Locus 4918

Sequence ID 3L_DroMel_CAF1
Location 13,669,679 – 13,669,858
Length 179
Max. P 0.942646
window7763 window7764 window7765 window7766

overview

Window 3

Location 13,669,679 – 13,669,799
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -31.32
Consensus MFE -30.00
Energy contribution -30.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.96
SVM decision value 0.69
SVM RNA-class probability 0.824972
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13669679 120 - 23771897
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCCGGGCUCGUAAACACCUCCGAAAGUCCUCAACCGCCA
..............((((..((((((((......))))))))..)))).((((.(..(((((((((((((((...))))))).((((...(....)...))))..))).)))))))))). ( -34.50)
>DroSec_CAF1 77069 120 - 1
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCCGGGCUCGUAAACACCUCCGAAAGUCCUCAACCACCA
............(.((((..((((((((......))))))))..)))).)(.(((..(((((((((((((((...))))))).((((...(....)...))))..))).))))).)))). ( -30.20)
>DroSim_CAF1 87211 120 - 1
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCCGGGCUCGUAAACACCUCCGAAAGUCCUCAACCACAA
............(.((((..((((((((......))))))))..)))).)..(((..(((((((((((((((...))))))).((((...(....)...))))..))).))))).))).. ( -31.00)
>DroEre_CAF1 82273 120 - 1
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCUGGGCUCGUAAACACCUCCGAAAGUCCUCAACCACCG
.....(((......((((..((((((((......))))))))..)))).((.((....((((.(((((((((...)))))))..)).))))...)).)).......)))........... ( -30.00)
>DroYak_CAF1 85583 120 - 1
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCUGGGCUCGUAAACACCUCCGAAAGUCCUCGACCACCA
..............((((..((((((((......))))))))..))))(((((.((((((((.(((((((((...)))))))..)).)))(....)........)))))..)).)))... ( -30.90)
>consensus
UUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUUGCCCGGGCUCGUAAACACCUCCGAAAGUCCUCAACCACCA
.....(((......((((..((((((((......))))))))..)))).((.((....((((.(((((((((...)))))))..)).))))...)).)).......)))........... (-30.00 = -30.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,669,719 – 13,669,824
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.51
Mean single sequence MFE -19.19
Consensus MFE -17.50
Energy contribution -17.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.26
Structure conservation index 0.91
SVM decision value 0.58
SVM RNA-class probability 0.787743
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13669719 105 + 23771897
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCUUCCU---------CCUGCUCC------
.............((((....(((...(((........((((((((......))))))))......((((........)))).....))).)))...---------.))))...------ ( -20.50)
>DroSec_CAF1 77109 105 + 1
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCAUCCU---------CCAGCUCC------
.(((.((..(((((..((.((.(((.......))).))((((((((......)))))))).))..)))))..)).))).........((........---------...))...------ ( -17.70)
>DroSim_CAF1 87251 105 + 1
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCAUCCU---------CCUGCUCC------
.............((((..........(((........((((((((......))))))))......((((........)))).....))).......---------.))))...------ ( -19.07)
>DroEre_CAF1 82313 105 + 1
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCAUCCU---------CCUGCUCC------
.............((((..........(((........((((((((......))))))))......((((........)))).....))).......---------.))))...------ ( -19.07)
>DroYak_CAF1 85623 120 + 1
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCAUCCCCCUGAUCCUCCUGCUCCUGCUCC
.............((((......(((((((........((((((((......))))))))......((((........)))).....))).........))))....))))......... ( -19.60)
>consensus
AAUUAAUUUAACUGCAGUCUCAAGUCACGCCAGCUAGAGGCCAUAACUAAAUUUAUGGCCAACAACAGUUUUGUCAAUAACUUUUAUGCGCCAUCCU_________CCUGCUCC______
.(((.((..(((((..((.((.(((.......))).))((((((((......)))))))).))..)))))..)).))).......................................... (-17.50 = -17.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,669,719 – 13,669,824
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.51
Mean single sequence MFE -29.64
Consensus MFE -25.14
Energy contribution -25.38
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.85
SVM decision value 1.33
SVM RNA-class probability 0.942646
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13669719 105 - 23771897
------GGAGCAGG---------AGGAAGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
------...((((.---------...(((((((.....(((((..(((((.....)))))((((((((......))))))))..))))).))))..)))....))))............. ( -28.30)
>DroSec_CAF1 77109 105 - 1
------GGAGCUGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
------(.((((.(---------((....((((.....(((((..(((((.....)))))((((((((......))))))))..))))).))))..))).)).)).)............. ( -28.70)
>DroSim_CAF1 87251 105 - 1
------GGAGCAGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
------...((((.---------(((.(.((((.....(((((..(((((.....)))))((((((((......))))))))..))))).)))).))))....))))............. ( -29.10)
>DroEre_CAF1 82313 105 - 1
------GGAGCAGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
------...((((.---------(((.(.((((.....(((((..(((((.....)))))((((((((......))))))))..))))).)))).))))....))))............. ( -29.10)
>DroYak_CAF1 85623 120 - 1
GGAGCAGGAGCAGGAGGAUCAGGGGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
...((((...((((...(((.....))).((((.....(((((..(((((.....)))))((((((((......))))))))..))))).))))..))))...))))............. ( -33.00)
>consensus
______GGAGCAGG_________AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGGCCUCUAGCUGGCGUGACUUGAGACUGCAGUUAAAUUAAUU
.........((((..........(((.(.((((.....(((((..(((((.....)))))((((((((......))))))))..))))).)))).))))....))))............. (-25.14 = -25.38 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,669,759 – 13,669,858
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.13
Mean single sequence MFE -28.88
Consensus MFE -21.04
Energy contribution -21.48
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.40
Structure conservation index 0.73
SVM decision value 0.83
SVM RNA-class probability 0.862244
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13669759 99 - 23771897
GAUUAAUGAAGUGCCGGCUAGAUUAGGUGGCACA------------GGAGCAGG---------AGGAAGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
.............(((((((((((..(((((.((------------(.(((((.---------.(..((..((......))..))..)....))))).)))))))).))))))))..))) ( -23.60)
>DroSec_CAF1 77149 99 - 1
GAUUAAUGAAGUGCCGGCUAGAUUAGGUGGCCCA------------GGAGCUGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
............((((.(((...))).))))(((------------..((((((---------(..(((((.(((((.((((........)))).))).)))))))...))))))).))) ( -26.80)
>DroSim_CAF1 87291 99 - 1
GAUUAAUGAAGUGCCGGCUAGAUUAGGUGGCCCA------------GGAGCAGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
.............(((((((((((..((((((.(------------(.(((((.---------..((((((........)))))).......))))).)))))))).))))))))..))) ( -26.80)
>DroEre_CAF1 82353 99 - 1
GAUUAAUGAAGUGCCGGCUAGAUUGGGUGGCACA------------GGAGCAGG---------AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
.............(((((((((((..(((((.((------------(.(((((.---------..((((((........)))))).......))))).)))))))).))))))))..))) ( -28.00)
>DroYak_CAF1 85663 120 - 1
GAUUAAUGAAGUGCCGGCUAGAUUAGGUGGCACAUGGCCAGGAGCAGGAGCAGGAGGAUCAGGGGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
((((((....((((((.(((...))).))))))((((((((.(((((((.........))..(..((((((........))))))..)....))))).))))))))....)))))).... ( -39.20)
>consensus
GAUUAAUGAAGUGCCGGCUAGAUUAGGUGGCACA____________GGAGCAGG_________AGGAUGGCGCAUAAAAGUUAUUGACAAAACUGUUGUUGGCCAUAAAUUUAGUUAUGG
((((((....((((((.(((...))).)))))).................................(((((.(((((.((((........)))).))).)))))))....)))))).... (-21.04 = -21.48 +   0.44)

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 11:36:59 2006