Locus 711

Sequence ID 3R_DroMel_CAF1
Location 2,523,711 – 2,523,828
Length 117
Max. P 0.998165
window1124 window1125 window1126

overview

Window 4

Location 2,523,711 – 2,523,812
Length 101
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 76.95
Mean single sequence MFE -21.07
Consensus MFE -15.32
Energy contribution -15.43
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.78
Structure conservation index 0.73
SVM decision value 1.30
SVM RNA-class probability 0.939439
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2523711 101 + 27905053
------GGACUUAAUUGCGUCCGAAAGAGUAAUGAUAGCAUUUCUUUGGUAGUCUGGAGAUAUGUUUGAAUAUGUAAAUAUUAUUAAAUAUUUCUAGAUGUAUUUGC
------((((........))))...((((.((((....)))).))))....((((((((((((.....(((((....))))).....))))))))))))........ ( -24.40)
>DroSec_CAF1 53063 84 + 1
A---------------GCGUCCGAAAGAGUAAUGAUAGCAUUUCUUUGGUAGUCUGGAGGUAUGUUUGAAUAAGU--------UUAAAUAUUUCUAGAUGUAUUUAC
.---------------((..((.(((((..((((....)))))))))))..((((((((..(((((((((....)--------))))))))))))))))))...... ( -16.90)
>DroSim_CAF1 51994 94 + 1
UAUGGUGGACUUAAUUGCGUCCGAAAGACUAAUGAUAGCAUUUCUUUGGUUGGCUGGAGAUAUGUU-----AUGU--------UUAAAUAUUUCUAGAUGUAUUUAC
...........(((.((((((.((((...(((..(((((((.((((..(....)..)))).)))))-----))..--------)))....))))..)))))).))). ( -21.90)
>consensus
______GGACUUAAUUGCGUCCGAAAGAGUAAUGAUAGCAUUUCUUUGGUAGUCUGGAGAUAUGUUUGAAUAUGU________UUAAAUAUUUCUAGAUGUAUUUAC
...............(((((((....).........(((((.((((..(....)..)))).)))))..............................))))))..... (-15.32 = -15.43 +   0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,523,738 – 2,523,828
Length 90
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 80.81
Mean single sequence MFE -22.13
Consensus MFE -18.87
Energy contribution -18.43
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -3.90
Structure conservation index 0.85
SVM decision value 3.02
SVM RNA-class probability 0.998165
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2523738 90 + 27905053
GAUAGCAUUUCUUUGGUAGUCUGGAGAUAUGUUUGAAUAUGUAAAUAUUAUUAAAUAUUUCUAGAUGUAUUUGCAUUUAAGAAAUGGCGU----
.....((((((((..(((((((((((((((.....(((((....))))).....)))))))))))).....)))....))))))))....---- ( -23.80)
>DroSec_CAF1 53081 86 + 1
GAUAGCAUUUCUUUGGUAGUCUGGAGGUAUGUUUGAAUAAGU--------UUAAAUAUUUCUAGAUGUAUUUACAUUUAAGAAAUGACGUAGAA
....(((((((((..(((((((((((..(((((((((....)--------)))))))))))))))).....)))....)))))))).)...... ( -20.20)
>DroSim_CAF1 52027 75 + 1
GAUAGCAUUUCUUUGGUUGGCUGGAGAUAUGUU-----AUGU--------UUAAAUAUUUCUAGAUGUAUUUACAUUUAAGAAAUGA------A
.(((((((.((((..(....)..)))).)))))-----))..--------.....(((((((((((((....)))))).))))))).------. ( -22.40)
>consensus
GAUAGCAUUUCUUUGGUAGUCUGGAGAUAUGUUUGAAUAUGU________UUAAAUAUUUCUAGAUGUAUUUACAUUUAAGAAAUGACGU___A
...(((((.((((..(....)..)))).)))))......................(((((((((((((....)))))).)))))))........ (-18.87 = -18.43 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,523,738 – 2,523,828
Length 90
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 80.81
Mean single sequence MFE -7.37
Consensus MFE -5.20
Energy contribution -5.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.71
SVM decision value 0.52
SVM RNA-class probability 0.766795
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2523738 90 - 27905053
----ACGCCAUUUCUUAAAUGCAAAUACAUCUAGAAAUAUUUAAUAAUAUUUACAUAUUCAAACAUAUCUCCAGACUACCAAAGAAAUGCUAUC
----..((.(((((((...((......))(((.((.((((.....(((((....))))).....)))).)).)))......))))))))).... (  -8.50)
>DroSec_CAF1 53081 86 - 1
UUCUACGUCAUUUCUUAAAUGUAAAUACAUCUAGAAAUAUUUAA--------ACUUAUUCAAACAUACCUCCAGACUACCAAAGAAAUGCUAUC
......(.((((((((..((((....))))...(((.((.....--------...))))).....................))))))))).... (  -6.90)
>DroSim_CAF1 52027 75 - 1
U------UCAUUUCUUAAAUGUAAAUACAUCUAGAAAUAUUUAA--------ACAU-----AACAUAUCUCCAGCCAACCAAAGAAAUGCUAUC
.------.((((((((..((((....))))((.((.(((((((.--------...)-----)).)))).)).)).......))))))))..... (  -6.70)
>consensus
U___ACGUCAUUUCUUAAAUGUAAAUACAUCUAGAAAUAUUUAA________ACAUAUUCAAACAUAUCUCCAGACUACCAAAGAAAUGCUAUC
........((((((((..(((......))).((....))..........................................))))))))..... ( -5.20 =  -5.20 +   0.00)

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 09:49:59 2006