Locus 5377

Sequence ID	X_DroMel_CAF1
Location	13,979,663 – 13,979,757
Length	94
Max. P	0.990111

overview

Window 4

Location	13,979,663 – 13,979,757
Length	94
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	70.34
Mean single sequence MFE	-16.60
Consensus MFE	-2.39
Energy contribution	-3.31
Covariance contribution	0.92
Combinations/Pair	1.18
Mean z-score	-2.70
Structure conservation index	0.14
SVM decision value	2.20
SVM RNA-class probability	0.990111
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13979663 94 + 22224390
CUAACUAAA-GAAAAAAGUACAAAUGUACUUCUA---AAAUAGCAAUUAAAAUUUAGGGCUCCGUAAUUAGGAUG------ACAAAAUUGUUAUCCCAACAAAA
.........-.....((((((....))))))...---................(((.(....).)))...(((((------(((....))))))))........ ( -14.70)
>DroSec_CAF1 12712 92 + 1
CUCGCUAUA-AAAAGAAGUACGAAUGUACUUCUA---AAAUGGCAAUCAAAAUUUAAAGCUCAGUAAUUAGGAUA------ACUAAUUUGUUAUCCAACCAA--
...(((((.-...((((((((....)))))))).---..)))))..........................(((((------((......)))))))......-- ( -23.90)
>DroSim_CAF1 12794 92 + 1
CUCGCUAGA-AAAAGAAGUACAAAUGUACUUCUA---AAAUGGCAAUCAAAAUUUAAGGCUCAGUAAUUAGGAUA------ACAAAUUUGUUAUCCAACCAA--
...((((..-...((((((((....)))))))).---...))))..........................(((((------(((....))))))))......-- ( -24.60)
>DroEre_CAF1 7093 100 + 1
CUUGGUAGCAACAAAAAUUACAAAUUUACUUAUA---AAAUGGCUAUUAAAAUCUGAGGCUCAGUAUUUAUGUUACAAACGACCAAAUUCUUAUCCAAACCAA-
.(((((.(.((((.((((.((...((((....))---)).(((((.(((.....)))))).)))))))).)))).).....))))).................- (  -7.50)
>DroYak_CAF1 13563 87 + 1
CUAGCUA---ACAAAAUUAACAAAUGUACUUAUAGAUAAAUGAUAAUAAAAA-------GUAAGUAAUUAGGCUGCAAAU------AGUGUUAGCCAAUCAAA-
...((((---(((..(((..((..(.(((((((...................-------)))))))....)..))..)))------..)))))))........- ( -12.31)
>consensus
CUAGCUAGA_AAAAAAAGUACAAAUGUACUUCUA___AAAUGGCAAUCAAAAUUUAAGGCUCAGUAAUUAGGAUA______ACAAAAUUGUUAUCCAAACAAA_
...............((((((....)))))).......................................(((((................)))))........ ( -2.39 =  -3.31 +   0.92)

alignment

secondary structure

dotplot

Window 5

Location	13,979,663 – 13,979,757
Length	94
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	70.34
Mean single sequence MFE	-19.42
Consensus MFE	-2.54
Energy contribution	-3.86
Covariance contribution	1.32
Combinations/Pair	1.12
Mean z-score	-2.29
Structure conservation index	0.13
SVM decision value	1.39
SVM RNA-class probability	0.949470
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13979663 94 - 22224390
UUUUGUUGGGAUAACAAUUUUGU------CAUCCUAAUUACGGAGCCCUAAAUUUUAAUUGCUAUUU---UAGAAGUACAUUUGUACUUUUUUC-UUUAGUUAG
....((((((((.(((....)))------.))))))))......................((((...---.((((((((....))))))))...-..))))... ( -18.90)
>DroSec_CAF1 12712 92 - 1
--UUGGUUGGAUAACAAAUUAGU------UAUCCUAAUUACUGAGCUUUAAAUUUUGAUUGCCAUUU---UAGAAGUACAUUCGUACUUCUUUU-UAUAGCGAG
--(..((.(((((((......))------))))).....))..)..............((((.((..---.((((((((....))))))))...-.)).)))). ( -23.10)
>DroSim_CAF1 12794 92 - 1
--UUGGUUGGAUAACAAAUUUGU------UAUCCUAAUUACUGAGCCUUAAAUUUUGAUUGCCAUUU---UAGAAGUACAUUUGUACUUCUUUU-UCUAGCGAG
--(..((.((((((((....)))------))))).....))..)..............((((.....---.((((((((....))))))))...-....)))). ( -23.52)
>DroEre_CAF1 7093 100 - 1
-UUGGUUUGGAUAAGAAUUUGGUCGUUUGUAACAUAAAUACUGAGCCUCAGAUUUUAAUAGCCAUUU---UAUAAGUAAAUUUGUAAUUUUUGUUGCUACCAAG
-(((((...((((((((..((((..((........((((.(((.....))))))).))..))))..(---((((((....)))))))))))))))...))))). ( -16.40)
>DroYak_CAF1 13563 87 - 1
-UUUGAUUGGCUAACACU------AUUUGCAGCCUAAUUACUUAC-------UUUUUAUUAUCAUUUAUCUAUAAGUACAUUUGUUAAUUUUGU---UAGCUAG
-......(((((((((..------(((.((((......((((((.-------....((........))....))))))...)))).)))..)))---)))))). ( -15.20)
>consensus
_UUUGGUUGGAUAACAAUUUUGU______UAUCCUAAUUACUGAGCCUUAAAUUUUAAUUGCCAUUU___UAGAAGUACAUUUGUACUUUUUUU_UCUAGCGAG
.......................................................................((((((((....))))))))............. ( -2.54 =  -3.86 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:29 2006