Locus 4099

Sequence ID 3R_DroMel_CAF1
Location 11,198,673 – 11,198,774
Length 101
Max. P 0.814251
window6563 window6564

overview

Window 3

Location 11,198,673 – 11,198,774
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 77.48
Mean single sequence MFE -22.07
Consensus MFE -14.87
Energy contribution -14.98
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.47
Structure conservation index 0.67
SVM decision value 0.66
SVM RNA-class probability 0.814251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11198673 101 + 27905053
GAGUUCGUCAAAUAUUCCAAGAAGUUCAGCACAACGCUGAAGGAGUACUUCAAAGAAGGACAGUAAGUAUU-AAGA----AUCACCUGCAGUGA-UUAUUUACUAUA
......(((...((((((......((((((.....))))))))))))((((...)))))))((((((((..-....----(((((.....))))-)))))))))... ( -24.50)
>DroVir_CAF1 770 86 + 1
GAGUUCGUCAAAUAUUCAAAGAAGUUCAGCACAACGCUGAAGGAAUACUUCAAAGAAGGACAGUAAGUUGG---C-------UCAUU------G-----UUAUCGUU
((((.........))))...((((((((((.....)))))......)))))...((..((((((.((....---)-------).)))------)-----)).))... ( -16.30)
>DroPse_CAF1 5710 101 + 1
GAGUUUGUCAAAUAUUCCAAGAAGUUCAGCACAACGCUGAAGGAGUACUUCAAAGAAGGACAGUAAGUGUU-GUGACAAAGACACU-----UUGUCUAUUUAUCGUU
.....((((...((((((......((((((.....))))))))))))((((...))))))))(((((((..-..(((((((...))-----)))))))))))).... ( -24.30)
>DroGri_CAF1 1274 92 + 1
GAGUUCGUCAAAUAUUCAAAGAAGUUCAGCACAACGCUGAAGGAAUACUUCAAAGAAGGACAGUAAGUUGUUGGCA----ACCAUUU------G-----UUAUCAUU
((((.........))))...((((((((((.....)))))......)))))...((..(((((...((((....))----))...))------)-----)).))... ( -17.70)
>DroAna_CAF1 1058 102 + 1
GAGUUUGUCAAAUAUUCCAAGAAGUUCAGCACAACGCUGAAGGAGUACUUCAAAGAAGGACAGUAAGUACAGAACA----UUAAGCUCCGGCCAUGUAUUUAC-AUU
.....((((...((((((......((((((.....))))))))))))((((...))))))))(((((((((.....----....((....))..)))))))))-... ( -25.30)
>DroPer_CAF1 5563 101 + 1
GAGUUUGUCAAAUAUUCCAAGAAGUUCAGCACAACGCUGAAGGAGUACUUCAAAGAAGGACAGUAAGUGUU-GUGACAAAGACACU-----UUGUCUAUUUAUCGUU
.....((((...((((((......((((((.....))))))))))))((((...))))))))(((((((..-..(((((((...))-----)))))))))))).... ( -24.30)
>consensus
GAGUUCGUCAAAUAUUCCAAGAAGUUCAGCACAACGCUGAAGGAGUACUUCAAAGAAGGACAGUAAGUAUU_GACA____AACACUU____U_G__UAUUUAUCAUU
......(((...((((((......((((((.....))))))))))))((((...))))))).............................................. (-14.87 = -14.98 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,198,673 – 11,198,774
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 77.48
Mean single sequence MFE -19.68
Consensus MFE -13.03
Energy contribution -13.12
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.21
Structure conservation index 0.66
SVM decision value 0.12
SVM RNA-class probability 0.594339
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11198673 101 - 27905053
UAUAGUAAAUAA-UCACUGCAGGUGAU----UCUU-AAUACUUACUGUCCUUCUUUGAAGUACUCCUUCAGCGUUGUGCUGAACUUCUUGGAAUAUUUGACGAACUC
...((((((.((-((((.....)))))----).))-..))))...((((.((((..(((((......(((((.....))))))))))..)))).....))))..... ( -20.20)
>DroVir_CAF1 770 86 - 1
AACGAUAA-----C------AAUGA-------G---CCAACUUACUGUCCUUCUUUGAAGUAUUCCUUCAGCGUUGUGCUGAACUUCUUUGAAUAUUUGACGAACUC
..((...(-----(------(.(((-------(---....)))).)))..(((...(((((......(((((.....))))))))))...))).......))..... ( -14.00)
>DroPse_CAF1 5710 101 - 1
AACGAUAAAUAGACAA-----AGUGUCUUUGUCAC-AACACUUACUGUCCUUCUUUGAAGUACUCCUUCAGCGUUGUGCUGAACUUCUUGGAAUAUUUGACAAACUC
...(.(((((((((((-----(((((.........-.))))))..)))).((((..(((((......(((((.....))))))))))..)))))))))).)...... ( -22.20)
>DroGri_CAF1 1274 92 - 1
AAUGAUAA-----C------AAAUGGU----UGCCAACAACUUACUGUCCUUCUUUGAAGUAUUCCUUCAGCGUUGUGCUGAACUUCUUUGAAUAUUUGACGAACUC
........-----(------(((((((----((....)))).........(((...(((((......(((((.....))))))))))...)))))))))........ ( -16.10)
>DroAna_CAF1 1058 102 - 1
AAU-GUAAAUACAUGGCCGGAGCUUAA----UGUUCUGUACUUACUGUCCUUCUUUGAAGUACUCCUUCAGCGUUGUGCUGAACUUCUUGGAAUAUUUGACAAACUC
.((-((....))))(..((((((....----.))))))..)....((((.((((..(((((......(((((.....))))))))))..)))).....))))..... ( -23.40)
>DroPer_CAF1 5563 101 - 1
AACGAUAAAUAGACAA-----AGUGUCUUUGUCAC-AACACUUACUGUCCUUCUUUGAAGUACUCCUUCAGCGUUGUGCUGAACUUCUUGGAAUAUUUGACAAACUC
...(.(((((((((((-----(((((.........-.))))))..)))).((((..(((((......(((((.....))))))))))..)))))))))).)...... ( -22.20)
>consensus
AACGAUAAAUA__C_A____AAGUGAC____UCAC_AAAACUUACUGUCCUUCUUUGAAGUACUCCUUCAGCGUUGUGCUGAACUUCUUGGAAUAUUUGACAAACUC
.............................................((((.((((..(((((......(((((.....))))))))))..)))).....))))..... (-13.03 = -13.12 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:05 2006