Locus 8395

Sequence ID	3R_DroMel_CAF1
Location	22,362,693 – 22,362,883
Length	190
Max. P	0.922181

overview

Window 2

Location	22,362,693 – 22,362,803
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.91
Mean single sequence MFE	-34.64
Consensus MFE	-23.10
Energy contribution	-25.85
Covariance contribution	2.75
Combinations/Pair	1.03
Mean z-score	-2.53
Structure conservation index	0.67
SVM decision value	1.15
SVM RNA-class probability	0.922181
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22362693 110 + 27905053
CUUCGCUGU--------GGAGAGGAAGCAACAAAUGCGAUGCGUUGCGUUGC--GUUUCUUGUUUCUUUUAACUAACUACGUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAA
...((((.(--------((...((((((.....(((.((((((((((((..(--((.....(((......))).....)))..)))))))))))).))).)).))))..))))))).... ( -37.60)
>DroSim_CAF1 74393 106 + 1
CUUCGCUGU--------GGAGAGGAAGCAACAAAUGCGAUGCGUUGCGUUGC--GUUUCUUGUUUCGUUUAA----CUACGUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAA
..((((.((--------(((((.(((((((.(((((((((((...)))))))--)))).))))))).)))..----))))))))..............(((((((.......))))))). ( -36.80)
>DroEre_CAF1 73196 109 + 1
CUUCGUUGUCGAGUUGUCGAGAGGAAGCAACAAAUGCG-----UUGCGUUUC--GUUUCUUCUUCCUUUUAA----CUACGUGAUGCAAUGCGUUUAAUGGCAUUCCAACCAAGUGCCAA
((((.((.((((....)))).))))))....(((((((-----(((((((.(--((................----..))).))))))))))))))..(((((((.......))))))). ( -33.67)
>DroYak_CAF1 72735 111 + 1
CUUCGUUGUCGAGUUGUCGAGAGGAAGCAACAAAUGCG-----UUGCGUUUCUUGUUCCUUUUUGUUUUUAA----CUACGUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAA
((((.((.((((....)))).))))))....(((((((-----(((((((...(((................----..))).))))))))))))))..(((((((.......))))))). ( -30.47)
>consensus
CUUCGCUGU________CGAGAGGAAGCAACAAAUGCG_____UUGCGUUGC__GUUUCUUGUUUCUUUUAA____CUACGUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAA
((((.((.(((......))).))))))....(((((((.(((((..(((.............................)))..))))).)))))))..(((((((.......))))))). (-23.10 = -25.85 +   2.75)

alignment

secondary structure

dotplot

Window 3

Location	22,362,763 – 22,362,883
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-35.15
Consensus MFE	-35.10
Energy contribution	-35.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	1.00
SVM decision value	1.06
SVM RNA-class probability	0.908001
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22362763 120 + 27905053
GUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAAUUAGAAUUGAUUAUUAUUCAUUAUUUCGCUUAUUACCCACACAGGCGCGUGUUUGUGCGUUUGUGUGUAAGCGGCUCUCU
....((.(((((........))))).))....((.(((.....(((.((((........)))).)))(((((.....((((((((((((......)))))))))))))))))))).)).. ( -35.10)
>DroSim_CAF1 74459 120 + 1
GUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAAUUAGAAUUGAUUAUUAUUCAUUAUUUCGCUUAUUACCCACACAGGCGCGUGUUCGUGCGUUUGUGUGUAAGCGGCUCUCU
....((.(((((........))))).))....((.(((.....(((.((((........)))).)))(((((.....((((((((((((......)))))))))))))))))))).)).. ( -35.10)
>DroEre_CAF1 73265 120 + 1
GUGAUGCAAUGCGUUUAAUGGCAUUCCAACCAAGUGCCAAUUAGAAUUGAUUAUUAUUCAUUAUUUCGCUUAUUACCCACACAGGCGCGUGUUUGUGCGUUUGUGUGUAAGCGGCUCUCU
(((((.((((...((((((((((((.......)))))).)))))))))))))))...........(((((((.....((((((((((((......)))))))))))))))))))...... ( -35.30)
>DroYak_CAF1 72806 120 + 1
GUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAAUUAGAAUUGAUUAUUAUUCAUUAUUUCGCUUAUUACCCACACAGGCGCGUGUUUGUGCGUUUGUGUGUAAGCGGCUCUCU
....((.(((((........))))).))....((.(((.....(((.((((........)))).)))(((((.....((((((((((((......)))))))))))))))))))).)).. ( -35.10)
>consensus
GUGAUGCAAUGCGUUUUAUGGCAUUCCAACCAAGUGCCAAUUAGAAUUGAUUAUUAUUCAUUAUUUCGCUUAUUACCCACACAGGCGCGUGUUUGUGCGUUUGUGUGUAAGCGGCUCUCU
....((.(((((........))))).))....((.(((.....(((.((((........)))).)))(((((.....((((((((((((......)))))))))))))))))))).)).. (-35.10 = -35.10 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	22,362,763 – 22,362,883
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-30.40
Consensus MFE	-30.40
Energy contribution	-30.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	1.00
SVM decision value	0.84
SVM RNA-class probability	0.864870
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22362763 120 - 27905053
AGAGAGCCGCUUACACACAAACGCACAAACACGCGCCUGUGUGGGUAAUAAGCGAAAUAAUGAAUAAUAAUCAAUUCUAAUUGGCACUUGGUUGGAAUGCCAUAAAACGCAUUGCAUCAC
.(((.((((((((((((((..(((........)))..)))))).....)))))........((((........)))).....))).)))(((.(.(((((........))))).)))).. ( -30.40)
>DroSim_CAF1 74459 120 - 1
AGAGAGCCGCUUACACACAAACGCACGAACACGCGCCUGUGUGGGUAAUAAGCGAAAUAAUGAAUAAUAAUCAAUUCUAAUUGGCACUUGGUUGGAAUGCCAUAAAACGCAUUGCAUCAC
.(((.((((((((((((((..(((........)))..)))))).....)))))........((((........)))).....))).)))(((.(.(((((........))))).)))).. ( -30.40)
>DroEre_CAF1 73265 120 - 1
AGAGAGCCGCUUACACACAAACGCACAAACACGCGCCUGUGUGGGUAAUAAGCGAAAUAAUGAAUAAUAAUCAAUUCUAAUUGGCACUUGGUUGGAAUGCCAUUAAACGCAUUGCAUCAC
.(((.((((((((((((((..(((........)))..)))))).....)))))........((((........)))).....))).)))(((.(.(((((........))))).)))).. ( -30.40)
>DroYak_CAF1 72806 120 - 1
AGAGAGCCGCUUACACACAAACGCACAAACACGCGCCUGUGUGGGUAAUAAGCGAAAUAAUGAAUAAUAAUCAAUUCUAAUUGGCACUUGGUUGGAAUGCCAUAAAACGCAUUGCAUCAC
.(((.((((((((((((((..(((........)))..)))))).....)))))........((((........)))).....))).)))(((.(.(((((........))))).)))).. ( -30.40)
>consensus
AGAGAGCCGCUUACACACAAACGCACAAACACGCGCCUGUGUGGGUAAUAAGCGAAAUAAUGAAUAAUAAUCAAUUCUAAUUGGCACUUGGUUGGAAUGCCAUAAAACGCAUUGCAUCAC
.(((.((((((((((((((..(((........)))..)))))).....)))))........((((........)))).....))).)))(((.(.(((((........))))).)))).. (-30.40 = -30.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:31 2006