Locus 3650

Sequence ID 2L_DroMel_CAF1
Location 10,613,821 – 10,614,016
Length 195
Max. P 0.946220
window5756 window5757 window5758 window5759 window5760

overview

Window 6

Location 10,613,821 – 10,613,937
Length 116
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 86.65
Mean single sequence MFE -24.87
Consensus MFE -19.85
Energy contribution -20.47
Covariance contribution 0.61
Combinations/Pair 1.14
Mean z-score -2.82
Structure conservation index 0.80
SVM decision value 0.85
SVM RNA-class probability 0.865372
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10613821 116 + 22407834
UCACCCCUCUAAGUAAUACUUCCUUAUGAUAUACAAGUUCCCCCAUUUUCGUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAAC
...................((((((((((...................))))))).))).((((((......((((((.....)))))).....(((((.....))))))))))). ( -26.71)
>DroSec_CAF1 93441 104 + 1
UCACCCCUCUA-GUAAAACUUCUU-----------ACUUCCCCCAUUUUCGUGAGCGAAUUUGCGCACUUUAGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAAC
..........(-((((......))-----------))).........((((....)))).((((((...(((((((((.....)))))))))..(((((.....))))))))))). ( -27.60)
>DroSim_CAF1 93823 115 + 1
UCACCCCUCUA-GUAAUACAUCCUUUUGAUAUACAAGUUCCCCCAUUUUUUUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAAC
...........-(((...((......))...)))((((((.(.((......)).).))))))((((......((((((.....)))))).....(((((.....)))))))))... ( -22.90)
>DroEre_CAF1 94112 114 + 1
UCACCCCUC-A-AUAAUACUUCUUUUUGAUAUACGAGUUCCCCCAUUUUGGUGAGCGAUUUUGCGCAUUUUUAUGACACUAAAUGUCACUAAUUUGACAAGAAAUGUCAGCGCAAC
.........-.-........................((((.((......)).))))....((((((.......(((((.....)))))......(((((.....))))))))))). ( -22.90)
>DroYak_CAF1 96811 115 + 1
UCACCCCUCUA-AUAAUACUGCUUUUUGAUAUACAAGCUCCCCCAUUUUGGUGAGCGAAUUUGCGCACUUUUAUGACACUAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAAC
...........-........................((((.((......)).))))....((((((.......(((((.....)))))......(((((.....))))))))))). ( -25.10)
>DroAna_CAF1 95501 115 + 1
UCACCCCUCUA-AUAAUACUUUCUUUUGAAAUACAAGCUCCCCCAUUCGCCUGGCCAAAUUUGCGCAUUUUCGUGACACUAAAUGUCACUAAUUUGACAGAAAAUGUCAGCGCAGA
...........-.......((((....))))..((.((..........)).))......(((((((......((((((.....)))))).....(((((.....)))))))))))) ( -24.00)
>consensus
UCACCCCUCUA_AUAAUACUUCCUUUUGAUAUACAAGUUCCCCCAUUUUCGUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAAC
....................................((((.(........).))))....((((((......((((((.....)))))).....(((((.....))))))))))). (-19.85 = -20.47 +   0.61)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,613,821 – 10,613,937
Length 116
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 86.65
Mean single sequence MFE -32.57
Consensus MFE -25.43
Energy contribution -25.27
Covariance contribution -0.17
Combinations/Pair 1.16
Mean z-score -2.62
Structure conservation index 0.78
SVM decision value 0.48
SVM RNA-class probability 0.753613
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10613821 116 - 22407834
GUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCACGAAAAUGGGGGAACUUGUAUAUCAUAAGGAAGUAUUACUUAGAGGGGUGA
.((((((((((((...)))))).....(((((((...)))))))......))))))..((((((......(..((....))..)...((.((((.........)))))).)))))) ( -33.50)
>DroSec_CAF1 93441 104 - 1
GUUGCGCUGACAUUUUGUGUCAAAUUAGUGACAUUUAGUGUCACUAAAGUGCGCAAAUUCGCUCACGAAAAUGGGGGAAGU-----------AAGAAGUUUUAC-UAGAGGGGUGA
.((((((((((((...))))))..((((((((((...))))))))))...))))))..((((((.(.....(((..(((.(-----------....).)))..)-))..))))))) ( -33.20)
>DroSim_CAF1 93823 115 - 1
GUUGCGCUGACAUUUUGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCAAAAAAAUGGGGGAACUUGUAUAUCAAAAGGAUGUAUUAC-UAGAGGGGUGA
.(((((((((((((..((((((......))))))..))))))).......))))))..((((((........(((....)))(((((((.....)))))))...-.....)))))) ( -34.61)
>DroEre_CAF1 94112 114 - 1
GUUGCGCUGACAUUUCUUGUCAAAUUAGUGACAUUUAGUGUCAUAAAAAUGCGCAAAAUCGCUCACCAAAAUGGGGGAACUCGUAUAUCAAAAAGAAGUAUUAU-U-GAGGGGUGA
.(((((((((((((...(((((......)))))...))))))).......))))))..((((((..(((...(((....)))((((.((.....)).))))..)-)-)..)))))) ( -34.01)
>DroYak_CAF1 96811 115 - 1
GUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCAUAAAAGUGCGCAAAUUCGCUCACCAAAAUGGGGGAGCUUGUAUAUCAAAAAGCAGUAUUAU-UAGAGGGGUGA
.(((((((((((((..((((((......))))))..))))))).......))))))..((((((.((.....))....((((..........))))........-.....)))))) ( -32.81)
>DroAna_CAF1 95501 115 - 1
UCUGCGCUGACAUUUUCUGUCAAAUUAGUGACAUUUAGUGUCACGAAAAUGCGCAAAUUUGGCCAGGCGAAUGGGGGAGCUUGUAUUUCAAAAGAAAGUAUUAU-UAGAGGGGUGA
..((((((((((.....))))).....(((((((...)))))))......)))))......(((...(..(..((....))..).((((....)))).......-..)...))).. ( -27.30)
>consensus
GUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCACGAAAAUGGGGGAACUUGUAUAUCAAAAAGAAGUAUUAC_UAGAGGGGUGA
.(((((((((((.....))))).....(((((((...)))))))......)))))).(((.((((......)))).)))..................................... (-25.43 = -25.27 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,613,861 – 10,613,976
Length 115
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 93.18
Mean single sequence MFE -30.90
Consensus MFE -24.92
Energy contribution -25.00
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -2.50
Structure conservation index 0.81
SVM decision value 0.50
SVM RNA-class probability 0.760413
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10613861 115 + 22407834
CCCCAUUUUCGUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUG
..((((.(((((.((.....((((((......((((((.....)))))).....(((((.....)))))))))))))...))))).))))..((((.((..-....)))))).... ( -31.70)
>DroSec_CAF1 93469 115 + 1
CCCCAUUUUCGUGAGCGAAUUUGCGCACUUUAGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUG
..((((.(((((.((.....((((((...(((((((((.....)))))))))..(((((.....)))))))))))))...))))).))))..((((.((..-....)))))).... ( -35.10)
>DroSim_CAF1 93862 115 + 1
CCCCAUUUUUUUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUG
...((((((((((((((...((((((......((((((.....)))))).....(((((.....)))))))))))....)))...(((.....))))))))-))))))........ ( -30.30)
>DroEre_CAF1 94150 115 + 1
CCCCAUUUUGGUGAGCGAUUUUGCGCAUUUUUAUGACACUAAAUGUCACUAAUUUGACAAGAAAUGUCAGCGCAACUAAUGCGAGUAUGGAAUGUGUCAGA-AAAAUGCAUAACUG
.........(((..(((....)))((((((((.((((((....(((.(((...((((((.....))))))((((.....))))))))))....)))))).)-)))))))...))). ( -29.40)
>DroYak_CAF1 96850 115 + 1
CCCCAUUUUGGUGAGCGAAUUUGCGCACUUUUAUGACACUAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUG
...((((((((((.(((....))).))))....(((((.....)))))....(((((((((..((((...((((.....)))).))))....)))))))))-))))))........ ( -26.90)
>DroAna_CAF1 95540 116 + 1
CCCCAUUCGCCUGGCCAAAUUUGCGCAUUUUCGUGACACUAAAUGUCACUAAUUUGACAGAAAAUGUCAGCGCAGAUAAUGCGAAUAUGGAAUGUGUCGGAUAAAAUGCAUAACUG
((..((((((........((((((((......((((((.....)))))).....(((((.....)))))))))))))...))))))..)).((((((........))))))..... ( -32.00)
>consensus
CCCCAUUUUCGUGAGCGAAUUUGCGCACUUUUGUGACACUAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA_AAAAUGCAUAACUG
..((((........(((...((((((......((((((.....)))))).....(((((.....)))))))))))....)))....))))..((((.((.......)))))).... (-24.92 = -25.00 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,613,861 – 10,613,976
Length 115
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 93.18
Mean single sequence MFE -30.82
Consensus MFE -25.73
Energy contribution -25.70
Covariance contribution -0.03
Combinations/Pair 1.08
Mean z-score -2.32
Structure conservation index 0.83
SVM decision value 0.93
SVM RNA-class probability 0.884514
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10613861 115 - 22407834
CAGUUAUGCAUUUU-UCUGACACAUUCCAUAUUCGCAUUAGUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCACGAAAAUGGGG
(((..(......).-.)))......(((((.((((((.....)))(.(((((((..((((((......))))))..))))))))....(((.((......)).)))))).))))). ( -30.90)
>DroSec_CAF1 93469 115 - 1
CAGUUAUGCAUUUU-UCUGACACAUUCCAUAUUCGCAUUAGUUGCGCUGACAUUUUGUGUCAAAUUAGUGACAUUUAGUGUCACUAAAGUGCGCAAAUUCGCUCACGAAAAUGGGG
......(.((((((-(.(((((((.........((((.....)))).........)))))))..((((((((((...)))))))))).(((.((......)).)))))))))).). ( -34.27)
>DroSim_CAF1 93862 115 - 1
CAGUUAUGCAUUUU-UCUGACACAUUCCAUAUUCGCAUUAGUUGCGCUGACAUUUUGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCAAAAAAAUGGGG
.......(((((((-(.(((((((.........((((.....)))).........))))))).....(((((((...))))))))))))))).........((((......)))). ( -31.17)
>DroEre_CAF1 94150 115 - 1
CAGUUAUGCAUUUU-UCUGACACAUUCCAUACUCGCAUUAGUUGCGCUGACAUUUCUUGUCAAAUUAGUGACAUUUAGUGUCAUAAAAAUGCGCAAAAUCGCUCACCAAAAUGGGG
.......(((((((-(.((((((..........((((.....)))).(((((.....)))))...............)))))).))))))))((......))...((.....)).. ( -29.40)
>DroYak_CAF1 96850 115 - 1
CAGUUAUGCAUUUU-UCUGACACAUUCCAUAUUCGCAUUAGUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCAUAAAAGUGCGCAAAUUCGCUCACCAAAAUGGGG
.......(((((((-(.((((((..........((((.....))))..........((((((......))))))...)))))).))))))))((......))...((.....)).. ( -29.70)
>DroAna_CAF1 95540 116 - 1
CAGUUAUGCAUUUUAUCCGACACAUUCCAUAUUCGCAUUAUCUGCGCUGACAUUUUCUGUCAAAUUAGUGACAUUUAGUGUCACGAAAAUGCGCAAAUUUGGCCAGGCGAAUGGGG
..........................((.(((((((...((.((((((((((.....))))).....(((((((...)))))))......))))).))........))))))))). ( -29.50)
>consensus
CAGUUAUGCAUUUU_UCUGACACAUUCCAUAUUCGCAUUAGUUGCGCUGACAUUUCGUGUCAAAUUAGUGACAUUUAGUGUCACAAAAGUGCGCAAAUUCGCUCACGAAAAUGGGG
.......(((((((...((((((..........((((.....)))).(((((.....)))))...............))))))..))))))).........((((......)))). (-25.73 = -25.70 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,613,900 – 10,614,016
Length 116
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 93.07
Mean single sequence MFE -31.39
Consensus MFE -26.36
Energy contribution -26.42
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -2.54
Structure conservation index 0.84
SVM decision value 1.36
SVM RNA-class probability 0.946220
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10613900 116 + 22407834
UAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUGGCGAGCUUUUUACCAGUUUUCUGUCGCAUUAGUGGCCACA
.....((((((((.((((((.....))))))((((.....)))).........((((.((((-((........(((((..((...))..))))))))))).)))))))))))).... ( -31.60)
>DroSec_CAF1 93508 116 + 1
UAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUGGCGAGCUUUUUACCAGUAUUCUGUCGCAUUAGUGGCCACA
.....(((((((((((((((((..((((...((((.....)))).))))....)))))))))-....(((((((((((..((...))..)))))....))).))))))))))).... ( -32.30)
>DroSim_CAF1 93901 116 + 1
UAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUGGCGAGCUUUUUACCAGUUUUCUGUCGCAUUAGUGGCCACA
.....(((((((((((((((((..((((...((((.....)))).))))....)))))))))-....(((((((((((..((...))..)))))....))).))))))))))).... ( -32.30)
>DroEre_CAF1 94189 116 + 1
UAAAUGUCACUAAUUUGACAAGAAAUGUCAGCGCAACUAAUGCGAGUAUGGAAUGUGUCAGA-AAAAUGCAUAACUGGCAAGCUUUCUACCAGCUUUCUGUCGCAUUAGUGGCCACA
.....(((((((((.(((((.((((((((((((((.....)))).........((((.((..-....)))))).)))))).(((.......)))))))))))).))))))))).... ( -33.70)
>DroYak_CAF1 96889 116 + 1
UAAAUGUCACUAAUUUGACACGAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA-AAAAUGCAUAACUGGCAAGUUUUUUACCAGCUUUCUGUCGCAUUAGUGGACACA
....((((......((((((.....))))))....((((((((((....((((.((((.(((-((..(((.......)))..))))).))..)).)))).)))))))))).)))).. ( -30.20)
>DroAna_CAF1 95579 117 + 1
UAAAUGUCACUAAUUUGACAGAAAAUGUCAGCGCAGAUAAUGCGAAUAUGGAAUGUGUCGGAUAAAAUGCAUAACUGGCUAGCUUCUCCCCAACAAUCUGUCGCAUUAGAUGCCACA
..............((((((.....)))))).(((..((((((((....(((.(((...(((......((.......)).......)))...))).))).))))))))..))).... ( -28.22)
>consensus
UAAAUGUCACUAAUUUGACACAAAAUGUCAGCGCAACUAAUGCGAAUAUGGAAUGUGUCAGA_AAAAUGCAUAACUGGCGAGCUUUUUACCAGCUUUCUGUCGCAUUAGUGGCCACA
.....(((((((((.(((((......(((((((((.....)))).........((((.((.......)))))).)))))(((((.......)))))..))))).))))))))).... (-26.36 = -26.42 +   0.06)

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 10:57:47 2006