Locus 7430

Sequence ID X_DroMel_CAF1
Location 18,538,844 – 18,539,132
Length 288
Max. P 0.943555
window12183 window12184 window12185 window12186 window12187 window12188 window12189

overview

Window 3

Location 18,538,844 – 18,538,939
Length 95
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -34.97
Consensus MFE -33.79
Energy contribution -33.57
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.97
SVM decision value 1.34
SVM RNA-class probability 0.943555
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538844 95 + 22224390
ACACCUAAGCUCUAAACUC-GGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUACAUGGAGCAGUCGCCAUGGAGC
........((((((.....-(((((((......(((......((((....)))).....)))((((.(((....))).))))))))))).)))))) ( -31.80)
>DroSec_CAF1 3721 96 + 1
ACACCUAAGCUCUAAGCUAAGGCGGCUCAAUGAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCUGUGUCUGCAUGGAGCAGCCGCCAUGGAGC
........((((((.((.((((((((((((((((......))).)))).))))))))).(((((((((((....)))))))).)))))..)))))) ( -38.50)
>DroSim_CAF1 3808 96 + 1
ACACCUAAGCUCUAAGCUAAGGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGC
........((((((.((.((((((((((((((...........))))).))))))))).(((((((.(((....))).)))).)))))..)))))) ( -34.60)
>consensus
ACACCUAAGCUCUAAGCUAAGGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGC
........((((((......(((((((......(((......((((....)))).....)))((((..((....))..))))))))))).)))))) (-33.79 = -33.57 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,538,860 – 18,538,979
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -45.50
Consensus MFE -44.72
Energy contribution -44.50
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.45
Structure conservation index 0.98
SVM decision value 0.12
SVM RNA-class probability 0.591393
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538860 119 + 22224390
CUC-GGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUACAUGGAGCAGUCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCAAACAGCCCAUGUCC
...-(((((((......(((......((((....)))).....)))((((.(((....))).)))))))))))((((.((.((((.....))))((.(....))).....)))))).... ( -42.20)
>DroSec_CAF1 3737 120 + 1
CUAAGGCGGCUCAAUGAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCUGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCC
(((.(((((((......(((......((((....)))).....)))((((((((....))))))))))))))).)))....((((.....))))(((((..(((......)))..))))) ( -48.60)
>DroSim_CAF1 3824 120 + 1
CUAAGGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCC
(((.(((((((......(((......((((....)))).....)))((((.(((....))).))))))))))).)))....((((.....))))(((((..(((......)))..))))) ( -45.70)
>consensus
CUAAGGCGGCUCAAUUAGCUUCAAUUCGAUUGUGGUCGUCUUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCC
....(((((((......(((......((((....)))).....)))((((..((....))..)))))))))))((((.((.((((.....))))((.(....))).....)))))).... (-44.72 = -44.50 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,538,899 – 18,539,019
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -43.83
Consensus MFE -42.69
Energy contribution -42.47
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.97
SVM decision value 0.56
SVM RNA-class probability 0.782578
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538899 120 + 22224390
UUUGGCGCUCAGUGUCUACAUGGAGCAGUCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCAAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUAGUAGCCAAAUCAA
((((((((((.(((....))).))))....(((((((..(.((((.....))))(((((..(((......)))..)))))..)..))(((.....)))))))).......)))))).... ( -41.60)
>DroSec_CAF1 3777 120 + 1
UUUGGCGCUCUGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAA
((((((((((((((....)))))))).((((((((((..(.((((.....))))(((((..(((......)))..)))))..)..))(((.....))))))))...))).)))))).... ( -46.40)
>DroSim_CAF1 3864 120 + 1
UUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAA
((((((((((.(((....))).)))).((((((((((..(.((((.....))))(((((..(((......)))..)))))..)..))(((.....))))))))...))).)))))).... ( -43.50)
>consensus
UUUGGCGCUCAGUGUCUGCAUGGAGCAGCCGCCAUGGAGCAUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAA
((((((((((..((....))..))))(((((((((((..(.((((.....))))(((((..(((......)))..)))))..)..)))......))))..))))......)))))).... (-42.69 = -42.47 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 18,538,899 – 18,539,019
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -43.00
Consensus MFE -42.33
Energy contribution -42.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.98
SVM decision value 0.41
SVM RNA-class probability 0.725004
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538899 120 - 22224390
UUGAUUUGGCUACUAAAGCCAUACCAGUUAAGUGGGUCCAGGACAUGGGCUGUUUGGCCUUCGUCCUCCGCAUUUCGGAUGCUCCAUGGCGACUGCUCCAUGUAGACACUGAGCGCCAAA
....((((((.......(((((.........((((....(((((..(((((....)))))..))))))))).....((.....)))))))....((((..((....))..)))))))))) ( -42.50)
>DroSec_CAF1 3777 120 - 1
UUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCAGGACAUGGGCUGUUCGGCCUUCGUCCUCCGCAUUUCGGAUGCUCCAUGGCGGCUGCUCCAUGCAGACACAGAGCGCCAAA
(((((((((((.....)))))....))))))((((....(((((..(((((....)))))..))))))))).....((.(((((..((....((((.....)))).))..)))))))... ( -43.30)
>DroSim_CAF1 3864 120 - 1
UUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCAGGACAUGGGCUGUUCGGCCUUCGUCCUCCGCAUUUCGGAUGCUCCAUGGCGGCUGCUCCAUGCAGACACUGAGCGCCAAA
(((((((((((.....)))))....))))))((((....(((((..(((((....)))))..))))))))).....((.(((((..((....((((.....)))).))..)))))))... ( -43.20)
>consensus
UUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCAGGACAUGGGCUGUUCGGCCUUCGUCCUCCGCAUUUCGGAUGCUCCAUGGCGGCUGCUCCAUGCAGACACUGAGCGCCAAA
....((((((.......(((((.........((((....(((((..(((((....)))))..))))))))).....((.....)))))))....((((..((....))..)))))))))) (-42.33 = -42.33 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 18,538,939 – 18,539,059
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -40.47
Consensus MFE -38.83
Energy contribution -39.17
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.96
SVM decision value -0.05
SVM RNA-class probability 0.508872
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538939 120 + 22224390
AUCCGAAAUGCGGAGGACGAAGGCCAAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUAGUAGCCAAAUCAAUAACACCCGAUAAGCCGAUUGGUCGAGGGUAAUGGUGGCC
.((((.....))))(((((..(((......)))..))))).....(((((....((((.(((((.....))))).)))).....((((.....(((....)))...))))...))))).. ( -38.60)
>DroSec_CAF1 3817 120 + 1
AUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAAUAACACCCGAUAAGCCGACUGGGCGAGGGUAAUGGUGGCC
.((((.....))))(((((..(((......)))..))))).....(((((....((((.(((((.....))))).)))).....((((.....(((.....)))..))))...))))).. ( -41.40)
>DroSim_CAF1 3904 120 + 1
AUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAAUAACACCCGAUAAGCCGACUGGGCGAGGGUAAUGGUGGCC
.((((.....))))(((((..(((......)))..))))).....(((((....((((.(((((.....))))).)))).....((((.....(((.....)))..))))...))))).. ( -41.40)
>consensus
AUCCGAAAUGCGGAGGACGAAGGCCGAACAGCCCAUGUCCUGGACCCACUUAACUGGUAUGGCUUUGGUAGCCAAAUCAAUAACACCCGAUAAGCCGACUGGGCGAGGGUAAUGGUGGCC
.((((.....))))(((((..(((......)))..))))).....(((((....((((.(((((.....))))).)))).....((((.....(((.....)))..))))...))))).. (-38.83 = -39.17 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 18,538,979 – 18,539,099
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -38.83
Consensus MFE -37.51
Energy contribution -37.40
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.60
Structure conservation index 0.97
SVM decision value 0.22
SVM RNA-class probability 0.639877
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18538979 120 - 22224390
UUUUUGGAAAUCCGCGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGACCAAUCGGCUUAUCGGGUGUUAUUGAUUUGGCUACUAAAGCCAUACCAGUUAAGUGGGUCCA
....((((..(((((.(((((...((((((((....)))))))).....(((((((((....))))......))))).)))))...(((((.....)))))..........))))))))) ( -37.80)
>DroSec_CAF1 3857 120 - 1
UUUUUGGAAAUUCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUAUUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCA
....((((...((((.(((((...((((((((....)))))))).....(((((..(((.....))).....))))).)))))...(((((.....)))))..........)))).)))) ( -38.10)
>DroSim_CAF1 3944 120 - 1
UUUUUGGAAAUCCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUAUUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCA
....((((..(((((.(((((...((((((((....)))))))).....(((((..(((.....))).....))))).)))))...(((((.....)))))..........))))))))) ( -40.60)
>consensus
UUUUUGGAAAUCCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUAUUGAUUUGGCUACCAAAGCCAUACCAGUUAAGUGGGUCCA
....((((...((((.(((((...((((((((....)))))))).....(((((..(((.....))).....))))).)))))...(((((.....)))))..........)))).)))) (-37.51 = -37.40 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 18,539,019 – 18,539,132
Length 113
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 97.05
Mean single sequence MFE -37.53
Consensus MFE -34.36
Energy contribution -34.03
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -1.73
Structure conservation index 0.92
SVM decision value 0.08
SVM RNA-class probability 0.575863
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18539019 113 - 22224390
AACGAUGGUGGGCAAGUAGAUUCAAUUUCGAAAUUUUUGGAAAUCCGCGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGACCAAUCGGCUUAUCGGGUGUUA
(((((((((.((((.(..((((....(((((.....)))))))))..)....)))).((((((((....))))))))))))))((((((((....))))......))))))). ( -36.50)
>DroSec_CAF1 3897 113 - 1
AACGAUGGUGGGCAAGCAGAUUCAAUUUCGAAAUUUUUGGAAAUUCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUA
(((((((((.((((.((......((((((.((....)).))))))...))..)))).((((((((....))))))))))))))((((..(((.....))).....))))))). ( -38.00)
>DroSim_CAF1 3984 113 - 1
AACGAUGGUGGGCAAGUAGAUUCAAUUUCGAAAUUUUUGGAAAUCCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUA
(((((((((.((((.((.((((....(((((.....))))))))).))....)))).((((((((....))))))))))))))((((..(((.....))).....))))))). ( -38.10)
>consensus
AACGAUGGUGGGCAAGUAGAUUCAAUUUCGAAAUUUUUGGAAAUCCACGCAGUGCCAGGUCAUCGCAUGCGAUGGCCACCAUUACCCUCGCCCAGUCGGCUUAUCGGGUGUUA
(((((((((.((((.((...(((......))).....(((....))).))..)))).((((((((....))))))))))))))((((..(((.....))).....))))))). (-34.36 = -34.03 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:47 2006