Locus 6180

Sequence ID 3L_DroMel_CAF1
Location 16,366,085 – 16,366,303
Length 218
Max. P 0.849042
window9919 window9920 window9921

overview

Window 9

Location 16,366,085 – 16,366,201
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 92.53
Mean single sequence MFE -38.44
Consensus MFE -34.12
Energy contribution -34.49
Covariance contribution 0.38
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.89
SVM decision value 0.43
SVM RNA-class probability 0.734247
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16366085 116 + 23771897
UGUGUUCCCGGGUAAACGGGACAUUCCCCGGAUAAGCGGAUUGCUCCGAGUAACGGUGAAAUGAGCAGGAGCGAAUCCGAACCGAGCAGUUGCAGUGAACAGCGGCAACUGGAUGA
.((((.((((......))))))))....(((.....(((((((((((..((.............)).))))).))))))..)))..(((((((.((.....)).)))))))..... ( -41.02)
>DroSec_CAF1 6248 116 + 1
UGUGUUCCUGGAUAAACGGGACUUUCCCCGGAUAAGCGGAUUGCUCCGAGUAACGGUGAAAAGAGCAGGAGCGAAUCCGAACCGAGCAGUUGCAGUGAACAGCGGCAACUGGAUGA
.....(((((......))))).......(((.....(((((((((((..((.............)).))))).))))))..)))..(((((((.((.....)).)))))))..... ( -37.32)
>DroSim_CAF1 6362 116 + 1
UGUGUUCCCGGAUAAACGGGACUUUCCCCGGAUAAGCGGAUUGCUCCGAGUAACGGUGAAAAGAGCAGGAGCGAAUCCGAACCGAGCAGUUGCAGUGAACAGCGGCAACUGGAUGA
.....(((((......))))).......(((.....(((((((((((..((.............)).))))).))))))..)))..(((((((.((.....)).)))))))..... ( -39.52)
>DroEre_CAF1 6226 115 + 1
GGUUUU-CCGGAUAAACGGGAUACUCCCCGGAUAAACGGACUGCGUCAAGUAACGGUAAAAAGAGCAGGAGCGAAUGCGAACCGAGCAGUUGCAGUGAACAGCGGCAACUGGAUUA
((((((-(((..((..((((......))))..))..))))..((((...((..(.((.......)).)..))..)))))))))...(((((((.((.....)).)))))))..... ( -35.90)
>consensus
UGUGUUCCCGGAUAAACGGGACAUUCCCCGGAUAAGCGGAUUGCUCCGAGUAACGGUGAAAAGAGCAGGAGCGAAUCCGAACCGAGCAGUUGCAGUGAACAGCGGCAACUGGAUGA
........(((.....((((......))))......(((((((((((..((.............)).))))).))))))..)))..(((((((.((.....)).)))))))..... (-34.12 = -34.49 +   0.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,366,085 – 16,366,201
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 92.53
Mean single sequence MFE -34.73
Consensus MFE -30.41
Energy contribution -31.47
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.79
Structure conservation index 0.88
SVM decision value 0.78
SVM RNA-class probability 0.849042
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16366085 116 - 23771897
UCAUCCAGUUGCCGCUGUUCACUGCAACUGCUCGGUUCGGAUUCGCUCCUGCUCAUUUCACCGUUACUCGGAGCAAUCCGCUUAUCCGGGGAAUGUCCCGUUUACCCGGGAACACA
.....(((((((.(.......).)))))))(((((..((((((.(((((....................))))))))))).....)))))...(((((((......)))).))).. ( -37.65)
>DroSec_CAF1 6248 116 - 1
UCAUCCAGUUGCCGCUGUUCACUGCAACUGCUCGGUUCGGAUUCGCUCCUGCUCUUUUCACCGUUACUCGGAGCAAUCCGCUUAUCCGGGGAAAGUCCCGUUUAUCCAGGAACACA
.....(((((((.(.......).)))))))....(((((((((.(((((....................))))))))))(..((..(((((....)))))..))..)..))))... ( -33.85)
>DroSim_CAF1 6362 116 - 1
UCAUCCAGUUGCCGCUGUUCACUGCAACUGCUCGGUUCGGAUUCGCUCCUGCUCUUUUCACCGUUACUCGGAGCAAUCCGCUUAUCCGGGGAAAGUCCCGUUUAUCCGGGAACACA
.....(((((((.(.......).)))))))(((((..((((((.(((((....................))))))))))).....))))).....(((((......)))))..... ( -37.35)
>DroEre_CAF1 6226 115 - 1
UAAUCCAGUUGCCGCUGUUCACUGCAACUGCUCGGUUCGCAUUCGCUCCUGCUCUUUUUACCGUUACUUGACGCAGUCCGUUUAUCCGGGGAGUAUCCCGUUUAUCCGG-AAAACC
.....(((((((.(.......).)))))))...((((.((....))..((((((...............)).))))((((..((..((((......))))..))..)))-).)))) ( -30.06)
>consensus
UCAUCCAGUUGCCGCUGUUCACUGCAACUGCUCGGUUCGGAUUCGCUCCUGCUCUUUUCACCGUUACUCGGAGCAAUCCGCUUAUCCGGGGAAAGUCCCGUUUAUCCGGGAACACA
.....(((((((.(.......).)))))))(((((..((((((.(((((....................))))))))))).....))))).....(((((......)))))..... (-30.41 = -31.47 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,366,201 – 16,366,303
Length 102
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 92.69
Mean single sequence MFE -27.57
Consensus MFE -26.10
Energy contribution -26.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.95
SVM decision value 0.16
SVM RNA-class probability 0.610202
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16366201 102 - 23771897
GGGUGGAAAACCGAGGGGGGCAGAGGUGCUUUUACCGCUCAAAGGCAAAAAAAAG-GGAGAUGAAAGACACGCCAUCGAAAGGAGAGUCCACCCGAGCUCCGU
(((((((...((..((..(((....(((((((((.(.(((..............)-)).).)))))).)))))).))....))....)))))))......... ( -29.24)
>DroSec_CAF1 6364 95 - 1
GGGUGGAAAACCGAGGGGGG-------GCUUUUACCGCUCAAAGGCAAAAAAAAA-GGAGAUGAAAGACACGCCAUCGAAAGGAAAGUCCACCCGAGCUUCGU
(((((((...(((((.((..-------.......)).)))...(((.........-...............))).......))....)))))))......... ( -26.76)
>DroSim_CAF1 6478 96 - 1
GGGUGGAAAACCGAGGGGGG-------GCUUUUACCGCUCAAAGGCAAAAAAAAAGGGAGAUGAAAGACACGCCAUCGAAAGGAGAGUCCACCCGAGCUUCGU
(((((((...(((((.((..-------.......)).)))...(((.........................))).......))....)))))))......... ( -26.71)
>consensus
GGGUGGAAAACCGAGGGGGG_______GCUUUUACCGCUCAAAGGCAAAAAAAAA_GGAGAUGAAAGACACGCCAUCGAAAGGAGAGUCCACCCGAGCUUCGU
(((((((...(((((.((................)).)))...(((.........................))).......))....)))))))......... (-26.10 = -26.10 +  -0.00)

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 12:12:04 2006