Locus 1124

Sequence ID	3L_DroMel_CAF1
Location	3,290,595 – 3,290,746
Length	151
Max. P	0.899633

overview

Window 6

Location	3,290,595 – 3,290,707
Length	112
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	88.86
Mean single sequence MFE	-29.98
Consensus MFE	-24.11
Energy contribution	-26.30
Covariance contribution	2.19
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.80
SVM decision value	1.01
SVM RNA-class probability	0.899633
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3290595 112 + 23771897
CAGUCAACUGCGAGCUGCAUGUUAAAUGGUUUGAAUUAAUUGCGUAGGCCACGCAUGUCACGUGCGCCUCACAUAGGACUAUAUCUAACUAUAUGUGCAUAUAGUAUGAUAU--
.((((...((.(((.(((((((....((((....))))..(((((.....)))))....))))))).))).))...))))(((((..(((((((....)))))))..)))))-- ( -30.10)
>DroSec_CAF1 20327 114 + 1
CAGUCAACUGCGAGCUGCAUGUUAAAUGGUUUGAAUUAAUUGCGUAGGCCACGCAUGUCACGUGCGGCUCACAUAGGAAUAUAUCUAUCUAUAUGUGCAUAUAGUACGAUAUAU
...((...((.(((((((((((....((((....))))..(((((.....)))))....))))))))))).))...))(((((((...((((((....))))))...))))))) ( -33.60)
>DroSim_CAF1 21143 102 + 1
CAGUCAACUGCGAGCUGCAUGUUAAAUGGUUUGAAUUAAUUGCUUAGGCCACGCAUGUCACGUGCGGCUCACAUAGGAAUAUAUCUA------------UAUAGUACGAUAUAU
...((...((.(((((((((((....((((((((.........))))))))........))))))))))).))...))(((((((..------------........))))))) ( -28.00)
>DroEre_CAF1 22406 111 + 1
CAGUCAACUGUGAGCUGCAUGUUAAAUGGUUUGAAUUAAUUGCGUAGGCCACGCAUGUCACGUGCACUUCACAUAGGACUAUAUC-AUAUAUAUGUACAUAUAGUACGAUAU--
.((((...((((((.(((((((....((((....))))..(((((.....)))))....))))))).))))))...)))).....-..((((.(((((.....)))))))))-- ( -28.20)
>consensus
CAGUCAACUGCGAGCUGCAUGUUAAAUGGUUUGAAUUAAUUGCGUAGGCCACGCAUGUCACGUGCGCCUCACAUAGGAAUAUAUCUAUCUAUAUGUGCAUAUAGUACGAUAU__
.((((...((.(((((((((((....(((((((..(.....)..)))))))........))))))))))).))...))))(((((...((((((....))))))...))))).. (-24.11 = -26.30 +   2.19)

alignment

secondary structure

dotplot

Window 7

Location	3,290,595 – 3,290,707
Length	112
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	88.86
Mean single sequence MFE	-28.53
Consensus MFE	-19.90
Energy contribution	-22.77
Covariance contribution	2.88
Combinations/Pair	1.03
Mean z-score	-2.34
Structure conservation index	0.70
SVM decision value	0.57
SVM RNA-class probability	0.786792
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3290595 112 - 23771897
--AUAUCAUACUAUAUGCACAUAUAGUUAGAUAUAGUCCUAUGUGAGGCGCACGUGACAUGCGUGGCCUACGCAAUUAAUUCAAACCAUUUAACAUGCAGCUCGCAGUUGACUG
--(((((..(((((((....)))))))..)))))((((...((((((((.(((((.....))))))))).)))).................(((.(((.....)))))))))). ( -32.90)
>DroSec_CAF1 20327 114 - 1
AUAUAUCGUACUAUAUGCACAUAUAGAUAGAUAUAUUCCUAUGUGAGCCGCACGUGACAUGCGUGGCCUACGCAAUUAAUUCAAACCAUUUAACAUGCAGCUCGCAGUUGACUG
(((((((...((((((....))))))...)))))))((...(((((((.(((.((....((((((...))))))..(((..........))))).))).)))))))...))... ( -29.30)
>DroSim_CAF1 21143 102 - 1
AUAUAUCGUACUAUA------------UAGAUAUAUUCCUAUGUGAGCCGCACGUGACAUGCGUGGCCUAAGCAAUUAAUUCAAACCAUUUAACAUGCAGCUCGCAGUUGACUG
(((((((........------------..)))))))((...(((((((.(((.((...(((..(((..(((....)))..)))...)))...)).))).)))))))...))... ( -24.20)
>DroEre_CAF1 22406 111 - 1
--AUAUCGUACUAUAUGUACAUAUAUAU-GAUAUAGUCCUAUGUGAAGUGCACGUGACAUGCGUGGCCUACGCAAUUAAUUCAAACCAUUUAACAUGCAGCUCACAGUUGACUG
--((((((((.(((((....))))))))-)))))((((...(((((..((((.((....((((((...))))))..(((..........))))).))))..)))))...)))). ( -27.70)
>consensus
__AUAUCGUACUAUAUGCACAUAUAGAUAGAUAUAGUCCUAUGUGAGCCGCACGUGACAUGCGUGGCCUACGCAAUUAAUUCAAACCAUUUAACAUGCAGCUCGCAGUUGACUG
..(((((...((((((....))))))...)))))((((...(((((((.(((.((....((((((...))))))..(((..........))))).))).)))))))...)))). (-19.90 = -22.77 +   2.88)

alignment

secondary structure

dotplot

Window 8

Location	3,290,635 – 3,290,746
Length	111
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	85.40
Mean single sequence MFE	-25.23
Consensus MFE	-15.31
Energy contribution	-18.12
Covariance contribution	2.81
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.61
SVM decision value	0.09
SVM RNA-class probability	0.578956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3290635 111 + 23771897
UGCGUAGGCCACGCAUGUCACGUGCGCCUCACAUAGGACUAUAUCUAACUAUAUGUGCAUAUAGUAUGAUAU--AUUCCACCCCCCUUUCCACCCACAA-GUCCUUGAGCAAAG
(((((((((((((.......)))).)))).))...(((.((((((..(((((((....)))))))..)))))--).)))....................-........)))... ( -30.60)
>DroSec_CAF1 20367 112 + 1
UGCGUAGGCCACGCAUGUCACGUGCGGCUCACAUAGGAAUAUAUCUAUCUAUAUGUGCAUAUAGUACGAUAUAUAUACCAC-CCCCUUUCCACCCACAA-AUCCUUGAGCAAAG
(((((..(((.(((.......))).)))..))...((.(((((((...((((((....))))))...)))))))...))..-.................-........)))... ( -25.90)
>DroSim_CAF1 21183 101 + 1
UGCUUAGGCCACGCAUGUCACGUGCGGCUCACAUAGGAAUAUAUCUA------------UAUAGUACGAUAUAUAUACCACACCCCUUUCCAGCCACAA-AUCCUUGAGCAAAG
((((((((....(((((...)))))((((.....(((........((------------((((......)))))).........)))....))))....-...))))))))... ( -23.73)
>DroEre_CAF1 22446 110 + 1
UGCGUAGGCCACGCAUGUCACGUGCACUUCACAUAGGACUAUAUC-AUAUAUAUGUACAUAUAGUACGAUAU--ACGCCAA-CCCCUUUCCACCCACAACGUCCUUGAGCAAAG
(((..(((.(..(((((...)))))..........((..((((((-...(((((....)))))....)))))--)..))..-..................).)))...)))... ( -20.70)
>consensus
UGCGUAGGCCACGCAUGUCACGUGCGCCUCACAUAGGAAUAUAUCUAUCUAUAUGUGCAUAUAGUACGAUAU__AUACCAC_CCCCUUUCCACCCACAA_AUCCUUGAGCAAAG
(((..(((...((((((...)))))).........((.(((((((...((((((....))))))...)))))))...)).......................)))...)))... (-15.31 = -18.12 +   2.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:44 2006