Locus 1313

Sequence ID	3R_DroMel_CAF1
Location	3,862,867 – 3,862,970
Length	103
Max. P	0.986477

overview

Window 3

Location	3,862,867 – 3,862,970
Length	103
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	78.29
Mean single sequence MFE	-17.40
Consensus MFE	-14.87
Energy contribution	-15.53
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.85
SVM decision value	2.04
SVM RNA-class probability	0.986477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3862867 103 + 27905053
CAUCCCGCUUUUUGUCUUUGGCCAUUUGGCAUUCCUUUUCCCGCGAUUAUUUCGCAUUUUCCUCUUCUCCUUAA-ACCAUAUACUGUGCUCAAUUUGACCAAUA----------------
.............(((.((((((....)))............((((.....))))...................-...............)))...))).....---------------- ( -13.50)
>DroSec_CAF1 3712 110 + 1
CAUCCCGCUUUUGGUCUUUGGCCAUUUGGCAUUCUUUACCUCGCGAUUAUUUCGGAUUUUCCUGUUUUCCUUGAAACCAUGUACUGUGCUCAAUUUGACCAAUAAAUUAU----------
..........((((((.(((..(((...((((........((.(((.....))))).......(((((....))))).))))...)))..)))...))))))........---------- ( -18.50)
>DroSim_CAF1 3745 113 + 1
CAUCCCGCUUUUGGUCUUUGGCCAUUUGGCAUUCCUUACCUCGCGAUUAUUUCGCAUUUUCCUGUUUUUCUUGAAACCU-------UGCUCAAUUUGACCAAUAANNNNNNNNNNNNNNN
..........((((((.((((((....)))............((((.....))))........(((((....)))))..-------....)))...)))))).................. ( -20.20)
>consensus
CAUCCCGCUUUUGGUCUUUGGCCAUUUGGCAUUCCUUACCUCGCGAUUAUUUCGCAUUUUCCUGUUUUCCUUGAAACCAU_UACUGUGCUCAAUUUGACCAAUAA_______________
..........((((((.((((((....)))............((((.....))))...................................)))...)))))).................. (-14.87 = -15.53 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	3,862,867 – 3,862,970
Length	103
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	78.29
Mean single sequence MFE	-20.68
Consensus MFE	-13.75
Energy contribution	-14.20
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-1.85
Structure conservation index	0.66
SVM decision value	0.82
SVM RNA-class probability	0.859391
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3862867 103 - 27905053
----------------UAUUGGUCAAAUUGAGCACAGUAUAUGGU-UUAAGGAGAAGAGGAAAAUGCGAAAUAAUCGCGGGAAAAGGAAUGCCAAAUGGCCAAAGACAAAAAGCGGGAUG
----------------..(((((((..((((((.((.....))))-))))((............(((((.....)))))............))...)))))))................. ( -20.55)
>DroSec_CAF1 3712 110 - 1
----------AUAAUUUAUUGGUCAAAUUGAGCACAGUACAUGGUUUCAAGGAAAACAGGAAAAUCCGAAAUAAUCGCGAGGUAAAGAAUGCCAAAUGGCCAAAGACCAAAAGCGGGAUG
----------........((((((...(((.((.((.....(((((((..........((.....))......(((....)))...))).))))..))))))).)))))).......... ( -21.10)
>DroSim_CAF1 3745 113 - 1
NNNNNNNNNNNNNNNUUAUUGGUCAAAUUGAGCA-------AGGUUUCAAGAAAAACAGGAAAAUGCGAAAUAAUCGCGAGGUAAGGAAUGCCAAAUGGCCAAAGACCAAAAGCGGGAUG
..................((((((...(((((..-------....)))))........((....(((((.....))))).((((.....))))......))...)))))).......... ( -20.40)
>consensus
_______________UUAUUGGUCAAAUUGAGCACAGUA_AUGGUUUCAAGGAAAACAGGAAAAUGCGAAAUAAUCGCGAGGUAAGGAAUGCCAAAUGGCCAAAGACCAAAAGCGGGAUG
..................(((((((..(((.(((..........((((...........)))).(((((.....)))))..........)))))).)))))))................. (-13.75 = -14.20 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:34 2006