Locus 4143

Sequence ID	3R_DroMel_CAF1
Location	11,304,611 – 11,304,716
Length	105
Max. P	0.987805

overview

Window 7

Location	11,304,611 – 11,304,716
Length	105
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	77.30
Mean single sequence MFE	-27.55
Consensus MFE	-16.18
Energy contribution	-17.35
Covariance contribution	1.17
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.59
SVM decision value	1.35
SVM RNA-class probability	0.945205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11304611 105 + 27905053
GCAAAAAUCAAACUCAAUUACUGCCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGU-GAAUCGC---CGGCAUCCAAAU------CGGAAUAGGAAUAGAGAGGCAUGCGUAAGAG
(((....(((...((.(((.(((((((((.....))))))))).))).))....)-))...((---(..(.(((....------.......)))...)...))).)))....... ( -30.10)
>DroVir_CAF1 49748 81 + 1
GCAAAAAUCAAACUCAAUUACGUGCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGG-GAAUCGG---------------------------------UCAAAGACAUGCGUAAGAG
(((.........(((((((.(.(((((((.....)))).))).).....))))))-).....(---------------------------------((...))).)))....... ( -19.00)
>DroGri_CAF1 45082 82 + 1
GCAAAAAUCAAAGUCAAUUACGUGCGCUGUCAAUCAGCGGCAGGAAUCGAACUCAAAAAUCGG---------------------------------ACAAAGACAUGCGUAAGAG
(((....((...(((.....(.(((((((.....)))).))).)...(((.........))))---------------------------------))...))..)))....... ( -15.20)
>DroSec_CAF1 39202 105 + 1
GCAAAAAUCAAACUCAAUUACUGCCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGU-GAAUCGC---CGGCAUCCAAAU------CGGAAUACGAAUAGAGAGGCAUGCGUAAGAG
(((....(((...((.(((.(((((((((.....))))))))).))).))....)-))...((---(....((....(------((.....)))...))..))).)))....... ( -32.10)
>DroEre_CAF1 38540 102 + 1
GCAAAAAUCAAACUCAAUUACUGCCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGG-GAAUC------GGCAUCCCAAU------CGGAAUCGGAAUAGAGAGGCAUGCGUAAGAG
(((....((...........(((((((((.....)))))))))((.((..(((((-((...------....)))))))------..)).))........))....)))....... ( -33.90)
>DroYak_CAF1 40072 114 + 1
GCAAAAAUCAAACUCAAUUACUGCCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGG-GAAUCUCCAUCGCCAUCCAAAUCGGAAUCGGAAUCGGAAUAGAGAGCCAUGCGUAAGAG
............(((((((.(((((((((.....)))))))))......))))))-)...(((...(((..(((.....)))...((..((......))...))..)))...))) ( -35.00)
>consensus
GCAAAAAUCAAACUCAAUUACUGCCGCUGUCAAUCAGCGGCAGGAAUCGAAUUGG_GAAUCGC____GGCAUCCAAAU______CGGAAU_GGAAUAGAGAGGCAUGCGUAAGAG
(((.................(((((((((.....)))))))))((.((........)).))............................................)))....... (-16.18 = -17.35 +   1.17)

alignment

secondary structure

dotplot

Window 8

Location	11,304,611 – 11,304,716
Length	105
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.30
Mean single sequence MFE	-30.27
Consensus MFE	-20.17
Energy contribution	-21.20
Covariance contribution	1.03
Combinations/Pair	1.06
Mean z-score	-2.76
Structure conservation index	0.67
SVM decision value	2.09
SVM RNA-class probability	0.987805
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11304611 105 - 27905053
CUCUUACGCAUGCCUCUCUAUUCCUAUUCCG------AUUUGGAUGCCG---GCGAUUC-ACAAUUCGAUUCCUGCCGCUGAUUGACAGCGGCAGUAAUUGAGUUUGAUUUUUGC
......(((..((.(((..(((........)------))..))).))..---)))..((-(.(((((((((.(((((((((.....))))))))).))))))))))))....... ( -35.40)
>DroVir_CAF1 49748 81 - 1
CUCUUACGCAUGUCUUUGA---------------------------------CCGAUUC-CCAAUUCGAUUCCUGCCGCUGAUUGACAGCGCACGUAAUUGAGUUUGAUUUUUGC
.......(((.(((...))---------------------------------)......-(.((((((((((.(((.((((.....))))))).).))))))))).).....))) ( -16.20)
>DroGri_CAF1 45082 82 - 1
CUCUUACGCAUGUCUUUGU---------------------------------CCGAUUUUUGAGUUCGAUUCCUGCCGCUGAUUGACAGCGCACGUAAUUGACUUUGAUUUUUGC
.......(((.(((...((---------------------------------((((.........))).....(((.((((.....))))))).......)))...)))...))) ( -15.30)
>DroSec_CAF1 39202 105 - 1
CUCUUACGCAUGCCUCUCUAUUCGUAUUCCG------AUUUGGAUGCCG---GCGAUUC-ACAAUUCGAUUCCUGCCGCUGAUUGACAGCGGCAGUAAUUGAGUUUGAUUUUUGC
......(((..((.(((....(((.....))------)...))).))..---)))..((-(.(((((((((.(((((((((.....))))))))).))))))))))))....... ( -36.90)
>DroEre_CAF1 38540 102 - 1
CUCUUACGCAUGCCUCUCUAUUCCGAUUCCG------AUUGGGAUGCC------GAUUC-CCAAUUCGAUUCCUGCCGCUGAUUGACAGCGGCAGUAAUUGAGUUUGAUUUUUGC
.......(((....((..(((((((((....------)))))))))..------))...-(.(((((((((.(((((((((.....))))))))).))))))))).).....))) ( -34.80)
>DroYak_CAF1 40072 114 - 1
CUCUUACGCAUGGCUCUCUAUUCCGAUUCCGAUUCCGAUUUGGAUGGCGAUGGAGAUUC-CCAAUUCGAUUCCUGCCGCUGAUUGACAGCGGCAGUAAUUGAGUUUGAUUUUUGC
.......((((((.(((((((((((..(((((.......)))))))).))))))))...-)))((((((((.(((((((((.....))))))))).))))))))........))) ( -43.00)
>consensus
CUCUUACGCAUGCCUCUCUAUUCC_AUUCCG______AUUUGGAUGCC____GCGAUUC_CCAAUUCGAUUCCUGCCGCUGAUUGACAGCGGCAGUAAUUGAGUUUGAUUUUUGC
..............................................................(((((((((.(((((((((.....))))))))).))))))))).......... (-20.17 = -21.20 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:17 2006