Locus 7538

Sequence ID 3R_DroMel_CAF1
Location 20,183,497 – 20,183,653
Length 156
Max. P 0.917887
window12166 window12167 window12168

overview

Window 6

Location 20,183,497 – 20,183,613
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.77
Mean single sequence MFE -35.53
Consensus MFE -28.50
Energy contribution -27.33
Covariance contribution -1.16
Combinations/Pair 1.24
Mean z-score -1.73
Structure conservation index 0.80
SVM decision value 1.12
SVM RNA-class probability 0.917887
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20183497 116 + 27905053
C--CUGUGGCGUUCUCUGUCUGCAGGGCCGUUGCCGCAUUUUGGUCCAGCUUGUUCAAAAUGUUUUCGGCCUUGUCCGCCAGUCCUGUGAUCCAGGAUGACAUAUUUUUCUAAGAAA--A
.--...(((((..........(((((((((.....(((((((((..........)))))))))...))))))))).)))))((((((.....))))))...................--. ( -35.60)
>DroPse_CAF1 9224 109 + 1
CAACGCUG---UUUCCAG-UUGCAGGGCCGUGGCCGCAUUCUGGUCGAUCUUGUUCAGAAUGUUCUCGGCCUUAUCUGCCAAUCCUGUGAUCCAGGAUGACAUUU-----UAAACGA--A
....((((---....)))-).(((((((((.((..((((((((..((....))..)))))))))).)))))....))))..((((((.....)))))).......-----.......--. ( -33.90)
>DroEre_CAF1 8471 102 + 1
C--CGGUGGAGUUCUCUGUCUGCAGGGCCGUUGCCGCAUUUUGGUCCAGCUUGUUCAAAAUGUUUUCGGCCUUAUCUGCCAGUCCUGUGAUCCAGGAUGACAUA----------------
.--.((..((.....(((....)))(((((.....(((((((((..........)))))))))...)))))...))..)).((((((.....))))))......---------------- ( -34.40)
>DroYak_CAF1 8435 116 + 1
C--CGGUGGAGUUCUCUGUUUGGAGGGCUGUUGCCGCAUUUUGGUCCAGCUUGUUCAAGAUGUUUUCGGCCUUGUCCGCCAGUCCUGUGAUCCAGGAUGACAUAUUUUUCUAAAACA--A
.--.(((((((((((((....)))))))....((((((((((((..........))))))))....))))....)))))).((((((.....))))))...................--. ( -36.10)
>DroAna_CAF1 8199 118 + 1
C--CGGCUUGAUUAUCCGUCUGUAGGGCUGUCGCCGCAUUCUGAUCGAUCUUGUUCAGAAUGUUUUCGGCCUUGUCCGCCAAUCCUGUUAUCCAGGAUGACAUUUUUUGCUCGGAAAUAA
(--((((..((......(((((..((((.((((..(((((((((.((....)).)))))))))...))))...))))..))((((((.....)))))))))...))..)).)))...... ( -36.60)
>DroPer_CAF1 9243 112 + 1
CAACGCUGUCGUUUCCAG-UUGCAGGGCCGUGGCCGCAUUCUGGUCGAUCUUGUUCAGAAUGUUCUCGGCCUUAUCUGCCAAUCCUGUGAUCCAGGAUGACAUUU-----UAAACGA--A
.......((((...((((-.(((..(((....))))))..)))).)))).(((((.((((((((...(((.......))).((((((.....)))))))))))))-----).)))))--. ( -36.60)
>consensus
C__CGGUGGAGUUCUCUGUCUGCAGGGCCGUUGCCGCAUUCUGGUCCAGCUUGUUCAAAAUGUUUUCGGCCUUAUCCGCCAAUCCUGUGAUCCAGGAUGACAUAU_____UAAAAAA__A
.................(((...(((((((.....(((((((((..........)))))))))...)))))))........((((((.....)))))))))................... (-28.50 = -27.33 +  -1.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,183,497 – 20,183,613
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.77
Mean single sequence MFE -32.63
Consensus MFE -24.65
Energy contribution -24.40
Covariance contribution -0.25
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.76
SVM decision value 1.06
SVM RNA-class probability 0.908069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20183497 116 - 27905053
U--UUUCUUAGAAAAAUAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUUUUGAACAAGCUGGACCAAAAUGCGGCAACGGCCCUGCAGACAGAGAACGCCACAG--G
.--....................(((((.....))))).(((((..(..((((.....(((((((..(.....)...))))))).(....)))))(((....))).)..)))))...--. ( -30.80)
>DroPse_CAF1 9224 109 - 1
U--UCGUUUA-----AAAUGUCAUCCUGGAUCACAGGAUUGGCAGAUAAGGCCGAGAACAUUCUGAACAAGAUCGACCAGAAUGCGGCCACGGCCCUGCAA-CUGGAAA---CAGCGUUG
.--((((...-----...((((((((((.....))))).))))).....(((((....(((((((..(......)..))))))))))))))))........-(((....---)))..... ( -35.60)
>DroEre_CAF1 8471 102 - 1
----------------UAUGUCAUCCUGGAUCACAGGACUGGCAGAUAAGGCCGAAAACAUUUUGAACAAGCUGGACCAAAAUGCGGCAACGGCCCUGCAGACAGAGAACUCCACCG--G
----------------..((((.(((((.....)))))...((((....((((.....(((((((..(.....)...))))))).(....))))))))).)))).............--. ( -29.90)
>DroYak_CAF1 8435 116 - 1
U--UGUUUUAGAAAAAUAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUCUUGAACAAGCUGGACCAAAAUGCGGCAACAGCCCUCCAAACAGAGAACUCCACCG--G
(--(((((.(((.......(((((((((.....))))).))))((......)).......))).))))))(.((((.........(((....)))(((......)))...)))).).--. ( -28.80)
>DroAna_CAF1 8199 118 - 1
UUAUUUCCGAGCAAAAAAUGUCAUCCUGGAUAACAGGAUUGGCGGACAAGGCCGAAAACAUUCUGAACAAGAUCGAUCAGAAUGCGGCGACAGCCCUACAGACGGAUAAUCAAGCCG--G
......(((.((......((((((((((.....))))).)))))((.....(((....((((((((.(......).)))))))).(((....))).......)))....))..))))--) ( -35.80)
>DroPer_CAF1 9243 112 - 1
U--UCGUUUA-----AAAUGUCAUCCUGGAUCACAGGAUUGGCAGAUAAGGCCGAGAACAUUCUGAACAAGAUCGACCAGAAUGCGGCCACGGCCCUGCAA-CUGGAAACGACAGCGUUG
.--.......-----...((((((((((.....))))).))))).....(((((....(((((((..(......)..)))))))))))).((((.(((...-.((....)).))).)))) ( -34.90)
>consensus
U__UCUUUUA_____AAAUGUCAUCCUGGAUCACAGGACUGGCAGACAAGGCCGAAAACAUUCUGAACAAGAUCGACCAAAAUGCGGCAACGGCCCUGCAAACAGAGAACGCCACCG__G
..................((((((((((.....))))).))))).....(((((....(((((((............)))))))......)))))......................... (-24.65 = -24.40 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,183,535 – 20,183,653
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.14
Mean single sequence MFE -28.82
Consensus MFE -19.91
Energy contribution -19.68
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.50
Structure conservation index 0.69
SVM decision value 0.55
SVM RNA-class probability 0.777400
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20183535 118 - 27905053
AGUGUGAUAUUGUUUACGUGUUUUACUCGAAGAGAUUUGUU--UUUCUUAGAAAAAUAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUUUUGAACAAGCUGGACCAA
.((.((...(((((((.(((((((.........(((.((((--((((...)))))))).))).(((((.....))))).((((.......)))))))))))..)))))))..)).))... ( -27.30)
>DroPse_CAF1 9260 102 - 1
------AUUUUGUUUACGUGUUUCAC-----AAGAUUUAUU--UCGUUUA-----AAAUGUCAUCCUGGAUCACAGGAUUGGCAGAUAAGGCCGAGAACAUUCUGAACAAGAUCGACCAG
------((((((((((.(((((((..-----..((......--))((((.-----...((((((((((.....))))).)))))....)))).))).))))..))))))))))....... ( -25.50)
>DroSim_CAF1 8899 118 - 1
AGUGUUAUAUUGUUUACGUGUUUUGCUCGAAGAGAUUUGUU--UUUCUUAGAAAAAUAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUUUUGAACAAGCUGGACCAA
..((((....(((((.((.((((((..((.((.(((.((((--((((...)))))))).))).(((((.....)))))))..))..)))))))).))))).....))))........... ( -32.20)
>DroYak_CAF1 8473 118 - 1
ACUGUGAUAUUGUUUACGUGUUUUGCUCGCAGAGAUUAGUU--UGUUUUAGAAAAAUAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUCUUGAACAAGCUGGACCAA
.((((((...................))))))...((((((--(((((.(((.......(((((((((.....))))).))))((......)).......))).)))))))))))..... ( -31.71)
>DroAna_CAF1 8237 119 - 1
UAAUAGAUAUUGUUUACGUGUUUGG-UUGACAAGAUUGUUUUAUUUCCGAGCAAAAAAUGUCAUCCUGGAUAACAGGAUUGGCGGACAAGGCCGAAAACAUUCUGAACAAGAUCGAUCAG
.....(((.(((((((.((((((..-.(((((...((((((.......))))))....)))))(((((.....)))))(((((.......)))))))))))..))))))).)))...... ( -31.10)
>DroPer_CAF1 9282 102 - 1
------UUUUUGUUUACGUGUUUCAC-----AAGAUUUAUU--UCGUUUA-----AAAUGUCAUCCUGGAUCACAGGAUUGGCAGAUAAGGCCGAGAACAUUCUGAACAAGAUCGACCAG
------.(((((((((.(((((((..-----..((......--))((((.-----...((((((((((.....))))).)))))....)))).))).))))..)))))))))........ ( -25.10)
>consensus
A_UGUGAUAUUGUUUACGUGUUUUACUCGAAAAGAUUUGUU__UUUCUUAGAAAAAAAUGUCAUCCUGGAUCACAGGACUGGCGGACAAGGCCGAAAACAUUCUGAACAAGAUCGACCAA
.........(((((((.((((((........................................(((((.....))))).((((.......)))).))))))..))))))).......... (-19.91 = -19.68 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:20 2006