Locus 8521

Sequence ID 3L_DroMel_CAF1
Location 22,308,681 – 22,308,841
Length 160
Max. P 0.999873
window13953 window13954 window13955 window13956

overview

Window 3

Location 22,308,681 – 22,308,801
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.00
Mean single sequence MFE -34.62
Consensus MFE -32.91
Energy contribution -32.91
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.27
Structure conservation index 0.95
SVM decision value 0.42
SVM RNA-class probability 0.730695
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22308681 120 + 23771897
UCCAAUCUACUCCCGGCCAUUACGCACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCA
..............(((((...(((...((....)).)))(((..(((((......))))))))........)))))........(((((((..(....)..)))).)))((.....)). ( -34.10)
>DroSec_CAF1 67347 120 + 1
UCCAAUCUACUCCCGGCCAUUACGCACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCA
..............(((((...(((...((....)).)))(((..(((((......))))))))........)))))........(((((((..(....)..)))).)))((.....)). ( -34.10)
>DroSim_CAF1 49389 120 + 1
UCCAAUCUACUCCCGGCCAUUACGCACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCA
..............(((((...(((...((....)).)))(((..(((((......))))))))........)))))........(((((((..(....)..)))).)))((.....)). ( -34.10)
>DroEre_CAF1 65825 120 + 1
UCCAAUCUACGCCCGGCCAUUGCGAACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCA
...............((..(((((((...((((..((((((((....))))...(((..(.(((((.....))))))..)))...))))..))))...)))))))...))((.....)). ( -37.60)
>DroYak_CAF1 43009 120 + 1
UCCCAUCUACUCCCGGCCAUUACGCACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAUCCAGCUUUUGUGCCAAUUUGCAGACAGCGCUACUUGCA
..............(((((...(((...((....)).)))(((..(((((......))))))))........)))))........((((((((........))))).)))((.....)). ( -33.20)
>consensus
UCCAAUCUACUCCCGGCCAUUACGCACACCCACUGGGGCGGGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCA
...........(((((................)))))((((((....))))....(((((.(((((.....))))))........((((((((........))))).)))))))...)). (-32.91 = -32.91 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,308,681 – 22,308,801
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.00
Mean single sequence MFE -41.98
Consensus MFE -37.98
Energy contribution -38.42
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.39
Structure conservation index 0.90
SVM decision value 0.40
SVM RNA-class probability 0.722804
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22308681 120 - 23771897
UGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUGCGUAAUGGCCGGGAGUAGAUUGGA
.((.....))(((.((.((..(((((((((...(((((..((.((((((.....)))))).))......((((....))))...)))))...)))).))))).)).)).)))........ ( -41.00)
>DroSec_CAF1 67347 120 - 1
UGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUGCGUAAUGGCCGGGAGUAGAUUGGA
.((.....))(((.((.((..(((((((((...(((((..((.((((((.....)))))).))......((((....))))...)))))...)))).))))).)).)).)))........ ( -41.00)
>DroSim_CAF1 49389 120 - 1
UGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUGCGUAAUGGCCGGGAGUAGAUUGGA
.((.....))(((.((.((..(((((((((...(((((..((.((((((.....)))))).))......((((....))))...)))))...)))).))))).)).)).)))........ ( -41.00)
>DroEre_CAF1 65825 120 - 1
UGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUUCGCAAUGGCCGGGCGUAGAUUGGA
.((.....)).(.((((((.(((((((.(((....((((....((((((.....)))))).))))..))))))))))(((((..(((.((.(....).)).))).))))))))))).).. ( -43.20)
>DroYak_CAF1 43009 120 - 1
UGCAAGUAGCGCUGUCUGCAAAUUGGCACAAAAGCUGGAUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUGCGUAAUGGCCGGGAGUAGAUGGGA
.((.....)).((((((((...(..((......))..).(.((((((.......((((....))))((((.(((...((((((....)))))).))).)))))))))).))))))))).. ( -43.70)
>consensus
UGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCCCGCCCCAGUGGGUGUGCGUAAUGGCCGGGAGUAGAUUGGA
.((.....))(((.((.((..(((((((((...(((((..((.((((((.....)))))).))......((((....))))...)))))...)))).))))).)).)).)))........ (-37.98 = -38.42 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,308,721 – 22,308,841
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -28.18
Consensus MFE -27.84
Energy contribution -27.68
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.78
Structure conservation index 0.99
SVM decision value 4.33
SVM RNA-class probability 0.999873
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22308721 120 + 23771897
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCAUUAAAUUGCAAAUCCACACAAACACAUUAAAACACAAUUA
(((..(((((......)))))(((((.....))))).........)))((((((...((((((((.....((.....))......))))))))...)))))).................. ( -27.90)
>DroSec_CAF1 67387 120 + 1
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCAUCAAAUUGCAAAUACACACAAACACAUUAAAACACAAUUA
(((..(((((......)))))(((((.....))))).........)))((((((...((((((((.....((.....))......))))))))...)))))).................. ( -27.90)
>DroSim_CAF1 49429 120 + 1
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCAUCAAAUUGCAAAUCCACACAAACACAUUAAAACACAAUUA
(((..(((((......)))))(((((.....))))).........)))((((((...((((((((.....((.....))......))))))))...)))))).................. ( -27.90)
>DroEre_CAF1 65865 120 + 1
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCAUCAAAUUGCAAGUCCACACAAACACAUUAAAACACAAUUA
(((((((((((((.((((...(((((.....)))))......))))...))).))))))).((.....)))))(((((((......)))))))........................... ( -30.40)
>DroYak_CAF1 43049 120 + 1
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAUCCAGCUUUUGUGCCAAUUUGCAGACAGCGCUACUUGCAUCAAAUUGCAAAUCCACACAAACACAUUAAAACACAAUUA
(((..(((((......)))))(((((.....))))).........)))((((((...((((((((.....((.....))......))))))))...)))))).................. ( -26.80)
>consensus
GGCAAUUGCCCAAUUUGGCGAGCCAAUUAUUUUGGCCAACAACCAGCUUUUGUGGCAAUUUGCAGACAGCGCUACUUGCAUCAAAUUGCAAAUCCACACAAACACAUUAAAACACAAUUA
(((..(((((......)))))(((((.....))))).........)))((((((...((((((((.....((.....))......))))))))...)))))).................. (-27.84 = -27.68 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,308,721 – 22,308,841
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -34.20
Consensus MFE -31.74
Energy contribution -31.78
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.93
SVM decision value 1.65
SVM RNA-class probability 0.969869
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22308721 120 - 23771897
UAAUUGUGUUUUAAUGUGUUUGUGUGGAUUUGCAAUUUAAUGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
(((((((.(......(((((((((..((((((((...((.(((.....))).))..))))))))..))))))(((..((((((......))))))..))))))......).))))))).. ( -33.40)
>DroSec_CAF1 67387 120 - 1
UAAUUGUGUUUUAAUGUGUUUGUGUGUAUUUGCAAUUUGAUGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
.....................((((.((((((((......)))))))))))).....((((.(((((.(((....((((....((((((.....)))))).))))..)))))))))))). ( -33.10)
>DroSim_CAF1 49429 120 - 1
UAAUUGUGUUUUAAUGUGUUUGUGUGGAUUUGCAAUUUGAUGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
(((((((.(......(((((((((..((((((((....(.(((.....))))....))))))))..))))))(((..((((((......))))))..))))))......).))))))).. ( -33.50)
>DroEre_CAF1 65865 120 - 1
UAAUUGUGUUUUAAUGUGUUUGUGUGGACUUGCAAUUUGAUGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
.....................((((..(((((((......))))))).)))).....((((.(((((.(((....((((....((((((.....)))))).))))..)))))))))))). ( -35.40)
>DroYak_CAF1 43049 120 - 1
UAAUUGUGUUUUAAUGUGUUUGUGUGGAUUUGCAAUUUGAUGCAAGUAGCGCUGUCUGCAAAUUGGCACAAAAGCUGGAUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
(((((((........((.(((((((.((((((((....(.(((.....))))....)))))))).))))))).))(((.((..((((((.....)))))))))))......))))))).. ( -35.60)
>consensus
UAAUUGUGUUUUAAUGUGUUUGUGUGGAUUUGCAAUUUGAUGCAAGUAGCGCUGUCUGCAAAUUGCCACAAAAGCUGGUUGUUGGCCAAAAUAAUUGGCUCGCCAAAUUGGGCAAUUGCC
...(((((...((((.(((..((((..(((((((......))))))).)))).....))).)))).))))).(((..((((((......))))))..))).(((......)))....... (-31.74 = -31.78 +   0.04)

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 13:17:54 2006