Locus 3866

Sequence ID 3R_DroMel_CAF1
Location 10,522,160 – 10,522,319
Length 159
Max. P 0.636496
window6191 window6192 window6193

overview

Window 1

Location 10,522,160 – 10,522,266
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.88
Mean single sequence MFE -31.68
Consensus MFE -17.27
Energy contribution -17.58
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -1.60
Structure conservation index 0.55
SVM decision value 0.21
SVM RNA-class probability 0.636496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10522160 106 - 27905053
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCAGUCGGAAGGAGAAAAGUCAAAAGGUGAGUUCCCUGAAAAGUCGCU-----------UAAGUCCGGGGGAAAUUCAAAUGC
...((((....(((((..((((((((((.((((.---((.....)).))))....)))...(((.(....)))).....))))))-----------)..).)))).)))).......... ( -30.80)
>DroSec_CAF1 172402 108 - 1
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCAUCAUCAGUCGGAAGGAGAAAAGCCAAAAGGUGAGUUCCCGGAAAAGUCGCU-----------UAAGUU-GCGGGAAAAUCAAAUGA
...(((((((((......(((((((....((((....((.....)).((.(((..(((....)))...)))))))))..))))))-----------)..)))-))))))........... ( -34.50)
>DroSim_CAF1 68983 105 - 1
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCAGUCGGAAGGAGAAAAGCCAAAAGGUGAGUUCCCGGAAAAGUCGCU-----------UAAGUU-GGGGGAAAAUCAAAUGA
...((((....(((((..(((((((....((((.---((.....)).((.(((..(((....)))...)))))))))..))))))-----------)..)))-)).)))).......... ( -32.60)
>DroEre_CAF1 68443 103 - 1
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCAGUCGGAAGGAGAAAAGCCAAAAGGUGAGUUCCCGGAAAAGUAGCA-----------UAAGUC---GGAAGGUUUAAAUCC
.....((((.((((((....))..)))).((((.---((.....)).((.(((..(((....)))...)))))))))..))))..-----------(((..(---....)..)))..... ( -30.60)
>DroYak_CAF1 69376 94 - 1
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCAGUCGGAAGGAGAAAAGCCAAAAGGUGAGUUCCCGGAAAAGUU-----------------------GGGAAAAUCAAAUCC
...((((.(.((((((....))..)))).((((.---......))))).))))..(((....)))((.(((((((.....))-----------------------)))))..))...... ( -27.80)
>DroAna_CAF1 57067 100 - 1
--------CUGCCAGCGGAAGCUGCCGCGG---------AGGGCGGCGGGGGAAAGCCAAGAGGUGAGUCGCCGGAAAAUGGGAAAACUCCCAAUAAAAGUC---UGAAAGUGCAUGUGC
--------((((((((....))))..))))---------.((((..(((.((...(((....)))...)).))).....(((((....)))))......)))---).............. ( -33.80)
>consensus
ACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA___UCAGUCGGAAGGAGAAAAGCCAAAAGGUGAGUUCCCGGAAAAGUCGCU___________UAAGUC___GGGAAAAUCAAAUGC
..........((((((....))..)))).((((..........))))((.(((..(((....)))...)))))............................................... (-17.27 = -17.58 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,522,229 – 10,522,319
Length 90
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 82.56
Mean single sequence MFE -29.77
Consensus MFE -19.31
Energy contribution -20.32
Covariance contribution 1.00
Combinations/Pair 1.17
Mean z-score -1.68
Structure conservation index 0.65
SVM decision value -0.04
SVM RNA-class probability 0.512543
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10522229 90 + 27905053
UGA---UGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGCAGCAGCGGUAGCAAAAACAAAUGCAAG
.((---(((....)))))(((.((((..(((((...(((((((......))))))).....)))))....)))).)))............... ( -31.30)
>DroPse_CAF1 66985 78 + 1
U---------CAGCUGUGGCCUCCGCAA-CCCCACAG-----UGCUGCCAACAUAUGUUGAGCGAGAGCAACAACAGUGCCAGCAGUUGCAGC
.---------..(((((((.........-..))))))-----)(((((.(((...(((((.((....))..)))))((....)).)))))))) ( -25.60)
>DroSec_CAF1 172470 93 + 1
UGAUGAUGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGCAGCAGCGGUAGCAAAAACAAAUGCAAG
....(((((....)))))(((.((((..(((((...(((((((......))))))).....)))))....)))).)))............... ( -31.30)
>DroSim_CAF1 69051 90 + 1
UGA---UGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGCAGCAGCGGUAGCAAAAACAAAUGCAAG
.((---(((....)))))(((.((((..(((((...(((((((......))))))).....)))))....)))).)))............... ( -31.30)
>DroEre_CAF1 68509 90 + 1
UGA---UGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGAAGCAGCGGUAGCAAAAACAAAUGCAAG
.((---(((....)))))(((.((((.(.((((...(((((((......))))))).....))))...).)))).)))............... ( -27.80)
>DroYak_CAF1 69433 90 + 1
UGA---UGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGCAGCAGCGGUAGCAGAAACAAAUGCAAG
.((---(((....)))))(((.((((..(((((...(((((((......))))))).....)))))....)))).)))............... ( -31.30)
>consensus
UGA___UGGAACGCCGUCGCUUCCGCCGGCUGCAGAAUGUGUUGUUGCAAGCAUGUGUUGAGCAGCAGCAGCGGUAGCAAAAACAAAUGCAAG
............((((.((....)).))))((((.....(((((((((.(((....)))..)))))))))((....)).........)))).. (-19.31 = -20.32 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,522,229 – 10,522,319
Length 90
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 82.56
Mean single sequence MFE -25.95
Consensus MFE -21.53
Energy contribution -21.07
Covariance contribution -0.47
Combinations/Pair 1.50
Mean z-score -1.36
Structure conservation index 0.83
SVM decision value 0.08
SVM RNA-class probability 0.572253
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10522229 90 - 27905053
CUUGCAUUUGUUUUUGCUACCGCUGCUGCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCA
.........((..(((((.((((((..(((((............................))))))))))).)))))..))......---... ( -25.79)
>DroPse_CAF1 66985 78 - 1
GCUGCAACUGCUGGCACUGUUGUUGCUCUCGCUCAACAUAUGUUGGCAGCA-----CUGUGGGG-UUGCGGAGGCCACAGCUG---------A
.(..((.((((..(((.(((((..((....)).)))))..)))..))))..-----.))..)((-(((.((...)).))))).---------. ( -27.50)
>DroSec_CAF1 172470 93 - 1
CUUGCAUUUGUUUUUGCUACCGCUGCUGCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCAUCAUCA
.........((..(((((.((((((..(((((............................))))))))))).)))))..))............ ( -25.79)
>DroSim_CAF1 69051 90 - 1
CUUGCAUUUGUUUUUGCUACCGCUGCUGCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCA
.........((..(((((.((((((..(((((............................))))))))))).)))))..))......---... ( -25.79)
>DroEre_CAF1 68509 90 - 1
CUUGCAUUUGUUUUUGCUACCGCUGCUUCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCA
...(((........)))..(((.((((((((((........(((.(((...........)))))).)))))))))).))).......---... ( -24.00)
>DroYak_CAF1 69433 90 - 1
CUUGCAUUUGUUUCUGCUACCGCUGCUGCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA---UCA
...((..(((((((((((...((((((((.((.........))..)))............))))).)))))))))))..))......---... ( -26.80)
>consensus
CUUGCAUUUGUUUUUGCUACCGCUGCUGCUGCUCAACACAUGCUUGCAACAACACAUUCUGCAGCCGGCGGAAGCGACGGCGUUCCA___UCA
.........(((.(((((.((((((((((...........((....))............)))).)))))).))))).)))............ (-21.53 = -21.07 +  -0.47)

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 11:12:00 2006