Locus 3167

Sequence ID	3R_DroMel_CAF1
Location	8,393,567 – 8,393,698
Length	131
Max. P	0.995659

overview

Window 2

Location	8,393,567 – 8,393,676
Length	109
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	85.10
Mean single sequence MFE	-32.65
Consensus MFE	-22.76
Energy contribution	-24.32
Covariance contribution	1.56
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.70
SVM decision value	0.57
SVM RNA-class probability	0.786046
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8393567 109 - 27905053
GCUGGGAAAAUACUUCAGUUUUUCCGAGGCAAAACGAGGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUAAGCUGUUUUCGGGUUAUCCUUGCCAUCCUUG
(((.((((((.((....))))))))..)))....((((((....(((........)))..........((((((..(((.(((....))).)))..)))))).)))))) ( -37.00)
>DroSim_CAF1 54753 109 - 1
GCUGGGCAAAUACUCCAGUUUUUCCGAGGGAAAACGAAGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUAAGCUGUUUUCGGGCUAUCCUUGCCAUCCUUG
....(((.....((((.(((((((....)))))))...)))).(((......))))))..........((((((..((.(((.......)))))..))))))....... ( -32.90)
>DroEre_CAF1 57330 106 - 1
GCUCGGAAAAUUCGUCAGUUUUGC--AGGGAAAACGAAGGAGAAGGCUUUUCCCUGCCAAUAGAACGUGGCAAGCUUAAGCUGUUUUCGGGUUACCCUUGC-GUCCUUC
(((((((((....(((((((((((--(((((((((..........).))))))))))....))))).)))).(((....))).))))))))).........-....... ( -30.80)
>DroYak_CAF1 57046 97 - 1
GCUGGGAAAAUACUUCAGUUUUC-----------CGAGGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUAAGCUGUUUUCGGGUAAACCUUGC-UUCCUUC
....(((((((......))))))-----------)(((((((((((.(((.(((((((..........))))(((....)))......))).))))))).)-)))))). ( -29.90)
>consensus
GCUGGGAAAAUACUUCAGUUUUUC__AGGGAAAACGAAGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUAAGCUGUUUUCGGGUUAUCCUUGC_AUCCUUC
((((((.......))))))................((((((...(((........)))..........((((((..(((.(((....))).)))..)))))).)))))) (-22.76 = -24.32 +   1.56)

alignment

secondary structure

dotplot

Window 3

Location	8,393,598 – 8,393,698
Length	100
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	72.80
Mean single sequence MFE	-28.52
Consensus MFE	-15.97
Energy contribution	-16.94
Covariance contribution	0.98
Combinations/Pair	1.28
Mean z-score	-2.60
Structure conservation index	0.56
SVM decision value	2.60
SVM RNA-class probability	0.995659
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8393598 100 + 27905053
UAAACUUGCCUUGUUUUAUUGGCAGGGAAAAGCCUUCUCCCUCGUUUUGCCUCGGAAAAACUGAAGUAUUUUCCCAGCUGUGCCUAAUGGCACCUGCAGC
......((((..........))))(((((((..((((......(((((.(....).))))).))))..))))))).((.(((((....)))))..))... ( -31.60)
>DroSec_CAF1 55528 78 + 1
----------------------AAGGGAAAAGCCUUCUCCCUCGUUUUCCCUCGGAAAAACUGAAGCAUUUUCCCAGCUGUGCCUAAUGGCACCUGCAGC
----------------------..(((((((..((((.......((((((...))))))...))))..))))))).((.(((((....)))))..))... ( -28.10)
>DroSim_CAF1 54784 100 + 1
UAAACUUGCCUUGUUUUAUUGGCAGGGAAAAGCCUUCUCCUUCGUUUUCCCUCGGAAAAACUGGAGUAUUUGCCCAGCUGCGCCUAAUGGCACCUGCAGC
......((((..........))))(((.(((.....((((....((((((...))))))...))))..))).))).((((((((....)))....))))) ( -31.00)
>DroEre_CAF1 57360 98 + 1
UAAGCUUGCCACGUUCUAUUGGCAGGGAAAAGCCUUCUCCUUCGUUUUCCCU--GCAAAACUGACGAAUUUUCCGAGCUGUGCCUAAUGGCACCUGCAGC
..((((((...((((......((((((((((.............))))))))--))......)))).......))))))(((((....)))))....... ( -30.82)
>DroYak_CAF1 57076 89 + 1
UAAACUUGCCUUGUUUUAUUGGCAGGGAAAAGCCUUCUCCCUCG-----------GAAAACUGAAGUAUUUUCCCAGCUGUGCCUAAUGGCACCUGCAGC
......((((..........))))(((((((..(((((((...)-----------)).....))))..))))))).((.(((((....)))))..))... ( -30.00)
>DroAna_CAF1 57560 84 + 1
UCAACUUC--GCAUUUUAUUGGCUUGAAGGAGCAGUC--------------CAGGGAAAAGCAAAGUAUUUGGCCAGCUGUGCCUAAUGGUAUCUGCACC
...((((.--((.((((.((((.(((......))).)--------------))).)))).)).)))).........((.(((((....)))))..))... ( -19.60)
>consensus
UAAACUUGCCUUGUUUUAUUGGCAGGGAAAAGCCUUCUCCCUCGUUUUCCCUCGGAAAAACUGAAGUAUUUUCCCAGCUGUGCCUAAUGGCACCUGCAGC
........................(((((((..((((.........................))))..))))))).((.(((((....)))))..))... (-15.97 = -16.94 +   0.98)

alignment

secondary structure

dotplot

Window 4

Location	8,393,598 – 8,393,698
Length	100
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	72.80
Mean single sequence MFE	-28.82
Consensus MFE	-12.24
Energy contribution	-14.46
Covariance contribution	2.22
Combinations/Pair	1.11
Mean z-score	-2.03
Structure conservation index	0.42
SVM decision value	0.75
SVM RNA-class probability	0.840456
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8393598 100 - 27905053
GCUGCAGGUGCCAUUAGGCACAGCUGGGAAAAUACUUCAGUUUUUCCGAGGCAAAACGAGGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUA
(((((..(((((....))))).))(((((((((......))))))))).))).((((.(((((((.....)))))))(((..........)))..)))). ( -33.60)
>DroSec_CAF1 55528 78 - 1
GCUGCAGGUGCCAUUAGGCACAGCUGGGAAAAUGCUUCAGUUUUUCCGAGGGAAAACGAGGGAGAAGGCUUUUCCCUU----------------------
...((..(((((....))))).)).(((((((..((((.(((((((....)))))))...)))).....)))))))..---------------------- ( -28.90)
>DroSim_CAF1 54784 100 - 1
GCUGCAGGUGCCAUUAGGCGCAGCUGGGCAAAUACUCCAGUUUUUCCGAGGGAAAACGAAGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUA
(((((..(((((....))))).))..(((.....((((.(((((((....)))))))...)))).(((......))))))..........)))....... ( -32.10)
>DroEre_CAF1 57360 98 - 1
GCUGCAGGUGCCAUUAGGCACAGCUCGGAAAAUUCGUCAGUUUUGC--AGGGAAAACGAAGGAGAAGGCUUUUCCCUGCCAAUAGAACGUGGCAAGCUUA
(((((..(((((....))))).))...........(((((((((((--(((((((((..........).))))))))))....))))).)))).)))... ( -32.60)
>DroYak_CAF1 57076 89 - 1
GCUGCAGGUGCCAUUAGGCACAGCUGGGAAAAUACUUCAGUUUUC-----------CGAGGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUA
...((..(((((....))))).))..(((((((......))))))-----------).(((((((.....)))))))(((..........)))....... ( -28.20)
>DroAna_CAF1 57560 84 - 1
GGUGCAGAUACCAUUAGGCACAGCUGGCCAAAUACUUUGCUUUUCCCUG--------------GACUGCUCCUUCAAGCCAAUAAAAUGC--GAAGUUGA
((((....))))....(((.(....))))....(((((((((((...((--------------(.((.........)))))..)))).))--)))))... ( -17.50)
>consensus
GCUGCAGGUGCCAUUAGGCACAGCUGGGAAAAUACUUCAGUUUUUCCGAGGGAAAACGAGGGAGAAGGCUUUUCCCUGCCAAUAAAACAAGGCAAGUUUA
.......(((((....))))).((.(((((((..((((.........................))))..))))))).))..................... (-12.24 = -14.46 +   2.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:45 2006