Locus 4851

Sequence ID 3R_DroMel_CAF1
Location 12,710,635 – 12,710,777
Length 142
Max. P 0.959515
window7944 window7945 window7946 window7947

overview

Window 4

Location 12,710,635 – 12,710,748
Length 113
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 93.92
Mean single sequence MFE -45.18
Consensus MFE -40.72
Energy contribution -41.13
Covariance contribution 0.42
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.90
SVM decision value 1.50
SVM RNA-class probability 0.959515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12710635 113 + 27905053
GGCUUUGGACAGGCUGGAUGUGCGCAGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAA
((((((((.(((((((........))))))).(((....)))..))(((((......)))...(((((((.(((((....))))).)))))))..)).))))))......... ( -45.50)
>DroSec_CAF1 86373 113 + 1
GGCUUUGGACAGGCUGGAUGUGCGCGGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAA
(((((((((...((..(...(((((((.....(((....)))..)))).)))..)..))))).(((((((.(((((....))))).))))))).....))))))......... ( -46.70)
>DroSim_CAF1 87538 113 + 1
GGCUUUGGACAGGCUGGAUGUGCGCGGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAA
(((((((((...((..(...(((((((.....(((....)))..)))).)))..)..))))).(((((((.(((((....))))).))))))).....))))))......... ( -46.70)
>DroEre_CAF1 91761 113 + 1
GGCUUUGGACAGGCUGGAUGUGCGCGGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUGUCGA
.......(((((((.((.(.(((((((((((((((....)))..))).)))....(((((((.(((((((...))).))))..))))))).))).))).)..))))))))).. ( -47.30)
>DroYak_CAF1 81228 113 + 1
GGCUUUGGACAGGCUGGAUGUGCGCGGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGAAGCCACCGCAGCAGAAGCCGCUUGGCAA
(((((((((...((..(...(((((((.....(((....)))..)))).)))..)..))))).(((((((..((((....))))..))))))).....))))))......... ( -45.30)
>DroAna_CAF1 72950 113 + 1
GGCUGUGACCAGGCUGGAUGUGUGUGGCGUGGCAUAUUGAUGAACCGCAACAAAUUGGCUACACGGUGGCAAUGCCAACUGCCGGAGCCACAGAAGCAGAAGCCGUAUGUCAA
.....((((..((((...(((.(((((((((((...(((.((.....)).)))....))))).(((((((...)))....))))..))))))...)))..))))....)))). ( -39.60)
>consensus
GGCUUUGGACAGGCUGGAUGUGCGCGGCUUGGCAUAUUGAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAA
((((((((...(((..(...(((((((.....(((....)))..)))).)))..)..))))).(((((((..((((....))))..))))))).....))))))......... (-40.72 = -41.13 +   0.42)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,710,635 – 12,710,748
Length 113
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 93.92
Mean single sequence MFE -42.49
Consensus MFE -36.20
Energy contribution -36.95
Covariance contribution 0.75
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.85
SVM decision value 0.67
SVM RNA-class probability 0.818084
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12710635 113 - 27905053
UUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCUGCGCACAUCCAGCCUGUCCAAAGCC
(((.((.((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......))...))))).... ( -42.10)
>DroSec_CAF1 86373 113 - 1
UUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCCGCGCACAUCCAGCCUGUCCAAAGCC
(((.((.((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......))...))))).... ( -44.30)
>DroSim_CAF1 87538 113 - 1
UUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCCGCGCACAUCCAGCCUGUCCAAAGCC
(((.((.((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......))...))))).... ( -44.30)
>DroEre_CAF1 91761 113 - 1
UCGACAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAUUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCCGCGCACAUCCAGCCUGUCCAAAGCC
..((((.((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......)).))))....... ( -48.10)
>DroYak_CAF1 81228 113 - 1
UUGCCAAGCGGCUUCUGCUGCGGUGGCUUCGCCAGUUGGCAUUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCCGCGCACAUCCAGCCUGUCCAAAGCC
(((.((.((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......)).))..))).... ( -43.80)
>DroAna_CAF1 72950 113 - 1
UUGACAUACGGCUUCUGCUUCUGUGGCUCCGGCAGUUGGCAUUGCCACCGUGUAGCCAAUUUGUUGCGGUUCAUCAAUAUGCCACGCCACACACAUCCAGCCUGGUCACAGCC
.((((....((((........((((((...(((((.((((...)))).).((((((......))))))...........))))..)))))).......))))..))))..... ( -32.36)
>consensus
UUGACAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUCAAUAUGCCAAGCCGCGCACAUCCAGCCUGUCCAAAGCC
.......((((((((....((((((((...(((....)))...))))))))))))))....(((.(((((((((....)))...)))))))))......))............ (-36.20 = -36.95 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,710,673 – 12,710,777
Length 104
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 88.21
Mean single sequence MFE -36.03
Consensus MFE -31.74
Energy contribution -31.97
Covariance contribution 0.22
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 0.88
SVM decision value 0.35
SVM RNA-class probability 0.701464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12710673 104 + 27905053
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAAGCGCCGCACAGUGGAUA------UAAAUAACAGAA-
......((((.........(((...(((((((.(((((....))))).))))))).)))....((((((.....))))..))...))))...------............- ( -35.40)
>DroSec_CAF1 86411 104 + 1
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAAGCGCCGCACAGUGGGUA------CGAACAACAGAA-
......((((.........(((...(((((((.(((((....))))).))))))).)))....((((((.....))))..))...))))...------............- ( -35.60)
>DroSim_CAF1 87576 104 + 1
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAUUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAAGCGCCGCACAGUGGGUA------CAAUCAACAGAA-
(((...((((.........(((...(((((((.(((((....))))).))))))).)))....((((((.....))))..))...))))...------..))).......- ( -37.20)
>DroEre_CAF1 91799 104 + 1
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUGUCGAGCGCCGCACAGUGGGCA------CAAGCAACAUAC-
.(((..............(((((..(((((((..((((....))))..))))))).....).))))((((((...((.((((...)))))))------)))))..)))..- ( -39.80)
>DroYak_CAF1 81266 104 + 1
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGAAGCCACCGCAGCAGAAGCCGCUUGGCAAGCGCCGCACAGUGGGUU------GAAACAACAGGA-
......((........(..((.((((((((((..((((....))))..))))))((.((....(((....)))....)).))...)))))).------.).......)).- ( -38.56)
>DroAna_CAF1 72988 110 + 1
GAUGAACCGCAACAAAUUGGCUACACGGUGGCAAUGCCAACUGCCGGAGCCACAGAAGCAGAAGCCGUAUGUCAAGCGCCGCACUGUGGUUUUUGGUUUAAAUA-UAGAAC
..((((((((..(....(((((...(((((((...)))....)))).)))))..)..))(((((((((((((........))).))))))))))))))))....-...... ( -29.60)
>consensus
GAUGAACCGCAGCAAAUUGGCUCCACGGUGGCAAUGCCAACUGGCGGAGCCACCGCAGCAGAAGCCGCUUCUCAAGCGCCGCACAGUGGGUA______CAAACAACAGAA_
......((((.........(((...(((((((..((((....))))..))))))).)))....(((((((...)))))..))...))))...................... (-31.74 = -31.97 +   0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,710,673 – 12,710,777
Length 104
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 88.21
Mean single sequence MFE -40.58
Consensus MFE -36.59
Energy contribution -37.45
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -1.79
Structure conservation index 0.90
SVM decision value 1.06
SVM RNA-class probability 0.908925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12710673 104 - 27905053
-UUCUGUUAUUUA------UAUCCACUGUGCGGCGCUUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
-............------.........(((((((((.....)))((((((....((((((((...(((....)))...)))))))))))))).....))))))....... ( -41.80)
>DroSec_CAF1 86411 104 - 1
-UUCUGUUGUUCG------UACCCACUGUGCGGCGCUUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
-...........(------.(((......((((((((.....)))((((((....((((((((...(((....)))...)))))))))))))).....)))))))).)... ( -41.90)
>DroSim_CAF1 87576 104 - 1
-UUCUGUUGAUUG------UACCCACUGUGCGGCGCUUGAGAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
-..........((------.(((......((((((((.....)))((((((....((((((((...(((....)))...)))))))))))))).....)))))))).)).. ( -42.30)
>DroEre_CAF1 91799 104 - 1
-GUAUGUUGCUUG------UGCCCACUGUGCGGCGCUCGACAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAUUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
-((.(((((...(------(((((.....).))))).))))).))((((((....((((((((...(((....)))...)))))))))))))).................. ( -44.10)
>DroYak_CAF1 81266 104 - 1
-UCCUGUUGUUUC------AACCCACUGUGCGGCGCUUGCCAAGCGGCUUCUGCUGCGGUGGCUUCGCCAGUUGGCAUUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
-.((.((((...)------))).......((((((((.....)))((((((....((((((((...(((....)))...)))))))))))))).....)))))))...... ( -42.80)
>DroAna_CAF1 72988 110 - 1
GUUCUA-UAUUUAAACCAAAAACCACAGUGCGGCGCUUGACAUACGGCUUCUGCUUCUGUGGCUCCGGCAGUUGGCAUUGCCACCGUGUAGCCAAUUUGUUGCGGUUCAUC
......-......((((.....((((((.((((.(((........)))..))))..))))))...(((((((((((..(((......)))))))).)))))).)))).... ( -30.60)
>consensus
_UUCUGUUGUUUG______UACCCACUGUGCGGCGCUUGACAAGCGGCUUCUGCUGCGGUGGCUCCGCCAGUUGGCAAUGCCACCGUGGAGCCAAUUUGCUGCGGUUCAUC
............................(((((((((.....)))((((((....((((((((...(((....)))...)))))))))))))).....))))))....... (-36.59 = -37.45 +   0.86)

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 11:40:23 2006