Locus 3738

Sequence ID 3R_DroMel_CAF1
Location 10,146,738 – 10,146,870
Length 132
Max. P 0.825963
window5990 window5991 window5992 window5993

overview

Window 0

Location 10,146,738 – 10,146,853
Length 115
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 86.36
Mean single sequence MFE -21.48
Consensus MFE -15.24
Energy contribution -15.17
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -1.68
Structure conservation index 0.71
SVM decision value 0.26
SVM RNA-class probability 0.656244
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10146738 115 + 27905053
UUUUUCCUUACUUGGGAUACUUCCGAAAUCCUUGUUAUUAAUUUGUAUCUUUUCUUUUUUGGUCAUCUAUGAUAAAU-CUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUU
...........((.(((....))).)).................((((((((.......(((((((.((((((((..-......)))))))).....)))))))...)))))))). ( -18.10)
>DroSec_CAF1 5391 114 + 1
UUUCUCUUCACUUGGGAUACUUCCGAAAUCCUUGUUUUUAAUUCGUAUCUUUUGU--UUUGGUCAUCUAUGAUGAUUCCUUAUGUUGUUACAUUGAUAUGACCGCAUAGAGAUAUU
..(((((..((..(((((((.....(((........))).....)))))))..))--...(((((((.(((.((((..(....)..))))))).))..)))))....))))).... ( -22.00)
>DroSim_CAF1 4454 114 + 1
UUUCUCUUCACUUGGGAUACUUCCGAAAUCCUUGUUUUUAAUUUGUAUCUUUUGU--UUUGGUCAUCUAUGAUGAGUCCUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUU
..((((...((..(((((((.....(((........))).....)))))))..))--...(((((((...)))))..)).(((((.((((((....)))))).))))))))).... ( -22.40)
>DroYak_CAF1 4472 112 + 1
UUUUAAUUCAUUGGGGAUAUUUCUGAAAUCUGUUUUGUUUUAUUGUAUCUGUUGU--UUUGGUCAUCUAGGAUAAAU-CUUAUGUAGUUAU-UUGAUAUGACCGCAUACAGAUAUU
...(((..((..(.((((.........)))).)..))..)))..(((((((((((--...((((((...((((((..-(....)...))))-))...))))))))).)))))))). ( -23.40)
>consensus
UUUCUCUUCACUUGGGAUACUUCCGAAAUCCUUGUUUUUAAUUUGUAUCUUUUGU__UUUGGUCAUCUAUGAUAAAU_CUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUU
..............(((....)))....................(((((((..........(((......))).......(((((.((((((....)))))).)))))))))))). (-15.24 = -15.17 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,146,738 – 10,146,853
Length 115
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 86.36
Mean single sequence MFE -17.43
Consensus MFE -10.73
Energy contribution -11.48
Covariance contribution 0.75
Combinations/Pair 1.16
Mean z-score -2.09
Structure conservation index 0.62
SVM decision value 0.10
SVM RNA-class probability 0.581477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10146738 115 - 27905053
AAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAG-AUUUAUCAUAGAUGACCAAAAAAGAAAAGAUACAAAUUAAUAACAAGGAUUUCGGAAGUAUCCCAAGUAAGGAAAAA
......(((.(((((((((......((((.........-..)))).....)))))).............................((((..(....).))))...))).))).... ( -16.00)
>DroSec_CAF1 5391 114 - 1
AAUAUCUCUAUGCGGUCAUAUCAAUGUAACAACAUAAGGAAUCAUCAUAGAUGACCAAA--ACAAAAGAUACGAAUUAAAAACAAGGAUUUCGGAAGUAUCCCAAGUGAAGAGAAA
....(((((.(((..((.((((.((((....))))..((..(((((...)))))))...--......)))).))...........((((..(....).))))...))).))))).. ( -21.70)
>DroSim_CAF1 4454 114 - 1
AAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAGGACUCAUCAUAGAUGACCAAA--ACAAAAGAUACAAAUUAAAAACAAGGAUUUCGGAAGUAUCCCAAGUGAAGAGAAA
....(((((.(((((((((.............(....)............))))))...--........................((((..(....).))))...))).))))).. ( -19.31)
>DroYak_CAF1 4472 112 - 1
AAUAUCUGUAUGCGGUCAUAUCAA-AUAACUACAUAAG-AUUUAUCCUAGAUGACCAAA--ACAACAGAUACAAUAAAACAAAACAGAUUUCAGAAAUAUCCCCAAUGAAUUAAAA
..(((((((.((.((((((.....-((((((.....))-..)))).....))))))...--.)))))))))..................((((.............))))...... ( -12.72)
>consensus
AAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAG_AUUCAUCAUAGAUGACCAAA__ACAAAAGAUACAAAUUAAAAACAAGGAUUUCGGAAGUAUCCCAAGUGAAGAAAAA
....(((((.(((((((((...............................)))))).............................((((..(....).))))...))).))))).. (-10.73 = -11.48 +   0.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,146,778 – 10,146,870
Length 92
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 88.93
Mean single sequence MFE -21.62
Consensus MFE -15.52
Energy contribution -15.90
Covariance contribution 0.38
Combinations/Pair 1.04
Mean z-score -2.30
Structure conservation index 0.72
SVM decision value 0.70
SVM RNA-class probability 0.825963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10146778 92 + 27905053
AUUUGUAUCUUUUCUUUUUUGGUCAUCUAUGAUAAAU-CUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUUGCAUGCUAUCGGAUGCA
....((((((((.......(((((((.((((((((..-......)))))))).....)))))))...))))))))(((((.(....).))))) ( -19.80)
>DroSec_CAF1 5431 91 + 1
AUUCGUAUCUUUUGU--UUUGGUCAUCUAUGAUGAUUCCUUAUGUUGUUACAUUGAUAUGACCGCAUAGAGAUAUUGCAUGCUAACAGAUGCA
....(((((((((((--...(((((((.(((.((((..(....)..))))))).))..)))))))).))))))))(((((........))))) ( -20.80)
>DroSim_CAF1 4494 91 + 1
AUUUGUAUCUUUUGU--UUUGGUCAUCUAUGAUGAGUCCUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUUGCAUGCUAACAGAUGCA
...(((((((.(((.--..((.(((((...)))))(((.((((((.((((((....)))))).)))))).)))....))...))).))))))) ( -21.50)
>DroYak_CAF1 4512 89 + 1
UAUUGUAUCUGUUGU--UUUGGUCAUCUAGGAUAAAU-CUUAUGUAGUUAU-UUGAUAUGACCGCAUACAGAUAUUGCAUGCAAACAGCUGCA
....(((((((((((--...((((((...((((((..-(....)...))))-))...))))))))).))))))))((((.((.....)))))) ( -24.40)
>consensus
AUUUGUAUCUUUUGU__UUUGGUCAUCUAUGAUAAAU_CUUAUGUUGUUAUAUUGAUAUGACCGCAUAGAGAUAUUGCAUGCUAACAGAUGCA
....(((((((..........(((......))).......(((((.((((((....)))))).))))))))))))(((((........))))) (-15.52 = -15.90 +   0.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,146,778 – 10,146,870
Length 92
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 88.93
Mean single sequence MFE -15.02
Consensus MFE -10.24
Energy contribution -10.30
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -1.69
Structure conservation index 0.68
SVM decision value -0.03
SVM RNA-class probability 0.519891
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10146778 92 - 27905053
UGCAUCCGAUAGCAUGCAAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAG-AUUUAUCAUAGAUGACCAAAAAAGAAAAGAUACAAAU
.((((..((((........))))...))))((((((......((((.........-..)))).....)))))).................... ( -12.20)
>DroSec_CAF1 5431 91 - 1
UGCAUCUGUUAGCAUGCAAUAUCUCUAUGCGGUCAUAUCAAUGUAACAACAUAAGGAAUCAUCAUAGAUGACCAAA--ACAAAAGAUACGAAU
.(.((((....(((((.........)))))((((((....((((....))))...((....))....))))))...--.....)))).).... ( -14.10)
>DroSim_CAF1 4494 91 - 1
UGCAUCUGUUAGCAUGCAAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAGGACUCAUCAUAGAUGACCAAA--ACAAAAGAUACAAAU
((((((.....).))))).(((((.((((..((.(((....))).))..)))).((..(((((...)))))))...--.....)))))..... ( -13.60)
>DroYak_CAF1 4512 89 - 1
UGCAGCUGUUUGCAUGCAAUAUCUGUAUGCGGUCAUAUCAA-AUAACUACAUAAG-AUUUAUCCUAGAUGACCAAA--ACAACAGAUACAAUA
((...(((((.(((((((.....)))))))((((((.....-((((((.....))-..)))).....))))))...--..)))))...))... ( -20.20)
>consensus
UGCAUCUGUUAGCAUGCAAUAUCUCUAUGCGGUCAUAUCAAUAUAACAACAUAAG_AUUCAUCAUAGAUGACCAAA__ACAAAAGAUACAAAU
(((((........))))).(((((.((((..((.(((....))).))..)))).....(((((...)))))............)))))..... (-10.24 = -10.30 +   0.06)

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 11:08:52 2006