Locus 4487

Sequence ID 3L_DroMel_CAF1
Location 12,975,623 – 12,975,777
Length 154
Max. P 0.966107
window7001 window7002 window7003

overview

Window 1

Location 12,975,623 – 12,975,737
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.63
Mean single sequence MFE -33.59
Consensus MFE -22.44
Energy contribution -25.52
Covariance contribution 3.08
Combinations/Pair 1.09
Mean z-score -2.64
Structure conservation index 0.67
SVM decision value 1.59
SVM RNA-class probability 0.966107
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12975623 114 + 23771897
UUUUUAGAUCCCAGUCCAAGCAAUUGAAUGAUGUCAGUCAAACACACACACACACACAUAUGGAGACAAG------GUCUCUAAGGAUAAGUCGAUUUGUGUGUCUGUGUGGGCUGGAAA
..........(((((((......((((.((....)).))))....(((((.(((((((..(((((((...------)))))))..((....))....))))))).))))))))))))... ( -38.40)
>DroSec_CAF1 92996 114 + 1
UUUUUAGAUCCCAGUCCAAGCAAUUGAAUGAUGUCAGUCAAACACACACACACACAUAUAUGGAGACAAG------CUCUCUAAGGAUAAGUCGAUUUGUGUGUCUGUGUGGGCUGGAAA
..........(((((((......((((.((....)).))))..(((((.(((((((....((((((....------.))))))..((....))....))))))).))))))))))))... ( -36.50)
>DroSim_CAF1 102703 110 + 1
UUUUUAGAUCCCAGUCCAAGCAAUUGAAUGAUGUCAGUCAAACACUC----ACACAUAUAUGGAGACAAG------CUCUCUAAGGAUAAGUCGAUUUGUGUGUCUGUGUGGGCUGGAAA
..........(((((((......((((.((....)).))))((((..----(((((((..((((((....------.))))))..((....))....)))))))..)))))))))))... ( -33.00)
>DroEre_CAF1 98736 114 + 1
UUUUUAGAUCCAGGUCCAAGGAAUUGAAUGGUGCCAGUCAAACACCCACACACACACA----GAAGCAAGCGUUCUCUUUCUAAGGAUAAGUCGAUUUGUGUGUAUGUGUGGGCUAG--G
.........((.((((((.((..((((.((....)).))))...))((((.(((((((----((.......(((((.......))))).......))))))))).)))))))))).)--) ( -30.84)
>DroYak_CAF1 96932 101 + 1
UUUUUAGACCCAAGUCCAAGCAAUUGAAUGGUGCCAGUCAAACAGACACACACA-------------------UCUCUUUCUAAGGAUAAGUCGAUUUGUCUGUCUGUGUGGGCUGGAAA
.......(((...((.(((....))).))))).((((((..(((((((.(((.(-------------------((.(((((....)).)))..))).))).)))))))...))))))... ( -29.20)
>consensus
UUUUUAGAUCCCAGUCCAAGCAAUUGAAUGAUGUCAGUCAAACACACACACACACACAUAUGGAGACAAG______CUCUCUAAGGAUAAGUCGAUUUGUGUGUCUGUGUGGGCUGGAAA
..........(((((((......((((.((....)).))))(((((.(((((((......((((((...........))))))..((....))....))))))).))))))))))))... (-22.44 = -25.52 +   3.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,975,623 – 12,975,737
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.63
Mean single sequence MFE -31.08
Consensus MFE -17.18
Energy contribution -19.86
Covariance contribution 2.68
Combinations/Pair 1.04
Mean z-score -2.54
Structure conservation index 0.55
SVM decision value 0.82
SVM RNA-class probability 0.858318
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12975623 114 - 23771897
UUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAC------CUUGUCUCCAUAUGUGUGUGUGUGUGUGUUUGACUGACAUCAUUCAAUUGCUUGGACUGGGAUCUAAAAA
.((((((((((((((.(((((((....((....))....(((((------...)))))....))))))).))))))...((((.((....)).))))......)).))))))........ ( -35.60)
>DroSec_CAF1 92996 114 - 1
UUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG------CUUGUCUCCAUAUAUGUGUGUGUGUGUGUUUGACUGACAUCAUUCAAUUGCUUGGACUGGGAUCUAAAAA
.((((((((((((((.(((((((....((....))....((((.------....))))......))))))).)))))).((((.((....)).))))......)).))))))........ ( -33.70)
>DroSim_CAF1 102703 110 - 1
UUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG------CUUGUCUCCAUAUAUGUGU----GAGUGUUUGACUGACAUCAUUCAAUUGCUUGGACUGGGAUCUAAAAA
.((((((.(((......((((((....((....))....((((.------....))))......)))))----)(((..((((.((....)).))))..)))))).))))))........ ( -25.00)
>DroEre_CAF1 98736 114 - 1
C--CUAGCCCACACAUACACACAAAUCGACUUAUCCUUAGAAAGAGAACGCUUGCUUC----UGUGUGUGUGUGGGUGUUUGACUGGCACCAUUCAAUUCCUUGGACCUGGAUCUAAAAA
.--...((((((((((((((.......((....))...((((.(((....)))..)))----)))))))))))))))..((((.((....)).)))).(((........)))........ ( -32.90)
>DroYak_CAF1 96932 101 - 1
UUUCCAGCCCACACAGACAGACAAAUCGACUUAUCCUUAGAAAGAGA-------------------UGUGUGUGUCUGUUUGACUGGCACCAUUCAAUUGCUUGGACUUGGGUCUAAAAA
...((((..((.(((((((.(((.(((..(((.((....))))).))-------------------).))).))))))).)).))))..............((((((....))))))... ( -28.20)
>consensus
UUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG______CUUGUCUCCAUAUAUGUGUGUGUGUGUGUUUGACUGACAUCAUUCAAUUGCUUGGACUGGGAUCUAAAAA
.((((((((((((((.(((((((.........................................))))))).)))))).((((.((....)).))))......)).))))))........ (-17.18 = -19.86 +   2.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,975,663 – 12,975,777
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.15
Mean single sequence MFE -28.22
Consensus MFE -15.54
Energy contribution -18.54
Covariance contribution 3.00
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.55
SVM decision value 0.73
SVM RNA-class probability 0.836214
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12975663 114 - 23771897
AAUUUAAUAAACGAAAACCAAAAAUGCCCUCAGAGUAGGUUUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAC------CUUGUCUCCAUAUGUGUGUGUGUGUGUGUU
............(((((((.....((....)).....))))))).(((.((((((.(((((((....((....))....(((((------...)))))....))))))).)))))).))) ( -31.40)
>DroSec_CAF1 93036 114 - 1
AAAUUAAUAAACGAAAACCAAAAAUGCCCUAAGGGUUGGUUUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG------CUUGUCUCCAUAUAUGUGUGUGUGUGUGUU
............((((((((.....((((...)))))))))))).....((((((.(((((((....((....))....((((.------....))))......))))))).)))))).. ( -33.60)
>DroSim_CAF1 102743 110 - 1
AAUUUAAUAAACGAAAACCAAAAAUGCCCUCAGAGUUGGUUUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG------CUUGUCUCCAUAUAUGUGU----GAGUGUU
............(((((((((...((....))...)))))))))......((((...((((((....((....))....((((.------....))))......)))))----).)))). ( -21.40)
>DroEre_CAF1 98776 114 - 1
AAUUUAAUAACCGAAAACCAAAAAUGCCCUCAGAGUAGGUC--CUAGCCCACACAUACACACAAAUCGACUUAUCCUUAGAAAGAGAACGCUUGCUUC----UGUGUGUGUGUGGGUGUU
...........................(((......)))..--...((((((((((((((.......((....))...((((.(((....)))..)))----)))))))))))))))... ( -28.00)
>DroYak_CAF1 96972 101 - 1
AAUUUAAUAACCGAAAACCAAAAAUGCCCUCAGAGUUGGUUUUCCAGCCCACACAGACAGACAAAUCGACUUAUCCUUAGAAAGAGA-------------------UGUGUGUGUCUGUU
............(((((((((...((....))...)))))))))........(((((((.(((.(((..(((.((....))))).))-------------------).))).))))))). ( -26.70)
>consensus
AAUUUAAUAAACGAAAACCAAAAAUGCCCUCAGAGUUGGUUUUCCAGCCCACACAGACACACAAAUCGACUUAUCCUUAGAGAG______CUUGUCUCCAUAUAUGUGUGUGUGUGUGUU
............(((((((((...((....))...))))))))).....((((((.(((((((.........................................))))))).)))))).. (-15.54 = -18.54 +   3.00)

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 11:24:38 2006