Locus 6346

Sequence ID	2R_DroMel_CAF1
Location	19,907,017 – 19,907,137
Length	120
Max. P	0.969587

overview

Window 2

Location	19,907,017 – 19,907,137
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.33
Mean single sequence MFE	-28.18
Consensus MFE	-23.87
Energy contribution	-25.07
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.85
SVM decision value	1.64
SVM RNA-class probability	0.969587
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19907017 120 + 20766785
CCGACGUUGAGCAAUAAACGCAUUGUUCGCAAAUUCUAUCUGUUAUUGCUCCAUAAACAAUAUCUAAGUCUUAACGUAAGGAGCUUAUAGAUAGUGAAACUGACACUUUUGUCAGCUAUG
.....((.(((((((......))))))))).....((((((((....(((((...........................)))))..)))))))).....((((((....))))))..... ( -27.93)
>DroSec_CAF1 140327 108 + 1
CCGACGUUGAGCAAUAAACGCAUUGUUCGCAAAUUCUAUCUGUUAUUGCUCCAUAAACAAUAUCUA------------AGGAGCUUAUAGAUAGUGAAACUGACACUUUUGUCAGCUAUG
.....((.(((((((......))))))))).....((((((((....(((((..............------------.)))))..)))))))).....((((((....))))))..... ( -28.56)
>DroSim_CAF1 118642 120 + 1
CCGACGUUGAGCAAUAAACGCAUUGUUCGCAAAUUCUAUCUGUUAUUGCUCCAUAAACAAUAUCUAAGUCUUAACGUAAGGAGCUUAUAGAUAGUGAAACUGACACUUUUGUCAGCUAUG
.....((.(((((((......))))))))).....((((((((....(((((...........................)))))..)))))))).....((((((....))))))..... ( -27.93)
>DroEre_CAF1 144592 119 + 1
CUGACUUUGAGCA-AAGUCGCAUUGUUCGCAAAGUCUAUCAGUUAUUGCUCCAUAAACAAUAUCUAUGUCUUAACGUAAGGAGCUUAUAGAUAGUGAAACUGACACGUUUGCCAGCUAUG
..((((((....)-))))).(((.(((.(((((((...((((((...((((((((.....))).(((((....))))).)))))((((.....)))))))))).)).))))).))).))) ( -26.40)
>DroYak_CAF1 142834 120 + 1
CCGACUUUGAGCAUGAAACGCAUUGUUCGCAAAGUCUAUCUGUUAUUGCUCCAUAAACAAUAUCUAUGUCUUAACGUAAGGAGCUUAUAGAUAGUGAAACUGACACGUUUGUCAGCUAUG
..(((((((.(((((.....)).)))...)))))))(((((((....((((((((.....))).(((((....))))).)))))..)))))))......((((((....))))))..... ( -30.10)
>consensus
CCGACGUUGAGCAAUAAACGCAUUGUUCGCAAAUUCUAUCUGUUAUUGCUCCAUAAACAAUAUCUAAGUCUUAACGUAAGGAGCUUAUAGAUAGUGAAACUGACACUUUUGUCAGCUAUG
........(((((((......))))))).......((((((((....(((((...........................)))))..)))))))).....((((((....))))))..... (-23.87 = -25.07 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	19,907,017 – 19,907,137
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.33
Mean single sequence MFE	-27.16
Consensus MFE	-23.05
Energy contribution	-23.29
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.33
Structure conservation index	0.85
SVM decision value	0.23
SVM RNA-class probability	0.646354
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19907017 120 - 20766785
CAUAGCUGACAAAAGUGUCAGUUUCACUAUCUAUAAGCUCCUUACGUUAAGACUUAGAUAUUGUUUAUGGAGCAAUAACAGAUAGAAUUUGCGAACAAUGCGUUUAUUGCUCAACGUCGG
...((((((((....))))))))...((((((....(((((..(((...............)))....)))))......))))))......(((.....(((.....)))......))). ( -26.16)
>DroSec_CAF1 140327 108 - 1
CAUAGCUGACAAAAGUGUCAGUUUCACUAUCUAUAAGCUCCU------------UAGAUAUUGUUUAUGGAGCAAUAACAGAUAGAAUUUGCGAACAAUGCGUUUAUUGCUCAACGUCGG
...((((((((....))))))))...((((((....(((((.------------(((((...))))).)))))......))))))......(((.....(((.....)))......))). ( -28.00)
>DroSim_CAF1 118642 120 - 1
CAUAGCUGACAAAAGUGUCAGUUUCACUAUCUAUAAGCUCCUUACGUUAAGACUUAGAUAUUGUUUAUGGAGCAAUAACAGAUAGAAUUUGCGAACAAUGCGUUUAUUGCUCAACGUCGG
...((((((((....))))))))...((((((....(((((..(((...............)))....)))))......))))))......(((.....(((.....)))......))). ( -26.16)
>DroEre_CAF1 144592 119 - 1
CAUAGCUGGCAAACGUGUCAGUUUCACUAUCUAUAAGCUCCUUACGUUAAGACAUAGAUAUUGUUUAUGGAGCAAUAACUGAUAGACUUUGCGAACAAUGCGACUU-UGCUCAAAGUCAG
(((.(.(.(((((..((((((((......(((((((((...(((.((....)).))).....))))))))).....))))))))...))))).).).))).(((((-(....)))))).. ( -28.00)
>DroYak_CAF1 142834 120 - 1
CAUAGCUGACAAACGUGUCAGUUUCACUAUCUAUAAGCUCCUUACGUUAAGACAUAGAUAUUGUUUAUGGAGCAAUAACAGAUAGACUUUGCGAACAAUGCGUUUCAUGCUCAAAGUCGG
...((((((((....))))))))....(((((....(((((........(((((.......)))))..)))))......)))))(((((((.(....(((.....))).).))))))).. ( -27.50)
>consensus
CAUAGCUGACAAAAGUGUCAGUUUCACUAUCUAUAAGCUCCUUACGUUAAGACAUAGAUAUUGUUUAUGGAGCAAUAACAGAUAGAAUUUGCGAACAAUGCGUUUAUUGCUCAACGUCGG
...((((((((....))))))))...((((((....(((((...........................)))))......))))))......(((.....(((.....)))......))). (-23.05 = -23.29 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:52 2006