Locus 5618

Sequence ID	3R_DroMel_CAF1
Location	14,811,775 – 14,811,980
Length	205
Max. P	0.918797

overview

Window 9

Location	14,811,775 – 14,811,872
Length	97
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	93.10
Mean single sequence MFE	-35.24
Consensus MFE	-25.70
Energy contribution	-26.06
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-3.27
Structure conservation index	0.73
SVM decision value	1.12
SVM RNA-class probability	0.918797
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14811775 97 + 27905053
CGAAUGGCCAUUUAUGUGGCAAGUGCUGCAGUUGUUGUU---GCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCCGCAGUGGCUGUCAAACUUCGUGA
((((..(((((....)))))..((...(((((..(((((---((((((((.......))))))))))).((....))..))..)))))...))))))... ( -36.70)
>DroSec_CAF1 4389 100 + 1
CGAAUGUCCAUUUAUGUGGCAAGUGCUGCAGUUGUUGCUGUAGCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGA
........(((.....(((((..((((((((.((...((((.((((((((.......)))))))).))))..)).))))))))..)))))......))). ( -35.00)
>DroSim_CAF1 4397 100 + 1
CGAAUGGCCAUUUAUGUGGCAAGUGCUGCAGUUGUUGUUGUAGCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGA
.((.((((((((..((..((....))..))((((((((((((((((......))))))))))))))))...........))))))))))........... ( -38.70)
>DroEre_CAF1 6153 91 + 1
CGAAUGGCCAUUUAUGUGGCAAGUGCUGCAGUUGUUG---------UUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGA
.((.((((((((..((..((....))..))(((((((---------((((.......)))))))))))...........))))))))))........... ( -31.50)
>DroYak_CAF1 4623 91 + 1
CGAAUGGCCAUUUAUGUGGCAAGUGCCGCAGUUGUUG---------UUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGA
.((.((((((((..((((((....))))))(((((((---------((((.......)))))))))))...........))))))))))........... ( -34.30)
>consensus
CGAAUGGCCAUUUAUGUGGCAAGUGCUGCAGUUGUUG_U___GCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGA
((((..(((((....)))))..((...(((((..((((................(((((....))))).((....))))))..)))))...))))))... (-25.70 = -26.06 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	14,811,775 – 14,811,872
Length	97
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	93.10
Mean single sequence MFE	-24.64
Consensus MFE	-18.22
Energy contribution	-18.10
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-2.25
Structure conservation index	0.74
SVM decision value	0.45
SVM RNA-class probability	0.741600
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14811775 97 - 27905053
UCACGAAGUUUGACAGCCACUGCGGAUAACCUGUUGCUGUUGCAACUAGAACAACAGC---AACAACAACUGCAGCACUUGCCACAUAAAUGGCCAUUCG
...((((............((((((......(((((((((((.........)))))))---))))....)))))).....((((......))))..)))) ( -29.10)
>DroSec_CAF1 4389 100 - 1
UCACGAAGUUUGACAGCCACUGCAGAUAACCUGUUGCUGUUGCAACUAGAACAACAGCUACAGCAACAACUGCAGCACUUGCCACAUAAAUGGACAUUCG
...((((............((((((.....((((.(((((((.........))))))).))))......))))))....(((((......))).)))))) ( -26.70)
>DroSim_CAF1 4397 100 - 1
UCACGAAGUUUGACAGCCACUGCAGAUAACCUGUUGCUGUUGCAACUAGAACAACAGCUACAACAACAACUGCAGCACUUGCCACAUAAAUGGCCAUUCG
...((((............((((((......(((.(((((((.........))))))).))).......)))))).....((((......))))..)))) ( -25.92)
>DroEre_CAF1 6153 91 - 1
UCACGAAGUUUGACAGCCACUGCAGAUAACCUGUUGCUGUUGCAACUAGAACAA---------CAACAACUGCAGCACUUGCCACAUAAAUGGCCAUUCG
...((((............((((((......(((((.((((........)))).---------))))).)))))).....((((......))))..)))) ( -20.30)
>DroYak_CAF1 4623 91 - 1
UCACGAAGUUUGACAGCCACUGCAGAUAACCUGUUGCUGUUGCAACUAGAACAA---------CAACAACUGCGGCACUUGCCACAUAAAUGGCCAUUCG
...(((((.....).((((..((((......(((((.((((........)))).---------))))).))))(((....))).......))))..)))) ( -21.20)
>consensus
UCACGAAGUUUGACAGCCACUGCAGAUAACCUGUUGCUGUUGCAACUAGAACAACAGC___A_CAACAACUGCAGCACUUGCCACAUAAAUGGCCAUUCG
...(((((((((.(((...))))))))....((((((.((((........................)))).))))))...((((......))))..)))) (-18.22 = -18.10 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	14,811,803 – 14,811,912
Length	109
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	87.87
Mean single sequence MFE	-30.50
Consensus MFE	-21.80
Energy contribution	-25.80
Covariance contribution	4.00
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.71
SVM decision value	0.62
SVM RNA-class probability	0.801487
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14811803 109 + 27905053
CAGUUGUUGUU---GCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCCGCAGUGGCUGUCAAACUUCGUGAUAUGCCCAAAUCCGAAUAUAUUUUCUCGUCUAUCCGCAUU
.......((((---((((((((.......))))))))))))((....))((.(.((((((((.......))))).))))......(((......)))..........))... ( -30.10)
>DroSec_CAF1 4417 105 + 1
CAGUUGUUGCUGUAGCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGAUAUGCCCAAAUCCGAAUAUAUUUCCUCGGCUAU-------
((((..(((((((.((((((((.......)))))))).)))((....))))))..))))......((((.(((........))))))).................------- ( -28.60)
>DroSim_CAF1 4425 112 + 1
CAGUUGUUGUUGUAGCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGAUAUGCCCAAAACCGAAUUUAUUUCCUCGGCUAUUCGCACU
..((((((((((((((((......))))))))))))))))........(((.(.((((((((.......))))).))))....((((..........))))......))).. ( -35.80)
>DroEre_CAF1 6181 102 + 1
CAGUUGUUG---------UUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGAUAUGCCCAAAUCCGAUUUUAUUUCCUCGGCUCUCCGCG-U
..(((((((---------((((.......))))))))))).........((.(.((((((((.......))))).))))....((((..........))))......)).-. ( -27.50)
>consensus
CAGUUGUUGUU___GCUGUUGUUCUAGUUGCAACAGCAACAGGUUAUCUGCAGUGGCUGUCAAACUUCGUGAUAUGCCCAAAUCCGAAUAUAUUUCCUCGGCUAUCCGCA_U
..((((((((((((((((......)))))))))))))))).........((.(.((((((((.......))))).))))....((((..........))))......))... (-21.80 = -25.80 +   4.00)

alignment

secondary structure

dotplot

Window 2

Location	14,811,872 – 14,811,980
Length	108
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	87.72
Mean single sequence MFE	-23.80
Consensus MFE	-15.30
Energy contribution	-15.63
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.64
SVM decision value	0.12
SVM RNA-class probability	0.591916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14811872 108 - 27905053
AAAUUCGGAUUGCAAGCAGAAAACAA------AAAUGUAAAGGCGAUAAAGUGCCGAGCGAAGCAAAGUGCUAAAAUGCGGAUAGACGAGAAAAUAUAUUCGGAUUUGGGCAUA
.........((((..((.....(((.------...)))...((((......))))..))...)))).(((((.((((.((((((............)))))).)))).))))). ( -24.60)
>DroSec_CAF1 4489 107 - 1
AAAUUCGGAUUGCAAGCAGAAAAUGAAAAUGAAAAUGAAAAGGCGAUAAAGUGCCGAGCGAAGCAAAGUGCUAA-------AUAGCCGAGGAAAUAUAUUCGGAUUUGGGCAUA
.........((((..((.....((....))...........((((......))))..))...)))).(((((..-------....(((((........))))).....))))). ( -22.20)
>DroSim_CAF1 4497 114 - 1
AAAUUCGGAUUGCAAGCAGAAAAUGAAAAUGAAAAUGAAAAGGCGAUAAAGUGCCGAGCGAAGCAAAGUGCUAAAGUGCGAAUAGCCGAGGAAAUAAAUUCGGUUUUGGGCAUA
........(((((...((....((....)).....)).....)))))...(((((..(((.(((.....)))....)))....(((((((........)))))))...))))). ( -24.60)
>consensus
AAAUUCGGAUUGCAAGCAGAAAAUGAAAAUGAAAAUGAAAAGGCGAUAAAGUGCCGAGCGAAGCAAAGUGCUAAA_UGCG_AUAGCCGAGGAAAUAUAUUCGGAUUUGGGCAUA
........(((((...((.................)).....)))))...(((((.((...(((.....))).............(((((........)))))..)).))))). (-15.30 = -15.63 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:29 2006