Locus 7007

Sequence ID 2L_DroMel_CAF1
Location 19,506,176 – 19,506,276
Length 100
Max. P 0.975440
window11173 window11174

overview

Window 3

Location 19,506,176 – 19,506,276
Length 100
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 75.82
Mean single sequence MFE -21.69
Consensus MFE -14.31
Energy contribution -14.75
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -2.12
Structure conservation index 0.66
SVM decision value 1.75
SVM RNA-class probability 0.975440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19506176 100 + 22407834
AAAAUAAAAGGUGUAGAUAAGAGAAGGGCUAUUCCAAGAGAUUCCCAGAACCAGACCCUGCUGAUCAUUGCCUUUUAUAGUAUAAAUAACCCU----------------UAAAGAA
...((((((((((..(((.((...((((((.(((...(.....)...)))..)).)))).)).)))..))))))))))...............----------------....... ( -19.00)
>DroSec_CAF1 1501 89 + 1
AAAAUAAAAGGUUUACAUAAGAGCAGGG-----------GAUUCCUAGAACCAGACCCUGCUGAUCAUUGCCUUUUAUAGUAUAAAUAACCCU----------------UAAAGAA
...(((((((((.........(((((((-----------................))))))).......)))))))))...............----------------....... ( -20.48)
>DroSim_CAF1 1007 89 + 1
AAAAUAAAAGGUUUACAUAAGAGCAGGG-----------GAUUCCUAGAACCAGACCCUGCUGAUCAUUGCCUUUUAUAGUAUAAAUAACCCU----------------UAAAGAA
...(((((((((.........(((((((-----------................))))))).......)))))))))...............----------------....... ( -20.48)
>DroEre_CAF1 1199 110 + 1
UAAAUAAAAGGUUUACAUAUGUGUAGGGCUGUUUCAAGGAAUUCCUGGAACCAGACCCUGGUGAUCAUUACCUUUUAUAGUGUAAGU------GACGUGUCGUUUAAGUUAAAGAA
...(((((((((.(((....)))((((((((.(((.(((....))).))).))).))))).........)))))))))....(((((------((....))))))).......... ( -26.80)
>consensus
AAAAUAAAAGGUUUACAUAAGAGCAGGG___________GAUUCCUAGAACCAGACCCUGCUGAUCAUUGCCUUUUAUAGUAUAAAUAACCCU________________UAAAGAA
...(((((((((.........(((((((...........................))))))).......)))))))))...................................... (-14.31 = -14.75 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 19,506,176 – 19,506,276
Length 100
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 75.82
Mean single sequence MFE -22.35
Consensus MFE -12.69
Energy contribution -13.56
Covariance contribution 0.87
Combinations/Pair 1.09
Mean z-score -2.30
Structure conservation index 0.57
SVM decision value 1.50
SVM RNA-class probability 0.959398
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19506176 100 - 22407834
UUCUUUA----------------AGGGUUAUUUAUACUAUAAAAGGCAAUGAUCAGCAGGGUCUGGUUCUGGGAAUCUCUUGGAAUAGCCCUUCUCUUAUCUACACCUUUUAUUUU
.......----------------...............((((((((....(((.((.(((((...((((..((.....))..)))).)))))...)).)))....))))))))... ( -24.20)
>DroSec_CAF1 1501 89 - 1
UUCUUUA----------------AGGGUUAUUUAUACUAUAAAAGGCAAUGAUCAGCAGGGUCUGGUUCUAGGAAUC-----------CCCUGCUCUUAUGUAAACCUUUUAUUUU
.......----------------...............((((((((..((((..(((((((...(((((...)))))-----------))))))).)))).....))))))))... ( -20.60)
>DroSim_CAF1 1007 89 - 1
UUCUUUA----------------AGGGUUAUUUAUACUAUAAAAGGCAAUGAUCAGCAGGGUCUGGUUCUAGGAAUC-----------CCCUGCUCUUAUGUAAACCUUUUAUUUU
.......----------------...............((((((((..((((..(((((((...(((((...)))))-----------))))))).)))).....))))))))... ( -20.60)
>DroEre_CAF1 1199 110 - 1
UUCUUUAACUUAAACGACACGUC------ACUUACACUAUAAAAGGUAAUGAUCACCAGGGUCUGGUUCCAGGAAUUCCUUGAAACAGCCCUACACAUAUGUAAACCUUUUAUUUA
...............((....))------.........(((((((((...........(((.(((.(((.(((....))).))).))))))((((....)))).)))))))))... ( -24.00)
>consensus
UUCUUUA________________AGGGUUAUUUAUACUAUAAAAGGCAAUGAUCAGCAGGGUCUGGUUCUAGGAAUC___________CCCUGCUCUUAUGUAAACCUUUUAUUUU
......................................((((((((..((((..(((((((((((....))))...............))))))).)))).....))))))))... (-12.69 = -13.56 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:04 2006