Locus 9209

Sequence ID	3R_DroMel_CAF1
Location	24,548,554 – 24,548,687
Length	133
Max. P	0.988579

overview

Window 0

Location	24,548,554 – 24,548,657
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.54
Mean single sequence MFE	-36.82
Consensus MFE	-14.88
Energy contribution	-15.63
Covariance contribution	0.75
Combinations/Pair	1.27
Mean z-score	-3.94
Structure conservation index	0.40
SVM decision value	1.01
SVM RNA-class probability	0.899941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24548554 103 + 27905053
ACUUCCCC-CCAGAAGUAUGCAU--ACUUGCACUCCG------CUCGCACUUUGUCG----CCCCA-ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUU-G-CCCAACCGACAAGCGC
(((((...-...))))).((((.--...)))).....------..(((...((((((----(((..-...))))((((((((((.........)))))))-)-)).....)))))))). ( -38.40)
>DroSec_CAF1 46792 103 + 1
ACUUCCCC-CCAGAAGUAUGCAU--ACUUGCACUCCG------CUCACACUUUGUCG----CCCUA-ACCGGGCUGCAAAGCCAAUCCAGUUCUGGCUUU-G-CCCAACCGACAAGCGC
(((((...-...))))).((((.--...))))...((------((.......(((((----(((..-...)))).(((((((((.........)))))))-)-)......)))))))). ( -34.31)
>DroSim_CAF1 48603 103 + 1
ACUUCCCC-CCAGAAGUAUGCAU--ACUUGCACUCCG------CUCACACUUUGUCG----CCCCA-ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUU-G-GCCAACCGACAAGCGC
(((((...-...))))).((((.--...))))...((------((.....(((((((----(((..-...))))))))))(((((.(((....)))..))-)-)).........)))). ( -36.30)
>DroEre_CAF1 51131 103 + 1
ACUUCCUC-CCAUAAGUAUGCAU--ACUUGCACUCCG------CUCGCACUUUGUCG----CCCCA-GCCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUU-G-CCCGACCGACAAGCGA
........-.........((((.--...)))).....------.((((...((((((----(((..-...))))((((((((((.........)))))))-)-)).....))))))))) ( -36.50)
>DroYak_CAF1 47896 105 + 1
ACUUCCCCACCAGAAGUAUGCAU--ACUUGCACUCCG------CUCGCACUUUGUCG----CCCCAAACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUU-G-CCCAACCGACAAGCGC
(((((.......))))).((((.--...)))).....------..(((...((((((----(((......))))((((((((((.........)))))))-)-)).....)))))))). ( -38.10)
>DroAna_CAF1 46967 114 + 1
AGA---CC-CUUAAAGUAUGCAAGGACUCCUACUCCCCGACUCCUUCCAUUUUACCGGAUUCCCGG-AUCAAGUCGGCAAGCCAAUCCAUUUUUGGCUGUUGUUCUGGCCGACGAGGGC
...---((-(((.....(((.(((((.((.........)).))))).)))....((((....))))-.....((((((.((((((.......)))))).........))))))))))). ( -37.30)
>consensus
ACUUCCCC_CCAGAAGUAUGCAU__ACUUGCACUCCG______CUCGCACUUUGUCG____CCCCA_ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUU_G_CCCAACCGACAAGCGC
.........((((((.(.((((......)))).................((((((((....(((......))))))))))).......).))))))....................... (-14.88 = -15.63 +   0.75)

alignment

secondary structure

dotplot

Window 1

Location	24,548,554 – 24,548,657
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-43.08
Consensus MFE	-22.21
Energy contribution	-23.77
Covariance contribution	1.56
Combinations/Pair	1.22
Mean z-score	-2.69
Structure conservation index	0.52
SVM decision value	0.42
SVM RNA-class probability	0.727854
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24548554 103 - 27905053
GCGCUUGUCGGUUGGG-C-AAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU-UGGGG----CGACAAAGUGCGAG------CGGAGUGCAAGU--AUGCAUACUUCUGG-GGGGAAGU
.(((((((...(((((-(-((((((((.......)))))))))))((((...-..)))----)..)))...)))))------))..(((((...--.)))))((((((..-..)))))) ( -46.50)
>DroSec_CAF1 46792 103 - 1
GCGCUUGUCGGUUGGG-C-AAAGCCAGAACUGGAUUGGCUUUGCAGCCCGGU-UAGGG----CGACAAAGUGUGAG------CGGAGUGCAAGU--AUGCAUACUUCUGG-GGGGAAGU
(((((((((......(-(-((((((((.......)))))))))).((((...-..)))----)))).))))))...------....(((((...--.)))))((((((..-..)))))) ( -41.10)
>DroSim_CAF1 48603 103 - 1
GCGCUUGUCGGUUGGC-C-AAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU-UGGGG----CGACAAAGUGUGAG------CGGAGUGCAAGU--AUGCAUACUUCUGG-GGGGAAGU
((((((((((((.(((-(-((..(((....))).))))))..)))((((...-..)))----)))).))))))...------....(((((...--.)))))((((((..-..)))))) ( -41.70)
>DroEre_CAF1 51131 103 - 1
UCGCUUGUCGGUCGGG-C-AAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGC-UGGGG----CGACAAAGUGCGAG------CGGAGUGCAAGU--AUGCAUACUUAUGG-GAGGAAGU
(((((((((.(((.((-(-((((((((.......)))))))))))((((...-..)))----))))...).)))))------))).(((((...--.))))).(((....-)))..... ( -44.20)
>DroYak_CAF1 47896 105 - 1
GCGCUUGUCGGUUGGG-C-AAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGUUUGGGG----CGACAAAGUGCGAG------CGGAGUGCAAGU--AUGCAUACUUCUGGUGGGGAAGU
.(((((((...(((((-(-((((((((.......)))))))))))((((......)))----)..)))...)))))------))..(((((...--.)))))((((((.....)))))) ( -46.70)
>DroAna_CAF1 46967 114 - 1
GCCCUCGUCGGCCAGAACAACAGCCAAAAAUGGAUUGGCUUGCCGACUUGAU-CCGGGAAUCCGGUAAAAUGGAAGGAGUCGGGGAGUAGGAGUCCUUGCAUACUUUAAG-GG---UCU
(((((.((((((.((.....((((((....))).))).)).)))))).....-((((....))))....(((.(((((.((.........)).))))).)))......))-))---).. ( -38.30)
>consensus
GCGCUUGUCGGUUGGG_C_AAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU_UGGGG____CGACAAAGUGCGAG______CGGAGUGCAAGU__AUGCAUACUUCUGG_GGGGAAGU
((((((((((.........((((((((.......))))))))....(((......)))....)))).)))))).............(((((......)))))((((((.....)))))) (-22.21 = -23.77 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	24,548,588 – 24,548,687
Length	99
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	78.69
Mean single sequence MFE	-30.43
Consensus MFE	-18.93
Energy contribution	-20.82
Covariance contribution	1.89
Combinations/Pair	1.05
Mean z-score	-3.38
Structure conservation index	0.62
SVM decision value	2.13
SVM RNA-class probability	0.988579
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24548588 99 + 27905053
CUCGCACUUUGUCGCCCCA-ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUUGCCCAACCGACAAGCGCACAAACAUCAUAACCACAUCAGCA--------CGUGAA
...((.(((.(((((((..-...))))((((((((((.........)))))))))).....)))))).))..............(((.......--------.))).. ( -34.70)
>DroVir_CAF1 41501 82 + 1
CUUUGCCCUUAAAGCGCCA-UACGC---------GCAAUCCAUUUUUCGUA--G----CUUGGCAAAAGCGCAAACAUCAAAACCACAUCAGCG--------GC--AU
...((((((....((((..-...))---------))............((.--(----(((.....))))))..................)).)--------))--). ( -16.70)
>DroSec_CAF1 46826 99 + 1
CUCACACUUUGUCGCCCUA-ACCGGGCUGCAAAGCCAAUCCAGUUCUGGCUUUGCCCAACCGACAAGCGCACAAACAUCAUAACCACAUCAGCA--------CGUGAA
.((((...(((((((((..-...)))).(((((((((.........)))))))))......)))))((.......................)).--------.)))). ( -30.50)
>DroSim_CAF1 48637 99 + 1
CUCACACUUUGUCGCCCCA-ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUUGGCCAACCGACAAGCGCACAAACAUCAUAACCACAUCAGCA--------CGUGAA
.((((...(((((((((..-...))))((((((((((.........))))))).)))....)))))((.......................)).--------.)))). ( -31.20)
>DroEre_CAF1 51165 107 + 1
CUCGCACUUUGUCGCCCCA-GCCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUUGCCCGACCGACAAGCGAACAAACAUCAUAACCACAUCAGCAGAGGAGCAGGGGAG
.((((...(((((((((..-...))))((((((((((.........)))))))))).....))))))))).............((.(....((......))..))).. ( -35.90)
>DroYak_CAF1 47931 100 + 1
CUCGCACUUUGUCGCCCCAAACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUUGCCCAACCGACAAGCGCACAAACAUCAUAACCACAUCAGCA--------GGGGAA
...((.(((.(((((((......))))((((((((((.........)))))))))).....)))))).)).......((....((.........--------)).)). ( -33.60)
>consensus
CUCGCACUUUGUCGCCCCA_ACCGGGCGGCAAAGCCAAUCCAGUUCUGGCUUUGCCCAACCGACAAGCGCACAAACAUCAUAACCACAUCAGCA________CGUGAA
........(((((((((......))))((((((((((.........)))))))))).....))))).......................................... (-18.93 = -20.82 +   1.89)

alignment

secondary structure

dotplot

Window 3

Location	24,548,588 – 24,548,687
Length	99
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	78.69
Mean single sequence MFE	-36.50
Consensus MFE	-25.64
Energy contribution	-26.78
Covariance contribution	1.14
Combinations/Pair	1.26
Mean z-score	-1.87
Structure conservation index	0.70
SVM decision value	1.11
SVM RNA-class probability	0.917274
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24548588 99 - 27905053
UUCACG--------UGCUGAUGUGGUUAUGAUGUUUGUGCGCUUGUCGGUUGGGCAAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU-UGGGGCGACAAAGUGCGAG
.(((((--------(....))))))............((((((((((.....(((((((((((.......)))))))))))((((...-..))))))).))))))).. ( -42.20)
>DroVir_CAF1 41501 82 - 1
AU--GC--------CGCUGAUGUGGUUUUGAUGUUUGCGCUUUUGCCAAG----C--UACGAAAAAUGGAUUGC---------GCGUA-UGGCGCUUUAAGGGCAAAG
.(--((--------(.(((((.(..(((((..(((((.((....))))))----)--..)))))...).)))((---------((...-..))))....))))))... ( -22.40)
>DroSec_CAF1 46826 99 - 1
UUCACG--------UGCUGAUGUGGUUAUGAUGUUUGUGCGCUUGUCGGUUGGGCAAAGCCAGAACUGGAUUGGCUUUGCAGCCCGGU-UAGGGCGACAAAGUGUGAG
.(((((--------(((.(((((.......)))))...))))(((((......((((((((((.......)))))))))).((((...-..)))))))))...)))). ( -38.00)
>DroSim_CAF1 48637 99 - 1
UUCACG--------UGCUGAUGUGGUUAUGAUGUUUGUGCGCUUGUCGGUUGGCCAAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU-UGGGGCGACAAAGUGUGAG
.(((((--------(((.(((((.......)))))...))))((((((((.((((((..(((....))).))))))..)))((((...-..)))))))))...)))). ( -38.60)
>DroEre_CAF1 51165 107 - 1
CUCCCCUGCUCCUCUGCUGAUGUGGUUAUGAUGUUUGUUCGCUUGUCGGUCGGGCAAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGC-UGGGGCGACAAAGUGCGAG
......(((.(..(..(....)..)........(((((.((((.(((((.(((.(((((((((.......)))))))))))).)))))-...)))))))))).))).. ( -37.70)
>DroYak_CAF1 47931 100 - 1
UUCCCC--------UGCUGAUGUGGUUAUGAUGUUUGUGCGCUUGUCGGUUGGGCAAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGUUUGGGGCGACAAAGUGCGAG
.....(--------..(....)..)............((((((((((.....(((((((((((.......)))))))))))((((......))))))).))))))).. ( -40.10)
>consensus
UUCACC________UGCUGAUGUGGUUAUGAUGUUUGUGCGCUUGUCGGUUGGGCAAAGCCAGAACUGGAUUGGCUUUGCCGCCCGGU_UGGGGCGACAAAGUGCGAG
...............((.(((((.......))))).))(((((((((.....(((((((((((.......)))))))))))((((......))))))).))))))... (-25.64 = -26.78 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:02 2006