Locus 8619

Sequence ID	3L_DroMel_CAF1
Location	22,425,796 – 22,426,026
Length	230
Max. P	0.801900

overview

Window 8

Location	22,425,796 – 22,425,912
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-30.13
Consensus MFE	-28.15
Energy contribution	-27.93
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.80
Structure conservation index	0.93
SVM decision value	0.37
SVM RNA-class probability	0.710752
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22425796 116 + 23771897
AAAAAUUAUACUCCAUUUAAUUUUCCAGUUCAGUUCUUGUCUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCCUCCGGGUGUC----UGUUCCCGGAG
.(((((((.........)))))))...(((.(((....(.((((((..(((((....)))))..)))))).).....))).)))..........(((((((....----....))))))) ( -31.40)
>DroSec_CAF1 2978 120 + 1
AAAAAUUAUACUCCAUUUAAUUUUCCAGUUCAGUUCUUGUCUGGUCCCGGAACGCUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAG
.(((((((.........)))))))...(((.(((....(.((((((..(((((....)))))..)))))).).....))).)))............(((((.((......)).))))).. ( -29.50)
>DroSim_CAF1 2315 120 + 1
AAAAAUUAUACUCCAUUUAAUUUUCCAGUUCAGUUCUUGUCUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAG
.(((((((.........)))))))...(((.(((....(.((((((..(((((....)))))..)))))).).....))).)))............(((((.((......)).))))).. ( -29.50)
>consensus
AAAAAUUAUACUCCAUUUAAUUUUCCAGUUCAGUUCUUGUCUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAG
..........((((.............(((.(((....(.((((((..(((((....)))))..)))))).).....))).)))..............(((.(........).))))))) (-28.15 = -27.93 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	22,425,836 – 22,425,946
Length	110
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	94.74
Mean single sequence MFE	-43.00
Consensus MFE	-39.13
Energy contribution	-38.47
Covariance contribution	-0.66
Combinations/Pair	1.06
Mean z-score	-1.63
Structure conservation index	0.91
SVM decision value	-0.04
SVM RNA-class probability	0.514206
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22425836 110 + 23771897
CUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCCUCCGGGUGUC----UGUUCCCGGAGCCGGUGUUUGGUGUCAAGUUUGACUGGCCCAGGC
(((.....(((((....)))))..((((((((.....(((..(((((.(.(((.(((((((....----....))))))).))).)...)))))..)))..))))))))))).. ( -46.00)
>DroSec_CAF1 3018 114 + 1
CUGGUCCCGGAACGCUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAGCCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGC
(((.....(((((....)))))..((((((((.....(((..(((((.....(((((((((.((......)).))))).....))))..)))))..)))..))))))))))).. ( -41.50)
>DroSim_CAF1 2355 114 + 1
CUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAGCCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGC
(((.....(((((....)))))..((((((((.....(((..(((((.....(((((((((.((......)).))))).....))))..)))))..)))..))))))))))).. ( -41.50)
>consensus
CUGGUCCCGGAACGGUCGUUUCCCGGCCAGUCCUUCUGCUCAACAUCUCCCUGCACCCGGGUGUCUAUCUGCUCCCGGAGCCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGC
(((.....(((((....)))))..((((((((.....(((..(((((.....(((.(((((.(........).)))))....)))....)))))..)))..))))))))))).. (-39.13 = -38.47 +  -0.66)

alignment

secondary structure

dotplot

Window 0

Location	22,425,836 – 22,425,946
Length	110
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	94.74
Mean single sequence MFE	-43.20
Consensus MFE	-40.92
Energy contribution	-40.70
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.48
Structure conservation index	0.95
SVM decision value	-0.02
SVM RNA-class probability	0.522944
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22425836 110 - 23771897
GCCUGGGCCAGUCAAACUUGACACCAAACACCGGCUCCGGGAACA----GACACCCGGAGGCAGGGAGAUGUUGAGCAGAAGGACUGGCCGGGAAACGACCGUUCCGGGACCAG
.((((((((((((...((..(((.(.....(((.(((((((....----....))))))).).))..).)))..))......)))))))(((.......)))..)))))..... ( -46.70)
>DroSec_CAF1 3018 114 - 1
GCCUGGGCCAGUCAAACUUGACACCAAACACAGGCUCCGGGAGCAGAUAGACACCCGGGUGCAGGGAGAUGUUGAGCAGAAGGACUGGCCGGGAAACGAGCGUUCCGGGACCAG
.((((((((((((...((..(((.(.....(..((((((((.(........).)))))).))..)..).)))..))......)))))))).(....)........))))..... ( -41.20)
>DroSim_CAF1 2355 114 - 1
GCCUGGGCCAGUCAAACUUGACACCAAACACAGGCUCCGGGAGCAGAUAGACACCCGGGUGCAGGGAGAUGUUGAGCAGAAGGACUGGCCGGGAAACGACCGUUCCGGGACCAG
.((((((((((((...((..(((.(.....(..((((((((.(........).)))))).))..)..).)))..))......)))))))(((.......)))..)))))..... ( -41.70)
>consensus
GCCUGGGCCAGUCAAACUUGACACCAAACACAGGCUCCGGGAGCAGAUAGACACCCGGGUGCAGGGAGAUGUUGAGCAGAAGGACUGGCCGGGAAACGACCGUUCCGGGACCAG
.((((((((((((...((..(((.(...(....((((((((............)))))).))..)..).)))..))......)))))))).(....)........))))..... (-40.92 = -40.70 +  -0.22)

alignment

secondary structure

dotplot

Window 1

Location	22,425,912 – 22,426,026
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	98.25
Mean single sequence MFE	-37.53
Consensus MFE	-34.43
Energy contribution	-35.10
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.92
SVM decision value	0.62
SVM RNA-class probability	0.801900
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22425912 114 + 23771897
CCGGUGUUUGGUGUCAAGUUUGACUGGCCCAGGCUCGGCGCCACUACGGGUUUUAGGUUUUGAGCUCGGGUUCAGGUUUCUGAGUUGACGUUAUGCAUUGAAAUUAAUUAAAUC
.((((((.(..((((((.((.((((.((((..((((((.(((.(....)......))).))))))..))))...))))...)).))))))..).)))))).............. ( -38.60)
>DroSec_CAF1 3098 114 + 1
CCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGCUCGGCGGCACUACGGGUUUUAGGUUUUGAGCUUGGGUUCAGGUUUCUGAGUUGACGUUAUGCAUUGAAAUUAAUUAAAUC
.(.((((.(..((((((.((.((((.((((((((((((.(((.(((.......))))))))))))))))))...))))...)).))))))..).)))).).............. ( -37.00)
>DroSim_CAF1 2435 114 + 1
CCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGCUCGGCGGCACUACGGGUUUUAGGUUUUGAGCUUGGGUUCAGGUUUCUGAGUUGACGUUAUGCAUUGAAAUUAAUUAAAUC
.(.((((.(..((((((.((.((((.((((((((((((.(((.(((.......))))))))))))))))))...))))...)).))))))..).)))).).............. ( -37.00)
>consensus
CCUGUGUUUGGUGUCAAGUUUGACUGGCCCAGGCUCGGCGGCACUACGGGUUUUAGGUUUUGAGCUUGGGUUCAGGUUUCUGAGUUGACGUUAUGCAUUGAAAUUAAUUAAAUC
.(.((((.(..((((((.((.((((.((((((((((((.(((.(((.......))))))))))))))))))...))))...)).))))))..).)))).).............. (-34.43 = -35.10 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:30 2006