Locus 3233

Sequence ID X_DroMel_CAF1
Location 8,550,720 – 8,550,943
Length 223
Max. P 0.954147
window5308 window5309 window5310

overview

Window 8

Location 8,550,720 – 8,550,840
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.26
Mean single sequence MFE -22.63
Consensus MFE -20.32
Energy contribution -20.72
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.90
SVM decision value 1.44
SVM RNA-class probability 0.954147
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8550720 120 + 22224390
UUUUUGUUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCACCAGGGCCGUCAGAGGGGAAAAUAAAUAGAAGGAAAAAAGGGGC
(((((.(((((((.....(((...((((((((.(.((((((...)))))).)....))))))))...)))(((((....)))))))))))).)))))....................... ( -26.30)
>DroSec_CAF1 11530 113 + 1
------UUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCACCAGGGCCGACAGAGGGGAAAAUAAAUAGAAGGAAA-AAGGGGC
------(((((.......(((...((((((((.(.((((((...)))))).)....))))))))...)))(((((....)))))..))))).....................-....... ( -20.20)
>DroSim_CAF1 17740 113 + 1
------UUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCACCAGGGCCGACAGAGGGGAAAAUAAAUAGAAGGAAA-AAGGGGC
------(((((.......(((...((((((((.(.((((((...)))))).)....))))))))...)))(((((....)))))..))))).....................-....... ( -20.20)
>DroEre_CAF1 12134 109 + 1
------UUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCCCCAGGGCCGUCAGAGGGGAAAA---AGA-GCGGGAA-AGGGGUG
------.((((((((.........((((((((.(.((((((...)))))).)....))))))))))))))))..((((....((((............---...-))))...-.)))).. ( -24.16)
>DroYak_CAF1 13260 110 + 1
------UUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCACCAGGGCCGUCAGAGGGAAAAA---AGAAGAGGAAA-AAGGGGG
------(((((((.....(((...((((((((.(.((((((...)))))).)....))))))))...)))(((((....)))))))))))).......---...........-....... ( -22.30)
>consensus
______UUCUGAUUGAAUUGAAAACAUUUUAUGCAUUUGAUUUAAUCAAAAGAAAAAUAGAAUGCAGUCAGGUUCACCAGGGCCGUCAGAGGGGAAAAUAAAUAGAAGGAAA_AAGGGGC
......(((((((.....(((...((((((((.(.((((((...)))))).)....))))))))...)))(((((....))))))))))))............................. (-20.32 = -20.72 +   0.40)

alignment

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secondary structure

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Window 9

Location 8,550,720 – 8,550,840
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.26
Mean single sequence MFE -15.74
Consensus MFE -13.02
Energy contribution -13.42
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.83
SVM decision value 0.21
SVM RNA-class probability 0.634873
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8550720 120 - 22224390
GCCCCUUUUUUCCUUCUAUUUAUUUUCCCCUCUGACGGCCCUGGUGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAACAAAAA
..............................(((((.......((....))(((..(((((.(((......((((((...))))))...))).)))))..)))......)))))....... ( -14.60)
>DroSec_CAF1 11530 113 - 1
GCCCCUU-UUUCCUUCUAUUUAUUUUCCCCUCUGUCGGCCCUGGUGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAA------
(((....-............................))).((((((((..(((..(((((.(((......((((((...))))))...))).)))))..))).))).)))))..------ ( -14.35)
>DroSim_CAF1 17740 113 - 1
GCCCCUU-UUUCCUUCUAUUUAUUUUCCCCUCUGUCGGCCCUGGUGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAA------
(((....-............................))).((((((((..(((..(((((.(((......((((((...))))))...))).)))))..))).))).)))))..------ ( -14.35)
>DroEre_CAF1 12134 109 - 1
CACCCCU-UUCCCGC-UCU---UUUUCCCCUCUGACGGCCCUGGGGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAA------
..((((.-...(((.-((.---...........)))))....))))...((((.((((((..((((.((....))..))))..)))))).....((....))......))))..------ ( -20.80)
>DroYak_CAF1 13260 110 - 1
CCCCCUU-UUUCCUCUUCU---UUUUUCCCUCUGACGGCCCUGGUGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAA------
.......-...........---........(((((.......((....))(((..(((((.(((......((((((...))))))...))).)))))..)))......))))).------ ( -14.60)
>consensus
GCCCCUU_UUUCCUUCUAUUUAUUUUCCCCUCUGACGGCCCUGGUGAACCUGACUGCAUUCUAUUUUUCUUUUGAUUAAAUCAAAUGCAUAAAAUGUUUUCAAUUCAAUCAGAA______
..............................(((((.......((....))(((..(((((.(((......((((((...))))))...))).)))))..)))......)))))....... (-13.02 = -13.42 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,550,840 – 8,550,943
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -21.90
Consensus MFE -19.56
Energy contribution -19.96
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.89
SVM decision value 0.14
SVM RNA-class probability 0.604201
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8550840 103 - 22224390
GGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUUCAUUUCAUUUCAAUGCCCAGCACC-----------------CCACCACCCCCUUGACCCCGUUGACCCCCGUGCA
((((...(((((......(((((((.(((((((((........)))).)))))..))))((...))...-----------------...........)))......)))))))))..... ( -19.30)
>DroSec_CAF1 11643 94 - 1
GGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUGCAUUUCAUUUCAAUGCCCAC-------------------------CGCCCCC-UGACCCCGUUGACCCCCGUGCA
((((...(((((..((((((((..((((......))))...)))))))).....(((..((....-------------------------.))....-))).....)))))))))..... ( -23.20)
>DroSim_CAF1 17853 101 - 1
NGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUGCAUUUCAUUUCAAUGCCCACCGC------------------CCACCGCCCCC-UGACCCCGUUGACCCCCGUGCA
.(((...(((((..((((((((..((((......))))...)))))))).................((------------------.....))....-........))))).)))..... ( -20.50)
>DroEre_CAF1 12243 94 - 1
GGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUGCAUUUCAUUUCAAUGCCCACCA-------------------------CCCCC-UGACCCCUUUGACCCCCGUGCG
((((...((((((..((((.....))))((((((((((......))).)))))))............-------------------------.....-.......))))))))))..... ( -22.40)
>DroYak_CAF1 13370 119 - 1
GGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUGCAUUUCAUUUCAAUGCCCACCAACCCACCAAAGCAACCAACCCACCGCCCCC-UGACCCCUUUGACCCCCGUGCA
((((...((((((.((((((((..((((......))))...)))))))).........(((................))).................-.......))))))))))..... ( -24.09)
>consensus
GGGGACCGUCAAACAAUGCAAAUUGCAUGAAUGAAUGCCAUUUUGCAUUUCAUUUCAAUGCCCACCA___________________CCACCGCCCCC_UGACCCCGUUGACCCCCGUGCA
((((...(((((...((((.....))))((((((((((......))).)))))))...................................................)))))))))..... (-19.56 = -19.96 +   0.40)

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 10:54:30 2006