Locus 7366

Sequence ID 2L_DroMel_CAF1
Location 20,519,159 – 20,519,320
Length 161
Max. P 0.890886
window11827 window11828 window11829

overview

Window 7

Location 20,519,159 – 20,519,249
Length 90
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 76.39
Mean single sequence MFE -14.75
Consensus MFE -10.95
Energy contribution -11.12
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.74
SVM decision value 0.96
SVM RNA-class probability 0.890886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20519159 90 - 22407834
A-CCACCCAAA--AAAUAGG-AAAAAAAA-----CAC-----------CCUUCA--CCCCUUAACCUUAACGAGCCACAAGCGACACUU-CGUACCGCCUUUGGUUCUCAUGU
.-....((...--.....))-........-----...-----------......--...............((((((...(((......-.....)))...))))))...... ( -11.00)
>DroSec_CAF1 40474 92 - 1
A-CCACCCAAA-AAAAUAGGGAAAAAAAA-----CAC-----------CUUCCA--CCCCUUAACCUUAACGAGCCACAAGCGACACUU-CGUACCGCCUUUGGUUCCCAUGU
.-...(((...-......)))........-----...-----------......--...............((((((...(((......-.....)))...))))))...... ( -13.30)
>DroSim_CAF1 41345 91 - 1
A-CCACCAAAA-AAAAUAGG-AAAAAAAA-----CAC-----------CUUCCA--CCCCUUAACCUUAACGAGCCACAAGCGACACUU-CGUACCGCCUUUGGUUCUCAUGU
.-.........-......((-((......-----...-----------.)))).--...............((((((...(((......-.....)))...))))))...... ( -12.90)
>DroEre_CAF1 34143 87 - 1
--CCACUCCAA----AUACUGAAAAAAGG-----C-A-----------CCUCCG--CCCCUUAACCUUAACGAGCCACAAGCGACACUU-CGUAGCGCCUUUGGUUCCCAUGU
--.........----............((-----(-.-----------.....)--)).............((((((...(((..((..-.))..)))...))))))...... ( -14.70)
>DroYak_CAF1 35747 83 - 1
A-CCUCUCCAG----AUAAAGAACA-----------C-----------CCUCCA--CCCCUUAACCUUAACGAGCCACAAGCGACACUU-CGUACCGCCUUUGGUUCUCAUGU
.-.........----..........-----------.-----------......--...............((((((...(((......-.....)))...))))))...... ( -10.40)
>DroAna_CAF1 32135 113 - 1
AUAUACCCUAAAAAAAAACCUAAAAAAAAGGAGGCAGCAGGGUGGUGGUUGCCAGCCCACCCAACCUUAACGAGCCACAAGCGACACUCGCAUUUCGCCUUUGGUUCUCAUGU
..................(((.......)))..(((...(((((((((...)))..)))))).........((((((...((((..........))))...))))))...))) ( -26.20)
>consensus
A_CCACCCAAA__AAAUAGGGAAAAAAAA_____CAC___________CCUCCA__CCCCUUAACCUUAACGAGCCACAAGCGACACUU_CGUACCGCCUUUGGUUCUCAUGU
.......................................................................((((((...(((..((....))..)))...))))))...... (-10.95 = -11.12 +   0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,519,197 – 20,519,289
Length 92
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -13.92
Consensus MFE -6.52
Energy contribution -6.20
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.47
SVM decision value 0.12
SVM RNA-class probability 0.591118
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20519197 92 - 22407834
CACUCCACGGUUAUCAGUGGCAGCCCAACAGCUAGUCCGCACCACCCAAA-AAAUAGG-AAAAAAAACACCCUUCACCCCUUAACCUUAACGAG
..(((...(((((...((((((((......))).).)))).....((...-.....))-......................))))).....))) ( -13.80)
>DroSec_CAF1 40512 94 - 1
CACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCACCACCCAAAAAAAUAGGGAAAAAAAACACCUUCCACCCCUUAACCUUAACGAG
.....((((((....((.((((((......))).))))).))).(((.........)))................................))) ( -16.00)
>DroSim_CAF1 41383 93 - 1
CACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCACCACCAAAAAAAAUAGG-AAAAAAAACACCUUCCACCCCUUAACCUUAACGAG
.....((((((....((.((((((......))).)))))....)))..........((-((..........))))................))) ( -16.20)
>DroEre_CAF1 34181 77 - 1
CACUCCUCGGUUAUCAGUGGCAGCCCAA-------------CCACUCCAA---AUACUGAAAAAAGGC-ACCUCCGCCCCUUAACCUUAACGAG
..(((.(((((....(((((........-------------)))))....---..))))).....(((-......))).............))) ( -14.80)
>DroYak_CAF1 35785 85 - 1
CACUCCUCGGUUAUCAGUGGUAUUCCAACAGCUAGCCCACACCUCUCCAG---AUAAAGAACA------CCCUCCACCCCUUAACCUUAACGAG
.....((((((((.(..(((....)))...).)))))......(((....---....)))...------......................))) (  -8.80)
>consensus
CACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCACCACCCAAA_AAAUAGGGAAAAAAAACACCCUCCACCCCUUAACCUUAACGAG
..(((...(((((...((((.....................................................))))....))))).....))) ( -6.52 =  -6.20 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,519,221 – 20,519,320
Length 99
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 72.23
Mean single sequence MFE -16.73
Consensus MFE -8.30
Energy contribution -9.18
Covariance contribution 0.88
Combinations/Pair 1.33
Mean z-score -1.66
Structure conservation index 0.50
SVM decision value 0.03
SVM RNA-class probability 0.549065
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20519221 99 - 22407834
UCACGCUGCAAAUGAUAUCCAAAGACUAAUCCACUCCACGGUUAUCAGUGGCAGCCCAACAGCUAGUCCGCA-CCACCCAAA--AAAUAGG-AAAAAAAA-----CAC---
....(((((...(((((.((...................)).)))))...)))))......((......)).-....((...--.....))-........-----...--- ( -17.01)
>DroSec_CAF1 40536 101 - 1
ACACGCUGCAAAUGAUAUCCAAAGACUAAUCCACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCA-CCACCCAAA-AAAAUAGGGAAAAAAAA-----CAC---
....(((((...(((((.((...................)).)))))...))))).................-...(((...-......)))........-----...--- ( -18.41)
>DroSim_CAF1 41407 100 - 1
ACACGCUGCAAAUGAUAUCCAAAGACUAAUCCACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCA-CCACCAAAA-AAAAUAGG-AAAAAAAA-----CAC---
....(((((...(((((.((...................)).)))))...))))).................-.........-........-........-----...--- ( -15.11)
>DroYak_CAF1 35809 92 - 1
ACCCGCUGCAAACGAUAACCAGAGACUAAUCCACUCCUCGGUUAUCAGUGGUAUUCCAACAGCUAGCCCACA-CCUCUCCAG----AUAAAGAACA-----------C---
....(((((....(((((((.(((............))))))))))..(((....)))...)).))).....-.........----..........-----------.--- ( -18.50)
>DroAna_CAF1 32208 100 - 1
-UACAUGGCAAAGGACUUGCUGAGACUAAUCCACUCUCCGGUUAUCAGUGGUACUUC----------CCUUAUAUACCCUAAAAAAAAACCUAAAAAAAAGGAGGCAGCAG
-................(((((...((............((((((.((.((.....)----------))).))).)))...........(((.......))))).))))). ( -14.60)
>consensus
ACACGCUGCAAAUGAUAUCCAAAGACUAAUCCACUCCUCGGUUAUCAGUGGCAGCCCAACAGCUAGCCCUCA_CCACCCAAA_AAAAUAGG_AAAAAAAA_____CAC___
....(((((...(((((.((.(.((.........)).).)).)))))...)))))........................................................ ( -8.30 =  -9.18 +   0.88)

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 12:34:55 2006