Locus 1572

Sequence ID 3R_DroMel_CAF1
Location 4,503,560 – 4,503,720
Length 160
Max. P 0.999946
window2595 window2596 window2597

overview

Window 5

Location 4,503,560 – 4,503,680
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -46.32
Consensus MFE -42.28
Energy contribution -41.64
Covariance contribution -0.64
Combinations/Pair 1.11
Mean z-score -1.71
Structure conservation index 0.91
SVM decision value 2.09
SVM RNA-class probability 0.987638
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503560 120 + 27905053
CUUCCACAAGGGCUGCUAUGUGGGCCAGGAGCUAACUGCCCGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCAAUUGAUGUGGGUUCCAGCCA
..((((((.(((((.....((((((.((.......))))))))(((.(((....(((((((((((....).))).)))))))....))).))))))))(....).))))))......... ( -48.80)
>DroSec_CAF1 3542 120 + 1
CUUCCACAAGGGCUGCUAUGUGGGCCAGGAGCUAACAGCCCGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCA
..........(((((..((..(((((.((.((.....))))..(((.(((....(((((((((((....).))).)))))))....))).))))))))((((....))))))..))))). ( -48.20)
>DroSim_CAF1 3539 120 + 1
CUUCCACAAGGGCUGCUAUGUGGGCCAGGAGCUAACAGCCCGCGUCCAUCAUUCGGGCGUGAUACGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCA
..........(((((..((..(((((.((.((.....))))..(((.(((....(((((((((.((....)))).)))))))....))).))))))))((((....))))))..))))). ( -44.50)
>DroEre_CAF1 3539 120 + 1
CUUCCAAAAGGGCUGCUAUGUGGGCCAGGAGUUGACUGCCCGCGUUCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCUCCUAUUGAUUUGGGUUCCAGCCA
..........((((.....((((((.((.......))))))))(((.(((....(((((((((((....).))).)))))))....))).)))((..((((......))))..)))))). ( -46.10)
>DroYak_CAF1 3552 120 + 1
CUUCCAAAAGGGCUGCUAUGUCGGCCAGGAGUUGACCGCCCGCGUCCAUCAUUCGGGCGUGAUCCGAAAGAGAUACAUGCCCAUCCGGUUGACAGCUCCUAUUGAUUUGGGUUCCAACCA
..((((((..(((((......)))))((((((((.(.(((...(.....)....(((((((((((....).))).)))))))....))).).)))))))).....))))))......... ( -44.00)
>consensus
CUUCCACAAGGGCUGCUAUGUGGGCCAGGAGCUAACAGCCCGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCA
..((((((.(((((.....((((((............))))))(((.(((....(((((((((((....).))).)))))))....))).))))))))(....).))))))......... (-42.28 = -41.64 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,503,600 – 4,503,720
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.17
Mean single sequence MFE -55.14
Consensus MFE -50.44
Energy contribution -51.28
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -3.97
Structure conservation index 0.91
SVM decision value 4.75
SVM RNA-class probability 0.999946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503600 120 + 27905053
CGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCAAUUGAUGUGGGUUCCAGCCAGGACGUAACUUCUUUGGCUGGAGCGAAACUUGGACGCGUC
((((((((...((((((((((((((....).))).)))))))..(((.....)))..(((.......)))(((((((((((((.......)).))))))))))))))...)))))))).. ( -57.60)
>DroSec_CAF1 3582 120 + 1
CGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCAGGACGUAACUUCUUUGGCUGGAGCGAAACUUGGACGCGUC
((((((((...((((((((((((((....).))).)))))))..(((.....)))...((((....))))(((((((((((((.......)).))))))))))))))...)))))))).. ( -57.50)
>DroSim_CAF1 3579 120 + 1
CGCGUCCAUCAUUCGGGCGUGAUACGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCAGGACGUAACUUCUUUGGCUGGAGCGAAACUUGGACGCGUC
((((((((...((((((((((((.((....)))).)))))))..(((.....)))...((((....))))(((((((((((((.......)).))))))))))))))...)))))))).. ( -53.80)
>DroEre_CAF1 3579 120 + 1
CGCGUUCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCUCCUAUUGAUUUGGGUUCCAGCCAGGAUGUAACUUCUGUGGCUGGAGCGAAACUUGGACGCGUC
((((((((...((((((((((((((....).))).)))))))..(((.....)))...............(((((((((((((.......))).)))))))))))))...)))))))).. ( -54.60)
>DroYak_CAF1 3592 120 + 1
CGCGUCCAUCAUUCGGGCGUGAUCCGAAAGAGAUACAUGCCCAUCCGGUUGACAGCUCCUAUUGAUUUGGGUUCCAACCAGGACGUAACUUCUGUUGCUGGAGCGAAACUAGGACGCGUC
(((((((.......(((((((((((....).))).)))))))....((((....(((((......(((((.......)))))..(((((....))))).)))))..)))).))))))).. ( -52.20)
>consensus
CGCGUCCAUCAUUCGGGCGUGAUCCGCAAGCGAUACAUGCCCAUCCGGUUGACGGCCCCUAUUGAUGUGGGUUCCAGCCAGGACGUAACUUCUUUGGCUGGAGCGAAACUUGGACGCGUC
((((((((...((((((((((((((....).))).)))))))..(((.....)))...............(((((((((((((.......))).)))))))))))))...)))))))).. (-50.44 = -51.28 +   0.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,503,600 – 4,503,720
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.17
Mean single sequence MFE -43.10
Consensus MFE -37.76
Energy contribution -38.64
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.35
SVM RNA-class probability 0.700021
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503600 120 - 27905053
GACGCGUCCAAGUUUCGCUCCAGCCAAAGAAGUUACGUCCUGGCUGGAACCCACAUCAAUUGGGGCCGUCAACCGGAUGGGCAUGUAUCGCUUGCGGAUCACGCCCGAAUGAUGGACGCG
..((((((((...(((..((((((((..((.......)).)))))))).((((.......)))).(((.....)))..((((.((..(((....)))..)).)))))))...)))))))) ( -47.20)
>DroSec_CAF1 3582 120 - 1
GACGCGUCCAAGUUUCGCUCCAGCCAAAGAAGUUACGUCCUGGCUGGAACCCACAUCAAUAGGGGCCGUCAACCGGAUGGGCAUGUAUCGCUUGCGGAUCACGCCCGAAUGAUGGACGCG
..((((((((...(((..((((((((..((.......)).)))))))).(((.........))).(((.....)))..((((.((..(((....)))..)).)))))))...)))))))) ( -45.90)
>DroSim_CAF1 3579 120 - 1
GACGCGUCCAAGUUUCGCUCCAGCCAAAGAAGUUACGUCCUGGCUGGAACCCACAUCAAUAGGGGCCGUCAACCGGAUGGGCAUGUAUCGCUUGCGUAUCACGCCCGAAUGAUGGACGCG
..((((((((...(((..((((((((..((.......)).)))))))).(((.........))).(((.....)))..((((.((...((....))...)).)))))))...)))))))) ( -45.90)
>DroEre_CAF1 3579 120 - 1
GACGCGUCCAAGUUUCGCUCCAGCCACAGAAGUUACAUCCUGGCUGGAACCCAAAUCAAUAGGAGCCGUCAACCGGAUGGGCAUGUAUCGCUUGCGGAUCACGCCCGAAUGAUGAACGCG
..(((((.((...(((..((((((((..((.......)).)))))))).................(((.....)))..((((.((..(((....)))..)).)))))))...)).))))) ( -36.10)
>DroYak_CAF1 3592 120 - 1
GACGCGUCCUAGUUUCGCUCCAGCAACAGAAGUUACGUCCUGGUUGGAACCCAAAUCAAUAGGAGCUGUCAACCGGAUGGGCAUGUAUCUCUUUCGGAUCACGCCCGAAUGAUGGACGCG
..(((((((....(((((....))............((((.((((((..(((.........)).)...))))))))))((((.((.((((.....)))))).)))))))....))))))) ( -40.40)
>consensus
GACGCGUCCAAGUUUCGCUCCAGCCAAAGAAGUUACGUCCUGGCUGGAACCCACAUCAAUAGGGGCCGUCAACCGGAUGGGCAUGUAUCGCUUGCGGAUCACGCCCGAAUGAUGGACGCG
..((((((((...(((..((((((((..((.......)).)))))))).(((.........))).(((.....)))..((((.((...((....))...)).)))))))...)))))))) (-37.76 = -38.64 +   0.88)

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 10:13:52 2006