Locus 3042

Sequence ID 2L_DroMel_CAF1
Location 8,679,094 – 8,679,252
Length 158
Max. P 0.975248
window4839 window4840 window4841 window4842

overview

Window 9

Location 8,679,094 – 8,679,214
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.90
Mean single sequence MFE -37.62
Consensus MFE -29.93
Energy contribution -29.93
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.24
Structure conservation index 0.80
SVM decision value 0.15
SVM RNA-class probability 0.607930
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8679094 120 + 22407834
UUUUACGAAAUUGAUGCCAAGUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGUGAGAGAUUCGUUUAAUUUUUUGU
(((((((...(((....))).((((((((........((((......(((((.......))))).))))((((.......))))))))))))..)))))))................... ( -35.50)
>DroPse_CAF1 1872 114 + 1
UUUGACGGCGGGAGAACCACAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUUCCA---AUUAGUUUUAUUUUU---
..(((((((((((.((((((((.((....)).)).))))))....).)))))).))))..(((....)))((..((...(((((...)))))))..)).---...............--- ( -40.00)
>DroEre_CAF1 2371 114 + 1
UUGUACAAAGGCAGUACCAAGUCCUCGAUAGUUUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGCGAGCGAUUCGUAUU--UUU----
..((((...((.....)).((((((((...(((............(((((.((((.....)))).(((.((((.......))))))))))))))).)))).)))).)))).--...---- ( -35.40)
>DroYak_CAF1 2150 113 + 1
UUGUACCAAAGUA-CACCAAGUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGCGAGUGAAUCGUAUU--UAU----
.(((((....)))-)).....((((((((........((((......(((((.......))))).))))((((.......))))))))))))(((((((.....)))))))--...---- ( -39.40)
>DroAna_CAF1 2694 106 + 1
UUCUACCGAUUGGAUUCCAUGUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGG--------------UUAAUUUUUUUU
..(((.(((..((((.....))))))).)))......((((((..(((((.((((.....)))).(((.((((.......))))))))))))..--------------))))))...... ( -35.40)
>DroPer_CAF1 1871 114 + 1
CUUGACGGCGGGAGAACCACAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUUCCA---AUUUGUUUUAUUUUU---
..(((((((((((.((((((((.((....)).)).))))))....).)))))).))))..(((....)))((..((...(((((...)))))))..)).---...............--- ( -40.00)
>consensus
UUUUACGAAGGGAGUACCAAGUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGCGA___AUUCGUUUUAUUUUU___
.....................((((((((........((((......(((((.......))))).))))((((.......))))))))))))............................ (-29.93 = -29.93 +   0.00)

alignment

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secondary structure

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Window 0

Location 8,679,094 – 8,679,214
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.90
Mean single sequence MFE -34.68
Consensus MFE -27.33
Energy contribution -27.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.79
SVM decision value 0.75
SVM RNA-class probability 0.840273
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8679094 120 - 22407834
ACAAAAAAUUAAACGAAUCUCUCACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACUUGGCAUCAAUUUCGUAAAA
............(((((.......((..(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..))........))))).... ( -33.26)
>DroPse_CAF1 1872 114 - 1
---AAAAAUAAAACUAAU---UGGAAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUGUGGUUCUCCCGCCGUCAAA
---...............---.((.....)).((.((((..((((.....))))..))))))((((.(((((((.....((((((....((....))...)))))).))))))))))).. ( -37.30)
>DroEre_CAF1 2371 114 - 1
----AAA--AAUACGAAUCGCUCGCGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAAACUAUCGAGGACUUGGUACUGCCUUUGUACAA
----...--....(((.((.((((.((.((((((.(((((.......)))))(((........)))...)))))).))((.....))......)))))).)))((((.......)))).. ( -33.00)
>DroYak_CAF1 2150 113 - 1
----AUA--AAUACGAUUCACUCGCAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACUUGGUG-UACUUUGGUACAA
----...--....(((.....)))((..(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..)).((-(((....))))). ( -34.30)
>DroAna_CAF1 2694 106 - 1
AAAAAAAAUUAA--------------CCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACAUGGAAUCCAAUCGGUAGAA
............--------------..((((((.(((((.......)))))(((........)))...))))))..............((((((((((.......)))..))))))).. ( -32.90)
>DroPer_CAF1 1871 114 - 1
---AAAAAUAAAACAAAU---UGGAAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUGUGGUUCUCCCGCCGUCAAG
---...............---.((.....)).((.((((..((((.....))))..))))))((((.(((((((.....((((((....((....))...)))))).))))))))))).. ( -37.30)
>consensus
___AAAAAUAAAACGAAU___UCGCAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACUUGGUACUCCCUCCGUAAAA
............................(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..................... (-27.33 = -27.33 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,679,134 – 8,679,252
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.17
Mean single sequence MFE -35.17
Consensus MFE -26.79
Energy contribution -26.57
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.50
Structure conservation index 0.76
SVM decision value 1.75
SVM RNA-class probability 0.975248
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8679134 118 + 22407834
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGUGAGAGAUUCGUUUAAUUUUUUGU--UGUUCCUCUCUUAGAAUCUUUUUUGUUUUGCUUAUUUA
.(((((((((.((((.....)))).(((.((((.......))))))))))))((((.(((((((((..............--.............))))))))).)))).))))...... ( -36.53)
>DroSec_CAF1 2367 119 + 1
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGUGAGAGAUUCGUUUUAUUUUUUGUGUUUUUCCUCUCUUAGAAUCUUU-AUGUUUGGCUUAUUUA
.......(((((.......))))).(((.((((.......)))))))((..(((((..((((((.......))))))..)))))..))...............-................ ( -35.50)
>DroSim_CAF1 2320 116 + 1
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGCGAGAGGAUCGUUUUAUUUUUUGUGU---UCCUCUCUUAGAAUCUUU-AUGUUUGGCUUAUUUA
..((.(((((.((((.....)))).(((.((((.......)))))))))))).))(((((((((.((............)).---)))))))...((((....-..)))).))....... ( -38.40)
>DroEre_CAF1 2411 103 + 1
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGCGAGCGAUUCGUAUU--UUU---------UUCUCUCUCAGAA----U-AUG-UUUGCUUAUUUA
..((.(((((.((((.....)))).(((.((((.......)))))))))))).))..((((((..((((((--((.---------.........))))----)-)))-.))))))..... ( -37.00)
>DroYak_CAF1 2189 105 + 1
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGCGAGUGAAUCGUAUU--UAU---------UUGUUUUUCCUCU---UU-UUGUUUUGCUUAUUUA
.((((..(((((.......))))).(((.((((.......)))))))(((((((.((((((((((...)))--)))---------)))).))))))).---..-......))))...... ( -36.40)
>DroPer_CAF1 1911 91 + 1
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUUCCA---AUUUGUUUUAUUUUU-----------CUUCAGAGAAU--UU-AAUU------------
.....(((((.((((.....)))).(((.((((.......)))))))))))).......---...........((((-----------(....))))).--..-....------------ ( -27.20)
>consensus
UAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGCGAGAGAUUCGUUUUAUUUUU________UCCUCUCUUAGAAU__UU_AUGUUUUGCUUAUUUA
..((.(((((.((((.....)))).(((.((((.......)))))))))))).))................................................................. (-26.79 = -26.57 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,679,134 – 8,679,252
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.17
Mean single sequence MFE -29.32
Consensus MFE -23.67
Energy contribution -24.00
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.81
SVM decision value 1.61
SVM RNA-class probability 0.967283
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8679134 118 - 22407834
UAAAUAAGCAAAACAAAAAAGAUUCUAAGAGAGGAACA--ACAAAAAAUUAAACGAAUCUCUCACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
............................((((((....--.................))))))..((.((((((.(((((.......)))))(((........)))...)))))).)).. ( -30.30)
>DroSec_CAF1 2367 119 - 1
UAAAUAAGCCAAACAU-AAAGAUUCUAAGAGAGGAAAAACACAAAAAAUAAAACGAAUCUCUCACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
................-...........((((((.......................))))))..((.((((((.(((((.......)))))(((........)))...)))))).)).. ( -30.20)
>DroSim_CAF1 2320 116 - 1
UAAAUAAGCCAAACAU-AAAGAUUCUAAGAGAGGA---ACACAAAAAAUAAAACGAUCCUCUCGCGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
................-...........(((((((---.(..............).)))))))..((.((((((.(((((.......)))))(((........)))...)))))).)).. ( -35.54)
>DroEre_CAF1 2411 103 - 1
UAAAUAAGCAAA-CAU-A----UUCUGAGAGAGAA---------AAA--AAUACGAAUCGCUCGCGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
.......((...-((.-.----...)).(((.((.---------...--........)).)))))((.((((((.(((((.......)))))(((........)))...)))))).)).. ( -29.00)
>DroYak_CAF1 2189 105 - 1
UAAAUAAGCAAAACAA-AA---AGAGGAAAAACAA---------AUA--AAUACGAUUCACUCGCAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
................-..---.((((((......---------...--.......))).))).....((((((.(((((.......)))))(((........)))...))))))..... ( -26.09)
>DroPer_CAF1 1911 91 - 1
------------AAUU-AA--AUUCUCUGAAG-----------AAAAAUAAAACAAAU---UGGAAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
------------....-..--.((((....))-----------)).............---(((.((((((((..(((((.......)))))(((........))).)).)))))).))) ( -24.80)
>consensus
UAAAUAAGCAAAACAU_AA__AUUCUAAGAGAGGA________AAAAAUAAAACGAAUCUCUCGCGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUA
.................................................................((.((((((.(((((.......)))))(((........)))...)))))).)).. (-23.67 = -24.00 +   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 10:42:54 2006