Locus 1349

Sequence ID 3R_DroMel_CAF1
Location 3,983,246 – 3,983,345
Length 99
Max. P 0.778897
window2208 window2209

overview

Window 8

Location 3,983,246 – 3,983,345
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 84.84
Mean single sequence MFE -29.89
Consensus MFE -20.22
Energy contribution -21.78
Covariance contribution 1.56
Combinations/Pair 1.14
Mean z-score -2.52
Structure conservation index 0.68
SVM decision value -0.03
SVM RNA-class probability 0.517136
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3983246 99 + 27905053
UAAAAGAGAAAAGGGUUAGAAAAUGCACAAGCAACCCUUUUCUGGU-GGGGGUGCUGU-CGGC--UUGUGCUGUAACCUGUGCAGAAUUAUGCAUUUGCAUAU
......((((((((((.......(((....))))))))))))).((-(.((((.....-((((--....))))..)))).))).....(((((....))))). ( -31.51)
>DroSec_CAF1 29647 99 + 1
UAAAAGAGAAAAGGGUUAGAAAAUGCACAAGCAACCCUUUUCUGGU-GGGGGUGCUGU-UGGG--UUGUGCUGUAACCUGUGCAGAAUUAUGCAUUUGCAUAU
......((((((((((.......(((....))))))))))))).((-(.((((((...-....--(((..(........)..)))......)))))).))).. ( -29.33)
>DroSim_CAF1 31336 100 + 1
UAAAAGAGAAAAGGGUUAGGAAAUGCACAAGCAACCCUUUUCUGGUUGGGGGUGCUGU-UGGG--UUGUGCUGUAACCUGUGCAGAAUUAUGCAUUUGCAUAU
......((((((((((.......(((....)))))))))))))(((((.(.(..(...-....--..)..)).)))))((((((((........)))))))). ( -29.11)
>DroEre_CAF1 30460 99 + 1
UAAAAACGAAAAGGGUUAGAAAAUGCAUAAGCAACCCUUUUCUGGU-GGGGGCGCUGU-UGGG--GUGUGCUGUAACCUGUGCAAAAUUAUGCAUUUGCAUAU
.......(((((((((.......(((....)))))))))))).(((-.(.(((((...-....--..))))).).)))((((((((........)))))))). ( -30.41)
>DroYak_CAF1 31760 101 + 1
UAAAAUGGAAAAGGGUUAGAAAAUGCAUAAGCAACCCUUUUCUGGU-GGG-GUGCUGUGUGGGGUGUGUGCUGUAACCUGUGCAAAAUUAUGCAUUUGCAUAU
......((((((((((.......(((....)))))))))))))(((-(.(-(..(............)..)).).)))((((((((........)))))))). ( -27.61)
>DroPer_CAF1 33072 88 + 1
UGGA----AAAAGGGUUAGAAAAUGCACUGGCAACCCUCAACCC--------UGUCCC-UAGG--GUGGGGGGAAACCUGUGCAAAAUUAUGCAUUUGCAUAU
....----...............(((((.((...(((((.((((--------((....-))))--)).)))))...)).)))))....(((((....))))). ( -31.40)
>consensus
UAAAAGAGAAAAGGGUUAGAAAAUGCACAAGCAACCCUUUUCUGGU_GGGGGUGCUGU_UGGG__GUGUGCUGUAACCUGUGCAAAAUUAUGCAUUUGCAUAU
......((((((((((.......(((....)))))))))))))(((....(((((............)))))...)))((((((((........)))))))). (-20.22 = -21.78 +   1.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,983,246 – 3,983,345
Length 99
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 84.84
Mean single sequence MFE -23.63
Consensus MFE -16.92
Energy contribution -17.28
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -3.12
Structure conservation index 0.72
SVM decision value 0.55
SVM RNA-class probability 0.778897
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3983246 99 - 27905053
AUAUGCAAAUGCAUAAUUCUGCACAGGUUACAGCACAA--GCCG-ACAGCACCCCC-ACCAGAAAAGGGUUGCUUGUGCAUUUUCUAACCCUUUUCUCUUUUA
.(((((....)))))....(((...((((........)--))).-...))).....-...(((((((((((((....))).......))))))))))...... ( -24.31)
>DroSec_CAF1 29647 99 - 1
AUAUGCAAAUGCAUAAUUCUGCACAGGUUACAGCACAA--CCCA-ACAGCACCCCC-ACCAGAAAAGGGUUGCUUGUGCAUUUUCUAACCCUUUUCUCUUUUA
.(((((....)))))....(((...((((.......))--))..-...))).....-...(((((((((((((....))).......))))))))))...... ( -22.11)
>DroSim_CAF1 31336 100 - 1
AUAUGCAAAUGCAUAAUUCUGCACAGGUUACAGCACAA--CCCA-ACAGCACCCCCAACCAGAAAAGGGUUGCUUGUGCAUUUCCUAACCCUUUUCUCUUUUA
.(((((....)))))....(((...((((.......))--))..-...))).........(((((((((((((....))).......))))))))))...... ( -22.11)
>DroEre_CAF1 30460 99 - 1
AUAUGCAAAUGCAUAAUUUUGCACAGGUUACAGCACAC--CCCA-ACAGCGCCCCC-ACCAGAAAAGGGUUGCUUAUGCAUUUUCUAACCCUUUUCGUUUUUA
...((((((........))))))..(((....((.(..--....-...).))....-))).((((((((((((....))).......)))))))))....... ( -22.71)
>DroYak_CAF1 31760 101 - 1
AUAUGCAAAUGCAUAAUUUUGCACAGGUUACAGCACACACCCCACACAGCAC-CCC-ACCAGAAAAGGGUUGCUUAUGCAUUUUCUAACCCUUUUCCAUUUUA
...((((((........))))))..(((....((..............))..-...-))).((((((((((((....))).......)))))))))....... ( -20.35)
>DroPer_CAF1 33072 88 - 1
AUAUGCAAAUGCAUAAUUUUGCACAGGUUUCCCCCCAC--CCUA-GGGACA--------GGGUUGAGGGUUGCCAGUGCAUUUUCUAACCCUUUU----UCCA
.(((((....)))))....(((((.(((..(((.(.((--(((.-.....)--------)))).).)))..))).)))))...............----.... ( -30.20)
>consensus
AUAUGCAAAUGCAUAAUUCUGCACAGGUUACAGCACAA__CCCA_ACAGCACCCCC_ACCAGAAAAGGGUUGCUUGUGCAUUUUCUAACCCUUUUCUCUUUUA
.(((((....)))))..............................................((((((((((((....))).......)))))))))....... (-16.92 = -17.28 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:26 2006