Locus 661

Sequence ID	X_DroMel_CAF1
Location	1,855,130 – 1,855,265
Length	135
Max. P	0.995111

overview

Window 4

Location	1,855,130 – 1,855,225
Length	95
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	76.21
Mean single sequence MFE	-44.86
Consensus MFE	-25.08
Energy contribution	-25.64
Covariance contribution	0.56
Combinations/Pair	1.26
Mean z-score	-2.24
Structure conservation index	0.56
SVM decision value	1.66
SVM RNA-class probability	0.970450
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1855130 95 - 22224390
GCUGUGUGAGAUGUUGCAUGGACUGACUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCUCUUGCGCAGCGUCAGCGGCUGUGUGAGUUGCUGGUGAAGA
((((((..(((.((.((.(.(.((.((.((((....))------------------------)).)).))).))).)))))..)))))).(((((((((.....)))))))))...... ( -43.00)
>DroPse_CAF1 89827 119 - 1
GCUGGGUGAGGUGCUGCAUGGACUGGCUGAGCAGGUGCUGCGGACUCUGGCCCAGCUGCAGCUCCAUUGGCGGGCUGUUCUUCCGCAGGGUCAGCGGCUGUGUCAGUUGCUGGUGCAGG
(((((((.((((.(((((.(.(((.((...)).))).)))))))).)).)))))))((((...((....(((((.......)))))..))((((((((((...)))))))))))))).. ( -54.20)
>DroSec_CAF1 55996 95 - 1
GCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCUCUUGCGCAGCGUCAGCGGCUGUGUGAGUUGCUGGUGAAGA
((((.(..(((.((.((.(.(.((.((.((((....))------------------------)).)).))).))).)))))..).)))).(((((((((.....)))))))))...... ( -41.10)
>DroSim_CAF1 48952 95 - 1
GCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCUCUUGCGCAGCGUCAGCGGCUGUGUGAGUUGCUGGUGAAGA
((((.(..(((.((.((.(.(.((.((.((((....))------------------------)).)).))).))).)))))..).)))).(((((((((.....)))))))))...... ( -41.10)
>DroWil_CAF1 89572 119 - 1
GCUGCGUCAAAUGCUGCAUGGACUGGCUAAGCAAAUGCUGUGGACUCUGGCCCAAUUGCAGAUCUGUGGGCGGGCUAGUCUUUCGCAAGGUCAGCGGUUGGGUUAGCUGCUGAUGCAAA
..(((((((...(((((((.(.((((((.(((....)))(((((..(((((((..(..((....))..)..)))))))...)))))..))))))).))...).))))...))))))).. ( -44.90)
>consensus
GCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC________________________UCUGUGGGCGGGCUGCUCUUGCGCAGCGUCAGCGGCUGUGUGAGUUGCUGGUGAAGA
((((.(..(((.((.((.....(((......))).............................(((....))))).)))))..).)))).(((((((((.....)))))))))...... (-25.08 = -25.64 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	1,855,170 – 1,855,265
Length	95
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	75.22
Mean single sequence MFE	-44.80
Consensus MFE	-26.32
Energy contribution	-27.16
Covariance contribution	0.84
Combinations/Pair	1.28
Mean z-score	-2.48
Structure conservation index	0.59
SVM decision value	2.54
SVM RNA-class probability	0.995111
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1855170 95 - 22224390
UGCUGCUGGCCAAGUAGGUGAUGCAGGUGGAUCGCCUGCUGCUGUGUGAGAUGUUGCAUGGACUGACUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCU
.((.(((.(((.((((((((((.(....).)))))))))).(((((..(....)..)))))....((.((((....))------------------------)).)).))).))).)). ( -41.80)
>DroPse_CAF1 89867 119 - 1
UGUUGCUGGCCGAGUAGGUGAUGCAGGUGGAGCUGUUGCUGCUGGGUGAGGUGCUGCAUGGACUGGCUGAGCAGGUGCUGCGGACUCUGGCCCAGCUGCAGCUCCAUUGGCGGGCUGUU
....(((.(((..(((.....))).(((((((((((....(((((((.((((.(((((.(.(((.((...)).))).)))))))).)).))))))).)))))))))))))).))).... ( -60.90)
>DroSec_CAF1 56036 95 - 1
UGCUGCUGGCCAAGUAGGUGAUGCAGGUGGAUCGCCUGCUGCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCU
.((.(((.(((.((((((((((.(....).))))))))))((..((((........)))...)..)).((((....))------------------------))....))).))).)). ( -39.80)
>DroSim_CAF1 48992 95 - 1
UGCUGCUGGCCAAGUAGGUGAUGCAGGUGGAUCGCCUGCUGCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC------------------------UCUGUGGGCGGGCUGCU
.((.(((.(((.((((((((((.(....).))))))))))((..((((........)))...)..)).((((....))------------------------))....))).))).)). ( -39.80)
>DroWil_CAF1 89612 119 - 1
UGUUGCUGUCCUAGUAAAUGAUGCAAAUGCAUUUGCUGUUGCUGCGUCAAAUGCUGCAUGGACUGGCUAAGCAAAUGCUGUGGACUCUGGCCCAAUUGCAGAUCUGUGGGCGGGCUAGU
.(((((((((((((((..(((((((...(((........))))))))))..)))))...)))).)))..(((....)))...))).(((((((..(..((....))..)..))))))). ( -41.70)
>consensus
UGCUGCUGGCCAAGUAGGUGAUGCAGGUGGAUCGCCUGCUGCUGGGUGAGAUGUUGCAUGGACUGGCUGAGCAGGUGC________________________UCUGUGGGCGGGCUGCU
.((.(((.(((.((((((((((.(....).))))))))))(((.(((.((.(.(.....).))).))).)))....................................))).))).)). (-26.32 = -27.16 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:33 2006