00 0.00 2.59
3853 4061 8.740906 TGAAAGAAAGACATCGAAGTATAGTCT 58.259 33.333 0.00 0.00 40.99 3.24
3856 4064 8.967664 AGAAAGACATCGAAGTATAGTCTACT 57.032 34.615 0.00 0.00 38.51 2.57
3857 4065 8.832521 AGAAAGACATCGAAGTATAGTCTACTG 58.167 37.037 0.00 0.00 38.51 2.74
3858 4066 8.734218 AAAGACATCGAAGTATAGTCTACTGA 57.266 34.615 0.00 0.00 38.51 3.41
3859 4067 8.911918 AAGACATCGAAGTATAGTCTACTGAT 57.088 34.615 0.00 0.00 38.51 2.90
3860 4068 9.999660 AAGACATCGAAGTATAGTCTACTGATA 57.000 33.333 0.00 0.00 38.51 2.15
3861 4069 9.999660 AGACATCGAAGTATAGTCTACTGATAA 57.000 33.333 0.00 0.00 37.75 1.75
3874 4082 8.798859 AGTCTACTGATAAAACATTGCAATCT 57.201 30.769 9.53 0.00 0.00 2.40
3875 4083 8.671921 AGTCTACTGATAAAACATTGCAATCTG 58.328 33.333 9.53 3.40 0.00 2.90
3876 4084 7.430502 GTCTACTGATAAAACATTGCAATCTGC 59.569 37.037 9.53 0.00 45.29 4.26
3892 4100 2.412937 GCATAAATTGCCGCCGCT 59.587 55.556 0.00 0.00 46.15 5.52
3893 4101 1.658409 GCATAAATTGCCGCCGCTC 60.658 57.895 0.00 0.00 46.15 5.03
3894 4102 1.008538 CATAAATTGCCGCCGCTCC 60.009 57.895 0.00 0.00 35.36 4.70
3895 4103 1.152963 ATAAATTGCCGCCGCTCCT 60.153 52.632 0.00 0.00 35.36 3.69
3896 4104 1.447317 ATAAATTGCCGCCGCTCCTG 61.447 55.000 0.00 0.00 35.36 3.86
3897 4105 2.813226 TAAATTGCCGCCGCTCCTGT 62.813 55.000 0.00 0.00 35.36 4.00
3898 4106 4.722700 ATTGCCGCCGCTCCTGTT 62.723 61.111 0.00 0.00 35.36 3.16
3904 4112 3.730761 GCCGCTCCTGTTGCAGTG 61.731 66.667 0.00 0.00 0.00 3.66
3905 4113 2.031012 CCGCTCCTGTTGCAGTGA 59.969 61.111 0.00 0.00 0.00 3.41
3906 4114 1.597854 CCGCTCCTGTTGCAGTGAA 60.598 57.895 0.00 0.00 0.00 3.18
3907 4115 1.572085 CCGCTCCTGTTGCAGTGAAG 61.572 60.000 0.00 0.00 0.00 3.02
3908 4116 1.578423 GCTCCTGTTGCAGTGAAGC 59.422 57.895 0.00 0.00 0.00 3.86
3909 4117 1.860484 GCTCCTGTTGCAGTGAAGCC 61.860 60.000 0.00 0.00 0.00 4.35
3910 4118 0.535780 CTCCTGTTGCAGTGAAGCCA 60.536 55.000 0.00 0.00 0.00 4.75
3911 4119 0.819259 TCCTGTTGCAGTGAAGCCAC 60.819 55.000 0.00 0.00 43.50 5.01
3912 4120 1.656441 CTGTTGCAGTGAAGCCACC 59.344 57.895 0.00 0.00 44.22 4.61
3913 4121 1.799258 CTGTTGCAGTGAAGCCACCC 61.799 60.000 0.00 0.00 44.22 4.61
3914 4122 2.594303 TTGCAGTGAAGCCACCCG 60.594 61.111 0.00 0.00 44.22 5.28
3915 4123 3.113514 TTGCAGTGAAGCCACCCGA 62.114 57.895 0.00 0.00 44.22 5.14
3916 4124 2.743928 GCAGTGAAGCCACCCGAG 60.744 66.667 0.00 0.00 44.22 4.63
3917 4125 2.743718 CAGTGAAGCCACCCGAGT 59.256 61.111 0.00 0.00 44.22 4.18
3918 4126 1.071471 CAGTGAAGCCACCCGAGTT 59.929 57.895 0.00 0.00 44.22 3.01
3919 4127 0.951040 CAGTGAAGCCACCCGAGTTC 60.951 60.000 0.00 0.00 44.22 3.01
3920 4128 1.070786 GTGAAGCCACCCGAGTTCA 59.929 57.895 0.00 0.00 37.33 3.18
3921 4129 0.321653 GTGAAGCCACCCGAGTTCAT 60.322 55.000 0.00 0.00 37.33 2.57
3922 4130 0.400213 TGAAGCCACCCGAGTTCATT 59.600 50.000 0.00 0.00 0.00 2.57
3923 4131 0.804989 GAAGCCACCCGAGTTCATTG 59.195 55.000 0.00 0.00 0.00 2.82
3924 4132 0.110486 AAGCCACCCGAGTTCATTGT 59.890 50.000 0.00 0.00 0.00 2.71
3925 4133 0.981183 AGCCACCCGAGTTCATTGTA 59.019 50.000 0.00 0.00 0.00 2.41
3926 4134 1.559682 AGCCACCCGAGTTCATTGTAT 59.440 47.619 0.00 0.00 0.00 2.29
3927 4135 2.026262 AGCCACCCGAGTTCATTGTATT 60.026 45.455 0.00 0.00 0.00 1.89
3928 4136 2.097466 GCCACCCGAGTTCATTGTATTG 59.903 50.000 0.00 0.00 0.00 1.90
3929 4137 3.605634 CCACCCGAGTTCATTGTATTGA 58.394 45.455 0.00 0.00 0.00 2.57
3930 4138 4.199310 CCACCCGAGTTCATTGTATTGAT 58.801 43.478 0.00 0.00 0.00 2.57
3931 4139 4.273480 CCACCCGAGTTCATTGTATTGATC 59.727 45.833 0.00 0.00 0.00 2.92
3932 4140 4.875536 CACCCGAGTTCATTGTATTGATCA 59.124 41.667 0.00 0.00 0.00 2.92
3933 4141 4.876107 ACCCGAGTTCATTGTATTGATCAC 59.124 41.667 0.00 0.00 0.00 3.06
3934 4142 4.273480 CCCGAGTTCATTGTATTGATCACC 59.727 45.833 0.00 0.00 0.00 4.02
3935 4143 5.118990 CCGAGTTCATTGTATTGATCACCT 58.881 41.667 0.00 0.00 0.00 4.00
3936 4144 5.235186 CCGAGTTCATTGTATTGATCACCTC 59.765 44.000 0.00 0.00 0.00 3.85
3937 4145 6.045318 CGAGTTCATTGTATTGATCACCTCT 58.955 40.000 0.00 0.00 0.00 3.69
3938 4146 7.203218 CGAGTTCATTGTATTGATCACCTCTA 58.797 38.462 0.00 0.00 0.00 2.43
3939 4147 7.168302 CGAGTTCATTGTATTGATCACCTCTAC 59.832 40.741 0.00 0.00 0.00 2.59
3940 4148 7.851228 AGTTCATTGTATTGATCACCTCTACA 58.149 34.615 0.00 0.00 0.00 2.74
3941 4149 7.766278 AGTTCATTGTATTGATCACCTCTACAC 59.234 37.037 0.00 0.00 0.00 2.90
3942 4150 7.181569 TCATTGTATTGATCACCTCTACACA 57.818 36.000 0.00 0.00 0.00 3.72
3943 4151 7.619965 TCATTGTATTGATCACCTCTACACAA 58.380 34.615 0.00 0.00 0.00 3.33
3944 4152 8.267183 TCATTGTATTGATCACCTCTACACAAT 58.733 33.333 0.00 0.00 33.32 2.71
3945 4153 8.554528 CATTGTATTGATCACCTCTACACAATC 58.445 37.037 0.00 0.00 32.03 2.67
3946 4154 6.582636 TGTATTGATCACCTCTACACAATCC 58.417 40.000 0.00 0.00 31.85 3.01
3947 4155 3.801114 TGATCACCTCTACACAATCCG 57.199 47.619 0.00 0.00 0.00 4.18
3948 4156 2.159099 TGATCACCTCTACACAATCCGC 60.159 50.000 0.00 0.00 0.00 5.54
3949 4157 0.535335 TCACCTCTACACAATCCGCC 59.465 55.000 0.00 0.00 0.00 6.13
3950 4158 0.537188 CACCTCTACACAATCCGCCT 59.463 55.000 0.00 0.00 0.00 5.52
3951 4159 0.824759 ACCTCTACACAATCCGCCTC 59.175 55.000 0.00 0.00 0.00 4.70
3952 4160 0.105039 CCTCTACACAATCCGCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
3953 4161 0.824109 CTCTACACAATCCGCCTCCA 59.176 55.000 0.00 0.00 0.00 3.86
3954 4162 0.535335 TCTACACAATCCGCCTCCAC 59.465 55.000 0.00 0.00 0.00 4.02
3955 4163 0.462047 CTACACAATCCGCCTCCACC 60.462 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 209 9.798885 GTATCATGTTTAAGCGTATGAAAGATC 57.201 33.333 0.00 0.00 33.71 2.75
182 210 9.325198 TGTATCATGTTTAAGCGTATGAAAGAT 57.675 29.630 0.00 0.00 33.71 2.40
183 211 8.710835 TGTATCATGTTTAAGCGTATGAAAGA 57.289 30.769 0.00 0.00 33.71 2.52
184 212 9.935682 ATTGTATCATGTTTAAGCGTATGAAAG 57.064 29.630 0.00 0.00 33.71 2.62
186 214 9.103861 TGATTGTATCATGTTTAAGCGTATGAA 57.896 29.630 0.00 0.00 33.71 2.57
187 215 8.655651 TGATTGTATCATGTTTAAGCGTATGA 57.344 30.769 0.00 0.00 33.59 2.15
206 234 3.149196 AGCAGGTCACGAAAATGATTGT 58.851 40.909 0.00 0.00 0.00 2.71
211 239 2.972625 TCCTAGCAGGTCACGAAAATG 58.027 47.619 0.00 0.00 36.53 2.32
285 320 5.659440 TGAAAGAACAAGGCAGAAAACTT 57.341 34.783 0.00 0.00 0.00 2.66
287 322 7.168135 CACTAATGAAAGAACAAGGCAGAAAAC 59.832 37.037 0.00 0.00 0.00 2.43
317 352 4.830600 TGCATGACCATATAGGAGTACGAA 59.169 41.667 0.00 0.00 41.22 3.85
318 353 4.403734 TGCATGACCATATAGGAGTACGA 58.596 43.478 0.00 0.00 41.22 3.43
319 354 4.783764 TGCATGACCATATAGGAGTACG 57.216 45.455 0.00 0.00 41.22 3.67
320 355 7.545965 GTGTTATGCATGACCATATAGGAGTAC 59.454 40.741 18.01 2.44 41.22 2.73
347 391 5.677567 CATAACTAACGGAAATGGGTAGGT 58.322 41.667 0.00 0.00 0.00 3.08
348 392 4.514066 GCATAACTAACGGAAATGGGTAGG 59.486 45.833 0.00 0.00 0.00 3.18
349 393 4.514066 GGCATAACTAACGGAAATGGGTAG 59.486 45.833 0.00 0.00 0.00 3.18
350 394 4.453751 GGCATAACTAACGGAAATGGGTA 58.546 43.478 0.00 0.00 0.00 3.69
656 711 4.023107 GTCCTTAAAGAAAACAGCTGGACC 60.023 45.833 19.93 4.12 36.42 4.46
657 712 4.578928 TGTCCTTAAAGAAAACAGCTGGAC 59.421 41.667 19.93 11.30 41.06 4.02
679 737 1.202687 TGTGCTCCAGTTCCTGTCTTG 60.203 52.381 0.00 0.00 0.00 3.02
974 1078 3.633986 CACTCAAGCAACTCTCCCTTTTT 59.366 43.478 0.00 0.00 0.00 1.94
979 1083 0.957888 GCCACTCAAGCAACTCTCCC 60.958 60.000 0.00 0.00 0.00 4.30
980 1084 0.957888 GGCCACTCAAGCAACTCTCC 60.958 60.000 0.00 0.00 0.00 3.71
981 1085 0.250467 TGGCCACTCAAGCAACTCTC 60.250 55.000 0.00 0.00 0.00 3.20
986 1090 1.179152 CATCATGGCCACTCAAGCAA 58.821 50.000 8.16 0.00 0.00 3.91
997 1101 2.196776 CCCACCTCCCATCATGGC 59.803 66.667 0.00 0.00 35.79 4.40
1020 1124 2.265904 CGCCATGCCCTGATCCATG 61.266 63.158 3.44 3.44 38.78 3.66
1347 1451 3.793144 GACTGCCGCGGCTTCAAG 61.793 66.667 45.79 36.41 42.51 3.02
2214 2333 0.526954 CTTTCATGGGCGCTTGCATC 60.527 55.000 7.64 0.00 41.71 3.91
2340 2459 1.515736 GTACCCGTAGTCGCTGTGC 60.516 63.158 0.00 0.00 35.54 4.57
2384 2503 1.672356 CAGGTGTACTGGTGGCTGC 60.672 63.158 0.00 0.00 43.70 5.25
2478 2597 0.960861 GGTTCTGCTGGTTGTAGGCC 60.961 60.000 0.00 0.00 0.00 5.19
2654 2773 2.279120 CCTCGTCCATCTGCGCTC 60.279 66.667 9.73 0.00 0.00 5.03
2656 2775 3.665675 AACCCTCGTCCATCTGCGC 62.666 63.158 0.00 0.00 0.00 6.09
2657 2776 1.079127 AAACCCTCGTCCATCTGCG 60.079 57.895 0.00 0.00 0.00 5.18
2658 2777 0.250513 AGAAACCCTCGTCCATCTGC 59.749 55.000 0.00 0.00 0.00 4.26
2659 2778 2.744202 CAAAGAAACCCTCGTCCATCTG 59.256 50.000 0.00 0.00 0.00 2.90
2660 2779 2.290323 CCAAAGAAACCCTCGTCCATCT 60.290 50.000 0.00 0.00 0.00 2.90
2661 2780 2.084546 CCAAAGAAACCCTCGTCCATC 58.915 52.381 0.00 0.00 0.00 3.51
2749 2874 3.670377 TGCTTGCTGCTGCTGCTG 61.670 61.111 27.67 21.23 43.37 4.41
2750 2875 3.671411 GTGCTTGCTGCTGCTGCT 61.671 61.111 27.67 0.00 43.37 4.24
2841 2987 2.412605 GATGCTGCCCATCTGGTTC 58.587 57.895 0.00 0.00 45.58 3.62
2971 3120 8.188799 GGTTTTAAAAGCTTATGATGACCCTAC 58.811 37.037 20.18 0.00 33.81 3.18
3240 3401 9.645059 TCAAGAAATACACAAACAATTTGACAA 57.355 25.926 8.24 0.00 43.26 3.18
3251 3412 6.488683 AGGAACGGAATCAAGAAATACACAAA 59.511 34.615 0.00 0.00 0.00 2.83
3326 3487 5.713025 ACAATTGAAAATCATCACCGGAAG 58.287 37.500 13.59 0.00 0.00 3.46
3327 3488 5.720371 ACAATTGAAAATCATCACCGGAA 57.280 34.783 13.59 0.00 0.00 4.30
3328 3489 5.720371 AACAATTGAAAATCATCACCGGA 57.280 34.783 13.59 0.00 0.00 5.14
3329 3490 6.783892 AAAACAATTGAAAATCATCACCGG 57.216 33.333 13.59 0.00 0.00 5.28
3379 3582 7.775053 AGCTGTCTATTTTACCAAAATTCCA 57.225 32.000 2.49 0.00 41.16 3.53
3408 3614 1.679139 TCCACAAGCCTGACAAACAG 58.321 50.000 0.00 0.00 45.36 3.16
3415 3621 2.224257 GGCAAAATTTCCACAAGCCTGA 60.224 45.455 0.00 0.00 37.67 3.86
3422 3628 5.792741 CCTAATTCAGGCAAAATTTCCACA 58.207 37.500 0.00 0.00 37.70 4.17
3462 3669 3.670625 TCTTGGTTGGTCCGTTTCTATG 58.329 45.455 0.00 0.00 39.52 2.23
3485 3692 4.499188 CCGAAAGTTCAGGGGAAGAAAAAC 60.499 45.833 0.00 0.00 32.62 2.43
3517 3725 2.098117 GCAGCTCAGCGGTATGAATTTT 59.902 45.455 0.00 0.00 0.00 1.82
3526 3734 0.536006 AAAAGAAGCAGCTCAGCGGT 60.536 50.000 0.00 0.00 40.15 5.68
3528 3736 3.058639 ACTTAAAAAGAAGCAGCTCAGCG 60.059 43.478 0.00 0.00 40.15 5.18
3530 3738 4.212214 ACGACTTAAAAAGAAGCAGCTCAG 59.788 41.667 0.00 0.00 0.00 3.35
3535 3743 5.234329 TCTCACACGACTTAAAAAGAAGCAG 59.766 40.000 0.00 0.00 0.00 4.24
3548 3756 3.936453 GTCACTAGATCTCTCACACGACT 59.064 47.826 0.00 0.00 0.00 4.18
3551 3759 4.955925 AAGTCACTAGATCTCTCACACG 57.044 45.455 0.00 0.00 0.00 4.49
3667 3875 9.369672 TCTAATAAAGAGGCCCAAGTTTAAAAA 57.630 29.630 0.00 0.00 0.00 1.94
3668 3876 8.943594 TCTAATAAAGAGGCCCAAGTTTAAAA 57.056 30.769 0.00 0.00 0.00 1.52
3669 3877 9.185680 GATCTAATAAAGAGGCCCAAGTTTAAA 57.814 33.333 0.00 0.00 37.74 1.52
3670 3878 8.333235 TGATCTAATAAAGAGGCCCAAGTTTAA 58.667 33.333 0.00 0.00 37.74 1.52
3671 3879 7.867921 TGATCTAATAAAGAGGCCCAAGTTTA 58.132 34.615 0.00 0.00 37.74 2.01
3672 3880 6.731467 TGATCTAATAAAGAGGCCCAAGTTT 58.269 36.000 0.00 0.00 37.74 2.66
3673 3881 6.327386 TGATCTAATAAAGAGGCCCAAGTT 57.673 37.500 0.00 0.00 37.74 2.66
3674 3882 5.975988 TGATCTAATAAAGAGGCCCAAGT 57.024 39.130 0.00 0.00 37.74 3.16
3675 3883 6.603201 TGTTTGATCTAATAAAGAGGCCCAAG 59.397 38.462 0.00 0.00 37.74 3.61
3676 3884 6.489603 TGTTTGATCTAATAAAGAGGCCCAA 58.510 36.000 0.00 0.00 37.74 4.12
3677 3885 6.073447 TGTTTGATCTAATAAAGAGGCCCA 57.927 37.500 0.00 0.00 37.74 5.36
3678 3886 6.183360 GGTTGTTTGATCTAATAAAGAGGCCC 60.183 42.308 0.00 0.00 37.74 5.80
3679 3887 6.458342 CGGTTGTTTGATCTAATAAAGAGGCC 60.458 42.308 0.00 0.00 37.74 5.19
3680 3888 6.093633 ACGGTTGTTTGATCTAATAAAGAGGC 59.906 38.462 1.03 0.00 37.74 4.70
3681 3889 7.611213 ACGGTTGTTTGATCTAATAAAGAGG 57.389 36.000 1.03 0.00 37.74 3.69
3682 3890 9.968743 GTAACGGTTGTTTGATCTAATAAAGAG 57.031 33.333 3.07 0.02 39.54 2.85
3683 3891 9.491675 TGTAACGGTTGTTTGATCTAATAAAGA 57.508 29.630 3.07 0.00 39.54 2.52
3686 3894 9.438228 TGATGTAACGGTTGTTTGATCTAATAA 57.562 29.630 3.07 0.00 39.54 1.40
3687 3895 9.607988 ATGATGTAACGGTTGTTTGATCTAATA 57.392 29.630 3.07 0.00 39.54 0.98
3688 3896 7.915293 TGATGTAACGGTTGTTTGATCTAAT 57.085 32.000 3.07 0.00 39.54 1.73
3689 3897 7.065324 GGATGATGTAACGGTTGTTTGATCTAA 59.935 37.037 3.07 0.00 39.54 2.10
3690 3898 6.537301 GGATGATGTAACGGTTGTTTGATCTA 59.463 38.462 3.07 0.00 39.54 1.98
3691 3899 5.354234 GGATGATGTAACGGTTGTTTGATCT 59.646 40.000 3.07 0.00 39.54 2.75
3692 3900 5.123186 TGGATGATGTAACGGTTGTTTGATC 59.877 40.000 3.07 0.35 39.54 2.92
3693 3901 5.007034 TGGATGATGTAACGGTTGTTTGAT 58.993 37.500 3.07 0.00 39.54 2.57
3694 3902 4.214545 GTGGATGATGTAACGGTTGTTTGA 59.785 41.667 3.07 0.00 39.54 2.69
3695 3903 4.472286 GTGGATGATGTAACGGTTGTTTG 58.528 43.478 3.07 0.00 39.54 2.93
3696 3904 3.504520 GGTGGATGATGTAACGGTTGTTT 59.495 43.478 3.07 0.00 39.54 2.83
3697 3905 3.078837 GGTGGATGATGTAACGGTTGTT 58.921 45.455 3.07 0.00 42.19 2.83
3698 3906 2.039216 TGGTGGATGATGTAACGGTTGT 59.961 45.455 3.07 0.00 0.00 3.32
3699 3907 2.677836 CTGGTGGATGATGTAACGGTTG 59.322 50.000 3.07 0.00 0.00 3.77
3700 3908 2.939640 GCTGGTGGATGATGTAACGGTT 60.940 50.000 0.00 0.00 0.00 4.44
3701 3909 1.406887 GCTGGTGGATGATGTAACGGT 60.407 52.381 0.00 0.00 0.00 4.83
3702 3910 1.299541 GCTGGTGGATGATGTAACGG 58.700 55.000 0.00 0.00 0.00 4.44
3703 3911 1.299541 GGCTGGTGGATGATGTAACG 58.700 55.000 0.00 0.00 0.00 3.18
3704 3912 2.418368 TGGCTGGTGGATGATGTAAC 57.582 50.000 0.00 0.00 0.00 2.50
3705 3913 2.779430 AGATGGCTGGTGGATGATGTAA 59.221 45.455 0.00 0.00 0.00 2.41
3706 3914 2.369860 GAGATGGCTGGTGGATGATGTA 59.630 50.000 0.00 0.00 0.00 2.29
3707 3915 1.142465 GAGATGGCTGGTGGATGATGT 59.858 52.381 0.00 0.00 0.00 3.06
3708 3916 1.142262 TGAGATGGCTGGTGGATGATG 59.858 52.381 0.00 0.00 0.00 3.07
3709 3917 1.142465 GTGAGATGGCTGGTGGATGAT 59.858 52.381 0.00 0.00 0.00 2.45
3710 3918 0.543277 GTGAGATGGCTGGTGGATGA 59.457 55.000 0.00 0.00 0.00 2.92
3711 3919 0.253894 TGTGAGATGGCTGGTGGATG 59.746 55.000 0.00 0.00 0.00 3.51
3712 3920 0.994247 TTGTGAGATGGCTGGTGGAT 59.006 50.000 0.00 0.00 0.00 3.41
3713 3921 0.994247 ATTGTGAGATGGCTGGTGGA 59.006 50.000 0.00 0.00 0.00 4.02
3714 3922 2.171237 TCTATTGTGAGATGGCTGGTGG 59.829 50.000 0.00 0.00 0.00 4.61
3715 3923 3.548745 TCTATTGTGAGATGGCTGGTG 57.451 47.619 0.00 0.00 0.00 4.17
3716 3924 4.082665 CATCTATTGTGAGATGGCTGGT 57.917 45.455 5.65 0.00 46.16 4.00
3723 3931 2.224378 CCACCGGCATCTATTGTGAGAT 60.224 50.000 0.00 0.00 36.58 2.75
3724 3932 1.138859 CCACCGGCATCTATTGTGAGA 59.861 52.381 0.00 0.00 0.00 3.27
3725 3933 1.134401 ACCACCGGCATCTATTGTGAG 60.134 52.381 0.00 0.00 0.00 3.51
3726 3934 0.908910 ACCACCGGCATCTATTGTGA 59.091 50.000 0.00 0.00 0.00 3.58
3727 3935 1.670811 GAACCACCGGCATCTATTGTG 59.329 52.381 0.00 0.00 0.00 3.33
3728 3936 1.408266 GGAACCACCGGCATCTATTGT 60.408 52.381 0.00 0.00 0.00 2.71
3729 3937 1.134098 AGGAACCACCGGCATCTATTG 60.134 52.381 0.00 0.00 44.74 1.90
3730 3938 1.141053 GAGGAACCACCGGCATCTATT 59.859 52.381 0.00 0.00 44.74 1.73
3731 3939 0.759346 GAGGAACCACCGGCATCTAT 59.241 55.000 0.00 0.00 44.74 1.98
3732 3940 1.672854 CGAGGAACCACCGGCATCTA 61.673 60.000 0.00 0.00 44.74 1.98
3733 3941 2.990479 GAGGAACCACCGGCATCT 59.010 61.111 0.00 0.00 44.74 2.90
3734 3942 2.511600 CGAGGAACCACCGGCATC 60.512 66.667 0.00 0.00 44.74 3.91
3735 3943 3.000819 TCGAGGAACCACCGGCAT 61.001 61.111 0.00 0.00 44.74 4.40
3736 3944 3.998672 GTCGAGGAACCACCGGCA 61.999 66.667 0.00 0.00 44.74 5.69
3737 3945 4.754667 GGTCGAGGAACCACCGGC 62.755 72.222 0.00 0.00 44.74 6.13
3738 3946 4.078516 GGGTCGAGGAACCACCGG 62.079 72.222 0.00 0.00 39.63 5.28
3739 3947 3.307906 TGGGTCGAGGAACCACCG 61.308 66.667 0.00 0.00 42.31 4.94
3743 3951 0.392595 GGATTGTGGGTCGAGGAACC 60.393 60.000 0.00 0.00 40.41 3.62
3744 3952 0.739813 CGGATTGTGGGTCGAGGAAC 60.740 60.000 0.00 0.00 0.00 3.62
3745 3953 1.594833 CGGATTGTGGGTCGAGGAA 59.405 57.895 0.00 0.00 0.00 3.36
3746 3954 2.355986 CCGGATTGTGGGTCGAGGA 61.356 63.158 0.00 0.00 0.00 3.71
3747 3955 2.186903 CCGGATTGTGGGTCGAGG 59.813 66.667 0.00 0.00 0.00 4.63
3748 3956 2.186903 CCCGGATTGTGGGTCGAG 59.813 66.667 0.73 0.00 42.07 4.04
3761 3969 0.171679 GCGGTTTTTAATCCACCCGG 59.828 55.000 0.00 0.00 36.05 5.73
3762 3970 0.171679 GGCGGTTTTTAATCCACCCG 59.828 55.000 0.00 0.00 38.45 5.28
3763 3971 1.203758 CTGGCGGTTTTTAATCCACCC 59.796 52.381 0.00 0.00 0.00 4.61
3764 3972 1.403647 GCTGGCGGTTTTTAATCCACC 60.404 52.381 0.00 0.00 0.00 4.61
3765 3973 1.403647 GGCTGGCGGTTTTTAATCCAC 60.404 52.381 0.00 0.00 0.00 4.02
3766 3974 0.892063 GGCTGGCGGTTTTTAATCCA 59.108 50.000 0.00 0.00 0.00 3.41
3767 3975 1.182667 AGGCTGGCGGTTTTTAATCC 58.817 50.000 0.00 0.00 0.00 3.01
3768 3976 2.223502 GCTAGGCTGGCGGTTTTTAATC 60.224 50.000 7.22 0.00 0.00 1.75
3769 3977 1.749063 GCTAGGCTGGCGGTTTTTAAT 59.251 47.619 7.22 0.00 0.00 1.40
3770 3978 1.170442 GCTAGGCTGGCGGTTTTTAA 58.830 50.000 7.22 0.00 0.00 1.52
3771 3979 0.326927 AGCTAGGCTGGCGGTTTTTA 59.673 50.000 17.53 0.00 37.57 1.52
3772 3980 0.326927 TAGCTAGGCTGGCGGTTTTT 59.673 50.000 17.53 1.02 40.10 1.94
3773 3981 0.107654 CTAGCTAGGCTGGCGGTTTT 60.108 55.000 17.53 1.79 40.10 2.43
3774 3982 1.522569 CTAGCTAGGCTGGCGGTTT 59.477 57.895 17.53 2.20 40.10 3.27
3775 3983 3.221222 CTAGCTAGGCTGGCGGTT 58.779 61.111 17.53 2.59 40.10 4.44
3780 3988 1.273048 CTCATGAGCTAGCTAGGCTGG 59.727 57.143 19.38 4.65 40.10 4.85
3781 3989 2.229543 CTCTCATGAGCTAGCTAGGCTG 59.770 54.545 19.38 12.49 40.40 4.85
3782 3990 2.108075 TCTCTCATGAGCTAGCTAGGCT 59.892 50.000 19.38 18.14 43.26 4.58
3783 3991 2.228822 GTCTCTCATGAGCTAGCTAGGC 59.771 54.545 19.38 8.10 40.03 3.93
3784 3992 3.253188 GTGTCTCTCATGAGCTAGCTAGG 59.747 52.174 19.38 10.29 40.03 3.02
3785 3993 3.882288 TGTGTCTCTCATGAGCTAGCTAG 59.118 47.826 19.38 16.84 40.03 3.42
3786 3994 3.891049 TGTGTCTCTCATGAGCTAGCTA 58.109 45.455 19.38 6.79 40.03 3.32
3787 3995 2.732763 TGTGTCTCTCATGAGCTAGCT 58.267 47.619 19.45 19.45 40.03 3.32
3788 3996 3.516981 TTGTGTCTCTCATGAGCTAGC 57.483 47.619 18.36 6.62 40.03 3.42
3789 3997 5.220624 GCAAATTGTGTCTCTCATGAGCTAG 60.221 44.000 18.36 11.24 40.03 3.42
3790 3998 4.633126 GCAAATTGTGTCTCTCATGAGCTA 59.367 41.667 18.36 5.30 40.03 3.32
3791 3999 3.439476 GCAAATTGTGTCTCTCATGAGCT 59.561 43.478 18.36 0.00 40.03 4.09
3792 4000 3.427233 GGCAAATTGTGTCTCTCATGAGC 60.427 47.826 18.36 4.87 40.03 4.26
3793 4001 4.008330 AGGCAAATTGTGTCTCTCATGAG 58.992 43.478 17.07 17.07 37.84 2.90
3794 4002 4.025040 AGGCAAATTGTGTCTCTCATGA 57.975 40.909 0.00 0.00 37.84 3.07
3802 4010 1.734465 CCTCGAGAGGCAAATTGTGTC 59.266 52.381 15.71 0.00 42.44 3.67
3803 4011 1.813513 CCTCGAGAGGCAAATTGTGT 58.186 50.000 15.71 0.00 42.44 3.72
3814 4022 0.891373 TCTTTCACTGCCCTCGAGAG 59.109 55.000 15.71 0.16 0.00 3.20
3815 4023 1.338107 TTCTTTCACTGCCCTCGAGA 58.662 50.000 15.71 0.00 0.00 4.04
3816 4024 2.072298 CTTTCTTTCACTGCCCTCGAG 58.928 52.381 5.13 5.13 0.00 4.04
3817 4025 1.691976 TCTTTCTTTCACTGCCCTCGA 59.308 47.619 0.00 0.00 0.00 4.04
3818 4026 1.801178 GTCTTTCTTTCACTGCCCTCG 59.199 52.381 0.00 0.00 0.00 4.63
3819 4027 2.851195 TGTCTTTCTTTCACTGCCCTC 58.149 47.619 0.00 0.00 0.00 4.30
3820 4028 3.416156 GATGTCTTTCTTTCACTGCCCT 58.584 45.455 0.00 0.00 0.00 5.19
3821 4029 2.160417 CGATGTCTTTCTTTCACTGCCC 59.840 50.000 0.00 0.00 0.00 5.36
3822 4030 3.067106 TCGATGTCTTTCTTTCACTGCC 58.933 45.455 0.00 0.00 0.00 4.85
3823 4031 4.212214 ACTTCGATGTCTTTCTTTCACTGC 59.788 41.667 0.00 0.00 0.00 4.40
3824 4032 5.914085 ACTTCGATGTCTTTCTTTCACTG 57.086 39.130 0.00 0.00 0.00 3.66
3825 4033 8.524487 ACTATACTTCGATGTCTTTCTTTCACT 58.476 33.333 7.29 0.00 0.00 3.41
3826 4034 8.690680 ACTATACTTCGATGTCTTTCTTTCAC 57.309 34.615 7.29 0.00 0.00 3.18
3827 4035 8.740906 AGACTATACTTCGATGTCTTTCTTTCA 58.259 33.333 7.29 0.00 34.78 2.69
3830 4038 9.398538 AGTAGACTATACTTCGATGTCTTTCTT 57.601 33.333 7.29 0.00 38.67 2.52
3831 4039 8.832521 CAGTAGACTATACTTCGATGTCTTTCT 58.167 37.037 7.29 8.21 38.67 2.52
3832 4040 8.828644 TCAGTAGACTATACTTCGATGTCTTTC 58.171 37.037 7.29 1.47 38.67 2.62
3833 4041 8.734218 TCAGTAGACTATACTTCGATGTCTTT 57.266 34.615 7.29 0.00 38.67 2.52
3834 4042 8.911918 ATCAGTAGACTATACTTCGATGTCTT 57.088 34.615 7.29 0.08 38.67 3.01
3835 4043 9.999660 TTATCAGTAGACTATACTTCGATGTCT 57.000 33.333 7.29 7.00 40.52 3.41
3848 4056 9.890629 AGATTGCAATGTTTTATCAGTAGACTA 57.109 29.630 18.59 0.00 0.00 2.59
3849 4057 8.671921 CAGATTGCAATGTTTTATCAGTAGACT 58.328 33.333 18.59 0.00 0.00 3.24
3850 4058 7.430502 GCAGATTGCAATGTTTTATCAGTAGAC 59.569 37.037 18.59 0.00 44.26 2.59
3851 4059 7.475015 GCAGATTGCAATGTTTTATCAGTAGA 58.525 34.615 18.59 0.00 44.26 2.59
3852 4060 7.675270 GCAGATTGCAATGTTTTATCAGTAG 57.325 36.000 18.59 0.00 44.26 2.57
3876 4084 1.008538 GGAGCGGCGGCAATTTATG 60.009 57.895 19.21 0.00 43.41 1.90
3877 4085 1.152963 AGGAGCGGCGGCAATTTAT 60.153 52.632 19.21 0.00 43.41 1.40
3878 4086 2.112198 CAGGAGCGGCGGCAATTTA 61.112 57.895 19.21 0.00 43.41 1.40
3879 4087 3.443045 CAGGAGCGGCGGCAATTT 61.443 61.111 19.21 0.00 43.41 1.82
3880 4088 4.722700 ACAGGAGCGGCGGCAATT 62.723 61.111 19.21 0.00 43.41 2.32
3881 4089 4.722700 AACAGGAGCGGCGGCAAT 62.723 61.111 19.21 0.00 43.41 3.56
3887 4095 3.730761 CACTGCAACAGGAGCGGC 61.731 66.667 0.00 0.00 42.07 6.53
3888 4096 1.572085 CTTCACTGCAACAGGAGCGG 61.572 60.000 0.00 0.00 43.90 5.52
3889 4097 1.864862 CTTCACTGCAACAGGAGCG 59.135 57.895 0.00 0.00 35.51 5.03
3890 4098 1.578423 GCTTCACTGCAACAGGAGC 59.422 57.895 0.00 0.00 35.51 4.70
3891 4099 0.535780 TGGCTTCACTGCAACAGGAG 60.536 55.000 0.00 0.00 35.51 3.69
3892 4100 0.819259 GTGGCTTCACTGCAACAGGA 60.819 55.000 0.00 0.00 36.89 3.86
3893 4101 1.656441 GTGGCTTCACTGCAACAGG 59.344 57.895 0.00 0.00 36.89 4.00
3894 4102 1.656441 GGTGGCTTCACTGCAACAG 59.344 57.895 0.00 0.00 38.57 3.16
3895 4103 1.827789 GGGTGGCTTCACTGCAACA 60.828 57.895 0.00 0.00 38.57 3.33
3896 4104 2.908073 CGGGTGGCTTCACTGCAAC 61.908 63.158 0.00 0.00 41.00 4.17
3897 4105 2.594303 CGGGTGGCTTCACTGCAA 60.594 61.111 0.00 0.00 41.00 4.08
3898 4106 3.535629 CTCGGGTGGCTTCACTGCA 62.536 63.158 0.00 0.00 41.00 4.41
3899 4107 2.743928 CTCGGGTGGCTTCACTGC 60.744 66.667 0.00 0.00 41.00 4.40
3900 4108 0.951040 GAACTCGGGTGGCTTCACTG 60.951 60.000 0.00 0.00 41.00 3.66
3901 4109 1.371558 GAACTCGGGTGGCTTCACT 59.628 57.895 0.00 0.00 41.00 3.41
3902 4110 0.321653 ATGAACTCGGGTGGCTTCAC 60.322 55.000 0.00 0.00 40.52 3.18
3903 4111 0.400213 AATGAACTCGGGTGGCTTCA 59.600 50.000 0.00 0.00 0.00 3.02
3904 4112 0.804989 CAATGAACTCGGGTGGCTTC 59.195 55.000 0.00 0.00 0.00 3.86
3905 4113 0.110486 ACAATGAACTCGGGTGGCTT 59.890 50.000 0.00 0.00 0.00 4.35
3906 4114 0.981183 TACAATGAACTCGGGTGGCT 59.019 50.000 0.00 0.00 0.00 4.75
3907 4115 2.038387 ATACAATGAACTCGGGTGGC 57.962 50.000 0.00 0.00 0.00 5.01
3908 4116 3.605634 TCAATACAATGAACTCGGGTGG 58.394 45.455 0.00 0.00 0.00 4.61
3909 4117 4.875536 TGATCAATACAATGAACTCGGGTG 59.124 41.667 0.00 0.00 32.06 4.61
3910 4118 4.876107 GTGATCAATACAATGAACTCGGGT 59.124 41.667 0.00 0.00 32.06 5.28
3911 4119 4.273480 GGTGATCAATACAATGAACTCGGG 59.727 45.833 0.00 0.00 32.06 5.14
3912 4120 5.118990 AGGTGATCAATACAATGAACTCGG 58.881 41.667 0.00 0.00 32.06 4.63
3913 4121 6.045318 AGAGGTGATCAATACAATGAACTCG 58.955 40.000 0.00 0.00 32.06 4.18
3914 4122 7.981789 TGTAGAGGTGATCAATACAATGAACTC 59.018 37.037 0.00 0.00 32.06 3.01
3915 4123 7.766278 GTGTAGAGGTGATCAATACAATGAACT 59.234 37.037 0.00 0.00 32.06 3.01
3916 4124 7.549134 TGTGTAGAGGTGATCAATACAATGAAC 59.451 37.037 0.00 0.00 32.06 3.18
3917 4125 7.619965 TGTGTAGAGGTGATCAATACAATGAA 58.380 34.615 0.00 0.00 32.06 2.57
3918 4126 7.181569 TGTGTAGAGGTGATCAATACAATGA 57.818 36.000 0.00 0.00 0.00 2.57
3919 4127 7.848223 TTGTGTAGAGGTGATCAATACAATG 57.152 36.000 0.00 0.00 0.00 2.82
3920 4128 7.716998 GGATTGTGTAGAGGTGATCAATACAAT 59.283 37.037 15.27 15.27 38.40 2.71
3921 4129 7.047891 GGATTGTGTAGAGGTGATCAATACAA 58.952 38.462 8.51 8.51 33.52 2.41
3922 4130 6.582636 GGATTGTGTAGAGGTGATCAATACA 58.417 40.000 0.00 2.20 0.00 2.29
3923 4131 5.692204 CGGATTGTGTAGAGGTGATCAATAC 59.308 44.000 0.00 0.00 0.00 1.89
3924 4132 5.739070 GCGGATTGTGTAGAGGTGATCAATA 60.739 44.000 0.00 0.00 0.00 1.90
3925 4133 4.697514 CGGATTGTGTAGAGGTGATCAAT 58.302 43.478 0.00 0.00 0.00 2.57
3926 4134 3.678806 GCGGATTGTGTAGAGGTGATCAA 60.679 47.826 0.00 0.00 0.00 2.57
3927 4135 2.159099 GCGGATTGTGTAGAGGTGATCA 60.159 50.000 0.00 0.00 0.00 2.92
3928 4136 2.474816 GCGGATTGTGTAGAGGTGATC 58.525 52.381 0.00 0.00 0.00 2.92
3929 4137 1.139058 GGCGGATTGTGTAGAGGTGAT 59.861 52.381 0.00 0.00 0.00 3.06
3930 4138 0.535335 GGCGGATTGTGTAGAGGTGA 59.465 55.000 0.00 0.00 0.00 4.02
3931 4139 0.537188 AGGCGGATTGTGTAGAGGTG 59.463 55.000 0.00 0.00 0.00 4.00
3932 4140 0.824759 GAGGCGGATTGTGTAGAGGT 59.175 55.000 0.00 0.00 0.00 3.85
3933 4141 0.105039 GGAGGCGGATTGTGTAGAGG 59.895 60.000 0.00 0.00 0.00 3.69
3934 4142 0.824109 TGGAGGCGGATTGTGTAGAG 59.176 55.000 0.00 0.00 0.00 2.43
3935 4143 0.535335 GTGGAGGCGGATTGTGTAGA 59.465 55.000 0.00 0.00 0.00 2.59
3936 4144 0.462047 GGTGGAGGCGGATTGTGTAG 60.462 60.000 0.00 0.00 0.00 2.74
3937 4145 1.600107 GGTGGAGGCGGATTGTGTA 59.400 57.895 0.00 0.00 0.00 2.90
3938 4146 2.351276 GGTGGAGGCGGATTGTGT 59.649 61.111 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.