Locus 8433

Sequence ID	dm3.chr3L
Location	22,694,545 – 22,694,676
Length	131
Max. P	0.905815

overview

Window 4

Location	22,694,545 – 22,694,645
Length	100
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	76.68
Shannon entropy	0.43427
G+C content	0.59463
Mean single sequence MFE	-36.93
Consensus MFE	-20.19
Energy contribution	-20.78
Covariance contribution	0.59
Combinations/Pair	1.30
Mean z-score	-1.41
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.04
SVM RNA-class probability	0.516477
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22694545 100 - 24543557
--CAACCAAGCAGGGCCGAAUAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-CCCUCGAGAGGUCACCGGGGUCCC--UGUCGGCCC-----------
--..........(((((((...(((((.((.((((((.(((.....))))))))).))...........-.(((....)))......)))))..--..)))))))----------- ( -38.00, z-score =  -2.02, R)
>droSim1.chr3L 21981071 113 - 22553184
--CAACCAAGCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-ACCUCGAGAGGUCACCGGGGUCCCGUCCUCUGUUCCCUGUCGGCCC
--..........(((((((((((.....((.((((((.(((.....))))))))).))..)))).....-......(((((....(((....))).)))))........))))))) ( -43.60, z-score =  -2.47, R)
>droSec1.super_11 2614557 113 - 2888827
--CAACCAAGCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-CCCUCGAGAGGUCACCGGGGUCCCGUCCUCUGUUCCCUGUCGGCCC
--..........(((((((((((.....((.((((((.(((.....))))))))).))..)))).....-......(((((....(((....))).)))))........))))))) ( -43.60, z-score =  -2.33, R)
>droYak2.chr3L 23181874 108 - 24197627
--CAACCACCCAGGGCCGAACAGAUCCGACCUGAGCCAUUCCACCAGGAGGCUGAAGUGGCUGUAUUAA-CCCUCGAGAGGUCACC-GGGUCCCGUUCUCCGUUCCAUGUCG----
--..........((..((...(((...(((((((((((((.((((....)).)).))))))).......-.(((....)))....)-)))))....))).))..))......---- ( -29.70, z-score =   0.87, R)
>droEre2.scaffold_4784 22345368 111 - 25762168
ACCAACCAACCAGGCCCGAACAGAUUCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUGGCUGUAUUAA-CCCUCGAGAGGUCACCGGGGUCCCGUUCCCUGUUCCCUGUUG----
......((((.(((...((((((....((((((((((.(((.....))))))))..(.((.(......)-.)).)...)))))..(((....)))....)))))))))))))---- ( -37.10, z-score =  -1.38, R)
>droAna3.scaffold_13337 22435310 96 - 23293914
-----------CAAUUUGAUCCGAGCCGGCCUGAGCCGACAUAACGUGAGGUUAAAGUGGCUUUAUUAACCCCUUGAGAGGUCACGGGGGCCACAACCUCCUUUUCG---------
-----------..........((((.((((....)))).......(.((((((...(((((........((((.(((....))).))))))))))))))))..))))--------- ( -29.60, z-score =  -1.12, R)
>consensus
__CAACCAAGCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA_CCCUCGAGAGGUCACCGGGGUCCCGUCCUCUGUUCCCUGUCG____
............(((((..((((.....((.((((((.(((.....))))))))).))..)))).......(((....))).......)))))....................... (-20.19 = -20.78 +   0.59)

alignment

secondary structure

dotplot

Window 5

Location	22,694,571 – 22,694,676
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	77.86
Shannon entropy	0.42423
G+C content	0.51617
Mean single sequence MFE	-36.48
Consensus MFE	-20.37
Energy contribution	-22.07
Covariance contribution	1.70
Combinations/Pair	1.15
Mean z-score	-1.76
Structure conservation index	0.56
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.73
SVM RNA-class probability	0.800617
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22694571 105 + 24543557
UCGAGGG-UUAAUACAGCUACUUGAGCCUCCUGGUGGGAUGGCUCAGGUCGGAUCUAUUCGGCCCUGCUUGGUUGGG---GGCCAAUCGAUUCGUAGGAAUAUUUAAAU
..(((.(-((..(((....((((((((((((.....))).))))))))).(((((.(((.((((((.(......)))---))))))).))))))))..))).))).... ( -38.80, z-score =  -1.90, R)
>droSim1.chr3L 21981110 105 + 22553184
UCGAGGU-UUAAUACAGCUACUUGAGCCUCCUGGUGGGAUGGCUCAGGUCGGAUCUGUUCGGCCCUGCUUGGUUGGG---GGCCAAUCGAUUCGGAGGAACAUUUAAAU
.....((-((.........((((((((((((.....))).)))))))))((((((.(((.((((((.(......)))---))))))).))))))...))))........ ( -39.60, z-score =  -1.84, R)
>droSec1.super_11 2614596 105 + 2888827
UCGAGGG-UUAAUACAGCUACUUGAGCCUCCUGGUGGGAUGGCUCAGGUCGGAUCUGUUCGGCCCUGCUUGGUUGGG---GGCCAAUCGAUUCGGAGAAACAUUUAAAU
(((((((-(..(.((((((((((((((((((.....))).))))))))).))..)))))..))))...((((((((.---..)))))))).)))).............. ( -38.30, z-score =  -1.50, R)
>droYak2.chr3L 23181908 103 + 24197627
UCGAGGG-UUAAUACAGCCACUUCAGCCUCCUGGUGGAAUGGCUCAGGUCGGAUCUGUUCGGCCCUGGGUGGUUGG-----GCGAAUCGAUUUGGAGGAACAUUUAAAU
.....((-((.....)))).(((((((((((....)))..))))((((((((.((.((((((((......))))))-----)))).))))))))))))........... ( -33.30, z-score =  -0.25, R)
>droEre2.scaffold_4784 22345403 108 + 25762168
UCGAGGG-UUAAUACAGCCACUUGAGCCUCCUGGUGGGAUGGCUCAGGUCGAAUCUGUUCGGGCCUGGUUGGUUGGUUGUGGCGAAUCGAUAUGGAGGAACAUUUAAAU
((((.((-((.....)))).(((((((((((.....))).))))))))))))...(((((...((..(((((((.((....)).)))))))..))..)))))....... ( -37.90, z-score =  -1.80, R)
>droAna3.scaffold_13337 22435340 90 + 23293914
UCAAGGGGUUAAUAAAGCCACUUUAACCUCACGUUAUGUCGGCUCAGGCCGGCUCGGAUCAAAUUGAGUCGGGUCGGA--GGGCAUUCAAAC-----------------
....((((((((..........))))))))......((...((((...((((((((..((.....))..)))))))).--))))...))...----------------- ( -31.00, z-score =  -3.27, R)
>consensus
UCGAGGG_UUAAUACAGCCACUUGAGCCUCCUGGUGGGAUGGCUCAGGUCGGAUCUGUUCGGCCCUGCUUGGUUGGG___GGCCAAUCGAUUCGGAGGAACAUUUAAAU
((((..........((((((..(((((((((.....))).))))))(((((((....))))))).....))))))...........))))................... (-20.37 = -22.07 +   1.70)

alignment

secondary structure

dotplot

Window 6

Location	22,694,571 – 22,694,676
Length	105
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	77.86
Shannon entropy	0.42423
G+C content	0.51617
Mean single sequence MFE	-27.62
Consensus MFE	-14.62
Energy contribution	-15.79
Covariance contribution	1.17
Combinations/Pair	1.32
Mean z-score	-2.11
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.18
SVM RNA-class probability	0.905815
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22694571 105 - 24543557
AUUUAAAUAUUCCUACGAAUCGAUUGGCC---CCCAACCAAGCAGGGCCGAAUAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-CCCUCGA
.....(((((..(((((.(((..((((((---(...........)))))))...))).)....((((((.(((.....))))))))).))))..)))))..-....... ( -33.10, z-score =  -3.77, R)
>droSim1.chr3L 21981110 105 - 22553184
AUUUAAAUGUUCCUCCGAAUCGAUUGGCC---CCCAACCAAGCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-ACCUCGA
...................((((((((((---(...........)))))))((((.....((.((((((.(((.....))))))))).))..)))).....-...)))) ( -32.10, z-score =  -2.94, R)
>droSec1.super_11 2614596 105 - 2888827
AUUUAAAUGUUUCUCCGAAUCGAUUGGCC---CCCAACCAAGCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA-CCCUCGA
...................((((((((((---(...........)))))))((((.....((.((((((.(((.....))))))))).))..)))).....-...)))) ( -32.10, z-score =  -2.88, R)
>droYak2.chr3L 23181908 103 - 24197627
AUUUAAAUGUUCCUCCAAAUCGAUUCGC-----CCAACCACCCAGGGCCGAACAGAUCCGACCUGAGCCAUUCCACCAGGAGGCUGAAGUGGCUGUAUUAA-CCCUCGA
...................((((.((((-----((.........))).)))((((..((.((.(.((((..(((....))))))).).)))))))).....-...)))) ( -23.50, z-score =  -0.30, R)
>droEre2.scaffold_4784 22345403 108 - 25762168
AUUUAAAUGUUCCUCCAUAUCGAUUCGCCACAACCAACCAACCAGGCCCGAACAGAUUCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUGGCUGUAUUAA-CCCUCGA
...................((((...(((((............(((..((((....)))).)))(((((.(((.....))))))))..))))).((....)-)..)))) ( -27.00, z-score =  -2.52, R)
>droAna3.scaffold_13337 22435340 90 - 23293914
-----------------GUUUGAAUGCCC--UCCGACCCGACUCAAUUUGAUCCGAGCCGGCCUGAGCCGACAUAACGUGAGGUUAAAGUGGCUUUAUUAACCCCUUGA
-----------------...((((.((((--(..((((((..((.....))..)).(.((((....)))).).........))))..)).)))))))............ ( -17.90, z-score =  -0.26, R)
>consensus
AUUUAAAUGUUCCUCCGAAUCGAUUGGCC___CCCAACCAACCAGGGCCGAACAGAUCCGACCUGAGCCAUCCCACCAGGAGGCUCAAGUAGCUGUAUUAA_CCCUCGA
...................((((((((((................))))))((((.....((.((((((.(((.....))))))))).))..)))).........)))) (-14.62 = -15.79 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:45:34 2011