Locus 4347

Sequence ID	3R_DroMel_CAF1
Location	11,464,742 – 11,464,938
Length	196
Max. P	0.983835

overview

Window 7

Location	11,464,742 – 11,464,859
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.33
Mean single sequence MFE	-28.12
Consensus MFE	-24.23
Energy contribution	-24.48
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.86
SVM decision value	0.39
SVM RNA-class probability	0.716904
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464742 117 + 27905053
AUAUAUAUUACAUUAU---CCCUAGUCUGAUUUCUGGCAGUGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGA
................---.............((((((((((........)))).(((((..((..(((((....))))).....))..))))).((((.....))))......)))))) ( -30.80)
>DroSec_CAF1 198604 120 + 1
AUAUAUAUUACAUUAUUACUCCUAGGCUGAUUUCUUGCAGUGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGA
........................(((.(((.......((((........)))).(((((..((..(((((....))))).....))..))))).((((.....))))...))))))... ( -26.40)
>DroSim_CAF1 193752 120 + 1
AUAUAUAUUACAUUAUUAUUGCUUGGCUGAUUUUUUGCAGUGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGA
......................(((((...........((((........)))).(((((..((..(((((....))))).....))..))))).)))))....((((......)))).. ( -27.70)
>DroYak_CAF1 190907 113 + 1
----AUAUUACCUAAU---UCCUAGGCUGAUUUCUUGCAGUGCAUUUACACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAACGCCAGA
----..((((((((..---...)))).)))).(((.((.(((......)))....(((((..((..(((((....))))).....))..))))).((((.....))))......)).))) ( -27.60)
>consensus
AUAUAUAUUACAUUAU___UCCUAGGCUGAUUUCUUGCAGUGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGA
........................(((...........((((........)))).(((((..((..(((((....))))).....))..))))).)))......((((......)))).. (-24.23 = -24.48 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	11,464,742 – 11,464,859
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-36.65
Consensus MFE	-31.86
Energy contribution	-31.92
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.35
Structure conservation index	0.87
SVM decision value	1.58
SVM RNA-class probability	0.965470
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464742 117 - 27905053
UCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCACUGCCAGAAAUCAGACUAGGG---AUAAUGUAAUAUAUAU
((((((.....(((((.....)))))(((((.(((....((((((....)))))).))).))))).((((((....)))))))))))).............---................ ( -39.00)
>DroSec_CAF1 198604 120 - 1
UCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCACUGCAAGAAAUCAGCCUAGGAGUAAUAAUGUAAUAUAUAU
(((((((((..(((((.....)))))(((((.(((....((((((....)))))).))).))))).((((((....)))))).......))).))).))).................... ( -35.20)
>DroSim_CAF1 193752 120 - 1
UCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCACUGCAAAAAAUCAGCCAAGCAAUAAUAAUGUAAUAUAUAU
..(((((....)))))...((((((.(((((.(((....((((((....)))))).))).))))).((((((....))))))...........))))))..................... ( -36.20)
>DroYak_CAF1 190907 113 - 1
UCUGGCGUUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUGUAAAUGCACUGCAAGAAAUCAGCCUAGGA---AUUAGGUAAUAU----
(((.((.....(((((.....)))))(((((.(((....((((((....)))))).))).))))).(((((......))))))).))).....((((((..---.)))))).....---- ( -36.20)
>consensus
UCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCACUGCAAGAAAUCAGCCUAGGA___AUAAUGUAAUAUAUAU
..(((((....)))))......(((.(((((.(((....((((((....)))))).))).))))).((((((....))))))...........)))........................ (-31.86 = -31.92 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	11,464,779 – 11,464,899
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-35.60
Consensus MFE	-35.51
Energy contribution	-35.58
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.86
Structure conservation index	1.00
SVM decision value	1.96
SVM RNA-class probability	0.983835
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464779 120 + 27905053
UGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUA
.((............(((((..((..(((((....))))).....))..))))).((((.....))))......))..........((((((...((((((....))))))..)))))). ( -36.70)
>DroSec_CAF1 198644 120 + 1
UGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUA
.((............(((((..((..(((((....))))).....))..))))).((((.....))))......))..........((((((...((((((....))))))..)))))). ( -36.70)
>DroSim_CAF1 193792 120 + 1
UGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUA
.((............(((((..((..(((((....))))).....))..))))).((((.....))))......))..........((((((...((((((....))))))..)))))). ( -36.70)
>DroYak_CAF1 190940 120 + 1
UGCAUUUACACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAACGCCAGAGACAACGGAGGAUAAAGGAAGCUGACUUCCUAUUCCUAUA
.((............(((((..((..(((((....))))).....))..))))).((((.....))))......))............((((...((((((....))))))..))))... ( -32.30)
>consensus
UGCAUUUAUACACUUGUGGCAACGUAUUUCCGACAGGAAACCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUA
.((............(((((..((..(((((....))))).....))..))))).((((.....))))......))..........((((((...((((((....))))))..)))))). (-35.51 = -35.58 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	11,464,779 – 11,464,899
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-43.25
Consensus MFE	-41.97
Energy contribution	-42.47
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.94
Structure conservation index	0.97
SVM decision value	1.83
SVM RNA-class probability	0.979237
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464779 120 - 27905053
UAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCA
.((((((..((((((....))))))...))))))(((((.....)))))..(((((.....)))))(((((.(((....((((((....)))))).))).)))))..((((....)))). ( -44.20)
>DroSec_CAF1 198644 120 - 1
UAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCA
.((((((..((((((....))))))...))))))(((((.....)))))..(((((.....)))))(((((.(((....((((((....)))))).))).)))))..((((....)))). ( -44.20)
>DroSim_CAF1 193792 120 - 1
UAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCA
.((((((..((((((....))))))...))))))(((((.....)))))..(((((.....)))))(((((.(((....((((((....)))))).))).)))))..((((....)))). ( -44.20)
>DroYak_CAF1 190940 120 - 1
UAUAGGAAUAGGAAGUCAGCUUCCUUUAUCCUCCGUUGUCUCUGGCGUUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUGUAAAUGCA
...((((..((((((....))))))...)))).(((((....(((((....))))).....)))))(((((.(((....((((((....)))))).))).)))))..((((....)))). ( -40.40)
>consensus
UAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGGUUUCCUGUCGGAAAUACGUUGCCACAAGUGUAUAAAUGCA
(((((((..((((((....))))))...))))))).........(((....(((((.....)))))(((((.(((....((((((....)))))).))).)))))...........))). (-41.97 = -42.47 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	11,464,819 – 11,464,938
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	82.22
Mean single sequence MFE	-30.77
Consensus MFE	-25.60
Energy contribution	-26.13
Covariance contribution	0.53
Combinations/Pair	1.04
Mean z-score	-2.10
Structure conservation index	0.83
SVM decision value	1.21
SVM RNA-class probability	0.930880
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464819 119 + 27905053
CCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUAUGUAGACCCGCGCCUGGAACUCCACAUACACAUCCUCGC-
(((..(((.(((((.........))))).............(((..((((((...((((((....))))))..)))))).)))......)))..)))......................- ( -32.20)
>DroSec_CAF1 198684 120 + 1
CCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUAUGUAGACCCGCGCCUGGAACUCCUCAUACUCCUCCUCGCA
(((..(((.(((((.........))))).............(((..((((((...((((((....))))))..)))))).)))......)))..)))....................... ( -32.20)
>DroYak_CAF1 190980 101 + 1
CCAUUCGCAGCCACCGCCAAAAUGUGGCAACAACGCCAGAGACAACGGAGGAUAAAGGAAGCUGACUUCCUAUUCCUAUAUGG-------------------UAUGUACUCCUCCUCGCA
......((.(((((.........)))))..................((((((...((((((....))))))...((.....))-------------------.......))))))..)). ( -27.90)
>consensus
CCAUUCGCAGCCACCGCCAAAAUGUGGCAACAUCGCCAGAGACAACAGAGGAUGAAGGAAGCUUACUUCCUAUUCCUCUAUGUAGACCCGCGCCUGGAACUCCACAUACUCCUCCUCGCA
......((.(((((.........)))))..........(((.....((((((...((((((....))))))..))))))................((....))...........))))). (-25.60 = -26.13 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	11,464,819 – 11,464,938
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-39.87
Consensus MFE	-31.17
Energy contribution	-32.17
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.78
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11464819 119 - 27905053
-GCGAGGAUGUGUAUGUGGAGUUCCAGGCGCGGGUCUACAUAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGG
-((.(((((.((..(.(((....))).)..)).))).((((((((((..((((((....))))))...))))))).)))..)).))..(((.(((((.........))))).)))..... ( -44.20)
>DroSec_CAF1 198684 120 - 1
UGCGAGGAGGAGUAUGAGGAGUUCCAGGCGCGGGUCUACAUAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGG
(((........))).........(((..(((((..((((((((((((..((((((....))))))...))))))))((((..(((((....)))))......)))))))))))))..))) ( -40.60)
>DroYak_CAF1 190980 101 - 1
UGCGAGGAGGAGUACAUA-------------------CCAUAUAGGAAUAGGAAGUCAGCUUCCUUUAUCCUCCGUUGUCUCUGGCGUUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGG
.((((((((((.......-------------------((.....))...((((((....))))))...)))))).)))).....((((..((((((.....))))))..)).))...... ( -34.80)
>consensus
UGCGAGGAGGAGUAUGUGGAGUUCCAGGCGCGGGUCUACAUAGAGGAAUAGGAAGUAAGCUUCCUUCAUCCUCUGUUGUCUCUGGCGAUGUUGCCACAUUUUGGCGGUGGCUGCGAAUGG
.((.((((.................((((....))))..((((((((..((((((....))))))...))))))))..)).)).))..(((.(((((.........))))).)))..... (-31.17 = -32.17 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:58 2006