Locus 1065

Sequence ID 3R_DroMel_CAF1
Location 3,288,908 – 3,289,068
Length 160
Max. P 0.849120
window1721 window1722 window1723

overview

Window 1

Location 3,288,908 – 3,289,010
Length 102
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 86.41
Mean single sequence MFE -17.55
Consensus MFE -13.15
Energy contribution -14.53
Covariance contribution 1.38
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.75
SVM decision value 0.78
SVM RNA-class probability 0.849120
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3288908 102 - 27905053
UUUUAACGAGCUGCCAUUUGCCUCCCUUUUUCCCGCCAUAUCUCUUCGUAUAUAUCCAUAUCCGUGGCACAUAUGCAAGUUUAUAUGCCACUUACA------------CACACA
.......((((........).)))..........(.(((((..(((.((((((..((((....))))...)))))))))...))))).).......------------...... ( -13.30)
>DroSec_CAF1 41857 114 - 1
UUUUAACGAGCUGGCAUUUGCCUCCCUUUUUCCCGCCAUAUCUCUCCGUAUAUAUCCAUAUCCGUGCCACAUAUGCAAGCUUAUAUGCCACUUACACGCACACACUCACACACA
.......(((..(((....)))............((...........((((((...(((....)))....))))))..((......)).........)).....)))....... ( -13.60)
>DroEre_CAF1 43594 106 - 1
UUUUAACGAGCUGCCAUUCGCCUCCCUUUUUCCCGCCAUAUCUCUCUGUGUAUAUCCAUAUCCGUGGCACAUAUGCAAGUUUAUAUGGCACUUCC--------ACACACUCGCA
......((((..((.....)).............(((((((..((.(((((((..((((....))))...)))))))))...)))))))......--------.....)))).. ( -21.40)
>DroYak_CAF1 61276 114 - 1
UUUUAACGAGCUGCCAUUCGCCUCCCUUUUUCCCGCCGUAUCUCUUUGUAUAUAUCCAUAUCCGUGGCACAUAUGCAAGUUUAUAUGGCACUUACCCACACACACACACUCACA
.......(((..((.....)).............(((((((...(((((((((..((((....))))...)))))))))...)))))))...................)))... ( -21.90)
>consensus
UUUUAACGAGCUGCCAUUCGCCUCCCUUUUUCCCGCCAUAUCUCUCCGUAUAUAUCCAUAUCCGUGGCACAUAUGCAAGUUUAUAUGCCACUUACA_______ACACACACACA
.......((((........).)))..........(((((((...(((((((((..((((....))))...)))))))))...)))))))......................... (-13.15 = -14.53 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,288,976 – 3,289,068
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -20.50
Consensus MFE -18.96
Energy contribution -18.84
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.15
Structure conservation index 0.92
SVM decision value -0.02
SVM RNA-class probability 0.523547
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3288976 92 + 27905053
GGGAAAAAGGGAGGCAAAUGGCAGCUCGUUAAAAGGAGAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUCC
.........((((((...((((..(((........))).)))).))......((((.((((.....)))).)))).............)))) ( -22.00)
>DroSec_CAF1 41937 92 + 1
GGGAAAAAGGGAGGCAAAUGCCAGCUCGUUAAAAGGAAAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUCC
.(((....(((.(((....)))..)))....(((.((((((((((((.........))))......)))))))).)))...........))) ( -20.90)
>DroSim_CAF1 43116 92 + 1
GGGAAAAGGGGAGGCAAAUGGCAGCUCGUUAAAAGGAAAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUCC
.(((.((.(((..((.....))..))).)).(((.((((((((((((.........))))......)))))))).)))...........))) ( -20.50)
>DroEre_CAF1 43666 92 + 1
GGGAAAAAGGGAGGCGAAUGGCAGCUCGUUAAAAGGAAAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUCC
.........((((((........))((.((.(((.((((((((((((.........))))......)))))))).)))..)).))...)))) ( -20.40)
>DroYak_CAF1 61356 92 + 1
GGGAAAAAGGGAGGCGAAUGGCAGCUCGUUAAAAGGAAAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUGU
........(((..((.....))..)))....(((.((((((((((((.........))))......)))))))).))).............. ( -18.70)
>consensus
GGGAAAAAGGGAGGCAAAUGGCAGCUCGUUAAAAGGAAAGCCGGGCGAAAUUCAAGUGCCGGAAAAUGGCUUUUGUUUAGAAGGAAAACUCC
.........((((((........))((.((.(((.((((((((((((.........))))......)))))))).)))..)).))...)))) (-18.96 = -18.84 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,288,976 – 3,289,068
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -15.32
Consensus MFE -13.52
Energy contribution -13.76
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.42
Structure conservation index 0.88
SVM decision value 0.42
SVM RNA-class probability 0.729194
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3288976 92 - 27905053
GGAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUCUCCUUUUAACGAGCUGCCAUUUGCCUCCCUUUUUCCC
((((.............(((..(((.......)))..))).........((((((..........))))))........))))......... ( -16.90)
>DroSec_CAF1 41937 92 - 1
GGAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUUUCCUUUUAACGAGCUGGCAUUUGCCUCCCUUUUUCCC
((((.............(((..(((.......)))..)))......(((.(((((..........))))))))......))))......... ( -18.70)
>DroSim_CAF1 43116 92 - 1
GGAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUUUCCUUUUAACGAGCUGCCAUUUGCCUCCCCUUUUCCC
((((.............(((..(((.......)))..)))..........(((.(((........)))..)))......))))......... ( -14.80)
>DroEre_CAF1 43666 92 - 1
GGAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUUUCCUUUUAACGAGCUGCCAUUCGCCUCCCUUUUUCCC
((((.............(((..(((.......)))..)))..........(((.(((........)))..)))......))))......... ( -14.80)
>DroYak_CAF1 61356 92 - 1
ACAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUUUCCUUUUAACGAGCUGCCAUUCGCCUCCCUUUUUCCC
.((((((.......(((..((((((.......(((...........))).))))))..)))....))))))..................... ( -11.40)
>consensus
GGAGUUUUCCUUCUAAACAAAAGCCAUUUUCCGGCACUUGAAUUUCGCCCGGCUUUCCUUUUAACGAGCUGCCAUUUGCCUCCCUUUUUCCC
((((.............(((..(((.......)))..))).........((((((..........))))))........))))......... (-13.52 = -13.76 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:40 2006