Locus 6018

Sequence ID	dm3.chr3L
Location	3,095,717 – 3,095,869
Length	152
Max. P	0.977201

overview

Window 1

Location	3,095,717 – 3,095,869
Length	152
Sequences	11
Columns	156
Reading direction	forward
Mean pairwise identity	74.11
Shannon entropy	0.56910
G+C content	0.47959
Mean single sequence MFE	-43.05
Consensus MFE	-29.80
Energy contribution	-29.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.94
SVM RNA-class probability	0.975786
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3095717 152 + 24543557
GGUCACUCGAAUCCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGUUGCUCCCCCCAGUCCGAAUACAAAGUAUAU----UUUUUUCUGAUCACU
(((((......((...(((((((....(((.(((.(((...(((......)))..((((((.((.((((((.......))))).).)).))))))..)))...)))..)))..)))))))..))((((...))))..----.......)))))... ( -44.20, z-score =  -0.95, R)
>droSim1.chr3L 2618613 150 + 22553184
GGUCGCGCGAACUCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUGCUCCCC--AGUUCAAAUAUAAAGUAUAU----UUUUUUCUGAUCAGU
((((...........(((((((((..((((.....(((...(((......)))..((((((.((.((((((.......))))).).)).))))))..))).....)))).)))))--)))).(((((((...)))))----))......))))... ( -47.90, z-score =  -1.95, R)
>droSec1.super_2 3089240 149 + 7591821
GGUCGCGCGAACUCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUGCUCCC---AGUUCAAAUAUAAAGUAUAU----UUUUUUCUGAUCAGC
((((...........((((((((...((((.....(((...(((......)))..((((((.((.((((((.......))))).).)).))))))..))).....)))).))))---)))).(((((((...)))))----))......))))... ( -43.60, z-score =  -0.83, R)
>droYak2.chr3L 15345744 156 - 24197627
GGUCGCGCGAACUCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGUUGCUGCCUGCUCCCCAGUUCUAAAAUGUAUAUAAUUUUCUCUGAUCAGU
(((((.(.((.....(((((((((....((.((((..(((((((......)))..((((((.((.((((((.......))))).).)).)))))).......))))..))))...)))))))))))...((((.......)))))).))))))... ( -48.00, z-score =  -1.26, R)
>droEre2.scaffold_4784 3103888 149 + 25762168
GGUCGCGCGGAGUGCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUCCCC-----AGUUUUACUAAAAUUUAUAUAU--UUUUGUCUGAUCAGU
(((((.(((.((((.(((((((((....((((.......))))........((((((((((.((.((((((.......))))).).)).))))))........)))))))))-----)))).))))(((((......))--)))))).)))))... ( -50.20, z-score =  -2.29, R)
>droAna3.scaffold_13337 14271035 143 - 23293914
AGCCGCGCUUGCUCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUUUUGUUCUUUU------UCCAACCUU--UCUUUAU-----UUUUCCUGAUCAAU
.((.(((..(((((..((((((.......))))))....)))))..)).).)).(((((.((((.((((((.......))))).).))..((((..(((......))).....------.))))....--.......-----...)).)))))... ( -39.10, z-score =  -0.71, R)
>dp4.chrXR_group8 3960930 155 + 9212921
GGCCGGUCGAAGCCCAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGAGUAACCUUUUUUCCUCUUUUUUUUUUACUUAACUC-AACAUUUCAGCUUUCUUUUGAUCAAU
.((.(((((((.(((....)))......((((.......)))).))))))))).((((((((((..(((((.......)))))(((....((((((((....................))))))))...-.))).........))))))))))... ( -44.35, z-score =  -1.30, R)
>droPer1.super_29 192478 154 + 1099123
GGCCGGUCGAAGCCCAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGAGUAACCUUUUUUCCUCUUUUUUUUU-ACUUAUCUC-AACAUUUCAGCGUUCUUUUGAUCAAU
.((.(((((((.(((....)))......((((.......)))).))))))))).((((((((((..(((((.......)))))(((.....(((((((...................))-)))))....-.))).........))))))))))... ( -44.01, z-score =  -1.09, R)
>droVir3.scaffold_13049 144849 116 + 25233164
AGUCGCUCGGUUUGCAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAAC-UUUUUAUUAUAUACAAC---------------------------------------
........(((((((....(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...))))))-)................--------------------------------------- ( -37.20, z-score =  -1.60, R)
>droMoj3.scaffold_6680 23767141 133 - 24764193
AGUCGCUGGCAACGUAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUUUCACAUUAUUUGUUUAUUUAAAAUG-AAUG----------------------
.......(....).(((((((((.....((((.......))))....(((....((((....))))(((((.......))))).))))))))))))..............((((..(((.....)))..-))))---------------------- ( -37.10, z-score =  -0.85, R)
>droGri2.scaffold_15110 1479851 131 + 24565398
AGUCGUCGCAGUUGUAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUUUGUACACAAUGCUUUUUUUAGAAUA-AG------------------------
.......((((((.(((((((((.....((((.......))))....(((....((((....))))(((((.......))))).)))))))))))))))....(((....)))))).............-..------------------------ ( -37.90, z-score =  -1.26, R)
>consensus
GGUCGCGCGAACUCCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUGCUCCCU__UGUUCUAAUAUA_AAUAUAU____UUUUUUCUGAUCAGU
...................(((((((..((((.......))))...........((((....))))(((((.......)))))))))))).................................................................. (-29.80 = -29.80 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	3,095,717 – 3,095,869
Length	152
Sequences	11
Columns	156
Reading direction	reverse
Mean pairwise identity	74.11
Shannon entropy	0.56910
G+C content	0.47959
Mean single sequence MFE	-42.37
Consensus MFE	-28.90
Energy contribution	-28.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.68
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.97
SVM RNA-class probability	0.977201
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3095717 152 - 24543557
AGUGAUCAGAAAAAA----AUAUACUUUGUAUUCGGACUGGGGGGAGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGGAUUCGAGUGACC
...............----...(((((...((((.(((((((((.(((........((((((((..(((....))).)))..)))))(((((.(..(((((.....)))))..).))).)).....)))...))))))))).))))..)))))... ( -50.70, z-score =  -1.43, R)
>droSim1.chr3L 2618613 150 - 22553184
ACUGAUCAGAAAAAA----AUAUACUUUAUAUUUGAACU--GGGGAGCAGCAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGUUCGCGCGACC
...............----...........((((.((((--(((((((((......((....)).(((((...(((((.......)))))..)))))....))))........((((.......))))....))))))))).)))).......... ( -47.70, z-score =  -1.88, R)
>droSec1.super_2 3089240 149 - 7591821
GCUGAUCAGAAAAAA----AUAUACUUUAUAUUUGAACU---GGGAGCAGCAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGUUCGCGCGACC
((((.((((....((----(((((...)))))))...))---))...)))).....((((......(((....)))(..(((.(((.(((((....(((((.....)))))..((((.......))))....))))).))).)))..)....)))) ( -46.40, z-score =  -1.71, R)
>droYak2.chr3L 15345744 156 + 24197627
ACUGAUCAGAGAAAAUUAUAUACAUUUUAGAACUGGGGAGCAGGCAGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGUUCGCGCGACC
..............................(((((((((((((((...........((....)).(((((...(((((.......)))))..))))).).)))))........((((.......))))....)))))))))............... ( -46.50, z-score =  -0.86, R)
>droEre2.scaffold_4784 3103888 149 - 25762168
ACUGAUCAGACAAAA--AUAUAUAAAUUUUAGUAAAACU-----GGGGAGCAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGCACUCCGCGCGACC
...............--.............(((..((((-----((((((((....((....)).(((((...(((((.......)))))..))))).....)))........((((.......))))....)))))))))..))).......... ( -44.40, z-score =  -1.68, R)
>droAna3.scaffold_13337 14271035 143 + 23293914
AUUGAUCAGGAAAA-----AUAAAGA--AAGGUUGGA------AAAAGAACAAAAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGCAAGCGCGGCU
...((((.......-----.......--..(((....------....((((......))))))).(((((...(((((.......)))))..))))).))))...(((((..(((((((..((((...........)))))))))))....))))) ( -39.50, z-score =  -0.38, R)
>dp4.chrXR_group8 3960930 155 - 9212921
AUUGAUCAAAAGAAAGCUGAAAUGUU-GAGUUAAGUAAAAAAAAAAGAGGAAAAAAGGUUACUCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGGGCUUCGACCGGCC
...((((.......((((.(.....)-.)))).............(((((................(....).(((((.......)))))..))))).)))).((.((((((.((((.......))))......(((....))).))))))..)). ( -41.60, z-score =  -0.30, R)
>droPer1.super_29 192478 154 - 1099123
AUUGAUCAAAAGAACGCUGAAAUGUU-GAGAUAAGU-AAAAAAAAAGAGGAAAAAAGGUUACUCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGGGCUUCGACCGGCC
...............((((...(((.-.((((....-.........(((............))).(((((...(((((.......)))))..)))))..)))))))((((((.((((.......))))......(((....))).)))))))))). ( -42.00, z-score =  -0.45, R)
>droVir3.scaffold_13049 144849 116 - 25233164
---------------------------------------GUUGUAUAUAAUAAAAA-GUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGCAAACCGAGCGACU
---------------------------------------(((((............-.........(((....))).((((((..(.(((((....(((((.....)))))..((((.......))))....))))).)...))))))..))))). ( -36.10, z-score =  -2.22, R)
>droMoj3.scaffold_6680 23767141 133 + 24764193
----------------------CAUU-CAUUUUAAAUAAACAAAUAAUGUGAAAAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUACGUUGCCAGCGACU
----------------------..((-(((.(((..........))).)))))....((((((((.(((....)))))))..)))).(((((....(((((.....)))))..((((.......))))....)))))......((((....)))). ( -33.90, z-score =  -1.19, R)
>droGri2.scaffold_15110 1479851 131 - 24565398
------------------------CU-UAUUCUAAAAAAAGCAUUGUGUACAAAAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUACAACUGCGACGACU
------------------------..-.............(((((((((........((((((((.(((....)))))))..)))).(((((....(((((.....)))))..((((.......))))....)))))..)))))).)))....... ( -37.30, z-score =  -2.41, R)
>consensus
ACUGAUCAGAAAAAA____AUAUACU_UAUAUUAGAAAA__AGAAAGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGUUCGAGCGACC
..................................................................(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))................... (-28.90 = -28.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:59:43 2011