Locus 13676

Sequence ID dm3.chrX
Location 8,305,393 – 8,305,605
Length 212
Max. P 0.997994
window18817 window18818 window18819 window18820 window18821

overview

Window 7

Location 8,305,393 – 8,305,510
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.69
Shannon entropy 0.42242
G+C content 0.43496
Mean single sequence MFE -30.26
Consensus MFE -14.94
Energy contribution -15.34
Covariance contribution 0.40
Combinations/Pair 1.32
Mean z-score -2.74
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979058
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8305393 117 + 22422827
GUAUCGUUGGUUUACAAUGGGCACAUUGGAACACUCUUCUAUGGAAAGUGCACCACUUGC---CCACUGUGUUUUUUCUCUCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGC
....((..((..((((.((((((...(((..((((.(((....)))))))..)))..)))---))).)))).................(((((....)))))..........))...)). ( -30.70, z-score =  -2.47, R)
>droEre2.scaffold_4690 11945831 113 - 18748788
--AUCGUUGGUUUACAAUGAGC--AUUAGAACACACUCCUAUGGAUAGUGCUUAUUUUGC---UCACUGUAUUUUUCUCCGUUUUUUGGCUGCCCCAGCGGGAAAUCUUUAUCCUUUCGC
--..((((((..((((.(((((--(....(((((..(((...)))..))).))....)))---))).)))).......(((.....))).....))))))(((........)))...... ( -26.60, z-score =  -1.62, R)
>droYak2.chrX 8761902 94 - 21770863
UUAUCGUUGGUUUACAAUGGGC--AUGGAAAUACUCUUCUAUGAAAAGUGCUUCUUUUGC---CCACUGUGUUUUUCUCCAUUUUUCGAAUCCUUUCGA---------------------
.......(((..((((.(((((--(.((((.((((.(((...))).)))).))))..)))---))).)))).......)))....(((((....)))))--------------------- ( -24.80, z-score =  -3.75, R)
>droSec1.super_35 155681 120 + 471130
GUAUCGUUGGUUUACAAUGGGCACAUUGGAGCACUUUUCUAUGGAAAGUGCACCACUUGCCGCCCAAUGUGUUUUUUCUCUCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGC
....((..((..((((.(((((.((.(((.((((((((.....)))))))).)))..))..))))).)))).................(((((....)))))..........))...)). ( -36.70, z-score =  -3.41, R)
>droSim1.chrX 6611356 120 + 17042790
GUAUCGUUGGUUUACAAUGGGCACAUUGGAACACUUUUCUAUGGAAAGUGCACCACUUGCCGCCCAAUGUGUUUUUUCUCUCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGC
....((..((..((((.(((((.((.(((..(((((((.....)))))))..)))..))..))))).)))).................(((((....)))))..........))...)). ( -32.50, z-score =  -2.47, R)
>consensus
GUAUCGUUGGUUUACAAUGGGCACAUUGGAACACUCUUCUAUGGAAAGUGCACCACUUGC___CCACUGUGUUUUUUCUCUCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGC
............((((.((((((...(((..((((.(((...))).))))..)))..)))...))).)))).................(((((....))))).................. (-14.94 = -15.34 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 8,305,393 – 8,305,510
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.69
Shannon entropy 0.42242
G+C content 0.43496
Mean single sequence MFE -32.84
Consensus MFE -18.26
Energy contribution -21.06
Covariance contribution 2.80
Combinations/Pair 1.17
Mean z-score -3.09
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.01
SVM RNA-class probability 0.996926
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8305393 117 - 22422827
GCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGAGAGAAAAAACACAGUGG---GCAAGUGGUGCACUUUCCAUAGAAGAGUGUUCCAAUGUGCCCAUUGUAAACCAACGAUAC
......((.......(((((.((....)).)))))...............(((((((---(((..(((.(((((((.......))))))).)))...))))))))))...))........ ( -37.90, z-score =  -3.85, R)
>droEre2.scaffold_4690 11945831 113 + 18748788
GCGAAAGGAUAAAGAUUUCCCGCUGGGGCAGCCAAAAAACGGAGAAAAAUACAGUGA---GCAAAAUAAGCACUAUCCAUAGGAGUGUGUUCUAAU--GCUCAUUGUAAACCAACGAU--
......((.......(((((((.(((.....))).....))).))))..((((((((---(((.....(((((..(((...)))..)))))....)--))))))))))..))......-- ( -30.30, z-score =  -2.72, R)
>droYak2.chrX 8761902 94 + 21770863
---------------------UCGAAAGGAUUCGAAAAAUGGAGAAAAACACAGUGG---GCAAAAGAAGCACUUUUCAUAGAAGAGUAUUUCCAU--GCCCAUUGUAAACCAACGAUAA
---------------------(((((....)))))....(((.(.....)(((((((---(((...((((.(((((((...))))))).))))..)--)))))))))...)))....... ( -27.50, z-score =  -4.98, R)
>droSec1.super_35 155681 120 - 471130
GCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGAGAGAAAAAACACAUUGGGCGGCAAGUGGUGCACUUUCCAUAGAAAAGUGCUCCAAUGUGCCCAUUGUAAACCAACGAUAC
......((.......(((((.((....)).)))))...............(((.((((((.((..(((.(((((((.......))))))).))).)))))))).)))...))........ ( -35.40, z-score =  -2.23, R)
>droSim1.chrX 6611356 120 - 17042790
GCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGAGAGAAAAAACACAUUGGGCGGCAAGUGGUGCACUUUCCAUAGAAAAGUGUUCCAAUGUGCCCAUUGUAAACCAACGAUAC
......((.......(((((.((....)).)))))...............(((.((((((.((..(((.(((((((.......))))))).))).)))))))).)))...))........ ( -33.10, z-score =  -1.64, R)
>consensus
GCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGAGAGAAAAAACACAGUGG___GCAAGUGGUGCACUUUCCAUAGAAGAGUGUUCCAAUGUGCCCAUUGUAAACCAACGAUAC
......((.......(((((.((....)).)))))...............(((((((...(((..(((.(((((((.......))))))).)))...))))))))))...))........ (-18.26 = -21.06 +   2.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,305,470 – 8,305,570
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.76
Shannon entropy 0.21115
G+C content 0.52375
Mean single sequence MFE -36.29
Consensus MFE -22.57
Energy contribution -22.89
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.523730
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8305470 100 + 22422827
UCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGCAUCGAAUUCGCCAUCUAACAGUGUGCGUUAACAUG-------AAAGCGCUAACAGCGGCAGGGC-AGC------------
........(((((((..((.((.............((((...))))..............((..(((((......-------..)))))..)).)).)).))))-)))------------ ( -27.60, z-score =  -0.72, R)
>droEre2.scaffold_4690 11945904 120 - 18748788
GUUUUUUGGCUGCCCCAGCGGGAAAUCUUUAUCCUUUCGCAUCAAAUUCGCCCUCUAACAGUCUGCGUUAACAUGCUGUUAGAAAGCGCUAACAGUAGCGGGGCGAGCGACAGGGGCAGC
........((((((((.(((..(...........)..)))......((((((((((((((((.((......)).)))))))))...(((((....)))))))))))).....)))))))) ( -53.10, z-score =  -4.79, R)
>droSec1.super_35 155761 100 + 471130
UCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGCAUCAAAUUCGCCCUCUAACAGUGCGCGUUAACAUG-------AAAGCGCUAACAGCGGCGGGGC-AGC------------
........((((((((.((((...............)))).........(((((.....(((((.(((....)))-------...)))))...)).))))))))-)))------------ ( -32.86, z-score =  -2.04, R)
>droSim1.chrX 6611436 100 + 17042790
UCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGCAUCGAAUUCGCCCUCUAACAGUGUGCGUUAACAUG-------AAAGCGCUAACAGCGGCGGGGC-AGC------------
........((((((((.((.((.............((((...))))..............((..(((((......-------..)))))..)).)).)))))))-)))------------ ( -31.60, z-score =  -1.39, R)
>consensus
UCUUUUUCGCUGCCCCAGCGGCAAAUCUUUAUCCUUUCGCAUCAAAUUCGCCCUCUAACAGUGUGCGUUAACAUG_______AAAGCGCUAACAGCGGCGGGGC_AGC____________
........((((((((.((.((................((.........)).........((..(((((...............)))))..)).)).))))))).)))............ (-22.57 = -22.89 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 8,305,470 – 8,305,570
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.76
Shannon entropy 0.21115
G+C content 0.52375
Mean single sequence MFE -44.52
Consensus MFE -33.43
Energy contribution -33.74
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -3.86
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.997994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8305470 100 - 22422827
------------GCU-GCCCUGCCGCUGUUAGCGCUUU-------CAUGUUAACGCACACUGUUAGAUGGCGAAUUCGAUGCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGA
------------(((-(((((((.((.(((((((....-------..)))))))))............((((((((..((.(....).))...)))))))))).))))))))........ ( -40.00, z-score =  -3.27, R)
>droEre2.scaffold_4690 11945904 120 + 18748788
GCUGCCCCUGUCGCUCGCCCCGCUACUGUUAGCGCUUUCUAACAGCAUGUUAACGCAGACUGUUAGAGGGCGAAUUUGAUGCGAAAGGAUAAAGAUUUCCCGCUGGGGCAGCCAAAAAAC
((((((((.((((.(((((((((((....)))))...((((((((..(((....)))..))))))))))))))...))))(((...(((........)))))).))))))))........ ( -52.60, z-score =  -5.25, R)
>droSec1.super_35 155761 100 - 471130
------------GCU-GCCCCGCCGCUGUUAGCGCUUU-------CAUGUUAACGCGCACUGUUAGAGGGCGAAUUUGAUGCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGA
------------(((-((((((((((.(((((((....-------..))))))))))...........(((((((((.((.(....).))..))))))))))).))))))))........ ( -43.30, z-score =  -3.50, R)
>droSim1.chrX 6611436 100 - 17042790
------------GCU-GCCCCGCCGCUGUUAGCGCUUU-------CAUGUUAACGCACACUGUUAGAGGGCGAAUUCGAUGCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGA
------------(((-(((((((.((.(((((((....-------..)))))))))............((((((((..((.(....).))...)))))))))).))))))))........ ( -42.20, z-score =  -3.44, R)
>consensus
____________GCU_GCCCCGCCGCUGUUAGCGCUUU_______CAUGUUAACGCACACUGUUAGAGGGCGAAUUCGAUGCGAAAGGAUAAAGAUUUGCCGCUGGGGCAGCGAAAAAGA
............(((.(((((((.((.(((((((.............)))))))))............((((((((..((.(....).))...)))))))))).))))))))........ (-33.43 = -33.74 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,305,510 – 8,305,605
Length 95
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 78.60
Shannon entropy 0.34106
G+C content 0.55730
Mean single sequence MFE -28.58
Consensus MFE -14.87
Energy contribution -14.35
Covariance contribution -0.52
Combinations/Pair 1.25
Mean z-score -2.02
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.532375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8305510 95 - 22422827
AACUCUCC----CCCUCACCCUUUCGCCUUGUGGCUCUGGCU-------------GCCCUGCCGCUGUUAGCGCUUU-------CAUGUUAACGCACACUGUUAGAUGGCGAAUUCGAU
........----..........((((((.(.((((...(((.-------------.....)))((.(((((((....-------..))))))))).....)))).).))))))...... ( -25.20, z-score =  -1.72, R)
>droEre2.scaffold_4690 11945944 118 + 18748788
AGCUCUCUCUCCCCCUCCCCCUUUCGCCAUGU-UCUCUGGCUGCCCCUGUCGCUCGCCCCGCUACUGUUAGCGCUUUCUAACAGCAUGUUAACGCAGACUGUUAGAGGGCGAAUUUGAU
.........................((((...-....)))).......((((.(((((((((((....)))))...((((((((..(((....)))..))))))))))))))...)))) ( -33.30, z-score =  -2.16, R)
>droYak2.chrX 8761996 115 + 21770863
AGCUCUC---CCCCCACCCCCUAUCAUCAUGC-UCUCUGGCUGCCCCUGCCGUUCGCCCCGCUACUGUUAGCGCUUUCUAACAGCAUGUUAACGCAGACUGUUAGAGGGCGCAUUUGAU
.......---............((((..((((-.....(((.......)))....(((((((((....)))))...((((((((..(((....)))..)))))))))))))))).)))) ( -35.10, z-score =  -2.94, R)
>droSec1.super_35 155801 96 - 471130
AACUCUCC--CUCCCUCACCCUUUCGCUUUGU-UCUCUGGCU-------------GCCCCGCCGCUGUUAGCGCUUU-------CAUGUUAACGCGCACUGUUAGAGGGCGAAUUUGAU
........--.....((.((((((.((..(((-.....(((.-------------.....)))((.(((((((....-------..))))))))))))..)).)))))).))....... ( -25.60, z-score =  -1.65, R)
>droSim1.chrX 6611476 96 - 17042790
AACUCUCC--CCCCCUCCCCCUUUCGCCUUGU-UCUCUGGCU-------------GCCCCGCCGCUGUUAGCGCUUU-------CAUGUUAACGCACACUGUUAGAGGGCGAAUUCGAU
........--.............(((..((((-((((((((.-------------.....)))((.(((((((....-------..)))))))))........)))))))))...))). ( -23.70, z-score =  -1.63, R)
>consensus
AACUCUCC__CCCCCUCCCCCUUUCGCCUUGU_UCUCUGGCU_____________GCCCCGCCGCUGUUAGCGCUUU_______CAUGUUAACGCACACUGUUAGAGGGCGAAUUUGAU
...............((.((((((.((..(((.....((((...................))))..(((((((.............))))))))))....)).)))))).))....... (-14.87 = -14.35 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:25:46 2011