Locus 8662

Sequence ID	3L_DroMel_CAF1
Location	22,472,821 – 22,472,924
Length	103
Max. P	0.919837

overview

Window 5

Location	22,472,821 – 22,472,924
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.69
Mean single sequence MFE	-27.27
Consensus MFE	-18.29
Energy contribution	-17.60
Covariance contribution	-0.69
Combinations/Pair	1.23
Mean z-score	-1.49
Structure conservation index	0.67
SVM decision value	0.65
SVM RNA-class probability	0.810083
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22472821 103 + 23771897
UGUGUGAGUGCGCGGUUAGCAA----------AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGC------UGCAGGCUAUGAAAAAUGCAGCUGAAGAGAUCUC
..((.((((((((((((.....----------))))))....)))))).))...((((......)))).((....((((------((((............))))))))...))..... ( -28.60)
>DroVir_CAF1 66918 96 + 1
---AUGUGUGUGUGGUUGGAAA----------AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGCCAAAGCUGCA-GCUAUGAAAAAUGUAUUCUG---------
---..((((.((..(((.....----------)))..))...))))(((((...((((......))))(((...(((((....))))))-))..)))))...........--------- ( -23.60)
>DroGri_CAF1 24797 97 + 1
U--GUGUAUAUGUGGCUAGGAA----------AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGCCAGAGUUGCA-GCUAUGAAAAAUGCAGUCAG---------
.--((((((.((..(((.....----------)))..)).))))))(((((...((((......))))(((...(((((....))))))-))..)))))...........--------- ( -26.10)
>DroEre_CAF1 26607 113 + 1
UGUGUAAGUGCGCGGUUAGCAAAUGCUGCAAAAGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGC------UGCAGGCCAUGAAAAAUGCAGCUGGAGAGAGCUC
.((((....)))).....(((..(((.((....)).)))..)))(((((((((.((((......)))))))....((((------((((............))))))))..)))))).. ( -36.00)
>DroYak_CAF1 28305 103 + 1
UGUGCGAGUGCGCGGUUAGCAA----------AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGC------UGCAGGCUAUGAAAAAUUCAGCUGGAGAGAGCUU
...((.(((((((((((.....----------))))))....)))))(((((((((............((....))(((------.....))).........)))))))))....)).. ( -27.10)
>DroAna_CAF1 20675 102 + 1
-AUGUAUGUGCGCGGUUGGAAA----------AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCUGC------UGCAGGCUAUGAAAAAUGCAUCCGAGAAAACCUG
-......((((((((((.....----------))))))......((((.((((.((((......))))((....)).))------)).))))..........))))............. ( -22.20)
>consensus
UGUGUGAGUGCGCGGUUAGCAA__________AGCUGCAAAUGCGCUUUCAGUUGAUUAAAUUAAAUCGCUAAAGCAGC______UGCAGGCUAUGAAAAAUGCAGCCGGAGAGA_CU_
...............(((((............(((((((...(((((((.(((.((((......)))))))))))).))......)))).)))............)))))......... (-18.29 = -17.60 +  -0.69)

alignment

secondary structure

dotplot

Window 6

Location	22,472,821 – 22,472,924
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.69
Mean single sequence MFE	-23.10
Consensus MFE	-16.11
Energy contribution	-15.67
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.74
Structure conservation index	0.70
SVM decision value	1.13
SVM RNA-class probability	0.919837
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22472821 103 - 23771897
GAGAUCUCUUCAGCUGCAUUUUUCAUAGCCUGCA------GCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU----------UUGCUAACCGCGCACUCACACA
(((.......((((((((............))))------))))..(((((((((......)))).....(((((((....)).)))----------))))))).......)))..... ( -27.50)
>DroVir_CAF1 66918 96 - 1
---------CAGAAUACAUUUUUCAUAGC-UGCAGCUUUGGCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU----------UUUCCAACCACACACACAU---
---------(((...............((-((((((....)))))...)))((((......))))..)))(((((((....)).)))----------)).................--- ( -20.50)
>DroGri_CAF1 24797 97 - 1
---------CUGACUGCAUUUUUCAUAGC-UGCAACUCUGGCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU----------UUCCUAGCCACAUAUACAC--A
---------.....((((.((.....)).-))))....(((((((....))((((......))))....((((((((....)).)))----------)))..))))).........--. ( -20.20)
>DroEre_CAF1 26607 113 - 1
GAGCUCUCUCCAGCUGCAUUUUUCAUGGCCUGCA------GCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCUUUUGCAGCAUUUGCUAACCGCGCACUUACACA
..(((.....((((((((............))))------))))....)))((((......))))........((((.......((....))(((....)))....))))......... ( -28.90)
>DroYak_CAF1 28305 103 - 1
AAGCUCUCUCCAGCUGAAUUUUUCAUAGCCUGCA------GCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU----------UUGCUAACCGCGCACUCGCACA
..((......((((((................))------))))..(((((((((......)))).....(((((((....)).)))----------)))))))..))((....))... ( -23.19)
>DroAna_CAF1 20675 102 - 1
CAGGUUUUCUCGGAUGCAUUUUUCAUAGCCUGCA------GCAGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU----------UUUCCAACCGCGCACAUACAU-
((((((......((........))..))))))..------((.((......((((......))))....((((((((....)).)))----------)))......))))........- ( -18.30)
>consensus
_AG_UCUCUCCAGCUGCAUUUUUCAUAGCCUGCA______GCUGCUUUAGCGAUUUAAUUUAAUCAACUGAAAGCGCAUUUGCAGCU__________UUGCUAACCGCGCACACACACA
...........(((............(((.((((......((.(((((((.((((......))))..))).))))))...)))))))............)))................. (-16.11 = -15.67 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:41 2006