Locus 5209

Sequence ID X_DroMel_CAF1
Location 13,618,374 – 13,618,528
Length 154
Max. P 0.999824
window8443 window8444 window8445 window8446

overview

Window 3

Location 13,618,374 – 13,618,494
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.99
Mean single sequence MFE -54.40
Consensus MFE -52.42
Energy contribution -51.50
Covariance contribution -0.92
Combinations/Pair 1.18
Mean z-score -2.28
Structure conservation index 0.96
SVM decision value 4.05
SVM RNA-class probability 0.999775
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13618374 120 + 22224390
UACCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAAGGCUGCGCCGCCCACGCAGGGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGC
((((.((........((((((((((....)).))))))))((((((((((((.....)))....)))))))))(((((......))))))).))))....((((.(......).)))).. ( -54.40)
>DroSec_CAF1 4246 120 + 1
UACCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAAGGCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGC
.....((........((((((((((....)).))))))))((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))))) ( -56.20)
>DroSim_CAF1 4222 120 + 1
UACCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAAGGCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGC
.....((........((((((((((....)).))))))))((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))))) ( -56.20)
>DroEre_CAF1 4197 118 + 1
--CCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAGGGUUGCGCCGCCCACGUAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGUCGCCAAGGCCGUCGGCGC
--...((........((((((((((....)).))))))))((((((.......))))))(((((((((...(((((...((((((((...))))))))..)))))....))))))))))) ( -51.70)
>DroYak_CAF1 3983 118 + 1
--CCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAAGGCUGUGCCGCCAACGCAGCGUCGGUGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGC
--...((........((((((((((....)).))))))))(((((((((((.(((...))).)))))))))))(((((......)))))(((((......(((.....)))..))))))) ( -53.50)
>consensus
UACCAGCAUCAUCGACUUAAUCCGUUCGAGCGGGAUUAAGGCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGC
.....((........((((((((((....)).))))))))((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))))) (-52.42 = -51.50 +  -0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,618,374 – 13,618,494
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.99
Mean single sequence MFE -57.60
Consensus MFE -53.86
Energy contribution -54.90
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -2.18
Structure conservation index 0.94
SVM decision value 3.48
SVM RNA-class probability 0.999275
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13618374 120 - 22224390
GCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACCCUGCGUGGGCGGCGCAGCCUUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGGUA
.((((((.....))))))......((((((((((((......)))))(((((((((((.((.....)).)))))))))))((((((((.........))))))))........))))))) ( -59.80)
>DroSec_CAF1 4246 120 - 1
GCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGCCUUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGGUA
.((((((.....))))))......((((((((((((......)))))(((((((((((.(((...))).)))))))))))((((((((.........))))))))........))))))) ( -61.20)
>DroSim_CAF1 4222 120 - 1
GCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGCCUUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGGUA
.((((((.....))))))......((((((((((((......)))))(((((((((((.(((...))).)))))))))))((((((((.........))))))))........))))))) ( -61.20)
>DroEre_CAF1 4197 118 - 1
GCGCCGACGGCCUUGGCGACUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUACGUGGGCGGCGCAACCCUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGG--
(((.((.((((...(((((((.((((((((...))))))))..)))))))((((((((.(((...))).)))))))).....((((((.........)))))).)))).)).)))...-- ( -53.70)
>DroYak_CAF1 3983 118 - 1
GCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCACCGACGCUGCGUUGGCGGCACAGCCUUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGG--
.((((((.....))))))........((((((((((......)))))((((.(((.((((((...)))))).))).))))((((((((.........))))))))........)))))-- ( -52.10)
>consensus
GCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGCCUUAAUCCCGCUCGAACGGAUUAAGUCGAUGAUGCUGGUA
.((((((.....)))))).......(((((((((((......)))))(((((((((((.((.....)).)))))))))))((((((((.........))))))))........)))))). (-53.86 = -54.90 +   1.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,618,414 – 13,618,528
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.72
Mean single sequence MFE -50.33
Consensus MFE -41.82
Energy contribution -41.06
Covariance contribution -0.76
Combinations/Pair 1.23
Mean z-score -2.70
Structure conservation index 0.83
SVM decision value 2.91
SVM RNA-class probability 0.997684
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13618414 114 + 22224390
GCUGCGCCGCCCACGCAGGGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGCUACACAGAAAGAAAUGUAAAGG------UAGAAUUGGUCU
((((((((((((.....)))....)))))))))(((((..(((((((.((((((......(((.....)))..))))))))..(((........)))...))------)))...))))). ( -48.70)
>DroSec_CAF1 4286 114 + 1
GCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGCUACACAGAAAGAAAUGUACAGG------UAGAAGUGACCU
((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))).((((......(....)......)------)))......... ( -48.90)
>DroSim_CAF1 4262 114 + 1
GCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGCUACACAGAAAGAAAUGUACAGG------UAGAAGUGACCU
((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))).((((......(....)......)------)))......... ( -48.90)
>DroEre_CAF1 4235 114 + 1
GUUGCGCCGCCCACGUAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGUCGCCAAGGCCGUCGGCGCUACACAGAAAGAAAAGUAAAAG------UAGAAGGGGCCU
........((((..((((((((((((((...(((((...((((((((...))))))))..)))))....))))))))))))))((..........)).....------......)))).. ( -52.90)
>DroYak_CAF1 4021 120 + 1
GCUGUGCCGCCAACGCAGCGUCGGUGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGCUACACUGCAAGAAAAGUAAAAGUGAAAGUAAAGGUGGCCU
(((((((((((.(((...))).)))))))))))(((((......)))))(.((((.....)))).).(((((..(...(((.((((..............))))..)))...)..))))) ( -52.24)
>consensus
GCUGCGCCGCCCACGCAGCGUCGACGGCGCAGCGACCGCAUUACCGGUCGCCGGUAAUUAGCCGCCAAGGCCGUCGGCGCUACACAGAAAGAAAUGUAAAGG______UAGAAGUGGCCU
((((((.......))))))(((((((((...(((((((......)))))))((((.....)))).....))))))))).......................................... (-41.82 = -41.06 +  -0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,618,414 – 13,618,528
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.72
Mean single sequence MFE -52.66
Consensus MFE -47.46
Energy contribution -47.94
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -2.76
Structure conservation index 0.90
SVM decision value 4.17
SVM RNA-class probability 0.999824
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13618414 114 - 22224390
AGACCAAUUCUA------CCUUUACAUUUCUUUCUGUGUAGCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACCCUGCGUGGGCGGCGCAGC
.((((.......------...((((((........))))))((((((.....))))))((..((((((((...))))))))))))))(((((((((((.((.....)).))))))))))) ( -53.60)
>DroSec_CAF1 4286 114 - 1
AGGUCACUUCUA------CCUGUACAUUUCUUUCUGUGUAGCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGC
((((.......)------)))........((.((..(((((((.(((((((...(((((((.((((((((...))))))))..)))))))..))))))).)))))))..)).))...... ( -53.60)
>DroSim_CAF1 4262 114 - 1
AGGUCACUUCUA------CCUGUACAUUUCUUUCUGUGUAGCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGC
((((.......)------)))........((.((..(((((((.(((((((...(((((((.((((((((...))))))))..)))))))..))))))).)))))))..)).))...... ( -53.60)
>DroEre_CAF1 4235 114 - 1
AGGCCCCUUCUA------CUUUUACUUUUCUUUCUGUGUAGCGCCGACGGCCUUGGCGACUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUACGUGGGCGGCGCAAC
..((.((.((((------(....((..........))((((((.(((((((...(((((((.((((((((...))))))))..)))))))..))))))).))))))))))).)).))... ( -55.70)
>DroYak_CAF1 4021 120 - 1
AGGCCACCUUUACUUUCACUUUUACUUUUCUUGCAGUGUAGCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCACCGACGCUGCGUUGGCGGCACAGC
..(((.((...((..........(((........)))((((((.((..(((...(((((((.((((((((...))))))))..)))))))..)))..)).)))))))).)).)))..... ( -46.80)
>consensus
AGGCCACUUCUA______CCUUUACAUUUCUUUCUGUGUAGCGCCGACGGCCUUGGCGGCUAAUUACCGGCGACCGGUAAUGCGGUCGCUGCGCCGUCGACGCUGCGUGGGCGGCGCAGC
.............................((.((..(((((((.(((((((...(((((((.((((((((...))))))))..)))))))..))))))).)))))))..)).))...... (-47.46 = -47.94 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:22 2006