Locus 2601

Sequence ID 2R_DroMel_CAF1
Location 9,178,631 – 9,178,773
Length 142
Max. P 0.843277
window4285 window4286

overview

Window 5

Location 9,178,631 – 9,178,738
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.68
Mean single sequence MFE -36.38
Consensus MFE -20.42
Energy contribution -21.53
Covariance contribution 1.11
Combinations/Pair 1.19
Mean z-score -2.10
Structure conservation index 0.56
SVM decision value 0.76
SVM RNA-class probability 0.843277
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9178631 107 - 20766785
UUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUAUUGUUCACGCCGAGAAGAUUGUCUACCAGAAGAAGUUCGCUGAACAAAUCGCGAU------U---GAGGAGGCUAAA----
.((...(((((((((((((((.....)))))))))))))))...)).(((.....((((((((......))).((((...))))......))))------)---.....)))....---- ( -32.50)
>DroSec_CAF1 62935 107 - 1
UUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUGUUGUUCAUGCCGAGAAGAUGGUCUACCAGAAGAAGUUCGCUGAACAAAUUGCGAU------U---GAGGAGGCUAUA----
((((((...((((((((((((.....)))))))))))).(((((((.((.(((....(((....))).......)))))))))))).)))))).------.---............---- ( -34.20)
>DroSim_CAF1 55274 107 - 1
UUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUGUUGUUCAUGCCGAGAAGAUGGUCUACCAGAAAAAGUUCGCUGAACAAAUUGCGAU------U---GAGGAGGCUAUA----
((((((...((((((((((((.....)))))))))))).(((((((.((.(((....(((....))).......)))))))))))).)))))).------.---............---- ( -34.20)
>DroEre_CAF1 59730 107 - 1
UUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUGUUGUUCACGCCGAGAAGAUUGUCUACCAGCAGAAGUUCGCUGAACAAAUUGCGGC------U---GAGGAGGCGGAG----
((((..((..((((((((((.......))))))))))..)).((((.((((...((.((((....((((........)))).)))).)).))))------)---)))...))))..---- ( -32.60)
>DroYak_CAF1 54147 107 - 1
UUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUACUGUGCAUGCCGAGAAGCUUGUCUACCAGCAGAAGUUUGCUGAACAAAUUGCGGC------U---GAGGAGGCAGAG----
.((((.((((((((((((((.......)))))))))))))).))))((((.(((......)))..((((...((((((.....))))))...))------)---)....))))...---- ( -40.50)
>DroAna_CAF1 57496 120 - 1
UGGUCCGCUGCAUGCUGAAGGGCAUUAAGAAGGGCUGCCUGCUCCACGCCCAGAAGAAGAUCUGCGCCCAGAAGGACGCCAAGCAGAAUGCGGCAGCCAUUGCCGCCGAGGCGGAGAAGG
((((..(((((((.(((...(((........((((.....)).))..((.((((......)))).))((....))..)))...))).))))))).))))...((((....))))...... ( -44.30)
>consensus
UUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUGUUGUUCACGCCGAGAAGAUGGUCUACCAGAAGAAGUUCGCUGAACAAAUUGCGAC______U___GAGGAGGCUAAA____
.((...((((((((((((((.......))))))))))))))...)).(((.(((......)))............((((..........))))................)))........ (-20.42 = -21.53 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,178,658 – 9,178,773
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.11
Mean single sequence MFE -39.17
Consensus MFE -23.33
Energy contribution -24.72
Covariance contribution 1.39
Combinations/Pair 1.11
Mean z-score -1.91
Structure conservation index 0.60
SVM decision value 0.40
SVM RNA-class probability 0.721730
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9178658 115 - 20766785
AAAGCCUCA-----GGGUGAUCCCAAGUCUGUAGAUUCUCUUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUAUUGUUCACGCCGAGAAGAUUGUCUACCAGAAGAAGUUCGCU
..(((....-----(((....)))...(((((((((..((((....(((((((((((((((.....))))))))))))))).(((.....)))))))..))))).))))........))) ( -39.40)
>DroSec_CAF1 62962 115 - 1
AAAGCCGAA-----GGGUGAUCCCAAGGCCGUAGAUUCUCUUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUGUUGUUCAUGCCGAGAAGAUGGUCUACCAGAAGAAGUUCGCU
..(((.(((-----(((....))).(((((((...(((((.((...((..(((((((((((.....)))))))))))..))...))....))))).)))))))...........)))))) ( -43.40)
>DroSim_CAF1 55301 115 - 1
AAAGCCGAA-----GGGUGAUCCCAAGGCCGUAGAUUCUCUUGUAAAGUGCAUGCUUUCUGGCAUACAGAAGGCGUGUGUUGUUCAUGCCGAGAAGAUGGUCUACCAGAAAAAGUUCGCU
..(((.(((-----(((....))).(((((((...(((((.((...((..(((((((((((.....)))))))))))..))...))....))))).)))))))...........)))))) ( -43.40)
>DroEre_CAF1 59757 115 - 1
GAAGCAGCA-----GGGGGAUCCCAAGUCCGUAGAUUCUCUUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUGUUGUUCACGCCGAGAAGAUUGUCUACCAGCAGAAGUUCGCU
..((((((.-----(((....)))..((..((((((..((((....((..((((((((((.......))))))))))..)).(((.....)))))))..))))))..))....))).))) ( -35.80)
>DroYak_CAF1 54174 115 - 1
AAAGCCACA-----GGGUGAUCCCAAGUCCGUAGAUUCACUUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUACUGUGCAUGCCGAGAAGCUUGUCUACCAGCAGAAGUUUGCU
..(((.((.-----(((....)))..((..((((((.....((((.((((((((((((((.......)))))))))))))).)))).((......))..))))))..))....))..))) ( -37.50)
>DroAna_CAF1 57536 120 - 1
GAAAAGGAAUUCUCGCACGAUCCCCCCGCCGUGGACAAGCUGGUCCGCUGCAUGCUGAAGGGCAUUAAGAAGGGCUGCCUGCUCCACGCCCAGAAGAAGAUCUGCGCCCAGAAGGACGCC
.....(...((((((((.((((.....((.((((((......)))))).))........((((....((.(((....))).))....)))).......))))))))...))))...)... ( -35.50)
>consensus
AAAGCCGAA_____GGGUGAUCCCAAGGCCGUAGAUUCUCUUGUAAAGUGCAUGCUUUCUGGCAUAAAGAAGGCGUGUGUUGUUCACGCCGAGAAGAUGGUCUACCAGAAGAAGUUCGCU
..(((.........(((....)))......((((((..((((.(.......(((((....)))))......((((((.......)))))).).))))..))))))............))) (-23.33 = -24.72 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:11 2006