Locus 5790

Sequence ID	dm3.chr3L
Location	1,219,871 – 1,219,988
Length	117
Max. P	0.998643

overview

Window 8

Location	1,219,871 – 1,219,988
Length	117
Sequences	6
Columns	129
Reading direction	forward
Mean pairwise identity	57.09
Shannon entropy	0.76122
G+C content	0.46509
Mean single sequence MFE	-33.27
Consensus MFE	-19.58
Energy contribution	-19.72
Covariance contribution	0.14
Combinations/Pair	1.27
Mean z-score	-1.61
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.43
SVM RNA-class probability	0.998643
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1219871 117 + 24543557
-------UAAGCCUAGAUAUAUAAGAUAUACAUAAGAACGCCGCUCCGCUGCUGGCGUACCCGGCAGCGCAGCUACGCGGAUU-AGCCUAAGUCCAA---AUAUAUAAAAAACUGUAAAAUCGGAGAG-
-------..........((((((................((.(((.(((((((((.....))))))))).)))...))(((((-......)))))..---.)))))).....(((......)))....- ( -31.10, z-score =  -1.46, R)
>droSim1.chr3h_random 862046 109 + 1452968
-------UAACUAUAUAUAUGUAGGAAACGCAAAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUGGACUU-AGGCUAAGAAACC---AUUGUAUUUAGAUCGCCAAA---------
-------...(((.((((((.(((((.((((......)))).((.(((((((.(((...))).))))))).))))))).)...-.((........))---..))))).))).........--------- ( -35.90, z-score =  -1.65, R)
>droSec1.super_6 688995 109 - 4358794
-------AAUAUAUAUAUAUGUAGGAAACGCAAAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUU-AGGCUAAGAAACC---AUUGUAUUUAGAUCGCCAAA---------
-------............((.((((.((((......)))).((.(((((((.(((...))).))))))).))))))))....-.(((.........---..............)))...--------- ( -32.70, z-score =  -0.95, R)
>droYak2.chrX_random 1263049 101 - 1802292
------------------GAAUCAAG-AUAU-UAAGAGAGCCGCUCCGCUGCUGUCGUAUCCGGCAGCGCAGCUACGCGGCUU-AGCCUUCGACGAA---AUAUAAUUAAGAAUCACAAAACAGA----
------------------((.((...-....-.....(((((((...((((((((((....)))))..)))))...)))))))-....(((...)))---..........)).))..........---- ( -26.10, z-score =  -0.78, R)
>droEre2.scaffold_4855 234970 104 - 242605
-----------------UAAGCACAG-AUAUAUAAGAGAGCCGCUCCGCUGCUGGCGUAGCUGGCAGCGCAGCUACGCGGUUUUAGGUUUAGCCGAA---AUAUACUUAAGAAUGUAUCGCCAGA----
-----------------........(-((((((...((((((((..((((((..((...))..)))))).......)))))))).((.....))...---............)))))))......---- ( -33.00, z-score =  -0.63, R)
>droPer1.super_81 10280 128 + 277874
UACAUACUAACAUAUAAGGGAUAAGA-ACACAUAGUUCUGCCGCUCCGCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGGCUUUUGGCUUACAAAAGCCCAAAAAAUUCAGAAUAUAAAAACCAAUAAA
..................((...(((-((.....))))).))(((.(((((((((.....))))))))).)))...(.((((((((.....)))))))))............................. ( -40.80, z-score =  -4.21, R)
>consensus
_______UAA___UA_AUAUAUAAGA_ACACAUAAGAGCGCCGCUCCGCUGCUGGCGUAGCCGGCAGCGCAGCUACGCGGCUU_AGGCUAAGAAAAA___AUAUAAUUAAGAAUGUAAAA_C_GA____
.......................................((((((.(((((((((.....))))))))).))).....)))................................................ (-19.58 = -19.72 +   0.14)

alignment

secondary structure

dotplot

Window 9

Location	1,219,871 – 1,219,988
Length	117
Sequences	6
Columns	129
Reading direction	reverse
Mean pairwise identity	57.09
Shannon entropy	0.76122
G+C content	0.46509
Mean single sequence MFE	-33.41
Consensus MFE	-17.70
Energy contribution	-18.53
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-0.82
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.65
SVM RNA-class probability	0.958110
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1219871 117 - 24543557
-CUCUCCGAUUUUACAGUUUUUUAUAUAU---UUGGACUUAGGCU-AAUCCGCGUAGCUGCGCUGCCGGGUACGCCAGCAGCGGAGCGGCGUUCUUAUGUAUAUCUUAUAUAUCUAGGCUUA-------
-...(((((....................---)))))..((((((-.....((((.(((.((((((.((.....)).)))))).))).))))...((((((.....))))))....))))))------- ( -34.15, z-score =  -0.79, R)
>droSim1.chr3h_random 862046 109 - 1452968
---------UUUGGCGAUCUAAAUACAAU---GGUUUCUUAGCCU-AAGUCCAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUUUGCGUUUCCUACAUAUAUAUAGUUA-------
---------...(((.....((((.....---.))))....))).-......((((((.(((((((.(((...))).))))))).))(((((......)))))))))...............------- ( -35.40, z-score =  -1.63, R)
>droSec1.super_6 688995 109 + 4358794
---------UUUGGCGAUCUAAAUACAAU---GGUUUCUUAGCCU-AAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUUUGCGUUUCCUACAUAUAUAUAUAUU-------
---------....((..............---.((((((..((..-..))..)))))).(((((((.(((...))).))))))).))(((((......)))))...................------- ( -35.60, z-score =  -1.80, R)
>droYak2.chrX_random 1263049 101 + 1802292
----UCUGUUUUGUGAUUCUUAAUUAUAU---UUCGUCGAAGGCU-AAGCCGCGUAGCUGCGCUGCCGGAUACGACAGCAGCGGAGCGGCUCUCUUA-AUAU-CUUGAUUC------------------
----...(...((((((.....)))))).---..)....((((..-.((((((....((((((((.((....)).)))).)))).)))))).)))).-....-........------------------ ( -27.30, z-score =   0.13, R)
>droEre2.scaffold_4855 234970 104 + 242605
----UCUGGCGAUACAUUCUUAAGUAUAU---UUCGGCUAAACCUAAAACCGCGUAGCUGCGCUGCCAGCUACGCCAGCAGCGGAGCGGCUCUCUUAUAUAU-CUGUGCUUA-----------------
----................((((((((.---...((.....)).......((...(((.((((((..((...))..)))))).))).))............-.))))))))----------------- ( -25.60, z-score =   1.17, R)
>droPer1.super_81 10280 128 - 277874
UUUAUUGGUUUUUAUAUUCUGAAUUUUUUGGGCUUUUGUAAGCCAAAAGCCGCGGAGCUGCGCUGCCAGUGACGCCGGCAGCGGAGCGGCAGAACUAUGUGU-UCUUAUCCCUUAUAUGUUAGUAUGUA
............(((((.((((........((((((((.....))))))))..((((((.(((((((.(.....).))))))).)))...(((((.....))-)))..)))........)))).))))) ( -42.40, z-score =  -2.01, R)
>consensus
____UC_G_UUUGACAUUCUUAAUUAUAU___UUUGUCUAAGCCU_AAGCCGCGGAGCUGCGCUGCCGGCUACGCCAGCAGCGGAGCGGCGCUCUUAUGUAU_UCUUACAUAU_UA___UUA_______
.....................................................(..(((.((((((.((.....)).)))))).)))..)....................................... (-17.70 = -18.53 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:55:10 2011