Locus 2561

Sequence ID	2L_DroMel_CAF1
Location	7,081,605 – 7,081,697
Length	92
Max. P	0.700795

overview

Window 2

Location	7,081,605 – 7,081,697
Length	92
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	81.28
Mean single sequence MFE	-25.26
Consensus MFE	-15.22
Energy contribution	-15.62
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-1.95
Structure conservation index	0.60
SVM decision value	0.35
SVM RNA-class probability	0.700795
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7081605 92 + 22407834
GCGACAG-----CAUUGUGCUGAUAAGCGAUUAAUCGCAGAAUCUAAAAAUGAUUGUCGUCAGCUUUGGGGAAAUCCGAAGCUAUGUAUAU------AUUCAA
(((((((-----((((.....(((..((((....))))...)))....)))).))))))).(((((((((....)))))))))........------...... ( -28.00)
>DroSec_CAF1 23433 88 + 1
GCGACGG-----CCUUGGGCUGAUAAGCGAUUAAUCGCAGAAUCUAAAAAUGAUUGUCGCCAGCUUUGGGGAAAUCCAACGCUA----UAC------UUUUAA
(((((((-----((...)))).....((((....))))..((((.......))))))))).(((.(((((....))))).))).----...------...... ( -25.40)
>DroSim_CAF1 23604 88 + 1
GCGACGG-----CCUUGGGCUGAUAAGCGAUUAAUCGCAGAAUCUAAAAAUGAUUGUCGCCAGCUUUGGGGAAAUCCAACGCUA----UAU------UUUUAA
(((((((-----((...)))).....((((....))))..((((.......))))))))).(((.(((((....))))).))).----...------...... ( -25.40)
>DroEre_CAF1 27108 91 + 1
ACCCAGGCUGAACCUUGGGCUGAUAAGCGAUUAAUCGCAGAAUCUAAAAGUGAUUGUCGCCGG--UUGGGGAAAUCCAAAGCUA----UAU------GUUCAU
.((((((......))))))(..((..(((((.((((((...........)))))))))))..)--)..)((....)).......----...------...... ( -24.60)
>DroYak_CAF1 27935 92 + 1
ACGCAGG-----CCUUGGACUGAUAAGCGAUUCAACGCAGAAUCUAAAAGUGAUUGUCGCCCGCUUUGGGGAAAUCCAAAGCAA----UAUUAAACUGUUA--
..((((.-----....((..........(((((......))))).....(((.....)))))((((((((....))))))))..----.......))))..-- ( -22.90)
>consensus
GCGACGG_____CCUUGGGCUGAUAAGCGAUUAAUCGCAGAAUCUAAAAAUGAUUGUCGCCAGCUUUGGGGAAAUCCAAAGCUA____UAU______GUUCAA
.................(((.(((..(((......)))..((((.......))))))))))(((.(((((....))))).))).................... (-15.22 = -15.62 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	7,081,605 – 7,081,697
Length	92
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	81.28
Mean single sequence MFE	-23.44
Consensus MFE	-12.42
Energy contribution	-14.02
Covariance contribution	1.60
Combinations/Pair	1.10
Mean z-score	-2.10
Structure conservation index	0.53
SVM decision value	0.27
SVM RNA-class probability	0.662905
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7081605 92 - 22407834
UUGAAU------AUAUACAUAGCUUCGGAUUUCCCCAAAGCUGACGACAAUCAUUUUUAGAUUCUGCGAUUAAUCGCUUAUCAGCACAAUG-----CUGUCGC
......------.......((((((.((......)).)))))).((((...........(((...((((....))))..)))(((.....)-----)))))). ( -22.30)
>DroSec_CAF1 23433 88 - 1
UUAAAA------GUA----UAGCGUUGGAUUUCCCCAAAGCUGGCGACAAUCAUUUUUAGAUUCUGCGAUUAAUCGCUUAUCAGCCCAAGG-----CCGUCGC
......------...----((((.((((......)))).))))(((((...........(((...((((....))))..))).(((...))-----).))))) ( -24.90)
>DroSim_CAF1 23604 88 - 1
UUAAAA------AUA----UAGCGUUGGAUUUCCCCAAAGCUGGCGACAAUCAUUUUUAGAUUCUGCGAUUAAUCGCUUAUCAGCCCAAGG-----CCGUCGC
......------...----((((.((((......)))).))))(((((...........(((...((((....))))..))).(((...))-----).))))) ( -24.90)
>DroEre_CAF1 27108 91 - 1
AUGAAC------AUA----UAGCUUUGGAUUUCCCCAA--CCGGCGACAAUCACUUUUAGAUUCUGCGAUUAAUCGCUUAUCAGCCCAAGGUUCAGCCUGGGU
......------...----..(((((((......))))--..)))..............(((...((((....))))..))).(((((.((.....))))))) ( -21.90)
>DroYak_CAF1 27935 92 - 1
--UAACAGUUUAAUA----UUGCUUUGGAUUUCCCCAAAGCGGGCGACAAUCACUUUUAGAUUCUGCGUUGAAUCGCUUAUCAGUCCAAGG-----CCUGCGU
--.............----..(((((((((((((((.....))).))............(((...(((......)))..))))))))))))-----)...... ( -23.20)
>consensus
UUAAAA______AUA____UAGCUUUGGAUUUCCCCAAAGCUGGCGACAAUCAUUUUUAGAUUCUGCGAUUAAUCGCUUAUCAGCCCAAGG_____CCGUCGC
...................((((.((((......)))).))))(((((...........(((...(((......)))..))).......((.....))))))) (-12.42 = -14.02 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:49 2006