Locus 5114

Sequence ID	3R_DroMel_CAF1
Location	13,471,311 – 13,471,424
Length	113
Max. P	0.962317

overview

Window 0

Location	13,471,311 – 13,471,424
Length	113
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	82.96
Mean single sequence MFE	-39.03
Consensus MFE	-31.90
Energy contribution	-31.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.37
Structure conservation index	0.82
SVM decision value	0.02
SVM RNA-class probability	0.543505
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13471311 113 + 27905053
UGGCCGUCCCCAAACUAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCAG-UAUAUAAUUUUUGG-----UAUUU
..((((..............((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))...-...........)))-----).... ( -35.09)
>DroPse_CAF1 29782 116 + 1
GGGACGCCUCAAAUGGAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGGAUUUA---UUUUUGUUCGGCUUCCC
((((.(((..........(.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))))((((...---.....))))))).)))) ( -45.20)
>DroEre_CAF1 17390 113 + 1
UGGCCAUUCUGAAAUUAAUAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGA-UUUAUUUCUUUUGC-----UUCUU
.(((......(((((.(((.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))..)-)).)))))....))-----).... ( -36.50)
>DroWil_CAF1 22096 114 + 1
CGGCUGUCGGAACUCGAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGGCAAUAUAUUUUUUUG-----UUUCA
.((((.(((..(((((((((((((....))))).((((......)))).)))))))).)))..))))((((((((((.......))))))))))...............-----..... ( -38.10)
>DroYak_CAF1 23306 113 + 1
UGGCGGUCCUAAAAUUAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGA-CUUUUUUAUUUUAC-----UUCUU
.........((((((.((((((.((..........(((.....(((((((.......)))))))..)))((((((((.......))))))))))-)))))).)))))).-----..... ( -33.70)
>DroPer_CAF1 26535 116 + 1
GGGACGCCCAAAAUGGAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGGAUCUA---UUUUUGUUCGGCUUCCU
((((.(((.((((((((.(.((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))))...))))---)))).....))).)))) ( -45.60)
>consensus
UGGCCGUCCCAAAACGAAGAGGCUCAAUGGUCUAGGGGUAUGAUUCUCGCUUUGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGG_UUUAU_UUUUUUGC_____UUCCU
....................((((((((.......(((.....(((((((.......)))))))..)))(((.......))).))))))))............................ (-31.90 = -31.90 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	13,471,311 – 13,471,424
Length	113
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	82.96
Mean single sequence MFE	-36.28
Consensus MFE	-30.48
Energy contribution	-30.48
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.07
Structure conservation index	0.84
SVM decision value	1.54
SVM RNA-class probability	0.962317
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13471311 113 - 27905053
AAAUA-----CCAAAAAUUAUAUA-CUGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUAGUUUGGGGACGGCCA
.....-----((..((((((....-..(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))..))))))..))....... ( -35.50)
>DroPse_CAF1 29782 116 - 1
GGGAAGCCGAACAAAAA---UAAAUCCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUCCAUUUGAGGCGUCCC
((((.(((...((((..---.......(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))......)))).))).)))) ( -41.56)
>DroEre_CAF1 17390 113 - 1
AAGAA-----GCAAAAGAAAUAAA-UCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUAUUAAUUUCAGAAUGGCCA
.....-----((....(((((.((-(.(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))))).)))))......)).. ( -35.30)
>DroWil_CAF1 22096 114 - 1
UGAAA-----CAAAAAAAUAUAUUGCCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUCGAGUUCCGACAGCCG
.....-----..............((.(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))..(((.....)))..)).. ( -31.90)
>DroYak_CAF1 23306 113 - 1
AAGAA-----GUAAAAUAAAAAAG-UCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUAAUUUUAGGACCGCCA
.....-----......(((((...-..(((((((((((((.......)))))((..((((((.......)))))).))..............)))))))).....)))))((....)). ( -32.10)
>DroPer_CAF1 26535 116 - 1
AGGAAGCCGAACAAAAA---UAGAUCCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUCCAUUUUGGGCGUCCC
.(((.(((.....((((---(.((...(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))..)).))))).))).))). ( -41.30)
>consensus
AAGAA_____ACAAAAAA_AUAAA_CCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCAAAGCGAGAAUCAUACCCCUAGACCAUUGAGCCUCUUAAAUUUAGGACGGCCA
...........................(((((((((((((.......)))))((..((((((.......)))))).))..............))))))))................... (-30.48 = -30.48 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:36 2006