Locus 8182

Sequence ID X_DroMel_CAF1
Location 20,345,415 – 20,345,629
Length 214
Max. P 0.937459
window13443 window13444 window13445

overview

Window 3

Location 20,345,415 – 20,345,530
Length 115
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 97.00
Mean single sequence MFE -29.10
Consensus MFE -28.30
Energy contribution -28.55
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.97
SVM decision value 1.02
SVM RNA-class probability 0.900735
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20345415 115 + 22224390
--CCACCCACCCACUUCAGUGGCACUUGCCACCGCUUUGCUGCCAUUGUCGUUCCACUUUAGAAUUAUUUGCACAAAAUCUUUCGGCGGCAGCAAGGAUUUCUCGCUACUGUGCUUC
--.........(((....(((((....)))))..((((((((((...((((.....)....(((..((((.....))))..)))))))))))))))).............))).... ( -29.60)
>DroSec_CAF1 13210 117 + 1
ACCCACCCACCCACUUCAGUGGCACUUGCCACCGCUUUGCUGCCAUUGUCGUUUCACUUUAGAAUUAUUUGCACAAAAUCUUUCGGCGGCAGCAAGGAUUUCUCGCUACUGUGCUUC
...........(((....(((((....)))))..((((((((((...((((.....)....(((..((((.....))))..)))))))))))))))).............))).... ( -29.60)
>DroSim_CAF1 14998 116 + 1
AC-CACCCACCCACUUCAGUGGCACUUGCCACCGCUUUGCUGCCAUUGUCGUUCCACUUUAGAAUUAUUUGCACAAAAUCUUUCGGCGGCAGCAAGGAUUUCUCGCUACUGUGCUUC
..-........(((....(((((....)))))..((((((((((...((((.....)....(((..((((.....))))..)))))))))))))))).............))).... ( -29.60)
>DroEre_CAF1 9932 114 + 1
---CACCCACCCACUUCAGUGGCACUUGCCACCGCUUUGCAGCCAUUGUCGUUCCACUUUAGAAUUAUUUGCACAAAAUCUUUCGGCGGCAGCAAGGAUUUCUCGCUGCUGUGCUUC
---...............(((((....)))))......((((((...((......))....(((..((((.....))))..))))))((((((.((.....)).)))))).)))... ( -27.60)
>consensus
___CACCCACCCACUUCAGUGGCACUUGCCACCGCUUUGCUGCCAUUGUCGUUCCACUUUAGAAUUAUUUGCACAAAAUCUUUCGGCGGCAGCAAGGAUUUCUCGCUACUGUGCUUC
...........(((....(((((....)))))..((((((((((...((((.....)....(((..((((.....))))..)))))))))))))))).............))).... (-28.30 = -28.55 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,345,415 – 20,345,530
Length 115
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -37.07
Consensus MFE -35.51
Energy contribution -35.13
Covariance contribution -0.37
Combinations/Pair 1.06
Mean z-score -2.19
Structure conservation index 0.96
SVM decision value 1.26
SVM RNA-class probability 0.937459
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20345415 115 - 22224390
GAAGCACAGUAGCGAGAAAUCCUUGCUGCCGCCGAAAGAUUUUGUGCAAAUAAUUCUAAAGUGGAACGACAAUGGCAGCAAAGCGGUGGCAAGUGCCACUGAAGUGGGUGGGUGG--
....(((.((((((((.....))))))))((((......((((((((......((((.....))))........))).)))))(((((((....))))))).....)))).))).-- ( -37.04)
>DroSec_CAF1 13210 117 - 1
GAAGCACAGUAGCGAGAAAUCCUUGCUGCCGCCGAAAGAUUUUGUGCAAAUAAUUCUAAAGUGAAACGACAAUGGCAGCAAAGCGGUGGCAAGUGCCACUGAAGUGGGUGGGUGGGU
...(((((((((((((.....))))))))...(....)....)))))......(((......)))....((.(.((..((...(((((((....)))))))...)).)).).))... ( -36.40)
>DroSim_CAF1 14998 116 - 1
GAAGCACAGUAGCGAGAAAUCCUUGCUGCCGCCGAAAGAUUUUGUGCAAAUAAUUCUAAAGUGGAACGACAAUGGCAGCAAAGCGGUGGCAAGUGCCACUGAAGUGGGUGGGUG-GU
....(((.((((((((.....))))))))((((......((((((((......((((.....))))........))).)))))(((((((....))))))).....)))).)))-.. ( -37.04)
>DroEre_CAF1 9932 114 - 1
GAAGCACAGCAGCGAGAAAUCCUUGCUGCCGCCGAAAGAUUUUGUGCAAAUAAUUCUAAAGUGGAACGACAAUGGCUGCAAAGCGGUGGCAAGUGCCACUGAAGUGGGUGGGUG---
...(((((((((((((.....))))))))...(....)....)))))......((((.....))))...((.(.(((.((...(((((((....)))))))...))))).).))--- ( -37.80)
>consensus
GAAGCACAGUAGCGAGAAAUCCUUGCUGCCGCCGAAAGAUUUUGUGCAAAUAAUUCUAAAGUGGAACGACAAUGGCAGCAAAGCGGUGGCAAGUGCCACUGAAGUGGGUGGGUG___
....(((.((((((((.....))))))))((((......((((((((......(((......))).........)).))))))(((((((....))))))).....)))).)))... (-35.51 = -35.13 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,345,530 – 20,345,629
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.51
Mean single sequence MFE -44.20
Consensus MFE -33.92
Energy contribution -34.70
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.77
SVM decision value 0.79
SVM RNA-class probability 0.852706
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20345530 99 + 22224390
UCGAGCUUCCGGCGACCGACUUGCUUCAUAAUUGUCCUUCCUCUGGCGU------AAGGGAAGGGGGGAAG---GGGGGAUGGUG------------UGGGUGGUUGGUGGGCGGCGGUG
....(((((((.(((((.(((..(.((((...(.((((((((((..(..------....)...))))))))---)).).)))).)------------..)))))))).)))).))).... ( -40.50)
>DroSec_CAF1 13327 120 + 1
UCGAGCUUCCGGCGACCAACUUGCUUCAUAAUUGUCCUUCCUCCGGCGAUGGUGGAGGGGGAAGGGGGAAGGGGGGGGGCUGGUGUGUGUGGUUGAGUGGGUGGUUGGUGGGCGGCGGUG
....(((((((.((((((.((..(((((((.((.((((((((((.((....))...)))))))))).)).........((....)).))))...)))..)))))))).)))).))).... ( -44.50)
>DroSim_CAF1 15114 109 + 1
UCGAGCUUCCGGCGACCAACUUGCUUCAUAAUUGUCCUUCCUCCGGCGA------AGGGGGAACGG-----GGGGGGGGCUGGUGUGGGUGGUUGAGUGGGUGGUUGGUGGGCGGCGGUG
....(((((((.((((((.((..(((((((...((((((((((((....------........)))-----)))))))))...)))).......)))..)))))))).)))).))).... ( -47.61)
>consensus
UCGAGCUUCCGGCGACCAACUUGCUUCAUAAUUGUCCUUCCUCCGGCGA______AGGGGGAAGGGGGAAGGGGGGGGGCUGGUGUG_GUGGUUGAGUGGGUGGUUGGUGGGCGGCGGUG
....(((.(((.(.(((((((.(((((....((.((((((((((............)))))))))).))......)))))......................))))))).).))).))). (-33.92 = -34.70 +   0.78)

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 12:57:48 2006