Locus 1907

Sequence ID	3L_DroMel_CAF1
Location	5,343,509 – 5,343,634
Length	125
Max. P	0.989535

overview

Window 9

Location	5,343,509 – 5,343,602
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	76.45
Mean single sequence MFE	-22.93
Consensus MFE	-14.32
Energy contribution	-15.52
Covariance contribution	1.20
Combinations/Pair	1.21
Mean z-score	-2.25
Structure conservation index	0.62
SVM decision value	1.89
SVM RNA-class probability	0.981387
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5343509 93 + 23771897
AUGGUUACACCUUUGGUUUGCAUUUCCAUUGCUGCCUUCGAUGGAAUCCUUUCCCAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA
..(((..(((...(((.......((((((((.......)))))))).......))).((((((......))))))....)))..)))...... ( -24.64)
>DroSec_CAF1 91522 93 + 1
AUGGUUACACCUUUGGUUUGCACUUCCAUUGCUGCCUCCGAUGAAAUUCUUUCCCAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA
..((.....))...(((...(((((.(((((.......)))))..............((((((......))))))..)))))..)))...... ( -20.60)
>DroSim_CAF1 93267 93 + 1
AUGGUUACACCUUUGGUUUGAACUUCCAUUGCUGCCUCCGAUUGAAUCCUUUCCCAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA
.((((((.(((...))).))).....(((..((..........(((....)))....((((((......))))))...))..))).))).... ( -18.00)
>DroEre_CAF1 91433 70 + 1
-----------UUGGGCUUGUAUCUCUUGUG------------GAAUCCACUCCCAUUGACCCACUUUCGGGUCAUCGAGUGAUGCCCACAUC
-----------.(((((.....(((.....)------------))...(((((....((((((......))))))..)))))..))))).... ( -25.00)
>DroYak_CAF1 100069 93 + 1
GUGACUACGCUUUGGGCUUGUAUCUCAUAUGCUGAUUGCGCUUGAAUCCUUUUCCAUUGACCCACUUUCGGGUCAUCGAGUGUUGCCCACAUC
(((....)))..(((((..((((.....)))).....((((((((............((((((......)))))))))))))).))))).... ( -26.40)
>consensus
AUGGUUACACCUUUGGUUUGCAUUUCCAUUGCUGCCUCCGAUGGAAUCCUUUCCCAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA
..............(((...(((.(((((((.......)))))))............((((((......))))))....)))..)))...... (-14.32 = -15.52 +   1.20)

alignment

secondary structure

dotplot

Window 0

Location	5,343,509 – 5,343,602
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	76.45
Mean single sequence MFE	-24.90
Consensus MFE	-13.82
Energy contribution	-14.18
Covariance contribution	0.36
Combinations/Pair	1.25
Mean z-score	-1.88
Structure conservation index	0.56
SVM decision value	0.58
SVM RNA-class probability	0.790174
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5343509 93 - 23771897
UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUGGGAAAGGAUUCCAUCGAAGGCAGCAAUGGAAAUGCAAACCAAAGGUGUAACCAU
...((((....(((((..(((((((....))))))).(((.......((((((.(.......).)))))).......))).)))))...)))) ( -26.14)
>DroSec_CAF1 91522 93 - 1
UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUGGGAAAGAAUUUCAUCGGAGGCAGCAAUGGAAGUGCAAACCAAAGGUGUAACCAU
...((((....(((((..(((((((....))))))).(((.......((((((.(.......).)))))).......))).)))))...)))) ( -24.44)
>DroSim_CAF1 93267 93 - 1
UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUGGGAAAGGAUUCAAUCGGAGGCAGCAAUGGAAGUUCAAACCAAAGGUGUAACCAU
...((((....(((((..(((((((....))))))).((((((....))).........((....))..........))).)))))...)))) ( -22.00)
>DroEre_CAF1 91433 70 - 1
GAUGUGGGCAUCACUCGAUGACCCGAAAGUGGGUCAAUGGGAGUGGAUUC------------CACAAGAGAUACAAGCCCAA-----------
....(((((....((((.(((((((....))))))).)))).((((...)------------)))...........))))).----------- ( -28.00)
>DroYak_CAF1 100069 93 - 1
GAUGUGGGCAACACUCGAUGACCCGAAAGUGGGUCAAUGGAAAAGGAUUCAAGCGCAAUCAGCAUAUGAGAUACAAGCCCAAAGCGUAGUCAC
(...(((((.....(((.(((((((....))))))).))).......((((...((.....))...))))......)))))...)........ ( -23.90)
>consensus
UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUGGGAAAGGAUUCAAUCGGAGGCAGCAAUGGAAAUACAAACCAAAGGUGUAACCAU
.....((......((((.(((((((....))))))).))))......((((((.(.......).)))))).......)).............. (-13.82 = -14.18 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	5,343,543 – 5,343,634
Length	91
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	69.04
Mean single sequence MFE	-26.73
Consensus MFE	-11.37
Energy contribution	-11.82
Covariance contribution	0.45
Combinations/Pair	1.29
Mean z-score	-2.42
Structure conservation index	0.43
SVM decision value	2.17
SVM RNA-class probability	0.989535
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5343543 91 + 23771897
C--CUUCGAUG--GAAUCCUUUCC-------CAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA------------UGGA-CAGGAUUCUUGCAAAAAGGACUC-GCUAC
(--(((....(--(((((((.(((-------...((((((......))))))....(((.....)))...------------.)))-.))))))))......))))....-..... ( -29.50)
>DroSec_CAF1 91556 91 + 1
C--CUCCGAUG--AAAUUCUUUCC-------CAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA------------UGGA-CAGGGUUCUGGCAAAAAGGCUUC-CCUAC
.--.((((...--...........-------...((((((......))))))....(((.....)))...------------))))-.((((....(((......))).)-))).. ( -23.10)
>DroSim_CAF1 93301 91 + 1
C--CUCCGAUU--GAAUCCUUUCC-------CAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA------------UGGA-CGGGGUUCUUGCAAAAAGGCUUC-CCUAC
.--....(...--(((((((.(((-------...((((((......))))))....(((.....)))...------------.)))-.)))))))...)....(((....-))).. ( -26.40)
>DroEre_CAF1 91453 77 + 1
-------------GAAUCCACUCC-------CAUUGACCCACUUUCGGGUCAUCGAGUGAUGCCCACAUC-----------------GAGGUUCCUUGCUAAAAGGAUCC--CUGC
-------------.....(((((.-------...((((((......))))))..)))))...........-----------------.(((.(((((.....)))))..)--)).. ( -24.60)
>DroYak_CAF1 100103 87 + 1
A--UUGCGCUU--GAAUCCUUUUC-------CAUUGACCCACUUUCGGGUCAUCGAGUGUUGCCCACAUC-----------------GAGGGUCCUUGCUAAAAGGAUCC-CCCAC
.--..((((((--((.........-------...((((((......))))))))))))))..........-----------------..((((((((.....))))))))-..... ( -28.40)
>DroPer_CAF1 139102 115 + 1
UCUUUCCCAUUACCAAUCGCUUCCCAUUGCGCAUUGACCUAGUUUCGGGUCAUCAAAUGAUGCC-ACAUUGAGUGUCACAUAUGGGGCACGCCCAGUGGAAAAAGGAUCUCAGUUC
.............(((((((........))).)))).(((..((((.((.((((....))))))-.(((((.(((((........)))))...))))))))).))).......... ( -28.40)
>consensus
C__CUCCGAUU__GAAUCCUUUCC_______CAUUGACCCACAUUCGGGUCAUCAAGUGAUGCCCACAUA____________UGGA_CAGGGUCCUUGCAAAAAGGAUCC_CCUAC
...............((((...............((((((......))))))....(((.....)))......................))))((((.....)))).......... (-11.37 = -11.82 +   0.45)

alignment

secondary structure

dotplot

Window 2

Location	5,343,543 – 5,343,634
Length	91
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	69.04
Mean single sequence MFE	-29.78
Consensus MFE	-16.09
Energy contribution	-16.40
Covariance contribution	0.31
Combinations/Pair	1.35
Mean z-score	-1.76
Structure conservation index	0.54
SVM decision value	1.16
SVM RNA-class probability	0.924361
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5343543 91 - 23771897
GUAGC-GAGUCCUUUUUGCAAGAAUCCUG-UCCA------------UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUG-------GGAAAGGAUUC--CAUCGAAG--G
...(.-(((((((((((.((((.....((-((((------------....))))))...)))).(((((((....)))))))...-------)))))))))))--).......--. ( -32.10)
>DroSec_CAF1 91556 91 - 1
GUAGG-GAAGCCUUUUUGCCAGAACCCUG-UCCA------------UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUG-------GGAAAGAAUUU--CAUCGGAG--G
..(((-....))).....((....(((((-((((------------(((.((((((((....)))).)))).))))))).))..)-------))...((....--..))))..--. ( -27.50)
>DroSim_CAF1 93301 91 - 1
GUAGG-GAAGCCUUUUUGCAAGAACCCCG-UCCA------------UAUGUGGGCAUCACUUGAUGACCCGAAUGUGGGUCAAUG-------GGAAAGGAUUC--AAUCGGAG--G
.....-(((.(((((..........((((-((((------------(((.((((((((....)))).)))).))))))....)))-------))))))).)))--........--. ( -27.60)
>DroEre_CAF1 91453 77 - 1
GCAG--GGAUCCUUUUAGCAAGGAACCUC-----------------GAUGUGGGCAUCACUCGAUGACCCGAAAGUGGGUCAAUG-------GGAGUGGAUUC-------------
...(--((.(((((.....))))).))).-----------------((((....)))).((((.(((((((....))))))).))-------)).........------------- ( -25.90)
>DroYak_CAF1 100103 87 - 1
GUGGG-GGAUCCUUUUAGCAAGGACCCUC-----------------GAUGUGGGCAACACUCGAUGACCCGAAAGUGGGUCAAUG-------GAAAAGGAUUC--AAGCGCAA--U
(((..-((((((((((..((..(((((((-----------------((.(((.....))))))).....(....).)))))..))-------.))))))))))--...)))..--. ( -33.40)
>DroPer_CAF1 139102 115 - 1
GAACUGAGAUCCUUUUUCCACUGGGCGUGCCCCAUAUGUGACACUCAAUGU-GGCAUCAUUUGAUGACCCGAAACUAGGUCAAUGCGCAAUGGGAAGCGAUUGGUAAUGGGAAAGA
...........((((..(.((..(.(((..(((((.((((.(((.....))-)...........(((((........)))))...)))))))))..))).)..))...)..)))). ( -32.20)
>consensus
GUAGG_GAAUCCUUUUUGCAAGAACCCUG_UCCA____________UAUGUGGGCAUCACUUGAUGACCCGAAAGUGGGUCAAUG_______GGAAAGGAUUC__AAUCGGAG__G
......((((((((((.................................(((.....)))....(((((((....)))))))...........))))))))))............. (-16.09 = -16.40 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:38 2006