Locus 6113

Sequence ID dm3.chr3L
Location 3,798,000 – 3,798,065
Length 65
Max. P 0.949554
window8409 window8410

overview

Window 9

Location 3,798,000 – 3,798,065
Length 65
Sequences 11
Columns 70
Reading direction forward
Mean pairwise identity 70.18
Shannon entropy 0.61064
G+C content 0.44605
Mean single sequence MFE -16.56
Consensus MFE -6.76
Energy contribution -8.02
Covariance contribution 1.27
Combinations/Pair 1.46
Mean z-score -1.94
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949554
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 3798000 65 + 24543557
GCUGUC-GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAAUAAAAAUUG----
((((((-((((((((....((........))....)))))).....))))))))............---- ( -18.50, z-score =  -3.12, R)
>droEre2.scaffold_4784 6495527 56 + 25762168
GCUGUC-GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAA-------------
((((((-((((((((....((........))....)))))).....))))))))...------------- ( -18.50, z-score =  -3.13, R)
>droYak2.chr3L 4354879 56 + 24197627
GCUGUC-GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAA-------------
((((((-((((((((....((........))....)))))).....))))))))...------------- ( -18.50, z-score =  -3.13, R)
>droSec1.super_2 3792156 65 + 7591821
GCUGUC-GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAAUAAAAAUUG----
((((((-((((((((....((........))....)))))).....))))))))............---- ( -18.50, z-score =  -3.12, R)
>droSim1.chr3L 3338345 65 + 22553184
GCUGUC-GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAAUAAAAAUUG----
((((((-((((((((....((........))....)))))).....))))))))............---- ( -18.50, z-score =  -3.12, R)
>dp4.chrXR_group6 6857940 68 + 13314419
GCUGUC-GUCGCCAUCGCUGCACAGUUUGUCAUAAACGGCGCCAUAUUGACAGCAAACACUAAAAAAAA-
((((((-(.((((...(((....)))..((.....))))))......)))))))...............- ( -15.70, z-score =  -1.20, R)
>droPer1.super_41 216688 69 + 728894
GCUGUC-GUCGCCAUCGCUGCACAGUUUGUCAUAAACGGCGCCAUAUUGACAGCAAACACUAAAAAAAAA
((((((-(.((((...(((....)))..((.....))))))......)))))))................ ( -15.70, z-score =  -1.19, R)
>droWil1.scaffold_180955 1707224 65 + 2875958
GCUGUC-GUCGCCAUCAUUGCACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCUAAAAAAGGAAA----
((((((-(.((((((...((.((.....))))...))))))......)))))))............---- ( -18.80, z-score =  -2.42, R)
>droVir3.scaffold_13049 21008698 51 - 25233164
---GCUUGCGAU-GCUGUUGGCCAGCUUGUCAUAAAUGACGCCAUCCUGUCAGCU---------------
---(((.(((..-((((.....))))..((((....)))).......))).))).--------------- ( -12.00, z-score =   0.16, R)
>droMoj3.scaffold_6680 2641888 55 + 24764193
GCUGUUUGCCAUCAUUGUAGCCAAGUUUGUCAUAAACGUUGCCAUAUUGACAGCA---------------
((((.......(((.(((.((...(((((...)))))...)).))).))))))).--------------- ( -10.11, z-score =  -0.09, R)
>droGri2.scaffold_15110 10574724 58 + 24565398
-------GCGUUUGCUGUGCGCAAGCUUGUCAUAAAUGGCGCCAUAUAGACAGCAAUAAUAAGCA-----
-------((..(((((((((....))..((((....)))).........)))))))......)).----- ( -17.40, z-score =  -1.02, R)
>consensus
GCUGUC_GACGCCAUCAUCGAACAGUUUGUCAUAAAUGGCGCCAUAUUGACAGCAAA_A_AAA_______
((((((.(.((((((....................)))))).).....))))))................ ( -6.76 =  -8.02 +   1.27)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,798,000 – 3,798,065
Length 65
Sequences 11
Columns 70
Reading direction reverse
Mean pairwise identity 70.18
Shannon entropy 0.61064
G+C content 0.44605
Mean single sequence MFE -18.66
Consensus MFE -6.20
Energy contribution -6.20
Covariance contribution 0.00
Combinations/Pair 1.54
Mean z-score -2.23
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911356
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 3798000 65 - 24543557
----CAAUUUUUAUUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC-GACAGC
----............((((((.....(((((((((...(((.....)))....)))))))))-)))))) ( -22.10, z-score =  -3.66, R)
>droEre2.scaffold_4784 6495527 56 - 25762168
-------------UUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC-GACAGC
-------------...((((((.....(((((((((...(((.....)))....)))))))))-)))))) ( -22.10, z-score =  -3.92, R)
>droYak2.chr3L 4354879 56 - 24197627
-------------UUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC-GACAGC
-------------...((((((.....(((((((((...(((.....)))....)))))))))-)))))) ( -22.10, z-score =  -3.92, R)
>droSec1.super_2 3792156 65 - 7591821
----CAAUUUUUAUUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC-GACAGC
----............((((((.....(((((((((...(((.....)))....)))))))))-)))))) ( -22.10, z-score =  -3.66, R)
>droSim1.chr3L 3338345 65 - 22553184
----CAAUUUUUAUUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC-GACAGC
----............((((((.....(((((((((...(((.....)))....)))))))))-)))))) ( -22.10, z-score =  -3.66, R)
>dp4.chrXR_group6 6857940 68 - 13314419
-UUUUUUUUAGUGUUUGCUGUCAAUAUGGCGCCGUUUAUGACAAACUGUGCAGCGAUGGCGAC-GACAGC
-...............((((((.......(((((((..((((.....)).))..)))))))..-)))))) ( -18.20, z-score =  -0.62, R)
>droPer1.super_41 216688 69 - 728894
UUUUUUUUUAGUGUUUGCUGUCAAUAUGGCGCCGUUUAUGACAAACUGUGCAGCGAUGGCGAC-GACAGC
................((((((.......(((((((..((((.....)).))..)))))))..-)))))) ( -18.20, z-score =  -0.61, R)
>droWil1.scaffold_180955 1707224 65 - 2875958
----UUUCCUUUUUUAGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUGCAAUGAUGGCGAC-GACAGC
----............((((((.......(((((((..((((.....)).))..)))))))..-)))))) ( -18.40, z-score =  -2.36, R)
>droVir3.scaffold_13049 21008698 51 + 25233164
---------------AGCUGACAGGAUGGCGUCAUUUAUGACAAGCUGGCCAACAGC-AUCGCAAGC---
---------------.((((...((..(((((((....))))..)))..))..))))-..(....).--- ( -13.70, z-score =  -0.66, R)
>droMoj3.scaffold_6680 2641888 55 - 24764193
---------------UGCUGUCAAUAUGGCAACGUUUAUGACAAACUUGGCUACAAUGAUGGCAAACAGC
---------------((((((((.(.((((...((((.....))))...)))).).))))))))...... ( -14.40, z-score =  -2.10, R)
>droGri2.scaffold_15110 10574724 58 - 24565398
-----UGCUUAUUAUUGCUGUCUAUAUGGCGCCAUUUAUGACAAGCUUGCGCACAGCAAACGC-------
-----.((........((((((((.(((....))).)).))).)))((((.....))))..))------- ( -11.90, z-score =   0.59, R)
>consensus
_______UUU_U_UUUGCUGUCAAUAUGGCGCCAUUUAUGACAAACUGUUCGAUGAUGGCGUC_GACAGC
................(((((....)))))((((((..((..........))..)))))).......... ( -6.20 =  -6.20 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:01:30 2011