Locus 12464

Sequence ID	dm3.chrX
Location	370,473 – 370,587
Length	114
Max. P	0.903749

overview

Window 5

Location	370,473 – 370,579
Length	106
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.06
Shannon entropy	0.38428
G+C content	0.46973
Mean single sequence MFE	-24.02
Consensus MFE	-17.38
Energy contribution	-19.22
Covariance contribution	1.84
Combinations/Pair	1.16
Mean z-score	-1.65
Structure conservation index	0.72
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.17
SVM RNA-class probability	0.903749
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 370473 106 - 22422827
ACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGGAAUUAGAACCGCGAGCAAGCGGAGCUCACAGUGACCGUAAC-
...((((((((....)))))))).-...((((.......))))(((((((.(((....))).))))....((..((((......))))..)).........)))...- ( -27.90, z-score =  -1.94, R)
>droSim1.chrX 269312 106 - 17042790
ACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGGAAUUAGAACCGCGAGCAAGCGGAGCUCACAGUGACCCCUAC-
...((((((((....)))))))).-...((((.......))))((.((((.(((....))).))))....((..((((......))))..))....)).........- ( -26.70, z-score =  -1.92, R)
>droSec1.super_10 228198 106 - 3036183
ACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGGAAUUAGAACCGCGAGCAAGCGGAGCUCACAGUGACCCCUAC-
...((((((((....)))))))).-...((((.......))))((.((((.(((....))).))))....((..((((......))))..))....)).........- ( -26.70, z-score =  -1.92, R)
>droYak2.chrX 299692 106 - 21770863
ACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGAGUGCUGAUGCGAUCGGAAUUAGAACCGCGAGCAAGCGGAGCUCAUAGUGACCCCCAC-
...((((((((....)))))))).-...((((.......))))...((((.(((....))).)))).((.((..((((......))))..)).)).(((.....)))- ( -27.10, z-score =  -1.88, R)
>droEre2.scaffold_4644 317917 106 - 2521924
ACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGAGUGCUGAUGCGAUCGGAAUCAGAACCGCGUGCAAGCGGAGCUUAUAGUGACCCCCAC-
...((((((((....)))))))).-.......((........((..((((.(((....))).))))..))....((((......)))).)).....(((.....)))- ( -27.40, z-score =  -1.60, R)
>droVir3.scaffold_13042 1512614 96 + 5191987
-----------AAAAAUUCAAAUAUAAAUCAUGAAAUUCUUAGCAAACAACUGCUAAUGCACUCAAAUCACUUAUCAC-CGCUAGCACCGAGCACAAAACCGCACACC
-----------....................(((.....((((((......)))))).....))).............-.(((.......)))............... (  -8.30, z-score =  -0.65, R)
>consensus
ACCUUUUGUGUAAAGACACAAAGA_AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGGAAUUAGAACCGCGAGCAAGCGGAGCUCACAGUGACCCCCAC_
...((((((((....)))))))).....((((.......))))...((((.(((....))).))))....((..((((......))))..))................ (-17.38 = -19.22 +   1.84)

alignment

secondary structure

dotplot

Window 6

Location	370,482 – 370,587
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	81.31
Shannon entropy	0.35253
G+C content	0.44974
Mean single sequence MFE	-29.63
Consensus MFE	-17.47
Energy contribution	-20.20
Covariance contribution	2.72
Combinations/Pair	1.07
Mean z-score	-2.03
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.77
SVM RNA-class probability	0.811173
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 370482 105 + 22422827
ACUGUGAGCUCCGCUUGCUCGCGGUUCUAAUU---CCGAUCGCAUCAGCAGUCGGCGUCCAUUAAUUGCAUGGUUU-UCUUUGUGUCUUUACACAAAAGGUGGCCAAAA-
(((((((((.......))))))))).......---(((((.((....)).)))))...............((((..-(((((((((....)))).)))))..))))...- ( -33.80, z-score =  -2.80, R)
>droSim1.chrX 269321 105 + 17042790
ACUGUGAGCUCCGCUUGCUCGCGGUUCUAAUU---CCGAUCGCAUCAGCAGUCGGCGUCCAUUAAUUGCAUGGUUU-UCUUUGUGUCUUUACACAAAAGGUGGCCAAAA-
(((((((((.......))))))))).......---(((((.((....)).)))))...............((((..-(((((((((....)))).)))))..))))...- ( -33.80, z-score =  -2.80, R)
>droSec1.super_10 228207 105 + 3036183
ACUGUGAGCUCCGCUUGCUCGCGGUUCUAAUU---CCGAUCGCAUCAGCAGUCGGCGUCCAUUAAUUGCAUGGUUU-UCUUUGUGUCUUUACACAAAAGGUGGCCAAAA-
(((((((((.......))))))))).......---(((((.((....)).)))))...............((((..-(((((((((....)))).)))))..))))...- ( -33.80, z-score =  -2.80, R)
>droYak2.chrX 299701 105 + 21770863
ACUAUGAGCUCCGCUUGCUCGCGGUUCUAAUU---CCGAUCGCAUCAGCACUCGGCGUCCAUUAAUUGCAUGGUUU-UCUUUGUGUCUUUACACAAAAGGUGGCCAAAA-
...(((..(.(((..((((.((((((......---..))))))...))))..))).)..)))........((((..-(((((((((....)))).)))))..))))...- ( -30.20, z-score =  -2.21, R)
>droEre2.scaffold_4644 317926 106 + 2521924
ACUAUAAGCUCCGCUUGCACGCGGUUCUGAUU---CCGAUCGCAUCAGCACUCGGCGUCCAUUAAUUGCAUGGUUU-UCUUUGUGUCUUUACACAAAAGGUGGCCAAAAA
.......((.((((......))))....(((.---((((..((....))..)))).)))........)).((((..-(((((((((....)))).)))))..)))).... ( -28.90, z-score =  -1.65, R)
>droVir3.scaffold_13042 1512622 88 - 5191987
GUUUUGUGCUCGG--UGCUAGCGGUGAUAAGUGAUUUGAGUGCAUUAGCAGUUGUUUGCUAAGAAUUUCAUGAUUUAUAUUUGAAUUUUU--------------------
....((..(((((--.....((........))...)))))..))(((((((....))))))).........((((((....))))))...-------------------- ( -17.30, z-score =   0.05, R)
>consensus
ACUGUGAGCUCCGCUUGCUCGCGGUUCUAAUU___CCGAUCGCAUCAGCAGUCGGCGUCCAUUAAUUGCAUGGUUU_UCUUUGUGUCUUUACACAAAAGGUGGCCAAAA_
.....((((.......))))((((((.........((((..((....))..))))........)))))).(((((....((((((......))))))....))))).... (-17.47 = -20.20 +   2.72)

alignment

secondary structure

dotplot

Window 7

Location	370,482 – 370,587
Length	105
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.31
Shannon entropy	0.35253
G+C content	0.44974
Mean single sequence MFE	-26.17
Consensus MFE	-16.23
Energy contribution	-18.45
Covariance contribution	2.22
Combinations/Pair	1.09
Mean z-score	-1.73
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.39
SVM RNA-class probability	0.671842
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 370482 105 - 22422827
-UUUUGGCCACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGG---AAUUAGAACCGCGAGCAAGCGGAGCUCACAGU
-..(((((....((((((((....)))))))).-...((((.......))))..)))))(((.(((.((..((..---.....)).((((......)))).)))))))). ( -30.10, z-score =  -2.12, R)
>droSim1.chrX 269321 105 - 17042790
-UUUUGGCCACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGG---AAUUAGAACCGCGAGCAAGCGGAGCUCACAGU
-..(((((....((((((((....)))))))).-...((((.......))))..)))))(((.(((.((..((..---.....)).((((......)))).)))))))). ( -30.10, z-score =  -2.12, R)
>droSec1.super_10 228207 105 - 3036183
-UUUUGGCCACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGG---AAUUAGAACCGCGAGCAAGCGGAGCUCACAGU
-..(((((....((((((((....)))))))).-...((((.......))))..)))))(((.(((.((..((..---.....)).((((......)))).)))))))). ( -30.10, z-score =  -2.12, R)
>droYak2.chrX 299701 105 - 21770863
-UUUUGGCCACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGAGUGCUGAUGCGAUCGG---AAUUAGAACCGCGAGCAAGCGGAGCUCAUAGU
-....(((....((((((((....)))))))).-...((((.......))))..)))((((.(((.(((...(((---........)))...)))..))).))))..... ( -29.70, z-score =  -1.87, R)
>droEre2.scaffold_4644 317926 106 - 2521924
UUUUUGGCCACCUUUUGUGUAAAGACACAAAGA-AAACCAUGCAAUUAAUGGACGCCGAGUGCUGAUGCGAUCGG---AAUCAGAACCGCGUGCAAGCGGAGCUUAUAGU
....(((.....((((((((....)))))))).-...))).((........((..((((.(((....))).))))---..))....((((......)))).))....... ( -28.70, z-score =  -1.14, R)
>droVir3.scaffold_13042 1512622 88 + 5191987
--------------------AAAAAUUCAAAUAUAAAUCAUGAAAUUCUUAGCAAACAACUGCUAAUGCACUCAAAUCACUUAUCACCGCUAGCA--CCGAGCACAAAAC
--------------------....................(((.....((((((......)))))).....)))..............(((....--...)))....... (  -8.30, z-score =  -1.03, R)
>consensus
_UUUUGGCCACCUUUUGUGUAAAGACACAAAGA_AAACCAUGCAAUUAAUGGACGCCGACUGCUGAUGCGAUCGG___AAUUAGAACCGCGAGCAAGCGGAGCUCACAGU
............((((((((....)))))))).....((((.......))))...((((.(((....))).))))...........((((......)))).......... (-16.23 = -18.45 +   2.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:45 2011