Locus 1368

Sequence ID 2R_DroMel_CAF1
Location 5,280,930 – 5,281,076
Length 146
Max. P 0.629347
window2360 window2361

overview

Window 0

Location 5,280,930 – 5,281,037
Length 107
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 86.50
Mean single sequence MFE -43.67
Consensus MFE -31.25
Energy contribution -33.61
Covariance contribution 2.36
Combinations/Pair 1.10
Mean z-score -1.77
Structure conservation index 0.72
SVM decision value 0.20
SVM RNA-class probability 0.629347
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5280930 107 - 20766785
CAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCACCCCUUCCAGUAACAUCAAUGGGUGCAGCCACUA-
......((((((.((((.(((((....))))).....(((((((....)))))))..))))))))))(((((((((.................))))))))).....- ( -47.03)
>DroSec_CAF1 4640 101 - 1
CAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGG------CUGCUGCCCCCCUUCCAGCAACGUCAAUGGGUGCAGCCAUUA-
.((.((((((((.(((..(((((....))))).....(((((((....)))))))..))------).)))))))).))............(((((......))))).- ( -43.40)
>DroSim_CAF1 8965 107 - 1
CAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCCCCCCUUCCAGCAACAUCAAUGGGUGCAGCCACUA-
.((.(((((((((((((.(((((....))))).....(((((((....)))))))..))))).....)))))))).))....((..((((....))))..)).....- ( -43.40)
>DroEre_CAF1 4358 102 - 1
-----UGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGCUGCUCCUCUUGCUCCCCUUCCCGCAACAUCAGCGGAGGCAGCCACUG-
-----.((((((((....(((((....))))).....(((((((....))))))).))))))))......(((.((....((((.......)))).)).))).....- ( -39.80)
>DroYak_CAF1 4791 108 - 1
CCGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUCAUGAUGCUCCUCUUCCAGCAACAUCAUCCGCGGCGGCCACUGC
...((.(((.(((((...(((((....))))).....(((((((....)))))))..(((((...(((.((((........)))).))))))))))))).))).)).. ( -44.70)
>consensus
CAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUCCUGCUGCCCCCCUUCCAGCAACAUCAAUGGGUGCAGCCACUA_
...((.((((.(((....(((((....))))).....(((((((....))))))).))).)))).))(((((((((.................)))))))))...... (-31.25 = -33.61 +   2.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,280,957 – 5,281,076
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.28
Mean single sequence MFE -50.66
Consensus MFE -32.68
Energy contribution -35.96
Covariance contribution 3.28
Combinations/Pair 1.14
Mean z-score -1.71
Structure conservation index 0.65
SVM decision value -0.03
SVM RNA-class probability 0.516683
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5280957 119 - 20766785
ACCCACGGCUGGAGCACCAAUGCUUGUCAGCGGAGCCGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCACCCCUUC
..((.(.(((((((((....)))))..)))).)...((((((((.((...)).))))).))).....)).......(((((((....)))))))..((((((.......)))))).... ( -50.30)
>DroSec_CAF1 4667 113 - 1
ACCCACGGCAGGAGCACCAAUGCUUGUCGGUGGAGCGGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGG------CUGCUGCCCCCCUUC
..((((.(.(.(((((....))))).)).)))).......((.((((((((.(((..(((((....))))).....(((((((....)))))))..))------).)))))))).)).. ( -52.30)
>DroSim_CAF1 8992 119 - 1
ACCCACGGCAGGAGCACCAAUGCUUGUCGGCGGAGCAGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUGCUGCUGCCCCCCUUC
.....((((((.((((((..((.(((((((((((((.(((.........))))))))).)))))))))........(((((((....)))))))...)))))).))))))......... ( -58.50)
>DroEre_CAF1 4385 98 - 1
ACCCACCGCUGGGGCACCAAUGG---------------------UGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGCUGCUCCUCUUGCUCCCCUUC
..........((((...(((.((---------------------..(((((((....(((((....))))).....(((((((....))))))).)))))))..)).)))..))))... ( -41.80)
>DroYak_CAF1 4819 119 - 1
ACCCACGGCAGGAGCAUCAAUGCUUACUGGGGAAGGAGGCCGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUCAUGAUGCUCCUCUUC
......((.((((((((((.......((.((........)).))(((((.(((....(((((....))))).....(((((((....))))))).))).))))).)))))))))))).. ( -50.40)
>consensus
ACCCACGGCAGGAGCACCAAUGCUUGUCGGCGGAGCAGGCAGAGGGGCAGCCGCUCUGACCGAUAACGGUUUUAUGGCCGCAGGUGUCUGUGGCAUGGGUGCUCCUGCUGCCCCCCUUC
.....((((((.((((((...((((((.......))))))...(((((....)))))(((((....))))).....(((((((....)))))))...)))))).))))))......... (-32.68 = -35.96 +   3.28)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:17 2006