Locus 1961

Sequence ID	3L_DroMel_CAF1
Location	5,431,921 – 5,432,080
Length	159
Max. P	0.998485

overview

Window 7

Location	5,431,921 – 5,432,041
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-42.75
Consensus MFE	-35.08
Energy contribution	-36.20
Covariance contribution	1.12
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.82
SVM decision value	0.40
SVM RNA-class probability	0.719228
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5431921 120 + 23771897
AUAGGGGAGUCGUUUCUCGUUCCACCUGCUAAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCAAAAGGUGAGCAGGAAGGGGA
.((((((((.((.....)))))).))))...............(.(((.(((((((.(..((((.((((.....))))..))))(((((......)))))...).)))))))..))).). ( -37.90)
>DroSec_CAF1 2092 120 + 1
GUGGGGGAGUCGUUUCUCGUUCCACCUGCUAAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGUA
(..((((((.((.....)))))).))..).............((((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).)))). ( -46.90)
>DroSim_CAF1 2166 120 + 1
AUGGGGGAGUCCUUUCUCGUUCCACCUGCUAAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGA
.((((((((......))).)))))...................(((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).))).. ( -40.50)
>DroEre_CAF1 2016 119 + 1
ACGGGGGACACCCUUCUCGUUCCACCUGCUAAUUCGAAUUUAAUGCCU-CUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAGGCGGA
..(((((((.........))))).)).................(((((-(((((((.((((.....))))........((((((.((((......)))))))))))))))).)))))).. ( -45.70)
>consensus
AUGGGGGAGUCCUUUCUCGUUCCACCUGCUAAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGA
.((((((((.((.....)))))).))))...............(((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).))).. (-35.08 = -36.20 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	5,431,921 – 5,432,041
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-39.32
Consensus MFE	-36.06
Energy contribution	-36.00
Covariance contribution	-0.06
Combinations/Pair	1.10
Mean z-score	-2.10
Structure conservation index	0.92
SVM decision value	1.37
SVM RNA-class probability	0.947010
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5431921 120 - 23771897
UCCCCUUCCUGCUCACCUUUUGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUUAGCAGGUGGAACGAGAAACGACUCCCCUAU
...((..((((((..((((((((((......))))))).))).....((((.((((((......))))))...)))).............)))))).))...(((......)))...... ( -33.50)
>DroSec_CAF1 2092 120 - 1
UACGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUUAGCAGGUGGAACGAGAAACGACUCCCCCAC
...((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).))))...................((((...(((......)))..)))) ( -40.40)
>DroSim_CAF1 2166 120 - 1
UCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUUAGCAGGUGGAACGAGAAAGGACUCCCCCAU
...((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).))))..................((.((...(((......))))))).. ( -39.90)
>DroEre_CAF1 2016 119 - 1
UCCGCCUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAG-AGGCAUUAAAUUCGAAUUAGCAGGUGGAACGAGAAGGGUGUCCCCCGU
(((((((.(((((((((((((((((......)))).))))))........((((.....)))).)))))))-..((...............))))))))).......(((.....))).. ( -43.46)
>consensus
UCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUUAGCAGGUGGAACGAGAAACGACUCCCCCAU
...((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).))))..................((.(((............))).)).. (-36.06 = -36.00 +  -0.06)

alignment

secondary structure

dotplot

Window 9

Location	5,431,961 – 5,432,080
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	87.16
Mean single sequence MFE	-40.15
Consensus MFE	-33.70
Energy contribution	-34.70
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.84
SVM decision value	1.68
SVM RNA-class probability	0.971663
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5431961 119 + 23771897
UAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCAAAAGGUGAGCAGGAAGGGGAGGAGGGCGGCUUGUUUGCGGUUGUUCACGCCAGAAGGGC
....((((.(((((((.(..((((.((((.....))))..))))(((((......)))))...).)))))))...((.(.(((.(((.((......)).))).))).).))....)))) ( -43.30)
>DroSec_CAF1 2132 99 + 1
UAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGUAGGAGUGCGACUUGUUUGCG--------------------
..((((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).))))......((((.....)))).-------------------- ( -37.60)
>DroSim_CAF1 2206 99 + 1
UAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCG--------------------
.....(((((((((...((((.....))))...)))..((((((.((((......))))))))))..))))))..(((((.(((.....))).))))).-------------------- ( -39.30)
>DroEre_CAF1 2056 98 + 1
UAAUGCCU-CUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAGGCGGAGGAGUGCGGCUUGUUUGCG--------------------
....((((-(((((((.((((.....))))........((((((.((((......)))))))))))))))).)))))(((.(((.....))).)))...-------------------- ( -40.40)
>consensus
UAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCG____________________
.........(((((((.((((.....))))........((((((.((((......)))))))))))))))))...(((((.(((.....))).)))))..................... (-33.70 = -34.70 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	5,431,961 – 5,432,080
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	87.16
Mean single sequence MFE	-35.83
Consensus MFE	-32.65
Energy contribution	-32.77
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-3.57
Structure conservation index	0.91
SVM decision value	3.12
SVM RNA-class probability	0.998485
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5431961 119 - 23771897
GCCCUUCUGGCGUGAACAACCGCAAACAAGCCGCCCUCCUCCCCUUCCUGCUCACCUUUUGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUA
(((.....((((....)....((......)).)))............(((((((((((((((((......))))))).)))........((((.....)))).)))))))..))).... ( -34.50)
>DroSec_CAF1 2132 99 - 1
--------------------CGCAAACAAGUCGCACUCCUACGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUA
--------------------.((.........))........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).... ( -35.40)
>DroSim_CAF1 2206 99 - 1
--------------------CGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUA
--------------------.((......))...........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).... ( -35.50)
>DroEre_CAF1 2056 98 - 1
--------------------CGCAAACAAGCCGCACUCCUCCGCCUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAG-AGGCAUUA
--------------------.((......))...........(((((.((((((((((((((((......)))).))))))........((((.....)))).)))))))-)))).... ( -37.90)
>consensus
____________________CGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUA
.....................((.........))........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).... (-32.65 = -32.77 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:10 2006