Locus 4397

Sequence ID 3L_DroMel_CAF1
Location 12,877,161 – 12,877,277
Length 116
Max. P 0.975837
window6817 window6818

overview

Window 7

Location 12,877,161 – 12,877,277
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.58
Mean single sequence MFE -40.85
Consensus MFE -25.38
Energy contribution -26.88
Covariance contribution 1.51
Combinations/Pair 1.45
Mean z-score -2.71
Structure conservation index 0.62
SVM decision value 1.76
SVM RNA-class probability 0.975837
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12877161 116 + 23771897
---GGCAGUAAAAGUUCGUGGCCGGUGAUGCGUUUCAUGGCUAUGUACUGGCCGCAAAUCUGCGGUAGAAAGAUCUCCGAUUCGUGGACAUUACAUUCUACGAGCACUACGCUGCCAUU
---((((((........((((((((((..((........))....)))))))))).....(((((.(((....)))))...(((((((........))))))))))....))))))... ( -44.70)
>DroVir_CAF1 13279 119 + 1
ACACAUUGCGCCAACUCGCCAGCGGAGACGCGCUUCAUGGCAACGCAAUGACUAGAAAUUUGAGGCAGAAAUAUCUCAGAUUCGUAGCCAUUACAUUCCACAAGCACCACGUUUCCGUU
.......(((......))).((((((((((.((((..(((.((.(.((((.(((..((((((((..(....)..))))))))..))).)))).).))))).))))....)))))))))) ( -35.40)
>DroSec_CAF1 4150 116 + 1
---GGCAGUAAAAGUUCGCGGCCGGUGAUGCGUUUCAUGGCUAUGUACUGACCGCAAAUCUGCGGUAGAAAGAUCUCCGAUUCGUGGACAUUGCAUUCCACGAGCACUACGCUGCCAUU
---((((((...(((.((..((((.(((......)))))))..)).))).((((((....))))))............(.((((((((........))))))))).....))))))... ( -42.10)
>DroEre_CAF1 5135 116 + 1
---GGCAGUACAAGUUCAUGGGCGGUGAUGCGUUUCAUGGUUAUGUACUGACCGCAAACCUGCGGUAGAAAUAUCUCCGAUUCGUGGACAUUACAUUCCACGAGCACCACGCUGCCAUU
---((((((....(((....))).(((.(((......(((..((((....((((((....))))))....))))..)))..(((((((........)))))))))).)))))))))... ( -43.30)
>DroYak_CAF1 1714 116 + 1
---GGCAGUACAAGUUCAUGGCCGGUGAUGCGUUUCAUGGCCAUGUACUGGCCGCAAAUUUGCGGUAGAAAGAUCUCCGAUUCGUGGACAUUACAUUCCACGAGCACCACGCUGCCAUU
---((((((...(((.((((((((.(((......))))))))))).))).((((((....))))))............(.((((((((........))))))))).....))))))... ( -48.50)
>DroAna_CAF1 2429 116 + 1
---CACUGGAUUAGUUCAUUGGCGGUAACGCGUUUCAUGGCAAUGAAUUGGCCAGAAAGAUAUGGCAGAAAUAUUUCCGAUUCGUGACCACUAGACUCCACGAGGACCACUUUUUCGUU
---....(((...........(((....)))((((..(((..((((((((((((........)))).(((....)))))))))))..)))..)))))))(((((((.....))))))). ( -31.10)
>consensus
___GGCAGUACAAGUUCAUGGCCGGUGAUGCGUUUCAUGGCUAUGUACUGACCGCAAAUCUGCGGUAGAAAGAUCUCCGAUUCGUGGACAUUACAUUCCACGAGCACCACGCUGCCAUU
...((((((...(((.(((((.(.((((......)))).)))))).))).((((((....))))))..............((((((((........))))))))......))))))... (-25.38 = -26.88 +   1.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,877,161 – 12,877,277
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.58
Mean single sequence MFE -37.47
Consensus MFE -22.39
Energy contribution -24.28
Covariance contribution 1.89
Combinations/Pair 1.30
Mean z-score -1.73
Structure conservation index 0.60
SVM decision value 0.43
SVM RNA-class probability 0.734346
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12877161 116 - 23771897
AAUGGCAGCGUAGUGCUCGUAGAAUGUAAUGUCCACGAAUCGGAGAUCUUUCUACCGCAGAUUUGCGGCCAGUACAUAGCCAUGAAACGCAUCACCGGCCACGAACUUUUACUGCC---
...(((((...(((..((((...(((((.((.((.(((((((((((....))).))...)))))).)).)).))))).(((.(((......)))..))).)))))))....)))))--- ( -32.90)
>DroVir_CAF1 13279 119 - 1
AACGGAAACGUGGUGCUUGUGGAAUGUAAUGGCUACGAAUCUGAGAUAUUUCUGCCUCAAAUUUCUAGUCAUUGCGUUGCCAUGAAGCGCGUCUCCGCUGGCGAGUUGGCGCAAUGUGU
.(((....))).(((((((((((((((((((((((.((((.((((..........)))).)))).))))))))))))).)))).)))))).....(((..(((......)))...))). ( -45.70)
>DroSec_CAF1 4150 116 - 1
AAUGGCAGCGUAGUGCUCGUGGAAUGCAAUGUCCACGAAUCGGAGAUCUUUCUACCGCAGAUUUGCGGUCAGUACAUAGCCAUGAAACGCAUCACCGGCCGCGAACUUUUACUGCC---
...(((((.....((((((((((........)))))))...(((((....))).)))))..(((((((((.((.....((........))...)).)))))))))......)))))--- ( -37.40)
>DroEre_CAF1 5135 116 - 1
AAUGGCAGCGUGGUGCUCGUGGAAUGUAAUGUCCACGAAUCGGAGAUAUUUCUACCGCAGGUUUGCGGUCAGUACAUAACCAUGAAACGCAUCACCGCCCAUGAACUUGUACUGCC---
...(((((.(((((((((((((.(((((.((.((.(((((((((((....))).)))...))))).)).)).)))))..))))))...)))))))....((......))..)))))--- ( -40.50)
>DroYak_CAF1 1714 116 - 1
AAUGGCAGCGUGGUGCUCGUGGAAUGUAAUGUCCACGAAUCGGAGAUCUUUCUACCGCAAAUUUGCGGCCAGUACAUGGCCAUGAAACGCAUCACCGGCCAUGAACUUGUACUGCC---
.(((((.(.((((((((((((((........))))))).(((((((....))).))(((....)))(((((.....)))))..))...)))))))).)))))..............--- ( -44.40)
>DroAna_CAF1 2429 116 - 1
AACGAAAAAGUGGUCCUCGUGGAGUCUAGUGGUCACGAAUCGGAAAUAUUUCUGCCAUAUCUUUCUGGCCAAUUCAUUGCCAUGAAACGCGUUACCGCCAAUGAACUAAUCCAGUG---
.........(((((...((((...((..(((((...((((.((((....))))((((........))))..))))...)))))))..))))..)))))..................--- ( -23.90)
>consensus
AAUGGCAGCGUGGUGCUCGUGGAAUGUAAUGUCCACGAAUCGGAGAUAUUUCUACCGCAGAUUUGCGGCCAGUACAUAGCCAUGAAACGCAUCACCGCCCACGAACUUGUACUGCC___
...(((((.(((((((((((((.(((((.((.((.(((((((((((....))).)))...))))).)).)).)))))..))))))...)))))))((....))........)))))... (-22.39 = -24.28 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:38 2006