Locus 7501

Sequence ID	3L_DroMel_CAF1
Location	20,132,167 – 20,132,293
Length	126
Max. P	0.907511

overview

Window 8

Location	20,132,167 – 20,132,265
Length	98
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	72.39
Mean single sequence MFE	-28.68
Consensus MFE	-15.01
Energy contribution	-15.85
Covariance contribution	0.84
Combinations/Pair	1.29
Mean z-score	-1.61
Structure conservation index	0.52
SVM decision value	-0.03
SVM RNA-class probability	0.517506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20132167 98 + 23771897
-GAUCGCCGGUACAAAAAGCUUAAUCUCGUUGGCGCAAAGAGAGCGGGA-AAGAGAGGAACUAAGUUAGUUC--A--------CCUAACCGCUCUCUUCAACUUCGUGCG
-...((((((........(((..........)))...((((((((((..-...((..((((((...))))))--.--------.))..)))))))))).....))).))) ( -31.30)
>DroSec_CAF1 46353 98 + 1
-GAUCGCCGGUACAAAAAGCUCAAGCUCGCCGGUGCAAAGAGAGCGGAA-AAGAGAGGAACUAAGUUAGUUC--A--------ACUAGUCGCUCUCUUCAACUUCGUGCG
-....((((((......(((....))).))))))(((((((((((((..-...((..((((((...))))))--.--------.))..))))))))))........))). ( -32.70)
>DroSim_CAF1 46530 98 + 1
-GAUCGCCGGUACAAAAAGCUCAAGCUCGCUGGCGCAAAGAGAGCGGGA-AAGAGAGGAACUAAGUUAGUUC--A--------ACUAACCGCUCUCUUCAACUUCGUGCG
-....((((((......(((....))).))))))(((((((((((((..-...((..((((((...))))))--.--------.))..))))))))))........))). ( -35.70)
>DroEre_CAF1 48370 95 + 1
UGAUCUCCGGUCCAAAAAGC------UCGCUGGUGCAAAGAGCGCGGAAGAAGAGAAAA----AAUUGGUGUUUAAGAGAAGAGCC----ACUCUC-UCGACUUUGUACA
.......((((.........------..))))(((((((((((((.((...........----..)).)))))...((((.(((..----.)))))-))..)))))))). ( -20.22)
>DroYak_CAF1 50746 99 + 1
UGAUCGCCGGUCCAAAAAGC------UCGCUGGCGCA-AGAGAGCGCAAAAAGAGAACA----AAUUAGAUCUAAGAAGAAGAGCCAUGCACUCUCUUCGACUUUGUGUG
....(((((((.........------..)))))))..-.....(((((((...(((.(.----.....).)))..(((((.(((.......))))))))...))))))). ( -23.50)
>consensus
_GAUCGCCGGUACAAAAAGCU_AA_CUCGCUGGCGCAAAGAGAGCGGAA_AAGAGAGGAACUAAGUUAGUUC__A________ACUAACCGCUCUCUUCAACUUCGUGCG
....(((((((.................)))))))..((((((((((.........................................))))))))))............ (-15.01 = -15.85 +   0.84)

alignment

secondary structure

dotplot

Window 9

Location	20,132,167 – 20,132,265
Length	98
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	72.39
Mean single sequence MFE	-29.46
Consensus MFE	-14.50
Energy contribution	-15.90
Covariance contribution	1.40
Combinations/Pair	1.18
Mean z-score	-1.87
Structure conservation index	0.49
SVM decision value	0.76
SVM RNA-class probability	0.843631
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20132167 98 - 23771897
CGCACGAAGUUGAAGAGAGCGGUUAGG--------U--GAACUAACUUAGUUCCUCUCUU-UCCCGCUCUCUUUGCGCCAACGAGAUUAAGCUUUUUGUACCGGCGAUC-
...........(((((((((((..(((--------.--((((((...))))))....)))-..))))))))))).((((.((((((.......))))))...))))...- ( -34.60)
>DroSec_CAF1 46353 98 - 1
CGCACGAAGUUGAAGAGAGCGACUAGU--------U--GAACUAACUUAGUUCCUCUCUU-UUCCGCUCUCUUUGCACCGGCGAGCUUGAGCUUUUUGUACCGGCGAUC-
(((.((..(..((((((((.(((((((--------(--(...)))).))))).)))))))-)..)((((..(((((....)))))...)))).........)))))...- ( -32.40)
>DroSim_CAF1 46530 98 - 1
CGCACGAAGUUGAAGAGAGCGGUUAGU--------U--GAACUAACUUAGUUCCUCUCUU-UCCCGCUCUCUUUGCGCCAGCGAGCUUGAGCUUUUUGUACCGGCGAUC-
(((.((.....(((((((((((..((.--------.--((((((...))))))....)).-..)))))))))))....(((.((((....)))).)))...)))))...- ( -33.40)
>DroEre_CAF1 48370 95 - 1
UGUACAAAGUCGA-GAGAGU----GGCUCUUCUCUUAAACACCAAUU----UUUUCUCUUCUUCCGCGCUCUUUGCACCAGCGA------GCUUUUUGGACCGGAGAUCA
...........((-(((((.----.....)))))))...........----...(((((...((((.((((...((....))))------))....))))..)))))... ( -19.00)
>DroYak_CAF1 50746 99 - 1
CACACAAAGUCGAAGAGAGUGCAUGGCUCUUCUUCUUAGAUCUAAUU----UGUUCUCUUUUUGCGCUCUCU-UGCGCCAGCGA------GCUUUUUGGACCGGCGAUCA
........((((((((((((.....)))).)))))...(.(((((..----.((((.((....((((.....-.)))).)).))------))...))))).))))..... ( -27.90)
>consensus
CGCACGAAGUUGAAGAGAGCGGUUAGC________U__GAACUAACUUAGUUCCUCUCUU_UUCCGCUCUCUUUGCGCCAGCGAG_UU_AGCUUUUUGUACCGGCGAUC_
.(((.(((((((((((((((((.........................................)))))))))))((....)).......)))))).)))........... (-14.50 = -15.90 +   1.40)

alignment

secondary structure

dotplot

Window 0

Location	20,132,197 – 20,132,293
Length	96
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	71.32
Mean single sequence MFE	-33.04
Consensus MFE	-14.04
Energy contribution	-14.68
Covariance contribution	0.64
Combinations/Pair	1.36
Mean z-score	-1.98
Structure conservation index	0.42
SVM decision value	1.05
SVM RNA-class probability	0.907511
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20132197 96 + 23771897
GGCGCAAAGAGAGCGGGA-AAGAGAGGAACUAAGUUAGUUC--A--------CCUAACCGCUCUCUUCAACUUCGUGCGUGCGUGUG--UGUGUGUAUGUUGCCGCGCA
.((((.((((((((((..-...((..((((((...))))))--.--------.))..))))))))))......((((((..((....--))..)))))).....)))). ( -41.00)
>DroSec_CAF1 46383 98 + 1
GGUGCAAAGAGAGCGGAA-AAGAGAGGAACUAAGUUAGUUC--A--------ACUAGUCGCUCUCUUCAACUUCGUGCGUGAGUGUGUGUGUGUGUAUGUUGCCUCGCA
.(((((((((((((((..-...((..((((((...))))))--.--------.))..))))))))))..((..((..(....)..))...)).)))))........... ( -30.90)
>DroSim_CAF1 46560 98 + 1
GGCGCAAAGAGAGCGGGA-AAGAGAGGAACUAAGUUAGUUC--A--------ACUAACCGCUCUCUUCAACUUCGUGCGUGCGUGUGUGUGUGUGUAUGUUGCCUCGCA
.(((..((((((((((..-...((..((((((...))))))--.--------.))..))))))))))((((..((..((..(....)..))..))...))))...))). ( -37.10)
>DroEre_CAF1 48395 96 + 1
GGUGCAAAGAGCGCGGAAGAAGAGAAAA----AAUUGGUGUUUAAGAGAAGAGCC----ACUCUC-UCGACUUUGUACAUGUGCGUGUGUGUGUGC----UGCGGCGCA
.((((...(((((((((((..((((...----...((((.(((.....))).)))----)...))-))..)))).(((((....)))))..)))))----).).)))). ( -25.80)
>DroYak_CAF1 50771 104 + 1
GGCGCA-AGAGAGCGCAAAAAGAGAACA----AAUUAGAUCUAAGAAGAAGAGCCAUGCACUCUCUUCGACUUUGUGUGCGUGAGUGUGUGUGUGCUGACUGCGACGCA
.(((((-.....(((((.(((((((.(.----.....).)))..(((((.(((.......))))))))..)))).))))).....)))))((((((.....)).)))). ( -30.40)
>consensus
GGCGCAAAGAGAGCGGAA_AAGAGAGGAACUAAGUUAGUUC__A________ACUAACCGCUCUCUUCAACUUCGUGCGUGCGUGUGUGUGUGUGUAUGUUGCCGCGCA
.(((((((((((((((.........................................))))))))))........))))).........(((((((.....)).))))) (-14.04 = -14.68 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:52 2006