Locus 4218

Sequence ID	2L_DroMel_CAF1
Location	12,081,387 – 12,081,486
Length	99
Max. P	0.934944

overview

Window 0

Location	12,081,387 – 12,081,486
Length	99
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	90.13
Mean single sequence MFE	-38.44
Consensus MFE	-28.98
Energy contribution	-30.18
Covariance contribution	1.20
Combinations/Pair	1.06
Mean z-score	-2.26
Structure conservation index	0.75
SVM decision value	1.03
SVM RNA-class probability	0.903730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12081387 99 + 22407834
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUCGCUGCGCGA-AAGAGAUGGAGUGCAUGUGCGAGUGCGAGC---
(((((((..((((((((((..((.(((((..(((((((...(((...)))..))))))).))))).(..-..)))..)))))))).))))).))))....--- ( -39.90)
>DroSec_CAF1 17763 100 + 1
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUCGCUGCGAGA-AAGAGAUGGCGUACAUGUGCGAGUGCGAGUG--
((((((((........((((.((.(((((..(((((((...(((...)))..))))))).))))).)).-)))))))))))).(((.(((....))).)))-- ( -36.20)
>DroSim_CAF1 17748 99 + 1
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUCGCUGCGAGA-AAGAGAUGGCGCACAUGUGCGAAUGCGAGC---
((((((((........((((.((.(((((..(((((((...(((...)))..))))))).))))).)).-)))))))))))).....(((....)))...--- ( -36.80)
>DroEre_CAF1 17978 98 + 1
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUGGCUGCGAGA-AAG----GGAGUGCGAGUGCGAGUGCGAGCAGG
(((((((..(((((((((((.((.(((((..(((((((...(((...)))..))))))).))))).)).-..)----))))))).)))))).))))....... ( -41.00)
>DroYak_CAF1 18756 99 + 1
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUGGCUGCGCGAGAAG----GGAGUGCGAGUGUGAGUGCGAGCGGG
.((((((.(((((((((((((.(((((((..(((((((...(((...)))..))))))).))))).)).))..----))))))).)))).....))).))).. ( -38.30)
>consensus
GCGCCGUUUACUGCAUUCUUCCUGGCAGCAAAGGAUUAUUUCCGAAACGGCCUAAUCCUCGCUGCGAGA_AAGAGAUGGAGUGCAUGUGCGAGUGCGAGC___
(((((((..((((((((((..((.(((((..(((((((...(((...)))..))))))).))))).)).........)))))))).))))).))))....... (-28.98 = -30.18 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	12,081,387 – 12,081,486
Length	99
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	90.13
Mean single sequence MFE	-35.64
Consensus MFE	-26.46
Energy contribution	-27.14
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-2.57
Structure conservation index	0.74
SVM decision value	1.24
SVM RNA-class probability	0.934944
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12081387 99 - 22407834
---GCUCGCACUCGCACAUGCACUCCAUCUCUU-UCGCGCAGCGAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
---...(((....((....))(((.(((.((((-((..(((((((((((((..(((...)))...)))))).)))))))..))))))))).))).....))). ( -35.90)
>DroSec_CAF1 17763 100 - 1
--CACUCGCACUCGCACAUGUACGCCAUCUCUU-UCUCGCAGCGAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
--..........(((.....(((..(((.((((-(((.(((((((((((((..(((...)))...)))))).))))))).))))))))))..)))....))). ( -37.00)
>DroSim_CAF1 17748 99 - 1
---GCUCGCAUUCGCACAUGUGCGCCAUCUCUU-UCUCGCAGCGAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
---....((....))......(((((...((((-(((.(((((((((((((..(((...)))...)))))).))))))).))))))).....(....)))))) ( -39.20)
>DroEre_CAF1 17978 98 - 1
CCUGCUCGCACUCGCACUCGCACUCC----CUU-UCUCGCAGCCAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
...(((.((....))(((.(((....----(((-(((.(((((.(((((((..(((...)))...)))))))..))))).))))))..))))))....))).. ( -33.80)
>DroYak_CAF1 18756 99 - 1
CCCGCUCGCACUCACACUCGCACUCC----CUUCUCGCGCAGCCAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
......(((......(((.(((....----((((..(.(((((.(((((((..(((...)))...)))))))..))))))..))))..)))))).....))). ( -32.30)
>consensus
___GCUCGCACUCGCACAUGCACUCCAUCUCUU_UCUCGCAGCGAGGAUUAGGCCGUUUCGGAAAUAAUCCUUUGCUGCCAGGAAGAAUGCAGUAAACGGCGC
...(((.(((.((((....)).............(((.(((((((((((((..(((...)))...)))))).))))))).)))..)).))))))......... (-26.46 = -27.14 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:37 2006