Locus 2710

Sequence ID 2R_DroMel_CAF1
Location 9,517,988 – 9,518,165
Length 177
Max. P 0.999624
window4482 window4483 window4484 window4485 window4486

overview

Window 2

Location 9,517,988 – 9,518,108
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -30.78
Consensus MFE -30.90
Energy contribution -30.58
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 1.00
SVM decision value 1.24
SVM RNA-class probability 0.935452
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9517988 120 - 20766785
AUUUAUUUUGUUUUACGGGCGCGAAAAUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
........(((....(((((((...(((((((((....))))))))).((((((....))))))......(((((((..(((........)))..)))))))))))))).....)))... ( -31.90)
>DroSec_CAF1 14979 120 - 1
AUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
........(((....(((((((((..((((((((....))))))))))((((((....))))))......(((((((..(((........)))..)))))))))))))).....)))... ( -30.30)
>DroSim_CAF1 15014 120 - 1
AUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
........(((....(((((((((..((((((((....))))))))))((((((....))))))......(((((((..(((........)))..)))))))))))))).....)))... ( -30.30)
>DroEre_CAF1 14883 120 - 1
AUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUGUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
..................(((((..(((((((((....)))))))))..))).))..((((((((((((((((((((..(((........)))..)))))))))))....)))))).))) ( -31.10)
>DroYak_CAF1 14841 120 - 1
AUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
........(((....(((((((((..((((((((....))))))))))((((((....))))))......(((((((..(((........)))..)))))))))))))).....)))... ( -30.30)
>consensus
AUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAUUGGAACUAAACGAGAUGUUCGAGUGCCCGGAAAUGCACAC
........(((....(((((((((..((((((((....))))))))))((((((....))))))......(((((((..(((........)))..)))))))))))))).....)))... (-30.90 = -30.58 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,518,028 – 9,518,148
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.17
Mean single sequence MFE -24.62
Consensus MFE -23.62
Energy contribution -23.30
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.96
SVM decision value 3.80
SVM RNA-class probability 0.999624
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9518028 120 + 20766785
AUUUGUUCAAAUAUAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAAUUUUCGCGCCCGUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGA
.(((((............((.....)).((..(((((.((((....)))).)))))..))((((((((((((.......(((....))).....)))))))))))))))))......... ( -21.30)
>DroSec_CAF1 15019 120 + 1
AUUUGUUCAAAUAUAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGA
......................(..(((((.(((.(((((....))))))))......(.((((((((((((.......(((....))).....)))))))))))).)..).))))..). ( -24.20)
>DroSim_CAF1 15054 120 + 1
AUUUGUUCAAAUAUAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGA
......................(..(((((.(((.(((((....))))))))......(.((((((((((((.......(((....))).....)))))))))))).)..).))))..). ( -24.20)
>DroEre_CAF1 14923 120 + 1
AUUUGUUCAAAUACAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACGAGACUGUCUAA
.(((((......)))))........((((..(((.(((((....))))))))..(((((.((((((((((((.......(((....))).....)))))))))))).))))))))).... ( -29.70)
>DroYak_CAF1 14881 120 + 1
AUUUGUUCAAAUAUAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUAA
.........................(((((.(((.(((((....))))))))......(.((((((((((((.......(((....))).....)))))))))))).)..).)))).... ( -23.70)
>consensus
AUUUGUUCAAAUAUAAACGCCACUCGCAGCAUGAAUUAAUUAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGA
.(((((......)))))........(((((.(((.(((((....))))))))......(.((((((((((((.......(((....))).....)))))))))))).)..).)))).... (-23.62 = -23.30 +  -0.32)

alignment

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secondary structure

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Window 4

Location 9,518,028 – 9,518,148
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -28.66
Consensus MFE -28.92
Energy contribution -28.64
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 1.01
SVM decision value 3.21
SVM RNA-class probability 0.998735
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9518028 120 - 20766785
UCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUACGGGCGCGAAAAUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAU
.....((.((((((((((..((((((.....(((....))).......))))))..)))))))).(((((((((....)))))))))........)).))..(((((....))))).... ( -26.10)
>DroSec_CAF1 15019 120 - 1
UCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAU
.....((.(((((((((((.((((((.....(((....))).......)))))).))))))))).(((((((((....)))))))))........)).))..(((((....))))).... ( -28.90)
>DroSim_CAF1 15054 120 - 1
UCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAU
.....((.(((((((((((.((((((.....(((....))).......)))))).))))))))).(((((((((....)))))))))........)).))..(((((....))))).... ( -28.90)
>DroEre_CAF1 14923 120 - 1
UUAGACAGUCUCGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUGUAUUUGAACAAAU
.....((.(((((((((((.((((((.....(((....))).......)))))).))))))))).(((((((((....)))))))))........)).))..((((((......)))))) ( -30.50)
>DroYak_CAF1 14881 120 - 1
UUAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAU
.....((.(((((((((((.((((((.....(((....))).......)))))).))))))))).(((((((((....)))))))))........)).))..(((((....))))).... ( -28.90)
>consensus
UCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUAAUUAAUUCAUGCUGCGAGUGGCGUUUAUAUUUGAACAAAU
.....((.(((((((((((.((((((.....(((....))).......)))))).))))))))).(((((((((....)))))))))........)).))..(((((....))))).... (-28.92 = -28.64 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,518,068 – 9,518,165
Length 97
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 93.32
Mean single sequence MFE -24.20
Consensus MFE -21.04
Energy contribution -20.85
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -3.09
Structure conservation index 0.87
SVM decision value 1.95
SVM RNA-class probability 0.983673
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9518068 97 + 20766785
UAACGUUAAUCAAUUUUCGCGCCCGUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGAAUGGCAUUUAGUACAUG---
....((((.(((((..((..((((((((((((.......(((....))).....))))))))))))....))..)).))).))))............--- ( -19.20)
>DroSec_CAF1 15059 100 + 1
UAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUGAAUGGCAUUUAGUGAAUGGAA
.........((....(((((((((((((((((.......(((....))).....)))))))))))).......((((.....))))....)))))..)). ( -26.70)
>DroEre_CAF1 14963 99 + 1
UAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACGAGACUGUCUAAAUGGCAUUUCGUACUUGGA-
.........((((.......((((((((((((.......(((....))).....))))))))))))((((((.((((.....))))))))))..)))).- ( -28.20)
>DroYak_CAF1 14921 100 + 1
UAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUAAAUGGCAUUUCGUACUUAGAA
..(((.............(.((((((((((((.......(((....))).....)))))))))))).).....((((.....))))...)))........ ( -22.70)
>consensus
UAACGUUAAUCAACUUUCGCGCCCAUAAAACAAAAUAAAUAGAAAACUAGAAAAUGUUUUGUGGGCACAAGACUGUCUAAAUGGCAUUUAGUACAUGGA_
....................((((((((((((.......(((....))).....))))))))))))((.(((.((((.....))))))).))........ (-21.04 = -20.85 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,518,068 – 9,518,165
Length 97
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 93.32
Mean single sequence MFE -21.07
Consensus MFE -20.51
Energy contribution -20.33
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -1.75
Structure conservation index 0.97
SVM decision value 1.17
SVM RNA-class probability 0.925188
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9518068 97 - 20766785
---CAUGUACUAAAUGCCAUUCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUACGGGCGCGAAAAUUGAUUAACGUUA
---......................((((.((((((((..((((((.....(((....))).......))))))..))))))))..)))).......... ( -18.00)
>DroSec_CAF1 15059 100 - 1
UUCCAUUCACUAAAUGCCAUUCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUA
............((((....((((......(((((((((.((((((.....(((....))).......)))))).)))))))))...))))....)))). ( -21.70)
>DroEre_CAF1 14963 99 - 1
-UCCAAGUACGAAAUGCCAUUUAGACAGUCUCGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUA
-......................(((....(((((((((.((((((.....(((....))).......)))))).)))))))))..(((....)))))). ( -22.40)
>DroYak_CAF1 14921 100 - 1
UUCUAAGUACGAAAUGCCAUUUAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUA
.(((((((..........)))))))(((..(((((((((.((((((.....(((....))).......)))))).))))))).))..))).......... ( -22.20)
>consensus
_UCCAAGUACGAAAUGCCAUUCAGACAGUCUUGUGCCCACAAAACAUUUUCUAGUUUUCUAUUUAUUUUGUUUUAUGGGCGCGAAAGUUGAUUAACGUUA
............((((....((((......(((((((((.((((((.....(((....))).......)))))).)))))))))...))))....)))). (-20.51 = -20.33 +  -0.19)

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 10:37:24 2006