Multiple sequence alignment - TraesCS5D01G141800

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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 TraesCS5D01G141800 chr5D 100.000 4131 0 0 1 4131 227702183 227706313 0.000000e+00 7629.0
1 TraesCS5D01G141800 chr5D 87.387 222 15 3 2499 2720 227704466 227704674 4.130000e-60 243.0
2 TraesCS5D01G141800 chr5D 87.387 222 15 3 2284 2492 227704681 227704902 4.130000e-60 243.0
3 TraesCS5D01G141800 chr5B 94.018 3778 149 29 1 3754 251248804 251252528 0.000000e+00 5653.0
4 TraesCS5D01G141800 chr5B 90.909 231 16 2 2490 2720 251251069 251251294 5.190000e-79 305.0
5 TraesCS5D01G141800 chr5A 96.123 3069 96 9 1 3050 305553961 305557025 0.000000e+00 4987.0
6 TraesCS5D01G141800 chr5A 95.928 221 7 2 3241 3460 305557023 305557242 1.410000e-94 357.0
7 TraesCS5D01G141800 chr5A 93.778 225 14 0 2499 2723 305556246 305556470 5.120000e-89 339.0
8 TraesCS5D01G141800 chr5A 88.929 280 18 3 3487 3758 305557239 305557513 2.380000e-87 333.0
9 TraesCS5D01G141800 chr5A 86.937 222 16 3 2284 2492 305556474 305556695 1.920000e-58 237.0
10 TraesCS5D01G141800 chr5A 93.878 49 1 1 301 347 101414430 101414478 5.730000e-09 73.1
11 TraesCS5D01G141800 chr2D 96.094 384 15 0 3748 4131 52635092 52635475 9.750000e-176 627.0
12 TraesCS5D01G141800 chr7D 96.306 379 12 1 3753 4131 503847660 503848036 4.540000e-174 621.0
13 TraesCS5D01G141800 chr7D 95.812 382 13 2 3747 4128 449553879 449553501 7.590000e-172 614.0
14 TraesCS5D01G141800 chr7D 95.288 382 17 1 3747 4128 449676798 449677178 4.570000e-169 604.0
15 TraesCS5D01G141800 chr7D 94.565 92 5 0 4029 4120 503847970 503848061 4.300000e-30 143.0
16 TraesCS5D01G141800 chr7D 90.291 103 7 3 3087 3189 574068353 574068254 9.320000e-27 132.0
17 TraesCS5D01G141800 chr7D 89.691 97 7 2 3087 3181 573968696 573968601 2.020000e-23 121.0
18 TraesCS5D01G141800 chr7D 89.831 59 6 0 3752 3810 578518492 578518434 4.430000e-10 76.8
19 TraesCS5D01G141800 chr1D 95.756 377 16 0 3755 4131 195189887 195189511 3.530000e-170 608.0
20 TraesCS5D01G141800 chr3D 94.879 371 17 2 3744 4112 474540418 474540788 2.770000e-161 579.0
21 TraesCS5D01G141800 chr6B 93.264 386 16 3 3751 4127 644447610 644447994 1.000000e-155 560.0
22 TraesCS5D01G141800 chr4A 91.099 382 14 7 3751 4131 27183566 27183204 2.220000e-137 499.0
23 TraesCS5D01G141800 chr7B 79.710 414 49 21 2547 2934 633000245 632999841 2.450000e-67 267.0
24 TraesCS5D01G141800 chr7B 87.879 132 15 1 3087 3218 632999755 632999625 1.990000e-33 154.0
25 TraesCS5D01G141800 chr7B 80.288 208 17 11 2066 2272 632800686 632800870 7.200000e-28 135.0
26 TraesCS5D01G141800 chr7B 87.500 88 10 1 2185 2272 633000965 633000879 2.630000e-17 100.0
27 TraesCS5D01G141800 chr7A 90.517 116 11 0 2157 2272 663574552 663574437 1.990000e-33 154.0


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 TraesCS5D01G141800 chr5D 227702183 227706313 4130 False 2705.0 7629 91.591333 1 4131 3 chr5D.!!$F1 4130
1 TraesCS5D01G141800 chr5B 251248804 251252528 3724 False 2979.0 5653 92.463500 1 3754 2 chr5B.!!$F1 3753
2 TraesCS5D01G141800 chr5A 305553961 305557513 3552 False 1250.6 4987 92.339000 1 3758 5 chr5A.!!$F2 3757

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
520 522 1.216977 CTCCGGCGACCACAATGTA 59.783 57.895 9.30 0.00 0.00 2.29 F
1045 1051 1.004745 GAGGAGAATCAAAGCCACCCA 59.995 52.381 0.00 0.00 36.25 4.51 F
1064 1070 1.305633 CCTGCACCCCTCTCTGAGA 60.306 63.158 7.24 7.24 0.00 3.27 F
2944 2976 0.741221 GACTGCGCCCTCTTCGAAAT 60.741 55.000 4.18 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2527 0.811281 GCCACAGGCCACAGTAAATC 59.189 55.000 5.01 0.0 44.06 2.17 R
2944 2976 2.542020 TCTGGAACAAGTTGCGATGA 57.458 45.000 1.81 0.0 38.70 2.92 R
3038 3070 4.761739 TCAATCCTGGATCAAACACTGAAC 59.238 41.667 10.14 0.0 37.67 3.18 R
3887 3928 0.104120 TGTGTTCAGTGGTCTGGTCG 59.896 55.000 0.00 0.0 41.59 4.79 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
84 85 6.011122 ACTGGATCAAGGCTTTTAGATGAT 57.989 37.500 1.23 0.00 33.64 2.45
272 274 6.838612 AGTTGAAATTAATGGGCTAGCCATTA 59.161 34.615 34.09 27.71 38.59 1.90
299 301 4.081365 TCAACGGGTATGCACTAAGAATGA 60.081 41.667 0.00 0.00 0.00 2.57
362 364 2.453080 TGCTAGTTATTACCGTTCGCG 58.547 47.619 0.00 0.00 40.93 5.87
403 405 2.610374 GCACAAACCAAGAACGACACTA 59.390 45.455 0.00 0.00 0.00 2.74
520 522 1.216977 CTCCGGCGACCACAATGTA 59.783 57.895 9.30 0.00 0.00 2.29
902 908 2.338620 CCACCAGTCAGCGAACGA 59.661 61.111 0.00 0.00 0.00 3.85
1037 1043 3.703001 AGAAAGCCGAGGAGAATCAAA 57.297 42.857 0.00 0.00 36.25 2.69
1045 1051 1.004745 GAGGAGAATCAAAGCCACCCA 59.995 52.381 0.00 0.00 36.25 4.51
1064 1070 1.305633 CCTGCACCCCTCTCTGAGA 60.306 63.158 7.24 7.24 0.00 3.27
1074 1080 1.405105 CCTCTCTGAGAGAAGCTTCGG 59.595 57.143 31.14 12.63 45.07 4.30
1108 1114 1.320344 CGATGGAGGTGTTCGAGGGA 61.320 60.000 0.00 0.00 34.92 4.20
1743 1757 2.285488 GCTAGAGTTATTTCTGGCGCAC 59.715 50.000 10.83 0.00 40.97 5.34
1763 1777 3.751175 CACTTCTTTGATTCCCGTGCTTA 59.249 43.478 0.00 0.00 0.00 3.09
1846 1865 4.771114 TCAGTTGGAGTTCTTCTTTCCA 57.229 40.909 0.00 0.00 39.16 3.53
1932 1951 4.763279 TGATTTTGTGATGATGTGCAGTCT 59.237 37.500 0.00 0.00 0.00 3.24
2287 2306 8.923683 GTCAGTGTACTTCTGAATTTACTTACC 58.076 37.037 17.90 4.09 42.42 2.85
2336 2355 3.605486 GCAGTTCTGAATCACGAATTTGC 59.395 43.478 3.84 13.19 0.00 3.68
2418 2437 3.191371 GCTTACCTGAAGAATGTTGTGGG 59.809 47.826 0.00 0.00 37.33 4.61
2578 2610 5.776744 CTTGATTTCTGCTGGCTTAGTTTT 58.223 37.500 0.00 0.00 0.00 2.43
2791 2823 7.011950 GCTTTTTAGTTTTTACCACTTGCCATT 59.988 33.333 0.00 0.00 0.00 3.16
2944 2976 0.741221 GACTGCGCCCTCTTCGAAAT 60.741 55.000 4.18 0.00 0.00 2.17
3038 3070 4.389374 TCTGAACTCCAACTTTTAGCAGG 58.611 43.478 0.00 0.00 0.00 4.85
3073 3105 2.744202 CCAGGATTGAAGTTTCCAGTCG 59.256 50.000 0.00 0.00 34.27 4.18
3129 3161 4.746611 GCAGAAATCAAAGTTTTGTCAGGG 59.253 41.667 4.67 0.00 39.18 4.45
3130 3162 5.682212 GCAGAAATCAAAGTTTTGTCAGGGT 60.682 40.000 4.67 0.00 39.18 4.34
3131 3163 6.340522 CAGAAATCAAAGTTTTGTCAGGGTT 58.659 36.000 4.67 0.00 39.18 4.11
3132 3164 6.256321 CAGAAATCAAAGTTTTGTCAGGGTTG 59.744 38.462 4.67 0.00 39.18 3.77
3133 3165 3.518634 TCAAAGTTTTGTCAGGGTTGC 57.481 42.857 4.67 0.00 39.18 4.17
3134 3166 2.167487 TCAAAGTTTTGTCAGGGTTGCC 59.833 45.455 4.67 0.00 39.18 4.52
3135 3167 2.159179 AAGTTTTGTCAGGGTTGCCT 57.841 45.000 0.00 0.00 0.00 4.75
3136 3168 1.402787 AGTTTTGTCAGGGTTGCCTG 58.597 50.000 0.00 0.00 39.01 4.85
3137 3169 1.111277 GTTTTGTCAGGGTTGCCTGT 58.889 50.000 0.00 0.00 38.77 4.00
3138 3170 1.067060 GTTTTGTCAGGGTTGCCTGTC 59.933 52.381 0.00 0.00 38.77 3.51
3139 3171 0.550914 TTTGTCAGGGTTGCCTGTCT 59.449 50.000 0.00 0.00 38.77 3.41
3140 3172 0.550914 TTGTCAGGGTTGCCTGTCTT 59.449 50.000 0.00 0.00 38.77 3.01
3141 3173 0.179020 TGTCAGGGTTGCCTGTCTTG 60.179 55.000 0.00 0.00 38.77 3.02
3142 3174 1.228245 TCAGGGTTGCCTGTCTTGC 60.228 57.895 0.00 0.00 38.77 4.01
3143 3175 1.529010 CAGGGTTGCCTGTCTTGCA 60.529 57.895 0.00 0.00 36.84 4.08
3144 3176 1.529244 AGGGTTGCCTGTCTTGCAC 60.529 57.895 0.00 0.00 38.72 4.57
3425 3458 1.211703 TGTGCTCTGGGACAAAACTCA 59.788 47.619 0.00 0.00 40.71 3.41
3464 3497 7.722795 TGTACATGTGCAATATATTAAGCGT 57.277 32.000 14.70 0.00 0.00 5.07
3545 3578 6.348540 GGAACAGTCAGGTGTGTATTTCATTC 60.349 42.308 0.00 0.00 0.00 2.67
3633 3666 9.104965 TCATTCTTGTTGGTATAATTTAGTCGG 57.895 33.333 0.00 0.00 0.00 4.79
3680 3721 3.891366 CGAAATCCATAGGGGCATCTTTT 59.109 43.478 0.00 0.00 36.21 2.27
3708 3749 5.528870 AGCATTTTTCCCGTTTTCAGTTAG 58.471 37.500 0.00 0.00 0.00 2.34
3719 3760 5.163693 CCGTTTTCAGTTAGGTTTCAGTGTT 60.164 40.000 0.00 0.00 0.00 3.32
3721 3762 6.617879 GTTTTCAGTTAGGTTTCAGTGTTGT 58.382 36.000 0.00 0.00 0.00 3.32
3724 3765 5.492895 TCAGTTAGGTTTCAGTGTTGTTCA 58.507 37.500 0.00 0.00 0.00 3.18
3725 3766 5.353123 TCAGTTAGGTTTCAGTGTTGTTCAC 59.647 40.000 0.00 0.00 46.46 3.18
3754 3795 5.425630 AGGAACGTGGACCATTAGAATTAC 58.574 41.667 0.00 0.00 0.00 1.89
3758 3799 4.081531 ACGTGGACCATTAGAATTACGGAA 60.082 41.667 0.00 0.00 34.90 4.30
3759 3800 5.054477 CGTGGACCATTAGAATTACGGAAT 58.946 41.667 0.00 0.00 0.00 3.01
3760 3801 5.176958 CGTGGACCATTAGAATTACGGAATC 59.823 44.000 0.00 0.00 0.00 2.52
3761 3802 5.176958 GTGGACCATTAGAATTACGGAATCG 59.823 44.000 0.00 0.00 43.02 3.34
3762 3803 5.069383 TGGACCATTAGAATTACGGAATCGA 59.931 40.000 0.00 0.00 40.11 3.59
3763 3804 6.164176 GGACCATTAGAATTACGGAATCGAT 58.836 40.000 0.00 0.00 40.11 3.59
3764 3805 7.039574 TGGACCATTAGAATTACGGAATCGATA 60.040 37.037 0.00 0.00 40.11 2.92
3765 3806 7.816031 GGACCATTAGAATTACGGAATCGATAA 59.184 37.037 0.00 0.00 40.11 1.75
3766 3807 8.530269 ACCATTAGAATTACGGAATCGATAAC 57.470 34.615 0.00 0.00 40.11 1.89
3767 3808 8.365647 ACCATTAGAATTACGGAATCGATAACT 58.634 33.333 0.00 0.00 40.11 2.24
3768 3809 8.861101 CCATTAGAATTACGGAATCGATAACTC 58.139 37.037 0.00 0.00 40.11 3.01
3769 3810 8.861101 CATTAGAATTACGGAATCGATAACTCC 58.139 37.037 0.00 0.78 40.11 3.85
3770 3811 5.780984 AGAATTACGGAATCGATAACTCCC 58.219 41.667 8.68 1.07 40.11 4.30
3771 3812 3.631145 TTACGGAATCGATAACTCCCG 57.369 47.619 16.24 16.24 42.30 5.14
3772 3813 1.683943 ACGGAATCGATAACTCCCGA 58.316 50.000 21.44 0.00 40.10 5.14
3773 3814 2.026641 ACGGAATCGATAACTCCCGAA 58.973 47.619 21.44 0.00 40.10 4.30
3774 3815 2.223665 ACGGAATCGATAACTCCCGAAC 60.224 50.000 21.44 0.00 40.10 3.95
3775 3816 2.391879 GGAATCGATAACTCCCGAACG 58.608 52.381 0.00 0.00 38.36 3.95
3776 3817 2.033801 GGAATCGATAACTCCCGAACGA 59.966 50.000 0.00 0.00 38.36 3.85
3777 3818 2.770699 ATCGATAACTCCCGAACGAC 57.229 50.000 0.00 0.00 38.36 4.34
3778 3819 0.734889 TCGATAACTCCCGAACGACC 59.265 55.000 0.00 0.00 0.00 4.79
3779 3820 0.248784 CGATAACTCCCGAACGACCC 60.249 60.000 0.00 0.00 0.00 4.46
3780 3821 0.248784 GATAACTCCCGAACGACCCG 60.249 60.000 0.00 0.00 0.00 5.28
3781 3822 0.967380 ATAACTCCCGAACGACCCGT 60.967 55.000 0.00 0.00 43.97 5.28
3782 3823 0.322098 TAACTCCCGAACGACCCGTA 60.322 55.000 0.00 0.00 39.99 4.02
3783 3824 1.866853 AACTCCCGAACGACCCGTAC 61.867 60.000 0.00 0.00 39.99 3.67
3784 3825 2.034066 TCCCGAACGACCCGTACT 59.966 61.111 0.00 0.00 39.99 2.73
3785 3826 1.589716 CTCCCGAACGACCCGTACTT 61.590 60.000 0.00 0.00 39.99 2.24
3786 3827 1.178534 TCCCGAACGACCCGTACTTT 61.179 55.000 0.00 0.00 39.99 2.66
3787 3828 0.319813 CCCGAACGACCCGTACTTTT 60.320 55.000 0.00 0.00 39.99 2.27
3788 3829 0.785979 CCGAACGACCCGTACTTTTG 59.214 55.000 0.00 0.00 39.99 2.44
3789 3830 1.602668 CCGAACGACCCGTACTTTTGA 60.603 52.381 0.00 0.00 39.99 2.69
3790 3831 2.126467 CGAACGACCCGTACTTTTGAA 58.874 47.619 0.00 0.00 39.99 2.69
3791 3832 2.733026 CGAACGACCCGTACTTTTGAAT 59.267 45.455 0.00 0.00 39.99 2.57
3792 3833 3.181537 CGAACGACCCGTACTTTTGAATC 60.182 47.826 0.00 0.00 39.99 2.52
3793 3834 3.672767 ACGACCCGTACTTTTGAATCT 57.327 42.857 0.00 0.00 38.73 2.40
3794 3835 3.582780 ACGACCCGTACTTTTGAATCTC 58.417 45.455 0.00 0.00 38.73 2.75
3795 3836 2.597305 CGACCCGTACTTTTGAATCTCG 59.403 50.000 0.00 0.00 0.00 4.04
3796 3837 3.582780 GACCCGTACTTTTGAATCTCGT 58.417 45.455 0.00 0.00 0.00 4.18
3797 3838 3.582780 ACCCGTACTTTTGAATCTCGTC 58.417 45.455 0.00 0.00 0.00 4.20
3798 3839 2.928116 CCCGTACTTTTGAATCTCGTCC 59.072 50.000 0.00 0.00 0.00 4.79
3799 3840 2.928116 CCGTACTTTTGAATCTCGTCCC 59.072 50.000 0.00 0.00 0.00 4.46
3800 3841 2.597305 CGTACTTTTGAATCTCGTCCCG 59.403 50.000 0.00 0.00 0.00 5.14
3801 3842 3.671433 CGTACTTTTGAATCTCGTCCCGA 60.671 47.826 0.00 0.00 0.00 5.14
3802 3843 3.396260 ACTTTTGAATCTCGTCCCGAA 57.604 42.857 0.00 0.00 34.74 4.30
3803 3844 3.064931 ACTTTTGAATCTCGTCCCGAAC 58.935 45.455 0.00 0.00 34.74 3.95
3811 3852 3.266964 CGTCCCGAACGTGTCCTA 58.733 61.111 0.00 0.00 46.42 2.94
3812 3853 1.580942 CGTCCCGAACGTGTCCTAA 59.419 57.895 0.00 0.00 46.42 2.69
3813 3854 0.039256 CGTCCCGAACGTGTCCTAAA 60.039 55.000 0.00 0.00 46.42 1.85
3814 3855 1.422388 GTCCCGAACGTGTCCTAAAC 58.578 55.000 0.00 0.00 0.00 2.01
3815 3856 0.318120 TCCCGAACGTGTCCTAAACC 59.682 55.000 0.00 0.00 0.00 3.27
3816 3857 1.010419 CCCGAACGTGTCCTAAACCG 61.010 60.000 0.00 0.00 0.00 4.44
3817 3858 0.318955 CCGAACGTGTCCTAAACCGT 60.319 55.000 0.00 0.00 36.67 4.83
3818 3859 1.055338 CGAACGTGTCCTAAACCGTC 58.945 55.000 0.00 0.00 34.89 4.79
3819 3860 1.600164 CGAACGTGTCCTAAACCGTCA 60.600 52.381 0.00 0.00 34.89 4.35
3820 3861 2.056577 GAACGTGTCCTAAACCGTCAG 58.943 52.381 0.00 0.00 34.89 3.51
3821 3862 1.321474 ACGTGTCCTAAACCGTCAGA 58.679 50.000 0.00 0.00 31.81 3.27
3822 3863 1.891150 ACGTGTCCTAAACCGTCAGAT 59.109 47.619 0.00 0.00 31.81 2.90
3823 3864 2.259618 CGTGTCCTAAACCGTCAGATG 58.740 52.381 0.00 0.00 0.00 2.90
3824 3865 2.094906 CGTGTCCTAAACCGTCAGATGA 60.095 50.000 0.00 0.00 0.00 2.92
3825 3866 3.512680 GTGTCCTAAACCGTCAGATGAG 58.487 50.000 0.00 0.00 0.00 2.90
3826 3867 2.094182 TGTCCTAAACCGTCAGATGAGC 60.094 50.000 0.00 0.00 0.00 4.26
3827 3868 1.480954 TCCTAAACCGTCAGATGAGCC 59.519 52.381 0.00 0.00 0.00 4.70
3828 3869 1.560923 CTAAACCGTCAGATGAGCCG 58.439 55.000 0.00 0.00 0.00 5.52
3829 3870 0.459585 TAAACCGTCAGATGAGCCGC 60.460 55.000 0.00 0.00 0.00 6.53
3830 3871 2.449031 AAACCGTCAGATGAGCCGCA 62.449 55.000 0.00 0.00 0.00 5.69
3831 3872 2.887568 CCGTCAGATGAGCCGCAC 60.888 66.667 0.00 0.00 0.00 5.34
3832 3873 2.182791 CGTCAGATGAGCCGCACT 59.817 61.111 0.00 0.00 0.00 4.40
3833 3874 1.433471 CGTCAGATGAGCCGCACTA 59.567 57.895 0.00 0.00 0.00 2.74
3834 3875 0.179137 CGTCAGATGAGCCGCACTAA 60.179 55.000 0.00 0.00 0.00 2.24
3835 3876 1.536922 CGTCAGATGAGCCGCACTAAT 60.537 52.381 0.00 0.00 0.00 1.73
3836 3877 2.131183 GTCAGATGAGCCGCACTAATC 58.869 52.381 0.00 0.00 36.57 1.75
3837 3878 2.034878 TCAGATGAGCCGCACTAATCT 58.965 47.619 0.00 0.00 46.33 2.40
3838 3879 2.432146 TCAGATGAGCCGCACTAATCTT 59.568 45.455 1.49 0.00 43.29 2.40
3839 3880 2.543012 CAGATGAGCCGCACTAATCTTG 59.457 50.000 1.49 0.00 43.29 3.02
3840 3881 2.432146 AGATGAGCCGCACTAATCTTGA 59.568 45.455 0.00 0.00 43.29 3.02
3841 3882 2.988010 TGAGCCGCACTAATCTTGAT 57.012 45.000 0.00 0.00 0.00 2.57
3842 3883 2.554142 TGAGCCGCACTAATCTTGATG 58.446 47.619 0.00 0.00 0.00 3.07
3843 3884 1.262683 GAGCCGCACTAATCTTGATGC 59.737 52.381 0.00 0.00 34.66 3.91
3844 3885 1.016627 GCCGCACTAATCTTGATGCA 58.983 50.000 0.00 0.00 37.97 3.96
3845 3886 1.401552 GCCGCACTAATCTTGATGCAA 59.598 47.619 0.00 0.00 37.97 4.08
3846 3887 2.159393 GCCGCACTAATCTTGATGCAAA 60.159 45.455 0.00 0.00 37.97 3.68
3847 3888 3.688272 CCGCACTAATCTTGATGCAAAG 58.312 45.455 0.00 0.00 37.97 2.77
3848 3889 3.103738 CGCACTAATCTTGATGCAAAGC 58.896 45.455 0.00 0.00 37.97 3.51
3849 3890 3.103738 GCACTAATCTTGATGCAAAGCG 58.896 45.455 0.00 0.00 38.00 4.68
3850 3891 3.103738 CACTAATCTTGATGCAAAGCGC 58.896 45.455 0.00 0.00 42.89 5.92
3864 3905 2.179018 GCGCAATGCCACGTCATT 59.821 55.556 0.30 0.00 37.16 2.57
3865 3906 1.444212 GCGCAATGCCACGTCATTT 60.444 52.632 0.30 0.00 34.68 2.32
3866 3907 1.008361 GCGCAATGCCACGTCATTTT 61.008 50.000 0.30 0.00 34.68 1.82
3867 3908 0.709467 CGCAATGCCACGTCATTTTG 59.291 50.000 0.00 0.00 34.68 2.44
3868 3909 1.782044 GCAATGCCACGTCATTTTGT 58.218 45.000 0.00 0.00 34.68 2.83
3869 3910 2.134346 GCAATGCCACGTCATTTTGTT 58.866 42.857 0.00 0.00 34.68 2.83
3870 3911 2.543430 GCAATGCCACGTCATTTTGTTT 59.457 40.909 0.00 0.00 34.68 2.83
3871 3912 3.604314 GCAATGCCACGTCATTTTGTTTG 60.604 43.478 0.00 0.00 34.68 2.93
3872 3913 3.724508 ATGCCACGTCATTTTGTTTGA 57.275 38.095 0.00 0.00 0.00 2.69
3873 3914 3.077229 TGCCACGTCATTTTGTTTGAG 57.923 42.857 0.00 0.00 0.00 3.02
3874 3915 1.786579 GCCACGTCATTTTGTTTGAGC 59.213 47.619 0.00 0.00 0.00 4.26
3875 3916 2.043411 CCACGTCATTTTGTTTGAGCG 58.957 47.619 0.00 0.00 0.00 5.03
3876 3917 2.540769 CCACGTCATTTTGTTTGAGCGT 60.541 45.455 0.00 0.00 33.96 5.07
3877 3918 3.105203 CACGTCATTTTGTTTGAGCGTT 58.895 40.909 0.00 0.00 32.53 4.84
3878 3919 3.177643 CACGTCATTTTGTTTGAGCGTTC 59.822 43.478 0.00 0.00 32.53 3.95
3879 3920 2.397154 CGTCATTTTGTTTGAGCGTTCG 59.603 45.455 0.00 0.00 0.00 3.95
3880 3921 2.719046 GTCATTTTGTTTGAGCGTTCGG 59.281 45.455 0.00 0.00 0.00 4.30
3881 3922 2.050691 CATTTTGTTTGAGCGTTCGGG 58.949 47.619 0.00 0.00 0.00 5.14
3882 3923 1.380524 TTTTGTTTGAGCGTTCGGGA 58.619 45.000 0.00 0.00 0.00 5.14
3883 3924 0.658897 TTTGTTTGAGCGTTCGGGAC 59.341 50.000 0.00 0.00 0.00 4.46
3896 3937 3.756727 GGGACGACCGACCAGACC 61.757 72.222 12.33 0.00 36.97 3.85
3897 3938 2.987547 GGACGACCGACCAGACCA 60.988 66.667 6.08 0.00 0.00 4.02
3898 3939 2.257676 GACGACCGACCAGACCAC 59.742 66.667 0.00 0.00 0.00 4.16
3899 3940 2.203451 ACGACCGACCAGACCACT 60.203 61.111 0.00 0.00 0.00 4.00
3900 3941 2.258591 CGACCGACCAGACCACTG 59.741 66.667 0.00 0.00 43.12 3.66
3901 3942 2.265904 CGACCGACCAGACCACTGA 61.266 63.158 0.00 0.00 46.03 3.41
3902 3943 1.802337 CGACCGACCAGACCACTGAA 61.802 60.000 0.00 0.00 46.03 3.02
3903 3944 0.319641 GACCGACCAGACCACTGAAC 60.320 60.000 0.00 0.00 46.03 3.18
3904 3945 1.046472 ACCGACCAGACCACTGAACA 61.046 55.000 0.00 0.00 46.03 3.18
3905 3946 0.600255 CCGACCAGACCACTGAACAC 60.600 60.000 0.00 0.00 46.03 3.32
3906 3947 0.104120 CGACCAGACCACTGAACACA 59.896 55.000 0.00 0.00 46.03 3.72
3907 3948 1.270305 CGACCAGACCACTGAACACAT 60.270 52.381 0.00 0.00 46.03 3.21
3908 3949 2.417719 GACCAGACCACTGAACACATC 58.582 52.381 0.00 0.00 46.03 3.06
3909 3950 1.270305 ACCAGACCACTGAACACATCG 60.270 52.381 0.00 0.00 46.03 3.84
3910 3951 1.432514 CAGACCACTGAACACATCGG 58.567 55.000 0.00 0.00 46.03 4.18
3911 3952 0.320771 AGACCACTGAACACATCGGC 60.321 55.000 0.00 0.00 38.03 5.54
3912 3953 0.320771 GACCACTGAACACATCGGCT 60.321 55.000 0.00 0.00 38.03 5.52
3913 3954 0.108585 ACCACTGAACACATCGGCTT 59.891 50.000 0.00 0.00 38.03 4.35
3914 3955 1.346395 ACCACTGAACACATCGGCTTA 59.654 47.619 0.00 0.00 38.03 3.09
3915 3956 2.027192 ACCACTGAACACATCGGCTTAT 60.027 45.455 0.00 0.00 38.03 1.73
3916 3957 2.609459 CCACTGAACACATCGGCTTATC 59.391 50.000 0.00 0.00 38.03 1.75
3917 3958 2.609459 CACTGAACACATCGGCTTATCC 59.391 50.000 0.00 0.00 38.03 2.59
3918 3959 2.236146 ACTGAACACATCGGCTTATCCA 59.764 45.455 0.00 0.00 38.03 3.41
3919 3960 2.609459 CTGAACACATCGGCTTATCCAC 59.391 50.000 0.00 0.00 34.01 4.02
3920 3961 2.236146 TGAACACATCGGCTTATCCACT 59.764 45.455 0.00 0.00 34.01 4.00
3921 3962 2.604046 ACACATCGGCTTATCCACTC 57.396 50.000 0.00 0.00 34.01 3.51
3922 3963 1.202417 ACACATCGGCTTATCCACTCG 60.202 52.381 0.00 0.00 34.01 4.18
3923 3964 0.249489 ACATCGGCTTATCCACTCGC 60.249 55.000 0.00 0.00 34.01 5.03
3924 3965 0.946221 CATCGGCTTATCCACTCGCC 60.946 60.000 0.00 0.00 39.14 5.54
3925 3966 2.100879 ATCGGCTTATCCACTCGCCC 62.101 60.000 0.00 0.00 39.34 6.13
3926 3967 2.908015 GGCTTATCCACTCGCCCA 59.092 61.111 0.00 0.00 36.56 5.36
3927 3968 1.523938 GGCTTATCCACTCGCCCAC 60.524 63.158 0.00 0.00 36.56 4.61
3928 3969 1.523938 GCTTATCCACTCGCCCACC 60.524 63.158 0.00 0.00 0.00 4.61
3929 3970 1.146263 CTTATCCACTCGCCCACCC 59.854 63.158 0.00 0.00 0.00 4.61
3930 3971 2.325393 CTTATCCACTCGCCCACCCC 62.325 65.000 0.00 0.00 0.00 4.95
3931 3972 3.627332 TATCCACTCGCCCACCCCA 62.627 63.158 0.00 0.00 0.00 4.96
3942 3983 4.641645 CACCCCAGCCAACGCTCA 62.642 66.667 0.00 0.00 43.95 4.26
3943 3984 4.643387 ACCCCAGCCAACGCTCAC 62.643 66.667 0.00 0.00 43.95 3.51
3944 3985 4.335647 CCCCAGCCAACGCTCACT 62.336 66.667 0.00 0.00 43.95 3.41
3945 3986 2.281761 CCCAGCCAACGCTCACTT 60.282 61.111 0.00 0.00 43.95 3.16
3946 3987 1.898574 CCCAGCCAACGCTCACTTT 60.899 57.895 0.00 0.00 43.95 2.66
3947 3988 1.455383 CCCAGCCAACGCTCACTTTT 61.455 55.000 0.00 0.00 43.95 2.27
3948 3989 0.385390 CCAGCCAACGCTCACTTTTT 59.615 50.000 0.00 0.00 43.95 1.94
3949 3990 1.600413 CCAGCCAACGCTCACTTTTTC 60.600 52.381 0.00 0.00 43.95 2.29
3950 3991 0.668535 AGCCAACGCTCACTTTTTCC 59.331 50.000 0.00 0.00 43.95 3.13
3951 3992 0.318699 GCCAACGCTCACTTTTTCCC 60.319 55.000 0.00 0.00 0.00 3.97
3952 3993 0.313987 CCAACGCTCACTTTTTCCCC 59.686 55.000 0.00 0.00 0.00 4.81
3953 3994 1.318576 CAACGCTCACTTTTTCCCCT 58.681 50.000 0.00 0.00 0.00 4.79
3954 3995 1.681264 CAACGCTCACTTTTTCCCCTT 59.319 47.619 0.00 0.00 0.00 3.95
3955 3996 2.067365 ACGCTCACTTTTTCCCCTTT 57.933 45.000 0.00 0.00 0.00 3.11
3956 3997 1.954382 ACGCTCACTTTTTCCCCTTTC 59.046 47.619 0.00 0.00 0.00 2.62
3957 3998 2.230660 CGCTCACTTTTTCCCCTTTCT 58.769 47.619 0.00 0.00 0.00 2.52
3958 3999 2.623416 CGCTCACTTTTTCCCCTTTCTT 59.377 45.455 0.00 0.00 0.00 2.52
3959 4000 3.304726 CGCTCACTTTTTCCCCTTTCTTC 60.305 47.826 0.00 0.00 0.00 2.87
3960 4001 3.636764 GCTCACTTTTTCCCCTTTCTTCA 59.363 43.478 0.00 0.00 0.00 3.02
3961 4002 4.499865 GCTCACTTTTTCCCCTTTCTTCAC 60.500 45.833 0.00 0.00 0.00 3.18
3962 4003 4.605183 TCACTTTTTCCCCTTTCTTCACA 58.395 39.130 0.00 0.00 0.00 3.58
3963 4004 5.208121 TCACTTTTTCCCCTTTCTTCACAT 58.792 37.500 0.00 0.00 0.00 3.21
3964 4005 5.301805 TCACTTTTTCCCCTTTCTTCACATC 59.698 40.000 0.00 0.00 0.00 3.06
3965 4006 5.068987 CACTTTTTCCCCTTTCTTCACATCA 59.931 40.000 0.00 0.00 0.00 3.07
3966 4007 5.069119 ACTTTTTCCCCTTTCTTCACATCAC 59.931 40.000 0.00 0.00 0.00 3.06
3967 4008 3.874383 TTCCCCTTTCTTCACATCACA 57.126 42.857 0.00 0.00 0.00 3.58
3968 4009 3.874383 TCCCCTTTCTTCACATCACAA 57.126 42.857 0.00 0.00 0.00 3.33
3969 4010 3.754965 TCCCCTTTCTTCACATCACAAG 58.245 45.455 0.00 0.00 0.00 3.16
3970 4011 2.229784 CCCCTTTCTTCACATCACAAGC 59.770 50.000 0.00 0.00 0.00 4.01
3971 4012 2.095567 CCCTTTCTTCACATCACAAGCG 60.096 50.000 0.00 0.00 0.00 4.68
3972 4013 2.095567 CCTTTCTTCACATCACAAGCGG 60.096 50.000 0.00 0.00 0.00 5.52
3973 4014 0.874390 TTCTTCACATCACAAGCGGC 59.126 50.000 0.00 0.00 0.00 6.53
3974 4015 1.133253 CTTCACATCACAAGCGGCG 59.867 57.895 0.51 0.51 0.00 6.46
3975 4016 2.244436 CTTCACATCACAAGCGGCGG 62.244 60.000 9.78 0.00 0.00 6.13
3976 4017 2.723586 TTCACATCACAAGCGGCGGA 62.724 55.000 9.78 0.00 0.00 5.54
3977 4018 2.434884 ACATCACAAGCGGCGGAG 60.435 61.111 9.78 0.00 0.00 4.63
3978 4019 2.125552 CATCACAAGCGGCGGAGA 60.126 61.111 9.78 0.00 0.00 3.71
3979 4020 2.125512 ATCACAAGCGGCGGAGAC 60.126 61.111 9.78 0.00 0.00 3.36
3992 4033 4.878774 GAGACGAGCTCCTGTGTG 57.121 61.111 8.47 0.00 37.69 3.82
3993 4034 1.214062 GAGACGAGCTCCTGTGTGG 59.786 63.158 8.47 0.00 37.69 4.17
3994 4035 1.528292 GAGACGAGCTCCTGTGTGGT 61.528 60.000 8.47 0.00 37.69 4.16
3995 4036 1.373497 GACGAGCTCCTGTGTGGTG 60.373 63.158 8.47 0.00 37.07 4.17
3996 4037 2.047844 CGAGCTCCTGTGTGGTGG 60.048 66.667 8.47 0.00 37.07 4.61
3997 4038 2.359230 GAGCTCCTGTGTGGTGGC 60.359 66.667 0.87 0.00 37.07 5.01
3998 4039 2.851102 AGCTCCTGTGTGGTGGCT 60.851 61.111 0.00 0.00 39.54 4.75
3999 4040 2.670934 GCTCCTGTGTGGTGGCTG 60.671 66.667 0.00 0.00 37.07 4.85
4000 4041 2.670934 CTCCTGTGTGGTGGCTGC 60.671 66.667 0.00 0.00 37.07 5.25
4001 4042 4.269523 TCCTGTGTGGTGGCTGCC 62.270 66.667 12.87 12.87 37.07 4.85
4003 4044 4.275508 CTGTGTGGTGGCTGCCCT 62.276 66.667 17.53 0.00 0.00 5.19
4004 4045 4.584518 TGTGTGGTGGCTGCCCTG 62.585 66.667 17.53 0.00 0.00 4.45
4008 4049 4.980702 TGGTGGCTGCCCTGCAAG 62.981 66.667 17.53 0.00 38.41 4.01
4009 4050 4.982701 GGTGGCTGCCCTGCAAGT 62.983 66.667 17.53 0.00 38.41 3.16
4010 4051 3.677648 GTGGCTGCCCTGCAAGTG 61.678 66.667 17.53 0.00 38.41 3.16
4011 4052 4.208403 TGGCTGCCCTGCAAGTGT 62.208 61.111 17.53 0.00 38.41 3.55
4012 4053 3.368571 GGCTGCCCTGCAAGTGTC 61.369 66.667 7.66 0.00 38.41 3.67
4013 4054 2.595463 GCTGCCCTGCAAGTGTCA 60.595 61.111 0.00 0.00 38.41 3.58
4014 4055 2.912624 GCTGCCCTGCAAGTGTCAC 61.913 63.158 0.00 0.00 38.41 3.67
4015 4056 2.203337 TGCCCTGCAAGTGTCACC 60.203 61.111 0.00 0.00 34.76 4.02
4016 4057 3.357079 GCCCTGCAAGTGTCACCG 61.357 66.667 0.00 0.00 0.00 4.94
4017 4058 2.669569 CCCTGCAAGTGTCACCGG 60.670 66.667 0.00 0.00 0.00 5.28
4018 4059 2.425592 CCTGCAAGTGTCACCGGA 59.574 61.111 9.46 0.00 0.00 5.14
4019 4060 1.669115 CCTGCAAGTGTCACCGGAG 60.669 63.158 9.46 0.00 0.00 4.63
4020 4061 1.367471 CTGCAAGTGTCACCGGAGA 59.633 57.895 9.46 1.33 0.00 3.71
4021 4062 0.946221 CTGCAAGTGTCACCGGAGAC 60.946 60.000 23.40 23.40 37.57 3.36
4022 4063 1.668151 GCAAGTGTCACCGGAGACC 60.668 63.158 26.35 18.04 38.02 3.85
4024 4065 3.222354 AAGTGTCACCGGAGACCGC 62.222 63.158 26.35 19.20 46.86 5.68
4074 4115 4.899239 CGGCGTGGGGATGAGCTC 62.899 72.222 6.82 6.82 0.00 4.09
4075 4116 4.899239 GGCGTGGGGATGAGCTCG 62.899 72.222 9.64 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.073650 AGCCTTGATCCAGTCTTCAAAGT 59.926 43.478 0.00 0.00 31.85 2.66
229 231 8.477419 TTTCAACTTGAGGGAAATAACAAGAT 57.523 30.769 0.00 0.00 41.16 2.40
237 239 7.623630 CCCATTAATTTCAACTTGAGGGAAAT 58.376 34.615 4.62 0.00 41.58 2.17
272 274 2.489938 AGTGCATACCCGTTGAATGT 57.510 45.000 0.00 0.00 0.00 2.71
348 350 1.642728 ATGCACGCGAACGGTAATAA 58.357 45.000 15.93 0.00 46.04 1.40
362 364 4.225984 TGCATCGTTTTGTTCTTATGCAC 58.774 39.130 3.83 0.00 43.32 4.57
489 491 0.394565 GCCGGAGATGCCTATTCAGT 59.605 55.000 5.05 0.00 0.00 3.41
493 495 1.367840 GTCGCCGGAGATGCCTATT 59.632 57.895 12.23 0.00 0.00 1.73
520 522 2.145397 TATCTCTTCTCACGGCCACT 57.855 50.000 2.24 0.00 0.00 4.00
528 530 7.317842 AGTCGTTTATCGTTATCTCTTCTCA 57.682 36.000 0.00 0.00 40.80 3.27
708 711 7.974482 AACTATTTTACTACAGCTTTTCGGT 57.026 32.000 0.00 0.00 0.00 4.69
710 713 9.872757 TTCAAACTATTTTACTACAGCTTTTCG 57.127 29.630 0.00 0.00 0.00 3.46
739 742 9.559958 CCTGTTTGATATAGCAAAGTAAAAGTG 57.440 33.333 16.10 1.98 38.33 3.16
742 745 7.363443 GGCCCTGTTTGATATAGCAAAGTAAAA 60.363 37.037 16.10 0.61 38.33 1.52
743 746 6.096282 GGCCCTGTTTGATATAGCAAAGTAAA 59.904 38.462 16.10 2.83 38.33 2.01
859 865 0.108615 CATCCAGTCAGTCCGGTCAC 60.109 60.000 0.00 0.00 0.00 3.67
1045 1051 1.611851 CTCAGAGAGGGGTGCAGGT 60.612 63.158 0.00 0.00 0.00 4.00
1064 1070 1.375268 GCTGCAGACCGAAGCTTCT 60.375 57.895 23.50 6.40 34.05 2.85
1074 1080 3.423162 ATCGCTCTCCGCTGCAGAC 62.423 63.158 20.43 8.06 36.73 3.51
1108 1114 3.616721 AGCCGCACGAAGTCCACT 61.617 61.111 0.00 0.00 41.61 4.00
1262 1268 2.439883 GCGGAGGAGGACGTAGGT 60.440 66.667 0.00 0.00 0.00 3.08
1263 1269 3.584052 CGCGGAGGAGGACGTAGG 61.584 72.222 0.00 0.00 0.00 3.18
1743 1757 4.003648 AGTAAGCACGGGAATCAAAGAAG 58.996 43.478 0.00 0.00 0.00 2.85
1763 1777 6.427853 TGATTGATTGATTCTTTCACACGAGT 59.572 34.615 0.00 0.00 32.84 4.18
1932 1951 1.376466 GAAGAGCTTGCCCCACTCA 59.624 57.895 0.00 0.00 32.71 3.41
1978 1997 2.112297 GAACCACCGCACCCAGAA 59.888 61.111 0.00 0.00 0.00 3.02
2418 2437 4.806247 ACTGCTTTCTTAGTGCATATCGAC 59.194 41.667 0.00 0.00 36.07 4.20
2495 2527 0.811281 GCCACAGGCCACAGTAAATC 59.189 55.000 5.01 0.00 44.06 2.17
2578 2610 9.591792 CTCTCAGAAATGTCACATTACTAATCA 57.408 33.333 2.67 0.00 0.00 2.57
2627 2659 4.100035 TCGCTAGTTTCAGATGATCCACAT 59.900 41.667 0.00 0.00 42.47 3.21
2944 2976 2.542020 TCTGGAACAAGTTGCGATGA 57.458 45.000 1.81 0.00 38.70 2.92
3038 3070 4.761739 TCAATCCTGGATCAAACACTGAAC 59.238 41.667 10.14 0.00 37.67 3.18
3129 3161 0.592247 CAACGTGCAAGACAGGCAAC 60.592 55.000 6.65 0.00 43.91 4.17
3130 3162 0.746204 TCAACGTGCAAGACAGGCAA 60.746 50.000 6.65 0.00 43.91 4.52
3131 3163 1.153269 TCAACGTGCAAGACAGGCA 60.153 52.632 6.65 0.00 37.69 4.75
3132 3164 1.279840 GTCAACGTGCAAGACAGGC 59.720 57.895 6.65 0.00 37.69 4.85
3133 3165 1.229428 ATGTCAACGTGCAAGACAGG 58.771 50.000 6.65 0.00 44.51 4.00
3134 3166 2.602933 CCAATGTCAACGTGCAAGACAG 60.603 50.000 6.65 0.23 44.51 3.51
3135 3167 1.333308 CCAATGTCAACGTGCAAGACA 59.667 47.619 6.65 10.55 45.26 3.41
3136 3168 1.925946 GCCAATGTCAACGTGCAAGAC 60.926 52.381 6.65 4.82 0.00 3.01
3137 3169 0.310543 GCCAATGTCAACGTGCAAGA 59.689 50.000 6.65 0.00 0.00 3.02
3138 3170 0.311790 AGCCAATGTCAACGTGCAAG 59.688 50.000 0.00 0.00 0.00 4.01
3139 3171 1.265635 GTAGCCAATGTCAACGTGCAA 59.734 47.619 0.00 0.00 0.00 4.08
3140 3172 0.871722 GTAGCCAATGTCAACGTGCA 59.128 50.000 0.00 0.00 0.00 4.57
3141 3173 0.871722 TGTAGCCAATGTCAACGTGC 59.128 50.000 0.00 0.00 0.00 5.34
3142 3174 1.135972 GCTGTAGCCAATGTCAACGTG 60.136 52.381 0.00 0.00 34.31 4.49
3143 3175 1.156736 GCTGTAGCCAATGTCAACGT 58.843 50.000 0.00 0.00 34.31 3.99
3144 3176 1.155889 TGCTGTAGCCAATGTCAACG 58.844 50.000 0.80 0.00 41.18 4.10
3248 3280 5.810587 GGAGCGTGTTTCATATCACTTAAGA 59.189 40.000 10.09 0.00 33.07 2.10
3251 3283 4.081365 TGGGAGCGTGTTTCATATCACTTA 60.081 41.667 0.00 0.00 33.07 2.24
3418 3451 6.996509 ACATATGCAATTTCAGGTGAGTTTT 58.003 32.000 1.58 0.00 0.00 2.43
3425 3458 6.681120 GCACATGTACATATGCAATTTCAGGT 60.681 38.462 29.50 7.41 40.71 4.00
3464 3497 2.416836 GGCGTATACAGTGCAGAGACAA 60.417 50.000 3.32 0.00 0.00 3.18
3545 3578 6.799441 CAGACTACAATAACTATAGCTGAGCG 59.201 42.308 0.00 0.00 0.00 5.03
3680 3721 5.661458 TGAAAACGGGAAAAATGCTAACAA 58.339 33.333 0.00 0.00 0.00 2.83
3708 3749 2.011222 TCCGTGAACAACACTGAAACC 58.989 47.619 0.00 0.00 46.24 3.27
3719 3760 1.321474 ACGTTCCTAGTCCGTGAACA 58.679 50.000 8.81 0.00 38.59 3.18
3724 3765 1.246737 GGTCCACGTTCCTAGTCCGT 61.247 60.000 0.00 0.00 34.71 4.69
3725 3766 1.246056 TGGTCCACGTTCCTAGTCCG 61.246 60.000 0.00 0.00 0.00 4.79
3727 3768 3.698040 TCTAATGGTCCACGTTCCTAGTC 59.302 47.826 0.00 0.00 0.00 2.59
3728 3769 3.705051 TCTAATGGTCCACGTTCCTAGT 58.295 45.455 0.00 0.00 0.00 2.57
3729 3770 4.730949 TTCTAATGGTCCACGTTCCTAG 57.269 45.455 0.00 0.00 0.00 3.02
3730 3771 5.687166 AATTCTAATGGTCCACGTTCCTA 57.313 39.130 0.00 0.00 0.00 2.94
3731 3772 4.569719 AATTCTAATGGTCCACGTTCCT 57.430 40.909 0.00 0.00 0.00 3.36
3754 3795 2.391879 GTTCGGGAGTTATCGATTCCG 58.608 52.381 1.71 9.97 35.06 4.30
3758 3799 1.336125 GGTCGTTCGGGAGTTATCGAT 59.664 52.381 2.16 2.16 35.25 3.59
3759 3800 0.734889 GGTCGTTCGGGAGTTATCGA 59.265 55.000 0.00 0.00 0.00 3.59
3760 3801 0.248784 GGGTCGTTCGGGAGTTATCG 60.249 60.000 0.00 0.00 0.00 2.92
3761 3802 0.248784 CGGGTCGTTCGGGAGTTATC 60.249 60.000 0.00 0.00 0.00 1.75
3762 3803 0.967380 ACGGGTCGTTCGGGAGTTAT 60.967 55.000 0.00 0.00 36.35 1.89
3763 3804 0.322098 TACGGGTCGTTCGGGAGTTA 60.322 55.000 0.00 0.00 41.54 2.24
3764 3805 1.603455 TACGGGTCGTTCGGGAGTT 60.603 57.895 0.00 0.00 41.54 3.01
3765 3806 2.034066 TACGGGTCGTTCGGGAGT 59.966 61.111 0.00 0.00 41.54 3.85
3766 3807 1.589716 AAGTACGGGTCGTTCGGGAG 61.590 60.000 0.00 0.00 41.54 4.30
3767 3808 1.178534 AAAGTACGGGTCGTTCGGGA 61.179 55.000 0.00 0.00 41.54 5.14
3768 3809 0.319813 AAAAGTACGGGTCGTTCGGG 60.320 55.000 0.00 0.00 41.54 5.14
3769 3810 0.785979 CAAAAGTACGGGTCGTTCGG 59.214 55.000 0.00 0.00 41.54 4.30
3770 3811 1.769733 TCAAAAGTACGGGTCGTTCG 58.230 50.000 0.00 0.00 41.54 3.95
3771 3812 3.992427 AGATTCAAAAGTACGGGTCGTTC 59.008 43.478 0.00 0.00 41.54 3.95
3772 3813 3.992427 GAGATTCAAAAGTACGGGTCGTT 59.008 43.478 0.00 0.00 41.54 3.85
3773 3814 3.582780 GAGATTCAAAAGTACGGGTCGT 58.417 45.455 0.00 0.00 44.35 4.34
3774 3815 2.597305 CGAGATTCAAAAGTACGGGTCG 59.403 50.000 0.00 0.00 0.00 4.79
3775 3816 3.582780 ACGAGATTCAAAAGTACGGGTC 58.417 45.455 0.00 0.00 0.00 4.46
3776 3817 3.582780 GACGAGATTCAAAAGTACGGGT 58.417 45.455 0.00 0.00 0.00 5.28
3777 3818 2.928116 GGACGAGATTCAAAAGTACGGG 59.072 50.000 0.00 0.00 0.00 5.28
3778 3819 2.928116 GGGACGAGATTCAAAAGTACGG 59.072 50.000 0.00 0.00 0.00 4.02
3795 3836 1.422388 GTTTAGGACACGTTCGGGAC 58.578 55.000 0.34 0.00 0.00 4.46
3796 3837 0.318120 GGTTTAGGACACGTTCGGGA 59.682 55.000 0.34 0.00 0.00 5.14
3797 3838 1.010419 CGGTTTAGGACACGTTCGGG 61.010 60.000 0.00 0.00 0.00 5.14
3798 3839 0.318955 ACGGTTTAGGACACGTTCGG 60.319 55.000 0.00 0.00 33.38 4.30
3799 3840 1.055338 GACGGTTTAGGACACGTTCG 58.945 55.000 0.00 0.00 36.00 3.95
3800 3841 2.056577 CTGACGGTTTAGGACACGTTC 58.943 52.381 0.00 0.00 36.00 3.95
3801 3842 1.682854 TCTGACGGTTTAGGACACGTT 59.317 47.619 0.00 0.00 36.00 3.99
3802 3843 1.321474 TCTGACGGTTTAGGACACGT 58.679 50.000 0.00 0.00 37.69 4.49
3803 3844 2.094906 TCATCTGACGGTTTAGGACACG 60.095 50.000 0.00 0.00 0.00 4.49
3804 3845 3.512680 CTCATCTGACGGTTTAGGACAC 58.487 50.000 0.00 0.00 0.00 3.67
3805 3846 2.094182 GCTCATCTGACGGTTTAGGACA 60.094 50.000 0.00 0.00 0.00 4.02
3806 3847 2.541556 GCTCATCTGACGGTTTAGGAC 58.458 52.381 0.00 0.00 0.00 3.85
3807 3848 1.480954 GGCTCATCTGACGGTTTAGGA 59.519 52.381 0.00 0.00 0.00 2.94
3808 3849 1.802880 CGGCTCATCTGACGGTTTAGG 60.803 57.143 0.00 0.00 0.00 2.69
3809 3850 1.560923 CGGCTCATCTGACGGTTTAG 58.439 55.000 0.00 0.00 0.00 1.85
3810 3851 0.459585 GCGGCTCATCTGACGGTTTA 60.460 55.000 0.00 0.00 0.00 2.01
3811 3852 1.741770 GCGGCTCATCTGACGGTTT 60.742 57.895 0.00 0.00 0.00 3.27
3812 3853 2.125512 GCGGCTCATCTGACGGTT 60.126 61.111 0.00 0.00 0.00 4.44
3813 3854 3.381983 TGCGGCTCATCTGACGGT 61.382 61.111 0.00 0.00 0.00 4.83
3814 3855 2.004808 TAGTGCGGCTCATCTGACGG 62.005 60.000 0.00 0.00 0.00 4.79
3815 3856 0.179137 TTAGTGCGGCTCATCTGACG 60.179 55.000 0.00 0.00 0.00 4.35
3816 3857 2.131183 GATTAGTGCGGCTCATCTGAC 58.869 52.381 0.00 0.00 0.00 3.51
3817 3858 2.034878 AGATTAGTGCGGCTCATCTGA 58.965 47.619 0.00 0.00 36.94 3.27
3818 3859 2.522836 AGATTAGTGCGGCTCATCTG 57.477 50.000 0.00 0.00 36.94 2.90
3819 3860 2.432146 TCAAGATTAGTGCGGCTCATCT 59.568 45.455 0.00 0.37 39.22 2.90
3820 3861 2.826428 TCAAGATTAGTGCGGCTCATC 58.174 47.619 0.00 0.00 0.00 2.92
3821 3862 2.988010 TCAAGATTAGTGCGGCTCAT 57.012 45.000 0.00 0.00 0.00 2.90
3822 3863 2.554142 CATCAAGATTAGTGCGGCTCA 58.446 47.619 0.00 0.00 0.00 4.26
3823 3864 1.262683 GCATCAAGATTAGTGCGGCTC 59.737 52.381 0.00 0.00 0.00 4.70
3824 3865 1.303309 GCATCAAGATTAGTGCGGCT 58.697 50.000 0.00 0.00 0.00 5.52
3825 3866 1.016627 TGCATCAAGATTAGTGCGGC 58.983 50.000 0.00 0.00 40.34 6.53
3826 3867 3.688272 CTTTGCATCAAGATTAGTGCGG 58.312 45.455 0.00 0.00 40.34 5.69
3827 3868 3.103738 GCTTTGCATCAAGATTAGTGCG 58.896 45.455 2.23 0.00 40.34 5.34
3828 3869 3.103738 CGCTTTGCATCAAGATTAGTGC 58.896 45.455 2.23 0.00 38.05 4.40
3829 3870 3.103738 GCGCTTTGCATCAAGATTAGTG 58.896 45.455 0.00 0.00 45.45 2.74
3830 3871 3.411415 GCGCTTTGCATCAAGATTAGT 57.589 42.857 0.00 0.00 45.45 2.24
3842 3883 3.472298 CGTGGCATTGCGCTTTGC 61.472 61.111 21.83 21.83 46.70 3.68
3843 3884 2.050168 ACGTGGCATTGCGCTTTG 60.050 55.556 9.73 7.42 41.91 2.77
3844 3885 1.865788 ATGACGTGGCATTGCGCTTT 61.866 50.000 9.73 0.00 41.91 3.51
3845 3886 1.865788 AATGACGTGGCATTGCGCTT 61.866 50.000 9.73 0.00 41.91 4.68
3846 3887 1.865788 AAATGACGTGGCATTGCGCT 61.866 50.000 9.73 0.00 38.42 5.92
3847 3888 1.008361 AAAATGACGTGGCATTGCGC 61.008 50.000 0.00 0.00 38.42 6.09
3848 3889 0.709467 CAAAATGACGTGGCATTGCG 59.291 50.000 0.86 0.00 38.42 4.85
3849 3890 1.782044 ACAAAATGACGTGGCATTGC 58.218 45.000 0.86 0.00 38.42 3.56
3850 3891 3.801050 TCAAACAAAATGACGTGGCATTG 59.199 39.130 0.86 0.00 38.42 2.82
3851 3892 4.050553 CTCAAACAAAATGACGTGGCATT 58.949 39.130 0.00 0.00 40.04 3.56
3852 3893 3.641648 CTCAAACAAAATGACGTGGCAT 58.358 40.909 0.00 0.00 0.00 4.40
3853 3894 2.797792 GCTCAAACAAAATGACGTGGCA 60.798 45.455 0.00 0.00 0.00 4.92
3854 3895 1.786579 GCTCAAACAAAATGACGTGGC 59.213 47.619 0.00 0.00 0.00 5.01
3855 3896 2.043411 CGCTCAAACAAAATGACGTGG 58.957 47.619 0.00 0.00 0.00 4.94
3856 3897 2.715268 ACGCTCAAACAAAATGACGTG 58.285 42.857 0.00 0.00 35.14 4.49
3857 3898 3.359654 GAACGCTCAAACAAAATGACGT 58.640 40.909 0.00 0.00 36.69 4.34
3858 3899 2.397154 CGAACGCTCAAACAAAATGACG 59.603 45.455 0.00 0.00 0.00 4.35
3859 3900 2.719046 CCGAACGCTCAAACAAAATGAC 59.281 45.455 0.00 0.00 0.00 3.06
3860 3901 2.287308 CCCGAACGCTCAAACAAAATGA 60.287 45.455 0.00 0.00 0.00 2.57
3861 3902 2.050691 CCCGAACGCTCAAACAAAATG 58.949 47.619 0.00 0.00 0.00 2.32
3862 3903 1.950909 TCCCGAACGCTCAAACAAAAT 59.049 42.857 0.00 0.00 0.00 1.82
3863 3904 1.064357 GTCCCGAACGCTCAAACAAAA 59.936 47.619 0.00 0.00 0.00 2.44
3864 3905 0.658897 GTCCCGAACGCTCAAACAAA 59.341 50.000 0.00 0.00 0.00 2.83
3865 3906 1.492319 CGTCCCGAACGCTCAAACAA 61.492 55.000 0.00 0.00 45.76 2.83
3866 3907 1.952133 CGTCCCGAACGCTCAAACA 60.952 57.895 0.00 0.00 45.76 2.83
3867 3908 2.851104 CGTCCCGAACGCTCAAAC 59.149 61.111 0.00 0.00 45.76 2.93
3879 3920 3.756727 GGTCTGGTCGGTCGTCCC 61.757 72.222 4.41 0.57 0.00 4.46
3880 3921 2.987547 TGGTCTGGTCGGTCGTCC 60.988 66.667 0.00 0.00 0.00 4.79
3881 3922 2.257676 GTGGTCTGGTCGGTCGTC 59.742 66.667 0.00 0.00 0.00 4.20
3882 3923 2.203451 AGTGGTCTGGTCGGTCGT 60.203 61.111 0.00 0.00 0.00 4.34
3883 3924 1.802337 TTCAGTGGTCTGGTCGGTCG 61.802 60.000 0.00 0.00 41.59 4.79
3884 3925 0.319641 GTTCAGTGGTCTGGTCGGTC 60.320 60.000 0.00 0.00 41.59 4.79
3885 3926 1.046472 TGTTCAGTGGTCTGGTCGGT 61.046 55.000 0.00 0.00 41.59 4.69
3886 3927 0.600255 GTGTTCAGTGGTCTGGTCGG 60.600 60.000 0.00 0.00 41.59 4.79
3887 3928 0.104120 TGTGTTCAGTGGTCTGGTCG 59.896 55.000 0.00 0.00 41.59 4.79
3888 3929 2.417719 GATGTGTTCAGTGGTCTGGTC 58.582 52.381 0.00 0.00 41.59 4.02
3889 3930 1.270305 CGATGTGTTCAGTGGTCTGGT 60.270 52.381 0.00 0.00 41.59 4.00
3890 3931 1.432514 CGATGTGTTCAGTGGTCTGG 58.567 55.000 0.00 0.00 41.59 3.86
3891 3932 1.432514 CCGATGTGTTCAGTGGTCTG 58.567 55.000 0.00 0.00 42.54 3.51
3892 3933 0.320771 GCCGATGTGTTCAGTGGTCT 60.321 55.000 0.00 0.00 0.00 3.85
3893 3934 0.320771 AGCCGATGTGTTCAGTGGTC 60.321 55.000 0.00 0.00 0.00 4.02
3894 3935 0.108585 AAGCCGATGTGTTCAGTGGT 59.891 50.000 0.00 0.00 0.00 4.16
3895 3936 2.093306 TAAGCCGATGTGTTCAGTGG 57.907 50.000 0.00 0.00 0.00 4.00
3896 3937 2.609459 GGATAAGCCGATGTGTTCAGTG 59.391 50.000 0.00 0.00 0.00 3.66
3897 3938 2.236146 TGGATAAGCCGATGTGTTCAGT 59.764 45.455 0.00 0.00 40.66 3.41
3898 3939 2.609459 GTGGATAAGCCGATGTGTTCAG 59.391 50.000 0.00 0.00 40.66 3.02
3899 3940 2.236146 AGTGGATAAGCCGATGTGTTCA 59.764 45.455 0.00 0.00 40.66 3.18
3900 3941 2.866762 GAGTGGATAAGCCGATGTGTTC 59.133 50.000 0.00 0.00 40.66 3.18
3901 3942 2.738643 CGAGTGGATAAGCCGATGTGTT 60.739 50.000 0.00 0.00 40.66 3.32
3902 3943 1.202417 CGAGTGGATAAGCCGATGTGT 60.202 52.381 0.00 0.00 40.66 3.72
3903 3944 1.491670 CGAGTGGATAAGCCGATGTG 58.508 55.000 0.00 0.00 40.66 3.21
3904 3945 0.249489 GCGAGTGGATAAGCCGATGT 60.249 55.000 0.00 0.00 40.66 3.06
3905 3946 0.946221 GGCGAGTGGATAAGCCGATG 60.946 60.000 0.00 0.00 40.17 3.84
3906 3947 1.367840 GGCGAGTGGATAAGCCGAT 59.632 57.895 0.00 0.00 40.17 4.18
3907 3948 2.812499 GGCGAGTGGATAAGCCGA 59.188 61.111 0.00 0.00 40.17 5.54
3910 3951 1.523938 GGTGGGCGAGTGGATAAGC 60.524 63.158 0.00 0.00 0.00 3.09
3911 3952 1.146263 GGGTGGGCGAGTGGATAAG 59.854 63.158 0.00 0.00 0.00 1.73
3912 3953 2.372074 GGGGTGGGCGAGTGGATAA 61.372 63.158 0.00 0.00 0.00 1.75
3913 3954 2.766651 GGGGTGGGCGAGTGGATA 60.767 66.667 0.00 0.00 0.00 2.59
3932 3973 0.318699 GGGAAAAAGTGAGCGTTGGC 60.319 55.000 0.00 0.00 40.37 4.52
3933 3974 0.313987 GGGGAAAAAGTGAGCGTTGG 59.686 55.000 0.00 0.00 0.00 3.77
3934 3975 1.318576 AGGGGAAAAAGTGAGCGTTG 58.681 50.000 0.00 0.00 0.00 4.10
3935 3976 2.067365 AAGGGGAAAAAGTGAGCGTT 57.933 45.000 0.00 0.00 0.00 4.84
3936 3977 1.954382 GAAAGGGGAAAAAGTGAGCGT 59.046 47.619 0.00 0.00 0.00 5.07
3937 3978 2.230660 AGAAAGGGGAAAAAGTGAGCG 58.769 47.619 0.00 0.00 0.00 5.03
3938 3979 3.636764 TGAAGAAAGGGGAAAAAGTGAGC 59.363 43.478 0.00 0.00 0.00 4.26
3939 3980 4.644685 TGTGAAGAAAGGGGAAAAAGTGAG 59.355 41.667 0.00 0.00 0.00 3.51
3940 3981 4.605183 TGTGAAGAAAGGGGAAAAAGTGA 58.395 39.130 0.00 0.00 0.00 3.41
3941 3982 5.068987 TGATGTGAAGAAAGGGGAAAAAGTG 59.931 40.000 0.00 0.00 0.00 3.16
3942 3983 5.069119 GTGATGTGAAGAAAGGGGAAAAAGT 59.931 40.000 0.00 0.00 0.00 2.66
3943 3984 5.068987 TGTGATGTGAAGAAAGGGGAAAAAG 59.931 40.000 0.00 0.00 0.00 2.27
3944 3985 4.959210 TGTGATGTGAAGAAAGGGGAAAAA 59.041 37.500 0.00 0.00 0.00 1.94
3945 3986 4.541705 TGTGATGTGAAGAAAGGGGAAAA 58.458 39.130 0.00 0.00 0.00 2.29
3946 3987 4.177537 TGTGATGTGAAGAAAGGGGAAA 57.822 40.909 0.00 0.00 0.00 3.13
3947 3988 3.874383 TGTGATGTGAAGAAAGGGGAA 57.126 42.857 0.00 0.00 0.00 3.97
3948 3989 3.754965 CTTGTGATGTGAAGAAAGGGGA 58.245 45.455 0.00 0.00 0.00 4.81
3949 3990 2.229784 GCTTGTGATGTGAAGAAAGGGG 59.770 50.000 0.00 0.00 0.00 4.79
3950 3991 2.095567 CGCTTGTGATGTGAAGAAAGGG 60.096 50.000 0.00 0.00 0.00 3.95
3951 3992 2.095567 CCGCTTGTGATGTGAAGAAAGG 60.096 50.000 0.00 0.00 0.00 3.11
3952 3993 2.666619 GCCGCTTGTGATGTGAAGAAAG 60.667 50.000 0.00 0.00 0.00 2.62
3953 3994 1.266718 GCCGCTTGTGATGTGAAGAAA 59.733 47.619 0.00 0.00 0.00 2.52
3954 3995 0.874390 GCCGCTTGTGATGTGAAGAA 59.126 50.000 0.00 0.00 0.00 2.52
3955 3996 1.291184 CGCCGCTTGTGATGTGAAGA 61.291 55.000 0.00 0.00 0.00 2.87
3956 3997 1.133253 CGCCGCTTGTGATGTGAAG 59.867 57.895 0.00 0.00 0.00 3.02
3957 3998 2.324330 CCGCCGCTTGTGATGTGAA 61.324 57.895 0.00 0.00 0.00 3.18
3958 3999 2.741985 CCGCCGCTTGTGATGTGA 60.742 61.111 0.00 0.00 0.00 3.58
3959 4000 2.741985 TCCGCCGCTTGTGATGTG 60.742 61.111 0.00 0.00 0.00 3.21
3960 4001 2.434884 CTCCGCCGCTTGTGATGT 60.435 61.111 0.00 0.00 0.00 3.06
3961 4002 2.125552 TCTCCGCCGCTTGTGATG 60.126 61.111 0.00 0.00 0.00 3.07
3962 4003 2.125512 GTCTCCGCCGCTTGTGAT 60.126 61.111 0.00 0.00 0.00 3.06
3963 4004 4.717629 CGTCTCCGCCGCTTGTGA 62.718 66.667 0.00 0.00 0.00 3.58
3964 4005 4.717629 TCGTCTCCGCCGCTTGTG 62.718 66.667 0.00 0.00 0.00 3.33
3965 4006 4.421479 CTCGTCTCCGCCGCTTGT 62.421 66.667 0.00 0.00 0.00 3.16
3975 4016 1.214062 CCACACAGGAGCTCGTCTC 59.786 63.158 5.82 0.00 41.22 3.36
3976 4017 1.531840 ACCACACAGGAGCTCGTCT 60.532 57.895 5.82 0.00 41.22 4.18
3977 4018 1.373497 CACCACACAGGAGCTCGTC 60.373 63.158 5.82 0.00 41.22 4.20
3978 4019 2.737180 CACCACACAGGAGCTCGT 59.263 61.111 7.83 5.12 41.22 4.18
3979 4020 2.047844 CCACCACACAGGAGCTCG 60.048 66.667 7.83 0.00 41.22 5.03
3980 4021 2.359230 GCCACCACACAGGAGCTC 60.359 66.667 4.71 4.71 41.22 4.09
3981 4022 2.851102 AGCCACCACACAGGAGCT 60.851 61.111 0.00 0.00 42.86 4.09
3982 4023 2.670934 CAGCCACCACACAGGAGC 60.671 66.667 0.00 0.00 41.22 4.70
3983 4024 2.670934 GCAGCCACCACACAGGAG 60.671 66.667 0.00 0.00 41.22 3.69
3984 4025 4.269523 GGCAGCCACCACACAGGA 62.270 66.667 6.55 0.00 41.22 3.86
3986 4027 4.275508 AGGGCAGCCACCACACAG 62.276 66.667 15.19 0.00 0.00 3.66
3987 4028 4.584518 CAGGGCAGCCACCACACA 62.585 66.667 15.19 0.00 0.00 3.72
3991 4032 4.980702 CTTGCAGGGCAGCCACCA 62.981 66.667 15.19 3.60 40.61 4.17
3992 4033 4.982701 ACTTGCAGGGCAGCCACC 62.983 66.667 15.19 0.56 40.61 4.61
3993 4034 3.677648 CACTTGCAGGGCAGCCAC 61.678 66.667 15.19 2.38 40.61 5.01
3994 4035 4.208403 ACACTTGCAGGGCAGCCA 62.208 61.111 15.19 0.00 40.61 4.75
3995 4036 3.368571 GACACTTGCAGGGCAGCC 61.369 66.667 1.26 1.26 40.61 4.85
3996 4037 2.595463 TGACACTTGCAGGGCAGC 60.595 61.111 0.00 0.00 40.61 5.25
3997 4038 2.263741 GGTGACACTTGCAGGGCAG 61.264 63.158 5.39 0.00 40.61 4.85
3998 4039 2.203337 GGTGACACTTGCAGGGCA 60.203 61.111 5.39 0.00 36.47 5.36
3999 4040 3.357079 CGGTGACACTTGCAGGGC 61.357 66.667 5.39 0.00 0.00 5.19
4000 4041 2.669569 CCGGTGACACTTGCAGGG 60.670 66.667 5.39 0.00 0.00 4.45
4001 4042 1.669115 CTCCGGTGACACTTGCAGG 60.669 63.158 0.00 0.00 0.00 4.85
4002 4043 0.946221 GTCTCCGGTGACACTTGCAG 60.946 60.000 27.42 2.50 36.97 4.41
4003 4044 1.069090 GTCTCCGGTGACACTTGCA 59.931 57.895 27.42 0.00 36.97 4.08
4004 4045 1.668151 GGTCTCCGGTGACACTTGC 60.668 63.158 31.48 14.67 38.61 4.01
4005 4046 1.372997 CGGTCTCCGGTGACACTTG 60.373 63.158 31.48 17.41 44.15 3.16
4006 4047 3.048602 CGGTCTCCGGTGACACTT 58.951 61.111 31.48 0.00 44.15 3.16
4057 4098 4.899239 GAGCTCATCCCCACGCCG 62.899 72.222 9.40 0.00 0.00 6.46
4058 4099 4.899239 CGAGCTCATCCCCACGCC 62.899 72.222 15.40 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.