Locus 3969

Sequence ID X_DroMel_CAF1
Location 10,525,935 – 10,526,069
Length 134
Max. P 0.832445
window6524 window6525 window6526 window6527

overview

Window 4

Location 10,525,935 – 10,526,033
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.35
Mean single sequence MFE -21.42
Consensus MFE -7.40
Energy contribution -7.88
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.96
Structure conservation index 0.35
SVM decision value 0.72
SVM RNA-class probability 0.832445
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10525935 98 + 22224390
CAGUGGCAAAUGCAAUUUGCGAAAUUAAAACCGAAAGUAGUAGUGAAAACUUUUCACUGACCACCACCGC---------------------CAAACCAAACUCCUUU-CGGCCAUUGUCA
(((((((...(((.....)))..........((((((.(((((((((.....))))))(.....).....---------------------........))).))))-)))))))))... ( -24.00)
>DroSec_CAF1 57113 98 + 1
CAUUGGCAAAUGCAAUUUGCGAAAUUAAAACCGAAAGUGGUAGUGAAAACUUUUCACCGACCACCAACGC---------------------CAAACCAAACUACUUU-CGACCAUUGUCA
..(((((...(((.....)))...............(((((.(((((.....)))))..)))))....))---------------------))).............-.(((....))). ( -21.80)
>DroSim_CAF1 60743 98 + 1
CAUUGGCAAAUGCAAUUUGCGAAAUUAAAACCGAAAGUAGUAGUGAAAACUUUUCACCGACCACCAACGC---------------------CAAACCAAACUCCUUU-CGACCAUUGUCA
...((((((.(((.....)))..........((((((.(((.(((((.....)))))((........)).---------------------........))).))))-))....)))))) ( -17.50)
>DroEre_CAF1 59107 90 + 1
CACGGGCGAAUGCAAUUUGCGAAAUUAAAACCGAAAGUAGUAGUGACAACUUUUCACCCACCGCCAC-----------------------------CAAACUCCAUU-CGACCAUUGUCA
....((((..(((.....)))...........((((((.((....)).)))))).......))))..-----------------------------...........-.(((....))). ( -14.40)
>DroAna_CAF1 61921 114 + 1
CAUUGGCGAAUGCAAUUUGCGAAAUUAAAACCGAAAGUAGUGG---GAUC-CUUCAGGGACUC-CUCCACUUUGGCCUCCUUUUUGGCCAACUU-CUCAUCUCCAUCCUGGCCAUUGUCA
((.((((....((.....))(((..........(((((.(.((---..((-(.....)))..)-).).)))))((((........))))...))-)..............)))).))... ( -29.40)
>consensus
CAUUGGCAAAUGCAAUUUGCGAAAUUAAAACCGAAAGUAGUAGUGAAAACUUUUCACCGACCACCACCGC_____________________CAAACCAAACUCCUUU_CGACCAUUGUCA
....(((((.(((.((((.((..........)).)))).)))(((((.....))))).........................................................))))). ( -7.40 =  -7.88 +   0.48)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,525,935 – 10,526,033
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.35
Mean single sequence MFE -29.42
Consensus MFE -13.16
Energy contribution -14.96
Covariance contribution 1.80
Combinations/Pair 1.23
Mean z-score -1.81
Structure conservation index 0.45
SVM decision value 0.14
SVM RNA-class probability 0.604170
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10525935 98 - 22224390
UGACAAUGGCCG-AAAGGAGUUUGGUUUG---------------------GCGGUGGUGGUCAGUGAAAAGUUUUCACUACUACUUUCGGUUUUAAUUUCGCAAAUUGCAUUUGCCACUG
...(((...((.-...))...)))...((---------------------((((.((((((.((((((.....)))))))))))).))............((.....))....))))... ( -27.80)
>DroSec_CAF1 57113 98 - 1
UGACAAUGGUCG-AAAGUAGUUUGGUUUG---------------------GCGUUGGUGGUCGGUGAAAAGUUUUCACUACCACUUUCGGUUUUAAUUUCGCAAAUUGCAUUUGCCAAUG
...((.(((.((-((.(((((((((((.(---------------------.((..((((((.((((((.....))))))))))))..)).)...)))....)))))))).))))))).)) ( -29.90)
>DroSim_CAF1 60743 98 - 1
UGACAAUGGUCG-AAAGGAGUUUGGUUUG---------------------GCGUUGGUGGUCGGUGAAAAGUUUUCACUACUACUUUCGGUUUUAAUUUCGCAAAUUGCAUUUGCCAAUG
...(((...((.-...))...)))..(((---------------------(((..((((((.((((((.....))))))))))))..)............((.....))....))))).. ( -25.90)
>DroEre_CAF1 59107 90 - 1
UGACAAUGGUCG-AAUGGAGUUUG-----------------------------GUGGCGGUGGGUGAAAAGUUGUCACUACUACUUUCGGUUUUAAUUUCGCAAAUUGCAUUCGCCCGUG
.....((((.((-((((.((((((-----------------------------((((.((..(.(....).)..)).))))......(((........))))))))).)))))).)))). ( -27.40)
>DroAna_CAF1 61921 114 - 1
UGACAAUGGCCAGGAUGGAGAUGAG-AAGUUGGCCAAAAAGGAGGCCAAAGUGGAG-GAGUCCCUGAAG-GAUC---CCACUACUUUCGGUUUUAAUUUCGCAAAUUGCAUUCGCCAAUG
...((.((((..(((((.((.((.(-(((((((((........))))(((((((.(-(..(((.....)-))..---)).))))))).......)))))).))..)).))))))))).)) ( -36.10)
>consensus
UGACAAUGGUCG_AAAGGAGUUUGGUUUG_____________________GCGGUGGUGGUCGGUGAAAAGUUUUCACUACUACUUUCGGUUUUAAUUUCGCAAAUUGCAUUUGCCAAUG
...((.((((.........................................((..((((((.((((((.....))))))))))))..))...........((.....))....)))).)) (-13.16 = -14.96 +   1.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,525,975 – 10,526,069
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 88.65
Mean single sequence MFE -19.55
Consensus MFE -14.65
Energy contribution -15.15
Covariance contribution 0.50
Combinations/Pair 1.20
Mean z-score -1.68
Structure conservation index 0.75
SVM decision value 0.28
SVM RNA-class probability 0.666279
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10525975 94 + 22224390
UAGUGAAAACUUUUCACUGACCACCACCGCCAAACCAAACUCCUUUCGGCCAUUGUCAGUCGUCUUAUCGGCGACAGCAAUCAUUUCUGCGGCU
(((((((.....))))))).........(((................(((....))).((((((.....)))))).(((........)))))). ( -23.10)
>DroSec_CAF1 57153 94 + 1
UAGUGAAAACUUUUCACCGACCACCAACGCCAAACCAAACUACUUUCGACCAUUGUCAGUCGUCUUAUCGGUGACAGCAAUCAUUUCUGCGGCU
..(((((.....)))))...........(((......................(((((.(((......))))))))(((........)))))). ( -18.10)
>DroSim_CAF1 60783 94 + 1
UAGUGAAAACUUUUCACCGACCACCAACGCCAAACCAAACUCCUUUCGACCAUUGUCAGUCGUCUUAUCGGUGACAGCAAUCAUUUCUGCGGCU
..(((((.....)))))...........(((......................(((((.(((......))))))))(((........)))))). ( -18.10)
>DroEre_CAF1 59147 86 + 1
UAGUGACAACUUUUCACCCACCGCCAC--------CAAACUCCAUUCGACCAUUGUCAGUCGCCUUAUCGGUGGCAGCCAUCAUUUCUGCGGCC
..((((.......))))...((((...--------............(((....))).((((((.....)))))).............)))).. ( -18.90)
>consensus
UAGUGAAAACUUUUCACCGACCACCAACGCCAAACCAAACUCCUUUCGACCAUUGUCAGUCGUCUUAUCGGUGACAGCAAUCAUUUCUGCGGCU
..(((((.....)))))...........(((................(((....))).((((((.....)))))).(((........)))))). (-14.65 = -15.15 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,525,975 – 10,526,069
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 88.65
Mean single sequence MFE -29.80
Consensus MFE -19.01
Energy contribution -20.07
Covariance contribution 1.06
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.64
SVM decision value 0.04
SVM RNA-class probability 0.555204
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10525975 94 - 22224390
AGCCGCAGAAAUGAUUGCUGUCGCCGAUAAGACGACUGACAAUGGCCGAAAGGAGUUUGGUUUGGCGGUGGUGGUCAGUGAAAAGUUUUCACUA
............(((..(..(((((((..((((..((......))((....)).))))...)))))))..)..)))((((((.....)))))). ( -32.70)
>DroSec_CAF1 57153 94 - 1
AGCCGCAGAAAUGAUUGCUGUCACCGAUAAGACGACUGACAAUGGUCGAAAGUAGUUUGGUUUGGCGUUGGUGGUCGGUGAAAAGUUUUCACUA
...........(((..(((.((((((((..((((.(..((((....(....)....)))..)..)))))....))))))))..)))..)))... ( -26.10)
>DroSim_CAF1 60783 94 - 1
AGCCGCAGAAAUGAUUGCUGUCACCGAUAAGACGACUGACAAUGGUCGAAAGGAGUUUGGUUUGGCGUUGGUGGUCGGUGAAAAGUUUUCACUA
...........(((..(((.((((((((..((((.(..((((...((....))...)))..)..)))))....))))))))..)))..)))... ( -27.60)
>DroEre_CAF1 59147 86 - 1
GGCCGCAGAAAUGAUGGCUGCCACCGAUAAGGCGACUGACAAUGGUCGAAUGGAGUUUG--------GUGGCGGUGGGUGAAAAGUUGUCACUA
(((((((....)).)))))((((((((..(..(((((......)))))..).....)))--------)))))....(((((.......))))). ( -32.80)
>consensus
AGCCGCAGAAAUGAUUGCUGUCACCGAUAAGACGACUGACAAUGGUCGAAAGGAGUUUGGUUUGGCGGUGGUGGUCGGUGAAAAGUUUUCACUA
...........(((..(((..(((((((...((.((((.(((...((....))...)))......)))).)).)))))))...)))..)))... (-19.01 = -20.07 +   1.06)

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 11:13:11 2006