Locus 7895

Sequence ID	3R_DroMel_CAF1
Location	21,161,086 – 21,161,199
Length	113
Max. P	0.910824

overview

Window 3

Location	21,161,086 – 21,161,199
Length	113
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	80.24
Mean single sequence MFE	-34.80
Consensus MFE	-24.35
Energy contribution	-26.30
Covariance contribution	1.95
Combinations/Pair	1.12
Mean z-score	-1.93
Structure conservation index	0.70
SVM decision value	0.85
SVM RNA-class probability	0.865550
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21161086 113 + 27905053
AAAAUCAUGAGCUAAGCGAGCUCACUACGGAAAAAAUGCUUCCGUCGGACGUGUGCCGCACCUGUGCGGUGCAGAACAGCCAAUUGCUGCCCUUGUCCACUUGCCUGGACAAA
.......((((((.....))))))..((((((.......)))))).((...((..(((((....)))))..))...((((.....)))).))(((((((......))))))). ( -41.10)
>DroPse_CAF1 14816 85 + 1
----------------------------AGUAAAAAUCCUGCCUAGCAAUAUUUGCCGCACGUGUGCCCUGCAAAACAGCAAUUUGCUGCCCCUCUCCACUUCCUUGGACAAG
----------------------------...........(((...)))...(((((.(((....)))...))))).((((.....))))......((((......)))).... ( -14.20)
>DroSec_CAF1 5552 113 + 1
AUAAUCAUGAGCUAAGCGAGCUCACUACGGAAAAAAUGCUUCCGUCGGAUAUGUGCCGCACAUGUGCGGUGCAGAACAGCCAAUUGCUGCCCUUGUCCACUUGCCUGGACAGA
...(((.((((((.....))))))(.((((((.......)))))).)))).((..(((((....)))))..))...((((.....))))...(((((((......))))))). ( -41.30)
>DroSim_CAF1 5531 113 + 1
AAAAUCAUGAGCUAAGCGAGCUCACUACGGAAAAAAUGCUUCCGUCGGAUAUGUGCCGCACCUGUGCGGUGCAGAACAGCCAAUUGCUGCCCUUGUCCACUUGCCUGGACAGA
...(((.((((((.....))))))(.((((((.......)))))).)))).((..(((((....)))))..))...((((.....))))...(((((((......))))))). ( -41.30)
>DroEre_CAF1 5558 113 + 1
AAAAGCAUGAGCUAAGUGAGCUCACGACGUCUAAAAUGCUUCCGUCGGAUAUUUGCCGCACCUGUGCGGUGCAGAACAACCGAUUGCUGCCCUUGUCCACUUGCCUGGACAGA
...((((((((((.....))))))(((((.............))))).......((((((....))))))..............))))....(((((((......))))))). ( -34.12)
>DroYak_CAF1 5616 113 + 1
AAAAUCAUGAGCUAAGUGAGCUCACCCCGGCAAAAAUGCUUCCGUCGGAUAUUUGCCGCACCUGUGCGGCGCAGAACAACCAAUUGCUGCCCUUGUCCACUCGCCUGGACAGA
.......((((((.....))))))..(((((............)))))......((((((....))))))((((..(((....)))))))..(((((((......))))))). ( -36.80)
>consensus
AAAAUCAUGAGCUAAGCGAGCUCACUACGGAAAAAAUGCUUCCGUCGGAUAUGUGCCGCACCUGUGCGGUGCAGAACAGCCAAUUGCUGCCCUUGUCCACUUGCCUGGACAGA
.......((((((.....))))))(.((((((.......)))))).).......((((((....))))))((((..(((....)))))))..(((((((......))))))). (-24.35 = -26.30 +   1.95)

alignment

secondary structure

dotplot

Window 4

Location	21,161,086 – 21,161,199
Length	113
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	80.24
Mean single sequence MFE	-39.59
Consensus MFE	-29.94
Energy contribution	-30.40
Covariance contribution	0.46
Combinations/Pair	1.20
Mean z-score	-2.06
Structure conservation index	0.76
SVM decision value	1.07
SVM RNA-class probability	0.910824
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21161086 113 - 27905053
UUUGUCCAGGCAAGUGGACAAGGGCAGCAAUUGGCUGUUCUGCACCGCACAGGUGCGGCACACGUCCGACGGAAGCAUUUUUUCCGUAGUGAGCUCGCUUAGCUCAUGAUUUU
.(((((((......)))))))(((((((.....)))((.(((((((.....))))))).))..)))).(((((((.....))))))).(((((((.....)))))))...... ( -46.00)
>DroPse_CAF1 14816 85 - 1
CUUGUCCAAGGAAGUGGAGAGGGGCAGCAAAUUGCUGUUUUGCAGGGCACACGUGCGGCAAAUAUUGCUAGGCAGGAUUUUUACU----------------------------
(((.((((......)))).)))((((((.....))))))((((...(((....)))((((.....))))..))))..........---------------------------- ( -23.50)
>DroSec_CAF1 5552 113 - 1
UCUGUCCAGGCAAGUGGACAAGGGCAGCAAUUGGCUGUUCUGCACCGCACAUGUGCGGCACAUAUCCGACGGAAGCAUUUUUUCCGUAGUGAGCUCGCUUAGCUCAUGAUUAU
..((((((......))))))((((((((.....))))))))...(((((....)))))..........(((((((.....))))))).(((((((.....)))))))...... ( -41.20)
>DroSim_CAF1 5531 113 - 1
UCUGUCCAGGCAAGUGGACAAGGGCAGCAAUUGGCUGUUCUGCACCGCACAGGUGCGGCACAUAUCCGACGGAAGCAUUUUUUCCGUAGUGAGCUCGCUUAGCUCAUGAUUUU
..((((((......))))))((((((((.....))))))))(((((.....)))))............(((((((.....))))))).(((((((.....)))))))...... ( -42.50)
>DroEre_CAF1 5558 113 - 1
UCUGUCCAGGCAAGUGGACAAGGGCAGCAAUCGGUUGUUCUGCACCGCACAGGUGCGGCAAAUAUCCGACGGAAGCAUUUUAGACGUCGUGAGCUCACUUAGCUCAUGCUUUU
..((((((......))))))((((((((.....))))))))(((((.....)))))((((......(((((.............)))))((((((.....))))))))))... ( -40.92)
>DroYak_CAF1 5616 113 - 1
UCUGUCCAGGCGAGUGGACAAGGGCAGCAAUUGGUUGUUCUGCGCCGCACAGGUGCGGCAAAUAUCCGACGGAAGCAUUUUUGCCGGGGUGAGCUCACUUAGCUCAUGAUUUU
.....((.((((((.(((..((((((((.....))))))))..((((((....)))))).....)))(.(....))...)))))).))(((((((.....)))))))...... ( -43.40)
>consensus
UCUGUCCAGGCAAGUGGACAAGGGCAGCAAUUGGCUGUUCUGCACCGCACAGGUGCGGCAAAUAUCCGACGGAAGCAUUUUUUCCGUAGUGAGCUCGCUUAGCUCAUGAUUUU
..((((((......))))))((((((((.....))))))))(((((.....)))))............((((...........)))).(((((((.....)))))))...... (-29.94 = -30.40 +   0.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:25 2006