Locus 4099

Sequence ID 3L_DroMel_CAF1
Location 11,955,628 – 11,955,750
Length 122
Max. P 0.927579
window6376 window6377 window6378

overview

Window 6

Location 11,955,628 – 11,955,719
Length 91
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -37.68
Consensus MFE -27.38
Energy contribution -28.33
Covariance contribution 0.95
Combinations/Pair 1.22
Mean z-score -1.91
Structure conservation index 0.73
SVM decision value 0.93
SVM RNA-class probability 0.883808
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11955628 91 + 23771897
UGCGGGGCAGUGUAUCCUGCCGGCGGAGCGGAGUGGA-------AACUGCUCCAACGGAGAGAGUAGAUCCGUGGUGGGCAGUUGCCACAGCUACGAA
.....(((((......)))))..((.(((...((((.-------(((((((((.(((((.........))))).).)))))))).)))).))).)).. ( -38.90)
>DroVir_CAF1 8922 97 + 1
UGCCAAUCAGUGCCGCCUGAACGUU-AGUCAAGUGGAAUCCACUGGCUGCUUGCAUGGACAAAAACGCGCCUUGGCCACCAGCUGCCACUUAUACGAA
......((((......)))).(((.-....((((((......((((..(((.((.((........)).))...)))..))))...))))))..))).. ( -22.00)
>DroSec_CAF1 8488 91 + 1
UGCGGGGCAGUGUAUCCUGCCGGCGGAGCGUAGUGGA-------AGCUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAA
.....(((((......)))))..((.(((...((((.-------(((((((((.(((((.........))))).).)))))))).)))).))).)).. ( -41.30)
>DroSim_CAF1 8436 91 + 1
UGCGGGGCAGUGUAUCCUGCCGGCGGAGCGGAGUGGA-------AACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAA
.((..((((((....((..((...(((((((......-------..))))))).(((((.........)))))))..))..))))))...))...... ( -41.10)
>DroEre_CAF1 8799 91 + 1
UGCGGGGAUGUGCUUCCUGCCGGCAGAGCGGAGAGGA-------AACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAA
.((..((((.((((..((.(((((...))((((((..-------..)).))))..)))))..)))).))))((((..(....)..)))).))...... ( -42.50)
>DroYak_CAF1 6778 91 + 1
UGCGGGGCAGUGUGUCCUGCCGGCGGAGCGGAGUGAA-------AGCUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGUUGCCACAGCUACGAC
..((..((.(((.((.(((((.(((((((((......-------..))))))).(((((.........))))).)).)))))..))))).))..)).. ( -40.30)
>consensus
UGCGGGGCAGUGUAUCCUGCCGGCGGAGCGGAGUGGA_______AACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAA
..((.(((.(((....(((((.(((((((((...............))))))).(((((.........))))).)).)))))....))).))).)).. (-27.38 = -28.33 +   0.95)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,955,628 – 11,955,719
Length 91
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 80.07
Mean single sequence MFE -35.02
Consensus MFE -23.30
Energy contribution -23.72
Covariance contribution 0.42
Combinations/Pair 1.26
Mean z-score -2.39
Structure conservation index 0.67
SVM decision value 1.18
SVM RNA-class probability 0.927579
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11955628 91 - 23771897
UUCGUAGCUGUGGCAACUGCCCACCACGGAUCUACUCUCUCCGUUGGAGCAGUU-------UCCACUCCGCUCCGCCGGCAGGAUACACUGCCCCGCA
...(.(((.((((.(((((((((..(((((.........)))))))).))))))-------.))))...))).)((.(((((......)))))..)). ( -37.70)
>DroVir_CAF1 8922 97 - 1
UUCGUAUAAGUGGCAGCUGGUGGCCAAGGCGCGUUUUUGUCCAUGCAAGCAGCCAGUGGAUUCCACUUGACU-AACGUUCAGGCGGCACUGAUUGGCA
...((...((((.(.(((.((((.(((((.....))))).))))...))).((((((((...)))))((((.-...).))))))).)))).....)). ( -28.40)
>DroSec_CAF1 8488 91 - 1
UUCGUAGCUGUGGCAGCUGCCCACCACGGAUCUGCUCUCUCCGUUGGAGCAGCU-------UCCACUACGCUCCGCCGGCAGGAUACACUGCCCCGCA
...(.(((.((((.(((((((((..(((((.........)))))))).))))))-------.))))...))).)((.(((((......)))))..)). ( -40.10)
>DroSim_CAF1 8436 91 - 1
UUCGUAGCUGUGGCAGCUGCCCACCACGGAUCUGCUCUCUCCGUUGGAGCAGUU-------UCCACUCCGCUCCGCCGGCAGGAUACACUGCCCCGCA
...(.(((.((((.(((((((((..(((((.........)))))))).))))))-------.))))...))).)((.(((((......)))))..)). ( -37.70)
>DroEre_CAF1 8799 91 - 1
UUCGUAGCUGUGGCAGCUGCCCACCACGGAUCUGCUCUCUCCGUUGGAGCAGUU-------UCCUCUCCGCUCUGCCGGCAGGAAGCACAUCCCCGCA
...(((((((...))))))).......((((.((((..(((((..(((((.(..-------......).)))))..))).))..)))).))))..... ( -35.00)
>DroYak_CAF1 6778 91 - 1
GUCGUAGCUGUGGCAACUGCCCACCACGGAUCUGCUCUCUCCGUUGGAGCAGCU-------UUCACUCCGCUCCGCCGGCAGGACACACUGCCCCGCA
...(.(((.((((...(((((((..(((((.........)))))))).))))..-------.))))...))).)((.(((((......)))))..)). ( -31.20)
>consensus
UUCGUAGCUGUGGCAGCUGCCCACCACGGAUCUGCUCUCUCCGUUGGAGCAGCU_______UCCACUCCGCUCCGCCGGCAGGAUACACUGCCCCGCA
.........((((.(((((((((..(((((.........)))))))).)))))).......................(((((......))))))))). (-23.30 = -23.72 +   0.42)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,955,653 – 11,955,750
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 82.43
Mean single sequence MFE -33.42
Consensus MFE -23.14
Energy contribution -24.00
Covariance contribution 0.86
Combinations/Pair 1.26
Mean z-score -1.49
Structure conservation index 0.69
SVM decision value 0.00
SVM RNA-class probability 0.533773
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11955653 97 + 23771897
GAGCGGAGUGGAAACUGCUCCAACGGAGAGAGUAGAUCCGUGGUGGGCAGUUGCCACAGCUACGAAGUGUGCUCGGAUAAUGGCCAGUGGAUAAGGA
(((((..((((.(((((((((.(((((.........))))).).)))))))).)))).(((....))).)))))((.......))............ ( -33.70)
>DroSec_CAF1 8513 97 + 1
GAGCGUAGUGGAAGCUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAAUUGUGCUCGGAUAAUGGCCAGUGGAUGAGGA
((((...((((.(((((((((.(((((.........))))).).)))))))).)))).((........))))))((.......))............ ( -35.30)
>DroSim_CAF1 8461 97 + 1
GAGCGGAGUGGAAACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAACUGUGCUCGGAUAAUGGCCAGUGGAUGAGGC
(((((.((((((..(((((((......).)))))).)))(((((.(((....)))...)))))..))).)))))........(((.........))) ( -36.80)
>DroEre_CAF1 8824 94 + 1
GAGCGGAGAGGAAACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAACUGUGCUCGGG---UGGCCAGUGGAGGAGGA
(((((.((.(((..(((((((......).)))))).)))(((((.(((....)))...)))))...)).)))))((.---...))............ ( -35.20)
>DroYak_CAF1 6803 94 + 1
GAGCGGAGUGAAAGCUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGUUGCCACAGCUACGACCUGUGUGCGGA---UGGCCAGUGGAUGAGGA
..(((((.......(((((((......).)))))).)))))(.(((.((.(((((((((.......))))).)))).---)).))).)......... ( -31.80)
>DroAna_CAF1 8711 94 + 1
GACGAGAAAGCAAACUGUUCGGCCGGAGAUAAUCGUGCUCUGGUGGGCAGCUGCCAUAGCUAUGAGCUGUGCCAGGA---GGAAAAAUGGAUCACAA
...((.........(((((((.((((((.........)))))))))))))(((.((((((.....)))))).)))..---...........)).... ( -27.70)
>consensus
GAGCGGAGUGGAAACUGCUCCAACGGAGAGAGCAGAUCCGUGGUGGGCAGCUGCCACAGCUACGAACUGUGCUCGGA___UGGCCAGUGGAUGAGGA
(((((.((......(((((((......).))))))...((((((.(((....)))...))))))..)).)))))....................... (-23.14 = -24.00 +   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 11:14:27 2006