Locus 467

Sequence ID	3L_DroMel_CAF1
Location	1,339,613 – 1,339,776
Length	163
Max. P	0.973173

overview

Window 8

Location	1,339,613 – 1,339,704
Length	91
Sequences	4
Columns	93
Reading direction	forward
Mean pairwise identity	90.98
Mean single sequence MFE	-32.18
Consensus MFE	-28.39
Energy contribution	-29.45
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-2.29
Structure conservation index	0.88
SVM decision value	1.71
SVM RNA-class probability	0.973173
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1339613 91 + 23771897
CAAUAAACUGCACAAGUUGCGCAUACGACGCGUGUUCCUCCCUCGAGAGGAAACGAGGUGGCUAAAG--ACGAAGCCAACUAGGUGCAGCAAA
.......((((((..((((......)))).(((.((((((......)))))))))((.(((((....--....))))).))..)))))).... ( -29.10)
>DroSec_CAF1 11842 88 + 1
CAAUAAACUGCACAAGUUGCGCAUACGACGCGUGUUC---CCUCGGGAGGAAACGGGGCGGCUGCAG--ACGCAGCCAACUAGGUGCAGCAAA
.......((((((.((((((((.......))))....---(((((........))))).((((((..--..))))))))))..)))))).... ( -34.40)
>DroSim_CAF1 11934 88 + 1
CAAUAAACUGCACAAGUUGCGCAUACGACGCGUGUUC---CCUCGGGAGGAAACGGGGCGGCUGCAG--ACGCAGCCAACUAGGUGCAGCAAA
.......((((((.((((((((.......))))....---(((((........))))).((((((..--..))))))))))..)))))).... ( -34.40)
>DroEre_CAF1 12196 90 + 1
CAAUAAACUGCACAAGUUGCGCAUACGACGCGUGUUC---CCUCGAGAGCAAACUGGGCGGCUGGGGGCGCGAAGCCAACUAGGUGCAGCAAA
.......((((((.(((((.((........(((((((---((......((.......))....)))))))))..)))))))..)))))).... ( -30.80)
>consensus
CAAUAAACUGCACAAGUUGCGCAUACGACGCGUGUUC___CCUCGAGAGGAAACGGGGCGGCUGCAG__ACGAAGCCAACUAGGUGCAGCAAA
.......((((((.((((((((.......)))).......(((((........))))).((((((......))))))))))..)))))).... (-28.39 = -29.45 +   1.06)

alignment

secondary structure

dotplot

Window 9

Location	1,339,613 – 1,339,704
Length	91
Sequences	4
Columns	93
Reading direction	reverse
Mean pairwise identity	90.98
Mean single sequence MFE	-34.35
Consensus MFE	-27.91
Energy contribution	-28.98
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-2.65
Structure conservation index	0.81
SVM decision value	1.49
SVM RNA-class probability	0.958404
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1339613 91 - 23771897
UUUGCUGCACCUAGUUGGCUUCGU--CUUUAGCCACCUCGUUUCCUCUCGAGGGAGGAACACGCGUCGUAUGCGCAACUUGUGCAGUUUAUUG
...(((((((..((((((((....--....)))).....(((((((((....))))))).))((((.....)))))))).)))))))...... ( -33.80)
>DroSec_CAF1 11842 88 - 1
UUUGCUGCACCUAGUUGGCUGCGU--CUGCAGCCGCCCCGUUUCCUCCCGAGG---GAACACGCGUCGUAUGCGCAACUUGUGCAGUUUAUUG
...(((((((..((((((((((..--..)))))).....(((((((....)))---))))..((((.....)))))))).)))))))...... ( -37.90)
>DroSim_CAF1 11934 88 - 1
UUUGCUGCACCUAGUUGGCUGCGU--CUGCAGCCGCCCCGUUUCCUCCCGAGG---GAACACGCGUCGUAUGCGCAACUUGUGCAGUUUAUUG
...(((((((..((((((((((..--..)))))).....(((((((....)))---))))..((((.....)))))))).)))))))...... ( -37.90)
>DroEre_CAF1 12196 90 - 1
UUUGCUGCACCUAGUUGGCUUCGCGCCCCCAGCCGCCCAGUUUGCUCUCGAGG---GAACACGCGUCGUAUGCGCAACUUGUGCAGUUUAUUG
...(((((((..(((((((..(((((((((((..((.......)).)).).))---).....))).))...)).))))).)))))))...... ( -27.80)
>consensus
UUUGCUGCACCUAGUUGGCUGCGU__CUGCAGCCGCCCCGUUUCCUCCCGAGG___GAACACGCGUCGUAUGCGCAACUUGUGCAGUUUAUUG
...(((((((..(((((((((((....))))))).....(((((((....)))...))))..((((.....)))))))).)))))))...... (-27.91 = -28.98 +   1.06)

alignment

secondary structure

dotplot

Window 0

Location	1,339,676 – 1,339,776
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.24
Mean single sequence MFE	-38.78
Consensus MFE	-26.04
Energy contribution	-26.48
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-1.66
Structure conservation index	0.67
SVM decision value	0.12
SVM RNA-class probability	0.591921
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1339676 100 - 23771897
AGUGGGGGGAGGGGGGGCGGCAUGUG--------UGUGUGCGGUUAGAAGGGCGUGGCAGCCGCAAUUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUUCGU--CUUU----------
.......(((((.(((((.((((...--------...))))...(((..(((.(..(((((((((.....))))))......)))..).)))..)))))))).)--))))---------- ( -33.60)
>DroSec_CAF1 11902 95 - 1
-GUGGGG--------GGCGGCAUGUGUGUG----UGUGUGCGGUUAGGAGGGCGUGGCAGCCGCAACUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUGCGU--CUGC----------
-...(.(--------(((.(((..(....)----..)))((((((((..(((.(..(((((((((.....))))))......)))..).)))..))))))))))--)).)---------- ( -36.20)
>DroSim_CAF1 11994 100 - 1
UGUGGGG--------GGCGGCAUGUGAGUGUGUGUGAGUGCGGUUAGGAGGGCGUGGCAGCCGCAAUUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUGCGU--CUGC----------
....(.(--------(((.(((..(....)..)))....((((((((..(((.(..(((((((((.....))))))......)))..).)))..))))))))))--)).)---------- ( -36.20)
>DroEre_CAF1 12256 92 - 1
UGUGGGG--------GGCGGCAAGUG--------UGUGUGCGGUUAGG--GGCGGGGCAGCCGCAAUUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUUCGCGCCCCC----------
...((((--------(((((((((((--------(.(((.(.((....--.)).).)))((((((.....)))))).))))))))))).((.....)).......)))))---------- ( -40.30)
>DroYak_CAF1 12840 104 - 1
UGUGGGG--------GGCGGCAUAUG--------UGUGUGCGGUUAGGAGGGCGUGGCAGCCGCAAUUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUUCGCCCCCCUAACUUGCCAC
...((((--------(((((((((..--------..)))))((((((..(((.(..(((((((((.....))))))......)))..).)))..)))))).))))))))........... ( -47.60)
>consensus
UGUGGGG________GGCGGCAUGUG________UGUGUGCGGUUAGGAGGGCGUGGCAGCCGCAAUUGAUGUGGCAAUAUUUGCUGCACCUAGUUGGCUUCGU__CUCC__________
................(((((((((..........))))))((((((..(((.((((((((((((.....))))))......)))))).)))..)))))).)))................ (-26.04 = -26.48 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:40 2006