Locus 2393

Sequence ID 3L_DroMel_CAF1
Location 6,732,069 – 6,732,254
Length 185
Max. P 0.997444
window3690 window3691 window3692 window3693

overview

Window 0

Location 6,732,069 – 6,732,183
Length 114
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 87.36
Mean single sequence MFE -32.82
Consensus MFE -23.73
Energy contribution -25.60
Covariance contribution 1.87
Combinations/Pair 1.06
Mean z-score -1.94
Structure conservation index 0.72
SVM decision value 0.55
SVM RNA-class probability 0.779753
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6732069 114 + 23771897
CAAAGUGGAGAAGCGGGCAUGGAGUUGCCCAGGUGGGAGCCACCAAUUAGUAAGCCUCGACCCAGUUCAACAAACUGCUCAUGCAGCAAA---AAAGCUGCAGACUUUUUGAAAAGG
....((.(((..(((((((......))))).(((((...))))).........))))).))((..(((((......(.((.((((((...---...)))))))))...)))))..)) ( -37.00)
>DroSec_CAF1 4998 116 + 1
CAAAGAGGAGGAGCGAGCAUGGAGUUGCCCAGGUGGGAGCCACCAAUUAGUAAGCCUCGACCCAGUUCAACAAACUGCUCAUGCAGCAAAAAAAAAGCUGCACACUUUUUGAA-AGG
((((((((((...(((((.(((......)))(((((...))))).........).))))...(((((.....)))))))).((((((.........))))))..)))))))..-... ( -34.70)
>DroSim_CAF1 3209 116 + 1
CAAAGAGGAGGAGCGAACAUGGAGUUGCCCAGGUGGGAGCCACCAAUUAGUAAGCCUCGACCCAGUUCAACAAACUGCUCAUGCAGCAAAAAAAAAGCUGCACACUUUUUGAA-AGG
((((((((((((((..((.(((......)))(((((...))))).....))..).)))....(((((.....)))))))).((((((.........))))))..)))))))..-... ( -33.90)
>DroYak_CAF1 5049 105 + 1
CAAAUGGCA------GGCAAGGAGUUGCCCAGGUGGGAGCCACCAAUUAGUAAGCCUCGACCCAGUUCAACAAACUGCUCAUGCAGAAAA---AUGGAUGCAUACUUGUACAA-A--
.....(((.------(((((....)))))..(((((...))))).........)))........(((((.....((((....))))....---.)))))(((....)))....-.-- ( -25.70)
>consensus
CAAAGAGGAGGAGCGAGCAUGGAGUUGCCCAGGUGGGAGCCACCAAUUAGUAAGCCUCGACCCAGUUCAACAAACUGCUCAUGCAGCAAA___AAAGCUGCACACUUUUUGAA_AGG
(((((((.......(((((.(..((((..(.(((.(..((.((......))..))..).)))..)..))))...)))))).((((((.........))))))..)))))))...... (-23.73 = -25.60 +   1.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 6,732,069 – 6,732,183
Length 114
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -35.00
Consensus MFE -29.21
Energy contribution -30.40
Covariance contribution 1.19
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.83
SVM decision value 1.08
SVM RNA-class probability 0.911755
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6732069 114 - 23771897
CCUUUUCAAAAAGUCUGCAGCUUU---UUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUGGCUCCCACCUGGGCAACUCCAUGCCCGCUUCUCCACUUUG
.........(((((.((((((...---...))))))....((((((...))))))((..(((((.........(((((...))))).(((((......)))))))))).))))))). ( -39.10)
>DroSec_CAF1 4998 116 - 1
CCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUGGCUCCCACCUGGGCAACUCCAUGCUCGCUCCUCCUCUUUG
...-..((((.((.(((((((.........)))))))(((((....((((..(..(((.(..(((.(((....))))))..).)))..).))))....))))).......)).)))) ( -37.30)
>DroSim_CAF1 3209 116 - 1
CCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUGGCUCCCACCUGGGCAACUCCAUGUUCGCUCCUCCUCUUUG
...-..((((.((.(((((((.........)))))))(((((....((((..(..(((.(..(((.(((....))))))..).)))..).))))....))))).......)).)))) ( -34.90)
>DroYak_CAF1 5049 105 - 1
--U-UUGUACAAGUAUGCAUCCAU---UUUUCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUGGCUCCCACCUGGGCAACUCCUUGCC------UGCCAUUUG
--.-.....(((((.((.(((((.---(((.((((....))))......))).))))))).(((.........(((((...))))).((((((....)))))------))))))))) ( -28.70)
>consensus
CCU_UUCAAAAAGUGUGCAGCUUU___UUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUGGCUCCCACCUGGGCAACUCCAUGCCCGCUCCUCCUCUUUG
..............(((((((.........)))))))(((((....((((..(..(((.(..(((.(((....))))))..).)))..).))))....))))).............. (-29.21 = -30.40 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,732,109 – 6,732,223
Length 114
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 94.86
Mean single sequence MFE -33.23
Consensus MFE -33.12
Energy contribution -33.57
Covariance contribution 0.45
Combinations/Pair 1.02
Mean z-score -2.66
Structure conservation index 1.00
SVM decision value 2.20
SVM RNA-class probability 0.990245
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6732109 114 - 23771897
CCAUUUAUGUAGUAAUCCUUUUAAGUUGCACAUUUACGAACCUUUUCAAAAAGUCUGCAGCUUU---UUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUG
(((......((((((.(((..(((((.....)))))(((.((..(((((.(((((((((((...---...)))))).))....))).)))))..)).)))))).))))))..))).. ( -28.10)
>DroSec_CAF1 5038 116 - 1
CCAUUUAUGCAGUAUUCCUUUGAAGUUGCACAUUUAAGAACCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUG
((((((((((((((.......((((((((((((((..((....-.))...)))))))))))))).....)))))))))))((((((...))))))(((....))).......))).. ( -36.00)
>DroSim_CAF1 3249 116 - 1
CCAUUUAUGCAGUAAUCCUUUUAAGUUGCACAUUUAAGAACCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUG
(((((((((((((((.......(((((((((((((..((....-.))...))))))))))))).....))))))))))))((((((...))))))(((....))).......))).. ( -35.60)
>consensus
CCAUUUAUGCAGUAAUCCUUUUAAGUUGCACAUUUAAGAACCU_UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAGCAGUUUGUUGAACUGGGUCGAGGCUUACUAAUUGGUG
(((((((((((((((.......(((((((((((((..(((....)))...))))))))))))).....))))))))))))((((((...))))))(((....))).......))).. (-33.12 = -33.57 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,732,146 – 6,732,254
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.86
Mean single sequence MFE -26.77
Consensus MFE -26.82
Energy contribution -27.27
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.92
Structure conservation index 1.00
SVM decision value 2.86
SVM RNA-class probability 0.997444
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6732146 108 - 23771897
---------ACAUAGAUAUCAUAUUUAUUAGAGAACUUAACCAUUUAUGUAGUAAUCCUUUUAAGUUGCACAUUUACGAACCUUUUCAAAAAGUCUGCAGCUUU---UUUGCUGCAUGAG
---------..(((((((...)))))))................(((((((((((.......((((((((.((((..(((....)))...)))).)))))))).---.))))))))))). ( -21.30)
>DroSec_CAF1 5075 119 - 1
GAACUUAAAACAUAGAUAUAAUAUUUACUAGAGAACUUAACCAUUUAUGCAGUAUUCCUUUGAAGUUGCACAUUUAAGAACCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAG
............................................((((((((((.......((((((((((((((..((....-.))...)))))))))))))).....)))))))))). ( -29.70)
>DroSim_CAF1 3286 119 - 1
GAACUUAAAACAUAGAUAUAAUAUUUACUAGAGAACUUAACCAUUUAUGCAGUAAUCCUUUUAAGUUGCACAUUUAAGAACCU-UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAG
............................................(((((((((((.......(((((((((((((..((....-.))...))))))))))))).....))))))))))). ( -29.30)
>consensus
GAACUUAAAACAUAGAUAUAAUAUUUACUAGAGAACUUAACCAUUUAUGCAGUAAUCCUUUUAAGUUGCACAUUUAAGAACCU_UUCAAAAAGUGUGCAGCUUUUUUUUUGCUGCAUGAG
............................................(((((((((((.......(((((((((((((..(((....)))...))))))))))))).....))))))))))). (-26.82 = -27.27 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:14 2006