Locus 1839

Sequence ID 2L_DroMel_CAF1
Location 5,080,167 – 5,080,309
Length 142
Max. P 0.994335
window2954 window2955 window2956

overview

Window 4

Location 5,080,167 – 5,080,271
Length 104
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 84.44
Mean single sequence MFE -22.47
Consensus MFE -16.99
Energy contribution -17.30
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.76
SVM decision value 0.85
SVM RNA-class probability 0.865998
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5080167 104 + 22407834
CCACCGCGGAAUCUCCAGAGCUUUGCACACGAAAUGCCAAAGGCAAGUAUGAGCAAGAAAAAAAAAAAAAAAAAUGGGAGAGAAAAC-----UGUUU-UUUCUCCAAAUG
.....((((.....))...((((((((.......)))..)))))........))......................(((((((((..-----...))-)))))))..... ( -20.10)
>DroSec_CAF1 9597 96 + 1
CCACCGCGGAAUCUCCAGCGCUUUGCACACGAAAUGCCAAAGGCAAGUAUGAGU---------AAAAAAAAAAAUGGGAGAGAAAAC-----UGUUUUUUUCUCCAAAUG
....(((((.....)).))).(((((.((.(...((((...))))..).)).))---------)))..........((((((((((.-----...))))))))))..... ( -22.20)
>DroSim_CAF1 11749 100 + 1
CCACCGCGGAAUCUCCAGCGCUUUGCACACUAAAUGCCAAAGGCAAGUAUGAGUCA-----AAAAAAAAAAAAAUUGGAGAGAAAAC-----UGUUUUUUUCUCCAAAUG
....(((((.....)).))).((((.((.(((..((((...))))..)).).))))-----))...........((((((((((((.-----...))))))))))))... ( -23.80)
>DroYak_CAF1 10912 99 + 1
-CACCGCGGAAUCUCCAGCGCUUUGCACACGAAAUGCCAACGGCAACUAUAAGCCA-----CAA-----AAAAAGGGGAGAAAAACCGUUUUUGUUUUUUUCUCCAAAUG
-...(((((.....)).)))....(((.......)))....(((........))).-----...-----.....((((((((((((.......))))))))))))..... ( -23.80)
>consensus
CCACCGCGGAAUCUCCAGCGCUUUGCACACGAAAUGCCAAAGGCAAGUAUGAGCCA_____AAAAAAAAAAAAAUGGGAGAGAAAAC_____UGUUUUUUUCUCCAAAUG
.....((((.....))...((((((((.......)))..)))))........))......................((((((((((.........))))))))))..... (-16.99 = -17.30 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,080,197 – 5,080,309
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 85.55
Mean single sequence MFE -26.93
Consensus MFE -20.86
Energy contribution -21.55
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -3.38
Structure conservation index 0.77
SVM decision value 2.47
SVM RNA-class probability 0.994335
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5080197 112 + 22407834
GAAAUGCCAAAGGCAAGUAUGAGCAAGAAAAAAAAAAAAAAAAAUGGGAGAGAAAAC-----UGUUU-UUUCUCCAAAUGCCGUUUUUGGCCAAAAUUCCAUUGACAAAGGUCAUAGU
...(((((...((((.((....))......................(((((((((..-----...))-)))))))...))))(((..(((........)))..)))...)).)))... ( -25.20)
>DroSec_CAF1 9627 104 + 1
GAAAUGCCAAAGGCAAGUAUGAGU---------AAAAAAAAAAAUGGGAGAGAAAAC-----UGUUUUUUUCUCCAAAUGCCGUUUUUGGCCAAAAUUCCAUUGACAAAGGUCAUAGU
.....(((((((((..((((....---------.............((((((((((.-----...))))))))))..)))).)))))))))...........((((....)))).... ( -24.81)
>DroSim_CAF1 11779 108 + 1
UAAAUGCCAAAGGCAAGUAUGAGUCA-----AAAAAAAAAAAAAUUGGAGAGAAAAC-----UGUUUUUUUCUCCAAAUGCCGUUUUUGGCCAAAAUUCCAUUGACAAAGGUCAUAUU
....((((...))))(((((((((((-----(............((((((((((((.-----...))))))))))))..((((....))))..........))))).....))))))) ( -28.90)
>DroYak_CAF1 10941 107 + 1
GAAAUGCCAACGGCAACUAUAAGCCA-----CAA-----AAAAAGGGGAGAAAAACCGUUUUUGUUUUUUUCUCCAAAUGCCGUU-UUGGCCAAAAUUCCAUUGACAAAGGUCAUAGU
.....((((((((((.(.....)...-----...-----.....((((((((((((.......))))))))))))...)))))).-.))))...........((((....)))).... ( -28.80)
>consensus
GAAAUGCCAAAGGCAAGUAUGAGCCA_____AAAAAAAAAAAAAUGGGAGAGAAAAC_____UGUUUUUUUCUCCAAAUGCCGUUUUUGGCCAAAAUUCCAUUGACAAAGGUCAUAGU
....((((...))))(((((((.(......................((((((((((.........))))))))))....((((....))))..................).))))))) (-20.86 = -21.55 +   0.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,080,197 – 5,080,309
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 85.55
Mean single sequence MFE -23.91
Consensus MFE -19.12
Energy contribution -19.38
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.80
SVM decision value 1.42
SVM RNA-class probability 0.952123
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5080197 112 - 22407834
ACUAUGACCUUUGUCAAUGGAAUUUUGGCCAAAAACGGCAUUUGGAGAAA-AAACA-----GUUUUCUCUCCCAUUUUUUUUUUUUUUUUUCUUGCUCAUACUUGCCUUUGGCAUUUC
.(((((((....))).)))).......((((((...((((...(((((((-(....-----.))))))))........................(......).))))))))))..... ( -20.10)
>DroSec_CAF1 9627 104 - 1
ACUAUGACCUUUGUCAAUGGAAUUUUGGCCAAAAACGGCAUUUGGAGAAAAAAACA-----GUUUUCUCUCCCAUUUUUUUUUUU---------ACUCAUACUUGCCUUUGGCAUUUC
.(((((((....))).)))).......((((((...((((....((((((((((.(-----(.............)).)))))))---------.))).....))))))))))..... ( -21.22)
>DroSim_CAF1 11779 108 - 1
AAUAUGACCUUUGUCAAUGGAAUUUUGGCCAAAAACGGCAUUUGGAGAAAAAAACA-----GUUUUCUCUCCAAUUUUUUUUUUUUU-----UGACUCAUACUUGCCUUUGGCAUUUA
..(((((.....(((((..(((.....(((......)))..(((((((.((((...-----.)))).))))))).......)))..)-----)))))))))..((((...)))).... ( -24.60)
>DroYak_CAF1 10941 107 - 1
ACUAUGACCUUUGUCAAUGGAAUUUUGGCCAA-AACGGCAUUUGGAGAAAAAAACAAAAACGGUUUUUCUCCCCUUUUU-----UUG-----UGGCUUAUAGUUGCCGUUGGCAUUUC
...........(((((((((((((..(((((.-..........(((((((((...........))))))))).......-----...-----)))))...)))).))))))))).... ( -29.70)
>consensus
ACUAUGACCUUUGUCAAUGGAAUUUUGGCCAAAAACGGCAUUUGGAGAAAAAAACA_____GUUUUCUCUCCCAUUUUUUUUUUUUU_____UGACUCAUACUUGCCUUUGGCAUUUC
...........((((((.((.......(((......)))....(((((...((((......))))..))))).................................)).)))))).... (-19.12 = -19.38 +   0.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:32 2006