Locus 1841

Sequence ID	3R_DroMel_CAF1
Location	5,277,384 – 5,277,542
Length	158
Max. P	0.804247

overview

Window 8

Location	5,277,384 – 5,277,479
Length	95
Sequences	3
Columns	106
Reading direction	reverse
Mean pairwise identity	86.04
Mean single sequence MFE	-20.03
Consensus MFE	-16.32
Energy contribution	-16.10
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-2.16
Structure conservation index	0.81
SVM decision value	0.63
SVM RNA-class probability	0.804247
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5277384 95 - 27905053
UGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACACCCGAGUAGCUCCAUUUUCCCAUUUUC--------CCAUCUUC---CCUUCGUCACGCCCCCUCAGCC
(((((((((((..(....)..))))))((((........))))............))))).....--------........---...................... ( -18.30)
>DroSim_CAF1 45235 98 - 1
UGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACAC-CGAGUAACUCCAUUUUCCCAUUUUCC-------CCAUCUUCCCCCCUUCGUCACGCCCCCUCAGCC
(((((((((((..(....)..))))))(((((.....))-)))............)))))......-------................................. ( -19.60)
>DroYak_CAF1 51909 103 - 1
UGGGAUCGGAUCUGAUCUCACAUCCGAUCGGUUCGAUCCCCGAGUAUCUCCAAUUCCCCAACUUCCCAUCUUUCCAUCUUC---CCUUCGUCACGCCCCCUCAGCC
.(((((((((.((((((........))))))))))))))).((((.......)))).........................---...................... ( -22.20)
>consensus
UGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACACCCGAGUAACUCCAUUUUCCCAUUUUCC_______CCAUCUUC___CCUUCGUCACGCCCCCUCAGCC
(((((((((((..(....)..))))))))((....((......))....))......))).............................................. (-16.32 = -16.10 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	5,277,408 – 5,277,517
Length	109
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	86.34
Mean single sequence MFE	-38.17
Consensus MFE	-30.43
Energy contribution	-32.10
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.80
SVM decision value	0.62
SVM RNA-class probability	0.800474
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5277408 109 - 27905053
ACGUCGAAAGCGGGACGCGGGUGGGUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACACCCGAGUAGCUCCAUUUUCCCAUUUUC--------CCAUCU
..(.(....))((((...(((.((((...((((((((((.((((.(((.......))).)))).)))))))))).))))(((...)))......)))....))--------)).... ( -40.20)
>DroSim_CAF1 45262 109 - 1
ACGUCGAAAGCGGGACGCGGGUGGGUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACAC-CGAGUAACUCCAUUUUCCCAUUUUCC-------CCAUCU
..(..(((((.((((...((((((((...((((((((((.((((.(((.......))).)))).)))))))))).))-)(((...)))))))))))).))))).-------.).... ( -37.10)
>DroYak_CAF1 51933 113 - 1
ACGACGAAAGCGGGACGCGG----GUCCUUUGAACCGAUGGGAUCGGAUCUGAUCUCACAUCCGAUCGGUUCGAUCCCCGAGUAUCUCCAAUUCCCCAACUUCCCAUCUUUCCAUCU
.....(((((.((((.(.((----(......((((((..(((((((((.((((((........))))))))))))))))).)).)).......)))...).))))..)))))..... ( -37.22)
>consensus
ACGUCGAAAGCGGGACGCGGGUGGGUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACACCCGAGUAACUCCAUUUUCCCAUUUUCC_______CCAUCU
.((.(....)))(((..((((((......((((((((((.((((.(((.......))).)))).))))))))))))))))......)))............................ (-30.43 = -32.10 +   1.67)

alignment

secondary structure

dotplot

Window 0

Location	5,277,439 – 5,277,542
Length	103
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	82.54
Mean single sequence MFE	-29.72
Consensus MFE	-21.54
Energy contribution	-23.10
Covariance contribution	1.56
Combinations/Pair	1.17
Mean z-score	-1.81
Structure conservation index	0.72
SVM decision value	0.55
SVM RNA-class probability	0.777022
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5277439 103 - 27905053
CAAUAAAAUCCAAACAAGCAUAAACACGUCGAAAGCGGGACGCGGGUGGGUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACACC
...........................(((......(((((.(....).)))))..((((((((.((((.(((.......))).)))).)))))))))))... ( -32.50)
>DroSim_CAF1 45294 102 - 1
CAAUAAAAUCCAAACAAGCAUAAACACGUCGAAAGCGGGACGCGGGUGGGUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACAC-
...........................(((......(((((.(....).)))))..((((((((.((((.(((.......))).)))).)))))))))))..- ( -32.50)
>DroYak_CAF1 51972 99 - 1
CAAUAAAAUCCAAACAAGCAUAAACACGACGAAAGCGGGACGCGG----GUCCUUUGAACCGAUGGGAUCGGAUCUGAUCUCACAUCCGAUCGGUUCGAUCCC
..........((((............((.(....)))((((....----)))))))).......(((((((((.((((((........))))))))))))))) ( -30.60)
>DroAna_CAF1 48793 93 - 1
CAAUAAAAUCCAAACAAGCAUAAACACGUCGAAAGCGGGUCGCAG----GACAUCCGAACCGGAUGGAUAGGAUGUGACAUUGCGCCCCAUAUCUUC------
...........................(.(....))(((.(((((----.((((((...((....))...))))))....))))).)))........------ ( -23.30)
>consensus
CAAUAAAAUCCAAACAAGCAUAAACACGUCGAAAGCGGGACGCGG____GUCCUUUGAACCGAUGGGAUCGGAUCUGACCUCUCAUCCGAUCGGUUCGACAC_
..........................((.(....)))((((........)))).((((((((((.((((.(((.......))).)))).)))))))))).... (-21.54 = -23.10 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:51 2006