Locus 5396

Sequence ID	3R_DroMel_CAF1
Location	14,181,705 – 14,181,836
Length	131
Max. P	0.999612

overview

Window 7

Location	14,181,705 – 14,181,812
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	84.74
Mean single sequence MFE	-42.40
Consensus MFE	-35.72
Energy contribution	-35.60
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-3.95
Structure conservation index	0.84
SVM decision value	3.78
SVM RNA-class probability	0.999612
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14181705 107 + 27905053
CGCGGCGUAUACGCAAUACGCGGAAUAGGUGGCGUAUACGUAACGCAAUGCAGAGUGAAAAUGUGUGUAUGUGUGUGUUUGGAAUACGCGGCGUAUACGCAAUGCGA
(((.((((((((((....(((.......)))((((((.((..((((((((((..((....))...))))).)))))...))..)))))).))))))))))...))). ( -41.40)
>DroSec_CAF1 173916 103 + 1
CGCGGCGUAUACGCAAAACGCGGAAUAGGUGGCGUAUACGUAACGCACUGCAGAGUGUAU----AUGUGUGUGUGUGUUUGGGUUACGCGGCGUAUACGCAAUGCGA
.(((((((((((((...((.(......))).))))))))))..)))..((((..((((((----((((.((((((.........))))))))))))))))..)))). ( -42.10)
>DroSim_CAF1 59213 105 + 1
CGCGGCGUAUACGCAAUACGCGGAAUAGGUGGCGUAUACGCAACGCACUGCAGAGUGUGU--GUCUGUGUGUGUGUGUUUGGGAUACGCGGCGUAUACGCAAUGCGA
(((.((((((((((.(((((((((.......(((....))).(((((((....)))))))--.)))))))))(((((((...))))))).))))))))))...))). ( -50.10)
>DroEre_CAF1 51759 93 + 1
CGCGGCGUAUACGCAAUACGUGGCAUAGGUGGCGUAUACGUAACGCACUGCACAGUG--------------GGUGUGUUUGGGGUACGCGGCGUAUACGCAAUGCGA
(((.((((((((((.((((((.((....)).)))))).((((.(.((..(((((...--------------..))))).)).).))))..))))))))))...))). ( -41.00)
>DroYak_CAF1 37045 93 + 1
CGCGGCGUAUACGCAAUACGUAGGAUGAGUGGCGUAUACGUAACGCAUUGCGGAGUG--------------UGUGUGUUUGGGGUACGCAGCGUAUACGCAAUGCGA
(((.((((((((((..(((.........)))((((((.((..((((((........)--------------)))))...))..)))))).))))))))))...))). ( -37.40)
>consensus
CGCGGCGUAUACGCAAUACGCGGAAUAGGUGGCGUAUACGUAACGCACUGCAGAGUG________UGU_UGUGUGUGUUUGGGAUACGCGGCGUAUACGCAAUGCGA
(((.((((((((((....(((.......)))((((((....(((((((........................)))))))....)))))).))))))))))...))). (-35.72 = -35.60 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	14,181,705 – 14,181,812
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	84.74
Mean single sequence MFE	-28.74
Consensus MFE	-24.14
Energy contribution	-24.30
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.80
Structure conservation index	0.84
SVM decision value	2.69
SVM RNA-class probability	0.996406
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14181705 107 - 27905053
UCGCAUUGCGUAUACGCCGCGUAUUCCAAACACACACAUACACACAUUUUCACUCUGCAUUGCGUUACGUAUACGCCACCUAUUCCGCGUAUUGCGUAUACGCCGCG
.(((...(((((((((..(((((.....................................)))))..)))))))))..........((((((.....)))))).))) ( -26.79)
>DroSec_CAF1 173916 103 - 1
UCGCAUUGCGUAUACGCCGCGUAACCCAAACACACACACACAU----AUACACUCUGCAGUGCGUUACGUAUACGCCACCUAUUCCGCGUUUUGCGUAUACGCCGCG
.(((...((((((((((.(((((((.((..((...........----........))...)).)))))))..((((..........))))...)))))))))).))) ( -28.11)
>DroSim_CAF1 59213 105 - 1
UCGCAUUGCGUAUACGCCGCGUAUCCCAAACACACACACACAGAC--ACACACUCUGCAGUGCGUUGCGUAUACGCCACCUAUUCCGCGUAUUGCGUAUACGCCGCG
.(((...((((((((((.((((((................((((.--......))))..)))))).))))))))))..........((((((.....)))))).))) ( -33.27)
>DroEre_CAF1 51759 93 - 1
UCGCAUUGCGUAUACGCCGCGUACCCCAAACACACC--------------CACUGUGCAGUGCGUUACGUAUACGCCACCUAUGCCACGUAUUGCGUAUACGCCGCG
..((((.(((((((((..((((((......((((..--------------...))))..))))))..))))))))).....))))..(((...(((....))).))) ( -29.50)
>DroYak_CAF1 37045 93 - 1
UCGCAUUGCGUAUACGCUGCGUACCCCAAACACACA--------------CACUCCGCAAUGCGUUACGUAUACGCCACUCAUCCUACGUAUUGCGUAUACGCCGCG
..((((((((.......((.((.......)).))..--------------.....))))))))((..(((((((((....(.......)....)))))))))..)). ( -26.04)
>consensus
UCGCAUUGCGUAUACGCCGCGUACCCCAAACACACACA_ACA________CACUCUGCAGUGCGUUACGUAUACGCCACCUAUUCCGCGUAUUGCGUAUACGCCGCG
.(((...((((((((((.((((.............................(((....)))((((.......))))..........))))...)))))))))).))) (-24.14 = -24.30 +   0.16)

alignment

secondary structure

dotplot

Window 9

Location	14,181,739 – 14,181,836
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	80.36
Mean single sequence MFE	-25.32
Consensus MFE	-15.54
Energy contribution	-15.14
Covariance contribution	-0.40
Combinations/Pair	1.24
Mean z-score	-1.82
Structure conservation index	0.61
SVM decision value	0.25
SVM RNA-class probability	0.651818
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14181739 97 + 27905053
UAUACGUAACGCAAUGCAGAGUGAAAAUGUGUGUAUGUGUGUGUUUGGAAUACGCGGCGUAUACGCAAUGCGAACGGGGACAAAAAGAAGAGACAGA
.....((..((((.(((...((....))..((((((((((((((.....)))))).))))))))))).))))...(....)...........))... ( -25.60)
>DroSec_CAF1 173950 93 + 1
UAUACGUAACGCACUGCAGAGUGUAU----AUGUGUGUGUGUGUUUGGGUUACGCGGCGUAUACGCAAUGCGAGCGGGUACAAAAAGAAGAGACAGA
.....(((.(((..((((..((((((----((((.((((((.........))))))))))))))))..)))).)))..)))................ ( -28.20)
>DroSim_CAF1 59247 95 + 1
UAUACGCAACGCACUGCAGAGUGUGU--GUCUGUGUGUGUGUGUUUGGGAUACGCGGCGUAUACGCAAUGCGAGCGGGGACAAAAAGAAGAGACAGA
((((((((((((((........))))--)).))))))))(((.(((......(((.(((....)))...)))...(....).......))).))).. ( -28.30)
>DroEre_CAF1 51793 73 + 1
UAUACGUAACGCACUGCACAGUG--------------GGUGUGUUUGGGGUACGCGGCGUAUACGCAAUGCGAGCGGGGACAAAAAG----------
....((.((((((((........--------------))))))))))..((.(((.(((....)))...))).))(....)......---------- ( -20.00)
>DroYak_CAF1 37079 83 + 1
UAUACGUAACGCAUUGCGGAGUG--------------UGUGUGUUUGGGGUACGCAGCGUAUACGCAAUGCGAGCGGGGACAAAAGGAAGUGACAGA
..(((....(((((((((..(((--------------(((((((.......))))).))))).)))))))))...(....)........)))..... ( -24.50)
>consensus
UAUACGUAACGCACUGCAGAGUG________UGU_UGUGUGUGUUUGGGAUACGCGGCGUAUACGCAAUGCGAGCGGGGACAAAAAGAAGAGACAGA
....((((((((((........................))))))).......(((((((....)))..)))).)))..................... (-15.54 = -15.14 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:43 2006