Locus 96

Sequence ID	3R_DroMel_CAF1
Location	601,384 – 601,502
Length	118
Max. P	0.846364

overview

Window 1

Location	601,384 – 601,502
Length	118
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	90.42
Mean single sequence MFE	-36.47
Consensus MFE	-28.35
Energy contribution	-28.10
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-2.12
Structure conservation index	0.78
SVM decision value	0.77
SVM RNA-class probability	0.846364
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 601384 118 + 27905053
ACCAAAAC-UGGGGCUUGAGUUGAAUUACCUGUUGGAAGACACAAUGCCACCCACGAUCAACAAUUCGGCGGUAAACAGUGCCGCCGAAAAGCGACCCCAGCGGCAAACGGAGCGCAAG
.((....(-(((((.(((.(((((....((....))..(.(.....).)........)))))..((((((((((.....))))))))))...))))))))).(.....)))........ ( -35.30)
>DroSec_CAF1 17466 117 + 1
ACCA-AAC-AGGGACUUAAGCUGAAUUACCUGUUGGAAGCCUCAAUGCCACCCACGAUCAACAAUUCGGCGGUAAACAGUGCCGCCGAAAAGCGACCCCAGCGGCAAACGGAGCGCAAG
.(((-(.(-(((................))))))))..(((((..((((...............((((((((((.....))))))))))..((.......))))))....))).))... ( -40.59)
>DroSim_CAF1 16618 117 + 1
ACCA-AAC-AGGGACUUAAGCUGAAUUACCUGUUGGAAGCCACAAUGCCACCCACGAUCAACAAUUCGGCGGUAAACAGUGCCGCCGAAAAGCGACCCCAGCGGCAAACGGAGCGCAAG
.(((-(.(-(((................))))))))..((..(..((((...............((((((((((.....))))))))))..((.......))))))...)..))..... ( -36.89)
>DroYak_CAF1 22143 119 + 1
CAAAAUAUAGAGGACUGAAGCAGAAUUACUUGUUGGAAGUCACAAUGCCACCUACGAUUAACAAUUCGGCGGUAAGCAGUGCCGCCGAAAAGCGAACCCAGCGGCAAACGGAGCGCAAG
............((((..(((((......)))))...))))....((((...............((((((((((.....))))))))))..((.......))))))............. ( -33.10)
>consensus
ACCA_AAC_AGGGACUUAAGCUGAAUUACCUGUUGGAAGCCACAAUGCCACCCACGAUCAACAAUUCGGCGGUAAACAGUGCCGCCGAAAAGCGACCCCAGCGGCAAACGGAGCGCAAG
...................((.......((....))..((..(..((((...............((((((((((.....))))))))))..((.......))))))...)..))))... (-28.35 = -28.10 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	601,384 – 601,502
Length	118
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	90.42
Mean single sequence MFE	-40.30
Consensus MFE	-31.65
Energy contribution	-32.53
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.79
SVM decision value	-0.01
SVM RNA-class probability	0.525989
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 601384 118 - 27905053
CUUGCGCUCCGUUUGCCGCUGGGGUCGCUUUUCGGCGGCACUGUUUACCGCCGAAUUGUUGAUCGUGGGUGGCAUUGUGUCUUCCAACAGGUAAUUCAACUCAAGCCCCA-GUUUUGGU
..............(((((((((((.....((((((((.........))))))))..(((((((.((((.(((.....))).))))...))....)))))....))))))-))...))) ( -39.80)
>DroSec_CAF1 17466 117 - 1
CUUGCGCUCCGUUUGCCGCUGGGGUCGCUUUUCGGCGGCACUGUUUACCGCCGAAUUGUUGAUCGUGGGUGGCAUUGAGGCUUCCAACAGGUAAUUCAGCUUAAGUCCCU-GUU-UGGU
...((.(((....(((((((.(((((((..((((((((.........))))))))..).))))).).)))))))..)))))..((((((((................)))-).)-))). ( -44.09)
>DroSim_CAF1 16618 117 - 1
CUUGCGCUCCGUUUGCCGCUGGGGUCGCUUUUCGGCGGCACUGUUUACCGCCGAAUUGUUGAUCGUGGGUGGCAUUGUGGCUUCCAACAGGUAAUUCAGCUUAAGUCCCU-GUU-UGGU
.....((..((..(((((((.(((((((..((((((((.........))))))))..).))))).).))))))).))..))..((((((((................)))-).)-))). ( -43.69)
>DroYak_CAF1 22143 119 - 1
CUUGCGCUCCGUUUGCCGCUGGGUUCGCUUUUCGGCGGCACUGCUUACCGCCGAAUUGUUAAUCGUAGGUGGCAUUGUGACUUCCAACAAGUAAUUCUGCUUCAGUCCUCUAUAUUUUG
.((((........(((((((.((((.((..((((((((.........))))))))..)).))))...)))))))((((........))))))))......................... ( -33.60)
>consensus
CUUGCGCUCCGUUUGCCGCUGGGGUCGCUUUUCGGCGGCACUGUUUACCGCCGAAUUGUUGAUCGUGGGUGGCAUUGUGGCUUCCAACAGGUAAUUCAGCUUAAGUCCCU_GUU_UGGU
((((.((......(((((((.(((((((..((((((((.........))))))))..).))))).).)))))))((((........))))........)).)))).............. (-31.65 = -32.53 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:58 2006