Locus 6845

Sequence ID dm3.chr3L
Location 10,244,814 – 10,244,919
Length 105
Max. P 0.791187
window9412 window9413

overview

Window 2

Location 10,244,814 – 10,244,919
Length 105
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 85.64
Shannon entropy 0.28966
G+C content 0.48099
Mean single sequence MFE -33.26
Consensus MFE -20.06
Energy contribution -22.77
Covariance contribution 2.71
Combinations/Pair 1.10
Mean z-score -2.12
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681545
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10244814 105 + 24543557
-UUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUUCGGAUCGUCAUCGCUGUCUGGCGCAGACAAAUGGUUGGCCAAAUGGCUAAAUGGCCAAU
-...((((((((((.............(((.(((..(((........)))..))))))...((((((...))))))....))))))))))(((((....))))).. ( -35.40, z-score =  -2.12, R)
>droSim1.chr3L 9634701 93 + 22553184
-UUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCC------------GGAUCGUCAUCGCUGUCUGGCGCAGACAAAUGGUUAGCCAAAUGGCUAAAUGGCCAAU
-....((((((((((..((....))...))).((((------------((((.((....)).))))))))...........((((((....)))))).))))))). ( -34.00, z-score =  -3.26, R)
>droSec1.super_0 2459710 105 + 21120651
-UUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUUCGGAUCGUCAUCGCUGUCUGGCGCAGACAAAUGGUUGGCCAAAUGUCUAAAUGGCCAUU
-.....((((((((.............(((.(((..(((........)))..)))))).(((....)))))(((((..(((....)))..)))))...)))))).. ( -31.20, z-score =  -1.36, R)
>droYak2.chr3L 10232042 105 + 24197627
-UUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUUCGGAUCGUCAUCGCUGUCUGCCGCAGACAAAUGGUUGGCCAAAUGGCUAAAUGGCCAAU
-...((((((((((.............(((.(((..(((........)))..))))))...((((((...))))))....))))))))))(((((....))))).. ( -35.40, z-score =  -2.38, R)
>droEre2.scaffold_4784 10234466 106 + 25762168
UUUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUCCGGAUCGUCAUCGCUGUCUGGCGCAGACAAAUGGUUGGCCAAAUGGCUAAAUGGCCAAU
....((((((((((.............(((.(((..(((........)))..))))))...((((((...))))))....))))))))))(((((....))))).. ( -34.90, z-score =  -1.79, R)
>droAna3.scaffold_13337 15159587 102 + 23293914
UUUUUUUGGCCCGAAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUGCGGAUCGUCAUCGGUGUCUGGCGCAGACAAAUGG----CCAAAUGGCUAAAUGGCCAAU
....((((((((((...((....))...((.(((..((((......))))..)))))))).((((((...))))))...))----)))))(((((....))))).. ( -31.40, z-score =  -0.96, R)
>droGri2.scaffold_15110 11925330 84 - 24565398
--UUUUUGGC----AAAUGUAAACAAAAUGCACGCCCCG----------------AGGCGACGUCUGUUGCAGACAAAUGUCUGGCCAAAUGGCCAAAUGGCCAAU
--..((((((----.......((((..(((..((((...----------------.)))).))).)))).(((((....)))))))))))(((((....))))).. ( -30.50, z-score =  -2.96, R)
>consensus
_UUUUUUGGCCAGCAAAUGUAAACAAAAUGCACGCCCCGUCGUCAUUCGGAUCGUCAUCGCUGUCUGGCGCAGACAAAUGGUUGGCCAAAUGGCUAAAUGGCCAAU
.....(((((((...........((..(((.(((..(((........)))..))))))...((((((...))))))..)).((((((....)))))).))))))). (-20.06 = -22.77 +   2.71)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,244,814 – 10,244,919
Length 105
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 85.64
Shannon entropy 0.28966
G+C content 0.48099
Mean single sequence MFE -33.06
Consensus MFE -22.22
Energy contribution -24.63
Covariance contribution 2.40
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.70
SVM RNA-class probability 0.791187
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10244814 105 - 24543557
AUUGGCCAUUUAGCCAUUUGGCCAACCAUUUGUCUGCGCCAGACAGCGAUGACGAUCCGAAUGACGACGGGGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAA-
..((((......))))((((((((..((((((((((...))))))..))))(((..(((........)))..)))(((...((....))..)))))))))))...- ( -34.10, z-score =  -1.81, R)
>droSim1.chr3L 9634701 93 - 22553184
AUUGGCCAUUUAGCCAUUUGGCUAACCAUUUGUCUGCGCCAGACAGCGAUGACGAUCC------------GGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAA-
.(((((((.((((((....))))))..........(((((.((...((....)).)).------------)))))(((...((....))..))))))))))....- ( -30.70, z-score =  -2.39, R)
>droSec1.super_0 2459710 105 - 21120651
AAUGGCCAUUUAGACAUUUGGCCAACCAUUUGUCUGCGCCAGACAGCGAUGACGAUCCGAAUGACGACGGGGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAA-
..((((((..((((((..(((....)))..))))))....((((((.(((((((..(((........)))..))).))))))))))........)))))).....- ( -34.50, z-score =  -2.33, R)
>droYak2.chr3L 10232042 105 - 24197627
AUUGGCCAUUUAGCCAUUUGGCCAACCAUUUGUCUGCGGCAGACAGCGAUGACGAUCCGAAUGACGACGGGGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAA-
..((((......))))((((((((..((((((((((...))))))..))))(((..(((........)))..)))(((...((....))..)))))))))))...- ( -34.10, z-score =  -1.62, R)
>droEre2.scaffold_4784 10234466 106 - 25762168
AUUGGCCAUUUAGCCAUUUGGCCAACCAUUUGUCUGCGCCAGACAGCGAUGACGAUCCGGAUGACGACGGGGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAAA
..((((......))))((((((((..((((((((((...))))))..))))(((..(((........)))..)))(((...((....))..))))))))))).... ( -35.40, z-score =  -1.83, R)
>droAna3.scaffold_13337 15159587 102 - 23293914
AUUGGCCAUUUAGCCAUUUGG----CCAUUUGUCUGCGCCAGACACCGAUGACGAUCCGCAUGACGACGGGGCGUGCAUUUUGUUUACAUUUUCGGGCCAAAAAAA
..((((......))))(((((----((...((((((...))))))..(((((((..(((........)))..))).))))...............))))))).... ( -31.40, z-score =  -1.17, R)
>droGri2.scaffold_15110 11925330 84 + 24565398
AUUGGCCAUUUGGCCAUUUGGCCAGACAUUUGUCUGCAACAGACGUCGCCU----------------CGGGGCGUGCAUUUUGUUUACAUUU----GCCAAAAA--
..(((((....)))))(((((((((((....))))).((((((.((((((.----------------...)))).))..)))))).......----))))))..-- ( -31.20, z-score =  -2.91, R)
>consensus
AUUGGCCAUUUAGCCAUUUGGCCAACCAUUUGUCUGCGCCAGACAGCGAUGACGAUCCGAAUGACGACGGGGCGUGCAUUUUGUUUACAUUUGCUGGCCAAAAAA_
..((((......))))((((((((......((((((...))))))..(((((((.((((........)))).))).))))..............)))))))).... (-22.22 = -24.63 +   2.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:15:30 2011