Locus 9634

Sequence ID 3R_DroMel_CAF1
Location 25,462,346 – 25,462,441
Length 95
Max. P 0.725894
window15403 window15404

overview

Window 3

Location 25,462,346 – 25,462,441
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 84.93
Mean single sequence MFE -14.90
Consensus MFE -9.46
Energy contribution -9.96
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.63
SVM decision value 0.41
SVM RNA-class probability 0.725894
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25462346 95 + 27905053
GCUUUUUCAAUUCUGGGCCAAUCUCCAAUCUCCUUGCUGCCCAUUUUCCCCAGCUCGCUGGUGAGUCAUAACCUUUAACCUCUUUUGGUUAAAUU
.............((((((((............)))..)))))..(((.((((....)))).)))........(((((((......))))))).. ( -19.50)
>DroSec_CAF1 145394 82 + 1
GCUUUUUCAAUUCUGGGCCAAU-------CUCCUUGCUGCCCAUUUUCCCCAGCUCGCUGGUGAUUCAUAACC------CUCUUUUGGUUAAAUU
.............((((((((.-------....)))..)))))...((.((((....)))).))....(((((------.......))))).... ( -16.90)
>DroEre_CAF1 152712 80 + 1
UCUUCUUCAAUUCUGGGCUAAU-------CUCCCUACUGCCCAUU-UCCACAGCUCCCUGGUGAGUCAUAACC------CUCU-UUAGUUAAAUU
.............(((((....-------.........)))))..-...........((((.(((........------))).-))))....... ( -10.82)
>DroYak_CAF1 155908 82 + 1
UCUUCUUCAAUUCUGGGCCAAU-------CUCCUUGCUGCCCAUUUUCCACAGCUCCCUGGUGAGUCAUAACC------CACUUUUAGUUAAAUU
.............((((((((.-------....)))..)))))........((((....((((.((....)).------))))...))))..... ( -12.40)
>consensus
GCUUCUUCAAUUCUGGGCCAAU_______CUCCUUGCUGCCCAUUUUCCACAGCUCCCUGGUGAGUCAUAACC______CUCUUUUAGUUAAAUU
.............(((((....................)))))...((.((((....)))).))....((((...............)))).... ( -9.46 =  -9.96 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 25,462,346 – 25,462,441
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 84.93
Mean single sequence MFE -18.50
Consensus MFE -13.18
Energy contribution -12.87
Covariance contribution -0.31
Combinations/Pair 1.16
Mean z-score -1.68
Structure conservation index 0.71
SVM decision value 0.29
SVM RNA-class probability 0.671925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25462346 95 - 27905053
AAUUUAACCAAAAGAGGUUAAAGGUUAUGACUCACCAGCGAGCUGGGGAAAAUGGGCAGCAAGGAGAUUGGAGAUUGGCCCAGAAUUGAAAAAGC
..(((((((......))))))).........((.((((....)))).))...(((((..(((.....))).......)))))............. ( -20.30)
>DroSec_CAF1 145394 82 - 1
AAUUUAACCAAAAGAG------GGUUAUGAAUCACCAGCGAGCUGGGGAAAAUGGGCAGCAAGGAG-------AUUGGCCCAGAAUUGAAAAAGC
....(((((.......------)))))....((.((((....)))).))...(((((..(((....-------.))))))))............. ( -18.80)
>DroEre_CAF1 152712 80 - 1
AAUUUAACUAA-AGAG------GGUUAUGACUCACCAGGGAGCUGUGGA-AAUGGGCAGUAGGGAG-------AUUAGCCCAGAAUUGAAGAAGA
...........-...(------(((((...(((.((.....(((((...-.....))))).)))))-------..)))))).............. ( -17.10)
>DroYak_CAF1 155908 82 - 1
AAUUUAACUAAAAGUG------GGUUAUGACUCACCAGGGAGCUGUGGAAAAUGGGCAGCAAGGAG-------AUUGGCCCAGAAUUGAAGAAGA
..((((((((...(((------(((....))))))(((....))))))....(((((..(((....-------.))))))))...)))))..... ( -17.80)
>consensus
AAUUUAACCAAAAGAG______GGUUAUGACUCACCAGCGAGCUGGGGAAAAUGGGCAGCAAGGAG_______AUUGGCCCAGAAUUGAAAAAGA
....(((((.............)))))....((.((((....)))).))...(((((..(((............))))))))............. (-13.18 = -12.87 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:48 2006