Locus 7662

Sequence ID 2L_DroMel_CAF1
Location 21,348,202 – 21,348,455
Length 253
Max. P 0.999772
window12308 window12309 window12310

overview

Window 8

Location 21,348,202 – 21,348,303
Length 101
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 79.30
Mean single sequence MFE -17.40
Consensus MFE -12.60
Energy contribution -12.72
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.65
Structure conservation index 0.72
SVM decision value 0.50
SVM RNA-class probability 0.759798
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21348202 101 + 22407834
UAUUUAAGUGAAUUACCCAUUAACGAAACUUCCUUAAGGCUAACGG-------CAAUUGGGCAAAAGCUGCCUUGCGGCACAAAAAAUAUCACUAUAUUUUGAAUUUG
......(((((....((((((((.((....)).))))(.(....).-------)...)))).....(((((...)))))..........))))).............. ( -18.60)
>DroSec_CAF1 58000 85 + 1
CAAUUAAGUGAAUUAC-CAUAAACGAAACUUCCUUAAGGCUAA--------------------AAAAAUGCCUUGAGGCACGAAAAAUAUCAAUAUAUUUUGAAUU--
.......(((......-(......)......(((((((((...--------------------......))))))))))))........((((......))))...-- ( -15.60)
>DroSim_CAF1 44475 105 + 1
CAAUUAAGUGAAUUAC-CAUAAACAAAACUUCCUUAAGGCUAACGGCUCUUAGCAAUUAGGCAAAAAAUGCCUUGAGGCACGAAAAAUAUCAAUAUAUUUUGAAUU--
.......(((......-)))...........(((((((((.....((.((........)))).......)))))))))...........((((......))))...-- ( -18.00)
>consensus
CAAUUAAGUGAAUUAC_CAUAAACGAAACUUCCUUAAGGCUAACGG_______CAAUU_GGCAAAAAAUGCCUUGAGGCACGAAAAAUAUCAAUAUAUUUUGAAUU__
...............................(((((((((.............................)))))))))..(((((.(((....))).)))))...... (-12.60 = -12.72 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,348,275 – 21,348,376
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 87.88
Mean single sequence MFE -21.33
Consensus MFE -18.06
Energy contribution -18.07
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.85
SVM decision value 0.39
SVM RNA-class probability 0.717487
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21348275 101 - 22407834
AGAAGCGAAAGUUUCCCAGAAGAGUAGGAGAUAAGGGCUCCCAAGCUUCAAACCUAAAACCGAAAUUCAAAUUCAAAUUCAAAAUAUAGUGAUAUUUUUUG
.(((((....)))))...((((..(.((((.......)))).)..))))..............................(((((.(((....))).))))) ( -19.70)
>DroSec_CAF1 58059 95 - 1
AGAAGCGAAAGCUUCCUAGAGGAGUAGGAGCUUAGGGCUCACAAGCGACAAACCUAAAACCGAAAUUUU------AAUUCAAAAUAUAUUGAUAUUUUUCG
.(((((....)))))...((((((((.((((.....)))).............................------...((((......)))))))))))). ( -21.80)
>DroSim_CAF1 44554 95 - 1
AGAAGCGAAAGUUUCCUAGAGGAGUAGGAGCUUAGGGCUCCCAAGCGACAAACCUAAAACCGAAAUUUU------AAUUCAAAAUAUAUUGAUAUUUUUCG
.(((((....)))))...(((((((((..((((.((....))))))..)....................------...((((......)))))))))))). ( -22.50)
>consensus
AGAAGCGAAAGUUUCCUAGAGGAGUAGGAGCUUAGGGCUCCCAAGCGACAAACCUAAAACCGAAAUUUU______AAUUCAAAAUAUAUUGAUAUUUUUCG
.(((((....)))))...((((((((((...((((((((....)))......)))))..)).................((((......)))))))))))). (-18.06 = -18.07 +   0.01)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,348,336 – 21,348,455
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.77
Mean single sequence MFE -35.67
Consensus MFE -19.04
Energy contribution -20.27
Covariance contribution 1.23
Combinations/Pair 1.13
Mean z-score -3.25
Structure conservation index 0.53
SVM decision value 4.05
SVM RNA-class probability 0.999772
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21348336 119 - 22407834
AAUAGAGGAUACGACGUUCAUCUUUUAUAGGUGAAGGUUGUGCUC-UUCAAAAAACUGGAAGCGCUUGGUCUAGUUCCCAAGAAGCGAAAGUUUCCCAGAAGAGUAGGAGAUAAGGGCUC
....(((((((((((.(((((((.....))))))).)))))).))-)))...........(((.((((.((((.((..(..(((((....)))))...)..)).))))...)))).))). ( -39.80)
>DroSec_CAF1 58114 93 - 1
---------------------A-UUUAUGUAUG-----UAUGCACGUGCAUAAACCCGGACCCAUUUGGUCUAGUUCCCAAGAAGCGAAAGCUUCCUAGAGGAGUAGGAGCUUAGGGCUC
---------------------.-((((((((((-----(....)))))))))))((((((((.....)))))((((((...(((((....)))))((.....))..))))))..)))... ( -34.80)
>DroSim_CAF1 44609 93 - 1
---------------------A-UUUAUGUAUG-----UAUGCACGUGCAUAAACCCGGACCCGUUUGGUCUAGUUCCCAAGAAGCGAAAGUUUCCUAGAGGAGUAGGAGCUUAGGGCUC
---------------------.-((((((((((-----(....)))))))))))((((((((.....)))))((((((...(((((....)))))((.....))..))))))..)))... ( -32.40)
>consensus
_____________________A_UUUAUGUAUG_____UAUGCACGUGCAUAAACCCGGACCCGUUUGGUCUAGUUCCCAAGAAGCGAAAGUUUCCUAGAGGAGUAGGAGCUUAGGGCUC
.......................((((((((((...........))))))))))((((((((.....)))))((((((...(((((....)))))(.....)....))))))..)))... (-19.04 = -20.27 +   1.23)

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 12:42:12 2006