Locus 636

Sequence ID	X_DroMel_CAF1
Location	1,773,888 – 1,774,001
Length	113
Max. P	0.988966

overview

Window 5

Location	1,773,888 – 1,774,001
Length	113
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	77.25
Mean single sequence MFE	-56.42
Consensus MFE	-38.48
Energy contribution	-38.73
Covariance contribution	0.26
Combinations/Pair	1.45
Mean z-score	-2.88
Structure conservation index	0.68
SVM decision value	2.14
SVM RNA-class probability	0.988966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1773888 113 + 22224390
AUUGG---AAAGGGUACCGCUGCAGCGGUGGCUGCAGUAGCAGCCGCCGAGGAGGAAGCUAACCAGGCUGAGGCUGCAGCGCUGGCGAACAAGCGGUUGGGCCAGUCCAUUGGUCU
..(((---(...(((((((((((((((((((((((....)))))))))........((((.....))))...))))))))(((........))))))...)))..))))....... ( -55.20)
>DroSim_CAF1 4628 113 + 1
AUUGG---AAAGGGUAGCGCUGCAGCGGUGGCUGCAGUAGCGGCCGCCGAGGAGGAAGCUAACCAGGCAGAGGCUGCAGCGUUGGCGAACAAGCGGUUGGGCCAGUCCAUUGGCCU
.....---....(.(((((((((((((((((((((....))))))))).........(((.....)))....)))))))))))).)............(((((((....))))))) ( -55.10)
>DroEre_CAF1 6930 113 + 1
GUUGG---AAAGGGUGGCGCUGCAGCGGCGGCGGCUGCAGCGGCCGCCAAGGAGGAAGCCAGCCAAGCCGAGGCUGCAGCGCUGGCGAACAAGCGAUUGGGUCAGUCCAUUGGCCU
(((..---....(.((((((((((((..(((((((((..((..((.(....).))..)))))))..))))..)))))))))))).).....)))....(((((((....))))))) ( -55.00)
>DroYak_CAF1 7074 113 + 1
AUUGG---CAAGGGUGCCGCUGCAGCGGCGGCUGCAGCAGCGGCUGCCGAGGAGGAAGCCAGCCAAGCGGAGGCUGCUGCGCUGGCGAACAAGCGAUUGGGCCAGUCCAUUGGCCU
...((---((....))))((((((((....)))))))).((((((.((.....)).)))).((((.(((.((....)).)))))))......))....(((((((....))))))) ( -56.90)
>DroMoj_CAF1 12034 113 + 1
AGCGGGACAAAGGGC---GCUGCGGCGGCGGCAGCUGCGGCUGCCGCUGAGGAUGCAGCGCGGAAGGCCGAGGCGCAGGUGGUGGCCAAUAAGCGUUUGGGUCAAAGCAUUGGGCU
.((..........((---((((((.((((((((((....))))))))))....))))))))....((((.((((((...(((...)))....)))))).))))...))........ ( -57.50)
>DroAna_CAF1 7172 110 + 1
---GG---CAAGGGAACAGCAGCUGCUGCCGCGGCUAUGGCUGCCGCGGAGGAGGCCGCCACCCAGGCGGAGGCCCAGGCGCUGGCCAACAAGCGGCUGGGCCAGUCGAUUGGACU
---.(---(..(((....((.(((.((.(((((((.......))))))).)).))).))..)))..))...(((((((.((((........)))).)))))))((((.....)))) ( -58.80)
>consensus
AUUGG___AAAGGGUACCGCUGCAGCGGCGGCUGCAGCAGCGGCCGCCGAGGAGGAAGCCAGCCAGGCCGAGGCUGCAGCGCUGGCGAACAAGCGGUUGGGCCAGUCCAUUGGCCU
..................(((((((((((((((((....))))))))).........((.......))....))))))))(((........)))....(((((((....))))))) (-38.48 = -38.73 +   0.26)

alignment

secondary structure

dotplot

Window 6

Location	1,773,888 – 1,774,001
Length	113
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	77.25
Mean single sequence MFE	-47.47
Consensus MFE	-21.54
Energy contribution	-24.48
Covariance contribution	2.95
Combinations/Pair	1.15
Mean z-score	-2.44
Structure conservation index	0.45
SVM decision value	1.00
SVM RNA-class probability	0.898085
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1773888 113 - 22224390
AGACCAAUGGACUGGCCCAACCGCUUGUUCGCCAGCGCUGCAGCCUCAGCCUGGUUAGCUUCCUCCUCGGCGGCUGCUACUGCAGCCACCGCUGCAGCGGUACCCUUU---CCAAU
.......((((..((....((((((.(....).)))((((((((....(((.((..........))..)))((((((....))))))...)))))))))))..))..)---))).. ( -48.00)
>DroSim_CAF1 4628 113 - 1
AGGCCAAUGGACUGGCCCAACCGCUUGUUCGCCAACGCUGCAGCCUCUGCCUGGUUAGCUUCCUCCUCGGCGGCCGCUACUGCAGCCACCGCUGCAGCGCUACCCUUU---CCAAU
.(((....((((.(((......))).)))))))..(((((((((....(((.((..........))..)))(((.((....)).)))...))))))))).........---..... ( -41.40)
>DroEre_CAF1 6930 113 - 1
AGGCCAAUGGACUGACCCAAUCGCUUGUUCGCCAGCGCUGCAGCCUCGGCUUGGCUGGCUUCCUCCUUGGCGGCCGCUGCAGCCGCCGCCGCUGCAGCGCCACCCUUU---CCAAC
.(((.((..(..(((.....))).)..)).))).((((((((((..((((..((((((((.((.....)).)))).....))))))))..))))))))))........---..... ( -47.50)
>DroYak_CAF1 7074 113 - 1
AGGCCAAUGGACUGGCCCAAUCGCUUGUUCGCCAGCGCAGCAGCCUCCGCUUGGCUGGCUUCCUCCUCGGCAGCCGCUGCUGCAGCCGCCGCUGCAGCGGCACCCUUG---CCAAU
.((((((((((..(((.....((((.(....).)))).....))))))).))))))((((.((.....)).))))(((((((((((....))))))))))).......---..... ( -52.60)
>DroMoj_CAF1 12034 113 - 1
AGCCCAAUGCUUUGACCCAAACGCUUAUUGGCCACCACCUGCGCCUCGGCCUUCCGCGCUGCAUCCUCAGCGGCAGCCGCAGCUGCCGCCGCCGCAGC---GCCCUUUGUCCCGCU
.(.(((((((((((...)))).))..))))).).......(((....(((.....(((((((.....(.((((((((....)))))))).)..)))))---)).....))).))). ( -38.90)
>DroAna_CAF1 7172 110 - 1
AGUCCAAUCGACUGGCCCAGCCGCUUGUUGGCCAGCGCCUGGGCCUCCGCCUGGGUGGCGGCCUCCUCCGCGGCAGCCAUAGCCGCGGCAGCAGCUGCUGUUCCCUUG---CC---
((((.....))))(((((((.((((.(....).)))).)))))))...((..(((.((((((...(((((((((.......))))))).))..))))))...)))..)---).--- ( -56.40)
>consensus
AGGCCAAUGGACUGGCCCAACCGCUUGUUCGCCAGCGCUGCAGCCUCCGCCUGGCUGGCUUCCUCCUCGGCGGCCGCUACAGCAGCCGCCGCUGCAGCGGUACCCUUU___CCAAU
.......(((((.(((......))).)))))....(((.(((((...(((.......)))........((((((.((....)).))))))))))).)))................. (-21.54 = -24.48 +   2.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:58 2006