Locus 8453

Sequence ID 3L_DroMel_CAF1
Location 22,264,622 – 22,264,850
Length 228
Max. P 0.958993
window13818 window13819 window13820 window13821 window13822

overview

Window 8

Location 22,264,622 – 22,264,736
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.16
Mean single sequence MFE -35.08
Consensus MFE -27.95
Energy contribution -29.07
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.80
SVM decision value 0.20
SVM RNA-class probability 0.628926
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22264622 114 + 23771897
UUGUUGGUUUGCGUUUUAUUUAAAUUUGCUUCUUUCGGCUGCCUUUUUGCUC------GUGCGGUGGUUGUUUGUCGCCCGAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUUCGUG
.....(((((((((((.....)))).(((((..(((((((((..((....((------(.((((..(....)..)))).)))......))..)))))))))))))).)).)))))..... ( -30.90)
>DroSec_CAF1 22959 111 + 1
UUGUUGGUUUGCGUUUUAUUUAAAUUUGCU---UUCGGCUGCCUUUUUGCUC------GCGCGGUGGUUGUUUGUCGCCCGAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUG
..((..((((((((((.....)))).((((---(((((((((..((....((------(.((((..(....)..)))).)))......))..))))))).)))))).)).))))..)).. ( -36.20)
>DroSim_CAF1 13176 114 + 1
UUGUUGGUUUGCGUUUUAUUUAAAUUUGCUUCUUUCGGCUGCCUUUUUGCUC------GCGCGGUGGUUGUUUGUCGCCCGAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUG
..((..((((((((((.....)))).(((((..(((((((((..((....((------(.((((..(....)..)))).)))......))..)))))))))))))).)).))))..)).. ( -36.20)
>DroEre_CAF1 22016 120 + 1
UUGUUGGUUUGCGUUUUAUUUAAAUUUGCUUCUUUCGGCUGGCUUUUUGCUCCUGCUUGCUCGGUGGUUGUCUGUCGCCCGAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUG
..(..((...(((..((.....))..)))..))..)(((..((((...((...(((((..(((((.((((((..((....))......)))))).))))).))))).)).))))..))). ( -37.00)
>consensus
UUGUUGGUUUGCGUUUUAUUUAAAUUUGCUUCUUUCGGCUGCCUUUUUGCUC______GCGCGGUGGUUGUUUGUCGCCCGAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUG
..((((((((((((((.....)))).(((((..(((((((((......((........))((((..(....)..))))..............)))))))))))))).)).)))))))).. (-27.95 = -29.07 +   1.12)

alignment

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secondary structure

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Window 9

Location 22,264,662 – 22,264,776
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.02
Mean single sequence MFE -31.61
Consensus MFE -25.73
Energy contribution -26.04
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.93
Structure conservation index 0.81
SVM decision value 0.36
SVM RNA-class probability 0.705093
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22264662 114 - 23771897
GCAAAUCAUUAAUUUGCUUUGAGCCAGAGCAAAAAGAAAGCACGAAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUCGGGCGACAAACAACCACCGCAC------GAGCAAAAAGGC
(((((((.....(((((((((...)))))))))..((((((.....))))((((.(((....))))))).)).)))))(((.(((............))).)------))))........ ( -28.00)
>DroSec_CAF1 22996 114 - 1
GCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUCGGGCGACAAACAACCACCGCGC------GAGCAAAAAGGC
(((((((.....(((((((((...)))))))))..((.((((((.(((.......))).....)))))).)).)))))(((.(((............))).)------))))........ ( -33.30)
>DroSim_CAF1 13216 114 - 1
GCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUCGGGCGACAAACAACCACCGCGC------GAGCAAAAAGGC
(((((((.....(((((((((...)))))))))..((.((((((.(((.......))).....)))))).)).)))))(((.(((............))).)------))))........ ( -33.30)
>DroEre_CAF1 22056 120 - 1
GCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUCGGGCGACAGACAACCACCGAGCAAGCAGGAGCAAAAAGCC
((..........(((((((((...)))))))))....((((.....)))).))..((((((..(((.((((..(....((((..............)))).)..)))).))).)))))). ( -31.84)
>consensus
GCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUCGGGCGACAAACAACCACCGCGC______GAGCAAAAAGGC
(((((((.....(((((((((...)))))))))..((.((((((.(((.......))).....)))))).)).))))).(((..............)))...........))........ (-25.73 = -26.04 +   0.31)

alignment

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secondary structure

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Window 0

Location 22,264,696 – 22,264,816
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -30.94
Consensus MFE -28.83
Energy contribution -30.57
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.93
SVM decision value 1.19
SVM RNA-class probability 0.927733
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22264696 120 + 23771897
GAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUUCGUGCUUUCUUUUUGCUCUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUG
....(((((.((((((((....))).))))((((((..((.(((...((((((.((((......((......))....))))...)))))).))).)).))))))....))))))..... ( -28.60)
>DroSec_CAF1 23030 120 + 1
GAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUGCUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUG
........((.(((((((....(((.......)))))))))).))..(((((((((...))))))))).....(((((((....((((.............))))....))))))).... ( -31.72)
>DroSim_CAF1 13250 120 + 1
GAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUGCUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUG
........((.(((((((....(((.......)))))))))).))..(((((((((...))))))))).....(((((((....((((.............))))....))))))).... ( -31.72)
>DroEre_CAF1 22096 120 + 1
GAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUGCUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUG
........((.(((((((....(((.......)))))))))).))..(((((((((...))))))))).....(((((((....((((.............))))....))))))).... ( -31.72)
>consensus
GAAAAUCUGACAGCAGCUGAAAAGCAUGCUAAGCUGGCUGCUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUG
....((((...(((((((....))).))))..(((....(((((...(((((((((...)))))))))......((((((......))))))......))))).....)))))))..... (-28.83 = -30.57 +   1.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,264,696 – 22,264,816
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -35.70
Consensus MFE -34.21
Energy contribution -34.02
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -3.19
Structure conservation index 0.96
SVM decision value 1.50
SVM RNA-class probability 0.958993
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22264696 120 - 23771897
CAGAGAUCUGCUUUGAAGCUUUUGAUUUAUUUGCUUGAUGGCAAAUCAUUAAUUUGCUUUGAGCCAGAGCAAAAAGAAAGCACGAAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUC
..(((((((((((((..((((((.....(((((((....)))))))......(((((((((...)))))))))..)))))).)))))).(((((.(((....))))))))..))))))). ( -38.10)
>DroSec_CAF1 23030 120 - 1
CAGAGAUCUGCUUUGAAGCUUUUGAUUUAUUUGCUUGAUGGCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUC
..(((((((((((((((((..(((((..(((((((....))))))).)))))...)))).....)))))).....((.((((((.(((.......))).....)))))).))))))))). ( -34.90)
>DroSim_CAF1 13250 120 - 1
CAGAGAUCUGCUUUGAAGCUUUUGAUUUAUUUGCUUGAUGGCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUC
..(((((((((((((((((..(((((..(((((((....))))))).)))))...)))).....)))))).....((.((((((.(((.......))).....)))))).))))))))). ( -34.90)
>DroEre_CAF1 22096 120 - 1
CAGAGAUCUGCUUUGAAGCUUUUGAUUUAUUUGCUUGAUGGCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUC
..(((((((((((((((((..(((((..(((((((....))))))).)))))...)))).....)))))).....((.((((((.(((.......))).....)))))).))))))))). ( -34.90)
>consensus
CAGAGAUCUGCUUUGAAGCUUUUGAUUUAUUUGCUUGAUGGCAAAUCAUUAAUUUGCUUUGAGCCAAAGCAAAAAGAAAGCAGCCAGCUUAGCAUGCUUUUCAGCUGCUGUCAGAUUUUC
..((((((((.......((((((.....(((((((....)))))))......(((((((((...)))))))))..))))))........(((((.(((....)))))))).)))))))). (-34.21 = -34.02 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,264,736 – 22,264,850
Length 114
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 89.24
Mean single sequence MFE -31.41
Consensus MFE -30.74
Energy contribution -31.60
Covariance contribution 0.86
Combinations/Pair 1.03
Mean z-score -1.42
Structure conservation index 0.98
SVM decision value 0.74
SVM RNA-class probability 0.838129
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22264736 114 + 23771897
CUUUCUUUUUGCUCUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUGGCUUAGCGCGCUGCGCUGUGGUGCGGUGCGAUGG-
.......((((((.((((......((......))....))))...))))))...(((....(((...((((((....)).)))))))(((((((((....))))))))))))..- ( -33.90)
>DroSec_CAF1 23070 115 + 1
CUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUGGCUUAGCGCGCUGCGCUGCGGUGCGGUGCGGUGGG
.......(((((((((...))))))))).....(((((((....((((.............))))....))))))).....((((.((((((((((....)))))))))).)))) ( -39.62)
>DroEre_CAF1 22136 99 + 1
CUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUGGCUUAGCGCG---------------GUGCGGUGG-
.......(((((((((...))))))))).....(((((((....((((.............))))....))))))).......((.(((.---------------..))).)).- ( -20.72)
>consensus
CUUUCUUUUUGCUUUGGCUCAAAGCAAAUUAAUGAUUUGCCAUCAAGCAAAUAAAUCAAAAGCUUCAAAGCAGAUCUCUGGCUUAGCGCGCUGCGCUG_GGUGCGGUGCGGUGG_
.......(((((((((...)))))))))...........(((((.................(((...((((((....)).)))))))(((((((((....)))))))))))))). (-30.74 = -31.60 +   0.86)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:45 2006