Locus 13941

Sequence ID dm3.chrX
Location 10,146,859 – 10,146,993
Length 134
Max. P 0.983875
window19175 window19176 window19177

overview

Window 5

Location 10,146,859 – 10,146,954
Length 95
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 78.80
Shannon entropy 0.32047
G+C content 0.41847
Mean single sequence MFE -24.17
Consensus MFE -18.12
Energy contribution -18.80
Covariance contribution 0.69
Combinations/Pair 1.13
Mean z-score -1.43
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.685399
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10146859 95 + 22422827
UUCUGAAUUUCUUGC-UGGAAUUGCAAACACAGAUUUCAUUUGAAAUGCAUUUA---------UUUUGCGAUGCACCUAGCCCACUGCACGUGGGCGCCAUCUGU
...((((((((....-.)))))).))...((((((..(........((((((..---------......))))))....((((((.....)))))))..)))))) ( -25.20, z-score =  -1.46, R)
>droSec1.super_15 858623 90 + 1954846
------UUGUAUAGUAUGGAAUUGCUAACACAGAUUUCAUUUGAAAUGCAUUUU---------UUUUGUGAUGCACCUCGCCCACUGCACGUGGGCGCCAUCUGU
------..((.(((((......)))))))((((((..(....((..((((((..---------......))))))..))((((((.....)))))))..)))))) ( -27.80, z-score =  -2.60, R)
>droYak2.chrX 18728187 93 + 21770863
------------UACAAAUAAUUACAAACACAGAUUUCCGUUGAAAUGCAUUUAAUGCAUGUAUUUUGUAAUGCACCUCGACCACUGCACGUGGGCGCCAUCUGU
------------.................((((((..(((((((..((((((.((((....))))....))))))..)))))(((.....)))))....)))))) ( -19.30, z-score =  -0.52, R)
>droSim1.chrX_random 527494 90 + 5698898
------UUGUAUAGUAUGGAAUUGCUAACACAGAUUUCAUUUGAAAUGCAUUUU---------UUUUGUGAUGCACCUCGCCCAGUGCACGUGGGCGCCAUCUGU
------..((.(((((......)))))))((((((..(....((..((((((..---------......))))))..))((((((....).))))))..)))))) ( -24.40, z-score =  -1.13, R)
>consensus
______UUGUAUAGCAUGGAAUUGCAAACACAGAUUUCAUUUGAAAUGCAUUUA_________UUUUGUGAUGCACCUCGCCCACUGCACGUGGGCGCCAUCUGU
...........(((((......)))))..((((((...........((((((.................))))))....((((((.....))))))...)))))) (-18.12 = -18.80 +   0.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,146,859 – 10,146,954
Length 95
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 78.80
Shannon entropy 0.32047
G+C content 0.41847
Mean single sequence MFE -26.98
Consensus MFE -24.16
Energy contribution -24.91
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983875
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10146859 95 - 22422827
ACAGAUGGCGCCCACGUGCAGUGGGCUAGGUGCAUCGCAAAA---------UAAAUGCAUUUCAAAUGAAAUCUGUGUUUGCAAUUCCA-GCAAGAAAUUCAGAA
((((((..(((((((.....)))))).((((((((.......---------...)))))))).....)..)))))).(((((.......-))))).......... ( -27.70, z-score =  -1.52, R)
>droSec1.super_15 858623 90 - 1954846
ACAGAUGGCGCCCACGUGCAGUGGGCGAGGUGCAUCACAAAA---------AAAAUGCAUUUCAAAUGAAAUCUGUGUUAGCAAUUCCAUACUAUACAA------
((((((..(((((((.....))))))(((((((((.......---------...)))))))))....)..)))))).......................------ ( -29.70, z-score =  -3.38, R)
>droYak2.chrX 18728187 93 - 21770863
ACAGAUGGCGCCCACGUGCAGUGGUCGAGGUGCAUUACAAAAUACAUGCAUUAAAUGCAUUUCAACGGAAAUCUGUGUUUGUAAUUAUUUGUA------------
(((((((((((((((.....))).....)))))((((((((....((((((...))))))....((((....)))).))))))))))))))).------------ ( -25.00, z-score =  -0.99, R)
>droSim1.chrX_random 527494 90 - 5698898
ACAGAUGGCGCCCACGUGCACUGGGCGAGGUGCAUCACAAAA---------AAAAUGCAUUUCAAAUGAAAUCUGUGUUAGCAAUUCCAUACUAUACAA------
((((((..((((((.(....))))))(((((((((.......---------...)))))))))....)..)))))).......................------ ( -25.50, z-score =  -2.15, R)
>consensus
ACAGAUGGCGCCCACGUGCAGUGGGCGAGGUGCAUCACAAAA_________AAAAUGCAUUUCAAAUGAAAUCUGUGUUAGCAAUUCCAUACAAUACAA______
((((((..(((((((.....))))))(((((((((...................)))))))))....)..))))))............................. (-24.16 = -24.91 +   0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,146,896 – 10,146,993
Length 97
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.15
Shannon entropy 0.28092
G+C content 0.49068
Mean single sequence MFE -34.19
Consensus MFE -26.50
Energy contribution -26.82
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -1.43
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.638675
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10146896 97 - 22422827
UACGCCAUGUAAUACAGCAGGCAGUUGCAUUUGCAUGCCACAGAUGGCGCCCACGUGCAGUGGGCUAGGUGCAUCGCAAAAUAAAUGCAUUUCAAAU---------
...(((.(((......))))))..((((...(((((((((....))))((((((.....))))))...)))))..))))..................--------- ( -33.70, z-score =  -1.37, R)
>droSec1.super_15 858655 97 - 1954846
UACGCCAUGUAAUACAGCAGGCAGUUGCAUUUGCAUGCUACAGAUGGCGCCCACGUGCAGUGGGCGAGGUGCAUCACAAAAAAAAUGCAUUUCAAAU---------
...(((((.(.....((((.((((......)))).))))..).)))))((((((.....))))))(((((((((..........)))))))))....--------- ( -37.70, z-score =  -3.32, R)
>droYak2.chrX 18728213 106 - 21770863
UACGCCGUGUAAUCCAGCAGGCAGUUGCACUUGCAUGCCACAGAUGGCGCCCACGUGCAGUGGUCGAGGUGCAUUACAAAAUACAUGCAUUAAAUGCAUUUCAACG
((((((.(((......))))))...(((((.((..(((((....)))))..)).))))))))((.((((((((((.................)))))))))).)). ( -32.63, z-score =  -0.55, R)
>droEre2.scaffold_4690 13774557 98 + 18748788
UUCGCCAUGUAGUCCAGCAAGCAGUUGCAUUUGCAUGCCACAGAUGGCGCCCGCGUGCAAUGGGUGGGCUGCAUAACAAUCUACAUGCAAUAAGUGCA--------
......((((((((((.(.....(((((((.((..(((((....)))))..)).))))))).).))))))))))...........((((.....))))-------- ( -33.40, z-score =   0.12, R)
>droSim1.chrX_random 527526 97 - 5698898
UACGCCAUGUAAUACAGCAGGCAGUUGCAUUUGCAUGCUACAGAUGGCGCCCACGUGCACUGGGCGAGGUGCAUCACAAAAAAAAUGCAUUUCAAAU---------
...(((((.(.....((((.((((......)))).))))..).)))))(((((.(....))))))(((((((((..........)))))))))....--------- ( -33.50, z-score =  -2.02, R)
>consensus
UACGCCAUGUAAUACAGCAGGCAGUUGCAUUUGCAUGCCACAGAUGGCGCCCACGUGCAGUGGGCGAGGUGCAUCACAAAAUAAAUGCAUUUCAAAU_________
...(((((.(......(((.((((......)))).)))...).)))))((((((.....))))))..(((((((..........)))))))............... (-26.50 = -26.82 +   0.32)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:30:39 2011