Locus 2018

Sequence ID	3R_DroMel_CAF1
Location	5,730,678 – 5,730,780
Length	102
Max. P	0.989564

overview

Window 6

Location	5,730,678 – 5,730,780
Length	102
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	84.00
Mean single sequence MFE	-18.28
Consensus MFE	-17.36
Energy contribution	-17.20
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-2.22
Structure conservation index	0.95
SVM decision value	2.17
SVM RNA-class probability	0.989564
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5730678 102 + 27905053
UCGCUUCCCUCCGCCC--UACCAUCCUUACAAUCACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
..((........))..--...........(((((.((.....((((((.....)))))).......(((.............)))..........)).))))). ( -18.02)
>DroSec_CAF1 22281 101 + 1
-CUCCCCACUCCUCAC--CGCCAUCCCUACAAUCACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
-...............--...........(((((.((.....((((((.....)))))).......(((.............)))..........)).))))). ( -17.72)
>DroSim_CAF1 22916 85 + 1
-------------------ACCAUCCCUACAAUCACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
-------------------..........(((((.((.....((((((.....)))))).......(((.............)))..........)).))))). ( -17.72)
>DroEre_CAF1 17804 98 + 1
CCACCUCGCCCCUCA------GGCCUGUACAAUUACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
.....(((((..(((------((...(((....))).....))))).....(((..((((((((((....))))))...))))..))).......))))).... ( -20.20)
>DroYak_CAF1 5450 104 + 1
CCCUUUCCCCCCUCUCGACACCGCCACUACAAUCACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
.............................(((((.((.....((((((.....)))))).......(((.............)))..........)).))))). ( -17.72)
>consensus
_C_CCUCCCCCCUCAC___ACCAUCCCUACAAUCACCAUCACCUGACCGUCAUGGUCAGCAAUUUAUGCUUAAAUUUCCGCUGCACAUUUUUCAAGGCGAUUGC
.............................(((((.((.....((((((.....)))))).......(((.............)))..........)).))))). (-17.36 = -17.20 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	5,730,678 – 5,730,780
Length	102
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	84.00
Mean single sequence MFE	-27.54
Consensus MFE	-24.96
Energy contribution	-25.16
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.91
SVM decision value	1.29
SVM RNA-class probability	0.940275
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5730678 102 - 27905053
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUGAUUGUAAGGAUGGUA--GGGCGGAGGGAAGCGA
(((((((((........(((((.............))))).((..((((((.....))))).)..)))))))))))..........--..((........)).. ( -27.62)
>DroSec_CAF1 22281 101 - 1
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUGAUUGUAGGGAUGGCG--GUGAGGAGUGGGGAG-
(((((((((........(((((.............))))).((..((((((.....))))).)..))))))))))).....(.((.--.......)).)....- ( -26.02)
>DroSim_CAF1 22916 85 - 1
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUGAUUGUAGGGAUGGU-------------------
(((((((((........(((((.............))))).((..((((((.....))))).)..))))))))))).........------------------- ( -25.92)
>DroEre_CAF1 17804 98 - 1
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUAAUUGUACAGGCC------UGAGGGGCGAGGUGG
.((.(((((((......(((((((..........((((.....)))).(((((.((......)).)))))..)))))))....------...)))))))..)). ( -31.22)
>DroYak_CAF1 5450 104 - 1
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUGAUUGUAGUGGCGGUGUCGAGAGGGGGGAAAGGG
(((((((((........(((((.............))))).((..((((((.....))))).)..)))))))))))........(.((....)).)........ ( -26.92)
>consensus
GCAAUCGCCUUGAAAAAUGUGCAGCGGAAAUUUAAGCAUAAAUUGCUGACCAUGACGGUCAGGUGAUGGUGAUUGUAGGGAUGGU___GUGAGGAGGGAAG_G_
(((((((((........(((((.............))))).((..((((((.....))))).)..)))))))))))............................ (-24.96 = -25.16 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:20 2006