Locus 7677

Sequence ID	3L_DroMel_CAF1
Location	20,581,303 – 20,581,503
Length	200
Max. P	0.969398

overview

Window 4

Location	20,581,303 – 20,581,423
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-38.24
Consensus MFE	-33.86
Energy contribution	-33.86
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.89
SVM decision value	0.35
SVM RNA-class probability	0.700108
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20581303 120 + 23771897
GUUCGUGGCCGUUUCUGUGCUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGG
..(((((.(((..((..(((((((((.(.((((....)))).)))))).....(((((((((((.....)))).....)))))))......))))...)).))))))))........... ( -39.40)
>DroSec_CAF1 25995 120 + 1
GUUCGUGGCCGUUUCUGUGCUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGG
..(((((.(((..((..(((((((((.(.((((....)))).)))))).....(((((((((((.....)))).....)))))))......))))...)).))))))))........... ( -39.40)
>DroAna_CAF1 47540 109 + 1
GUUCGU------UU-----CUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGG
((((((------(.-----..(((((.(.((((....)))).))))))..((((((((((((((.....)))).....))))))).((((........))))...)))..)))))))... ( -33.90)
>DroSim_CAF1 19556 120 + 1
GUUCGUGGCCGUUUCUGUGCUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGG
..(((((.(((..((..(((((((((.(.((((....)))).)))))).....(((((((((((.....)))).....)))))))......))))...)).))))))))........... ( -39.40)
>DroEre_CAF1 19183 120 + 1
GUUCGUGGCCGUUUCUGUGCUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGG
..((((.((((..((..(((((((((.(.((((....)))).)))))).....(((((((((((.....)))).....)))))))......))))...))..)).)).))))........ ( -39.10)
>consensus
GUUCGUGGCCGUUUCUGUGCUGUUAGAUGAAGCGCGAGUUUGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGG
((((((...............(((((.(.((((....)))).))))))..((((((((((((((.....)))).....))))))).((((........))))...)))...))))))... (-33.86 = -33.86 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	20,581,343 – 20,581,463
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-34.00
Consensus MFE	-31.60
Energy contribution	-31.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.93
SVM decision value	0.67
SVM RNA-class probability	0.816438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20581343 120 + 23771897
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGAACCUCCCCGAAGU
...(((.....(((((((((((((.....)))).....))))))..((((........)))))))((((((((((...(....))))))))))).........))).............. ( -34.00)
>DroSec_CAF1 26035 120 + 1
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGU
...(((.....(((((((((((((.....)))).....))))))..((((........)))))))((((((((((...(....))))))))))).........))).............. ( -34.00)
>DroAna_CAF1 47569 119 + 1
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGUCGC-CCCUUUGGU
.(((((....((.(((((((((((.....)))).....))))))).((((........)))))).((((((((((...(....))))))))))).........)))))((-(.....))) ( -36.20)
>DroSim_CAF1 19596 120 + 1
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGU
...(((.....(((((((((((((.....)))).....))))))..((((........)))))))((((((((((...(....))))))))))).........))).............. ( -34.00)
>DroEre_CAF1 19223 118 + 1
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGAC-CUCCCCG-AGU
......(((.((.(((((((((((.....)))).....))))))).((((........)))).(((.((((((((...(....)))))))))((((....))))....-)))..))-))) ( -31.80)
>consensus
UGACUGACUACGCCUGGCCAAAUGUUAGUCAUUAAUUAUGGCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGU
...........(((((((((((((.....)))).....))))))).((((........))))...))((((((((...(....)))))))))((((....))))................ (-31.60 = -31.60 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	20,581,343 – 20,581,463
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-39.52
Consensus MFE	-34.62
Energy contribution	-35.02
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.79
Structure conservation index	0.88
SVM decision value	1.64
SVM RNA-class probability	0.969398
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20581343 120 - 23771897
ACUUCGGGGAGGUUCUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCGCCGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
.(((....))).............((((((((((((..(...)..))))))))(((((((((........))))..((((((.....((((.....))))))))))))))).)))).... ( -39.70)
>DroSec_CAF1 26035 120 - 1
ACUUCGGGGAGGGUCUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCGCCGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
.(....).((..(.((((((....))))((((((((..(...)..))))))))(((((((((........))))..((((((.....((((.....))))))))))))))))).)..)). ( -39.90)
>DroAna_CAF1 47569 119 - 1
ACCAAAGGG-GCGACUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCUCGGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
.((....))-..(((((.(......(((((((((((..(...)..))))))))).))(((((........)))))(((((((.....((((.....))))))))))).....).))))). ( -40.20)
>DroSim_CAF1 19596 120 - 1
ACUUCGGGGAGGGUCUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCGCCGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
.(....).((..(.((((((....))))((((((((..(...)..))))))))(((((((((........))))..((((((.....((((.....))))))))))))))))).)..)). ( -39.90)
>DroEre_CAF1 19223 118 - 1
ACU-CGGGGAG-GUCUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCUCGGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
...-...((((-(((((.(((...((((((((((((..(...)..))))))))).)))......))).)))))))))(((((.....((((.....))))))))).(((.......))). ( -37.90)
>consensus
ACUUCGGGGAGGGUCUGUCAAUAAUGACGAUGAUGAGUCGCCGGUUCAUCAUCGCGCCGAUCAUUUGCUGGAUCUCUGGCCAUAAUUAAUGACUAACAUUUGGCCAGGCGUAGUCAGUCA
........................((((((((((((..(...)..))))))))((((.((((........)))).(((((((.....((((.....))))))))))))))).)))).... (-34.62 = -35.02 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	20,581,383 – 20,581,503
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-34.82
Consensus MFE	-27.74
Energy contribution	-28.74
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.80
SVM decision value	0.21
SVM RNA-class probability	0.633342
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20581383 120 + 23771897
GCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGAACCUCCCCGAAGUCCGCAGACCCCGCGAAACAUGUUCUUUAAACUUUGGCCUU
(((((((.....((......((((...((((((((...(....)))))))))((((....)))).........)))).(((....)))...))(((.....)))......)))))))... ( -33.00)
>DroSec_CAF1 26075 120 + 1
GCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGUCCGCGGACCCCGCGAAACAUGUUCUUUAAACUUUGGCCUU
(((((((....((...(((.((((...((((((((...(....)))))))))((((....)))).........))))....(((((...)))))...)))...)).....)))))))... ( -37.10)
>DroAna_CAF1 47609 118 + 1
GCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGUCGC-CCCUUUGGUCCUCCUCCCCCUCC-AGUGUGUUCUUUAAACUUUGGCCUU
(((((((....((((..((....(((.((.(((.((..(((((((.......((((....))))))))))-)...)).))).)))))......)-)...)))).......)))))))... ( -31.41)
>DroSim_CAF1 19636 120 + 1
GCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGUCCGCGGACCCCGCGAAACAUGUUCUUUAAACUUUGGCCUU
(((((((....((...(((.((((...((((((((...(....)))))))))((((....)))).........))))....(((((...)))))...)))...)).....)))))))... ( -37.10)
>DroEre_CAF1 19263 118 + 1
GCCAGAGAUCCAGCAAAUGAUCCGAGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGAC-CUCCCCG-AGUCCGCGGACCCCGCGAAACAUGUUCUUUAAACUUUGGCCUU
(((((((...((.....))....((((((((((((...(....)))))))))((((....)))).(((-.......-.)))(((((...)))))......))))......)))))))... ( -35.50)
>consensus
GCCAGAGAUCCAGCAAAUGAUCGGCGCGAUGAUGAACCGGCGACUCAUCAUCGUCAUUAUUGACAGACCCUCCCCGAAGUCCGCGGACCCCGCGAAACAUGUUCUUUAAACUUUGGCCUU
(((((((.....(..((((((....((((((((((...(....))))))))))).))))))..).................((((.....))))................)))))))... (-27.74 = -28.74 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:35 2006