Locus 6425

Sequence ID 3R_DroMel_CAF1
Location 16,821,565 – 16,821,707
Length 142
Max. P 0.863023
window10468 window10469 window10470

overview

Window 8

Location 16,821,565 – 16,821,667
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.90
Mean single sequence MFE -22.80
Consensus MFE -5.58
Energy contribution -8.66
Covariance contribution 3.08
Combinations/Pair 1.14
Mean z-score -1.94
Structure conservation index 0.24
SVM decision value 0.84
SVM RNA-class probability 0.863023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16821565 102 - 27905053
GACAAUUAGAAAUAAGUUUAUGCUGUAUA-GCUACUGUACAAUUUUAGUUGCUAAACAGCUUAUAUCUUUGAGAGUAUAA-ACUUGUUCCAUAGAUAACCA----------------AAA
........(.((((((((((((((((.((-((.((((........)))).)))).))..((((......)))))))))))-))))))).)...........----------------... ( -25.20)
>DroSec_CAF1 5485 102 - 1
GAUAAUUAGAAAUAAGUUGAAGCUGUGUA-GCUACUGUGCAAUUUUAGUUGCUAAACAGCUAAAAUCUUUGAGAGUAUAA-ACUUGUUCCAGAGAUGGCCA----------------AAC
.....(((....))).(((.((((((.((-((.((((........)))).)))).))))))...(((((((.(((((...-...))))))))))))...))----------------).. ( -25.80)
>DroSim_CAF1 3352 102 - 1
GAUAAUUAGAAAUAAGUUGAAGCUGUAUA-GCUACUGUGCAAUUUUAGUUGCUAAACAGCUUAUAUCUUUGAGAGUAUAA-ACUUGUUCCAGAGAUGGCCA----------------AAA
.....(((....))).((((((((((.((-((.((((........)))).)))).))))))).((((((((.(((((...-...)))))))))))))..))----------------).. ( -27.90)
>DroEre_CAF1 8696 106 - 1
AAUAAUUAGAAAUUACUUU-----GUAUA-GCUACUGUAAAAUAUGAGUUGCUAAACAGCUUACGCUUUG-AGCGUAUAAAACUUGUUUCAGAGACAACCAAUACGU-------UAGCAU
...................-----.....-((((.((((.....(((((((.....))))))).((((((-((((.........)).))))))).)......)))).-------)))).. ( -18.80)
>DroYak_CAF1 8786 115 - 1
AAUAAUUAUAAAUUAGUUU-----UUGUUGGAAAGUGGAAAGUGUGAGUAGCUAAACAGCCGACGUCUUGCAGAGUAUAAAACUUGUUUCAGAAGCCACAAUAACAUACAAGUUUCAAAA
...............(((.-----((((.((....(((((..((..((..(((....)))......))..))((((.....)))).)))))....)))))).)))............... ( -16.30)
>consensus
GAUAAUUAGAAAUAAGUUUA_GCUGUAUA_GCUACUGUACAAUUUUAGUUGCUAAACAGCUUACAUCUUUGAGAGUAUAA_ACUUGUUCCAGAGAUAACCA________________AAA
.....................(((((....((.((((........)))).))...)))))....(((((((.((((.....))))....)))))))........................ ( -5.58 =  -8.66 +   3.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,821,588 – 16,821,707
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 89.20
Mean single sequence MFE -24.90
Consensus MFE -15.32
Energy contribution -14.88
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -3.46
Structure conservation index 0.62
SVM decision value 0.10
SVM RNA-class probability 0.584010
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16821588 119 + 27905053
UUAUACUCUCAAAGAUAUAAGCUGUUUAGCAACUAAAAUUGUACAGUAGCUAUACAGCAUAAACUUAUUUCUAAUUGUCUGCCAAUUGUUUGCUAUAGAAUAGUAUCUAUGUAGAUAUG
.((((.(((((.((((((..(((((.((((.(((..........))).)))).)))))..........(((((...((..((.....))..))..)))))..)))))).)).))))))) ( -25.40)
>DroSec_CAF1 5508 114 + 1
UUAUACUCUCAAAGAUUUUAGCUGUUUAGCAACUAAAAUUGCACAGUAGCUACACAGCUUCAACUUAUUUCUAAUUAUCUACCAAUUGUUUG-UAUACUCUUG----UAUAUAGAUAUA
...........(((.((..((((((.((((.(((..........))).)))).))))))..)))))....................((((((-(((((....)----)))))))))).. ( -24.20)
>DroSim_CAF1 3375 114 + 1
UUAUACUCUCAAAGAUAUAAGCUGUUUAGCAACUAAAAUUGCACAGUAGCUAUACAGCUUCAACUUAUUUCUAAUUAUCUACCAAUUGUUUG-UAUACUCUUG----UAUAUAGAUAUA
............(((((.(((((((.((((.(((..........))).)))).)))))))...............)))))......((((((-(((((....)----)))))))))).. ( -25.09)
>consensus
UUAUACUCUCAAAGAUAUAAGCUGUUUAGCAACUAAAAUUGCACAGUAGCUAUACAGCUUCAACUUAUUUCUAAUUAUCUACCAAUUGUUUG_UAUACUCUUG____UAUAUAGAUAUA
....................(((((.((((.(((..........))).)))).))))).................((((((..............................)))))).. (-15.32 = -14.88 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,821,588 – 16,821,707
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 89.20
Mean single sequence MFE -25.00
Consensus MFE -19.17
Energy contribution -19.83
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.77
SVM decision value 0.39
SVM RNA-class probability 0.717797
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16821588 119 - 27905053
CAUAUCUACAUAGAUACUAUUCUAUAGCAAACAAUUGGCAGACAAUUAGAAAUAAGUUUAUGCUGUAUAGCUACUGUACAAUUUUAGUUGCUAAACAGCUUAUAUCUUUGAGAGUAUAA
....(((.((.(((((...(((((.........((((.....)))))))))..........(((((.((((.((((........)))).)))).)))))...))))).)))))...... ( -25.10)
>DroSec_CAF1 5508 114 - 1
UAUAUCUAUAUA----CAAGAGUAUA-CAAACAAUUGGUAGAUAAUUAGAAAUAAGUUGAAGCUGUGUAGCUACUGUGCAAUUUUAGUUGCUAAACAGCUAAAAUCUUUGAGAGUAUAA
..((((((((((----(....)))).-(((....)))))))))).(((....))).....((((((.((((.((((........)))).)))).))))))................... ( -24.10)
>DroSim_CAF1 3375 114 - 1
UAUAUCUAUAUA----CAAGAGUAUA-CAAACAAUUGGUAGAUAAUUAGAAAUAAGUUGAAGCUGUAUAGCUACUGUGCAAUUUUAGUUGCUAAACAGCUUAUAUCUUUGAGAGUAUAA
........((((----(....)))))-...((..(..(.(((((.(((....)))....(((((((.((((.((((........)))).)))).))))))).))))))..)..)).... ( -25.80)
>consensus
UAUAUCUAUAUA____CAAGAGUAUA_CAAACAAUUGGUAGAUAAUUAGAAAUAAGUUGAAGCUGUAUAGCUACUGUGCAAUUUUAGUUGCUAAACAGCUUAUAUCUUUGAGAGUAUAA
..............................((..(..(.(((((.(((....)))......(((((.((((.((((........)))).)))).)))))...))))))..)..)).... (-19.17 = -19.83 +   0.67)

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 12:21:11 2006