Locus 2788

Sequence ID	3R_DroMel_CAF1
Location	7,453,059 – 7,453,222
Length	163
Max. P	0.946742

overview

Window 5

Location	7,453,059 – 7,453,164
Length	105
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	83.43
Mean single sequence MFE	-34.26
Consensus MFE	-19.26
Energy contribution	-21.54
Covariance contribution	2.28
Combinations/Pair	1.16
Mean z-score	-2.34
Structure conservation index	0.56
SVM decision value	0.36
SVM RNA-class probability	0.705359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7453059 105 + 27905053
CGCCGGAUUGUCUGAACGAUCCAUUCGGGGAAGUCGAUGAAUACAUUGUGGAAUCCCCAGAAGAAGUUUUGGAUCAUG---AUAGUGAUGCUCAUCAUGAUCUGGAUG
....(((((((....))))))).((((((((...(((((....))))).....))))).))).....((..(((((((---((((.....)).)))))))))..)).. ( -37.20)
>DroSec_CAF1 6893 102 + 1
CGCCGGAUUGUCUGGACGAUCCUUUCGGGGAAGUCGAUGAAUACAUUGUGGAAUCCCCAGAAGAAGUUUUGGAUCGUGAUGAUAGUGAUGCGCAU------CUGGAUG
..((((((((((...((((((((((((((((...(((((....))))).....))))).)))).......)))))))...))))(((...)))))------))))... ( -31.91)
>DroSim_CAF1 6906 105 + 1
CGCCGGAUUGUCUGAACGAUCCUUUCGGGGAAGUCGAUGAAUACAUUGUGGAAUCCCCAGAAGAAAUUUUGGAUCGUG---AUAGUGAUGCGCAUCAUGAACUGGAUG
..((((..((((...(((((((....(((((...(((((....))))).....)))))((((....))))))))))))---)))(((((....)))))...))))... ( -33.40)
>DroEre_CAF1 7164 102 + 1
CGGCGGAUGAGCUGAACGAUCCAUUUGGGGAAGUCGAUGAAUACUUUGAGGAAUCCCCAG---AGUAUGGGGAUAGUG---AUAUUAAUGCACAUGAAGAUCUGGAUG
((((......))))....(((((((((((((..((((........))))....)))))))---)((((...((((...---.)))).))))...........))))). ( -28.30)
>DroYak_CAF1 7132 105 + 1
CGGCGGAUGAGCUGAACGAUCCAUUCGGGGAAGUCGAUGAAUACUUCGAAGAAUCCCCAGAUGAGGAUGCGGAUCGUG---AUAUUGAUGCGCAUCAAGAUCUGGAUG
((((......))))....((((....(((((..((((........))))....)))))((((...((((((.((((..---....)))).))))))...)))))))). ( -40.50)
>consensus
CGCCGGAUUGUCUGAACGAUCCAUUCGGGGAAGUCGAUGAAUACAUUGUGGAAUCCCCAGAAGAAGUUUUGGAUCGUG___AUAGUGAUGCGCAUCAAGAUCUGGAUG
..((((((.......((((((((((((((((...(((((....))))).....)))))....))))....))))))).......(((((....))))).))))))... (-19.26 = -21.54 +   2.28)

alignment

secondary structure

dotplot

Window 6

Location	7,453,127 – 7,453,222
Length	95
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-26.76
Consensus MFE	-16.70
Energy contribution	-17.30
Covariance contribution	0.60
Combinations/Pair	1.18
Mean z-score	-1.67
Structure conservation index	0.62
SVM decision value	0.08
SVM RNA-class probability	0.575439
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7453127 95 + 27905053
UUGGAUCAUG---AUAGUGAUGCUCAUCAUGAUCUGGAUGAGGAUAAUUAUAUUGAUUCUGUUGAAGAUGUUGAUGCGCUUCAAGAUAUGGCUGA------------AGU
..((((((..---(((((.((.((((((........)))))).)).)))))..))))))(.((((((.(((....))))))))).).........------------... ( -24.70)
>DroSec_CAF1 6961 104 + 1
UUGGAUCGUGAUGAUAGUGAUGCGCAU------CUGGAUGAGGAUCAUUAUAUUGAUUCUGUUGAAGAUGUUGAUGCACUUCAAGAUAUGGCAGAAGGUCAGCUAAAAGU
...((((......((((((((.(.(((------....))).).)))))))).....(((((((((((.(((....)))))))).......)))))))))).......... ( -25.51)
>DroSim_CAF1 6974 107 + 1
UUGGAUCGUG---AUAGUGAUGCGCAUCAUGAACUGGAUGAGGAUCAUUAUAUUGAUUCUGUCGAAGAUGUUGAUGCACUUCAAGAUAUGGCAGAAGGUCAGCUAAAAGU
...((((...---((((((((.(.((((........)))).).)))))))).....((((((((...((.((((......)))).)).)))))))))))).......... ( -30.50)
>DroEre_CAF1 7229 107 + 1
GGGGAUAGUG---AUAUUAAUGCACAUGAAGAUCUGGAUGAGGAUCAAUAUAUUGAAUCUGUUGAAGAUGUCGAUGUGCUGCAAGAUACGAAUGCAGUUCAGUUGGAAGC
...((((...---.))))..(.((..(((((((((......)))))..((((((((((((.....)))).))))))))(((((.........)))))))))..)).)... ( -21.80)
>DroYak_CAF1 7200 107 + 1
GCGGAUCGUG---AUAUUGAUGCGCAUCAAGAUCUGGAUGAGGACCAAUAUAUUGAUUCUAUUGAAGAUGCUGAUGCGCUUCAAGAUAUGGAUGCAGUUCAGCUGGAAGU
(((..(((((---...((((.((((((((..((((.....((((.(((....))).)))).....))))..)))))))).))))..))))).)))............... ( -31.30)
>consensus
UUGGAUCGUG___AUAGUGAUGCGCAUCAAGAUCUGGAUGAGGAUCAUUAUAUUGAUUCUGUUGAAGAUGUUGAUGCGCUUCAAGAUAUGGCUGAAGGUCAGCUAAAAGU
..((((((.....((((((((.(.((((........)))).).))))))))..))))))..((((((.(((....))))))))).......................... (-16.70 = -17.30 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	7,453,127 – 7,453,222
Length	95
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	79.21
Mean single sequence MFE	-17.68
Consensus MFE	-12.48
Energy contribution	-13.56
Covariance contribution	1.08
Combinations/Pair	1.24
Mean z-score	-2.10
Structure conservation index	0.71
SVM decision value	1.37
SVM RNA-class probability	0.946742
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7453127 95 - 27905053
ACU------------UCAGCCAUAUCUUGAAGCGCAUCAACAUCUUCAACAGAAUCAAUAUAAUUAUCCUCAUCCAGAUCAUGAUGAGCAUCACUAU---CAUGAUCCAA
.((------------((((.......))))))............................................((((((((((........)))---)))))))... ( -14.90)
>DroSec_CAF1 6961 104 - 1
ACUUUUAGCUGACCUUCUGCCAUAUCUUGAAGUGCAUCAACAUCUUCAACAGAAUCAAUAUAAUGAUCCUCAUCCAG------AUGCGCAUCACUAUCAUCACGAUCCAA
.......((.(.....).)).......(((.(((((((....(((.....)))((((......)))).........)------)))))).)))................. ( -14.30)
>DroSim_CAF1 6974 107 - 1
ACUUUUAGCUGACCUUCUGCCAUAUCUUGAAGUGCAUCAACAUCUUCGACAGAAUCAAUAUAAUGAUCCUCAUCCAGUUCAUGAUGCGCAUCACUAU---CACGAUCCAA
.......((.(.....).)).......(((.((((((((....((.....((.((((......)))).)).....))....)))))))).)))....---.......... ( -16.50)
>DroEre_CAF1 7229 107 - 1
GCUUCCAACUGAACUGCAUUCGUAUCUUGCAGCACAUCGACAUCUUCAACAGAUUCAAUAUAUUGAUCCUCAUCCAGAUCUUCAUGUGCAUUAAUAU---CACUAUCCCC
.........(((..((((.........))))((((((.((.((((.....((..((((....))))..)).....)))).)).)))))).......)---))........ ( -17.20)
>DroYak_CAF1 7200 107 - 1
ACUUCCAGCUGAACUGCAUCCAUAUCUUGAAGCGCAUCAGCAUCUUCAAUAGAAUCAAUAUAUUGGUCCUCAUCCAGAUCUUGAUGCGCAUCAAUAU---CACGAUCCGC
.......((......)).........((((.(((((((((.((((.....((.(((((....))))).)).....)))).))))))))).))))...---.......... ( -25.50)
>consensus
ACUUCCAGCUGAACUUCAGCCAUAUCUUGAAGCGCAUCAACAUCUUCAACAGAAUCAAUAUAAUGAUCCUCAUCCAGAUCAUGAUGCGCAUCACUAU___CACGAUCCAA
...........................(((.((((((((..((((.....((.((((......)))).)).....))))..)))))))).)))................. (-12.48 = -13.56 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:45 2006