Locus 7968

Sequence ID	3L_DroMel_CAF1
Location	21,097,462 – 21,097,622
Length	160
Max. P	0.970956

overview

Window 1

Location	21,097,462 – 21,097,582
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.50
Mean single sequence MFE	-33.20
Consensus MFE	-26.80
Energy contribution	-27.44
Covariance contribution	0.64
Combinations/Pair	1.09
Mean z-score	-2.07
Structure conservation index	0.81
SVM decision value	1.27
SVM RNA-class probability	0.938273
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21097462 120 + 23771897
CUGCAAUCCGAGUGGUCCUUGCCUUUGUUUAUCCUGCUGCCAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCCUACUGUCCUGCAGUUCCAGUUACU
(((((....(((.(((....)))...((.(((((((....))))))).)))))(((......))).....((((...(((((((....)))))))....)))).)))))........... ( -32.90)
>DroSec_CAF1 147654 120 + 1
CUGCAAUCCGAGUGGUCCUUGCCUUUGUUUAUCCUGCUGCCAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACU
(((((....(((.(((....)))...((.(((((((....))))))).)))))(((......))).....((((...(((((((....)))))))....)))).)))))........... ( -33.60)
>DroSim_CAF1 55186 120 + 1
CUGCAAUCCGAGUGGUCCUUGCCUUUGUUUAUCCUGCUGCCAGGAUGCACCUCGCACAUCCUUGUACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACU
(((((...((((.(((...(((....((.(((((((....))))))).))...))).)))))))......((((...(((((((....)))))))....)))).)))))........... ( -33.50)
>DroEre_CAF1 70017 120 + 1
CUGCAAUGCGAGUGGUCCUUGCCUUUGUUUAUCCUGCUGCCAUGUUGCAGCUCGCUUAUCCUUGCACCCUGGUACUUGCGCUUAUGAAUAAGCGUUUACUGUCCUGCAGUUCCAGUUACU
(((((.((((((.(((....)))............(((((......))))).........))))))....((((...(((((((....))))))).))))....)))))........... ( -31.90)
>DroYak_CAF1 41876 120 + 1
CUGCAAUCCGAGUGCUCCUUGCCUUUGUUUAUCCUGCUGCCAGGUUGCACCUUGCAUAUCCUUGCACUCUGACACUCGCGCUUAUGAAUAAGCGUUUACUGUCCUGCAGUUCCAGUUACU
(((((....((((((....(((...(((....((((....))))..)))....))).......)))))).((((...(((((((....)))))))....)))).)))))........... ( -34.10)
>consensus
CUGCAAUCCGAGUGGUCCUUGCCUUUGUUUAUCCUGCUGCCAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACU
(((((...((((.(((...(((....((.(((((((....))))))).))...))).)))))))......((((...(((((((....)))))))....)))).)))))........... (-26.80 = -27.44 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	21,097,462 – 21,097,582
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.50
Mean single sequence MFE	-39.22
Consensus MFE	-31.06
Energy contribution	-32.90
Covariance contribution	1.84
Combinations/Pair	1.03
Mean z-score	-2.56
Structure conservation index	0.79
SVM decision value	1.67
SVM RNA-class probability	0.970956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21097462 120 - 23771897
AGUAACUGGAACUGCAGGACAGUAGGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUGGCAGCAGGAUAAACAAAGGCAAGGACCACUCGGAUUGCAG
.((((((((..((((..((((.(..(((((((....))))))).).))))....(((.((((((..(...)..)))))).)))))))..........((......))..)))).)))).. ( -42.80)
>DroSec_CAF1 147654 120 - 1
AGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUGGCAGCAGGAUAAACAAAGGCAAGGACCACUCGGAUUGCAG
...........((((((..((((..(((((((....)))))))...((((..(.(((.((((((..(...)..)))))).))).)..))))......((......))))).)..)))))) ( -42.60)
>DroSim_CAF1 55186 120 - 1
AGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUACAAGGAUGUGCGAGGUGCAUCCUGGCAGCAGGAUAAACAAAGGCAAGGACCACUCGGAUUGCAG
.((((((((..((((..((((.(..(((((((....))))))).).))))...((...((((((..(...)..)))))).)).))))..........((......))..)))).)))).. ( -39.40)
>DroEre_CAF1 70017 120 - 1
AGUAACUGGAACUGCAGGACAGUAAACGCUUAUUCAUAAGCGCAAGUACCAGGGUGCAAGGAUAAGCGAGCUGCAACAUGGCAGCAGGAUAAACAAAGGCAAGGACCACUCGCAUUGCAG
...........((((((....((...(((((((((....((....))((....))....))))))))).(((((......))))).......))....((.((.....)).)).)))))) ( -34.00)
>DroYak_CAF1 41876 120 - 1
AGUAACUGGAACUGCAGGACAGUAAACGCUUAUUCAUAAGCGCGAGUGUCAGAGUGCAAGGAUAUGCAAGGUGCAACCUGGCAGCAGGAUAAACAAAGGCAAGGAGCACUCGGAUUGCAG
...........((((((((((.(...((((((....))))))..).)))).((((((.......(((.....))).(((.((....(......)....)).))).))))))...)))))) ( -37.30)
>consensus
AGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUGGCAGCAGGAUAAACAAAGGCAAGGACCACUCGGAUUGCAG
.((((((((..((((..........(((((((....)))))))...((((((((((((.(......)....))))))))))))))))..........((......))..)))).)))).. (-31.06 = -32.90 +   1.84)

alignment

secondary structure

dotplot

Window 3

Location	21,097,502 – 21,097,622
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.50
Mean single sequence MFE	-29.74
Consensus MFE	-25.50
Energy contribution	-25.66
Covariance contribution	0.16
Combinations/Pair	1.17
Mean z-score	-1.25
Structure conservation index	0.86
SVM decision value	0.06
SVM RNA-class probability	0.561356
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21097502 120 + 23771897
CAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCCUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGGCAAUUAUGCGCUUCUUAAAAAUAAA
.((((((.........)))))).(((....((((...(((((((....)))))))....))))...((((.......))))((((.......)))).....)))................ ( -30.50)
>DroSec_CAF1 147694 120 + 1
CAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGGCAAUUAUGCGCUUCUUAAAAAUAAA
.((((((.........)))))).(((....((((...(((((((....)))))))....))))...((((.......))))((((.......)))).....)))................ ( -31.20)
>DroSim_CAF1 55226 120 + 1
CAGGAUGCACCUCGCACAUCCUUGUACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGGCAAUUAUGCGCUUCUUAAAAAUAAA
.((((((.........))))))........((((...(((((((....)))))))....))))..(((....(((...)))((((.......)))).....)))................ ( -29.20)
>DroEre_CAF1 70057 120 + 1
CAUGUUGCAGCUCGCUUAUCCUUGCACCCUGGUACUUGCGCUUAUGAAUAAGCGUUUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGCCAAUUAUGCGCUUCUUAAAAAUAAA
((((((((((..(((........)).....((((...(((((((....))))))).)))))..))))))..........(((((........)))))..))))................. ( -27.30)
>DroYak_CAF1 41916 120 + 1
CAGGUUGCACCUUGCAUAUCCUUGCACUCUGACACUCGCGCUUAUGAAUAAGCGUUUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGGCAAUUAUGCGCUUCCUAAAAAUAAA
.(((..((....((((......))))....((((...(((((((....)))))))....))))..(((....(((...)))((((.......)))).....)))))..)))......... ( -30.50)
>consensus
CAGGAUGCACCUCGCACAUCCUUGCACCCUGACACUUGCGCUUAUGAAUAAGCGCUUACUGUCCUGCAGUUCCAGUUACUGGCCCAGUUACCGGGCAAUUAUGCGCUUCUUAAAAAUAAA
.((((.((.....(((......))).....((((...(((((((....)))))))....))))..(((....(((...)))((((.......)))).....))))).))))......... (-25.50 = -25.66 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	21,097,502 – 21,097,622
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.50
Mean single sequence MFE	-38.86
Consensus MFE	-30.32
Energy contribution	-32.36
Covariance contribution	2.04
Combinations/Pair	1.03
Mean z-score	-2.00
Structure conservation index	0.78
SVM decision value	0.65
SVM RNA-class probability	0.812272
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21097502 120 - 23771897
UUUAUUUUUAAGAAGCGCAUAAUUGCCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAGGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUG
..............((((....(((((((((.((((...)))).)))))....))))((((.(..(((((((....))))))).).))))...)))).((((((..(...)..)))))). ( -42.70)
>DroSec_CAF1 147694 120 - 1
UUUAUUUUUAAGAAGCGCAUAAUUGCCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUG
..............((((....(((((((((.((((...)))).)))))....))))((((.(..(((((((....))))))).).))))...)))).((((((..(...)..)))))). ( -41.90)
>DroSim_CAF1 55226 120 - 1
UUUAUUUUUAAGAAGCGCAUAAUUGCCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUACAAGGAUGUGCGAGGUGCAUCCUG
..............(((((....)))(((((.((((...)))).)))))....))..((((.(..(((((((....))))))).).))))........((((((..(...)..)))))). ( -38.40)
>DroEre_CAF1 70057 120 - 1
UUUAUUUUUAAGAAGCGCAUAAUUGGCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAAACGCUUAUUCAUAAGCGCAAGUACCAGGGUGCAAGGAUAAGCGAGCUGCAACAUG
..............((((...(((((((........))))))).((((...(....)..))))...(((((((((....((....))((....))....))))))))).)).))...... ( -33.10)
>DroYak_CAF1 41916 120 - 1
UUUAUUUUUAGGAAGCGCAUAAUUGCCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAAACGCUUAUUCAUAAGCGCGAGUGUCAGAGUGCAAGGAUAUGCAAGGUGCAACCUG
........((((..((((....(((((((((.((((...)))).)))))...((((.((((.(...((((((....))))))..).))))....)))).......)))).))))..)))) ( -38.20)
>consensus
UUUAUUUUUAAGAAGCGCAUAAUUGCCCGGUAACUGGGCCAGUAACUGGAACUGCAGGACAGUAAGCGCUUAUUCAUAAGCGCAAGUGUCAGGGUGCAAGGAUGUGCGAGGUGCAUCCUG
..............((((......((((((...))))))......((((.((((.....))))..(((((((....))))))).....)))).)))).(((((((((...))))))))). (-30.32 = -32.36 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:24 2006