Locus 8560

Sequence ID	3R_DroMel_CAF1
Location	22,875,638 – 22,875,789
Length	151
Max. P	0.855754

overview

Window 4

Location	22,875,638 – 22,875,749
Length	111
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	80.18
Mean single sequence MFE	-36.37
Consensus MFE	-30.47
Energy contribution	-30.37
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-1.38
Structure conservation index	0.84
SVM decision value	0.48
SVM RNA-class probability	0.754633
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22875638 111 - 27905053
ACUUCUUCCUGCUCUGGUGGUGGCACGUGCACGUAGAUGUGCUUCUGCACCAAGGUGGUGCCACCACCACCACCGCCGCCGCCUCCGAAUCCGCCAAUGCUGCCACCUGUG
..........((...((((((((((((....)))....((((....))))...(((((((....)))))))...))))))))).........((....)).))........ ( -38.70)
>DroWil_CAF1 27675 105 - 1
AUUUCCUCUUGCUCUGGUGGUGGGACAUGCACAUAGAUGUGCUUUUGCACUAGAGUGGUGCCACCACCA------CCGCCGCCUCCGAAACCACCUCCGAUGCUGCCUGUA
..............(((((((((.((..(((((....))))).....(((....))))).)))))))))------..((.((.((.((.......)).)).)).))..... ( -34.00)
>DroMoj_CAF1 31113 105 - 1
ACUUCCUCCUGCUCUGGUGGUGGCACAUGCACAUAGAUGUGCUUCUGCACCAGAGUGGUGCCGCCA---CCGCCGCCGCCGCCUCCGAAUCCACCGCCUAUG---CCUGUA
..........((..((((((((((....(((((....)))))....(((((.....))))).))))---))))))..)).......................---...... ( -36.40)
>consensus
ACUUCCUCCUGCUCUGGUGGUGGCACAUGCACAUAGAUGUGCUUCUGCACCAGAGUGGUGCCACCACCACC_CCGCCGCCGCCUCCGAAUCCACCACCGAUGC__CCUGUA
...............(((((((((....(((((....)))))....(((((.....))))).............)))))))))............................ (-30.47 = -30.37 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	22,875,678 – 22,875,789
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	84.95
Mean single sequence MFE	-42.94
Consensus MFE	-33.84
Energy contribution	-35.68
Covariance contribution	1.84
Combinations/Pair	1.16
Mean z-score	-1.91
Structure conservation index	0.79
SVM decision value	0.77
SVM RNA-class probability	0.845891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22875678 111 + 27905053
GGUGGUGGUGGCACCACCUUGGUGCAGAAGCACAUCUACGUGCACGUGCCACCACCAGAGCAGGAAGAAGUGCGCCAGCGCCCUAACCUGCCCAUUGGCCAGUCCCAGAAG
(((((((((((((((((....))).....((((......))))..))))))))))).(.(((((.....((((....)))).....))))).)....)))........... ( -49.80)
>DroGri_CAF1 23297 111 + 1
GGCGGCGGUGGCACCACUUUGGUUCAAAAGCACAUUUAUGUUCAUGUGCCACCACCAGAGCAGGAGGAAGUGCGUCAGCGCCCCAACAUUCCAGUCGGCCAAUCCCAGAAG
(((((.((((((((..((((......)))).(((....)))....)))))))).))......((((...((((....)))).......)))).....)))........... ( -33.70)
>DroSec_CAF1 21409 111 + 1
GGUGGUGGUGGCACCACCUUGGUGCAGAAGCACAUCUACGUGCACGUGCCGCCACCAGAGCAGGAAGAAGUGCGCCAGCGCCCUAACCUGCCCAUUGGCCAGUCCCAGAAG
(((((((((((((((((....))).....((((......))))..))))))))))).(.(((((.....((((....)))).....))))).)....)))........... ( -49.40)
>DroWil_CAF1 27711 109 + 1
--UGGUGGUGGCACCACUCUAGUGCAAAAGCACAUCUAUGUGCAUGUCCCACCACCAGAGCAAGAGGAAAUCCGUCAGCGUCCCAACUUGCCAGUUGGUCAGUCUCAGAAG
--(((((((((.(((((....))).....(((((....)))))..)).)))))))))((((..((((....)).))......((((((....))))))...).)))..... ( -37.40)
>DroMoj_CAF1 31150 108 + 1
GG---UGGCGGCACCACUCUGGUGCAGAAGCACAUCUAUGUGCAUGUGCCACCACCAGAGCAGGAGGAAGUGCGUCAGCGACCUAACCUGCCCGUCGGCCAGGCCCAGAAG
((---((((((((((.....)))))....(((((....)))))...)))))))....(.((((((((...(((....))).)))..))))).)...(((...)))...... ( -44.40)
>consensus
GGUGGUGGUGGCACCACUUUGGUGCAGAAGCACAUCUAUGUGCAUGUGCCACCACCAGAGCAGGAGGAAGUGCGUCAGCGCCCUAACCUGCCCGUUGGCCAGUCCCAGAAG
(((((((((((((((((....))).....((((......))))..)))))))))))...(((((..(..((((....))))..)..)))))......)))........... (-33.84 = -35.68 +   1.84)

alignment

secondary structure

dotplot

Window 6

Location	22,875,678 – 22,875,789
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	84.95
Mean single sequence MFE	-46.50
Consensus MFE	-37.36
Energy contribution	-38.64
Covariance contribution	1.28
Combinations/Pair	1.23
Mean z-score	-1.90
Structure conservation index	0.80
SVM decision value	0.81
SVM RNA-class probability	0.855754
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22875678 111 - 27905053
CUUCUGGGACUGGCCAAUGGGCAGGUUAGGGCGCUGGCGCACUUCUUCCUGCUCUGGUGGUGGCACGUGCACGUAGAUGUGCUUCUGCACCAAGGUGGUGCCACCACCACC
....(((......)))..(((((((..((((((....))).)))...)))))))((((((((((((..(((((....))))).....(((....))))))))))))))).. ( -53.60)
>DroGri_CAF1 23297 111 - 1
CUUCUGGGAUUGGCCGACUGGAAUGUUGGGGCGCUGACGCACUUCCUCCUGCUCUGGUGGUGGCACAUGAACAUAAAUGUGCUUUUGAACCAAAGUGGUGCCACCGCCGCC
.....((((..(((((((......))))).(((....)))....)))))).....(((((((((((....(((....)))(((((......))))).)))))))))))... ( -39.00)
>DroSec_CAF1 21409 111 - 1
CUUCUGGGACUGGCCAAUGGGCAGGUUAGGGCGCUGGCGCACUUCUUCCUGCUCUGGUGGCGGCACGUGCACGUAGAUGUGCUUCUGCACCAAGGUGGUGCCACCACCACC
....(((......)))..(((((((..((((((....))).)))...)))))))((((((.(((((..(((((....))))).....(((....)))))))).)))))).. ( -49.70)
>DroWil_CAF1 27711 109 - 1
CUUCUGAGACUGACCAACUGGCAAGUUGGGACGCUGACGGAUUUCCUCUUGCUCUGGUGGUGGGACAUGCACAUAGAUGUGCUUUUGCACUAGAGUGGUGCCACCACCA--
......(((....((((((....))))))...((.((.((....))))..)))))((((((((.((..(((((....))))).....(((....))))).)))))))).-- ( -41.10)
>DroMoj_CAF1 31150 108 - 1
CUUCUGGGCCUGGCCGACGGGCAGGUUAGGUCGCUGACGCACUUCCUCCUGCUCUGGUGGUGGCACAUGCACAUAGAUGUGCUUCUGCACCAGAGUGGUGCCGCCA---CC
......(((...)))...(((((((..((((.((....))))))...))))))).(((((((((((..(((((....)))))(((((...)))))..)))))))))---)) ( -49.10)
>consensus
CUUCUGGGACUGGCCAACGGGCAGGUUAGGGCGCUGACGCACUUCCUCCUGCUCUGGUGGUGGCACAUGCACAUAGAUGUGCUUCUGCACCAAAGUGGUGCCACCACCACC
....(((......)))..(((((((..((.(((....))).))....)))))))((((((((((((..(((((....))))).....(((....))))))))))))))).. (-37.36 = -38.64 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:08 2006