Locus 2098

Sequence ID 3R_DroMel_CAF1
Location 5,978,373 – 5,978,504
Length 131
Max. P 0.964012
window3430 window3431 window3432

overview

Window 0

Location 5,978,373 – 5,978,466
Length 93
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 79.13
Mean single sequence MFE -30.52
Consensus MFE -18.97
Energy contribution -19.75
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.62
SVM decision value 1.24
SVM RNA-class probability 0.934794
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5978373 93 + 27905053
AGCAACUUGGCAUCUUUUUGGGGGGAUAAUGCUCCCCAGCU--GG---GCACGAUCAAUGUGAAGAUCGUACAUCA-------UGCUGGCUGUUU-U---UUUUUUCGA
((((..(..((((((..((((((((......))))))))..--))---(.((((((........)))))).)...)-------)))..).)))).-.---......... ( -27.50)
>DroSec_CAF1 7065 101 + 1
AGCAACUUAGCAGCUUUUUGGGGGGAUAAUGCUCCCCAGCU--GG---GCACGAUCAAUGUGAAGAUCGUACAUCAUACAUCGUACUGGUUGUUUAU---UUUUUUCGA
(((((((..((.((((.((((((((......))))))))..--))---))((((((........))))))............))...)))))))...---......... ( -31.00)
>DroSim_CAF1 7128 97 + 1
AGCAACUUAGCAGCUUUUUGGGGGGAUAAUGCUCCCCAGCU--GG---GCACGAUCAAUUUGAAGAUCGUACAUCAUACAUCAUGCAGGUUGU-------UUUUUUCGA
((((((((.(((((((.((((((((......))))))))..--))---))((((((........)))))).............))))))))))-------)........ ( -34.50)
>DroEre_CAF1 7786 89 + 1
AGCAACUCUGCAUCUUUUUGGGGGGAUAAUGCUCCCCAGCU--GG---GCACGAUCAAUGUGAAGAUCGUACAUCA-------UACUGGUUGUU--------UUUUCGA
(((((((..((..((..((((((((......))))))))..--))---))((((((........))))))......-------....)))))))--------....... ( -27.00)
>DroYak_CAF1 7514 91 + 1
AGCAACUUGGCAUCUUUUUGG-GGGAUAAUGCUCCCCAGCU--GGGGUGCACGAUCAGUGUGAGGAUCGUACAUCA-------UACUGGUUGUU--------UUUUCGA
.(((.((..((..(.....)(-((((......))))).)).--.)).)))((((((((((((((.......).)))-------)))))))))).--------....... ( -35.10)
>DroAna_CAF1 5973 85 + 1
AGAAGG---GC---------GGGGGAUAGUGC-CCCCAGCUCCGG---GCACGAUCAAUGUGAAGAUCGUACAUUA-------UGUUGCUUAUAC-UCCGUGUUUUCGA
.((((.---((---------(((((((.((((-((........))---)))).)))((((((.......)))))).-------...........)-))))).))))... ( -28.00)
>consensus
AGCAACUUAGCAUCUUUUUGGGGGGAUAAUGCUCCCCAGCU__GG___GCACGAUCAAUGUGAAGAUCGUACAUCA_______UACUGGUUGUU______UUUUUUCGA
.((((((...........(((((((......)))))))((........))((((((........)))))).................))))))................ (-18.97 = -19.75 +   0.78)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,978,373 – 5,978,466
Length 93
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 79.13
Mean single sequence MFE -26.45
Consensus MFE -19.24
Energy contribution -19.43
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -2.50
Structure conservation index 0.73
SVM decision value 1.56
SVM RNA-class probability 0.964012
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5978373 93 - 27905053
UCGAAAAAA---A-AAACAGCCAGCA-------UGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCAUUAUCCCCCCAAAAAGAUGCCAAGUUGCU
.........---.-...((((..(((-------(...((((((((........))))))))---..--....(((((......)))))........))))...)))).. ( -26.40)
>DroSec_CAF1 7065 101 - 1
UCGAAAAAA---AUAAACAACCAGUACGAUGUAUGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCAUUAUCCCCCCAAAAAGCUGCUAAGUUGCU
.........---.....((((................((((((((........))))))))---.(--(((((((((......)))))......)))))....)))).. ( -27.20)
>DroSim_CAF1 7128 97 - 1
UCGAAAAAA-------ACAACCUGCAUGAUGUAUGAUGUACGAUCUUCAAAUUGAUCGUGC---CC--AGCUGGGGAGCAUUAUCCCCCCAAAAAGCUGCUAAGUUGCU
.........-------.((((..((............((((((((........))))))))---..--(((((((((......)))))......))))))...)))).. ( -27.40)
>DroEre_CAF1 7786 89 - 1
UCGAAAA--------AACAACCAGUA-------UGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCAUUAUCCCCCCAAAAAGAUGCAGAGUUGCU
.......--------..(((((.(((-------(...((((((((........))))))))---..--....(((((......)))))........)))).).)))).. ( -25.10)
>DroYak_CAF1 7514 91 - 1
UCGAAAA--------AACAACCAGUA-------UGAUGUACGAUCCUCACACUGAUCGUGCACCCC--AGCUGGGGAGCAUUAUCCC-CCAAAAAGAUGCCAAGUUGCU
.......--------..((((..(((-------(..(((((((((........)))))))))....--....(((((......))))-).......))))...)))).. ( -24.80)
>DroAna_CAF1 5973 85 - 1
UCGAAAACACGGA-GUAUAAGCAACA-------UAAUGUACGAUCUUCACAUUGAUCGUGC---CCGGAGCUGGGG-GCACUAUCCCCC---------GC---CCUUCU
..(((.....((.-((....))....-------....((((((((........))))))))---))((.((.((((-(......)))))---------))---))))). ( -27.80)
>consensus
UCGAAAAAA______AACAACCAGCA_______UGAUGUACGAUCUUCACAUUGAUCGUGC___CC__AGCUGGGGAGCAUUAUCCCCCCAAAAAGAUGCCAAGUUGCU
.................((((..((............((((((((........))))))))...........(((((......)))))..........))...)))).. (-19.24 = -19.43 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,978,402 – 5,978,504
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.04
Mean single sequence MFE -26.77
Consensus MFE -14.58
Energy contribution -14.83
Covariance contribution 0.25
Combinations/Pair 1.06
Mean z-score -1.95
Structure conservation index 0.54
SVM decision value 0.70
SVM RNA-class probability 0.825898
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5978402 102 - 27905053
--CAUAUCUCAAAGCUGGCAAUAAACGUGACAUAGAAGCCUCGAAAAAA---A-AAACAGCCAGCA-------UGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCA
--...........((((((..................))).........---.-......(((((.-------((..((((((((........))))))))---.)--))))))..))). ( -26.67)
>DroSec_CAF1 7094 93 - 1
------------------UAAUAAACGUGACAAAGA-CCCUCGAAAAAA---AUAAACAACCAGUACGAUGUAUGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCA
------------------................(.-.(((((......---.....((..((......))..))..((((((((........))))))))---..--...)))))..). ( -17.40)
>DroSim_CAF1 7157 104 - 1
--UAUCUC-CAAAGCUGGCAAUAAACGUGACAAAGA-CCCUCGAAAAAA-------ACAACCUGCAUGAUGUAUGAUGUACGAUCUUCAAAUUGAUCGUGC---CC--AGCUGGGGAGCA
--...(((-(..((((((.......((((.((....-............-------......)))))).........((((((((........))))))))---))--))))..)))).. ( -29.95)
>DroEre_CAF1 7815 98 - 1
UAUAUGUC-CGGAGCUGGCAAUAAACGUGACAAAGA-CUCUCGAAAA--------AACAACCAGUA-------UGAUGUACGAUCUUCACAUUGAUCGUGC---CC--AGCUGGGGAGCA
......((-(..((((((.......((.((......-.)).))....--------...........-------....((((((((........))))))))---))--))))..)))... ( -26.40)
>DroYak_CAF1 7542 99 - 1
--UAUCUC-CAGAGCUGGCAAUAAACGUGACAAAGA-CACUCGAAAA--------AACAACCAGUA-------UGAUGUACGAUCCUCACACUGAUCGUGCACCCC--AGCUGGGGAGCA
--...(((-(..((((((........(((.......-))).......--------...........-------...(((((((((........)))))))))..))--))))..)))).. ( -29.60)
>DroAna_CAF1 5990 104 - 1
--CAUCUC-CGAAGCCGGCACUAAUCGUGACAACGA-CCCUCGAAAACACGGA-GUAUAAGCAACA-------UAAUGUACGAUCUUCACAUUGAUCGUGC---CCGGAGCUGGGG-GCA
--..((((-((...((((.(((..(((((....((.-....))....))))))-))..........-------....((((((((........))))))))---))))...)))))-).. ( -30.60)
>consensus
__UAUCUC_CAAAGCUGGCAAUAAACGUGACAAAGA_CCCUCGAAAAAA______AACAACCAGCA_______UGAUGUACGAUCUUCACAUUGAUCGUGC___CC__AGCUGGGGAGCA
..........................((..(...((....))..................(((((............((((((((........))))))))........))))))..)). (-14.58 = -14.83 +   0.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:22 2006