Locus 7791

Sequence ID 3R_DroMel_CAF1
Location 20,872,418 – 20,872,615
Length 197
Max. P 0.997885
window12561 window12562 window12563

overview

Window 1

Location 20,872,418 – 20,872,535
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.00
Mean single sequence MFE -29.22
Consensus MFE -20.42
Energy contribution -21.07
Covariance contribution 0.64
Combinations/Pair 1.20
Mean z-score -1.36
Structure conservation index 0.70
SVM decision value 0.55
SVM RNA-class probability 0.779152
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20872418 117 + 27905053
---UUGAAUGCUAAACUUAUAAGAUUCUUUCGCAUUUAUUAGGCAACGAUAGUGGGGGCUACAGCUACAGCUCCCCGCCGAGCAACAGCUACUUGCCUCCAGCCACACCUGCUCCGGAGU
---.(((((((.(((............))).)))))))...(((.((....))((((((...((((...((((......))))...))))....)))))).)))...((......))... ( -31.30)
>DroSec_CAF1 1622 117 + 1
---UUAAAAGCUUAACUCAUAAGAUUUUUUUGCAUUUAUCAGGCAAUGAUAGUGGGGGCUACAGCUAUAGCUCCCCGCCGAGCAACAGCUACUUGCCUCCAGCCACUCCUGCUCCGGAGU
---..(((((((((.....)))).)))))..((..((((((.....))))))(((((((...((((...((((......))))...))))....))))))))).(((((......))))) ( -33.20)
>DroSim_CAF1 324 117 + 1
---UUAAAAGCUUAACUCAUAAGAUUAUUUUGAAUUUAUCAGGCAACGAUAGUGGGGGCUACAGCUACAGCUCCCCGCCGAGCAACAGCUACUUGCCUCCAGCCACUCCUGCUCCGGAGU
---((((((.((((.....))))....))))))........(((.((....))((((((...((((...((((......))))...))))....)))))).)))(((((......))))) ( -34.40)
>DroEre_CAF1 310 120 + 1
AAGUUGAAAUCUAGACUUACUUGAUUCUUUUGCAUUUAUUAGGCAACGACAGUGGGGGCUACAGCUACAGCUCCCCACCGAGCAACAGCUACCUACCUCCAGCCACUCCUGCACCGGAGU
.(((((.((((.((.....)).))))...((((........(....)..(.(((((((((........))).)))))).).)))))))))..............(((((......))))) ( -31.60)
>DroYak_CAF1 336 120 + 1
AAGUUGAAAGCUAGACUUACUUGAUUCUUUUGCAUUUACUAGGCAACGACAGUGGGGGCUACAGCUACAGCUCCCCACCCAGCAACAGUUACCUACCUCCAGCCACUCCUGCUCCGGAGU
.........(((.((..((..(((((...((((........(....)....(((((((((........))).))))))...)))).)))))..))..)).))).(((((......))))) ( -30.50)
>DroAna_CAF1 1838 95 + 1
------------------------UCCUUUUU-CUAAAUCAGGCAAUGAUAGCGGAGGAUAUAGCUAUAAUCCCCCACCAAAUAACAACUACCUGCCACCUGCAACACCUGCCCCGGAUU
------------------------........-...((((.((((.((.....((.((((.........)))).)).................(((.....))).))..))))...)))) ( -14.30)
>consensus
___UUGAAAGCUAAACUUAUAAGAUUCUUUUGCAUUUAUCAGGCAACGAUAGUGGGGGCUACAGCUACAGCUCCCCACCGAGCAACAGCUACCUGCCUCCAGCCACUCCUGCUCCGGAGU
.........................................(((.......(((((((((........))).))))))..(((....)))...........)))(((((......))))) (-20.42 = -21.07 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,872,418 – 20,872,535
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.00
Mean single sequence MFE -37.08
Consensus MFE -24.99
Energy contribution -24.68
Covariance contribution -0.30
Combinations/Pair 1.35
Mean z-score -1.48
Structure conservation index 0.67
SVM decision value 0.61
SVM RNA-class probability 0.798081
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20872418 117 - 27905053
ACUCCGGAGCAGGUGUGGCUGGAGGCAAGUAGCUGUUGCUCGGCGGGGAGCUGUAGCUGUAGCCCCCACUAUCGUUGCCUAAUAAAUGCGAAAGAAUCUUAUAAGUUUAGCAUUCAA---
.((((((.((....))..))))))((.....))((.((((..((((((.((((......)))))))).((.((((............)))).))..........))..))))..)).--- ( -34.60)
>DroSec_CAF1 1622 117 - 1
ACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCUCGGCGGGGAGCUAUAGCUGUAGCCCCCACUAUCAUUGCCUGAUAAAUGCAAAAAAAUCUUAUGAGUUAAGCUUUUAA---
(((((......)))))((((..((((((...((((.....))))((((.(((((....))))))))).......))))))................((....))....)))).....--- ( -37.30)
>DroSim_CAF1 324 117 - 1
ACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCUCGGCGGGGAGCUGUAGCUGUAGCCCCCACUAUCGUUGCCUGAUAAAUUCAAAAUAAUCUUAUGAGUUAAGCUUUUAA---
(((((......)))))((((..((((((...((((.....))))((((.((((......)))))))).......))))))....((((((.((.....)).)))))).)))).....--- ( -38.00)
>DroEre_CAF1 310 120 - 1
ACUCCGGUGCAGGAGUGGCUGGAGGUAGGUAGCUGUUGCUCGGUGGGGAGCUGUAGCUGUAGCCCCCACUGUCGUUGCCUAAUAAAUGCAAAAGAAUCAAGUAAGUCUAGAUUUCAACUU
.(((((((.((....))))))))).((((((((.(.....((((((((.((((......)))))))))))).)))))))))............(((((.((.....)).)))))...... ( -41.00)
>DroYak_CAF1 336 120 - 1
ACUCCGGAGCAGGAGUGGCUGGAGGUAGGUAACUGUUGCUGGGUGGGGAGCUGUAGCUGUAGCCCCCACUGUCGUUGCCUAGUAAAUGCAAAAGAAUCAAGUAAGUCUAGCUUUCAACUU
(((((......)))))((((((((.((((((((....((..(((((((.((((......))))))))))))).)))))))).)...(((...........)))..)))))))........ ( -41.50)
>DroAna_CAF1 1838 95 - 1
AAUCCGGGGCAGGUGUUGCAGGUGGCAGGUAGUUGUUAUUUGGUGGGGGAUUAUAGCUAUAUCCUCCGCUAUCAUUGCCUGAUUUAG-AAAAAGGA------------------------
..((..((.(((((..((((((((((((....))))))))))(((((((((.........)))))))))...))..))))).))..)-).......------------------------ ( -30.10)
>consensus
ACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCUCGGCGGGGAGCUGUAGCUGUAGCCCCCACUAUCGUUGCCUAAUAAAUGCAAAAGAAUCUUAUAAGUUUAGCUUUCAA___
(((((......)))))......((((((...((((.....))))((((.((((......)))))))).......))))))........................................ (-24.99 = -24.68 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,872,495 – 20,872,615
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.42
Mean single sequence MFE -42.96
Consensus MFE -40.08
Energy contribution -39.32
Covariance contribution -0.76
Combinations/Pair 1.14
Mean z-score -2.02
Structure conservation index 0.93
SVM decision value 2.95
SVM RNA-class probability 0.997885
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20872495 120 - 27905053
AUAGUUGUUGUUAGGCGGUGGCAGGUAGUUGUUGUUCGGCGGCGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGAGCAGGUGUGGCUGGAGGCAAGUAGCUGUUGCU
................((..((((.((.(((((.((((((.((((((.........)))).((((((..(((((.......)))))))))))..)).))))))))))).)).))))..)) ( -44.20)
>DroSec_CAF1 1699 120 - 1
AUAGUUGUUGUUAGGCGGUGGCAGGUAGUUGUUGUUCGGUGGCGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCU
................((..((((.((.(((((.((((((.((((((.........)))).((((((..(((((.......)))))))))))..)).))))))))))).)).))))..)) ( -42.90)
>DroSim_CAF1 401 120 - 1
AUAGUUGUUGUUAGGCGGUGGCAGGUAGUUGUUGUUCGGCGGCGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCU
................((..((((.((.(((((.((((((.((((((.........)))).((((((..(((((.......)))))))))))..)).))))))))))).)).))))..)) ( -44.40)
>DroEre_CAF1 390 120 - 1
AUAGUUGUUGUUCGGCGGUGGCAGGUAGUUGUUGUUCGGCGGUGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGUGCAGGAGUGGCUGGAGGUAGGUAGCUGUUGCU
...((((.....))))((..((((.((.((((((((..(((((((((.........)))))))))..)))))...(((.((((((......)))))).)))....))).)).))))..)) ( -42.70)
>DroYak_CAF1 416 120 - 1
AUAGUUGUUGUUGGGCGGUGGCAGGUAGUUGUUGUUUGGCGGCGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGAGCAGGAGUGGCUGGAGGUAGGUAACUGUUGCU
(((((((((((..(((((..((.....))..)))))..)))))........(..((.(((..(((((..(((((.......)))))))))))))...))..)........)))))).... ( -40.60)
>consensus
AUAGUUGUUGUUAGGCGGUGGCAGGUAGUUGUUGUUCGGCGGCGGAUUGUACUGGUAUCCAUUGUUCGGCGGAGGCAGGUACUCCGGAGCAGGAGUGGCUGGAGGCAAGUAGCUGUUGCU
................((..((((.((.(((((.((((((.((((((.........)))).((((((..(((((.......)))))))))))..)).))))))))))).)).))))..)) (-40.08 = -39.32 +  -0.76)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:45 2006