Locus 3373

Sequence ID 2L_DroMel_CAF1
Location 9,779,581 – 9,779,675
Length 94
Max. P 0.984245
window5340 window5341

overview

Window 0

Location 9,779,581 – 9,779,675
Length 94
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 87.60
Mean single sequence MFE -18.96
Consensus MFE -18.07
Energy contribution -18.19
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -2.15
Structure conservation index 0.95
SVM decision value 1.97
SVM RNA-class probability 0.984245
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9779581 94 + 22407834
GACGUCAGGAAAGUCAUUGAGCUAUAAUUUAAUAGCCAGCGACUGCUAUGUCUGGCCAAAAAGAACAAA-AAAGUGGUAACGAAA-----GCAAAAA-AA--A
(((((.((...((((.(((.(((((......)))))))).)))).)))))))..((((...........-....))))..(....-----)......-..--. ( -19.06)
>DroSec_CAF1 61923 94 + 1
GACGUCAGGAAAGUCAUUGAGCUAUAAUUUAAUAGCCAGCGACUGCUAUGUCUGGCCAAAAAGAGCAAA-AAAGUGGUAACGAAA-----GCAAAAA-AA--A
(((((.((...((((.(((.(((((......)))))))).)))).)))))))..((((...........-....))))..(....-----)......-..--. ( -19.06)
>DroEre_CAF1 60537 101 + 1
GACGUCAGGAAAGUCAUUGAGCUAUAAUUUAAUAGCCAGCGACUGCUACGUCUGGCCAAAAAGAACAAA--AAGUGGUAACAAAAAAUAAACAGAAAAAUACA
(((((.((...((((.(((.(((((......)))))))).)))).)))))))..((((...........--...))))......................... ( -20.44)
>DroYak_CAF1 62651 98 + 1
GACGUCAGGGAAGUCAUUGAGCCACAAUUUGAUAGCCAGCGACUGCUAUGUCUGGCCAAAAAGAACAAAAAAAGUGGCAACAAAA-----AUACAAAAAUACA
(((.........))).....(((((.........((((..(((......)))))))(.....)..........))))).......-----............. ( -17.30)
>consensus
GACGUCAGGAAAGUCAUUGAGCUAUAAUUUAAUAGCCAGCGACUGCUAUGUCUGGCCAAAAAGAACAAA_AAAGUGGUAACAAAA_____ACAAAAA_AA__A
(((((.((...((((.(((.(((((......)))))))).)))).)))))))..((((................))))......................... (-18.07 = -18.19 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 9,779,581 – 9,779,675
Length 94
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 87.60
Mean single sequence MFE -17.60
Consensus MFE -16.36
Energy contribution -15.55
Covariance contribution -0.81
Combinations/Pair 1.17
Mean z-score -1.26
Structure conservation index 0.93
SVM decision value 0.02
SVM RNA-class probability 0.545330
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9779581 94 - 22407834
U--UU-UUUUUGC-----UUUCGUUACCACUUU-UUUGUUCUUUUUGGCCAGACAUAGCAGUCGCUGGCUAUUAAAUUAUAGCUCAAUGACUUUCCUGACGUC
.--..-.......-----...(((((.......-((((..(.....)..))))......(((((.(((((((......))))).)).)))))....))))).. ( -16.40)
>DroSec_CAF1 61923 94 - 1
U--UU-UUUUUGC-----UUUCGUUACCACUUU-UUUGCUCUUUUUGGCCAGACAUAGCAGUCGCUGGCUAUUAAAUUAUAGCUCAAUGACUUUCCUGACGUC
.--..-.......-----...(((((.......-..((((.....((......)).))))((((.(((((((......))))).)).)))).....))))).. ( -16.20)
>DroEre_CAF1 60537 101 - 1
UGUAUUUUUCUGUUUAUUUUUUGUUACCACUU--UUUGUUCUUUUUGGCCAGACGUAGCAGUCGCUGGCUAUUAAAUUAUAGCUCAAUGACUUUCCUGACGUC
...........(((.......((((((.....--((((..(.....)..)))).))))))((((.(((((((......))))).)).))))......)))... ( -17.40)
>DroYak_CAF1 62651 98 - 1
UGUAUUUUUGUAU-----UUUUGUUGCCACUUUUUUUGUUCUUUUUGGCCAGACAUAGCAGUCGCUGGCUAUCAAAUUGUGGCUCAAUGACUUCCCUGACGUC
.((......((..-----..(((..(((((....((((.......(((((((((......)))..)))))).))))..))))).)))..)).......))... ( -20.42)
>consensus
U__AU_UUUUUGC_____UUUCGUUACCACUUU_UUUGUUCUUUUUGGCCAGACAUAGCAGUCGCUGGCUAUUAAAUUAUAGCUCAAUGACUUUCCUGACGUC
.....................(((((...((...((((..(.....)..))))...)).(((((.(((((((......))))).)).)))))....))))).. (-16.36 = -15.55 +  -0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:54 2006