Locus 1357

Sequence ID	3R_DroMel_CAF1
Location	3,998,080 – 3,998,276
Length	196
Max. P	0.798116

overview

Window 6

Location	3,998,080 – 3,998,200
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-29.05
Consensus MFE	-28.27
Energy contribution	-28.52
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.97
SVM decision value	0.33
SVM RNA-class probability	0.690719
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3998080 120 + 27905053
AAAAUAAAAGAAAAAAGGAGUACCAAAGAGGAAAAACAAUGAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACA
................((.(((((.....)).........((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))...)))...))... ( -29.30)
>DroSec_CAF1 3750 118 + 1
AAAAUAAAA--AAAAAGGACUACCAAAGAGGAAAAACAAUGAGAGCUAACCAGUUAACCAGCUCGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACA
.........--.....((((..((.....)).........((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))......)).))... ( -28.30)
>DroSim_CAF1 3798 118 + 1
AAAAUAAAA--AAAAAGGAGUACCAAAGAGGAAAAACAAUGAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACA
.........--.....((.(((((.....)).........((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))...)))...))... ( -29.30)
>DroYak_CAF1 3385 119 + 1
AAAACAAAAAAAAUAAGGAGUACCAAAGAGGAA-AACAAUGAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACA
................((.(((((.....))..-......((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))...)))...))... ( -29.30)
>consensus
AAAAUAAAA__AAAAAGGAGUACCAAAGAGGAAAAACAAUGAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACA
................((.(((((.....)).........((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))...)))...))... (-28.27 = -28.52 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	3,998,120 – 3,998,236
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.20
Mean single sequence MFE	-31.27
Consensus MFE	-30.30
Energy contribution	-30.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.97
SVM decision value	0.61
SVM RNA-class probability	0.798116
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3998120 116 + 27905053
GAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAACAA----AUACAACAAAAUAA
((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))(((....))).....(((((...)))))........----.............. ( -30.30)
>DroSec_CAF1 3788 116 + 1
GAGAGCUAACCAGUUAACCAGCUCGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAA----GUACAACAAAAUAA
..(((((............)))))(((((((((((((((.....)))))....)))))))(((((((((....))).....(((((...)))))....))))----))..)))....... ( -32.20)
>DroSim_CAF1 3836 114 + 1
GAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAA--AAAA----GUACAACAAAGUAA
((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))......((((.....(((((...)))))..--....----)))).......... ( -32.30)
>DroYak_CAF1 3424 120 + 1
GAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAUAUAUAUACAACAAAAUAA
((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))(((....))).....(((((...))))).......................... ( -30.30)
>consensus
GAGAGCUAACCAGUUAACCAGCUUGUUUGGGCCAACGUGUGAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAA____AUACAACAAAAUAA
((((((((((.((((....)))).))).(((((((((((.....)))))....)))))))))))))(((....))).....(((((...))))).......................... (-30.30 = -30.30 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	3,998,160 – 3,998,276
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.77
Mean single sequence MFE	-28.22
Consensus MFE	-25.60
Energy contribution	-25.85
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.91
SVM decision value	0.47
SVM RNA-class probability	0.748310
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3998160 116 + 27905053
GAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAACAA----AUACAACAAAAUAAAGGCAGGGAAAUGGGAAAACACGUUGACAACAACAAGCGC
.......(((.((((.(((.(((((((((....))).....(((((...)))))........----............)))))).)))...))))....)))((((....))))...... ( -26.90)
>DroSec_CAF1 3828 116 + 1
GAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAA----GUACAACAAAAUAAAGGCAUGGAAAUGGGAAAACACGUUGACAACAACAAGCGC
.......(((......((((((....))...((((((....(((((...)))))........----(.....)........))))))....))))....)))((((....))))...... ( -27.60)
>DroSim_CAF1 3876 114 + 1
GAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAA--AAAA----GUACAACAAAGUAAAGGCAGGGAAAUGGGAAAACACGUUGACAACAACAAGCGC
.......(((.((((.(((.((((((((....((((.....(((((...)))))..--....----))))......)))))))).)))...))))....)))((((....))))...... ( -31.10)
>DroYak_CAF1 3464 120 + 1
GAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAUAUAUAUACAACAAAAUAAAGGCAGGGAAAUGGGAAAACACGUUGACAACAACCAGCGC
.......(((.((((.(((.(((((((((....))).....(((((...)))))........................)))))).)))...))))....)))((((........)))).. ( -27.30)
>consensus
GAAUUACGUGGCCUGGCCCAGCUUUUGCAUACGUGCCACAAUGUGGUUGCCACAAAAAAAAA____AUACAACAAAAUAAAGGCAGGGAAAUGGGAAAACACGUUGACAACAACAAGCGC
.......(((.((((.(((.(((((((((....))).....(((((...)))))........................)))))).)))...))))....)))((((....))))...... (-25.60 = -25.85 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:52 2006