Locus 1699

Sequence ID 2L_DroMel_CAF1
Location 4,644,991 – 4,645,190
Length 199
Max. P 0.957544
window2723 window2724 window2725

overview

Window 3

Location 4,644,991 – 4,645,110
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 65.89
Mean single sequence MFE -28.28
Consensus MFE -13.16
Energy contribution -12.85
Covariance contribution -0.31
Combinations/Pair 1.39
Mean z-score -2.18
Structure conservation index 0.47
SVM decision value 1.48
SVM RNA-class probability 0.957544
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4644991 119 + 22407834
AUCCACCAGGAUCACAGAAGCCUCCUAAUGUGGGAAUAUACCCCCCAUCCACGGGCUGGAUUCCGCCAUCUGGGCCACUAACUCAAAGUGGACAUCCACCAGGAUCACUGUUGCCUCCU
...((.(((((((.....(((((....(((.(((........))))))....)))))(((((((((....((((.......))))..))))).)))).....)))).))).))...... ( -33.70)
>DroSec_CAF1 81813 119 + 1
AUCCACCAGGAUCACAGAAGCCUCCUAAUUCCGGUAUAUACCCCCCAUCCACGGGCUGGACUUUGCCAUCUGGGCUACCAAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGCCUCCA
........(((...(((((((((.........(((....)))..........)))))((......)).))))(((.((((.(((..(((((....)))))..)))...)))))))))). ( -36.21)
>DroEre_CAF1 86018 94 + 1
-------------------------UAAUUCUGGAUUACAUCCUCCACAACAGAACUGGAUUCUGCCUCCUGGACCACCAAACCAAGGUGAACAUCCACCUGGAUCACUGAUGCCUCCC
-------------------------.......(((...((((.((((...(((((.....))))).....))))........(((.((((......)))))))......))))..))). ( -20.20)
>DroYak_CAF1 85761 94 + 1
-------------------------UAACUUAGGAACAAACCCUUCAUUACCGGGCUGGAUUCUGCCUCCUGCGCCACCAAAUCUAGGUGGACAUCCACCAGGAACACAGCUGCCUCCU
-------------------------......((((......((.........))((((..((((((.....)).............(((((....))))).))))..))))....)))) ( -23.00)
>consensus
_________________________UAAUUCAGGAAUAUACCCCCCAUCAACGGGCUGGAUUCUGCCACCUGGGCCACCAAAUCAAGGUGGACAUCCACCAGGAUCACUGAUGCCUCCU
................................(((.....((.(((......)))..)).........(((((.(((((.......))))).......)))))............))). (-13.16 = -12.85 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,645,070 – 4,645,190
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -34.10
Consensus MFE -28.13
Energy contribution -29.47
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.83
SVM decision value 0.25
SVM RNA-class probability 0.651765
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4645070 120 + 22407834
AACUCAAAGUGGACAUCCACCAGGAUCACUGUUGCCUCCUAAUACUGGAUUGCCACCGGGCUCUAUUCCGCCUCUUCGACCACCAAAUCAAGGUGGACAUCCACCAGGAUCACAGAAGCC
...((...((((....))))...))...((((....((((.....(((((..(((((((((........))))....((........))..)))))..)))))..))))..))))..... ( -30.90)
>DroSec_CAF1 81892 120 + 1
AAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGCCUCCAAUUUCUGUAUUGCCACCGGGCUCUAUUCCGCCUCUUCGACCACCAAUUCAGGGUGGACAUCCACCAGGAUCACUGAAGCC
..(((..((((((..((((((..((....(((((....((((......)))).....((((........)))).......)))))..))..))))))..))))))..))).......... ( -37.10)
>DroSim_CAF1 74192 120 + 1
AAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGCCUCCAAUUUCUGUAUUGCCACCGGGCUCUAUUCCGCCUCUUCGACCACCAAUUCAAGGUGGACAACCACCAGGAUCACAGAAGCC
..(((..(((((....)))))..)))...(((.....))).(((((((.((((((((((((........))))....((........))..))))).)))((....))...))))))).. ( -34.30)
>consensus
AAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGCCUCCAAUUUCUGUAUUGCCACCGGGCUCUAUUCCGCCUCUUCGACCACCAAUUCAAGGUGGACAUCCACCAGGAUCACAGAAGCC
......((((((((...(((((.......))))).................(((....)))....))))))))((((..(((((.......)))))..((((....))))....)))).. (-28.13 = -29.47 +   1.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,645,070 – 4,645,190
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -43.57
Consensus MFE -37.45
Energy contribution -38.23
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.86
SVM decision value 0.05
SVM RNA-class probability 0.556992
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4645070 120 - 22407834
GGCUUCUGUGAUCCUGGUGGAUGUCCACCUUGAUUUGGUGGUCGAAGAGGCGGAAUAGAGCCCGGUGGCAAUCCAGUAUUAGGAGGCAACAGUGAUCCUGGUGGAUGUCCACUUUGAGUU
...........((..((((((((((((((.....((((..((((..(.(((........))))..))))...))))....((((.((....))..))))))))))))))))))..))... ( -44.80)
>DroSec_CAF1 81892 120 - 1
GGCUUCAGUGAUCCUGGUGGAUGUCCACCCUGAAUUGGUGGUCGAAGAGGCGGAAUAGAGCCCGGUGGCAAUACAGAAAUUGGAGGCACCAUUGAUCCUGGUGGAUUUCCACCUUGAUUU
.........((((..((((((.(((((((..(.((..(((((((..(.(((........))))..))((....(((...)))...)))))))..)).).))))))).))))))..)))). ( -43.20)
>DroSim_CAF1 74192 120 - 1
GGCUUCUGUGAUCCUGGUGGUUGUCCACCUUGAAUUGGUGGUCGAAGAGGCGGAAUAGAGCCCGGUGGCAAUACAGAAAUUGGAGGCACCAUUGAUCCUGGUGGAUUUCCACCUUGAUUU
.........((((..(((((..(((((((..((.(..(((((((..(.(((........))))..))((....(((...)))...)))))))..)))..)))))))..)))))..)))). ( -42.70)
>consensus
GGCUUCUGUGAUCCUGGUGGAUGUCCACCUUGAAUUGGUGGUCGAAGAGGCGGAAUAGAGCCCGGUGGCAAUACAGAAAUUGGAGGCACCAUUGAUCCUGGUGGAUUUCCACCUUGAUUU
.........((((..((((((.(((((((..((..(((((((((..(.(((........))))..))))....(.......)....)))))....))..))))))).))))))..)))). (-37.45 = -38.23 +   0.78)

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 10:08:52 2006