Locus 2616

Sequence ID 2R_DroMel_CAF1
Location 9,224,333 – 9,224,488
Length 155
Max. P 0.998682
window4314 window4315 window4316 window4317 window4318 window4319

overview

Window 4

Location 9,224,333 – 9,224,438
Length 105
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 91.51
Mean single sequence MFE -35.10
Consensus MFE -28.02
Energy contribution -28.27
Covariance contribution 0.25
Combinations/Pair 1.03
Mean z-score -1.75
Structure conservation index 0.80
SVM decision value 0.35
SVM RNA-class probability 0.699606
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224333 105 + 20766785
GGAGCUGUUUGUUGUUGAUGCUGCCGCUGGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUGCUAUUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCAUC
...((.(..(((....(((((((..((.(((((....((.((..(((((((((....))))))))).)).)).))))).))..)).)))))..)))..).))... ( -34.20)
>DroSec_CAF1 117733 100 + 1
GGAGCUGUUUGUUGUUGAUGCUGCCGCUGGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUGCUAUUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCU-----
(((((.(..((((((((..((((((((.(..(.......)..).))))))))((..((((.......))))...))....))))).)))..).)).))).----- ( -33.20)
>DroEre_CAF1 103181 98 + 1
GGAGCUGUUUGUUGUUGAUGC-GCCGCUAGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG------CCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCACC
((.((.(..(((....(((((-.......(((((((...(((..(((((((((....)))))------)))).)))...))))))))))))..)))..).)).)) ( -37.51)
>DroYak_CAF1 100748 99 + 1
GGAGCUGUUUGUUGUUGAUGCUGCCGCUAGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG------CCACUGCACUUGCAACAUGCAUUCUGCAUCCUGCACU
............(((.(((((....((..(((((((...(((..(((((((((....)))))------)))).)))...))))))))).....)))))..))).. ( -35.50)
>consensus
GGAGCUGUUUGUUGUUGAUGCUGCCGCUAGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG______CCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCACC
((((((((.((((((...(((.((.((((((...((((((......))))))..)))))).))..........)))...)))))).)))....)).)))...... (-28.02 = -28.27 +   0.25)

alignment

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secondary structure

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Window 5

Location 9,224,333 – 9,224,438
Length 105
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 91.51
Mean single sequence MFE -29.97
Consensus MFE -22.70
Energy contribution -22.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.76
SVM decision value 0.45
SVM RNA-class probability 0.739949
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224333 105 - 20766785
GAUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAAUAGCAGCCAGUCAACUGCCACAGACAACAGCAACACCAGCGGCAGCAUCAACAACAAACAGCUCC
(((((....(((.((.(((.(((((...((((((((((.......))).....)))).)))...))))))))...)).)))...)))))................ ( -29.20)
>DroSec_CAF1 117733 100 - 1
-----AGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAAUAGCAGCCAGUCAACUGCCACAGACAACAGCAACACCAGCGGCAGCAUCAACAACAAACAGCUCC
-----..(((((....(((.((((((...(((.((((((...((.....))....)))))).).))...))))))...)))...)))))................ ( -26.90)
>DroEre_CAF1 103181 98 - 1
GGUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGG------CAGCCAGUCAACUGCCACAGACAACAGCAACACUAGCGGC-GCAUCAACAACAAACAGCUCC
(((((...((((.....))))(((((.((((..((((------(((........))))))).(....).....)))).)))))-)))))................ ( -32.00)
>DroYak_CAF1 100748 99 - 1
AGUGCAGGAUGCAGAAUGCAUGUUGCAAGUGCAGUGG------CAGCCAGUCAACUGCCACAGACAACAGCAACACUAGCGGCAGCAUCAACAACAAACAGCUCC
.((....(((((....(((.((((((...(((.((((------(((........))))))).).))...))))))...)))...)))))....)).......... ( -31.80)
>consensus
GGUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGG______CAGCCAGUCAACUGCCACAGACAACAGCAACACCAGCGGCAGCAUCAACAACAAACAGCUCC
.......(((((....(((.((((((...(((.((((..........(((....))))))).).))...))))))...)))...)))))................ (-22.70 = -22.70 +  -0.00)

alignment

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secondary structure

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Window 6

Location 9,224,361 – 9,224,464
Length 103
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 78.08
Mean single sequence MFE -39.35
Consensus MFE -22.90
Energy contribution -26.77
Covariance contribution 3.88
Combinations/Pair 1.06
Mean z-score -3.26
Structure conservation index 0.58
SVM decision value 3.18
SVM RNA-class probability 0.998682
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224361 103 + 20766785
GGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUGCUAUUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCAUCCUGCAUC-------CUGCAGCGU-------GCAUGCUGCA
(((((....((.((..(((((((((....))))))))).)).)).)))))((((.(((((((.(((((...(((.....)))..-------.))))).))-------))))).)))) ( -42.20)
>DroSec_CAF1 117761 96 + 1
GGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUGCUAUUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCU-------GCAUC-------CUGCACCGU-------GCAUGCUGCA
.(((((((...(((..((((((((.(.(.....)).)))))))).)))...)))))))(((.(.(((((..(-------((...-------..)))..))-------))).).))). ( -36.40)
>DroEre_CAF1 103208 97 + 1
AGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG------CCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCACC--------------CUGAGCCCUGCAACCUGCGAACUGCA
.(((((((...(((..(((((((((....)))))------)))).)))...)))))))(((...((((...((((..--------------........))))...))))...))). ( -35.00)
>DroYak_CAF1 100776 111 + 1
AGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG------CCACUGCACUUGCAACAUGCAUUCUGCAUCCUGCACUCUGCAUCCUGCACUCUGCACCGUGCAACCUGCAACCUGCA
.(((((((...(((..(((((((((....)))))------)))).)))...)))))))(((...((((...(((((..((((..........))))..)))))...))))...))). ( -43.80)
>consensus
AGUGUUGCUGUUGUCUGUGGCAGUUGACUGGCUG______CCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCACC__GCAUC_______CUGCACCGU_______GCAAGCUGCA
.(((((((...(((..(((((((((....)))))......)))).)))...)))))))(((.(.((((...(((((..((((..........))))..)))))...)))).).))). (-22.90 = -26.77 +   3.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,224,361 – 9,224,464
Length 103
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 78.08
Mean single sequence MFE -39.40
Consensus MFE -19.25
Energy contribution -23.75
Covariance contribution 4.50
Combinations/Pair 1.03
Mean z-score -2.90
Structure conservation index 0.49
SVM decision value 1.38
SVM RNA-class probability 0.948162
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224361 103 - 20766785
UGCAGCAUGC-------ACGCUGCAG-------GAUGCAGGAUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAAUAGCAGCCAGUCAACUGCCACAGACAACAGCAACACC
((((((((((-------(..(((((.-------..(((.....)))...)))))..))))))))))).((((((((((.......))).....)))).)))................ ( -40.50)
>DroSec_CAF1 117761 96 - 1
UGCAGCAUGC-------ACGGUGCAG-------GAUGC-------AGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAAUAGCAGCCAGUCAACUGCCACAGACAACAGCAACACC
(((....(((-------((..(((((-------.((((-------(..........))))).))))).)))))((((((...((.....))....))))))........)))..... ( -33.50)
>DroEre_CAF1 103208 97 - 1
UGCAGUUCGCAGGUUGCAGGGCUCAG--------------GGUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGG------CAGCCAGUCAACUGCCACAGACAACAGCAACACU
(((.....))).(((((...((.(..--------------..(((((.((((.....)))).))))).).)).((((------(((........)))))))........)))))... ( -35.80)
>DroYak_CAF1 100776 111 - 1
UGCAGGUUGCAGGUUGCACGGUGCAGAGUGCAGGAUGCAGAGUGCAGGAUGCAGAAUGCAUGUUGCAAGUGCAGUGG------CAGCCAGUCAACUGCCACAGACAACAGCAACACU
((((..(((((..((((((..((((..........))))..))))))..)))))..))))((((((...(((.((((------(((........))))))).).))...)))))).. ( -47.80)
>consensus
UGCAGCAUGC_______ACGGUGCAG_______GAUGC__GGUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGG______CAGCCAGUCAACUGCCACAGACAACAGCAACACC
((((.((((((..(((((...((((..........))))...)))))..)))))).))))((((((...(((.((((..........(((....))))))).).))...)))))).. (-19.25 = -23.75 +   4.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,224,398 – 9,224,488
Length 90
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 79.34
Mean single sequence MFE -26.98
Consensus MFE -14.08
Energy contribution -16.12
Covariance contribution 2.04
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.52
SVM decision value 0.81
SVM RNA-class probability 0.857425
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224398 90 + 20766785
UUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCAUCCUGCAUC-------CUGCAGCGU-------GCAUGCUGCAACUAGCAACUCGACGCGUGUCUGG
...(((..(((((((((.(((((((.(((((...(((.....)))..-------.))))).))-------))))).)))))...((........)))))).))) ( -33.40)
>DroSec_CAF1 117798 83 + 1
UUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCU-------GCAUC-------CUGCACCGU-------GCAUGCUGCAACUAGCAACUCGACGCGUGUCUGG
...(((..(((((((((.(((((((..((((....-------.....-------.))))..))-------))))).)))))...((........)))))).))) ( -25.40)
>DroSim_CAF1 102004 83 + 1
UUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCU-------GCAUC-------CUGCACCGU-------GCAUGCUGCAACUAGCAACUCGACGCGUGUCUGG
...(((..(((((((((.(((((((..((((....-------.....-------.))))..))-------))))).)))))...((........)))))).))) ( -25.40)
>DroEre_CAF1 103242 87 + 1
---CCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCACC--------------CUGAGCCCUGCAACCUGCGAACUGCAACUCGCAACUCGACGCGUGUCUGG
---(((.(((....)))((((((.((.((((....((...--------------....))..))))...(((((........)))))....)).)))))).))) ( -20.10)
>DroYak_CAF1 100810 101 + 1
---CCACUGCACUUGCAACAUGCAUUCUGCAUCCUGCACUCUGCAUCCUGCACUCUGCACCGUGCAACCUGCAACCUGCAACGAGCAACUCGACGCGUGUCUGG
---(((.(((....)))((((((....((((...((((...(((((..(((.....)))..)))))...))))...)))).((((...))))..)))))).))) ( -30.60)
>consensus
UUGCCACUGCACUUGCAACAUGCAUCCUGCAUCCUGCA____GCAUC_______CUGCACCGU_______GCAUGCUGCAACUAGCAACUCGACGCGUGUCUGG
...(((..(((((((((.(((((.....((.....)).....(((..........)))............))))).)))))...((........)))))).))) (-14.08 = -16.12 +   2.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,224,398 – 9,224,488
Length 90
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 79.34
Mean single sequence MFE -35.28
Consensus MFE -18.86
Energy contribution -19.54
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -2.44
Structure conservation index 0.53
SVM decision value 1.43
SVM RNA-class probability 0.953083
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9224398 90 - 20766785
CCAGACACGCGUCGAGUUGCUAGUUGCAGCAUGC-------ACGCUGCAG-------GAUGCAGGAUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAA
...(((....)))..((..(((.(((((((((((-------(..(((((.-------..(((.....)))...)))))..)))))))))))).)..))..)).. ( -40.50)
>DroSec_CAF1 117798 83 - 1
CCAGACACGCGUCGAGUUGCUAGUUGCAGCAUGC-------ACGGUGCAG-------GAUGC-------AGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAA
...(((....)))..(((((.....))))).(((-------.((.((((.-------..(((-------((.((((.....)))).)))))..)))).))))). ( -32.00)
>DroSim_CAF1 102004 83 - 1
CCAGACACGCGUCGAGUUGCUAGUUGCAGCAUGC-------ACGGUGCAG-------GAUGC-------AGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAA
...(((....)))..(((((.....))))).(((-------.((.((((.-------..(((-------((.((((.....)))).)))))..)))).))))). ( -32.00)
>DroEre_CAF1 103242 87 - 1
CCAGACACGCGUCGAGUUGCGAGUUGCAGUUCGCAGGUUGCAGGGCUCAG--------------GGUGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGG---
.....((((((.((((((((((.((((.....)))).)))))..))))..--------------..(((((.((((.....)))).))))).)))).))).--- ( -33.20)
>DroYak_CAF1 100810 101 - 1
CCAGACACGCGUCGAGUUGCUCGUUGCAGGUUGCAGGUUGCACGGUGCAGAGUGCAGGAUGCAGAGUGCAGGAUGCAGAAUGCAUGUUGCAAGUGCAGUGG---
.....(((((((((((...))).(((((..(((((..((((((........))))))..)))))..))))))))))....(((((.......)))))))).--- ( -38.70)
>consensus
CCAGACACGCGUCGAGUUGCUAGUUGCAGCAUGC_______ACGGUGCAG_______GAUGC____UGCAGGAUGCAGGAUGCAUGUUGCAAGUGCAGUGGCAA
.....((((((((..(((((.....)))))................(((..........))).........)))))....(((((.......)))))))).... (-18.86 = -19.54 +   0.68)

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 10:34:42 2006