Locus 9003

Sequence ID dm3.chr3R
Location 3,311,414 – 3,311,601
Length 187
Max. P 0.966233
window12359 window12360 window12361 window12362

overview

Window 9

Location 3,311,414 – 3,311,533
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.98
Shannon entropy 0.20916
G+C content 0.45475
Mean single sequence MFE -32.74
Consensus MFE -28.82
Energy contribution -28.78
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -2.14
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.966233
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3311414 119 - 27905053
AUUUUAAGGGGUUCUGAGGGGGGUUUUAGGGUG-GCUUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
.....((((((((((((((..((((.......)-)))..)).....(((((((((((((.(((((((.(....).))))))).)......))))))))))))......)))))))))))) ( -42.50, z-score =  -4.26, R)
>droSim1.chr3R 3362951 104 - 27517382
----------------AGGGGAUUUUUAGGGGGUGCUUUCCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
----------------.(((((.((((((((((....)))).....(((((((((((((.(((((((.(....).))))))).......)))))))))))))......)))))).))))) ( -32.60, z-score =  -1.85, R)
>droSec1.super_6 3401098 104 - 4358794
----------------AGGGGAUUUUUAGGGGGUGCUUUCCAGGAGGGGUUAGCGCCCGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
----------------.(((((.((((((((((....)))).....(((((((((((((.(((((((.(....).))))))).......)))))))))))))......)))))).))))) ( -32.60, z-score =  -1.85, R)
>droYak2.chr3R 21806430 97 + 28832112
----------------------GUUUUUAGGGG-GCCUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
----------------------..((((((...-..(((....)))(((((((((((((.(((((((.(....).))))))).)......))))))))))))......))))))...... ( -28.10, z-score =  -1.00, R)
>droEre2.scaffold_4770 3573118 97 - 17746568
---------------------GUUUUUAGGGGGUG--UUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
---------------------..((((((..((..--..)).....(((((((((((((.(((((((.(....).))))))).)......))))))))))))......))))))...... ( -27.90, z-score =  -1.75, R)
>consensus
________________AGGGGAUUUUUAGGGGGUGCUUUCCAGGAGGGGUUAGCGCCUGGAUCCUGUUCAUGUGCACGGGGUGUAAAAAUGGGCGUUAACUCAAUAAAUUAGAAUUUUUU
........................(((..((((....))))..)))(((((((((((((.(((((((.(....).))))))).)......)))))))))))).................. (-28.82 = -28.78 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,311,494 – 3,311,599
Length 105
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.16
Shannon entropy 0.33780
G+C content 0.56072
Mean single sequence MFE -29.32
Consensus MFE -21.04
Energy contribution -21.44
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -1.51
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725260
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3311494 105 - 27905053
CACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGGCCGGGCAUGACCACCGGA-----UGGGGGAUUUUAAGGGGUUCUGAGGGGGGUUUUAGGGUGGCUUUC
..(((((((...((..(((.((((((((.((..(((.....))))).))))))))((...-----...)))))....)).)))))))..(..((((.......))))..) ( -31.80, z-score =  -0.78, R)
>droSim1.chr3R 3363031 89 - 27517382
CACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCACGGGCGUGACCACCGGAGGGGGAGGGGAUUUUUAGGGGGUGCUUUC---------------------
(((((.......)))))...((((((((.((((((....).))))).))))))))((....)).(((((.((((.....)))).)))))--------------------- ( -30.80, z-score =  -2.37, R)
>droSec1.super_6 3401178 89 - 4358794
CACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCACGGGCGUGACCACCGGAGGAGGAGGGGAUUUUUAGGGGGUGCUUUC---------------------
(((((.......)))))...((((((((.((((((....).))))).)))))))).........(((((.((((.....)))).)))))--------------------- ( -29.70, z-score =  -2.03, R)
>droYak2.chr3R 21806510 82 + 28832112
UACAGAAUUAGACUGUGUUAUGGUCAUGGCUGCGGCAUGCGCCCGGGCGUGACCAACGGA-----UGGGGGUUUUUAGGGGGCCUUC-----------------------
(((((.......)))))...((((((((.(((.(((....)))))).)))))))).....-----.((((((((.....))))))))----------------------- ( -31.80, z-score =  -2.08, R)
>droEre2.scaffold_4770 3573198 81 - 17746568
UACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCG-CCGGGCGUGACCAACGGA-----UGGGGGUUUUUAGGGGGUGUUC-----------------------
(((....(((((((.((((.((((((((.((..(((....)-)))).))))))))...))-----)).))...)))))...)))...----------------------- ( -22.50, z-score =  -0.31, R)
>consensus
CACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCCCGGGCGUGACCACCGGA_____UGGGGGUUUUUAGGGGGUGCUC_______________________
(((((.......)))))...((((((((.(((.(((....)))))).))))))))....................................................... (-21.04 = -21.44 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,311,502 – 3,311,601
Length 99
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 79.93
Shannon entropy 0.30626
G+C content 0.55770
Mean single sequence MFE -17.84
Consensus MFE -12.06
Energy contribution -12.86
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.718893
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3311502 99 + 27905053
CCCUAAAACCCCCCUCAGAACCCCUUAAAAUCCCCCA----UCCGGUGGUCAUGCCCGGCCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCA-
.....................................----....((((((((((..(((.....)))...).)))))))))..(((((.......)))))..- ( -21.50, z-score =  -2.45, R)
>droSim1.chr3R 3363040 83 + 27517382
---------------------CCCUAAAAAUCCCCUCCCCCUCCGGUGGUCACGCCCGUGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAA
---------------------........................(((((((.((..(((.(....)))).))..)))))))..(((((.......)))))... ( -18.40, z-score =  -2.17, R)
>droSec1.super_6 3401187 83 + 4358794
---------------------CCCUAAAAAUCCCCUCCUCCUCCGGUGGUCACGCCCGUGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCAA
---------------------........................(((((((.((..(((.(....)))).))..)))))))..(((((.......)))))... ( -18.40, z-score =  -2.20, R)
>droYak2.chr3R 21806517 76 - 28832112
---------------------CCCUAAAAACCCCCA-----UCCGUUGGUCACGCCCGGGCGCAUGCCGCAGCCAUGACCAUAACACAGUCUAAUUCUGUAC--
---------------------...............-----...((((((((.((...(((....)))...))..))))))..))((((.......))))..-- ( -15.60, z-score =  -0.46, R)
>droEre2.scaffold_4770 3573205 75 + 17746568
---------------------CCCUAAAAACCCCCA-----UCCGUUGGUCACGCCCGG-CGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUAC--
---------------------...............-----...((((((((.((..((-(....)))...))..))))))..))((((.......))))..-- ( -15.30, z-score =  -1.68, R)
>consensus
_____________________CCCUAAAAAUCCCCA_____UCCGGUGGUCACGCCCGGGCGCAUGCCACAGCCAUGACCAUAACACAGUCUAAUUCUGUGCA_
.............................................(((((((.((......))..((....))..)))))))..(((((.......)))))... (-12.06 = -12.86 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,311,502 – 3,311,601
Length 99
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 79.93
Shannon entropy 0.30626
G+C content 0.55770
Mean single sequence MFE -27.60
Consensus MFE -21.34
Energy contribution -21.74
Covariance contribution 0.40
Combinations/Pair 1.10
Mean z-score -1.75
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874969
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3311502 99 - 27905053
-UGCACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGGCCGGGCAUGACCACCGGA----UGGGGGAUUUUAAGGGGUUCUGAGGGGGGUUUUAGGG
-.((((((.......))))))..((((((((.((..(((.....))))).))))))))((...----(..(((((((....)))))))..)..))......... ( -29.40, z-score =  -0.56, R)
>droSim1.chr3R 3363040 83 - 27517382
UUGCACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCACGGGCGUGACCACCGGAGGGGGAGGGGAUUUUUAGGG---------------------
..((((((.......))))))..((((((((.((((((....).))))).))))))))((.(((((........))))).)).--------------------- ( -29.60, z-score =  -2.83, R)
>droSec1.super_6 3401187 83 - 4358794
UUGCACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCACGGGCGUGACCACCGGAGGAGGAGGGGAUUUUUAGGG---------------------
..((((((.......))))))..((((((((.((((((....).))))).))))))))((.(((((........))))).)).--------------------- ( -30.60, z-score =  -3.34, R)
>droYak2.chr3R 21806517 76 + 28832112
--GUACAGAAUUAGACUGUGUUAUGGUCAUGGCUGCGGCAUGCGCCCGGGCGUGACCAACGGA-----UGGGGGUUUUUAGGG---------------------
--.............((.((((.((((((((.(((.(((....)))))).))))))))...))-----)).))..........--------------------- ( -26.30, z-score =  -1.37, R)
>droEre2.scaffold_4770 3573205 75 - 17746568
--GUACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCG-CCGGGCGUGACCAACGGA-----UGGGGGUUUUUAGGG---------------------
--.............((.((((.((((((((.((..(((....)-)))).))))))))...))-----)).))..........--------------------- ( -22.10, z-score =  -0.66, R)
>consensus
_UGCACAGAAUUAGACUGUGUUAUGGUCAUGGCUGUGGCAUGCGCCCGGGCGUGACCACCGGA_____AGGGGAUUUUUAGGG_____________________
..((((((.......))))))..((((((((.(((.(((....)))))).)))))))).............................................. (-21.34 = -21.74 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:56:19 2011