Locus 3719

Sequence ID	3R_DroMel_CAF1
Location	10,102,241 – 10,102,390
Length	149
Max. P	0.992835

overview

Window 7

Location	10,102,241 – 10,102,350
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	97.43
Mean single sequence MFE	-39.82
Consensus MFE	-36.20
Energy contribution	-35.88
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.38
Structure conservation index	0.91
SVM decision value	0.54
SVM RNA-class probability	0.773889
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102241 109 + 27905053
AGUAAAGCGGCACUUAUAGGAAAGGUUCCACCUUGGGAGGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAACAGUGCUU
....(((((((............((((((.(((..((((....))))))))).))))..(((((.((((((((.....))).))))).))))))))((.....)))))) ( -43.10)
>DroSec_CAF1 11574 109 + 1
AGUAAAGCGGCACUUAUAGGAAAGGCUCCACCUUGCGACGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUU
........((((((....(....(((..((((..((.((.(((..(.((((....))..(((....)))...)).)..))))).)).))))..))).)....)))))). ( -37.20)
>DroSim_CAF1 7772 109 + 1
AGUAAAGCGGCACUUAUAGGAAAGGCUCCACCUUGCGACGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUU
........((((((....(....(((..((((..((.((.(((..(.((((....))..(((....)))...)).)..))))).)).))))..))).)....)))))). ( -37.20)
>DroEre_CAF1 11639 109 + 1
AGUAAAGCGGCACUUAUAGGAAAGGCUCCACCUUGCGAGGAUCCUCCUGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUU
........((((((....(....(((..((((.((((((....)))((((.....)))).)))..((((((((.....))).)))))))))..))).)....)))))). ( -40.80)
>DroYak_CAF1 11650 109 + 1
AGUAAAGCGGCACUUAUAGGAAAGGCUCCACCUUGCGAGGAUCCUCCUGGGGAAACCAGGGCACAGGCCAGUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUU
........((((((....(....(((..((((.((((((....)))((((.....)))).)))..((((((((.....))).)))))))))..))).)....)))))). ( -40.80)
>consensus
AGUAAAGCGGCACUUAUAGGAAAGGCUCCACCUUGCGAGGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUU
........((((((....(....(((..((((.............((..((....))..))....((((((((.....))).)))))))))..))).)....)))))). (-36.20 = -35.88 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	10,102,241 – 10,102,350
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	97.43
Mean single sequence MFE	-39.46
Consensus MFE	-33.10
Energy contribution	-33.54
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.84
SVM decision value	0.76
SVM RNA-class probability	0.842987
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102241 109 - 27905053
AAGCACUGUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCCUCCCAAGGUGGAACCUUUCCUAUAAGUGCCGCUUUACU
..(((((......((.(.(((.(((((.(((.....)))))))).)))))).((((((((..((((....))))...)).)))))).........)))))......... ( -38.70)
>DroSec_CAF1 11574 109 - 1
AAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCGUCGCAAGGUGGAGCCUUUCCUAUAAGUGCCGCUUUACU
..(((((....((((((((((.(((((.(((.....)))))))).)))((((((......)))).)).)))))))((((.....)))).......)))))......... ( -39.70)
>DroSim_CAF1 7772 109 - 1
AAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCGUCGCAAGGUGGAGCCUUUCCUAUAAGUGCCGCUUUACU
..(((((....((((((((((.(((((.(((.....)))))))).)))((((((......)))).)).)))))))((((.....)))).......)))))......... ( -39.70)
>DroEre_CAF1 11639 109 - 1
AAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCAGGAGGAUCCUCGCAAGGUGGAGCCUUUCCUAUAAGUGCCGCUUUACU
..(((((((..(.(((..(((((((((.(((.....))))))))..(((.((((.....))))(((....)))))).))))..)))...)..)).)))))......... ( -40.50)
>DroYak_CAF1 11650 109 - 1
AAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGACUGGCCUGUGCCCUGGUUUCCCCAGGAGGAUCCUCGCAAGGUGGAGCCUUUCCUAUAAGUGCCGCUUUACU
..(((((((..(.(((..(((((((((..((....))..)))))..(((.((((.....))))(((....)))))).))))..)))...)..)).)))))......... ( -38.70)
>consensus
AAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCCUCGCAAGGUGGAGCCUUUCCUAUAAGUGCCGCUUUACU
..(((((((..(.(((..(((((((((.(((.....))))))))..(((...((((..(....)..))))...))).))))..)))...)..)).)))))......... (-33.10 = -33.54 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	10,102,272 – 10,102,390
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-48.14
Consensus MFE	-41.80
Energy contribution	-42.36
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.87
SVM decision value	2.35
SVM RNA-class probability	0.992835
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102272 118 + 27905053
CUUGGGAGGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAACAGUGCUUUGAGACAUGCGCCUGAAAGGCCAGAGGUUGUUGCUUCACU
(((.((((....)))).))).....((((((((.((((((((.....))).)))))((.....)).......)))))))).....((.(((.....)))))(((((....)))))... ( -43.10)
>DroSec_CAF1 11605 118 + 1
CUUGCGACGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUUUAAGGCAUGCGCUGGAAAGGCCAGAGGUUGUUGCUUCACU
...(((((((.((((.((((....))..(((((.((((((((.....))).))))).))))).(((((....(((((....))))).)).))).....)).)))))))))))...... ( -49.80)
>DroSim_CAF1 7803 118 + 1
CUUGCGACGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUUUAAGGCAUGCGCUGGAAAGGCCAGAGGUUGUUGCUUCACU
...(((((((.((((.((((....))..(((((.((((((((.....))).))))).))))).(((((....(((((....))))).)).))).....)).)))))))))))...... ( -49.80)
>DroEre_CAF1 11670 118 + 1
CUUGCGAGGAUCCUCCUGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUUUAAGGCAUGCACUGGAAAGGCCAGAGGUUGUUGCUUCACA
...((((.(((((((((((.....))))).....((((..((((((...((((((.......))))))....(((((....)))))..))))))..)))))).)))).))))...... ( -47.60)
>DroYak_CAF1 11681 118 + 1
CUUGCGAGGAUCCUCCUGGGGAAACCAGGGCACAGGCCAGUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUUUAAGGCAUGAACUGGAAAGGCCAGAGGUUGUUGCUUCACA
...((((.(((((((((((.....))))).....((((..(((((((..((((((.......))))))....(((((....))))).)))))))..)))))).)))).))))...... ( -50.40)
>consensus
CUUGCGAGGAUCCUCCGGGGGAAACCAGGGCACAGGCCAAUCCAGUUGAUGUGGCCGGUGUCGCCACGAAUAGUGCUUUAAGGCAUGCGCUGGAAAGGCCAGAGGUUGUUGCUUCACU
...((((.((.(((((..((....))..).....((((..((((((...((((((.......))))))....(((((....)))))..))))))..)))).)))))).))))...... (-41.80 = -42.36 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	10,102,272 – 10,102,390
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-40.32
Consensus MFE	-33.86
Energy contribution	-33.94
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.38
SVM RNA-class probability	0.714570
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10102272 118 - 27905053
AGUGAAGCAACAACCUCUGGCCUUUCAGGCGCAUGUCUCAAAGCACUGUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCCUCCCAAG
.((......))..(((((((....(((((.((((.................(((....))).(((((.(((.....)))))))).)))))))))......)))))))........... ( -37.70)
>DroSec_CAF1 11605 118 - 1
AGUGAAGCAACAACCUCUGGCCUUUCCAGCGCAUGCCUUAAAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCGUCGCAAG
......((.((..(((((((.....((((.((((((......)).......(((....))).(((((.(((.....)))))))).)))).))))......)))))))...)).))... ( -40.00)
>DroSim_CAF1 7803 118 - 1
AGUGAAGCAACAACCUCUGGCCUUUCCAGCGCAUGCCUUAAAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCGUCGCAAG
......((.((..(((((((.....((((.((((((......)).......(((....))).(((((.(((.....)))))))).)))).))))......)))))))...)).))... ( -40.00)
>DroEre_CAF1 11670 118 - 1
UGUGAAGCAACAACCUCUGGCCUUUCCAGUGCAUGCCUUAAAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCAGGAGGAUCCUCGCAAG
(((((.(((.((......((((..((((((...(((......)))......(((((.......)))))....))))))..)))))))))(((((.....))))).......))))).. ( -42.20)
>DroYak_CAF1 11681 118 - 1
UGUGAAGCAACAACCUCUGGCCUUUCCAGUUCAUGCCUUAAAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGACUGGCCUGUGCCCUGGUUUCCCCAGGAGGAUCCUCGCAAG
(((((.(((.((......((((..(((((((..(((......)))......(((((.......)))))...)))))))..)))))))))(((((.....))))).......))))).. ( -41.70)
>consensus
AGUGAAGCAACAACCUCUGGCCUUUCCAGCGCAUGCCUUAAAGCACUAUUCGUGGCGACACCGGCCACAUCAACUGGAUUGGCCUGUGCCCUGGUUUCCCCCGGAGGAUCCUCGCAAG
.((((........(((((((((..(((((....(((......)))......(((((.......))))).....)))))..))))........((.....)).)))))....))))... (-33.86 = -33.94 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:20 2006