Locus 6975

Sequence ID dm3.chr3L
Location 11,239,470 – 11,239,566
Length 96
Max. P 0.748104
window9600 window9601

overview

Window 0

Location 11,239,470 – 11,239,566
Length 96
Sequences 12
Columns 120
Reading direction forward
Mean pairwise identity 64.74
Shannon entropy 0.65389
G+C content 0.54125
Mean single sequence MFE -33.58
Consensus MFE -12.46
Energy contribution -12.73
Covariance contribution 0.27
Combinations/Pair 1.21
Mean z-score -1.49
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.748104
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11239470 96 + 24543557
-----------AAAUGAAACGUUGCCGUUGAGCAACUUGAUUC----CAAUGGACUUG-----GCUCACUCAGUGAGUGAAAAACGGCAACGGCGCACGAGAGCC----GUGUGUGCAGG
-----------........((((((((((............((----(...))).((.-----((((((...)))))).)).))))))))))(((((((.....)----))))))..... ( -34.60, z-score =  -2.13, R)
>droSim1.chr3L 10633772 96 + 22553184
-----------AAAUGAAACGUUGCCGUUGAGCAACUUGAUUC----CAAUGGACUUG-----GCUCACUCAGUGAGUGAAAAUCGGCAACGGCGCACAAGAGCC----GUGUGUGCAGG
-----------........(((((((((..(((...(((....----)))..).))..-----))((((((...)))))).....)))))))(((((((......----.)))))))... ( -34.80, z-score =  -2.28, R)
>droSec1.super_0 3461189 96 + 21120651
-----------AAAUGAAACGUUGCCGUUGAGCAACUUGAUUC----CAAUGGACUUG-----GCUCACUCAGUGAGUGAAAAACGGCAACGGCGCACAAGAGCC----GUGUGUGCAGG
-----------........((((((((((............((----(...))).((.-----((((((...)))))).)).))))))))))(((((((......----.)))))))... ( -34.80, z-score =  -2.33, R)
>droYak2.chr3L 11280166 96 + 24197627
-----------AAAUGAAACGUUGCCGUUGAGCAACUUGAUUC----CAAUGGACGCG-----GCUCACUCAGUGAGUGAAAAUUGGCAACGGCGCACAAGAGCC----GUGUGUGCAGG
-----------........(((((((((((..(...(((....----)))..)...))-----))((((((...)))))).....)))))))(((((((......----.)))))))... ( -31.70, z-score =  -0.97, R)
>droEre2.scaffold_4784 11250414 96 + 25762168
-----------AAAUGAAACGUUGCCGUUGAGCAACUUGAUUC----CAAUGGACGCG-----GCUCACUCAGUGAGUGAAAAUUGGCAACGGCGCACAAGAGCC----GUGUGUGCAGG
-----------........(((((((((((..(...(((....----)))..)...))-----))((((((...)))))).....)))))))(((((((......----.)))))))... ( -31.70, z-score =  -0.97, R)
>droAna3.scaffold_13337 5534574 100 + 23293914
-----------AGAUGAAACGUUGCCGUUGAGCAACUGGCUUC----CAGGCCGCUUU-----UCUCACUCAGUAACUGAAAAUCGGCAACGCUGCCCCUAGCCCCAUCGUGUGUGCAGG
-----------.((((....(((((((.((((....(((((..----..)))))....-----.)))).((((...))))....)))))))((((....))))..))))........... ( -28.60, z-score =  -0.49, R)
>dp4.chrXR_group6 2854433 103 - 13314419
AACGUUGACGAGGAAGCAACGUUGCCGUUGAGCAACUCGUUCC----CAGGCAGCUCG-----UCUGGCCCAGUGUGUGAAAAUCGGCAACAGUGCACUGU--------GUGCAGGCAGG
...((((.(......)))))((((((...((((.....)))).----..))))))..(-----((((((.(((((..((.....)(....).)..))))).--------)).)))))... ( -34.80, z-score =   0.15, R)
>droPer1.super_20 1458764 103 - 1872136
AACGUUGACGAGGAAGCAACGUUGCCGUUGAGCAACUCGUUCC----CAGGCAGCUCG-----UCUGGCCCAGUGUGUGAAAAUCGGCAACAGUGCACUGU--------GUGCAGGCAGG
...((((.(......)))))((((((...((((.....)))).----..))))))..(-----((((((.(((((..((.....)(....).)..))))).--------)).)))))... ( -34.80, z-score =   0.15, R)
>droWil1.scaffold_180698 1635202 106 + 11422946
----AACACACAGAUGAAACGUUGCCGUUGAGCAACUCGUUUGGUGUUUGUCAGCCGAUCAGAGCUUGCCAAGUAAGUGAAAAACGGCAACAGUGCAACCCAGCAGCAGG----------
----(((((.(((((((...(((((......)))))))))))))))))(((..((((......((((((...))))))......)))).....(((......))))))..---------- ( -30.70, z-score =  -0.70, R)
>droVir3.scaffold_13049 1542571 81 - 25233164
-----------GAGCGCGACGUUGCCGUUGUACAACUCGUUUG----CAGGCGGCUCA-----GCUCACAAUGUGAGUGAAAAACGGCAACAAGGCG---CAGG----------------
-----------..((((...(((((((((.....((((..(((----..(((......-----)))..)))...))))....)))))))))...)))---)...---------------- ( -32.70, z-score =  -2.28, R)
>droGri2.scaffold_15110 13973502 81 + 24565398
-----------GAGUGCAACGUUGCCGUUGUUGAACUCGUUUG----UUGGCGGCUCA-----GCUUGCAGAGUGAGUGAAAAACGGCAACGAUGCG--UAAG-----------------
-----------....(((.((((((((((.....(((((((((----(.(((......-----))).))))).)))))....)))))))))).))).--....----------------- ( -36.60, z-score =  -4.23, R)
>droMoj3.scaffold_6680 6454149 81 - 24764193
-----------GAGCGCGACGUUGCCGCCGCUGAACUCGUUUG----CAGGCGGCUCA-----GCUCGCACCGUGAGUGAAAAUCGGCAACAGCGUG---CAGU----------------
-----------..(((((..((((((((((((...(......)----..))))))(((-----.(((((...)))))))).....))))))..))))---)...---------------- ( -37.20, z-score =  -1.73, R)
>consensus
___________AAAUGAAACGUUGCCGUUGAGCAACUCGUUUC____CAGGCGGCUCG_____GCUCACUCAGUGAGUGAAAAUCGGCAACGGCGCACAAGAGCC____GUGUGUGCAGG
....................(((((((((....)))............................(((((...)))))........))))))............................. (-12.46 = -12.73 +   0.27)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,239,470 – 11,239,566
Length 96
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 64.74
Shannon entropy 0.65389
G+C content 0.54125
Mean single sequence MFE -29.67
Consensus MFE -11.58
Energy contribution -11.53
Covariance contribution -0.05
Combinations/Pair 1.38
Mean z-score -1.22
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.613071
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11239470 96 - 24543557
CCUGCACACAC----GGCUCUCGUGCGCCGUUGCCGUUUUUCACUCACUGAGUGAGC-----CAAGUCCAUUG----GAAUCAAGUUGCUCAACGGCAACGUUUCAUUU-----------
...((((....----.......))))..((((((((((.(((((((...)))))))(-----(((.....)))----).............))))))))))........----------- ( -29.70, z-score =  -1.91, R)
>droSim1.chr3L 10633772 96 - 22553184
CCUGCACACAC----GGCUCUUGUGCGCCGUUGCCGAUUUUCACUCACUGAGUGAGC-----CAAGUCCAUUG----GAAUCAAGUUGCUCAACGGCAACGUUUCAUUU-----------
...(((((...----......)))))..((((((((((((((((((...)))))))(-----(((.....)))----)))))..(((....))))))))))........----------- ( -29.70, z-score =  -1.86, R)
>droSec1.super_0 3461189 96 - 21120651
CCUGCACACAC----GGCUCUUGUGCGCCGUUGCCGUUUUUCACUCACUGAGUGAGC-----CAAGUCCAUUG----GAAUCAAGUUGCUCAACGGCAACGUUUCAUUU-----------
...(((((...----......)))))..((((((((((.(((((((...)))))))(-----(((.....)))----).............))))))))))........----------- ( -30.70, z-score =  -2.17, R)
>droYak2.chr3L 11280166 96 - 24197627
CCUGCACACAC----GGCUCUUGUGCGCCGUUGCCAAUUUUCACUCACUGAGUGAGC-----CGCGUCCAUUG----GAAUCAAGUUGCUCAACGGCAACGUUUCAUUU-----------
...(((((...----......)))))..(((((((.......((((...))))((((-----.((.(((...)----)).....)).))))...)))))))........----------- ( -27.90, z-score =  -1.13, R)
>droEre2.scaffold_4784 11250414 96 - 25762168
CCUGCACACAC----GGCUCUUGUGCGCCGUUGCCAAUUUUCACUCACUGAGUGAGC-----CGCGUCCAUUG----GAAUCAAGUUGCUCAACGGCAACGUUUCAUUU-----------
...(((((...----......)))))..(((((((.......((((...))))((((-----.((.(((...)----)).....)).))))...)))))))........----------- ( -27.90, z-score =  -1.13, R)
>droAna3.scaffold_13337 5534574 100 - 23293914
CCUGCACACACGAUGGGGCUAGGGGCAGCGUUGCCGAUUUUCAGUUACUGAGUGAGA-----AAAGCGGCCUG----GAAGCCAGUUGCUCAACGGCAACGUUUCAUCU-----------
...........(((((.((.....))((((((((((...(((((...)))))((((.-----..((((((...----...))).))).)))).))))))))))))))).----------- ( -34.20, z-score =  -0.85, R)
>dp4.chrXR_group6 2854433 103 + 13314419
CCUGCCUGCAC--------ACAGUGCACUGUUGCCGAUUUUCACACACUGGGCCAGA-----CGAGCUGCCUG----GGAACGAGUUGCUCAACGGCAACGUUGCUUCCUCGUCAACGUU
..((((((...--------.))).)))..(((((((...........(((...))).-----.((((.((.((----....)).)).))))..)))))))(((((......).))))... ( -30.60, z-score =   0.32, R)
>droPer1.super_20 1458764 103 + 1872136
CCUGCCUGCAC--------ACAGUGCACUGUUGCCGAUUUUCACACACUGGGCCAGA-----CGAGCUGCCUG----GGAACGAGUUGCUCAACGGCAACGUUGCUUCCUCGUCAACGUU
..((((((...--------.))).)))..(((((((...........(((...))).-----.((((.((.((----....)).)).))))..)))))))(((((......).))))... ( -30.60, z-score =   0.32, R)
>droWil1.scaffold_180698 1635202 106 - 11422946
----------CCUGCUGCUGGGUUGCACUGUUGCCGUUUUUCACUUACUUGGCAAGCUCUGAUCGGCUGACAAACACCAAACGAGUUGCUCAACGGCAACGUUUCAUCUGUGUGUU----
----------(((......)))..((((((((((((((....((((..((((..((((......))))........))))..)))).....))))))))))........))))...---- ( -24.30, z-score =   1.34, R)
>droVir3.scaffold_13049 1542571 81 + 25233164
----------------CCUG---CGCCUUGUUGCCGUUUUUCACUCACAUUGUGAGC-----UGAGCCGCCUG----CAAACGAGUUGUACAACGGCAACGUCGCGCUC-----------
----------------...(---(((..((((((((((...(((((...((((..((-----......))..)----)))..))).))...))))))))))..))))..----------- ( -32.60, z-score =  -3.42, R)
>droGri2.scaffold_15110 13973502 81 - 24565398
-----------------CUUA--CGCAUCGUUGCCGUUUUUCACUCACUCUGCAAGC-----UGAGCCGCCAA----CAAACGAGUUCAACAACGGCAACGUUGCACUC-----------
-----------------....--.(((.((((((((((.((.((((.(((.......-----.)))..(....----)....))))..)).)))))))))).)))....----------- ( -25.50, z-score =  -3.43, R)
>droMoj3.scaffold_6680 6454149 81 + 24764193
----------------ACUG---CACGCUGUUGCCGAUUUUCACUCACGGUGCGAGC-----UGAGCCGCCUG----CAAACGAGUUCAGCGGCGGCAACGUCGCGCUC-----------
----------------...(---(.((.((((((((..((.(((.....))).))((-----(((((((....----....)).)))))))..)))))))).)).))..----------- ( -32.30, z-score =  -0.72, R)
>consensus
CCUGCACACAC____GGCUCUUGUGCGCCGUUGCCGAUUUUCACUCACUGAGUGAGC_____CGAGCCGACUG____GAAACGAGUUGCUCAACGGCAACGUUUCAUUU___________
............................(((((((........(((.......)))............................(((....))))))))))................... (-11.58 = -11.53 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:18:04 2011