Locus 1800

Sequence ID 3R_DroMel_CAF1
Location 5,146,234 – 5,146,331
Length 97
Max. P 0.630701
window2966 window2967

overview

Window 6

Location 5,146,234 – 5,146,331
Length 97
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 82.50
Mean single sequence MFE -27.27
Consensus MFE -16.54
Energy contribution -18.77
Covariance contribution 2.22
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.61
SVM decision value -0.01
SVM RNA-class probability 0.529485
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5146234 97 + 27905053
U------------GCCAGGACACUAUGCUCAUUGCCGCCUAUCUGCCGGCAGAGUUCGCUUAUCAAUUACAUUGAAUUUACCCAGGCAGAAAUGGCUUUUAGCCAUUCU
(------------(((.((.......((((..(((((.(.....).))))))))).......(((((...)))))......)).))))(((.((((.....))))))). ( -26.60)
>DroSec_CAF1 20286 97 + 1
U------------GCCAGGACACUCUGCUCAUUGCCGCCUAUCUGCCGGCAGAGUUCGCUUAUCAAUUACAUUGAAUUUACCCAGGCACAAAUGGCUUUUAGCCAUUCU
(------------(((.((.......((((..(((((.(.....).))))))))).......(((((...)))))......)).))))..((((((.....)))))).. ( -26.20)
>DroSim_CAF1 17271 97 + 1
U------------GCCAGGACACUCUGCUCAUUGCCGCCUAUCUGCCGGCAGAGUUCGCUUAUCAAUUACAUUGAAUUUACCCAGGCACAAAUGGCUUUUAGCCAUUCU
(------------(((.((.......((((..(((((.(.....).))))))))).......(((((...)))))......)).))))..((((((.....)))))).. ( -26.20)
>DroEre_CAF1 18702 109 + 1
UGCGUGGUAAGCAGCCAGGACACUCCGCUCAUUGCCGCCUAUCUGCCGGCGGAGUUCGCUUAUCAAUUACACUGAAUUUAGCCAGGCGCAAAUGGCUUUUAGCCAUUCC
((((((((((((.....((.....))((((...((((.(.....).)))).))))..))))))).......(((........))))))))((((((.....)))))).. ( -37.20)
>DroYak_CAF1 17669 102 + 1
UGU-------GCAGCCAGGACACUCUGCUCAUUGCCGCCUAUCUGCCGGCGGAGUUCGCUUAUCAAUUACAUUGAAUUUACCCAGGCACAAAUGGCUUUUAGCCAUUCU
(((-------(((((((((....)))).......(((((........))))).....)))..(((((...)))))..........)))))((((((.....)))))).. ( -27.60)
>DroAna_CAF1 40151 86 + 1
U--GU--------G-GAGAAGACUCCAGUCAUUGCCGCCUAUCUGCCGC---------CUUAUCAAUUACAUUGAAUUUACCCAGGCAAG---CACCCUGGGCAACUCU
.--.(--------(-(((....))))).........(((((..(((.((---------((....((((......)))).....))))..)---))...)))))...... ( -19.80)
>consensus
U____________GCCAGGACACUCUGCUCAUUGCCGCCUAUCUGCCGGCAGAGUUCGCUUAUCAAUUACAUUGAAUUUACCCAGGCACAAAUGGCUUUUAGCCAUUCU
.............(((.((.......((((..(((((.(.....).))))))))).......(((((...)))))......)).)))...(((((((...))))))).. (-16.54 = -18.77 +   2.22)

alignment

Postscript

secondary structure

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dotplot

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Window 7

Location 5,146,234 – 5,146,331
Length 97
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 82.50
Mean single sequence MFE -31.42
Consensus MFE -20.71
Energy contribution -20.97
Covariance contribution 0.26
Combinations/Pair 1.31
Mean z-score -1.93
Structure conservation index 0.66
SVM decision value 0.20
SVM RNA-class probability 0.630701
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5146234 97 - 27905053
AGAAUGGCUAAAAGCCAUUUCUGCCUGGGUAAAUUCAAUGUAAUUGAUAAGCGAACUCUGCCGGCAGAUAGGCGGCAAUGAGCAUAGUGUCCUGGC------------A
.(((((((.....)))))))..(((.((..(...(((((...)))))...((...(..(((((.(.....).)))))..).))....)..)).)))------------. ( -30.00)
>DroSec_CAF1 20286 97 - 1
AGAAUGGCUAAAAGCCAUUUGUGCCUGGGUAAAUUCAAUGUAAUUGAUAAGCGAACUCUGCCGGCAGAUAGGCGGCAAUGAGCAGAGUGUCCUGGC------------A
.(((((((.....))))))).((((.(((...((((.......(((.....))).((((((((.(.....).)))))..)))..))))..))))))------------) ( -31.00)
>DroSim_CAF1 17271 97 - 1
AGAAUGGCUAAAAGCCAUUUGUGCCUGGGUAAAUUCAAUGUAAUUGAUAAGCGAACUCUGCCGGCAGAUAGGCGGCAAUGAGCAGAGUGUCCUGGC------------A
.(((((((.....))))))).((((.(((...((((.......(((.....))).((((((((.(.....).)))))..)))..))))..))))))------------) ( -31.00)
>DroEre_CAF1 18702 109 - 1
GGAAUGGCUAAAAGCCAUUUGCGCCUGGCUAAAUUCAGUGUAAUUGAUAAGCGAACUCCGCCGGCAGAUAGGCGGCAAUGAGCGGAGUGUCCUGGCUGCUUACCACGCA
.(((((((.....)))))))..((.(((......(((((...)))))((((((.((((((((........))).((.....)))))))((....))))))))))).)). ( -34.60)
>DroYak_CAF1 17669 102 - 1
AGAAUGGCUAAAAGCCAUUUGUGCCUGGGUAAAUUCAAUGUAAUUGAUAAGCGAACUCCGCCGGCAGAUAGGCGGCAAUGAGCAGAGUGUCCUGGCUGC-------ACA
.(((((((.....)))))))(((((..((...((((..(((.....))).((.....(((((........)))))......)).))))..))..)..))-------)). ( -33.60)
>DroAna_CAF1 40151 86 - 1
AGAGUUGCCCAGGGUG---CUUGCCUGGGUAAAUUCAAUGUAAUUGAUAAG---------GCGGCAGAUAGGCGGCAAUGACUGGAGUCUUCUC-C--------AC--A
.((((((((((((...---....))))))).)))))...............---------((.((......)).))......(((((....)))-)--------).--. ( -28.30)
>consensus
AGAAUGGCUAAAAGCCAUUUGUGCCUGGGUAAAUUCAAUGUAAUUGAUAAGCGAACUCUGCCGGCAGAUAGGCGGCAAUGAGCAGAGUGUCCUGGC____________A
.((((((((...))))))))..(((.((..(...(((((...)))))...((.....(((((........)))))......))....)..)).)))............. (-20.71 = -20.97 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:52 2006