Locus 5771

Sequence ID	2R_DroMel_CAF1
Location	18,297,728 – 18,297,862
Length	134
Max. P	0.631696

overview

Window 5

Location	18,297,728 – 18,297,822
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	87.45
Mean single sequence MFE	-22.42
Consensus MFE	-16.46
Energy contribution	-18.26
Covariance contribution	1.80
Combinations/Pair	1.10
Mean z-score	-1.52
Structure conservation index	0.73
SVM decision value	-0.08
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18297728 94 + 20766785
ACCGGCGUAAGUAUUCACAAAGGAAUGCGUUAAGUAAUAGCAUUUAAGUAGUGCAAAUGGGAAAGUGUUGUGUUUAUCAAUGCACUUUAUGCAA
....((((((((((((......))))))....(((....(((((.....)))))..........((((((.......))))))))))))))).. ( -20.60)
>DroSec_CAF1 95008 94 + 1
UCCGGCGUAAGUAUUCACAAAGGAAUGCGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAA
....(((((.((((((......))))))((((.....)))).......((((((((.(((..((((.....)))).)))))))))))))))).. ( -23.80)
>DroSim_CAF1 95769 94 + 1
UCCGGCGUAAGUAUUCACAAAGGAAUGCGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAA
....(((((.((((((......))))))((((.....)))).......((((((((.(((..((((.....)))).)))))))))))))))).. ( -23.80)
>DroEre_CAF1 98749 78 + 1
UCCGGCGUAAGUAUUCACAAAGGAAUGCGUUA----AUAGCAUUUAAGGGGUGC------------UUCAUGUUUGCCAUUGCACUUUAGGCAA
...(((((((((((((......((((((....----...))))))...))))))------------)).)))))((((...........)))). ( -20.00)
>DroYak_CAF1 96749 94 + 1
UCCGGCGUAAGUAUUCACAAAGGAAUGCGUUAAGUAAUAGCAUUUAAGGAGUGCAAACGGAGAAGCGUUAUGUUUGUCAUUGCACUUUAGGCAA
....((.((.((((((......))))))((((.....)))).......((((((((...((.((((.....)))).)).)))))))))).)).. ( -23.90)
>consensus
UCCGGCGUAAGUAUUCACAAAGGAAUGCGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAA
....((((((((((((......))))))((((.....))))........(((((((...((.((((.....)))).)).))))))))))))).. (-16.46 = -18.26 +   1.80)

alignment

secondary structure

dotplot

Window 6

Location	18,297,755 – 18,297,862
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	80.60
Mean single sequence MFE	-24.62
Consensus MFE	-13.61
Energy contribution	-14.22
Covariance contribution	0.61
Combinations/Pair	1.24
Mean z-score	-1.96
Structure conservation index	0.55
SVM decision value	0.20
SVM RNA-class probability	0.631696
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18297755 107 + 20766785
CGUUAAGUAAUAGCAUUUAAGUAGUGCAAAUGGGAAAGUGUUGUGUUUAUCAAUGCACUUUAUGCAAAUGUGCAAAUAUUUCUUUAAUAUCUUUAAAAGUGCAACCA
............(((((.....)))))...(((......((((.......))))(((((((.((((....)))).(((((.....))))).....)))))))..))) ( -19.00)
>DroSec_CAF1 95035 107 + 1
CGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAAAUGUGCAAAUAUUUCUUUAAAAUCUUUAAAUGUGCAAGAU
............(((((((((((((((((.(((..((((.....)))).)))))))))....((((....))))...............)))))))))))....... ( -24.40)
>DroSim_CAF1 95796 107 + 1
CGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAAAUGUGCAAAUAUUUCUUUAAAAUCUUUAAAUGGGCAACCC
.((((.....))))(((((((((((((((.(((..((((.....)))).)))))))))....((((....))))...............)))))))))((....)). ( -24.30)
>DroEre_CAF1 98776 88 + 1
CGUUA----AUAGCAUUUAAGGGGUGC------------UUCAUGUUUGCCAUUGCACUUUAGGCAAAUGUGCAAAUAUUU---AAGGAUCCUUAAAAGUGCUCCCA
.....----..(((((((.((((((.(------------((.((((((((((((((.(....))).)))).))))))))..---))).))))))..))))))).... ( -27.30)
>DroYak_CAF1 96776 104 + 1
CGUUAAGUAAUAGCAUUUAAGGAGUGCAAACGGAGAAGCGUUAUGUUUGUCAUUGCACUUUAGGCAAAUGGGCAAAUAUUU---AAGGUUCUUUAUAAGUGUACCCA
.((((.....))))......((.(((((.(..(((((.(...(((((((((.((((.(....)))))...)))))))))..---..).)))))..)...))))))). ( -28.10)
>consensus
CGUUAAGUAAUAGCAUUUAAGGAGUGCAAAUGGGAAAGCGUUAUGUUUGUCAUUGCACUUUAUGCAAAUGUGCAAAUAUUUCUUUAAAAUCUUUAAAAGUGCAACCA
............(((((((((((.....((((......))))((((((((((((((.......)).)))).))))))))..........)))))))..))))..... (-13.61 = -14.22 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:01 2006