Locus 7473

Sequence ID X_DroMel_CAF1
Location 18,654,928 – 18,655,059
Length 131
Max. P 0.909865
window12258 window12259 window12260 window12261

overview

Window 8

Location 18,654,928 – 18,655,040
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.26
Mean single sequence MFE -36.90
Consensus MFE -26.20
Energy contribution -26.83
Covariance contribution 0.63
Combinations/Pair 1.25
Mean z-score -2.48
Structure conservation index 0.71
SVM decision value 0.53
SVM RNA-class probability 0.772460
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18654928 112 + 22224390
UCCACCGCCACGGCCAUAUCGGCCACCACGCAGGCAGCCACUGCUUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCAUACGCAUCCGCAUGCCC
......((...((((.....)))).....(((((..(((.(((....))).))).....(((((....))))).))))).)).......------...((((.((....)).)))).. ( -40.70)
>DroSec_CAF1 43 112 + 1
UCCACCGCCACGGCCAUAUCGGCCACCACGCAGGCAGCCACUGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCAUACGCAUCCGCAUGCCC
......((...((((.....)))).....(((((..(((.(((....))).))).....(((((....))))).))))).)).......------...((((.((....)).)))).. ( -40.70)
>DroEre_CAF1 482 112 + 1
UCCACCGCCACCGCCAUAUCGGCCACAACGCAGGCAGCCACCGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCACACGCAUCCGCAUGCCC
......((....(((.....)))......(((((.(((..((((.....))))..))).(((((....))))).))))).)).......------...(((..((....))..))).. ( -35.70)
>DroWil_CAF1 397 103 + 1
UCCACUGCCACCGCCAUUUCGGCGACCACACAGGCGGCCACAGCAUUUAGCGGCAGUUCGGUUGGCCAUCAUCAUCUGCAACAUCAUCA------UCCGCAC---CAUCCG------G
...((((((.(((((.....(....)......))))).....((.....)))))))).(((.(((...........(((..........------...))))---)).)))------. ( -26.32)
>DroYak_CAF1 343 112 + 1
UCCACCGCCACGGCCAUAUCGGCCACAACGCAGGCAGCCACUGCCUUCAGUGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCAUCA------CCAGCAUACGCAUCCGCAUGCCC
......((...((((.....)))).....(((((..(((((((....))))))).....(((((....))))).))))).)).......------...((((.((....)).)))).. ( -44.60)
>DroAna_CAF1 5848 115 + 1
UCCACUGCCACGGCCAUCUCCGCCACGACCCAGGCGGCCACUGCCUUCAGCGGCAGUUCCGUGGGUCACCACCACUUGCAGCACCACCAGCAUCCCCACCAGAAGCCUCAGCCUG---
....((((...(((.......)))..(((((..((((..((((((......)))))).)))))))))..........))))........((.((.......)).)).........--- ( -33.40)
>consensus
UCCACCGCCACGGCCAUAUCGGCCACCACGCAGGCAGCCACUGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA______CCAGCAUACGCAUCCGCAUGCCC
......((...((((.....)))).....(((((..(((.(((....))).))).....(((((....))))).)))))...................))....((....))...... (-26.20 = -26.83 +   0.63)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,654,928 – 18,655,040
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 83.26
Mean single sequence MFE -52.03
Consensus MFE -36.90
Energy contribution -39.37
Covariance contribution 2.46
Combinations/Pair 1.22
Mean z-score -2.30
Structure conservation index 0.71
SVM decision value 0.43
SVM RNA-class probability 0.732535
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18654928 112 - 22224390
GGGCAUGCGGAUGCGUAUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAAGCAGUGGCUGCCUGCGUGGUGGCCGAUAUGGCCGUGGCGGUGGA
.((((((((....)))))))).(------..(.....)..).(((((.(....))))))...(..((((((...((..((((..((.....))..)))).....))..))))))..). ( -53.90)
>DroSec_CAF1 43 112 - 1
GGGCAUGCGGAUGCGUAUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCAGUGGCUGCCUGCGUGGUGGCCGAUAUGGCCGUGGCGGUGGA
.((((((((....)))))))).(------..(.....)..).(((((.(....))))))...(..(((((...(((..((((..((.....))..)))).....)))..)))))..). ( -57.50)
>DroEre_CAF1 482 112 - 1
GGGCAUGCGGAUGCGUGUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCGGUGGCUGCCUGCGUUGUGGCCGAUAUGGCGGUGGCGGUGGA
.((((((((....))))))))..------.......((((((((((((((....))))).(((..((((.....))))..)))))))))((..(.(((.....))).)..)))))... ( -55.80)
>DroWil_CAF1 397 103 - 1
C------CGGAUG---GUGCGGA------UGAUGAUGUUGCAGAUGAUGAUGGCCAACCGAACUGCCGCUAAAUGCUGUGGCCGCCUGUGUGGUCGCCGAAAUGGCGGUGGCAGUGGA
.------(((.((---((.((..------...((......)).....))...)))).))).(((((((((.........((((((....))))))(((.....))))))))))))... ( -37.10)
>DroYak_CAF1 343 112 - 1
GGGCAUGCGGAUGCGUAUGCUGG------UGAUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCACUGAAGGCAGUGGCUGCCUGCGUUGUGGCCGAUAUGGCCGUGGCGGUGGA
.((((((((....))))))))..------.......((((((((((((((....))))).....(((((((....))))))).))))))((..(((((.....)))))..)))))... ( -56.80)
>DroAna_CAF1 5848 115 - 1
---CAGGCUGAGGCUUCUGGUGGGGAUGCUGGUGGUGCUGCAAGUGGUGGUGACCCACGGAACUGCCGCUGAAGGCAGUGGCCGCCUGGGUCGUGGCGGAGAUGGCCGUGGCAGUGGA
---...((((.(((((((.((.(.(((.(.(((((((((((.(((((..((..(....)..))..)))))....))))).)))))).).))).).)).).)).))))....))))... ( -51.10)
>consensus
GGGCAUGCGGAUGCGUAUGCUGG______UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCAGUGGCUGCCUGCGUGGUGGCCGAUAUGGCCGUGGCGGUGGA
.((((((((....))))))))...............((((((((((((((....))))).....(((((((....))))))).))))))((..(((((.....)))))..)))))... (-36.90 = -39.37 +   2.46)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,654,968 – 18,655,059
Length 91
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 68.70
Mean single sequence MFE -25.33
Consensus MFE -19.23
Energy contribution -19.57
Covariance contribution 0.34
Combinations/Pair 1.18
Mean z-score -1.01
Structure conservation index 0.76
SVM decision value 1.07
SVM RNA-class probability 0.909865
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18654968 91 + 22224390
CUGCUUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCAUACGCAUCCGCAUGCCC---CACAGCAGUCACAGUCACA-------------------
(((((....((.((((...(((((....)))))..)))).)).......------...((((.((....)).))))..---...)))))...........------------------- ( -27.50)
>DroSec_CAF1 83 90 + 1
CUGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCAUACGCAUCCGCAUGCCC---CACAGCAGUCACAGUCAC--------------------
((((.....((.((((...(((((....)))))..)))).)).......------...((((.((....)).))))..---....))))..........-------------------- ( -26.50)
>DroEre_CAF1 522 110 + 1
CCGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA------CCAGCACACGCAUCCGCAUGCCC---CACAGCAGUCGCAGUCACAGUCCCAGUCACUGACACAG
......((((.(((.....(((((....)))))..((((.((.......------.........((....)).(((..---....))))).))))...........))).))))..... ( -28.40)
>DroYak_CAF1 383 104 + 1
CUGCCUUCAGUGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCAUCA------CCAGCAUACGCAUCCGCAUGCCC---CACAGCAGUCC------CAGUCCCAGUCACAGCCACAU
.........(((((.....(((((....)))))..((((.((.......------...))....((((....))))..---....))))...------..............))))).. ( -28.20)
>DroAna_CAF1 5888 86 + 1
CUGCCUUCAGCGGCAGUUCCGUGGGUCACCACCACUUGCAGCACCACCAGCAUCCCCACCAGAAGCCUCAGCCUG--------CGGCAGUGACG-------------------------
(((((......)))))....((((....))))((((.((.(((......((.((.......)).)).......))--------).))))))...------------------------- ( -23.42)
>DroPer_CAF1 8535 95 + 1
CCGCAUUUAGCGGCAGUUCCGUGGGCCACCAUCACUUGCAGCACCACCA---------------GCAUCCGCACGCCCAUUCACAGCCCGCAACGCACC---------AACAACAACUG
((((.....))))(((((..((((((..........(((.((.......---------------))....)))............))))))...(....---------..)...))))) ( -17.95)
>consensus
CUGCCUUCAGCGGCAGCUCGGUGGGUCACCACCACCUGCAGCACCACCA______CCAGCAUACGCAUCCGCAUGCCC___CACAGCAGUCACAGUCAC____________________
((((.....((.((((...(((((....)))))..)))).))......................((....)).............)))).............................. (-19.23 = -19.57 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,654,968 – 18,655,059
Length 91
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 68.70
Mean single sequence MFE -39.67
Consensus MFE -26.34
Energy contribution -28.90
Covariance contribution 2.56
Combinations/Pair 1.21
Mean z-score -1.32
Structure conservation index 0.66
SVM decision value 0.99
SVM RNA-class probability 0.896059
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18654968 91 - 22224390
-------------------UGUGACUGUGACUGCUGUG---GGGCAUGCGGAUGCGUAUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAAGCAG
-------------------...........(((((...---.((((((((....))))))))((------(((..((......(((((.(....))))))..))..)))))...))))) ( -41.10)
>DroSec_CAF1 83 90 - 1
--------------------GUGACUGUGACUGCUGUG---GGGCAUGCGGAUGCGUAUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCAG
--------------------..........(((((...---.((((((((....))))))))((------(((..((......(((((.(....))))))..))..)))))...))))) ( -41.10)
>DroEre_CAF1 522 110 - 1
CUGUGUCAGUGACUGGGACUGUGACUGCGACUGCUGUG---GGGCAUGCGGAUGCGUGUGCUGG------UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCGG
...((.((((.((.......)).)))))).(((((...---.((((((((....))))))))((------(((..((......(((((.(....))))))..))..)))))...))))) ( -46.00)
>DroYak_CAF1 383 104 - 1
AUGUGGCUGUGACUGGGACUG------GGACUGCUGUG---GGGCAUGCGGAUGCGUAUGCUGG------UGAUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCACUGAAGGCAG
.((..((.((..(.......)------..)).(((((.---(((((((((....))))))))..------).)))))))..))(((((.(....))))))...(((((......))))) ( -39.50)
>DroAna_CAF1 5888 86 - 1
-------------------------CGUCACUGCCG--------CAGGCUGAGGCUUCUGGUGGGGAUGCUGGUGGUGCUGCAAGUGGUGGUGACCCACGGAACUGCCGCUGAAGGCAG
-------------------------.(((((..(((--------(..((.(..(((.(..((......))..).))).).))..))))..)))))........(((((......))))) ( -36.40)
>DroPer_CAF1 8535 95 - 1
CAGUUGUUGUU---------GGUGCGUUGCGGGCUGUGAAUGGGCGUGCGGAUGC---------------UGGUGGUGCUGCAAGUGAUGGUGGCCCACGGAACUGCCGCUAAAUGCGG
(((((......---------...((((((((.(((.......))).))).)))))---------------..((((.((..(.(....).)..))))))..)))))((((.....)))) ( -33.90)
>consensus
____________________GUGACUGUGACUGCUGUG___GGGCAUGCGGAUGCGUAUGCUGG______UGGUGGUGCUGCAGGUGGUGGUGACCCACCGAGCUGCCGCUGAAGGCAG
..............................(((((.......((((((((....)))))))).........(((((((((...(((((.(....)))))).))).))))))...))))) (-26.34 = -28.90 +   2.56)

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 12:39:50 2006