Locus 6146

Sequence ID 3L_DroMel_CAF1
Location 16,262,776 – 16,262,983
Length 207
Max. P 0.858625
window9873 window9874 window9875

overview

Window 3

Location 16,262,776 – 16,262,888
Length 112
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 90.00
Mean single sequence MFE -37.00
Consensus MFE -28.14
Energy contribution -29.18
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -2.04
Structure conservation index 0.76
SVM decision value 0.82
SVM RNA-class probability 0.858625
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16262776 112 + 23771897
UUUGCAUAGCUGACUCCCUCCCAUCUGC--GGAUCGCUGGCUGUGACUCGAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGUUGGACGCCACUCGGUCAAGGCCGUGCUUA
...(((((((.((.((((........).--))))))))((((.((((.((((((((.(((((...((((.....)))).....))))).)).)))))))))).))))))))... ( -39.90)
>DroSec_CAF1 14192 109 + 1
UUUGCAUAGCUGACUCC---CCAUCUGC--GGAUCGCUGGCUGUGACUCGAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGUUGGACGCCACUCGGUCAAGGCCGUGCUUA
...(((((((.((.(((---.(....).--))))))))((((.((((.((((((((.(((((...((((.....)))).....))))).)).)))))))))).))))))))... ( -39.70)
>DroSim_CAF1 12696 109 + 1
UUUGCAUAGCUGACUCC---CCAUCUGC--GGAUCGCUGGCUGUGACUCGAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGUUGGACGCCACUCGGUCAAGGCCGUGCUUA
...(((((((.((.(((---.(....).--))))))))((((.((((.((((((((.(((((...((((.....)))).....))))).)).)))))))))).))))))))... ( -39.70)
>DroEre_CAF1 14168 108 + 1
UUUGCAUAGCUGACUC----CCAUCUGC--GGAUCGCUGGCUGUGACUCGAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGUUGGACGCCACUCGGUCAAGGCCGUGCUUA
...(((((((.((.((----((....).--))))))))((((.((((.((((((((.(((((...((((.....)))).....))))).)).)))))))))).))))))))... ( -39.70)
>DroAna_CAF1 13482 108 + 1
UUUGCAUAGCGUAUUUU------UUUGAGGUGACUACCAUCUGUGACUCUAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGGUGUCCGCCACUCGGUCAAGGUCGUGCUUA
...(((..((.......------....(((((.....))))).(((((...(.(((((.(((.....)))..(.(((((....))))).)))))).))))))..))..)))... ( -26.00)
>consensus
UUUGCAUAGCUGACUCC___CCAUCUGC__GGAUCGCUGGCUGUGACUCGAGUGUGGCCAAUUAAGUAUUAAGUAUACCACAUGUUGGACGCCACUCGGUCAAGGCCGUGCUUA
...((((...............(((......)))....((((.((((.((((((((.(((((...((((.....)))).....))))).)).)))))))))).))))))))... (-28.14 = -29.18 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,262,776 – 16,262,888
Length 112
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -34.36
Consensus MFE -27.20
Energy contribution -27.72
Covariance contribution 0.52
Combinations/Pair 1.10
Mean z-score -1.81
Structure conservation index 0.79
SVM decision value 0.80
SVM RNA-class probability 0.853128
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16262776 112 - 23771897
UAAGCACGGCCUUGACCGAGUGGCGUCCAACAUGUGGUAUACUUAAUACUUAAUUGGCCACACUCGAGUCACAGCCAGCGAUCC--GCAGAUGGGAGGGAGUCAGCUAUGCAAA
...(((.(((..((((((((((..(.((((.....(((((.....)))))...)))).).)))))).))))..)))(((..(((--.(........))))....))).)))... ( -36.10)
>DroSec_CAF1 14192 109 - 1
UAAGCACGGCCUUGACCGAGUGGCGUCCAACAUGUGGUAUACUUAAUACUUAAUUGGCCACACUCGAGUCACAGCCAGCGAUCC--GCAGAUGG---GGAGUCAGCUAUGCAAA
...(((.(((..((((((((((..(.((((.....(((((.....)))))...)))).).)))))).))))..)))(((..(((--.(....).---)))....))).)))... ( -38.60)
>DroSim_CAF1 12696 109 - 1
UAAGCACGGCCUUGACCGAGUGGCGUCCAACAUGUGGUAUACUUAAUACUUAAUUGGCCACACUCGAGUCACAGCCAGCGAUCC--GCAGAUGG---GGAGUCAGCUAUGCAAA
...(((.(((..((((((((((..(.((((.....(((((.....)))))...)))).).)))))).))))..)))(((..(((--.(....).---)))....))).)))... ( -38.60)
>DroEre_CAF1 14168 108 - 1
UAAGCACGGCCUUGACCGAGUGGCGUCCAACAUGUGGUAUACUUAAUACUUAAUUGGCCACACUCGAGUCACAGCCAGCGAUCC--GCAGAUGG----GAGUCAGCUAUGCAAA
...(((.(((..((((((((((..(.((((.....(((((.....)))))...)))).).)))))).))))..)))(((..(((--.......)----))....))).)))... ( -36.40)
>DroAna_CAF1 13482 108 - 1
UAAGCACGACCUUGACCGAGUGGCGGACACCAUGUGGUAUACUUAAUACUUAAUUGGCCACACUAGAGUCACAGAUGGUAGUCACCUCAAA------AAAAUACGCUAUGCAAA
...((.((........)).(((((((((.(..((((((....(((.....)))...))))))...).)))...((.(((....)))))...------......))))))))... ( -22.10)
>consensus
UAAGCACGGCCUUGACCGAGUGGCGUCCAACAUGUGGUAUACUUAAUACUUAAUUGGCCACACUCGAGUCACAGCCAGCGAUCC__GCAGAUGG___GGAGUCAGCUAUGCAAA
...(((.(((..((((((((((..(.((((.....(((((.....)))))...)))).).)))))).))))..)))(((..((...............))....))).)))... (-27.20 = -27.72 +   0.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,262,888 – 16,262,983
Length 95
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 81.93
Mean single sequence MFE -21.88
Consensus MFE -14.14
Energy contribution -14.46
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -1.89
Structure conservation index 0.65
SVM decision value 0.38
SVM RNA-class probability 0.712065
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16262888 95 + 23771897
CCCCAGCCUUUGUCACAAUGUCGUGCACA--UUACAAUGUGUACAGCAAAGC------CUG------ACUAUUACUCGUUUUAUAAUGAUUAAUACCAAGAGGAACAGC---
......(((((((((...(((.(((((((--(....)))))))).)))....------.))------))(((((.(((((....))))).)))))...)))))......--- ( -23.40)
>DroSec_CAF1 14301 95 + 1
CCCCAGCCUUUGUCACAAUGUCGUGCACA--UUACAAUGUGUACAGCAAAGC------UCG------ACUAUUACUCGUUUUAUAAUGAUUAAUACCAAGAGGAACAGC---
......((((((((....(((.(((((((--(....)))))))).)))....------..)------))(((((.(((((....))))).)))))...)))))......--- ( -21.80)
>DroSim_CAF1 12805 95 + 1
CCCCAGCCUUUGUCACAAUGUCGUGCACA--UUACAAUGUGUACAGCAGAGC------UCG------ACUAUUACUCGUUUUAUAAUGAUUAAUACCAAGAGGAACAGC---
......((((((((....(((.(((((((--(....)))))))).)))....------..)------))(((((.(((((....))))).)))))...)))))......--- ( -22.90)
>DroEre_CAF1 14276 95 + 1
CCCCAGCCUUUGUCACAAUGUCGUGCACA--UUACAAUGUGUACAGCAAAAC------CCG------GCCAUUAUUCGUUUUAUAAUGAUUAAUACCAAGAGGAAUAGC---
......(((((.......(((.(((((((--(....)))))))).)))....------..(------(..((((.(((((....))))).)))).)).)))))......--- ( -22.70)
>DroAna_CAF1 13590 112 + 1
CUUCAGCCUUUGUCACAAUGUCGUGCACAUAUUACACUCUGCCAUGUAAAAUGCGAGUCUGGCUACAAUUAUUAUUUGUUUUUAAAUGAUUAAUUAUAAGAGCAACAACUGC
....((((..((((((......))).)))......((((.((.((.....))))))))..))))...........((((((((((((.....))).)))))))))....... ( -18.60)
>consensus
CCCCAGCCUUUGUCACAAUGUCGUGCACA__UUACAAUGUGUACAGCAAAGC______CCG______ACUAUUACUCGUUUUAUAAUGAUUAAUACCAAGAGGAACAGC___
......(((((.......(((.(((((((........))))))).)))......................((((.(((((....))))).))))....)))))......... (-14.14 = -14.46 +   0.32)

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 12:11:17 2006