Locus 3567

Sequence ID	X_DroMel_CAF1
Location	9,576,410 – 9,576,536
Length	126
Max. P	0.990049

overview

Window 5

Location	9,576,410 – 9,576,505
Length	95
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	94.96
Mean single sequence MFE	-26.32
Consensus MFE	-24.94
Energy contribution	-24.98
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.64
Structure conservation index	0.95
SVM decision value	2.19
SVM RNA-class probability	0.990049
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9576410 95 + 22224390
AGUUUAGCCCGAAAGUAUCUCAUAGAUACAUAUGUGGGCUCACUGCGCACAAGUGACUGGCAGGCAUUUGCUGACUUAGUCAUGAUUUGAUG--AAU
.(((((...((((.(((((.....)))))...((((.((.....)).)))).((((((((..(((....)))...))))))))..)))).))--))) ( -26.10)
>DroSec_CAF1 35463 94 + 1
AAUUUAGCCCGA-AGUAUCUCAUAGAUACAUAUGUGGGCUCACUGCGGACAAGUGACUGGCAGGCAUUUGCCGACUUAGUCAUGAUUUGAUG--AAU
......(((((.-.(((((.....))))).....)))))(((...((((...((((((((..(((....)))..).)))))))..)))).))--).. ( -28.60)
>DroSim_CAF1 21927 94 + 1
AAUUUAGCCCGA-AGUAUCUCAUAGAUACAUAUGUGGGCUCACUGCGGACAAGUGACUGGCAGGCAUUUGCCGACUUAGUCAUGAUUUGAUG--AAU
......(((((.-.(((((.....))))).....)))))(((...((((...((((((((..(((....)))..).)))))))..)))).))--).. ( -28.60)
>DroEre_CAF1 40266 94 + 1
AAUUUAGCCCGA-AGUAUCUCAUAGAUACAUAUGCGAGCGCACUGCAGACAAGUGACUGGCAGGCAUUUGCCGACUAAGUCAUGAUUUGAUG--AAU
.(((((((.((.-.(((((.....))))).....)).))......((((...((((((((..(((....)))..)).))))))..)))).))--))) ( -23.50)
>DroYak_CAF1 37270 96 + 1
AAUUUAGCCCGA-AGUAUCUCAUAGAUACAUAUGUGAGCUCACUGCAGACAAGUGACUGGCAGGCAUUUGCCGACUUAGUCAUGAUUUGAUGAGAAU
............-.(((((.....))))).........((((...((((...((((((((..(((....)))..).)))))))..)))).))))... ( -24.80)
>consensus
AAUUUAGCCCGA_AGUAUCUCAUAGAUACAUAUGUGGGCUCACUGCGGACAAGUGACUGGCAGGCAUUUGCCGACUUAGUCAUGAUUUGAUG__AAU
......(((((...(((((.....))))).....)))))......((((...((((((((..(((....)))..)).))))))..))))........ (-24.94 = -24.98 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	9,576,410 – 9,576,505
Length	95
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	94.96
Mean single sequence MFE	-22.32
Consensus MFE	-20.68
Energy contribution	-20.68
Covariance contribution	-0.00
Combinations/Pair	1.09
Mean z-score	-1.35
Structure conservation index	0.93
SVM decision value	0.97
SVM RNA-class probability	0.892933
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9576410 95 - 22224390
AUU--CAUCAAAUCAUGACUAAGUCAGCAAAUGCCUGCCAGUCACUUGUGCGCAGUGAGCCCACAUAUGUAUCUAUGAGAUACUUUCGGGCUAAACU
...--..........((((...))))((....))((((((........)).))))..(((((......(((((.....)))))....)))))..... ( -19.90)
>DroSec_CAF1 35463 94 - 1
AUU--CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCACAUAUGUAUCUAUGAGAUACU-UCGGGCUAAAUU
...--..........(((((..((.(((....))).)).)))))...(((((..(((....)))....(((((.....))))).-.)))))...... ( -23.50)
>DroSim_CAF1 21927 94 - 1
AUU--CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCACAUAUGUAUCUAUGAGAUACU-UCGGGCUAAAUU
...--..........(((((..((.(((....))).)).)))))...(((((..(((....)))....(((((.....))))).-.)))))...... ( -23.50)
>DroEre_CAF1 40266 94 - 1
AUU--CAUCAAAUCAUGACUUAGUCGGCAAAUGCCUGCCAGUCACUUGUCUGCAGUGCGCUCGCAUAUGUAUCUAUGAGAUACU-UCGGGCUAAAUU
...--..........(((((..((.(((....))).)).)))))...(((((..((((....))))..(((((.....))))).-.)))))...... ( -22.80)
>DroYak_CAF1 37270 96 - 1
AUUCUCAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCUGCAGUGAGCUCACAUAUGUAUCUAUGAGAUACU-UCGGGCUAAAUU
...............(((((..((.(((....))).)).)))))...(((((..(((....)))....(((((.....))))).-.)))))...... ( -21.90)
>consensus
AUU__CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCACAUAUGUAUCUAUGAGAUACU_UCGGGCUAAAUU
...............(((((..((.(((....))).)).)))))...(((((..(((....)))....(((((.....)))))...)))))...... (-20.68 = -20.68 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	9,576,444 – 9,576,536
Length	92
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	90.04
Mean single sequence MFE	-32.01
Consensus MFE	-26.12
Energy contribution	-25.48
Covariance contribution	-0.64
Combinations/Pair	1.10
Mean z-score	-1.66
Structure conservation index	0.82
SVM decision value	0.71
SVM RNA-class probability	0.831015
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9576444 92 - 22224390
AUGUCGAAGUGCACGAGUGUCUG---------CGGGAGGCAUU--CAUCAAAUCAUGACUAAGUCAGCAAAUGCCUGCCAGUCACUUGUGCGCAGUGAGCCCA
...(((..(((((((((((.((.---------.((.(((((((--..........((((...))))...))))))).)))).)))))))))))..)))..... ( -35.82)
>DroSec_CAF1 35496 92 - 1
AUGUCGAAGUGCACGAGUGUCUG---------CGGGAGGCAUU--CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCA
...(((..(((.(((((((.((.---------.((.(((((((--..........((((...))))...))))))).)))).))))))).)))..)))..... ( -28.52)
>DroSim_CAF1 21960 92 - 1
AUGUCGAAGUGCACGAGUGUCUG---------CGGGAGGCAUU--CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCA
...(((..(((.(((((((.((.---------.((.(((((((--..........((((...))))...))))))).)))).))))))).)))..)))..... ( -28.52)
>DroEre_CAF1 40299 92 - 1
AUGCCGAGGUGAACGAGUGUCUG---------UGGGAGGCAUU--CAUCAAAUCAUGACUUAGUCGGCAAAUGCCUGCCAGUCACUUGUCUGCAGUGCGCUCG
.((((((..(((..((((((((.---------....)))))))--).)))..))..(((...)))))))...((((((.((.(....).)))))).))..... ( -30.20)
>DroYak_CAF1 37303 103 - 1
AUGCCGAAGUGCACGAGUGUCUGGCAUUUGAGUGGGAGGCAUUCUCAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCUGCAGUGAGCUCA
..((...(.((((((((((.(((((((((((.((((((...)))))))))))....(((...)))(((....))))))))).)))))))..))).)..))... ( -37.00)
>consensus
AUGUCGAAGUGCACGAGUGUCUG_________CGGGAGGCAUU__CAUCAAAUCAUGACUAAGUCGGCAAAUGCCUGCCAGUCACUUGUCCGCAGUGAGCCCA
..((((..(((.(((((((.((...........((.(((((((............((((...))))...))))))).)))).))))))).)))..)).))... (-26.12 = -25.48 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:35 2006