Locus 6808

Sequence ID 3R_DroMel_CAF1
Location 18,005,888 – 18,006,020
Length 132
Max. P 0.998143
window11052 window11053 window11054 window11055

overview

Window 2

Location 18,005,888 – 18,005,982
Length 94
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 65.30
Mean single sequence MFE -21.12
Consensus MFE -9.55
Energy contribution -9.79
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.19
Structure conservation index 0.45
SVM decision value 3.02
SVM RNA-class probability 0.998143
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18005888 94 + 27905053
GUUAAGCCCUUUCUGCAAGUGUGAACUGUUCCAUUUUCUUAAAAUUCAGCUUUGGUCACACAACCAGUUUUAGUGUGACCAUCCCAUUC----------ACCCU
.....((.......)).((.((((((((..................)))...(((((((((...........))))))))).....)))----------)).)) ( -18.17)
>DroSim_CAF1 50559 81 + 1
CUUAAACCCUUUCUU-------------UUAAGGUUUCUACAAAUUCGACUUUGGUCACACACCCAGUUUAAAUGUGACCAUCCUGUUA----------ACCCU
.......((((....-------------..)))).............(((..((((((((.............))))))))....))).----------..... ( -14.02)
>DroEre_CAF1 50120 98 + 1
AUUAAACCCCUUUUGCAAGUGUGAACA------CUUGCUUCAACUUAAGCUCUGGUCACACAACAAAUUUAAAUGUGACCAUCGCAUUCGGAUAAAAGUACCCU
........((....(((((((....))------)))))..........((..((((((((.............))))))))..))....))............. ( -26.62)
>DroYak_CAF1 51286 98 + 1
CUUAAAUCCUUUCUGCUAGUGCGAACUCUUCAGCUUGCUUCAAAUUAAGCUUUGGUCACUCAACCCAUUUAAAUGUGACCAUCGUAUGCGGAUAAAAG------
...........(((((..((((((.......((((((........)))))).(((((((...............))))))))))))))))))......------ ( -25.66)
>consensus
CUUAAACCCUUUCUGCAAGUGUGAACU_UUCAGCUUGCUUCAAAUUAAGCUUUGGUCACACAACCAAUUUAAAUGUGACCAUCCCAUUC__________ACCCU
....................................................((((((((.............))))))))....................... ( -9.55 =  -9.79 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,005,888 – 18,005,982
Length 94
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 65.30
Mean single sequence MFE -23.55
Consensus MFE -12.16
Energy contribution -12.22
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.52
SVM decision value 1.71
SVM RNA-class probability 0.973608
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18005888 94 - 27905053
AGGGU----------GAAUGGGAUGGUCACACUAAAACUGGUUGUGUGACCAAAGCUGAAUUUUAAGAAAAUGGAACAGUUCACACUUGCAGAAAGGGCUUAAC
.((((----------(.......(((((((((...........))))))))).(((((..(((((......))))))))))..)))))((.......))..... ( -21.60)
>DroSim_CAF1 50559 81 - 1
AGGGU----------UAACAGGAUGGUCACAUUUAAACUGGGUGUGUGACCAAAGUCGAAUUUGUAGAAACCUUAA-------------AAGAAAGGGUUUAAG
.....----------........(((((((((...........)))))))))...............(((((((..-------------.....)))))))... ( -17.80)
>DroEre_CAF1 50120 98 - 1
AGGGUACUUUUAUCCGAAUGCGAUGGUCACAUUUAAAUUUGUUGUGUGACCAGAGCUUAAGUUGAAGCAAG------UGUUCACACUUGCAAAAGGGGUUUAAU
.(((((....)))))((((((..(((((((((...........)))))))))..))..........(((((------((....))))))).......))))... ( -31.90)
>DroYak_CAF1 51286 98 - 1
------CUUUUAUCCGCAUACGAUGGUCACAUUUAAAUGGGUUGAGUGACCAAAGCUUAAUUUGAAGCAAGCUGAAGAGUUCGCACUAGCAGAAAGGAUUUAAG
------(((..((((((......(((((((..((((.....)))))))))))..((((......))))..)).......(((((....)).))).))))..))) ( -22.90)
>consensus
AGGGU__________GAAUACGAUGGUCACAUUUAAACUGGUUGUGUGACCAAAGCUGAAUUUGAAGAAAGCUGAA_AGUUCACACUUGCAGAAAGGGUUUAAG
.......................(((((((((...........))))))))).................................................... (-12.16 = -12.22 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,005,912 – 18,006,020
Length 108
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 65.22
Mean single sequence MFE -20.30
Consensus MFE -10.47
Energy contribution -10.35
Covariance contribution -0.13
Combinations/Pair 1.09
Mean z-score -2.21
Structure conservation index 0.52
SVM decision value 2.35
SVM RNA-class probability 0.992807
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18005912 108 + 27905053
ACUGUUCCAUUUUCUUAAAAUUCAGCUUUGGUCACACAACCAGUUUUAGUGUGACCAUCCCAUUC----------ACCCUUUUUUGAGUUUAUCUAAGUUUGAACUCCAAUCGCUCCA
.......................(((..(((((((((...........)))))))))........----------..........(((((((........))))))).....)))... ( -22.30)
>DroSim_CAF1 50574 99 + 1
----UUAAGGUUUCUACAAAUUCGACUUUGGUCACACACCCAGUUUAAAUGUGACCAUCCUGUUA----------ACCCUUUCCUA-----UUUUAAGUUCGAACUCCGAUCGUUCCA
----....((.....((......(((..((((((((.............))))))))....))).----------...........-----......(.(((.....))).))).)). ( -14.52)
>DroEre_CAF1 50144 112 + 1
ACA------CUUGCUUCAACUUAAGCUCUGGUCACACAACAAAUUUAAAUGUGACCAUCGCAUUCGGAUAAAAGUACCCUUUGUUGAGUAUAUUUAAGUUCGAAUUCCGAUUACUCCA
...------...((((......))))..((((((((.............))))))))(((.((((((((..(((((..(((....)))..)))))..))))))))..)))........ ( -25.02)
>DroYak_CAF1 51310 104 + 1
ACUCUUCAGCUUGCUUCAAAUUAAGCUUUGGUCACUCAACCCAUUUAAAUGUGACCAUCGUAUGCGGAUAAAAG--------------UAUAUUAACGUUCGAAUUCCGAUUACUCUA
.......((((((........)))))).(((((((...............)))))))..(((..((((.....(--------------(......))........))))..))).... ( -19.38)
>consensus
ACU_UUCAGCUUGCUUCAAAUUAAGCUUUGGUCACACAACCAAUUUAAAUGUGACCAUCCCAUUC__________ACCCUUU_UUG__UAUAUUUAAGUUCGAACUCCGAUCACUCCA
............................((((((((.............))))))))..........................................(((.....)))........ (-10.47 = -10.35 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,005,912 – 18,006,020
Length 108
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 65.22
Mean single sequence MFE -24.05
Consensus MFE -15.00
Energy contribution -14.38
Covariance contribution -0.62
Combinations/Pair 1.23
Mean z-score -1.44
Structure conservation index 0.62
SVM decision value 1.30
SVM RNA-class probability 0.938953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18005912 108 - 27905053
UGGAGCGAUUGGAGUUCAAACUUAGAUAAACUCAAAAAAGGGU----------GAAUGGGAUGGUCACACUAAAACUGGUUGUGUGACCAAAGCUGAAUUUUAAGAAAAUGGAACAGU
........((((((((((..((((.....((((......))))----------...)))).(((((((((...........)))))))))....)))))))))).............. ( -26.70)
>DroSim_CAF1 50574 99 - 1
UGGAACGAUCGGAGUUCGAACUUAAAA-----UAGGAAAGGGU----------UAACAGGAUGGUCACAUUUAAACUGGGUGUGUGACCAAAGUCGAAUUUGUAGAAACCUUAA----
........((.((((((((.(((....-----.......(...----------...)....(((((((((...........))))))))))))))))))))...))........---- ( -20.90)
>DroEre_CAF1 50144 112 - 1
UGGAGUAAUCGGAAUUCGAACUUAAAUAUACUCAACAAAGGGUACUUUUAUCCGAAUGCGAUGGUCACAUUUAAAUUUGUUGUGUGACCAGAGCUUAAGUUGAAGCAAG------UGU
....(((.(((((.........((((..(((((......)))))..))))))))).)))..(((((((((...........)))))))))..((((......))))...------... ( -29.40)
>DroYak_CAF1 51310 104 - 1
UAGAGUAAUCGGAAUUCGAACGUUAAUAUA--------------CUUUUAUCCGCAUACGAUGGUCACAUUUAAAUGGGUUGAGUGACCAAAGCUUAAUUUGAAGCAAGCUGAAGAGU
..((....))...................(--------------(((((....((......(((((((..((((.....)))))))))))..((((......))))..))..)))))) ( -19.20)
>consensus
UGGAGCAAUCGGAAUUCGAACUUAAAUAUA__CAA_AAAGGGU__________GAAUACGAUGGUCACAUUUAAACUGGUUGUGUGACCAAAGCUGAAUUUGAAGAAAGCUGAA_AGU
..((((.......))))............................................(((((((((...........)))))))))............................ (-15.00 = -14.38 +  -0.62)

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 12:30:30 2006