Locus 2959

Sequence ID	2L_DroMel_CAF1
Location	8,498,491 – 8,498,676
Length	185
Max. P	0.680841

overview

Window 5

Location	8,498,491 – 8,498,596
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.26
Mean single sequence MFE	-37.08
Consensus MFE	-24.33
Energy contribution	-25.59
Covariance contribution	1.25
Combinations/Pair	1.12
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	0.07
SVM RNA-class probability	0.567729
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8498491 105 + 22407834
-----------CCGCAGUGGCCGCCGCAUUCAAAUCCCAUCGAGC-GGAAUAGGCCAAACAGUUUGGCCUGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAU
-----------..((..((((((((((((((...((.....))..-.))))(((((((.....)))))))))..))))))))..........(((((((......)))---)))).)).. ( -37.20)
>DroSim_CAF1 7155 105 + 1
-----------CCGCAGUGUCCGCAGCAUUCAAAUCCCAUCAAGC-GGAAUAGGCCAAACAGUUUGGGCUGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAU
-----------..(((((((..((((((((......(((((((((-((..(((((......)))))..))))))))))).............)))))))).......)---)))).)).. ( -33.81)
>DroEre_CAF1 7511 117 + 1
GAGUGGUCGGCAUGCCAUGGCCGCAGCAUUCAAAUCCCAUCAAAUGGGAAUUGGCCAAACAGCUUGGCCCGCUUGCUGGUUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACAGGCGU
(((((.(((((........)))).).)))))...((((((...))))))...((((((.....)))))).(((.(((((.((((.(.......).)))).))))).))---)........ ( -41.90)
>DroYak_CAF1 7935 108 + 1
-----------AUUCCAUGGCCGCAGCAUUCAAAUCCCAUCAAGC-GGAAUAGGCCAAACAGUGUGGGCCGCUCGGUGGUUAACCCAAAUCAAGUGUUGCCCAGUCAGCAGCACUGGCGU
-----------........(((..............(((((.(((-((..((.((......)).))..))))).))))).............((((((((.......))))))))))).. ( -35.40)
>consensus
___________ACGCAAUGGCCGCAGCAUUCAAAUCCCAUCAAGC_GGAAUAGGCCAAACAGUUUGGCCCGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG___CACUGGCAU
.................(((..((((((((......(((((((((.((..(((((......)))))..))))))))))).............)))))))))))(((((.....))))).. (-24.33 = -25.59 +   1.25)

alignment

secondary structure

dotplot

Window 6

Location	8,498,520 – 8,498,636
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.52
Mean single sequence MFE	-40.60
Consensus MFE	-28.30
Energy contribution	-29.05
Covariance contribution	0.75
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.654349
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8498520 116 + 22407834
CGAGC-GGAAUAGGCCAAACAGUUUGGCCUGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCUCCACAA
.((((-((...(((((((.....)))))))(((((((((.....)))..)))))).....)).(((((---(...((.((((((((....)))).)))).))..)))))).))))..... ( -41.10)
>DroSim_CAF1 7184 116 + 1
CAAGC-GGAAUAGGCCAAACAGUUUGGGCUGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAUUUGUCUAACGAGAUGAGAUUUCUGGCUGGCAGCUCCACUG
..((.-(((....((((..(((..(((((.(((((((((.....)))..))))))...)))))((((.---...)))).((..(((....)))..))....)))..))))...))).)). ( -37.60)
>DroEre_CAF1 7551 110 + 1
CAAAUGGGAAUUGGCCAAACAGCUUGGCCCGCUUGCUGGUUAACCCAAAUCAAGUGUUGCCCAGUCAG---CACAGGCGUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGC-------
....((((....((((((.....))))))((((((.(((.....)))...))))))...))))(((((---(.((((..((..(((....)))..))...))))))))))...------- ( -43.20)
>DroYak_CAF1 7964 116 + 1
CAAGC-GGAAUAGGCCAAACAGUGUGGGCCGCUCGGUGGUUAACCCAAAUCAAGUGUUGCCCAGUCAGCAGCACUGGCGUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCAC---AG
..(((-((..((.((......)).))..))))).(((.....)))........((((((((.((((((..((....)).((..(((....)))..))....))))))))))))))---.. ( -40.50)
>consensus
CAAGC_GGAAUAGGCCAAACAGUUUGGCCCGCUUGGUGGCUAACCCAAAUCAAGUGUUGCCCAGUCAG___CACUGGCAUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCUC___AG
.............((((..(((..(((((((((((.(((.....)))...))))))..)))))(((((.....))))).((..(((....)))..))....)))..)))).......... (-28.30 = -29.05 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	8,498,559 – 8,498,676
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.04
Mean single sequence MFE	-27.03
Consensus MFE	-19.41
Energy contribution	-19.41
Covariance contribution	-0.00
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.72
SVM decision value	0.31
SVM RNA-class probability	0.680841
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8498559 117 + 22407834
UAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCUCCACAACCAUCCACCCCACACCCACCUGCUACGCAAAACUCUCACC
.....((((((.(((((((......)))---)))).).)))))((....))..(((((......((((((((...........................)))))).)).....))))).. ( -22.93)
>DroSim_CAF1 7223 111 + 1
UAACCCAAAUCAAGUGUUGCCCAGUCAG---CACUGGCAUUUGUCUAACGAGAUGAGAUUUCUGGCUGGCAGCUCCACUGCCA------CUGCCCCCACCUGCUACGCAAAACUCUCACC
.....((((((.(((((((......)))---)))).).)))))((....))..(((((.....(((((((((.....))))))------..)))......(((...)))....))))).. ( -28.60)
>DroEre_CAF1 7591 95 + 1
UAACCCAAAUCAAGUGUUGCCCAGUCAG---CACAGGCGUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGC----------------------CCACCUGCCACGCAAAACUCUCACC
............(((.((((......((---(.((((..((..(((....)))..))...)))))))(((((.----------------------....)))))..)))).)))...... ( -26.80)
>DroYak_CAF1 8003 104 + 1
UAACCCAAAUCAAGUGUUGCCCAGUCAGCAGCACUGGCGUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCAC---AG-------------CCCCACCUGCCACGCAAAACUCUCACC
.....(((((..((((((((.......))))))))...)))))((....))..(((((......((((((((...---..-------------......)))))).)).....))))).. ( -29.80)
>consensus
UAACCCAAAUCAAGUGUUGCCCAGUCAG___CACUGGCAUUUGUCUAACGAGAUGAGAUUCCUGGCUGGCAGCUC___AG_____________CCCCACCUGCCACGCAAAACUCUCACC
........(((...(((((..(((((((.....)))))...))..))))).)))((((......((((((((...........................)))))).)).....))))... (-19.41 = -19.41 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:34 2006