Locus 110

Sequence ID	2L_DroMel_CAF1
Location	370,857 – 371,050
Length	193
Max. P	0.992123

overview

Window 0

Location	370,857 – 370,977
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-35.26
Consensus MFE	-34.88
Energy contribution	-34.92
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.99
SVM decision value	2.31
SVM RNA-class probability	0.992123
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 370857 120 + 22407834
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGUAACAAGUGGGCGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
..(((((((.....((((((.((..(((......)))..))...))))))......(....).)))))))..(((((((....))))))).(((((((...........))))))).... ( -35.50)
>DroSec_CAF1 38415 120 + 1
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGUAACAAGUGGGCGGGGCAGGGCAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
..(((((((......(((((.((..(((......)))..))...)))))((....))......)))))))..(((((((....))))))).(((((((...........))))))).... ( -35.70)
>DroSim_CAF1 39085 120 + 1
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGUAACAAGUGGGCGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
..(((((((.....((((((.((..(((......)))..))...))))))......(....).)))))))..(((((((....))))))).(((((((...........))))))).... ( -35.50)
>DroEre_CAF1 44953 120 + 1
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGUAACAAGUGGGCGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
..(((((((.....((((((.((..(((......)))..))...))))))......(....).)))))))..(((((((....))))))).(((((((...........))))))).... ( -35.50)
>DroYak_CAF1 39541 120 + 1
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGCAACAAGUGGGCGGGGCAGGACAGGGGCGGGAGAGUAGUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
.((((.((((....((((((..(.(.((((..(........)..))))..).)..))))))......)))).(((((((....))))))).(((((((...........))))))))))) ( -34.10)
>consensus
ACGCAAUGCAAAAAUCUUGUAGCAGGCUGUAACAAGUGGGCGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCG
..(((((((.....((((((.((..(((......)))..))...))))))......(....).)))))))..(((((((....))))))).(((((((...........))))))).... (-34.88 = -34.92 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	370,897 – 371,015
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.14
Mean single sequence MFE	-38.96
Consensus MFE	-35.92
Energy contribution	-36.56
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.20
Structure conservation index	0.92
SVM decision value	0.13
SVM RNA-class probability	0.599145
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 370897 118 + 22407834
CGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGAUUCGCU--
..............((((((......(((((.(((((((....))))))).(((((((...........)))))))))))).(((((((((((....)))))).)).)))..))))))-- ( -37.30)
>DroSec_CAF1 38455 118 + 1
CGGGGCAGGGCAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGAU--
((((((((.((((..((......)).))))..(((((((....))))))).........................))))...(((((((((((....)))))).)).)))..))))..-- ( -39.20)
>DroSim_CAF1 39125 118 + 1
CGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGCU--
..............((((((......(((((.(((((((....))))))).(((((((...........)))))))))))).(((((((((((....)))))).)).)))..))))))-- ( -39.90)
>DroEre_CAF1 44993 118 + 1
CGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCGGCGACCGACUCGCU--
..............((((((......(((((.(((((((....))))))).(((((((...........)))))))))))).(((((((((((....)))))).)).)))..))))))-- ( -39.90)
>DroYak_CAF1 39581 120 + 1
CGGGGCAGGACAGGGGCGGGAGAGUAGUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUGCGACGAGUCCAGCGACCGACUCGAUAU
(((.((.((((.(..((((....(((.((((.(((((((....))))))).(((((((...........)))))))))))....)))...))))..)..)))).))..)))......... ( -38.50)
>consensus
CGGGGCAGGACAGGGGCGGGAGAGUAUUGCAACAUGUGCAAAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGCU__
..............((((((......(((((.(((((((....))))))).(((((((...........)))))))))))).(((((((((((....)))))).)).)))..)))))).. (-35.92 = -36.56 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	370,937 – 371,050
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.99
Mean single sequence MFE	-30.48
Consensus MFE	-27.90
Energy contribution	-28.18
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.37
Structure conservation index	0.92
SVM decision value	0.95
SVM RNA-class probability	0.888259
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 370937 113 + 22407834
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGAUUCGCU-------UUGACCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....((.(((((((((((((((...(((.....))).(((((((..((((((....))))))(((((.....)))))-------...))).))))...))))).)))).)))))).)). ( -30.60)
>DroSec_CAF1 38495 113 + 1
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGAU-------UUGACCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....(((((((((((((...........))))))).))...(((((((((((....)))))).)).)))...((((.-------((((....))))...)))).......))))..... ( -27.70)
>DroSim_CAF1 39165 113 + 1
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGCU-------UUGACCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....((.(((((((((((((((...(((.....))).(((((((..((((((....))))))(((((.....)))))-------...))).))))...))))).)))).)))))).)). ( -30.60)
>DroEre_CAF1 45033 112 + 1
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCGGCGACCGACUCGCU--------UUGCCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....((.(((((((((((((((...(((.....))).(((((((.(((((((....)))))))((((.....)))).--------..))).))))...))))).)))).)))))).)). ( -31.80)
>DroYak_CAF1 39621 120 + 1
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUGCGACGAGUCCAGCGACCGACUCGAUAUUCGCAUUGACCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....((.(((((((((((((((...(((.....))).(((((((.(((..(((((((((((........))))))....))))))))))).))))...))))).)))).)))))).)). ( -31.70)
>consensus
AAUGCGCAUGCGUAAUUAUUGAAACAAGUUAAUUACUGCGAAGGUGCGGACUUCGACGAGUCCAGCGACCGACUCGCU_______UUGACCAUUCGAUAUUCGACUAAUAUAUGCAAGUA
.....((.(((((((((((((((...(((.....))).(((((((..((((((....))))))(((((.....)))))..........))).))))...))))).)))).)))))).)). (-27.90 = -28.18 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:04 2006