Locus 11

Sequence ID 4_DroMel_CAF1
Location 156,216 – 156,384
Length 168
Max. P 0.999483
window17 window18 window19 window20 window21

overview

Window 7

Location 156,216 – 156,321
Length 105
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 71.35
Mean single sequence MFE -26.80
Consensus MFE -13.03
Energy contribution -13.04
Covariance contribution 0.01
Combinations/Pair 1.24
Mean z-score -3.01
Structure conservation index 0.49
SVM decision value 2.55
SVM RNA-class probability 0.995194
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 156216 105 + 1281640
AAUAAAUAUGUAUA------UGCAUUUGUAUGUAUAUGAAGCAACAAAUCUGUUU-UCAGCGUUGUUGUAUUAAUAUAU----GCAUACAUACAUGUAUUGAUCAGCACAAGCCAG
......((((((((------(((....)))))))))))..(((((((..(((...-.)))..)))))))((((((((((----(........)))))))))))..((....))... ( -27.10)
>DroEre_CAF1 18144 116 + 1
AGUAUAUAUGCAUAUAUGAUUGCAUAUGUAGGUAUAUGAAACAACGAAUCUGUUUGACAGUGGUGCUAUAUUAAUAUGUACACACAUAUGUACACGUAUUGAUCAGCACAUGCCAG
..((((((((((........))))))))))(((((.(.(((((.......))))).).....(((((..((((((((((..(((....)))..)))))))))).)))))))))).. ( -33.40)
>DroYak_CAF1 18462 96 + 1
-------GUGCA-------------ACGUAUGCAUAUAAAACAACGAAUCUGUUUGACAGAGUUGCUGUAUUAAUAUGAACAUACAUACAUACAUGUAUUGAUCAGCAAAUGCCAG
-------.(((.-------------..((((((((((((.(((.(((.((((.....)))).))).))).)).)))))..)))))(((((....)))))......)))........ ( -19.90)
>consensus
A_UA_AUAUGCAUA______UGCAUAUGUAUGUAUAUGAAACAACGAAUCUGUUUGACAGAGUUGCUGUAUUAAUAUGUACA_ACAUACAUACAUGUAUUGAUCAGCACAUGCCAG
...............................((((...(((((.......))))).......((((((.((((((((((..............))))))))))))))))))))... (-13.03 = -13.04 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 156,216 – 156,321
Length 105
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 71.35
Mean single sequence MFE -22.66
Consensus MFE -14.94
Energy contribution -15.73
Covariance contribution 0.79
Combinations/Pair 1.25
Mean z-score -2.18
Structure conservation index 0.66
SVM decision value 3.64
SVM RNA-class probability 0.999483
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 156216 105 - 1281640
CUGGCUUGUGCUGAUCAAUACAUGUAUGUAUGC----AUAUAUUAAUACAACAACGCUGA-AAACAGAUUUGUUGCUUCAUAUACAUACAAAUGCA------UAUACAUAUUUAUU
..(((....)))....((((.((((.(((((((----((((((.....((((((..(((.-...)))..))))))....)))))........))))------)))).)))).)))) ( -19.90)
>DroEre_CAF1 18144 116 - 1
CUGGCAUGUGCUGAUCAAUACGUGUACAUAUGUGUGUACAUAUUAAUAUAGCACCACUGUCAAACAGAUUCGUUGUUUCAUAUACCUACAUAUGCAAUCAUAUAUGCAUAUAUACU
..((((.((((((........((((((((....)))))))).......))))))...))))((((((.....))))))...........(((((((........)))))))..... ( -25.56)
>DroYak_CAF1 18462 96 - 1
CUGGCAUUUGCUGAUCAAUACAUGUAUGUAUGUAUGUUCAUAUUAAUACAGCAACUCUGUCAAACAGAUUCGUUGUUUUAUAUGCAUACGU-------------UGCAC-------
..(((....)))..........(((((((((((((((..........(((((...((((.....))))...)))))...))))))))))).-------------)))).------- ( -22.52)
>consensus
CUGGCAUGUGCUGAUCAAUACAUGUAUGUAUGU_UGUACAUAUUAAUACAGCAACACUGUCAAACAGAUUCGUUGUUUCAUAUACAUACAUAUGCA______UAUGCAUAU_UA_U
..(((....))).........(((((((((((((.............(((((....(((.....)))....)))))..)))))))))))))......................... (-14.94 = -15.73 +   0.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 156,250 – 156,357
Length 107
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 79.50
Mean single sequence MFE -21.50
Consensus MFE -12.06
Energy contribution -12.07
Covariance contribution 0.00
Combinations/Pair 1.19
Mean z-score -2.02
Structure conservation index 0.56
SVM decision value 0.16
SVM RNA-class probability 0.613394
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 156250 107 + 1281640
GCAACAAAUCUGUUU-UCAGCGUUGUUGUAUUAAUAUAU----GCAUACAUACAUGUAUUGAUCAGCACAAGCCAGCUGCACAAAAAUUUGAAUGAAUAUACAUAUGUACA----U
(((((((..(((...-.)))..)))))))((((((((((----(........)))))))))))((((........)))).............(((.((((....)))).))----) ( -21.20)
>DroSec_CAF1 30746 94 + 1
GCAACGAAUCUUUUUGACAGUGUUGCUGUAUUAGUAUAU----GCAUACAUACAUGUAUUGAUCAGCACAUGCCAGCUGC--AAAAAUUUUAAUGAAUA----------------U
.((...((..((((((.(((((((((((.((((((((((----(........))))))))))))))))...))..)))))--)))))..))..))....----------------. ( -23.40)
>DroSim_CAF1 15880 93 + 1
GCAACGAAUCUUUUUGACAGUGUUGCUGUAUUAGUAUAU----GCAUACAUACAUGUAUUG-UCAGCACAUGCCAGCUGC--AAAAAUGUUAAUGAAUA----------------U
.((...(((.((((((.(((((((((((...((((((((----(........)))))))))-.)))))...))..)))))--))))).)))..))....----------------. ( -21.50)
>DroYak_CAF1 18482 103 + 1
ACAACGAAUCUGUUUGACAGAGUUGCUGUAUUAAUAUGAACAUACAUACAUACAUGUAUUGAUCAGCAAAUGCCAGCUGCACAAAAAUUUGUAUGAAU-------------UACAC
.(((((((((((.....))))((.((((((((....(((.(((((((......))))).)).)))...)))).)))).)).......))))).))...-------------..... ( -19.90)
>consensus
GCAACGAAUCUGUUUGACAGUGUUGCUGUAUUAAUAUAU____GCAUACAUACAUGUAUUGAUCAGCACAUGCCAGCUGC__AAAAAUUUGAAUGAAUA________________U
.................(((((((((((.((((((((((..............)))))))))))))))...))..))))..................................... (-12.06 = -12.07 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 156,288 – 156,384
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 86.86
Mean single sequence MFE -25.23
Consensus MFE -21.33
Energy contribution -21.67
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -4.29
Structure conservation index 0.85
SVM decision value 1.74
SVM RNA-class probability 0.974703
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 156288 96 + 1281640
GCAUACAUACAUGUAUUGAUCAGCACAAGCCAGCUGCACAAAAAUUUGAAUGAAUAUACAUAUGUACAUAUGUACGGUACAUGUGUAUGCAUUAAU
((((((..((((((((((..((((........))))....................(((((((....)))))))))))))))))))))))...... ( -28.80)
>DroSec_CAF1 30785 82 + 1
GCAUACAUACAUGUAUUGAUCAGCACAUGCCAGCUGC--AAAAAUUUUAAUGAAUA------------UAUGUACGGUACAUGUGUAUGCAUUAAU
((((((..((((((((((..((((........)))).--....((((....)))).------------......))))))))))))))))...... ( -22.80)
>DroSim_CAF1 15919 81 + 1
GCAUACAUACAUGUAUUG-UCAGCACAUGCCAGCUGC--AAAAAUGUUAAUGAAUA------------UAUGUACGGUACAUGUGUAUGCAUUAAU
((((((..((((((((((-(((((........)))).--....(((((....))))------------)....)))))))))))))))))...... ( -24.10)
>consensus
GCAUACAUACAUGUAUUGAUCAGCACAUGCCAGCUGC__AAAAAUUUUAAUGAAUA____________UAUGUACGGUACAUGUGUAUGCAUUAAU
((((((..((((((((((..((((........)))).......((((....))))...................))))))))))))))))...... (-21.33 = -21.67 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 156,288 – 156,384
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 86.86
Mean single sequence MFE -20.50
Consensus MFE -16.00
Energy contribution -16.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.78
SVM decision value 0.75
SVM RNA-class probability 0.840497
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 156288 96 - 1281640
AUUAAUGCAUACACAUGUACCGUACAUAUGUACAUAUGUAUAUUCAUUCAAAUUUUUGUGCAGCUGGCUUGUGCUGAUCAAUACAUGUAUGUAUGC
......(((((((((((((..((((((((....))))))))..............(((..((((........))))..))))))))))..)))))) ( -26.50)
>DroSec_CAF1 30785 82 - 1
AUUAAUGCAUACACAUGUACCGUACAUA------------UAUUCAUUAAAAUUUUU--GCAGCUGGCAUGUGCUGAUCAAUACAUGUAUGUAUGC
......(((((((((((((.....((..------------.(((......)))...)--)((((........)))).....)))))))..)))))) ( -16.60)
>DroSim_CAF1 15919 81 - 1
AUUAAUGCAUACACAUGUACCGUACAUA------------UAUUCAUUAACAUUUUU--GCAGCUGGCAUGUGCUGA-CAAUACAUGUAUGUAUGC
......(((((((.(((((...))))).------------.........((((..((--(((((........)))).-)))...)))).))))))) ( -18.40)
>consensus
AUUAAUGCAUACACAUGUACCGUACAUA____________UAUUCAUUAAAAUUUUU__GCAGCUGGCAUGUGCUGAUCAAUACAUGUAUGUAUGC
......(((((((((((((......(((((........))))).................((((........)))).....)))))))..)))))) (-16.00 = -16.33 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:08 2006