Locus 938

Sequence ID	3R_DroMel_CAF1
Location	3,122,335 – 3,122,633
Length	298
Max. P	0.999779

overview

Window 3

Location	3,122,335 – 3,122,443
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.46
Mean single sequence MFE	-27.98
Consensus MFE	-25.01
Energy contribution	-23.68
Covariance contribution	-1.33
Combinations/Pair	1.26
Mean z-score	-1.66
Structure conservation index	0.89
SVM decision value	0.82
SVM RNA-class probability	0.860042
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3122335 108 + 27905053
AAUACUAAUGCAAAUAAAUGUGAGUGCCAAUUGAAAUAGAAAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAA
..(((((.(((.......(((((((((...((........))...))))).)))).........((((.....)))))))------------.)))))..(((((.(....))))))... ( -26.10)
>DroPse_CAF1 9657 107 + 1
AAGACUAAUACAAAUAAAUGUGAGUGUCAAUUGAAAUAGAAAACCGCGUGCCACGCAAUCGAGGUGUCAAAGCGACGGCG------------ACGGCG-AUGCCGAGGAGACCGGCAAAA
..(((...((((......))))...)))...............(((((((((.((....)).)))(((.....))).)))------------.)))..-.(((((.(....))))))... ( -28.20)
>DroSec_CAF1 9942 108 + 1
AAUACUAAUGCAAAUAAAUGUGAGUGCCAAUUGAAAUAGAAAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAA
..(((((.(((.......(((((((((...((........))...))))).)))).........((((.....)))))))------------.)))))..(((((.(....))))))... ( -26.10)
>DroSim_CAF1 15251 108 + 1
AAUACUAAUGCAAAUAAAUGUGAGUGCCAAUUGAAAUAGAAAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAA
..(((((.(((.......(((((((((...((........))...))))).)))).........((((.....)))))))------------.)))))..(((((.(....))))))... ( -26.10)
>DroPer_CAF1 9631 107 + 1
AGGACUAAUACAAAUAAAUGUGAGUGUCAAUUGAAAUAGAAAACCGCGUGCCACGCAAUCGAGGUGUCAAAGCGACGGCG------------ACGGCG-AUGCCGAGGAGACCGGCAAAA
..(((...((((......))))...)))...............(((((((((.((....)).)))(((.....))).)))------------.)))..-.(((((.(....))))))... ( -28.00)
>DroYak_CAF1 13589 120 + 1
AAUACUAAUGCAAAUAAAUGUGAGUGCCAAUUGAAAUAGAAAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCGGCGGCGACGGCGAUGGUGAAUGUCGACGAGAGCGACAAAA
...(((...(((......))).)))((((..............(((((((..((((.......))))...)))).)))((.((....)).)).))))...(((((.(....))))))... ( -33.40)
>consensus
AAUACUAAUGCAAAUAAAUGUGAGUGCCAAUUGAAAUAGAAAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG____________AUGGUGAAUGUCGACGAGAGCGACAAAA
...(((...(((......))).)))((((..............(((((((..((((.......))))...)))).)))...............))))...(((((.(....))))))... (-25.01 = -23.68 +  -1.33)

alignment

secondary structure

dotplot

Window 4

Location	3,122,375 – 3,122,479
Length	104
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	94.55
Mean single sequence MFE	-36.55
Consensus MFE	-33.00
Energy contribution	-33.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.90
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3122375 104 + 27905053
AAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAAGUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAAC
......((((((((((.((((...((((.....)))).))------------)).))...(((((.(....))))))...))))))))..((((((.((((...)))))))))).. ( -35.30)
>DroSec_CAF1 9982 104 + 1
AAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAAGUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAAC
......((((((((((.((((...((((.....)))).))------------)).))...(((((.(....))))))...))))))))..((((((.((((...)))))))))).. ( -35.30)
>DroSim_CAF1 15291 104 + 1
AAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG------------AUGGUGAAUGUCGACGAGAGCGACAAAAGUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAAC
......((((((((((.((((...((((.....)))).))------------)).))...(((((.(....))))))...))))))))..((((((.((((...)))))))))).. ( -35.30)
>DroYak_CAF1 13629 116 + 1
AAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCGGCGGCGACGGCGAUGGUGAAUGUCGACGAGAGCGACAAAAGUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAAC
......((((((((((.(((..(.((((.....)))).)(.((....)).)))).))...(((((.(....))))))...))))))))..((((((.((((...)))))))))).. ( -40.30)
>consensus
AAACCGCGCUGCACACAAUCGAGGUGUCAAAGCGACGGCG____________AUGGUGAAUGUCGACGAGAGCGACAAAAGUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAAC
......((((((((........(.((((.....)))).).....................(((((.(....))))))...))))))))..((((((.((((...)))))))))).. (-33.00 = -33.00 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	3,122,443 – 3,122,543
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-28.04
Consensus MFE	-27.16
Energy contribution	-26.92
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-3.08
Structure conservation index	0.97
SVM decision value	4.06
SVM RNA-class probability	0.999779
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3122443 100 + 27905053
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGAAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACGCAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((...........(((....)))............((........)).)))))..))))......))))))))))))) ( -27.30)
>DroSec_CAF1 10050 100 + 1
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGAAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACGCAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((...........(((....)))............((........)).)))))..))))......))))))))))))) ( -27.30)
>DroSim_CAF1 15359 100 + 1
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGAAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACGCAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((...........(((....)))............((........)).)))))..))))......))))))))))))) ( -27.30)
>DroEre_CAF1 9766 100 + 1
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGGAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACACAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((............(((....)))...........((........)).)))))..))))......))))))))))))) ( -30.60)
>DroYak_CAF1 13709 100 + 1
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGAAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACACAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((...........(((....)))............((........)).)))))..))))......))))))))))))) ( -27.70)
>consensus
GUGCGGCGGCUUUUGGUGUUGGCCCAACUCAAAAACGUGAAAACGCAAAAAAUCGGAGCAAAACAAAGCAGGCCAAAACGCAACUAAAAAAGUGUUGCAU
((((((((.(((((.(((((((((............(((....)))...........((........)).)))))..))))......))))))))))))) (-27.16 = -26.92 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	3,122,443 – 3,122,543
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-28.46
Consensus MFE	-27.70
Energy contribution	-27.46
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.71
Structure conservation index	0.97
SVM decision value	3.80
SVM RNA-class probability	0.999627
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3122443 100 - 27905053
AUGCAACACUUUUUUAGUUGCGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUUCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
(((((((.........)))))))...(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).))).... ( -28.50)
>DroSec_CAF1 10050 100 - 1
AUGCAACACUUUUUUAGUUGCGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUUCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
(((((((.........)))))))...(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).))).... ( -28.50)
>DroSim_CAF1 15359 100 - 1
AUGCAACACUUUUUUAGUUGCGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUUCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
(((((((.........)))))))...(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).))).... ( -28.50)
>DroEre_CAF1 9766 100 - 1
AUGCAACACUUUUUUAGUUGUGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUCCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
.((((((((..........)))))..(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).)))))). ( -28.40)
>DroYak_CAF1 13709 100 - 1
AUGCAACACUUUUUUAGUUGUGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUUCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
.((((((((..........)))))..(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).)))))). ( -28.40)
>consensus
AUGCAACACUUUUUUAGUUGCGUUUUGGCCUGCUUUGUUUUGCUCCGAUUUUUUGCGUUUUCACGUUUUUGAGUUGGGCCAACACCAAAAGCCGCCGCAC
(((((((.........)))))))...(((..(((((((.(((..(((((((...((((....))))....)))))))..))).))..))))).))).... (-27.70 = -27.46 +  -0.24)

alignment

secondary structure

dotplot

Window 7

Location	3,122,543 – 3,122,633
Length	90
Sequences	3
Columns	90
Reading direction	reverse
Mean pairwise identity	98.52
Mean single sequence MFE	-26.73
Consensus MFE	-26.03
Energy contribution	-26.03
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.97
SVM decision value	1.19
SVM RNA-class probability	0.928054
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3122543 90 - 27905053
AAAGCAACAAAGCUAACGCUCAGCGGUUCACACCCACGCACACCCGCAUGUGUGUGGGCCUAUCACACAGUGGCCAACUCCCCUUGCGCU
...((((...(((....)))....(((.(((.((((((((((......))))))))))...........))))))........))))... ( -27.00)
>DroSec_CAF1 10150 90 - 1
AAAGCAACAAAGCUAAAGCUCAGCGGUUCACACCCACGCACACCCGCAUGUGUGUGGGCCUAUCACACAGUGGCCAACUCCCCUUGCGCU
..(((......)))..(((.(((.((........((((((((......))))))))((((...........)))).....)).))).))) ( -26.60)
>DroSim_CAF1 15459 90 - 1
AAAGCAACAAAGCUAACGCUCAGCGGUUCACACCCACGCACUCCCGCAUGUGUGUGGGCCUAUCACACAGUGGCCAACUCCCCUUGCGCU
...((((...(((....)))....(((.(((.(((((((((........)))))))))...........))))))........))))... ( -26.60)
>consensus
AAAGCAACAAAGCUAACGCUCAGCGGUUCACACCCACGCACACCCGCAUGUGUGUGGGCCUAUCACACAGUGGCCAACUCCCCUUGCGCU
..(((.....(((....)))..(((((((((((.((.((......)).)).)))))))))..((((...))))............))))) (-26.03 = -26.03 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:02 2006