Locus 1254

Sequence ID 2R_DroMel_CAF1
Location 4,905,721 – 4,905,997
Length 276
Max. P 0.951207
window2172 window2173 window2174 window2175

overview

Window 2

Location 4,905,721 – 4,905,841
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.17
Mean single sequence MFE -38.30
Consensus MFE -32.94
Energy contribution -31.74
Covariance contribution -1.20
Combinations/Pair 1.21
Mean z-score -1.48
Structure conservation index 0.86
SVM decision value 0.72
SVM RNA-class probability 0.833186
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4905721 120 + 20766785
AACCACCAUCCGAGCCUUGGAUGCCCAGCGCGUUCUGGAGAAGGAGUUCGACAGCUACCAGGAUGCGCACAGCUCUGCAUUUUUCAUGUACAUAAGUACAUCGCAGGCAUUUGGUUAUUG
(((((.(((((((...)))))))....(((((((((((((..(........)..)).)))))))))))...((.((((.......((((((....)))))).))))))...))))).... ( -42.50)
>DroSec_CAF1 38960 120 + 1
AACCACCAUCCGAGCCCAGGAUGCCCAGCGCGUUCUGGAGAAGGAGUUCGAUAGCUACCAGGAUGCGCACAGCUCCGCAUUUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUAG
(((((((...((((....(((.((...(((((((((((......(((......))).)))))))))))...)))))...........((((....))))))))..))....))))).... ( -36.10)
>DroSim_CAF1 57565 120 + 1
AACCACCAUCCGAGCCCUGGAUGCCCAGAGCGUUCUGGAGAAGGAGUUCGACAGCUACCAGGAUGCGCACAGCUCUGCAUUUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUUG
(((((......((((.((((....)))).(((((((((((..(........)..)).))))))))).....))))(((....(((..((((....))))...))).)))..))))).... ( -35.80)
>DroEre_CAF1 53535 120 + 1
AACAACCAUCCGAGCCUUGGAGGCUCAGCGCGUUCUGGAGAAGGAGUUCGAUAAUUACCAGGAUGCGCACAGCUCGGCAUUCUACAUGUACAUAAGUACCUCGGUGGCUUUUGGUUAUUG
...(((((...(((((.(.((((((..(((((((((((...................)))))))))))..)))..............((((....))))))).).))))).))))).... ( -39.81)
>DroYak_CAF1 58159 120 + 1
AACAACCAUCCGAGCCUUGGAAGCUCAGCGCGUUCUGGAGAAGGAGUUCGACAAUUACCAGGAUGCGCACAGCUCUGCAUUUUACAUGUACAUAAGUACUUCGAUGGCUUUCGGUUAUUA
...((((....((((((((((((((..(((((((((((.((..(.......)..)).)))))))))))..)))).............((((....))))))))).)))))..)))).... ( -37.30)
>consensus
AACCACCAUCCGAGCCUUGGAUGCCCAGCGCGUUCUGGAGAAGGAGUUCGACAGCUACCAGGAUGCGCACAGCUCUGCAUUUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUUG
............((((..(((((((..(((((((((((((..(........)..)).)))))))))))...................((((....))))......))))))))))).... (-32.94 = -31.74 +  -1.20)

alignment

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secondary structure

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Window 3

Location 4,905,801 – 4,905,921
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.25
Mean single sequence MFE -32.87
Consensus MFE -26.06
Energy contribution -26.18
Covariance contribution 0.12
Combinations/Pair 1.22
Mean z-score -1.90
Structure conservation index 0.79
SVM decision value 0.98
SVM RNA-class probability 0.893974
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4905801 120 + 20766785
UUUUCAUGUACAUAAGUACAUCGCAGGCAUUUGGUUAUUGUAUGAACUGCAUAUGCGUGAUUUAUAUAUCGAUCAUAACGCUUAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUG
.....((((((....)))))).....((...(((((..((((((((((((....))).).))))))))..)))))....))((((((((.((((((.......)))))).)))))))).. ( -32.30)
>DroSec_CAF1 39040 120 + 1
UUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUAGCAUGAACUGCAUAUGUGUGAUCUACAUAUCGAUCAUAACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUG
..(((((((((.(((((.((.....)).)))))))....)))))))..((.....(((((((........)))))))..))((((((((.((((((.......)))))).)))))))).. ( -34.50)
>DroSim_CAF1 57645 120 + 1
UUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUUGCAUGAACUGCAUAUGUGUGAUCUACAUAUCGAUCAUAACGCUCAGUUUUUUUGCCUUUCCUCCGGGCAACGGAGCGGAUG
..((((((((..(((((.((.....)).))))).....)))))))).........(((((((........))))))).(((((.((.....(((((.......))))))).))))).... ( -31.20)
>DroEre_CAF1 53615 120 + 1
UCUACAUGUACAUAAGUACCUCGGUGGCUUUUGGUUAUUGCAUGAACUGCAUAUGCGUGAUUUACAUAUCAAUCAUCACGCUCAGUUUCUUUGCCUUUCCGCCGGGCAACGGAGCUGAUG
....((((((((.((((((....)).)))).)).....))))))..........(((((((.............)))))))((((((((.((((((.......)))))).)))))))).. ( -34.42)
>DroYak_CAF1 58239 120 + 1
UUUACAUGUACAUAAGUACUUCGAUGGCUUUCGGUUAUUAUAUGAACAUCAUAUGCGUGAUUUACAUAUCGAUCAUUACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUG
.......((((....))))...((((((.....))))))(((((.....)))))(((((((.............)))))))((((((((.((((((.......)))))).)))))))).. ( -31.92)
>consensus
UUUUCAUGUACAUAAGUACCUCGAAGGCAUUUGGUUAUUGCAUGAACUGCAUAUGCGUGAUUUACAUAUCGAUCAUAACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUG
..((((((((..(((((.((.....)).))))).....))))))))........((((((((........))))...))))((((((((.((((((.......)))))).)))))))).. (-26.06 = -26.18 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,905,841 – 4,905,957
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.07
Mean single sequence MFE -37.26
Consensus MFE -28.14
Energy contribution -26.82
Covariance contribution -1.32
Combinations/Pair 1.22
Mean z-score -2.54
Structure conservation index 0.76
SVM decision value 1.41
SVM RNA-class probability 0.951207
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4905841 116 + 20766785
UAUGAACUGCAUAUGCGUGAUUUAUAUAUCGAUCAUAACGCUUAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUUGGUCUGGUCAUAACACAGGUAA----GCCAUUACACUA
........((....))(((((.........((((((((((.((((((((.((((((.......)))))).)))))))))))))...)))))........((...----.))))))).... ( -29.50)
>DroSec_CAF1 39080 120 + 1
CAUGAACUGCAUAUGUGUGAUCUACAUAUCGAUCAUAACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUGGGUCUGCUCAUAACACAGGUGAGCGAGCCAUCACACAA
.............((((((((.................(((((((((((.((((((.......)))))).)))))))).)))((..(((((((.......)))))))..)))))))))). ( -45.20)
>DroSim_CAF1 57685 120 + 1
CAUGAACUGCAUAUGUGUGAUCUACAUAUCGAUCAUAACGCUCAGUUUUUUUGCCUUUCCUCCGGGCAACGGAGCGGAUGUGGGUCUGGUCAUAACACAGGUGAGCGAGCCAUCACACAA
.............((((((((...((((((((.(.....).)).((((..((((((.......))))))..)))).))))))((..((.((((.......)))).))..)))))))))). ( -37.00)
>DroEre_CAF1 53655 116 + 1
CAUGAACUGCAUAUGCGUGAUUUACAUAUCAAUCAUCACGCUCAGUUUCUUUGCCUUUCCGCCGGGCAACGGAGCUGAUGUGGGUCUGGUCAUAACACAGGUGA----GCCAUCAUACAA
.((((.(..((...(((((((.............)))))))((((((((.((((((.......)))))).))))))))))..)...(((((((.......))))----.))))))).... ( -36.52)
>DroYak_CAF1 58279 115 + 1
UAUGAACAUCAUAUGCGUGAUUUACAUAUCGAUCAUUACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUCGGUCUGGUCAUCACACAGGUGA----G-CAUCAUACAA
(((((...((((.((.(((((...((.(((((.((......((((((((.((((((.......)))))).))))))))))))))).))...))))).)).))))----.-..)))))... ( -38.10)
>consensus
CAUGAACUGCAUAUGCGUGAUUUACAUAUCGAUCAUAACGCUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUGGGUCUGGUCAUAACACAGGUGA____GCCAUCACACAA
......(..((...((((((((........))))...))))((((((((.((((((.......)))))).))))))))))..)..(((.........)))((((........)))).... (-28.14 = -26.82 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,905,881 – 4,905,997
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.24
Mean single sequence MFE -34.56
Consensus MFE -25.39
Energy contribution -25.63
Covariance contribution 0.24
Combinations/Pair 1.21
Mean z-score -1.95
Structure conservation index 0.73
SVM decision value 0.52
SVM RNA-class probability 0.768209
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4905881 116 + 20766785
CUUAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUUGGUCUGGUCAUAACACAGGUAA----GCCAUUACACUAAAGCAGUCACUAUCACCUGCCAAUCACCUUUUGGUUACCC
.((((((((.((((((.......)))))).)))))))).((((((..(((.(((.....((...----.)).....(((.....)))...))).))).)))))).(((....)))..... ( -27.80)
>DroSec_CAF1 39120 118 + 1
CUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUGGGUCUGCUCAUAACACAGGUGAGCGAGCCAUCACACAAAUGUAGUCACUAUCACCUGUCAGUCU--CUUUGGUUACCC
.((((((((.((((((.......)))))).))))))))((((((....))))))..((((((((...((..((.(((....))).))..)).))))))))......--............ ( -36.00)
>DroSim_CAF1 57725 118 + 1
CUCAGUUUUUUUGCCUUUCCUCCGGGCAACGGAGCGGAUGUGGGUCUGGUCAUAACACAGGUGAGCGAGCCAUCACACAAAAGUAGUCACUAUCACCUGACAGUCC--CUUUGGUUACCC
.((.((((..((((((.......))))))..)))).))...(((.(((((....)).(((((((...((..((.((......)).))..)).))))))).))).))--)........... ( -32.40)
>DroEre_CAF1 53695 114 + 1
CUCAGUUUCUUUGCCUUUCCGCCGGGCAACGGAGCUGAUGUGGGUCUGGUCAUAACACAGGUGA----GCCAUCAUACAAAGGUAUUCACCAUCACCUGCCAGUCC--CUUUGAUUCUCC
.((((((((.((((((.......)))))).))))))))...(((.((((........(((((((----......((((....))))......))))))))))).))--)........... ( -40.50)
>DroYak_CAF1 58319 113 + 1
CUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUCGGUCUGGUCAUCACACAGGUGA----G-CAUCAUACAAAAGUAUUCACCAUCACCUGCCAGCCC--UUUUGGUUCCCC
.((((((((.((((((.......)))))).))))))))....((.((((........(((((((----.-....((((....))))......))))))))))).))--............ ( -36.10)
>consensus
CUCAGUUUCUUUGCCUUUCCUCCGGGCAACGGAGCUGAUGUGGGUCUGGUCAUAACACAGGUGA____GCCAUCACACAAAAGUAGUCACUAUCACCUGCCAGUCC__CUUUGGUUACCC
.((((((((.((((((.......)))))).))))))))...(((.((((........(((((((.........(........).........)))))))))))))).............. (-25.39 = -25.63 +   0.24)

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 10:00:10 2006