Locus 4117

Sequence ID	2L_DroMel_CAF1
Location	11,816,518 – 11,816,609
Length	91
Max. P	0.946215

overview

Window 0

Location	11,816,518 – 11,816,609
Length	91
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	86.87
Mean single sequence MFE	-42.12
Consensus MFE	-32.48
Energy contribution	-32.60
Covariance contribution	0.12
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.77
SVM decision value	1.36
SVM RNA-class probability	0.946215
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11816518 91 + 22407834
UCAGUUGGCCGCUGGCCGCCAGGUGGCGCAAUUGUCC-CCUUAGGCCGCAGCGCCAUCUGCCGGCUCCGCAGCUGGCUCACUCUGCUCGCCA
..(((.((((((((((((.((((((((((....(((.-.....)))....)))))))))).))))....)))).)))).))).......... ( -41.60)
>DroSec_CAF1 5423 91 + 1
UCAGUUGGCCGCUGGCCGCCAGGUGGCGCUGUUGCCC-CCUUAGUCUGCAGCGCCAUCUGCCGGAUCCGCAGCUACCUCACUCUGCUCGCCA
.....((((.((.(((((.(((((((((((((.((..-.....))..))))))))))))).))).)).))(((...........))).)))) ( -39.50)
>DroSim_CAF1 5406 90 + 1
UCAGUUGA-CGCUGGCCGCCAGGUGGCGCAGUUGCCC-CCCUAGGCCGCAGCGCCAUCUGCCGGAUCCGCAGCUGCCUCACUCUGCUCGCCA
.((((((.-((....(((.((((((((((.((.(((.-.....))).)).)))))))))).)))...))))))))................. ( -39.90)
>DroEre_CAF1 5457 90 + 1
UCAGCCUGCCGCCGGCCGACAGGUGGCGCACUGGCC--CCUUAGGCGGCAGCGCCAUCUGCCGGCUCCGCCGCGGGCUCACUCUGCUCUCCA
..(((((((.((.(((((.((((((((((....(((--((...)).))).)))))))))).)))).).)).))))))).............. ( -49.70)
>DroYak_CAF1 5528 92 + 1
UCAGCUUGCCGCCGGCCGACAGGUGGCGCCAUGGCCCCCCUUAGGCGGCAGCGCCAUCUGCCGGCUCCGCCGCCGACUCACUCUGCUCGCCA
..(((..((.((.(((((.((((((((((....(((((.....)).))).)))))))))).)))).).)).)).((.....)).)))..... ( -39.90)
>consensus
UCAGUUGGCCGCUGGCCGCCAGGUGGCGCAAUUGCCC_CCUUAGGCCGCAGCGCCAUCUGCCGGCUCCGCAGCUGCCUCACUCUGCUCGCCA
..((.((((.((.(((((.((((((((((....(((.......)))....)))))))))).))).)).)).)))).)).............. (-32.48 = -32.60 +   0.12)

alignment

secondary structure

dotplot

Window 1

Location	11,816,518 – 11,816,609
Length	91
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	86.87
Mean single sequence MFE	-45.08
Consensus MFE	-32.08
Energy contribution	-33.24
Covariance contribution	1.16
Combinations/Pair	1.15
Mean z-score	-1.82
Structure conservation index	0.71
SVM decision value	0.22
SVM RNA-class probability	0.640267
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11816518 91 - 22407834
UGGCGAGCAGAGUGAGCCAGCUGCGGAGCCGGCAGAUGGCGCUGCGGCCUAAGG-GGACAAUUGCGCCACCUGGCGGCCAGCGGCCAACUGA
((((..((...))..))))(((((.(.((((.(((.((((((....(((.....-)).)....)))))).))).))))).)))))....... ( -43.80)
>DroSec_CAF1 5423 91 - 1
UGGCGAGCAGAGUGAGGUAGCUGCGGAUCCGGCAGAUGGCGCUGCAGACUAAGG-GGGCAACAGCGCCACCUGGCGGCCAGCGGCCAACUGA
((((..((((..........))))((..(((.(((.((((((((....((....-))....)))))))).))).)))))....))))..... ( -38.60)
>DroSim_CAF1 5406 90 - 1
UGGCGAGCAGAGUGAGGCAGCUGCGGAUCCGGCAGAUGGCGCUGCGGCCUAGGG-GGGCAACUGCGCCACCUGGCGGCCAGCG-UCAACUGA
(((((.((((..........))))((..(((.(((.((((((.(..((((....-))))..).)))))).))).)))))..))-)))..... ( -41.90)
>DroEre_CAF1 5457 90 - 1
UGGAGAGCAGAGUGAGCCCGCGGCGGAGCCGGCAGAUGGCGCUGCCGCCUAAGG--GGCCAGUGCGCCACCUGUCGGCCGGCGGCAGGCUGA
..............((((.((.((.(.((((((((.((((((....(((.....--)))....)))))).))))))))).)).)).)))).. ( -50.20)
>DroYak_CAF1 5528 92 - 1
UGGCGAGCAGAGUGAGUCGGCGGCGGAGCCGGCAGAUGGCGCUGCCGCCUAAGGGGGGCCAUGGCGCCACCUGUCGGCCGGCGGCAAGCUGA
.......(((..((.(((((((((...)))(((((.((((((((((.((....)).)))...))))))).))))).))))))..))..))). ( -50.90)
>consensus
UGGCGAGCAGAGUGAGCCAGCUGCGGAGCCGGCAGAUGGCGCUGCCGCCUAAGG_GGGCAACUGCGCCACCUGGCGGCCAGCGGCCAACUGA
..........(((..(((.((((....((((.(((.((((((....((((.....))))....)))))).))).)))))))))))..))).. (-32.08 = -33.24 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:02 2006