Locus 4518

Sequence ID 2L_DroMel_CAF1
Location 12,956,174 – 12,956,277
Length 103
Max. P 0.965062
window7103 window7104

overview

Window 3

Location 12,956,174 – 12,956,277
Length 103
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 94.74
Mean single sequence MFE -32.75
Consensus MFE -29.70
Energy contribution -30.08
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.91
SVM decision value 0.23
SVM RNA-class probability 0.644821
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956174 103 + 22407834
CUCACUUGCUCUGCUCAACUGAUUGCUUACAGUGAGUGCAAACAGUAUUCUGAUUGGUUCAGGGCAAUCAGUGGCUGGGGAUCGCAGAACUACAGCGGGAUUU---
....((((((((((...(((.((((....)))).))).....((((...(((((((.(....).)))))))..))))......)))))......)))))....--- ( -29.80)
>DroSec_CAF1 936 103 + 1
CUCGCUUGCUCUGCUCAACUGAUUGCUUACAGUGAGUGCAAACAGUAUUCUGAUUGGUUCAGGGCAAUCAGUGGCUGGGGAUCGCAGAACUACAGCGGGAUUU---
((((((.(.(((((...(((.((((....)))).))).....((((...(((((((.(....).)))))))..))))......))))).)...))))))....--- ( -34.50)
>DroSim_CAF1 1039 105 + 1
CUCGCUUGCUCUGCUCAACUGAUUGCUUACACUGAGUGCAAACAGUAUUCUGAUUGGUUCAG-GCAAUCAGUGGCUGGGGAUCGCAGAUCUACAGCGGGAUUUUAA
((((((..(((.(((..(((((((((((..(((((((((.....)))))).....)))..))-)))))))))))).)))((((...))))...))))))....... ( -35.50)
>DroYak_CAF1 1078 103 + 1
CUCGCUUGCUCUGCUCAACUGAUUGCUUACAGUGAGUGCAAACAGUAUUCUGAUUGGUUCAGGGCAAUCAGUGGCUGGAGAUCCCAGAACUACAUCGAGAUUU---
((((.((((((((..(.(((.((((....)))).))).(((.(((....))).))))..))))))))...((((((((.....))))..))))..))))....--- ( -31.20)
>consensus
CUCGCUUGCUCUGCUCAACUGAUUGCUUACAGUGAGUGCAAACAGUAUUCUGAUUGGUUCAGGGCAAUCAGUGGCUGGGGAUCGCAGAACUACAGCGGGAUUU___
((((((.(.(((((((.(((((((((((.....((((((.....))))))(((.....)))))))))))))).....)))....)))).)...))))))....... (-29.70 = -30.08 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,956,174 – 12,956,277
Length 103
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 94.74
Mean single sequence MFE -31.65
Consensus MFE -28.44
Energy contribution -29.00
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.42
Structure conservation index 0.90
SVM decision value 1.58
SVM RNA-class probability 0.965062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956174 103 - 22407834
---AAAUCCCGCUGUAGUUCUGCGAUCCCCAGCCACUGAUUGCCCUGAACCAAUCAGAAUACUGUUUGCACUCACUGUAAGCAAUCAGUUGAGCAGAGCAAGUGAG
---......((((...(((((((.........(.(((((((((.((((.....))))........(((((.....)))))))))))))).).))))))).)))).. ( -30.80)
>DroSec_CAF1 936 103 - 1
---AAAUCCCGCUGUAGUUCUGCGAUCCCCAGCCACUGAUUGCCCUGAACCAAUCAGAAUACUGUUUGCACUCACUGUAAGCAAUCAGUUGAGCAGAGCAAGCGAG
---......((((...(((((((.........(.(((((((((.((((.....))))........(((((.....)))))))))))))).).))))))).)))).. ( -32.70)
>DroSim_CAF1 1039 105 - 1
UUAAAAUCCCGCUGUAGAUCUGCGAUCCCCAGCCACUGAUUGC-CUGAACCAAUCAGAAUACUGUUUGCACUCAGUGUAAGCAAUCAGUUGAGCAGAGCAAGCGAG
.........((((.....(((((.........(.(((((((((-((((.....)))).((((((........))))))..))))))))).).)))))...)))).. ( -33.00)
>DroYak_CAF1 1078 103 - 1
---AAAUCUCGAUGUAGUUCUGGGAUCUCCAGCCACUGAUUGCCCUGAACCAAUCAGAAUACUGUUUGCACUCACUGUAAGCAAUCAGUUGAGCAGAGCAAGCGAG
---....((((.....((((((((....))..(.(((((((((.((((.....))))........(((((.....)))))))))))))).)..))))))...)))) ( -30.10)
>consensus
___AAAUCCCGCUGUAGUUCUGCGAUCCCCAGCCACUGAUUGCCCUGAACCAAUCAGAAUACUGUUUGCACUCACUGUAAGCAAUCAGUUGAGCAGAGCAAGCGAG
.........((((...(((((((.........(.(((((((((.((((.....))))........(((((.....)))))))))))))).).))))))).)))).. (-28.44 = -29.00 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:43 2006