Locus 8836

Sequence ID 3R_DroMel_CAF1
Location 23,656,781 – 23,656,911
Length 130
Max. P 0.961679
window14186 window14187 window14188

overview

Window 6

Location 23,656,781 – 23,656,893
Length 112
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 79.88
Mean single sequence MFE -29.42
Consensus MFE -20.33
Energy contribution -20.08
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -1.29
Structure conservation index 0.69
SVM decision value 0.17
SVM RNA-class probability 0.617745
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23656781 112 + 27905053
-GACUAG-AAAAUUCUCUGGAGUCGCACAAACAAAUGCGCGUAAAUUUUGCUUAGCGCGCAAUUCAAGUGCAAAUACUUGACACCGCCGCACCUAAACUG-G--GAAAAGUGCGGGC
-..((((-(......)))))..((((((.......(((((((.((......)).)))))))..(((((((....)))))))..........(((.....)-)--)....)))))).. ( -31.50)
>DroPse_CAF1 122240 113 + 1
-GGGGAG-CAUAUUCUCUGGAGUGGCACAAACAAAUGCGCGUAAAUUUUGCUUAGCGCGCGAUUCAAGUGCAAAUACUUGACACUGCCACAACCAAAGUGCGAGGAUAAGCGGUA--
-.....(-(.((((((((((.((((((........(((((((.((......)).)))))))..(((((((....)))))))...))))))..)))......))))))).))....-- ( -36.10)
>DroSec_CAF1 118766 114 + 1
-GACGAG-GAAAUUCUCCGGAGUCGCACAAACAAAUGCGCGUAUAUUUUGCUUAGCGCGCAAUUCAAGUGCAAAUACUUGACACCGCCGCACCUAAACUG-GAGGAAAAGUGGGAAA
-(((..(-((.....)))...)))...........(((((((............)))))))..(((((((....)))))))..((((....(((......-.)))....)))).... ( -29.60)
>DroWil_CAF1 136386 98 + 1
UGUCGAACAAAAUUCUCUGGAGUCGUACAAACAAAUGCGCGUAAAUUUAGCUUAGCGCGCAAUUCAAGUGCAAAUACUUGACACUGCCGCACCUACAU-------------------
..................((.((.(((........(((((((.((......)).)))))))..(((((((....)))))))...))).)).)).....------------------- ( -20.80)
>DroAna_CAF1 121074 106 + 1
-G--------AACUCUCCGGAGUCGCACAAACAAAUGCGCGUAAAUUUUGCUUAGCGCGCAAUUCAAGUGCAAAUACUUGACACCGCCGCACCUAAGCCU-GGGCCAA-AUGGGAAA
-.--------.....(((((.((.((.........(((((((.((......)).)))))))..(((((((....)))))))....)).)).))...((..-..))...-...))).. ( -27.80)
>DroPer_CAF1 120507 113 + 1
-GGGGAG-CAUAUUCUCUGGAGUCGCACAAACAAAUGCGCGUAAAUUUUGCUUAGCGCGCGAUUCAAGUGCAAAUACUUGACACUGCCACAACCAAAGUGCGAGGAUAAGCGGUA--
-.....(-(.(((((((.(....)((((.......(((((((.((......)).)))))))..(((((((....)))))))................))))))))))).))....-- ( -30.70)
>consensus
_GACGAG_AAAAUUCUCUGGAGUCGCACAAACAAAUGCGCGUAAAUUUUGCUUAGCGCGCAAUUCAAGUGCAAAUACUUGACACCGCCGCACCUAAACUG_GAGGAAAAGUGGGA__
..................((.((.((.........(((((((............)))))))..(((((((....)))))))....)).)).))........................ (-20.33 = -20.08 +  -0.25)

alignment

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secondary structure

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Window 7

Location 23,656,781 – 23,656,893
Length 112
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 79.88
Mean single sequence MFE -31.82
Consensus MFE -21.80
Energy contribution -21.97
Covariance contribution 0.17
Combinations/Pair 1.16
Mean z-score -1.34
Structure conservation index 0.69
SVM decision value 0.21
SVM RNA-class probability 0.634675
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23656781 112 - 27905053
GCCCGCACUUUUC--C-CAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUACGCGCAUUUGUUUGUGCGACUCCAGAGAAUUUU-CUAGUC-
(((.((((((...--.-......)))))))))((.(((........((((......((((((.((((.....)))))))))).......))))))).))((((....))-))....- ( -32.02)
>DroPse_CAF1 122240 113 - 1
--UACCGCUUAUCCUCGCACUUUGGUUGUGGCAGUGUCAAGUAUUUGCACUUGAAUCGCGCGCUAAGCAAAAUUUACGCGCAUUUGUUUGUGCCACUCCAGAGAAUAUG-CUCCCC-
--..............(((((((((..((((((...((((((......))))))...(((((.((((.....))))))))).........)))))).))))))....))-).....- ( -34.50)
>DroSec_CAF1 118766 114 - 1
UUUCCCACUUUUCCUC-CAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUAUACGCGCAUUUGUUUGUGCGACUCCGGAGAAUUUC-CUCGUC-
.............(((-(.((((((.((((.((((.((((((......))))))))))))))))))))........((((((......)))))).....))))......-......- ( -35.50)
>DroWil_CAF1 136386 98 - 1
-------------------AUGUAGGUGCGGCAGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCUAAAUUUACGCGCAUUUGUUUGUACGACUCCAGAGAAUUUUGUUCGACA
-------------------...(((((((.(((((.((((((......)))))))))))(((.((((.....))))))))))))))..(((.(((...((((....)))).)))))) ( -23.30)
>DroAna_CAF1 121074 106 - 1
UUUCCCAU-UUGGCCC-AGGCUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUACGCGCAUUUGUUUGUGCGACUCCGGAGAGUU--------C-
(((((...-.......-..((((((.((((.((((.((((((......))))))))))))))))))))........((((((......)))))).....)))))...--------.- ( -35.50)
>DroPer_CAF1 120507 113 - 1
--UACCGCUUAUCCUCGCACUUUGGUUGUGGCAGUGUCAAGUAUUUGCACUUGAAUCGCGCGCUAAGCAAAAUUUACGCGCAUUUGUUUGUGCGACUCCAGAGAAUAUG-CUCCCC-
--..............(((((((((..((.(((...((((((......))))))...(((((.((((.....))))))))).........))).)).))))))....))-).....- ( -30.10)
>consensus
__UCCCACUUUUCCUC_CAGUUUAGGUGCGGCAGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUACGCGCAUUUGUUUGUGCGACUCCAGAGAAUUUG_CUCGCC_
....................(((((.((((.((((.((((((......))))))))))))))))))).........((((((......))))))....................... (-21.80 = -21.97 +   0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 23,656,819 – 23,656,911
Length 92
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 76.40
Mean single sequence MFE -25.90
Consensus MFE -15.23
Energy contribution -16.57
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.59
SVM decision value 1.53
SVM RNA-class probability 0.961679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23656819 92 - 27905053
CCCA-------UUCAC-------CAU-CGCCCAG---CCCGCACUUUUC--CCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUAC
....-------.....-------...-.((..((---(.(((((((...--.......)))))))(((((.((((((......)))))))))))..)))..))......... ( -24.30)
>DroGri_CAF1 154446 87 - 1
CUUUUAGUGUG-UCAC-------UGCUCGCAGAG---UAGGCACUUG-------UUUUAGGUGCGGCUGUGUCAAGUAUUUGCACUU-------GCGCUAAGCAAAAUUUAC
..(((((((((-((.(-------(((((...)))---)))(((((((-------...)))))))))).(((.(((....))))))..-------)))))))).......... ( -25.30)
>DroSec_CAF1 118804 89 - 1
-------------CAC-------CGCCCGCACUU---UUCCCACUUUUCCUCCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUAUAC
-------------(((-------((((.((((((---.....(((........)))..)))))))))))))((((((......)))))).((((.......))))....... ( -29.10)
>DroSim_CAF1 117743 94 - 1
CCCA-------UUCAC-------CAU-CGCCCAG---CCCGCACUUUUCCUCCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUAC
....-------.....-------...-.((..((---(.(((((((............)))))))(((((.((((((......)))))))))))..)))..))......... ( -24.10)
>DroEre_CAF1 118883 95 - 1
CCCA-------UUUCC-------CAC-CGCCCAACGCCCC--ACUUUUCCUCCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUAC
....-------.....-------(((-((((...((((..--(((........)))...)))).)))))))((((((......)))))).((((.......))))....... ( -26.30)
>DroYak_CAF1 123230 104 - 1
GCCA-------UUUCCCAACACCCAC-CGCCCAACACCCCACACUUUUCCACCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUAC
((..-------............(((-((((...((((....(((........)))...)))).)))))))((((((......))))))...))((.....))......... ( -26.30)
>consensus
CCCA_______UUCAC_______CAC_CGCCCAG___CCCGCACUUUUCCUCCAGUUUAGGUGCGGCGGUGUCAAGUAUUUGCACUUGAAUUGCGCGCUAAGCAAAAUUUAC
......................................................((((((.((((.((((.((((((......))))))))))))))))))))......... (-15.23 = -16.57 +   1.33)

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 13:20:54 2006