Locus 22

Sequence ID	4_DroMel_CAF1
Location	209,245 – 209,377
Length	132
Max. P	0.793777

overview

Window 6

Location	209,245 – 209,337
Length	92
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	78.71
Mean single sequence MFE	-17.87
Consensus MFE	-9.70
Energy contribution	-10.72
Covariance contribution	1.02
Combinations/Pair	1.21
Mean z-score	-2.08
Structure conservation index	0.54
SVM decision value	0.59
SVM RNA-class probability	0.793777
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 209245 92 - 1281640
UAGUGCUAUCCUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAAAAACGUAAAUACUACGUCUAGUGUAAGGACCCAAAAA-GGAAAAA-
.(((((((...)))))))...................(((((((......(((((.....)))))....)))))))..((.....-)).....- ( -18.10)
>DroSec_CAF1 3320 92 - 1
UAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAGAAACGUAAAUACUACGUGUAGUGUACGGACCCAAAAA-GGAAAAA-
.(((((((...))))))).................(((.((((((.....))))))((((((....))))))..))).((.....-)).....- ( -18.60)
>DroSim_CAF1 3664 92 - 1
UAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAGAAACGUAAAUACUACGUGUAGUGUACGGACCCAAAAA-GGAAAAA-
.(((((((...))))))).................(((.((((((.....))))))((((((....))))))..))).((.....-)).....- ( -18.60)
>DroEre_CAF1 2664 92 - 1
UAGUGCUAUACUAGCACUCACCAUAAAGGUUACCAUUCCUUACGUAAAAAACGUUCAUACUACGUAUAGUGUAAGGACCCAAAAA-GGAAAAC-
.(((((((...))))))).(((.....)))......((((((((......((((.......))))....)))))))).((.....-)).....- ( -19.30)
>DroYak_CAF1 1003 92 - 1
UAGUGCUAUACUAGCACUUACCAUUAAGGUUACCAUUCCUUACGUUAAAAACGUGCACACUACGUCUAGUGUAGGGGCCCAAAAA-GGAAAAA-
.(((((((...))))))).(((.....))).....((((((((((.....))))((...(((((.....)))))..)).....))-))))...- ( -21.90)
>DroMoj_CAF1 4991 84 - 1
UACUGCCCUAUUUGCAUUAACCGUUAAGGUAACUGUACCAUAUAUCCGAAAUGCCC------CAUGCA---UUA-AACACAAAAAUGAAAAUGC
.............(((((...((((..((((....))))..........(((((..------...)))---)).-........))))..))))) ( -10.70)
>consensus
UAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAAAAACGUAAAUACUACGUGUAGUGUAAGGACCCAAAAA_GGAAAAA_
.((((((.....))))))..((..................(((((.....))))).((((((....))))))..............))...... ( -9.70 = -10.72 +   1.02)

alignment

secondary structure

dotplot

Window 7

Location	209,262 – 209,377
Length	115
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	82.41
Mean single sequence MFE	-27.12
Consensus MFE	-15.36
Energy contribution	-15.20
Covariance contribution	-0.16
Combinations/Pair	1.33
Mean z-score	-2.26
Structure conservation index	0.57
SVM decision value	0.01
SVM RNA-class probability	0.536175
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 209262 115 - 1281640
AUGGGUUUACAAAACACGCUUUUAGCUAUGCUCUAGUAACUAGUGCUAUCCUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAAAAAC--GUAAAUACUACGUCUAGUGUAAG-
..(((............((.....)).......(((((((((((((((...))))))).........)))))))).)))((((((.....))--))))((((((....))))))...- ( -25.80)
>DroSec_CAF1 3337 115 - 1
AUGGCUUUACGAAACACGCUUUUAGCUAUGCUCUAGUAACUAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAGAAAC--GUAAAUACUACGUGUAGUGUACG-
((((((...((.....)).....))))))....(((((((((((((((...))))))).........))))))))....((((((.....))--))))((((((....))))))...- ( -26.70)
>DroSim_CAF1 3681 115 - 1
AUGGGUUUACGAAACACGCUUUUAGCUAUGCUCUAGUAACUAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAGAAAC--GUAAAUACUACGUGUAGUGUACG-
..(((............((.....)).......(((((((((((((((...))))))).........)))))))).)))((((((.....))--))))((((((....))))))...- ( -27.10)
>DroEre_CAF1 2681 115 - 1
AUGGAAUUACGAAACAUGCUUUAAGCUAUGCUCUUGUAACUAGUGCUAUACUAGCACUCACCAUAAAGGUUACCAUUCCUUACGUAAAAAAC--GUUCAUACUACGUAUAGUGUAAG-
((((..((((((..(((((.....)).)))...))))))..(((((((...)))))))..)))).((((........))))((((.....))--))..((((((....))))))...- ( -23.10)
>DroYak_CAF1 1020 115 - 1
AUGGGUUUACAAAAAACGUUUUUAGCUAUGCUAUUGUAACUAGUGCUAUACUAGCACUUACCAUUAAGGUUACCAUUCCUUACGUUAAAAAC--GUGCACACUACGUCUAGUGUAGG-
...............(((((((((((.........(((...(((((((...))))))))))...(((((........))))).)))))))))--))..((((((....))))))...- ( -28.00)
>DroPer_CAF1 3451 117 - 1
AUGGAAUUACAAAGCACGCUUUUAGCUGCGUGCUCGUGACCAGUGCGAUAGUAGCUCUUACCAUUAAGAUUACUACUCCGUAUGUAAGAAAUACGCAAUCACAAUCCCCAA-GAAAGA
.(((........(((((((........))))))).((((....(((((((((((.(((((....))))))))))).)).((((.......))))))).)))).....))).-...... ( -32.00)
>consensus
AUGGGUUUACAAAACACGCUUUUAGCUAUGCUCUAGUAACUAGUGCUAUACUAGCACUUACCAUUAAAGUUACUAUCCCUUACGUAAAAAAC__GUAAAUACUACGUCUAGUGUAAG_
..(((............((.....)).........(((((((((((((...))))))).........))))))...)))...................((((((....)))))).... (-15.36 = -15.20 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:38 2006