Locus 4176

Sequence ID 2L_DroMel_CAF1
Location 11,972,383 – 11,972,581
Length 198
Max. P 0.999782
window6597 window6598 window6599 window6600 window6601 window6602

overview

Window 7

Location 11,972,383 – 11,972,478
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 90.42
Mean single sequence MFE -25.66
Consensus MFE -19.54
Energy contribution -20.82
Covariance contribution 1.28
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.76
SVM decision value 0.84
SVM RNA-class probability 0.863269
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972383 95 + 22407834
GAAUAACAGCGGCAGAACAUGCUGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCU
.......((((((((..((((..(((..((((((((....))).)))))..)))..))))))))(((((((..((....))..))))))).)))) ( -27.00)
>DroSec_CAF1 191760 95 + 1
GAACAAAAGCGGCAGAACAUGCUGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCU
.......((((((((..((((..(((..((((((((....))).)))))..)))..))))))))(((((((..((....))..))))))).)))) ( -27.00)
>DroSim_CAF1 158122 95 + 1
GAACAACAGCGGCAGAACAUGCUGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCU
.......((((((((..((((..(((..((((((((....))).)))))..)))..))))))))(((((((..((....))..))))))).)))) ( -27.00)
>DroEre_CAF1 166455 95 + 1
GAACAACAGCGUCGGAAAGUGCAGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGGUCGCCACCGUUAGACGCU
.......((((((.......(((((....)...(((((((..(....)..)))))))...)))).((((((..((....))..)))))))))))) ( -28.20)
>DroYak_CAF1 163214 81 + 1
GAACA--------------UGCAGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGUUCGCCACCGUUAGACGCU
.....--------------.(((((....)...(((((((..(....)..)))))))...))))(((((((..((....))..)))))))..... ( -19.10)
>consensus
GAACAACAGCGGCAGAACAUGCUGAGAAAUAAAGAAAAACUUCAUUUGUCGUUUUUCAUGCUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCU
........((((((......((.((.((((.(((.....))).)))).))))......))))))(((((((..((....))..)))))))..... (-19.54 = -20.82 +   1.28)

alignment

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secondary structure

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Window 8

Location 11,972,383 – 11,972,478
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -26.76
Consensus MFE -22.26
Energy contribution -22.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.83
SVM decision value 2.71
SVM RNA-class probability 0.996561
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972383 95 - 22407834
AGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCAGCAUGUUCUGCCGCUGUUAUUC
((((..((((((..((....))..)))))).((((((((......((.((((((((.....)))))))).))..))))..))))))))....... ( -26.80)
>DroSec_CAF1 191760 95 - 1
AGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCAGCAUGUUCUGCCGCUUUUGUUC
((((..((((((..((....))..)))))).((((((((......((.((((((((.....)))))))).))..))))..))))))))....... ( -26.20)
>DroSim_CAF1 158122 95 - 1
AGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCAGCAUGUUCUGCCGCUGUUGUUC
((((..((((((..((....))..)))))).((((((((......((.((((((((.....)))))))).))..))))..))))))))....... ( -26.80)
>DroEre_CAF1 166455 95 - 1
AGCGUCUAACGGUGGCGACCGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCUGCACUUUCCGACGCUGUUGUUC
((((((((((((.(((....))).)))))).((((...(((((((..(....)..))))))).........)))).......))))))....... ( -30.00)
>DroYak_CAF1 163214 81 - 1
AGCGUCUAACGGUGGCGAACGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCUGCA--------------UGUUC
...(..((((((.(((....))).))))))..)((((((......((.((((((((.....)))))))).))..))--------------)))). ( -24.00)
>consensus
AGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAGCAUGAAAAACGACAAAUGAAGUUUUUCUUUAUUUCUCAGCAUGUUCUGCCGCUGUUGUUC
.(((..((((((..((....))..))))))..)............((.((((((((.....)))))))).)).)).................... (-22.26 = -22.26 +  -0.00)

alignment

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secondary structure

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Window 9

Location 11,972,443 – 11,972,545
Length 102
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 90.88
Mean single sequence MFE -32.96
Consensus MFE -25.28
Energy contribution -25.68
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.77
SVM decision value 1.24
SVM RNA-class probability 0.934628
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972443 102 + 22407834
CUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUA----------UGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUCGACGGCGAUCCCAACCAAA
.........((..(.((((((...(((((((.((((.......((....(----------((((((....)))))))))......))))))).)))))))))).)..))... ( -31.12)
>DroSec_CAF1 191820 102 + 1
CUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUA----------UGCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAA
....(((((((..((....))..))))))).(((((((...........(----------((((((....)))))))..((........)).)).)))))............ ( -27.30)
>DroSim_CAF1 158182 102 + 1
CUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUA----------UGCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAA
....(((((((..((....))..))))))).(((((((...........(----------((((((....)))))))..((........)).)).)))))............ ( -27.30)
>DroEre_CAF1 166515 112 + 1
CUGCUUAACGGAAGCGGUCGCCACCGUUAGACGCUGGAUCCAAAGCUAUAUGCAGCUAUAUGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUGGCCGGCGAUCCCGGCCAAA
..(..((((((..((....))..))))))..)(((((......((....(((((((((((......))))))))))))).....)))))..(((((((.....))))))).. ( -45.80)
>DroYak_CAF1 163260 107 + 1
CUGCUUAACGGAAGCGUUCGCCACCGUUAGACGCUGGAUCCAAAGCUAUA-----CUCUAAGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUUGCCGGCGAUCCCAGCCAAA
..(..((((((..((....))..))))))..)(((((.............-----......(((((....)))))......(((((.((....)).)).))).))))).... ( -33.30)
>consensus
CUGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUA__________UGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUUGCCGGCGAUCCCAACCAAA
....(((((((..((....))..))))))).(((((.........................(((((....)))))..(((.....))).......)))))............ (-25.28 = -25.68 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,972,443 – 11,972,545
Length 102
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 90.88
Mean single sequence MFE -43.78
Consensus MFE -37.74
Energy contribution -37.74
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -3.21
Structure conservation index 0.86
SVM decision value 4.07
SVM RNA-class probability 0.999782
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972443 102 - 22407834
UUUGGUUGGGAUCGCCGUCGAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCA----------UAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAG
...(((((.((((((((((.(((((((........(((((((....))))))----------).))))))).))))..))(.....))))).)))))((((.....)))).. ( -38.60)
>DroSec_CAF1 191820 102 - 1
UUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCA----------UAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAG
....(((((((((.(((((....))))))))))..(((((((....))))))----------).............))))(..((((((..((....))..))))))..).. ( -38.30)
>DroSim_CAF1 158182 102 - 1
UUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCA----------UAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAG
....(((((((((.(((((....))))))))))..(((((((....))))))----------).............))))(..((((((..((....))..))))))..).. ( -38.30)
>DroEre_CAF1 166515 112 - 1
UUUGGCCGGGAUCGCCGGCCAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUGCAUAUAGCUUUGGAUCCAGCGUCUAACGGUGGCGACCGCUUCCGUUAAGCAG
(((((((((.....)))))))))(((((.(((((((((((((((((......))))))))))......))))))))))))(..((((((.(((....))).))))))..).. ( -58.40)
>DroYak_CAF1 163260 107 - 1
UUUGGCUGGGAUCGCCGGCAAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCUUAGAG-----UAUAGCUUUGGAUCCAGCGUCUAACGGUGGCGAACGCUUCCGUUAAGCAG
....(((((((((.(((((....)))))))))).((((((((....)))))((((((-----.....)))))))))))))(..((((((.(((....))).))))))..).. ( -45.30)
>consensus
UUUGGUUGGGAUCGCCGGCAAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCA__________UAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCAG
....(((((((((.(((((....))))))))))....(((((....))))).........................))))(..((((((..((....))..))))))..).. (-37.74 = -37.74 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,972,478 – 11,972,581
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -27.30
Consensus MFE -26.93
Energy contribution -26.93
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.99
SVM decision value 1.48
SVM RNA-class probability 0.957673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972478 103 + 22407834
GCAUCCAAAGCUAUAUGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUCGACGGCGAUCCCAACCAAAUGCAAUUAGUUGCAGCAACAAACUGCAGCUGCUGCU
.........(((..(((((((....)))))))(((.....)))........)))..............(((..(((((((((.......))))))))).))). ( -28.10)
>DroSec_CAF1 191855 103 + 1
GCAUCCAAAGCUAUAUGCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAAUGCAAUUAGUUGCAGCAACAAACUGCAGCUGCUGCU
(((......((...(((((((....))))))).((.(((((..........)).)))..)).......))...(((((((((.......))))))))).))). ( -26.90)
>DroSim_CAF1 158217 103 + 1
GCAUCCAAAGCUAUAUGCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAAUGCAAUUAGUUGCAGCAACAAACUGCAGCUGCUGCU
(((......((...(((((((....))))))).((.(((((..........)).)))..)).......))...(((((((((.......))))))))).))). ( -26.90)
>consensus
GCAUCCAAAGCUAUAUGCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAAUGCAAUUAGUUGCAGCAACAAACUGCAGCUGCUGCU
(((......((...(((((((....))))))).((.(((((..(....)..)).)))..)).......))...(((((((((.......))))))))).))). (-26.93 = -26.93 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,972,478 – 11,972,581
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 98.06
Mean single sequence MFE -42.83
Consensus MFE -42.87
Energy contribution -43.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -4.27
Structure conservation index 1.00
SVM decision value 2.18
SVM RNA-class probability 0.989771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11972478 103 - 22407834
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGUCGAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUUGGAUGC
.((((((((........))))))))........((((((((((((((((.(((.(....).))))))))..(((((((....))))))).)))))..)))))) ( -41.90)
>DroSec_CAF1 191855 103 - 1
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUUGGAUGC
.((((((((........))))))))........((((((((((((((((.(((((....))))))))))..(((((((....))))))).)))))..)))))) ( -43.30)
>DroSim_CAF1 158217 103 - 1
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUUGGAUGC
.((((((((........))))))))........((((((((((((((((.(((((....))))))))))..(((((((....))))))).)))))..)))))) ( -43.30)
>consensus
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUUGGAUGC
.((((((((........))))))))........((((((((((((((((.(((((....))))))))))..(((((((....))))))).)))))..)))))) (-42.87 = -43.20 +   0.33)

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 11:11:40 2006