Locus 7622

Sequence ID 3R_DroMel_CAF1
Location 20,426,429 – 20,426,565
Length 136
Max. P 0.999990
window12300 window12301 window12302 window12303

overview

Window 0

Location 20,426,429 – 20,426,525
Length 96
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 89.21
Mean single sequence MFE -27.32
Consensus MFE -25.40
Energy contribution -25.56
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.93
SVM decision value 3.87
SVM RNA-class probability 0.999674
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20426429 96 + 27905053
UACAUACAUAUAGAAGCCGAA-------AUCGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGC
....(((((.(((..((((..-------..))))(((((........((((((((((........)))))).)))))))))..))).)))))........... ( -27.00)
>DroSec_CAF1 9437 93 + 1
---AUACAUAUAGAAGCCAAA-------AUCGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGC
---.(((((.(((..(((...-------...)))(((((........((((((((((........)))))).)))))))))..))).)))))........... ( -24.20)
>DroSim_CAF1 9024 93 + 1
---AUACAUAUAGAAGCCGAA-------AUCGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGC
---.(((((.(((..((((..-------..))))(((((........((((((((((........)))))).)))))))))..))).)))))........... ( -27.00)
>DroEre_CAF1 8930 87 + 1
---------UUGGAAGCCGAA-------AUCGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGCACUGGUUAAGUGUAGAAACCAUUGC
---------......((((..-------..))))(((..........((((((((((........)))))).))))(((((.....)))))....)))..... ( -30.20)
>DroYak_CAF1 9458 94 + 1
---------AUAGAAGCCGAAAGCCAAAAACGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGCACUGGUUAAGUGUAGAAACCAUUGC
---------......((((...........))))(((..........((((((((((........)))))).))))(((((.....)))))....)))..... ( -28.20)
>consensus
___AUACAUAUAGAAGCCGAA_______AUCGGCGGUGCAAGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGC
...............(((((.........)))))(((..........((((((((((........)))))).))))(((((.....)))))....)))..... (-25.40 = -25.56 +   0.16)

alignment

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secondary structure

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Window 1

Location 20,426,429 – 20,426,525
Length 96
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 89.21
Mean single sequence MFE -25.16
Consensus MFE -25.14
Energy contribution -24.94
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -2.00
Structure conservation index 1.00
SVM decision value 3.18
SVM RNA-class probability 0.998678
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20426429 96 - 27905053
GCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGAU-------UUCGGCUUCUAUAUGUAUGUA
(((((((((.........)))))....((((.(((((..........)))))))))......))))...((((..-------..))))............... ( -25.30)
>DroSec_CAF1 9437 93 - 1
GCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGAU-------UUUGGCUUCUAUAUGUAU---
(((((((((.........)))))....((((.(((((..........)))))))))......))))...((((..-------..))))............--- ( -22.50)
>DroSim_CAF1 9024 93 - 1
GCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGAU-------UUCGGCUUCUAUAUGUAU---
(((((((((.........)))))....((((.(((((..........)))))))))......))))...((((..-------..))))............--- ( -25.30)
>DroEre_CAF1 8930 87 - 1
GCAAUGGUUUCUACACUUAACCAGUGCGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGAU-------UUCGGCUUCCAA---------
(((.(((((.........))))).)))((((.(((((..........))))))))).............((((..-------..))))......--------- ( -26.90)
>DroYak_CAF1 9458 94 - 1
GCAAUGGUUUCUACACUUAACCAGUGCGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGUUUUUGGCUUUCGGCUUCUAU---------
(((.(((((.........))))).)))((((.(((((..........)))))))))........((...((((....)))).....))......--------- ( -25.80)
>consensus
GCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCUUGCACCGCCGAU_______UUCGGCUUCUAUAUGUAU___
(((((((((.........)))))....((((.(((((..........)))))))))......))))...(((((.........)))))............... (-25.14 = -24.94 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,426,462 – 20,426,565
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 93.91
Mean single sequence MFE -29.41
Consensus MFE -28.55
Energy contribution -28.15
Covariance contribution -0.40
Combinations/Pair 1.09
Mean z-score -2.95
Structure conservation index 0.97
SVM decision value 5.56
SVM RNA-class probability 0.999990
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20426462 103 + 27905053
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGCUUUUCGGCCAUUUCUAUACAGCUAUUAAAUUGGUCAAUUA
.(((...((((((((((........)))))).))))....(((((..(((((((((...(((.....)))...))))))))))))))........)))..... ( -26.80)
>DroSec_CAF1 9467 101 + 1
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGCUUUUCGGCCAUUUCU--ACUGCUAUUAACUUGGCCAAUUA
.......((((((((((........)))))).))))....((((((((((((((((...(((.....)))...)))))--))........))))))))).... ( -29.40)
>DroSim_CAF1 9054 101 + 1
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGCUUUUCGGCCAUUUCU--ACUGCUAUUAACUUGGCCAAUUA
.......((((((((((........)))))).))))....((((((((((((((((...(((.....)))...)))))--))........))))))))).... ( -29.40)
>DroEre_CAF1 8954 101 + 1
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGCACUGGUUAAGUGUAGAAACCAUUGCUUUUCGGCCAUUUCU--ACAGCUAUUUAAUUGGCCAAUUU
.......((((((((((........)))))).))))(((.(((((.........))))).))).....(((((.....--.............)))))..... ( -30.07)
>DroYak_CAF1 9489 101 + 1
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGCACUGGUUAAGUGUAGAAACCAUUGCUUUUUGGCCAUUUCU--ACGACCAUUUAAUUGGCCAAUUU
.......((((((((((........)))))).))))(((.(((((.........))))).)))...(((((((.....--.............)))))))... ( -31.37)
>consensus
AGAUAAAGCGGGCUAAUUACAUAACGUUAGCACCGCGUACUGGUUAAGUGUAGAAACCACUGCUUUUCGGCCAUUUCU__ACAGCUAUUAAAUUGGCCAAUUA
.......((((((((((........)))))).))))(((.(((((.........))))).))).....(((((....................)))))..... (-28.55 = -28.15 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,426,462 – 20,426,565
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 93.91
Mean single sequence MFE -26.66
Consensus MFE -21.97
Energy contribution -22.01
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.82
SVM decision value 1.21
SVM RNA-class probability 0.931451
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20426462 103 - 27905053
UAAUUGACCAAUUUAAUAGCUGUAUAGAAAUGGCCGAAAAGCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
.....................((.(((((((.((.(.....).)).))))))).))...........((((.(((((..........)))))))))....... ( -20.30)
>DroSec_CAF1 9467 101 - 1
UAAUUGGCCAAGUUAAUAGCAGU--AGAAAUGGCCGAAAAGCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
..(((((..((((........((--((((((.((.(.....).)).))))))))))))..)))))..((((.(((((..........)))))))))....... ( -26.80)
>DroSim_CAF1 9054 101 - 1
UAAUUGGCCAAGUUAAUAGCAGU--AGAAAUGGCCGAAAAGCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
..(((((..((((........((--((((((.((.(.....).)).))))))))))))..)))))..((((.(((((..........)))))))))....... ( -26.80)
>DroEre_CAF1 8954 101 - 1
AAAUUGGCCAAUUAAAUAGCUGU--AGAAAUGGCCGAAAAGCAAUGGUUUCUACACUUAACCAGUGCGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
...(((((((.((..((....))--..)).)))))))...(((.(((((.........))))).)))((((.(((((..........)))))))))....... ( -29.20)
>DroYak_CAF1 9489 101 - 1
AAAUUGGCCAAUUAAAUGGUCGU--AGAAAUGGCCAAAAAGCAAUGGUUUCUACACUUAACCAGUGCGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
...(((((((.((..((....))--..)).)))))))...(((.(((((.........))))).)))((((.(((((..........)))))))))....... ( -30.20)
>consensus
UAAUUGGCCAAUUUAAUAGCAGU__AGAAAUGGCCGAAAAGCAGUGGUUUCUACACUUAACCAGUACGCGGUGCUAACGUUAUGUAAUUAGCCCGCUUUAUCU
...(((((((....................))))))).......(((((.........)))))....((((.(((((..........)))))))))....... (-21.97 = -22.01 +   0.04)

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 12:50:28 2006