Locus 8308

Sequence ID 3R_DroMel_CAF1
Location 22,185,106 – 22,185,231
Length 125
Max. P 0.696592
window13396 window13397 window13398

overview

Window 6

Location 22,185,106 – 22,185,205
Length 99
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.36
Mean single sequence MFE -31.46
Consensus MFE -18.82
Energy contribution -20.13
Covariance contribution 1.31
Combinations/Pair 1.34
Mean z-score -1.75
Structure conservation index 0.60
SVM decision value 0.34
SVM RNA-class probability 0.696592
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22185106 99 - 27905053
-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUCUUGGCCAAACUAUGUGGCGCAGAGUGGAUUUG---------------AAUUCACCUG
-.....(((((((.......))).))))......(((((.((..(....)..)).))))).((((.......)))).(((.((((((...---------------.))))))))) ( -33.70)
>DroPse_CAF1 55943 104 - 1
UUAAUUGGCCUCAUUAGAUUUAAUGGC--UGAAUGGUAUGUGUGUUUGC--------UCGGAGGAAACGUUGUUUCGCCGA-UGGCCUUGUGAUAAAAGAAGGCGAGAACACCUU
....(..(((..............)))--..).........((((((..--------((((..(((((...))))).))))-..(((((.(......).)))))..))))))... ( -27.34)
>DroSec_CAF1 29630 99 - 1
-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGAGAUGUGUGCGUGAGUGCGGGUUUUGGCCAAACUAUGUGGCGCAGAGUGGAUUUG---------------AAUUCACCUG
-.....(((((((.......))).))))......(((((.((..(....)..)).))))).((((.......)))).(((.((((((...---------------.))))))))) ( -31.90)
>DroSim_CAF1 28462 99 - 1
-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUUUUGGCCAAACUAUGUGGUGCAGAGUGGAUUUG---------------GAUUCACCUG
-...((((((((((((....))))))(((.....)))((.((..(....)..)).))...))))))...........(((.((((((...---------------.))))))))) ( -29.60)
>DroEre_CAF1 43817 99 - 1
-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAAGGAUGUGCGCGUGAGUGUGGGUUCUGGCCAAACUAUGUUGCGUAGGGUGGAUGUG---------------AAUUCACCUG
-...((((((((((((....))))))........(((((.(((((....))))).))))))))))).(((((...)))))(((((((...---------------.))))))).. ( -35.20)
>DroYak_CAF1 35946 99 - 1
-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAAGGAUGUGUGCGUGGGUGUGGAUUCUGGCCAAACUAUGUUGCGCAGGGUGGAUUUG---------------AAUUCACCUG
-.....(((((((.......))).))))..........(((((((((((...(((.......)))..))))).))))))((((((((...---------------.)))))))). ( -31.00)
>consensus
_UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUUCUGGCCAAACUAUGUGGCGCAGAGUGGAUUUG_______________AAUUCACCUG
....((((((((((((....))))))........(((((.(((((....))))).)))))))))))...........(((.(((((((.................)))))))))) (-18.82 = -20.13 +   1.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,185,126 – 22,185,231
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -20.20
Consensus MFE -14.41
Energy contribution -15.00
Covariance contribution 0.59
Combinations/Pair 1.25
Mean z-score -1.83
Structure conservation index 0.71
SVM decision value 0.04
SVM RNA-class probability 0.551781
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22185126 105 + 27905053
CUGCGCCACAUAGUUUGGCCAAGACCCGCACUCACGCACACAUCCCUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA-AACCACACACUCUAGUGUUGGCCCCA
....((((......((((((.......((......))......(((.....)))................))))))...-......((((....)))))))).... ( -23.60)
>DroPse_CAF1 55977 94 + 1
CGGCGAAACAACGUUUCCUCCGA--------GCAAACACACAUACCAUUCA--GCCAUUAAAUCUAAUGAGGCCAAUUAAAACCACAUACUCU--UACUCUACGCA
(((.(((((...)))))..))).--------((..................--..(((((....))))).((..........)).........--........)). (  -9.50)
>DroSec_CAF1 29650 105 + 1
CUGCGCCACAUAGUUUGGCCAAAACCCGCACUCACGCACACAUCUCUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA-AACCACACACUCCAGUGUUGGCCCCA
.((.(((.(((((..(((((.......((......))...((........)))))))......)).))).)))))....-..(((.((((....)))))))..... ( -22.80)
>DroSim_CAF1 28482 105 + 1
CUGCACCACAUAGUUUGGCCAAAACCCGCACUCACGCACACAUCCCUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA-AACCACACACUCCAGUGUUGGCCCCA
..............((((((.......((......))......(((.....)))................))))))...-..(((.((((....)))))))..... ( -21.60)
>DroEre_CAF1 43837 105 + 1
CUACGCAACAUAGUUUGGCCAGAACCCACACUCACGCGCACAUCCUUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA-AACCACACACUCCAGUAUUGGCCCCA
..........(((..(((((((((.......................)))).)))))......))).((.(((((((..-................))))))).)) ( -18.37)
>DroYak_CAF1 35966 105 + 1
CUGCGCAACAUAGUUUGGCCAGAAUCCACACCCACGCACACAUCCUUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA-AGCCACACACUCCAGUGUUGGCCCCA
..((.(((((((((.(((((((((.......................)))))((((.(((.......))))))).....-.))))...)))...)))))))).... ( -25.30)
>consensus
CUGCGCAACAUAGUUUGGCCAAAACCCGCACUCACGCACACAUCCCUUUCUGGGCCAUCAAAUCUAAUGAGGCCAAUUA_AACCACACACUCCAGUGUUGGCCCCA
................((((((..............................((((.(((.......))))))).............(((....)))))))))... (-14.41 = -15.00 +   0.59)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,185,126 – 22,185,231
Length 105
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -33.51
Consensus MFE -23.81
Energy contribution -24.40
Covariance contribution 0.59
Combinations/Pair 1.48
Mean z-score -1.74
Structure conservation index 0.71
SVM decision value -0.03
SVM RNA-class probability 0.517409
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22185126 105 - 27905053
UGGGGCCAACACUAGAGUGUGUGGUU-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUCUUGGCCAAACUAUGUGGCGCAG
..(.((((((((....))))((((((-(....(((((((.......))).))))......(((((.((..(....)..)).)))))....))))))).)))).).. ( -38.00)
>DroPse_CAF1 55977 94 - 1
UGCGUAGAGUA--AGAGUAUGUGGUUUUAAUUGGCCUCAUUAGAUUUAAUGGC--UGAAUGGUAUGUGUGUUUGC--------UCGGAGGAAACGUUGUUUCGCCG
......(((((--((..((((((.(.....(..(((..............)))--..)..).))))))..)))))--------))((..(((((...))))).)). ( -21.54)
>DroSec_CAF1 29650 105 - 1
UGGGGCCAACACUGGAGUGUGUGGUU-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGAGAUGUGUGCGUGAGUGCGGGUUUUGGCCAAACUAUGUGGCGCAG
..(.((((((((....))))((((((-(....(((((((.......))).))))......(((((.((..(....)..)).)))))....))))))).)))).).. ( -36.20)
>DroSim_CAF1 28482 105 - 1
UGGGGCCAACACUGGAGUGUGUGGUU-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUUUUGGCCAAACUAUGUGGUGCAG
..(.((((((((....))))((((((-....(((((((((((....))))))(((.....)))((.((..(....)..)).))...))))))))))).)))).).. ( -34.10)
>DroEre_CAF1 43837 105 - 1
UGGGGCCAAUACUGGAGUGUGUGGUU-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAAGGAUGUGCGCGUGAGUGUGGGUUCUGGCCAAACUAUGUUGCGUAG
((((((((((..((((.(....).))-))))))))))))..........(((((......(((((.(((((....))))).))))))))))..(((((...))))) ( -35.60)
>DroYak_CAF1 35966 105 - 1
UGGGGCCAACACUGGAGUGUGUGGCU-UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAAGGAUGUGUGCGUGGGUGUGGAUUCUGGCCAAACUAUGUUGCGCAG
..((((((((((....))))(.((((-.....)))).)...........)))))).........(((((((((((...(((.......)))..))))).)))))). ( -35.60)
>consensus
UGGGGCCAACACUGGAGUGUGUGGUU_UAAUUGGCCUCAUUAGAUUUGAUGGCCCAGAAAGGGAUGUGUGCGUGAGUGCGGGUUCUGGCCAAACUAUGUGGCGCAG
..((((((.((.......(((.((((......)))).)))......)).)))))).....(((((.(((((....))))).))))).((((.......)))).... (-23.81 = -24.40 +   0.59)

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 13:08:30 2006