Locus 7344

Sequence ID	2L_DroMel_CAF1
Location	20,485,979 – 20,486,187
Length	208
Max. P	0.998826

overview

Window 3

Location	20,485,979 – 20,486,096
Length	117
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.62
Mean single sequence MFE	-33.38
Consensus MFE	-21.06
Energy contribution	-23.13
Covariance contribution	2.07
Combinations/Pair	1.03
Mean z-score	-1.44
Structure conservation index	0.63
SVM decision value	0.07
SVM RNA-class probability	0.566811
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20485979 117 - 22407834
GGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC--GGAAUGCUUUUGGGAGGACCGGUGGAUGGGUGAA
((((((((.....))))))))....((((((....(((((((((((.........)))))))(((.(((((((((.((.....--.)).)))))))))...))).))))..)))).)). ( -36.00)
>DroPse_CAF1 40050 101 - 1
--------------UCCGGCUGGAGUCCCCCAUGAUAUCGCACAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGAAG-GAGUCCUGCAG-GAGGAG-GGCGGAG-GGCGGA
--------------((((.((...((((.((.(((((.((((((((.........)))))))).)))))................-...(((....)-)))).)-)))...)-).)))) ( -33.90)
>DroSec_CAF1 3092 106 - 1
GGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC--GGAAUGCUGUUGGG-----------AUGGGUGGA
((((((((.....))))))))...(((((...(((((.((((((((.........)))))))).)))))...........(((--((....))))))))-----------))....... ( -32.90)
>DroSim_CAF1 8458 106 - 1
GGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC--GGAAUGCUGUUGGG-----------AUGGGUGGA
((((((((.....))))))))...(((((...(((((.((((((((.........)))))))).)))))...........(((--((....))))))))-----------))....... ( -32.90)
>DroEre_CAF1 2980 92 - 1
GGCUGCACUUGUUGUGCGGCAGGACUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC--GGAAUGCUG-------------------------
.(((((((.....)))))))((.(.(((....(((((.((((((((.........)))))))).)))))...((.......))--))).).)).------------------------- ( -29.20)
>DroYak_CAF1 2301 117 - 1
GGCUGCACUUGUUGUGCGGCUUGACUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC--GGAAUGCUGGUGGGAGGACUGGUGGAUAGGUGGA
((((((((.....))))))))...((((((..(((((.((((((((.........)))))))).)))))..((((.((.....--.)).)))).).)))))..(((.....)))..... ( -35.40)
>consensus
GGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAGAGC__GGAAUGCUGUUGGG___________AUGGGUGGA
.(((((((.....))))))).......((((.(((((.((((((((.........)))))))).)))))..((((.((........)).))))..)))).................... (-21.06 = -23.13 +   2.07)

alignment

secondary structure

dotplot

Window 4

Location	20,486,016 – 20,486,118
Length	102
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	94.32
Mean single sequence MFE	-32.46
Consensus MFE	-23.10
Energy contribution	-23.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.71
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20486016 102 + 22407834
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGACUCAAGCCGCACGACAAGUGCAGCCGCCCUGCGGGGGGAUUCCC---------CAA
...(((((...........((......))..........)))))....(((((((.((...((((((.....))))..((((...)))))).)).))))---------))) ( -30.50)
>DroSec_CAF1 3118 102 + 1
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGACUCAAGCCGCACGACAAGUGCAGCCGCCCUGCGGGGGGAUUCCC---------CAA
...(((((...........((......))..........)))))....(((((((.((...((((((.....))))..((((...)))))).)).))))---------))) ( -30.50)
>DroSim_CAF1 8484 102 + 1
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGACUCAAGCCGCACGACAAGUGCAGCCGCCCUGCGGGGGGAUUCCC---------CAA
...(((((...........((......))..........)))))....(((((((.((...((((((.....))))..((((...)))))).)).))))---------))) ( -30.50)
>DroEre_CAF1 2992 101 + 1
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGAGUCCUGCCGCACAACAAGUGCAGCCGCCCUGCGGG-GGAUUCCC---------CAA
...(((((...........((......))..........)))))....((((((((((((...((((.....))))..((((...)))))-))))))))---------))) ( -36.10)
>DroYak_CAF1 2338 111 + 1
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGAGUCAAGCCGCACAACAAGUGCAGCCGCCCUGCGGGGGGAUUCCCCAGGAAUCCCAA
...(((((...........((......))..........))))).((.((((((((((...((((((.....))))..((((...)))))).))))))))))))....... ( -34.70)
>consensus
CUAAUCGCUUCUAAUAACGCACAAAAUUGAAAAACUUAUGCGAUAUCAUUGGGGACUCAAGCCGCACGACAAGUGCAGCCGCCCUGCGGGGGGAUUCCC_________CAA
...(((((...........((......))..........))))).......((((.((..((.((((.....)))).))(.(((...))).))).))))............ (-23.10 = -23.10 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	20,486,016 – 20,486,118
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	94.32
Mean single sequence MFE	-40.26
Consensus MFE	-32.94
Energy contribution	-33.34
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-3.28
Structure conservation index	0.82
SVM decision value	2.95
SVM RNA-class probability	0.997857
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20486016 102 - 22407834
UUG---------GGGAAUCCCCCCGCAGGGCGGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
..(---------(((....))))(((.((((((((((((.....))))))))...))))....(((((.((((((((.........)))))))).)))))...)))..... ( -39.00)
>DroSec_CAF1 3118 102 - 1
UUG---------GGGAAUCCCCCCGCAGGGCGGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
..(---------(((....))))(((.((((((((((((.....))))))))...))))....(((((.((((((((.........)))))))).)))))...)))..... ( -39.00)
>DroSim_CAF1 8484 102 - 1
UUG---------GGGAAUCCCCCCGCAGGGCGGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
..(---------(((....))))(((.((((((((((((.....))))))))...))))....(((((.((((((((.........)))))))).)))))...)))..... ( -39.00)
>DroEre_CAF1 2992 101 - 1
UUG---------GGGAAUCC-CCCGCAGGGCGGCUGCACUUGUUGUGCGGCAGGACUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
(((---------((((.(((-..(((...)))(((((((.....))))))).))).)))))))(((((.((((((((.........)))))))).)))))........... ( -41.00)
>DroYak_CAF1 2338 111 - 1
UUGGGAUUCCUGGGGAAUCCCCCCGCAGGGCGGCUGCACUUGUUGUGCGGCUUGACUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
..((((((((...))))))))..(((.(((.((((((((.....))))))))......)))..(((((.((((((((.........)))))))).)))))...)))..... ( -43.30)
>consensus
UUG_________GGGAAUCCCCCCGCAGGGCGGCUGCACUUGUCGUGCGGCUUGAGUCCCCAAUGAUAUCGCAUAAGUUUUUCAAUUUUGUGCGUUAUUAGAAGCGAUUAG
............(((......)))((.((((.(((((((.....)))))))....))))....(((((.((((((((.........)))))))).)))))...))...... (-32.94 = -33.34 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	20,486,096 – 20,486,187
Length	91
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-36.82
Consensus MFE	-31.04
Energy contribution	-31.24
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.89
Structure conservation index	0.84
SVM decision value	3.24
SVM RNA-class probability	0.998826
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20486096 91 - 22407834
CUCGUCCUGUUUACUUUGCUGGCCCUGCCUCAUGUGCUUAAAGUUGUCACAAGUUGUCGGGUCCAGUUCUUG---------GGGAAUCCCCCCGCAGGGC
...(((((((.......((((((((.((..(.(((((........).)))).)..)).))).)))))....(---------(((.....))))))))))) ( -35.60)
>DroSec_CAF1 3198 91 - 1
CUCGUCCUGUUUACUUUGCUGGCCCUGCCUCAUGUGCUUAAAGUUGUCACAAGUUGUCGGGUCCAGUUCUUG---------GGGAAUCCCCCCGCAGGGC
...(((((((.......((((((((.((..(.(((((........).)))).)..)).))).)))))....(---------(((.....))))))))))) ( -35.60)
>DroSim_CAF1 8564 91 - 1
CUCGUCCUGUUUACUUUGCUGGCCCUGCCUCAUGUGCUUAAAGUUGUCACAAGUUGUCGGGUCCAGUUCUUG---------GGGAAUCCCCCCGCAGGGC
...(((((((.......((((((((.((..(.(((((........).)))).)..)).))).)))))....(---------(((.....))))))))))) ( -35.60)
>DroEre_CAF1 3072 90 - 1
CUCGUCCUGUUUACUUUGCGGGCCCUGCCUCAUGUGCUUAAAGUUGUCACAAGUUGUCGGGUCCAGUUCUUG---------GGGAAUCC-CCCGCAGGGC
...(((((((.........((((((.((..(.(((((........).)))).)..)).)))))).......(---------(((....)-)))))))))) ( -35.50)
>DroYak_CAF1 2418 100 - 1
CUCGUCCUGUUGACUUUGCUGGCCCUGCCCCAUGUGCUUAAAGUUGUCACAAGUUGUGGGGUCCAGUUCUUGGGAUUCCUGGGGAAUCCCCCCGCAGGGC
...(((((((.(.....((((((((..(..(.(((((........).)))).)..)..))).)))))....((((((((...)))))))).).))))))) ( -41.80)
>consensus
CUCGUCCUGUUUACUUUGCUGGCCCUGCCUCAUGUGCUUAAAGUUGUCACAAGUUGUCGGGUCCAGUUCUUG_________GGGAAUCCCCCCGCAGGGC
...(((((((.......((((((((..(..(.(((((........).)))).)..)..))).)))))..............(((......)))))))))) (-31.04 = -31.24 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:17 2006