Locus 6311

Sequence ID 3L_DroMel_CAF1
Location 16,848,345 – 16,848,447
Length 102
Max. P 0.855440
window10124 window10125

overview

Window 4

Location 16,848,345 – 16,848,447
Length 102
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 82.53
Mean single sequence MFE -21.40
Consensus MFE -12.19
Energy contribution -13.04
Covariance contribution 0.85
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.57
SVM decision value 0.21
SVM RNA-class probability 0.634979
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16848345 102 + 23771897
AUCCACGCCGGCAACUGCAACAUCAACAUCCGAUUCGCGGCAGCAACUGCAACUGCAACUGAA------GCUGCCACUGCCACAAACAUAUGCAUACCCCCCGUCCCC
.........((((...((...(((.......)))..))((((((..((((....)))...)..------))))))..))))........................... ( -21.60)
>DroSec_CAF1 37892 98 + 1
AUCUAAGCCGACAACUGCAACAUCAACAUCCGAUUCGCAGCAGCAACUGCAACUGCAACUGAA------GCUGCCACUGCCACAAACAUAUGCAUGCAUCCCCU----
...............((((.................(((((..((..(((....)))..))..------)))))...(((...........)))))))......---- ( -16.70)
>DroSim_CAF1 40630 98 + 1
AUCCAAGCCGGCAACUGCAACAUCAACAUCCGAUUCGCGGCAGCAACUGCAACUGCAACUGAA------GCUGCCACUGCCACAAACAUAUGCAUGCAUCUCCC----
.........((((...((...(((.......)))..))((((((..((((....)))...)..------))))))..)))).......................---- ( -21.60)
>DroEre_CAF1 38603 96 + 1
AUCCACGGCGGCUACUGCAACAUCAACAUCCGAUCCGCGGCAGCAACUG------CAACUGAAGCUGCCACUGCCACUGCCACAAACAUAUUCAUUCGACCC------
......((((((....((...(((.......)))..))((((((..(..------.....)..))))))...)))...))).....................------ ( -21.90)
>DroYak_CAF1 38045 102 + 1
AUCCACAGCGGCCACUGCAACAUCAACAUCCGAUCCGCGGCAGCAACUGCAGCUGCAACUGAAGCUGCUACUGCCACUGCCACAAACAUAUUCAAUCCCCCC------
.......(.(((....((...(((.......)))..))(((((.....((((((........))))))..)))))...))).)...................------ ( -25.20)
>consensus
AUCCACGCCGGCAACUGCAACAUCAACAUCCGAUUCGCGGCAGCAACUGCAACUGCAACUGAA______GCUGCCACUGCCACAAACAUAUGCAUGCACCCC______
.........(((....((...(((.......)))..))((((((...(((....)))............))))))...)))........................... (-12.19 = -13.04 +   0.85)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,848,345 – 16,848,447
Length 102
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 82.53
Mean single sequence MFE -35.98
Consensus MFE -24.57
Energy contribution -24.06
Covariance contribution -0.51
Combinations/Pair 1.13
Mean z-score -2.10
Structure conservation index 0.68
SVM decision value 0.81
SVM RNA-class probability 0.855440
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16848345 102 - 23771897
GGGGACGGGGGGUAUGCAUAUGUUUGUGGCAGUGGCAGC------UUCAGUUGCAGUUGCAGUUGCUGCCGCGAAUCGGAUGUUGAUGUUGCAGUUGCCGGCGUGGAU
((.((((.((.((..((((..((((((((((((.(((((------(.(....).))))))....))))))))))))...))))..)).)).).))).))......... ( -37.00)
>DroSec_CAF1 37892 98 - 1
----AGGGGAUGCAUGCAUAUGUUUGUGGCAGUGGCAGC------UUCAGUUGCAGUUGCAGUUGCUGCUGCGAAUCGGAUGUUGAUGUUGCAGUUGUCGGCUUAGAU
----.((.((((((.((((((((((((.((((..(((((------(.(((......))).))))))..)))).)..)))))))..)))))))).)).))......... ( -31.40)
>DroSim_CAF1 40630 98 - 1
----GGGAGAUGCAUGCAUAUGUUUGUGGCAGUGGCAGC------UUCAGUUGCAGUUGCAGUUGCUGCCGCGAAUCGGAUGUUGAUGUUGCAGUUGCCGGCUUGGAU
----((.((.((((.((((..((((((((((((.(((((------(.(....).))))))....))))))))))))...))))......)))).)).))......... ( -36.10)
>DroEre_CAF1 38603 96 - 1
------GGGUCGAAUGAAUAUGUUUGUGGCAGUGGCAGUGGCAGCUUCAGUUG------CAGUUGCUGCCGCGGAUCGGAUGUUGAUGUUGCAGUAGCCGCCGUGGAU
------...............(((..((((.(((((((..((.((.......)------).))..))))))).....((.(((.......)))....))))))..))) ( -34.90)
>DroYak_CAF1 38045 102 - 1
------GGGGGGAUUGAAUAUGUUUGUGGCAGUGGCAGUAGCAGCUUCAGUUGCAGCUGCAGUUGCUGCCGCGGAUCGGAUGUUGAUGUUGCAGUGGCCGCUGUGGAU
------......((..(...(((((((((((((.(((((.(((((....))))).)))))....))))))))))).))....)..)).(..((((....))))..).. ( -40.50)
>consensus
______GGGAGGAAUGCAUAUGUUUGUGGCAGUGGCAGC______UUCAGUUGCAGUUGCAGUUGCUGCCGCGAAUCGGAUGUUGAUGUUGCAGUUGCCGGCGUGGAU
.....................(((((((((((..((.(.........)...(((....)))))..)))))))))))(((.(((.......)))....)))........ (-24.57 = -24.06 +  -0.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:22 2006