Locus 6544

Sequence ID 3R_DroMel_CAF1
Location 17,249,458 – 17,249,725
Length 267
Max. P 0.992290
window10651 window10652 window10653 window10654 window10655 window10656 window10657

overview

Window 1

Location 17,249,458 – 17,249,576
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.60
Mean single sequence MFE -17.66
Consensus MFE -14.46
Energy contribution -15.86
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.82
SVM decision value 0.26
SVM RNA-class probability 0.659229
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249458 118 - 27905053
UAC--UAUACACUGUGCCAUACGACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
...--.........((((.......))))..............................((.(((((((..((((..............))))..((((....))))...))))))).)) ( -20.64)
>DroSec_CAF1 45884 115 - 1
-----CAAACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
-----.........((((.......))))..............................((.(((((((..((((..............))))..((((....))))...))))))).)) ( -20.64)
>DroEre_CAF1 47700 120 - 1
UACCACAUACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACCUUAUGACGGCCUCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
..............((((.......))))..............................((.(.(((((..((((..............))))..((((....))))...))))).).)) ( -17.74)
>DroYak_CAF1 68705 120 - 1
UACUACAUACACUGUACCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
...........((((...........)))).............................((.(((((((..((((..............))))..((((....))))...))))))).)) ( -17.34)
>DroAna_CAF1 37495 107 - 1
--------ACA-----CAGCACAACACCGGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACAGCCCCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
--------...-----...........................................((.(((((((...(((..............)))...((((....))))...))))))).)) ( -11.94)
>consensus
UAC__CAUACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACAUACAAACUUGGCCUAGACAAUAGUGUCAACCAUAAAGAGA
..............((((.......))))..............................((.(((((((..((((..............))))..((((....))))...))))))).)) (-14.46 = -15.86 +   1.40)

alignment

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secondary structure

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Window 2

Location 17,249,498 – 17,249,614
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 85.55
Mean single sequence MFE -33.67
Consensus MFE -28.46
Energy contribution -28.68
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -3.28
Structure conservation index 0.85
SVM decision value 1.90
SVM RNA-class probability 0.981944
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249498 116 + 27905053
UGUGGGGCCGUCAUAAAGUGAUGAAUGCAUUAUUAUUAUUGUUAUUGUGGCUGCCGUCGUAUGGCACAGUGUAUA--GUAUAGUAUAGUGUAUAGUGUACAUUGUGUAUUGCUGGCUG
.....(((.(((((((((((((((........))))))))....))))))).)))((((((..((((((((((((--.((((........)))).))))))))))))..))).))).. ( -38.00)
>DroSec_CAF1 45924 106 + 1
UGUGGGGCCGUCAUAAAGUGAUGAAUGCAUUAUUAUUAUUGUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUUUG-----UA-------GUAUAGUGUACAUUGUGUAUUGCUGGCUG
.....(((((.((....(..(((..((((((((.(((((...(((((((.((((....))).).)))))))...)-----))-------)))))))))))))..)....)).))))). ( -31.00)
>DroEre_CAF1 47740 104 + 1
UGUGAGGCCGUCAUAAGGUGAUGAAUGCAUUAUUAUUAUUGUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUAUGUGGUAUAG--------------UACAUUGUGUAUUGCUGGCUG
.....(((((..((((((((((((........)))))))).))))..)))))((((..(((..(((((((((((........)--------------))))))))))..))))))).. ( -32.00)
>consensus
UGUGGGGCCGUCAUAAAGUGAUGAAUGCAUUAUUAUUAUUGUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUAUG__GUAUAG______GUAUAGUGUACAUUGUGUAUUGCUGGCUG
.....(((.(((((((((((((((........))))))))....))))))).)))((((((..(((((((((((......................)))))))))))..))).))).. (-28.46 = -28.68 +   0.23)

alignment

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secondary structure

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Window 3

Location 17,249,498 – 17,249,614
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 85.55
Mean single sequence MFE -15.43
Consensus MFE -13.63
Energy contribution -13.63
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.88
SVM decision value 1.07
SVM RNA-class probability 0.910102
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249498 116 - 27905053
CAGCCAGCAAUACACAAUGUACACUAUACACUAUACUAUAC--UAUACACUGUGCCAUACGACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACA
..(((.(((....(((.((((.(.((((........)))).--).)))).)))(((.......))).......................)))..((((......)))).)))...... ( -16.50)
>DroSec_CAF1 45924 106 - 1
CAGCCAGCAAUACACAAUGUACACUAUAC-------UA-----CAAACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACA
..(((.(((........((((........-------))-----)).......((((.......))))......................)))..((((......)))).)))...... ( -14.60)
>DroEre_CAF1 47740 104 - 1
CAGCCAGCAAUACACAAUGUA--------------CUAUACCACAUACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACCUUAUGACGGCCUCACA
..(((.(((....(((.((((--------------..........)))).)))(((.......))).......................)))..((((......)))).)))...... ( -15.20)
>consensus
CAGCCAGCAAUACACAAUGUACACUAUAC______CUAUAC__CAUACACUGUGCCAUACAACGGCAGCCACAAUAACAAUAAUAAUAAUGCAUUCAUCACUUUAUGACGGCCCCACA
..(((.(((.(((.....)))...............................((((.......))))......................)))..((((......)))).)))...... (-13.63 = -13.63 +   0.00)

alignment

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secondary structure

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Window 4

Location 17,249,538 – 17,249,654
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 86.71
Mean single sequence MFE -29.75
Consensus MFE -25.12
Energy contribution -25.78
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.84
SVM decision value 0.11
SVM RNA-class probability 0.589601
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249538 116 + 27905053
GUUAUUGUGGCUGCCGUCGUAUGGCACAGUGUAUA--GUAUAGUAUAGUGUAUAGUGUACAUUGUGUAUUGCUGGCUGGGCCUUUGUUGAAAAGCGUUAAUUGAGUGUUGCGAAUGUG
....(((..((.(((((((((..((((((((((((--.((((........)))).))))))))))))..))).)))..)))....(((....)))...........))..)))..... ( -34.40)
>DroSec_CAF1 45964 106 + 1
GUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUUUG-----UA-------GUAUAGUGUACAUUGUGUAUUGCUGGCUGGGCCUUUGUUGAAAAGCGUUAAUUGAGUGUUGCGAAUGUG
....((((((((((((..(((..(((((((((...-----..-------.........)))))))))..)))))))..))))...(((....)))..............))))..... ( -25.44)
>DroEre_CAF1 47780 104 + 1
GUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUAUGUGGUAUAG--------------UACAUUGUGUAUUGCUGGCUGGGCCUUUGUUGAAAAGCGUUAAUUGAGUGUUGCGAAUGUG
....((((((((((((..(((..(((((((((((........)--------------))))))))))..)))))))..))))...(((....)))..............))))..... ( -29.40)
>consensus
GUUAUUGUGGCUGCCGUUGUAUGGCACAGUGUAUG__GUAUAG______GUAUAGUGUACAUUGUGUAUUGCUGGCUGGGCCUUUGUUGAAAAGCGUUAAUUGAGUGUUGCGAAUGUG
....(((..((.((((..(((..(((((((((((......................)))))))))))..)))))))..(((((((.....)))).)))........))..)))..... (-25.12 = -25.78 +   0.67)

alignment

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secondary structure

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Window 5

Location 17,249,538 – 17,249,654
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 86.71
Mean single sequence MFE -13.81
Consensus MFE -12.02
Energy contribution -12.35
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.87
SVM decision value 0.26
SVM RNA-class probability 0.659374
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249538 116 - 27905053
CACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUACACUAUACUAUAC--UAUACACUGUGCCAUACGACGGCAGCCACAAUAAC
.......((..............((((((....))))))...(((..(....((((.((((.(.((((........)))).--).)))).))))......)..))).))......... ( -15.10)
>DroSec_CAF1 45964 106 - 1
CACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUAC-------UA-----CAAACACUGUGCCAUACAACGGCAGCCACAAUAAC
.......((..............((((((....))))))...(((.......((((.(((.........-------..-----...))).)))).........))).))......... ( -12.53)
>DroEre_CAF1 47780 104 - 1
CACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUA--------------CUAUACCACAUACACUGUGCCAUACAACGGCAGCCACAAUAAC
.......((..............((((((....))))))...(((.......((((.((((--------------..........)))).)))).........))).))......... ( -13.79)
>consensus
CACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUAC______CUAUAC__CAUACACUGUGCCAUACAACGGCAGCCACAAUAAC
.......((..............((((((....))))))...(((.......((((.((((........................)))).)))).........))).))......... (-12.02 = -12.35 +   0.33)

alignment

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secondary structure

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Window 6

Location 17,249,576 – 17,249,694
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.42
Mean single sequence MFE -19.84
Consensus MFE -18.33
Energy contribution -18.53
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.92
SVM decision value 2.32
SVM RNA-class probability 0.992290
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249576 118 - 27905053
GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUACACUAU--ACUA
(((.(((((.((((.................)))).)))))......................((((((....))))))...)))............((((.....))))....--.... ( -20.13)
>DroSec_CAF1 45999 111 - 1
GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUAC---------UA
(((.(((((.((((.................)))).)))))......................((((((....))))))...)))........................---------.. ( -19.73)
>DroEre_CAF1 47820 104 - 1
GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUA----------------CUA
(((.(((((.((((.................)))).)))))......................((((((....))))))...)))................----------------... ( -19.73)
>DroYak_CAF1 68825 120 - 1
GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUACACUAUCCACUA
(((.(((((.((((.................)))).)))))......................((((((....))))))...)))............((((.....)))).......... ( -20.13)
>DroAna_CAF1 37602 97 - 1
GGCAACAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCGGCCAGCAAAACGGCA-----------------------
.((......(((..(((............(((((..(((((......)))))...)))))...((((((....))))))..)))..))).....)).----------------------- ( -19.50)
>consensus
GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCCCAGCCAGCAAUACACAAUGUACACUAUAC________CUA
(((.(((((.((((.................)))).)))))......................((((((....))))))...)))................................... (-18.33 = -18.53 +   0.20)

alignment

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secondary structure

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Window 7

Location 17,249,614 – 17,249,725
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.26
Mean single sequence MFE -24.84
Consensus MFE -21.74
Energy contribution -21.98
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.88
SVM decision value 1.98
SVM RNA-class probability 0.984682
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17249614 111 - 27905053
CAUUACA-------CAUCAUUGAGCAUGAGCUAAGGCU--GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
.......-------....((((((..........((((--.((((...)))).))))...................(((((......))))).))))))....((((((....)))))). ( -23.80)
>DroSec_CAF1 46030 111 - 1
CGUUACA-------CAUUAUUGAGCAUGAGCUACGGCU--GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
.((((..-------....((((((....(((....)))--((((((....))..((.....)).........))))(((((......))))).))))))))))((((((....)))))). ( -27.10)
>DroEre_CAF1 47844 118 - 1
CAUUACACAUUGCACAUUAUUGGGCAUGAGCUACGGCA--GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
..........(((.((....)).)))((((....((((--(((((...))))..((.....))........)))))(((((......))))).))))......((((((....)))))). ( -26.40)
>DroYak_CAF1 68865 118 - 1
CAUUACACAUUACACAUUAUUGAGCAUGAGCUACGGCA--GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
..................((((((.....((....)).--((((((....))..((.....)).........))))(((((......))))).))))))....((((((....)))))). ( -25.30)
>DroAna_CAF1 37619 111 - 1
CAUUAC---------AUUAUUGAACAUGAGCCCGGGCCGCGGCAACAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
......---------...........((((....(((.((((......))))..((.....))..........)))(((((......))))).))))......((((((....)))))). ( -21.60)
>consensus
CAUUACA_______CAUUAUUGAGCAUGAGCUACGGCA__GGCAGCAACUGCAAGUCAUAAACAAUUUCAAUUGCCGUUGCACAUUCGCAACACUCAAUUAACGCUUUUCAACAAAGGCC
..................((((((.....((....))...((((((....))..((.....)).........))))(((((......))))).))))))....((((((....)))))). (-21.74 = -21.98 +   0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:09 2006