Locus 563

Sequence ID X_DroMel_CAF1
Location 1,616,263 – 1,616,412
Length 149
Max. P 0.979439
window885 window886 window887

overview

Window 5

Location 1,616,263 – 1,616,377
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 72.84
Mean single sequence MFE -39.55
Consensus MFE -21.44
Energy contribution -24.82
Covariance contribution 3.38
Combinations/Pair 1.14
Mean z-score -2.26
Structure conservation index 0.54
SVM decision value 1.73
SVM RNA-class probability 0.974571
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1616263 114 - 22224390
GCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUGAGUAUGUUCAUGUGUGAGUAUCUUAAAGGACUACU------
.......((((((....(((((((((.....))).))))))((((((....))))))))))))((.(((((.....(((((.(((((((....)))))))))))).))))).))------ ( -42.60)
>DroSec_CAF1 11975 118 - 1
GCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG--CAUGUCCAUGUGCGAGUAUCUUAAAGGAGGACUAAUCUC
...(((.((((((....(((((((((.....))).))))))((((((....))))))))))))...(((((.....(((--(((......))))))...(((....))))))))..))). ( -44.10)
>DroSim_CAF1 27884 118 - 1
GCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG--CAUGUCCAUGUGCGAGUAUCUUAAAGGACGACUACUCUC
...((((((((((....(((((((((.....))).))))))((((((....)))))))))))....))))).......(--(((......))))((((((((....)))....))))).. ( -44.20)
>DroYak_CAF1 13799 98 - 1
GCAGGACUGGCGAUCAAGCUGUUG---------------GGGCCCAGCA----AUCACAGCAAAGGAGCCCAAGUAGCCAG-GCAUCCAUG--UACAUAUCUUAAAGGGUGAAUACCUAC
..(((.(((((......(((....---------------((((((.((.----......))...)).)))).))).)))))-.(((((...--.............)))))....))).. ( -27.29)
>consensus
GCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG__CAUGUCCAUGUGCGAGUAUCUUAAAGGACGACUACUCUC
...((((((((......(((((((((.....))).))))))((((((....))))))..)))....)))))............(((((..................)))))......... (-21.44 = -24.82 +   3.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,616,297 – 1,616,412
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 97.66
Mean single sequence MFE -35.40
Consensus MFE -34.20
Energy contribution -34.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.97
SVM decision value 0.51
SVM RNA-class probability 0.763442
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1616297 115 + 22224390
UCAACACUUGGACUCCUUGGCAAGGACCUUUUCAGGUCCGCUGUGAUUGCUGGCCAACACAGCUUGAUCGCCAGUCCUGCGUGAAUCCCCCGUCCACAAGGCCCAGAGAUCAUUC
....(((..(((((....(((..((((((....))))))((((((.(((.....)))))))))......))))))))...)))......((........)).............. ( -34.50)
>DroSec_CAF1 12014 112 + 1
-CAACACUUGGACUCCUUGGCAAGGACCUUUUCAGGUCCGCUGUGAUUGCUGGCCAACACAGCUUGAUCGCCAGUCCUGCGUGAAUCCCC--UCCACAAGGCCCAGAGAUCAUUC
-...(((..(((((....(((..((((((....))))))((((((.(((.....)))))))))......))))))))...))).....((--(.....))).............. ( -34.60)
>DroSim_CAF1 27923 112 + 1
-CAACACUUGGACUCCUUGGCAAGGACCUUUUCAGGUCCGCUGUGAUUGCUGGCCAACACAGCUUGAUCGCCAGUCCUGCGUGAAUCCCC--UUCACAAGGCCCAGAGAUCAUUC
-.......(((.(((.(((((..((((((....))))))((((((.(((.....)))))))))......))))).(((..(((((.....--))))).)))....))).)))... ( -37.10)
>consensus
_CAACACUUGGACUCCUUGGCAAGGACCUUUUCAGGUCCGCUGUGAUUGCUGGCCAACACAGCUUGAUCGCCAGUCCUGCGUGAAUCCCC__UCCACAAGGCCCAGAGAUCAUUC
........(((.(((.(((((..((((((....))))))((((((.(((.....)))))))))......))))).(((..(((...........))).)))....))).)))... (-34.20 = -34.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,616,297 – 1,616,412
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 97.66
Mean single sequence MFE -46.50
Consensus MFE -44.57
Energy contribution -44.90
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.96
SVM decision value 1.84
SVM RNA-class probability 0.979439
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1616297 115 - 22224390
GAAUGAUCUCUGGGCCUUGUGGACGGGGGAUUCACGCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUGA
....(((((((.(.((....)).).)))))))(((...((((((((((....(((((((((.....))).))))))((((((....)))))))))))....)))))..))).... ( -48.40)
>DroSec_CAF1 12014 112 - 1
GAAUGAUCUCUGGGCCUUGUGGA--GGGGAUUCACGCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG-
....(((((((...((....)).--)))))))(((...((((((((((....(((((((((.....))).))))))((((((....)))))))))))....)))))..)))...- ( -46.60)
>DroSim_CAF1 27923 112 - 1
GAAUGAUCUCUGGGCCUUGUGAA--GGGGAUUCACGCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG-
...((..((((.(((((((((((--.....)))))).))).))(((((....(((((((((.....))).))))))((((((....)))))))))))..))))..)).......- ( -44.50)
>consensus
GAAUGAUCUCUGGGCCUUGUGGA__GGGGAUUCACGCAGGACUGGCGAUCAAGCUGUGUUGGCCAGCAAUCACAGCGGACCUGAAAAGGUCCUUGCCAAGGAGUCCAAGUGUUG_
....(((((((...((....))...)))))))(((...((((((((((....(((((((((.....))).))))))((((((....)))))))))))....)))))..))).... (-44.57 = -44.90 +   0.33)

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 09:47:50 2006