Locus 4864

Sequence ID dm3.chr2R
Location 16,074,994 – 16,075,101
Length 107
Max. P 0.987796
window6684 window6685

overview

Window 4

Location 16,074,994 – 16,075,101
Length 107
Sequences 8
Columns 123
Reading direction forward
Mean pairwise identity 73.45
Shannon entropy 0.46666
G+C content 0.58233
Mean single sequence MFE -42.88
Consensus MFE -26.36
Energy contribution -25.82
Covariance contribution -0.53
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.940215
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16074994 107 + 21146708
AAUGAAUGUCAGGCUUGGCUUC-----------UUGCGAACUGACGCCAAUGCGUCAGGGGGCGUGGCCCCGUCUGCC-----UCAUAAUACGUAUACGCAGGGGGGGCUGUGCUGGCCGUCG
...........(((..((((..-----------.......(((((((....)))))))..((((..(((((.(((((.-----..(((.....)))..))))).)))))..))))))))))). ( -46.80, z-score =  -1.84, R)
>droSim1.chr2R 14732824 94 + 19596830
AAUGAAUGUCAGGCUUGGCUUC-----------UUGCGAACUGACGCCAAUGCGUCAGGGGGCGUGGCCCCGUCUGCC-----UCAUAAUACGUAUACGCAGGGGGGGCU-------------
.........((.((((.((...-----------..))...(((((((....))))))).)))).))(((((.(((((.-----..(((.....)))..))))).))))).------------- ( -38.30, z-score =  -1.52, R)
>droSec1.super_1 13635843 94 + 14215200
AAUGAAUGUCAGGCUUGGCUUC-----------UUGCGAACUGACGCCAAUGCGUCAGGGGGCGUGGCCCCGUCUGCC-----UCAUAAUACGUAUACGCAGGGGGGGCU-------------
.........((.((((.((...-----------..))...(((((((....))))))).)))).))(((((.(((((.-----..(((.....)))..))))).))))).------------- ( -38.30, z-score =  -1.52, R)
>droYak2.chr2R 8008920 107 - 21139217
AAUGAAUGUCAGGCUUGGCUUC-----------UUGCGAACUGACGCCAAUGCGUCAGGGGGCGUGGCCCCGUCUGCU-----UCAUAAUACGUAUACGCAGGGGGGGCUGCAGUGCCUGUUG
.........(((((...(((((-----------.......(((((((....))))))))))))(..(((((.(((((.-----...............))))).)))))..)...)))))... ( -46.80, z-score =  -2.44, R)
>droEre2.scaffold_4845 10225567 112 + 22589142
AAUGAAUGUCAGGCUUGGCUUC-----------UUGCGAACUGACGCCCAUGCGUCAGGGGGCGUGGCCCCGUCUGCCCCGUCUCAUAAUACGUAUACGCAAGGGGGGCUGCAGUGCCGGUUG
...........((((...((((-----------(((((..(((((((....)))))))((((((.(((...))))))))).................)))))))))(((......))))))). ( -44.00, z-score =  -0.34, R)
>droAna3.scaffold_13266 10618726 94 - 19884421
AGCGAAUGUCAGGCUUGGUUUC-----------CUACGAACUGACGCCAAUGCGUCAGAGGGCGUGGCCCUGUGUGCC-----UCAUAAUACGUAUACGUACCGUAUGAU-------------
.(((..(((.((((........-----------.......(((((((....)))))))(((((...)))))....)))-----).))).((((....)))).))).....------------- ( -29.80, z-score =  -0.78, R)
>dp4.chr3 13212817 104 + 19779522
ACAGAAUAUCAGGCUUGGCUUGGCCAGGUCGGGUCCGGGGCUGACGCCUAUGCGUCAGAGGGCGUGGCCCUGCCUGGC-----UCAUA-UGUACAUAGGUAUUUCUGCCA-------------
.(((((((((.((((((((...))))))))(((.(((((.(((((((....)))))))(((((...))))).))))))-----))...-........)))).)))))...------------- ( -49.20, z-score =  -2.63, R)
>droPer1.super_2 624981 104 - 9036312
ACAUAAUGUCAGGCUUGGCUUGGCCAGGUCGGGUCCGGGGCUGACGCCUAUGCGUCAGAGGGCGUGGCCCUGCCUGGC-----UCAUA-UGUACAUAGGUAUUUCUGCCA-------------
(((((..(((((((.((((...))))(((((.((((....(((((((....))))))).)))).)))))..)))))))-----...))-))).....((((....)))).------------- ( -49.80, z-score =  -2.74, R)
>consensus
AAUGAAUGUCAGGCUUGGCUUC___________UUGCGAACUGACGCCAAUGCGUCAGGGGGCGUGGCCCCGUCUGCC_____UCAUAAUACGUAUACGCAGGGGGGGCU_____________
.........(((((..........................(((((((....)))))))(((((...))))))))))............................................... (-26.36 = -25.82 +  -0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 16,074,994 – 16,075,101
Length 107
Sequences 8
Columns 123
Reading direction reverse
Mean pairwise identity 73.45
Shannon entropy 0.46666
G+C content 0.58233
Mean single sequence MFE -36.76
Consensus MFE -21.97
Energy contribution -21.87
Covariance contribution -0.09
Combinations/Pair 1.07
Mean z-score -2.25
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.29
SVM RNA-class probability 0.987796
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16074994 107 - 21146708
CGACGGCCAGCACAGCCCCCCCUGCGUAUACGUAUUAUGA-----GGCAGACGGGGCCACGCCCCCUGACGCAUUGGCGUCAGUUCGCAA-----------GAAGCCAAGCCUGACAUUCAUU
....(((..((...(((((..((((.((((.....)))).-----.))))..)))))........(((((((....)))))))(((....-----------)))))...)))........... ( -37.30, z-score =  -1.84, R)
>droSim1.chr2R 14732824 94 - 19596830
-------------AGCCCCCCCUGCGUAUACGUAUUAUGA-----GGCAGACGGGGCCACGCCCCCUGACGCAUUGGCGUCAGUUCGCAA-----------GAAGCCAAGCCUGACAUUCAUU
-------------.(((((..((((.((((.....)))).-----.))))..)))))((.((...(((((((....)))))))(((....-----------))).....)).))......... ( -33.30, z-score =  -2.35, R)
>droSec1.super_1 13635843 94 - 14215200
-------------AGCCCCCCCUGCGUAUACGUAUUAUGA-----GGCAGACGGGGCCACGCCCCCUGACGCAUUGGCGUCAGUUCGCAA-----------GAAGCCAAGCCUGACAUUCAUU
-------------.(((((..((((.((((.....)))).-----.))))..)))))((.((...(((((((....)))))))(((....-----------))).....)).))......... ( -33.30, z-score =  -2.35, R)
>droYak2.chr2R 8008920 107 + 21139217
CAACAGGCACUGCAGCCCCCCCUGCGUAUACGUAUUAUGA-----AGCAGACGGGGCCACGCCCCCUGACGCAUUGGCGUCAGUUCGCAA-----------GAAGCCAAGCCUGACAUUCAUU
...(((((...((.(((((..((((.((((.....)))).-----.))))..)))))........(((((((....)))))))(((....-----------)))))...)))))......... ( -41.00, z-score =  -3.66, R)
>droEre2.scaffold_4845 10225567 112 - 22589142
CAACCGGCACUGCAGCCCCCCUUGCGUAUACGUAUUAUGAGACGGGGCAGACGGGGCCACGCCCCCUGACGCAUGGGCGUCAGUUCGCAA-----------GAAGCCAAGCCUGACAUUCAUU
.....(((...((.(((((.....((((.......))))....)))))....(((((...)))))(((((((....)))))))(((....-----------)))))...)))........... ( -42.20, z-score =  -1.65, R)
>droAna3.scaffold_13266 10618726 94 + 19884421
-------------AUCAUACGGUACGUAUACGUAUUAUGA-----GGCACACAGGGCCACGCCCUCUGACGCAUUGGCGUCAGUUCGUAG-----------GAAACCAAGCCUGACAUUCGCU
-------------.(((((..(((((....))))))))))-----(((..(((((((...)))))(((((((....)))))))...)).(-----------....)...)))........... ( -31.00, z-score =  -2.10, R)
>dp4.chr3 13212817 104 - 19779522
-------------UGGCAGAAAUACCUAUGUACA-UAUGA-----GCCAGGCAGGGCCACGCCCUCUGACGCAUAGGCGUCAGCCCCGGACCCGACCUGGCCAAGCCAAGCCUGAUAUUCUGU
-------------((((.....(((....)))..-..((.-----((((((..(((((.......(((((((....)))))))....)).)))..)))))))).))))............... ( -38.00, z-score =  -1.92, R)
>droPer1.super_2 624981 104 + 9036312
-------------UGGCAGAAAUACCUAUGUACA-UAUGA-----GCCAGGCAGGGCCACGCCCUCUGACGCAUAGGCGUCAGCCCCGGACCCGACCUGGCCAAGCCAAGCCUGACAUUAUGU
-------------((((.....(((....)))..-..((.-----((((((..(((((.......(((((((....)))))))....)).)))..)))))))).))))............... ( -38.00, z-score =  -2.09, R)
>consensus
_____________AGCCCCCCCUGCGUAUACGUAUUAUGA_____GGCAGACGGGGCCACGCCCCCUGACGCAUUGGCGUCAGUUCGCAA___________GAAGCCAAGCCUGACAUUCAUU
.............................................(((....(((((...)))))(((((((....)))))))..........................)))........... (-21.97 = -21.87 +  -0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:37:28 2011