Locus 103

Sequence ID	3R_DroMel_CAF1
Location	629,972 – 630,103
Length	131
Max. P	0.996107

overview

Window 2

Location	629,972 – 630,069
Length	97
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	83.01
Mean single sequence MFE	-30.78
Consensus MFE	-20.91
Energy contribution	-22.72
Covariance contribution	1.81
Combinations/Pair	1.12
Mean z-score	-3.49
Structure conservation index	0.68
SVM decision value	2.65
SVM RNA-class probability	0.996107
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 629972 97 + 27905053
AAAUCGUUUAGGUAUGCUCGUCUUGAAUACG--------UGUAUGAAUGUAGAACCUAUGAUUUAGAGCACAUUUGCCGAAAUCGGCAAGUGCCU-CACCACGAUA
..(((((...(((.((((((((.....((((--------(......)))))........)))...)))))(((((((((....)))))))))...-.)))))))). ( -29.42)
>DroSec_CAF1 45751 96 + 1
AAAUCGUUUAGGAAUGCUCGUCUUGAAUUCA--------UGUACGAAUGUAGAUCCUAUCAUUUAGAGCACAUUUGCCGAAAUCGGCAAGUGCCUACACCACGA--
...((((.((((..(((((....(((....(--------(.(((....))).))....)))....)))))(((((((((....)))))))))))))....))))-- ( -29.50)
>DroSim_CAF1 47377 98 + 1
AAAUCGGUUAGGAAUGCUCGUCUUGAAUUCA--------UGUACGAAUGUAGAUCCUAUCAUUUAGAGCACAUUUGCCGAAAUCGGCAAGUGCCUACACCACGAUA
.....(((((((..(((((....(((....(--------(.(((....))).))....)))....)))))(((((((((....))))))))))))).)))...... ( -32.00)
>DroEre_CAF1 49173 106 + 1
AAAUCGUUUAGAAUCGUUCAGAUGUAAUACGAAUGGUUUUGUACGAAUGAAGAUAGUAUCGUUUAGAGAACAUUUGCCGAAAUCGGCAAAUGCCUACGCCACGAUA
...((((.(((((((((((...........))))))))))).))))..........((((((...(((..(((((((((....))))))))).)).)...)))))) ( -32.20)
>consensus
AAAUCGUUUAGGAAUGCUCGUCUUGAAUACA________UGUACGAAUGUAGAUCCUAUCAUUUAGAGCACAUUUGCCGAAAUCGGCAAGUGCCUACACCACGAUA
..(((((.((((..(((((........((((((....)))))).(((((..........))))).)))))(((((((((....)))))))))))))....))))). (-20.91 = -22.72 +   1.81)

alignment

secondary structure

dotplot

Window 3

Location	629,972 – 630,069
Length	97
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	83.01
Mean single sequence MFE	-26.56
Consensus MFE	-17.48
Energy contribution	-18.35
Covariance contribution	0.87
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.66
SVM decision value	1.06
SVM RNA-class probability	0.907923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 629972 97 - 27905053
UAUCGUGGUG-AGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUCAUAGGUUCUACAUUCAUACA--------CGUAUUCAAGACGAGCAUACCUAAACGAUUU
.(((((....-(((...((((((....)))))).(((((((......(((.((.............)--------).))).......))))))))))..))))).. ( -24.04)
>DroSec_CAF1 45751 96 - 1
--UCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUACA--------UGAAUUCAAGACGAGCAUUCCUAAACGAUUU
--((((....(((((((((((((....))))))..)))).))).....(((((......(((((.(.--------((....)).))))))...))))).))))... ( -28.20)
>DroSim_CAF1 47377 98 - 1
UAUCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUACA--------UGAAUUCAAGACGAGCAUUCCUAACCGAUUU
.....((((.(((((((((((((....))))))..)))).))).....(((((......(((((.(.--------((....)).))))))...))))))))).... ( -28.50)
>DroEre_CAF1 49173 106 - 1
UAUCGUGGCGUAGGCAUUUGCCGAUUUCGGCAAAUGUUCUCUAAACGAUACUAUCUUCAUUCGUACAAAACCAUUCGUAUUACAUCUGAACGAUUCUAAACGAUUU
((((((...(..(((((((((((....)))))))))))..)...))))))........................((((.....(((.....))).....))))... ( -25.50)
>consensus
UAUCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUACA________CGAAUUCAAGACGAGCAUUCCUAAACGAUUU
..((((....(((((((((((((....))))))..)))).))).....(((((......(((((.....................)))))...))))).))))... (-17.48 = -18.35 +   0.87)

alignment

secondary structure

dotplot

Window 4

Location	630,004 – 630,103
Length	99
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	89.50
Mean single sequence MFE	-31.03
Consensus MFE	-22.17
Energy contribution	-23.93
Covariance contribution	1.75
Combinations/Pair	1.12
Mean z-score	-1.74
Structure conservation index	0.71
SVM decision value	0.13
SVM RNA-class probability	0.596457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 630004 99 - 27905053
UUCUGGGUUGGGUGUUUGGAACGAGUGCACUAACUAUCGUGGUG-AGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUCAUAGGUUCUACAUUCAUAC
........(((((((..(((((.(((......)))...(((((.-.(((((((((((....))))))..)))))....)))))..))))))))))))... ( -30.60)
>DroSec_CAF1 45783 93 - 1
UUCUGGGUUGGGUGUUUGGAACUAGCGCA-------UCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUAC
...((.(((((..........))))).))-------.((.(((((((((((((((((....))))))..))))((((.....))))..)))))))))... ( -27.50)
>DroSim_CAF1 47409 100 - 1
UUCUGGGUUGGGUGUUUGGAACUAGCGCACUGACUAUCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUAC
...(((((((((((((.......))))).))..(((((((....(((((((((((((....))))))..)))).))).)))))))))))))......... ( -32.20)
>DroEre_CAF1 49213 100 - 1
UUCUGGGUUGGGUGUUUGGAACGAGCGCACUGACUAUCGUGGCGUAGGCAUUUGCCGAUUUCGGCAAAUGUUCUCUAAACGAUACUAUCUUCAUUCGUAC
.....(((..((((((((...))))))).)..)))(((((...(..(((((((((((....)))))))))))..)...)))))................. ( -33.80)
>consensus
UUCUGGGUUGGGUGUUUGGAACGAGCGCACUGACUAUCGUGGUGUAGGCACUUGCCGAUUUCGGCAAAUGUGCUCUAAAUGAUAGGAUCUACAUUCGUAC
...((((((((((((((.....)))))).....(((((((....(((((((((((((....))))))..)))).))).)))))))...))).)))))... (-22.17 = -23.93 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:18 2006