Locus 4919

Sequence ID	3L_DroMel_CAF1
Location	13,670,081 – 13,670,313
Length	232
Max. P	0.997917

overview

Window 7

Location	13,670,081 – 13,670,195
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.08
Mean single sequence MFE	-38.32
Consensus MFE	-33.13
Energy contribution	-33.56
Covariance contribution	0.43
Combinations/Pair	1.08
Mean z-score	-1.71
Structure conservation index	0.86
SVM decision value	1.27
SVM RNA-class probability	0.938297
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670081 114 - 23771897
---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGUUCGUGUCGGGUUCCCUGCCACUGGCAGUUGCUCCU---CCU
---....((((((((((((((...(((...)))...)))))))))((((....))))...)))))..((((((....((..(((.((((...)))).)))..)).))))))...---... ( -36.10)
>DroSec_CAF1 77471 114 - 1
---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCUCGUGUCGGGUUCCCUGCUACUGGCAGUUGCUCCU---CCU
---(((.((((((((((((((...(((...)))...)))))))))((((....))))...)))))..))).....((((...((((((...........))))))...))))..---... ( -37.20)
>DroSim_CAF1 87613 117 - 1
---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCUCGUGUCGGGUUCCCUGCCACUGGCAGUUGCUCCUCCUCCU
---....((((((((((((((...(((...)))...)))))))))((((....))))...)))))..((((((....(((.(((.((((...)))).))).))).))))))......... ( -38.30)
>DroEre_CAF1 82673 117 - 1
---GCUCCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCUCGUGUCGGGUUCCCAGCCAGUGGCAGUUGCACCUCCCCCC
---((..((((.((((((.....(((((.(((....)))(((..(((((....)))))..))).)))))......(((((((...))))..))).).)))))))))..)).......... ( -38.70)
>DroYak_CAF1 86022 108 - 1
GCUGCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCUCCU------------GCCAGUGGCAGUUGCUCCUCUCCCC
((((...((((((((((((((...(((...)))...)))))))))((((....))))...))))).)))).....((((..((------------(((...)))))..))))........ ( -41.30)
>consensus
___GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCUCGUGUCGGGUUCCCUGCCACUGGCAGUUGCUCCUC__CCU
.......((((((((((((((...(((...)))...)))))))))((((....))))...)))))...(((((....(((.(((.((((...)))).))).))).))))).......... (-33.13 = -33.56 +   0.43)

alignment

secondary structure

dotplot

Window 8

Location	13,670,118 – 13,670,235
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.97
Mean single sequence MFE	-36.64
Consensus MFE	-34.20
Energy contribution	-34.24
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.93
SVM decision value	1.14
SVM RNA-class probability	0.920779
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670118 117 + 23771897
AACCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGAAGC---AGCAUCCGCCCAAUAAUGUUUCCACGUAAUGCGGCAUCUA
.........(((((.(((((((.((((....))))...((((((.(((((...))))).)))))).)))))))...)---))))...(((((...((((....))))..)).)))..... ( -36.50)
>DroSec_CAF1 77508 117 + 1
AGCCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGAAGC---AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUA
.........(((((.(((((((.((((....))))...((((((.(((((...))))).)))))).)))))))...)---))))...(((((...((((....))))..)).)))..... ( -36.50)
>DroSim_CAF1 87653 117 + 1
AGCCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGAAGC---AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUA
.........(((((.(((((((.((((....))))...((((((.(((((...))))).)))))).)))))))...)---))))...(((((...((((....))))..)).)))..... ( -36.50)
>DroEre_CAF1 82713 117 + 1
AGCCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGGAGC---AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUA
.(((...(((((((((((((((.((((....))))...((((((.(((((...))))).)))))).)))))))((((---(((....)).......)))))))).)))))..)))..... ( -36.01)
>DroYak_CAF1 86050 120 + 1
AGCCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGAAGCAGCAGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUA
.(((.....((((..(((((((.((((....))))...((((((.(((((...))))).)))))).))))))).))))(((((....))......((((....))))..))))))..... ( -37.70)
>consensus
AGCCCGAAUUGCUGGCUGCAUAAAUUCUGAUGAAUCACUGCACCUUUUGGCUGCCAGGUGGUGCAAUGUGCAGAAGC___AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUA
.(((...((((((((..((((...(((((......((.((((((.(((((...))))).)))))).))..)))))......((....))......))))..))).)))))..)))..... (-34.20 = -34.24 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	13,670,118 – 13,670,235
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.97
Mean single sequence MFE	-41.70
Consensus MFE	-37.48
Energy contribution	-37.48
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.52
Structure conservation index	0.90
SVM decision value	2.96
SVM RNA-class probability	0.997917
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670118 117 - 23771897
UAGAUGCCGCAUUACGUGGAAACAUUAUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGUU
.....(((.((.((.(((....))))).)))))(((((((---(...((((((((((((((...(((...)))...)))))))))((((....))))...))))).)))).))))..... ( -40.80)
>DroSec_CAF1 77508 117 - 1
UAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCU
.....(((((.....(((....)))......))(((((((---(...((((((((((((((...(((...)))...)))))))))((((....))))...))))).)))).)))).))). ( -41.60)
>DroSim_CAF1 87653 117 - 1
UAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCU
.....(((((.....(((....)))......))(((((((---(...((((((((((((((...(((...)))...)))))))))((((....))))...))))).)))).)))).))). ( -41.60)
>DroEre_CAF1 82713 117 - 1
UAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUCCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCU
.....(((((.....(((....)))......))(((((((---(...((((((((((((((...(((...)))...)))))))))((((....))))...))))).)))).)))).))). ( -41.60)
>DroYak_CAF1 86050 120 - 1
UAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCUGCUGCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCU
.....(((((.....(((....)))......))(((((((((((((((((..(((((((((...(((...)))...)))))))))......))))).....)))).)))).)))).))). ( -42.90)
>consensus
UAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU___GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUGCAGUGAUUCAUCAGAAUUUAUGCAGCCAGCAAUUCGGGCU
.((...((((.....(((....)))......))))...))...(((.((((((((((((((...(((...)))...)))))))))((((....))))...)))))..))).......... (-37.48 = -37.48 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,670,158 – 13,670,273
Length	115
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	97.42
Mean single sequence MFE	-36.24
Consensus MFE	-34.94
Energy contribution	-34.70
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.31
Structure conservation index	0.96
SVM decision value	0.81
SVM RNA-class probability	0.856682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670158 115 - 23771897
GUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUAUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
.....((((((((((((.(((....((((........)))).))).)).....(((....)))....))))))))))(---(((..(((.....)))......))))(((....))). ( -33.70)
>DroSec_CAF1 77548 115 - 1
GUUCCGCGUUCGCCCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
.....((((((((((((.(((....((((........)))).))).)).....(((....)))....))))))))))(---(((..(((.....)))......))))(((....))). ( -36.70)
>DroSim_CAF1 87693 115 - 1
GUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
.....((((((((((((.(((....((((........)))).))).)).....(((....)))....))))))))))(---(((..(((.....)))......))))(((....))). ( -33.70)
>DroEre_CAF1 82753 115 - 1
GCUCCGCGUUCGCCCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU---GCUCCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
((...((((((((((((.(((....((((........)))).))).)).....(((....)))....))))))))))(---((....)))....))..(((((..........))))) ( -38.40)
>DroYak_CAF1 86090 118 - 1
GUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCUGCUGCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
...((((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))).((((((..(((.....)))......)))))).....)).. ( -38.70)
>consensus
GUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU___GCUUCUGCACAUUGCACCACCUGGCAGCCAAAAGGUG
.....((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))).........(((.....))).(((((..........))))) (-34.94 = -34.70 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	13,670,195 – 13,670,313
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	97.97
Mean single sequence MFE	-25.40
Consensus MFE	-22.72
Energy contribution	-22.88
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.89
SVM decision value	1.54
SVM RNA-class probability	0.962529
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670195 118 + 23771897
AGCAUCCGCCCAAUAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGAGCGAACGCGGAACCAAAUUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((..(((((...((((....))))..)).))).(((.............(((((.....)))))....((((((.....)))))))))))))....................... ( -23.60)
>DroSec_CAF1 77585 118 + 1
AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGGGCGAACGCGGAACCAAAUUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((.(((((....((((....))))...((.((((((((........))))...)))).)))))))...((((((.....))))))...))))....................... ( -28.70)
>DroSim_CAF1 87730 118 + 1
AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGAGCGAACGCGGAACCAAAUUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((..(((((...((((....))))..)).))).(((.............(((((.....)))))....((((((.....)))))))))))))....................... ( -23.60)
>DroEre_CAF1 82790 118 + 1
AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGGGCGAACGCGGAGCCAAAAUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((.(((((....((((....))))...((.((((((((........))))...)))).)))))))...(((((.......)))))...))))....................... ( -28.50)
>DroYak_CAF1 86130 118 + 1
AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGAGCGAACGCGGAACCAGAAUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((..(((((...((((....))))..)).))).(((.............(((((.....)))))....(((((.......))))))))))))....................... ( -22.60)
>consensus
AGCAUCCGCCCAAAAAUGUUUCCACGUAAUGCGGCAUCUAAUAAUAAAUUUAGCUUGUGCAGCGAGCGAACGCGGAACCAAAUUUCGCAGAAUGCAUAAUUCAAAAUAAUUCAAAACA
.((((..(((((...((((....))))..)).))).(((.............(((((.....)))))....((((((.....)))))))))))))....................... (-22.72 = -22.88 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	13,670,195 – 13,670,313
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	97.97
Mean single sequence MFE	-33.14
Consensus MFE	-30.78
Energy contribution	-31.14
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.19
Structure conservation index	0.93
SVM decision value	2.86
SVM RNA-class probability	0.997430
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13670195 118 - 23771897
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAAUUUGGUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUAUUGGGCGGAUGCU
..............(..((((.(((.....))).))))..)....((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). ( -32.20)
>DroSec_CAF1 77585 118 - 1
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAAUUUGGUUCCGCGUUCGCCCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU
..............(..((((.(((.....))).))))..)....((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). ( -35.20)
>DroSim_CAF1 87730 118 - 1
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAAUUUGGUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU
..............(..((((.(((.....))).))))..)....((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). ( -32.20)
>DroEre_CAF1 82790 118 - 1
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAUUUUGGCUCCGCGUUCGCCCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU
.(((..(((((.....((((.....))))....))))).)))...((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). ( -32.60)
>DroYak_CAF1 86130 118 - 1
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAUUCUGGUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU
......((((((....(((((.(((.....)))))))))))))).((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). ( -33.50)
>consensus
UGUUUUGAAUUAUUUUGAAUUAUGCAUUCUGCGAAAUUUGGUUCCGCGUUCGCUCGCUGCACAAGCUAAAUUUAUUAUUAGAUGCCGCAUUACGUGGAAACAUUUUUGGGCGGAUGCU
..............(..((((.(((.....))).))))..)....((((((((((((.(((....((((........)))).))).)).....(((....)))....)))))))))). (-30.78 = -31.14 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:05 2006