Locus 6308

Sequence ID	dm3.chr3L
Location	5,428,646 – 5,428,777
Length	131
Max. P	0.974364

overview

Window 3

Location	5,428,646 – 5,428,777
Length	131
Sequences	11
Columns	143
Reading direction	forward
Mean pairwise identity	75.01
Shannon entropy	0.52722
G+C content	0.52131
Mean single sequence MFE	-35.91
Consensus MFE	-27.36
Energy contribution	-27.35
Covariance contribution	-0.01
Combinations/Pair	1.23
Mean z-score	-1.33
Structure conservation index	0.76
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.91
SVM RNA-class probability	0.974364
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5428646 131 + 24543557
--UAUCAACCUGCUUUUCCGUUUCCAUC----------UCUCUUUAUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
--........(((.(((((((.......----------.........................(((..(((((((((.........))))))))).))).((((..((((....))))...))))..))))))).)))..... ( -36.30, z-score =  -1.88, R)
>droGri2.scaffold_15110 7979056 125 + 24565398
----UCUACUUUCACUUCGCUUCGCGUC----------UCUUCAA----AUAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCGCAUCCCA
----...................(((((----------((.....----...(.(.((((((((((((((...)))))))).....)))))).).).(.(((((..((((....))))...))))))...)))))))...... ( -38.90, z-score =  -1.98, R)
>droMoj3.scaffold_6680 9464392 120 + 24764193
--------UCUGCUUCUCUCCAUUCACC----------UCUCUU-----GCAGUCUCGCCCAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCCCAUCCCA
--------..................((----------((....-----((((((..(((..((((((((...))))))))....(((((....))))).)))...((((....))))))))))......))))......... ( -33.70, z-score =  -0.78, R)
>droVir3.scaffold_13049 11361757 120 + 25233164
----UCUACUUUC--UCUGCCCCGCG-------------CUUUAU----UCAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCUCAUCCCA
----.........--...(((.((.(-------------......----.(((((..((((.((((((((...))))))))....(((((....)))))))))...((((....))))))))).....))).)))........ ( -32.60, z-score =  -0.36, R)
>droAna3.scaffold_13337 10178457 122 - 23293914
--UAUCAA--AAAUCUCUCUUUUUCAUU------------UCAA-----ACAGUUUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCACAUCCCA
--......--..................------------....-----........(((........(((((((((.........)))))))))..(((((((..((((....))))...))))....))))))........ ( -31.20, z-score =  -1.51, R)
>droEre2.scaffold_4784 8122021 131 + 25762168
--UAUCAACCAGCUUUUCCGUUUCCACC----------CCUCUGUAUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
--.........((.(((((((.......----------...((((....))))..........(((..(((((((((.........))))))))).))).((((..((((....))))...))))..))))))).))...... ( -37.30, z-score =  -1.73, R)
>droYak2.chr3L 5997706 140 + 24197627
--UAUCAACCUGCUUUUCCGUUUCCCUCUCUUAUUCC-CCUCUCUAUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCUCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
--........(((.(((((((................-..................((((((((((((((...)))))))).....))))))........((((..((((....))))...))))..))))))).)))..... ( -35.60, z-score =  -1.76, R)
>droSec1.super_2 5373795 131 + 7591821
--UAUCAACCUGUUUUUCCGUUUCCAUC----------CCUCUUCAUCCACAGUCUCGCCGAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
--...((((..(((.(((.((......(----------((...(((((..(......)..)))))...))).)).)))..)))..))))(((((((....((((..((((....))))...))))....)).)))))...... ( -38.10, z-score =  -1.89, R)
>droSim1.chr3L 4943248 131 + 22553184
--UAUCAACCUGUUUUUCCGUUUCCAUC----------CCUCUAUUUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
--................(((((((...----------.........................(((..(((((((((.........))))))))).))).((((..((((....))))...))))....)))))))....... ( -34.80, z-score =  -1.40, R)
>apiMel3.GroupUn 202380634 113 - 399230636
---------CCGAAUCCUUCGUUCGAUG------------UUUA-------AGUUUCGCCGAUGAUCUUCGUGCCGAAUCAGCUGGUCGGCGCACCGGCUGGCACGAACGUAACGAUCGAUUGUCACACGGAGGCUUAUCC--
---------......((((((((((...------------....-------.(.((((((((......))).).)))).).((..(((((....)))))..)).)))))((.((((....)))).))..))))).......-- ( -36.00, z-score =  -0.31, R)
>triCas2.ChLG1X 7529755 143 - 8109244
GAUCGUGAUUCGUUUUCGCUUUCGCAUUUGUAAAUAAAUGUGUUUUGUUACAGUUUCUCCGAUGAUUUGGGUUCCAAAUCAGUUGGUCGGGGCACCAGCCGGCACGGAUGUCACAAUAGACUGCCAUACAGAGGCAUACCCAA
((..((((.......))))..))((.((((((.......((.(.((((.(((.....((((.((((((((...))))))))((((((.((....)).)))))).))))))).)))).).)).....)))))).))........ ( -40.50, z-score =  -1.02, R)
>consensus
__UAUCAACCUGCUUUUCCGUUUCCAUC__________CCUCUAU____ACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCA
....................................................((((((((((((((((((...)))))))).....))))).........((((..((((....))))...)))).....)))))........ (-27.36 = -27.35 +  -0.01)

alignment

secondary structure

dotplot

Window 4

Location	5,428,646 – 5,428,777
Length	131
Sequences	11
Columns	143
Reading direction	reverse
Mean pairwise identity	75.01
Shannon entropy	0.52722
G+C content	0.52131
Mean single sequence MFE	-42.61
Consensus MFE	-20.41
Energy contribution	-20.71
Covariance contribution	0.30
Combinations/Pair	1.19
Mean z-score	-1.30
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.18
SVM RNA-class probability	0.580353
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5428646 131 - 24543557
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGUGGAUAAAGAGA----------GAUGGAAACGGAAAAGCAGGUUGAUA--
......(((((.((((.(((((...((((....))))..))))).)))))))))((((..(((..((((....(((..(((((.(((....))).))).....))----------..)))...))))..)))..))))...-- ( -44.70, z-score =  -1.62, R)
>droGri2.scaffold_15110 7979056 125 - 24565398
UGGGAUGCGCCUCGGUGUGGCAAUCGAUGGUUACAUCUGUGCCAGCUGGCGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUAU----UUGAAGA----------GACGCGAAGCGAAGUGAAAGUAGA----
......(((((..(((.(((((...((((....))))..)))))))))))))(((((.....(((((.((...)).))))))))))....((((----((.....----------..(((...)))......)))))).---- ( -38.52, z-score =   0.02, R)
>droMoj3.scaffold_6680 9464392 120 - 24764193
UGGGAUGGGCCUCGGUGUGGCAAUCGAUGGUUACAUCUGUGCCAGCUGGCGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUGGGCGAGACUGC-----AAGAGA----------GGUGAAUGGAGAGAAGCAGA--------
........(((((..((((((....((((....)))).(((((....))))))))....((((...(((...((((.....)))))))))))))-----)...))----------))).................-------- ( -35.60, z-score =   1.01, R)
>droVir3.scaffold_13049 11361757 120 - 25233164
UGGGAUGAGCCUCGGUGUGGCAAUCGAUGGUUACAUCUGUGCCAGCUGGCGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGA----AUAAAG-------------CGCGGGGCAGA--GAAAGUAGA----
........((((((((.((((....((((....)))).(((((....)))))))))))..(((.(((((((.(((((....)))).).).))))----))..))-------------).))))))...--.........---- ( -40.50, z-score =  -0.69, R)
>droAna3.scaffold_13337 10178457 122 + 23293914
UGGGAUGUGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAAACUGU-----UUGA------------AAUGAAAAAGAGAGAUUU--UUGAUA--
((((..(((((.((((.(((((...((((....))))..))))).)))))))))......((((...)))).))))..(((((..((((....)-----))).------------))))).............--......-- ( -38.90, z-score =  -1.51, R)
>droEre2.scaffold_4784 8122021 131 - 25762168
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGUGGAUACAGAGG----------GGUGGAAACGGAAAAGCUGGUUGAUA--
......(((((.((((.(((((...((((....))))..))))).)))))))))((((.((((..((((.(((((...((......))..((.((....)).)))----------))))....))))..)))).))))...-- ( -52.30, z-score =  -2.80, R)
>droYak2.chr3L 5997706 140 - 24197627
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGAGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGUGGAUAGAGAGG-GGAAUAAGAGAGGGAAACGGAAAAGCAGGUUGAUA--
......((((.(((((.(((((...((((....))))..))))).)))))))))((((..(((..(((....(((...(((((.(((....))).))).))...)-))..........(....))))..)))..))))...-- ( -47.30, z-score =  -2.11, R)
>droSec1.super_2 5373795 131 - 7591821
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUCGGCGAGACUGUGGAUGAAGAGG----------GAUGGAAACGGAAAAACAGGUUGAUA--
......(((((.((((.(((((...((((....))))..))))).)))))))))((((..(((..((((.(((((...(((((.(((....))).)))))...))----------).))....))))..)))..))))...-- ( -52.90, z-score =  -3.39, R)
>droSim1.chr3L 4943248 131 - 22553184
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGUGGAAAUAGAGG----------GAUGGAAACGGAAAAACAGGUUGAUA--
......(((((.((((.(((((...((((....))))..))))).)))))))))((((..(((..((((.(((((...((......))..((((....)))).))----------).))....))))..)))..))))...-- ( -47.60, z-score =  -2.36, R)
>apiMel3.GroupUn 202380634 113 + 399230636
--GGAUAAGCCUCCGUGUGACAAUCGAUCGUUACGUUCGUGCCAGCCGGUGCGCCGACCAGCUGAUUCGGCACGAAGAUCAUCGGCGAAACU-------UAAA------------CAUCGAACGAAGGAUUCGG---------
--......(((.....(((((........))))).(((((((((((.(((......))).))).....)))))))).......)))......-------....------------...(((((....).)))).--------- ( -32.40, z-score =   0.56, R)
>triCas2.ChLG1X 7529755 143 + 8109244
UUGGGUAUGCCUCUGUAUGGCAGUCUAUUGUGACAUCCGUGCCGGCUGGUGCCCCGACCAACUGAUUUGGAACCCAAAUCAUCGGAGAAACUGUAACAAAACACAUUUAUUUACAAAUGCGAAAGCGAAAACGAAUCACGAUC
..(((((((((...((((((..(((......)))..)))))).)))..))))))((......((((((((...))))))))(((.......(((((..............)))))..(((....)))....)))....))... ( -37.94, z-score =  -1.38, R)
>consensus
UGGGAUGCGCCUCCGUGUGGCAAUCGAUGGUUACAUCUGUGCCGGAUGGGGCGCCAACAAGUUGAUUCGGCACCCAAAUCAUUGGCGAGACUGU____AUAGAGA__________GAUGGAAACGGAAAAGCAGGUUGAUA__
.(((.....))).....(((((...((((....))))..)))))...((..((((((.....(((((.((...)).)))))))))))...))................................................... (-20.41 = -20.71 +   0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:05:11 2011