Locus 8374

Sequence ID 3L_DroMel_CAF1
Location 22,000,005 – 22,000,133
Length 128
Max. P 0.965072
window13695 window13696 window13697

overview

Window 5

Location 22,000,005 – 22,000,102
Length 97
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.38
Mean single sequence MFE -42.43
Consensus MFE -27.93
Energy contribution -28.97
Covariance contribution 1.03
Combinations/Pair 1.22
Mean z-score -2.70
Structure conservation index 0.66
SVM decision value 1.58
SVM RNA-class probability 0.965072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22000005 97 + 23771897
-----GGAGGGAGACCAGCUGAACGGCUCCUUCCGCCUGCAGUGCUCGAUGUCCUCCGUGGAUAUGGAGAGCGAGAGUGACCUCUCGCUGGCAUUCGAGCGC
-----((((((((.((........)))))))))).......((((((((((((((((((....))))))((((((((....)))))))))))).)))))))) ( -52.60)
>DroVir_CAF1 49 91 + 1
AGUAUUGAGCU---ACAGCUAAACAGCUCCUAUAUCCUUCAGUGCUCGAUGUCCUCGCUG------GAGAGCGAAAGUGACUUGUCGCUGGCCUUUGAAC--
.((((((((..---..((((....)))).........))))))))((((.(.(((((((.------...))))).(((((....))))))).).))))..-- ( -22.12)
>DroGri_CAF1 416 96 + 1
AGCAUUGAGCAACAACAGCUAAACAGCUCCAAUAUCCUACAGUGCUCACUGUCCUCGCUA------GACAGCGAAAGUGAUUUGUCGCUGGCCUUCGAGCGU
.((((((((.......((((....))))........)).))))))(((((....(((((.------...))))).))))).....((((.(....).)))). ( -24.76)
>DroSec_CAF1 1937 97 + 1
-----GGAGGGAGACCAGCUGAACGGCUCCUUCCGCCUGCAGUGCUCGAUGUCCUCCGUGGACAUGGAGAGCGAGAGUGACCUCUCGCUGGCCUUCGAGCGC
-----((((((((.((........)))))))))).......(((((((((((((.....))))).((..((((((((....))))))))..)).)))))))) ( -52.70)
>DroSim_CAF1 33 97 + 1
-----GGAGGGAGACCAGCUGAACGGCUCCUUCCGCCUGCAGUGCUCGAUGUCCUCCGUGGACAUGGAGAGCGAGAGUGACCUCUCGCUGGCCUUCGAGCGC
-----((((((((.((........)))))))))).......(((((((((((((.....))))).((..((((((((....))))))))..)).)))))))) ( -52.70)
>DroEre_CAF1 2014 97 + 1
-----GGAGGGAGACCAGCUGAACGGUUCCUUCCGCCUGCAGUGCUCGAUGUCCUCCGUGGACAUCGAGAGCGAGAGUGACCUCUCGCUGGCCUUCGAGCGC
-----((((((((.((........))))))))))(((.......((((((((((.....))))))))))((((((((....))))))))))).......... ( -49.70)
>consensus
_____GGAGGGAGACCAGCUGAACGGCUCCUUCCGCCUGCAGUGCUCGAUGUCCUCCGUGGACAUGGAGAGCGAGAGUGACCUCUCGCUGGCCUUCGAGCGC
.....((((((.....((((....)))))))))).......((((((((.((((((..........)))((((((((....)))))))))))..)))))))) (-27.93 = -28.97 +   1.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,000,005 – 22,000,102
Length 97
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.38
Mean single sequence MFE -38.50
Consensus MFE -22.10
Energy contribution -23.80
Covariance contribution 1.70
Combinations/Pair 1.21
Mean z-score -1.94
Structure conservation index 0.57
SVM decision value 0.45
SVM RNA-class probability 0.739558
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22000005 97 - 23771897
GCGCUCGAAUGCCAGCGAGAGGUCACUCUCGCUCUCCAUAUCCACGGAGGACAUCGAGCACUGCAGGCGGAAGGAGCCGUUCAGCUGGUCUCCCUCC-----
((((((((.((((((((((((....)))))))).(((........))))).)))))))).(....)))(((.(((((((......))).)))).)))----- ( -41.90)
>DroVir_CAF1 49 91 - 1
--GUUCAAAGGCCAGCGACAAGUCACUUUCGCUCUC------CAGCGAGGACAUCGAGCACUGAAGGAUAUAGGAGCUGUUUAGCUGU---AGCUCAAUACU
--((((..((((...(((...(((....(((((...------.))))).))).))).)).))...))))....((((((........)---)))))...... ( -21.30)
>DroGri_CAF1 416 96 - 1
ACGCUCGAAGGCCAGCGACAAAUCACUUUCGCUGUC------UAGCGAGGACAGUGAGCACUGUAGGAUAUUGGAGCUGUUUAGCUGUUGUUGCUCAAUGCU
..((....((((.(((((..........))))))))------)(((((.(((((((((((((.(((....))).)).)))))).))))).)))))....)). ( -30.20)
>DroSec_CAF1 1937 97 - 1
GCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACUGCAGGCGGAAGGAGCCGUUCAGCUGGUCUCCCUCC-----
((((((((.((..((((((((....))))))))..)).(((((.....))))))))))).(....)))(((.(((((((......))).)))).)))----- ( -46.00)
>DroSim_CAF1 33 97 - 1
GCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACUGCAGGCGGAAGGAGCCGUUCAGCUGGUCUCCCUCC-----
((((((((.((..((((((((....))))))))..)).(((((.....))))))))))).(....)))(((.(((((((......))).)))).)))----- ( -46.00)
>DroEre_CAF1 2014 97 - 1
GCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCGAUGUCCACGGAGGACAUCGAGCACUGCAGGCGGAAGGAACCGUUCAGCUGGUCUCCCUCC-----
......(.(((((((((((.(((..((..((((((((((((((.....)))))))))).......))))..))..))).))).)))))))).)....----- ( -45.61)
>consensus
GCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACUGCAGGCGGAAGGAGCCGUUCAGCUGGUCUCCCUCC_____
..((((((...((((((((((....)))))))).((..........))))...)))))).........(((.(((((((......)))).))).)))..... (-22.10 = -23.80 +   1.70)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,000,040 – 22,000,133
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -34.82
Consensus MFE -20.63
Energy contribution -22.05
Covariance contribution 1.42
Combinations/Pair 1.18
Mean z-score -1.83
Structure conservation index 0.59
SVM decision value 0.72
SVM RNA-class probability 0.831065
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22000040 93 - 23771897
CGUCGCAGCCGCCAUCCGGUAUUUGCUCCUCGCGCUCGAAUGCCAGCGAGAGGUCACUCUCGCUCUCCAUAUCCACGGAGGACAUCGAGCACU
....((((..(((....)))..)))).......((((((.((((((((((((....)))))))).(((........))))).))))))))... ( -36.70)
>DroVir_CAF1 86 78 - 1
CAUCACAGUCG---GCCGGUUCGCCCG------GUUCAAAGGCCAGCGACAAGUCACUUUCGCUCUC------CAGCGAGGACAUCGAGCACU
...........---((((((((((..(------((......))).))))...(((....(((((...------.))))).))))))).))... ( -21.30)
>DroGri_CAF1 456 84 - 1
CAUCACAGUCA---GCCGGUUCGUCCAGAUCACGCUCGAAGGCCAGCGACAAAUCACUUUCGCUGUC------UAGCGAGGACAGUGAGCACU
..((((.(((.---...((.....))........((((..((.((((((..........)))))).)------)..))))))).))))..... ( -24.60)
>DroSec_CAF1 1972 93 - 1
CGUCGCAGCCGCCAUCCGGGGUUUGCUCCUCGCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACU
....((((((.((....)))).)))).......((((((.((..((((((((....))))))))..)).(((((.....)))))))))))... ( -42.30)
>DroSim_CAF1 68 93 - 1
CGUCGCAGCCGCCAUCCGGGGUUUGCUCCUCGCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACU
....((((((.((....)))).)))).......((((((.((..((((((((....))))))))..)).(((((.....)))))))))))... ( -42.30)
>DroEre_CAF1 2049 93 - 1
CGUCGCAGCUGCCACCCGGGGACUGCUCCUCGCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCGAUGUCCACGGAGGACAUCGAGCACU
..(((.(((.((.....(((((....))))))))))))).....((((((((....))))))))((((((((((.....)))))))))).... ( -41.70)
>consensus
CGUCGCAGCCGCCAUCCGGGGUUUGCUCCUCGCGCUCGAAGGCCAGCGAGAGGUCACUCUCGCUCUCCAUGUCCACGGAGGACAUCGAGCACU
.................((((......))))..((((((...((((((((((....)))))))).((..........))))...))))))... (-20.63 = -22.05 +   1.42)

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 13:13:47 2006