Locus 8539

Sequence ID 3L_DroMel_CAF1
Location 22,320,057 – 22,320,328
Length 271
Max. P 0.945849
window13989 window13990 window13991 window13992

overview

Window 9

Location 22,320,057 – 22,320,152
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.75
Mean single sequence MFE -42.34
Consensus MFE -30.35
Energy contribution -33.23
Covariance contribution 2.88
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.72
SVM decision value -0.02
SVM RNA-class probability 0.522636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320057 95 - 23771897
-------------------CAUCCCAGUGUAGGGCAGCGGGAAGAUGAGACCCAAAAGCGAGCCCGGCAGUCUUAUCUCGUCCCGUACAUCGGGCUUUAACUUUUGGCUGGCAC------
-------------------.......((((..(((.(((((((((((((((((............))..)))))))))..)))))).((..((.......))..))))).))))------ ( -28.60)
>DroSec_CAF1 78731 120 - 1
UGCUUCGGCCAUCUCCAUUCAGCCCAGUGUAGGGCAGCGGGAAGAUGAGACCCAGAAGCGAGCCUGGCAGUCUUAUCUCGUCCCGUACAUCGGGCUUUAGCUUUUGGCUGGCACUCUGCA
(((..((((((.........(((((.((((......(((((((((((((((((((........))))..)))))))))..)))))))))).)))))........)))))))))....... ( -47.33)
>DroEre_CAF1 77099 120 - 1
UGGUUCGGCCAUCGCCAUUCAGCCCAGUGUAGGGCAGCGGGAAGAUGAGACCCAAAAGCGAGCCUGCCAGUCUUAUCUCGUCCCCUACAUCGGGCUUUAGCUUUUGCCUGGCACUCCGCA
(((.....)))..((((...(((((.((((((((..(((...(((((((((......(((....)))..)))))))))))).)))))))).)))))...((....)).))))........ ( -44.10)
>DroYak_CAF1 57120 120 - 1
UAGUUCGGCCAUCUCCAUUCAGCCCAGUGUAGGGCAGAGGGAAGAUGAGACCCAACAGCGAGCCUGGCAGUCUUAUCUUGUCCCCUGCAUCGGGCUUUAGCUUUUGGCUGGCACUCCGCA
.((((((((((.........(((((.((((((((....((.((((((((((....(((.....)))...)))))))))).)))))))))).)))))........))))))).)))..... ( -49.33)
>consensus
UGGUUCGGCCAUCUCCAUUCAGCCCAGUGUAGGGCAGCGGGAAGAUGAGACCCAAAAGCGAGCCUGGCAGUCUUAUCUCGUCCCCUACAUCGGGCUUUAGCUUUUGGCUGGCACUCCGCA
.....((((((.........(((((.((((((((..(((...((((((((((((..........)))..)))))))))))).)))))))).)))))........)))))).......... (-30.35 = -33.23 +   2.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,320,152 – 22,320,250
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.89
Mean single sequence MFE -37.58
Consensus MFE -25.86
Energy contribution -27.18
Covariance contribution 1.31
Combinations/Pair 1.12
Mean z-score -1.97
Structure conservation index 0.69
SVM decision value 0.81
SVM RNA-class probability 0.857355
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320152 98 + 23771897
---------------------AAGUGGCUGCCCAG-AAACUGGGUUCUAUUUGGGACCCAGAGUGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGACGGCACAGCACAUGU
---------------------..(((((((.((..-...(((((((((....))))))))).............(((((...(((....)))...)))))......))..)))).))).. ( -38.00)
>DroSec_CAF1 78851 119 + 1
GAUAUGCAGCAGGAUGCAAAGAAGCGGCUGCCCAG-AAACUGGGUUCUAUUUGGGACCCAGAGUGUAGAGAAUCCGGCGAUGCUGGAGACGGAACCGCCGAAAGAUGCCACAGCACAUGU
.....(((((....(((......))))))))....-...(((((((((....))))))))).((((.(.(.((((((((...(((....)))...)))))...)))..).).)))).... ( -43.00)
>DroEre_CAF1 77219 120 + 1
GAUAUGCAGCAGGAUGCAAGGAAGCGGCUGCCCAGAGAAGUGGCUUCUAUUUGGGACCUAGAGGGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGAUGCCACAGCACAUGU
....(((.((((..(((......))).))))........(((((.(((((((...(((.....)))...)))).(((((...(((....)))...)))))..))).))))).)))..... ( -40.80)
>DroYak_CAF1 57240 118 + 1
GAUAUGCAGUAGGAUGCAAGGAAGCGGCUGUUUAG-GAACUGGGUUCUAUUUGGUAC-GAGUGGGUAGAGAAUCUGGGGAUACUGGAGACGAAACUGCCAAAAGAUGCCACAGCAAAUGU
....((((......))))........(((((...(-((((...)))))....(((((-.....(((((.(..((..(.....)..))..)....)))))....).)))))))))...... ( -28.50)
>consensus
GAUAUGCAGCAGGAUGCAAGGAAGCGGCUGCCCAG_AAACUGGGUUCUAUUUGGGACCCAGAGGGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGAUGCCACAGCACAUGU
....((((......))))........((((.........(((((((((....))))))))).............(((((...(((....)))...)))))..........))))...... (-25.86 = -27.18 +   1.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,320,170 – 22,320,290
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.28
Mean single sequence MFE -41.94
Consensus MFE -34.26
Energy contribution -37.33
Covariance contribution 3.06
Combinations/Pair 1.07
Mean z-score -2.38
Structure conservation index 0.82
SVM decision value 1.36
SVM RNA-class probability 0.945849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320170 120 + 23771897
UGGGUUCUAUUUGGGACCCAGAGUGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGACGGCACAGCACAUGUGUCCCUGCAUUGGCAUUUUCUUUUGCUUUCUUUUCUCUCU
((((((((....))))))))(((.(.((((((...((((...(((....)))...))))((((((.((((((.....))))))..(((....)))...))))))...)))))).).))). ( -44.10)
>DroSec_CAF1 78890 120 + 1
UGGGUUCUAUUUGGGACCCAGAGUGUAGAGAAUCCGGCGAUGCUGGAGACGGAACCGCCGAAAGAUGCCACAGCACAUGUGUCCCUGCUCUGGCAUUAUCUUUUGCUUUCUUUUCCCUCU
((((((((....))))))))(((.(.((((((..(((((...(((....)))...)))))...(((((((.((((..........)))).)))))))..........)))))).).))). ( -47.00)
>DroEre_CAF1 77259 119 + 1
UGGCUUCUAUUUGGGACCUAGAGGGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGAUGCCACAGCACAUGUGUCCCUGCUCCGGCAUUUUCUUUUGCUUUCUUUC-CCUCU
.((.((((....)))))).((((((.((((((..(((((...(((....)))...))))).((((((((..((((..........))))..))))))))........)))))))-))))) ( -42.70)
>DroYak_CAF1 57279 119 + 1
UGGGUUCUAUUUGGUAC-GAGUGGGUAGAGAAUCUGGGGAUACUGGAGACGAAACUGCCAAAAGAUGCCACAGCAAAUGUGUCCCUGCUUUGGCAUUUUCUUUUGCUUUCUUUUCCCUCU
.(((........((((.-(((..(((((.(..((..(.....)..))..)....)))))..(((((((((.((((..........)))).)))))))))))).)))).......)))... ( -33.96)
>consensus
UGGGUUCUAUUUGGGACCCAGAGGGUAGAGAAUCUGGCGAUGCUGGAGACGGAACCGCCAAAAGAUGCCACAGCACAUGUGUCCCUGCUCUGGCAUUUUCUUUUGCUUUCUUUUCCCUCU
((((((((....))))))))(((((.((((((..(((((...(((....)))...))))).(((((((((.((((..........)))).)))))))))........)))))).))))). (-34.26 = -37.33 +   3.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,320,210 – 22,320,328
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.34
Mean single sequence MFE -31.96
Consensus MFE -25.52
Energy contribution -25.90
Covariance contribution 0.38
Combinations/Pair 1.16
Mean z-score -2.05
Structure conservation index 0.80
SVM decision value 0.85
SVM RNA-class probability 0.865874
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320210 118 - 23771897
AGAGAGGUUGAGCAAAAAGUAACAAAUAGUGUUGGGGC--AGAGAGAAAAGAAAGCAAAAGAAAAUGCCAAUGCAGGGACACAUGUGCUGUGCCGUCUUUUGGCGGUUCCGUCUCCAGCA
......((((.(((.....(((((.....))))).(((--(........................))))..))).((((((((.....)))((((((....))))))...))))))))). ( -27.16)
>DroSec_CAF1 78930 118 - 1
AGAGAGGUUGAGCAAAAAGUAUCAAAUAGUGUUGGGGC--AGAGGGAAAAGAAAGCAAAAGAUAAUGCCAGAGCAGGGACACAUGUGCUGUGGCAUCUUUCGGCGGUUCCGUCUCCAGCA
.......((((((.....)).))))....((((((...--(((.((((......((.(((((...(((((.((((.(......).)))).))))))))))..))..)))).))))))))) ( -34.90)
>DroEre_CAF1 77299 119 - 1
AGAGAGGUUGAGCAAAAAGUAACAAAUAGUGUUGGGGAAAAGAGG-GAAAGAAAGCAAAAGAAAAUGCCGGAGCAGGGACACAUGUGCUGUGGCAUCUUUUGGCGGUUCCGUCUCCAGCA
.............................(((((((((.....((-((..(....(((((((...(((((.((((.(......).)))).)))))))))))).)..)))).))))))))) ( -37.10)
>DroYak_CAF1 57318 118 - 1
AGUAAGGUUGAGCAAAAUGUAGCAAAUAGUGUUGGGAC--AGAGGGAAAAGAAAGCAAAAGAAAAUGCCAAAGCAGGGACACAUUUGCUGUGGCAUCUUUUGGCAGUUUCGUCUCCAGUA
.((.(.(((......))).).))........((((...--(((.((((..(....(((((((...(((((.((((((......)))))).)))))))))))).)..)))).))))))).. ( -28.70)
>consensus
AGAGAGGUUGAGCAAAAAGUAACAAAUAGUGUUGGGGC__AGAGGGAAAAGAAAGCAAAAGAAAAUGCCAAAGCAGGGACACAUGUGCUGUGGCAUCUUUUGGCGGUUCCGUCUCCAGCA
.............................((((((.....(((.((((..(....(((((((...(((((.((((.(......).)))).)))))))))))).)..)))).))))))))) (-25.52 = -25.90 +   0.38)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:29 2006