Locus 5070

Sequence ID	3R_DroMel_CAF1
Location	13,366,346 – 13,366,465
Length	119
Max. P	0.951127

overview

Window 7

Location	13,366,346 – 13,366,443
Length	97
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.48
Mean single sequence MFE	-47.05
Consensus MFE	-34.65
Energy contribution	-37.10
Covariance contribution	2.45
Combinations/Pair	1.13
Mean z-score	-2.35
Structure conservation index	0.74
SVM decision value	1.41
SVM RNA-class probability	0.951127
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13366346 97 + 27905053
--------------------AUGAGCGCCACGCCGCCGGACCUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCCGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCA
--------------------....(((.(..((((.((((......)))).))))((((..(((((....))))).))))).))).(((((.(((((((....))))))).))))). ( -51.10)
>DroSec_CAF1 45 111 + 1
GUGAAGGUGGUGAAAAAAGCAUGAGCGCCACGCCGCCGGACCUACUUUCGUUGUCGGCGUCCCGAGAAGUCUCGGCCGCA------GUCGCCGCCUCUGCCAACGGAGGCAGCGGCA
.....(((((((......((....))....))))))).(((..((....)).))).(((..(((((....))))).))).------(((((.(((((((....))))))).))))). ( -49.20)
>DroSim_CAF1 1 97 + 1
--------------------AUGAGCGCCACACCGCCGGACCUACUUUCGUUGUCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCA
--------------------....(((.(....((((((....((....))..))))))..(((((....))))).....).))).(((((.(((((((....))))))).))))). ( -42.80)
>DroEre_CAF1 1 91 + 1
--------------------AUGAGCGACACGCCGCCGGACUUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGU------CGGCGCCUCUGCCAACGGAGGCAGCGGCA
--------------------....(((..(((((((((.((........))))))))))).(((((....))))).))).((------((..(((((((....)))))))..)))). ( -46.20)
>DroYak_CAF1 1 97 + 1
--------------------AUGAGCGCCACGCCGCCGGACCUACUUUCCUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCUGCCUCUGCCAACGGAGGCAGCGGCA
--------------------....(((.((((((((((((.......)))..)))))))).(((((....))))).....).))).(((((((((((((....))))))))))))). ( -55.60)
>DroAna_CAF1 1 91 + 1
--------------------AUGAGUGAAACGCCGCCAGACUCACUUUUGGCGGCGGCGUCCCGAGAAGUCUCAGAAGUCUUGGCAG---CGGUCGCAGCCAACG---GCAGCGGAA
--------------------..........((((((((((......))))))))))...(((((((....)))....((((((((.(---(....)).))))).)---)).).))). ( -37.40)
>consensus
____________________AUGAGCGCCACGCCGCCGGACCUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCA
........................(((..((((((((.(((........))))))))))).(((((....))))).))).......(((((.(((((((....))))))).))))). (-34.65 = -37.10 +   2.45)

alignment

secondary structure

dotplot

Window 8

Location	13,366,346 – 13,366,443
Length	97
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-47.08
Consensus MFE	-34.60
Energy contribution	-35.88
Covariance contribution	1.28
Combinations/Pair	1.12
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	1.09
SVM RNA-class probability	0.913542
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13366346 97 - 27905053
UGCCGCUGCCUCCGUUGGCAGAGGCGGCGACUGCGACGGCGGCCGAGACUUCUCGGGACGCCGCCAACGAAAGUAGGUCCGGCGGCGUGGCGCUCAU--------------------
.(((((.(((.(((..(((...(((((((.((((....))))(((((....)))))..))))))).((....))..)))))).))))))))......-------------------- ( -53.00)
>DroSec_CAF1 45 111 - 1
UGCCGCUGCCUCCGUUGGCAGAGGCGGCGAC------UGCGGCCGAGACUUCUCGGGACGCCGACAACGAAAGUAGGUCCGGCGGCGUGGCGCUCAUGCUUUUUUCACCACCUUCAC
.(((.(((((......))))).)))((((.(------..((.(((((....)))))..(((((((.((....))..)).))))).))..)))))....................... ( -48.80)
>DroSim_CAF1 1 97 - 1
UGCCGCUGCCUCCGUUGGCAGAGGCGGCGACUGCGACUGCGGCCGAGACUUCUCGGGACGCCGACAACGAAAGUAGGUCCGGCGGUGUGGCGCUCAU--------------------
...(((((((((.(....).)))))))))...(((.(..((.(((((....)))))..(((((((.((....))..)).))))).))..))))....-------------------- ( -48.10)
>DroEre_CAF1 1 91 - 1
UGCCGCUGCCUCCGUUGGCAGAGGCGCCG------ACUGCGGCCGAGACUUCUCGGGACGCCGCCAACGAAAGUAAGUCCGGCGGCGUGUCGCUCAU--------------------
.(((.(((((......))))).)))((.(------((.....(((((....))))).((((((((.((....))......)))))))))))))....-------------------- ( -46.30)
>DroYak_CAF1 1 97 - 1
UGCCGCUGCCUCCGUUGGCAGAGGCAGCGACUGCGACUGCGGCCGAGACUUCUCGGGACGCCGCCAAGGAAAGUAGGUCCGGCGGCGUGGCGCUCAU--------------------
.(((((((((((.(....).))))))))..((((....))))(((((....))))).((((((((..(((.......))))))))))))))......-------------------- ( -51.50)
>DroAna_CAF1 1 91 - 1
UUCCGCUGC---CGUUGGCUGCGACCG---CUGCCAAGACUUCUGAGACUUCUCGGGACGCCGCCGCCAAAAGUGAGUCUGGCGGCGUUUCACUCAU--------------------
...((((((---(..((((.((....)---).))))(((((((((((....)))))))......(((.....))).)))))))))))..........-------------------- ( -34.80)
>consensus
UGCCGCUGCCUCCGUUGGCAGAGGCGGCGACUGCGACUGCGGCCGAGACUUCUCGGGACGCCGCCAACGAAAGUAGGUCCGGCGGCGUGGCGCUCAU____________________
((((.(((((......))))).))))............(((.(((((....))))).((((((((...............))))))))..)))........................ (-34.60 = -35.88 +   1.28)

alignment

secondary structure

dotplot

Window 9

Location	13,366,366 – 13,366,465
Length	99
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	83.81
Mean single sequence MFE	-44.98
Consensus MFE	-29.09
Energy contribution	-31.53
Covariance contribution	2.45
Combinations/Pair	1.13
Mean z-score	-2.44
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.577504
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13366366 99 + 27905053
CCUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCCGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCAGAAG---CGCUGAUAAGGAGCGUUC
......(((((.(((((((..(((((....))))).))))))))).(((((.(((((((....))))))).))))).)))(---((((.......))))).. ( -50.10)
>DroSec_CAF1 85 93 + 1
CCUACUUUCGUUGUCGGCGUCCCGAGAAGUCUCGGCCGCA------GUCGCCGCCUCUGCCAACGGAGGCAGCGGCAGAAG---CGCUGAUAAGGAGCGCUC
......(((.((((((((((.(((((....))))).....------(((((.(((((((....))))))).)))))....)---))))))))).)))..... ( -45.90)
>DroSim_CAF1 21 99 + 1
CCUACUUUCGUUGUCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCAGAAA---CGCUGAUAAGGAGCGCUC
......(((.((((((((((.(((((....)))))..((....)).(((((.(((((((....))))))).)))))....)---))))))))).)))..... ( -46.50)
>DroEre_CAF1 21 93 + 1
CUUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGU------CGGCGCCUCUGCCAACGGAGGCAGCGGCAAAAG---CACUGAUAAGGAGCGCUC
.........((((((.(((..(((((....))))).))).))------))))(((.(((((......))))).)))...((---(.((.......)).))). ( -39.00)
>DroYak_CAF1 21 99 + 1
CCUACUUUCCUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCUGCCUCUGCCAACGGAGGCAGCGGCAAAAG---CGCUGAUAAGGAUCGAUC
....(..((((((.((((((.(((((....)))))..((....)).(((((((((((((....)))))))))))))....)---))))).))))))..)... ( -50.70)
>DroAna_CAF1 21 96 + 1
CUCACUUUUGGCGGCGGCGUCCCGAGAAGUCUCAGAAGUCUUGGCAG---CGGUCGCAGCCAACG---GCAGCGGAAGAAGCGGCGCUGAUAAAGAGCGCUC
....(((((((((((.((...((((((..((...))..))))))..)---).))))).(((...)---))..))))))....((((((.......)))))). ( -37.70)
>consensus
CCUACUUUCGUUGGCGGCGUCCCGAGAAGUCUCGGCCGCAGUCGCAGUCGCCGCCUCUGCCAACGGAGGCAGCGGCAGAAG___CGCUGAUAAGGAGCGCUC
....((((.((((((((((..(((((....))))).))).......(((((.(((((((....))))))).)))))........)))))))))))....... (-29.09 = -31.53 +   2.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:29 2006