Locus 8398

Sequence ID 3L_DroMel_CAF1
Location 22,080,438 – 22,080,601
Length 163
Max. P 0.997881
window13732 window13733 window13734

overview

Window 2

Location 22,080,438 – 22,080,540
Length 102
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 91.70
Mean single sequence MFE -37.60
Consensus MFE -26.29
Energy contribution -27.23
Covariance contribution 0.95
Combinations/Pair 1.11
Mean z-score -4.03
Structure conservation index 0.70
SVM decision value 0.36
SVM RNA-class probability 0.706396
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22080438 102 - 23771897
AUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAUAAAAUGGGCACAACA-----CCAGCGUCGUCGAA
........((.((((((...........)))))).)).((((.(((.((((((((((((....................))).)))))-----)))).))).)))). ( -39.85)
>DroSec_CAF1 65869 102 - 1
AUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAUAAAAUGGGCACAACA-----CCAGCGUCGUCGAA
........((.((((((...........)))))).)).((((.(((.((((((((((((....................))).)))))-----)))).))).)))). ( -39.85)
>DroSim_CAF1 72222 102 - 1
AUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAUAAAAUGGGCACAACA-----CCAGCGUCGUCGAA
........((.((((((...........)))))).)).((((.(((.((((((((((((....................))).)))))-----)))).))).)))). ( -39.85)
>DroEre_CAF1 66054 107 - 1
AUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAUAAAAUGGGCACAACACCACACCAGCGUCGUCGGA
........((.((((((...........)))))).)).((((.(((.(((((((((((...)))))...........(((........))))))))).))).)))). ( -36.90)
>DroYak_CAF1 80946 102 - 1
AUAAAACGACCGCUGCAAAAUGCCAGAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAAGCUAAGAACAAUAAAAUGGCCACAGCA-----CCAGCGUCGUCGGA
........((.((((((...........)))))).)).((((.(((.(((((((((((((.................))))))..)))-----)))).))).)))). ( -39.53)
>DroAna_CAF1 87577 101 - 1
AUA-AACGGGCGCUGAAAAAUGCCAAAAUGCAGCCGAGGCGAGGACCCUGGUGAUGGCCGGGCCAAGAACAAUAAAAUGUGCACAGCA-----CCAGCGUCGAAAUA
...-....(((((((.....(((......)))(((..(((.(..((....))..).))).)))...............((((...)))-----))))))))...... ( -29.60)
>consensus
AUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAUAAAAUGGGCACAACA_____CCAGCGUCGUCGAA
........((.((((((...........)))))).)).((((.(((.((((((((((((....................))).))))).....)))).))).)))). (-26.29 = -27.23 +   0.95)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,080,467 – 22,080,561
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 98.72
Mean single sequence MFE -21.50
Consensus MFE -20.86
Energy contribution -20.90
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.97
SVM decision value 2.95
SVM RNA-class probability 0.997881
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22080467 94 - 23771897
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.(.(((((....))))))))......... ( -22.50)
>DroSec_CAF1 65898 94 - 1
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.(.(((((....))))))))......... ( -22.50)
>DroSim_CAF1 72251 94 - 1
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.(.(((((....))))))))......... ( -22.50)
>DroEre_CAF1 66088 94 - 1
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.(.(((((....))))))))......... ( -22.50)
>DroYak_CAF1 80975 94 - 1
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAGAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAAGCUAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.((.((((....))))))))......... ( -17.50)
>consensus
CAAAAUAAAAAAGAUACGAAAAUAAAACGACCGCUGCAAAAUGCCAAAAUGCAGCCGUGUCGAGGACUCUGGUGUUGGCCAGGCCAAGAACAAU
...........................(((((((((((...........))))).)).)))).((.(.(((((....))))))))......... (-20.86 = -20.90 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,080,502 – 22,080,601
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 96.30
Mean single sequence MFE -22.07
Consensus MFE -20.58
Energy contribution -20.63
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -0.89
Structure conservation index 0.93
SVM decision value 0.04
SVM RNA-class probability 0.554857
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22080502 99 + 23771897
CACGGCUGCAUUUUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).((...........)).))..))))))))))).)))))................. ( -21.90)
>DroSec_CAF1 65933 99 + 1
CACGGCUGCAUUUUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).((...........)).))..))))))))))).)))))................. ( -21.90)
>DroSim_CAF1 72286 99 + 1
CACGGCUGCAUUUUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).((...........)).))..))))))))))).)))))................. ( -21.90)
>DroEre_CAF1 66123 99 + 1
CACGGCUGCAUUUUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).((...........)).))..))))))))))).)))))................. ( -21.90)
>DroYak_CAF1 81010 99 + 1
CACGGCUGCAUUCUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).((...........)).))..))))))))))).)))))................. ( -24.50)
>DroAna_CAF1 87641 96 + 1
CUCGGCUGCAUUUUGGCAUUUUUCAGCGCCCGUU-UAUUUUUGUG--UUUUUUAGUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.((((((((((((((((((((.......-(((....)))--.......).))))))...))))))))))).)))))................. ( -20.34)
>consensus
CACGGCUGCAUUUUGGCAUUUUGCAGCGGUCGUUUUAUUUUCGUAUCUUUUUUAUUUUGAAGUUUAAUGCCAGAGUCGUGCCUCAUAUUUCGACGAUGG
...(((.(((((((((((((..((.((((...........)))).....(((......)))))..))))))))))).)))))................. (-20.58 = -20.63 +   0.06)

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 13:14:21 2006