Locus 5715

Sequence ID 2L_DroMel_CAF1
Location 16,259,759 – 16,259,922
Length 163
Max. P 0.862893
window9052 window9053 window9054 window9055

overview

Window 2

Location 16,259,759 – 16,259,851
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.90
Mean single sequence MFE -31.87
Consensus MFE -23.01
Energy contribution -23.07
Covariance contribution 0.06
Combinations/Pair 1.26
Mean z-score -1.58
Structure conservation index 0.72
SVM decision value 0.63
SVM RNA-class probability 0.803799
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16259759 92 + 22407834
GAAGAAGAGUUUC-UUCAAUU---CAAAUC-CGGGUCUCAACA--GUGGCGUCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUGUU
((((((....)))-)))....---......-((.((((((...--.((((..((.(((.(((((((...))))))).)))))..)))))))))).)).. ( -34.40)
>DroSec_CAF1 1176 93 + 1
GAACAAGAGCUUC-UUCAAUU---CGAAUCGCGGGUCUCAACA--GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUU
....((((((...-(((....---.)))..))..((((((...--.(((((((..(((.(((((((...))))))).)))))).)))))))))).)))) ( -32.40)
>DroSim_CAF1 1178 93 + 1
GAACAAGAGCUUC-UUCAAUU---CGAAUCGCGGGUCUCAACA--GUGGCGCCCCAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUU
....((((((...-(((....---.)))..))..((((((...--.((((...(((((.(((((((...))))))).)))))..)))))))))).)))) ( -34.60)
>DroEre_CAF1 1166 91 + 1
GAAGAAGAGUUUC-UUCAAUU---CGAAUC--GGGUCUCUACA--GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUAAGACGUUUU
((((((....)))-)))....---......--..((((.....--((((((((..(((.(((((((...))))))).)))))).))))).))))..... ( -30.50)
>DroYak_CAF1 1212 91 + 1
AAAGAAGAGCUUC-UUCAUUU---CGAAUC--GGGUCUCUACA--GUGGCGCCCGAGCAGGAACACUUGGUGUCCUAGCUGGUAGCCAUGACACUUGUU
...((((.....)-)))....---.....(--((((.((....--(((((..((.(((((((.(((...))))))).)))))..))))))).))))).. ( -27.50)
>DroAna_CAF1 2139 88 + 1
GAAU---GGCUUCCCACCAUCCUACGAUG--CUGGUCA-AAUGGUCUGGCGCCUGAGCAG-GACACUUGGUGUCCUAGAUGGCUGCUGGCUGCCG----
....---(((...(((.((((....))))--.)))...-...((.(..(((((....(((-(((((...))))))).)..))).))..)))))).---- ( -31.80)
>consensus
GAAGAAGAGCUUC_UUCAAUU___CGAAUC_CGGGUCUCAACA__GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUU
..................................(((((......((((((((..(((.(((((((...))))))).)))))).))))))))))..... (-23.01 = -23.07 +   0.06)

alignment

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secondary structure

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Window 3

Location 16,259,794 – 16,259,887
Length 93
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 79.60
Mean single sequence MFE -30.75
Consensus MFE -20.64
Energy contribution -20.03
Covariance contribution -0.61
Combinations/Pair 1.33
Mean z-score -1.87
Structure conservation index 0.67
SVM decision value 0.84
SVM RNA-class probability 0.862893
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16259794 93 + 22407834
ACA--GUGGCGUCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUGUUGAACAAA--GUCAAGAAGAAACUGAAAUUGCACAGCGC
...--(((((..((.(((.(((((((...))))))).)))))..))))).....((((((..(((.--.(((.........)))..)))..)))))) ( -30.10)
>DroSec_CAF1 1212 95 + 1
ACA--GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUUGAACGAAACGUCAAGAAGAAACUGAAAUUGCACGGCGC
...--...(((((..(((.(((((((...))))))).))).((((...(.((...((((((.((...)))))))).....)).)..))))..))))) ( -31.30)
>DroSim_CAF1 1214 95 + 1
ACA--GUGGCGCCCCAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUUGAACAAAACGUCAAGAAGAAACUGACAUUGCACAGCGC
...--...((((.(((((.(((((((...))))))).)))))..((.(((.(((((.((....)).))))).((......))..))).))...)))) ( -33.30)
>DroEre_CAF1 1200 90 + 1
ACA--GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUAAGACGUUUUGAAUAAA--GUUA---AGAAACUGAAAUUGCACAGCGC
...--((((((((..(((.(((((((...))))))).)))))).)))))....((((.(((((..(--(((.---...))))...))).)).)))). ( -28.30)
>DroYak_CAF1 1246 90 + 1
ACA--GUGGCGCCCGAGCAGGAACACUUGGUGUCCUAGCUGGUAGCCAUGACACUUGUUGAACAAA--GUUA---AGAAACUGAAAUUGCACAGCGC
...--(((((..((.(((((((.(((...))))))).)))))..))))).......((((..(((.--.(((---......)))..)))..)))).. ( -25.30)
>DroAna_CAF1 2173 81 + 1
AUGGUCUGGCGCCUGAGCAG-GACACUUGGUGUCCUAGAUGGCUGCUGGCUGCCG----GAAU----C-------GGCUGUUGGAAUCGCUCAGCGU
........((((.(((((((-(((((...))))))).(((.....(..((.((((----....----)-------))).))..).)))))))))))) ( -36.20)
>consensus
ACA__GUGGCGCCCGAGCAGGGACACUUGGUGUCCUAGCUGGCAGCUAUGAGACGUCUUGAACAAA__GUCA___AGAAACUGAAAUUGCACAGCGC
.....((((((((..(((.(((((((...))))))).)))))).)))))...............................(((........)))... (-20.64 = -20.03 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,259,794 – 16,259,887
Length 93
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 79.60
Mean single sequence MFE -28.93
Consensus MFE -18.58
Energy contribution -18.72
Covariance contribution 0.14
Combinations/Pair 1.26
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value 0.80
SVM RNA-class probability 0.854846
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16259794 93 - 22407834
GCGCUGUGCAAUUUCAGUUUCUUCUUGAC--UUUGUUCAACACGUCUCAUAGCUGCCAGCUAGGACACCAAGUGUCCCUGCUCGGACGCCAC--UGU
(((.(((((((..((((.......)))).--.))))...))))))......((..(((((..((((((...))))))..))).))..))...--... ( -23.80)
>DroSec_CAF1 1212 95 - 1
GCGCCGUGCAAUUUCAGUUUCUUCUUGACGUUUCGUUCAAGACGUCUCAUAGCUGCCAGCUAGGACACCAAGUGUCCCUGCUCGGGCGCCAC--UGU
(((((.........(((((.......(((((((......)))))))....)))))(.(((..((((((...))))))..))).))))))...--... ( -32.80)
>DroSim_CAF1 1214 95 - 1
GCGCUGUGCAAUGUCAGUUUCUUCUUGACGUUUUGUUCAAGACGUCUCAUAGCUGCCAGCUAGGACACCAAGUGUCCCUGCUGGGGCGCCAC--UGU
(((((.........(((((.......((((((((....))))))))....)))))(((((..((((((...))))))..))))))))))...--... ( -38.70)
>DroEre_CAF1 1200 90 - 1
GCGCUGUGCAAUUUCAGUUUCU---UAAC--UUUAUUCAAAACGUCUUAUAGCUGCCAGCUAGGACACCAAGUGUCCCUGCUCGGGCGCCAC--UGU
((((..........(((((...---..((--(((.....))).)).....)))))(((((..((((((...))))))..))).))))))...--... ( -23.20)
>DroYak_CAF1 1246 90 - 1
GCGCUGUGCAAUUUCAGUUUCU---UAAC--UUUGUUCAACAAGUGUCAUGGCUACCAGCUAGGACACCAAGUGUUCCUGCUCGGGCGCCAC--UGU
(((((.((.(((...((((...---.)))--)..)))))...)))))..((((..(((((..((((((...))))))..))).))..)))).--... ( -25.70)
>DroAna_CAF1 2173 81 - 1
ACGCUGAGCGAUUCCAACAGCC-------G----AUUC----CGGCAGCCAGCAGCCAUCUAGGACACCAAGUGUC-CUGCUCAGGCGCCAGACCAU
..((((.(((....)....(((-------(----....----)))).)))))).(((...((((((((...)))))-)))....))).......... ( -29.40)
>consensus
GCGCUGUGCAAUUUCAGUUUCU___UGAC__UUUGUUCAACACGUCUCAUAGCUGCCAGCUAGGACACCAAGUGUCCCUGCUCGGGCGCCAC__UGU
((((((.(((.......................................((((.....))))((((((...)))))).))).))).)))........ (-18.58 = -18.72 +   0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,259,828 – 16,259,922
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -29.68
Consensus MFE -16.65
Energy contribution -17.18
Covariance contribution 0.53
Combinations/Pair 1.26
Mean z-score -1.86
Structure conservation index 0.56
SVM decision value 0.61
SVM RNA-class probability 0.798082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16259828 94 + 22407834
AGCUGGCAGCUAUGAGACGUGUUGAACAAA--GUCAAGAAGAAACUGAAAUUGCACAGCGCAGACGCAGCUUGGCGAAG-GCAGACAGCUGCAGCAU---
.((((.(((((....(((.((.....))..--))).........(((...((((..(((((....)).)))..))))..-.)))..)))))))))..--- ( -28.80)
>DroSec_CAF1 1246 96 + 1
AGCUGGCAGCUAUGAGACGUCUUGAACGAAACGUCAAGAAGAAACUGAAAUUGCACGGCGCAGACGCAGCCUGGCGAAG-GGAGACAGCUGCAGCAU---
.((((.(((((....(((((.((....)).)))))...............((((..(((((....)).)))..))))..-(....))))))))))..--- ( -32.10)
>DroSim_CAF1 1248 96 + 1
AGCUGGCAGCUAUGAGACGUCUUGAACAAAACGUCAAGAAGAAACUGACAUUGCACAGCGCAGACGCAGCUUGGCGAAG-GGAGACAGCUGCAGCAU---
.((((.(((((....(((((.((....)).))))).........((..(.((((..(((((....)).)))..)))).)-..))..)))))))))..--- ( -31.20)
>DroEre_CAF1 1234 91 + 1
AGCUGGCAGCUAUAAGACGUUUUGAAUAAA--GUUA---AGAAACUGAAAUUGCACAGCGCAGACGCAGCUUGGCGAAG-GGAGACAGCCGCUGCAU---
.((((((((.....((...((((((.....--.)))---)))..))....)))).))))......(((((..(((....-(....).))))))))..--- ( -27.70)
>DroYak_CAF1 1280 91 + 1
AGCUGGUAGCCAUGACACUUGUUGAACAAA--GUUA---AGAAACUGAAAUUGCACAGCGCAGACGCAGCUUGGCGAAG-GGAGACAGCUGCAACAU---
.((((((((....(((....)))......(--(((.---...))))....)))).))))((((.(((......)))...-(....)..)))).....--- ( -20.70)
>DroAna_CAF1 2208 85 + 1
AGAUGGCUGCUGGCUGCCG----GAAU----C-------GGCUGUUGGAAUCGCUCAGCGUCGGCGCGGCUUGGCAGAGGAGAGGCAGCUGCGGCAGAUC
.(((.(((((.(((((((.----...(----(-------..((((..(....(((..(((....)))))))..))))..))..))))))))))))..))) ( -37.60)
>consensus
AGCUGGCAGCUAUGAGACGUCUUGAACAAA__GUCA___AGAAACUGAAAUUGCACAGCGCAGACGCAGCUUGGCGAAG_GGAGACAGCUGCAGCAU___
.((((.(((((.......................................((((..(((((....)).)))..))))...(....))))))))))..... (-16.65 = -17.18 +   0.53)

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 11:50:54 2006