Locus 7129

Sequence ID	3L_DroMel_CAF1
Location	19,176,791 – 19,176,991
Length	200
Max. P	0.997966

overview

Window 3

Location	19,176,791 – 19,176,911
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-32.92
Consensus MFE	-29.60
Energy contribution	-30.40
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.30
Structure conservation index	0.90
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19176791 120 - 23771897
GAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCGAACUUUGGACUAACAAACCGCUU
((((((((((.((((((((((((.........)))))).((....)).))))))....))))))........(((((....))))).)))).........((((......))))...... ( -33.00)
>DroSec_CAF1 5308 120 - 1
GAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCGAACUUUGGACUAACAAACCGCUU
((((((((((.((((((((((((.........)))))).((....)).))))))....))))))........(((((....))))).)))).........((((......))))...... ( -33.00)
>DroSim_CAF1 8345 120 - 1
GAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCAAACUUUGGACUAACAAACCGCUU
((((((((((.((((((((((((.........)))))).((....)).))))))....))))))........(((((....))))).)))).........((((......))))...... ( -33.00)
>DroEre_CAF1 8048 120 - 1
GAAGGCAAGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCGAACUUUGGACUAACAAACCGCUU
..((((.....((((((((((((.........)))))).((....)).))))))...((....((((..((((((((....)))))..(((.....))).....))).))))..)))))) ( -30.90)
>DroYak_CAF1 10129 120 - 1
GAACGCCAGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCGAACUUUGGACUAACAAACCGCUU
....((((...((((((((((((.........)))))).((....)).))))))..))))..(((.(((((.(((((....)))))..((((..........))))...))))).))).. ( -34.70)
>consensus
GAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCAGGAGUCACUUCAUCUCGAACUUUGGACUAACAAACCGCUU
((((((((((.((((((((((((.........)))))).((....)).))))))....))))))........(((((....))))).)))).........((((......))))...... (-29.60 = -30.40 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	19,176,831 – 19,176,951
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-41.38
Consensus MFE	-38.44
Energy contribution	-38.88
Covariance contribution	0.44
Combinations/Pair	1.02
Mean z-score	-1.47
Structure conservation index	0.93
SVM decision value	1.08
SVM RNA-class probability	0.912428
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19176831 120 - 23771897
UGGACUUGGACUUGGCCAUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
.(((..(.(((..((((((.((((....)))).))))))((((.((((((.((((((((((((.........)))))).((....)).))))))....)))))).))))))).)..))). ( -42.80)
>DroSec_CAF1 5348 120 - 1
UGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
..((((..((((.((((...))))))))))))(((.(.(((((.((((((.((((((((((((.........)))))).((....)).))))))....)))))).))))).).))).... ( -41.70)
>DroSim_CAF1 8385 120 - 1
UGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
..((((..((((.((((...))))))))))))(((.(.(((((.((((((.((((((((((((.........)))))).((....)).))))))....)))))).))))).).))).... ( -41.70)
>DroEre_CAF1 8088 120 - 1
UGGACUUGGACGUGGCCCUUGGCUGGUUGGUCAGUGGUCGGAAGGCAAGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
..(((..(.(((((.((....(((((((.((((.(.(((....))).).)))).((.((((((.........)))))).)).....))))).))...))))))).)...)))........ ( -39.20)
>DroYak_CAF1 10169 120 - 1
UGGACUUGGACUUGGCCCUUGGCUGGUUGGUCAGUGGUUGGAACGCCAGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
..(((..(((((..(((.((((((....)))))).)))..)...((((...((((((((((((.........)))))).((....)).))))))..))))....)))).)))........ ( -41.50)
>consensus
UGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCACAAGUAUGACCAUGUAAUGGCAUGUGUUUUGUCGACUUUCA
..((((..(((.(((((...))))))))))))(((.(.(((((.((((((.((((((((((((.........)))))).((....)).))))))....)))))).))))).).))).... (-38.44 = -38.88 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	19,176,871 – 19,176,991
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.17
Mean single sequence MFE	-47.90
Consensus MFE	-44.42
Energy contribution	-44.86
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.03
Structure conservation index	0.93
SVM decision value	2.97
SVM RNA-class probability	0.997966
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19176871 120 - 23771897
UCCCUUGUUAUGGCUGGUUCUUGGGAUCUGGCCAGGUCUUUGGACUUGGACUUGGCCAUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((.(((((((((..(.((....)).)..)))..((((((.((((..((((.((((...))))....))))...)))).))))))..)))))).))((((((.........)))))).. ( -49.10)
>DroSec_CAF1 5388 120 - 1
UCCCUUGUUAUGGCUGGUUCUUGGGAUCUGGCCAGUUCUUUGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((.(((((((((..(.((....)).)..))).((.((((.((((..((((.((((...))))....))))...)))).))))))..)))))).))((((((.........)))))).. ( -45.50)
>DroSim_CAF1 8425 120 - 1
UCCCUUGUUAUGGCUGGUUCUUGGGAUCUGGCCAGGUCUUUGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((.(((((((((..(.((....)).)..)))..((((((.((((..((((.((((...))))....))))...)))).))))))..)))))).))((((((.........)))))).. ( -49.10)
>DroEre_CAF1 8128 120 - 1
UCCCUUGUUAUAGCUGGUUCUUGGGAUCUGGCCAGGUCCUUGGACUUGGACGUGGCCCUUGGCUGGUUGGUCAGUGGUCGGAAGGCAAGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((.((((((.((((..(..(.((.((.(((((.((((........)))).)))))...)))).)..)..)))).(((....)))..)))))).))((((((.........)))))).. ( -48.00)
>DroYak_CAF1 10209 120 - 1
UCCCUUGUUAUAGCUGGUUCUUGGGAUCUGGCCAGGUCUUUGGACUUGGACUUGGCCCUUGGCUGGUUGGUCAGUGGUUGGAACGCCAGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((......((((..(((...(((.((.(((((((((....))))))).)).)))))..)))..))))((((.((((......)))).))))..))((((((.........)))))).. ( -47.80)
>consensus
UCCCUUGUUAUGGCUGGUUCUUGGGAUCUGGCCAGGUCUUUGGACUUGGACUUGGCCCUCGGCUGGUUGGUCAGUGGUCGGAAGGCAUGUGACAUGGGCAGACAUUCCACAAGUCUGCAC
..((.((((((.((((..(..(.((....((((((((((........)))))))))).....)).)..)..)))).(((....)))..)))))).))((((((.........)))))).. (-44.42 = -44.86 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:45 2006