Locus 4892

Sequence ID 3L_DroMel_CAF1
Location 13,630,388 – 13,630,552
Length 164
Max. P 0.909583
window7721 window7722 window7723

overview

Window 1

Location 13,630,388 – 13,630,492
Length 104
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 75.99
Mean single sequence MFE -24.93
Consensus MFE -16.15
Energy contribution -18.14
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.65
SVM decision value 0.48
SVM RNA-class probability 0.751001
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13630388 104 - 23771897
AAAAAGGCAACCACCGCAUGGCUACAACUACUGCUGC------UGAUUCUGCUGCCAACUAUGAGCCAGGGGAAGUCCCCAGUCUAC-CCAGUUGCCCUUUCCUUUCCUGC
.....((((((.......(((((.((......((.((------.......)).))......)))))))((((....)))).......-...)))))).............. ( -28.90)
>DroSec_CAF1 37862 92 - 1
AAAAAGGCAACCACCGCAUGGCUACAACUACUGC------------------UGCCAACUAUGAGCCAGGGGAAGUCCCCAGUCUCC-UCAGUUGCCCUGUCCCUUCCUUC
.....((((((.......((((..((.....)).------------------.)))).....(((.(.((((....)))).).))).-...)))))).............. ( -25.60)
>DroSim_CAF1 47678 92 - 1
AAAAAGGCAACCACCGCAUGGCUACAACUACUGC------------------UGCCAACUAUGAGCCAGGGGAAGUCCCCAGUCUCC-UCAGUUGCCCUGUCCCUUCCUUC
.....((((((.......((((..((.....)).------------------.)))).....(((.(.((((....)))).).))).-...)))))).............. ( -25.60)
>DroEre_CAF1 40176 93 - 1
AAAAAGGCAACCACCGCACGACUACAACUACUGCUGCUGCUUUUGCUUCUGCUGCCAACUAUGAGCCAGGGGAAGUCCCCAGUCUCCCCCCCA------------------
.....((((......(((.............))).((.((....))....))))))......(((.(.((((....)))).).))).......------------------ ( -19.62)
>consensus
AAAAAGGCAACCACCGCAUGGCUACAACUACUGC__________________UGCCAACUAUGAGCCAGGGGAAGUCCCCAGUCUCC_CCAGUUGCCCUGUCCCUUCCUUC
.....((((((........((((.((......((.((.............)).))......)))))).((((....))))...........)))))).............. (-16.15 = -18.14 +   2.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,630,455 – 13,630,552
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.31
Mean single sequence MFE -25.32
Consensus MFE -16.84
Energy contribution -16.73
Covariance contribution -0.11
Combinations/Pair 1.19
Mean z-score -1.65
Structure conservation index 0.67
SVM decision value 1.07
SVM RNA-class probability 0.909583
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13630455 97 + 23771897
---GCAGCAGUAGUUGUAGCCAUGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCA------CAGAGCAAAAAAAAAAAG-------------GA-GG
---...((((..(((....(((((((((((..((......))..)))).)))))))..)))..))))......((((.------....))))..........-------------..-.. ( -26.60)
>DroPse_CAF1 21528 80 + 1
----------------UAGUCG--UGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCA------CACAGCACACAAA--AAG-------------AU-AG
----------------..((.(--((.((..(((...(((((((((((....)))).........)))))))...)))------..)).)))))...--...-------------..-.. ( -20.70)
>DroSec_CAF1 37920 93 + 1
------GCAGUAGUUGUAGCCAUGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCA------CAGAGCAAAAA-AAAAAG-------------AA-GG
------((((..(((....(((((((((((..((......))..)))).)))))))..)))..))))......((((.------....))))...-......-------------..-.. ( -26.40)
>DroSim_CAF1 47736 94 + 1
------GCAGUAGUUGUAGCCAUGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCA------CAGAGCAAAAAAAAAAAG-------------AA-GG
------((((..(((....(((((((((((..((......))..)))).)))))))..)))..))))......((((.------....))))..........-------------..-.. ( -26.40)
>DroEre_CAF1 40229 120 + 1
GCAGCAGCAGUAGUUGUAGUCGUGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCACAGGCACAGAGCAAAAAAGAAAAAAAAAAAAAGAAUAAACGG
((.(((((....))))).((((((((((....)))..(((((((((((....)))).........)))))))...)))).))).....)).............................. ( -27.30)
>DroAna_CAF1 74056 76 + 1
-----------------AGCCGAGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUGGCACAAACUUGCA------CGG--CAAAAA-GAUAAA------------------
-----------------.((((.(((((...((((((((..(((......)))..)))).....))))...)).))).------)))--).....-......------------------ ( -24.50)
>consensus
______GCAGUAGUUGUAGCCAUGCGGUGGUUGCCUUUUUGUGCCCAUGCGCAUGGAAAAUAGUUGCACAAACUUGCA______CAGAGCAAAAAAAAAAAG_____________AA_GG
...................(((((((((((..((......))..)))).))))))).........(((......)))........................................... (-16.84 = -16.73 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,630,455 – 13,630,552
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.31
Mean single sequence MFE -20.62
Consensus MFE -14.23
Energy contribution -14.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.69
SVM decision value 0.15
SVM RNA-class probability 0.608427
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13630455 97 - 23771897
CC-UC-------------CUUUUUUUUUUUGCUCUG------UGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCAUGGCUACAACUACUGCUGC---
..-.(-------------((((((.....(((((((------((((((((.....))))........)))))).))))).)))))))........((((((......))).)))...--- ( -20.10)
>DroPse_CAF1 21528 80 - 1
CU-AU-------------CUU--UUUGUGUGCUGUG------UGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCA--CGACUA----------------
..-.(-------------(((--(((((((.(((((------((((((((.....))))........)))))))))))))))))))).........--......---------------- ( -22.80)
>DroSec_CAF1 37920 93 - 1
CC-UU-------------CUUUUU-UUUUUGCUCUG------UGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCAUGGCUACAACUACUGC------
..-..-------------......-...(((((.((------(((.....((((((...........))))))...)))))....))))).....((((((......))).)))------ ( -18.70)
>DroSim_CAF1 47736 94 - 1
CC-UU-------------CUUUUUUUUUUUGCUCUG------UGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCAUGGCUACAACUACUGC------
..-..-------------..........(((((.((------(((.....((((((...........))))))...)))))....))))).....((((((......))).)))------ ( -18.70)
>DroEre_CAF1 40229 120 - 1
CCGUUUAUUCUUUUUUUUUUUUUCUUUUUUGCUCUGUGCCUGUGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCACGACUACAACUACUGCUGCUGC
.(((...................((((((((((((((((.((((((......)))).........)).))))).))))).))))))((.......))))).................... ( -21.20)
>DroAna_CAF1 74056 76 - 1
------------------UUUAUC-UUUUUG--CCG------UGCAAGUUUGUGCCACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCUCGGCU-----------------
------------------......-.....(--(((------.((...((((((((.(................)))))))))..((......)))).)))).----------------- ( -22.19)
>consensus
CC_UU_____________CUUUUUUUUUUUGCUCUG______UGCAAGUUUGUGCAACUAUUUUCCAUGCGCAUGGGCACAAAAAGGCAACCACCGCACGGCUACAACUACUGC______
..........................................(((...(((((((.........((((....)))))))))))...)))............................... (-14.23 = -14.23 +  -0.00)

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 11:36:17 2006