Locus 1738

Sequence ID 3R_DroMel_CAF1
Location 5,008,073 – 5,008,171
Length 98
Max. P 0.875749
window2859 window2860

overview

Window 9

Location 5,008,073 – 5,008,171
Length 98
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -21.52
Consensus MFE -11.83
Energy contribution -12.17
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.55
SVM decision value 0.79
SVM RNA-class probability 0.851946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5008073 98 + 27905053
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG---------UAAGCUAUUGCAAACACCCGCACAACUGAACGCACUCUUAUUU---------U
..(((((((((.(((((((.....(((.......)))......)))))))...)---------)))))...(((........))).....))).............---------. ( -19.30)
>DroSec_CAF1 114695 97 + 1
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG---------UAAACUAUUGCACACACAAGCACA-CUGCACGCACUCCUAUUU---------U
.....((((.(.((((.((((....(((((...((((.....)))).....)))---------))....)))))))).).))))...-..................---------. ( -17.70)
>DroSim_CAF1 118614 98 + 1
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG---------UAAGCUAUUGCACACACAAGCACAACUGCACGCACUCCUAUUU---------U
.....((((((.(((((((.....(((.......)))......)))))))...)---------)))))..............(((....)))..............---------. ( -19.10)
>DroEre_CAF1 116222 107 + 1
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG---------UAAGCUAUUGCACACAUUCGCACAACUGCACGCACUCUUACUGUGUGCUGUGU
.....((((((.(((((((.....(((.......)))......)))))))...)---------)))))..............(((((...(((((((.......)))))))))))) ( -30.10)
>DroYak_CAF1 117413 107 + 1
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUGUGCAAGUAGUAAGCUAUUGCACACACCCGCACUGCUGCACGCACUCGUACUG---------A
...((((......))))......(((((.....((((.....)))).......(((((.(((((..((...((....))...))))))))))))))))).......---------. ( -25.30)
>DroAna_CAF1 110746 79 + 1
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG---------UCGGGUCAAACACACCCACGCA-------------------UA---------U
.....((.....(((((((.....(((.......)))......)))))))...(---------(.((((.......)))))))).-------------------..---------. ( -17.60)
>consensus
CUUUCGCUUAUUUGUGACAAUUAAGUGCAAAUUACACAUUCUGUGUCACACUUG_________UAAGCUAUUGCACACACACGCACAACUGCACGCACUCCUAUUU_________U
.....((.....(((((((.....(((.......)))......)))))))................((....))........))................................ (-11.83 = -12.17 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,008,073 – 5,008,171
Length 98
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -27.82
Consensus MFE -15.61
Energy contribution -16.98
Covariance contribution 1.36
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.56
SVM decision value 0.89
SVM RNA-class probability 0.875749
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5008073 98 - 27905053
A---------AAAUAAGAGUGCGUUCAGUUGUGCGGGUGUUUGCAAUAGCUUA---------CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
.---------(((((...(..((......))..)...)))))......(((((---------....(((((((...((.((((.....))))))...)))))))..)))))..... ( -24.20)
>DroSec_CAF1 114695 97 - 1
A---------AAAUAGGAGUGCGUGCAG-UGUGCUUGUGUGUGCAAUAGUUUA---------CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
.---------........(..((..(((-.....)))..))..)....(((((---------....(((((((...((.((((.....))))))...)))))))..)))))..... ( -24.70)
>DroSim_CAF1 118614 98 - 1
A---------AAAUAGGAGUGCGUGCAGUUGUGCUUGUGUGUGCAAUAGCUUA---------CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
.---------........(..((..(((......)))..))..)....(((((---------....(((((((...((.((((.....))))))...)))))))..)))))..... ( -27.30)
>DroEre_CAF1 116222 107 - 1
ACACAGCACACAGUAAGAGUGCGUGCAGUUGUGCGAAUGUGUGCAAUAGCUUA---------CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
.....(((((((......(..((......))..)...)))))))....(((((---------....(((((((...((.((((.....))))))...)))))))..)))))..... ( -33.60)
>DroYak_CAF1 117413 107 - 1
U---------CAGUACGAGUGCGUGCAGCAGUGCGGGUGUGUGCAAUAGCUUACUACUUGCACAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
(---------(.(((((....))))).((.(((((((((((.((....)).))).))))))))...(((((((...((.((((.....))))))...))))))).....))))... ( -36.10)
>DroAna_CAF1 110746 79 - 1
A---------UA-------------------UGCGUGGGUGUGUUUGACCCGA---------CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
.---------..-------------------(((((((((.......)))).)---------)...(((((((...((.((((.....))))))...))))))).....))).... ( -21.00)
>consensus
A_________AAAUAAGAGUGCGUGCAGUUGUGCGUGUGUGUGCAAUAGCUUA_________CAAGUGUGACACAGAAUGUGUAAUUUGCACUUAAUUGUCACAAAUAAGCGAAAG
...................((((..((..........))..))))...(((((.............(((((((...((.((((.....))))))...)))))))..)))))..... (-15.61 = -16.98 +   1.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:08 2006