Locus 5957

Sequence ID	2L_DroMel_CAF1
Location	16,778,751 – 16,778,911
Length	160
Max. P	0.997812

overview

Window 3

Location	16,778,751 – 16,778,871
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.00
Mean single sequence MFE	-35.70
Consensus MFE	-33.74
Energy contribution	-34.05
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-1.20
Structure conservation index	0.95
SVM decision value	1.03
SVM RNA-class probability	0.903760
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778751 120 + 22407834
UUCCAGCAGAAGAAGAAGGCCGAUCAGGAGAUCUCUGGCCUGAAGAAGGACAUCGAGGAUCUGGAAUUGAACGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((((((....))))..((((((...((......)).....((((((........))))))))))))..........)))).....(((((....))))))) ( -37.10)
>DroVir_CAF1 8873 120 + 1
UUCCAGCAGAAGAAGAAGGCCGAUCAGGAGAUCUCUGGCCUGAAGAAGGACAUCGAGGAUCUGGAAUUGAGCGUCCAGAAGGCCGAACAGGAUAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((((((....))))..((((((......((((.((((..........))))..))))...))))))..........)))).....(((((....))))))) ( -37.10)
>DroGri_CAF1 9071 120 + 1
UUCCAGCAGAAGAAGAAGGCCGAUCAAGAGAUCUCUGGCCUGAAGAAGGACAUCGAAGAUAUGGAGCUGAACAUCCAGAAGGCCGAACAGGAUAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((((((....))))..((((((...((......)).......((((........))))..))))))..........)))).....(((((....))))))) ( -33.40)
>DroWil_CAF1 8472 120 + 1
UUCCAACAGAAGAAGAAGGCCGACCAGGAGAUCUCUGGCUUGAAGAAGGAUAUCGAAGAUCUGGAAUUGAACAUCCAGAAGGCCGAGCAAGACAAGGCCACCAAGGAUCACCAGAUCCGC
.................((((..(((((.....)))))((((..........(((....((((((........))))))....))).))))....)))).....(((((....))))).. ( -32.10)
>DroMoj_CAF1 9068 120 + 1
UUCCAGCAGAAGAAGAAGGCCGAUCAGGAGAUCUCCGGCUUGAAGAAGGACAUCGAGGAUCUGGAAUUGAGCGUCCAGAAGGCCGAGCAGGAUAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((((((....))))(((.(((((..((......)).....((((((........))))))....))))).)))...)))).....(((((....))))))) ( -37.80)
>DroAna_CAF1 8583 120 + 1
UUCCAGCAGAAGAAGAAGGCCGACCAGGAGAUCUCUGGCCUGAAGAAGGACAUCGAGGAUCUGGAGCUGAAUGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((..(((((.....)))))((((..((......))..((.((((((.(.....)))))))...))...))))....)))).....(((((....))))))) ( -36.70)
>consensus
UUCCAGCAGAAGAAGAAGGCCGAUCAGGAGAUCUCUGGCCUGAAGAAGGACAUCGAGGAUCUGGAAUUGAACGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGC
.....((..........((((((((....))))..((((((...((......)).....((((((........))))))))))))..........)))).....(((((....))))))) (-33.74 = -34.05 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	16,778,751 – 16,778,871
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.00
Mean single sequence MFE	-37.83
Consensus MFE	-36.68
Energy contribution	-36.35
Covariance contribution	-0.33
Combinations/Pair	1.10
Mean z-score	-1.48
Structure conservation index	0.97
SVM decision value	2.26
SVM RNA-class probability	0.991254
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778751 120 - 22407834
GCGGAUCUGGUGAUCCUUGGUGGCCUUGUCCUGCUCGGCCUUCUGGACGUUCAAUUCCAGAUCCUCGAUGUCCUUCUUCAGGCCAGAGAUCUCCUGAUCGGCCUUCUUCUUCUGCUGGAA
((.((((.((.((((.(((((((((..(.....)..)))).((((((........))))))....................))))).)))).)).)))).)).....(((......))). ( -38.90)
>DroVir_CAF1 8873 120 - 1
GCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGUUCGGCCUUCUGGACGCUCAAUUCCAGAUCCUCGAUGUCCUUCUUCAGGCCAGAGAUCUCCUGAUCGGCCUUCUUCUUCUGCUGGAA
(((((((....)))))..((.((((...........(((((((((((........)))))).....((......))...)))))...((((....)))))))).)).......))..... ( -37.70)
>DroGri_CAF1 9071 120 - 1
GCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGUUCGGCCUUCUGGAUGUUCAGCUCCAUAUCUUCGAUGUCCUUCUUCAGGCCAGAGAUCUCUUGAUCGGCCUUCUUCUUCUGCUGGAA
(((((((....)))))..((.((((...........(((((...(((((((.((........))..)))))))......)))))...((((....)))))))).)).......))..... ( -34.80)
>DroWil_CAF1 8472 120 - 1
GCGGAUCUGGUGAUCCUUGGUGGCCUUGUCUUGCUCGGCCUUCUGGAUGUUCAAUUCCAGAUCUUCGAUAUCCUUCUUCAAGCCAGAGAUCUCCUGGUCGGCCUUCUUCUUCUGUUGGAA
((.((((.((.((((.(((((((((..(.....)..)))).((((((........))))))....................))))).)))).)).)))).)).....(((......))). ( -39.10)
>DroMoj_CAF1 9068 120 - 1
GCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGCUCGGCCUUCUGGACGCUCAAUUCCAGAUCCUCGAUGUCCUUCUUCAAGCCGGAGAUCUCCUGAUCGGCCUUCUUCUUCUGCUGGAA
(((((((....)))))..((.((((...(((.((((((...((((((........))))))...))))((........)).)).)))((((....)))))))).)).......))..... ( -36.90)
>DroAna_CAF1 8583 120 - 1
GCGGAUCUGGUGAUCCUUGGUGGCCUUGUCCUGCUCGGCCUUCUGGACAUUCAGCUCCAGAUCCUCGAUGUCCUUCUUCAGGCCAGAGAUCUCCUGGUCGGCCUUCUUCUUCUGCUGGAA
((((((..(((.((.....)).)))..)))).))..((((....(((((((.((.........)).))))))).......((((((.(....)))))))))))....(((......))). ( -39.60)
>consensus
GCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGCUCGGCCUUCUGGACGUUCAAUUCCAGAUCCUCGAUGUCCUUCUUCAGGCCAGAGAUCUCCUGAUCGGCCUUCUUCUUCUGCUGGAA
((.((((.((.((((..((((((((...........)))).((((((........))))))....................))))..)))).)).)))).)).....(((......))). (-36.68 = -36.35 +  -0.33)

alignment

secondary structure

dotplot

Window 5

Location	16,778,791 – 16,778,911
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.72
Mean single sequence MFE	-34.28
Consensus MFE	-32.80
Energy contribution	-32.97
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.16
Structure conservation index	0.96
SVM decision value	1.21
SVM RNA-class probability	0.930832
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778791 120 + 22407834
UGAAGAAGGACAUCGAGGAUCUGGAAUUGAACGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
............(((((..((((((........)))))).((((...........)))).....(((((....)))))....)))))..((.(((.(((.((....)).))).))).)). ( -35.30)
>DroVir_CAF1 8913 120 + 1
UGAAGAAGGACAUCGAGGAUCUGGAAUUGAGCGUCCAGAAGGCCGAACAGGAUAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
............(((((..((((((........)))))).((((...........)))).....(((((....)))))....)))))..((.(((.(((.((....)).))).))).)). ( -35.30)
>DroGri_CAF1 9111 120 + 1
UGAAGAAGGACAUCGAAGAUAUGGAGCUGAACAUCCAGAAGGCCGAACAGGAUAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
.......................(((((...(((((....((((...........)))).....(((((....)))))((..((((.....))))...))......)))))))))).... ( -30.80)
>DroWil_CAF1 8512 120 + 1
UGAAGAAGGAUAUCGAAGAUCUGGAAUUGAACAUCCAGAAGGCCGAGCAAGACAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
(.(((..((..........((((((........)))))).((((...........)))).))..(((((....)))))....))).)..((.(((.(((.((....)).))).))).)). ( -33.60)
>DroMoj_CAF1 9108 120 + 1
UGAAGAAGGACAUCGAGGAUCUGGAAUUGAGCGUCCAGAAGGCCGAGCAGGAUAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
............(((((..((((((........)))))).((((...........)))).....(((((....)))))....)))))..((.(((.(((.((....)).))).))).)). ( -35.30)
>DroAna_CAF1 8623 120 + 1
UGAAGAAGGACAUCGAGGAUCUGGAGCUGAAUGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
............(((((..((((((.(.....))))))).((((...........)))).....(((((....)))))....)))))..((.(((.(((.((....)).))).))).)). ( -35.40)
>consensus
UGAAGAAGGACAUCGAGGAUCUGGAAUUGAACGUCCAGAAGGCCGAGCAGGACAAGGCCACCAAGGAUCACCAGAUCCGCAACUUGAACGACGAGAUCGCCCACCAGGAUGAGCUCAUCA
(.(((..((..........((((((........)))))).((((...........)))).))..(((((....)))))....))).)..((.(((.(((.((....)).))).))).)). (-32.80 = -32.97 +   0.17)

alignment

secondary structure

dotplot

Window 6

Location	16,778,791 – 16,778,911
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.72
Mean single sequence MFE	-40.02
Consensus MFE	-39.14
Energy contribution	-39.08
Covariance contribution	-0.05
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.98
SVM decision value	2.94
SVM RNA-class probability	0.997812
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778791 120 - 22407834
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUGUCCUGCUCGGCCUUCUGGACGUUCAAUUCCAGAUCCUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((..(.....)..)))).)).)))...)))...)))))))).))))........... ( -41.90)
>DroVir_CAF1 8913 120 - 1
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGUUCGGCCUUCUGGACGCUCAAUUCCAGAUCCUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((...........)))).)).)))...)))...)))))))).))))........... ( -40.60)
>DroGri_CAF1 9111 120 - 1
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGUUCGGCCUUCUGGAUGUUCAGCUCCAUAUCUUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))(((.(((.((.(((.((((..((((..((.((((...........)))).)).))))..)))).))).)).))).)))........... ( -35.50)
>DroWil_CAF1 8512 120 - 1
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUGUCUUGCUCGGCCUUCUGGAUGUUCAAUUCCAGAUCUUCGAUAUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((..(.....)..)))).)).)))...)))...)))))))).))))........... ( -39.60)
>DroMoj_CAF1 9108 120 - 1
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGCUCGGCCUUCUGGACGCUCAAUUCCAGAUCCUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((...........)))).)).)))...)))...)))))))).))))........... ( -40.60)
>DroAna_CAF1 8623 120 - 1
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUGUCCUGCUCGGCCUUCUGGACAUUCAGCUCCAGAUCCUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((..(.....)..)))).)).)))...)))...)))))))).))))........... ( -41.90)
>consensus
UGAUGAGCUCAUCCUGGUGGGCGAUCUCGUCGUUCAAGUUGCGGAUCUGGUGAUCCUUGGUGGCCUUAUCCUGCUCGGCCUUCUGGACGUUCAAUUCCAGAUCCUCGAUGUCCUUCUUCA
.((((((.((..((....))..)).))))))......((((.((((((((((((((..((.((((...........)))).)).)))...)))...)))))))).))))........... (-39.14 = -39.08 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:29 2006