Locus 2328

Sequence ID X_DroMel_CAF1
Location 6,259,292 – 6,259,573
Length 281
Max. P 0.886657
window3774 window3775 window3776 window3777 window3778

overview

Window 4

Location 6,259,292 – 6,259,399
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 98.75
Mean single sequence MFE -23.20
Consensus MFE -23.20
Energy contribution -23.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 1.00
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259292 107 + 22224390
UUUUUUUUUUUUUGUUUUUUUGUCACUUCACUGGAAGCGCGCUCAAAGGAGGCUAAAUAUUGCAUUACGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUU
.............................((((((.....((((((.((((((((.....((((...........)))).....))))..)))))))))))))))). ( -23.20)
>DroSec_CAF1 941 107 + 1
CUAUUUUUUUUUUGUUUUUUUGUCACUUCACUGGAAGCGCGCUCAAAGGAGGCUAAAUAUUGCAUUACGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUU
.............................((((((.....((((((.((((((((.....((((...........)))).....))))..)))))))))))))))). ( -23.20)
>DroSim_CAF1 945 107 + 1
CUAUUUUUUUUUUGUUUUUUUGUCACUUCACUGGAAGCGCGCUCAAAGGAGGCUAAAUAUUGCAUUACGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUU
.............................((((((.....((((((.((((((((.....((((...........)))).....))))..)))))))))))))))). ( -23.20)
>consensus
CUAUUUUUUUUUUGUUUUUUUGUCACUUCACUGGAAGCGCGCUCAAAGGAGGCUAAAUAUUGCAUUACGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUU
.............................((((((.....((((((.((((((((.....((((...........)))).....))))..)))))))))))))))). (-23.20 = -23.20 +  -0.00)

alignment

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secondary structure

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Window 5

Location 6,259,292 – 6,259,399
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -20.60
Consensus MFE -20.60
Energy contribution -20.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 1.00
SVM decision value 0.18
SVM RNA-class probability 0.619584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259292 107 - 22224390
AACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACGUAAUGCAAUAUUUAGCCUCCUUUGAGCGCGCUUCCAGUGAAGUGACAAAAAAACAAAAAAAAAAAAA
.......(((.((((((..((..((((.((((.(....)....))))...)))))))))))).).))(((((((....)))))).)..................... ( -20.60)
>DroSec_CAF1 941 107 - 1
AACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACGUAAUGCAAUAUUUAGCCUCCUUUGAGCGCGCUUCCAGUGAAGUGACAAAAAAACAAAAAAAAAAUAG
.......(((.((((((..((..((((.((((.(....)....))))...)))))))))))).).))(((((((....)))))).)..................... ( -20.60)
>DroSim_CAF1 945 107 - 1
AACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACGUAAUGCAAUAUUUAGCCUCCUUUGAGCGCGCUUCCAGUGAAGUGACAAAAAAACAAAAAAAAAAUAG
.......(((.((((((..((..((((.((((.(....)....))))...)))))))))))).).))(((((((....)))))).)..................... ( -20.60)
>consensus
AACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACGUAAUGCAAUAUUUAGCCUCCUUUGAGCGCGCUUCCAGUGAAGUGACAAAAAAACAAAAAAAAAAUAG
.......(((.((((((..((..((((.((((.(....)....))))...)))))))))))).).))(((((((....)))))).)..................... (-20.60 = -20.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,259,359 – 6,259,466
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.32
Mean single sequence MFE -36.03
Consensus MFE -32.42
Energy contribution -33.05
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.90
SVM decision value 0.94
SVM RNA-class probability 0.886657
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259359 107 + 22224390
CGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUUUCUGGAAUUCCUCGAAGGUGUCCUUCGCCCUAACUGGGCUGGAAUGCGAGCAGCCACCAUU-------------UGCCAG
......((.(((..(..(((((((((.......(((((...)))))(((((..(((((...)))))((((.....)))).)))))..)))))))))..)..-------------))).)) ( -40.30)
>DroSec_CAF1 1008 106 + 1
CGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUUUCUGGAAUUCCUCGAAGGUGUCCUCCGCCCUAACUGGGCUGGAAUGCGAGCAGCCACCAU--------------UGCCAG
......((.(((.....(((((((((...((((.((...(((.((....))..))))).))))(((((((.....)))).)))....)))))))))....--------------))).)) ( -39.10)
>DroSim_CAF1 1012 93 + 1
CGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUUUCUGGAAUUCCUCGAAGGUGUCCUCCGCCCUAACUGGGCUGGAAUGCGAGCAG---------------------------
.(((....))).........((((((...((((.((...(((.((....))..))))).))))(((((((.....)))).)))....))))))--------------------------- ( -29.00)
>DroYak_CAF1 546 120 + 1
CGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUUUCUGGAAUUCCUCGAAGGUAUCCUCCGCUCUAACUGGGCUGGAAUGCGAGCAGCCACCAUUACCAGCUACCAGCUACCAG
.(((....)))......(((((((((((((((.(((((...)))))...)))..)))((((..(((((((.....)))).))))))))))))))))........(((.....)))..... ( -35.70)
>consensus
CGUAUCCUUGCACUUUAUGGCUGCUCCUUGGGCUCUAGUUUCUGGAAUUCCUCGAAGGUGUCCUCCGCCCUAACUGGGCUGGAAUGCGAGCAGCCACCAU______________UGCCAG
.(((....)))......(((((((((...((((.((...(((.((....))..))))).))))(((((((.....)))).)))....)))))))))........................ (-32.42 = -33.05 +   0.63)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,259,359 – 6,259,466
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.32
Mean single sequence MFE -36.38
Consensus MFE -30.69
Energy contribution -31.75
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.84
SVM decision value 0.64
SVM RNA-class probability 0.807656
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259359 107 - 22224390
CUGGCA-------------AAUGGUGGCUGCUCGCAUUCCAGCCCAGUUAGGGCGAAGGACACCUUCGAGGAAUUCCAGAAACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACG
((.(((-------------....(((((((((((.(((((.((((.....))))(((((...)))))..))))).)......((........))))))))))))....))).))...... ( -42.30)
>DroSec_CAF1 1008 106 - 1
CUGGCA--------------AUGGUGGCUGCUCGCAUUCCAGCCCAGUUAGGGCGGAGGACACCUUCGAGGAAUUCCAGAAACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACG
((.(((--------------...(((((((((((.(((((.((((.....))))(((((...)))))..))))).)......((........))))))))))))....))).))...... ( -41.40)
>DroSim_CAF1 1012 93 - 1
---------------------------CUGCUCGCAUUCCAGCCCAGUUAGGGCGGAGGACACCUUCGAGGAAUUCCAGAAACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACG
---------------------------(((((((.(((((.((((.....))))(((((...)))))..))))).)......((........)))))))).................... ( -25.70)
>DroYak_CAF1 546 120 - 1
CUGGUAGCUGGUAGCUGGUAAUGGUGGCUGCUCGCAUUCCAGCCCAGUUAGAGCGGAGGAUACCUUCGAGGAAUUCCAGAAACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACG
....((((.....))))(((...((((((((((((......))...(((..((((((((...)))))).((....)).....))..))).....))))))))))....)))......... ( -36.10)
>consensus
CUGGCA______________AUGGUGGCUGCUCGCAUUCCAGCCCAGUUAGGGCGGAGGACACCUUCGAGGAAUUCCAGAAACUAGAGCCCAAGGAGCAGCCAUAAAGUGCAAGGAUACG
.......................(((((((((((.(((((.((((.....))))(((((...)))))..))))).)......((........))))))))))))................ (-30.69 = -31.75 +   1.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,259,466 – 6,259,573
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 89.59
Mean single sequence MFE -23.43
Consensus MFE -17.59
Energy contribution -18.03
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.58
Structure conservation index 0.75
SVM decision value 0.40
SVM RNA-class probability 0.722315
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259466 107 + 22224390
CUACCAUGGCGAUGGCACGAUGAUCUAUCCUACCCGAAAAUCCAACCCUGGCACACCCCGUGCUGUCCUUUCCCAUUUCGCAUCAUCCAUUUCCGUGGAGAACACUU
((.((((((.(((((...((((............(((((..........(((((.....)))))...........)))))))))..))))).))))))))....... ( -25.30)
>DroSec_CAF1 1114 102 + 1
CUACCAUGGCGAUGGCACGAUG-UCUAUCCCACCCGAAAAUCCACCCCGGGCACCCCCUCCG----CCCUUCCCAUUUCACAUCAUCCAUUUCCGUGGAGAACACUU
((.((((((.(((((...((((-(...((......))...........((((.........)----)))..........)))))..))))).))))))))....... ( -25.90)
>DroSim_CAF1 1105 103 + 1
CUACCAUAGCAAUGGCACGAUGAUCUAUCCUACCCGAAAAUCCACCCCGGGCACUCCCUCCG----CCCUUCCCAUUUCGCAUCAUCCAUUUCCGUGGAGAACACUU
((.(((..(.(((((...((((.....((......))...........((((.........)----)))...........))))..))))).)..)))))....... ( -19.10)
>consensus
CUACCAUGGCGAUGGCACGAUGAUCUAUCCUACCCGAAAAUCCACCCCGGGCACACCCUCCG____CCCUUCCCAUUUCGCAUCAUCCAUUUCCGUGGAGAACACUU
((.((((((.(((((...((((.....((......))...........(((....)))......................))))..))))).))))))))....... (-17.59 = -18.03 +   0.45)

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 10:31:44 2006