Locus 3915

Sequence ID	X_DroMel_CAF1
Location	10,473,843 – 10,474,000
Length	157
Max. P	0.537039

overview

Window 2

Location	10,473,843 – 10,473,962
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.85
Mean single sequence MFE	-23.54
Consensus MFE	-17.16
Energy contribution	-17.32
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-1.59
Structure conservation index	0.73
SVM decision value	-0.02
SVM RNA-class probability	0.524293
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10473843 119 - 22224390
CGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGUCUGGCAAUGUCAAUUCAAAGCAGAAAGCAAAUAAAUAUGUACACAAUUAAUUAAUGAAACAAGAUUUAAAAUAUCGCC-
........((((((...(((((((((((((((............).))))))))))))))((.....))............................................))))))- ( -22.30)
>DroSec_CAF1 4722 119 - 1
CGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAAAAUGUACACAAUUAAUUAAAGAAUUAAGAUUUAAAAUCUUGCC-
.(((........)))..(((((((((((((((............).))))))))))))))((((((.(((........)))......((((((....)))))).........)))))).- ( -24.70)
>DroSim_CAF1 4854 119 - 1
CGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAAAAUGUACACAAUUAAUUAAAGAAUUAAGAUUUAAAAUCUCGCC-
........((((((((.(((((((((((((((............).))))))))))))))((.....)).........)).))....((((((....))))))............))))- ( -22.30)
>DroEre_CAF1 5825 118 - 1
CGACAAGUGGCGGUCAAUUUGAAUGGGCAUUCCAAUUGAGCCUGGCAAUGUCAAUUCAAAGCAGGCAGCAAAUAAA-CUCUCCACAAUUAAUCAAAAAAUCAAGAUUUAAAAUGUCAGC-
.((((.((((.((....(((((((.(((((((((........))).)))))).)))))))((.....)).......-.)).))))....((((..........)))).....))))...- ( -26.50)
>DroYak_CAF1 6354 119 - 1
CGACAAGUGGCGGUCAAUUUGAAUGGGCAUUCAAUUUGAGCCUGGCAAUGUCAAUUCAAAGCAUGUAGCAUUUAAA-CCGUACACAUUUAAUUAAAGAAUCAAGAUUUAAAAGUACCCCU
......((((((((....(((((((.((((....((((((..((((...)))).))))))..))))..))))))))-)))).)))................................... ( -21.90)
>consensus
CGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAA_AUGUACACAAUUAAUUAAAGAAUCAAGAUUUAAAAUCUCGCC_
......(((........(((((((((((((((............).))))))))))))))((.....)).............)))................................... (-17.16 = -17.32 +   0.16)

alignment

secondary structure

dotplot

Window 3

Location	10,473,882 – 10,474,000
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.14
Mean single sequence MFE	-27.30
Consensus MFE	-18.58
Energy contribution	-20.83
Covariance contribution	2.25
Combinations/Pair	1.07
Mean z-score	-1.23
Structure conservation index	0.68
SVM decision value	0.01
SVM RNA-class probability	0.537039
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10473882 118 - 22224390
AAAAUUAAAGAGAGCGAGAGUGGCGCAUGUGG--GGAACGCGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGUCUGGCAAUGUCAAUUCAAAGCAGAAAGCAAAUAAAUAUG
.............((..((.((.(((.(((.(--......).))).))).)).))..(((((((((((((((............).)))))))))))))))).................. ( -28.80)
>DroSec_CAF1 4761 118 - 1
AAAAUUAAAGAGAGCGAGAGUGGCGCAUGUGG--GGAACGCGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAAAAUG
.............((..((.((.(((.(((.(--......).))).))).)).))..(((((((((((((((............).)))))))))))))))).................. ( -28.80)
>DroSim_CAF1 4893 118 - 1
AACAUUAAAGAGAGCGAGAGUGGCGCAUGUGG--GGAACGCGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAAAAUG
.............((..((.((.(((.(((.(--......).))).))).)).))..(((((((((((((((............).)))))))))))))))).................. ( -28.80)
>DroEre_CAF1 5864 117 - 1
AGAGUCAAAGAGAGCGAGAGUGGCGCAUGUGA--GGAACGCGACAAGUGGCGGUCAAUUUGAAUGGGCAUUCCAAUUGAGCCUGGCAAUGUCAAUUCAAAGCAGGCAGCAAAUAAA-CUC
.((((........((....)).((((.(((..--.((.(((.(....).))).))..(((((((.(((((((((........))).)))))).)))))))))).)).))......)-))) ( -30.80)
>DroYak_CAF1 6394 117 - 1
AGAGCCAAAGAGAGCGAGAGUGGCGCAUGUGG--GGAACGCGACAAGUGGCGGUCAAUUUGAAUGGGCAUUCAAUUUGAGCCUGGCAAUGUCAAUUCAAAGCAUGUAGCAUUUAAA-CCG
...(((.......((....)))))((((((..--.(((...((((..((.(((((((.((((((....)))))).)))).)).).)).))))..)))...))))))..........-... ( -30.51)
>DroAna_CAF1 4030 98 - 1
GAGAGCGAAGAGAGAGAGAGUGGCGCAUGUGAAGAGAGUGCGACAAGUGGCGGUCAAUUUGAAUUU-UAUU------UUGUUUGAAAACUUUGA--------------CAAAAAAA-GUC
..((((((((.((((..((((.((((...........))))(((........))).))))...)))-).))------))))))....(((((..--------------.....)))-)). ( -16.10)
>consensus
AAAAUCAAAGAGAGCGAGAGUGGCGCAUGUGG__GGAACGCGACAAGUGGCGGUCAAUUUGAAUUGACAUUCAAUUUUAGCCUGGCAAUGUCAAUUCAAAGCAAGAAGCAAAUAAA_AUG
.............((..((.((.(((.(((.(........).))).))).)).))..((((((((((((((...............)))))))))))))).......))........... (-18.58 = -20.83 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:36 2006