Locus 4831

Sequence ID	2R_DroMel_CAF1
Location	15,872,186 – 15,872,336
Length	150
Max. P	0.998724

overview

Window 0

Location	15,872,186 – 15,872,299
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	96.99
Mean single sequence MFE	-20.72
Consensus MFE	-18.18
Energy contribution	-18.22
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.63
Structure conservation index	0.88
SVM decision value	1.02
SVM RNA-class probability	0.901909
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15872186 113 + 20766785
CUCCCUUAAGCGCAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGCGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCC
.........((((((((((((..........((((.((.....))))))((....))))))))))......(((.......))).....)))).................... ( -22.00)
>DroSec_CAF1 9495 113 + 1
CUCCCUUAAGCGAAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGUGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCC
........(((....)))............((((..(((....(((((.((....)).)))))........(((.......)))....)))..))))................ ( -19.70)
>DroSim_CAF1 6930 113 + 1
CUCCCUUAAGCGCAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGCGCUGCUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCC
.........((((((((((((..........((((.((.....))))))((....))))))))))......(((.......))).....)))).................... ( -22.00)
>DroEre_CAF1 7351 113 + 1
CUCCCUUAAGCGCAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGCGCUACUGCUUCAGCAUUUACCUGGCUUCCUUUGCUUUUCAGUGCCACAUCAUCUCUCUUCCUCC
.........((((..((((((..........((((.((.....))))))((....))))))))........(((.......))).....)))).................... ( -20.10)
>DroYak_CAF1 9774 113 + 1
CUCCCUUAAGCGCAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGCGCUACAGCUUCAGCAUUUACCUGGCUUCCUUUGCUUUUCAGUGCCACAUCAUCUCUCUUCCUCC
.........((((..((((((..........((((.((.....))))))((....))))))))........(((.......))).....)))).................... ( -19.80)
>consensus
CUCCCUUAAGCGCAAGUUGAACAUUUCAUUUGUCAUGCUUUUUGCUGGCGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCC
.........((((..((((((..........((((.((.....))))))((....))))))))........(((.......))).....)))).................... (-18.18 = -18.22 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	15,872,226 – 15,872,336
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.91
Mean single sequence MFE	-22.73
Consensus MFE	-21.75
Energy contribution	-21.75
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-1.27
Structure conservation index	0.96
SVM decision value	0.72
SVM RNA-class probability	0.831713
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15872226 110 + 20766785
UUUGCUGGCGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGCC
...(((((.((....)).)))))........(((.((.((.(((((...(((((((((......................))))))))).)))))....))..))..))) ( -23.95)
>DroSec_CAF1 9535 110 + 1
UUUGCUGGUGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGCC
...(((((.((....)).)))))........(((.((.((.(((((...(((((((((......................))))))))).)))))....))..))..))) ( -23.95)
>DroSim_CAF1 6970 110 + 1
UUUGCUGGCGCUGCUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGCC
...(((((.((....)).)))))........(((.((.((.(((((...(((((((((......................))))))))).)))))....))..))..))) ( -23.95)
>DroEre_CAF1 7391 110 + 1
UUUGCUGGCGCUACUGCUUCAGCAUUUACCUGGCUUCCUUUGCUUUUCAGUGCCACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGCC
..((((((.((....)).)))))).................((...(((((........................((((.....)))).(((.....))))))))..)). ( -21.00)
>DroYak_CAF1 9814 110 + 1
UUUGCUGGCGCUACAGCUUCAGCAUUUACCUGGCUUCCUUUGCUUUUCAGUGCCACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGUC
...((((......)))).((((((...((.((((.......((........)).......................(((.....)))))))..))...)).))))..... ( -20.80)
>consensus
UUUGCUGGCGCUACUGCUUCAGCUUUUACCUGGCUUCCUCUGCUUUUCAGUGCGACAUCAUCUCUCUUCCUCCCACGCAUAUGUUGCGCCAAAGUUUUUGACUGAUUGCC
...(((((.((....)).)))))........(((.((.((.(((((...(((((((((......................))))))))).)))))....))..))..))) (-21.75 = -21.75 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	15,872,226 – 15,872,336
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.91
Mean single sequence MFE	-29.66
Consensus MFE	-27.52
Energy contribution	-27.72
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.93
SVM decision value	3.20
SVM RNA-class probability	0.998724
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15872226 110 - 20766785
GGCAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUCGCACUGAAAAGCAGAGGAAGCCAGGUAAAAGCUGAAGCAGUAGCGCCAGCAAA
(((.((((.((.....((((.(((((.....))))).)))).....))..)))).((.(.(((.....))).))).)))........((((..((....))..))))... ( -29.90)
>DroSec_CAF1 9535 110 - 1
GGCAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUCGCACUGAAAAGCAGAGGAAGCCAGGUAAAAGCUGAAGCAGUAGCACCAGCAAA
(((.((((.((.....((((.(((((.....))))).)))).....))..)))).((.(.(((.....))).))).)))........((((..((....))..))))... ( -29.50)
>DroSim_CAF1 6970 110 - 1
GGCAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUCGCACUGAAAAGCAGAGGAAGCCAGGUAAAAGCUGAAGCAGCAGCGCCAGCAAA
(((.((((.((.....((((.(((((.....))))).)))).....))..)))).((.(.(((.....))).))).)))........((((..((....))..))))... ( -29.90)
>DroEre_CAF1 7391 110 - 1
GGCAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUGGCACUGAAAAGCAAAGGAAGCCAGGUAAAUGCUGAAGCAGUAGCGCCAGCAAA
(((..(((((......((((.(((((.....))))).))))...........((.((((.((.........))...)))).))....))))).((....)))))...... ( -29.80)
>DroYak_CAF1 9814 110 - 1
GACAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUGGCACUGAAAAGCAAAGGAAGCCAGGUAAAUGCUGAAGCUGUAGCGCCAGCAAA
(((.....))).....((((.(((((.....))))).))))...........((.((((.((.........))...)))).))...(((((..((....))..))))).. ( -29.20)
>consensus
GGCAAUCAGUCAAAAACUUUGGCGCAACAUAUGCGUGGGAGGAAGAGAGAUGAUGUCGCACUGAAAAGCAGAGGAAGCCAGGUAAAAGCUGAAGCAGUAGCGCCAGCAAA
(((.((((.((.....((((.(((((.....))))).)))).....))..))))...((........)).......)))........((((..((....))..))))... (-27.52 = -27.72 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:19 2006