Locus 2758

Sequence ID 3L_DroMel_CAF1
Location 7,786,421 – 7,786,556
Length 135
Max. P 0.956311
window4311 window4312

overview

Window 1

Location 7,786,421 – 7,786,522
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.00
Mean single sequence MFE -19.30
Consensus MFE -10.79
Energy contribution -12.68
Covariance contribution 1.89
Combinations/Pair 1.16
Mean z-score -1.96
Structure conservation index 0.56
SVM decision value 1.46
SVM RNA-class probability 0.956311
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7786421 101 - 23771897
AGGCUACCAUAGCUUAAGUUGAGGCGUAAACGAAAGCUAGAUCAAAGCAUAACUUAAAGCCUAAGAAAAGGCAAGAUAACUUCAUUUGGUACUCAA-------------------AACAC
.(..(((((((((((..(((........)))..)))))).(((.(((.....)))...((((......))))..))).........)))))..)..-------------------..... ( -20.90)
>DroGri_CAF1 34171 94 - 1
AGG----CAUAAAUUAAAU---GGCU------AACGCUAAAGCUAAACAUAAUUUAGAAC-UAACAAUUUGUAAAGCGUUUGUAUUAGUAACAUAAAA-----------CUAAA-AAGGA
..(----((((((((...(---(((.------...))))...(((((.....)))))...-....)))))))...)).......(((((........)-----------)))).-..... ( -11.40)
>DroSec_CAF1 26668 100 - 1
AGGCUACCAUAGCUUAAGUUGAGGCGUAAACGAAAGCUAGAUCAAAGCAUAACUUA-AGCCUGAGAAAAGGCAAGAAAACUUCAUUUGGUACUCAA-------------------AACAC
.(..(((((((((((..(((........)))..)))))).................-.((((......))))..............)))))..)..-------------------..... ( -21.40)
>DroEre_CAF1 27059 120 - 1
AGGCUACCAUAGCUUAAGUUGAGGCUUAAACGAAAGCUAGAUCAAAGCUUAACUUAAAGCCUAAGAGAGGGCAAGAAAACUUCAUUUGGUACUCAAAAUAAAAAAUAAAACAAAAAACAC
.(..(((((.(((((..(((..(((((......))))).)))..))))).........((((......))))..............)))))..).......................... ( -22.00)
>DroYak_CAF1 28717 115 - 1
AGGCUACCAUAGCUUAAGUUGUGGCUUAAACGAAAGCUAGAUCAAAGCUUAACUUAAAGCCAAAGAAA-GGCAAGAAAACUUCAUUUGGUACUCAAAA---AAAAUA-AAUAAAAAACAC
(((((.(((((((....)))))))......(....).........)))))........((((((..((-(.........)))..))))))........---......-............ ( -20.80)
>consensus
AGGCUACCAUAGCUUAAGUUGAGGCUUAAACGAAAGCUAGAUCAAAGCAUAACUUAAAGCCUAAGAAAAGGCAAGAAAACUUCAUUUGGUACUCAAAA_____________AAA_AACAC
.((.((((.((((((..(((........)))..))))))...................((((......))))...............)))).)).......................... (-10.79 = -12.68 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 7,786,442 – 7,786,556
Length 114
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 91.12
Mean single sequence MFE -20.50
Consensus MFE -16.35
Energy contribution -16.73
Covariance contribution 0.37
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.80
SVM decision value 0.80
SVM RNA-class probability 0.853490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7786442 114 - 23771897
GUAAAAAGCUGAAGGUAAA-UUCAUAAAUAACACAAGGCUACCAUAGCUUAAGUUGAGGCGUAAACGAAAGCUAGAUCAAAGCAUAACUUAAAGCCUAAGAAAAGGCAAGAUAAC
.......(((...((((..-...................)))).((((((..(((........)))..))))))......)))..........((((......))))........ ( -19.30)
>DroSec_CAF1 26689 113 - 1
GUGAAAAGCUGAAGGUAAA-UUCAUAAAUAAAACAAGGCUACCAUAGCUUAAGUUGAGGCGUAAACGAAAGCUAGAUCAAAGCAUAACUUA-AGCCUGAGAAAAGGCAAGAAAAC
.......(((...((((..-...................)))).((((((..(((........)))..))))))......)))........-.((((......))))........ ( -20.20)
>DroEre_CAF1 27099 113 - 1
AA-AGAAACUGAUGGUAAA-UUCAUAAAUAACACAAGGCUACCAUAGCUUAAGUUGAGGCUUAAACGAAAGCUAGAUCAAAGCUUAACUUAAAGCCUAAGAGAGGGCAAGAAAAC
.(-((......((((((..-...................))))))(((((..(((..(((((......))))).)))..)))))...)))...((((......))))........ ( -19.90)
>DroYak_CAF1 28753 114 - 1
AAAAGAAACUGAAGGUAAACUUCAUAAAUAACACAAGGCUACCAUAGCUUAAGUUGUGGCUUAAACGAAAGCUAGAUCAAAGCUUAACUUAAAGCCAAAGAAA-GGCAAGAAAAC
.........(((((.....)))))............((((.(((((((....))))))).........(((((.......))))).......)))).......-........... ( -22.60)
>consensus
AAAAAAAACUGAAGGUAAA_UUCAUAAAUAACACAAGGCUACCAUAGCUUAAGUUGAGGCGUAAACGAAAGCUAGAUCAAAGCAUAACUUAAAGCCUAAGAAAAGGCAAGAAAAC
....................(((..............(((....((((((..(((........)))..))))))......)))..........((((......))))..)))... (-16.35 = -16.73 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:02 2006