Locus 8280

Sequence ID X_DroMel_CAF1
Location 20,600,213 – 20,600,392
Length 179
Max. P 0.997801
window13597 window13598 window13599 window13600

overview

Window 7

Location 20,600,213 – 20,600,313
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.82
Mean single sequence MFE -38.77
Consensus MFE -18.70
Energy contribution -18.18
Covariance contribution -0.52
Combinations/Pair 1.21
Mean z-score -2.15
Structure conservation index 0.48
SVM decision value 1.09
SVM RNA-class probability 0.913325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20600213 100 + 22224390
GGACG--------------AGCGCAGCUGGGAGUGGUGGGCAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCACGGCUUAU
....(--------------(((((((((((..((((((((.((((.....(((((((..........))))....)))....))))))))))------))..))))))))....)))).. ( -39.40)
>DroPse_CAF1 5679 113 + 1
GGUCGGCCGUUGGGGCAUUGUCACAGCU-GGAGUUAUGGAAAUAAAAACUGUCUGCCAUAUCCGUUUGCCGAUUUGAUUAAGUUGUCAGAGG------AGGCUCCCGGAGGACCCAAGAG
(((((((.((((.(((...))).)))).-(...((((....))))...).....)))...((((...(((..((((((......))))))..------.)))...)))).))))...... ( -33.10)
>DroSec_CAF1 4755 99 + 1
GGUCG--------------AGCGCAGCA-GGAGUGGUGGGCAUAAAAACUGUCUGACAUAUCCGCUGGUCGACUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCUUGGCUUAC
(((((--------------((.(((((.-((.((((((((((........(((.(((..........))))))..........)).))))))------))..)).))))))))))))... ( -38.47)
>DroEre_CAF1 4688 105 + 1
GGACG--------------AGCGCAGCU-GGAGUGGUGGGCAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUCGACCAUGCGACCAGCUGCCUUGGCACAC
...((--------------((.((((((-((.(((..(((((.......)))))..)))...(((((((((((..(((......)))..)))))))).))).))))))))))))...... ( -46.30)
>DroYak_CAF1 4827 99 + 1
GGACG--------------AGCGCAGCU-GGAGUGGUGGACAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCUUGGCACAC
...((--------------((.((((((-((.((((((((((.......)))).............((.((((((....)))))).))))))------))..))))))))))))...... ( -36.60)
>consensus
GGACG______________AGCGCAGCU_GGAGUGGUGGGCAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC______GCGACCAGCUGCCUUGGCACAC
.....................((((((..((((((..(((((.......)))))..))).))))))((.((((((....)))))).))..........)))....(((.....))).... (-18.70 = -18.18 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,600,239 – 20,600,353
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.21
Mean single sequence MFE -33.15
Consensus MFE -24.34
Energy contribution -27.96
Covariance contribution 3.62
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.73
SVM decision value 0.64
SVM RNA-class probability 0.807056
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20600239 114 + 22224390
CAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCACGGCUUAUAGCUGGCCAAAAGAAUAGGACAAAUUUCGGGCUUGGUUUU
....((((((((((((.((.(((((((((((....(((......))).....------.)))))))).((((..((.....))))))..........)))...)).))))))..)))))) ( -33.70)
>DroSec_CAF1 4780 114 + 1
CAUAAAAACUGUCUGACAUAUCCGCUGGUCGACUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCUUGGCUUACAGCUGGCCAAGAUAAUAGGACAAAUUUCGGAUUUGGUUUU
....((((((((((((.((.(((((((((((....(((......))).....------.))))))))...(((((((.......)))))))......)))...)).))))))..)))))) ( -37.40)
>DroEre_CAF1 4713 114 + 1
CAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUCGACCAUGCGACCAGCUGCCUUGGCACACAGCGAGCCAAAAUAUUAGGAGCAAUGU------GGGUUUU
............((.((((...(((((((((((..(((......)))..)))))))).)))....(((.(((((((.(.....).)))).......)))))).))))------.)).... ( -33.11)
>DroYak_CAF1 4852 108 + 1
CAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC------GCGACCAGCUGCCUUGGCACACAGCUGGCCAAAAUAAUAGGACAAAUGU------GCGUUUU
....(((((.((...((((.(((((((((((....(((......))).....------.))))))))....(((((.((....))))))).......)))...))))------))))))) ( -28.40)
>consensus
CAUAAAAACUGUCUGACAUAUCCGCUGGUCGAUUUGAUUAAGUUGUCCCAUC______GCGACCAGCUGCCUUGGCACACAGCUGGCCAAAAUAAUAGGACAAAUGU______GGGUUUU
....(((((((((((((((.(((((((((((....(((......)))............))))))))....(((((.........))))).......)))...)))))))))..)))))) (-24.34 = -27.96 +   3.62)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,600,239 – 20,600,353
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.21
Mean single sequence MFE -33.55
Consensus MFE -26.04
Energy contribution -27.10
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.78
SVM decision value 0.65
SVM RNA-class probability 0.811481
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20600239 114 - 22224390
AAAACCAAGCCCGAAAUUUGUCCUAUUCUUUUGGCCAGCUAUAAGCCGUGGCAGCUGGUCGC------GAUGGGACAACUUAAUCAAAUCGACCAGCGGAUAUGUCAGACAGUUUUUAUG
..........(((....((((((((((....(((((((((....((....))))))))))).------)))))))))).....((.....))....)))..................... ( -29.30)
>DroSec_CAF1 4780 114 - 1
AAAACCAAAUCCGAAAUUUGUCCUAUUAUCUUGGCCAGCUGUAAGCCAAGGCAGCUGGUCGC------GAUGGGACAACUUAAUCAAGUCGACCAGCGGAUAUGUCAGACAGUUUUUAUG
.....((.(((((.....(((((((((....(((((((((((........))))))))))).------)))))))))((((....)))).......))))).))................ ( -36.30)
>DroEre_CAF1 4713 114 - 1
AAAACCC------ACAUUGCUCCUAAUAUUUUGGCUCGCUGUGUGCCAAGGCAGCUGGUCGCAUGGUCGAUGGGACAACUUAAUCAAAUCGACCAGCGGAUAUGUCAGACAGUUUUUAUG
.......------((((...(((.........((((.(((((.(....).))))).))))((.((((((((..((........))..))))))))))))).))))............... ( -34.00)
>DroYak_CAF1 4852 108 - 1
AAAACGC------ACAUUUGUCCUAUUAUUUUGGCCAGCUGUGUGCCAAGGCAGCUGGUCGC------GAUGGGACAACUUAAUCAAAUCGACCAGCGGAUAUGUCAGACAGUUUUUAUG
....(((------....((((((((((....(((((((((((.(....).))))))))))).------)))))))))).....((.....))...)))...................... ( -34.60)
>consensus
AAAACCA______AAAUUUGUCCUAUUAUUUUGGCCAGCUGUAAGCCAAGGCAGCUGGUCGC______GAUGGGACAACUUAAUCAAAUCGACCAGCGGAUAUGUCAGACAGUUUUUAUG
(((((............((((((((((....(((((((((((........))))))))))).......))))))))))............(((..........))).....))))).... (-26.04 = -27.10 +   1.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,600,279 – 20,600,392
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.57
Mean single sequence MFE -29.58
Consensus MFE -24.01
Energy contribution -25.07
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -2.73
Structure conservation index 0.81
SVM decision value 2.93
SVM RNA-class probability 0.997801
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20600279 113 - 22224390
AAGAGGCACUUUUAUAAGAAUUAAAAUGAA-UAAAUACAAAAAACCAAGCCCGAAAUUUGUCCUAUUCUUUUGGCCAGCUAUAAGCCGUGGCAGCUGGUCGC------GAUGGGACAACU
..(.(((.(((....)))........((..-......)).........)))).....((((((((((....(((((((((....((....))))))))))).------)))))))))).. ( -30.30)
>DroSec_CAF1 4820 112 - 1
AAGA-GCACUUUUAUAAGAAUUAAAAUGUA-UGAAUACAAAAAACCAAAUCCGAAAUUUGUCCUAUUAUCUUGGCCAGCUGUAAGCCAAGGCAGCUGGUCGC------GAUGGGACAACU
....-(((.(((((.......)))))))).-..........................((((((((((....(((((((((((........))))))))))).------)))))))))).. ( -31.50)
>DroEre_CAF1 4753 114 - 1
AAGAAACGUUUCUAAGAUAAUUAAAAUAAAUUGAAUACAAAAAACCC------ACAUUGCUCCUAAUAUUUUGGCUCGCUGUGUGCCAAGGCAGCUGGUCGCAUGGUCGAUGGGACAACU
.((((....))))................................((------.(((((..((........(((((.(((((.(....).))))).)))))...)).)))))))...... ( -20.30)
>DroYak_CAF1 4892 108 - 1
AAGAAAACAUUUUAAAAGAAUUAAAAUGAAGUGAAUACAAAAAACGC------ACAUUUGUCCUAUUAUUUUGGCCAGCUGUGUGCCAAGGCAGCUGGUCGC------GAUGGGACAACU
.......((((((((.....))))))))..(((.............)------))..((((((((((....(((((((((((.(....).))))))))))).------)))))))))).. ( -36.22)
>consensus
AAGAAACACUUUUAAAAGAAUUAAAAUGAA_UGAAUACAAAAAACCA______AAAUUUGUCCUAUUAUUUUGGCCAGCUGUAAGCCAAGGCAGCUGGUCGC______GAUGGGACAACU
.........................................................((((((((((....(((((((((((........))))))))))).......)))))))))).. (-24.01 = -25.07 +   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 13:00:04 2006