Locus 746

Sequence ID	3L_DroMel_CAF1
Location	2,236,022 – 2,236,204
Length	182
Max. P	0.995130

overview

Window 4

Location	2,236,022 – 2,236,141
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	94.12
Mean single sequence MFE	-38.65
Consensus MFE	-34.76
Energy contribution	-33.95
Covariance contribution	-0.81
Combinations/Pair	1.15
Mean z-score	-1.63
Structure conservation index	0.90
SVM decision value	0.46
SVM RNA-class probability	0.744492
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2236022 119 - 23771897
AGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUCAUACUCAUGCUCACUUGGUCGUGAUCUUGGAAUGUGAGAU
.(((((.(((((..(((((.((.....))((((.(.(((((.(.....).))))).).)))).)))))..))))).))))).(((((..((.(..(((....)))..)))..))))).. ( -39.40)
>DroSec_CAF1 16993 119 - 1
AGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAACUUUUUGAGUCCUUUAUACUCAUGCUCACUUGGUCGUGAUCUUGGAAUGUGAGAU
.(((((.(((((.((((((.....)))).((((.(.(((((.(.....).))))).).))))..))....))))).))))).(((((..((.(..(((....)))..)))..))))).. ( -34.30)
>DroSim_CAF1 17027 119 - 1
AGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUUAUACUCAUGCUCACUUGGUCGUGAUCUUGGAAUGUGAGAU
.(((((.(((((..(((((.((.....))((((.(.(((((.(.....).))))).).)))).)))))..))))).))))).(((((..((.(..(((....)))..)))..))))).. ( -37.30)
>DroEre_CAF1 30035 119 - 1
AUUGGAAGACUUUGGGGGCACGUAGCUCGGGGUGAAUGAUAGCGAAAGCGUGUCGAUGACCCAGCUCUUUGAGUCUUUUAGAUUCAUGCUCUCUUGGUCGUGUUCGUGGAAUGUGAGAU
.(((((((((((..(((((.((.....))((((.(.(((((((....)).))))).).)))).)))))..))))))))))).(((((..(((..(((......))).)))..))))).. ( -43.60)
>consensus
AGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUUAUACUCAUGCUCACUUGGUCGUGAUCUUGGAAUGUGAGAU
.(((((.(((((..(((((.((.....))((((.(.(((((.(....)..))))).).)))).)))))..))))).))))).(((((..((.(..(((....)))..)))..))))).. (-34.76 = -33.95 +  -0.81)

alignment

secondary structure

dotplot

Window 5

Location	2,236,061 – 2,236,174
Length	113
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	92.48
Mean single sequence MFE	-38.67
Consensus MFE	-33.67
Energy contribution	-33.30
Covariance contribution	-0.37
Combinations/Pair	1.17
Mean z-score	-1.40
Structure conservation index	0.87
SVM decision value	0.03
SVM RNA-class probability	0.547232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2236061 113 - 23771897
CUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUCA
(((((((((.((...(((.(((.((((....)))).))).).))..))))))..((((((..((((.(.(((((.(.....).))))).).)))))))))))))))....... ( -38.50)
>DroSec_CAF1 17032 113 - 1
CUCGAGCUCUCCUUCUGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAACUUUUUGAGUCCUUUA
((((((((.....(((((((((...((.(((.....))).))....))))))).))))))).((((.(.(((((.(.....).))))).).))))........)))....... ( -38.20)
>DroSim_CAF1 17066 113 - 1
CUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUUA
(((((((((.((...(((.(((.((((....)))).))).).))..))))))..((((((..((((.(.(((((.(.....).))))).).)))))))))))))))....... ( -38.50)
>DroEre_CAF1 30074 113 - 1
AUCGAGCUCCUCUUCAGCCUCGUCUUCUCCUGAAUUGGAAGACUUUGGGGGCACGUAGCUCGGGGUGAAUGAUAGCGAAAGCGUGUCGAUGACCCAGCUCUUUGAGUCUUUUA
..((((((.(......((((((((((((........)))))))....)))))..).))))))((((.(.(((((((....)).))))).).)))).((((...))))...... ( -39.50)
>consensus
CUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGACAGUGAAAGAGUGUCGAUGACCCAGCUUUUUGAGUCCUUUA
..(((((((((((..(((.(((.((((....)))).))).).))..))))).....))))))((((.(.(((((.(....)..))))).).)))).((((...))))...... (-33.67 = -33.30 +  -0.37)

alignment

secondary structure

dotplot

Window 6

Location	2,236,101 – 2,236,204
Length	103
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	88.67
Mean single sequence MFE	-35.53
Consensus MFE	-31.08
Energy contribution	-31.95
Covariance contribution	0.87
Combinations/Pair	1.07
Mean z-score	-3.05
Structure conservation index	0.87
SVM decision value	2.54
SVM RNA-class probability	0.995130
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2236101 103 - 23771897
CUCCAGUUCAUCGCCUUCAGAUACAUUUUCCUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGAC
.........(((.......))).(((((.((((((((((((((..(((.(((.((((....)))).))).).))..))))).....))))))))).))))).. ( -36.00)
>DroSec_CAF1 17072 103 - 1
CUCCAGCUCAUUACCCUCAGAUUCAUUUUCCUCGAGCUCUCCUUCUGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGAC
......................((((((.(((((((((.....(((((((((...((.(((.....))).))....))))))).))))))))))).)))))). ( -37.40)
>DroSim_CAF1 17106 103 - 1
CUCCAGCUCAUUUCCCUCAGAUUCAUUUUCCUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGAC
......................((((((.((((((((((((((..(((.(((.((((....)))).))).).))..))))).....))))))))).)))))). ( -36.70)
>DroEre_CAF1 30114 103 - 1
CUCCAAGUCAUCCUCUUCAUACUCAUUUACAUCGAGCUCCUCUUCAGCCUCGUCUUCUCCUGAAUUGGAAGACUUUGGGGGCACGUAGCUCGGGGUGAAUGAU
......................((((((((..((((((.(......((((((((((((........)))))))....)))))..).))))))..)))))))). ( -32.00)
>consensus
CUCCAGCUCAUCACCCUCAGAUUCAUUUUCCUCGAGCUCUCCUUCAGCCUCCUCUUCAUCCGAAGUGGAAGACUUUGGGGGCACGAAGCUCGGGGUGAAUGAC
......................((((((.((((((((((((((..(((.(((.((((....)))).))).).))..))))).....))))))))).)))))). (-31.08 = -31.95 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:06 2006