Locus 4433

Sequence ID 3R_DroMel_CAF1
Location 11,703,927 – 11,704,115
Length 188
Max. P 0.999919
window7243 window7244 window7245 window7246

overview

Window 3

Location 11,703,927 – 11,704,047
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.98
Mean single sequence MFE -35.50
Consensus MFE -11.34
Energy contribution -13.88
Covariance contribution 2.54
Combinations/Pair 1.04
Mean z-score -2.32
Structure conservation index 0.32
SVM decision value 2.08
SVM RNA-class probability 0.987409
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11703927 120 + 27905053
AAUCAUAGGGUACGUGUCUUAACGCCUGUUGUUAUAAUGCUCAUGGCCGAUGUGCCACCCAUUUUUGAUUCAAAAGACCCAUGGGCGUUAUUUCACUUUUGAAAGUGUCACAACACCCUG
.....((((((..((((....))))..(((((.(((((((((((((.(((.(((.....)))..)))..((....)).)))))))))))))..(((((....)))))..))))))))))) ( -32.60)
>DroSec_CAF1 41241 119 + 1
AAUUGUAGGGUAAGUG-CUUGGUGACUGGAGUUAAAUUGCUCCUGGACGAUGCGCCACCCAUUUUUGAUUCAAAAGGCCCAUGGGCGUUAUGUCACUUUUGAAAGUGUCACAACACCCUG
.......((((..(((-(.(.((..(.(((((......))))).).)).).))))......((((((...))))))))))..(((.(((.((.(((((....))))).)).))).))).. ( -35.80)
>DroSim_CAF1 42837 119 + 1
AAUUGUAGGGUAAGUG-CCUGGUGACUGGAGUUAAAUUGCUCCUGGGCGAUGUGCCACCCAUUUUUGAUUCAAAAGGCCCAUGGGCGUUAUGUCACUUUUGAAAGUGUCACAACACCCUG
.....((((((....(-((((....).(((((......))))).))))(.((((.(((.((....)).(((((((((((....)))(......).)))))))).))).)))).))))))) ( -40.10)
>DroEre_CAF1 40980 115 + 1
AAUAGCAGGGUAAACGUCUUAACGACAAGUUUUAUAACGCGCACGGGCGUUAUGCCACACAUUUUUGUGUCAUAAGGCCCACUGGCG--CUGUCACUUUUGAAAGUGUCAUAAGUGC---
....((.........(((.....)))..(((....)))))((((((((.(((((.((((......)))).))))).))))..(((((--((.(((....))).)))))))...))))--- ( -39.50)
>DroYak_CAF1 41023 103 + 1
AACAGUAGGUU-ACCAACUUAACGUCAAGUUGCAUGACGCU----------------CACAUUUUUGUGGCAUAAGGCCCACUGGCAAAAUGUCACUUUUGAAAGUGUCAUAACACCCAG
.......(((.-..((((((......)))))).((((((((----------------..((.....(((((((...(((....)))...)))))))...))..))))))))...)))... ( -29.50)
>consensus
AAUAGUAGGGUAAGUG_CUUAACGACUGGUGUUAUAAUGCUCAUGGGCGAUGUGCCACCCAUUUUUGAUUCAAAAGGCCCAUGGGCGUUAUGUCACUUUUGAAAGUGUCACAACACCCUG
.......((((.................................((........)).....((((((...))))))))))..(((.(((.((.(((((....))))).)).))).))).. (-11.34 = -13.88 +   2.54)

alignment

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secondary structure

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Window 4

Location 11,703,927 – 11,704,047
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.98
Mean single sequence MFE -36.20
Consensus MFE -16.30
Energy contribution -19.84
Covariance contribution 3.54
Combinations/Pair 1.19
Mean z-score -2.85
Structure conservation index 0.45
SVM decision value 3.59
SVM RNA-class probability 0.999418
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11703927 120 - 27905053
CAGGGUGUUGUGACACUUUCAAAAGUGAAAUAACGCCCAUGGGUCUUUUGAAUCAAAAAUGGGUGGCACAUCGGCCAUGAGCAUUAUAACAACAGGCGUUAAGACACGUACCCUAUGAUU
..(((((((((..(((((....)))))..)))))))))..((((((.(((..(((....)))(((((......)))))...........))).))((((......))))))))....... ( -33.90)
>DroSec_CAF1 41241 119 - 1
CAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCGCAUCGUCCAGGAGCAAUUUAACUCCAGUCACCAAG-CACUUACCCUACAAUU
..((((((((((.(((((....))))).))))))))))..(((..(((((...)))))...(((((((.......).((((........)))).))))))...-......)))....... ( -37.40)
>DroSim_CAF1 42837 119 - 1
CAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCACAUCGCCCAGGAGCAAUUUAACUCCAGUCACCAGG-CACUUACCCUACAAUU
..((((((((((.(((((....))))).))))))))))....((((..(((........(((((((....)))))))((((........))))..)))..)))-)............... ( -44.00)
>DroEre_CAF1 40980 115 - 1
---GCACUUAUGACACUUUCAAAAGUGACAG--CGCCAGUGGGCCUUAUGACACAAAAAUGUGUGGCAUAACGCCCGUGCGCGUUAUAAAACUUGUCGUUAAGACGUUUACCCUGCUAUU
---(((.(((((((((((....))))....(--(((...(((((.(((((.((((......)))).))))).))))).))))))))))).....(((.....)))........))).... ( -35.40)
>DroYak_CAF1 41023 103 - 1
CUGGGUGUUAUGACACUUUCAAAAGUGACAUUUUGCCAGUGGGCCUUAUGCCACAAAAAUGUG----------------AGCGUCAUGCAACUUGACGUUAAGUUGGU-AACCUACUGUU
...((((..(((.(((((....))))).)))..))))((((((....((((((((....))))----------------.))))....(((((((....)))))))..-..))))))... ( -30.30)
>consensus
CAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCACAUCGCCCAGGAGCAUUAUAACACCAGUCGUUAAG_CACUUACCCUACAAUU
..((((((((((.(((((....))))).))))))))))(((((..(((((...))))).((((((......))))))..................................))))).... (-16.30 = -19.84 +   3.54)

alignment

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secondary structure

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Window 5

Location 11,703,967 – 11,704,080
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 79.20
Mean single sequence MFE -33.00
Consensus MFE -22.80
Energy contribution -24.17
Covariance contribution 1.38
Combinations/Pair 1.27
Mean z-score -2.64
Structure conservation index 0.69
SVM decision value 2.55
SVM RNA-class probability 0.995184
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11703967 113 - 27905053
ACUUAACUUGAAGAGCAAUCGAUAAUUAGUCAGCAGGGUGUUGUGACACUUUCAAAAGUGAAAUAACGCCCAUGGGUCUUUUGAAUCAAAAAUGGGUGGCACAUCGGCCAUGA
.........(((((.(....(((.....)))....(((((((((..(((((....)))))..)))))))))...).)))))..............(((((......))))).. ( -30.90)
>DroSec_CAF1 41280 113 - 1
ACUUAAUUCAAAGAGCAAUCGAUAAUUAGCCUGCAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCGCAUCGUCCAGGA
.....(((((((((....))........((((...((((((((((.(((((....))))).))))))))))..))))..)))))))......(((..((....))..)))... ( -35.90)
>DroSim_CAF1 42876 113 - 1
AAUUAAUUUAAAGAGCAAUCGAUAAUUAGCCUGCAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCACAUCGCCCAGGA
.....(((((((((....))........((((...((((((((((.(((((....))))).))))))))))..))))..)))))))......(((((((....)))))))... ( -38.50)
>DroYak_CAF1 41062 97 - 1
ACUUACCUCAAGGCGCAGGCCAAAAUUAGCCUUCUGGGUGUUAUGACACUUUCAAAAGUGACAUUUUGCCAGUGGGCCUUAUGCCACAAAAAUGUG----------------A
.........(((((.(((((........))).....((((..(((.(((((....))))).)))..))))..)).)))))....((((....))))----------------. ( -26.70)
>consensus
ACUUAACUCAAAGAGCAAUCGAUAAUUAGCCUGCAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAUGGGCCUUUUGAAUCAAAAAUGGGUGGCACAUCG_CCAGGA
.......(((((((....))........((((...((((((((((.(((((....))))).))))))))))..))))..)))))........(((((((....)))))))... (-22.80 = -24.17 +   1.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,704,007 – 11,704,115
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 72.38
Mean single sequence MFE -23.57
Consensus MFE -16.95
Energy contribution -17.40
Covariance contribution 0.45
Combinations/Pair 1.18
Mean z-score -2.42
Structure conservation index 0.72
SVM decision value 4.55
SVM RNA-class probability 0.999919
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11704007 108 - 27905053
UCAUAAAUUACUGCUACAUUUUUGAUUUUAUAUUUACUUAACUUGAAGAGCAAUCGAUAAUUAGUCAGCAGGGUGUUGUGACACUUUCAAAAGUGAAAUAACGCCCAU
..........((((((.(((.((((((.....((((.......))))....)))))).)))))).)))..(((((((((..(((((....)))))..))))))))).. ( -25.90)
>DroSec_CAF1 41320 92 - 1
----------------AAUUUUUGUUUUUAUAUUUACUUAAUUCAAAGAGCAAUCGAUAAUUAGCCUGCAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAU
----------------..((((((...(((........)))..))))))(((..(........)..))).((((((((((.(((((....))))).)))))))))).. ( -25.90)
>DroYak_CAF1 41086 99 - 1
UCA---------CCUACAUGUUUGUUUUAACAUUAACUUACCUCAAGGCGCAGGCCAAAAUUAGCCUUCUGGGUGUUAUGACACUUUCAAAAGUGACAUUUUGCCAGU
...---------(((....((..(((........)))..))....))).(.((((........)))).)..((((..(((.(((((....))))).)))..))))... ( -18.90)
>consensus
UCA__________CUACAUUUUUGUUUUUAUAUUUACUUAACUCAAAGAGCAAUCGAUAAUUAGCCUGCAGGGUGUUGUGACACUUUCAAAAGUGACAUAACGCCCAU
...............................................((....))...............((((((((((.(((((....))))).)))))))))).. (-16.95 = -17.40 +   0.45)

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 11:29:08 2006