Locus 1914

Sequence ID 2L_DroMel_CAF1
Location 5,225,769 – 5,225,923
Length 154
Max. P 0.995490
window3078 window3079 window3080

overview

Window 8

Location 5,225,769 – 5,225,884
Length 115
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 79.97
Mean single sequence MFE -26.19
Consensus MFE -19.88
Energy contribution -20.38
Covariance contribution 0.50
Combinations/Pair 1.05
Mean z-score -2.39
Structure conservation index 0.76
SVM decision value 2.08
SVM RNA-class probability 0.987564
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5225769 115 - 22407834
AAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUCAAAAAAAAAAAAUAGGAAUAUGAAAGCGCGGUCUAUUUGGUUCGCCACUGUUCGAAA
........((((((((....(((((((..(((....)))..)))))))((((((((((...............)))).)))))).....)))))))).((((........)))). ( -29.76)
>DroSec_CAF1 3241 99 - 1
AAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAAU------AUA----------GUAUUUUGUUCCCCGCUACUCGAAA
..........(((((.....(((((((..(((....)))..))))))).((((.....)))).((((((((------(..----------.)))))))))..)))))........ ( -24.30)
>DroSim_CAF1 4131 99 - 1
AAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAGU------AUA----------GUAUUUGGUUCCCCGCUACUCGAAA
..........(((((.....(((((((..(((....)))..)))))))..........(((.(((((....------...----------.)))))..))).)))))........ ( -23.20)
>DroYak_CAF1 4285 111 - 1
AAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGAAAAUGCCCUGCCAAUAGGAAAAAAU----UAGAAAUAUGAAAAUGUAGUGUAUUUUGUUCCCCACUACUCAAAA
..........(((((.....(((((((..(((....)))..))))))).........(((((((((----.....((((....)))).....))))).)))))))))........ ( -27.50)
>consensus
AAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAAU______AUA__________GUAUUUGGUUCCCCACUACUCGAAA
..........(((((.....(((((((..(((....)))..))))))).((((.....))))........................................)))))........ (-19.88 = -20.38 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,225,806 – 5,225,923
Length 117
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 85.59
Mean single sequence MFE -19.52
Consensus MFE -17.74
Energy contribution -18.30
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.91
SVM decision value 2.32
SVM RNA-class probability 0.992251
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5225806 117 + 22407834
UAUUCCUAUUUUUUUUUUUUGAAUUGAAAGGGCAUUUCCCAGUCACCUGUUAAAUACCAAAUUCCACUUGUGGCAUUUGUGCUUUUCUGCACGUUUUCCUCCGUUCAAUUUU-UUUAU
....................((((((((.(((.........(((((..((..(((.....)))..))..)))))....((((......)))).......))).)))))))).-..... ( -21.10)
>DroSec_CAF1 3268 112 + 1
U------AUUCUAUUUUUUCUAAUUGAAAGGGCAUUUCCCAGUCACCUGUUAAAUACCAAAUUCCACUUGUGGCAUUUGUGCUUUUCCGCACGUUUUCCUCCAUUCAAUUUUUUUUAU
.------..............(((((((.(((.........(((((..((..(((.....)))..))..)))))....((((......)))).......))).)))))))........ ( -19.20)
>DroSim_CAF1 4158 106 + 1
U------ACUCUAUUUUUUCUAAUUGAAAGGGCAUUUCCCAGUCACCUGUUAAAUACCAAAUUCCACUUGUGGCAUUUGUGCUUUUCCGCACGUUUUCCUCCAUUCAAUUUU------
.------..............(((((((.(((.........(((((..((..(((.....)))..))..)))))....((((......)))).......))).)))))))..------ ( -19.20)
>DroYak_CAF1 4322 114 + 1
UAUUUCUA----AUUUUUUCCUAUUGGCAGGGCAUUUUCCAGUCACCUGUUAAAUACCAAAUUCCACUUGUGGCAUUUGUGCUUUUCUGCACGUUUUCCUCCGUUCAUUUUGUUUUUG
........----.............((.((((.........(((((..((..(((.....)))..))..)))))....((((......))))....))))))................ ( -18.60)
>consensus
U______AUUCUAUUUUUUCUAAUUGAAAGGGCAUUUCCCAGUCACCUGUUAAAUACCAAAUUCCACUUGUGGCAUUUGUGCUUUUCCGCACGUUUUCCUCCAUUCAAUUUU_UUUAU
.....................(((((((.(((.........(((((..((..(((.....)))..))..)))))....((((......)))).......))).)))))))........ (-17.74 = -18.30 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,225,806 – 5,225,923
Length 117
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -29.90
Consensus MFE -28.56
Energy contribution -28.62
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -5.15
Structure conservation index 0.96
SVM decision value 2.58
SVM RNA-class probability 0.995490
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5225806 117 - 22407834
AUAAA-AAAAUUGAACGGAGGAAAACGUGCAGAAAAGCACAAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUCAAAAAAAAAAAAUAGGAAUA
.....-....(((((.(((((.....((((......))))((((.(((....))).))))(((((((..(((....)))..))))))))))))..))))).................. ( -30.50)
>DroSec_CAF1 3268 112 - 1
AUAAAAAAAAUUGAAUGGAGGAAAACGUGCGGAAAAGCACAAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAAU------A
..........((((.((((((.....((((......))))((((.(((....))).))))(((((((..(((....)))..))))))))))))).))))............------. ( -31.30)
>DroSim_CAF1 4158 106 - 1
------AAAAUUGAAUGGAGGAAAACGUGCGGAAAAGCACAAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAGU------A
------....((((.((((((.....((((......))))((((.(((....))).))))(((((((..(((....)))..))))))))))))).))))............------. ( -31.30)
>DroYak_CAF1 4322 114 - 1
CAAAAACAAAAUGAACGGAGGAAAACGUGCAGAAAAGCACAAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGAAAAUGCCCUGCCAAUAGGAAAAAAU----UAGAAAUA
................((.((.....((((......))))((((.(((....))).))))(((((((..(((....)))..))))))))).)).............----........ ( -26.50)
>consensus
AUAAA_AAAAUUGAACGGAGGAAAACGUGCAGAAAAGCACAAAUGCCACAAGUGGAAUUUGGUAUUUAACAGGUGACUGGGAAAUGCCCUUUCAAUUAGAAAAAAUAGAAU______A
................(((((.....((((......))))((((.(((....))).))))(((((((..(((....)))..))))))))))))......................... (-28.56 = -28.62 +   0.06)

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 10:14:33 2006