Locus 8599

Sequence ID 3L_DroMel_CAF1
Location 22,386,951 – 22,387,243
Length 292
Max. P 0.933078
window14091 window14092 window14093 window14094 window14095

overview

Window 1

Location 22,386,951 – 22,387,044
Length 93
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 82.43
Mean single sequence MFE -27.28
Consensus MFE -19.07
Energy contribution -20.02
Covariance contribution 0.95
Combinations/Pair 1.12
Mean z-score -2.17
Structure conservation index 0.70
SVM decision value 0.52
SVM RNA-class probability 0.767722
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386951 93 - 23771897
----------C-UCUGGGGAAAAUGCGUUACCAACCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUC-CCCCACCC-----------
----------.-...((((((((.(((((.....((((((((.((((((......)))))).)).(....)))))).)......)))))..)))))-))).....----------- ( -24.20)
>DroSec_CAF1 38076 91 - 1
----------C-UCGGGGGAAAAUGCGUUGCCAACCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUC-CCCCAC-------------
----------.-..(((((((((.((((((((((...((.(((((((((......))))))....))).))..))).))).....))))..)))))-))))..------------- ( -29.10)
>DroSim_CAF1 53660 93 - 1
----------C-UCGGGGGAAAAUGCGUUGCCAACCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUC-CCCCACCC-----------
----------.-..(((((((((.((((((((((...((.(((((((((......))))))....))).))..))).))).....))))..)))))-))))....----------- ( -29.10)
>DroEre_CAF1 54352 94 - 1
----------C-UCGGGGGAAAAUGCGUUGCCAACCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUCCCCCCACCA-----------
----------.-..(((((((((.((((((((((...((.(((((((((......))))))....))).))..))).))).....))))..))))))))).....----------- ( -28.20)
>DroYak_CAF1 54611 78 - 1
----------C-UCGGGGGAAA----------------UCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUUCCCCCACCA-----------
----------.-..((((((((----------------...((((((((......))))))(((..(((........)))..)))..))....))))))))....----------- ( -22.40)
>DroPer_CAF1 95126 115 - 1
GGCGGCGCCACACCAGGGGAAAAUGCGUUGGCUGCCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGCUUUUUUC-CUCCUCCUUCUCCCUACAU
(((...))).....(((((((((.(((((.(.((((((((((.((((((......)))))).)).(....)))))).)))..).)))))..)))))-).))).............. ( -30.70)
>consensus
__________C_UCGGGGGAAAAUGCGUUGCCAACCAGUCCGCAAAUGUAAAUUGACAUUUUCGAGUGCACGAUUGAGCAAAUGAACGUUUUUUUC_CCCCACCA___________
..............(((((((((.(((((...........((.((((((......)))))).))..(((........)))....)))))..))))).))))............... (-19.07 = -20.02 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 22,387,044 – 22,387,149
Length 105
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 91.78
Mean single sequence MFE -36.95
Consensus MFE -31.09
Energy contribution -31.15
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.84
SVM decision value 1.02
SVM RNA-class probability 0.902200
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22387044 105 + 23771897
AGGCAAUACGGCCCCAGCCAGCUUAAGUUGACUUUAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGC---------GGUGGCCAAGGGAAAUGCGAAGGCAUUCCA
.........((((((((.((((....)))).)).....(((((..((...((........))..))....)))))---------)).))))...((((.(((....))))))). ( -35.40)
>DroSec_CAF1 38167 105 + 1
AGGCAAUCCGGCCCCAGCCAGCUUAAGUUGACUUUAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUUGAGGC---------GGAGGCCAAGGGAAAUGCGAAGGCAUUCCA
.((....))((((((((.((((....)))).)).....((((((((....((........)).....))))))))---------)).))))...((((.(((....))))))). ( -37.70)
>DroEre_CAF1 54446 114 + 1
AGGCAAUCGGGCCCCAGCCAGCUUAAGUUGACUUUAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGCGGAGGAGGCGGAGGCCAAGGGAAAUGCAAAGGCAUUCCA
.........((((((((.((((....)))).)).....(((((..(((.((((.((.(.....).)).)))).)))...))))))).))))...((((.(((....))))))). ( -41.40)
>DroYak_CAF1 54689 105 + 1
AGGCAAUCCGGCCCAAGCCAGCUUAAGUUGACUUUAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGU---------GGAGGCCAAUGGAACUGCGAAGGCAUUCCA
.((....))((((((((.((((....)))).)))...((((((..((...((........))..))....)))))---------)).))))..(((((.(((....)))))))) ( -33.30)
>consensus
AGGCAAUCCGGCCCCAGCCAGCUUAAGUUGACUUUAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGC_________GGAGGCCAAGGGAAAUGCGAAGGCAUUCCA
.........((((((((.((((....)))).)).....(((((..((...((........))..))....))))).........)).))))...((((.(((....))))))). (-31.09 = -31.15 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 22,387,078 – 22,387,171
Length 93
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 92.31
Mean single sequence MFE -28.38
Consensus MFE -22.43
Energy contribution -22.75
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.79
SVM decision value 0.16
SVM RNA-class probability 0.610736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22387078 93 + 23771897
UAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGC---------GGUGGCCAAGGGAAAUGCGAAGGCAUUCCAUAUAGGAGAAAGUUUUUGUGUG
....(((....(((.((((.((.(.....).)).)))).))---------)..)))....((((.(((....)))))))(((((((((....))))))))). ( -25.80)
>DroSec_CAF1 38201 93 + 1
UAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUUGAGGC---------GGAGGCCAAGGGAAAUGCGAAGGCAUUCCAUAUAGGAGAAAGUUUUUGUGUG
...(((((((((....((........)).....))))))))---------).........((((.(((....)))))))(((((((((....))))))))). ( -27.70)
>DroEre_CAF1 54480 102 + 1
UAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGCGGAGGAGGCGGAGGCCAAGGGAAAUGCAAAGGCAUUCCAUAUAGGAGAAAGUUUUUGUGUG
...((((((..(((.((((.((.(.....).)).)))).)))...)))))).............((((((((((.((((.....))))...)))))))))). ( -32.30)
>DroYak_CAF1 54723 93 + 1
UAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGU---------GGAGGCCAAUGGAACUGCGAAGGCAUUCCAUAUAGGAGAAAGUUUUUGUGUG
....(((((...((.((((.((.(.....).)).)))).))---------.)))))..((((((.(((....)))))))))(((.((((....)))).))). ( -27.70)
>consensus
UAACGCCUCAAUGCAUCCAACUAGAAGGCCCAGAUGGAGGC_________GGAGGCCAAGGGAAAUGCGAAGGCAUUCCAUAUAGGAGAAAGUUUUUGUGUG
....(((((...((.((((.((.(.....).)).)))).))..........)))))....((((.(((....)))))))(((((((((....))))))))). (-22.43 = -22.75 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 22,387,078 – 22,387,171
Length 93
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 92.31
Mean single sequence MFE -25.60
Consensus MFE -21.35
Energy contribution -21.85
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.83
SVM decision value 1.23
SVM RNA-class probability 0.933078
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22387078 93 - 23771897
CACACAAAAACUUUCUCCUAUAUGGAAUGCCUUCGCAUUUCCCUUGGCCACC---------GCCUCCAUCUGGGCCUUCUAGUUGGAUGCAUUGAGGCGUUA
...............(((.....)))(((((((.(((........(((....---------)))((((.((((.....)))).)))))))...))))))).. ( -24.20)
>DroSec_CAF1 38201 93 - 1
CACACAAAAACUUUCUCCUAUAUGGAAUGCCUUCGCAUUUCCCUUGGCCUCC---------GCCUCAAUCUGGGCCUUCUAGUUGGAUGCAUUGAGGCGUUA
...............(((.....)))(((((((.((((((..((.(((((..---------..........)))))....))..))))))...))))))).. ( -24.60)
>DroEre_CAF1 54480 102 - 1
CACACAAAAACUUUCUCCUAUAUGGAAUGCCUUUGCAUUUCCCUUGGCCUCCGCCUCCUCCGCCUCCAUCUGGGCCUUCUAGUUGGAUGCAUUGAGGCGUUA
.................(((...(((((((....)))))))...)))....((((((....((.((((.((((.....)))).)))).))...))))))... ( -29.00)
>DroYak_CAF1 54723 93 - 1
CACACAAAAACUUUCUCCUAUAUGGAAUGCCUUCGCAGUUCCAUUGGCCUCC---------ACCUCCAUCUGGGCCUUCUAGUUGGAUGCAUUGAGGCGUUA
........(((..........(((((((((....))).))))))..(((((.---------.(.((((.((((.....)))).)))).)....)))))))). ( -24.60)
>consensus
CACACAAAAACUUUCUCCUAUAUGGAAUGCCUUCGCAUUUCCCUUGGCCUCC_________GCCUCCAUCUGGGCCUUCUAGUUGGAUGCAUUGAGGCGUUA
...............(((.....)))(((((((.((((((..((.((((.......................))))....))..))))))...))))))).. (-21.35 = -21.85 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 22,387,149 – 22,387,243
Length 94
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 97.04
Mean single sequence MFE -22.27
Consensus MFE -20.05
Energy contribution -20.30
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.90
SVM decision value 0.42
SVM RNA-class probability 0.728319
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22387149 94 + 23771897
UAUAGGAGAAAGUUUUUGUGUGUGCAACGGGGAA-AAA-GAAAACUUUUUAUUAAAGUCAGCUGAAAUGGGUGGAACUCGUUUCGGUUUCGAAUUU
..(((.(((((((((((.....(.(....).)..-...-))))))))))).))).....((((((((((((.....))))))))))))........ ( -21.30)
>DroSec_CAF1 38272 95 + 1
UAUAGGAGAAAGUUUUUGUGUGUGCAACAGGGAAAAAA-GAAAACUUUUUAUUAAAGUCAGCUGAAAUGGGUGGAACUCGUUUCGGUCUCGAAUUU
..(((.(((((((((((.....(.(.....).).....-))))))))))).)))...((((((((((((((.....)))))))))).)).)).... ( -21.20)
>DroEre_CAF1 54560 96 + 1
UAUAGGAGAAAGUUUUUGUGUGUGCAACAGGGAAAAAAGGAAAACUUUUUAUUAAAGUCAGCUGAAAUGGGUGGAACUCGUUUCGGUUUCGGAUUU
..(((.(((((((((((.(.....(......).....).))))))))))).)))(((((.(((((((((((.....)))))))))))....))))) ( -23.30)
>DroYak_CAF1 54794 96 + 1
UAUAGGAGAAAGUUUUUGUGUGUGCAACAGGGAAAAAAGGAAAACUUUUUAUUAAAGUCAGCUGAAAUGGGUGGAACUCGUUUCGGUUUCGGAUUU
..(((.(((((((((((.(.....(......).....).))))))))))).)))(((((.(((((((((((.....)))))))))))....))))) ( -23.30)
>consensus
UAUAGGAGAAAGUUUUUGUGUGUGCAACAGGGAAAAAA_GAAAACUUUUUAUUAAAGUCAGCUGAAAUGGGUGGAACUCGUUUCGGUUUCGAAUUU
..(((.(((((((((((.(.....(......).....).))))))))))).))).....((((((((((((.....))))))))))))........ (-20.05 = -20.30 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:05 2006