Locus 5658

Sequence ID 3L_DroMel_CAF1
Location 15,534,153 – 15,534,284
Length 131
Max. P 0.986379
window8947 window8948 window8949

overview

Window 7

Location 15,534,153 – 15,534,253
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.75
Mean single sequence MFE -33.92
Consensus MFE -25.82
Energy contribution -26.43
Covariance contribution 0.61
Combinations/Pair 1.17
Mean z-score -2.30
Structure conservation index 0.76
SVM decision value 0.74
SVM RNA-class probability 0.838761
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15534153 100 + 23771897
UCUAGGGGAUACACCGCCCUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUGCCAUC--CACAUA------------------
..((((((......).)))))....((..((((((.((((.(((((..........)))))..((((....)))))))).))))))...))...--......------------------ ( -32.00)
>DroSec_CAF1 4203 100 + 1
UCUAGGGGAUACACCGCCCUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUCCCAAC--CACAAA------------------
..((((((......).)))))....(((.((((((.((((.(((((..........)))))..((((....)))))))).)))))).)))....--......------------------ ( -33.70)
>DroAna_CAF1 8434 99 + 1
UCCCGCGGCUACACAGCCCUGCUUCGAAAGAUCUCCUACCAGCAGCACACCAACUCGCUGCGAGGAGUUAGCAGCGGUAAGCCA---CCCGAGCAGCACAUG------------------
..((((((((....)))).((((((....)).(((((....(((((..........))))).)))))..))))))))...(((.---...).))........------------------ ( -32.90)
>DroSim_CAF1 5386 100 + 1
UCUAGGGGAUACACCGCCCUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUCCCAAC--CACAUA------------------
..((((((......).)))))....(((.((((((.((((.(((((..........)))))..((((....)))))))).)))))).)))....--......------------------ ( -33.70)
>DroEre_CAF1 7479 97 + 1
UCUAGGGGAUACACCGCCUUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGUUGCGCGCUGUUAGCAGCGGUAAGAGAAUAUCCCCGC--CAC---------------------
....(((((((..(((........)))....((((.((((.(((((..........)))))..((((....)))))))).)))).)))))))..--...--------------------- ( -34.40)
>DroYak_CAF1 5798 118 + 1
UCUAGGGGAUACACCGCCUUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGCUGCGCGCUGUCAGCAGCGGUAAGAGAAUAUCCCCAC--CACACAACCAAUUUCUGCUGCUUU
....(((((((..(((........)))....((((.((((.(((((..........)))))..((((....)))))))).)))).)))))))..--........................ ( -36.80)
>consensus
UCUAGGGGAUACACCGCCCUGCUCCGGAAGAUCUCCUAUCAGCAGCACACCAACUCGCUGCGCGCUGUCAGCAGCGGUAAGAGAUUAUCCCAAC__CACAUA__________________
.....((((((.............(....).((((.((((.(((((..........)))))..((((....)))))))).)))).))))))............................. (-25.82 = -26.43 +   0.61)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,534,193 – 15,534,284
Length 91
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 68.19
Mean single sequence MFE -18.28
Consensus MFE -15.50
Energy contribution -15.10
Covariance contribution -0.40
Combinations/Pair 1.20
Mean z-score -0.54
Structure conservation index 0.85
SVM decision value 2.04
SVM RNA-class probability 0.986379
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15534193 91 + 23771897
AGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUGCCAUCCACAUA---------------------------AAAAAACCUCAUGUUGUUUAUGAAAUGACUU
(((((((......((((((((.(((.....))))))))..))).(((((.......))))---------------------------)..........)))))))............. ( -20.50)
>DroSec_CAF1 4243 73 + 1
AGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUCCCAACCACAAA----------------------------AAAA-----------------AAUAGAUUU
.(((((..........)))))..((((....))))(((..((.....))...))).....----------------------------....-----------------......... ( -15.80)
>DroSim_CAF1 5426 74 + 1
AGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUCCCAACCACAUA---------------------------AAAAA-----------------GAAAGAUUU
.(((((..........)))))..((((....))))(((..((.....))...))).....---------------------------.....-----------------......... ( -15.80)
>DroEre_CAF1 7519 97 + 1
AGCAGCACACCAACUCGUUGCGCGCUGUUAGCAGCGGUAAGAGAAUAUCCCCGCCAC---------------------AAUUCGUUCGAAGAACCUUAUAUUUAUUAUGAAAAGAUUU
.(((((..........))))).(((((....)))))(((((.((((...........---------------------.))))((((...)))))))))................... ( -17.70)
>DroYak_CAF1 5838 118 + 1
AGCAGCACACCAACUCGCUGCGCGCUGUCAGCAGCGGUAAGAGAAUAUCCCCACCACACAACCAAUUUCUGCUGCUUUAAUUUGUUAGAAGAACCAUUUAUUUGUUAUGAAAAGAUUU
(((((((.........(((((.........)))))(((..((.....))...)))..............)))))))....................(((((.....)))))....... ( -21.60)
>consensus
AGCAGCACACCAACUCGCUGCGCGCUGUCAGCGGCGGUAAGAGAUUAUCCCAACCACAUA___________________________AAAAAACC___U_UU__UUAUGAAAAGAUUU
.(((((..........))))).(((((....))))).................................................................................. (-15.50 = -15.10 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,534,193 – 15,534,284
Length 91
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 68.19
Mean single sequence MFE -24.28
Consensus MFE -17.16
Energy contribution -16.84
Covariance contribution -0.32
Combinations/Pair 1.18
Mean z-score -0.86
Structure conservation index 0.71
SVM decision value 0.18
SVM RNA-class probability 0.623200
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15534193 91 - 23771897
AAGUCAUUUCAUAAACAACAUGAGGUUUUUU---------------------------UAUGUGGAUGGCAUAAUCUCUUACCGCCGCUGACAGCGCGCAGCGAGUUGGUGUGCUGCU
..(((((((((((((.(((.....)))..))---------------------------)))).))))))).............(((((..((.((.....))..))..))).)).... ( -23.10)
>DroSec_CAF1 4243 73 - 1
AAAUCUAUU-----------------UUUU----------------------------UUUGUGGUUGGGAUAAUCUCUUACCGCCGCUGACAGCGCGCAGCGAGUUGGUGUGCUGCU
.........-----------------....----------------------------...(((((.(((.....)))..)))))......((((((((.........)))))))).. ( -19.60)
>DroSim_CAF1 5426 74 - 1
AAAUCUUUC-----------------UUUUU---------------------------UAUGUGGUUGGGAUAAUCUCUUACCGCCGCUGACAGCGCGCAGCGAGUUGGUGUGCUGCU
.........-----------------.....---------------------------...(((((.(((.....)))..)))))......((((((((.........)))))))).. ( -19.60)
>DroEre_CAF1 7519 97 - 1
AAAUCUUUUCAUAAUAAAUAUAAGGUUCUUCGAACGAAUU---------------------GUGGCGGGGAUAUUCUCUUACCGCUGCUAACAGCGCGCAACGAGUUGGUGUGCUGCU
........................((((...)))).....---------------------(..(((((((.....)))..))))..)...((((((((((....)).)))))))).. ( -23.50)
>DroYak_CAF1 5838 118 - 1
AAAUCUUUUCAUAACAAAUAAAUGGUUCUUCUAACAAAUUAAAGCAGCAGAAAUUGGUUGUGUGGUGGGGAUAUUCUCUUACCGCUGCUGACAGCGCGCAGCGAGUUGGUGUGCUGCU
..........................................(((((((..((((.((((((((((((((......)))))))((((....))))))))))).))))....))))))) ( -35.60)
>consensus
AAAUCUUUUCAUAA__AA_A___GGUUUUUC___________________________UAUGUGGUUGGGAUAAUCUCUUACCGCCGCUGACAGCGCGCAGCGAGUUGGUGUGCUGCU
.............................................................(((((.((............)))))))...((((((((((....)).)))))))).. (-17.16 = -16.84 +  -0.32)

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 11:55:54 2006