Locus 822

Sequence ID 3L_DroMel_CAF1
Location 2,505,112 – 2,505,240
Length 128
Max. P 0.974062
window1263 window1264 window1265

overview

Window 3

Location 2,505,112 – 2,505,203
Length 91
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 90.27
Mean single sequence MFE -18.96
Consensus MFE -16.12
Energy contribution -17.36
Covariance contribution 1.24
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 1.72
SVM RNA-class probability 0.974062
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2505112 91 + 23771897
GAUUGCGCUCGAAUUACACUUAACACAAAUUUCAUUUGAAUAAACUAAAUG---------GCCAAAGGAGACGGGCUGCAUAAUCAGCAAAAAAAAAAAA
(((((.((........................((((((.......))))))---------(((...(....).))).)).)))))............... ( -15.20)
>DroSec_CAF1 128211 91 + 1
GAUUGCGCUCGAAUUACACUUAACACAAUUUUCAUUUGAAUAAACUAAAUGAAAUGCACGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA---------
..((((........................((((((((.......))))))))(((((..(((...(....).)))))))).....)))).--------- ( -20.60)
>DroSim_CAF1 123546 90 + 1
GAUUGCGCUCGAA-UACACUUAACACAAAUUUCAUUUGAAUAAACUAAAUGGAAUGCACGGCCAAAGGAGACGGGAUGCAUAAUCAGCAAA---------
..((((.......-................((((((((.......))))))))(((((...((...(....).)).))))).....)))).--------- ( -17.70)
>DroEre_CAF1 128763 91 + 1
GAUUGCGCUCGAAUUACACUUAACACAAAUUUCAUUUGAAUAAACUAAAUGAAAUGCAUGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA---------
(((((.((....................((((((((((.......))))))))))....((((...(....).)))))).)))))......--------- ( -20.90)
>DroYak_CAF1 127198 91 + 1
GAUUGCGCUCGAAUUACACUUAACACAAAUUUCAUUUGAAUAAACUAAAUGGAAUGCAUGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA---------
(((((.((....................((((((((((.......))))))))))....((((...(....).)))))).)))))......--------- ( -20.40)
>consensus
GAUUGCGCUCGAAUUACACUUAACACAAAUUUCAUUUGAAUAAACUAAAUGAAAUGCACGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA_________
(((((.((....................((((((((((.......))))))))))....((((...(....).)))))).)))))............... (-16.12 = -17.36 +   1.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,505,148 – 2,505,240
Length 92
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 89.26
Mean single sequence MFE -16.84
Consensus MFE -13.34
Energy contribution -13.58
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.79
SVM decision value 0.79
SVM RNA-class probability 0.851494
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2505148 92 + 23771897
UGAAUAAACUAAAUG---------GCCAAAGGAGACGGGCUGCAUAAUCAGCAAAAAAAAAAAAAAAACUCAUUAAAAUGUUUAAUCAGGAAAAUGGGUGG
..............(---------(((...(....).))))((.......))...............(((((((....((......))....))))))).. ( -15.20)
>DroSec_CAF1 128247 91 + 1
UGAAUAAACUAAAUGAAAUGCACGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA----------AAACUCAUUAAAAUGUUUAAUCAGGAAAAUGGGUGG
.............(((.(((((..(((...(....).))))))))..))).....----------..(((((((....((......))....))))))).. ( -18.60)
>DroSim_CAF1 123581 91 + 1
UGAAUAAACUAAAUGGAAUGCACGGCCAAAGGAGACGGGAUGCAUAAUCAGCAAA----------AAACUCAUUAAAAUGUUUAAUCAGGAAAAUGGGUGG
.................(((((...((...(....).)).)))))..........----------..(((((((....((......))....))))))).. ( -15.50)
>DroEre_CAF1 128799 91 + 1
UGAAUAAACUAAAUGAAAUGCAUGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA----------AAACUCAUUAAAAUGUUUAAUCACGAAAAUGGGUUG
.............(((.(((((..(((...(....).))))))))..))).....----------.((((((((....((......))....)))))))). ( -18.40)
>DroYak_CAF1 127234 91 + 1
UGAAUAAACUAAAUGGAAUGCAUGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA----------AAACUCAUUAAAAUGUUUAAUCACGAAAAUGGCUGG
.................(((((..(((...(....).))))))))...((((...----------......(((((.....)))))..........)))). ( -16.51)
>consensus
UGAAUAAACUAAAUGAAAUGCACGGCCAAAGGAGACGGGCUGCAUAAUCAGCAAA__________AAACUCAUUAAAAUGUUUAAUCAGGAAAAUGGGUGG
(((.(((((..(((((........(((...(....).)))(((.......)))................))))).....))))).)))............. (-13.34 = -13.58 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,505,148 – 2,505,240
Length 92
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 89.26
Mean single sequence MFE -14.70
Consensus MFE -10.80
Energy contribution -11.60
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.73
SVM decision value 0.02
SVM RNA-class probability 0.542716
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2505148 92 - 23771897
CCACCCAUUUUCCUGAUUAAACAUUUUAAUGAGUUUUUUUUUUUUUUUUGCUGAUUAUGCAGCCCGUCUCCUUUGGC---------CAUUUAGUUUAUUCA
..............((.(((((...........................((((......))))..(((......)))---------......))))).)). ( -11.50)
>DroSec_CAF1 128247 91 - 1
CCACCCAUUUUCCUGAUUAAACAUUUUAAUGAGUUU----------UUUGCUGAUUAUGCAGCCCGUCUCCUUUGGCCGUGCAUUUCAUUUAGUUUAUUCA
..............((.(((((....((((.(((..----------...))).))))(((((((.(......).)))..)))).........))))).)). ( -15.30)
>DroSim_CAF1 123581 91 - 1
CCACCCAUUUUCCUGAUUAAACAUUUUAAUGAGUUU----------UUUGCUGAUUAUGCAUCCCGUCUCCUUUGGCCGUGCAUUCCAUUUAGUUUAUUCA
..............((.(((((....((((.(((..----------...))).))))(((((...(((......))).))))).........))))).)). ( -15.90)
>DroEre_CAF1 128799 91 - 1
CAACCCAUUUUCGUGAUUAAACAUUUUAAUGAGUUU----------UUUGCUGAUUAUGCAGCCCGUCUCCUUUGGCCAUGCAUUUCAUUUAGUUUAUUCA
.............(((.(((((....((((.(((..----------...))).))))(((((((.(......).)))..)))).........))))).))) ( -15.40)
>DroYak_CAF1 127234 91 - 1
CCAGCCAUUUUCGUGAUUAAACAUUUUAAUGAGUUU----------UUUGCUGAUUAUGCAGCCCGUCUCCUUUGGCCAUGCAUUCCAUUUAGUUUAUUCA
.............(((.(((((....((((.(((..----------...))).))))(((((((.(......).)))..)))).........))))).))) ( -15.40)
>consensus
CCACCCAUUUUCCUGAUUAAACAUUUUAAUGAGUUU__________UUUGCUGAUUAUGCAGCCCGUCUCCUUUGGCCAUGCAUUCCAUUUAGUUUAUUCA
.............(((.(((((....((((.(((...............))).))))((((..(((.......)))...)))).........))))).))) (-10.80 = -11.60 +   0.80)

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 09:52:03 2006