Locus 998

Sequence ID X_DroMel_CAF1
Location 2,900,953 – 2,901,066
Length 113
Max. P 0.995693
window1614 window1615 window1616

overview

Window 4

Location 2,900,953 – 2,901,050
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.94
Mean single sequence MFE -24.02
Consensus MFE -21.07
Energy contribution -21.73
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.88
SVM decision value 0.16
SVM RNA-class probability 0.610405
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2900953 97 + 22224390
-----------------------GGAGAAUCAAAUUGCAAAACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUA
-----------------------...((((((..((((......))))......((((((((((((..((...........))..)))))))))).((((....)))).))))))))... ( -24.60)
>DroPse_CAF1 394691 97 + 1
-----------------------AGAGAAUCAAAUUGCAAAACAGCAGCCAACUGGGAAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAAGAGCCUGAUUUAUA
-----------------------...((((((..((((......))))((....))..((((((((..((...........))..))))))))((.((........)))).))))))... ( -16.80)
>DroEre_CAF1 311390 97 + 1
-----------------------GGAGAAUCAAAUUGCAAAACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUA
-----------------------...((((((..((((......))))......((((((((((((..((...........))..)))))))))).((((....)))).))))))))... ( -24.60)
>DroYak_CAF1 295999 97 + 1
-----------------------GGAGAAUCAAAUUGCAAAACGGCAGCCAUCUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUA
-----------------------...((((((..((((......))))......((((((((((((..((...........))..)))))))))).((((....)))).))))))))... ( -24.60)
>DroAna_CAF1 454231 120 + 1
GGGGGGCACCGCCACCCCACCGAAGAGAAUCAAAUUGCAAAACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUG
(((((((...))).))))........((((((..((((......))))......((((((((((((..((...........))..)))))))))).((((....)))).))))))))... ( -36.70)
>DroPer_CAF1 415192 97 + 1
-----------------------AGAGAAUCAAAUUGCAAAACAGCAGCCAACUGGGAAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAAGAGCCUGAUUUAUA
-----------------------...((((((..((((......))))((....))..((((((((..((...........))..))))))))((.((........)))).))))))... ( -16.80)
>consensus
_______________________AGAGAAUCAAAUUGCAAAACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUA
..........................((((((..((((......))))......((((((((((((..((...........))..)))))))))).((((....)))).))))))))... (-21.07 = -21.73 +   0.67)

alignment

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secondary structure

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Window 5

Location 2,900,970 – 2,901,066
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -26.72
Consensus MFE -23.32
Energy contribution -23.52
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.87
SVM decision value 0.90
SVM RNA-class probability 0.878098
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2900970 96 + 22224390
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGCCCCAGCUCUGGUCC
...((..((((.((((((((((((((..((...........))..)))))))))).((((....))))...............))))...)))))) ( -26.00)
>DroSec_CAF1 287755 96 + 1
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGCCCCAGCUCUGGUCC
...((..((((.((((((((((((((..((...........))..)))))))))).((((....))))...............))))...)))))) ( -26.00)
>DroSim_CAF1 258046 96 + 1
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGCCCCAGCUCUGGUCC
...((..((((.((((((((((((((..((...........))..)))))))))).((((....))))...............))))...)))))) ( -26.00)
>DroEre_CAF1 311407 96 + 1
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGACCCAGCUCUGGUCC
...(((..((....))((((((((((..((...........))..)))))))))).((((....))))))).........((((.......)))). ( -26.60)
>DroYak_CAF1 296016 96 + 1
AACGGCAGCCAUCUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGCCCCAGCUCUGUUCC
(((((.(((.....((((((((((((..((...........))..))))))))((.((((....))))))..........))))..)))))))).. ( -25.90)
>DroAna_CAF1 454271 96 + 1
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUGGCCCCAGUCAGUGGGA
........((((((((((((((((((..((...........))..)))))))))).((((....))))(((........))).)))))...))).. ( -29.80)
>consensus
AACGGCAGCCAACUGGGCAAGCGAAACACGUUUCAAAACCUCGCAUUUCGCUUGCGUCAUUAAAAUGAGCCUGAUUUAUAGCCCCAGCUCUGGUCC
...(((..((....))((((((((((..((...........))..)))))))))))))........((((.((...........))))))...... (-23.32 = -23.52 +   0.19)

alignment

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secondary structure

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Window 6

Location 2,900,970 – 2,901,066
Length 96
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -34.43
Consensus MFE -30.57
Energy contribution -30.85
Covariance contribution 0.28
Combinations/Pair 1.12
Mean z-score -2.48
Structure conservation index 0.89
SVM decision value 2.60
SVM RNA-class probability 0.995693
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2900970 96 - 22224390
GGACCAGAGCUGGGGCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
((.(((..(((((((((........))))............((((((((((((((...........))))))))))))))))))))))...))... ( -34.60)
>DroSec_CAF1 287755 96 - 1
GGACCAGAGCUGGGGCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
((.(((..(((((((((........))))............((((((((((((((...........))))))))))))))))))))))...))... ( -34.60)
>DroSim_CAF1 258046 96 - 1
GGACCAGAGCUGGGGCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
((.(((..(((((((((........))))............((((((((((((((...........))))))))))))))))))))))...))... ( -34.60)
>DroEre_CAF1 311407 96 - 1
GGACCAGAGCUGGGUCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
((.(((..((((((((..((((..........))))..)))((((((((((((((...........))))))))))))))))))))))...))... ( -33.90)
>DroYak_CAF1 296016 96 - 1
GGAACAGAGCUGGGGCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGAUGGCUGCCGUU
((..(((..((((((((........))))............((((((((((((((...........))))))))))))))))))....)))))... ( -32.70)
>DroAna_CAF1 454271 96 - 1
UCCCACUGACUGGGGCCAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
...(((..(((((((((........))))............((((((((((((((...........)))))))))))))))))))..).))..... ( -36.20)
>consensus
GGACCAGAGCUGGGGCUAUAAAUCAGGCUCAUUUUAAUGACGCAAGCGAAAUGCGAGGUUUUGAAACGUGUUUCGCUUGCCCAGUUGGCUGCCGUU
((.....((((((((((........))))............((((((((((((((...........)))))))))))))))))))).....))... (-30.57 = -30.85 +   0.28)

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 09:59:00 2006