Locus 8022

Sequence ID 3R_DroMel_CAF1
Location 21,546,570 – 21,546,700
Length 130
Max. P 0.845767
window12911 window12912 window12913

overview

Window 1

Location 21,546,570 – 21,546,676
Length 106
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 86.56
Mean single sequence MFE -19.28
Consensus MFE -13.22
Energy contribution -13.86
Covariance contribution 0.64
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.69
SVM decision value 0.01
SVM RNA-class probability 0.538412
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21546570 106 - 27905053
UUAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUCCAAGUAUUCAAUAAGACUUGUG-GUACGAAAUCUUCAUCCCCAUCACCAACACAAAUAUGUAAAUAUUCUA
....((((((..(((((((((((((((((.......))))).))))))))).)))(((-((..((........))...))))).................)))))). ( -20.90)
>DroSec_CAF1 44197 107 - 1
UCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAGGACUUGUGGGUACGAAAUCUUCAUUAUCAUCACCAACACAAAUAUGUAAAUAUUCAA
.....(((((..((((((((((((((((((.....)))))).))))))))).)))((((((..((...........))...)))..)))...........))))).. ( -21.90)
>DroSim_CAF1 38496 107 - 1
UCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAGGACUUGUGGGUACGAAAUCUUCAUCAUCAUCACCAACACAAAUAUGUAAAUAUUCAA
.....(((((..((((((((((((((((((.....)))))).))))))))).)))((((....((........))....)))).................))))).. ( -21.90)
>DroEre_CAF1 34295 101 - 1
UCAAAGAAUGAAAAGCUUACUGCAACUUGAUUGCUUUAAGUAUUCAAUAAGUCAUGUGGGCACAAAGUGUUUA------UCACCAACACAAAUAUGUAAAUAUUGUA
..............(((((((((...((((.(((.....))).))))...).)).)))))).....(((((..------.....))))).(((((....)))))... ( -16.40)
>DroYak_CAF1 37495 101 - 1
UCAAAGAAUGAAGAGCUUAUUGCAACUUGAUUGCUUUAAGUAUUCAAUAAGUCUUGCAGGUACGAAGUCUUUA------UCACCAACACAAAUUUGUAAAUAUAUUA
.((((...((((((.(((((((..((((((.....))))))...))))))))))).))(((..((........------)))))........))))........... ( -15.30)
>consensus
UCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAAGACUUGUGGGUACGAAAUCUUCAU___CAUCACCAACACAAAUAUGUAAAUAUUCUA
.....(((((..((((((((((((((((((.....)))))).))))))))).)))..............................(((......)))...))))).. (-13.22 = -13.86 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,546,605 – 21,546,700
Length 95
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 89.67
Mean single sequence MFE -21.16
Consensus MFE -15.22
Energy contribution -16.42
Covariance contribution 1.20
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21546605 95 + 27905053
GAAGAUUUCGUAC-CACAAGUCUUAUUGAAUACUUGGAGCAAUCAAGUUUCAAUAAGCUUUUCAUUCUUUAAGUGAUUACAUCCAUUUGGUUUGAG--
.......(((.((-((.(((.(((((((((.((((((.....)))))))))))))))))).(((((.....)))))...........)))).))).-- ( -21.50)
>DroSec_CAF1 44232 96 + 1
GAAGAUUUCGUACCCACAAGUCCUAUUGAAUACUUGAAGCAAUCAAGUUUCAAUAAGCUUUUCAUUCUUUGAGUGAUUACAUCCAUUUGGUUUGAG--
.......(((.(((...((((..(((((((.((((((.....))))))))))))).)))).((((((...))))))............))).))).-- ( -20.20)
>DroSim_CAF1 38531 96 + 1
GAAGAUUUCGUACCCACAAGUCCUAUUGAAUACUUGAAGCAAUCAAGUUUCAAUAAGCUUUUCAUUCUUUGAGUGAUUACAUCCAUUUGGUUUGAG--
.......(((.(((...((((..(((((((.((((((.....))))))))))))).)))).((((((...))))))............))).))).-- ( -20.20)
>DroEre_CAF1 34324 96 + 1
AAACACUUUGUGCCCACAUGACUUAUUGAAUACUUAAAGCAAUCAAGUUGCAGUAAGCUUUUCAUUCUUUGAGUGAUUACAUCCAUUGGGCUUGAG--
.....(((...(((((.(((.(((((((...((((.........))))..)))))))....((((((...)))))).......))))))))..)))-- ( -22.20)
>DroYak_CAF1 37524 98 + 1
AAAGACUUCGUACCUGCAAGACUUAUUGAAUACUUAAAGCAAUCAAGUUGCAAUAAGCUCUUCAUUCUUUGAGUGAUUACAUGCAUUUGGUUUGAGUU
...(((((...(((((((((((((((((...((((.........))))..))))))).)))((((((...)))))).....))))...)))..))))) ( -21.70)
>consensus
GAAGAUUUCGUACCCACAAGUCUUAUUGAAUACUUGAAGCAAUCAAGUUUCAAUAAGCUUUUCAUUCUUUGAGUGAUUACAUCCAUUUGGUUUGAG__
.......(((.(((...(((.(((((((((.((((((.....)))))))))))))))))).((((((...))))))............))).)))... (-15.22 = -16.42 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,546,605 – 21,546,700
Length 95
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 89.67
Mean single sequence MFE -20.88
Consensus MFE -16.10
Energy contribution -16.94
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -1.92
Structure conservation index 0.77
SVM decision value 0.77
SVM RNA-class probability 0.845767
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21546605 95 - 27905053
--CUCAAACCAAAUGGAUGUAAUCACUUAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUCCAAGUAUUCAAUAAGACUUGUG-GUACGAAAUCUUC
--......((....)).((((.(((((((.....))).(((((((((((((((((.......))))).))))))))).))))))-)))))........ ( -18.80)
>DroSec_CAF1 44232 96 - 1
--CUCAAACCAAAUGGAUGUAAUCACUCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAGGACUUGUGGGUACGAAAUCUUC
--......((....)).((((..((((((.....))).((((((((((((((((((.....)))))).))))))))).))))))..))))........ ( -24.00)
>DroSim_CAF1 38531 96 - 1
--CUCAAACCAAAUGGAUGUAAUCACUCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAGGACUUGUGGGUACGAAAUCUUC
--......((....)).((((..((((((.....))).((((((((((((((((((.....)))))).))))))))).))))))..))))........ ( -24.00)
>DroEre_CAF1 34324 96 - 1
--CUCAAGCCCAAUGGAUGUAAUCACUCAAAGAAUGAAAAGCUUACUGCAACUUGAUUGCUUUAAGUAUUCAAUAAGUCAUGUGGGCACAAAGUGUUU
--.....(((((...(((....((.......)).((((..(((((..((((.....))))..))))).))))....)))...)))))........... ( -20.70)
>DroYak_CAF1 37524 98 - 1
AACUCAAACCAAAUGCAUGUAAUCACUCAAAGAAUGAAGAGCUUAUUGCAACUUGAUUGCUUUAAGUAUUCAAUAAGUCUUGCAGGUACGAAGUCUUU
.......(((...((((.....(((.((...)).)))(((.(((((((..((((((.....))))))...)))))))))))))))))........... ( -16.90)
>consensus
__CUCAAACCAAAUGGAUGUAAUCACUCAAAGAAUGAAAAGCUUAUUGAAACUUGAUUGCUUCAAGUAUUCAAUAAGACUUGUGGGUACGAAAUCUUC
.................((((.(((((((.....))).((((((((((((((((((.....)))))).))))))))).))))))).))))........ (-16.10 = -16.94 +   0.84)

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 13:00:36 2006