Locus 4908

Sequence ID	3L_DroMel_CAF1
Location	13,657,478 – 13,657,603
Length	125
Max. P	0.631280

overview

Window 6

Location	13,657,478 – 13,657,589
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.81
Mean single sequence MFE	-19.27
Consensus MFE	-11.65
Energy contribution	-11.07
Covariance contribution	-0.58
Combinations/Pair	1.17
Mean z-score	-1.79
Structure conservation index	0.60
SVM decision value	-0.03
SVM RNA-class probability	0.520829
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13657478 111 - 23771897
CCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA----CUCAAAUACAGCGUCACAACAUCAGUUACAAAAG-----
..((((((((((...(((((.(((((.......)))))...)))))...)))))...........(((((.(((...----.....))).)))))..))))).............----- ( -19.40)
>DroPse_CAF1 49919 111 - 1
UUUGUUGAUUUAGUCAGCGCUCAUAAUACAAAUUUAUAUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA----CGCAAAUAUGUUGGAAAAACAACAGCAACGCAAC-----
..((((.(((((...(((((.((((...........)))).)))))...))))).))))..................----.((.....(((((......))))).....))...----- ( -21.20)
>DroEre_CAF1 70012 111 - 1
CCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAGUUUCUACGCUAUAUAAA----CUCAAAUACAGCGUCACUACAUCAGUUACAAAAA-----
.(((((.(((((...(((((.(((((.......)))))...)))))...))))).))))).....(((((.(((...----.....))).)))))....................----- ( -20.80)
>DroYak_CAF1 73058 111 - 1
CCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA----CUCAAAUACGGCGUCACUACAUCAGUUACAAAAG-----
.(((.(((((((...(((((.(((((.......)))))...)))))...)))))...........((((..(((...----.....)))..)))).....)).))).........----- ( -18.60)
>DroAna_CAF1 108070 110 - 1
AUUGUUUAUUUAACCAGCGCUUGUAAUUCAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCCACGCUACUUAAAUAUACUAAAAUA--ACAUCGCAA--------ACCAAAAACCAU
..((((((((((...(((((.(((((.......)))))...)))))...))))))))))..............................--.........--------............ ( -14.40)
>DroPer_CAF1 51146 111 - 1
UUUGUUGAUUUAGUCAGCGCUCAUAAUACAAAUUUAUAUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA----CGCAAAUAUGUUGGAAAAACAACAGCAACGCAAC-----
..((((.(((((...(((((.((((...........)))).)))))...))))).))))..................----.((.....(((((......))))).....))...----- ( -21.20)
>consensus
CCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA____CUCAAAUACGGCGUCACAACAUCAGUUACAAAAA_____
..((((.(((((...(((((.((((...........)))).)))))...))))).))))............................................................. (-11.65 = -11.07 +  -0.58)

alignment

secondary structure

dotplot

Window 7

Location	13,657,512 – 13,657,603
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.31
Mean single sequence MFE	-18.08
Consensus MFE	-11.65
Energy contribution	-11.07
Covariance contribution	-0.58
Combinations/Pair	1.17
Mean z-score	-1.37
Structure conservation index	0.64
SVM decision value	0.20
SVM RNA-class probability	0.631280
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13657512 91 - 23771897
--------------------------UUUACCAAAAAUGCCCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA---
--------------------------................((((.(((((...(((((.(((((.......)))))...)))))...))))).))))..................--- ( -12.50)
>DroPse_CAF1 49953 117 - 1
GGCGAAACCCAACCCUCCAGCUGGGGGCUACUAAAUACGCUUUGUUGAUUUAGUCAGCGCUCAUAAUACAAAUUUAUAUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA---
((((.........(((((....)))))...............((((.(((((...(((((.((((...........)))).)))))...))))).)))).......)))).......--- ( -25.80)
>DroEre_CAF1 70046 91 - 1
--------------------------UUUACCAAAAAUGCCCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAGUUUCUACGCUAUAUAAA---
--------------------------...............(((((.(((((...(((((.(((((.......)))))...)))))...))))).))))).................--- ( -15.30)
>DroYak_CAF1 73092 91 - 1
--------------------------UUUACCAAAAAUGCCCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA---
--------------------------................((((.(((((...(((((.(((((.......)))))...)))))...))))).))))..................--- ( -12.50)
>DroAna_CAF1 108100 93 - 1
--------------------------UUUACCAAA-AGGCAUUGUUUAUUUAACCAGCGCUUGUAAUUCAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCCACGCUACUUAAAUAU
--------------------------.........-.((...((((((((((...(((((.(((((.......)))))...)))))...))))))))))....))............... ( -16.60)
>DroPer_CAF1 51180 117 - 1
GGCGAAACCCAACCCUCCAGCUGGGGGCUACUAAAUACGCUUUGUUGAUUUAGUCAGCGCUCAUAAUACAAAUUUAUAUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA---
((((.........(((((....)))))...............((((.(((((...(((((.((((...........)))).)))))...))))).)))).......)))).......--- ( -25.80)
>consensus
__________________________UUUACCAAAAAUGCCCUGUUGAUUUAGUCAGCGCUUAUAAUACAAAUUUAUGUGUGUGCUUAAUAAAUAAACAUUUUCUACGCUAUAUAAA___
..........................................((((.(((((...(((((.((((...........)))).)))))...))))).))))..................... (-11.65 = -11.07 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:41 2006