Locus 53

Sequence ID	3R_DroMel_CAF1
Location	310,903 – 311,063
Length	160
Max. P	0.991423

overview

Window 6

Location	310,903 – 311,023
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.78
Mean single sequence MFE	-52.73
Consensus MFE	-49.29
Energy contribution	-49.60
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-1.40
Structure conservation index	0.93
SVM decision value	0.26
SVM RNA-class probability	0.656468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 310903 120 + 27905053
ACGGCGGGGAUUCUCUGACGGCGGAGCACGAGUCGGCGGCGGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAACUCCACUGAAGACU
.(((.((((..((.(((((..((.....)).))))).))((((((((((...(((....)))........(.(((((.....))))).))))))))))).......)))).)))...... ( -54.70)
>DroSec_CAF1 47845 120 + 1
ACGGCGGGGAUUCUCUCACGGCGGAGCACGAGUCGGCGGCGGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGUGCUUCGGCCGGAACUAAUUCCGCUGAAGACU
.(((((((.(((...((.(((((((((((..((((.((.((((..(.((....)).)..))))...)).))))((((.....)))).))))))).))))))...))))))))))...... ( -56.00)
>DroSim_CAF1 48701 120 + 1
ACGGCGGGGAUUCUCUCACGGCGGAGCACGAGUCGGCGGCGGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAAUUCCGCUGAAGACU
.((.(((((.....))).)).)).......((((..(((((((((((((...(((....)))........(.(((((.....))))).))))))))))((((....))))))))..)))) ( -57.60)
>DroYak_CAF1 51123 117 + 1
ACGGCGGGGAUUCUCUGAUGGCGGAACACGAGUCGGU---GGCUGAGGCUCAGGCAUUGGCUGAAUUGGUGGCCGGCGAAAAGAUGGGCGCUUCGGUAGGGACUGAUUCCGCUGAAGACU
.((((((((..((((((..((((...(((..((((((---.((..(...((((.(...).)))).)..)).)))))).....).))..))))....))))))....))))))))...... ( -42.60)
>consensus
ACGGCGGGGAUUCUCUCACGGCGGAGCACGAGUCGGCGGCGGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAAUUCCGCUGAAGACU
.((((((((...........((.((((...(((((....)))))...))))..)).((((((((...((((.(((((.....))))).))))))))))))......))))))))...... (-49.29 = -49.60 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	310,943 – 311,063
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-56.62
Consensus MFE	-52.72
Energy contribution	-52.10
Covariance contribution	-0.62
Combinations/Pair	1.12
Mean z-score	-2.88
Structure conservation index	0.93
SVM decision value	2.27
SVM RNA-class probability	0.991423
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 310943 120 + 27905053
GGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAACUCCACUGAAGACUCGCCGCGCUGUCCAAAGGAGGAGGUGCCCGAGUACUCGGA
(((.(((..((((.....((((((...((((.(((((.....))))).))))))))))(((......))).))))...))))))(((((.(((......))))))))((((....)))). ( -59.80)
>DroSec_CAF1 47885 120 + 1
GGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGUGCUUCGGCCGGAACUAAUUCCGCUGAAGACUCGCCGCGCUGUCCAAAGGAAGAGGUGCCCGAGUACUCGGA
(((.(((.((..(((...((((((...((((.(((((.....))))).))))))))))((((....)))))))..)).))))))(((((.(((...)))...)))))((((....)))). ( -58.20)
>DroSim_CAF1 48741 120 + 1
GGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAAUUCCGCUGAAGACUGGCCGUGCUGUCCAAAGGAAGAGGUGCCCGAGUACUCGGA
..(((((((((.(((.((((((((...((((.(((((.....))))).)))))))))))).(((..((((..((..(((.(((...))))))))..))))..)))))).)))).))))). ( -57.90)
>DroYak_CAF1 51160 120 + 1
GGCUGAGGCUCAGGCAUUGGCUGAAUUGGUGGCCGGCGAAAAGAUGGGCGCUUCGGUAGGGACUGAUUCCGCUGAAGACUCGCCGCGCUGUCCAAAGGAAGAGGUGCCCGAGUACUCGGA
..(((((((((.((((((..((...((((((((((((((.....(.((((..(((((....)))))...)))).)....)))))).)))).))))....)).)))))).)))).))))). ( -50.60)
>consensus
GGCUGAGGCUCAGGCAUUGGCCGAAUUGGUGGCCGGCGAAAAGCCGGGCGCUUCGGCCGGAACUAAUUCCGCUGAAGACUCGCCGCGCUGUCCAAAGGAAGAGGUGCCCGAGUACUCGGA
..(((((((((.(((.((((((((...((((.(((((.....))))).)))))))))))).(((..((((..((..(((..........)))))..))))..)))))).)))).))))). (-52.72 = -52.10 +  -0.62)

alignment

secondary structure

dotplot

Window 8

Location	310,943 – 311,063
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-44.57
Consensus MFE	-39.10
Energy contribution	-39.98
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	-0.01
SVM RNA-class probability	0.530775
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 310943 120 - 27905053
UCCGAGUACUCGGGCACCUCCUCCUUUGGACAGCGCGGCGAGUCUUCAGUGGAGUUAGUUCCGGCCGAAGCGCCCGGCUUUUCGCCGGCCACCAAUUCGGCCAAUGCCUGAGCCUCAGCC
...(((..((((((((.((((..((..((((.((...))..))))..)).))))........((((((((.(.(((((.....))))).).)...)))))))..)))))))).))).... ( -49.30)
>DroSec_CAF1 47885 120 - 1
UCCGAGUACUCGGGCACCUCUUCCUUUGGACAGCGCGGCGAGUCUUCAGCGGAAUUAGUUCCGGCCGAAGCACCCGGCUUUUCGCCGGCCACCAAUUCGGCCAAUGCCUGAGCCUCAGCC
...(((..((((((((.......((..((((.((...))..))))..)).((((....))))(((((((....(((((.....))))).......)))))))..)))))))).))).... ( -46.20)
>DroSim_CAF1 48741 120 - 1
UCCGAGUACUCGGGCACCUCUUCCUUUGGACAGCACGGCCAGUCUUCAGCGGAAUUAGUUCCGGCCGAAGCGCCCGGCUUUUCGCCGGCCACCAAUUCGGCCAAUGCCUGAGCCUCAGCC
...(((..((((((((((.........)).......((((.(.((((.((((((....)))).)).)))))(.(((((.....))))).)........))))..)))))))).))).... ( -46.30)
>DroYak_CAF1 51160 120 - 1
UCCGAGUACUCGGGCACCUCUUCCUUUGGACAGCGCGGCGAGUCUUCAGCGGAAUCAGUCCCUACCGAAGCGCCCAUCUUUUCGCCGGCCACCAAUUCAGCCAAUGCCUGAGCCUCAGCC
...(((..((((((((.........((((...((.(((((((......(((...((.((....)).))..))).......)))))))))..)))).........)))))))).))).... ( -36.49)
>consensus
UCCGAGUACUCGGGCACCUCUUCCUUUGGACAGCGCGGCGAGUCUUCAGCGGAAUUAGUUCCGGCCGAAGCGCCCGGCUUUUCGCCGGCCACCAAUUCGGCCAAUGCCUGAGCCUCAGCC
...(((..((((((((....((((...((((.((...))..)))).....))))........(((((((....(((((.....))))).......)))))))..)))))))).))).... (-39.10 = -39.98 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:31 2006