Locus 1944

Sequence ID 3L_DroMel_CAF1
Location 5,398,607 – 5,398,804
Length 197
Max. P 0.924087
window3036 window3037 window3038 window3039

overview

Window 6

Location 5,398,607 – 5,398,725
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.61
Mean single sequence MFE -36.35
Consensus MFE -31.43
Energy contribution -31.43
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 0.86
SVM decision value 1.16
SVM RNA-class probability 0.924087
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5398607 118 - 23771897
GACUUGUGCUGGUGGGAGCAGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCAGGAGCCAUGGGGC--AGGAUCCAGAUCCUGCAGGAGCAAA
..(((.(((((.((....)).))))).).))....((((...................(((((......))))).((((((((....((((..--....))))..))))))))..)))). ( -37.20)
>DroSec_CAF1 47511 112 - 1
GACUUGUGCUGG---G---AGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCAGGAGACAUGGGGC--AGGAUCCAGAUCCUGCAGGAGCAAG
..(((((((((.---.---(((((((.......))))))...................((....))...)..))))(((((((....((((..--....))))..)))))))...))))) ( -36.10)
>DroYak_CAF1 47453 114 - 1
GACUUGUGCUGG---A---AGCAGCAGGGAGAGUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCAGGAGCCAUGGGGCACAGGAUCCAGAUCCUGCUGGAGCAAA
...((.(((((.---.---..))))).)).(((((((((........................)))))))))..(((.(((..(((....))).((((((....))))))))).)))... ( -35.76)
>consensus
GACUUGUGCUGG___G___AGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCAGGAGCCAUGGGGC__AGGAUCCAGAUCCUGCAGGAGCAAA
...((((((((.........((((((.......)))))).............(((((.((....)).))))))))).((((((....((((........))))..))))))....)))). (-31.43 = -31.43 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,398,645 – 5,398,765
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.79
Mean single sequence MFE -28.74
Consensus MFE -24.01
Energy contribution -24.13
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.84
SVM decision value 0.29
SVM RNA-class probability 0.670760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5398645 120 - 23771897
GAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGGUGGGAGCAGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCA
..........(((((..........)))))...(((((.....((.(((((.((....)).))))).)).(((((((((........................)))))))))..))))). ( -29.86)
>DroSec_CAF1 47549 114 - 1
GAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGG---G---AGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCA
..........(((((..........)))))...(((((.....((.(((((.---.---..))))).)).(((((((((........................)))))))))..))))). ( -26.76)
>DroYak_CAF1 47493 114 - 1
GAUAUUAAAAACAAGAGAGAAAGGACUAGUGCAGCAGCAGGACUUGUGCUGG---A---AGCAGCAGGGAGAGUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCA
.............................((((((.((((.((((.(((((.---.---..)))))....)))).))))...................(((((......))))))))))) ( -29.60)
>consensus
GAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGG___G___AGCAGCAGGGAGAAUGUUGCAUAAACUUAACAUAAAUAAUGGAAGCAAUAUUUCAGCUGCA
..........(((((..........)))))...(((((....((((((((.........)))).))))..(((((((((........................)))))))))..))))). (-24.01 = -24.13 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 5,398,685 – 5,398,804
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.20
Mean single sequence MFE -23.13
Consensus MFE -19.73
Energy contribution -20.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.85
SVM decision value 0.17
SVM RNA-class probability 0.615936
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5398685 119 + 23771897
UGCAACAUUCUCCCUGCUGCUGCUCCCACCAGCACAAGUCCUGCUGCAGCACAAGUCCUUCCUCUCUUGUUUUUAAUAUCCUUCAGCUUGUAAAGGAAUUACUCCUCAAGCCGGCA-ACU
(((............(((((((((......))))..((.....)))))))(((((..........)))))...............(((((...((((.....)))))))))..)))-... ( -24.10)
>DroSec_CAF1 47589 113 + 1
UGCAACAUUCUCCCUGCUGCU---C---CCAGCACAAGUCCUGCUGCAGCACAAGUCCUUCCUCUCUUGUUUUUAAUAUCCUUCAGCUUGUAAAGGAAUUACUCCUCAAGCCGGCA-ACU
(((............(((((.---.---..((((.......)))))))))(((((..........)))))...............(((((...((((.....)))))))))..)))-... ( -23.70)
>DroYak_CAF1 47533 114 + 1
UGCAACACUCUCCCUGCUGCU---U---CCAGCACAAGUCCUGCUGCUGCACUAGUCCUUUCUCUCUUGUUUUUAAUAUCCUUCAGCUUGUAAAGGAAUUACUCCUCAAGCCGGCAAACU
(((..........(((.(((.---.---.(((((.......)))))..))).)))..............................(((((...((((.....)))))))))..))).... ( -21.60)
>consensus
UGCAACAUUCUCCCUGCUGCU___C___CCAGCACAAGUCCUGCUGCAGCACAAGUCCUUCCUCUCUUGUUUUUAAUAUCCUUCAGCUUGUAAAGGAAUUACUCCUCAAGCCGGCA_ACU
.(((.((..((...(((((..........)))))..))...)).))).(((((((..........)))))...............(((((...((((.....)))))))))..))..... (-19.73 = -20.07 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,398,685 – 5,398,804
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.20
Mean single sequence MFE -33.70
Consensus MFE -29.23
Energy contribution -29.57
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.87
SVM decision value 0.49
SVM RNA-class probability 0.758406
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5398685 119 - 23771897
AGU-UGCCGGCUUGAGGAGUAAUUCCUUUACAAGCUGAAGGAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGGUGGGAGCAGCAGCAGGGAGAAUGUUGCA
...-.(((((((((..(((......)))..))))))).............(((((..........))))))).((((((....((.(((((.((....)).))))).))....)))))). ( -36.10)
>DroSec_CAF1 47589 113 - 1
AGU-UGCCGGCUUGAGGAGUAAUUCCUUUACAAGCUGAAGGAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGG---G---AGCAGCAGGGAGAAUGUUGCA
...-.(((((((((..(((......)))..))))))).............(((((..........))))))).((((((....((.(((((.---.---..))))).))....)))))). ( -33.00)
>DroYak_CAF1 47533 114 - 1
AGUUUGCCGGCUUGAGGAGUAAUUCCUUUACAAGCUGAAGGAUAUUAAAAACAAGAGAGAAAGGACUAGUGCAGCAGCAGGACUUGUGCUGG---A---AGCAGCAGGGAGAGUGUUGCA
....((((((((((..(((......)))..)))))))..............((..((........))..))..)))((((.((((.(((((.---.---..)))))....)))).)))). ( -32.00)
>consensus
AGU_UGCCGGCUUGAGGAGUAAUUCCUUUACAAGCUGAAGGAUAUUAAAAACAAGAGAGGAAGGACUUGUGCUGCAGCAGGACUUGUGCUGG___G___AGCAGCAGGGAGAAUGUUGCA
.....(((((((((..(((......)))..))))))).............(((((..........))))))).((((((...((((((((.........)))).)))).....)))))). (-29.23 = -29.57 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:41 2006