Locus 201

Sequence ID	2L_DroMel_CAF1
Location	606,174 – 606,304
Length	130
Max. P	0.831661

overview

Window 1

Location	606,174 – 606,270
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-32.95
Consensus MFE	-21.39
Energy contribution	-22.08
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-1.79
Structure conservation index	0.65
SVM decision value	0.72
SVM RNA-class probability	0.831661
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 606174 96 + 22407834
CCGACAACAAACUGCGCCUGCGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGC------------------------GAUGUCGCCACAAAC
.(((((......(((((.(((((.((((((.....)))(((.....)))......)))))))).))))).(((......))------------------------).)))))........ ( -32.30)
>DroVir_CAF1 47824 85 + 1
UCAGGUACAAACUGCGGCAGUGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCC------------------------------GCUGUC-----CAGU
..........((((.(((((((.((((((.......((((((...(....)...))))))....))))...)).)------------------------------))))))-----)))) ( -27.60)
>DroEre_CAF1 38051 96 + 1
CCGACAACAAACUGCGCCUGCGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGC------------------------GAUGUCGCCACAAAC
.(((((......(((((.(((((.((((((.....)))(((.....)))......)))))))).))))).(((......))------------------------).)))))........ ( -32.30)
>DroYak_CAF1 38068 96 + 1
CCGACAACAAACUGCGCCUGCGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGC------------------------GAUGUCGCCACAAAC
.(((((......(((((.(((((.((((((.....)))(((.....)))......)))))))).))))).(((......))------------------------).)))))........ ( -32.30)
>DroMoj_CAF1 46860 85 + 1
UCAGCUACAAACUGCGAAAGCACACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCC------------------------------GCUGUC-----CAGU
.((((.......(((....)))...((((.......((((((...(....)...))))))....)))).......------------------------------))))..-----.... ( -24.30)
>DroAna_CAF1 37053 120 + 1
UCGAUAACUAACUGCGCCUGCGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGGUGCCCGGUUCGGUGCUGGUGCCGGGCUGAUGUCGCCACAAAC
.(((((......(((((.(((((.((((((.....)))(((.....)))......)))))))).))))).((.(((((..((.(((.....)))))..))))).)).)))))........ ( -48.90)
>consensus
CCGACAACAAACUGCGCCUGCGCACGCGUUCAAUUAGCUGCAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGC________________________GAUGUCGCCACAAAC
............(((((.(((((.((((((.....)))(((.....)))......)))))))).)))))................................................... (-21.39 = -22.08 +   0.69)

alignment

secondary structure

dotplot

Window 2

Location	606,214 – 606,304
Length	90
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	79.17
Mean single sequence MFE	-31.67
Consensus MFE	-16.39
Energy contribution	-17.95
Covariance contribution	1.56
Combinations/Pair	1.11
Mean z-score	-2.31
Structure conservation index	0.52
SVM decision value	0.70
SVM RNA-class probability	0.825301
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 606214 90 + 22407834
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGCGAUGUCGCCACAAACGGCGGCAACAUGU------UGCUGCUGCUGCUGCUGCAAC
....(((((......((((((((.(((((((((......))(.(((((((......))))))).)..))------))).))))).)))))))))). ( -35.60)
>DroVir_CAF1 47864 82 + 1
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCC------GCUGUC-----CAGUGGCAACAACAUGUAGCUUUUGCUGCUGCUGCCGUUGC---
......((((..((.(((((((....))...(.((------(((...-----.))))))........(((((....))))).)))))))))))--- ( -26.40)
>DroSec_CAF1 37651 81 + 1
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGCGAUGUCGCCACAAACGGCGGCAACAUGU------UGCU---------GCUGCAAC
....(((((......((((((((((((((.((...)).)))).(((((((......))))))).)))).------))))---------))))))). ( -32.60)
>DroEre_CAF1 38091 82 + 1
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGCGAUGUCGCCACAAACGGCGGCAACAUGU------UGCUGC------UGCUGCA--
.....((((.....((.(((((((.((((.((...)).))))))).)))).))..(((((((((....)------))))))------)).))))-- ( -33.70)
>DroYak_CAF1 38108 84 + 1
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGCGAUGUCGCCACAAACGGCGGCAACAUGU------UGCUGC------UGCUGCAAC
....(((((.....((.(((((((.((((.((...)).))))))).)))).))..(((((((((....)------))))))------)).))))). ( -35.20)
>DroMoj_CAF1 46900 76 + 1
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCC------GCUGUC-----CAGUGGUAACAACAUGU------UGCUGCCGCUGCUGUUGC---
......((((.....((((((...(((((((((((------(((...-----.))))).......))))------))).))))))))..))))--- ( -26.51)
>consensus
CAAAUUGCAAAUCGUGCGGCGCAUGCGCAACGUCCCGAUGCGAUGUCGCCACAAACGGCGGCAACAUGU______UGCUGC______UGCUGCA__
......(((......(((((((....)).............(.(((((((......))))))).)...........)))))......)))...... (-16.39 = -17.95 +   1.56)

alignment

secondary structure

dotplot

Window 3

Location	606,214 – 606,304
Length	90
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-32.47
Consensus MFE	-17.06
Energy contribution	-18.50
Covariance contribution	1.44
Combinations/Pair	1.06
Mean z-score	-2.02
Structure conservation index	0.53
SVM decision value	0.26
SVM RNA-class probability	0.656233
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 606214 90 - 22407834
GUUGCAGCAGCAGCAGCAGCA------ACAUGUUGCCGCCGUUUGUGGCGACAUCGCAUCGGGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
((((((((.((.((((((...------...)))))).)).)).(((((((.(((((((.((...)).)))).)))))))))).....))))))... ( -37.10)
>DroVir_CAF1 47864 82 - 1
---GCAACGGCAGCAGCAGCAAAAGCUACAUGUUGUUGCCACUG-----GACAGC------GGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
---((((.((((((((((((....))....))))))))))....-----....((------((.(((.......))))))).....))))...... ( -30.50)
>DroSec_CAF1 37651 81 - 1
GUUGCAGC---------AGCA------ACAUGUUGCCGCCGUUUGUGGCGACAUCGCAUCGGGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
((((((((---------.(((------(....)))).))(((..((((((.(((((((.((...)).)))).))))))))))))...))))))... ( -32.40)
>DroEre_CAF1 38091 82 - 1
--UGCAGCA------GCAGCA------ACAUGUUGCCGCCGUUUGUGGCGACAUCGCAUCGGGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
--((((((.------(((((.------....))))).))(((..((((((.(((((((.((...)).)))).))))))))))))...))))..... ( -33.30)
>DroYak_CAF1 38108 84 - 1
GUUGCAGCA------GCAGCA------ACAUGUUGCCGCCGUUUGUGGCGACAUCGCAUCGGGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
((((((((.------(((((.------....))))).))(((..((((((.(((((((.((...)).)))).))))))))))))...))))))... ( -34.90)
>DroMoj_CAF1 46900 76 - 1
---GCAACAGCAGCGGCAGCA------ACAUGUUGUUACCACUG-----GACAGC------GGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
---((((.....(((((.(((------((.(((((((.......-----))))))------)...)))))(....)))))).....))))...... ( -26.60)
>consensus
__UGCAGCA______GCAGCA______ACAUGUUGCCGCCGUUUGUGGCGACAUCGCAUCGGGACGUUGCGCAUGCGCCGCACGAUUUGCAAUUUG
...((((.......................(((((((((.....)))))))))............((.(((....))).)).....))))...... (-17.06 = -18.50 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:09 2006