Locus 8062

Sequence ID 3R_DroMel_CAF1
Location 21,643,681 – 21,643,803
Length 122
Max. P 0.994214
window12979 window12980 window12981

overview

Window 9

Location 21,643,681 – 21,643,780
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.85
Mean single sequence MFE -35.12
Consensus MFE -18.75
Energy contribution -19.67
Covariance contribution 0.92
Combinations/Pair 1.31
Mean z-score -2.88
Structure conservation index 0.53
SVM decision value 2.46
SVM RNA-class probability 0.994214
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21643681 99 - 27905053
ACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGAGGCGUGUC---CGGGGGGCAGGCAUUUGGAUUUUGAUUCGGA------------UGCG
..(((((((((..(...(((------((((((((((((((....)))))))))..........((.((((---(...))))).)))))))))).)..)))))))------------)).. ( -39.30)
>DroSec_CAF1 132993 99 - 1
ACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGGGGCGUGUC---UGGGGGGCAGGCAUUUGGAUUUGGAUUCGGU------------UGGG
.(((.(((((((.(...(((------((((((((((((((....)))))))))...(....).((.((((---.....)))).)))))))))).).))))))).------------))). ( -37.20)
>DroSim_CAF1 129605 99 - 1
ACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGGGGCGUGUC---UGGGGGGCAGGCAUUUGGAUUUGGAUUCGGU------------UGGG
.(((.(((((((.(...(((------((((((((((((((....)))))))))...(....).((.((((---.....)))).)))))))))).).))))))).------------))). ( -37.20)
>DroEre_CAF1 129735 111 - 1
ACCAUCUGAAUUGGUGAAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCAGUUCGAGGCGUGUC---UGUGGGGCAGGCAUUUGGAUUUGGAUUCAGAUUCUGUUUCUGAUUCU
((((.......))))(((((------((((((((((((((....)))))))))..........((.((((---.....)))).))))))))))))(((.(((((.......))))).))) ( -36.30)
>DroYak_CAF1 130274 105 - 1
ACCAUCUGAAUUGGUGUAUUCGAGUUCGAGUAUCGAAAUGAAUACAUUUCGCUUCAGUUUGAGGCGUGUC---UGGGUGGCAGGCAUUUGGAUUUGGAUUCCGA------------UUCG
.......(((((((...((((((((((((((...((((((....))))))(((((.....)))))..(((---((.....))))))))))))))))))).))))------------))). ( -39.00)
>DroAna_CAF1 112525 82 - 1
UCCGUUCGCAUUGG--------------AGUGUUGAAAUGAAUACAUUUUGGCCCAGUUUGUGGCAUGACGAGUGGGGGGCGGUGACUAGGAUUUG------------------------
.((((((...(..(--------------(((((..........))))))..)((((.(((((......))))))))))))))).............------------------------ ( -21.70)
>consensus
ACCAUCUGAAUUGGUGUAUU______CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGAGGCGUGUC___UGGGGGGCAGGCAUUUGGAUUUGGAUUCGGA____________UGCG
.....(((((((.................(.(((((((((....))))))))).)..((((((((.((((........)))).)).))))))....)))))))................. (-18.75 = -19.67 +   0.92)

alignment

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secondary structure

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Window 0

Location 21,643,709 – 21,643,803
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.35
Mean single sequence MFE -27.60
Consensus MFE -17.13
Energy contribution -18.85
Covariance contribution 1.72
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.62
SVM decision value 0.54
SVM RNA-class probability 0.774722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21643709 94 + 27905053
CCCCCCG---GACACGCCUCGAAGUGAACCGAAAUGUAUUCAUUUCGGUACUCG------AAUACACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGGGUC-----------------
..(((((---((......((((.((..(((((((((....))))))))))))))------)...(((((.......))))).............)))))))..----------------- ( -35.10)
>DroSec_CAF1 133021 94 + 1
CCCCCCA---GACACGCCCCGAAGUGAACCGAAAUGUAUUCAUUUCGGUACUCG------AAUACACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGGGUC-----------------
.......---.....((((((..(.(.(((((((((....))))))))).).).------....(((((.......)))))...............)))))).----------------- ( -28.80)
>DroSim_CAF1 129633 94 + 1
CCCCCCA---GACACGCCCCGAAGUGAACCGAAAUGUAUUCAUUUCGGUACUCG------AAUACACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGGGUC-----------------
.......---.....((((((..(.(.(((((((((....))))))))).).).------....(((((.......)))))...............)))))).----------------- ( -28.80)
>DroEre_CAF1 129775 94 + 1
CCCCACA---GACACGCCUCGAACUGAACCGAAAUGUAUUCAUUUCGGUACUCG------AAUUCACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGAGUC-----------------
.((....---((((......((((((.(((((((((....))))))))).....------....(((((.......))))).)))))).))))....))....----------------- ( -22.90)
>DroYak_CAF1 130302 100 + 1
CCACCCA---GACACGCCUCAAACUGAAGCGAAAUGUAUUCAUUUCGAUACUCGAACUCGAAUACACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGGGUC-----------------
...(((.---((...((...((((((...(((((((....)))))))....(((....)))...(((((.......))))).))))))..))..)).)))...----------------- ( -24.50)
>DroAna_CAF1 112541 106 + 1
CCCCCCACUCGUCAUGCCACAAACUGGGCCAAAAUGUAUUCAUUUCAACACU--------------CCAAUGCGAACGGAGGGAGUUUUUGUUAUACCGAGUCCGGCUCUGGGGUCUGGG
...((((((((..(((.((.(((((...((.(((((....))))).....((--------------((.........))))))))))).)).)))..)))))..((((....)))).))) ( -25.50)
>consensus
CCCCCCA___GACACGCCUCGAACUGAACCGAAAUGUAUUCAUUUCGGUACUCG______AAUACACCAAUUCAGAUGGUGCCAGUUUUUGUUAUCCGGGGUC_________________
...............((((((......(((((((((....)))))))))...............(((((.......)))))...............)))))).................. (-17.13 = -18.85 +   1.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,643,709 – 21,643,803
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.35
Mean single sequence MFE -36.27
Consensus MFE -22.12
Energy contribution -22.68
Covariance contribution 0.56
Combinations/Pair 1.31
Mean z-score -3.15
Structure conservation index 0.61
SVM decision value 1.85
SVM RNA-class probability 0.979936
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21643709 94 - 27905053
-----------------GACCCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGAGGCGUGUC---CGGGGGG
-----------------..(((((((((..........((((((.......)))))).((------((((((((((((((....)))))))))..)).)))))...))))---))))).. ( -42.00)
>DroSec_CAF1 133021 94 - 1
-----------------GACCCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGGGGCGUGUC---UGGGGGG
-----------------..(((((((((..........((((((.......)))))).((------((((((((((((((....)))))))))..)).)))))...))))---))))).. ( -38.80)
>DroSim_CAF1 129633 94 - 1
-----------------GACCCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGUAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGGGGCGUGUC---UGGGGGG
-----------------..(((((((((..........((((((.......)))))).((------((((((((((((((....)))))))))..)).)))))...))))---))))).. ( -38.80)
>DroEre_CAF1 129775 94 - 1
-----------------GACUCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGAAUU------CGAGUACCGAAAUGAAUACAUUUCGGUUCAGUUCGAGGCGUGUC---UGUGGGG
-----------------..(((((((((...........(((((.......)))))..((------((((.(((((((((....)))))))))....))))))...))))---)).))). ( -31.10)
>DroYak_CAF1 130302 100 - 1
-----------------GACCCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGUAUUCGAGUUCGAGUAUCGAAAUGAAUACAUUUCGCUUCAGUUUGAGGCGUGUC---UGGGUGG
-----------------..(((((((((.(..((((((((((((.......))))))(((((....)))))..(((((((....)))))))...))))))..)...))))---)))).). ( -36.10)
>DroAna_CAF1 112541 106 - 1
CCCAGACCCCAGAGCCGGACUCGGUAUAACAAAAACUCCCUCCGUUCGCAUUGG--------------AGUGUUGAAAUGAAUACAUUUUGGCCCAGUUUGUGGCAUGACGAGUGGGGGG
(((...((((......))(((((.(((..((.(((((..(((((.......)))--------------)).((..(((((....)))))..))..))))).))..))).))))))).))) ( -30.80)
>consensus
_________________GACCCCGGAUAACAAAAACUGGCACCAUCUGAAUUGGUGUAUU______CGAGUACCGAAAUGAAUACAUUUCGGUUCACUUCGAGGCGUGUC___UGGGGGG
...................(((((....(((....((.((((((.......)))))).........((((.(((((((((....)))))))))....))))))...)))....))))).. (-22.12 = -22.68 +   0.56)

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 13:01:41 2006