Locus 5708

Sequence ID 2R_DroMel_CAF1
Location 18,071,677 – 18,071,868
Length 191
Max. P 0.768192
window9140 window9141 window9142

overview

Window 0

Location 18,071,677 – 18,071,776
Length 99
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.67
Mean single sequence MFE -43.02
Consensus MFE -21.40
Energy contribution -20.93
Covariance contribution -0.47
Combinations/Pair 1.32
Mean z-score -2.38
Structure conservation index 0.50
SVM decision value 0.52
SVM RNA-class probability 0.768192
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18071677 99 - 20766785
AUGGCAGUGGGAGCAGGAGCAGGAGCAGGAG---CAACCGGACCUGG---CGGACAGCCGAAGGUUACGACGGCCGCCUAGAAUUGGUUGUGCUCGCUGCUGUUC
..(((((..(((((....((....))....(---(((((((..((((---((....((((..(....)..)))))))).))..)))))))))))).)..))))). ( -40.70)
>DroPse_CAF1 31718 94 - 1
-----AGCAGGAGCAGGA------GCUGGAGCUACAGCCGAGCCUGGUGGCGGCCAGGCCAAGGUCACGACGGCCGCCUAGAAUUGGCUGUGCUCGCUGCUGUUC
-----.....((((((.(------((..((((.((((((((..(((..(((((((.(((....))).....))))))))))..))))))))))))))).)))))) ( -51.00)
>DroSec_CAF1 29194 93 - 1
GUGGCAGUGGGAGCAGGA------GCAGGAG---CAACCGGACCUGG---CGGACAGCCGAAGGUCACGACGGCCGCCUAGAAUUGGUUGUGCUCGCUGCUGUUC
(..((((((((.((....------))....(---(((((((..((((---((....((((..(....)..)))))))).))..)))))))).))))))))..).. ( -39.30)
>DroYak_CAF1 29972 92 - 1
-CAGGAGCAGGAGCAGGA------GCAGGAG---CAACCGGACCUGG---UGGACAGCCGAAGGUGACGACGGCCGCCUAGAAUUGGUUGUGCUCGCUGCUGUUC
-...((((((.(((..((------((....(---(((((((..((((---((....((((..(....)..)))))))).))..))))))))))))))).)))))) ( -41.40)
>DroAna_CAF1 29384 85 - 1
--------GGCAGAAGGA------GGAUCUG---CUGUUGGUCCUGG---GGGACAGCCGAAGGUGACGACGGCUGCCUAGAAUUGGUUGUGCUCGCUGCUGUUC
--------(((((..(((------(((((..---.....))))))..---(((.((((((..(....)..))))))))).............))..))))).... ( -34.70)
>DroPer_CAF1 32135 94 - 1
-----AGCAGGAGCAGGA------GCUGGAGCUACAGCCGAGCCUGGUGGCGGCCAGGCCAAGGUCACGACGGCCGCCUAGAAUUGGCUGUGCUCGCUGCUGUUC
-----.....((((((.(------((..((((.((((((((..(((..(((((((.(((....))).....))))))))))..))))))))))))))).)))))) ( -51.00)
>consensus
_____AGCAGGAGCAGGA______GCAGGAG___CAACCGGACCUGG___CGGACAGCCGAAGGUCACGACGGCCGCCUAGAAUUGGUUGUGCUCGCUGCUGUUC
.....(((((((((......................(((....(((........))).....)))....(((((((........))))))))))).))))).... (-21.40 = -20.93 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,071,776 – 18,071,868
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 65.10
Mean single sequence MFE -32.20
Consensus MFE -15.48
Energy contribution -15.85
Covariance contribution 0.37
Combinations/Pair 1.28
Mean z-score -1.54
Structure conservation index 0.48
SVM decision value 0.51
SVM RNA-class probability 0.762660
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18071776 92 + 20766785
GCCGCCAACUCCCACUCCUGCAUCUGCGCCCGCCUCGAGGGAUGCGGGUGCCGCCGAGAUCUCGUCCAGCUGCUGUUGGAGCAGCUGCUCCU
..............(((..((((((((((((.......))).)))))))))....))).....(..((((((((.....))))))))..).. ( -34.70)
>DroPse_CAF1 31812 73 + 1
----CCCACUGCUC------CUCCAGCAGUGGCCUCAGCCGUCACUGUCGCCGUUGAGAUCUCGUCCAGCUGCAGCU---------CCGUGU
----.((((((((.------....))))))))..........(((.((.((.((((.(((...))))))).)).)).---------..))). ( -22.20)
>DroSec_CAF1 29287 92 + 1
GCCGCCCACUCCCACUCCUGCGUCUGCGCCCGCCUCCAAGGAUGCGGGUGCCGCCGAGAUCUCGUCCAGCUGCUGCUGGAGCAUCUGCUCCU
...((.........(((..(((...((((((((.((....)).))))))))))).)))......((((((....)))))))).......... ( -36.80)
>DroSim_CAF1 29434 92 + 1
GCCGCCCACUACCACUCCUGCGUCUGCGCCCGCCUCCAAGGAUGCGGGUGCCGCCGAGAUCUCGUCCAGCUGCUGCUGGAGCAGCUGCUCCU
((.((.........(((..(((...((((((((.((....)).))))))))))).)))......((((((....)))))))).))....... ( -39.00)
>DroYak_CAF1 30064 72 + 1
--------------------CUCCUACUCCCGCCUCCAGGGAGGCGGGUGCUGCCGAGAUCUCGUCCAGCUGUUGCUGGAGCAGCUGCUCCU
--------------------........((((((((....)))))))).((((((((....)))((((((....)))))))))))....... ( -38.30)
>DroPer_CAF1 32229 73 + 1
----CCCACUGCUC------CUCCAGCAGUGGCCUCAGCCGUCACUGUCGCCGUUGAGAUCUCGUCCAGCUGCAGCU---------CCGUGU
----.((((((((.------....))))))))..........(((.((.((.((((.(((...))))))).)).)).---------..))). ( -22.20)
>consensus
____CCCACUCCCA______CUCCUGCGCCCGCCUCCAAGGAUGCGGGUGCCGCCGAGAUCUCGUCCAGCUGCUGCUGGAGCAGCUGCUCCU
.........................((.(((((.((....)).))))).))...(((....)))((((((....))))))............ (-15.48 = -15.85 +   0.37)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,071,776 – 18,071,868
Length 92
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 65.10
Mean single sequence MFE -35.95
Consensus MFE -15.85
Energy contribution -18.55
Covariance contribution 2.70
Combinations/Pair 1.14
Mean z-score -1.59
Structure conservation index 0.44
SVM decision value 0.38
SVM RNA-class probability 0.711849
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18071776 92 - 20766785
AGGAGCAGCUGCUCCAACAGCAGCUGGACGAGAUCUCGGCGGCACCCGCAUCCCUCGAGGCGGGCGCAGAUGCAGGAGUGGGAGUUGGCGGC
.(((((....)))))..((((.((((..(((....))).)))).(((((.(((((((...)))).((....)).)))))))).))))..... ( -37.10)
>DroPse_CAF1 31812 73 - 1
ACACGG---------AGCUGCAGCUGGACGAGAUCUCAACGGCGACAGUGACGGCUGAGGCCACUGCUGGAG------GAGCAGUGGG----
...((.---------.((((..((((...((....))..))))..))))..)).......((((((((....------.)))))))).---- ( -29.80)
>DroSec_CAF1 29287 92 - 1
AGGAGCAGAUGCUCCAGCAGCAGCUGGACGAGAUCUCGGCGGCACCCGCAUCCUUGGAGGCGGGCGCAGACGCAGGAGUGGGAGUGGGCGGC
.(((((....))))).((.((.((((..(((....))).)))).(((((.((((((...((....))...)).))))))))).))..))... ( -38.70)
>DroSim_CAF1 29434 92 - 1
AGGAGCAGCUGCUCCAGCAGCAGCUGGACGAGAUCUCGGCGGCACCCGCAUCCUUGGAGGCGGGCGCAGACGCAGGAGUGGUAGUGGGCGGC
....((.(((((((((((....))))))......(((.(((((.(((((.((....)).))))).))...)))..)))..)))))..))... ( -39.90)
>DroYak_CAF1 30064 72 - 1
AGGAGCAGCUGCUCCAGCAACAGCUGGACGAGAUCUCGGCAGCACCCGCCUCCCUGGAGGCGGGAGUAGGAG--------------------
....((.(((((((((((....))))))(((....)))))))).((((((((....)))))))).)).....-------------------- ( -40.40)
>DroPer_CAF1 32229 73 - 1
ACACGG---------AGCUGCAGCUGGACGAGAUCUCAACGGCGACAGUGACGGCUGAGGCCACUGCUGGAG------GAGCAGUGGG----
...((.---------.((((..((((...((....))..))))..))))..)).......((((((((....------.)))))))).---- ( -29.80)
>consensus
AGGAGCAGCUGCUCCAGCAGCAGCUGGACGAGAUCUCGGCGGCACCCGCAUCCCUGGAGGCGGGCGCAGAAG______UGGCAGUGGG____
.(((((....)))))....((.((((..(((....))).)))).(((((.((....)).))))).))......................... (-15.85 = -18.55 +   2.70)

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 11:52:22 2006