Locus 2411

Sequence ID 3L_DroMel_CAF1
Location 6,783,586 – 6,783,733
Length 147
Max. P 0.897076
window3724 window3725 window3726

overview

Window 4

Location 6,783,586 – 6,783,705
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 81.22
Mean single sequence MFE -36.68
Consensus MFE -24.32
Energy contribution -24.36
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.66
SVM decision value 1.00
SVM RNA-class probability 0.897076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6783586 119 + 23771897
UUUUUAGCCCAAAUUUUCGACAUUGAAUUUCCAGGAUCGAACUUUAAUUUCAGUGUGGUCCGCGGCACAACAUAUUUGCGCUGUGGCACCGUGGUCAACCAGGGCACUUACGCAGUGCC
......((((.........((((((((.((..((.......))..)).))))))))((((((((((.(((.....))).))))))).))).(((....))))))).............. ( -37.00)
>DroSec_CAF1 44363 105 + 1
UUUUAAACCCAAAUUUUC--------------GGUAUCGAACUUUAAUCUCAGUGUGGUCCGCGGCACAACAUAUUUGCGCUGUGGCACCGUGGUCAACCAGGGCACUUACGCAGUGCC
......((((.....(((--------------(....))))...............((((((((((.(((.....))).))))))).)))).))).......((((((.....)))))) ( -29.30)
>DroSim_CAF1 47917 119 + 1
UUUUAAACCAAAAUUUUCGAGAUUGAAUUUUUGGUAUCGAACUUUAAUCUCAGUGUGGUCCGCGGCACAACAUAUUUGCGCUGUGGCACGGUGGUCAACCAGGGCACUUACGCAGUGCC
......(((.........(((((((((..((((....)))).)))))))))...(((..(((((((.(((.....))).)))))))))))))((....))..((((((.....)))))) ( -37.20)
>DroEre_CAF1 57687 113 + 1
UUUGUAGACCAGCACUUUGAAA-UGAUUUCCUA--AUC---AUUUAAUCUCAGUGUGGUCCGCGGCACAACAUAUUUGCGCUGUGGUCCCGUGGUCAACCAGGGCACUUACGCAGUGCC
......((((((((((..((((-(((((....)--)))---)))...))..)))))((.(((((((.(((.....))).))))))).))..)))))......((((((.....)))))) ( -42.40)
>DroYak_CAF1 47963 113 + 1
UUUGUCGACUACCAUUUUGAAA-UGAGUGUUCA--AUG---AUUUAAUCUCAGUGUGGUCAGCGGCACAACAUAUUUGCGCUGUGGUCCCGUGGUCAACCGGGGCACUUACGCAGUGCC
..(((((.(((((((.((((..-(((((.....--...---)))))...)))).))))).)))))))..........((((((((((((((.(.....))))))).....)))))))). ( -37.50)
>consensus
UUUUUAGCCCAAAUUUUCGAAA_UGAAUUUCCAG_AUCGAACUUUAAUCUCAGUGUGGUCCGCGGCACAACAUAUUUGCGCUGUGGCACCGUGGUCAACCAGGGCACUUACGCAGUGCC
....................................................((((.(....).)))).........((((((((...((.(((....))).))......)))))))). (-24.32 = -24.36 +   0.04)

alignment

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secondary structure

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Window 5

Location 6,783,586 – 6,783,705
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -35.12
Consensus MFE -22.56
Energy contribution -22.96
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.64
SVM decision value 0.47
SVM RNA-class probability 0.749534
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6783586 119 - 23771897
GGCACUGCGUAAGUGCCCUGGUUGACCACGGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAAAUUAAAGUUCGAUCCUGGAAAUUCAAUGUCGAAAAUUUGGGCUAAAAA
((((((.....)))))).(((....))).(((.((.(.((((((.....)))))).).)))))...((.(((((....((((((..(((....)))..))))))))))).))....... ( -34.00)
>DroSec_CAF1 44363 105 - 1
GGCACUGCGUAAGUGCCCUGGUUGACCACGGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGUUCGAUACC--------------GAAAAUUUGGGUUUAAAA
((((((.....)))))).(((....))).(((.((.(.((((((.....)))))).).)))))..(((.(((((....((((....)--------------)))))))).)))...... ( -31.40)
>DroSim_CAF1 47917 119 - 1
GGCACUGCGUAAGUGCCCUGGUUGACCACCGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGUUCGAUACCAAAAAUUCAAUCUCGAAAAUUUUGGUUUAAAA
((((((.....))))))......((((((((((.(((((((......))))))).))))).......(((((((.((...............)).))))))).......)))))..... ( -34.46)
>DroEre_CAF1 57687 113 - 1
GGCACUGCGUAAGUGCCCUGGUUGACCACGGGACCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAU---GAU--UAGGAAAUCA-UUUCAAAGUGCUGGUCUACAAA
(((((.(((((.((((..(((((........)))))..))))...))))).)))))(..(((((((((..((...(((---(((--(....)))))-))))..)))).)))))..)... ( -43.10)
>DroYak_CAF1 47963 113 - 1
GGCACUGCGUAAGUGCCCCGGUUGACCACGGGACCACAGCGCAAAUAUGUUGUGCCGCUGACCACACUGAGAUUAAAU---CAU--UGAACACUCA-UUUCAAAAUGGUAGUCGACAAA
((((((.....))))))...(((((((((((...(((((((......)))))))))).))((((...((((((.....---...--.........)-)))))...)))).))))))... ( -32.63)
>consensus
GGCACUGCGUAAGUGCCCUGGUUGACCACGGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGUUCGAU_CUAAAAAUUCA_UUUCGAAAAUUUGGGCUAAAAA
((((((.....))))))..(((...((.(((...(((((((......)))))))))).)))))........................................................ (-22.56 = -22.96 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,783,626 – 6,783,733
Length 107
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 92.96
Mean single sequence MFE -38.08
Consensus MFE -32.18
Energy contribution -33.07
Covariance contribution 0.89
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.84
SVM decision value 0.26
SVM RNA-class probability 0.657778
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6783626 107 - 23771897
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCUGGUUGACCACGGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAAAUUAAAGU
.((((((.((((.((((((((((..(((((((((.....))))))..))))))))...((((....)))).........))))).)))))))...)))......... ( -40.30)
>DroSec_CAF1 44389 107 - 1
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCUGGUUGACCACGGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGU
.((((((.((((.((((((((((..(((((((((.....))))))..))))))))...((((....)))).........))))).)))))))...)))......... ( -40.30)
>DroSim_CAF1 47957 107 - 1
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCUGGUUGACCACCGUGCCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGU
.((((((.((((.((((((((...((((((((((.....))))))..))))....))))))))...((((((.....))))))..)))))))...)))......... ( -41.80)
>DroEre_CAF1 57722 106 - 1
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCUGGUUGACCACGGGACCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAU-
.((((((.((((.(((.((((((..(((((((((.....))))))..))))))))).......((((((......))))))))).)))))))...)))........- ( -38.40)
>DroYak_CAF1 47998 106 - 1
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCCGGUUGACCACGGGACCACAGCGCAAAUAUGUUGUGCCGCUGACCACACUGAGAUUAAAU-
.((((((((....))).(((((..(((.(((((.(((((.((((((((........))))......))))...))))).))))))))))))))).)))........- ( -36.30)
>DroAna_CAF1 54834 107 - 1
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGGACUGCGUAAGUGCCCUGGUUGACCACGAGACCACAGCGCAAAUAUGUUGUAGGGCGAAUUACACAGAAAGAAAAUU
......(((((((..(.((((((..((((((.(.((....))).)))))))))))).)...))((((((......)))))))))))..................... ( -31.40)
>consensus
AUCAUGGCUCUGGGGCAUGGUUAAAGCCGGCACUGCGUAAGUGCCCUGGUUGACCACGGGACCACAGCGCAAAUAUGUUGUGCCGCGGACCACACUGAGAUUAAAGU
.((((((.((((.(((.((((((..(((((((((.....))))))..))))))))).......((((((......))))))))).)))))))...)))......... (-32.18 = -33.07 +   0.89)

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 10:31:45 2006