Locus 3404

Sequence ID 2L_DroMel_CAF1
Location 9,848,582 – 9,848,704
Length 122
Max. P 0.997241
window5387 window5388 window5389

overview

Window 7

Location 9,848,582 – 9,848,678
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 75.28
Mean single sequence MFE -23.27
Consensus MFE -18.43
Energy contribution -19.10
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.09
Structure conservation index 0.79
SVM decision value 0.29
SVM RNA-class probability 0.672311
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9848582 96 + 22407834
UGCGAGAUGCCUUCACUCCUUGGCGCCAACAAGGACGUCGCCAGGACCCAUCCAGGAAUCACACACAUAUACAUAUGUACUACACAUAUACGCACG
((((.(((.(((....((((.((((((.....))....)))))))).......))).)))............((((((.....)))))).)))).. ( -22.90)
>DroSec_CAF1 57310 75 + 1
UGCGAGAUGCCUUUGGUCCUUGGCGCCAACGAGGACGACGCCAGGACCCAUCCAGGAUUCACACACA---------------------CACGCACU
((((.((((.....((((((.((((((.....))....))))))))))))))..(......).....---------------------..)))).. ( -22.70)
>DroEre_CAF1 59888 73 + 1
UGCGAGAUGCCUUUGGUCCUUGGCGCCAAGGAGGACGUCGCCAGGACCCAUCCAGGAUCCACACACA---------------------C--GCACG
((((.((((((.....((((((....)))))))).))))....(((.((.....)).))).......---------------------)--))).. ( -24.20)
>consensus
UGCGAGAUGCCUUUGGUCCUUGGCGCCAACGAGGACGUCGCCAGGACCCAUCCAGGAUUCACACACA_____________________CACGCACG
((((.((((.....((((((.((((((.....))....))))))))))))))).(......).............................))).. (-18.43 = -19.10 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,848,582 – 9,848,678
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 75.28
Mean single sequence MFE -29.60
Consensus MFE -23.54
Energy contribution -23.43
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -1.05
Structure conservation index 0.80
SVM decision value 0.21
SVM RNA-class probability 0.637283
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9848582 96 - 22407834
CGUGCGUAUAUGUGUAGUACAUAUGUAUAUGUGUGUGAUUCCUGGAUGGGUCCUGGCGACGUCCUUGUUGGCGCCAAGGAGUGAAGGCAUCUCGCA
...((((((((((((.....))))))))))))(((.(((.(((...(.(.((((((((.((.......)).)))).)))).).)))).))).))). ( -30.70)
>DroSec_CAF1 57310 75 - 1
AGUGCGUG---------------------UGUGUGUGAAUCCUGGAUGGGUCCUGGCGUCGUCCUCGUUGGCGCCAAGGACCAAAGGCAUCUCGCA
........---------------------..((((.((..(((.....(((((((((((((.......))))))).))))))..)))..)).)))) ( -30.40)
>DroEre_CAF1 59888 73 - 1
CGUGC--G---------------------UGUGUGUGGAUCCUGGAUGGGUCCUGGCGACGUCCUCCUUGGCGCCAAGGACCAAAGGCAUCUCGCA
.....--.---------------------..((((.(((((((.....((((((((((.((.......)).)))).))))))..))).)))))))) ( -27.70)
>consensus
CGUGCGUG_____________________UGUGUGUGAAUCCUGGAUGGGUCCUGGCGACGUCCUCGUUGGCGCCAAGGACCAAAGGCAUCUCGCA
...............................((((.((..(((.....((((((((((.((.......)).)))).))))))..)))..)).)))) (-23.54 = -23.43 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,848,611 – 9,848,704
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 71.71
Mean single sequence MFE -31.67
Consensus MFE -17.12
Energy contribution -17.56
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.59
Structure conservation index 0.54
SVM decision value 2.82
SVM RNA-class probability 0.997241
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9848611 93 - 22407834
CACACAAACAUACGCAUACUGGCGUGCGUGCGUAUAUGUGUAGUACAUAUGUAUAUGUGUGUGAUUCCUGGAUGGGUCCUGGCGACGUCCUUG
((((((....(((((((......))))))).(((((((((.....)))))))))...))))))......(((((.((....))..)))))... ( -30.40)
>DroSec_CAF1 57339 70 - 1
CACACA--CAUACGCAUGCUGGCAUGAGUGCGUG---------------------UGUGUGUGAAUCCUGGAUGGGUCCUGGCGUCGUCCUCG
((((((--(((((((((.(......).)))))))---------------------))))))))......((((((((....)).))))))... ( -33.60)
>DroEre_CAF1 59917 70 - 1
CACACACCCAUACGCAUGCAGGCUUGCGUGC--G---------------------UGUGUGUGGAUCCUGGAUGGGUCCUGGCGACGUCCUCC
.......(((((((((((((.(....).)))--)---------------------))))))))).....(((((.((....))..)))))... ( -31.00)
>consensus
CACACA__CAUACGCAUGCUGGCAUGCGUGCGUG_____________________UGUGUGUGAAUCCUGGAUGGGUCCUGGCGACGUCCUCG
((((((....(((((((.(......).))))))).......................))))))......(((((.((....))..)))))... (-17.12 = -17.56 +   0.45)

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 10:51:40 2006