Locus 2292

Sequence ID 3R_DroMel_CAF1
Location 6,511,371 – 6,511,473
Length 102
Max. P 0.926476
window3705 window3706

overview

Window 5

Location 6,511,371 – 6,511,473
Length 102
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 82.91
Mean single sequence MFE -20.08
Consensus MFE -12.54
Energy contribution -11.98
Covariance contribution -0.56
Combinations/Pair 1.32
Mean z-score -2.39
Structure conservation index 0.62
SVM decision value 0.93
SVM RNA-class probability 0.883817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6511371 102 + 27905053
AAGCA-----CAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGU--------GAAUGGUGAAAGAAACCGAAAGUAAAAUCAGAAAAAAAUAUGUUAAGGA-
.(((.-----((.....)))))....(....)((.........((((..(((((((..--------..)))))))...))))(....).....))....................- ( -15.80)
>DroSec_CAF1 276022 109 + 1
AAGCA-----CAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAAAUUGUGAAUGGUAAAGGAAACCGAAAGUAAAAUCGGAA-AAAAUACGUUAAGGA-
...((-----((.(((((((......(....)...((.(((....))).)).)))))))....))))..............((((........))))..-...............- ( -18.80)
>DroSim_CAF1 306442 109 + 1
AAGCA-----CAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAAAUUGUGAAUGGUGAACGAAACCGAAAGUAAAAUCGGAA-AAAAUAUGUUAAGGA-
...((-----((.(((((((......(....)...((.(((....))).)).)))))))....))))..............((((........))))..-...............- ( -18.80)
>DroEre_CAF1 289709 107 + 1
CAGUACACAACAGCACAUGGCUAUAAGGAAACGGAAAAUAAACGCUUAGUUGCCAUGU--------GAGUGGUAGAAGAAAUCGAAAGUAAAAUCGAAA-AAAAUGUGUUAAGGGA
....(((((.((.((((((((.....(....)........(((.....))))))))))--------)..))..........((((........))))..-....)))))....... ( -24.00)
>DroYak_CAF1 285927 107 + 1
AAGUACACAACAGCACAUGGCUAUAAGGAAACGGAAAAUAAAUGUUUAGGUACCAUGU--------GAAUGGUGAAAGAAACCGAGAGUAAGAUCGCAA-GAAAUGUGUUAAGGGA
....(((((((..(((((((.(((....(((((.........)))))..)))))))))--------)..((((.......))))...))....((....-))..)))))....... ( -23.00)
>consensus
AAGCA_____CAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGU________GAAUGGUGAAAGAAACCGAAAGUAAAAUCGGAA_AAAAUAUGUUAAGGA_
..((........)).(.((((.....(....).........((((((..(((((((............)))))))......((((........))))....)))))))))).)... (-12.54 = -11.98 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,511,371 – 6,511,473
Length 102
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 82.91
Mean single sequence MFE -16.60
Consensus MFE -10.50
Energy contribution -9.98
Covariance contribution -0.52
Combinations/Pair 1.27
Mean z-score -2.53
Structure conservation index 0.63
SVM decision value 1.18
SVM RNA-class probability 0.926476
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6511371 102 - 27905053
-UCCUUAACAUAUUUUUUUCUGAUUUUACUUUCGGUUUCUUUCACCAUUC--------ACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUG-----UGCUU
-..................((((........))))..........(((.(--------(((((((((..((((...........))))..))...))))))))..)-----))... ( -13.00)
>DroSec_CAF1 276022 109 - 1
-UCCUUAACGUAUUUU-UUCCGAUUUUACUUUCGGUUUCCUUUACCAUUCACAAUUUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUG-----UGCUU
-........(((....-..((((........)))).......)))....((((....((((((((((..((((...........))))..))...)))))))).))-----))... ( -17.32)
>DroSim_CAF1 306442 109 - 1
-UCCUUAACAUAUUUU-UUCCGAUUUUACUUUCGGUUUCGUUCACCAUUCACAAUUUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUG-----UGCUU
-...............-..((((........))))..............((((....((((((((((..((((...........))))..))...)))))))).))-----))... ( -16.00)
>DroEre_CAF1 289709 107 - 1
UCCCUUAACACAUUUU-UUUCGAUUUUACUUUCGAUUUCUUCUACCACUC--------ACAUGGCAACUAAGCGUUUAUUUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUACUG
.......(((((....-..((((........))))...........((.(--------(((((((....(((((.........))))).......))))))))..))))))).... ( -20.90)
>DroYak_CAF1 285927 107 - 1
UCCCUUAACACAUUUC-UUGCGAUCUUACUCUCGGUUUCUUUCACCAUUC--------ACAUGGUACCUAAACAUUUAUUUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUACUU
.......(((((....-................(((.......)))...(--------(((((((....((((...........)))).......))))))))....))))).... ( -15.80)
>consensus
_UCCUUAACAUAUUUU_UUCCGAUUUUACUUUCGGUUUCUUUCACCAUUC________ACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUG_____UGCUU
...................((((........)))).......................(((((((....((((...........)))).......))))))).............. (-10.50 =  -9.98 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:47 2006