Locus 2052

Sequence ID 3R_DroMel_CAF1
Location 5,817,724 – 5,817,851
Length 127
Max. P 0.994785
window3359 window3360 window3361

overview

Window 9

Location 5,817,724 – 5,817,822
Length 98
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 73.23
Mean single sequence MFE -32.65
Consensus MFE -21.84
Energy contribution -24.53
Covariance contribution 2.69
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.67
SVM decision value 2.35
SVM RNA-class probability 0.992778
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5817724 98 + 27905053
UUUGAGCGAAUCGGACCGUGGACUUUGGACUUUGGA-------ACUCCGCACGGGCAUAUCUAAGUUAUAUCCGUGAGAGUUCGCUUCCGGUUCCGGGCAGAAUC
((((.(.((((((((..(((((((((.......((.-------...)).(((((..(((.......)))..)))))))))))))).)))))))))...))))... ( -34.50)
>DroSim_CAF1 110029 78 + 1
UUUGAGCGAAUCGGACCCUGGACUUUG---------------------------GCAUAUCUAGGUUAUAUCCGUGAGAGUCCGCUUCCGGUUCCGGGCAGAUUC
((((.(.((((((((...((((((((.---------------------------((.......((......)))).))))))))..)))))))))...))))... ( -24.71)
>DroEre_CAF1 106284 94 + 1
UUUGAGCGAUUCGGACCUGGGACCUUGGACUUCGGA-------ACUCCGCACGGAUAUAUG----UUAUAUCCGUGGGAUUCCACUUCCGAUUCCGGCCAGAAUC
.......(((((((.((.((((..(((((....(((-------(.(((.((((((((((..----.)))))))))))))))))...))))))))))))).))))) ( -37.90)
>DroYak_CAF1 95386 105 + 1
UUUGAGCGAUUCGCACUUCGGACUUUGGACUUCGGACUUUGGUACUCCGCACGGAUGUAUGUUUGUUAUAUCCGUGAGAUUCCACUUCCGUUUCCGGGCAGAAUC
.......(((((((.(....)...(((((...((((...(((...((..((((((((((.......)))))))))).))..)))..))))..))))))).))))) ( -33.50)
>consensus
UUUGAGCGAAUCGGACCUUGGACUUUGGACUUCGGA_______ACUCCGCACGGACAUAUCUA_GUUAUAUCCGUGAGAGUCCACUUCCGGUUCCGGGCAGAAUC
((((.(.((((((((....(((((((......((((.........))))((((((((((.......)))))))))))))))))...)))))))))...))))... (-21.84 = -24.53 +   2.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,817,724 – 5,817,822
Length 98
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 73.23
Mean single sequence MFE -31.33
Consensus MFE -16.52
Energy contribution -19.02
Covariance contribution 2.50
Combinations/Pair 1.12
Mean z-score -2.64
Structure conservation index 0.53
SVM decision value 2.51
SVM RNA-class probability 0.994785
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5817724 98 - 27905053
GAUUCUGCCCGGAACCGGAAGCGAACUCUCACGGAUAUAACUUAGAUAUGCCCGUGCGGAGU-------UCCAAAGUCCAAAGUCCACGGUCCGAUUCGCUCAAA
((.((.(((.(((...(((...((((((((((((.((((.......)))).))))).)))))-------)).....)))....)))..)))..)).))....... ( -28.60)
>DroSim_CAF1 110029 78 - 1
GAAUCUGCCCGGAACCGGAAGCGGACUCUCACGGAUAUAACCUAGAUAUGC---------------------------CAAAGUCCAGGGUCCGAUUCGCUCAAA
(((((.(((((....)))..))(((((((...((((...............---------------------------....))))))))))))))))....... ( -23.01)
>DroEre_CAF1 106284 94 - 1
GAUUCUGGCCGGAAUCGGAAGUGGAAUCCCACGGAUAUAA----CAUAUAUCCGUGCGGAGU-------UCCGAAGUCCAAGGUCCCAGGUCCGAAUCGCUCAAA
(((((.((((((.((((((..((((((((((((((((((.----..)))))))))).))).)-------))))...)))..))).)).)))).)))))....... ( -42.00)
>DroYak_CAF1 95386 105 - 1
GAUUCUGCCCGGAAACGGAAGUGGAAUCUCACGGAUAUAACAAACAUACAUCCGUGCGGAGUACCAAAGUCCGAAGUCCAAAGUCCGAAGUGCGAAUCGCUCAAA
(((((.((.((....)(((..((((....(((((((.((.......)).)))))))((((.(.....).))))...))))...)))...).)))))))....... ( -31.70)
>consensus
GAUUCUGCCCGGAACCGGAAGCGGAAUCUCACGGAUAUAAC_UACAUAUACCCGUGCGGAGU_______UCCGAAGUCCAAAGUCCAAGGUCCGAAUCGCUCAAA
(((((...(((....)))....(((((..((((((((((.......)))))))))).(((.........))).........))))).......)))))....... (-16.52 = -19.02 +   2.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,817,755 – 5,817,851
Length 96
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 77.39
Mean single sequence MFE -35.90
Consensus MFE -27.00
Energy contribution -30.62
Covariance contribution 3.62
Combinations/Pair 1.09
Mean z-score -2.22
Structure conservation index 0.75
SVM decision value 2.13
SVM RNA-class probability 0.988661
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5817755 96 - 27905053
GCAGGCCGCAGCCACGGUCGCUGAGCUUCGAUUCUGCCCGGAACCGGAAGCGAACUCUCACGGAUAUAACUUAGAUAUGCCCGUGCGGAGU-------UCCAA
((.(((((......)))))))...((((((.((((....)))).).)))))((((((((((((.((((.......)))).))))).)))))-------))... ( -35.40)
>DroSim_CAF1 110056 80 - 1
GCAGGCCGCAGCCACGGUCGCUGAGCUUCGAAUCUGCCCGGAACCGGAAGCGGACUCUCACGGAUAUAACCUAGAUAUGC-----------------------
((.(((((......)))))))...((.((((.((((((((....)))..))))).))....((......))..))...))----------------------- ( -22.10)
>DroEre_CAF1 106315 92 - 1
GCAGGCCGCAGCCACGGUCGCAGAGCUCCGAUUCUGGCCGGAAUCGGAAGUGGAAUCCCACGGAUAUAA----CAUAUAUCCGUGCGGAGU-------UCCGA
((.(((((......)))))))...(((((((((((....)))))))).)))(((((((((((((((((.----..)))))))))).))).)-------))).. ( -44.80)
>DroYak_CAF1 95417 103 - 1
GCAGGCCGCAGCCACGGUCGCUGAGCUCCGAUUCUGCCCGGAAACGGAAGUGGAAUCUCACGGAUAUAACAAACAUACAUCCGUGCGGAGUACCAAAGUCCGA
...(((....))).(((.(..((.((((((((((..((((....)))..)..))))).(((((((.((.......)).))))))).)))))..))..).))). ( -41.30)
>consensus
GCAGGCCGCAGCCACGGUCGCUGAGCUCCGAUUCUGCCCGGAACCGGAAGCGGAAUCUCACGGAUAUAAC_UACAUAUACCCGUGCGGAGU_______UCCGA
((.(((((......)))))))...((((((((((((((((....)))..)))))))).((((((((((.......)))))))))).)))))............ (-27.00 = -30.62 +   3.62)

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 10:26:13 2006