Locus 1035

Sequence ID 3L_DroMel_CAF1
Location 3,066,390 – 3,066,484
Length 94
Max. P 0.995453
window1599 window1600

overview

Window 9

Location 3,066,390 – 3,066,484
Length 94
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 88.20
Mean single sequence MFE -25.25
Consensus MFE -19.02
Energy contribution -20.62
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.75
SVM decision value 1.42
SVM RNA-class probability 0.952275
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3066390 94 + 23771897
UUGUACGUA--UAUUCGUCUAUAUGCUAUAUAGCGAAUUCAAGGCCAAUAUCACUUGUUUUCUCUUCGUACAUUGGCAAGAGGCAUUGGCCCCGUA
...((((..--.(((((.((((((...)))))))))))....(((((((..(.((((((...............)))))).)..))))))).)))) ( -26.06)
>DroSec_CAF1 27212 96 + 1
UUGUACGUACGUAUUCGUCUAUAUGCUAUAUAGCGAAUUCAAGGCCAAUAUCACUUGUUUUCUCUUCGUACAUUGGCAAGAGGCAUUGGCCCCGUA
...((((...(.(((((.((((((...))))))))))).)..(((((((..(.((((((...............)))))).)..))))))).)))) ( -27.16)
>DroSim_CAF1 27178 96 + 1
UUGUACGUACGUAUUCGUCUAUAUGCUAUAUAGCGAAUUCAAGGCCAAUAUCACUUGUUUUCUCUUCGUACAUUGGCAAGAGGCAUUGGCCCCGUA
...((((...(.(((((.((((((...))))))))))).)..(((((((..(.((((((...............)))))).)..))))))).)))) ( -27.16)
>DroYak_CAF1 27417 92 + 1
UUUUACG----UAUUCGUCUAUAUGCUAUAUAGCGAUUUCAAGGCCAAUAUCACUUGUUUUCUCUUCAUACAUUGGCAAGAGGCAUUGGCCCCGUA
...((((----...(((.((((((...)))))))))......(((((((..(.((((((...............)))))).)..))))))).)))) ( -24.56)
>DroAna_CAF1 29110 85 + 1
U------UACUUAUUCAAGUAUAUGCGA-----AGAAUUCAAGGCCAAUAUCACUUGAUUUCUCUUCGGACGUUGGCAAGAGGCAUUGGCCCGGUA
.------(((((....))))).......-----.........(((((((..(.((((....(((....)).)....)))).)..)))))))..... ( -21.30)
>consensus
UUGUACGUAC_UAUUCGUCUAUAUGCUAUAUAGCGAAUUCAAGGCCAAUAUCACUUGUUUUCUCUUCGUACAUUGGCAAGAGGCAUUGGCCCCGUA
............(((((.((((((...)))))))))))....(((((((..(.((((((...............)))))).)..)))))))..... (-19.02 = -20.62 +   1.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,066,390 – 3,066,484
Length 94
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 88.20
Mean single sequence MFE -24.47
Consensus MFE -21.47
Energy contribution -23.07
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.88
SVM decision value 2.58
SVM RNA-class probability 0.995453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3066390 94 - 23771897
UACGGGGCCAAUGCCUCUUGCCAAUGUACGAAGAGAAAACAAGUGAUAUUGGCCUUGAAUUCGCUAUAUAGCAUAUAGACGAAUA--UACGUACAA
..(((((((((((.(.((((...................)))).).))))))))))).(((((((((((...)))))).))))).--......... ( -26.51)
>DroSec_CAF1 27212 96 - 1
UACGGGGCCAAUGCCUCUUGCCAAUGUACGAAGAGAAAACAAGUGAUAUUGGCCUUGAAUUCGCUAUAUAGCAUAUAGACGAAUACGUACGUACAA
..(((((((((((.(.((((...................)))).).))))))))))).(((((((((((...)))))).)))))............ ( -26.51)
>DroSim_CAF1 27178 96 - 1
UACGGGGCCAAUGCCUCUUGCCAAUGUACGAAGAGAAAACAAGUGAUAUUGGCCUUGAAUUCGCUAUAUAGCAUAUAGACGAAUACGUACGUACAA
..(((((((((((.(.((((...................)))).).))))))))))).(((((((((((...)))))).)))))............ ( -26.51)
>DroYak_CAF1 27417 92 - 1
UACGGGGCCAAUGCCUCUUGCCAAUGUAUGAAGAGAAAACAAGUGAUAUUGGCCUUGAAAUCGCUAUAUAGCAUAUAGACGAAUA----CGUAAAA
..(((((((((((.(.((((...................)))).).)))))))))))...(((((((((...)))))).)))...----....... ( -24.61)
>DroAna_CAF1 29110 85 - 1
UACCGGGCCAAUGCCUCUUGCCAACGUCCGAAGAGAAAUCAAGUGAUAUUGGCCUUGAAUUCU-----UCGCAUAUACUUGAAUAAGUA------A
..(.(((((((((.(.((((......((......))...)))).).))))))))).)......-----.......(((((....)))))------. ( -18.20)
>consensus
UACGGGGCCAAUGCCUCUUGCCAAUGUACGAAGAGAAAACAAGUGAUAUUGGCCUUGAAUUCGCUAUAUAGCAUAUAGACGAAUA_GUACGUACAA
..(((((((((((.(.((((...................)))).).))))))))))).(((((((((((...)))))).)))))............ (-21.47 = -23.07 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:23 2006