Locus 13057

Sequence ID	dm3.chrX
Location	4,100,155 – 4,100,247
Length	92
Max. P	0.980770

overview

Window 3

Location	4,100,155 – 4,100,247
Length	92
Sequences	7
Columns	109
Reading direction	forward
Mean pairwise identity	65.70
Shannon entropy	0.63035
G+C content	0.55347
Mean single sequence MFE	-28.30
Consensus MFE	-11.21
Energy contribution	-11.09
Covariance contribution	-0.12
Combinations/Pair	1.58
Mean z-score	-1.36
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.45
SVM RNA-class probability	0.702335
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 4100155 92 + 22422827
-----CCACAGCUAUUGCCGCGCCACAAGAUC-UGGCAACCCCAAAUGUUGCCAGCCGAUGCG---ACGCAGCAUGUUGCCAAC--------CGAAAGUAAUCAAGCAA
-----...((((...(((.(((.(.((....(-(((((((.......))))))))....)).)---.))).))).)))).....--------(....)........... ( -25.60, z-score =  -1.69, R)
>droAna3.scaffold_13117 273503 109 - 5790199
CCGAGGCCCACUGUGAAGUGAGCGCAGCGACAGCACCAACAUGAAGCGGCGAGAGCGGAUUUUCGCGGCAACAAGGUUGCCGAGGCAUGUUGCAGAGGCAGGCGGGCAA
.....((((.((((...((....)).((((((((..(...........(((((((....)))))))((((((...)))))))..)).))))))....))))..)))).. ( -41.30, z-score =  -0.96, R)
>droEre2.scaffold_4690 1470417 92 + 18748788
-----CCACAGCUAUUGCCGCGCCACAAGAUC-UGGCAACCCCCAAUGUUGCCAGCAGAUGCG---ACGCAGCAUGUUGCCAAC--------CAAAAGUAAACCAGCGA
-----...((((...(((.(((.(.((....(-(((((((.......))))))))....)).)---.))).))).)))).....--------................. ( -25.10, z-score =  -1.66, R)
>droYak2.chrX 17433304 92 - 21770863
-----CCACAGCUAUCGCCGCGCCACAAGAUC-UGGCAACCCCCAAUGUUGCCAGCAGAUGCG---ACGCAGCAUGUUGCCAAC--------CAAAAGUAAGCGAGCGA
-----.........(((((((...........-(((((((.....(((((((..((....)).---..))))))))))))))..--------.........))).)))) ( -30.05, z-score =  -2.81, R)
>droSec1.super_4 3548257 92 - 6179234
-----CCACAGCUAUUGCCGCGCCACAAGAUC-UGGCAACCCCAAAUGUUGCCAGCAGAUGCG---UGGCAGCAUGUUGCCAAC--------CGAAAGUAAACGAGCAA
-----.....(((.(((((((((........(-(((((((.......)))))))).....)))---))))))..((((......--------(....)..))))))).. ( -30.32, z-score =  -2.18, R)
>droSim1.chrX 3063921 92 + 17042790
-----CCACAGCUAUUGCCGCGCCACAAGAUC-UGGCAACCCCAAAUGUUGCCAGCAGAUGCG---UGGCAGCAUGUUGCCAAC--------CGAAAGUAAACGAGCAA
-----.....(((.(((((((((........(-(((((((.......)))))))).....)))---))))))..((((......--------(....)..))))))).. ( -30.32, z-score =  -2.18, R)
>droWil1.scaffold_181150 2642132 96 - 4952429
-------GAAAUGGAAAUGCCGCCAGAUGAUGAUGAUGACCGGAGACGACGUUCGAAAAUGUU---GCUAAGCAUGUUGCCAGCGC---UCACAGCAGUAAACCGACAA
-------....(((........)))...............(((((.(((((((....))))))---)))..((.(((.((....))---..)))))......))).... ( -15.40, z-score =   1.93, R)
>consensus
_____CCACAGCUAUUGCCGCGCCACAAGAUC_UGGCAACCCCAAAUGUUGCCAGCAGAUGCG___ACGCAGCAUGUUGCCAAC________CAAAAGUAAACGAGCAA
..........((....))...((..........(((((((.......)))))))((((((((.........)))).)))).........................)).. (-11.21 = -11.09 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	4,100,155 – 4,100,247
Length	92
Sequences	7
Columns	109
Reading direction	reverse
Mean pairwise identity	65.70
Shannon entropy	0.63035
G+C content	0.55347
Mean single sequence MFE	-35.10
Consensus MFE	-16.04
Energy contribution	-15.11
Covariance contribution	-0.93
Combinations/Pair	1.76
Mean z-score	-1.86
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.06
SVM RNA-class probability	0.980770
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 4100155 92 - 22422827
UUGCUUGAUUACUUUCG--------GUUGGCAACAUGCUGCGU---CGCAUCGGCUGGCAACAUUUGGGGUUGCCA-GAUCUUGUGGCGCGGCAAUAGCUGUGG-----
...............((--------((((....).((((((((---((((....((((((((.......)))))))-)....))))))))))))..)))))...----- ( -39.90, z-score =  -3.40, R)
>droAna3.scaffold_13117 273503 109 + 5790199
UUGCCCGCCUGCCUCUGCAACAUGCCUCGGCAACCUUGUUGCCGCGAAAAUCCGCUCUCGCCGCUUCAUGUUGGUGCUGUCGCUGCGCUCACUUCACAGUGGGCCUCGG
..((((((.((......(((((((....((((((...))))))(((......)))...........)))))))((((.......))))........))))))))..... ( -35.50, z-score =  -0.93, R)
>droEre2.scaffold_4690 1470417 92 - 18748788
UCGCUGGUUUACUUUUG--------GUUGGCAACAUGCUGCGU---CGCAUCUGCUGGCAACAUUGGGGGUUGCCA-GAUCUUGUGGCGCGGCAAUAGCUGUGG-----
..((((((..((.....--------))..))....((((((((---((((....((((((((.......)))))))-)....)))))))))))).)))).....----- ( -41.50, z-score =  -3.62, R)
>droYak2.chrX 17433304 92 + 21770863
UCGCUCGCUUACUUUUG--------GUUGGCAACAUGCUGCGU---CGCAUCUGCUGGCAACAUUGGGGGUUGCCA-GAUCUUGUGGCGCGGCGAUAGCUGUGG-----
..(((.(((.((.....--------)).)))....((((((((---((((....((((((((.......)))))))-)....))))))))))))..))).....----- ( -41.50, z-score =  -3.20, R)
>droSec1.super_4 3548257 92 + 6179234
UUGCUCGUUUACUUUCG--------GUUGGCAACAUGCUGCCA---CGCAUCUGCUGGCAACAUUUGGGGUUGCCA-GAUCUUGUGGCGCGGCAAUAGCUGUGG-----
...............((--------((((....).((((((..---((((....((((((((.......)))))))-)....))))..))))))..)))))...----- ( -32.80, z-score =  -0.92, R)
>droSim1.chrX 3063921 92 - 17042790
UUGCUCGUUUACUUUCG--------GUUGGCAACAUGCUGCCA---CGCAUCUGCUGGCAACAUUUGGGGUUGCCA-GAUCUUGUGGCGCGGCAAUAGCUGUGG-----
...............((--------((((....).((((((..---((((....((((((((.......)))))))-)....))))..))))))..)))))...----- ( -32.80, z-score =  -0.92, R)
>droWil1.scaffold_181150 2642132 96 + 4952429
UUGUCGGUUUACUGCUGUGA---GCGCUGGCAACAUGCUUAGC---AACAUUUUCGAACGUCGUCUCCGGUCAUCAUCAUCAUCUGGCGGCAUUUCCAUUUC-------
...(((((((((....))))---))((((((.....)).))))---........))).....(((.((((.............)))).)))...........------- ( -21.72, z-score =  -0.02, R)
>consensus
UUGCUCGUUUACUUUUG________GUUGGCAACAUGCUGCGU___CGCAUCUGCUGGCAACAUUUGGGGUUGCCA_GAUCUUGUGGCGCGGCAAUAGCUGUGG_____
.........................((((....)).))........((((.....(((((((.......)))))))......)))).((((((....))))))...... (-16.04 = -15.11 +  -0.93)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:13:47 2011