Locus 2020

Sequence ID	3R_DroMel_CAF1
Location	5,734,525 – 5,734,680
Length	155
Max. P	0.831196

overview

Window 0

Location	5,734,525 – 5,734,627
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	93.28
Mean single sequence MFE	-24.14
Consensus MFE	-21.23
Energy contribution	-21.57
Covariance contribution	0.34
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.88
SVM decision value	0.18
SVM RNA-class probability	0.622118
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5734525 102 + 27905053
GCGGAAAAUGGCCAAAGAAUUUCCCUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCC
........((((((((.((.....((((....))))....((.((((((..((((....)))))))-))).))..)).))))))))...(((((....))))) ( -25.80)
>DroPse_CAF1 31950 100 + 1
G-GGAAAAUGGCAAAAGAAUUUCACUCAAACGUGAGAAUAGUGGCGAAAUAAUUGAGAACGAUUUC-UGUGGCAUUUGUUUUGCCAA-AGGAAAUUGAUUUUC
.-.((((((.((.......((((((......))))))......))..............(((((((-(.(((((.......))))).-.)))))))))))))) ( -23.62)
>DroSim_CAF1 26706 102 + 1
GCGGAAAAUGGCCAAAGAAUUUCCCUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCC
........((((((((.((.....((((....))))....((.((((((..((((....)))))))-))).))..)).))))))))...(((((....))))) ( -25.80)
>DroEre_CAF1 21719 102 + 1
GCGGAAAAUGGCCAAAGAAUUUCCCUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUAACCUGGCCAAAAGGAAAUUGAUUUCC
........((((((..........((((....))))..(((((.((....(((((....)))))..-..)).)))))...))))))...(((((....))))) ( -23.10)
>DroYak_CAF1 9440 103 + 1
GCGGAAAAUGGCCAAAGAAAUUCCCUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUUGUGUGGCAUUAGCCUGGCCAAAAGGAAAUUGAUUUCC
........((((((......((((((((..(....)..))).)).)))......................(((....)))))))))...(((((....))))) ( -22.90)
>DroPer_CAF1 31591 100 + 1
G-GGAAAAUGGCAAAAGAAUUUCACUCAAACGUGAGAAUAGUGGCGAAAUAAUUGAGAACGAUUUC-UGUGGCAUUUGUUUUGCCAA-AGGAAAUUGAUUUUC
.-.((((((.((.......((((((......))))))......))..............(((((((-(.(((((.......))))).-.)))))))))))))) ( -23.62)
>consensus
GCGGAAAAUGGCCAAAGAAUUUCCCUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU_UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCC
........((((((((.((.....((((....))))....((.(((....(((((....)))))...))).))..)).))))))))...(((((....))))) (-21.23 = -21.57 +   0.34)

alignment

secondary structure

dotplot

Window 1

Location	5,734,549 – 5,734,642
Length	93
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.80
Mean single sequence MFE	-25.58
Consensus MFE	-16.16
Energy contribution	-16.80
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-1.95
Structure conservation index	0.63
SVM decision value	0.72
SVM RNA-class probability	0.831196
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5734549 93 + 27905053
CUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCCAAUACUAGAA-------------------------ACAAA
((((....))))..(((((((.((((((.((...((((...)-)))..)).)))))).)))....(((((....)))))...))))...-------------------------..... ( -21.50)
>DroPse_CAF1 31973 117 + 1
CUCAAACGUGAGAAUAGUGGCGAAAUAAUUGAGAACGAUUUC-UGUGGCAUUUGUUUUGCCAA-AGGAAAUUGAUUUUCAAUAAAAGAGUUUUCGUUGCCUCGGGGCCUGCCGAGGAAA
((((....))))....(..((((((..(((((((((((((((-(.(((((.......))))).-.)))))))).))))))))........))))))..)(((((......))))).... ( -38.70)
>DroSec_CAF1 26120 93 + 1
CUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCCAAUACUAGAA-------------------------ACAAA
((((....))))..(((((((.((((((.((...((((...)-)))..)).)))))).)))....(((((....)))))...))))...-------------------------..... ( -21.50)
>DroEre_CAF1 21743 93 + 1
CUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU-UGUGGCAUUAACCUGGCCAAAAGGAAAUUGAUUUCCUAUAGCAGAA-------------------------ACAAA
((((....))))....((.((...(((...((((.(((((((-(.((((.........))))...)))))))).)))).))).))....-------------------------))... ( -17.10)
>DroYak_CAF1 9464 94 + 1
CUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUUGUGUGGCAUUAGCCUGGCCAAAAGGAAAUUGAUUUCCAAUACCAGAA-------------------------ACAAA
((((....))))..(((((((.....(((((....)))))......(((....)))..)))....(((((....)))))...))))...-------------------------..... ( -19.80)
>DroPer_CAF1 31614 117 + 1
CUCAAACGUGAGAAUAGUGGCGAAAUAAUUGAGAACGAUUUC-UGUGGCAUUUGUUUUGCCAA-AGGAAAUUGAUUUUCAAUAAGAGAGUUUUCGUUGCCUAGGGGCCUGCCGAGGAAA
(((...(....)......((((.....(((((((((((((((-(.(((((.......))))).-.)))))))).))))))))...............(((....))).))))))).... ( -34.90)
>consensus
CUCAAACGUGAGAAUGGUGGCGAAAUAAUUGAGAACGAUUUU_UGUGGCAUUUGUUUGGCCAAAAGGAAAUUGAUUUCCAAUACCAGAA_________________________ACAAA
((((....)))).....((((.((((((.((...(((......)))..)).)))))).))))...(((((....)))))........................................ (-16.16 = -16.80 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	5,734,588 – 5,734,680
Length	92
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-16.24
Consensus MFE	-13.44
Energy contribution	-12.24
Covariance contribution	-1.20
Combinations/Pair	1.32
Mean z-score	-1.29
Structure conservation index	0.83
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5734588 92 - 27905053
GAAAUGCUUUCAUUCCCGUUUGCCAGAUAAAUAAAACUUUUGUUUCUAGUAUUGGAAAUCAAUUUCCUUUUGGCCAAACAAAUGCCACA-AAA
.................((((((((((......((((....))))........(((((....))))).))))).)))))..........-... ( -14.40)
>DroSec_CAF1 26159 91 - 1
GAAAUGCUUUCUUUCCCGUUUGCCAAAUAAAA-AAACUUUUGUUUCUAGUAUUGGAAAUCAAUUUCCUUUUGGCCAAACAAAUGCCACA-AAA
.................((((((((((.....-((((....))))........(((((....))))).))))).)))))..........-... ( -14.30)
>DroSim_CAF1 26769 91 - 1
GAAAUGCUUUCUUUCCCGUUUGCCAAAUAAAC-AAGCUUUUGUUUCUGGUAUUGGAAAUCAAUUUCCUUUUGGCCAAACAAAUGCCACA-AAA
.................(((((.....)))))-..((.((((((..((((...(((((....))))).....)))))))))).))....-... ( -15.90)
>DroEre_CAF1 21782 92 - 1
GAAAUGCUUUCUUUCCCGUUUGCCAGAUAAAGCAAACUUUUGUUUCUGCUAUAGGAAAUCAAUUUCCUUUUGGCCAGGUUAAUGCCACA-AAA
.................((((((........)))))).(((((....((((.((((((....))))))..))))..(((....))))))-)). ( -20.10)
>DroYak_CAF1 9503 87 - 1
GAAAUGCUU----UCCCGUUUGUCAGAUAAA--AAACUUUUGUUUCUGGUAUUGGAAAUCAAUUUCCUUUUGGCCAGGCUAAUGCCACACAAA
(((((..((----(((....(..((((..((--(....)))...))))..)..)))))...)))))..((((....(((....)))...)))) ( -16.50)
>consensus
GAAAUGCUUUCUUUCCCGUUUGCCAGAUAAA__AAACUUUUGUUUCUGGUAUUGGAAAUCAAUUUCCUUUUGGCCAAACAAAUGCCACA_AAA
.................((((((((((......((((....))))........(((((....))))).))))).))))).............. (-13.44 = -12.24 +  -1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:25 2006