Locus 4291

Sequence ID X_DroMel_CAF1
Location 11,303,035 – 11,303,187
Length 152
Max. P 0.969631
window7054 window7055 window7056

overview

Window 4

Location 11,303,035 – 11,303,147
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 76.51
Mean single sequence MFE -19.47
Consensus MFE -11.45
Energy contribution -11.23
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.59
SVM decision value 0.67
SVM RNA-class probability 0.816658
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11303035 112 - 22224390
AAAAUAGAGAAGUUUCGUGAAAAGCGAGACUACUUGGCAAGAAUUAAAGUAGAAAAUGACGUACUUUACUGUCUUGAAGACUUAACAGUCCCCACUUGUACUCCCUAAGUAU
..........((((((((.....))))))))(((((((((((..(((((((..........)))))))...)))))..((((....))))..............)))))).. ( -24.80)
>DroSec_CAF1 6578 91 - 1
AAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGAAAAUAAUCAAAGUAGAAAAUAA---------------------CCUAACAGUCCCUACUUCAACUGACUAAUUAU
....((((((.(((((((.....)))))))...((((......))))............---------------------)))..((((..........)))).)))..... ( -15.10)
>DroSim_CAF1 7633 91 - 1
AAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGGCAAGAAUCAAAGUAGAAAAUGA---------------------CCUAACAGUCCCUACUUCAUCUCACUAAUUAU
...........(((((((.....))))))).((((((..(((....((((((.....((---------------------(......))).))))))..)))..)))))).. ( -18.50)
>consensus
AAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGGCAAGAAUCAAAGUAGAAAAUGA_____________________CCUAACAGUCCCUACUUCAACUCACUAAUUAU
...........(((((((.....))))))).((((((...((....((((((.......................................))))))....)).)))))).. (-11.45 = -11.23 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,303,068 – 11,303,187
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -18.06
Consensus MFE -14.42
Energy contribution -14.53
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.70
Structure conservation index 0.80
SVM decision value 0.72
SVM RNA-class probability 0.833163
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11303068 119 + 22224390
CUUCAAGACAGUAAAGUACGUCAUUUUCUACUUUAAUUCUUGCCAAGUAGUCUCGCUUUUCACGAAACUUCUCUAUUUUGUGAGGCCAAAAACUCUUACGUUAAAGCUCUAGUGACACU
...(((((...(((((((.(......).)))))))..)))))......(((.(((((..((((((((........))))))))(((....(((......)))...)))..))))).))) ( -21.30)
>DroSec_CAF1 6610 99 + 1
--------------------UUAUUUUCUACUUUGAUUAUUUUCAAUUUGUCUCGCUUUUCACGAAACUCCUCUAUUUUGUGAGGCCAAAAACCCUCACGUUUAAGCUUUAGCGACACU
--------------------............((((......))))...((.(((((.......((((...........((((((........)))))))))).......))))).)). ( -17.14)
>DroSim_CAF1 7665 99 + 1
--------------------UCAUUUUCUACUUUGAUUCUUGCCAAUUUGUCUCGCUUUUCACGAAACUCCUCUAUUUUGUGAGGCCAAAAACCCUCACGUUUAAGCUUUAGCGACACU
--------------------.............................((.(((((.......((((...........((((((........)))))))))).......))))).)). ( -15.74)
>consensus
____________________UCAUUUUCUACUUUGAUUCUUGCCAAUUUGUCUCGCUUUUCACGAAACUCCUCUAUUUUGUGAGGCCAAAAACCCUCACGUUUAAGCUUUAGCGACACU
.................................................((.(((((..((((((((........))))))))(((...((((......))))..)))..))))).)). (-14.42 = -14.53 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 11,303,068 – 11,303,187
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -24.87
Consensus MFE -18.41
Energy contribution -18.97
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.74
SVM decision value 1.64
SVM RNA-class probability 0.969631
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11303068 119 - 22224390
AGUGUCACUAGAGCUUUAACGUAAGAGUUUUUGGCCUCACAAAAUAGAGAAGUUUCGUGAAAAGCGAGACUACUUGGCAAGAAUUAAAGUAGAAAAUGACGUACUUUACUGUCUUGAAG
.(((...((((((((((......)))).))))))...)))......(((.((((((((.....)))))))).)))..(((((..(((((((..........)))))))...)))))... ( -28.40)
>DroSec_CAF1 6610 99 - 1
AGUGUCGCUAAAGCUUAAACGUGAGGGUUUUUGGCCUCACAAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGAAAAUAAUCAAAGUAGAAAAUAA--------------------
.((...((....))....)).(((..(((((..(((((........)))).(((((((.....)))))))...)..)))))..))).............-------------------- ( -22.00)
>DroSim_CAF1 7665 99 - 1
AGUGUCGCUAAAGCUUAAACGUGAGGGUUUUUGGCCUCACAAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGGCAAGAAUCAAAGUAGAAAAUGA--------------------
......(((((.........((((((.(....).))))))...........(((((((.....)))))))...))))).....................-------------------- ( -24.20)
>consensus
AGUGUCGCUAAAGCUUAAACGUGAGGGUUUUUGGCCUCACAAAAUAGAGGAGUUUCGUGAAAAGCGAGACAAAUUGGCAAGAAUCAAAGUAGAAAAUGA____________________
............((((...(....)((((((((.((((........)))).(((((((.....))))))).......)))))))).))))............................. (-18.41 = -18.97 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:23 2006