Locus 7030

Sequence ID	3L_DroMel_CAF1
Location	19,030,526 – 19,030,784
Length	258
Max. P	0.786673

overview

Window 2

Location	19,030,526 – 19,030,646
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.11
Mean single sequence MFE	-41.52
Consensus MFE	-24.34
Energy contribution	-24.90
Covariance contribution	0.56
Combinations/Pair	1.50
Mean z-score	-1.93
Structure conservation index	0.59
SVM decision value	0.57
SVM RNA-class probability	0.786673
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19030526 120 - 23771897
UUACAAGCACCCAACCAAAAGGGUCUGGAAUGGAGCAUUAAUCCACUUGAUGCGCCUGUAGGCAGGCAGUUUCUCCAGCCUCUCCAUUAUCAAUGGCAGCACCAGCAUUCCGGGCGCCGC
......((.(((..((....))(.((((..(((((((((((.....)))))))(((((....)))))......))))(((..............)))....))))).....))).))... ( -39.44)
>DroVir_CAF1 178892 120 - 1
UUACAAGCAGCCCACCAUGAGCGUUUGGAAGGGUGCAUUGAUCCAUUUGAUGCGCCUGUAUGCGGGCAACUUCUCCAGUCGCUGCAUAAUGACGGGCAGCAACAACAUGCCCGGCGCUGC
......(((((((...(((((((.(((((..(((((((..(.....)..))))(((((....))))).)))..))))).)))).)))......(((((.........))))))).))))) ( -53.60)
>DroGri_CAF1 168129 120 - 1
UUACAAGCAGCCCACCAUCAGUGUUUGGAAUGGCGCAUUGAUCCAUUUGAUGCGUGCAUAGGCGGGCAGCUUCUCCAGCCUCUGCAUAAUCACUGGCAGCACCAGCAUGCCGGGUGCAGC
......(((.(((......((((.(((.....((((((..(.....)..))))))(((.((((.((.((...)))).)))).))).))).))))((((((....)).))))))))))... ( -44.40)
>DroWil_CAF1 209789 120 - 1
UUACAAGCAGCCAACCAUUAGAGUCUGGAAUGGUGCAUUUGCCCAUUUGAUUUUCUUAUACACUGGGAAUUUCUCCAAUUUCUCCAUGAUCAAUGGCAACACCAACAUGCCAGGUGCUGC
......(((((..(((...((((..((((((((.((....))))))..((..((((((.....))))))..))))))..))))..........(((((.........))))))))))))) ( -33.20)
>DroMoj_CAF1 188828 120 - 1
UCACAAGCAGCCCACCAUGAGCGUUUGGAACGGCGCAUUGAUCCACUUGAUGCGUUUGUACGCUGGCAGUUUCUCCAGUCGCUCCAUGACAACGGGCAGUAGCAGCAUACCCGGGGCUGC
......(((((((..((((((((.(((((...((((((..(.....)..))))))((((......))))....))))).)))).))))....((((..((....))...))))))))))) ( -46.90)
>DroPer_CAF1 172645 120 - 1
UUACAAGCAUCCAACCAUCAGGGUUUGGAAAGGGGCAUUUAUCCAUUUGAUGCGGCUGUAGGCGGGCAGCUUUUCCAAUCGCUCCAUGAUCAAAGGCAGUACCAGCAUCCCGGGCGCUGC
.....(((..((....(((((((((((((((((.(((((.........)))))(.(((....))).)..)))))))))..)).)).))))....((.....))........))..))).. ( -31.60)
>consensus
UUACAAGCAGCCAACCAUCAGCGUUUGGAAUGGCGCAUUGAUCCAUUUGAUGCGCCUGUAGGCGGGCAGCUUCUCCAGUCGCUCCAUGAUCAAUGGCAGCACCAGCAUGCCGGGCGCUGC
......(((((...((...((((.(((((..((((((((((.....)))))))(((((....))))).)))..))))).))))..........(((.............))))).))))) (-24.34 = -24.90 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	19,030,566 – 19,030,670
Length	104
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.62
Mean single sequence MFE	-31.25
Consensus MFE	-23.32
Energy contribution	-23.02
Covariance contribution	-0.30
Combinations/Pair	1.22
Mean z-score	-1.31
Structure conservation index	0.75
SVM decision value	0.08
SVM RNA-class probability	0.575652
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19030566 104 - 23771897
AGUGGUCGUAG--AUGAUAA--AGUUACUUACAAGCACCCAACCAAAAGGGUCUGGAAUGGAGCAUUAAUCCACUUGAUGCGCCUGUAGGCAGGCAGUUUCUCCAGCC
.(((.(.((((--.((((..--.)))).)))).).)))((((((.....))).)))..(((((((((((.....)))))))(((((....)))))......))))... ( -30.40)
>DroSec_CAF1 164289 104 - 1
AGUGCUCGUAG--ACGGUAA--AGUUACUUACAAGCACCCAACCAAUAGGGUCUGGAAUGGAGCAUUGAUCCACUUGAUGCGCCUGUACGCAGGCAGUUUCUCCAGUU
.(((((.((((--((.....--.)))...))).)))))((((((.....))).)))..((((((((..(.....)..))))(((((....)))))......))))... ( -34.30)
>DroSim_CAF1 173360 102 - 1
AGUGGUGGUAG--AUGAU----AGUUACUUACAAGCACCCUACCAAUAAGGUCUGGAAUGGAGCAUUGAUCCACUUGAUGCGCCUGUACGCAGGCAGUUUCUCCAGCC
.....((((((--.((..----.((.....))...))..))))))....((.(((((.....((((..(.....)..))))(((((....)))))......))))))) ( -32.00)
>DroYak_CAF1 187004 101 - 1
AGUGGUCG-----AGGGUAA--AUUUACUUACAAGCACCCAACCAAUAGGGUCUGGAAUGGAGCAUUAAUCCACUUGAUGCGCCUGUAGGCAGGCAGUUUCUCCAGCC
..((((..-----.((((..--..............)))).))))....((.(((((.....(((((((.....)))))))(((((....)))))......))))))) ( -31.29)
>DroAna_CAF1 161408 101 - 1
-UU--ACGUAGUUAUCUU----AACGACUUACAAGCACCCAACCAUCAGGGUCUGGAAGGGAGCAUUUAUCCACUUGAUGCGCCUGUAGGCGGGCAGCUUCUCCAGCC
-..--..((((((.....----...))).)))....((((........))))(((((..((.(((((.........)))))(((((....)))))..))..))))).. ( -29.00)
>DroPer_CAF1 172685 106 - 1
AUUGCUUAUAG--GUGAUCGUGAUCCCCUUACAAGCAUCCAACCAUCAGGGUUUGGAAAGGGGCAUUUAUCCAUUUGAUGCGGCUGUAGGCGGGCAGCUUUUCCAAUC
..(((((..((--(.(((....))).)))...)))))(((((((.....)).)))))..((((((((.........)))))((((((......))))))..))).... ( -30.50)
>consensus
AGUGGUCGUAG__AUGAUAA__AGUUACUUACAAGCACCCAACCAAUAGGGUCUGGAAUGGAGCAUUAAUCCACUUGAUGCGCCUGUAGGCAGGCAGUUUCUCCAGCC
....................................((((........))))(((((..((.(((((((.....)))))))(((((....)))))..))..))))).. (-23.32 = -23.02 +  -0.30)

alignment

secondary structure

dotplot

Window 4

Location	19,030,670 – 19,030,784
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	84.52
Mean single sequence MFE	-30.17
Consensus MFE	-25.54
Energy contribution	-25.65
Covariance contribution	0.11
Combinations/Pair	1.18
Mean z-score	-1.64
Structure conservation index	0.85
SVM decision value	0.27
SVM RNA-class probability	0.663894
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19030670 114 - 23771897
GGUGCGCAUAAUCGAAGUGUCCAAGGAACACUGCUGUGGGAACAGGGCGCAGGCAGUGGGCACCAUGAAGCAAAGGCUAAACAUCAAAGA---AUAAAAAGAUCAGUUAAAGGAACA
(((((.(((..((..((((((....).)))))(((.((....)).)))...))..))).)))))....(((....)))............---........................ ( -29.00)
>DroSec_CAF1 164393 114 - 1
GGUGCGCAUAAUCGAAGUGUCCAAGGAACACUGCUGUGGGAACAGGGCGCAGGCAGUGGGCACCAUGAAGCAAAGGCUAAACAUCAAAGA---AUUGCAAGAUUAGCUAAAGGAACU
(((((.(((..((..((((((....).)))))(((.((....)).)))...))..))).)))))..........((((((.(..(((...---.)))...).))))))......... ( -31.80)
>DroSim_CAF1 173462 114 - 1
GGUGCGCAUAAUCGAAGUGUCCAAGGAACACUGCUGUGGGAACAGGGCGCAGGCAGUGGGCACCAUGAAGCAAAGGCUAAACAUCAAAUA---AGUGCAAGAUUAGCUAAAGGAUCU
..(((((....(((..(((((((..(.....((((.((....)).))))....)..)))))))..)))(((....)))............---.)))))(((((........))))) ( -32.30)
>DroEre_CAF1 165631 113 - 1
GGUGCGCAUAAUCGAAGUGUCCAAGGAACACUGCUGUGGAAACAGGGCGCAGGCAGUGGGCACCAUGAAGCAAAGGCUAAA-GUUAACGA---AUAGAUAGAUUAGCUGAAGGAACU
(((((.(((..((..((((((....).)))))(((.((....)).)))...))..))).)))))..........((((((.-.(((.(..---...).))).))))))......... ( -33.30)
>DroYak_CAF1 187105 114 - 1
GGUGCGCAUAAUCGAAGUGUCCAAAGAACACUGCUGGGGAAACAGGGCGCAGGCAGUGGGCACCAUAAAGCAGAGGCUAAACAUUAAAGA---AAAGAUAUAUUAGCUGAAAGAACU
(((((.(((..((..(((((.......)))))(((..(....)..)))...))..))).)))))..........((((((..(((.....---...)))...))))))......... ( -28.10)
>DroAna_CAF1 161509 114 - 1
GGUGCGCAUGGUGGACGUGUCCAAGGAGCAUUGUUGCGGGAACAGAGCGCAGGCAGAGGGCACCAUGAAGCAGAGGCUGAAA-UUGAUAAGAAAUUUUAUUAUUA--UUGAGGAAUA
..(((.(((((((..(.((((....(.((.(((((.....))))).)).).))))..)..)))))))..)))....((.((.-.(((((((....)))))))...--)).))..... ( -26.50)
>consensus
GGUGCGCAUAAUCGAAGUGUCCAAGGAACACUGCUGUGGGAACAGGGCGCAGGCAGUGGGCACCAUGAAGCAAAGGCUAAACAUCAAAGA___AUAGAAAGAUUAGCUAAAGGAACU
(((((.(((......((((((....).)))))(((.((....)).))).......))).)))))....(((....)))....................................... (-25.54 = -25.65 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:58 2006