Locus 4177

Sequence ID	2L_DroMel_CAF1
Location	11,973,318 – 11,973,456
Length	138
Max. P	0.785889

overview

Window 3

Location	11,973,318 – 11,973,427
Length	109
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-25.22
Consensus MFE	-13.61
Energy contribution	-13.65
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.82
Structure conservation index	0.54
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11973318 109 + 22407834
UACACUGUCAUCGAACCGUGACGAUGCGUUGCUGCUGCUGCUGUUGUUGUUGUUGUGAUGUACCUGUACCUACAUAUG-UAGGUAUAUUACAUACAUAUAUGUAUGUAUG
......((((((((((.(..((((((.((.((....)).))))))))..).))).))))).)).(((((((((....)-)))))))).((((((((....)))))))).. ( -34.60)
>DroSec_CAF1 192839 89 + 1
UACAUUGUCAUCGAACCGUGACGAUGCGUUGCUGCU------------GUUGUUGUGAUGUACCUGUACCUACAUAUG-UACGUAUAUUACAUAU--------AUGUAUG
..(((((((((......)))))))))......((((------------((...((((((((((..((((........)-))))))))))))).))--------).))).. ( -23.00)
>DroSim_CAF1 159222 89 + 1
UACAUUGUCAUCGAACCGUGACGAUGCGUUGCUGCU------------GUUGUUGUGAUGUACCUGUACCUACAUAUG-UACGUAUAUUACAUAC--------AUGUAUG
..(((((((((......)))))))))......((((------------((...((((((((((..((((........)-))))))))))))).))--------).))).. ( -24.90)
>DroEre_CAF1 167261 86 + 1
UACAUUGUCAUCGAACCGUGACGAUGCGUUGCCGCUG---U------UGUUGUUGCGAUGUACCUGUACCUACAUACGA-------AUACUAUAU--------ACGUAUG
(((((((((((......)))))))((((((((.((..---.------....)).))))))))..))))....((((((.-------(((...)))--------.)))))) ( -22.00)
>DroYak_CAF1 164061 99 + 1
UACAUUGUCAUCGAACCGUGACGAUGCGUUGCUGCUG---UGGUUGCUGUUGUUGUGAUGUACCUGUACCUACAUACGAUAUAUACAUACCAUCC--------AUAUAUA
..(((((((((......)))))))))..........(---((((((.((((((((((.((((........))))))))))).))))).)))))..--------....... ( -21.60)
>consensus
UACAUUGUCAUCGAACCGUGACGAUGCGUUGCUGCUG__________UGUUGUUGUGAUGUACCUGUACCUACAUAUG_UACGUAUAUUACAUAC________AUGUAUG
(((((((((((......)))))))((((((((.((................)).))))))))..)))).......................................... (-13.61 = -13.65 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	11,973,355 – 11,973,456
Length	101
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	75.68
Mean single sequence MFE	-24.42
Consensus MFE	-12.49
Energy contribution	-12.55
Covariance contribution	0.06
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.51
SVM decision value	0.57
SVM RNA-class probability	0.785889
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11973355 101 - 22407834
UGCGGGGGCUAUACCGCCU--------GUGUAUAUGGCAUACAUACAUAUAUGUAUGUAAUAUACCUA-CAUAUGUAGGUACAGGUACAUCACAACAACAACAACAGCAG
(((((........))((((--------((((((((.(((((((((....))))))))).)))))((((-(....))))))))))))....................))). ( -32.30)
>DroSec_CAF1 192875 82 - 1
UGCGGGGGCUAUACCGCCU--------GUCUAUAUGGCAUACAU--------AUAUGUAAUAUACGUA-CAUAUGUAGGUACAGGUACAUCACAACAAC-----------
((.((.(.((.(((((((.--------........)))....((--------(((((((.......))-))))))).)))).)).)...)).)).....----------- ( -18.60)
>DroSim_CAF1 159258 82 - 1
UGCGGAGGCUAUACCGCCU--------GUUUAUAUGGCAUACAU--------GUAUGUAAUAUACGUA-CAUAUGUAGGUACAGGUACAUCACAACAAC-----------
....((.(((.(((((((.--------........))).(((((--------(((((((...))))))-))..))))))))..)))...))........----------- ( -19.70)
>DroYak_CAF1 164098 99 - 1
UGCGGGGGUUAAACUGCCUGUUUGUCUGUCUAUAUGGUAUAUAU--------GGAUGGUAUGUAUAUAUCGUAUGUAGGUACAGGUACAUCACAACAACAGCAACCA---
(((.(..(((....(((((((...((((..((((((((((((((--------(.......))))))))))))))))))).)))))))......)))..).)))....--- ( -27.10)
>consensus
UGCGGGGGCUAUACCGCCU________GUCUAUAUGGCAUACAU________GUAUGUAAUAUACGUA_CAUAUGUAGGUACAGGUACAUCACAACAAC___________
.((((........)))).............(((((.((((((..........)))))).))))).........(((..(((....)))...)))................ (-12.49 = -12.55 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:42 2006