Locus 6446

Sequence ID X_DroMel_CAF1
Location 16,156,523 – 16,156,880
Length 357
Max. P 0.980143
window10523 window10524 window10525 window10526 window10527

overview

Window 3

Location 16,156,523 – 16,156,643
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.17
Mean single sequence MFE -43.66
Consensus MFE -42.94
Energy contribution -42.34
Covariance contribution -0.60
Combinations/Pair 1.11
Mean z-score -1.41
Structure conservation index 0.98
SVM decision value 1.53
SVM RNA-class probability 0.961640
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16156523 120 - 22224390
AGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAGAUACAGGAAGCGUCGCCCAAGGGCGAACUGGAUGUGGUCUUCAACAAGUACUGCAGCCGGCGUUCGAAUGCCGUCG
(((((.......((((((((........))))))))....(((((((((...((..(((((....))))).))...))).)))))).....)))))...(.((((((....)))))).). ( -43.10)
>DroSec_CAF1 2465 120 - 1
AGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAAAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUGGUUUUCAACAAGUACUGCAGCCGGCGUUCCAAUGCUGUCG
...(((.....)))((((((........))))))(((((((......).((((.(((((((....))))).((((.((..((...........))..)).))))))))))..)))))).. ( -40.50)
>DroSim_CAF1 3241 120 - 1
AGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAAAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUGGUUUUCAACAAGUACUGCAGCCGGCGUUCCAAUGCCGUCG
((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))((.((..((...........))..)).))(((((....))))).... ( -42.80)
>DroEre_CAF1 2410 120 - 1
AGUGCCUCAAUGGCAUUGUCAACUACACGGCGAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUGGUCUUCAACAAGUACUGCAGCCGGCGUUCGAAUGCCGUGG
((((((.....))))))........(((((((((((..(..(.....)..)..)))))(((....)))(((((((.((..(((((....))).))..)).)))..))))....)))))). ( -45.40)
>DroYak_CAF1 3289 120 - 1
AGUGCCUCAAUGGCAUCGUCAACUACACGGCGAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUGGUCUUUAACAAGUACUGCAGCCGGCGUUCGAAUGCCGUGG
((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))((.((..(((((....))).))..)).))(((((....))))).... ( -46.50)
>consensus
AGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUGGUCUUCAACAAGUACUGCAGCCGGCGUUCGAAUGCCGUCG
((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))((.((..(((((....))).))..)).))(((((....))))).... (-42.94 = -42.34 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,156,563 – 16,156,683
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -44.04
Consensus MFE -39.20
Energy contribution -38.64
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -1.36
Structure conservation index 0.89
SVM decision value 0.56
SVM RNA-class probability 0.783099
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16156563 120 - 22224390
GCAUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAGAUACAGGAAGCGUCGCCCAAGGGCGAACUGGAUGUG
((.....))........((((((.(((..(..(((..((..(((.(((....((((((((........)))))))).....))).))).)).)))..)(((....))))))))))))... ( -41.20)
>DroSec_CAF1 2505 120 - 1
GCGUACGGUGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAAAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUG
..((((.(((((.(((....))).))))).))))...((.((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))))..... ( -45.60)
>DroSim_CAF1 3281 120 - 1
GCGUACGGUGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAAAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUG
..((((.(((((.(((....))).))))).))))...((.((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))))..... ( -45.60)
>DroEre_CAF1 2450 120 - 1
GCGUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUGACGGAGUGCCUCAAUGGCAUUGUCAACUACACGGCGAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUG
.(((.(((((..((.((((....))))))..)))))))).((((((((....((((((((........))))))))....(......)..))))).(((((....))))))))....... ( -41.40)
>DroYak_CAF1 3329 120 - 1
GCGUUCGGCGAGAUCGAAUCCGGAUUUAUGGUGCUAACCGAGUGCCUCAAUGGCAUCGUCAACUACACGGCGAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUG
((((((((......((..(((.......((((....)))).(((.(((....((((((((........)))))))).....))).))).)))..))(((((....))))).)))))))). ( -46.40)
>consensus
GCGUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCAGGAGAUACAGGAGGCGUCGCCCAAGGGCGAACUGGAUGUG
((.....))........((((((((((..(((....)))))))(((((....((((((((........))))))))....(......)..))))).(((((....))))).))))))... (-39.20 = -38.64 +  -0.56)

alignment

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secondary structure

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Window 5

Location 16,156,603 – 16,156,723
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.00
Mean single sequence MFE -47.12
Consensus MFE -43.62
Energy contribution -43.14
Covariance contribution -0.48
Combinations/Pair 1.14
Mean z-score -1.14
Structure conservation index 0.93
SVM decision value 0.13
SVM RNA-class probability 0.596229
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16156603 120 - 22224390
CAAAUGCAUCGAGGUGGCCGGCGAGGAGGCGGGCGUCGAGGCAUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCA
....(((.....(..(.(((.(.....).))).)..)(((((((.(((..(((((((((....))))..))).))..))).)))))))....((((((((........)))))))).))) ( -45.50)
>DroSec_CAF1 2545 120 - 1
CAAAUGCAUCGAGGUGGCCGGCGAGGAGGCGGGCGGCGAGGCGUACGGUGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCA
....(((......((.(((.((......)).))).))((((((..((((.(((((((((....))))..))).)).))))..))))))....((((((((........)))))))).))) ( -47.20)
>DroSim_CAF1 3321 120 - 1
CAAAUGCAUCGAGGUGGCCGGCGAGGAGGCGGGCGGCGAGGCGUACGGUGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCA
....(((......((.(((.((......)).))).))((((((..((((.(((((((((....))))..))).)).))))..))))))....((((((((........)))))))).))) ( -47.20)
>DroEre_CAF1 2490 120 - 1
CAAAUGCGUCGAGGUGGCCGGCGAGGAGGCGGGCGGCGAGGCGUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUGACGGAGUGCCUCAAUGGCAUUGUCAACUACACGGCGAUGCAGCA
....(((((((..((((((.((......)).)))(((....(((.(((((..((.((((....))))))..)))))))).((((((.....))))))))).....)))..)))))))... ( -47.20)
>DroYak_CAF1 3369 120 - 1
CAAAUGCAUCGAGGUGGCCGGCGAGGAGGCGGGCGGCGAGGCGUUCGGCGAGAUCGAAUCCGGAUUUAUGGUGCUAACCGAGUGCCUCAAUGGCAUCGUCAACUACACGGCGAUGCAGCA
....(((......((.(((.((......)).))).))(((((((((((..(((((((((....))))..))).))..)))))))))))....((((((((........)))))))).))) ( -48.50)
>consensus
CAAAUGCAUCGAGGUGGCCGGCGAGGAGGCGGGCGGCGAGGCGUACGGCGAGAUCGAGUCCGGAUUCAUGGUGCUAACCGAGUGCCUCAAUGGCAUUGUCAACUACACGGCAAUGCAGCA
....(((......((.(((.((......)).))).))((((((..(((..(((((((((....))))..))).))..)))..))))))....((((((((........)))))))).))) (-43.62 = -43.14 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,156,723 – 16,156,843
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.83
Mean single sequence MFE -48.76
Consensus MFE -40.00
Energy contribution -40.24
Covariance contribution 0.24
Combinations/Pair 1.11
Mean z-score -2.23
Structure conservation index 0.82
SVM decision value 1.85
SVM RNA-class probability 0.980143
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16156723 120 + 22224390
UUGCGAAAUAGCUCCUUGGCGUCGUUCACGCUAAAGUUUGACUUCCUCAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUAUGCCGGCAGUGGCGAAUAUA
(((((((..((((..(((((((.....)))))))))))....)))....((((((..(((((((((..((((((...))))))..))))))..))).....))))))....))))..... ( -46.40)
>DroSec_CAF1 2665 120 + 1
UUGCGAAAUAGCUCCUUGGCGUCAUUCACGCUAAAGUUCGAGUUGCUUAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUACGCCGGCAGUGGCGAGUAUA
..........((((.(((((((.....))))))).......((..((..((((((..(((((((((..((((((...))))))..))))))..))).....))))))))..))))))... ( -50.40)
>DroSim_CAF1 3441 120 + 1
UUGCGAAAUAGCUCCUUGGCGUCAUUCACGCUAAAGUUCGACUUGGUUAGCUGGUCGGGCAGCUGAGUCUGGAUCUGCUCAAGGUCUAGCUGGGCCAUUACGCCGGCAGUGGAGAGUAUA
...........(((((((((((.....)))))))...............(((((.((....(((.((.((((((((.....)))))))))).))).....)))))))...))))...... ( -40.90)
>DroEre_CAF1 2610 120 + 1
UUGCGGAUUAGCUCCUUGGCGUCGUUGACGCUAAAGUUCGACUUGCUCAGCUGGUCGGGCAGUUGGGUCUGGAUCUGAUCCAGGUCCAGCUGGGCCACUAUGCCAGGAGUUGCCAGUACA
.(((((..(((((((((((((((...)))))))).((((((((.((...)).))))))))((((((..((((((...))))))..)))))).(((......))).))))))))).))).. ( -55.20)
>DroYak_CAF1 3489 120 + 1
UUGCGGAUUAGCUCCUUGGCGUCGUUAACGCUAAAGUUUGACUUGCUCAGCUGGUCGGGCAGUUGGGUCUGGAUCUGGUCCAGGUCCAGCUGGGCCAUUAUGCCAGCCGCUGCCAGUACC
..(((..((((((..(((((((.....))))))))).))))..)))...(((((((((.(((((((..((((((...))))))..)))))))(((......)))..)))..))))))... ( -50.90)
>consensus
UUGCGAAAUAGCUCCUUGGCGUCGUUCACGCUAAAGUUCGACUUGCUCAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUAUGCCGGCAGUGGCGAGUAUA
..(((.(((.((((.(((((((.....))))))).((((((((.(.....).))))))))((((((..(((((.....)))))..)))))))))).))).)))................. (-40.00 = -40.24 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,156,763 – 16,156,880
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.90
Mean single sequence MFE -44.70
Consensus MFE -35.66
Energy contribution -37.94
Covariance contribution 2.28
Combinations/Pair 1.09
Mean z-score -1.87
Structure conservation index 0.80
SVM decision value 0.87
SVM RNA-class probability 0.870578
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16156763 117 + 22224390
ACUUCCUCAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUAUGCCGGCAGUGGCGAAUAUAACCAGCCAAAUGGCGUAUAUCGCAUGGCUUACAUA---UG
.........((((((..(((((((((..((((((...))))))..))))))..))).....))))))(((.((((.((((....(((....))).))))))))...)))......---.. ( -46.80)
>DroSec_CAF1 2705 117 + 1
AGUUGCUUAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUACGCCGGCAGUGGCGAGUAUAACCAACCAAAUGGCGCAUAUCGCAUGGCUUACAUA---UA
.((..((..((((((..(((((((((..((((((...))))))..))))))..))).....))))))))..))..(((...(((.((....)).((.....)).)))..)))...---.. ( -45.70)
>DroSim_CAF1 3481 117 + 1
ACUUGGUUAGCUGGUCGGGCAGCUGAGUCUGGAUCUGCUCAAGGUCUAGCUGGGCCAUUACGCCGGCAGUGGAGAGUAUAACCAACCAAAUGGCGCAUAUCGCAUGGCUUACAUA---UA
..((((((.(((((.((....(((.((.((((((((.....)))))))))).))).....)))))))...((.........))))))))...(((.....)))(((.....))).---.. ( -36.60)
>DroEre_CAF1 2650 120 + 1
ACUUGCUCAGCUGGUCGGGCAGUUGGGUCUGGAUCUGAUCCAGGUCCAGCUGGGCCACUAUGCCAGGAGUUGCCAGUACAACCAGCCAAAUGGCACAUAUCGCAUGGCGUACAUACAGUG
.........((((...((.(((((((..((((((...))))))..)))))).).))..((((((((((((((......))))..(((....))).....)).).)))))))....)))). ( -45.50)
>DroYak_CAF1 3529 117 + 1
ACUUGCUCAGCUGGUCGGGCAGUUGGGUCUGGAUCUGGUCCAGGUCCAGCUGGGCCAUUAUGCCAGCCGCUGCCAGUACCACCAGCCAAAUGGCGCAUAUCGCUUGGCUUACAUA---UG
.........(((((((((.(((((((..((((((...))))))..)))))))(((......)))..)))..))))))......(((((...((((.....)))))))))......---.. ( -48.90)
>consensus
ACUUGCUCAGCUGGUCGGGCAGCUGGGUCUGGAUCUGAUCCAGGUCUAGCUGGGCCAUUAUGCCGGCAGUGGCGAGUAUAACCAGCCAAAUGGCGCAUAUCGCAUGGCUUACAUA___UG
(((((((..((((((..(((((((((..(((((.....)))))..))))))..))).....))))))...))))))).......((((....(((.....))).))))............ (-35.66 = -37.94 +   2.28)

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 12:13:59 2006