Locus 5247

Sequence ID	2R_DroMel_CAF1
Location	17,078,301 – 17,078,429
Length	128
Max. P	0.779821

overview

Window 0

Location	17,078,301 – 17,078,394
Length	93
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	78.79
Mean single sequence MFE	-23.18
Consensus MFE	-14.99
Energy contribution	-15.38
Covariance contribution	0.39
Combinations/Pair	1.11
Mean z-score	-1.62
Structure conservation index	0.65
SVM decision value	0.55
SVM RNA-class probability	0.779821
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17078301 93 - 20766785
UGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCGUAAACUGA--------------AAACUUUUC-AUUUGCAAAAUGCCCCGA
.(((((.((((...))))((((((...((((((....))).)))...))))))....(((((.(((--------------(.....)))-))))))..)))))..... ( -24.10)
>DroVir_CAF1 23820 81 - 1
UGCAUUGGAUCAACGAUCACCAUUGACGGUGGAGUCCUCCUGCCCCAAACGGUGAGUA--AAUCUCA-------------AUCC--------AAGCAAAA----CAAA
(((.((((((......(((((.((...((((((....))).)))...)).)))))...--.......-------------))))--------)))))...----.... ( -21.49)
>DroSec_CAF1 15774 93 - 1
UGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCGUAAACUGA--------------AAACUUUUC-AUUUGCAAAAUGCCCCGA
.(((((.((((...))))((((((...((((((....))).)))...))))))....(((((.(((--------------(.....)))-))))))..)))))..... ( -24.10)
>DroSim_CAF1 15882 92 - 1
UGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCA-ACGGUAAGCAUAAACUGA--------------AAACUUUUC-AUUUGCAAAAUGCCCCGA
.(((((.((((...))))(((((((..((((((....))).))).))-)))))..(((.....(((--------------(.....)))-)..)))..)))))..... ( -24.00)
>DroYak_CAF1 17677 107 - 1
UGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCGUAAAUUGAAAACUAAAAACUGAAAACUUUUC-AUUUGCAAAAUGCCCCAA
.(((((.((((...))))((((((...((((((....))).)))...))))))....((((((.(((((...............)))))-))))))..)))))..... ( -24.46)
>DroMoj_CAF1 18792 89 - 1
UGCAUUGGAUCAACGAUCACCAUUGACGGUGGAGUCCUCGUGUCCCAAGCGGUAAGUA--AAUUCCA-------------ACGCUUUUCUAGCAGCAAAG----CAAA
(((.((((..((.((((((((......))))).....)))))..))))((((......--....)).-------------..(((.....))).))...)----)).. ( -20.90)
>consensus
UGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCAUAAACUGA______________AAACUUUUC_AUUUGCAAAAUGCCCCAA
(((....((((...))))((((((...((((((....))).)))...)))))).........................................)))........... (-14.99 = -15.38 +   0.39)

alignment

secondary structure

dotplot

Window 1

Location	17,078,328 – 17,078,429
Length	101
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.21
Mean single sequence MFE	-31.37
Consensus MFE	-24.45
Energy contribution	-24.98
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	0.78
SVM decision value	0.33
SVM RNA-class probability	0.693304
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17078328 101 + 20766785
UCAGUUUA---CGCUUACCGUUUGGGGCAGGAGGAAUCCACCGUCAACGGUGAUCGUUGAUCCAAUGCAACAAACGGAGUUCUGUUU-UUGGGAGG-AAAG---CAAAG
........---.((((.(((((((..((((((..(((.(((((....)))))...)))..)))..)))..)))))))..((((.(..-...).)))-))))---).... ( -32.30)
>DroPse_CAF1 47832 96 + 1
U----------UGCUCACCGUUUGGGGCAGGAGGAAUCCACCGUCAACGGUGAUCGUUGAUCCAAUGCAACAAACGGAGUCCUGUGC-GGGGGAGAGAAAU--CGAAAG
.----------..(((.(((((((..((((((..(((.(((((....)))))...)))..)))..)))..)))))))..((((....-..)))))))....--...... ( -33.50)
>DroSec_CAF1 15801 102 + 1
UCAGUUUA---CGCUUACCGUUUGGGGCAGGAGGAAUCCACCGUCAACGGUGAUCGUUGAUCCAAUGCAACAAACGGAGUUCUGUUUUUUGGGAGG-AAAG---CAAAG
........---.((((.(((((((..((((((..(((.(((((....)))))...)))..)))..)))..)))))))..((((.((....)).)))-))))---).... ( -33.00)
>DroSim_CAF1 15909 100 + 1
UCAGUUUA---UGCUUACCGU-UGGGGCAGGAGGAAUCCACCGUCAACGGUGAUCGUUGAUCCAAUGCAACAAACGGAGUUCUGUUU-UUGGAAGG-AAAG---CAAUG
........---(((((.((((-(((((..(((....))).))(((((((.....)))))))))))).(((.((((((....))))))-)))...))-.)))---))... ( -30.20)
>DroWil_CAF1 55848 97 + 1
UGAGUUCAAUUCACUUACCGUUUGGGGCAAGAGGAAUCCACCGUCAACGGUGAUCUUUGAUCCAAUGCAACAAAUGGAGUUCUGUGG---AGCAGG---------AAAC
(((((.......)))))(((((((..(((...(((.(((((((....)))))......)))))..)))..)))))))..(((((...---..))))---------)... ( -27.90)
>DroAna_CAF1 17743 101 + 1
---UUUUC---GACUUACCGUUUGGGGCAGGAGGAAUCCACCGUCAACGGCGAUCGUUGAUCCAAUGCAACAAACGGAGUUCUGUUU-UUGGUAAG-AGAUUUGGAGAG
---(((((---((....(((((((..((((((....)))...(((((((.....)))))))....)))..)))))))...(((.((.-.....)).-))).))))))). ( -31.30)
>consensus
UCAGUUUA___CGCUUACCGUUUGGGGCAGGAGGAAUCCACCGUCAACGGUGAUCGUUGAUCCAAUGCAACAAACGGAGUUCUGUUU_UUGGGAGG_AAAG___CAAAG
.................(((((((..((((((..(((.(((((....)))))...)))..)))..)))..)))))))................................ (-24.45 = -24.98 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	17,078,328 – 17,078,429
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	82.21
Mean single sequence MFE	-25.37
Consensus MFE	-20.69
Energy contribution	-20.88
Covariance contribution	0.19
Combinations/Pair	1.05
Mean z-score	-1.39
Structure conservation index	0.82
SVM decision value	0.15
SVM RNA-class probability	0.605740
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17078328 101 - 20766785
CUUUG---CUUU-CCUCCCAA-AAACAGAACUCCGUUUGUUGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCG---UAAACUGA
....(---(((.-((..((((-.((((((......))))))...)))).((((((.....)))))).((((((....))).)))......)).)))).---........ ( -24.60)
>DroPse_CAF1 47832 96 - 1
CUUUCG--AUUUCUCUCCCCC-GCACAGGACUCCGUUUGUUGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUGAGCA----------A
......--....(((....((-.....))...(((((((..(((..(((.......((((((....))))))..)))...)))..))))))).)))..----------. ( -24.80)
>DroSec_CAF1 15801 102 - 1
CUUUG---CUUU-CCUCCCAAAAAACAGAACUCCGUUUGUUGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCG---UAAACUGA
....(---(((.-((..((((..((((((......))))))...)))).((((((.....)))))).((((((....))).)))......)).)))).---........ ( -25.00)
>DroSim_CAF1 15909 100 - 1
CAUUG---CUUU-CCUUCCAA-AAACAGAACUCCGUUUGUUGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCA-ACGGUAAGCA---UAAACUGA
...((---(((.-...(((((-.((((((......))))))...))))).........(((((((..((((((....))).))).))-))))))))))---........ ( -27.20)
>DroWil_CAF1 55848 97 - 1
GUUU---------CCUGCU---CCACAGAACUCCAUUUGUUGCAUUGGAUCAAAGAUCACCGUUGACGGUGGAUUCCUCUUGCCCCAAACGGUAAGUGAAUUGAACUCA
...(---------(((((.---..(((((......))))).)))..)))((((...((((((....)))))).(((..((((((......)))))).)))))))..... ( -24.80)
>DroAna_CAF1 17743 101 - 1
CUCUCCAAAUCU-CUUACCAA-AAACAGAACUCCGUUUGUUGCAUUGGAUCAACGAUCGCCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGUC---GAAAA---
.........((.-((((((..-.((((((......))))))...((((.((((((.....)))))).((((((....))).)))))))..))))))..---))...--- ( -25.80)
>consensus
CUUUG___CUUU_CCUCCCAA_AAACAGAACUCCGUUUGUUGCAUUGGAUCAACGAUCACCGUUGACGGUGGAUUCCUCCUGCCCCAAACGGUAAGCG___UAAACUGA
................................(((((((..(((..(((.......((((((....))))))..)))...)))..)))))))................. (-20.69 = -20.88 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:07 2006