Locus 5004

Sequence ID 3L_DroMel_CAF1
Location 13,760,070 – 13,760,224
Length 154
Max. P 0.999867
window7913 window7914 window7915 window7916

overview

Window 3

Location 13,760,070 – 13,760,184
Length 114
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 97.99
Mean single sequence MFE -31.16
Consensus MFE -28.02
Energy contribution -28.30
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.90
SVM decision value 2.22
SVM RNA-class probability 0.990636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13760070 114 + 23771897
AAUAAUUGAUGCCAGCUCUUGAAGAGGAAGCCCGUGGCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAG
...............(((.....)))((((((.((((((((((((.....(((..-....))).(((.((((((........)))))))))..))))))).))))).)))))).. ( -31.20)
>DroSec_CAF1 6636 114 + 1
AAUAAUUGAUGCCAGCUCUUGAAGAGGAAGCCCGUGGCUUGUGUUCCUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAG
...............(((.....)))((((((.((((((((((((.....(((..-....))).(((.((((((........)))))))))..))))))).))))).)))))).. ( -31.20)
>DroSim_CAF1 2769 114 + 1
AAUAAUUGAUGCCAGCUCUUGAAGAGGAAGCCCGUGGCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAG
...............(((.....)))((((((.((((((((((((.....(((..-....))).(((.((((((........)))))))))..))))))).))))).)))))).. ( -31.20)
>DroEre_CAF1 5799 114 + 1
AAUAAUUGAUGCCAGGUCUUGAAGAGGAAGACCGUGGCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCCGGCUUCAG
......(((.(((.((((((.......))))))((((((((((((.....(((..-....))).(((.((((((........)))))))))..))))))).))))).))).))). ( -32.40)
>DroYak_CAF1 2873 115 + 1
AAUAAUUGAUGCCAGUUCUUGAAGAGGAAGCCCGUGGCUUGUGUUCUUUCUGAUCCCUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAG
...(((((....))))).........((((((.(((((((((((((.....))...........(((.((((((........)))))))))...)))))).))))).)))))).. ( -29.80)
>consensus
AAUAAUUGAUGCCAGCUCUUGAAGAGGAAGCCCGUGGCUUGUGUUCUUUCUGAUC_CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAG
...............(((.....)))((((((.(((((((((((((.....))...........(((.((((((........)))))))))...)))))).))))).)))))).. (-28.02 = -28.30 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,760,070 – 13,760,184
Length 114
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 97.99
Mean single sequence MFE -25.14
Consensus MFE -21.64
Energy contribution -22.04
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 0.99
SVM RNA-class probability 0.895289
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13760070 114 - 23771897
CUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGCCACGGGCUUCCUCUUCAAGAGCUGGCAUCAAUUAUU
..((((((((.(((......((((((((((((..........))))).))).))))...-..((.....))......))).))))))))(((.....)))............... ( -25.40)
>DroSec_CAF1 6636 114 - 1
CUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAGGAACACAAGCCACGGGCUUCCUCUUCAAGAGCUGGCAUCAAUUAUU
..((((((((.(((......((((((((((((..........))))).))).))))..(-..((....))..)....))).))))))))(((.....)))............... ( -25.70)
>DroSim_CAF1 2769 114 - 1
CUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGCCACGGGCUUCCUCUUCAAGAGCUGGCAUCAAUUAUU
..((((((((.(((......((((((((((((..........))))).))).))))...-..((.....))......))).))))))))(((.....)))............... ( -25.40)
>DroEre_CAF1 5799 114 - 1
CUGAAGCCGGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGCCACGGUCUUCCUCUUCAAGACCUGGCAUCAAUUAUU
((((.(((...)))......((((((((((((..........))))).))).))))...-..))))...........((((.((((((.......)))))))))).......... ( -25.10)
>DroYak_CAF1 2873 115 - 1
CUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAGGGAUCAGAAAGAACACAAGCCACGGGCUUCCUCUUCAAGAACUGGCAUCAAUUAUU
..((((((((.(((......((((((((((((..........))))).))).))))......((.....))......))).)))))))).......................... ( -24.10)
>consensus
CUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG_GAUCAGAAAGAACACAAGCCACGGGCUUCCUCUUCAAGAGCUGGCAUCAAUUAUU
..((((((((.(((......((((((((((((..........))))).))).))))......((.....))......))).)))))))).......................... (-21.64 = -22.04 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,760,106 – 13,760,224
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 98.65
Mean single sequence MFE -28.60
Consensus MFE -28.44
Energy contribution -28.44
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.99
SVM decision value 2.55
SVM RNA-class probability 0.995221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13760106 118 + 23771897
GCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAGAUGUUGAACGCCAGCCGUGGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((..-...((((.(((.((((((........)))))))))))))......(((...))).)))))....))))))((((....)))).)).............. ( -29.00)
>DroSec_CAF1 6672 118 + 1
GCUUGUGUUCCUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAGAUGUUGAACGCCAGCCGUUGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((..-...((((.(((.((((((........)))))))))))))......(((...))).)))))....))))))((((....)))).)).............. ( -26.20)
>DroSim_CAF1 2805 118 + 1
GCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAGAUGUUGAACGCCAGCCGUGGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((..-...((((.(((.((((((........)))))))))))))......(((...))).)))))....))))))((((....)))).)).............. ( -29.00)
>DroEre_CAF1 5835 118 + 1
GCUUGUGUUCUUUCUGAUC-CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCCGGCUUCAGAUGUUGAACGCCAGCCGUGGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((..-...((((.(((.((((((........)))))))))))))......(((...))).)))))....))))))((((....)))).)).............. ( -29.00)
>DroYak_CAF1 2909 119 + 1
GCUUGUGUUCUUUCUGAUCCCUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAGAUGUUGAACGCCAGCCGUGGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((..(((.....((((((((.(((..((.((......)).))))).)))))))).)))..)))))....))))))((((....)))).)).............. ( -29.80)
>consensus
GCUUGUGUUCUUUCUGAUC_CUUUUUAUGGUAUUAAGUUAUUAUGUGCUUAAACCUAAAUAUAAUGCCGCAGGCUUCAGAUGUUGAACGCCAGCCGUGGCUGUGCUUUUAUUGUUUAUU
((..((((((..(((((......((((.(((.((((((........)))))))))))))......(((...))).)))))....))))))((((....)))).)).............. (-28.44 = -28.44 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,760,106 – 13,760,224
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 98.65
Mean single sequence MFE -25.72
Consensus MFE -25.72
Energy contribution -25.72
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 1.00
SVM decision value 4.31
SVM RNA-class probability 0.999867
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13760106 118 - 23771897
AAUAAACAAUAAAAGCACAGCCACGGCUGGCGUUCAACAUCUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))...-..)))))..))))...... ( -25.80)
>DroSec_CAF1 6672 118 - 1
AAUAAACAAUAAAAGCACAGCAACGGCUGGCGUUCAACAUCUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAGGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))...-..)))))..))))...... ( -25.40)
>DroSim_CAF1 2805 118 - 1
AAUAAACAAUAAAAGCACAGCCACGGCUGGCGUUCAACAUCUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))...-..)))))..))))...... ( -25.80)
>DroEre_CAF1 5835 118 - 1
AAUAAACAAUAAAAGCACAGCCACGGCUGGCGUUCAACAUCUGAAGCCGGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG-GAUCAGAAAGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))...-..)))))..))))...... ( -25.80)
>DroYak_CAF1 2909 119 - 1
AAUAAACAAUAAAAGCACAGCCACGGCUGGCGUUCAACAUCUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAGGGAUCAGAAAGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))......)))))..))))...... ( -25.80)
>consensus
AAUAAACAAUAAAAGCACAGCCACGGCUGGCGUUCAACAUCUGAAGCCUGCGGCAUUAUAUUUAGGUUUAAGCACAUAAUAACUUAAUACCAUAAAAAG_GAUCAGAAAGAACACAAGC
..............((.((((....))))))((((....(((((.(((...)))......((((((((((((..........))))).))).))))......)))))..))))...... (-25.72 = -25.72 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:21 2006