Locus 2178

Sequence ID	2R_DroMel_CAF1
Location	8,059,785 – 8,059,900
Length	115
Max. P	0.809039

overview

Window 8

Location	8,059,785 – 8,059,900
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-26.96
Consensus MFE	-23.72
Energy contribution	-23.92
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.88
SVM decision value	0.58
SVM RNA-class probability	0.789742
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8059785 115 + 20766785
CGAAAACGUAGCUACUAUUUUGGCCGCUGCUGUGCAUACAUAAGCGGGCGGUGGUAAUAUGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
.................(((((((((.((((((((........))...(((((((....(((.(......).)))....)))))))))))))....)))...))))))....... ( -26.00)
>DroSec_CAF1 24965 115 + 1
CAAAAACGUAGCUAUUAUUUCGGCCGCUGCUGUGCCUAUAUAAGCGGGCGGUGGUAAUAUGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
.................(((((((((.((((((((((........))))((((((....(((.(......).)))....)))))).))))))....)))...))))))....... ( -30.60)
>DroSim_CAF1 8877 115 + 1
CAAAAACGUAGCUAUUAUUUCGGCCGCUGCUGUGCCUACAUAAGCGGGCGGUGGUAAUAUGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
.................(((((((((.(((((((((..(....)..)))((((((....(((.(......).)))....)))))).))))))....)))...))))))....... ( -31.30)
>DroEre_CAF1 23240 115 + 1
CGAAAACGUAGCUAAUACUUUGGCCGCUGCUGUGCAUACAUAAGCGGGCGGUGGUAAUAUGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
.......(..(((((....)))))..)((((((((........))...(((((((....(((.(......).)))....)))))))))))))....(((...))).......... ( -27.50)
>DroYak_CAF1 23150 112 + 1
---AGACGUAGCUAGCACUUUGACCGCAGCUGUGCGAACAUAAGCGGGCGAUGGUAAUACGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
---....((.(((..........((((...(((....)))...)))).((.((((...(((((.....)))))......)))).))..))).....(((...)))..))...... ( -19.40)
>consensus
CAAAAACGUAGCUAUUAUUUUGGCCGCUGCUGUGCAUACAUAAGCGGGCGGUGGUAAUAUGAAAUUAAUUUGUUAGACAACCACCGACAGCAUAAACGGUAACCGAAACAACAAA
..................((((((((.((((((((........))...(((((((...(((((.....)))))......)))))))))))))....)))...)))))........ (-23.72 = -23.92 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	8,059,785 – 8,059,900
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-30.36
Consensus MFE	-25.28
Energy contribution	-25.08
Covariance contribution	-0.20
Combinations/Pair	1.17
Mean z-score	-1.54
Structure conservation index	0.83
SVM decision value	0.64
SVM RNA-class probability	0.809039
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8059785 115 - 20766785
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCAUAUUACCACCGCCCGCUUAUGUAUGCACAGCAGCGGCCAAAAUAGUAGCUACGUUUUCG
.(((((((((.((...((((...(((((((((((((........................)))))))...((........)))))))))))))).)))))))))........... ( -26.66)
>DroSec_CAF1 24965 115 - 1
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCAUAUUACCACCGCCCGCUUAUAUAGGCACAGCAGCGGCCGAAAUAAUAGCUACGUUUUUG
.((((((((((((...((((...(((((((((((((........................)))))))...((((....))))))))))))))))))))))))))........... ( -36.76)
>DroSim_CAF1 8877 115 - 1
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCAUAUUACCACCGCCCGCUUAUGUAGGCACAGCAGCGGCCGAAAUAAUAGCUACGUUUUUG
.((((((((((((...((((...((((((.((((((........................))))))(((..(....)..)))))))))))))))))))))))))........... ( -39.86)
>DroEre_CAF1 23240 115 - 1
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCAUAUUACCACCGCCCGCUUAUGUAUGCACAGCAGCGGCCAAAGUAUUAGCUACGUUUUCG
...((((...(.....((((...(((((((((((((........................)))))))...((........)))))))))))).....)...)))).......... ( -24.96)
>DroYak_CAF1 23150 112 - 1
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCGUAUUACCAUCGCCCGCUUAUGUUCGCACAGCUGCGGUCAAAGUGCUAGCUACGUCU---
...((.(((.((.(((((((....(((((.((((((........................))))))((..((....))..))))))).)))))..)).))..))).))....--- ( -23.56)
>consensus
UUUGUUGUUUCGGUUACCGUUUAUGCUGUCGGUGGUUGUCUAACAAAUUAAUUUCAUAUUACCACCGCCCGCUUAUGUAGGCACAGCAGCGGCCAAAAUAAUAGCUACGUUUUCG
.(((((((((.((...((((...(((((((((((((........................)))))))...((........)))))))))))))).)))))))))........... (-25.28 = -25.08 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:13 2006