Locus 1765

Sequence ID 2R_DroMel_CAF1
Location 6,601,000 – 6,601,141
Length 141
Max. P 0.991788
window2938 window2939 window2940 window2941

overview

Window 8

Location 6,601,000 – 6,601,110
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 87.11
Mean single sequence MFE -42.65
Consensus MFE -35.40
Energy contribution -36.03
Covariance contribution 0.62
Combinations/Pair 1.03
Mean z-score -2.97
Structure conservation index 0.83
SVM decision value 2.29
SVM RNA-class probability 0.991788
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6601000 110 + 20766785
AGAAGG--GGGCUUGACGGUGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCAAGUGAGCCCCAAUGCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACAG
....((--((((((((((((......)))..)))))))))...(((((((((...(((((....)))))........)))))))))((((.....))))......))..... ( -46.00)
>DroSec_CAF1 153484 100 + 1
AGAAGG--GGGCUUGGCGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCGCUCAGGACGAGAAAAACCAACAG
....((--(((((((((..(((....)))..)))))))))...(((((((((....(((..-..)---------)).)))))))))...(((.....))).....))..... ( -41.60)
>DroSim_CAF1 140281 102 + 1
AGAAGGGGGGGCUUGGCGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACGG
........(((((((((..(((....)))..)))))))))..(((((........((((((-(..---------...))))))).(((((.....))))).....)).))). ( -44.80)
>DroYak_CAF1 159979 95 + 1
AGAAGG--GGGCUUGACGCGGUUUGGGCCAAGUCGAGCUCAACGUGGCUCCGAUCGGCUCA-G--------------GUGAGCCACUCGCACAGAGCGAGAAAAACCAACAG
....((--(((((((((..(((....)))..)))))))))...(((((((..(((......-)--------------)))))))))((((.....))))......))..... ( -38.20)
>consensus
AGAAGG__GGGCUUGACGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA_GUG_________GCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACAG
........(((((((((..(((....)))..)))))))))....(((........((((((.(((..........))))))))).(((((.....))))).....))).... (-35.40 = -36.03 +   0.62)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,601,000 – 6,601,110
Length 110
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 87.11
Mean single sequence MFE -35.40
Consensus MFE -29.81
Energy contribution -30.00
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.32
SVM RNA-class probability 0.687272
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6601000 110 - 20766785
CUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGCAUUGGGGCUCACUUGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACACCGUCAAGCCC--CCUUCU
..((((((((..(((((.....))))(((((((((........(((((....)))))...))))))))))..)))).))))(((((.........)))))....--...... ( -38.10)
>DroSec_CAF1 153484 100 - 1
CUGUUGGUUUUUCUCGUCCUGAGCGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAGCCC--CCUUCU
...(((((....(((((.....)))))((((((((...---------..)-)))))))......((((.((((....)))).)))).........)))))....--...... ( -32.60)
>DroSim_CAF1 140281 102 - 1
CCGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAGCCCCCCCUUCU
...(((((....(((((.....)))))((((((((...---------..)-)))))))......((((.((((....)))).)))).........)))))............ ( -35.30)
>DroYak_CAF1 159979 95 - 1
CUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAC--------------C-UGAGCCGAUCGGAGCCACGUUGAGCUCGACUUGGCCCAAACCGCGUCAAGCCC--CCUUCU
.....(((((..(((((.....)))))((((((..--------------.-.))))))...((.((((.((((....)))).)))))))))))((.....))..--...... ( -35.60)
>consensus
CUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGC_________CAC_UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAGCCC__CCUUCU
.....(((((..(((((.....)))))((((((((((..........))).)))))))......((((.((((....)))).))))............)))))......... (-29.81 = -30.00 +   0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,601,036 – 6,601,141
Length 105
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 84.46
Mean single sequence MFE -35.75
Consensus MFE -25.31
Energy contribution -26.50
Covariance contribution 1.19
Combinations/Pair 1.07
Mean z-score -2.94
Structure conservation index 0.71
SVM decision value 1.95
SVM RNA-class probability 0.983766
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6601036 105 + 20766785
UCAACGUGGCUCAGAUCGGCUCAAGUGAGCCCCAAUGCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACAGAGACCA-GAGACUGUUCAAGCGUCUCUGGAGC
.....(((((((((...(((((....)))))........)))))))))((((.....))))................(((-(((((.((....))))))))))... ( -42.30)
>DroSec_CAF1 153520 96 + 1
UCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCGCUCAGGACGAGAAAAACCAACAGAGACCAACAGACUGUUCAAGCGUCUGUGGACC
......((((((.....((((((-(..---------...))))))).(((((....).))))...........))).)))((((((.((....))))))))..... ( -32.90)
>DroSim_CAF1 140319 96 + 1
UCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACGGAGACCAACAGACUGUUCAAGCGUCUGUGGAGC
((..(((((........((((((-(..---------...))))))).(((((.....))))).....)).)))..))(((.(((((.((....))))))))))... ( -37.00)
>DroYak_CAF1 160015 86 + 1
UCAACGUGGCUCCGAUCGGCUCA-G--------------GUGAGCCACUCGCACAGAGCGAGAAAAACCAACAGAAACCG-----CUGUUCAAGCGUCUCUGGAGC
........(((((....(((((.-.--------------..))))).(((((.....)))))..........(((...((-----((.....))))..)))))))) ( -30.80)
>consensus
UCAACGUGGCUCAGAUCGGCUCA_GUG_________GCACUGAGCCACUCGCACAGAGCGAGAAAAACCAACAGAGACCA_CAGACUGUUCAAGCGUCUCUGGAGC
((....(((........((((((.(((..........))))))))).(((((.....))))).....)))...))..(((.(((((.((....))))))))))... (-25.31 = -26.50 +   1.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,601,036 – 6,601,141
Length 105
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 84.46
Mean single sequence MFE -37.47
Consensus MFE -28.01
Energy contribution -28.82
Covariance contribution 0.81
Combinations/Pair 1.12
Mean z-score -2.23
Structure conservation index 0.75
SVM decision value 1.21
SVM RNA-class probability 0.931235
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6601036 105 - 20766785
GCUCCAGAGACGCUUGAACAGUCUC-UGGUCUCUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGCAUUGGGGCUCACUUGAGCCGAUCUGAGCCACGUUGA
...((((((((.........)))))-)))................((((.....))))(((((((((........(((((....)))))...)))))))))..... ( -42.70)
>DroSec_CAF1 153520 96 - 1
GGUCCACAGACGCUUGAACAGUCUGUUGGUCUCUGUUGGUUUUUCUCGUCCUGAGCGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGA
(..(.((((((.........)))))).)..).....((((((..(((((.....)))))((((((((...---------..)-)))))))....))))))...... ( -34.50)
>DroSim_CAF1 140319 96 - 1
GCUCCACAGACGCUUGAACAGUCUGUUGGUCUCCGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGA
...((((((((.........))))).)))((..(((.(((((..(((((.....)))))((((((((...---------..)-)))))))....))))))))..)) ( -37.90)
>DroYak_CAF1 160015 86 - 1
GCUCCAGAGACGCUUGAACAG-----CGGUUUCUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAC--------------C-UGAGCCGAUCGGAGCCACGUUGA
((((((((((((((.....))-----).))))))...((((...(((((.....))))).(((((..--------------.-.))))))))))))))........ ( -34.80)
>consensus
GCUCCACAGACGCUUGAACAGUCUG_UGGUCUCUGUUGGUUUUUCUCGCUCUGUGCGAGUGGCUCAGUGC_________CAC_UGAGCCGAUCUGAGCCACGUUGA
...((((((((.........))))).)))((..(((.(((((..(((((.....)))))((((((((((..........))).)))))))....))))))))..)) (-28.01 = -28.82 +   0.81)

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 10:12:40 2006