Locus 1268

Sequence ID 3L_DroMel_CAF1
Location 3,667,388 – 3,667,503
Length 115
Max. P 0.917299
window1981 window1982 window1983

overview

Window 1

Location 3,667,388 – 3,667,483
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -26.58
Consensus MFE -23.78
Energy contribution -23.87
Covariance contribution 0.09
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.89
SVM decision value 1.11
SVM RNA-class probability 0.917299
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3667388 95 + 23771897
CAAUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCA
...(((...((((.((.((((((((.(((((((((((.((......)).)))))))....))))...))))))))))(((.....)))))))))) ( -28.60)
>DroSec_CAF1 62530 91 + 1
CAAUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAUCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCA----CA
....((.....(((((.((((((((.(((((((((.(.((......)).).)))))....))))...))))))))))))).....))..----.. ( -21.70)
>DroSim_CAF1 57305 95 + 1
CAAUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCA
...(((...((((.((.((((((((.(((((((((((.((......)).)))))))....))))...))))))))))(((.....)))))))))) ( -28.60)
>DroEre_CAF1 56750 95 + 1
CAUUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCA
((((((.((........((((((((.(((((((((((.((......)).)))))))....))))...)))))))))).)))))).(((...))). ( -28.80)
>DroYak_CAF1 43025 95 + 1
CAAUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCA
...(((...((((.((.((((((((.(((((((((((.((......)).)))))))....))))...))))))))))(((.....)))))))))) ( -28.60)
>DroAna_CAF1 59786 78 + 1
---CGUGGACAGUUGAAUUGUCAGUCAUUUUGUCAGGCGCUUAAUUGCAGCUGGCAAUUCGAAUAAAGCUGGCAAUCGGC--------------A
---........(((((.((((((((.((((((((((..((......))..))))))....))))...)))))))))))))--------------. ( -23.20)
>consensus
CAAUGCAGACAGUUGAAUUGUCAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCA
...........(((((.((((((((.(((((((((((.((......)).)))))))....))))...)))))))))))))............... (-23.78 = -23.87 +   0.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,667,409 – 3,667,503
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 92.03
Mean single sequence MFE -27.97
Consensus MFE -22.51
Energy contribution -24.73
Covariance contribution 2.22
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.80
SVM decision value 0.53
SVM RNA-class probability 0.772652
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3667409 94 + 23771897
CAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCAACUGCCAGCCAAAGCCAAAC
...((...((((((((.((......)).))))))))...)).......((((....(((.....))).(((((....))))).....))))... ( -31.70)
>DroSec_CAF1 62551 90 + 1
CAGUCAUUUUGUCAUCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCA----CAACUGCCAGCCAAAGCCAAAC
...((...((((((.(.((......)).).))))))...)).......((((....(((....(((..----.....))).)))...))))... ( -21.20)
>DroSim_CAF1 57326 94 + 1
CAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCAACUGCCAGCCAAAGCCAAAC
...((...((((((((.((......)).))))))))...)).......((((....(((.....))).(((((....))))).....))))... ( -31.70)
>DroEre_CAF1 56771 94 + 1
CAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCAACUGCCAGCCAAAGCCAAAC
...((...((((((((.((......)).))))))))...)).......((((....(((.....))).(((((....))))).....))))... ( -31.70)
>DroYak_CAF1 43046 94 + 1
CAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCAACUGCCAGCCAAAGCCAAAC
...((...((((((((.((......)).))))))))...)).......((((....(((.....))).(((((....))))).....))))... ( -31.70)
>DroAna_CAF1 59804 80 + 1
CAGUCAUUUUGUCAGGCGCUUAAUUGCAGCUGGCAAUUCGAAUAAAGCUGGCAAUCGGC--------------AACUGGAAGCCAAAGCCAAAC
..............(((((......)).((..((............))..))....(((--------------........)))...))).... ( -19.80)
>consensus
CAGUCAUUUUGUCAGCCGCUUAAUUGCAGUUGGCAAUUCGAAUAAAACUGGCAAUCGGCAAUGGGCCACUGGCAACUGCCAGCCAAAGCCAAAC
...((...((((((((.((......)).))))))))...)).......((((....(((.....))).(((((....))))).....))))... (-22.51 = -24.73 +   2.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,667,409 – 3,667,503
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 92.03
Mean single sequence MFE -28.70
Consensus MFE -25.47
Energy contribution -26.83
Covariance contribution 1.36
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.89
SVM decision value 0.89
SVM RNA-class probability 0.874618
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3667409 94 - 23771897
GUUUGGCUUUGGCUGGCAGUUGCCAGUGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGCUGACAAAAUGACUG
.((((..(..((((((((((((.(((((...))))).))))))))))))..)..))))(((.((.((((......)))).)).)))........ ( -30.70)
>DroSec_CAF1 62551 90 - 1
GUUUGGCUUUGGCUGGCAGUUG----UGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGAUGACAAAAUGACUG
(((....((((((((((((((.----.(((.....))))))))))))).(((((((((((((.....))))))...)))))))))))..))).. ( -28.20)
>DroSim_CAF1 57326 94 - 1
GUUUGGCUUUGGCUGGCAGUUGCCAGUGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGCUGACAAAAUGACUG
.((((..(..((((((((((((.(((((...))))).))))))))))))..)..))))(((.((.((((......)))).)).)))........ ( -30.70)
>DroEre_CAF1 56771 94 - 1
GUUUGGCUUUGGCUGGCAGUUGCCAGUGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGCUGACAAAAUGACUG
.((((..(..((((((((((((.(((((...))))).))))))))))))..)..))))(((.((.((((......)))).)).)))........ ( -30.70)
>DroYak_CAF1 43046 94 - 1
GUUUGGCUUUGGCUGGCAGUUGCCAGUGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGCUGACAAAAUGACUG
.((((..(..((((((((((((.(((((...))))).))))))))))))..)..))))(((.((.((((......)))).)).)))........ ( -30.70)
>DroAna_CAF1 59804 80 - 1
GUUUGGCUUUGGCUUCCAGUU--------------GCCGAUUGCCAGCUUUAUUCGAAUUGCCAGCUGCAAUUAAGCGCCUGACAAAAUGACUG
..(((((.(((((........--------------)))))..)))))......(((..(((.(((.(((......))).))).)))..)))... ( -21.20)
>consensus
GUUUGGCUUUGGCUGGCAGUUGCCAGUGGCCCAUUGCCGAUUGCCAGUUUUAUUCGAAUUGCCAACUGCAAUUAAGCGGCUGACAAAAUGACUG
.((((..(..((((((((((((.(((((...))))).))))))))))))..)..))))(((.((.((((......)))).)).)))........ (-25.47 = -26.83 +   1.36)

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 10:03:27 2006