Locus 7555

Sequence ID 3R_DroMel_CAF1
Location 20,238,959 – 20,239,109
Length 150
Max. P 0.999968
window12193 window12194 window12195 window12196 window12197

overview

Window 3

Location 20,238,959 – 20,239,053
Length 94
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 94.71
Mean single sequence MFE -20.86
Consensus MFE -20.80
Energy contribution -20.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.15
Structure conservation index 1.00
SVM decision value 0.73
SVM RNA-class probability 0.834121
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20238959 94 - 27905053
UGCUCCUUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAAUAUAUA--
.........((((((..................(((((...((((......))))..)))))(((.......))))))))).............-- ( -20.80)
>DroSec_CAF1 50038 94 - 1
UGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAAUAUAUA--
.........((((((..................(((((...((((......))))..)))))(((.......))))))))).............-- ( -20.80)
>DroSim_CAF1 54027 92 - 1
UGCUCCGUUGACCACCAUGAAACCCCAACCCGAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAACAUA----
......(((.((.((((((.....((((.....(((((...((((......))))..)))))........)))))))))).))...)))...---- ( -20.92)
>DroEre_CAF1 51196 96 - 1
CGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAAUACAUAUA
.........((((((..................(((((...((((......))))..)))))(((.......)))))))))(((....)))..... ( -21.00)
>DroYak_CAF1 52398 91 - 1
UGCUCCGUUGACCACCGUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAAUAC-----
.........((((((..................(((((...((((......))))..)))))(((.......)))))))))..........----- ( -20.80)
>consensus
UGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUCCCACUUGGCGUGGUCGUAUAAAUAUAUA__
.........((((((..................(((((...((((......))))..)))))(((.......)))))))))............... (-20.80 = -20.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,238,987 – 20,239,093
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 97.74
Mean single sequence MFE -36.74
Consensus MFE -35.34
Energy contribution -35.38
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.13
Structure conservation index 0.96
SVM decision value 0.04
SVM RNA-class probability 0.553692
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20238987 106 + 27905053
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUUGGGUUGGGGUUUCAUGGUGGUCAAAGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((.((.((((((...((((........))))((......))))))))..)).)))))))) ( -36.20)
>DroSec_CAF1 50066 106 + 1
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((.((.(((((((((((((..(((....))))).)))))..))))))..)).)))))))) ( -37.20)
>DroSim_CAF1 54053 106 + 1
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUCGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((.((.(((((((((((((..(((....))))).)))))..))))))..)).)))))))) ( -37.20)
>DroEre_CAF1 51226 106 + 1
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCGGGAGCACGCUUGCUUUUGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((.((.((((((.....(((((((((....)))))))))..))))))..)).)))))))) ( -37.80)
>DroYak_CAF1 52423 106 + 1
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUUGGGUUGGGGUUUCACGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((....(((((((((((((..(((....))))).)))))..)))))).....)))))))) ( -35.30)
>consensus
GAGCCAUCACACUGGGGAUUACCAGAGUUGAUAUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCC
.(((((((((.((((......)))).).))))....))))((((((((.((.((((((...((((........))))((......))))))))..)).)))))))) (-35.34 = -35.38 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,238,987 – 20,239,093
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 97.74
Mean single sequence MFE -34.46
Consensus MFE -34.04
Energy contribution -34.12
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.99
SVM decision value 3.78
SVM RNA-class probability 0.999606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20238987 106 - 27905053
GGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCUUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((......))(((((......)))))...)))))).)))))))..)).......(((((...((((......))))..))))).... ( -33.30)
>DroSec_CAF1 50066 106 - 1
GGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))..)).......(((((...((((......))))..))))).... ( -37.00)
>DroSim_CAF1 54053 106 - 1
GGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCGAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))..)).......(((((...((((......))))..))))).... ( -37.00)
>DroEre_CAF1 51226 106 - 1
GGAAUUUCGUGCUUGGUCAGCACAAAAGCAAGCGUGCUCCCGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((.(....)..((((......))))..)))))))).)))))))..)).......(((((...((((......))))..))))).... ( -31.40)
>DroYak_CAF1 52423 106 - 1
GGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCGUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))..)).......(((((...((((......))))..))))).... ( -33.60)
>consensus
GGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCAAUAUCAACUCUGGUAAUCCCCAGUGUGAUGGCUC
((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))..)).......(((((...((((......))))..))))).... (-34.04 = -34.12 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,239,019 – 20,239,109
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -30.76
Consensus MFE -29.02
Energy contribution -28.90
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.87
Structure conservation index 0.94
SVM decision value 2.46
SVM RNA-class probability 0.994221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20239019 90 + 27905053
AUUGGGUUGGGGUUUCAUGGUGGUCAAAGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
.....(((((((((((.((.((((((...((((........))))((......))))))))..)).))))..)))))))........... ( -29.80)
>DroSec_CAF1 50098 90 + 1
AUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
.....(((((((((((.((.(((((((((((((..(((....))))).)))))..))))))..)).))))..)))))))........... ( -30.80)
>DroSim_CAF1 54085 90 + 1
AUCGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
((((((...(((((((.((.(((((((((((((..(((....))))).)))))..))))))..)).)))))))))))))........... ( -32.40)
>DroEre_CAF1 51258 90 + 1
AUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCGGGAGCACGCUUGCUUUUGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
.....(((((((((((.((.((((((.....(((((((((....)))))))))..))))))..)).))))..)))))))........... ( -31.40)
>DroYak_CAF1 52455 90 + 1
AUUGGGUUGGGGUUUCACGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
.....(((((((..(..((.(((((((((((((..(((....))))).)))))..))))))....))..)..)))))))........... ( -29.40)
>consensus
AUUGGGUUGGGGUUUCAUGGUGGUCAACGGAGCAGGAGCACGCUCGCUUUCGUGCUGACCAAGCACGAAAUUCCCCGAUAAUUGCAAAUA
((((((...(((((((.((.((((((...((((........))))((......))))))))..)).)))))))))))))........... (-29.02 = -28.90 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,239,019 – 20,239,109
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -30.58
Consensus MFE -30.14
Energy contribution -30.22
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -3.10
Structure conservation index 0.99
SVM decision value 5.01
SVM RNA-class probability 0.999968
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20239019 90 - 27905053
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCUUUGACCACCAUGAAACCCCAACCCAAU
..............((((..(((((((..((((((((......))(((((......)))))...)))))).)))))))))))........ ( -29.40)
>DroSec_CAF1 50098 90 - 1
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCAAU
..............((((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))))))........ ( -33.10)
>DroSim_CAF1 54085 90 - 1
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCGAU
...........((((((...(((((((..((((((((.(....).(((((......))))).)))))))).)))))))......)))))) ( -33.20)
>DroEre_CAF1 51258 90 - 1
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACAAAAGCAAGCGUGCUCCCGCUCCGUUGACCACCAUGAAACCCCAACCCAAU
..............((((..(((((((..((((((((.(....)..((((......))))..)))))))).)))))))))))........ ( -27.50)
>DroYak_CAF1 52455 90 - 1
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCGUGAAACCCCAACCCAAU
..............((((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))))))........ ( -29.70)
>consensus
UAUUUGCAAUUAUCGGGGAAUUUCGUGCUUGGUCAGCACGAAAGCGAGCGUGCUCCUGCUCCGUUGACCACCAUGAAACCCCAACCCAAU
..............((((..(((((((..((((((((.(....).(((((......))))).)))))))).)))))))))))........ (-30.14 = -30.22 +   0.08)

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 12:48:48 2006