Locus 932

Sequence ID	3R_DroMel_CAF1
Location	3,118,761 – 3,118,918
Length	157
Max. P	0.999876

overview

Window 5

Location	3,118,761 – 3,118,863
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	95.88
Mean single sequence MFE	-37.46
Consensus MFE	-32.14
Energy contribution	-32.98
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.54
Structure conservation index	0.86
SVM decision value	0.72
SVM RNA-class probability	0.831120
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118761 102 + 27905053
GCAGAUAAUUGCUGGGGACCGUCCUCCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUG
((((....)))).((((......))))(((((((((((((.....))))..(.(((((((....).))))))))))).(((((.....))))).)))))... ( -36.20)
>DroSec_CAF1 6410 102 + 1
GCAGAUAAUUGCUGGGGCCGGUCCUCCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUG
((((....))))..((((((....(((((((((..(((((.....)))))..)).))))....(((....))))))..(((((.....)))))..)))))). ( -38.70)
>DroSim_CAF1 11718 102 + 1
GCAGAUAAUUGCUGGGGCCGGUCCUCCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUG
((((....))))..((((((....(((((((((..(((((.....)))))..)).))))....(((....))))))..(((((.....)))))..)))))). ( -38.70)
>DroEre_CAF1 6178 100 + 1
GCAGAUAAUUGCUGGC--CCGUCCUCCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACGGUGGCCUG
((((....)))).(((--(...(((((((((((..(((((.....)))))..)).))))....(((....))))))..(((((.....))))))).)))).. ( -38.10)
>DroYak_CAF1 10092 102 + 1
GCAGAUAAUUGCUGCCCCCCGUCCACCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCACUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUG
((((.......)))).....(.((((.((((((..(((((.....)))))..)).))))..(((((....)))))...(((((.....))))).)))).).. ( -35.60)
>consensus
GCAGAUAAUUGCUGGGGCCCGUCCUCCGCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUG
((((....)))).((((......))))(((((((((((((.....))))..(.(((((((....).))))))))))..(((((.....)))))))))))... (-32.14 = -32.98 +   0.84)

alignment

secondary structure

dotplot

Window 6

Location	3,118,788 – 3,118,900
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	97.68
Mean single sequence MFE	-39.58
Consensus MFE	-37.54
Energy contribution	-37.78
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.01
Structure conservation index	0.95
SVM decision value	2.77
SVM RNA-class probability	0.996910
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118788 112 + 27905053
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGAAAGCUGAAGCUUUUCAGCGGCAUUUCAAAUGGACGA
.(((.....((((.....))))((((((((((((.((((....))).....(((((.....)))))).))))).....((((((....))))))))).))))...))).... ( -38.40)
>DroSec_CAF1 6437 112 + 1
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGA
.(((.....((((.....))))((((((((((((.((((....))).....(((((.....)))))).))))).....((((((....))))))))).))))...))).... ( -39.80)
>DroSim_CAF1 11745 112 + 1
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGA
.(((.....((((.....))))((((((((((((.((((....))).....(((((.....)))))).))))).....((((((....))))))))).))))...))).... ( -39.80)
>DroEre_CAF1 6203 112 + 1
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACGGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGA
.(((.....((((.....))))((((((((((((.((((....))).....(((((.....)))))).))))).....((((((....))))))))).))))...))).... ( -39.80)
>DroYak_CAF1 10119 112 + 1
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCACUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGAAAGCUAAAGCUCCUCAGCGGCAUUUCAAAUGGACGA
(((...(((((((.....)))).)))(((((((((((((....))).....(((((.....)))))))))))).((.(((....)))..))))))))............... ( -40.10)
>consensus
GCCACUUCUGUGUUAAUUACACGAGAGCUGGCCAGUGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGA
.(((.....((((.....))))((((((((((((.((((....))).....(((((.....)))))).))))).....((((((....))))))))).))))...))).... (-37.54 = -37.78 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	3,118,788 – 3,118,900
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	97.68
Mean single sequence MFE	-37.88
Consensus MFE	-35.94
Energy contribution	-35.66
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.95
SVM decision value	2.70
SVM RNA-class probability	0.996453
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118788 112 - 27905053
UCGUCCAUUUGAAAUGCCGCUGAAAAGCUUCAGCUUUCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCACUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............(((((((.((((.(((((((..(((....)))......))))))))))).)))).)))((((((.......(((.((((.....))))))))))))) ( -37.51)
>DroSec_CAF1 6437 112 - 1
UCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCACUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............((((((((.(((((((((((..(((....)))......)))))).......(((..(.....)..))))))))))((((.....))))...)))))) ( -37.40)
>DroSim_CAF1 11745 112 - 1
UCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCACUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............((((((((.(((((((((((..(((....)))......)))))).......(((..(.....)..))))))))))((((.....))))...)))))) ( -37.40)
>DroEre_CAF1 6203 112 - 1
UCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACCGUUCAUUAGCUGAACUUUCCGGCUGGCGCCACUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............((((((((.(((((((((((....(((....)))....)))))).......(((..(.....)..))))))))))((((.....))))...)))))) ( -36.00)
>DroYak_CAF1 10119 112 - 1
UCGUCCAUUUGAAAUGCCGCUGAGGAGCUUUAGCUUUCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCAGUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............(((((((((((((....))))...((((((((..(.(((((((.......))))))).).))))))))....)))((((.....))))...)))))) ( -41.10)
>consensus
UCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCACUGGCCAGCUCUCGUGUAAUUAACACAGAAGUGGC
...............(((((((.((((.(((((((..(((....)))......))))))))))).).((((((.......))))))(((.((((.....))))))))))))) (-35.94 = -35.66 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	3,118,823 – 3,118,918
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	97.68
Mean single sequence MFE	-33.54
Consensus MFE	-33.04
Energy contribution	-33.00
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.69
Structure conservation index	0.99
SVM decision value	2.20
SVM RNA-class probability	0.990120
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118823 95 + 27905053
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGAAAGCUGAAGCUUUUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
...(((((....(((((((((.....))))).((.((..((((((....))))))..)).)).))))...))).)).(((((.......))))). ( -34.40)
>DroSec_CAF1 6472 95 + 1
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
...(((((....(((((((((.....)))))....(((.....((((((....))))))))).))))...))).)).(((((.......))))). ( -33.40)
>DroSim_CAF1 11780 95 + 1
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
...(((((....(((((((((.....)))))....(((.....((((((....))))))))).))))...))).)).(((((.......))))). ( -33.40)
>DroEre_CAF1 6238 95 + 1
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACGGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
..((.(((((((....(((((.....)))))..))).))))..((((((....)))))).))...............(((((.......))))). ( -34.00)
>DroYak_CAF1 10154 95 + 1
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGAAAGCUAAAGCUCCUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
...(((((....(((((((((.....))))).((.((.(((.(((....)))..))))).)).))))...))).)).(((((.......))))). ( -32.50)
>consensus
UGGCGCCAGCCGGAAAGUUCAGCUAAUGAACAGUGGCCUGGAAGCUGAAGCUCUUCAGCGGCAUUUCAAAUGGACGACCGGCAAUAUGAGCCGGG
...(((((....(((((((((.....))))).((.((.(((((((....))).)))))).)).))))...))).)).(((((.......))))). (-33.04 = -33.00 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	3,118,823 – 3,118,918
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	97.68
Mean single sequence MFE	-34.14
Consensus MFE	-33.54
Energy contribution	-33.26
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-2.61
Structure conservation index	0.98
SVM decision value	4.34
SVM RNA-class probability	0.999876
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118823 95 - 27905053
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAAAAGCUUCAGCUUUCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((.((((.(((((((..(((....)))......))))))))))).)))).))).... ( -34.90)
>DroSec_CAF1 6472 95 - 1
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((.((((.(((((((..(((....)))......))))))))))).)))).))).... ( -34.30)
>DroSim_CAF1 11780 95 - 1
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((.((((.(((((((..(((....)))......))))))))))).)))).))).... ( -34.30)
>DroEre_CAF1 6238 95 - 1
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACCGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((.((((.(((((((....(((....)))....))))))))))).)))).))).... ( -32.90)
>DroYak_CAF1 10154 95 - 1
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAGGAGCUUUAGCUUUCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((..(((.(((((((..(((....)))......))))))))))..)))).))).... ( -34.30)
>consensus
CCCGGCUCAUAUUGCCGGUCGUCCAUUUGAAAUGCCGCUGAAGAGCUUCAGCUUCCAGGCCACUGUUCAUUAGCUGAACUUUCCGGCUGGCGCCA
.(((((.......)))))...............(((((((.((((.(((((((..(((....)))......))))))))))).)))).))).... (-33.54 = -33.26 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:45 2006