Locus 9719

Sequence ID 3R_DroMel_CAF1
Location 25,706,694 – 25,706,858
Length 164
Max. P 0.999312
window15523 window15524 window15525 window15526 window15527

overview

Window 3

Location 25,706,694 – 25,706,797
Length 103
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 84.52
Mean single sequence MFE -23.02
Consensus MFE -13.82
Energy contribution -14.94
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -2.18
Structure conservation index 0.60
SVM decision value 0.18
SVM RNA-class probability 0.620153
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25706694 103 + 27905053
AAUAACUCAAAAAAUGGCACAUUAUAUGAGGGAAUUUCUAUUGUUCAU---------UAAAUGUGUGUAUAAUGCGGGAAAAAAUUUGAAUUUUUCCAUGCAUUACACAAGU
................(((((((..(((((.((.......)).)))))---------..)))))))((.((((((((((((((.......))))))).))))))).)).... ( -25.30)
>DroSec_CAF1 11314 103 + 1
AUUGACUCCAAAAAUGGCGCAUUAUAUGAGGGAAUUUCUAUUAUUCAU---------UAAACGUGUGUAUAAUGCGCGGAAAAAUUUUAAUUUUUCCAUGCAUUACACAAGU
............((((((((((((((((.(.((((.......))))..---------....)...))))))))))))((((((((....))))))))...))))........ ( -24.00)
>DroSim_CAF1 11523 112 + 1
AUUAACUCCAAAAAUGGCGCAUUAUAUGAGGGAAUUUCUAUUAUUCAUUAAAUUCAUUAAAUGUGUGUAUAAUGCGCGGAAAAAUUUUAGUUUUUCCAUGCAUUACACAAGU
................(((((((..(((((.((((.......))))......)))))..)))))))((.(((((((.((((((((....)))))))).))))))).)).... ( -27.50)
>DroEre_CAF1 12567 102 + 1
GUUAGCUCCAA-GAUGGCACUUUAUAUGAGGGAAUUUCUAUUAUUCAC---------UAAAUGUGGAUAUAAUGCGCAGAAAAAUUGCAAUCUCUCCAUGCAUUACACAAGC
....((.((..-...))..........((((((........(((((((---------.....)))))))......((((.....))))..))))))...))........... ( -17.70)
>DroYak_CAF1 11722 103 + 1
GUUAACUCCAAAAAUGCCACAUUAUACGAGGGAAUUUCUAUUAUUCAC---------UAAGUGUGGCUAUAAUGCGGUUAAAAAUUUCAAUUUUUCCAUGCAUUACACAAGC
...............((((((((.....((.((((.......)))).)---------).))))))))..(((((((...((((((....))))))...)))))))....... ( -20.60)
>consensus
AUUAACUCCAAAAAUGGCACAUUAUAUGAGGGAAUUUCUAUUAUUCAU_________UAAAUGUGUGUAUAAUGCGCGGAAAAAUUUCAAUUUUUCCAUGCAUUACACAAGU
.....(((....((((...))))....))).((((.......))))...............((((....(((((((.((((((((....)))))))).)))))))))))... (-13.82 = -14.94 +   1.12)

alignment

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secondary structure

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Window 4

Location 25,706,694 – 25,706,797
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 84.52
Mean single sequence MFE -23.42
Consensus MFE -17.24
Energy contribution -16.96
Covariance contribution -0.28
Combinations/Pair 1.33
Mean z-score -2.51
Structure conservation index 0.74
SVM decision value 1.52
SVM RNA-class probability 0.961118
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25706694 103 - 27905053
ACUUGUGUAAUGCAUGGAAAAAUUCAAAUUUUUUCCCGCAUUAUACACACAUUUA---------AUGAACAAUAGAAAUUCCCUCAUAUAAUGUGCCAUUUUUUGAGUUAUU
(((((((((((((..(((((((.......))))))).))))))))).((((((..---------((((.....(....)....))))..)))))).........)))).... ( -24.30)
>DroSec_CAF1 11314 103 - 1
ACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCAUUAUACACACGUUUA---------AUGAAUAAUAGAAAUUCCCUCAUAUAAUGCGCCAUUUUUGGAGUCAAU
...((((((((((.(((((((((....))))))))).))))))))))(.((((..---------((((.....(....)....))))..)))).)(((....)))....... ( -24.90)
>DroSim_CAF1 11523 112 - 1
ACUUGUGUAAUGCAUGGAAAAACUAAAAUUUUUCCGCGCAUUAUACACACAUUUAAUGAAUUUAAUGAAUAAUAGAAAUUCCCUCAUAUAAUGCGCCAUUUUUGGAGUUAAU
...((((((((((.((((((((......)))))))).))))))))))..........((((((............)))))).......((((...(((....))).)))).. ( -24.80)
>DroEre_CAF1 12567 102 - 1
GCUUGUGUAAUGCAUGGAGAGAUUGCAAUUUUUCUGCGCAUUAUAUCCACAUUUA---------GUGAAUAAUAGAAAUUCCCUCAUAUAAAGUGCCAUC-UUGGAGCUAAC
(((((((((((((..((((((((....))))))))..))))))))).(((.((((---------((((.....(....)....)))).))))))).....-...)))).... ( -22.70)
>DroYak_CAF1 11722 103 - 1
GCUUGUGUAAUGCAUGGAAAAAUUGAAAUUUUUAACCGCAUUAUAGCCACACUUA---------GUGAAUAAUAGAAAUUCCCUCGUAUAAUGUGGCAUUUUUGGAGUUAAC
((((.((((((((....((((((....))))))....))))))))((((((...(---------(.((((.......)))).)).......)))))).......)))).... ( -20.40)
>consensus
ACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCAUUAUACACACAUUUA_________AUGAAUAAUAGAAAUUCCCUCAUAUAAUGUGCCAUUUUUGGAGUUAAU
(((((((((((((.(((((((((....))))))))).)))))))))..................((((.....(....)....)))).................)))).... (-17.24 = -16.96 +  -0.28)

alignment

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secondary structure

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Window 5

Location 25,706,726 – 25,706,837
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.39
Mean single sequence MFE -23.76
Consensus MFE -18.36
Energy contribution -20.24
Covariance contribution 1.88
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.77
SVM decision value 1.21
SVM RNA-class probability 0.930483
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25706726 111 + 27905053
AAUUUCUAUUGUUCAU---------UAAAUGUGUGUAUAAUGCGGGAAAAAAUUUGAAUUUUUCCAUGCAUUACACAAGUGCAUUUCAAAAGCGAAACGUAUAUAAUUGAAAUAACUCGG
.(((((.(((((....---------......((((((..((((((((((((.......))))))).))))))))))).((((.((((......)))).))))))))).)))))....... ( -25.50)
>DroSec_CAF1 11346 111 + 1
AAUUUCUAUUAUUCAU---------UAAACGUGUGUAUAAUGCGCGGAAAAAUUUUAAUUUUUCCAUGCAUUACACAAGUGCAUUUCAAAAGCGAAUCGUAUAUAAUUGAAAUAACUCGG
.(((((.(((((....---------......((((((..(((((.((((((((....)))))))).))))))))))).((((..(((......)))..))))))))).)))))....... ( -26.40)
>DroSim_CAF1 11555 120 + 1
AAUUUCUAUUAUUCAUUAAAUUCAUUAAAUGUGUGUAUAAUGCGCGGAAAAAUUUUAGUUUUUCCAUGCAUUACACAAGUGCAUUUCAAAAGCGAAUCGUAUAUAAUUGAAAUAACUCGG
.(((((.(((((...................((((((..(((((.((((((((....)))))))).))))))))))).((((..(((......)))..))))))))).)))))....... ( -27.00)
>DroEre_CAF1 12598 111 + 1
AAUUUCUAUUAUUCAC---------UAAAUGUGGAUAUAAUGCGCAGAAAAAUUGCAAUCUCUCCAUGCAUUACACAAGCGCAUUUCAAUAGCGAAACGUAUAUAAUUGAAAUAACUCGG
.(((((...(((((((---------.....))))))).(((((((........((((.........))))........))))))).......................)))))....... ( -20.19)
>DroYak_CAF1 11754 111 + 1
AAUUUCUAUUAUUCAC---------UAAGUGUGGCUAUAAUGCGGUUAAAAAUUUCAAUUUUUCCAUGCAUUACACAAGCGCAUUUCAAUAGCGAAACGUAUAUAAUUGAAAUAGCUCGG
.(((((.(((((..((---------...((((.....(((((((...((((((....))))))...))))))).....)))).((((......)))).))..))))).)))))....... ( -19.70)
>consensus
AAUUUCUAUUAUUCAU_________UAAAUGUGUGUAUAAUGCGCGGAAAAAUUUCAAUUUUUCCAUGCAUUACACAAGUGCAUUUCAAAAGCGAAACGUAUAUAAUUGAAAUAACUCGG
.(((((.(((((.................((((....(((((((.((((((((....)))))))).))))))))))).((((.((((......)))).))))))))).)))))....... (-18.36 = -20.24 +   1.88)

alignment

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secondary structure

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Window 6

Location 25,706,726 – 25,706,837
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.39
Mean single sequence MFE -25.56
Consensus MFE -22.77
Energy contribution -22.89
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -2.67
Structure conservation index 0.89
SVM decision value 3.50
SVM RNA-class probability 0.999312
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25706726 111 - 27905053
CCGAGUUAUUUCAAUUAUAUACGUUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUCAAAUUUUUUCCCGCAUUAUACACACAUUUA---------AUGAACAAUAGAAAUU
..((((((((((((.................)))))))).))))(((((((((..(((((((.......))))))).))))))))).........---------................ ( -24.33)
>DroSec_CAF1 11346 111 - 1
CCGAGUUAUUUCAAUUAUAUACGAUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCAUUAUACACACGUUUA---------AUGAAUAAUAGAAAUU
....(((((((..((((...(((....((.........))...((((((((((.(((((((((....))))))))).))))))))))..))).))---------)))))))))....... ( -27.90)
>DroSim_CAF1 11555 120 - 1
CCGAGUUAUUUCAAUUAUAUACGAUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAACUAAAAUUUUUCCGCGCAUUAUACACACAUUUAAUGAAUUUAAUGAAUAAUAGAAAUU
.......(((((.(((((.((.(((((((.........))...((((((((((.((((((((......)))))))).))))))))))..........)))))...)).))))).))))). ( -27.40)
>DroEre_CAF1 12598 111 - 1
CCGAGUUAUUUCAAUUAUAUACGUUUCGCUAUUGAAAUGCGCUUGUGUAAUGCAUGGAGAGAUUGCAAUUUUUCUGCGCAUUAUAUCCACAUUUA---------GUGAAUAAUAGAAAUU
.......(((((.(((((...(((((((....)))))))((((((((((((((..((((((((....))))))))..))))))....))))...)---------))).))))).))))). ( -25.70)
>DroYak_CAF1 11754 111 - 1
CCGAGCUAUUUCAAUUAUAUACGUUUCGCUAUUGAAAUGCGCUUGUGUAAUGCAUGGAAAAAUUGAAAUUUUUAACCGCAUUAUAGCCACACUUA---------GUGAAUAAUAGAAAUU
.((((((((((((((...............))))))))).)))))((((((((....((((((....))))))....))))))))..(((.....---------)))............. ( -22.46)
>consensus
CCGAGUUAUUUCAAUUAUAUACGUUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCAUUAUACACACAUUUA_________AUGAAUAAUAGAAAUU
..((((((((((((.................)))))))).))))(((((((((.(((((((((....))))))))).))))))))).................................. (-22.77 = -22.89 +   0.12)

alignment

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secondary structure

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Window 7

Location 25,706,757 – 25,706,858
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 87.23
Mean single sequence MFE -26.18
Consensus MFE -19.07
Energy contribution -19.11
Covariance contribution 0.04
Combinations/Pair 1.21
Mean z-score -2.23
Structure conservation index 0.73
SVM decision value 0.86
SVM RNA-class probability 0.869483
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25706757 101 - 27905053
GCAUGAAGAGAGUGAGUCGCACCGAGUUAUUUCAAUUAUAUACGUUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUCAAAUUUUUUCCCGCA
((((...(((((((((.((.....((((.....)))).....)).)))))))))...))))..........(((..(((((((.......))))))).))) ( -23.70)
>DroSec_CAF1 11377 101 - 1
GCAUGAAGAGAGCGAGUCGCACCGAGUUAUUUCAAUUAUAUACGAUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCA
((((...((((((((((((.....((((.....)))).....))))))))))))...))))..........(((.(((((((((....))))))))).))) ( -33.60)
>DroSim_CAF1 11595 101 - 1
GCAUGAAGAGAGCGAGUCGCACCGAGUUAUUUCAAUUAUAUACGAUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAACUAAAAUUUUUCCGCGCA
((((...((((((((((((.....((((.....)))).....))))))))))))...))))..........(((.((((((((......)))))))).))) ( -32.50)
>DroEre_CAF1 12629 87 - 1
--------------AGUCGCACCGAGUUAUUUCAAUUAUAUACGUUUCGCUAUUGAAAUGCGCUUGUGUAAUGCAUGGAGAGAUUGCAAUUUUUCUGCGCA
--------------.((..(((.(((((((((((((...............))))))))).)))))))..))((..((((((((....))))))))..)). ( -20.56)
>DroYak_CAF1 11785 101 - 1
GCAUGAAGAGUGUGAGUCGCACCGAGCUAUUUCAAUUAUAUACGUUUCGCUAUUGAAAUGCGCUUGUGUAAUGCAUGGAAAAAUUGAAAUUUUUAACCGCA
((.........(((.((..(((.(((((((((((((...............))))))))).)))))))..)).)))((((((((....))))))..)))). ( -20.56)
>consensus
GCAUGAAGAGAGCGAGUCGCACCGAGUUAUUUCAAUUAUAUACGUUUCGCUUUUGAAAUGCACUUGUGUAAUGCAUGGAAAAAUUAAAAUUUUUCCGCGCA
...............((..(((.((((((((((((.................)))))))).)))))))..))((.(((((((((....))))))))).)). (-19.07 = -19.11 +   0.04)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:36 2006