Locus 3480

Sequence ID 3R_DroMel_CAF1
Location 9,409,019 – 9,409,131
Length 112
Max. P 0.621980
window5597 window5598

overview

Window 7

Location 9,409,019 – 9,409,131
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 81.44
Mean single sequence MFE -23.35
Consensus MFE -19.41
Energy contribution -19.73
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.49
Structure conservation index 0.83
SVM decision value 0.18
SVM RNA-class probability 0.621980
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9409019 112 + 27905053
GCAUUUGGGCAUACUUUGCACGCCGGCACAUUGGCAAUUGCAUUCACAUACCAUAAGCCGGGUGUUUCCCCCCCCCUCCCCCUUCCAGCACUCUAGCAUUCCAGUGCCAAAA
(((((.(((........((((.(((((....(((....((......))..)))...)))))))))........)))...........((......)).....)))))..... ( -25.99)
>DroSec_CAF1 38622 88 + 1
GCAUUUGGGCAUACUUUGCACGCCGGCACAUUGGCAAUUGCAUUCACAUACCAUAAGCCGGGUGUUUCCCCCC------------------------UUUCCAGUUCACAAA
......(((........((((.(((((....(((....((......))..)))...))))))))).....)))------------------------............... ( -19.72)
>DroEre_CAF1 39659 86 + 1
GCAUUUGGGCAUACUUUGCACGCCGGCACAUUGGCAAUUGCAUUCACAUACCAUAAGCCGGGUGUUCCCUC--------------------------AUCCCGCUGCCAAAA
(((..((((........((((.(((((....(((....((......))..)))...)))))))))......--------------------------..)))).)))..... ( -23.79)
>DroYak_CAF1 40723 85 + 1
GCAUUUGGGCAUACUUUGCACGCCGGCACAUUGGCAAUUGCAUUCACAUACCAUAAGCCGGGUGUUUCCUC--------------------------AUUCCAGUGCCAAA-
(((((.(((........((((.(((((....(((....((......))..)))...)))))))))......--------------------------..))))))))....- ( -23.89)
>consensus
GCAUUUGGGCAUACUUUGCACGCCGGCACAUUGGCAAUUGCAUUCACAUACCAUAAGCCGGGUGUUUCCCC__________________________AUUCCAGUGCCAAAA
(((((.(((((.....)))((.(((((....(((....((......))..)))...))))))).....................................)))))))..... (-19.41 = -19.73 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 9,409,019 – 9,409,131
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 81.44
Mean single sequence MFE -29.98
Consensus MFE -23.15
Energy contribution -24.90
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.77
SVM decision value 0.10
SVM RNA-class probability 0.584643
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9409019 112 - 27905053
UUUUGGCACUGGAAUGCUAGAGUGCUGGAAGGGGGAGGGGGGGGGAAACACCCGGCUUAUGGUAUGUGAAUGCAAUUGCCAAUGUGCCGGCGUGCAAAGUAUGCCCAAAUGC
(((..(((((..........)))))..))).........(((.(....).)))(((...((((((((....)))..)))))....)))(((((((...)))))))....... ( -36.90)
>DroSec_CAF1 38622 88 - 1
UUUGUGAACUGGAAA------------------------GGGGGGAAACACCCGGCUUAUGGUAUGUGAAUGCAAUUGCCAAUGUGCCGGCGUGCAAAGUAUGCCCAAAUGC
........((....)------------------------)((((....).)))(((...((((((((....)))..)))))....)))(((((((...)))))))....... ( -28.00)
>DroEre_CAF1 39659 86 - 1
UUUUGGCAGCGGGAU--------------------------GAGGGAACACCCGGCUUAUGGUAUGUGAAUGCAAUUGCCAAUGUGCCGGCGUGCAAAGUAUGCCCAAAUGC
....((((..(((.(--------------------------(......)))))(((.....((((....))))....)))....))))(((((((...)))))))....... ( -27.60)
>DroYak_CAF1 40723 85 - 1
-UUUGGCACUGGAAU--------------------------GAGGAAACACCCGGCUUAUGGUAUGUGAAUGCAAUUGCCAAUGUGCCGGCGUGCAAAGUAUGCCCAAAUGC
-...(((((......--------------------------..(....)....(((.....((((....))))....)))...)))))(((((((...)))))))....... ( -27.40)
>consensus
UUUUGGCACUGGAAU__________________________GAGGAAACACCCGGCUUAUGGUAUGUGAAUGCAAUUGCCAAUGUGCCGGCGUGCAAAGUAUGCCCAAAUGC
....(((((..............................(((.(....).)))(((.....((((....))))....)))...)))))(((((((...)))))))....... (-23.15 = -24.90 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:14 2006