Locus 1083

Sequence ID	2R_DroMel_CAF1
Location	4,375,782 – 4,375,919
Length	137
Max. P	0.993540

overview

Window 5

Location	4,375,782 – 4,375,883
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	93.96
Mean single sequence MFE	-28.95
Consensus MFE	-23.38
Energy contribution	-23.82
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-1.57
Structure conservation index	0.81
SVM decision value	0.35
SVM RNA-class probability	0.698613
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4375782 101 - 20766785
GAAUCGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAACGUAUUUAUUUAU
((((((....((.((((.......((((((((.((((((((((....))))))))))....)))))...))).......)))).))..)).))))...... ( -28.24)
>DroSec_CAF1 46430 101 - 1
GAAUUGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAACGUAUUUAUUUAU
((((...(..((.((((.......((((((((.((((((((((....))))))))))....)))))...))).......)))).))..)..))))...... ( -28.04)
>DroSim_CAF1 46636 101 - 1
GAAUUGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAACGUAUUUAUUUAU
((((...(..((.((((.......((((((((.((((((((((....))))))))))....)))))...))).......)))).))..)..))))...... ( -28.04)
>DroEre_CAF1 43079 100 - 1
GAAUCGGACUUGGGGG-CCACAAGCAGAUACAAAGAUACACGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAACGUAUUUAUUUAU
((((((...(((((((-(((((.((((.........(((((((....))))))).))))..))))..............)))))))).)).))))...... ( -34.43)
>DroYak_CAF1 44897 101 - 1
GAAUCGGGCCUGAGGGCCCACAAAGAGAUACAGAGAUAUUCGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAAUGUAUUUAUUUAU
.....(((((....)))))......(((((((........(((....)))..(((..((((..((......))....))))..)))..)))))))...... ( -26.00)
>consensus
GAAUCGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGAUGUGUAAACUCAACUUUUGCCCCCAAACGUAUUUAUUUAU
((((((....((.((((.......((((((((.((((((((((....))))))))))....)))))...))).......)))).))..)).))))...... (-23.38 = -23.82 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	4,375,822 – 4,375,919
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	90.47
Mean single sequence MFE	-20.07
Consensus MFE	-17.37
Energy contribution	-17.69
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-1.53
Structure conservation index	0.87
SVM decision value	0.84
SVM RNA-class probability	0.864094
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4375822 97 + 20766785
UCGCAGCCACACGGACAUCCGUGUAACUUUGUAUCUCUUUGUGGGCCCGCAGGCUCGAUUCCCACACACCGCAACAGAAAUUCAAUAAAUACCGAAU
(((.((((((((((....))))))...............((((....)))))))))))....................................... ( -22.60)
>DroSec_CAF1 46470 97 + 1
UCGCAGCCACACGGACAUCCGUGUAACUUUGUAUCUCUUUGUGGGCCCGCAGGCUCAAUUCCCACACACCGCAUCAGAAAUUCAAUAAAUACCGAAU
..((....((((((....)))))).....(((.........((((((....))))))........)))..))......................... ( -20.43)
>DroSim_CAF1 46676 92 + 1
UCGCAGCCACACGGACAUCCGUGUAACUUUGUAUCUCUUUGUGGGCCCGCAGGCUCAAUUCCCACACACCGCAACAGAAAUUCAAUAAAUAC-----
..((....((((((....)))))).....(((.........((((((....))))))........)))..))....................----- ( -20.43)
>DroEre_CAF1 43119 91 + 1
UCGCAGCCACACGGACAUCCGUGUAUCUUUGUAUCUGCUUGUGG-CCCCCAAGUCCGAUUCCCACACACCGCAACAGAAAUUCAAUAAAUAC-----
..((((..((((((....))))))....)))).((((.((((((-.......................))))))))))..............----- ( -19.50)
>DroYak_CAF1 44937 92 + 1
UCGCAGCCACACGGACAUCCGAAUAUCUCUGUAUCUCUUUGUGGGCCCUCAGGCCCGAUUCCCACACACCGCAACAGAAAUUCAAUAAAUAC-----
..((((.....(((....))).......))))...((((((((((((....)))))(.....).......)))).)))..............----- ( -17.40)
>consensus
UCGCAGCCACACGGACAUCCGUGUAACUUUGUAUCUCUUUGUGGGCCCGCAGGCUCGAUUCCCACACACCGCAACAGAAAUUCAAUAAAUAC_____
..((....((((((....)))))).....(((.........((((((....))))))........)))..))......................... (-17.37 = -17.69 +   0.32)

alignment

secondary structure

dotplot

Window 7

Location	4,375,822 – 4,375,919
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	90.47
Mean single sequence MFE	-31.59
Consensus MFE	-27.66
Energy contribution	-28.42
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-2.08
Structure conservation index	0.88
SVM decision value	2.41
SVM RNA-class probability	0.993540
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4375822 97 - 20766785
AUUCGGUAUUUAUUGAAUUUCUGUUGCGGUGUGUGGGAAUCGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGA
..(((.......(((.((((((..((.(((.((..((.......))..)).)))))...)))))).)))((((((((((....)))))))))).))) ( -36.40)
>DroSec_CAF1 46470 97 - 1
AUUCGGUAUUUAUUGAAUUUCUGAUGCGGUGUGUGGGAAUUGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGA
..(((.......(((.((((((..((.(((.((..((.......))..)).)))))...)))))).)))((((((((((....)))))))))).))) ( -36.40)
>DroSim_CAF1 46676 92 - 1
-----GUAUUUAUUGAAUUUCUGUUGCGGUGUGUGGGAAUUGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGA
-----.......(((.((((((..((.(((.((..((.......))..)).)))))...)))))).)))((((((((((....)))))))))).... ( -35.00)
>DroEre_CAF1 43119 91 - 1
-----GUAUUUAUUGAAUUUCUGUUGCGGUGUGUGGGAAUCGGACUUGGGGG-CCACAAGCAGAUACAAAGAUACACGGAUGUCCGUGUGGCUGCGA
-----.......(((....(((((((.(((.(.((((.......)))).).)-)).).))))))..)))((.(((((((....))))))).)).... ( -24.30)
>DroYak_CAF1 44937 92 - 1
-----GUAUUUAUUGAAUUUCUGUUGCGGUGUGUGGGAAUCGGGCCUGAGGGCCCACAAAGAGAUACAGAGAUAUUCGGAUGUCCGUGUGGCUGCGA
-----(((.((((...((((((((.......((((((..(((....)))...)))))).......))))))))...(((....))).)))).))).. ( -25.84)
>consensus
_____GUAUUUAUUGAAUUUCUGUUGCGGUGUGUGGGAAUCGAGCCUGCGGGCCCACAAAGAGAUACAAAGUUACACGGAUGUCCGUGUGGCUGCGA
............(((.((((((..((.(((.((((((.......)))))).)))))...)))))).)))((((((((((....)))))))))).... (-27.66 = -28.42 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:04 2006