Locus 4601

Sequence ID	dm3.chr2R
Location	14,461,269 – 14,461,406
Length	137
Max. P	0.994627

overview

Window 7

Location	14,461,269 – 14,461,373
Length	104
Sequences	7
Columns	107
Reading direction	forward
Mean pairwise identity	63.79
Shannon entropy	0.70146
G+C content	0.37598
Mean single sequence MFE	-22.40
Consensus MFE	-13.12
Energy contribution	-14.03
Covariance contribution	0.90
Combinations/Pair	1.42
Mean z-score	-1.40
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.72
SVM RNA-class probability	0.994627
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14461269 104 + 21146708
-UUUGUAGUUGGAGGGGGGAGGAGUAGGUAGGCUUUGUAUAUUUUGUUGUUGCCUU--UACCGCUUGAUUAAUUUUUGGUGCGUUUGGCAACAGCGAAAAACUUUUA
-........((((((.....(((((......))))).....(((((((((((((..--.((((((.((......)).)))).))..)))))))))))))..)))))) ( -28.10, z-score =  -1.68, R)
>droSim1.chr2R 13176938 99 + 19596830
-UUUUUGGUAGGUGGGGGGAGG----GGUAGGCUUUGUAUAUUUUGUUGUUGCCUU--UACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUA
-...........((((((((((----......)))).....(((((((((((((..--.((((((.((.....)).-)))).))..)))))))))))))..)))))) ( -25.50, z-score =  -1.12, R)
>droSec1.super_1 11929886 99 + 14215200
-UUUUUGGUAGGUGGGGGGAGG----GGUAGGCUUUGUAUAUUUUGUUGUUGCCUU--UACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUA
-...........((((((((((----......)))).....(((((((((((((..--.((((((.((.....)).-)))).))..)))))))))))))..)))))) ( -25.50, z-score =  -1.12, R)
>droYak2.chr2R 6411095 87 - 21139217
-----------------UCUACUUUUGUUGGGUUUUGAAUAUUUUGUUGUUGCCUU--UACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUA
-----------------((.((((.....))))...))...(((((((((((((..--.((((((.((.....)).-)))).))..)))))))))))))........ ( -24.10, z-score =  -3.52, R)
>droEre2.scaffold_4845 8663928 98 + 22589142
UCGUUUUGUUGUUGGGGAGGGG------GAGCCUUUGAAUAUUUUGUUGUUGCCUU--UACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUA
..(((((.........(((((.------...))))).......(((((((((((..--.((((((.((.....)).-)))).))..))))))))))))))))..... ( -29.00, z-score =  -2.13, R)
>droWil1.scaffold_180699 1075864 86 + 2593675
--------------------AUCGUUGCUUGGUUUUCGCUUUUUUUUUUCUUUUUUGGUAACGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUA
--------------------............(((((((....................((((((..(......).-.).)))))((....)))))))))....... ( -15.70, z-score =  -0.59, R)
>droGri2.scaffold_15074 590753 84 + 7742996
-----------------CCCAAAGUUGUCAAAAAUUCUGAAUGAAAAUCUUGUGUC--AAAAGCUUACUUUGAUUCUCCCUGAUUUGAAGAAGAUAAAAAUCA----
-----------------.......(((((.....(((.....)))...........--.........(((..(.((.....)).)..)))..)))))......---- (  -8.90, z-score =   0.38, R)
>consensus
___U_U_GU_G__GGGGGGAGG__U_GGUAGGCUUUGUAUAUUUUGUUGUUGCCUU__UACCGCUUGAUUAAUUUU_GGUGCGUUUGGCAACAGCGAAAAACUUUUA
.........................................(((((((((((((.......((((.((......)).)))).....)))))))))))))........ (-13.12 = -14.03 +   0.90)

alignment

secondary structure

dotplot

Window 8

Location	14,461,308 – 14,461,406
Length	98
Sequences	8
Columns	103
Reading direction	forward
Mean pairwise identity	71.71
Shannon entropy	0.59507
G+C content	0.37232
Mean single sequence MFE	-25.14
Consensus MFE	-10.10
Energy contribution	-11.97
Covariance contribution	1.88
Combinations/Pair	1.44
Mean z-score	-2.57
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.47
SVM RNA-class probability	0.991285
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14461308 98 + 21146708
--AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUUUGGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCUCGAUGCCACUUUAUGUGAG---
--.(((((((((((((...((((((.((......)).)))).))..)))))))))))))..........(((((........)))))(((.....)))..--- ( -31.20, z-score =  -4.42, R)
>droSim1.chr2R 13176973 99 + 19596830
--AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCUCGAUGCCACUUUAUGUGAGUG-
--.(((((((((((((...((((((.((.....)).-)))).))..)))))))))))))..........(((((........)))))(((((.....)))))- ( -32.10, z-score =  -4.44, R)
>droSec1.super_1 11929921 99 + 14215200
--AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUAAUGCGUCAUUUUCUCGAUGCCACUUUAUCUGAGUG-
--.(((((((((((((...((((((.((.....)).-)))).))..)))))))))))))..........(((((........)))))(((((.....)))))- ( -31.90, z-score =  -4.94, R)
>droYak2.chr2R 6411118 100 - 21139217
--AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCUCGAUGCCGCUUUCUGUGUGUAU
--.(((((((((((((...((((((.((.....)).-)))).))..))))))))))))).((....((((((.((((.....)))).))))))....)).... ( -32.10, z-score =  -4.32, R)
>droEre2.scaffold_4845 8663962 99 + 22589142
--AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCUCGAUGCCGCAUUCGGUGUGUG-
--.(((((((((((((...((((((.((.....)).-)))).))..)))))))))))))..........(((((........)))))(((((.....)))))- ( -31.80, z-score =  -3.26, R)
>dp4.chr3 11031057 93 - 19779522
---------UUUUGUUUUAACCGCUUGAUUAAUUUU-UGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCCCUGUGCCUCUGUGCCGCUGUGC
---------...((((..((((((..((.....)).-.))).))).))))((((((....((.......(((.((.......)))))....))..)))))).. ( -14.80, z-score =   1.20, R)
>droWil1.scaffold_180699 1075884 89 + 2593675
UUUUUUUUUCUUUUUUGGUAACGCUUGAUUAAUUUU-GGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCCUCAUUUGGUUGGUAUGUG-------------
....((((((.((.(((.(((((((..(......).-.).))).))).))).)).)))))).......((((......))))........------------- ( -14.50, z-score =   0.46, R)
>droGri2.scaffold_15074 590776 88 + 7742996
--AUGAAAAUCUUGUGUCAAAAGCUUACUUUGAUUCUCCCUGAUUUGAAGAAGAUAAAAA----UCAAAUCUUCAUGUUUUUGUAACUCUUUUA---------
--...........((..(((((((....((..(.((.....)).)..))((((((.....----....))))))..)))))))..)).......--------- ( -12.70, z-score =  -0.84, R)
>consensus
__AUUUUGUUGUUGCCUUUACCGCUUGAUUAAUUUU_GGUGCGUUUGGCAACAGCGAAAAACUUUUAAAGCGUCAUUUUCUCGAUGCCACUUUAUGUGAGUG_
...(((((((.(((((...((((((.((......)).)))).))..))))).)))))))..........(((((........)))))................ (-10.10 = -11.97 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:32:19 2011