Locus 2330

Sequence ID	2L_DroMel_CAF1
Location	6,325,520 – 6,325,632
Length	112
Max. P	0.975275

overview

Window 7

Location	6,325,520 – 6,325,632
Length	112
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.51
Mean single sequence MFE	-40.60
Consensus MFE	-29.10
Energy contribution	-29.13
Covariance contribution	0.03
Combinations/Pair	1.33
Mean z-score	-2.47
Structure conservation index	0.72
SVM decision value	1.45
SVM RNA-class probability	0.955424
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6325520 112 + 22407834
GGAGGCCGAGGAGAUUGACCUCUCCGGCCUGGUGGAGUCCGUUGUGGACUCUGACGAGGAGGACCUGGCGGAGAGCAUGGAUGUAAGUGGAUAAAACAUCCAAUGUAUACAU--
..((((((..(((......)))..)))))).(((...(((((((.(..((((.....))))..).)))))))..((((((((((...........)))))).)))).)))..-- ( -42.30)
>DroVir_CAF1 34921 106 + 1
GGAGGCCGAGGAGAUUGAUCUCUCCGGCCUCGUUGAGUCUGUGGUGGACUCCGAUGAGGAGGAUCUUGCCGAGAGCAUGGAUGUGAGUUGGU--CAUAUCGAGCAAAA------
.(((((((..((((....))))..)))))))......(((.(((..(.((((.....))))....)..))))))((.(.(((((((.....)--)))))).)))....------ ( -44.00)
>DroGri_CAF1 8919 106 + 1
GGAGGCCGAGGAGAUCGAUCUCUCCGGCCUCGUCGAGUCUGUGGUCGACUCCGAUGAGGAGGAUCUCGCCGAGAGCAUGGAUGUGAGUCGGU--CAUAUCAAGCCAAA------
.(((((((..((((....))))..)))))))........((((..((((((((.((((......)))).))...(((....)))))))))..--))))..........------ ( -42.50)
>DroSec_CAF1 16640 108 + 1
GGAGGCCGAGGAGAUUGACCUCUCCGGCCUGGUGGAGUCCGUCGUGGACUCUGAUGAGGAGGAUCUAGCGGAGAGCAUGGAUGUAAGUAGACAAACCUUCGAAUAUAU------
..((((((..(((......)))..))))))...(((((((.....))))))).....((((((((((((.....)).)))))((......))...)))))........------ ( -39.40)
>DroSim_CAF1 16829 108 + 1
GGAGGCCGAGGAGAUUGACCUCUCCGGCCUGGUGGAGUCCGUAGUGGACUCUGACGAGGAGGAUCUAGCGGAGAGCAUGGAUGUAAAUAGACAAAACAUCGAAUAUAU------
..((((((..(((......)))..))))))((((((((((.....)))))).........(.(((((((.....)).))))).)............))))........------ ( -36.10)
>DroWil_CAF1 57563 113 + 1
GGAGGCCGAAGAGAUUGAUCUCUCCGGCCUUGUCGAAUCGGUAGUCGAUUCCGAUGAGGAGGAUCUUGCUGAGAGUAUGGAUGUGAGUUAUGGUCAUAUCGGA-GUAUAGAUCU
.(((((((.(((((....))))).)))))))(((((((((.....))))).)))).....((((((((((.......(.(((((((.......))))))).))-))).)))))) ( -39.31)
>consensus
GGAGGCCGAGGAGAUUGACCUCUCCGGCCUGGUGGAGUCCGUAGUGGACUCCGAUGAGGAGGAUCUAGCGGAGAGCAUGGAUGUAAGUAGAUAAAACAUCGAAUAUAU______
..((((((.((((......)))).)))))).......(((((((.(..((((.....))))..).))))))).......(((((...........))))).............. (-29.10 = -29.13 +   0.03)

alignment

secondary structure

dotplot

Window 8

Location	6,325,520 – 6,325,632
Length	112
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.51
Mean single sequence MFE	-33.70
Consensus MFE	-24.43
Energy contribution	-24.10
Covariance contribution	-0.33
Combinations/Pair	1.19
Mean z-score	-3.32
Structure conservation index	0.73
SVM decision value	1.75
SVM RNA-class probability	0.975275
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6325520 112 - 22407834
--AUGUAUACAUUGGAUGUUUUAUCCACUUACAUCCAUGCUCUCCGCCAGGUCCUCCUCGUCAGAGUCCACAACGGACUCCACCAGGCCGGAGAGGUCAAUCUCCUCGGCCUCC
--..........(((((((...........)))))))........((.(((....))).))..((((((.....))))))....((((((..((((....))))..)))))).. ( -36.20)
>DroVir_CAF1 34921 106 - 1
------UUUUGCUCGAUAUG--ACCAACUCACAUCCAUGCUCUCGGCAAGAUCCUCCUCAUCGGAGUCCACCACAGACUCAACGAGGCCGGAGAGAUCAAUCUCCUCGGCCUCC
------((((((.(((((((--.............))))...)))))))))............(((((.......)))))...(((((((..((((....))))..))))))). ( -34.42)
>DroGri_CAF1 8919 106 - 1
------UUUGGCUUGAUAUG--ACCGACUCACAUCCAUGCUCUCGGCGAGAUCCUCCUCAUCGGAGUCGACCACAGACUCGACGAGGCCGGAGAGAUCGAUCUCCUCGGCCUCC
------...(((..(((.((--(.....))).)))...)))..((..(((......)))..))(((((.......)))))...(((((((..((((....))))..))))))). ( -37.80)
>DroSec_CAF1 16640 108 - 1
------AUAUAUUCGAAGGUUUGUCUACUUACAUCCAUGCUCUCCGCUAGAUCCUCCUCAUCAGAGUCCACGACGGACUCCACCAGGCCGGAGAGGUCAAUCUCCUCGGCCUCC
------........((.((...(((((...........((.....)))))))...))))....((((((.....))))))....((((((..((((....))))..)))))).. ( -30.80)
>DroSim_CAF1 16829 108 - 1
------AUAUAUUCGAUGUUUUGUCUAUUUACAUCCAUGCUCUCCGCUAGAUCCUCCUCGUCAGAGUCCACUACGGACUCCACCAGGCCGGAGAGGUCAAUCUCCUCGGCCUCC
------........((((....(((((...........((.....)))))))......)))).((((((.....))))))....((((((..((((....))))..)))))).. ( -30.50)
>DroWil_CAF1 57563 113 - 1
AGAUCUAUAC-UCCGAUAUGACCAUAACUCACAUCCAUACUCUCAGCAAGAUCCUCCUCAUCGGAAUCGACUACCGAUUCGACAAGGCCGGAGAGAUCAAUCUCUUCGGCCUCC
.(((((...(-(..((((((...............)))).))..))..)))))..........((((((.....))))))....((((((((((((....)))))))))))).. ( -32.46)
>consensus
______AUAUAUUCGAUAUGUUAUCAACUCACAUCCAUGCUCUCCGCAAGAUCCUCCUCAUCAGAGUCCACCACGGACUCCACCAGGCCGGAGAGAUCAAUCUCCUCGGCCUCC
................................(((...((.....))..)))...........((((((.....))))))....((((((..((((....))))..)))))).. (-24.43 = -24.10 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:27 2006