Locus 2408

Sequence ID 2R_DroMel_CAF1
Location 8,674,981 – 8,675,126
Length 145
Max. P 0.883622
window3988 window3989 window3990

overview

Window 8

Location 8,674,981 – 8,675,091
Length 110
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 88.73
Mean single sequence MFE -32.70
Consensus MFE -26.90
Energy contribution -28.14
Covariance contribution 1.24
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.82
SVM decision value 0.93
SVM RNA-class probability 0.883622
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8674981 110 - 20766785
AAAAAUAGGGUAAAAA------CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACAACACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
................------.((.((((((((((((((..((((.......)))).))))))))).))))).))((((..((((((.......))))))..))))......... ( -35.50)
>DroSec_CAF1 329 110 - 1
AAAAAUAGUGUAAAAA------CGUGAUGGUUUGCCUGCUGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACACCACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
.......((((.....------.((..((((((((((((.((..........)).)))))))))))).))....))))....((((((.......))))))(((((.....))))) ( -31.20)
>DroSim_CAF1 59 110 - 1
AAAAAUAGUGUAAAAA------CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACACCACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
.......((((.....------.((.((((((((((((((..((((.......)))).))))))))).))))).))))))..((((((.......))))))(((((.....))))) ( -35.10)
>DroEre_CAF1 59 114 - 1
AGAAAUAGGGCAAAAAC--GAGCGUGAUAGCUGGCCGGCCGUACAAAAAUCAGCUGUAGGCAAGCCAGACUAUAGCAUACCACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
........(((((....--..((...(((((((((..(((.((((.........)))))))..))))).)))).))......((((((.......))))))..)))))........ ( -32.90)
>DroYak_CAF1 59 112 - 1
AGAAAUAUGCCAAAAUCAAAAGCGUGAUAGUUGGC----CGCACAAAAAUCAGCUGUAGGCAGGCCAGACUAUAGCAUGCCACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
........(((..((((....((((((((((((((----((((((.........)))..)).))))).)))))..)))))..((((((.......))))))))))...)))..... ( -28.80)
>consensus
AAAAAUAGGGUAAAAA______CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACACCACUUACGUUCAUCUUGUAGGGAUUGUCGGUCAGUC
.......................((.((((((((((((((..((((.......)))).)))))))))).)))).))......((((((.......))))))(((((.....))))) (-26.90 = -28.14 +   1.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,675,017 – 8,675,126
Length 109
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 85.97
Mean single sequence MFE -27.94
Consensus MFE -19.36
Energy contribution -20.88
Covariance contribution 1.52
Combinations/Pair 1.16
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value 0.17
SVM RNA-class probability 0.617140
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8675017 109 + 20766785
UUGUGCUAUAGUCUGGCCUGCCUACAACUGAUUUUUGUGCGGCAGGCCAACCAUCACG------UUUUUACCCUAUUUUUGGCAGCAGUUUUGUUAUCUCACAGCACGCACUUCA
..(((((...(..((((((((((((((.......))))).)))))))))..)......------...............((((((.....))))))......)))))........ ( -32.00)
>DroSec_CAF1 365 109 + 1
GUGUGCUAUAGUCUGGCCUGCCUACAACUGAUUUUUGUGCAGCAGGCAAACCAUCACG------UUUUUACACUAUUUUUGGCAGCAGUUUUGUUAUCUCACAGCACUCACUCCA
(.((((((((((...((((((.(((((.......)))))..))))))((((......)------)))....)))))...((((((.....))))))......))))).)...... ( -24.00)
>DroSim_CAF1 95 109 + 1
GUGUGCUAUAGUCUGGCCUGCCUACAACUGAUUUUUGUGCGGCAGGCCAACCAUCACG------UUUUUACACUAUUUUUGGCAGCAGUUUUGUUAUCUCACAGCACUCACUCCA
(.((((((((((.((((((((((((((.......))))).)))))))))........(------(....)))))))...((((((.....))))))......))))).)...... ( -32.70)
>DroEre_CAF1 95 113 + 1
GUAUGCUAUAGUCUGGCUUGCCUACAGCUGAUUUUUGUACGGCCGGCCAGCUAUCACGCUC--GUUUUUGCCCUAUUUCUGUCAGCAGUUUGGUUAUCUCAUAUCACUCACUCCA
...((((((((.((((((.((((((((.......))))).))).))))))))))...((..--......))............))))(..((((........))))..)...... ( -27.60)
>DroYak_CAF1 95 110 + 1
GCAUGCUAUAGUCUGGCCUGCCUACAGCUGAUUUUUGUGCG----GCCAACUAUCACGCUUUUGAUUUUGGCAUAUUUCUGGCAGCAGUUUUGUUAUCUCAUAGC-CUCACUCCA
((.(((((((((.(((((.((..((((.......)))))))----))))))))....(((.........))).......))))))).(((.((......)).)))-......... ( -23.40)
>consensus
GUGUGCUAUAGUCUGGCCUGCCUACAACUGAUUUUUGUGCGGCAGGCCAACCAUCACG______UUUUUACCCUAUUUUUGGCAGCAGUUUUGUUAUCUCACAGCACUCACUCCA
..(((((...((.((((((((((((((.......))))).))))))))))).............................(..(((......)))..)....)))))........ (-19.36 = -20.88 +   1.52)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,675,017 – 8,675,126
Length 109
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 85.97
Mean single sequence MFE -31.82
Consensus MFE -21.82
Energy contribution -24.46
Covariance contribution 2.64
Combinations/Pair 1.09
Mean z-score -2.37
Structure conservation index 0.69
SVM decision value 0.78
SVM RNA-class probability 0.849184
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8675017 109 - 20766785
UGAAGUGCGUGCUGUGAGAUAACAAAACUGCUGCCAAAAAUAGGGUAAAAA------CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACAA
....((((((..(((......)))..))...((((........))))....------....((((((((((((((..((((.......)))).))))))))).))))).)))).. ( -37.20)
>DroSec_CAF1 365 109 - 1
UGGAGUGAGUGCUGUGAGAUAACAAAACUGCUGCCAAAAAUAGUGUAAAAA------CGUGAUGGUUUGCCUGCUGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACAC
((((((.(((..(((......)))..)))))).)))......((((.....------.((..((((((((((((.((..........)).)))))))))))).))....)))).. ( -33.30)
>DroSim_CAF1 95 109 - 1
UGGAGUGAGUGCUGUGAGAUAACAAAACUGCUGCCAAAAAUAGUGUAAAAA------CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACAC
((((((.(((..(((......)))..)))))).)))......((......)------)(((((((((((((((((..((((.......)))).))))))))).)))))..))).. ( -36.90)
>DroEre_CAF1 95 113 - 1
UGGAGUGAGUGAUAUGAGAUAACCAAACUGCUGACAGAAAUAGGGCAAAAAC--GAGCGUGAUAGCUGGCCGGCCGUACAAAAAUCAGCUGUAGGCAAGCCAGACUAUAGCAUAC
....((.(((..(.((.......)).)..))).)).................--..((...(((((((((..(((.((((.........)))))))..))))).)))).)).... ( -27.70)
>DroYak_CAF1 95 110 - 1
UGGAGUGAG-GCUAUGAGAUAACAAAACUGCUGCCAGAAAUAUGCCAAAAUCAAAAGCGUGAUAGUUGGC----CGCACAAAAAUCAGCUGUAGGCAGGCCAGACUAUAGCAUGC
....(((.(-((((.............(((....)))...(((((...........))))).....))))----).)))........(((((((..........))))))).... ( -24.00)
>consensus
UGGAGUGAGUGCUGUGAGAUAACAAAACUGCUGCCAAAAAUAGGGUAAAAA______CGUGAUGGUUGGCCUGCCGCACAAAAAUCAGUUGUAGGCAGGCCAGACUAUAGCACAC
((((((.(((..(((......)))..)))))).)))......................((.((((((((((((((..((((.......)))).)))))))))).)))).)).... (-21.82 = -24.46 +   2.64)

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 10:29:27 2006