Locus 4558

Sequence ID	3L_DroMel_CAF1
Location	13,111,525 – 13,111,672
Length	147
Max. P	0.998744

overview

Window 8

Location	13,111,525 – 13,111,622
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	97.53
Mean single sequence MFE	-24.93
Consensus MFE	-22.76
Energy contribution	-23.36
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.91
SVM decision value	3.21
SVM RNA-class probability	0.998744
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13111525 97 + 23771897
CCGUCUUUUGUCGCAUCGCAUCAAUUAAAGCAUUACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCAGCAGCCGACGGA
(((((.....((.((((((..........)).......((((((.......))))))...............)))).))..(((....)))))))). ( -25.60)
>DroSec_CAF1 99189 96 + 1
CCGUCUUUUGUCGCAUCGCAUCAAUUAAAGCAU-ACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCAGCAGCCGACGGA
(((((..((((.((.((.(((((..........-....((((((.......))))))..............))))).))...)).))))..))))). ( -26.09)
>DroSim_CAF1 96960 97 + 1
CCGUCUUUUGUCGCAUCGCAUCAAUUAAAGCAUUACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCAGCAGCCGACGGA
(((((.....((.((((((..........)).......((((((.......))))))...............)))).))..(((....)))))))). ( -25.60)
>DroEre_CAF1 95879 97 + 1
UCGCCUUUUGUCGCAUCGCAUCAAUUAAAGCAUUACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCGGCAGCCGACACA
(((....(((((((.((.(((((...............((((((.......))))))..............))))).))...))))))).))).... ( -21.75)
>DroYak_CAF1 99210 97 + 1
CCGUCUUUUGUCGCAUCGCAUCAAUUAAAGCAUUACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCAGCAGCCGACGGA
(((((.....((.((((((..........)).......((((((.......))))))...............)))).))..(((....)))))))). ( -25.60)
>consensus
CCGUCUUUUGUCGCAUCGCAUCAAUUAAAGCAUUACAAUGUCAUAAUCAAAAUGACAAAUAGAAUUACGCAUGAUGGGAAAGGCAGCAGCCGACGGA
(((((.....((.((((((..........)).......((((((.......))))))...............)))).))..(((....)))))))). (-22.76 = -23.36 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	13,111,525 – 13,111,622
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	97.53
Mean single sequence MFE	-24.14
Consensus MFE	-23.50
Energy contribution	-23.38
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.41
Structure conservation index	0.97
SVM decision value	1.19
SVM RNA-class probability	0.928217
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13111525 97 - 23771897
UCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGUAAUGCUUUAAUUGAUGCGAUGCGACAAAAGACGG
.((((((((....)))..((.(((((.((((.((......((((((.......))))))..)).))))......))))).))..........))))) ( -24.60)
>DroSec_CAF1 99189 96 - 1
UCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGU-AUGCUUUAAUUGAUGCGAUGCGACAAAAGACGG
.((((((((....)))..((.(((((.(((((........((((((.......))))))...)-))))......))))).))..........))))) ( -25.80)
>DroSim_CAF1 96960 97 - 1
UCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGUAAUGCUUUAAUUGAUGCGAUGCGACAAAAGACGG
.((((((((....)))..((.(((((.((((.((......((((((.......))))))..)).))))......))))).))..........))))) ( -24.60)
>DroEre_CAF1 95879 97 - 1
UGUGUCGGCUGCCGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGUAAUGCUUUAAUUGAUGCGAUGCGACAAAAGGCGA
..((((...((.(((...((.(((((.((((.((......((((((.......))))))..)).))))......))))).)).))).))...)))). ( -21.10)
>DroYak_CAF1 99210 97 - 1
UCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGUAAUGCUUUAAUUGAUGCGAUGCGACAAAAGACGG
.((((((((....)))..((.(((((.((((.((......((((((.......))))))..)).))))......))))).))..........))))) ( -24.60)
>consensus
UCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUUUGUCAUUUUGAUUAUGACAUUGUAAUGCUUUAAUUGAUGCGAUGCGACAAAAGACGG
.((((((((....)))..((.(((((.((((.((......((((((.......))))))..)).))))......))))).))..........))))) (-23.50 = -23.38 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	13,111,582 – 13,111,672
Length	90
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	92.11
Mean single sequence MFE	-30.02
Consensus MFE	-25.46
Energy contribution	-25.94
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-1.39
Structure conservation index	0.85
SVM decision value	0.41
SVM RNA-class probability	0.724797
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13111582 90 - 23771897
--UACUGGGUGAUGCGGA---UUGCCGGCUAUCAACCACCACAAGAGGAGUU----AGCUCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUU
--...((((.((.((((.---..((((((..((...........))((((..----..))))))))))..)))).)).))))................. ( -28.60)
>DroSec_CAF1 99245 90 - 1
--UGCUGGGUGAUGCGGA---UUGCCGGCUAUCAACCACCACAAGAGGAGUU----AGCUCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUU
--((.((((.((.((((.---..((((((..((...........))((((..----..))))))))))..)))).)).)))).)).............. ( -29.50)
>DroSim_CAF1 97017 90 - 1
--UGCUGGGUGAUGCGGA---UUGCCGGCUAUCAACCACCACAAGAGGAGUU----AGCUCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUU
--((.((((.((.((((.---..((((((..((...........))((((..----..))))))))))..)))).)).)))).)).............. ( -29.50)
>DroEre_CAF1 95936 99 - 1
GGUGCUGGGUGCUGCGGACUAUUGCCGGCUAUCAACCACCACAAGAGGAGUUACAUAGCUGUGUCGGCUGCCGCCUUUCCCAUCAUGCGUAAUUCUAUU
.(((.((((....((((.(....((((((.........((......))((((....))))..)))))).)))))....)))).)))............. ( -28.30)
>DroYak_CAF1 99267 95 - 1
AGUGAUGGGUGAUGCGGACUAUUGCCGGGUAUCAACCACCACAAGAGGAGUU----AGCUCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUU
.((((((((.((.((((.(....(((((((....))).........((((..----..))))..)))).))))).)).))))))))............. ( -34.20)
>consensus
__UGCUGGGUGAUGCGGA___UUGCCGGCUAUCAACCACCACAAGAGGAGUU____AGCUCCGUCGGCUGCUGCCUUUCCCAUCAUGCGUAAUUCUAUU
..((.((((.((.((((......((((((..((...........))(((((......)))))))))))..)))).)).)))).)).............. (-25.46 = -25.94 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:33 2006