Locus 1200

Sequence ID X_DroMel_CAF1
Location 3,581,019 – 3,581,268
Length 249
Max. P 0.884881
window1926 window1927 window1928 window1929

overview

Window 6

Location 3,581,019 – 3,581,109
Length 90
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 84.64
Mean single sequence MFE -16.70
Consensus MFE -12.23
Energy contribution -12.90
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -2.52
Structure conservation index 0.73
SVM decision value 0.93
SVM RNA-class probability 0.884881
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3581019 90 + 22224390
AAACACUCCGGCAAUUUAACUGUCUUACCGGCUGCAUUACCUUUCAAUCAAACAUCAUCAGCCAUAACCAUCAUGGCCAUUGAU-----CCAUUC
.......((((................))))......................((((...(((((.......)))))...))))-----...... ( -11.39)
>DroSec_CAF1 39188 90 + 1
CUUCACUGUGGCAAUUUAACUGUCUUACCGACUGCAUUGCCUUUCAAUCAAACAUCAUCAGCCAUAACCAUCAUGGCCAGUGAU-----CCACUC
..((((((.((((((......(((.....)))...))))))...................(((((.......))))))))))).-----...... ( -21.30)
>DroEre_CAF1 34295 95 + 1
AAACACUUGGGCAAUUUAACUGUCUUGCCGGCUGCAUUGCCCUUCAAUCAAACAUCAUCACCCAUAACCCACAUGGCCAAUGAUCCGAUCCGCUC
........(((((((.((.(((......))).)).)))))))...........(((((...((((.......))))...)))))........... ( -17.40)
>consensus
AAACACUCCGGCAAUUUAACUGUCUUACCGGCUGCAUUGCCUUUCAAUCAAACAUCAUCAGCCAUAACCAUCAUGGCCAAUGAU_____CCACUC
.........((((((......(((.....)))...))))))............(((((..(((((.......)))))..)))))........... (-12.23 = -12.90 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,581,019 – 3,581,109
Length 90
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 84.64
Mean single sequence MFE -26.97
Consensus MFE -18.61
Energy contribution -18.50
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -2.36
Structure conservation index 0.69
SVM decision value 0.57
SVM RNA-class probability 0.785392
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3581019 90 - 22224390
GAAUGG-----AUCAAUGGCCAUGAUGGUUAUGGCUGAUGAUGUUUGAUUGAAAGGUAAUGCAGCCGGUAAGACAGUUAAAUUGCCGGAGUGUUU
......-----((((.(((((((((...))))))))).))))((...(((....)))...))..(((((((..........)))))))....... ( -23.30)
>DroSec_CAF1 39188 90 - 1
GAGUGG-----AUCACUGGCCAUGAUGGUUAUGGCUGAUGAUGUUUGAUUGAAAGGCAAUGCAGUCGGUAAGACAGUUAAAUUGCCACAGUGAAG
......-----.(((((((((((((...)))))))...................((((((((.(((.....))).))...)))))).)))))).. ( -27.00)
>DroEre_CAF1 34295 95 - 1
GAGCGGAUCGGAUCAUUGGCCAUGUGGGUUAUGGGUGAUGAUGUUUGAUUGAAGGGCAAUGCAGCCGGCAAGACAGUUAAAUUGCCCAAGUGUUU
((((((((((((((((((.(((((.....))))).))))))..)))))))...(((((((..(((.(......).)))..)))))))...))))) ( -30.60)
>consensus
GAGUGG_____AUCAAUGGCCAUGAUGGUUAUGGCUGAUGAUGUUUGAUUGAAAGGCAAUGCAGCCGGUAAGACAGUUAAAUUGCCAAAGUGUUU
...........((((..(((((((.....)))))))..))))............((((((..(((.(......).)))..))))))......... (-18.61 = -18.50 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,581,088 – 3,581,189
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.45
Mean single sequence MFE -33.76
Consensus MFE -26.67
Energy contribution -27.05
Covariance contribution 0.38
Combinations/Pair 1.19
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.53
SVM RNA-class probability 0.772076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3581088 101 - 22224390
UCGGCGUGAUUACGUGAGUAAUUCCCAAUGUUCGCCCAUGGGAAGACCAGCUUGAAAGGGUUAAGAUUGAGCCUAAGGUGGAAUGG-----AUCAAUGGCCAUGAU--------------
..(((.(((((((....))..((((((.((......))))))))..(((.(((...(((.(((....))).)))))).)))....)-----))))...))).....-------------- ( -28.90)
>DroSec_CAF1 39257 101 - 1
UCGGCUAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAUGGCAAGACCAGCUUGAAAGGGUUAAGAUUGAGCCUAAGGUGGAGUGG-----AUCACUGGCCAUGAU--------------
..(((((((((((....)))))).(((...((((((...(((..((.((((((....)))))..).))..)))...)))))).)))-----.....))))).....-------------- ( -31.90)
>DroEre_CAF1 34364 106 - 1
UUGGCCAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAAGGGAAGACCAGCUUGAUGGGGUUAAGAUUGAGCCUAGGGUGGAGCGGAUCGGAUCAUUGGCCAUGUG--------------
.((((((((((((....)))))(((...(((((((((..((.....)).......((((.(((....))).)))))))).)))))....)))...)))))))....-------------- ( -38.70)
>DroYak_CAF1 35593 115 - 1
UUGGCCAAGAUACGUGAGUAAUUCCCAAUGUUCACCCAAGGGAAGACCAGCUUAAAAGGGUUAAGAUUGAGCCUAGGGUGGAGCUG-----AUCAUUGGCCAUGAGGCAUCAGGGCUAUG
.(((((((..(((....))).(((((.............)))))((.((((((....(((((.......)))))......))))))-----.)).)))))))...(((......)))... ( -35.52)
>consensus
UCGGCCAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAAGGGAAGACCAGCUUGAAAGGGUUAAGAUUGAGCCUAAGGUGGAGCGG_____AUCAUUGGCCAUGAG______________
..(((((((((((....)))))).......(((((((..((.....))........(((.(((....))).))).)))))))..............)))))................... (-26.67 = -27.05 +   0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,581,149 – 3,581,268
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.20
Mean single sequence MFE -37.65
Consensus MFE -27.64
Energy contribution -29.39
Covariance contribution 1.75
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.73
SVM decision value 0.15
SVM RNA-class probability 0.607265
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3581149 119 - 22224390
UUGACCAGGAGGAAUUUGAAGGAGUUACCCAACCAUCAACGUGUGUUGACUGGGAAUCGAGUUAUUAUGUGAU-UCCCCCUCGGCGUGAUUACGUGAGUAAUUCCCAAUGUUCGCCCAUG
.......((..((((.....((((((((.((...((((.....((((((..((((((((.((....)).))))-))))..))))))))))....)).))))))))....))))..))... ( -33.80)
>DroSec_CAF1 39318 119 - 1
UUGACCAGGAGGAAUUCGGAGGAGUUACCCAACCAUCAACGUGUGUUGACUGGGAAUCGAGUUAUUAUGUGAU-UCCCCCUCGGCUAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAUG
.......((..((((...(.((((((((.......(((.((((.(((((..((((((((.((....)).))))-))))..))))).....))))))))))))))))...))))..))... ( -36.41)
>DroEre_CAF1 34430 119 - 1
UUGACCAGGAGGAAUUUUGAGGAGUUACCCAA-CAUCAACGUGUGUUGGCUGGGAAUCGAGUGAUUAUGUGAUUUCCCCUUUGGCCAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAAG
.......((..((((.(((.((((((((....-..(((.((((..((((((((((((((.((....)).)))))))).....))))))..)))))))))))))))))).))))..))... ( -38.90)
>DroYak_CAF1 35668 118 - 1
UUGACCAGAAGGAAUUUUGAGGAGUUGCCCAA-CAUCAACGUGUGUUGGCUGGGAAUCGAGUGAUUAUGUGAU-UCCCCUUUGGCCAAGAUACGUGAGUAAUUCCCAAUGUUCACCCAAG
...........((((.(((.((((((((....-..(((.(((((.((((((((((((((.((....)).))))-))))....)))))).))))))))))))))))))).))))....... ( -41.50)
>consensus
UUGACCAGGAGGAAUUUGGAGGAGUUACCCAA_CAUCAACGUGUGUUGACUGGGAAUCGAGUGAUUAUGUGAU_UCCCCCUCGGCCAAGUUACGUGAGUAAUUCCCAAUGUUCACCCAAG
.......((..((((.(((.((((((((.......(((.((((..((((((((((((((.((....)).)))).))))....))))))..)))))))))))))))))).))))..))... (-27.64 = -29.39 +   1.75)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:45 2006