Locus 7230

Sequence ID	3L_DroMel_CAF1
Location	19,379,127 – 19,379,227
Length	100
Max. P	0.780050

overview

Window 4

Location	19,379,127 – 19,379,227
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	92.18
Mean single sequence MFE	-30.42
Consensus MFE	-25.34
Energy contribution	-26.14
Covariance contribution	0.80
Combinations/Pair	1.07
Mean z-score	-1.31
Structure conservation index	0.83
SVM decision value	0.10
SVM RNA-class probability	0.581327
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19379127 100 + 23771897
AAUUCCGGUCCAGGAGGACCAAAGCCAGGUUCCCAGCCCGGUCUUGCACCUGAUCCAGCGGCAGUUAACCCCAACUGCAGCUAGUUAGUUAGUUUCUGGC
......(((((....)))))...((((((..(...((........))..(((((..(((.((((((......)))))).))).)))))...)..)))))) ( -32.80)
>DroSec_CAF1 11986 100 + 1
AAUCCCGGUCCAGGAGGACCAAAGCCAGGUUCCCAGCCCGGUCUUGCACCUGAUCCAGCGGCAGUUAACCCUAACUGCAGCUAGUUAGUUAGUUUCUGGC
......(((((....)))))...((((((..(...((........))..(((((..(((.(((((((....))))))).))).)))))...)..)))))) ( -34.10)
>DroSim_CAF1 9329 100 + 1
AAUCCCGGUCCAGGAGGACCAAAGCCAGGUACCCAGCCCGGGCNUGCACCAAAUCCAGCGGCAGUUAACCCCAACNGCAGCAAGUUAGUUAGUUUCUGGC
......(((((....)))))...(((((((((((.....)))..)))..........((.((.(((......))).)).))..............))))) ( -26.60)
>DroEre_CAF1 15781 96 + 1
AAUCCCGGUCCAG---GACUAAAGCCAGGUUCCCAGCCCGGACUUUCACCUGAUCCAGA-GCAGUUAACCCCAACUGCAGCUAGUUAGUUAGUUUCUGGC
..........(((---(...((((((.(((.....))).)).))))..))))..(((((-((((((......))))))((((((....))))))))))). ( -28.70)
>DroYak_CAF1 46200 97 + 1
AAUCCCGGUCCAG---GACUAAAGCCAGGUUCCCAGCCCGGACUUUCACCUGAUCCAGCGGCAGUUAACCCCAACUGCAGCUAGUUAGUUAGUUUCUGGC
......((..(((---(...((((((.(((.....))).)).))))..))))..))(((.((((((......)))))).))).(((((.......))))) ( -29.90)
>consensus
AAUCCCGGUCCAGGAGGACCAAAGCCAGGUUCCCAGCCCGGACUUGCACCUGAUCCAGCGGCAGUUAACCCCAACUGCAGCUAGUUAGUUAGUUUCUGGC
......(((((....)))))...((((((..(((.....))........(((((..(((.((((((......)))))).))).)))))...)..)))))) (-25.34 = -26.14 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	19,379,127 – 19,379,227
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.18
Mean single sequence MFE	-36.22
Consensus MFE	-30.54
Energy contribution	-31.62
Covariance contribution	1.08
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.84
SVM decision value	0.55
SVM RNA-class probability	0.780050
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19379127 100 - 23771897
GCCAGAAACUAACUAACUAGCUGCAGUUGGGGUUAACUGCCGCUGGAUCAGGUGCAAGACCGGGCUGGGAACCUGGCUUUGGUCCUCCUGGACCGGAAUU
(((((...(((.((..(((((.(((((((....))))))).)))))....(((.....))).)).)))....)))))((((((((....))))))))... ( -40.20)
>DroSec_CAF1 11986 100 - 1
GCCAGAAACUAACUAACUAGCUGCAGUUAGGGUUAACUGCCGCUGGAUCAGGUGCAAGACCGGGCUGGGAACCUGGCUUUGGUCCUCCUGGACCGGGAUU
(((((...(((.((..(((((.(((((((....))))))).)))))....(((.....))).)).)))....)))))((((((((....))))))))... ( -39.50)
>DroSim_CAF1 9329 100 - 1
GCCAGAAACUAACUAACUUGCUGCNGUUGGGGUUAACUGCCGCUGGAUUUGGUGCANGCCCGGGCUGGGUACCUGGCUUUGGUCCUCCUGGACCGGGAUU
((((((..(...(((((........)))))(((.....)))...)..)))))).....(((((((..(....)..)))).(((((....))))))))... ( -34.50)
>DroEre_CAF1 15781 96 - 1
GCCAGAAACUAACUAACUAGCUGCAGUUGGGGUUAACUGC-UCUGGAUCAGGUGAAAGUCCGGGCUGGGAACCUGGCUUUAGUC---CUGGACCGGGAUU
((.((...........)).)).(((((((....)))))))-(((((.(((((..((((.(((((.......)))))))))...)---)))).)))))... ( -31.60)
>DroYak_CAF1 46200 97 - 1
GCCAGAAACUAACUAACUAGCUGCAGUUGGGGUUAACUGCCGCUGGAUCAGGUGAAAGUCCGGGCUGGGAACCUGGCUUUAGUC---CUGGACCGGGAUU
.((.............(((((.(((((((....))))))).))))).(((((..((((.(((((.......)))))))))...)---))))...)).... ( -35.30)
>consensus
GCCAGAAACUAACUAACUAGCUGCAGUUGGGGUUAACUGCCGCUGGAUCAGGUGCAAGACCGGGCUGGGAACCUGGCUUUGGUCCUCCUGGACCGGGAUU
(((((...(((.((..(((((.(((((((....))))))).)))))....((.......)).)).)))....)))))((((((((....))))))))... (-30.54 = -31.62 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:39 2006