Locus 7076

Sequence ID 2L_DroMel_CAF1
Location 19,806,693 – 19,806,887
Length 194
Max. P 0.999939
window11283 window11284 window11285 window11286 window11287

overview

Window 3

Location 19,806,693 – 19,806,813
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.33
Mean single sequence MFE -36.64
Consensus MFE -36.64
Energy contribution -36.64
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 1.00
SVM decision value 3.19
SVM RNA-class probability 0.998702
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19806693 120 + 22407834
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). ( -36.40)
>DroSec_CAF1 73299 120 + 1
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). ( -36.40)
>DroSim_CAF1 75071 120 + 1
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). ( -36.40)
>DroEre_CAF1 74913 120 + 1
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAACACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). ( -36.40)
>DroYak_CAF1 76440 120 + 1
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGGAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). ( -37.60)
>consensus
GAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUA
..........((((((.((((((....))))))...))))))...........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))). (-36.64 = -36.64 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,806,693 – 19,806,813
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.33
Mean single sequence MFE -36.16
Consensus MFE -36.16
Energy contribution -36.16
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 1.00
SVM decision value 2.92
SVM RNA-class probability 0.997733
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19806693 120 - 22407834
UAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... ( -36.30)
>DroSec_CAF1 73299 120 - 1
UAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... ( -36.30)
>DroSim_CAF1 75071 120 - 1
UAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... ( -36.30)
>DroEre_CAF1 74913 120 - 1
UAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUGUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... ( -36.30)
>DroYak_CAF1 76440 120 - 1
UAUUUUUAAUGGCCCUCUCGGGCUCCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... ( -35.60)
>consensus
UAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUAAAGUUUUCAACUAGCAAUAAUCGCACCUCAGUAGAACUUC
.((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).)))))(((((..((((((..(((.......)))..)))))).)))))........... (-36.16 = -36.16 +   0.00)

alignment

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secondary structure

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Window 5

Location 19,806,733 – 19,806,849
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.94
Mean single sequence MFE -33.82
Consensus MFE -30.34
Energy contribution -30.22
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -2.45
Structure conservation index 0.90
SVM decision value 3.26
SVM RNA-class probability 0.998862
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19806733 116 + 22407834
UAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAAAUUAGUCUUUAGUUAAUAAUGAG----CUCU
((((.........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))).....................))))........----.... ( -30.40)
>DroSec_CAF1 73339 120 + 1
UAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUUUUAAGUUAAUAAUGAGCAUGCUCU
((((.........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))).....................)))).....(((....))). ( -32.90)
>DroSim_CAF1 75111 120 + 1
UAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCAAAUAUUAGUCUUUAGUUAAUAAUGAGUAGGCUCU
...((........(((.((((((((........))))).))).))).((((((((..((((....))))..))))))))..(((((..((((((.(....))))))).))))).)).... ( -33.50)
>DroEre_CAF1 74953 117 + 1
UAACCAAUACCCCGCCAUGGGGACGUGAAACACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUAAAUUCGAACAUUAGUCUAUAGUCUCUGUUGGGCA---CCG
...((((((....(((.((((((((........))))).))).))).((((((((..((((....))))..))))))))..........................))))))...---... ( -35.30)
>DroYak_CAF1 76480 117 + 1
UAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGGAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUCUUUAGUUGGUUUUAGAGC---CUA
.(((((((.....(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))).....................))))))).......---... ( -37.00)
>consensus
UAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUCUUUAGUUAAUAAUGAGCA__CUCU
((((.........(((.((((((((........))))).))).))).((((((((..((((....))))..)))))))).....................)))).....(((....))). (-30.34 = -30.22 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,806,733 – 19,806,849
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.94
Mean single sequence MFE -37.48
Consensus MFE -36.86
Energy contribution -36.22
Covariance contribution -0.64
Combinations/Pair 1.14
Mean z-score -2.69
Structure conservation index 0.98
SVM decision value 4.69
SVM RNA-class probability 0.999939
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19806733 116 - 22407834
AGAG----CUCAUUAUUAACUAAAGACUAAUUUUCGAAUGUAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
....----................((((((((..(......((((((...(((((....)))))...)))))).(((((.(.(((((........)))))).))))))..).))))))). ( -33.90)
>DroSec_CAF1 73339 120 - 1
AGAGCAUGCUCAUUAUUAACUUAAAACUAAUAUUCGAAUGUAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
.(((....))).............(((((((((((......((((((...(((((....)))))...))))))((((((.(.(((((........)))))).))))))))))))))))). ( -40.30)
>DroSim_CAF1 75111 120 - 1
AGAGCCUACUCAUUAUUAACUAAAGACUAAUAUUUGAAUGUAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
.(((....))).............(((((((((((......((((((...(((((....)))))...))))))((((((.(.(((((........)))))).))))))))))))))))). ( -37.30)
>DroEre_CAF1 74953 117 - 1
CGG---UGCCCAACAGAGACUAUAGACUAAUGUUCGAAUUUAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUGUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
(((---(((((..............................((((((...(((((....)))))...))))))((((((.(.(((((........)))))).)))))))))))))).... ( -38.40)
>DroYak_CAF1 76480 117 - 1
UAG---GCUCUAAAACCAACUAAAGACUAAUAUUCGAAUGUAUUUUUAAUGGCCCUCUCGGGCUCCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
..(---(........)).......(((((((((((......((((((...(((((....)))))...))))))((((((.(.(((((........)))))).))))))))))))))))). ( -37.50)
>consensus
AGAG__UGCUCAUUAUUAACUAAAGACUAAUAUUCGAAUGUAUUUUUAAUGGCCCUCUCGGGCUUCCAAAAAUUGCCGUAGUGGACGGUAUUUCACGUCCCCAUGGCGGGGUAUUGGUUA
.(((....))).............(((((((((((......((((((...(((((....)))))...))))))((((((.(.(((((........)))))).))))))))))))))))). (-36.86 = -36.22 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,806,773 – 19,806,887
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.61
Mean single sequence MFE -28.80
Consensus MFE -19.96
Energy contribution -19.76
Covariance contribution -0.20
Combinations/Pair 1.10
Mean z-score -1.80
Structure conservation index 0.69
SVM decision value 0.34
SVM RNA-class probability 0.697161
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19806773 114 + 22407834
UACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAAAUUAGUCUUUAGUUAAUAAUGAG----CUCUCUU--AAAACAGUGCUGAGCUCAUCCUCGCAUUAAUCUGA
...(((((((((((((.((((....)))).............)))))))))).))).(((((((((.(((((----(((....--...........))))))))......))))).)))) ( -27.30)
>DroSec_CAF1 73379 118 + 1
UACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUUUUAAGUUAAUAAUGAGCAUGCUCUCUU--AAAACAUUGCUGAGCUCAUCAUCUCAUUAAUGUGA
..(((((((((((((..((((....))))..))))))))..............((((((((........(((....))).)))--)))))..)))))...........((((....)))) ( -29.00)
>DroSim_CAF1 75151 118 + 1
UACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCAAAUAUUAGUCUUUAGUUAAUAAUGAGUAGGCUCUCUU--AAAACAGUGCUGAGCUCAUCAUCUCAUUAAUGUGA
.......((((((((..((((....))))..))))))))(((((....((((((.(....)))))))((((((.(((.((...--.....)).)))..)))))).........))))).. ( -25.90)
>DroEre_CAF1 74993 109 + 1
UACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUAAAUUCGAACAUUAGUCUAUAGUCUCUGUUGGGCA---CCGCUU------CGGUGCUGAGCUCAGCAU--CAUUAAUGAGA
..(((..((((((((..((((....))))..))))))))....)))..(((((((.....(.((..(((.((((---(((...------))))))).)))..)))..--.)))))))... ( -32.80)
>DroYak_CAF1 76520 113 + 1
UACGGCAAUUUUUGGGAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUCUUUAGUUGGUUUUAGAGC---CUACUUGAAAAACGGAGCUGAGCUCAGCAU--CAUUAAUG--A
..((...((((((((..((((....))))..))))))))...(((((....(((.((((((......)))))).---))).)))))...))((((((....)))).)--).......--. ( -29.00)
>consensus
UACGGCAAUUUUUGGAAGCCCGAGAGGGCCAUUAAAAAUACAUUCGAAUAUUAGUCUUUAGUUAAUAAUGAGCA__CUCUCUU__AAAACAGUGCUGAGCUCAUCAUC_CAUUAAUGUGA
..(((((((((((((..((((....))))..))))))))..............................(((....))).............)))))....................... (-19.96 = -19.76 +  -0.20)

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 12:26:46 2006