Locus 2640

Sequence ID dm3.chr2L
Location 20,645,822 – 20,645,901
Length 79
Max. P 0.998384
window3623 window3624

overview

Window 3

Location 20,645,822 – 20,645,901
Length 79
Sequences 8
Columns 95
Reading direction forward
Mean pairwise identity 68.82
Shannon entropy 0.53799
G+C content 0.29530
Mean single sequence MFE -12.64
Consensus MFE -9.10
Energy contribution -9.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.23
SVM RNA-class probability 0.986335
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20645822 79 + 23011544
UUCAGUAUUUUUUGCAGAGUUUAUUUGGUGCACAAGCACCGGUAGU--------------CAAUAUAAUU-AUAAUUACAUUAAACCA-CCUAAA
....(((.....))).(.(((((..((((((....))))))(((((--------------..(((....)-)).)))))..)))))).-...... ( -13.60, z-score =  -1.62, R)
>droSim1.chr2L 20245340 79 + 22036055
UUCAGUAUUUUUUGCAGAAUUUAUUUGGUGCACAAGCACCGGUAGU--------------CAAUAUAAUU-AUAAUUACAUUAAACCA-CCUAAA
(((.(((.....))).))).......(((((....)))))(((.((--------------.(((.((((.-...)))).)))..)).)-)).... ( -12.50, z-score =  -1.39, R)
>droSec1.super_18 565099 79 + 1342155
UUCAGUAUUUUUUGCAGAAUUUAUUUGGUGCACAAGCACCGGUAGU--------------CAAUAUAAUU-AUAAUUACAUUAAACCA-CCUAAA
(((.(((.....))).))).......(((((....)))))(((.((--------------.(((.((((.-...)))).)))..)).)-)).... ( -12.50, z-score =  -1.39, R)
>droYak2.chr2R 6988645 80 + 21139217
UUCAGUAUUUUUCGCAGAAUUUAUUUGGUGCACUAGCACCGGUUGU--------------CAAUAUAAUU-AUAAUUACAUUAAACCCUCCUAAA
..........................(((((....)))))((((..--------------.(((.((((.-...)))).))).))))........ ( -11.40, z-score =  -0.99, R)
>droAna3.scaffold_12916 7151735 71 + 16180835
--------CAUCACCGUUCACUAUUUGGUGCACAAGCACCGGUUGC--------------CAAUAUAAUU-AUAAUUACUUUUACACA-AAUAAA
--------....((((....).....(((((....))))))))...--------------..........-.................-...... (  -9.20, z-score =  -0.70, R)
>dp4.chr4_group3 4027796 66 - 11692001
--------------CGUAAAUUAUUUGGUGCACAAGCACCGGUUGC--------------CAAUACAAUUUAUAAAUAUUUUUACACA-AAUAAA
--------------.(((((.((((((((((....)))))(((((.--------------.....)))))...)))))..)))))...-...... ( -13.70, z-score =  -2.35, R)
>droPer1.super_1 1172322 66 - 10282868
--------------CGUAAAUUAUUUGGUGCACAAGCACCGGUUGC--------------CAAUACAAUUUAUAAAUAUUUUUACACA-AAUAAA
--------------.(((((.((((((((((....)))))(((((.--------------.....)))))...)))))..)))))...-...... ( -13.70, z-score =  -2.35, R)
>droGri2.scaffold_15252 234391 88 + 17193109
-------UUGAGUAUUUUGGUAUUUUGGUGCACAAGCACCGGUAAUAAUCUUUUUUUAUACAAUACACAUUAUAAUUCUAUAUAAAUAAUCCAAA
-------..((((((..(((((((.((((((....))))))(((.(((.......))))))))))).))..)).))))................. ( -14.50, z-score =  -1.60, R)
>consensus
_______UUUUUUGCAGAAUUUAUUUGGUGCACAAGCACCGGUAGU______________CAAUAUAAUU_AUAAUUACAUUAAAACA_CCUAAA
........................(((((((....)))))))..................................................... ( -9.10 =  -9.10 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 20,645,822 – 20,645,901
Length 79
Sequences 8
Columns 95
Reading direction reverse
Mean pairwise identity 68.82
Shannon entropy 0.53799
G+C content 0.29530
Mean single sequence MFE -18.55
Consensus MFE -9.40
Energy contribution -9.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998384
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20645822 79 - 23011544
UUUAGG-UGGUUUAAUGUAAUUAU-AAUUAUAUUG--------------ACUACCGGUGCUUGUGCACCAAAUAAACUCUGCAAAAAAUACUGAA
....((-(((((.((((((((...-.)))))))))--------------))))))(((((....))))).......................... ( -23.00, z-score =  -4.68, R)
>droSim1.chr2L 20245340 79 - 22036055
UUUAGG-UGGUUUAAUGUAAUUAU-AAUUAUAUUG--------------ACUACCGGUGCUUGUGCACCAAAUAAAUUCUGCAAAAAAUACUGAA
....((-(((((.((((((((...-.)))))))))--------------))))))(((((....))))).......................... ( -23.00, z-score =  -4.58, R)
>droSec1.super_18 565099 79 - 1342155
UUUAGG-UGGUUUAAUGUAAUUAU-AAUUAUAUUG--------------ACUACCGGUGCUUGUGCACCAAAUAAAUUCUGCAAAAAAUACUGAA
....((-(((((.((((((((...-.)))))))))--------------))))))(((((....))))).......................... ( -23.00, z-score =  -4.58, R)
>droYak2.chr2R 6988645 80 - 21139217
UUUAGGAGGGUUUAAUGUAAUUAU-AAUUAUAUUG--------------ACAACCGGUGCUAGUGCACCAAAUAAAUUCUGCGAAAAAUACUGAA
..(((((.(((((((((((((...-.)))))))))--------------)..)))(((((....))))).......))))).............. ( -19.60, z-score =  -2.99, R)
>droAna3.scaffold_12916 7151735 71 - 16180835
UUUAUU-UGUGUAAAAGUAAUUAU-AAUUAUAUUG--------------GCAACCGGUGCUUGUGCACCAAAUAGUGAACGGUGAUG--------
......-..(((.((.(((((...-.))))).)).--------------)))((((((((....))))).....(....))))....-------- ( -14.50, z-score =  -0.76, R)
>dp4.chr4_group3 4027796 66 + 11692001
UUUAUU-UGUGUAAAAAUAUUUAUAAAUUGUAUUG--------------GCAACCGGUGCUUGUGCACCAAAUAAUUUACG--------------
..((((-(......)))))....((((((((...(--------------....).(((((....)))))..))))))))..-------------- ( -13.70, z-score =  -1.51, R)
>droPer1.super_1 1172322 66 + 10282868
UUUAUU-UGUGUAAAAAUAUUUAUAAAUUGUAUUG--------------GCAACCGGUGCUUGUGCACCAAAUAAUUUACG--------------
..((((-(......)))))....((((((((...(--------------....).(((((....)))))..))))))))..-------------- ( -13.70, z-score =  -1.51, R)
>droGri2.scaffold_15252 234391 88 - 17193109
UUUGGAUUAUUUAUAUAGAAUUAUAAUGUGUAUUGUAUAAAAAAAGAUUAUUACCGGUGCUUGUGCACCAAAAUACCAAAAUACUCAA-------
(((((....(((((((((.((........)).)))))))))..............(((((....)))))......)))))........------- ( -17.90, z-score =  -2.36, R)
>consensus
UUUAGG_UGGUUAAAUGUAAUUAU_AAUUAUAUUG______________ACAACCGGUGCUUGUGCACCAAAUAAAUUAUGCAAAAAA_______
.......................................................(((((....))))).......................... ( -9.40 =  -9.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:55:02 2011