Locus 3995

Sequence ID 2R_DroMel_CAF1
Location 13,217,903 – 13,218,044
Length 141
Max. P 0.777107
window6449 window6450

overview

Window 9

Location 13,217,903 – 13,218,006
Length 103
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.07
Mean single sequence MFE -20.99
Consensus MFE -9.73
Energy contribution -11.65
Covariance contribution 1.92
Combinations/Pair 1.16
Mean z-score -2.44
Structure conservation index 0.46
SVM decision value 0.55
SVM RNA-class probability 0.777107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13217903 103 - 20766785
AGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA-AAAUGAUAAGCU----GGCAAAAAUUUAA-AGCAAAUACUUACCACAAAAGUUCAGCUGA-------AUCACAA---
.(..((((((((....(((((((....(((((.....))))-)...)))))))(----((.((..((((..-...))))..)).))).........))))))-------))..)..--- ( -22.30)
>DroSec_CAF1 11859 104 - 1
AGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAAAAAAUGAUAAGCU----GGCAAGAAUUAAA-AACAAAUACUUACCACAAAAGUUCAGCUGA-------AUCACAA---
.(..((((((((....(((((((....(((((.....)))))....)))))))(----((.(((.(((...-....))).))).))).........))))))-------))..)..--- ( -25.30)
>DroSim_CAF1 12959 103 - 1
AGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA-AAAUGAUAAGCU----GGCGAGAAUUAAA-AACAAAUACUUACCACAAAAGUUCAGCUGA-------AUCACAA---
.(..((((((((....(((((((....(((((.....))))-)...)))))))(----((..((.(((...-....))).))..))).........))))))-------))..)..--- ( -26.00)
>DroEre_CAF1 11296 104 - 1
AGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCUUCAAGAAA-AAAUGAUAAUCU----UGCAAGAAUUUAA---AAAAUACUUACCACCAUAGUUUAGCAGA-------AUCACAAUCG
.(..((((.((((...(((......(((.((((((((((..-.........)))----)).))))).....---.........))).....))).)))).))-------))..)..... ( -14.76)
>DroYak_CAF1 14257 103 - 1
AGAAAUUCAGCUAUAUGCUUGCCUAGGUUUUCAUCAAGAAA-AAAUGAUAACCU----GGCACGAAAUAAAAAAAAAAUACUUACCAC-AAAGUUCAGUUGA-------UUCACAA---
.(((..((((((.......((((.(((((.((((.......-..)))).)))))----)))).................((((.....-.))))..))))))-------)))....--- ( -20.80)
>DroPer_CAF1 11319 112 - 1
AAACAUUCAGGUAUAUGCUUGUCAAGGUAUUCGUCAUGAAA-UGG-AAUCAGCGGAGGGUCAACAAAUUAA---AUAUUACGUACCAU--UAGCUCACAAGAGGGCCAUGCCACAAUCC
.........(((((.(((((....)))))(((((..(((..-...-..)))))))).((((....(((...---..))).........--...(((....))))))))))))....... ( -16.80)
>consensus
AGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA_AAAUGAUAAGCU____GGCAAGAAUUAAA_AAAAAAUACUUACCACAAAAGUUCAGCUGA_______AUCACAA___
......((((((....(((((((.....((((.....)))).....))))))).....((.(((.(((........))).))).))..........))))))................. ( -9.73 = -11.65 +   1.92)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,217,932 – 13,218,044
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -25.67
Consensus MFE -14.88
Energy contribution -16.43
Covariance contribution 1.56
Combinations/Pair 1.17
Mean z-score -2.27
Structure conservation index 0.58
SVM decision value 0.28
SVM RNA-class probability 0.665358
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13217932 112 - 20766785
AUAAAUAUGACUU--GAUCAGUCGCGUGAGUUGUCGACAGAGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA-AAAUGAUAAGCU----GGCAAAAAUUUAA-AGCAAAUA
........((((.--....))))((.((((((.((....))..))))))((((...(((((((....(((((.....))))-)...))))))))----)))..........-.))..... ( -25.50)
>DroSec_CAF1 11888 112 - 1
AUAAAUGUGACUU---AUCAGUCGCGUGAGAUGUCGACAGAGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAAAAAAUGAUAAGCU----GGCAAGAAUUAAA-AACAAAUA
....((((((((.---...))))))))..((..((......))...)).((((...(((((((....(((((.....)))))....))))))))----)))..........-........ ( -25.70)
>DroSim_CAF1 12988 111 - 1
AUAAAUGUGACUU---AUCAGUCGCGUGAGUUGUCGACAGAGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA-AAAUGAUAAGCU----GGCGAGAAUUAAA-AACAAAUA
....((((((((.---...))))))))(((((.((....))..))))).((((...(((((((....(((((.....))))-)...))))))))----)))..........-........ ( -27.40)
>DroEre_CAF1 11328 109 - 1
AUAAAUGUGACUG---AUCAGUCACAUGAGUUUUCGACAGAGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCUUCAAGAAA-AAAUGAUAAUCU----UGCAAGAAUUUAA---AAAAUA
....((((((((.---...))))))))(((((((.(...((((......((.....))(((((....(((((.....))))-)...))))))))----).).)))))))..---...... ( -23.00)
>DroYak_CAF1 14285 112 - 1
AUAAAUGUGACUG---AUCAGUCACGUGUGUUAUCGACAGAGAAAUUCAGCUAUAUGCUUGCCUAGGUUUUCAUCAAGAAA-AAAUGAUAACCU----GGCACGAAAUAAAAAAAAAAUA
....((((((((.---...)))))))).((((.(((............(((.....)))((((.(((((.((((.......-..)))).)))))----)))))))))))........... ( -28.10)
>DroPer_CAF1 11356 115 - 1
AUGGGUGUGCUUGGGGAUCAGUCAAGUGUGUAUUCGACAUAAACAUUCAGGUAUAUGCUUGUCAAGGUAUUCGUCAUGAAA-UGG-AAUCAGCGGAGGGUCAACAAAUUAA---AUAUUA
...(((((..(((..((((.(.(((((((((((..((.........))..))))))))))).)......(((((..(((..-...-..)))))))).))))..))).....---))))). ( -24.30)
>consensus
AUAAAUGUGACUG___AUCAGUCACGUGAGUUGUCGACAGAGAAAUUCAGCUAUAUGCUUGUCUAGGUUUUCAUCAAGAAA_AAAUGAUAAGCU____GGCAAGAAUUAAA_AAAAAAUA
....((((((((.......))))))))(((((.((......))))))).(((....(((((((.....((((.....)))).....))))))).....)))................... (-14.88 = -16.43 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:15 2006