Locus 2592

Sequence ID 3L_DroMel_CAF1
Location 7,202,724 – 7,203,001
Length 277
Max. P 0.634480
window4039 window4040 window4041

overview

Window 9

Location 7,202,724 – 7,202,844
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.35
Mean single sequence MFE -33.48
Consensus MFE -27.40
Energy contribution -27.46
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.82
SVM decision value 0.21
SVM RNA-class probability 0.634480
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7202724 120 - 23771897
CGCAUGCAUACUUUGGCAGGGUUAGAGUUAAAAAAAAAAAACGGCGUGACUCCAGCUGGAAGCCAAAUCCGGCAAUAACUGUCUUGAGUCGGGAAUCAGGAAUCACCAAGGAUGCGAUGA
..(((((((.((((((...(((((((((((................))))))..((((((.......))))))..))))).((((((........))))))....)))))))))).))). ( -34.19)
>DroSec_CAF1 16140 116 - 1
CGCAUGCAUACUUUGGCAGGGUUAGAGUUAAAA----AAAACGGCGUGACUCCAGCUGUAAGGCAAAUCCGGCAAUAACUGUCUUGAGUCGGGAAUCAGGAAUCACCAAGGAUGCGAUGA
(((((.(..((((((((...)))))))).....----......(.((((.(((.(((....)))...((((((..............)))))).....))).)))))..).))))).... ( -30.94)
>DroEre_CAF1 16597 113 - 1
CGCAUGCAUACUUUGGCAGGA-CAGAGUUAAA------AAGCGGCGUGACUCCAGCCGAAAGCCAAAUCCGGCAAUAACUGUCUUGAGUCAGGAAUCAGGAAUACCCAAGGAUGCGAUGA
..(((((((.(((((((((((-(((.......------...((((.((....))))))...(((......))).....))))))))..((........)).....)))))))))).))). ( -34.30)
>DroYak_CAF1 13667 113 - 1
CGCAUGCAUACUUUGGCAGGG-UGGAGUUAAA------AAGCCGCGUGACUCCAGCUGAAAGCCAAAUCCGGCAAUAACUGUCUUGAGUCAGGAAUCAGGAAUAAGCAAGGAUGCGAUGU
(((((((....((((((.((.-((((((((..------........)))))))).))....))))))....)).....((.((((((........))))))...)).....))))).... ( -34.50)
>consensus
CGCAUGCAUACUUUGGCAGGG_UAGAGUUAAA______AAACGGCGUGACUCCAGCUGAAAGCCAAAUCCGGCAAUAACUGUCUUGAGUCAGGAAUCAGGAAUAACCAAGGAUGCGAUGA
..(((((((.(((((((((.....((((((................))))))..((((...........)))).....)))((((((........))))))....)))))))))).))). (-27.40 = -27.46 +   0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,202,844 – 7,202,961
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.15
Mean single sequence MFE -24.85
Consensus MFE -16.41
Energy contribution -18.22
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.66
SVM decision value -0.03
SVM RNA-class probability 0.515955
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7202844 117 + 23771897
AAAAUUGUUUGUGAAAAUGUACCGGCAAAUAUUUGGAAUGAAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAUGUGCCAAAAAAAA---UGGCGCACAAAUAAGCA
....(((((((((((..(((((..((.....((((.(.....).))))...))..))..((..........)).)))..))).....((((((.......---))))))))))))))... ( -23.10)
>DroSec_CAF1 16256 109 + 1
AAAAUUGUUUGUGAAAAUGUGGCGGCAAAUAUUUGGAAUGAAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAAAUUCAGGAUGUGCAAAAAAAAA-----------AAAAAAGCA
....((((((((.....(((.((.(((..(((.....)))..)))...)).))).....))))))))....((.(((.........))))).........-----------......... ( -18.20)
>DroEre_CAF1 16710 116 + 1
AAAAUUGUUUGUGAAAAUGUGGCGGCAAAUAUUUGGAAUGAAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAA----UGGCGCACAAAUAAGAA
....(((((((((((..(((.((.(((..(((.....)))..)))...((.((......)).).)......)).)))..))).....((((((......----))))))))))))))... ( -28.50)
>DroYak_CAF1 13780 120 + 1
AAAAUUGUUUGUGCAAAUGUGGCGGCAAAUAUUUGAAAUAAAUGCAAAACGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAAAAAUUGGCGCACAAAUAAGCA
....((((((((((...(((.((.(((..(((.....)))..)))....(.((......)).)........)).)))............(((((........)))))))))))))))... ( -29.60)
>consensus
AAAAUUGUUUGUGAAAAUGUGGCGGCAAAUAUUUGGAAUGAAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAAA___UGGCGCACAAAUAAGCA
....((((((((.....(((.((.(((..(((.....)))..)))...)).))).....))))))))....................((((((..........))))))........... (-16.41 = -18.22 +   1.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,202,884 – 7,203,001
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.18
Mean single sequence MFE -25.77
Consensus MFE -17.94
Energy contribution -19.25
Covariance contribution 1.31
Combinations/Pair 1.08
Mean z-score -1.62
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.597449
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7202884 117 + 23771897
AAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAUGUGCCAAAAAAAA---UGGCGCACAAAUAAGCAAAAACCCACGGAAUGCCAUGCUUAUUUUGCUGAGAAAUUG
.........(((((((((((((....((.((((((.....))....(((((((.......---))))))).......)).....((...))..)))).)))))).)))))))........ ( -26.90)
>DroSec_CAF1 16296 109 + 1
AAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAAAUUCAGGAUGUGCAAAAAAAAA-----------AAAAAAGCAAAACCAAACGGAAUGCCUUGCUUAUUUGGCUGAGAAAUUG
.........(((((((((((((...(((.((..((.....)).((...(((.........-----------......)))...))........)))))))))))))).))))........ ( -20.06)
>DroEre_CAF1 16750 115 + 1
AAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAA----UGGCGCACAAAUAAGAAGAA-CCAACGAAAUUCCUCGCUUGUUUUGCUGAGAAAUUG
..(((......)))......(((.(((((((((((..((((..(...((((((......----))))))........(.....-.)..)..))))..)))).))))))))))........ ( -27.20)
>DroYak_CAF1 13820 119 + 1
AAUGCAAAACGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAAAAAUUGGCGCACAAAUAAGCAGAA-CCAACGAAAUUCCUCGCUUAUUUUGCUGAGAAAUUG
.........(((((((((((((...((((..((((.....)).....(((((((........)))))))........)).(..-....).....)))))))))).)))))))........ ( -28.90)
>consensus
AAUGCAAAGCGGCAAGUAAGCGGACAGGACAGCGACAGAUUCAGGAAGUGCCAAAAAAAA___UGGCGCACAAAUAAGCAAAA_CCAACGAAAUGCCUCGCUUAUUUUGCUGAGAAAUUG
.........(((((((((((((...(((.....((.....)).....((((((..........))))))..........................)))))))))))).))))........ (-17.94 = -19.25 +   1.31)

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 10:36:43 2006