Locus 5784

Sequence ID	3L_DroMel_CAF1
Location	15,666,916 – 15,667,044
Length	128
Max. P	0.687775

overview

Window 9

Location	15,666,916 – 15,667,026
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	92.91
Mean single sequence MFE	-31.96
Consensus MFE	-27.10
Energy contribution	-27.54
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.31
Structure conservation index	0.85
SVM decision value	0.20
SVM RNA-class probability	0.631069
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15666916 110 + 23771897
CGUUGAGGAAAUGAAUCAGCAGAGAGGCUGGGGAGAUUAGCAAAAUGCCGGAGGUUGUCUGCGCAACGAUGACGUCUUGAAGACAGAGGACAGACAAUUAUCCGGGCAUU
.(((((.........(((((......))))).....)))))..((((((((((((((((((((((....)).)(((.....)))....).))))))))).))).)))))) ( -31.64)
>DroSec_CAF1 26633 110 + 1
CGUUGAGGAAAUGAAUCAGCAGAGAGGCUGGGGAGAUUAGCAAAAUGCCGGAGGUUGUCUUCGCAACGAUGACGUCUUGAAGACAGGGGACAGACAAUUAUACGGGCAUU
.(((((.........(((((......))))).....)))))..((((((.(....((((((((..(((....)))..))))))))(....)...........).)))))) ( -31.24)
>DroSim_CAF1 26614 110 + 1
CGUUGAGGAAAUGAAUCAGCAGAGAGGCUGGGGAGAUUAGCAAAAUGCCGGAGGUUGUCUUCGCAACGAUGACGUCUUGAAGACAGGGGACAGACAAUUAUCCGGGCAUU
.(((((.........(((((......))))).....)))))..(((((((((.((((((((((..(((....)))..))))))).(....).))).....))).)))))) ( -33.14)
>DroEre_CAF1 26212 109 + 1
CGUUGAGGAAAUGAAUCAGCAGAGCGGCUGG-GAGAUUAGCAAAAUGCCGGAGGCUGUCGGUGGAACGAUGACGUCUCCAAGACAGGGCACAGACAAUUAUCCGGGCAUU
.(((((.........)))))...((.(((((-....)))))......(((((..(((((..(((((((....))).)))).)))))(.......).....)))))))... ( -31.90)
>DroYak_CAF1 26786 110 + 1
CGCGGAGGAAAUGAAUCAGCAGAGAGGCUGGCGAGAUUAGCAAAAUGCCGGAGGUUGUCAGUGGUACGAUGACGUCUCGGAGACAGGGGACAGACAAUUAUCCGGGCAUU
.((.............((((......))))((.......))......((((((((((((.((.((...)).))((((((....)..))))).))))))).)))))))... ( -31.90)
>consensus
CGUUGAGGAAAUGAAUCAGCAGAGAGGCUGGGGAGAUUAGCAAAAUGCCGGAGGUUGUCUGCGCAACGAUGACGUCUUGAAGACAGGGGACAGACAAUUAUCCGGGCAUU
.(((((.........(((((......))))).....)))))..((((((((((((((((..............(((.....))).(....).))))))).))).)))))) (-27.10 = -27.54 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	15,666,916 – 15,667,026
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	92.91
Mean single sequence MFE	-25.08
Consensus MFE	-19.98
Energy contribution	-20.58
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.80
SVM decision value	0.30
SVM RNA-class probability	0.678506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15666916 110 - 23771897
AAUGCCCGGAUAAUUGUCUGUCCUCUGUCUUCAAGACGUCAUCGUUGCGCAGACAACCUCCGGCAUUUUGCUAAUCUCCCCAGCCUCUCUGCUGAUUCAUUUCCUCAACG
((((((.(((...((((((((.....(((.....)))(.((....)))))))))))..))))))))).............((((......))))................ ( -26.60)
>DroSec_CAF1 26633 110 - 1
AAUGCCCGUAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGAAGACAACCUCCGGCAUUUUGCUAAUCUCCCCAGCCUCUCUGCUGAUUCAUUUCCUCAACG
((((((((......)).........(((((((..((((....))))..)))))))......)))))).............((((......))))................ ( -22.30)
>DroSim_CAF1 26614 110 - 1
AAUGCCCGGAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGAAGACAACCUCCGGCAUUUUGCUAAUCUCCCCAGCCUCUCUGCUGAUUCAUUUCCUCAACG
((((((.(((((......)))))..(((((((..((((....))))..)))))))......)))))).............((((......))))................ ( -28.60)
>DroEre_CAF1 26212 109 - 1
AAUGCCCGGAUAAUUGUCUGUGCCCUGUCUUGGAGACGUCAUCGUUCCACCGACAGCCUCCGGCAUUUUGCUAAUCUC-CCAGCCGCUCUGCUGAUUCAUUUCCUCAACG
(((((((((((....)))))....(((((.(((((.((....)))))))..))))).....))))))...........-.((((......))))................ ( -26.30)
>DroYak_CAF1 26786 110 - 1
AAUGCCCGGAUAAUUGUCUGUCCCCUGUCUCCGAGACGUCAUCGUACCACUGACAACCUCCGGCAUUUUGCUAAUCUCGCCAGCCUCUCUGCUGAUUCAUUUCCUCCGCG
((((((.(((((......)))))..((((......(((....)))......))))......)))))).............((((......))))................ ( -21.60)
>consensus
AAUGCCCGGAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGCAGACAACCUCCGGCAUUUUGCUAAUCUCCCCAGCCUCUCUGCUGAUUCAUUUCCUCAACG
((((((.(((...((((((((.....(((.....)))(....).....))))))))..))))))))).............((((......))))................ (-19.98 = -20.58 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	15,666,948 – 15,667,044
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.44
Mean single sequence MFE	-26.12
Consensus MFE	-19.94
Energy contribution	-20.54
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-1.87
Structure conservation index	0.76
SVM decision value	0.32
SVM RNA-class probability	0.687775
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15666948 96 - 23771897
CCGCACUAACCAGAGAAGAAUGCCCGGAUAAUUGUCUGUCCUCUGUCUUCAAGACGUCAUCGUUGCGCAGACAACCUCCGGCAUUUUGCUAAUCUC
............((((((((((((.(((...((((((((.....(((.....)))(.((....)))))))))))..))))))))))).....)))) ( -26.60)
>DroSec_CAF1 26665 96 - 1
CCGCACUAACCAGAGAAGAAUGCCCGUAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGAAGACAACCUCCGGCAUUUUGCUAAUCUC
............((((((((((((((......)).........(((((((..((((....))))..)))))))......)))))))).....)))) ( -22.30)
>DroSim_CAF1 26646 96 - 1
CCGCACUAACCAGAGAAGAAUGCCCGGAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGAAGACAACCUCCGGCAUUUUGCUAAUCUC
............((((((((((((.(((((......)))))..(((((((..((((....))))..)))))))......)))))))).....)))) ( -28.60)
>DroEre_CAF1 26243 96 - 1
CCGCACUAACCGGAGAAGAAUGCCCGGAUAAUUGUCUGUGCCCUGUCUUGGAGACGUCAUCGUUCCACCGACAGCCUCCGGCAUUUUGCUAAUCUC
..(((....((((((......((.(((((....))))).)).(((((.(((((.((....)))))))..))))).)))))).....)))....... ( -31.50)
>DroYak_CAF1 26818 96 - 1
CCGCACUAACCAGAGAAGAAUGCCCGGAUAAUUGUCUGUCCCCUGUCUCCGAGACGUCAUCGUACCACUGACAACCUCCGGCAUUUUGCUAAUCUC
............((((((((((((.(((((......)))))..((((......(((....)))......))))......)))))))).....)))) ( -21.60)
>consensus
CCGCACUAACCAGAGAAGAAUGCCCGGAUAAUUGUCUGUCCCCUGUCUUCAAGACGUCAUCGUUGCGCAGACAACCUCCGGCAUUUUGCUAAUCUC
............((((((((((((.(((...((((((((.....(((.....)))(....).....))))))))..))))))))))).....)))) (-19.94 = -20.54 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:52 2006