Locus 6228

Sequence ID 3L_DroMel_CAF1
Location 16,552,037 – 16,552,154
Length 117
Max. P 0.567859
window9992 window9993

overview

Window 2

Location 16,552,037 – 16,552,154
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.88
Mean single sequence MFE -39.80
Consensus MFE -27.32
Energy contribution -26.72
Covariance contribution -0.60
Combinations/Pair 1.40
Mean z-score -1.48
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.567859
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16552037 117 + 23771897
UUGUCCAGCACCACCUUGAGGUGCUUCAUGUCCUUGGCCAGCUGCUCUAUUCCCGUCUGAAUGCUGCUUGUCAGUUGGACGAACUGGCUCGUCCUCGGAUUGAGCUGCUGCCGCUGG
....(((((..((((....))))............(((.(((.((((...(((.........((((.....)))).((((((......))))))..)))..)))).))))))))))) ( -43.50)
>DroSec_CAF1 4994 117 + 1
UUGUCCAGCACCACCUUGAGGUGCUUCACGUCCUUGGACAGCUGUUCAAUUCCCGUCUGUAUGCUGCUCGUCAGUUGGACGAACUGACUCGUCUUCUGAUUGAGCUGCUGCCGCUGG
(((..((((..((((....))))......(((....))).))))..)))...(((.(.(((.((.(((((((((..((((((......)))))).)))).))))).))))).).))) ( -43.40)
>DroSim_CAF1 4928 117 + 1
UUGUCCAGCACCACCUUGAGGUGCUUCACGUCCUUGGACAGCUGUUCAAUUCCCGUCUGUAUGCUGCUCGUCAGUUGGACGAACUGGCUCGUCUUCUGAUUGAGCUGCUGCCGCUGG
(((..((((..((((....))))......(((....))).))))..)))...(((.(.(((.((.(((((((((..((((((......)))))).)))).))))).))))).).))) ( -43.40)
>DroEre_CAF1 6238 117 + 1
UUAUCCAGCACCACCUUGAGGUGCUUCAGGUCCUUGUCCAGCUGCUCUAUUCCGGUCUGUAUGCUGCUUGUCAGUUGGACGUACGAGGUUGUCCUUUGAUUACACUGCUGACGUUGG
....(((((..((((....))))..((((......(((((((((..(.....((((......))))...).)))))))))(((.((((....))))....)))....)))).))))) ( -33.20)
>DroYak_CAF1 4856 117 + 1
UUGUCCAGCACCACCUUUAGGUGCUUCACGUCCUUGGCCAGCUGCUCUAUUCCGGUCUGUAUGCUGCUGGACAGUUGGACGUACGAGCUCGCCUUCUGAUUGAGUUGCUGACGCUGG
....(((((..((((....))))..(((((((((((.(((((.((..(((........))).)).))))).)))..))))))...((((((.........))))))...)).))))) ( -37.20)
>DroAna_CAF1 4390 117 + 1
UUGUCCAGGACCACUUUCAAGUGGUUCACAUCCUUUCCUAGCUGCUCUAGUCCGGAUUUUACGCUGGCCGUCAACUGAAGAUACUUAGCAUCUUUGGGAUUGAGCUGCUGGCGCUGG
....(((((((((((....))))))))..........(((((.((((.(((((.((......(((((..(((.......)))..)))))....)).))))))))).)))))...))) ( -38.10)
>consensus
UUGUCCAGCACCACCUUGAGGUGCUUCACGUCCUUGGCCAGCUGCUCUAUUCCCGUCUGUAUGCUGCUCGUCAGUUGGACGAACUGGCUCGUCUUCUGAUUGAGCUGCUGCCGCUGG
....(((((..((((....))))............((.((((.((((...((..........((((.....)))).(((((........)))))...))..)))).))))))))))) (-27.32 = -26.72 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,552,037 – 16,552,154
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.88
Mean single sequence MFE -37.55
Consensus MFE -24.39
Energy contribution -25.03
Covariance contribution 0.64
Combinations/Pair 1.31
Mean z-score -1.61
Structure conservation index 0.65
SVM decision value 0.03
SVM RNA-class probability 0.551072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16552037 117 - 23771897
CCAGCGGCAGCAGCUCAAUCCGAGGACGAGCCAGUUCGUCCAACUGACAAGCAGCAUUCAGACGGGAAUAGAGCAGCUGGCCAAGGACAUGAAGCACCUCAAGGUGGUGCUGGACAA
(((((((((((.((((..((((.(((((((....)))))))..((((..........)))).))))....)))).))).)))............((((....))))..))))).... ( -47.10)
>DroSec_CAF1 4994 117 - 1
CCAGCGGCAGCAGCUCAAUCAGAAGACGAGUCAGUUCGUCCAACUGACGAGCAGCAUACAGACGGGAAUUGAACAGCUGUCCAAGGACGUGAAGCACCUCAAGGUGGUGCUGGACAA
(((((((((((.((((..((((..((((((....))))))...)))).))))............(........).)))))).............((((....))))..))))).... ( -38.60)
>DroSim_CAF1 4928 117 - 1
CCAGCGGCAGCAGCUCAAUCAGAAGACGAGCCAGUUCGUCCAACUGACGAGCAGCAUACAGACGGGAAUUGAACAGCUGUCCAAGGACGUGAAGCACCUCAAGGUGGUGCUGGACAA
(((((((((((.((((..((((..((((((....))))))...)))).))))............(........).)))))).............((((....))))..))))).... ( -39.70)
>DroEre_CAF1 6238 117 - 1
CCAACGUCAGCAGUGUAAUCAAAGGACAACCUCGUACGUCCAACUGACAAGCAGCAUACAGACCGGAAUAGAGCAGCUGGACAAGGACCUGAAGCACCUCAAGGUGGUGCUGGAUAA
.....(((((...((....))..((((..........))))..)))))...((((((.(((.((....(((.....))).....))..)))...((((....))))))))))..... ( -28.50)
>DroYak_CAF1 4856 117 - 1
CCAGCGUCAGCAACUCAAUCAGAAGGCGAGCUCGUACGUCCAACUGUCCAGCAGCAUACAGACCGGAAUAGAGCAGCUGGCCAAGGACGUGAAGCACCUAAAGGUGGUGCUGGACAA
(((((..(.((...((.....))..))..(((..(((((((...((.(((((.((.................)).))))).)).))))))).)))(((....))))..))))).... ( -38.63)
>DroAna_CAF1 4390 117 - 1
CCAGCGCCAGCAGCUCAAUCCCAAAGAUGCUAAGUAUCUUCAGUUGACGGCCAGCGUAAAAUCCGGACUAGAGCAGCUAGGAAAGGAUGUGAACCACUUGAAAGUGGUCCUGGACAA
((((..(((((.((((..(((..(((((((...)))))))..((((.....)))).........)))...)))).))).))...........((((((....)))))).)))).... ( -32.80)
>consensus
CCAGCGGCAGCAGCUCAAUCAGAAGACGAGCCAGUACGUCCAACUGACGAGCAGCAUACAGACCGGAAUAGAGCAGCUGGCCAAGGACGUGAAGCACCUCAAGGUGGUGCUGGACAA
(((((((((((.((((........((((........))))...(((.....)))................)))).)))))).............((((....))))..))))).... (-24.39 = -25.03 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:15 2006