Locus 3718

Sequence ID X_DroMel_CAF1
Location 9,910,578 – 9,910,750
Length 172
Max. P 0.938516
window6092 window6093 window6094

overview

Window 2

Location 9,910,578 – 9,910,690
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -30.65
Consensus MFE -19.06
Energy contribution -19.62
Covariance contribution 0.56
Combinations/Pair 1.22
Mean z-score -1.74
Structure conservation index 0.62
SVM decision value 0.65
SVM RNA-class probability 0.812548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9910578 112 + 22224390
AUCGGCGAUU--GAAGCAACAAGCGGC--GAAAUAAACUUUUGCUGA--UGACACCCAGCUGGGAUAUUGAAGCAGAAUGGCCACAAAUGGAAAAAUGGAAGAGUUCAAGGGUCGCCG
..((((((((--...((..(((.((((--((((.....)))))))).--.....(((....)))...)))..)).((((..(((............)))....))))...)))))))) ( -31.40)
>DroPse_CAF1 10207 106 + 1
GGCAGCAAGCAACAAGCAACAAGCAACUCAACAUAGAGGCAUCCUGAAACAGGACCCUGCUGAGAGAUCGAAUCCAAGAGGUUUUCAAGGCAA-AA-------CUUU----GCCCCCU
(((((...((.....((.....))..(((......))))).(((((...)))))..)))))(((((.((........))..)))))..(((((-..-------..))----))).... ( -25.60)
>DroSec_CAF1 7984 112 + 1
AUCGGCGAUU--GAAGCAACAAGCGGC--GAAAUAAACUUUUGCCGA--UGGCACCCAGCUGGGAUAUCGAAGCAGAAUGGCCACAAAUGGAAAAAUGGAAGAGUUCAAGGGUCGCCG
..((((((..--...((......((((--((((.....)))))))).--..)).(((.(((..(....)..))).((((..(((............)))....))))..))))))))) ( -33.70)
>DroSim_CAF1 8028 112 + 1
AUCGGCGAUU--GAAGCAACAAGCGGC--GAAAUAAACUUUUGCUGA--UGGCACCCAGCUGGGAUAUCGAAGCAGAAUGGCCACAAAUGGAAAAAUGGAAGAGUUCAAGGGUCGCCG
..((((((..--...((......((((--((((.....)))))))).--..)).(((.(((..(....)..))).((((..(((............)))....))))..))))))))) ( -31.50)
>DroEre_CAF1 8296 103 + 1
AUCGGCGAUU--GAAGCAACAAGCGGC--GAAAUAAACU-UUGCUGA--UGGCACCCAGCUGGGAUAUCGAAACAGAAUGGCCACAAAU--------GGAAGAGUUCAAGGGUCGCCG
..((((((((--((.((......((((--(((......)-)))))).--..)).(((....)))...))......((((..(((....)--------))....))))...)))))))) ( -30.60)
>DroYak_CAF1 7927 104 + 1
AUCGGCGAUU--GAAGCAACAAGCGGC--GAAAUAAACUUUUGCUGA--UGGCACCCAGCUGGGAUAUCGAAACAGAAUGGCCACAAAU--------GGAAGAGUUCAAGGGUCGCCG
..((((((((--((.((......((((--((((.....)))))))).--..)).(((....)))...))......((((..(((....)--------))....))))...)))))))) ( -31.10)
>consensus
AUCGGCGAUU__GAAGCAACAAGCGGC__GAAAUAAACUUUUGCUGA__UGGCACCCAGCUGGGAUAUCGAAGCAGAAUGGCCACAAAUGGAA_AA_GGAAGAGUUCAAGGGUCGCCG
..((((((((..(((((.....))(((..............((((.....))))(((....)))................))).....................)))...)))))))) (-19.06 = -19.62 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,910,612 – 9,910,730
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 93.34
Mean single sequence MFE -27.81
Consensus MFE -27.68
Energy contribution -27.12
Covariance contribution -0.56
Combinations/Pair 1.11
Mean z-score -1.14
Structure conservation index 1.00
SVM decision value 0.67
SVM RNA-class probability 0.817420
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9910612 118 - 22224390
CACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCAUUCUGCUUCAAUAUCCCAGCUGGGUGUCAUCAGCAAAA
(((((((..((((((....)))))).(((..(((((.....)))))..)))..................))))))).......((((.......(((....))).......))))... ( -27.74)
>DroSec_CAF1 8018 118 - 1
CACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCAUUCUGCUUCGAUAUCCCAGCUGGGUGCCAUCGGCAAAA
(((((((..((((((....)))))).(((..(((((.....)))))..)))..................))))))).......(((..((((..(((....)))....)))))))... ( -28.60)
>DroSim_CAF1 8062 118 - 1
CACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCAUUCUGCUUCGAUAUCCCAGCUGGGUGCCAUCAGCAAAA
(((((((..((((((....)))))).(((..(((((.....)))))..)))..................))))))).......((((..(((..(((....)))....)))))))... ( -27.80)
>DroEre_CAF1 8330 109 - 1
CACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCC--------AUUUGUGGCCAUUCUGUUUCGAUAUCCCAGCUGGGUGCCAUCAGCAA-A
(((((((..((((((....)))))).(((..(((((.....)))))..)))..........--------)))))))......................(((((......)))))..-. ( -26.30)
>DroYak_CAF1 7961 110 - 1
CACAGAUAAUCAAGUUGAUGCUUGAAAAGUUUCGCCCCUCCGGCGACCCUUGAACUCUUCC--------AUUUGUGGCCAUUCUGUUUCGAUAUCCCAGCUGGGUGCCAUCAGCAAAA
(((((((..((((((....)))))).(((..(((((.....)))))..)))..........--------)))))))......................(((((......))))).... ( -28.60)
>consensus
CACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCAUUCUGCUUCGAUAUCCCAGCUGGGUGCCAUCAGCAAAA
(((((((..((((((....)))))).(((..(((((.....)))))..)))..................))))))).......((((.......(((....))).......))))... (-27.68 = -27.12 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,910,650 – 9,910,750
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 93.95
Mean single sequence MFE -22.78
Consensus MFE -21.50
Energy contribution -21.54
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.94
SVM decision value 1.29
SVM RNA-class probability 0.938516
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9910650 100 - 22224390
CUCGACUUCAGCUCGACUUGCACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCA
...((.((((((((((((((..........)))))))).)))....(((..(((((.....)))))..)))))).))..((((..........))))... ( -21.90)
>DroSec_CAF1 8056 100 - 1
CUCGACUUCAGCUCGACUUGCACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCA
...((.((((((((((((((..........)))))))).)))....(((..(((((.....)))))..)))))).))..((((..........))))... ( -21.90)
>DroSim_CAF1 8100 100 - 1
CUCGACUUCAGCUCGACUUGCACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCA
...((.((((((((((((((..........)))))))).)))....(((..(((((.....)))))..)))))).))..((((..........))))... ( -21.90)
>DroEre_CAF1 8367 92 - 1
CGCGACUUCAGCUCGACUUGCACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCC--------AUUUGUGGCCA
.((.((((((((((((((((..........)))))))).)).))))(((..(((((.....)))))..)))..........--------....)).)).. ( -24.10)
>DroYak_CAF1 7999 92 - 1
CUCGACUUCAGCUCGACUUGCACAGAUAAUCAAGUUGAUGCUUGAAAAGUUUCGCCCCUCCGGCGACCCUUGAACUCUUCC--------AUUUGUGGCCA
.(((((....).))))....(((((((..((((((....)))))).(((..(((((.....)))))..)))..........--------))))))).... ( -24.10)
>consensus
CUCGACUUCAGCUCGACUUGCACAGAUACUCAAGUUGAUGCUUGAAAAGUUUUGCCCCUCCGGCGACCCUUGAACUCUUCCAUUUUUCCAUUUGUGGCCA
.(((((....).))))....(((((((..((((((....)))))).(((..(((((.....)))))..)))..................))))))).... (-21.50 = -21.54 +   0.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:30 2006