Locus 1363

Sequence ID 3L_DroMel_CAF1
Location 3,971,590 – 3,971,696
Length 106
Max. P 0.998099
window2120 window2121

overview

Window 0

Location 3,971,590 – 3,971,696
Length 106
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 78.82
Mean single sequence MFE -34.28
Consensus MFE -20.98
Energy contribution -23.18
Covariance contribution 2.20
Combinations/Pair 1.14
Mean z-score -2.10
Structure conservation index 0.61
SVM decision value 1.05
SVM RNA-class probability 0.907270
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3971590 106 + 23771897
GCAUAGAAUACAUUGGGCGCGCUACAGAAAUCUCUAAGGA---CUUGAAGCCAAGUCGCAAUCCGGCUCGGGUGACCAGACUUAGACAUCUCUGUUGCACAACCGAUAA
...........(((((..(.((.(((((.((.((((((((---((((....))))))((......))..((....))...)))))).)).))))).)).)..))))).. ( -35.60)
>DroSec_CAF1 43934 106 + 1
GCAUAGAAUACAUUGGGCGCGCCACAGAAAUCUCUAAGGA---CUCGAAGCCAAGUCGCAAUCCGGCUCGGGGGACCAGACUUAGACAUCUCUGUGGCACUACCGAUAA
...........(((((..(.((((((((.((.((((((..---...((.(((............)))))((....))...)))))).)).)))))))).)..))))).. ( -38.20)
>DroSim_CAF1 47417 106 + 1
GCAUAGAAUACAUUGGGCGCGCCACAGAAAUCUCUGAGGA---CUCGAAGCCAAGUCGCAAUUCGGCUCGGGGGACCAGACUUAGAAAUCUCUGUUGCACUACCGAUAA
...........(((((..(.((.(((((.((.((((((((---..((((((......))..))))..))((....))...)))))).)).))))).)).)..))))).. ( -32.90)
>DroEre_CAF1 44989 109 + 1
GCAUGAAACACAUUGGCCGUGCCACAGAAAUCUCUGAGGAAAUCUUGAGACGGAGUCGUAAUCCGGCUCGGUGGACCAGACUUGGACGUUUCUGUUGCACCACCGGUAA
...........(((((..((((.((((((((.((..((........(((.((((.......)))).)))((....))...))..)).)))))))).))))..))))).. ( -38.60)
>DroYak_CAF1 47166 89 + 1
GCAUCAAACACAUUGGGCGCUACACAAAAAUC--------------------AAGUCGUGAUCCGGCUCGUUGGACCAGACUUGGGGAUUUCUGUUGCAACGCCGAUGA
..........(((((((.((.(((.(((..((--------------------(((((.((.(((((....))))).)))))))))...))).))).))..).)))))). ( -26.10)
>consensus
GCAUAGAAUACAUUGGGCGCGCCACAGAAAUCUCUAAGGA___CUCGAAGCCAAGUCGCAAUCCGGCUCGGGGGACCAGACUUAGACAUCUCUGUUGCACCACCGAUAA
...........(((((..(.((.(((((.((.((((((...............(((((.....))))).((....))...)))))).)).))))).)).)..))))).. (-20.98 = -23.18 +   2.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,971,590 – 3,971,696
Length 106
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 78.82
Mean single sequence MFE -39.14
Consensus MFE -22.96
Energy contribution -24.16
Covariance contribution 1.20
Combinations/Pair 1.15
Mean z-score -3.11
Structure conservation index 0.59
SVM decision value 3.01
SVM RNA-class probability 0.998099
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3971590 106 - 23771897
UUAUCGGUUGUGCAACAGAGAUGUCUAAGUCUGGUCACCCGAGCCGGAUUGCGACUUGGCUUCAAG---UCCUUAGAGAUUUCUGUAGCGCGCCCAAUGUAUUCUAUGC
.....((.(((((.((((((((.((((((((((((.......))))))....((((((....))))---)))))))).)))))))).))))).)).............. ( -41.80)
>DroSec_CAF1 43934 106 - 1
UUAUCGGUAGUGCCACAGAGAUGUCUAAGUCUGGUCCCCCGAGCCGGAUUGCGACUUGGCUUCGAG---UCCUUAGAGAUUUCUGUGGCGCGCCCAAUGUAUUCUAUGC
.....((..(((((((((((((.((((((((((((.......))))))....((((((....))))---)))))))).)))))))))))))..)).............. ( -47.50)
>DroSim_CAF1 47417 106 - 1
UUAUCGGUAGUGCAACAGAGAUUUCUAAGUCUGGUCCCCCGAGCCGAAUUGCGACUUGGCUUCGAG---UCCUCAGAGAUUUCUGUGGCGCGCCCAAUGUAUUCUAUGC
.....((..((((.((((((((((((.((.((.(....(((((.((.....)).)))))...).))---..)).)))))))))))).))))..)).............. ( -35.10)
>DroEre_CAF1 44989 109 - 1
UUACCGGUGGUGCAACAGAAACGUCCAAGUCUGGUCCACCGAGCCGGAUUACGACUCCGUCUCAAGAUUUCCUCAGAGAUUUCUGUGGCACGGCCAAUGUGUUUCAUGC
.....(((.((((.((((((..(((..((((((((.......))))))))..)))...(((((.((.....))..))))))))))).)))).))).............. ( -35.60)
>DroYak_CAF1 47166 89 - 1
UCAUCGGCGUUGCAACAGAAAUCCCCAAGUCUGGUCCAACGAGCCGGAUCACGACUU--------------------GAUUUUUGUGUAGCGCCCAAUGUGUUUGAUGC
.(((((((((((((.((((((((...(((((((((((........)))))).)))))--------------------)))))))))))))))))(.....)...)))). ( -35.70)
>consensus
UUAUCGGUAGUGCAACAGAGAUGUCUAAGUCUGGUCCCCCGAGCCGGAUUGCGACUUGGCUUCAAG___UCCUCAGAGAUUUCUGUGGCGCGCCCAAUGUAUUCUAUGC
.....((..((((.((((((((.((..((((((((.......))))))))((......))...............)).)))))))).))))..)).............. (-22.96 = -24.16 +   1.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:39 2006