Locus 116

Sequence ID	4_DroMel_CAF1
Location	823,448 – 823,547
Length	99
Max. P	0.624690

overview

Window 9

Location	823,448 – 823,547
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	78.72
Mean single sequence MFE	-33.47
Consensus MFE	-18.50
Energy contribution	-17.53
Covariance contribution	-0.97
Combinations/Pair	1.43
Mean z-score	-1.71
Structure conservation index	0.55
SVM decision value	0.02
SVM RNA-class probability	0.542070
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 823448 99 + 1281640
CCCGUACUGGCUGCUCAGAUGAUUGUGCAAUUCCUGAAGGCAGCUUUCGUGCUGCAGUCUCUGCACGUUCUGAAGUUGUUGUUGCUGUUGAGCACUCGC
........(..(((((((..((.((((((......((..(((((......)))))..))..)))))).))...(((.......))).)))))))..).. ( -29.20)
>DroPse_CAF1 2875 99 + 1
CCCGAACUGUGUAUUCAGCUGAUGAUGCAGCUCCUGCAGGCUACUCUCUUGCUGCAGCCUCUGCACAUUUUGGAGUUGCUGCUGCUGCUGAAUACUUGC
..........(((((((((.(.....((((((((.(((((.......)))))(((((...)))))......)))))))).....).))))))))).... ( -36.70)
>DroEre_CAF1 2232 99 + 1
UCCGAACUGGCUGCUCAGUUGAUUGUGCAAUUCCUGAAGGCAGCUUUCGUGCUGCAGUCUCUGCACGUUCUGAAGGCGUUGUUGCUGUUUAGCACUCGC
...(((..((((((((((..((((....)))).))))..)))))))))((((((((((....(((((((.....)))).))).)))))..))))).... ( -29.50)
>DroWil_CAF1 2306 96 + 1
CGAAAACUGAGCACUAAGCUGCUGGUGCAGCUCCUGCAGGCAGCUCUCCUGCUGCAAUCGCUGGACAUUGUGCAGUUG---CUGCUGCUGAAUGCUAGC
.((.......(((...((((((....))))))..)))..(((((......)))))..))(((((.((((..(((((..---..)))))..))))))))) ( -39.30)
>DroYak_CAF1 1897 99 + 1
CCCAAACUGGCUGCUCAGUUGAUUGUGCAAUUCCUGAAGGCAGCUUUCGUGCUGCAGUCUCUGCACGUUCUGAAGGUGUUGUUGCUGUUGAGCACUCGC
........((((((((((..((((....)))).))))..))))))...((((((((((..(.((((.(.....).)))).)..)))))..))))).... ( -29.40)
>DroPer_CAF1 2506 99 + 1
CCCGAACUGUGUAUUCAGCUGAUGAUGCAGCUCCUGCAGGCUACUCUCUUGCUGCAGCCUCUGCACAUUUUGGAGUUGCUGCUGCUGCUGAAUACUUGC
..........(((((((((.(.....((((((((.(((((.......)))))(((((...)))))......)))))))).....).))))))))).... ( -36.70)
>consensus
CCCGAACUGGCUACUCAGCUGAUGGUGCAACUCCUGAAGGCAGCUCUCGUGCUGCAGUCUCUGCACAUUCUGAAGUUGUUGCUGCUGCUGAACACUCGC
...........((((((((.(.....(((((..((....(((((......)))))....((..........))))..)))))..).))))))))..... (-18.50 = -17.53 +  -0.97)

alignment

secondary structure

dotplot

Window 0

Location	823,448 – 823,547
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	78.72
Mean single sequence MFE	-31.18
Consensus MFE	-17.42
Energy contribution	-16.78
Covariance contribution	-0.63
Combinations/Pair	1.39
Mean z-score	-1.78
Structure conservation index	0.56
SVM decision value	0.19
SVM RNA-class probability	0.624690
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 823448 99 - 1281640
GCGAGUGCUCAACAGCAACAACAACUUCAGAACGUGCAGAGACUGCAGCACGAAAGCUGCCUUCAGGAAUUGCACAAUCAUCUGAGCAGCCAGUACGGG
((...((((....)))).........(((((..((((((...(((..((((....).)))...)))...)))))).....)))))))..((.....)). ( -25.00)
>DroPse_CAF1 2875 99 - 1
GCAAGUAUUCAGCAGCAGCAGCAACUCCAAAAUGUGCAGAGGCUGCAGCAAGAGAGUAGCCUGCAGGAGCUGCAUCAUCAGCUGAAUACACAGUUCGGG
....(((((((((.((.(((((..((.((.....)).))..))))).))..((((((((((.....).))))).)).)).))))))))).......... ( -35.70)
>DroEre_CAF1 2232 99 - 1
GCGAGUGCUAAACAGCAACAACGCCUUCAGAACGUGCAGAGACUGCAGCACGAAAGCUGCCUUCAGGAAUUGCACAAUCAACUGAGCAGCCAGUUCGGA
(((..((((....))))....))).........((((((...(((..((((....).)))...)))...))))))......((((((.....)))))). ( -29.00)
>DroWil_CAF1 2306 96 - 1
GCUAGCAUUCAGCAGCAG---CAACUGCACAAUGUCCAGCGAUUGCAGCAGGAGAGCUGCCUGCAGGAGCUGCACCAGCAGCUUAGUGCUCAGUUUUCG
(((.(((.((.((((...---...)))).....(.....))).))))))..((((((((...(((.(((((((....)))))))..))).)))))))). ( -37.90)
>DroYak_CAF1 1897 99 - 1
GCGAGUGCUCAACAGCAACAACACCUUCAGAACGUGCAGAGACUGCAGCACGAAAGCUGCCUUCAGGAAUUGCACAAUCAACUGAGCAGCCAGUUUGGG
.....((((....))))......((........((((((...(((..((((....).)))...)))...))))))....(((((......))))).)). ( -23.80)
>DroPer_CAF1 2506 99 - 1
GCAAGUAUUCAGCAGCAGCAGCAACUCCAAAAUGUGCAGAGGCUGCAGCAAGAGAGUAGCCUGCAGGAGCUGCAUCAUCAGCUGAAUACACAGUUCGGG
....(((((((((.((.(((((..((.((.....)).))..))))).))..((((((((((.....).))))).)).)).))))))))).......... ( -35.70)
>consensus
GCGAGUACUCAACAGCAACAACAACUUCAGAACGUGCAGAGACUGCAGCACGAAAGCUGCCUGCAGGAACUGCACAAUCAGCUGAGCACCCAGUUCGGG
((..((.....)).)).................((((((...(((((((......)))))....))...))))))......((((((.....)))))). (-17.42 = -16.78 +  -0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:00 2006