Locus 5416

Sequence ID 2L_DroMel_CAF1
Location 15,449,721 – 15,449,864
Length 143
Max. P 0.981945
window8595 window8596 window8597

overview

Window 5

Location 15,449,721 – 15,449,828
Length 107
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 71.24
Mean single sequence MFE -23.27
Consensus MFE -16.23
Energy contribution -16.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.70
SVM decision value 1.90
SVM RNA-class probability 0.981945
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15449721 107 + 22407834
UCGCGCCUUUCCUUGCAUUUUUCUCAACCAAAGUUCCAUCUGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCCGUAU-------
.((.((.....((((............(((.((......))..))).........((((((((((((.......)))))).))))))....))))..-...))))...------- ( -24.10)
>DroSec_CAF1 187935 94 + 1
UAGC--AUUUUCCUAAAUUUUCCUCAACCAAACUUCCAUCUGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCC-CAAGUC------------------
....--............................((((.....))))........((((((((((((.......)))))).))))))...-......------------------ ( -19.10)
>DroSim_CAF1 193854 105 + 1
UCGC--AUUUUCCUGCAUUUUCCUCAAACAAACUUCCAUCUGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCCGUAA-------
..((--(......))).............((((((........(((....)))..((((((((((((.......)))))).)))))).....)))))-).........------- ( -23.50)
>DroEre_CAF1 198251 92 + 1
UCGCUGCUUUUCCAGAAUUUUCCCCGGCAAAAUU---------------UCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUG-UACGCCGUAA-------
...(((......))).........((((...(((---------------(.....((((((((((((.......)))))).)))))).....)))).-...))))...------- ( -24.00)
>DroYak_CAF1 195460 92 + 1
UCGCUCCUUUCCCUGCCUUUUCCCCAACAAAAUU---------------UCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCGGUAA-------
.............((((.................---------------......((((((((((((.......)))))).)))))).......((.-...)))))).------- ( -19.30)
>DroAna_CAF1 197311 108 + 1
------UUUUUCCCUGAUUUUCC-AUUCAAAAGUUCCAUCUGCCGUGGCUGCUCUGACAGGCUCAUUUGUUCCUGGUGAGCCUUGUCCCCCUAAAUAUUCCACGGUAGUACUCCG
------........(((......-..)))..(((.....(((((((((.......((((((((((((.......)))))))).))))............))))))))).)))... ( -29.61)
>consensus
UCGC__CUUUUCCUGCAUUUUCCUCAACAAAACUUCCAUCUGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU_UACGCCGUAA_______
.......................................................((((((((((((.......)))))))).))))............................ (-16.23 = -16.23 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,449,761 – 15,449,864
Length 103
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.56
Mean single sequence MFE -28.58
Consensus MFE -20.53
Energy contribution -21.37
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.72
SVM decision value 0.35
SVM RNA-class probability 0.699873
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15449761 103 + 22407834
UGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCCGUAU--------CUUCCAAAAUCCGGGCCUCAUUAGCCCGCCCAAGGC
...(((....)))..((((((((((((.......)))))).))))))..........-...((((...--------...).......(((((.......))))).....))) ( -28.00)
>DroSec_CAF1 187973 90 + 1
UGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCC-CAAGUC---------------------UCCAAAAUCCGGGCCUCAUUAGCCCGCCUAAGGC
.((((((.((.....((((((((((((.......)))))).))))))...-...)).---------------------)))......(((((.......))))).....))) ( -28.70)
>DroSim_CAF1 193892 103 + 1
UGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCCGUAA--------CUUCCAAAAUCCGGGCCUCAUUAGCCCGCCUAAGGC
.(((((((.......((((((((((((.......)))))).)))))).....(((((-........))--------))).....))))((((.......))))......))) ( -30.40)
>DroEre_CAF1 198285 94 + 1
---------UCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUG-UACGCCGUAA--------CUUUCACAAUCCGGGCCUCAUUAGCCCGCCUAAGGC
---------..((((((((((((((((.......)))))).))))))......))))-...(((((..--------.....))....(((((.......))))).....))) ( -28.60)
>DroYak_CAF1 195494 94 + 1
---------UCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU-UACGCGGUAA--------CUUCCACAAUCCGAGCCUUAUUAGCCCGUCUAAGGC
---------......((((((((((((.......)))))).))))))..........-...(.((...--------...)).).......((((((..........)))))) ( -23.10)
>DroAna_CAF1 197344 111 + 1
UGCCGUGGCUGCUCUGACAGGCUCAUUUGUUCCUGGUGAGCCUUGUCCCCCUAAAUAUUCCACGGUAGUACUCCGAAAUCCGAAAUCCGGCCCUCAUUAGCCAACCC-GGGC
((((((((.......((((((((((((.......)))))))).))))............)))))))).......((...(((.....)))...))....(((.....-.))) ( -32.71)
>consensus
UGCUGGAUAUCCACUGACAGGCUCAUUUGUUGCUGGUGAGCCCUGUCUCCCCAAGUU_UACGCCGUAA________CUUCCAAAAUCCGGGCCUCAUUAGCCCGCCUAAGGC
..........((...((((((((((((.......)))))))).))))........................................(((((.......))))).....)). (-20.53 = -21.37 +   0.83)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,449,761 – 15,449,864
Length 103
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.56
Mean single sequence MFE -33.15
Consensus MFE -23.39
Energy contribution -23.80
Covariance contribution 0.41
Combinations/Pair 1.19
Mean z-score -1.10
Structure conservation index 0.71
SVM decision value 0.10
SVM RNA-class probability 0.583078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15449761 103 - 22407834
GCCUUGGGCGGGCUAAUGAGGCCCGGAUUUUGGAAG--------AUACGGCGUA-AACUUGGGGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGAUAUCCAGCA
.(((..((((((((.....)))))).((.(((....--------...))).)).-..))..))).((((((.((((...........))))))))))..(((....)))... ( -33.70)
>DroSec_CAF1 187973 90 - 1
GCCUUAGGCGGGCUAAUGAGGCCCGGAUUUUGGA---------------------GACUUG-GGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGAUAUCCAGCA
(((...)))(((((.....)))))((((.(((..---------------------..)...-...((((((.((((...........))))))))))....)).)))).... ( -31.00)
>DroSim_CAF1 193892 103 - 1
GCCUUAGGCGGGCUAAUGAGGCCCGGAUUUUGGAAG--------UUACGGCGUA-AACUUGGGGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGAUAUCCAGCA
.(((((((((((((.....))))))..........(--------(....))...-..))))))).((((((.((((...........))))))))))..(((....)))... ( -33.60)
>DroEre_CAF1 198285 94 - 1
GCCUUAGGCGGGCUAAUGAGGCCCGGAUUGUGAAAG--------UUACGGCGUA-CACUUGGGGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGA---------
.(((((((((((((.....))))))...((((...(--------(....)).))-))))))))).((((((.((((...........))))))))))......--------- ( -33.60)
>DroYak_CAF1 195494 94 - 1
GCCUUAGACGGGCUAAUAAGGCUCGGAUUGUGGAAG--------UUACCGCGUA-AACUUGGGGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGA---------
.((((((.((((((.....))))))....((((...--------...))))...-...)))))).((((((.((((...........))))))))))......--------- ( -31.10)
>DroAna_CAF1 197344 111 - 1
GCCC-GGGUUGGCUAAUGAGGGCCGGAUUUCGGAUUUCGGAGUACUACCGUGGAAUAUUUAGGGGGACAAGGCUCACCAGGAACAAAUGAGCCUGUCAGAGCAGCCACGGCA
(((.-((.((((((......))))))((((((.....))))))....))((((.........(....)...((((..((((..(....)..))))...))))..))))))). ( -35.90)
>consensus
GCCUUAGGCGGGCUAAUGAGGCCCGGAUUUUGGAAG________UUACGGCGUA_AACUUGGGGAGACAGGGCUCACCAGCAACAAAUGAGCCUGUCAGUGGAUAUCCAGCA
.(((((((((((((.....))))))....................(((...)))...))))))).((((.((((((...........))))))))))............... (-23.39 = -23.80 +   0.41)

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 11:43:36 2006