Locus 627

Sequence ID 2R_DroMel_CAF1
Location 3,152,264 – 3,152,395
Length 131
Max. P 0.811719
window1120 window1121 window1122

overview

Window 0

Location 3,152,264 – 3,152,357
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 81.86
Mean single sequence MFE -32.42
Consensus MFE -23.04
Energy contribution -23.43
Covariance contribution 0.39
Combinations/Pair 1.33
Mean z-score -1.43
Structure conservation index 0.71
SVM decision value 0.10
SVM RNA-class probability 0.583996
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3152264 93 - 20766785
CGGAGAAGGCGCCUUUAUAUCAGAAGGCAUGGCCAUCGGGGAUACCACAAACUCAUUGGUUGUCUCUGUGAAUGCGGGCUCAUUCUCCUCCGG
(((((.(((.((((((......))))))((((((..(((((((((((.........))).))))))))........))).)))))).))))). ( -32.80)
>DroPse_CAF1 38345 84 - 1
---------AACUAUAAUAUCAGAUGGCGCGGCAGAGGAUGCUACGACGAACGUGUUUGUGGUUUCCGUAAAUGCGGGCUCAUGCUCCUCCGG
---------...............(((.(.(((((((...(((((((((....)).))))))).(((((....)))))))).)))).).))). ( -21.10)
>DroSec_CAF1 42004 93 - 1
CGGAGACGGCGCCUUUAUAUCAGAGGGCAUGGCCAUCGGGGACACCACAAACUCAUUGGUUGUCUCCGUGAAUGCGGGCUCGUUCUCCUCCGG
.((((((((.((((.(((.(((((.(((...))).))((((((((((.........))).))))))).)))))).))))))).)))))..... ( -36.40)
>DroSim_CAF1 44036 93 - 1
CGGAGAUGGCGCCUUUAUAUCAGAAGGCAUGGCCAUCGGGGACACCACAAACUCAUUGGUUGUCUCCGUGAAUGCGGGCUCAUUCUCCUCCGG
((((((((((((((((......))))))...))))))((((((((((.........))).)))))))(.(((((......))))).).)))). ( -38.10)
>DroEre_CAF1 41564 93 - 1
UGGAGAUGGCGCCUUAAUAUCAGAAGGCACUGCCAUCGGGGACACCACGAACUCAUUGGUGGUCUCUGUGAAUGCCGGCUCAUUCUCCUCCAG
(((((((((((((((........)))))...))))))(((((.(((((.((....)).))))).)))..(((((......))))).)))))). ( -33.60)
>DroYak_CAF1 42012 93 - 1
CGGAGAUGGCGCCUUAAUAUCGGAAGGCACUGCCAUCGGGGACACCACGAACUCAUUGGUUGUCUCUGUGAAUGCGGGCUCAUUCUCUUCCAG
.((((((((((((((........))))).((((...(((((((((((.........))).)))))))).....)))))).)).)))))..... ( -32.50)
>consensus
CGGAGAUGGCGCCUUAAUAUCAGAAGGCACGGCCAUCGGGGACACCACAAACUCAUUGGUUGUCUCCGUGAAUGCGGGCUCAUUCUCCUCCGG
.(((((.((((((((........))))).(.((...(((((((((((.........)))).))))))).....)).))))...)))))..... (-23.04 = -23.43 +   0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,152,304 – 3,152,395
Length 91
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -24.83
Consensus MFE -17.96
Energy contribution -19.93
Covariance contribution 1.97
Combinations/Pair 1.26
Mean z-score -1.63
Structure conservation index 0.72
SVM decision value 0.65
SVM RNA-class probability 0.811719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3152304 91 + 20766785
AGUUUGUGGUAUCCCCGAUGGCCAUGCCUUCUGAUAUAAAGGCGCCUUCUCCGACGCCACCUCCGCCACCAAUGAUAUUCCAGGAUGACUU
((((.((((..((...((.(((...(((((........)))))))).))...))..)))).(((..................))).)))). ( -20.57)
>DroPse_CAF1 38385 79 + 1
CGUUCGUCGUAGCAUCCUCUGCCGCGCCAUCUGAUAUUAUAGUU------------UCACUACCAUCACCCAUGGUGUUUCAAGAUGACUC
...(((((((((......)))).(((((((.((((....(((..------------...)))..))))...))))))).....)))))... ( -16.50)
>DroSec_CAF1 42044 91 + 1
AGUUUGUGGUGUCCCCGAUGGCCAUGCCCUCUGAUAUAAAGGCGCCGUCUCCGACGCUACCUCCGCCACCAAUGAUAUUCCAGGAUGACUU
((((.((((((((...((((((...(((............)))))))))...)))))))).(((..................))).)))). ( -23.67)
>DroSim_CAF1 44076 91 + 1
AGUUUGUGGUGUCCCCGAUGGCCAUGCCUUCUGAUAUAAAGGCGCCAUCUCCGACGCCACCUCCGCCACCAAUGAUAUUCCAGGAUGACUU
((((.((((((((...((((((...(((((........)))))))))))...)))))))).(((..................))).)))). ( -29.67)
>DroEre_CAF1 41604 91 + 1
AGUUCGUGGUGUCCCCGAUGGCAGUGCCUUCUGAUAUUAAGGCGCCAUCUCCAACGCCACCUCCUCCACCCAUGAUAUUCCAGGAUGACUU
.....(((((((....((((((...(((((........)))))))))))....)))))))......((.((.((......)))).)).... ( -27.20)
>DroYak_CAF1 42052 91 + 1
AGUUCGUGGUGUCCCCGAUGGCAGUGCCUUCCGAUAUUAAGGCGCCAUCUCCGACGCCACCUCCUCCACCAAUGAUAUUCCAGGACGACUU
.((((((((((((...((((((...(((((........)))))))))))...))))))))............((......))))))..... ( -31.40)
>consensus
AGUUCGUGGUGUCCCCGAUGGCCAUGCCUUCUGAUAUAAAGGCGCCAUCUCCGACGCCACCUCCGCCACCAAUGAUAUUCCAGGAUGACUU
.....((((((((...((((((...(((((........)))))))))))...))))))))............................... (-17.96 = -19.93 +   1.97)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,152,304 – 3,152,395
Length 91
Sequences 6
Columns 91
Reading direction reverse
Mean pairwise identity 80.07
Mean single sequence MFE -30.13
Consensus MFE -19.50
Energy contribution -19.87
Covariance contribution 0.37
Combinations/Pair 1.30
Mean z-score -1.71
Structure conservation index 0.65
SVM decision value 0.45
SVM RNA-class probability 0.742493
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3152304 91 - 20766785
AAGUCAUCCUGGAAUAUCAUUGGUGGCGGAGGUGGCGUCGGAGAAGGCGCCUUUAUAUCAGAAGGCAUGGCCAUCGGGGAUACCACAAACU
..((((((...(.....)...))))))...(((((((((......)))((((((......))))))...))))))((.....))....... ( -30.20)
>DroPse_CAF1 38385 79 - 1
GAGUCAUCUUGAAACACCAUGGGUGAUGGUAGUGA------------AACUAUAAUAUCAGAUGGCGCGGCAGAGGAUGCUACGACGAACG
..(((((((.((..((((...))))(((((.....------------.)))))....)))))))))(..(((.....)))..)........ ( -20.50)
>DroSec_CAF1 42044 91 - 1
AAGUCAUCCUGGAAUAUCAUUGGUGGCGGAGGUAGCGUCGGAGACGGCGCCUUUAUAUCAGAGGGCAUGGCCAUCGGGGACACCACAAACU
..(((.(((..(.....)...((((((.........((((....))))((((((......))))))...)))))))))))).......... ( -31.20)
>DroSim_CAF1 44076 91 - 1
AAGUCAUCCUGGAAUAUCAUUGGUGGCGGAGGUGGCGUCGGAGAUGGCGCCUUUAUAUCAGAAGGCAUGGCCAUCGGGGACACCACAAACU
..((((((...(.....)...))))))....((((.(((...((((((((((((......))))))...))))))...))).))))..... ( -35.10)
>DroEre_CAF1 41604 91 - 1
AAGUCAUCCUGGAAUAUCAUGGGUGGAGGAGGUGGCGUUGGAGAUGGCGCCUUAAUAUCAGAAGGCACUGCCAUCGGGGACACCACGAACU
...((((((((......)).)))))).....((((.(((...(((((((((((........)))))...))))))...))).))))..... ( -31.90)
>DroYak_CAF1 42052 91 - 1
AAGUCGUCCUGGAAUAUCAUUGGUGGAGGAGGUGGCGUCGGAGAUGGCGCCUUAAUAUCGGAAGGCACUGCCAUCGGGGACACCACGAACU
...((.(((...............))).)).((((.(((...(((((((((((........)))))...))))))...))).))))..... ( -31.86)
>consensus
AAGUCAUCCUGGAAUAUCAUUGGUGGCGGAGGUGGCGUCGGAGAUGGCGCCUUAAUAUCAGAAGGCACGGCCAUCGGGGACACCACAAACU
..(((..(((((.......((((((...((((((.((((...)))).))))))..))))))..(((...))).)))))))).......... (-19.50 = -19.87 +   0.37)

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 09:43:08 2006