Locus 9904

Sequence ID 3R_DroMel_CAF1
Location 26,458,383 – 26,458,477
Length 94
Max. P 0.601193
window15794 window15795

overview

Window 4

Location 26,458,383 – 26,458,477
Length 94
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 80.20
Mean single sequence MFE -32.05
Consensus MFE -21.01
Energy contribution -22.90
Covariance contribution 1.89
Combinations/Pair 1.07
Mean z-score -1.27
Structure conservation index 0.66
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26458383 94 + 27905053
CUUAACCCUUUGUCACCCCAGGAACGGUGACAUUUGGCGACGGCGGCCAAGGGUUAAGAGAAAGCGACAGCUGGUGCU----------CUGG-----UUUCCAGC---UUCG
((((((((..(((((((........))))))).(((((.......)))))))))))))......(((.((((((.((.----------...)-----)..)))))---)))) ( -39.50)
>DroSec_CAF1 50574 94 + 1
CUUAACCCUUUUACACCCUAGGAACGGCGACAUUUGGCGACGGCGGCCAAGGGUUAAGAGAAAGCGACAGCUGGUGCU----------CCGG-----UUUCCAGC---UUCG
((((((((.....(.((........)).)....(((((.......)))))))))))))......(((.((((((.((.----------...)-----)..)))))---)))) ( -30.20)
>DroSim_CAF1 50799 94 + 1
CUUAACCCUUUGUCACCCCAGGAACGGUGACAUUUGGCAACGGCGGCCAAGGGCUAAGAGAAAGCGACAGCUGGUGCU----------CCGG-----UUUCCAGC---UUCG
((((.(((..(((((((........))))))).(((((.......)))))))).))))......(((.((((((.((.----------...)-----)..)))))---)))) ( -35.10)
>DroEre_CAF1 58094 94 + 1
CUUAACCCUUUGUCACCCCAGGAACAGUCACAUUUGGCGACGGCGGCCAAGGGUUAAAAGAAAGCGACAGCUGGUGCU----------CUGG-----UUUCCAGC---AUCG
.(((((((((.(((.(((((((..........)))))....)).))).))))))))).......(((..(((((.((.----------...)-----)..)))))---.))) ( -27.80)
>DroYak_CAF1 52594 94 + 1
CUUAACCCUUUGUCACCCCAGCACCACUGACAUUUGGCAACGACGGCCAGGGGUUAAGAGAAAGCGACAGCUGGUGCU----------CUGG-----UUUCCAGC---AUCG
((((((((((.(((....(((.....)))....(((....))).))).))))))))))......(((..(((((.((.----------...)-----)..)))))---.))) ( -31.10)
>DroAna_CAF1 51394 104 + 1
CUUAACCCCUUAACA-----G---GGUCGACACUUGGCGACAUCGGCCAAGGGUUAAGAGAAAAUGACAGCUGUUGCCAGAGUGGAUUCUUGUUAUUUUUUUAGCGUGUUCU
((((((((((....)-----)---((((((....((....))))))))..))))))))((((((((((((......((.....))....))))))))))))........... ( -28.60)
>consensus
CUUAACCCUUUGUCACCCCAGGAACGGUGACAUUUGGCGACGGCGGCCAAGGGUUAAGAGAAAGCGACAGCUGGUGCU__________CUGG_____UUUCCAGC___UUCG
((((((((..((((((..........)))))).(((((.......)))))))))))))......(((..(((((..........................)))))....))) (-21.01 = -22.90 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 26,458,383 – 26,458,477
Length 94
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 80.20
Mean single sequence MFE -31.20
Consensus MFE -24.77
Energy contribution -25.72
Covariance contribution 0.95
Combinations/Pair 1.21
Mean z-score -1.14
Structure conservation index 0.79
SVM decision value 0.14
SVM RNA-class probability 0.601193
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26458383 94 - 27905053
CGAA---GCUGGAAA-----CCAG----------AGCACCAGCUGUCGCUUUCUCUUAACCCUUGGCCGCCGUCGCCAAAUGUCACCGUUCCUGGGGUGACAAAGGGUUAAG
((((---(((((...-----....----------....)))))).)))......(((((((((((((.......)))...(((((((.(....).))))))))))))))))) ( -37.30)
>DroSec_CAF1 50574 94 - 1
CGAA---GCUGGAAA-----CCGG----------AGCACCAGCUGUCGCUUUCUCUUAACCCUUGGCCGCCGUCGCCAAAUGUCGCCGUUCCUAGGGUGUAAAAGGGUUAAG
((((---(((((...-----....----------....)))))).)))......(((((((((((((.......)))......((((.(....).))))...)))))))))) ( -30.30)
>DroSim_CAF1 50799 94 - 1
CGAA---GCUGGAAA-----CCGG----------AGCACCAGCUGUCGCUUUCUCUUAGCCCUUGGCCGCCGUUGCCAAAUGUCACCGUUCCUGGGGUGACAAAGGGUUAAG
((((---(((((...-----....----------....)))))).)))......(((((((((((((.......)))...(((((((.(....).))))))))))))))))) ( -37.20)
>DroEre_CAF1 58094 94 - 1
CGAU---GCUGGAAA-----CCAG----------AGCACCAGCUGUCGCUUUCUUUUAACCCUUGGCCGCCGUCGCCAAAUGUGACUGUUCCUGGGGUGACAAAGGGUUAAG
((((---(((((...-----....----------....))))).)))).......(((((((((((..((.(((((.....))))).)).))...(....).))))))))). ( -29.70)
>DroYak_CAF1 52594 94 - 1
CGAU---GCUGGAAA-----CCAG----------AGCACCAGCUGUCGCUUUCUCUUAACCCCUGGCCGUCGUUGCCAAAUGUCAGUGGUGCUGGGGUGACAAAGGGUUAAG
((((---(((((...-----....----------....))))).))))......((((((((.((((.......)))).((.((((.....)))).))......)))))))) ( -28.80)
>DroAna_CAF1 51394 104 - 1
AGAACACGCUAAAAAAAUAACAAGAAUCCACUCUGGCAACAGCUGUCAUUUUCUCUUAACCCUUGGCCGAUGUCGCCAAGUGUCGACC---C-----UGUUAAGGGGUUAAG
......................((((...((.(((....)))..))....))))((((((.((((((.(....)))))))......((---(-----(....)))))))))) ( -23.90)
>consensus
CGAA___GCUGGAAA_____CCAG__________AGCACCAGCUGUCGCUUUCUCUUAACCCUUGGCCGCCGUCGCCAAAUGUCACCGUUCCUGGGGUGACAAAGGGUUAAG
(((....(((((..........................)))))..)))......(((((((((((((.......)))...(((((((........))))))))))))))))) (-24.77 = -25.72 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:35 2006