Locus 2720

Sequence ID 3R_DroMel_CAF1
Location 7,315,873 – 7,316,137
Length 264
Max. P 0.889050
window4410 window4411 window4412

overview

Window 0

Location 7,315,873 – 7,315,988
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.26
Mean single sequence MFE -40.00
Consensus MFE -26.37
Energy contribution -29.45
Covariance contribution 3.08
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.66
SVM decision value 0.74
SVM RNA-class probability 0.838094
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7315873 115 + 27905053
UUUGUUGCCGGGGUACGUGAGACCCGGCCGGGCU--ACCACCCCC-CUGCC-GAUUCAACCCCCCUUCCUGUCGACGGCGGCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA-
.....(((((((((.(....)))))(((((((..--.........-(((((-(..((.((..........)).)))))))).(((....))).......)))))))........)))))- ( -39.20)
>DroSec_CAF1 8745 117 + 1
UUUGUUGCCCGGGUACGUGAGACCCGGCCGGGCUUCACCACCCCCGCCACU-GAUUCAACCC-CCUUCCUGUCGACGGCGGCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA-
.....((((.((((.(....)))))(((((((...........(((((..(-(((.......-.......))))..))))).(((....))).......))))))).........))))- ( -38.64)
>DroSim_CAF1 4158 113 + 1
UUUGUUGCCCGGGUACGUGAGACCCGGCCCGGCUCCUCCACCGCC----CU-GAUUCAACCC-CCAUCCUGUCGACGGCGGCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA-
.((((((.((((((.(....)))))))...((((......(((((----.(-(((.......-.......))))..))))).(((....)))..........)))).....))))))..- ( -34.24)
>DroEre_CAF1 8690 104 + 1
UUUGUUGCCGGGGUACGUGAGACCCAGCCGGGCUC---------------GCCCCAAAACCC-CCUUUCUCUUGACGGCGGCGACGAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCAA
....((((((((((.(....))))).(((((((.(---------------(((.(((.....-........)))..))))))(((....)))........))))).........)))))) ( -39.62)
>DroYak_CAF1 3280 107 + 1
UUUGUUGCCGGGGUACGUGAGACCCAGCCGGGCAU------------UGGGGGGUUAAACCC-CCUUCCUGUCGACGGCGGCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCAA
(((((((((.((((.(....))))).((((((((.------------.((((((.....)))-)))...))))..)))))))))))))...............(((.........))).. ( -48.30)
>consensus
UUUGUUGCCGGGGUACGUGAGACCCGGCCGGGCUC__CCACC_CC____CG_GAUUCAACCC_CCUUCCUGUCGACGGCGGCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA_
(((((((((.((((.(....))))).(((((((.....................................)))..)))))))))))))...............(((.........))).. (-26.37 = -29.45 +   3.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,315,949 – 7,316,057
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.24
Mean single sequence MFE -31.72
Consensus MFE -26.56
Energy contribution -26.56
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.84
SVM decision value 0.38
SVM RNA-class probability 0.710848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7315949 108 + 27905053
GCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA------------GCAGCUACGGCAAUGCCGACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((.(....(((.........(((......)))..((((------------...((....))..)))))))((((((....((((....))))..(((...))).)))))).....)))) ( -30.90)
>DroSec_CAF1 8823 108 + 1
GCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA------------ACAGCUACGGCAAUGUCGACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((.(....(((.........(((......)))..((((------------...((....))..)))))))((((((....((((....))))..(((...))).)))))).....)))) ( -27.10)
>DroSim_CAF1 4232 108 + 1
GCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA------------ACAGCUACGGCAAUGCCGACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((.(....(((.........(((......)))..((((------------...((....))..)))))))((((((....((((....))))..(((...))).)))))).....)))) ( -29.80)
>DroEre_CAF1 8754 120 + 1
GCGACGAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCAAUGGCUACGGCAAUGGCUACGGCAAUGCCAACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((((....))).........((((((...((...))...)))))).((((...((....))..))))...((((((....((((....))))..(((...))).)))))).....)).. ( -37.50)
>DroYak_CAF1 3347 120 + 1
GCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCAACGAGAACGGCAACAGCUACGGCAAUGCCAACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((((....))).........((((.........((....)).....((((...((....))..))))......))))...((((......(((.(((...))).)))......)))))) ( -33.30)
>consensus
GCGACAAAAGUCUUUAAUUUCUGGCCAAUACCAACGGCA____________ACAGCUACGGCAAUGCCGACGAUGCCAAAAGCUUUUCAAAGCCACCGAAACGGGGGCGUUAACAAGCGC
(((((....)))...........(((.........)))................))...((((.((....)).))))....((((......(((.(((...))).)))......)))).. (-26.56 = -26.56 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,316,017 – 7,316,137
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.06
Mean single sequence MFE -34.80
Consensus MFE -31.82
Energy contribution -32.42
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.91
SVM decision value 0.95
SVM RNA-class probability 0.889050
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7316017 120 - 27905053
UCUUUUUUUCCAGUGCAUCUGGCUGUGUGUCUUUAUCUAGCUGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
.........((((.(((.((.(((((.(((.....((((((((.....)))))))).))).))))).))...)))..)))).((((.((((.(((.(((...))).))).)))).)))). ( -34.90)
>DroSec_CAF1 8891 118 - 1
A-UUU-UUUCCAGUGCAUCUGGCUGUGUGUCUUUAUCUAGCUGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
.-...-...((((.(((.((.(((((.(((.....((((((((.....)))))))).))).))))).))...)))..)))).((((.((((.(((.(((...))).))).)))).)))). ( -34.90)
>DroSim_CAF1 4300 119 - 1
A-UUUUUUUCCAGUGCAUCUGGCUGUGUGUCUUUAUCUAGCUGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
.-.......((((.(((.((.(((((.(((.....((((((((.....)))))))).))).))))).))...)))..)))).((((.((((.(((.(((...))).))).)))).)))). ( -34.90)
>DroEre_CAF1 8834 118 - 1
A-UUU-UUGCCAGUGCAUCUGUCUGUGUGUCUUUAUCUAGCCGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
.-...-..(((((.((((......))))...........(((((.((((........)))))))))...........)))))((((.((((.(((.(((...))).))).)))).)))). ( -32.70)
>DroYak_CAF1 3427 118 - 1
G-UUU-UUUCCAGUGCAUCUGGCUGUGUGGCUUUAUCUAGCCGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
(-(((-(((((((((((.(((((((.(((....))).)))))).).)))).))))))).))))((((.....))))......((((.((((.(((.(((...))).))).)))).)))). ( -36.60)
>consensus
A_UUU_UUUCCAGUGCAUCUGGCUGUGUGUCUUUAUCUAGCUGUGUUGUAGUUGGAAAUAAACGGCAAGUUUUGUCUCUGGCGCUUGUUAACGCCCCCGUUUCGGUGGCUUUGAAAAGCU
.........((((.(((.((.(((((.........((((((((.....)))))))).....))))).))...)))..)))).((((.((((.(((.(((...))).))).)))).)))). (-31.82 = -32.42 +   0.60)

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 10:43:03 2006