Locus 8676

Sequence ID 3R_DroMel_CAF1
Location 23,180,992 – 23,181,113
Length 121
Max. P 0.584062
window13934 window13935 window13936

overview

Window 4

Location 23,180,992 – 23,181,087
Length 95
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 85.44
Mean single sequence MFE -26.45
Consensus MFE -19.31
Energy contribution -19.12
Covariance contribution -0.19
Combinations/Pair 1.23
Mean z-score -2.16
Structure conservation index 0.73
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23180992 95 + 27905053
CUGCAGUGAACGCAGCCAA-GCGCCAUUGUUGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAGAAGC
((((((..(.(((......-)))......)..))))))........((((((((..(((......)))..)))))))).................. ( -28.20)
>DroVir_CAF1 31917 88 + 1
CUGCAAUGCAUGCAAC-------CCAUUGGUGUUGCAGCUACCAGCGUGGCACUAAUUAGAAGUAUAAAAGGUGCUACAACAACAUUUAAAG-AGC
(((....((.((((((-------((...)).))))))))...))).((((((((..(((......)))..))))))))..............-... ( -24.30)
>DroPse_CAF1 19078 90 + 1
CGGCAAUGUAUGCAGCC-----GCCAUUGUUGCUGCAGCCGGCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AAC
((((......((((((.-----((....)).)))))))))).....((((((((..(((......)))..))))))))..............-... ( -29.70)
>DroMoj_CAF1 39497 88 + 1
CUGCAAUGCAUGCAAG-------CCAUUGUUGUUGCAGCUACCAAUGUGGCACUAAUUAGAAGUAUAAAAGGUGCUACAACAACAGUUUAAG-AGC
(((((((....((((.-------...)))).))))))).......(((((((((..(((......)))..))))))))).............-... ( -22.30)
>DroAna_CAF1 26049 95 + 1
AUGCAAUGCAUGCUGCCGCCCCGCCAUUGUUGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AAC
.......((..(((((.((..((....))..)).))))).))....((((((((..(((......)))..))))))))..............-... ( -24.80)
>DroPer_CAF1 21778 90 + 1
CGGCAAUGUGUGCAGCC-----ACCAUUGUUGCUGCAGCCGGCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AAC
((((......((((((.-----((....)).)))))))))).....((((((((..(((......)))..))))))))..............-... ( -29.40)
>consensus
CUGCAAUGCAUGCAGCC_____GCCAUUGUUGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG_AAC
..((..((((.(((((............))))))))))).......((((((((..(((......)))..)))))))).................. (-19.31 = -19.12 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 23,180,992 – 23,181,087
Length 95
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 85.44
Mean single sequence MFE -27.72
Consensus MFE -21.29
Energy contribution -20.98
Covariance contribution -0.30
Combinations/Pair 1.19
Mean z-score -2.03
Structure conservation index 0.77
SVM decision value 0.09
SVM RNA-class probability 0.579203
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23180992 95 - 27905053
GCUUCUCUAACUGUUGUUGUGGCACCUUUUAUACUUCUAAUUAGUGCCACGUUGGCGGCUGCAGCAACAAUGGCGC-UUGGCUGCGUUCACUGCAG
..........(((((..((((((((...(((......)))...))))))))..)))))((((((......((((((-......))).))))))))) ( -29.10)
>DroVir_CAF1 31917 88 - 1
GCU-CUUUAAAUGUUGUUGUAGCACCUUUUAUACUUCUAAUUAGUGCCACGCUGGUAGCUGCAACACCAAUGG-------GUUGCAUGCAUUGCAG
(((-(......((.((((((((((((.....((((.......)))).......))).))))))))).))..))-------))((((.....)))). ( -22.60)
>DroPse_CAF1 19078 90 - 1
GUU-CUCUAACUGUUGUUGUGGCACCUUUUAUACUUCUAAUUAGUGCCACGUUGCCGGCUGCAGCAACAAUGGC-----GGCUGCAUACAUUGCCG
...-......(((((((((((((((...(((......)))...)))))))(((((.....)))))))))))))(-----(((..........)))) ( -28.80)
>DroMoj_CAF1 39497 88 - 1
GCU-CUUAAACUGUUGUUGUAGCACCUUUUAUACUUCUAAUUAGUGCCACAUUGGUAGCUGCAACAACAAUGG-------CUUGCAUGCAUUGCAG
...-.......(((((((((((((((.....((((.......)))).......))).))))))))))))....-------..((((.....)))). ( -25.80)
>DroAna_CAF1 26049 95 - 1
GUU-CUCUAACUGUUGUUGUGGCACCUUUUAUACUUCUAAUUAGUGCCACGUUGGCGGCUGCAGCAACAAUGGCGGGGCGGCAGCAUGCAUUGCAU
((.-.(((..((((((((((.(((((......(((.......)))(((.....))))).))).))))))))))..)))..)).(((.....))).. ( -30.30)
>DroPer_CAF1 21778 90 - 1
GUU-CUCUAACUGUUGUUGUGGCACCUUUUAUACUUCUAAUUAGUGCCACGUUGCCGGCUGCAGCAACAAUGGU-----GGCUGCACACAUUGCCG
...-.....((((((((((((((((...(((......)))...)))))))(((((.....))))))))))))))-----(((..........))). ( -29.70)
>consensus
GCU_CUCUAACUGUUGUUGUGGCACCUUUUAUACUUCUAAUUAGUGCCACGUUGGCGGCUGCAGCAACAAUGGC_____GGCUGCAUGCAUUGCAG
...........((((((((((((.........(((.......)))(((.....))).))))))))))))..............(((.....))).. (-21.29 = -20.98 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 6

Location 23,181,021 – 23,181,113
Length 92
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 83.42
Mean single sequence MFE -25.75
Consensus MFE -18.03
Energy contribution -17.78
Covariance contribution -0.25
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.70
SVM decision value 0.10
SVM RNA-class probability 0.584062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23181021 92 + 27905053
UGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAGAAGCA----GCAUCAUCCUUCUUC-------CCCCUGAGUG---
((((((..........((((((((..(((......)))..))))))))(((....)))......)))----)))............-------..........--- ( -24.50)
>DroPse_CAF1 19103 92 + 1
UGCUGCAGCCGGCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AACAGAGAGCAUCAUUCU---CC-------CAUCUGCUCU---
....((((..((....((((((((..(((......)))..))))))))...........(((-((..((.....)).))))---))-------)..))))...--- ( -25.00)
>DroEre_CAF1 27872 91 + 1
UGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AGCA----GCAUCAUCCUUGUUC-------CCCCUCAGUU---
((((((..........((((((((..(((......)))..))))))))(((....)))....-.)))----)))............-------..........--- ( -24.50)
>DroYak_CAF1 14564 98 + 1
UGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AGCAGC-AGCAUCAUCCUUGUUC-UUC--CCCCCUUACUU---
((((((.(((......((((((((..(((......)))..))))))))(((....)))...)-.)).))-))))............-...--...........--- ( -26.30)
>DroAna_CAF1 26079 101 + 1
UGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AACA----GCAUCAUCCUUCGUUCGUUCGCCCGCUUAGCCUGU
.((((.(((.((.(((((((((((..(((......)))..)))))))).............(-(((.----............))))))).))..))))))).... ( -27.22)
>DroPer_CAF1 21803 92 + 1
UGCUGCAGCCGGCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG-AACAGAGAGCAUCAUUCU---CU-------CAUCUGCUCU---
(((((....)))))..((((((((..(((......)))..))))))))..........((((-....(((((.......))---))-------).....))))--- ( -27.00)
>consensus
UGCUGCAGCCGCCAACGUGGCACUAAUUAGAAGUAUAAAAGGUGCCACAACAACAGUUAGAG_AACA____GCAUCAUCCUU_UUC_______CCCCUGAGCU___
((.(((..........((((((((..(((......)))..)))))))).......(((.....))).....))).))............................. (-18.03 = -17.78 +  -0.25)

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 13:17:01 2006