Locus 4239

Sequence ID 3L_DroMel_CAF1
Location 12,408,019 – 12,408,171
Length 152
Max. P 0.989416
window6561 window6562 window6563

overview

Window 1

Location 12,408,019 – 12,408,120
Length 101
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 78.22
Mean single sequence MFE -25.42
Consensus MFE -18.50
Energy contribution -17.98
Covariance contribution -0.52
Combinations/Pair 1.27
Mean z-score -1.68
Structure conservation index 0.73
SVM decision value 0.74
SVM RNA-class probability 0.838764
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12408019 101 - 23771897
AGUGCCGCUGCAGUGGGGAGUUGCAAUAACAACACCUCUGGCUGUGCAAAAAUCAUUUCACGUUAAAGGGCCCAA----AUACACAUGCAUGCAUA------------UGUACAUAC
.((((.((((((((((((.((((......)))).(((.((((.(((.(((.....)))))))))).))).)))..----...))).)))).))...------------.)))).... ( -25.80)
>DroSec_CAF1 10617 97 - 1
AGCGCGGCUGCAAUGAGGAGUUGCAAUAACAACACCUCUGGCUGUGCAAAAAUCACUUCACUUUAAAGGGCCCAA----ACACACAU----ACAUG------------UGUACAUAC
.((((((((.....((((.((((......)))).)))).))))))))............................----..(((((.----...))------------)))...... ( -26.30)
>DroSim_CAF1 10593 101 - 1
AGCGCGGUUGCAAUGGGGAGUUGCAAUAACAACACCUCUGGCUGUGCAAAAAUCACUUCACGUUAAAGGGCCCAA----ACACACAUACAUACAUG------------UGUACAUAC
.((((((((.....((((.((((......)))).)))).))))))))............................----..((((((......)))------------)))...... ( -24.20)
>DroEre_CAF1 10930 85 - 1
AGCGCGGCAGCAAUGGGGAGUUGCAACAACAACACCUCUGGUUGUGCAAAAAUCAUUUCAUGUUAAAGGGCCCAG----GCACA----------------------------CAUAC
.(((((((......((((.((((......)))).))))..)))))))............((((......((....----))..)----------------------------))).. ( -21.20)
>DroYak_CAF1 11465 113 - 1
AGCGCGGCAGCAAUGGGGAGUUGCAAAAACAACACCUCUGGUUGUGCAAAAAUCAUUUCAACUUAAAAGGGCCAAACAAGCACA----CAUGCAUAUGUAUGUAUGUAUGUACAUAC
.(((((((......((((.((((......)))).))))..)))))))............................(((.(((.(----(((((....)))))).))).)))...... ( -29.60)
>consensus
AGCGCGGCUGCAAUGGGGAGUUGCAAUAACAACACCUCUGGCUGUGCAAAAAUCAUUUCACGUUAAAGGGCCCAA____ACACACAU_CAUACAUA____________UGUACAUAC
.(((((((......((((.((((......)))).))))..)))))))...................................................................... (-18.50 = -17.98 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,408,080 – 12,408,171
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 88.69
Mean single sequence MFE -34.62
Consensus MFE -24.20
Energy contribution -24.36
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.70
SVM decision value 0.39
SVM RNA-class probability 0.716931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12408080 91 + 23771897
CAGAGGUGUUGUUAUUGCAACUCCCCACUGCAGCGGCACUUCUCUAUCCCCCCUUUCU-UUUCCAGUGGGUGUGACAGAGAGGCGGCGAACG
.(((((((((((...((((.........)))))))))))))))...((((.(((((((-.(..((.....))..).))))))).)).))... ( -28.80)
>DroSec_CAF1 10674 90 + 1
CAGAGGUGUUGUUAUUGCAACUCCUCAUUGCAGCCGCGCUUCUCUAUCCCC-CGUUCU-UUUUUAGUGGGUGUGACAGAGAGGCGGCGAACG
..((((.(((((....))))).))))......(((((.((.((((.(((((-((..((-.....)))))).).)).)))))))))))..... ( -35.80)
>DroSim_CAF1 10654 91 + 1
CAGAGGUGUUGUUAUUGCAACUCCCCAUUGCAACCGCGCUUCUCUAUCCCCCCUUUCU-UUUUUAGUGGGUGUGACAGAGAGGCGGCGAACG
..(.((.(((((....))))).)).)........(((((((((((.((((((((....-.....)).))).).)).)))))))).))).... ( -31.30)
>DroEre_CAF1 10975 91 + 1
CAGAGGUGUUGUUGUUGCAACUCCCCAUUGCUGCCGCGCUUUUCUAUGCCC-CGCUUUGAUUCCAGGGGGUGUGGCAGAGAGGCGGCGAACG
..(.((.(((((....))))).)).).((((((((...((((.((((((((-(.((........))))))))))).)))).))))))))... ( -40.10)
>DroYak_CAF1 11538 90 + 1
CAGAGGUGUUGUUUUUGCAACUCCCCAUUGCUGCCGCGCUUUUCUAUGCCC-CUCGUU-UUUCCAGGGGGUGUGACAGAGAGGCGGCGAACG
..(.((.(((((....))))).)).).((((((((...((((..(((((((-(..(..-....)..))))))))..)))).))))))))... ( -37.10)
>consensus
CAGAGGUGUUGUUAUUGCAACUCCCCAUUGCAGCCGCGCUUCUCUAUCCCC_CUUUCU_UUUCCAGUGGGUGUGACAGAGAGGCGGCGAACG
..(.((.(((((....))))).)).)........((((((((((((..(((.(............).)))..)...)))))))).))).... (-24.20 = -24.36 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,408,080 – 12,408,171
Length 91
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 88.69
Mean single sequence MFE -33.46
Consensus MFE -26.31
Energy contribution -27.19
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -2.71
Structure conservation index 0.79
SVM decision value 2.16
SVM RNA-class probability 0.989416
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12408080 91 - 23771897
CGUUCGCCGCCUCUCUGUCACACCCACUGGAAA-AGAAAGGGGGGAUAGAGAAGUGCCGCUGCAGUGGGGAGUUGCAAUAACAACACCUCUG
.((.((.(((.((((((((...(((.((.....-....))))).)))))))).))).))..))...((((.((((......)))).)))).. ( -32.30)
>DroSec_CAF1 10674 90 - 1
CGUUCGCCGCCUCUCUGUCACACCCACUAAAAA-AGAACG-GGGGAUAGAGAAGCGCGGCUGCAAUGAGGAGUUGCAAUAACAACACCUCUG
.((..((((((((((((((...(((........-.....)-)).))))))).)).))))).))...((((.((((......)))).)))).. ( -36.42)
>DroSim_CAF1 10654 91 - 1
CGUUCGCCGCCUCUCUGUCACACCCACUAAAAA-AGAAAGGGGGGAUAGAGAAGCGCGGUUGCAAUGGGGAGUUGCAAUAACAACACCUCUG
.((..((((((((((((((...(((.((.....-....))))).))))))).)).))))).))...((((.((((......)))).)))).. ( -34.90)
>DroEre_CAF1 10975 91 - 1
CGUUCGCCGCCUCUCUGCCACACCCCCUGGAAUCAAAGCG-GGGCAUAGAAAAGCGCGGCAGCAAUGGGGAGUUGCAACAACAACACCUCUG
.(((.(((((((.((((.....((((((........)).)-)))..))))..)).))))))))...((((.((((......)))).)))).. ( -30.70)
>DroYak_CAF1 11538 90 - 1
CGUUCGCCGCCUCUCUGUCACACCCCCUGGAAA-AACGAG-GGGCAUAGAAAAGCGCGGCAGCAAUGGGGAGUUGCAAAAACAACACCUCUG
.(((.(((((((.(((((.....(((((.(...-..).))-))).)))))..)).))))))))...((((.((((......)))).)))).. ( -33.00)
>consensus
CGUUCGCCGCCUCUCUGUCACACCCACUGGAAA_AGAAAG_GGGGAUAGAGAAGCGCGGCUGCAAUGGGGAGUUGCAAUAACAACACCUCUG
.....((((((((((((((...(((................)))))))))).)).)))))......((((.((((......)))).)))).. (-26.31 = -27.19 +   0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:33 2006