Locus 6665

Sequence ID	3L_DroMel_CAF1
Location	17,738,121 – 17,738,321
Length	200
Max. P	0.923702

overview

Window 7

Location	17,738,121 – 17,738,241
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-40.11
Consensus MFE	-36.84
Energy contribution	-37.02
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.92
SVM decision value	1.16
SVM RNA-class probability	0.923702
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17738121 120 + 23771897
CAUUAUCCUUUUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCACCUCCACAUAUCAGCUUACCAAUAAGAUGACUCCUGUCCUGGUUUCGGGCGUCAAGUGGCAUUAUCGCCA
....((((((.(((....)))..))))))((((((((.(((((((........))))....................((((.((((.........)))).))))..))).)))))))).. ( -36.30)
>DroSec_CAF1 19323 120 + 1
CAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGCGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUCCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCA
...(((((((((((....))).))))))))((((((((((.((((........))))...(((.((((....)))).)))................)))((((....))))..))))))) ( -40.80)
>DroSim_CAF1 22593 120 + 1
CAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGCGAUGACUCCUGCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCA
...(((((((((((....))).))))))))(((((((...(((.(((((((....................))))))).)))..((((((((..........)))).))))..))))))) ( -42.55)
>DroEre_CAF1 34095 119 + 1
CAUUAUCCUUGUGGGCAACCACCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUGCCCU-GUUUCGGGCGUCAAGUGGCAUUAUCGACG
...(((((((((((....))).))))))))(((((((.(((.(((...((((((...................))))))...)).((((.-.....))))....).))).)))))))... ( -40.81)
>consensus
CAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUGCCCUUGUUUCGGGCGUCAAGUGGCAUUAUCGCCA
...(((((((((((....))).))))))))(((((((.(((((((........))))....................((((.((((.........)))).))))..)))....))))))) (-36.84 = -37.02 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	17,738,161 – 17,738,281
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-31.08
Consensus MFE	-28.05
Energy contribution	-28.55
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.90
SVM decision value	0.07
SVM RNA-class probability	0.566363
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17738161 120 + 23771897
AGUGGUCGCACCUCCACAUAUCAGCUUACCAAUAAGAUGACUCCUGUCCUGGUUUCGGGCGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCAC
.((((........)))).......((((....)))).((((.((((.........)))).)))).(((((((..((....))...((((((.........)))))).......))))))) ( -30.70)
>DroSec_CAF1 19363 120 + 1
AGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUCCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAGUAUUAUGCCAC
.((((........)))).......((((....)))).((((....(((........))).)))).(((((((..((....))...((((((.........)))))).......))))))) ( -28.90)
>DroSim_CAF1 22633 120 + 1
AGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGCGAUGACUCCUGCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCAC
.((((........))))......((........))..((((.((((.........)))).)))).(((((((..((....))...((((((.........)))))).......))))))) ( -31.60)
>DroEre_CAF1 34135 119 + 1
AGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUGCCCU-GUUUCGGGCGUCAAGUGGCAUUAUCGACGGAACUGCUGUCAUGCCCUCCGACAACAAUUAUUAUGCCAC
.(((((..((((((...................))))))......((((.-.....))))(((.((.(((((....(((((.....))))))))))))..)))............))))) ( -33.11)
>consensus
AGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUGAGAUGACUCCUGCCCUUGUUUCGGGCGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCAC
.((((........))))....................((((.((((.........)))).)))).(((((((..((....))...((((((.........)))))).......))))))) (-28.05 = -28.55 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	17,738,201 – 17,738,321
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.03
Mean single sequence MFE	-29.23
Consensus MFE	-24.11
Energy contribution	-24.80
Covariance contribution	0.69
Combinations/Pair	1.07
Mean z-score	-2.27
Structure conservation index	0.82
SVM decision value	0.83
SVM RNA-class probability	0.861013
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17738201 120 + 23771897
CUCCUGUCCUGGUUUCGGGCGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCACUUCUUGGCAUUUAAUUACAAUUUUCUAGGCAAUUCCAGUU
.....((((.......))))(((....)))......(((((((..((((((.........))))))(((((..((((((.....)))))).)))))......)))).))).......... ( -30.10)
>DroSec_CAF1 19403 120 + 1
CUCCUCCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAGUAUUAUGCCACUUCUUGCCAUUUAAUUACAAUUUUCUAGGCAAUUCCAGUU
...(.(((........))).)..(((((((((..((....))...((((((.........)))))).......))))))))).(((((...................)))))........ ( -26.01)
>DroSim_CAF1 22673 120 + 1
CUCCUGCCCUUGUUUCGGGUGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCACUUCUUGCCAUUUAAUUACAAUUUUCUAGGCAAUUCCAGUU
.....((((.......))))...(((((((((..((....))...((((((.........)))))).......))))))))).(((((...................)))))........ ( -27.91)
>DroEre_CAF1 34175 119 + 1
CUCCUGCCCU-GUUUCGGGCGUCAAGUGGCAUUAUCGACGGAACUGCUGUCAUGCCCUCCGACAACAAUUAUUAUGCCACUUCUUGGCAUUUAAUUACAAUUUUCUAGGCAAUUCCAGUG
..(((((((.-.....))))(((.((.(((((....(((((.....))))))))))))..)))...(((((..((((((.....)))))).)))))..........)))........... ( -32.90)
>consensus
CUCCUGCCCUUGUUUCGGGCGUCAAGUGGCAUUAUCGCCAGAACAGUUGUCAUCCCCUUCGACAACAAUUAUUAUGCCACUUCUUGCCAUUUAAUUACAAUUUUCUAGGCAAUUCCAGUU
..(((((((.......))))((((((((((((..((....))...((((((.........)))))).......))))))))...))))..................)))........... (-24.11 = -24.80 +   0.69)

alignment

secondary structure

dotplot

Window 0

Location	17,738,201 – 17,738,321
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.03
Mean single sequence MFE	-33.91
Consensus MFE	-26.04
Energy contribution	-27.10
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-2.13
Structure conservation index	0.77
SVM decision value	0.12
SVM RNA-class probability	0.594163
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17738201 120 - 23771897
AACUGGAAUUGCCUAGAAAAUUGUAAUUAAAUGCCAAGAAGUGGCAUAAUAAUUGUUGUCGAAGGGGAUGACAACUGUUCUGGCGAUAAUGCCACUUGACGCCCGAAACCAGGACAGGAG
..((((......))))..............((((((.....)))))).....((((..((......))..))))(((((((((.......((........))......)))))))))... ( -30.62)
>DroSec_CAF1 19403 120 - 1
AACUGGAAUUGCCUAGAAAAUUGUAAUUAAAUGGCAAGAAGUGGCAUAAUACUUGUUGUCGAAGGGGAUGACAACUGUUCUGGCGAUAAUGCCACUUGACACCCGAAACAAGGGGAGGAG
........(((((...................))))).(((((((((......((((((((((.((........)).))).))))))))))))))))....(((.......)))...... ( -32.51)
>DroSim_CAF1 22673 120 - 1
AACUGGAAUUGCCUAGAAAAUUGUAAUUAAAUGGCAAGAAGUGGCAUAAUAAUUGUUGUCGAAGGGGAUGACAACUGUUCUGGCGAUAAUGCCACUUGACACCCGAAACAAGGGCAGGAG
..(((...(((((...................))))).(((((((((......((((((((((.((........)).))).))))))))))))))))....(((.......))))))... ( -34.11)
>DroEre_CAF1 34175 119 - 1
CACUGGAAUUGCCUAGAAAAUUGUAAUUAAAUGCCAAGAAGUGGCAUAAUAAUUGUUGUCGGAGGGCAUGACAGCAGUUCCGUCGAUAAUGCCACUUGACGCCCGAAAC-AGGGCAGGAG
..((((......)))).................((...(((((((((......(((((.(((((.((......))..))))).))))))))))))))...((((.....-.)))).)).. ( -38.40)
>consensus
AACUGGAAUUGCCUAGAAAAUUGUAAUUAAAUGCCAAGAAGUGGCAUAAUAAUUGUUGUCGAAGGGGAUGACAACUGUUCUGGCGAUAAUGCCACUUGACACCCGAAACAAGGGCAGGAG
..((((......))))......................(((((((((......((((((((((.((........)).))).))))))))))))))))...((((.......))))..... (-26.04 = -27.10 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:04 2006