Locus 7513

Sequence ID X_DroMel_CAF1
Location 18,775,787 – 18,775,986
Length 199
Max. P 0.981696
window12323 window12324 window12325 window12326 window12327

overview

Window 3

Location 18,775,787 – 18,775,907
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.50
Mean single sequence MFE -29.43
Consensus MFE -19.64
Energy contribution -20.20
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -1.65
Structure conservation index 0.67
SVM decision value 0.17
SVM RNA-class probability 0.618380
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18775787 120 + 22224390
CCUGAGCAAGGCGAACUCAAGUCCAAACUUCUACUCCUGAGCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUUGAAAGAGACUCGGAA
.(((((.((((((.....((((....))))....((((((.(.....((((((.....(....).....))))))...).))))))...)))))).......(((....))).))))).. ( -34.70)
>DroSec_CAF1 21093 120 + 1
CCUGAGGAAGGUGAACUGUAGUCCAAACUCCUACUCCUCAGCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAA
.(((((.((((((....((((.........))))((((....(((((((((((.....(....).....))))))..)))))))))...)))))).......(((....))).))))).. ( -35.10)
>DroEre_CAF1 21034 107 + 1
CCUUAGGAAUUCCAAC-------------UAUAGUCCUAAGCGACUUUCCUCUUUUCCGGAGUCCAUUCGGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAACAGACGCGGAA
.(((((((........-------------.....))))))).............(((((..(((..((((.(((((...((.(((......))).))..)))))))))...))).))))) ( -26.22)
>DroYak_CAF1 20810 93 + 1
CU---------------------------CAUCCUCCUAAGCGACUUUUCUCUUUUCCGGAGUUCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAA
..---------------------------..(((....(((((..(((((((((.(((.(((....)))...))).)))...)))))).)))))........(((....)))....))). ( -21.70)
>consensus
CCUGAGGAAGGCGAAC_____________CAUACUCCUAAGCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAA
..................................(((.(((((..(((((((((.(((.(((....)))...))).)))...)))))).)))))........(((....)))....))). (-19.64 = -20.20 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,775,827 – 18,775,947
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -35.30
Consensus MFE -32.41
Energy contribution -33.10
Covariance contribution 0.69
Combinations/Pair 1.08
Mean z-score -2.56
Structure conservation index 0.92
SVM decision value 1.89
SVM RNA-class probability 0.981696
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18775827 120 + 22224390
GCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUUGAAAGAGACUCGGAAAAGCGGAUGGCGAAAAAAAUCGCCGAAAAUGAAACGAAGC
.((....(((.((((((((.((.((.((((.(((((...((.(((......))).))..))))))))).).).)))))))))).)))((((((......)))))).........)).... ( -34.90)
>DroSec_CAF1 21133 119 + 1
GCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGCGAAA-AAAUCGCCGAAAAUGAAGCGAAGC
((.....(((.((((((((.((.((.(((.((((((...((.(((......))).))..))))))))).).).)))))))))).)))((((((..-...))))))........))..... ( -38.20)
>DroEre_CAF1 21061 118 + 1
GCGACUUUCCUCUUUUCCGGAGUCCAUUCGGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAACAGACGCGGAAAAGCGGAUGGGGAA--AAAUCGCCGAAAAUGAAACGAAGC
.((....(((.((((((((..(((..((((.(((((...((.(((......))).))..)))))))))...))).)))))))).)))(((.((.--...)).))).........)).... ( -34.90)
>DroYak_CAF1 20823 119 + 1
GCGACUUUUCUCUUUUCCGGAGUUCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGGGAAA-AAAUCGCCGAAAAUGAAACCAAGC
((.....(((.(((((((((..(((.(((.((((((...((.(((......))).))..))))))))).)))..))))))))).)))(((.((..-...)).))).............)) ( -33.20)
>consensus
GCGACUUUCCUCUUUUCCGGAGACCAUUCAGAGGAUAAGGUCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGCGAAA_AAAUCGCCGAAAAUGAAACGAAGC
((.....(((.((((((((.((((..((..((((((...((.(((......))).))..))))))..))..)))))))))))).)))((((((......)))))).............)) (-32.41 = -33.10 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,775,827 – 18,775,947
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -37.03
Consensus MFE -31.77
Energy contribution -33.77
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.94
Structure conservation index 0.86
SVM decision value 1.49
SVM RNA-class probability 0.958753
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18775827 120 - 22224390
GCUUCGUUUCAUUUUCGGCGAUUUUUUUCGCCAUCCGCUUUUCCGAGUCUCUUUCAAGGAUUUGUAAAGCGUUUUCCUGACCUUAUCCUCUGAAUGGUCUCCGGAAAAGAGGAAAGUCGC
((((............(((((......))))).(((.((((((((((.((..(((((((((.....(((.(((.....))))))))))).)))).)).)).)))))))).)))))))... ( -37.20)
>DroSec_CAF1 21133 119 - 1
GCUUCGCUUCAUUUUCGGCGAUUU-UUUCGCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGACCUUAUCCUCUGAAUGGUCUCCGGAAAAGAGGAAAGUCGC
....(((((.......(((((...-..))))).(((.((((((((((.((.(((.((((((.....(((.(((.....)))))))))))).))).)).)).)))))))).)))))).)). ( -39.50)
>DroEre_CAF1 21061 118 - 1
GCUUCGUUUCAUUUUCGGCGAUUU--UUCCCCAUCCGCUUUUCCGCGUCUGUUUCGAGGAUUUGUAAAGCGUUUUCCUGACCUUAUCCUCCGAAUGGACUCCGGAAAAGAGGAAAGUCGC
.................(((((((--.......(((.((((((((.((((((((.((((((.....(((.(((.....)))))))))))).))))))))..)))))))).)))))))))) ( -38.71)
>DroYak_CAF1 20823 119 - 1
GCUUGGUUUCAUUUUCGGCGAUUU-UUUCCCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGACCUUAUCCUCUGAAUGAACUCCGGAAAAGAGAAAAGUCGC
.................(((((((-(((.........(((((((((((.((.(((((((((.....(((.(((.....)))))))))))).))).))))).)))))))).)))))))))) ( -32.70)
>consensus
GCUUCGUUUCAUUUUCGGCGAUUU_UUUCCCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGACCUUAUCCUCUGAAUGGACUCCGGAAAAGAGGAAAGUCGC
((((............(((((......))))).(((.((((((((((((..(((.((((((.....(((.(((.....)))))))))))).)))..)))).)))))))).)))))))... (-31.77 = -33.77 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 18,775,867 – 18,775,986
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 95.36
Mean single sequence MFE -26.61
Consensus MFE -20.83
Energy contribution -21.95
Covariance contribution 1.13
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.78
SVM decision value 0.23
SVM RNA-class probability 0.644883
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18775867 119 + 22224390
UCAGGAAAACGCUUUACAAAUCCUUGAAAGAGACUCGGAAAAGCGGAUGGCGAAAAAAAUCGCCGAAAAUGAAACGAAGCGAAAAUAAAAUUUCCCAGCUAAUGACAAAAAUUUCCGGU
...(((((.((((((.(.....(((....))).....).))))))..((((((......))))))............(((((((......))))...)))...........)))))... ( -24.90)
>DroSec_CAF1 21173 118 + 1
UCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGCGAAA-AAAUCGCCGAAAAUGAAGCGAAGCGAAAAUAAAAUUUCCAAGCUAAUGACAAAAAUUUCCGGU
...(((((.((((((.(.....(((....))).....).))))))..((((((..-...)))))).......(((...(.((((......)))))..)))...........)))))... ( -29.70)
>DroEre_CAF1 21101 117 + 1
UCAGGAAAACGCUUUACAAAUCCUCGAAACAGACGCGGAAAAGCGGAUGGGGAA--AAAUCGCCGAAAAUGAAACGAAGCGAACAUAAAAUUUCCCAGCUAAUGACAAAAAUUUCCGGU
...(((((.((((((.....(((.((.......)).)))))))))..(((((((--...((((((.........))..))))........)))))))..............)))))... ( -24.20)
>DroYak_CAF1 20863 118 + 1
UCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGGGAAA-AAAUCGCCGAAAAUGAAACCAAGCGAAUAUAAAAUUUCCCAGCUAAUGACAAAAAUUUCCGGU
...(((((.((((((.(.....(((....))).....).))))))..(((((((.-...((((...............))))........)))))))..............)))))... ( -27.66)
>consensus
UCAGGAAAACGCUUUACAAAUCCUCGAAAGAGACUCGGAAAAGCGGAUGGCGAAA_AAAUCGCCGAAAAUGAAACGAAGCGAAAAUAAAAUUUCCCAGCUAAUGACAAAAAUUUCCGGU
...(((((.((((((.(.....(((....))).....).))))))..((((((......))))))............(((.................)))...........)))))... (-20.83 = -21.95 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 18,775,867 – 18,775,986
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 95.36
Mean single sequence MFE -27.05
Consensus MFE -22.54
Energy contribution -23.10
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 0.11
SVM RNA-class probability 0.589121
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18775867 119 - 22224390
ACCGGAAAUUUUUGUCAUUAGCUGGGAAAUUUUAUUUUCGCUUCGUUUCAUUUUCGGCGAUUUUUUUCGCCAUCCGCUUUUCCGAGUCUCUUUCAAGGAUUUGUAAAGCGUUUUCCUGA
...(((((....((.....(((.(..((......))..))))......)).....(((((......)))))...((((((..(((((((.......))))))).)))))).)))))... ( -28.50)
>DroSec_CAF1 21173 118 - 1
ACCGGAAAUUUUUGUCAUUAGCUUGGAAAUUUUAUUUUCGCUUCGCUUCAUUUUCGGCGAUUU-UUUCGCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGA
...(((((...........(((..(((((......)))).)...)))........(((((...-..)))))...((((((..((((((((....)).)))))).)))))).)))))... ( -28.10)
>DroEre_CAF1 21101 117 - 1
ACCGGAAAUUUUUGUCAUUAGCUGGGAAAUUUUAUGUUCGCUUCGUUUCAUUUUCGGCGAUUU--UUCCCCAUCCGCUUUUCCGCGUCUGUUUCGAGGAUUUGUAAAGCGUUUUCCUGA
...(((((...............((((((........(((((.............)))))..)--)))))....(((((((((.((.......)).))).....)))))).)))))... ( -23.82)
>DroYak_CAF1 20863 118 - 1
ACCGGAAAUUUUUGUCAUUAGCUGGGAAAUUUUAUAUUCGCUUGGUUUCAUUUUCGGCGAUUU-UUUCCCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGA
...(((((...............((((((........(((((.((........)))))))...-))))))....((((((..((((((((....)).)))))).)))))).)))))... ( -27.80)
>consensus
ACCGGAAAUUUUUGUCAUUAGCUGGGAAAUUUUAUUUUCGCUUCGUUUCAUUUUCGGCGAUUU_UUUCCCCAUCCGCUUUUCCGAGUCUCUUUCGAGGAUUUGUAAAGCGUUUUCCUGA
...(((((...........(((..((..(........)..))..)))........(((((......)))))...((((((..(((((((.......))))))).)))))).)))))... (-22.54 = -23.10 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:49 2006