Locus 1053

Sequence ID dm3.chr2L
Location 7,913,491 – 7,913,613
Length 122
Max. P 0.830873
window1437 window1438 window1439

overview

Window 7

Location 7,913,491 – 7,913,583
Length 92
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 91.29
Shannon entropy 0.16308
G+C content 0.46270
Mean single sequence MFE -22.49
Consensus MFE -19.84
Energy contribution -19.32
Covariance contribution -0.53
Combinations/Pair 1.22
Mean z-score -1.32
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7913491 92 + 23011544
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUU-CCCACAAAUCGGUGCGUGGCCGUUAUAUAUAU
.......(((((((...(((((((....................))))-)))......((.-((........)).))..)))))))........ ( -20.45, z-score =  -0.84, R)
>droAna3.scaffold_12943 3646246 89 - 5039921
UUCAAUCGAUGGCCUAUGAAUGAGUGUUCCUCUAAUUCUGUU-UCCCGGUUCCUGGAAAUUGCCCGCGAAUCGGUGCGUGGCCGUUAUAC----
.......(((((((...(((((((.....)))..)))).((.-..(((((((.(((.......))).))))))).))..)))))))....---- ( -26.00, z-score =  -1.86, R)
>droEre2.scaffold_4929 16835591 88 + 26641161
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUC-CCCACAAAUCGGUGCGUGGCCGUUAUAU----
.......(((((((...(((((((....................))))-)))......(..-((........))..)..)))))))....---- ( -20.95, z-score =  -1.04, R)
>droYak2.chr2L 17343214 89 - 22324452
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCUUCCCGGUUCCUGGAAGUA-CCCACAAAUCGGUGCGUGGCCGUUAUAU----
.......(((((((.(((...(((((.......))))).......((((((..(((.....-.)))..))))))..))))))))))....---- ( -24.20, z-score =  -1.52, R)
>droSec1.super_3 3427877 88 + 7220098
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUC-CCCACAAAUCGGUGCGUGGCCGUUAUAU----
.......(((((((...(((((((....................))))-)))......(..-((........))..)..)))))))....---- ( -20.95, z-score =  -1.04, R)
>droSim1.chr2L_random 411951 88 + 909653
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCAUCCCG-UUCCUGGAAGUC-UCCACAAAUCGGUGCGUGGCCGUUAUAU----
.......(((((((.((((..(((((.......)))))..)))).(((-((..((((....-))))..)).))).....)))))))....---- ( -22.40, z-score =  -1.65, R)
>consensus
UUCAAUCAAUGGCCUAUGAAUGGGUGUUUCUCUCACUUUAUCUUCCCG_UUCCUGGAAGUC_CCCACAAAUCGGUGCGUGGCCGUUAUAU____
.......(((((((.(((...(((((.......))))).......(((.((..(((.......)))..)).)))..))))))))))........ (-19.84 = -19.32 +  -0.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,913,491 – 7,913,583
Length 92
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 91.29
Shannon entropy 0.16308
G+C content 0.46270
Mean single sequence MFE -22.67
Consensus MFE -20.10
Energy contribution -20.02
Covariance contribution -0.08
Combinations/Pair 1.15
Mean z-score -1.57
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.796261
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7913491 92 - 23011544
AUAUAUAUAACGGCCACGCACCGAUUUGUGGG-AACUUCCAGGAA-CGGGAAGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
...........((((.....(((.(((.((((-....)))).)))-)))...((....(((.......)))....))...)))).......... ( -20.90, z-score =  -1.20, R)
>droAna3.scaffold_12943 3646246 89 + 5039921
----GUAUAACGGCCACGCACCGAUUCGCGGGCAAUUUCCAGGAACCGGGA-AACAGAAUUAGAGGAACACUCAUUCAUAGGCCAUCGAUUGAA
----.......((((..((.(((.....)))))..(((((.(....).)))-))..((((..(((.....)))))))...)))).......... ( -24.20, z-score =  -2.02, R)
>droEre2.scaffold_4929 16835591 88 - 26641161
----AUAUAACGGCCACGCACCGAUUUGUGGG-GACUUCCAGGAA-CGGGAAGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
----.......((((.((((......))))((-(.(((((.....-..))))).....((.......)).))).......)))).......... ( -22.60, z-score =  -1.40, R)
>droYak2.chr2L 17343214 89 + 22324452
----AUAUAACGGCCACGCACCGAUUUGUGGG-UACUUCCAGGAACCGGGAAGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
----.......((((.((...))....(((((-(.(((((.(....).))))).....((.......)))))))).....)))).......... ( -22.40, z-score =  -1.20, R)
>droSec1.super_3 3427877 88 - 7220098
----AUAUAACGGCCACGCACCGAUUUGUGGG-GACUUCCAGGAA-CGGGAAGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
----.......((((.((((......))))((-(.(((((.....-..))))).....((.......)).))).......)))).......... ( -22.60, z-score =  -1.40, R)
>droSim1.chr2L_random 411951 88 - 909653
----AUAUAACGGCCACGCACCGAUUUGUGGA-GACUUCCAGGAA-CGGGAUGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
----.......((((.....(((.(((.(((.-.....))).)))-))).((((....(((.......)))....)))).)))).......... ( -23.30, z-score =  -2.18, R)
>consensus
____AUAUAACGGCCACGCACCGAUUUGUGGG_GACUUCCAGGAA_CGGGAAGAUAAAGUGAGAGAAACACCCAUUCAUAGGCCAUUGAUUGAA
...........((((.....(((.(((.((((.....)))).))).))).........(((((.(.......).))))).)))).......... (-20.10 = -20.02 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,913,518 – 7,913,613
Length 95
Sequences 8
Columns 118
Reading direction forward
Mean pairwise identity 71.00
Shannon entropy 0.49259
G+C content 0.45915
Mean single sequence MFE -22.70
Consensus MFE -13.44
Energy contribution -12.97
Covariance contribution -0.47
Combinations/Pair 1.25
Mean z-score -1.35
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830873
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7913518 95 + 23011544
-----------UUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUU-CCCACAAAUCGGUGCGUGGCCGUUAUAUAUAUAUAAAAUA-CUAUAAUGCUGUGCCAGCAUCA---------
-----------..............(((((..-.....)))))..-..........(((((.((((((((((((((.......)))-.)))))))....))))))))).--------- ( -19.90, z-score =  -2.05, R)
>droPer1.super_1 3415301 110 - 10282868
ACAGACUCCAGACUCCACUCUCCGUUUUUUCUGUUCCUGGAAGCU----GGACAACGGUGCGUGGCGGCCUGUUG---UUGUCGUCGUUAU-AUGCUGUGCCAGCAUCAUCAUCAUCA
.(((....((((....((.....))....))))...)))((.(((----((...(((((..((((((((......---.....))))))))-..))))).))))).)).......... ( -30.00, z-score =  -0.09, R)
>dp4.chr4_group3 6316788 110 - 11692001
ACAGACUCCAGACUCCACUCUCCGUUUUUUCUGUUCCUGGAAGCU----GGACAACGGUGCGUGGCGGCCUGUUG---UUGUCGUCGUUAU-AUGCUGUGCCAGCAUCAUCAUCAUCA
.(((....((((....((.....))....))))...)))((.(((----((...(((((..((((((((......---.....))))))))-..))))).))))).)).......... ( -30.00, z-score =  -0.09, R)
>droAna3.scaffold_12943 3646273 93 - 5039921
-----------UCCUCUAAUUCUGU-UUCCCGGUUCCUGGAAAUUGCCCGCGAAUCGGUGCGUGGCCGUUAUAC----AUAAGAGAACUAUUAUGCUGUGCCAGCAUCA---------
-----------..((((......((-((((.(....).)))))).(((((((......)))).)))........----...)))).......((((((...))))))..--------- ( -23.50, z-score =  -0.82, R)
>droEre2.scaffold_4929 16835618 91 + 26641161
-----------UUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUC-CCCACAAAUCGGUGCGUGGCCGUUAUAU----AUAAAAUA-CUAUAAUGCUGUGCCAGCAUCA---------
-----------..............(((((..-.....)))))..-..........(((((.(((((((((((.----........-.)))))))....))))))))).--------- ( -19.40, z-score =  -2.13, R)
>droYak2.chr2L 17343241 92 - 22324452
-----------UUCUCUCACUUUAUCUUCCCGGUUCCUGGAAGUA-CCCACAAAUCGGUGCGUGGCCGUUAUAU----AUAAAAUA-CUAUAAUGCUGUGCCAGCAUCA---------
-----------..............(((((.(....).)))))..-..........(((((.(((((((((((.----........-.)))))))....))))))))).--------- ( -21.40, z-score =  -1.93, R)
>droSec1.super_3 3427904 91 + 7220098
-----------UUCUCUCACUUUAUCUUCCCG-UUCCUGGAAGUC-CCCACAAAUCGGUGCGUGGCCGUUAUAU----AUAAAAUA-CUAUAAUGCUGUGCCAGCAUCA---------
-----------..............(((((..-.....)))))..-..........(((((.(((((((((((.----........-.)))))))....))))))))).--------- ( -19.40, z-score =  -2.13, R)
>droSim1.chr2L_random 411978 91 + 909653
-----------UUCUCUCACUUUAUCAUCCCG-UUCCUGGAAGUC-UCCACAAAUCGGUGCGUGGCCGUUAUAU----AUAAAAUA-CUAUAAUGCUGUGCCAGCAUCA---------
-----------....................(-((..((((....-))))..))).(((((.(((((((((((.----........-.)))))))....))))))))).--------- ( -18.00, z-score =  -1.55, R)
>consensus
___________UUCUCUCACUUUAUCUUCCCG_UUCCUGGAAGUU_CCCACAAAUCGGUGCGUGGCCGUUAUAU____AUAAAAUA_CUAUAAUGCUGUGCCAGCAUCA_________
.........................(((((........))))).............(((((.((((.((.........................))...))))))))).......... (-13.44 = -12.97 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:42 2011