Locus 6879

Sequence ID	2L_DroMel_CAF1
Location	19,240,119 – 19,240,260
Length	141
Max. P	0.963322

overview

Window 3

Location	19,240,119 – 19,240,224
Length	105
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	72.76
Mean single sequence MFE	-22.94
Consensus MFE	-4.11
Energy contribution	-4.39
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-1.72
Structure conservation index	0.18
SVM decision value	0.52
SVM RNA-class probability	0.766607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19240119 105 + 22407834
CUAAAUGUU-------UGAAUGGACA--U-UGAAGCAUUGAUUAUG--CUCCAUAACAUAAAGGUGUAUAUAAAAUUCUCUCCAUUUCACUGGAUAAGUAAGAACUCUUUCAUUUCU
.........-------.(((((((..--.-((.(((((.....)))--)).))..((((....)))).............)))))))...((((..(((....)))..))))..... ( -15.90)
>DroSec_CAF1 59985 106 + 1
CCAAGUGUU-------UGAAUGGACA--CGUAUUGCAGUGAUUAUG--CUCCAUGCCAUACAGGUGUGUAUAAAAUUCUCUUCAUUUCACUGGAUAAGUAAGAACUCUUACUCUUCU
...((((..-------((((.(((((--(........))).(((((--(...(((((.....)))))))))))...))).))))...))))(((..((((((....))))))..))) ( -26.20)
>DroSim_CAF1 61362 106 + 1
CCAAGUGUU-------UGAAUGGACA--CGUAUUGCAUUGAUUAUG--CUCCAUACCAGACAGGUGUAUAUAAAAUUCUCUUCAUUUCACUGGAUAAGUAAGAACUCUUACUCUUCU
...((((..-------((((.(((..--......((((.....)))--)...(((((.....))))).........))).))))...))))(((..((((((....))))))..))) ( -24.50)
>DroEre_CAF1 59604 115 + 1
CAAAGUGUUUU-CCCUUGAAUGGUUGUCCAUACUAUAUGGACUAUAGUCUCCAGACCAUAAGUGUGCACA-AAAAUGCUCUCAAUUUCACUGCAUAUGUAGGAACUCCUACACUAUU
....((((...-(.(((..(((((((((((((...)))))))...........))))))))).).)))).-...((((.............)))).((((((....))))))..... ( -26.22)
>DroYak_CAF1 61625 111 + 1
CAAAGUGUUUUAUUCUUGAAUGGUUGUAUGGAC---GUUGACUAUG--CUCCAUACCAUACAUAUGCAUA-AAAAUCCCCUCAAUUUCUGUGCAAAAAUAAGAACUCUUACAGUAUU
..(((.(((((.....((.(((((...((((((---((.....)))--.)))))))))).))..((((((-.((((.......)))).))))))......))))).)))........ ( -21.90)
>consensus
CAAAGUGUU_______UGAAUGGACA__CGUACUGCAUUGAUUAUG__CUCCAUACCAUACAGGUGUAUAUAAAAUUCUCUCCAUUUCACUGGAUAAGUAAGAACUCUUACACUUCU
...................((((...........................))))...........................................(((((....)))))...... ( -4.11 =  -4.39 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	19,240,149 – 19,240,260
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	78.16
Mean single sequence MFE	-20.81
Consensus MFE	-4.34
Energy contribution	-5.50
Covariance contribution	1.16
Combinations/Pair	1.20
Mean z-score	-2.44
Structure conservation index	0.21
SVM decision value	1.55
SVM RNA-class probability	0.963322
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19240149 111 + 22407834
AUUAUG--CUCCAUAACAUAAAGGUGUAUAUAAAAUUCUCUCCAUUUCACUGGAUAAGUAAGAACUCUUUCAUUUCUUACCAGCUUGAUGAACCACCUGCCAGCAUAAUUCCA
((((((--((...........(((((..............((((......))))...(((((((.........))))))).............)))))...)))))))).... ( -18.94)
>DroSec_CAF1 60016 108 + 1
AUUAUG--CUCCAUGCCAUACAGGUGUGUAUAAAAUUCUCUUCAUUUCACUGGAUAAGUAAGAACUCUUACUCUUCUUAGCAGCUUGAUGAAC---CUGCCAGCAUAAUUCCA
((((((--((.((((((.....))))))............((((((...(((((..((((((....))))))..))....)))...)))))).---.....)))))))).... ( -25.50)
>DroSim_CAF1 61393 108 + 1
AUUAUG--CUCCAUACCAGACAGGUGUAUAUAAAAUUCUCUUCAUUUCACUGGAUAAGUAAGAACUCUUACUCUUCUUAGCAGCUUGAUGAAC---CUGCCAGCAUAAUUCCA
((((((--((..(((((.....))))).............((((((...(((((..((((((....))))))..))....)))...)))))).---.....)))))))).... ( -24.00)
>DroEre_CAF1 59643 97 + 1
ACUAUAGUCUCCAGACCAUAAGUGUGCACA-AAAAUGCUCUCAAUUUCACUGCAUAUGUAGGAACUCCUACACUAUUUACCAGCCUGAUGGAC---UUGCC------------
.....(((((.(((.......(((((((..-.((((.......))))...)))))))(((((....))))).............)))..))))---)....------------ ( -20.60)
>DroYak_CAF1 61662 107 + 1
ACUAUG--CUCCAUACCAUACAUAUGCAUA-AAAAUCCCCUCAAUUUCUGUGCAAAAAUAAGAACUCUUACAGUAUUUACCAGCUUGAUGAAC---UUGCCAGCAUAAUUCCA
..((((--((.......((((...((((((-.((((.......)))).))))))....((((....))))..))))......((..(.....)---..)).))))))...... ( -15.00)
>consensus
AUUAUG__CUCCAUACCAUACAGGUGUAUAUAAAAUUCUCUCCAUUUCACUGGAUAAGUAAGAACUCUUACACUUCUUACCAGCUUGAUGAAC___CUGCCAGCAUAAUUCCA
........................................((((((...(((....((((((....))))))........)))...))))))..................... ( -4.34 =  -5.50 +   1.16)

alignment

secondary structure

dotplot

Window 5

Location	19,240,149 – 19,240,260
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	78.16
Mean single sequence MFE	-27.28
Consensus MFE	-8.08
Energy contribution	-9.32
Covariance contribution	1.24
Combinations/Pair	1.33
Mean z-score	-1.89
Structure conservation index	0.30
SVM decision value	0.09
SVM RNA-class probability	0.580604
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19240149 111 - 22407834
UGGAAUUAUGCUGGCAGGUGGUUCAUCAAGCUGGUAAGAAAUGAAAGAGUUCUUACUUAUCCAGUGAAAUGGAGAGAAUUUUAUAUACACCUUUAUGUUAUGGAG--CAUAAU
....((((((((((((((((.(((((....((....))..)))))(((((((((.....((((......))))))))))))).....))))....))))....))--)))))) ( -24.90)
>DroSec_CAF1 60016 108 - 1
UGGAAUUAUGCUGGCAG---GUUCAUCAAGCUGCUAAGAAGAGUAAGAGUUCUUACUUAUCCAGUGAAAUGAAGAGAAUUUUAUACACACCUGUAUGGCAUGGAG--CAUAAU
....(((((((((((((---.((....)).))))))....(((((((....))))))).(((((((((((.......))))))).....((.....))..)))))--)))))) ( -28.10)
>DroSim_CAF1 61393 108 - 1
UGGAAUUAUGCUGGCAG---GUUCAUCAAGCUGCUAAGAAGAGUAAGAGUUCUUACUUAUCCAGUGAAAUGAAGAGAAUUUUAUAUACACCUGUCUGGUAUGGAG--CAUAAU
....(((((((((((((---.((....)).))))))....(((((((....))))))).(((((((((((.......)))))))....(((.....))).)))))--)))))) ( -29.90)
>DroEre_CAF1 59643 97 - 1
------------GGCAA---GUCCAUCAGGCUGGUAAAUAGUGUAGGAGUUCCUACAUAUGCAGUGAAAUUGAGAGCAUUUU-UGUGCACACUUAUGGUCUGGAGACUAUAGU
------------....(---(((..((((((((((.....(((((((....))))))).((((..((((((....).)))))-..)))).)))...))))))).))))..... ( -26.60)
>DroYak_CAF1 61662 107 - 1
UGGAAUUAUGCUGGCAA---GUUCAUCAAGCUGGUAAAUACUGUAAGAGUUCUUAUUUUUGCACAGAAAUUGAGGGGAUUUU-UAUGCAUAUGUAUGGUAUGGAG--CAUAGU
....((((((((...((---((((.((((.((((((((....(((((....))))).))))).)))...))))..))))))(-(((((....)))))).....))--)))))) ( -26.90)
>consensus
UGGAAUUAUGCUGGCAG___GUUCAUCAAGCUGGUAAGAAGUGUAAGAGUUCUUACUUAUCCAGUGAAAUGGAGAGAAUUUUAUAUACACCUGUAUGGUAUGGAG__CAUAAU
.....................(((((...((((....((.(((((((....))))))).))))))...)))))........................................ ( -8.08 =  -9.32 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:55 2006