Locus 166

Sequence ID 2R_DroMel_CAF1
Location 1,426,708 – 1,426,908
Length 200
Max. P 0.999070
window368 window369 window370 window371 window372

overview

Window 8

Location 1,426,708 – 1,426,828
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -40.82
Consensus MFE -36.28
Energy contribution -36.52
Covariance contribution 0.24
Combinations/Pair 1.08
Mean z-score -1.39
Structure conservation index 0.89
SVM decision value 0.79
SVM RNA-class probability 0.850611
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1426708 120 - 20766785
AUGUAAAUGAAAUGCCACUCGGCAGAGUGGCUUACCCUUUGGAAGAAGCUUCCUCUGAGAAGUUAACUGAGGUGAGGUGCCAGAACAGAUUGGUCGGACGGCCAUUGUCUGGGUCGACAA
.(((.........(((((((....)))))))..(((((((((.....(((((.(((.((.......)).))).))))).)))))..(((((((((....)))))..))))))))..))). ( -40.80)
>DroSec_CAF1 45149 120 - 1
AUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGCCAGAACAGAUUGGUCGGACGGCCAUUGUCUGGGGCGACAG
.(((.........(((((((....)))))))(((((.((((((.((.....)))))))).((....))..))))).((.(((((.(((..(((((....))))))))))))).)).))). ( -44.00)
>DroSim_CAF1 50205 120 - 1
AUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGCCAGAACAGAUUGGUCGGACGGCCAUUGUCUGGGUCGACAA
.(((..((.....(((((((....)))))))(((((.((((((.((.....)))))))).((....))..)))))....(((((.(((..(((((....)))))))))))))))..))). ( -40.40)
>DroEre_CAF1 43252 120 - 1
AUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGGAGGAGCUGCCUCCGAGAAGUUAAGCGAGGUGAGGUGCCAGAACAGAUUGGUCGGACGUCCAUUGUCUGGGUCGACAA
.(((..((.....(((((((....)))))))(((((((((.(((((.....))))).))).(.....)).)))))....(((((.(((..(((.(....).)))))))))))))..))). ( -39.30)
>DroYak_CAF1 47811 120 - 1
AUGUAAAUGAAAUGCCAAUCUGCAGAGUGGCUUACCCUUUGGAAGGAGCUUCUUUCGAGAAGUUAACUGAGGUGAGGUGCCAGAACGGAUUGGUCGGACGGCCAUUGUCUGGGCCGACAA
.(((.........(((((((((....(((.((((((..(..(....(((((((....)))))))..)..))))))).))).....)))))))))....(((((........)))))))). ( -39.60)
>consensus
AUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGCCAGAACAGAUUGGUCGGACGGCCAUUGUCUGGGUCGACAA
.(((.........(((((((....))))))).((((((((((....((((((......))))))..))))))...))))(((((.(((..(((((....)))))))))))))....))). (-36.28 = -36.52 +   0.24)

alignment

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secondary structure

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Window 9

Location 1,426,748 – 1,426,868
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.08
Mean single sequence MFE -31.64
Consensus MFE -28.90
Energy contribution -29.22
Covariance contribution 0.32
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.91
SVM decision value 1.87
SVM RNA-class probability 0.980831
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1426748 120 + 20766785
GCACCUCACCUCAGUUAACUUCUCAGAGGAAGCUUCUUCCAAAGGGUAAGCCACUCUGCCGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUU
...............((((...((((.(((((...)))))...((((..(((((((....))))))).........((((....)))).))))((.....)).)))).....)))).... ( -30.10)
>DroSec_CAF1 45189 120 + 1
GCACCUCACCUCAGUUAACUUCUCGGAGGAAGCUCCUUCCAAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCGCCCGCUUUCGGCACUGACAGUCGUUACUUU
..........(((((.........((((....)))).......(((((((((((((....)))))))....((((........))))))))))((.....)))))))............. ( -35.60)
>DroSim_CAF1 50245 120 + 1
GCACCUCACCUCAGUUAACUUCUCGGAGGAAGCUCCUUCCAAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCGCCCGCUUUCGGCACUGACAGUCGUUACUUU
..........(((((.........((((....)))).......(((((((((((((....)))))))....((((........))))))))))((.....)))))))............. ( -35.60)
>DroEre_CAF1 43292 120 + 1
GCACCUCACCUCGCUUAACUUCUCGGAGGCAGCUCCUCCCAAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUU
............(((.........(((((.....)))))....(((((((((((((....)))))))....((((........))))))))))......)))..((((....)))).... ( -34.50)
>DroYak_CAF1 47851 120 + 1
GCACCUCACCUCAGUUAACUUCUCGAAAGAAGCUCCUUCCAAAGGGUAAGCCACUCUGCAGAUUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUGUUUU
..........(((((...(((((....)))))...........((((..((((.((....)).)))).........((((....)))).))))((.....)))))))............. ( -22.40)
>consensus
GCACCUCACCUCAGUUAACUUCUCGGAGGAAGCUCCUUCCAAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUU
..........(((((.........(((((.....)))))....(((((((((((((....)))))))....((((........))))))))))((.....)))))))............. (-28.90 = -29.22 +   0.32)

alignment

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secondary structure

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Window 0

Location 1,426,748 – 1,426,868
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.08
Mean single sequence MFE -35.80
Consensus MFE -31.80
Energy contribution -31.88
Covariance contribution 0.08
Combinations/Pair 1.13
Mean z-score -1.24
Structure conservation index 0.89
SVM decision value 0.30
SVM RNA-class probability 0.677911
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1426748 120 - 20766785
AAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCGGCAGAGUGGCUUACCCUUUGGAAGAAGCUUCCUCUGAGAAGUUAACUGAGGUGAGGUGC
.......(...(.(((((.(((((...((((((((((........))))....(((((((....))))))))))))))))))....((((((......)))))).))))).)...).... ( -36.50)
>DroSec_CAF1 45189 120 - 1
AAAGUAACGACUGUCAGUGCCGAAAGCGGGCGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGC
.......(((.((((.((.((....).).)))))))))...............(((((((....)))))))(((((.((((((.((.....)))))))).((....))..)))))..... ( -34.80)
>DroSim_CAF1 50245 120 - 1
AAAGUAACGACUGUCAGUGCCGAAAGCGGGCGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGC
.......(((.((((.((.((....).).)))))))))...............(((((((....)))))))(((((.((((((.((.....)))))))).((....))..)))))..... ( -34.80)
>DroEre_CAF1 43292 120 - 1
AAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGGAGGAGCUGCCUCCGAGAAGUUAAGCGAGGUGAGGUGC
................(..((..(.((((((((((((........))))....(((((((....)))))))))))))(((.(((((.....))))).)))......))....)..))..) ( -41.30)
>DroYak_CAF1 47851 120 - 1
AAAACAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCAAUCUGCAGAGUGGCUUACCCUUUGGAAGGAGCUUCUUUCGAGAAGUUAACUGAGGUGAGGUGC
....((.(...(.(((((.(((((...((((((((((........))))....((((.((....)).)))))))))))))))....(((((((....))))))).))))).)...).)). ( -31.60)
>consensus
AAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUUGGAAGGAGCUUCCUCCGAGAAGUUAACUGAGGUGAGGUGC
................(..((....((((((((((((........))))....(((((((....)))))))))))))(((((.(((.....))))))))............))..))..) (-31.80 = -31.88 +   0.08)

alignment

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secondary structure

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Window 1

Location 1,426,788 – 1,426,908
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -33.66
Consensus MFE -32.04
Energy contribution -32.44
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.63
Structure conservation index 0.95
SVM decision value 2.17
SVM RNA-class probability 0.989458
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1426788 120 + 20766785
AAAGGGUAAGCCACUCUGCCGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUUCCGUUACAAAUCAAUUGCCAACUUAUGGCCGUGACGAGCC
...((((..(((((((....))))))).........((((....)))).))))......(((..((((....)))).....((((((.........((((.....)))).)))))).))) ( -33.10)
>DroSec_CAF1 45229 120 + 1
AAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCGCCCGCUUUCGGCACUGACAGUCGUUACUUUCCGUUACAAAUCAAUUGCCAACUUAUGGCCGUGACGAGCC
...(((((((((((((....)))))))....((((........))))))))))......(((..((((....)))).....((((((.........((((.....)))).)))))).))) ( -36.90)
>DroSim_CAF1 50285 120 + 1
AAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCGCCCGCUUUCGGCACUGACAGUCGUUACUUUCCGUUACAAAUCAAUUGCCAACUUAUGGCCGUGACGAGCC
...(((((((((((((....)))))))....((((........))))))))))......(((..((((....)))).....((((((.........((((.....)))).)))))).))) ( -36.90)
>DroEre_CAF1 43332 120 + 1
AAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUUCCGCUACAAAUCAAUUGCCAACUUAUGGCCGUGACGAGCC
...(((((((((((((....)))))))....((((........))))))))))((((.(((...((((....))))....))).......(((...((((.....))))..))).)))). ( -36.80)
>DroYak_CAF1 47891 120 + 1
AAAGGGUAAGCCACUCUGCAGAUUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUGUUUUCCGUUGCAAAUCAAUUGCCAUCUUAUGACCGUGACGAGCC
...((((..((((.((....)).)))).........((((....)))).))))((((((((((.(((......((((........)))).)))..)))).((....))....)).)))). ( -24.60)
>consensus
AAAGGGUGAGCCACUCUGCGGAGUGGCAUUUCAUUUACAUUUCAAUGUCACCCGCUUUCGGCACUGACAAUCGUUAUUUUCCGUUACAAAUCAAUUGCCAACUUAUGGCCGUGACGAGCC
...(((((((((((((....)))))))....((((........))))))))))((((.(((...((((....))))....))).......(((...((((.....))))..))).)))). (-32.04 = -32.44 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,426,788 – 1,426,908
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -38.64
Consensus MFE -36.24
Energy contribution -36.64
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -2.08
Structure conservation index 0.94
SVM decision value 3.36
SVM RNA-class probability 0.999070
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1426788 120 - 20766785
GGCUCGUCACGGCCAUAAGUUGGCAAUUGAUUUGUAACGGAAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCGGCAGAGUGGCUUACCCUUU
((((......)))).....((((((.(((((......((........))...)))))))))))....((((((((((........))))....(((((((....)))))))))))))... ( -39.50)
>DroSec_CAF1 45229 120 - 1
GGCUCGUCACGGCCAUAAGUUGGCAAUUGAUUUGUAACGGAAAGUAACGACUGUCAGUGCCGAAAGCGGGCGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUU
((((......)))).....((((((.(((((((((.((.....)).))))..)))))))))))....(((.((((((........))))....(((((((....))))))))).)))... ( -39.50)
>DroSim_CAF1 50285 120 - 1
GGCUCGUCACGGCCAUAAGUUGGCAAUUGAUUUGUAACGGAAAGUAACGACUGUCAGUGCCGAAAGCGGGCGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUU
((((......)))).....((((((.(((((((((.((.....)).))))..)))))))))))....(((.((((((........))))....(((((((....))))))))).)))... ( -39.50)
>DroEre_CAF1 43332 120 - 1
GGCUCGUCACGGCCAUAAGUUGGCAAUUGAUUUGUAGCGGAAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUU
((((......)))).....((((((.(((((......((........))...)))))))))))....((((((((((........))))....(((((((....)))))))))))))... ( -41.60)
>DroYak_CAF1 47891 120 - 1
GGCUCGUCACGGUCAUAAGAUGGCAAUUGAUUUGCAACGGAAAACAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCAAUCUGCAGAGUGGCUUACCCUUU
((...(((((.......((((((((.((.(((((((.((........))..(((((.(..(....)..).)))))......))))))).)).)))).)))).....)))))...)).... ( -33.10)
>consensus
GGCUCGUCACGGCCAUAAGUUGGCAAUUGAUUUGUAACGGAAAAUAACGAUUGUCAGUGCCGAAAGCGGGUGACAUUGAAAUGUAAAUGAAAUGCCACUCCGCAGAGUGGCUCACCCUUU
((((......)))).....((((((.(((((......((........))...)))))))))))....((((((((((........))))....(((((((....)))))))))))))... (-36.24 = -36.64 +   0.40)

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 09:30:49 2006