Locus 8124

Sequence ID	3L_DroMel_CAF1
Location	21,397,769 – 21,397,901
Length	132
Max. P	0.999282

overview

Window 4

Location	21,397,769 – 21,397,870
Length	101
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	79.62
Mean single sequence MFE	-27.80
Consensus MFE	-19.06
Energy contribution	-18.70
Covariance contribution	-0.36
Combinations/Pair	1.35
Mean z-score	-2.20
Structure conservation index	0.69
SVM decision value	1.19
SVM RNA-class probability	0.927837
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21397769 101 + 23771897
CGCUUUUAAUAAUCUCACUGAUGAUGGCUUCUUGUGGA-UGCAGAUAAGUAUCUCGCCCAAGUGGCUGCUAUUCGUC-AGAUACUUAUCAAUUAAUGUUGAAA
.................(((((((.((((.((((.((.-((.((((....)))))))))))).)))).....)))))-)).......(((((....))))).. ( -24.90)
>DroSec_CAF1 30454 91 + 1
CGUUUUUAAUAAUCUCG----------CUUCUUGUGGA-UGCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUC-GGAUACUUAUCAAUUAAUGCUGAAA
.((..(((((.(((.((----------(.....)))))-)...((((((((((.((..(((((((...))))))).)-))))))))))).))))).))..... ( -29.00)
>DroSim_CAF1 30558 101 + 1
CGUUUUUAAUAAUCUCGCUGAUGAUGGCUUCUUGUGGA-UGCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUC-GGAUACUUAUCAAUUAAUGCUGAAA
.((..(((((.(((.(((.((........))..)))))-)...((((((((((.((..(((((((...))))))).)-))))))))))).))))).))..... ( -29.30)
>DroEre_CAF1 31554 99 + 1
CGUUUUUAAUAAUCUCGCUGAUGAUGGCUUCUUGUGGG-UACAGAUAAGUAU--CGCUCGAGUGGCUGCCAUUAGGC-GGAUACUUAUCAAUUAAUGCUGGAA
...........(((.((((((((..((((.((((.(((-(((......))))--).).)))).))))..))))).))-))))..................... ( -26.40)
>DroYak_CAF1 31569 100 + 1
CGUUUUUCAUAAUCUCGCUGAUGAUGGCUUCUUGUGGA-UACAGAUAAGCAUCUCGCUCGAGUGGCUGCCAUUCGUG-GGAUGCUUAUCAAUUAAUGCUA-AA
.((..(((((((....(((......)))...)))))))-.)).((((((((((((((..((((((...)))))))))-)))))))))))...........-.. ( -34.60)
>DroPer_CAF1 17258 86 + 1
GGUUUUUAAUAAUCUCGCUGA---UAGCUACUUGUGGCCCGUUGAUAAGUAUCUCACUCAAGUGGCCUGCAUGUGCCGGGAUACUUAUU--------------
((.........(((.....))---).((((....))))))...((((((((((((((....))((((.....).)))))))))))))))-------------- ( -22.60)
>consensus
CGUUUUUAAUAAUCUCGCUGAUGAUGGCUUCUUGUGGA_UGCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUC_GGAUACUUAUCAAUUAAUGCUGAAA
.((.....((((....(((......)))...)))).....)).(((((((((((....((((((.....))))))...))))))))))).............. (-19.06 = -18.70 +  -0.36)

alignment

secondary structure

dotplot

Window 5

Location	21,397,808 – 21,397,901
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	82.90
Mean single sequence MFE	-29.18
Consensus MFE	-22.40
Energy contribution	-22.28
Covariance contribution	-0.12
Combinations/Pair	1.22
Mean z-score	-4.45
Structure conservation index	0.77
SVM decision value	3.48
SVM RNA-class probability	0.999282
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21397808 93 + 23771897
GCAGAUAAGUAUCUCGCCCAAGUGGCUGCUAUUCGUCAGAUACUUAUCAAUUAAUGUUGAAAUUAUAGCACUUUAAGUAGCAACAUAAUUCAA
...(((((((((((.((...(((....)))....)).))))))))))).....((((((...(((........)))....))))))....... ( -21.30)
>DroSec_CAF1 30483 93 + 1
GCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUCGGAUACUUAUCAAUUAAUGCUGAAAUUAUAGCACUAUAAGUGGCAACCUAAUUUAG
...((((((((((.((..(((((((...))))))).))))))))))))......(((((...(((((....))))).)))))........... ( -30.00)
>DroSim_CAF1 30597 93 + 1
GCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUCGGAUACUUAUCAAUUAAUGCUGAAAUUAUAGCACUAUAAGUGGCAACACAAUUUAG
...((((((((((.((..(((((((...))))))).))))))))))))......(((((......)))))......(((....)))....... ( -32.60)
>DroEre_CAF1 31593 91 + 1
ACAGAUAAGUAU--CGCUCGAGUGGCUGCCAUUAGGCGGAUACUUAUCAAUUAAUGCUGGAAUUAUAGCAUUAUAAGUAGCAACAUAAUUUCA
...(((((((((--((((.....)))((((....))))))))))))))...((((((((......)))))))).................... ( -27.30)
>DroYak_CAF1 31608 77 + 1
ACAGAUAAGCAUCUCGCUCGAGUGGCUGCCAUUCGUGGGAUGCUUAUCAAUUAAUGCUA-AAUUAUAGCAUUAUAAGA---------------
...((((((((((((((..((((((...))))))))))))))))))))...((((((((-.....)))))))).....--------------- ( -34.70)
>consensus
GCAGAUAAGUAUCUCGCUCGAGUGGCUGCCAUUCGUCGGAUACUUAUCAAUUAAUGCUGAAAUUAUAGCACUAUAAGUAGCAACAUAAUUUAA
...(((((((((((....(((((((...)))))))..)))))))))))......(((((......)))))....................... (-22.40 = -22.28 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	21,397,808 – 21,397,901
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	82.90
Mean single sequence MFE	-25.36
Consensus MFE	-18.26
Energy contribution	-18.62
Covariance contribution	0.36
Combinations/Pair	1.16
Mean z-score	-3.33
Structure conservation index	0.72
SVM decision value	2.72
SVM RNA-class probability	0.996591
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21397808 93 - 23771897
UUGAAUUAUGUUGCUACUUAAAGUGCUAUAAUUUCAACAUUAAUUGAUAAGUAUCUGACGAAUAGCAGCCACUUGGGCGAGAUACUUAUCUGC
((((((((((..(((......)))..))))).)))))........((((((((((((.(.....)).(((.....))).)))))))))))... ( -22.10)
>DroSec_CAF1 30483 93 - 1
CUAAAUUAGGUUGCCACUUAUAGUGCUAUAAUUUCAGCAUUAAUUGAUAAGUAUCCGACGAAUGGCAGCCACUCGAGCGAGAUACUUAUCUGC
......(((((....)))))(((((((........)))))))...((((((((((((.(((.(((...))).)))..)).))))))))))... ( -26.30)
>DroSim_CAF1 30597 93 - 1
CUAAAUUGUGUUGCCACUUAUAGUGCUAUAAUUUCAGCAUUAAUUGAUAAGUAUCCGACGAAUGGCAGCCACUCGAGCGAGAUACUUAUCUGC
.......(((....)))...(((((((........)))))))...((((((((((((.(((.(((...))).)))..)).))))))))))... ( -26.20)
>DroEre_CAF1 31593 91 - 1
UGAAAUUAUGUUGCUACUUAUAAUGCUAUAAUUCCAGCAUUAAUUGAUAAGUAUCCGCCUAAUGGCAGCCACUCGAGCG--AUACUUAUCUGU
....................(((((((........)))))))...((((((((((.(((....))).(((....).)))--)))))))))... ( -24.50)
>DroYak_CAF1 31608 77 - 1
---------------UCUUAUAAUGCUAUAAUU-UAGCAUUAAUUGAUAAGCAUCCCACGAAUGGCAGCCACUCGAGCGAGAUGCUUAUCUGU
---------------.....((((((((.....-))))))))...((((((((((((.(((.(((...))).))).).).))))))))))... ( -27.70)
>consensus
CUAAAUUAUGUUGCCACUUAUAGUGCUAUAAUUUCAGCAUUAAUUGAUAAGUAUCCGACGAAUGGCAGCCACUCGAGCGAGAUACUUAUCUGC
....................(((((((........)))))))...((((((((((((.(((.(((...))).)))..)).))))))))))... (-18.26 = -18.62 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:52 2006