Locus 2492

Sequence ID	3L_DroMel_CAF1
Location	6,985,910 – 6,986,110
Length	200
Max. P	0.820312

overview

Window 6

Location	6,985,910 – 6,986,030
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-31.22
Consensus MFE	-30.83
Energy contribution	-30.83
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.99
SVM decision value	0.14
SVM RNA-class probability	0.602967
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6985910 120 - 23771897
GGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUUCGCAAUUCCGCAUAUAUGCAUACAAUUCCCCUCCACUUUUGCGGACACUUGUGCGUGGAAAUAAACCAACCGCAGACACU
(((.....((((((((..(((.((.....((((((((....))))))))(((....))).......................)).)))))))))))((.......)).)))......... ( -32.00)
>DroSec_CAF1 55749 120 - 1
GGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUUCGCAAUUCCGCAUAUAUGUAUACAAUUCCCCUCCACUUUUGCGGACACUUGUGCGUGGAAAUAAACCAACCGCAGACACU
(((.....((((((((..(((.((.....((((((((....))))))))(((...........................))))).)))))))))))((.......)).)))......... ( -30.83)
>DroSim_CAF1 55546 120 - 1
GGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUUCGCAAUUCCGCAUAUAUGUAUACAAUUCCCCUCCACUUUUGCGGACACUUGUGCGUGGAAAUAAACCAACCGCAGACACU
(((.....((((((((..(((.((.....((((((((....))))))))(((...........................))))).)))))))))))((.......)).)))......... ( -30.83)
>consensus
GGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUUCGCAAUUCCGCAUAUAUGUAUACAAUUCCCCUCCACUUUUGCGGACACUUGUGCGUGGAAAUAAACCAACCGCAGACACU
(((.....((((((((..(((.((.....((((((((....))))))))(((...........................))))).)))))))))))((.......)).)))......... (-30.83 = -30.83 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	6,985,950 – 6,986,070
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-32.67
Consensus MFE	-31.46
Energy contribution	-30.80
Covariance contribution	-0.66
Combinations/Pair	1.09
Mean z-score	-1.91
Structure conservation index	0.96
SVM decision value	0.68
SVM RNA-class probability	0.820312
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6985950 120 + 23771897
AAAAGUGGAGGGGAAUUGUAUGCAUAUAUGCGGAAUUGCGAAUGCAAUCCCAAACUGGCCACAUUUGUGCAUUGAUUACCCAGCGAAACGGAAGUGCCGCUUUAAUCUCAUAAUUUUACA
.(((((.(((((((((((.(((((((.(((.((.(((((....))))).((.....)))).))).)))))))))))).)))((((..((....))..)))).....)))...)))))... ( -36.90)
>DroSec_CAF1 55789 120 + 1
AAAAGUGGAGGGGAAUUGUAUACAUAUAUGCGGAAUUGCGAAUGCAAUCCCAAACUGGCCACAUUUGUGCAUUGAUUACCCAGCGAAACGGAAGUGCCGCUUUAAUUUCAUAGUUUUACA
....((((..((.....(((((....)))))((.(((((....))))).))...))..))))..(((((....(((((...((((..((....))..)))).))))).)))))....... ( -29.50)
>DroSim_CAF1 55586 120 + 1
AAAAGUGGAGGGGAAUUGUAUACAUAUAUGCGGAAUUGCGAAUGCAAUCCCAAACUGGCCACAUUUGUGCAUUGAUUACCCAGCGAAACGGAAGUGCCGCUUUAAUCUCAUAAUUUUACA
....((((..((.....(((((....)))))((.(((((....))))).))...))..))))..(((((....(((((...((((..((....))..)))).))))).)))))....... ( -31.60)
>consensus
AAAAGUGGAGGGGAAUUGUAUACAUAUAUGCGGAAUUGCGAAUGCAAUCCCAAACUGGCCACAUUUGUGCAUUGAUUACCCAGCGAAACGGAAGUGCCGCUUUAAUCUCAUAAUUUUACA
....((((..((.....(((((....)))))((.(((((....))))).))...))..))))..(((((....(((((...((((..((....))..)))).))))).)))))....... (-31.46 = -30.80 +  -0.66)

alignment

secondary structure

dotplot

Window 8

Location	6,985,990 – 6,986,110
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.21
Mean single sequence MFE	-28.47
Consensus MFE	-27.77
Energy contribution	-28.10
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.98
SVM decision value	-0.02
SVM RNA-class probability	0.524187
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6985990 120 - 23771897
AAAAAAGCAAUAAAAACAUAAGCUGCCAUCCGUUUGAAUCUGUAAAAUUAUGAGAUUAAAGCGGCACUUCCGUUUCGCUGGGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUU
......(((((.......((((((((((..((((((..((...........))(((((.(((((.((....)).)))))...)))))......))))))))).)))))))..)))))... ( -29.70)
>DroSec_CAF1 55829 118 - 1
A--AAAGCAAUAAAAACAUAAGCUGCCAUCCGUUUGAAUCUGUAAAACUAUGAAAUUAAAGCGGCACUUCCGUUUCGCUGGGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUU
.--...(((((.......((((((((((..((((((.......................(((((.((....)).)))))..(((.....))).))))))))).)))))))..)))))... ( -26.00)
>DroSim_CAF1 55626 117 - 1
---AAAGCAAUAAAAACAUAAGCUGCCAUCCGUUUGAAUCUGUAAAAUUAUGAGAUUAAAGCGGCACUUCCGUUUCGCUGGGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUU
---...(((((.......((((((((((..((((((..((...........))(((((.(((((.((....)).)))))...)))))......))))))))).)))))))..)))))... ( -29.70)
>consensus
A__AAAGCAAUAAAAACAUAAGCUGCCAUCCGUUUGAAUCUGUAAAAUUAUGAGAUUAAAGCGGCACUUCCGUUUCGCUGGGUAAUCAAUGCACAAAUGUGGCCAGUUUGGGAUUGCAUU
......(((((.......((((((((((..((((((..((...........))(((((.(((((.((....)).)))))...)))))......))))))))).)))))))..)))))... (-27.77 = -28.10 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:01 2006