Locus 661

Sequence ID 2R_DroMel_CAF1
Location 3,287,850 – 3,287,980
Length 130
Max. P 0.813190
window1170 window1171 window1172

overview

Window 0

Location 3,287,850 – 3,287,957
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 79.90
Mean single sequence MFE -19.15
Consensus MFE -13.96
Energy contribution -15.02
Covariance contribution 1.06
Combinations/Pair 1.10
Mean z-score -1.80
Structure conservation index 0.73
SVM decision value 0.66
SVM RNA-class probability 0.813190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3287850 107 + 20766785
ACCGACCAGAUCAUCAUAAAUAUUUAUACAAUAGUUCCUAACUAACUGAAUGAUCUGUCACGAUCGUUUAAUCGCAACAUUUGGUUGCCCACGUCCUGGGAUUAUUA
..(((((((((....................((((.....))))..(((((((((......)))))))))........)))))))))((((.....))))....... ( -23.10)
>DroSec_CAF1 56278 102 + 1
AACGACCAGAACAUCAUAAAUAUUUA-----UAGUUCCUAACUAACUGAAUAAUCUGUCACGAUCGUUUAAUCGCAACAUUUGGUUGCCCACGUCCUGGAAUUAUUA
..((((((((..........((((((-----((((.....))))..))))))...(((..((((......))))..))))))))))).(((.....)))........ ( -17.00)
>DroSim_CAF1 66817 102 + 1
AACGACCAGAGCAUCAUAAAUAUUUA-----UAGUUCCUAACUCACUGAAUGAUCUGUCACGAUCGUUUAAUCGCAACAUUUGGUUGCCCACGUCCUGGAAUUAUUA
.....((((..(..............-----...............(((((((((......)))))))))...(((((.....)))))....)..))))........ ( -22.30)
>DroYak_CAF1 55188 81 + 1
A---------------U--UUAUUUA-----UAGUUUCUAAGUA----AAUGAUCUGUCACGAUCGUUUUAUCGCAAUAUUUGGUUUCCUAAUUCCUGCGAUCAUUA
(---------------(--(((((((-----.......))))))----)))((((......)))).....((((((....((((....))))....))))))..... ( -14.20)
>consensus
AACGACCAGA_CAUCAUAAAUAUUUA_____UAGUUCCUAACUAACUGAAUGAUCUGUCACGAUCGUUUAAUCGCAACAUUUGGUUGCCCACGUCCUGGAAUUAUUA
...............................(((((((........(((((((((......)))))))))...(((((.....))))).........)))))))... (-13.96 = -15.02 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,287,850 – 3,287,957
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 79.90
Mean single sequence MFE -23.22
Consensus MFE -14.80
Energy contribution -15.68
Covariance contribution 0.87
Combinations/Pair 1.11
Mean z-score -1.90
Structure conservation index 0.64
SVM decision value 0.50
SVM RNA-class probability 0.761189
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3287850 107 - 20766785
UAAUAAUCCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUUAGUUAGGAACUAUUGUAUAAAUAUUUAUGAUGAUCUGGUCGGU
...(((((.(((.(..(((....)))..).))).)))))....((((...(((((((((((((.(((.....))))))).............)))))))))..)))) ( -26.51)
>DroSec_CAF1 56278 102 - 1
UAAUAAUUCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUUAUUCAGUUAGUUAGGAACUA-----UAAAUAUUUAUGAUGUUCUGGUCGUU
........(((((((((((....))...(((..(((((....)))))..)))(((((......)))))........-----............)))))))))..... ( -27.40)
>DroSim_CAF1 66817 102 - 1
UAAUAAUUCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUGAGUUAGGAACUA-----UAAAUAUUUAUGAUGCUCUGGUCGUU
........((((..(.(((....)))..(((..(((((....)))))..))).(((((.........(((...)))-----.........))))))..))))..... ( -24.17)
>DroYak_CAF1 55188 81 - 1
UAAUGAUCGCAGGAAUUAGGAAACCAAAUAUUGCGAUAAAACGAUCGUGACAGAUCAUU----UACUUAGAAACUA-----UAAAUAA--A---------------U
.....(((((((......(....)......))))))).....((((......))))...----.............-----.......--.---------------. ( -14.80)
>consensus
UAAUAAUCCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUUAGUUAGGAACUA_____UAAAUAUUUAUGAUG_UCUGGUCGUU
.(((((((........(((....)))..(((..(((((....)))))..))))))))))................................................ (-14.80 = -15.68 +   0.87)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,287,890 – 3,287,980
Length 90
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 81.67
Mean single sequence MFE -21.38
Consensus MFE -15.45
Energy contribution -16.95
Covariance contribution 1.50
Combinations/Pair 1.12
Mean z-score -1.83
Structure conservation index 0.72
SVM decision value 0.60
SVM RNA-class probability 0.795063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3287890 90 - 20766785
---UUCUAU-AUAGAGUG------------GAUAUUAAAUAAUAAUCCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUUAGU
---......-...(((((------------(........................(((....)))..(((..(((((....)))))..)))..))))))....... ( -21.80)
>DroSec_CAF1 56313 94 - 1
GUAUUCUAUAAUAGAGUG------------GAUAUUAAAUAAUAAUUCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUUAUUCAGUUAGU
.(((((((...)))))))------------...(((((..(((((((........(((....)))..(((..(((((....)))))..))))))))))...))))) ( -22.20)
>DroSim_CAF1 66852 94 - 1
GUAUUCUAUAAUAGAGUG------------GAUAUUAAAUAAUAAUUCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUGAGU
.............(((((------------(........................(((....)))..(((..(((((....)))))..)))..))))))....... ( -21.80)
>DroYak_CAF1 55206 102 - 1
AUUUUCUACAAUAGAGUAAAAUUGUCCAGCGAUAUUGAAUAAUGAUCGCAGGAAUUAGGAAACCAAAUAUUGCGAUAAAACGAUCGUGACAGAUCAUU----UACU
..............((((((.(((((..(((((...........(((((((......(....)......)))))))......))))))))))....))----)))) ( -19.73)
>consensus
GUAUUCUAUAAUAGAGUG____________GAUAUUAAAUAAUAAUCCCAGGACGUGGGCAACCAAAUGUUGCGAUUAAACGAUCGUGACAGAUCAUUCAGUUAGU
.(((((((...)))))))......................(((((((........(((....)))..(((..(((((....)))))..))))))))))........ (-15.45 = -16.95 +   1.50)

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 09:44:01 2006