Locus 2134

Sequence ID dm3.chr2L
Location 16,499,704 – 16,499,820
Length 116
Max. P 0.988607
window2935 window2936 window2937

overview

Window 5

Location 16,499,704 – 16,499,798
Length 94
Sequences 9
Columns 120
Reading direction forward
Mean pairwise identity 78.46
Shannon entropy 0.39616
G+C content 0.42880
Mean single sequence MFE -22.94
Consensus MFE -15.64
Energy contribution -15.77
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.33
SVM RNA-class probability 0.988607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16499704 94 + 23011544
-----------------------CUAACAACACAUGGAAUUAAUGGGUCGGACAACGACCCAAAACUGUGGAA-CAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAG--CUCAUC
-----------------------.............(((((..(((((((.....)))))))....((((...-)))))))))...((((.(..(((((....).))))..)--)))).. ( -22.40, z-score =  -2.26, R)
>droSim1.chr2L 16209120 94 + 22036055
-----------------------CUAACAACACAUGGAAUUAAUGGGUCGGACAACGACCCAAAACUGUGGAA-CAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAG--CUCAUC
-----------------------.............(((((..(((((((.....)))))))....((((...-)))))))))...((((.(..(((((....).))))..)--)))).. ( -22.40, z-score =  -2.26, R)
>droSec1.super_7 153522 94 + 3727775
-----------------------CUAACAACACAUGGAAUUAAUGGGUCGGACAACGACCCAAAACUGGGGAA-CAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAG--CUCAUC
-----------------------.............(((((..(((((((.....)))))))......(....-)...)))))...((((.(..(((((....).))))..)--)))).. ( -23.20, z-score =  -2.83, R)
>droYak2.chr2R 16543422 87 - 21139217
-----------------------------ACACAUGGAAU-AAUGGGUCGUACAACGACCCACAACUGGGGAA-CAUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAG--CUCAUC
-----------------------------.......((((-..(((((((.....)))))))......(....-)....))))...(((.((..(((((....).))))..)--)))).. ( -21.50, z-score =  -2.43, R)
>droEre2.scaffold_4845 19571186 87 + 22589142
-----------------------------ACACAUCGAAU-AAUGGGUCGGACAACGACCCAGAAGUGGGGAA-CAUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAG--CUCAUC
-----------------------------.......((((-..(((((((.....)))))))...(((.....-)))..))))...(((.((..(((((....).))))..)--)))).. ( -23.40, z-score =  -2.99, R)
>droAna3.scaffold_12916 126937 99 - 16180835
---------------------CCGCAUGCCGAGAGAGAAAUAAUAGGUCGGACAACGACCCAAAACUGGGGGGCCAUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAACUCUCAUC
---------------------.........(((((..........(((((.....)..((((....)))).)))).....(((.(((((........))))).)))......)))))... ( -22.20, z-score =  -0.91, R)
>dp4.chr4_group3 8227048 91 + 11692001
-----------------------------GCAAACAGCAAUAAUGGGUCGGACAACGACCCAAAACUGGGGCCUCAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGAACUCAUC
-----------------------------((.....)).....(((((((.....)))))))....((((((((((..........))))))..(((((....).)))).....)))).. ( -29.70, z-score =  -4.93, R)
>droPer1.super_1 9675998 91 + 10282868
-----------------------------GCAAACAGCAAUAAUGGGUCGGACAACGACCCAAAACUGGGGCCUCAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGAACUCAUC
-----------------------------((.....)).....(((((((.....)))))))....((((((((((..........))))))..(((((....).)))).....)))).. ( -29.70, z-score =  -4.93, R)
>droWil1.scaffold_180772 4771216 117 + 8906247
CUCUCAUCCAAUGGCCAUGUAGUGUAUAGUAUCCAAGUAAUAAUGGUUCGAGCAAUGACCCAAAACUCGUAAA-CAUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAA--CUCUUC
...........(((...((((...))))....))).........((((((....((((........))))...-......(((.(((((........))))).)))..))))--)).... ( -12.00, z-score =   1.92, R)
>consensus
_________________________A___ACACAUAGAAUUAAUGGGUCGGACAACGACCCAAAACUGGGGAA_CAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAG__CUCAUC
...........................................(((((((.....)))))))..................(((.(((((.(....).))))).))).............. (-15.64 = -15.77 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,499,704 – 16,499,798
Length 94
Sequences 9
Columns 120
Reading direction reverse
Mean pairwise identity 78.46
Shannon entropy 0.39616
G+C content 0.42880
Mean single sequence MFE -23.17
Consensus MFE -15.66
Energy contribution -15.64
Covariance contribution -0.01
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.935362
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16499704 94 - 23011544
GAUGAG--CUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUG-UUCCACAGUUUUGGGUCGUUGUCCGACCCAUUAAUUCCAUGUGUUGUUAG-----------------------
...(((--(....((((.(((((........))))).))))....)-)))((((.(..(((((((.....)))))))..)......)))).......----------------------- ( -23.10, z-score =  -2.13, R)
>droSim1.chr2L 16209120 94 - 22036055
GAUGAG--CUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUG-UUCCACAGUUUUGGGUCGUUGUCCGACCCAUUAAUUCCAUGUGUUGUUAG-----------------------
...(((--(....((((.(((((........))))).))))....)-)))((((.(..(((((((.....)))))))..)......)))).......----------------------- ( -23.10, z-score =  -2.13, R)
>droSec1.super_7 153522 94 - 3727775
GAUGAG--CUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUG-UUCCCCAGUUUUGGGUCGUUGUCCGACCCAUUAAUUCCAUGUGUUGUUAG-----------------------
...(((--(....((((.(((((........))))).))))....)-)))........(((((((.....))))))).((((..(....)..)))).----------------------- ( -21.10, z-score =  -1.94, R)
>droYak2.chr2R 16543422 87 + 21139217
GAUGAG--CUCGUGUUCUAUUGACACUUGCUUCAAUUGAAUUUAUG-UUCCCCAGUUGUGGGUCGUUGUACGACCCAUU-AUUCCAUGUGU-----------------------------
...(((--(..(((((.....)))))..))))((((((........-.....))))))(((((((.....)))))))..-...........----------------------------- ( -23.12, z-score =  -2.41, R)
>droEre2.scaffold_4845 19571186 87 - 22589142
GAUGAG--CUCGUGUUCUAUUGACACUUGCUUCAAUUGAAUUUAUG-UUCCCCACUUCUGGGUCGUUGUCCGACCCAUU-AUUCGAUGUGU-----------------------------
...(((--(....((((.(((((........))))).))))....)-)))..(((.(((((((((.....)))))))..-....)).))).----------------------------- ( -22.10, z-score =  -2.35, R)
>droAna3.scaffold_12916 126937 99 + 16180835
GAUGAGAGUUCGUGUUCUAUUGACACUUGCUUCAAUUGAAUUUAUGGCCCCCCAGUUUUGGGUCGUUGUCCGACCUAUUAUUUCUCUCUCGGCAUGCGG---------------------
((.(((((.((((((((.(((((........))))).))))..))))......(((..(((((((.....)))))))..))).))))))).........--------------------- ( -22.80, z-score =  -0.45, R)
>dp4.chr4_group3 8227048 91 - 11692001
GAUGAGUUCUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUGAGGCCCCAGUUUUGGGUCGUUGUCCGACCCAUUAUUGCUGUUUGC-----------------------------
...........(((((.....)))))..((((((..........))))))..((((..(((((((.....)))))))..))))........----------------------------- ( -26.70, z-score =  -3.09, R)
>droPer1.super_1 9675998 91 - 10282868
GAUGAGUUCUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUGAGGCCCCAGUUUUGGGUCGUUGUCCGACCCAUUAUUGCUGUUUGC-----------------------------
...........(((((.....)))))..((((((..........))))))..((((..(((((((.....)))))))..))))........----------------------------- ( -26.70, z-score =  -3.09, R)
>droWil1.scaffold_180772 4771216 117 - 8906247
GAAGAG--UUCGUGUUCUAUUGACACUUGCUUCAAUUGAAUUUAUG-UUUACGAGUUUUGGGUCAUUGCUCGAACCAUUAUUACUUGGAUACUAUACACUACAUGGCCAUUGGAUGAGAG
((((..--...(((((.....)))))...)))).(((.((((((((-(...(((((..((...))..)))))..(((........)))............))))))..))).)))..... ( -19.80, z-score =   1.01, R)
>consensus
GAUGAG__CUCGUGUUCUAUUGACACUUGCCUCAAUUGAAUUUAUG_UUCCCCAGUUUUGGGUCGUUGUCCGACCCAUUAAUUCCAUGUGU___U_________________________
..((((.....(((((.....)))))....))))........................(((((((.....)))))))........................................... (-15.66 = -15.64 +  -0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,499,721 – 16,499,820
Length 99
Sequences 8
Columns 103
Reading direction forward
Mean pairwise identity 85.82
Shannon entropy 0.27975
G+C content 0.40534
Mean single sequence MFE -26.61
Consensus MFE -15.56
Energy contribution -15.70
Covariance contribution 0.14
Combinations/Pair 1.06
Mean z-score -2.55
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871620
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16499721 99 + 23011544
UAAUGGGUCGGACAACGACCCAAAACUGUGGAAC-AUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGCUC--AUCCAUUUGUAAGUGUUC-UAUAACC
...(((((((.....)))))))....((((((((-((.....(((.((.(((..(((((....).))))..))).--...)).)))...))))))-))))... ( -30.80, z-score =  -3.88, R)
>droSim1.chr2L 16209137 99 + 22036055
UAAUGGGUCGGACAACGACCCAAAACUGUGGAAC-AUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGCUC--AUCCAUUUGUAAGUGUUC-UAUAACC
...(((((((.....)))))))....((((((((-((.....(((.((.(((..(((((....).))))..))).--...)).)))...))))))-))))... ( -30.80, z-score =  -3.88, R)
>droSec1.super_7 153539 99 + 3727775
UAAUGGGUCGGACAACGACCCAAAACUGGGGAAC-AUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGCUC--AUCCAUUUGUAAGUGUUC-UAUAACC
...(((((((.....))))))).......(((((-((.....(((.((.(((..(((((....).))))..))).--...)).)))...))))))-)...... ( -27.60, z-score =  -2.64, R)
>droYak2.chr2R 16543432 99 - 21139217
UAAUGGGUCGUACAACGACCCACAACUGGGGAAC-AUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAGCUC--AUCCAUUUUCAAGUGUUC-UAUAACC
...(((((((.....))))))).......(((((-((.........(((.((..(((((....).))))..))))--)...........))))))-)...... ( -25.95, z-score =  -2.86, R)
>droAna3.scaffold_12916 126956 102 - 16180835
UAAUAGGUCGGACAACGACCCAAAACUGGGGGGCCAUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAACUCUCAUCCAUAUGCAAGUUUUU-UAUAACU
.....(((((.....)))))......((((((..(.....(((....)))....(((((....).)))))..))))))..........((((...-...)))) ( -19.20, z-score =  -0.49, R)
>dp4.chr4_group3 8227059 103 + 11692001
UAAUGGGUCGGACAACGACCCAAAACUGGGGCCUCAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGAACUCAUCCAUAUGCAAGCAUUCAUGUGACU
...(((((((.....)))))))....((((((((((..........))))))..(((((....).)))).....))))..((((((........))))))... ( -32.70, z-score =  -3.60, R)
>droPer1.super_1 9676009 103 + 10282868
UAAUGGGUCGGACAACGACCCAAAACUGGGGCCUCAUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGAACUCAUCCAUAUGCAAGCAUUCAUGUGACU
...(((((((.....)))))))....((((((((((..........))))))..(((((....).)))).....))))..((((((........))))))... ( -32.70, z-score =  -3.60, R)
>droWil1.scaffold_180772 4771256 97 + 8906247
UAAUGGUUCGAGCAAUGACCCAAAACUCGUAAAC-AUAAAUUCAAUUGAAGCAAGUGUCAAUAGAACACGAACUCU--UCCAUUU-UACAUGUUG--AUGAUG
...(((.(((.....))).)))....((((.(((-((......(((.((((...(((((....).)))).....))--)).))).-...))))).--)))).. ( -13.10, z-score =   0.56, R)
>consensus
UAAUGGGUCGGACAACGACCCAAAACUGGGGAAC_AUAAAUUCAAUUGAGGCAAGUGUCAAUAGAACACGAGCUC__AUCCAUUUGCAAGUGUUC_UAUAACC
...(((((((.....)))))))..................(((.(((((.(....).))))).)))..................................... (-15.56 = -15.70 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:45:25 2011