Locus 3520

Sequence ID 3R_DroMel_CAF1
Location 9,510,839 – 9,511,199
Length 360
Max. P 0.996957
window5655 window5656 window5657 window5658

overview

Window 5

Location 9,510,839 – 9,510,959
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.39
Mean single sequence MFE -39.24
Consensus MFE -32.96
Energy contribution -32.96
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.84
SVM decision value 0.57
SVM RNA-class probability 0.784608
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9510839 120 - 27905053
UGUUUUUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAACCACUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGGUGAAG
.((.((((((((((((....)))))))))))).))((....))((((.(.((((((((((((((((..((....))..))))).......(((....)))))))))).)))).))))).. ( -44.50)
>DroSec_CAF1 140517 119 - 1
UGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAACCUCUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGGUGAAG
.(((-(((((((((((....)))))))))))).))((....))((((.(.(((((((.((((((((..((....))..))))).......(((....)))))).))).)))).))))).. ( -39.10)
>DroSim_CAF1 130678 119 - 1
UGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAACCUCUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGGUGAAG
.(((-(((((((((((....)))))))))))).))((....))((((.(.(((((((.((((((((..((....))..))))).......(((....)))))).))).)))).))))).. ( -39.10)
>DroEre_CAF1 148369 116 - 1
UCUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAAACAUUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGCAG---
...(-(((((((((((....)))))))))))).......(((((.((.((((...((((.((((((..(....)..)))))).))))...(((....))).))))))...)))))..--- ( -38.60)
>DroYak_CAF1 142125 119 - 1
UGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAAACACUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGAAGGAA
.(((-(((((((((((....)))))))))))).)).(((.((....(((.(((((((((.(((.(.......)))).))))(((....))).....))))).)))....)))))...... ( -34.90)
>consensus
UGUU_UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCGCGCUCACACACUAAACCACUCGCACAACCGAAGGCGUGUGUGCAUGUAUGCAAUUUUUUGGGGUGGUAUUGGCGGUGAAG
......(((((((((((.....((((((.......))))))...(((((((.....(..(((......)))..).))))))))))))))))))........................... (-32.96 = -32.96 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,510,919 – 9,511,039
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.55
Mean single sequence MFE -39.94
Consensus MFE -32.89
Energy contribution -33.13
Covariance contribution 0.24
Combinations/Pair 1.12
Mean z-score -2.72
Structure conservation index 0.82
SVM decision value 2.77
SVM RNA-class probability 0.996957
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9510919 120 - 27905053
UCUUCUUACUUUCGCCCCCAGCAAUGAAACGCCAUGAAUUGGGGGAGACGGAAUCUAACGAUUGCGAACGCGUCGUAUCUUGUUUUUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
...........((.(((((((..(((......)))...))))))).))((.((((....)))).))..((((.(((((.......(((((((((((....)))))))))))))))))))) ( -44.31)
>DroSec_CAF1 140597 119 - 1
UCUUCUUACUUUCGUCUCCAGCAAUGAAACUCCAUGAAUUGGGGGAGACUGAAUCUAACGAUUGCGAACGCGUUGUAUCUUGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
..........((((((((((....))...(((((.....))))))))))..((((....))))..)))(((((.((((......-(((((((((((....)))))))))))))))))))) ( -37.40)
>DroSim_CAF1 130758 119 - 1
UCUUCUUACUUUCGUCCCCAGCAAUGAAACGCCAUGAAUUGGGGGAGACGGAAUCUAACGAUUGCGAACGCGUUGUAUCUUGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
...........((..((((((..(((......)))...))))))..))((.((((....)))).))..(((((.((((......-(((((((((((....)))))))))))))))))))) ( -40.50)
>DroEre_CAF1 148446 119 - 1
UCUUCUUACUUUCUUCCCCAGCAAUGAAAAGCAAGAAAUUUGGGGAGAAGGAAUCAAACGAUUGCGAACGCGUCGUAUCUUCUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
..(((...((((((.(((((((........))((....)))))))))))))((((....))))..)))((((.(((((......-(((((((((((....)))))))))))))))))))) ( -38.90)
>DroYak_CAF1 142205 119 - 1
UCUUCUUACUUUCUUUCCCAGCAUUGAAACGUAAAGAAUUGGGGGAGAAGGAAUCAAACGAGUGCGAACGCGUCGUAUCUUGUU-UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
........((((((..(((((..((........))...)))))..)))))).................((((.(((((......-(((((((((((....)))))))))))))))))))) ( -38.60)
>consensus
UCUUCUUACUUUCGUCCCCAGCAAUGAAACGCCAUGAAUUGGGGGAGACGGAAUCUAACGAUUGCGAACGCGUCGUAUCUUGUU_UUUGCAUGCAUGACAAUGUGUGCAGAAUACGCGCG
..(((......((.(((((((..(((......)))...))))))).)).(.((((....)))).))))((((.(((((.......(((((((((((....)))))))))))))))))))) (-32.89 = -33.13 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,511,039 – 9,511,159
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -36.90
Consensus MFE -27.56
Energy contribution -29.16
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -1.59
Structure conservation index 0.75
SVM decision value -0.02
SVM RNA-class probability 0.521415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9511039 120 - 27905053
CACGCAUGGGCGCGAACGCUGCAAGUGUCCGUGUGAAGAAGGAGAAGGCGAAGAGGUGGGAAUCCAAAAGCUAAGGAUGCAGGACUUCAUUAGGAAGUGGUUCGCAUAUCCCUUUCGUUA
..(((((((((((...........)))))))))))...........(((((((.((((.(((((.....((.......))...(((((.....)))))))))).))...)).))))))). ( -37.10)
>DroSec_CAF1 140716 120 - 1
CACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGGCGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGCAGGACUUCAUAAGGAAGUGGUUCGCAUAUCCCUUUCGUUA
..(((((((((((...........)))))))))))...........(((((((....((((.(((....)))....((((.(((((.(........).))))))))).))))))))))). ( -37.50)
>DroSim_CAF1 130877 120 - 1
CACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGACGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGCAGGACUUCAUAAGGAAGUGGUUCGCAUAUCCCUUUCGUUA
..(((((((((((...........)))))))))))...........(((((((....((((.(((....)))....((((.(((((.(........).))))))))).))))))))))). ( -38.00)
>DroEre_CAF1 148565 120 - 1
CACCCAUGGGCGCGAAAGCUGCAAGUGUCCGUGAGAAAAAGGAGCAGGCGAAAAGGUGGGAAGGGAUAAGCUAAGGAUGCAGGACUCCAUAAGAAAGCGGUUCGCAUAUGCCUUUCGAUA
(((((((((((((...........)))))))))..........(....).....))))((((((.(((.((...(((........)))....(((.....))))).))).)))))).... ( -32.70)
>DroYak_CAF1 142324 120 - 1
GACACAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGACGAAAAGUUUGGAAGGGAUAAGCUAAGGAUGCACCAUUUCACAAGGAAGCGGUUCGCAUAUCCCUUUCGAUA
..(((((((((((...........))))))))))).....................((((((((((((.((.......))(((.((((.....)))).))).....)))))))))))).. ( -39.20)
>consensus
CACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGGCGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGCAGGACUUCAUAAGGAAGUGGUUCGCAUAUCCCUUUCGUUA
..(((((((((((...........)))))))))))...........(((((((....((((.(((....)))....((((.((((..(........)..)))))))).))))))))))). (-27.56 = -29.16 +   1.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,511,079 – 9,511,199
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.75
Mean single sequence MFE -42.19
Consensus MFE -34.80
Energy contribution -35.84
Covariance contribution 1.04
Combinations/Pair 1.06
Mean z-score -1.64
Structure conservation index 0.82
SVM decision value 0.81
SVM RNA-class probability 0.856595
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9511079 120 - 27905053
GGAGUCUCGCUGCUCUCUUCCUGUUCUUCGCACACAUACACACGCAUGGGCGCGAACGCUGCAAGUGUCCGUGUGAAGAAGGAGAAGGCGAAGAGGUGGGAAUCCAAAAGCUAAGGAUGC
(((.(((((((..(((((((.(.((((((((((....((((..(((...(((....))))))..))))..)))))))))).).))))).))...))))))).)))............... ( -43.20)
>DroSec_CAF1 140756 120 - 1
GGAGUCUCGCUGCUCUCUUCCUGUUCUUCGCACACAUACACACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGGCGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGC
...((((..(..(.((((((((((((((..(((((..((((..((....))((....)).....))))..)))))....)))))))))..))))))..)..))))............... ( -43.90)
>DroSim_CAF1 130917 120 - 1
GGAGUCUCGCUGCUCUCUUCCUGUUCUUCGCACACAUACACACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGACGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGC
...((((..(..(.((((((((((((((..(((((..((((..((....))((....)).....))))..)))))....))))))))..)))))))..)..))))............... ( -43.50)
>DroEre_CAF1 148605 120 - 1
GGAGUCUCGCUAUUCUCUUCCUGUUCUUCGCACACACACACACCCAUGGGCGCGAAAGCUGCAAGUGUCCGUGAGAAAAAGGAGCAGGCGAAAAGGUGGGAAGGGAUAAGCUAAGGAUGC
...((((.(((..((((((((..((.(((((............((((((((((...........))))))))).)............)))))..))..))))))))..)))...)))).. ( -38.25)
>DroYak_CAF1 142364 120 - 1
GGAGUCUUGCUGCUCUCUUCCUGUUUUUCGCACACAUACAGACACAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGACGAAAAGUUUGGAAGGGAUAAGCUAAGGAUGC
...((((((((..((((((((..((((((((...(((((.(((((.((.(.((....))).)).))))).)))))..(......).).)))))))...))))))))..)))..))))).. ( -42.10)
>consensus
GGAGUCUCGCUGCUCUCUUCCUGUUCUUCGCACACAUACACACGCAUGGGCGCGAAAGCUGCAAGUGUCCGUGUGAAGAAGGAGCAGGCGAAGAGGUGGGAAGGCAAAAGCUAAGGAUGC
...((((.(((....((((((..((((((((...........(((((((((((...........)))))))))))............))))))).)..))))))....)))...)))).. (-34.80 = -35.84 +   1.04)

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 11:03:13 2006