Locus 11831

Sequence ID	dm3.chr3R
Location	24,121,148 – 24,121,210
Length	62
Max. P	0.983352

overview

Window 1

Location	24,121,148 – 24,121,210
Length	62
Sequences	10
Columns	72
Reading direction	forward
Mean pairwise identity	67.28
Shannon entropy	0.65694
G+C content	0.44427
Mean single sequence MFE	-17.71
Consensus MFE	-7.12
Energy contribution	-7.42
Covariance contribution	0.30
Combinations/Pair	1.31
Mean z-score	-2.10
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.13
SVM RNA-class probability	0.983352
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24121148 62 + 27905053
UUCAAGCCGCCAUCGUUGCCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUG----------
.....(((((((....))((((((((((..((((........))))))))))))))))))).---------- ( -20.00, z-score =  -2.46, R)
>droSim1.chr3R 23805064 62 + 27517382
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUG----------
.....(((((((....))))((((((((..((((........)))))))))))).)))....---------- ( -20.20, z-score =  -2.38, R)
>droSec1.super_22 725282 62 + 1066717
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUG----------
.....(((((((....))))((((((((..((((........)))))))))))).)))....---------- ( -20.20, z-score =  -2.38, R)
>droYak2.chr3R 6448886 62 - 28832112
UUUAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUG----------
.....(((((((....))))((((((((..((((........)))))))))))).)))....---------- ( -20.20, z-score =  -2.27, R)
>droEre2.scaffold_4820 6543219 62 - 10470090
UUCCAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGCUG----------
.....(((((((....))))((((((((..((((........)))))))))))).)))....---------- ( -20.20, z-score =  -2.36, R)
>droVir3.scaffold_13047 3789179 52 - 19223366
-UGCAAGCGGCCCCGUUUGUGUUAUUUAUGGGCGCUCACAUAUGCAUAAAUAA-------------------
-.(((((((....))))))).(((((((((.(..........).)))))))))------------------- ( -12.60, z-score =  -0.06, R)
>droWil1.scaffold_181108 1368854 50 + 4707319
----------CAACGUUUCUGUUAUUUAUUUGCGCUCACAUGUGCAUAAAUAACAUGUAU------------
----------.........(((((((((..(((((......)))))))))))))).....------------ ( -13.10, z-score =  -3.12, R)
>dp4.chr2 22827207 65 - 30794189
-------CGCCACAGUCUGUGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGUGGACUGAGAGGGGGAG
-------(.((.(((((..(((((((((..((((........)))))))))))))..)))))....)).).. ( -23.40, z-score =  -3.88, R)
>droPer1.super_0 10021897 65 - 11822988
-------CGCCACAGUCUGUGCUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGUGGACUGAGAGGGGGAG
-------(.((.(((((..((.((((((..((((........)))))))))).))..)))))....)).).. ( -19.20, z-score =  -1.99, R)
>anoGam1.chr3R 6560650 62 - 53272125
AAUAGCGUGUCAUUUAUUUUUUGGUUCAUUUCCGGCACCACAUUCAAACACCACAAACGGUG----------
....(.(((((......................)))))).........((((......))))---------- (  -8.05, z-score =  -0.08, R)
>consensus
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUG__________
...................(((((((((..((((........)))))))))))))................. ( -7.12 =  -7.42 +   0.30)

alignment

secondary structure

dotplot

Window 2

Location	24,121,148 – 24,121,210
Length	62
Sequences	10
Columns	72
Reading direction	reverse
Mean pairwise identity	67.28
Shannon entropy	0.65694
G+C content	0.44427
Mean single sequence MFE	-15.49
Consensus MFE	-5.91
Energy contribution	-6.17
Covariance contribution	0.26
Combinations/Pair	1.38
Mean z-score	-1.40
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.53
SVM RNA-class probability	0.732718
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24121148 62 - 27905053
----------CACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGGCAACGAUGGCGGCUUGAA
----------..(((((.(((((((((.....(((....))).)))))))))(....)...)))))...... ( -18.40, z-score =  -1.49, R)
>droSim1.chr3R 23805064 62 - 27517382
----------CACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUGAA
----------....(((.(((((((((.....(((....))).)))))))))((((....)))))))..... ( -17.80, z-score =  -1.63, R)
>droSec1.super_22 725282 62 - 1066717
----------CACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUGAA
----------....(((.(((((((((.....(((....))).)))))))))((((....)))))))..... ( -17.80, z-score =  -1.63, R)
>droYak2.chr3R 6448886 62 + 28832112
----------CACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUAAA
----------....(((.(((((((((.....(((....))).)))))))))((((....)))))))..... ( -17.80, z-score =  -1.81, R)
>droEre2.scaffold_4820 6543219 62 + 10470090
----------CAGCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUGGAA
----------((((....(((((((((.....(((....))).)))))))))((((....)))).))))... ( -19.10, z-score =  -1.34, R)
>droVir3.scaffold_13047 3789179 52 + 19223366
-------------------UUAUUUAUGCAUAUGUGAGCGCCCAUAAAUAACACAAACGGGGCCGCUUGCA-
-------------------.............((..(((((((................))).))))..))- ( -14.29, z-score =  -1.33, R)
>droWil1.scaffold_181108 1368854 50 - 4707319
------------AUACAUGUUAUUUAUGCACAUGUGAGCGCAAAUAAAUAACAGAAACGUUG----------
------------.....((((((((((((.(......).)))..))))))))).........---------- (  -9.50, z-score =  -1.12, R)
>dp4.chr2 22827207 65 + 30794189
CUCCCCCUCUCAGUCCACGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACACAGACUGUGGCG-------
.....((...(((((...(((((((((.....(((....))).)))))))))...))))).))..------- ( -15.10, z-score =  -2.36, R)
>droPer1.super_0 10021897 65 + 11822988
CUCCCCCUCUCAGUCCACGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAGCACAGACUGUGGCG-------
.....((...(((((...(((((((((.....(((....))).)))))))))...))))).))..------- ( -15.10, z-score =  -1.77, R)
>anoGam1.chr3R 6560650 62 + 53272125
----------CACCGUUUGUGGUGUUUGAAUGUGGUGCCGGAAAUGAACCAAAAAAUAAAUGACACGCUAUU
----------...(((((.(((..((.......))..))).))))).......................... ( -10.00, z-score =   0.46, R)
>consensus
__________CACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACACAAACGAUGGCGGCUUGAA
.................((((((((((.....(((....))).))))))))))................... ( -5.91 =  -6.17 +   0.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:50:31 2011