Locus 3789

Sequence ID	2L_DroMel_CAF1
Location	11,069,373 – 11,069,517
Length	144
Max. P	0.996659

overview

Window 2

Location	11,069,373 – 11,069,482
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-38.90
Consensus MFE	-32.08
Energy contribution	-33.68
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.82
SVM decision value	1.18
SVM RNA-class probability	0.926987
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11069373 109 + 22407834
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCA
..((((........(((((....((....))...)))))....(((((((((..(((((((...(((.......)))...))))))).....)))))).)))...)))) ( -39.50)
>DroSec_CAF1 58010 109 + 1
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCA
..((((........(((((....((....))...)))))....(((((((((..(((((((...(((.......)))...))))))).....)))))).)))...)))) ( -39.50)
>DroSim_CAF1 58196 109 + 1
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCA
..((((........(((((....((....))...)))))....(((((((((..(((((((...(((.......)))...))))))).....)))))).)))...)))) ( -39.50)
>DroEre_CAF1 60822 104 + 1
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACUGCGCAGCCGCAGCAGCCGCAGCAGCAG-----AAGGUUGCUGAAGAAGCCGCGUCAGAAGGCCA
..............((((..(.(((...........((((((....)))))).((.((..(..(((((((..-----...)))))))..)..)).))))).)..)))). ( -36.20)
>DroYak_CAF1 60854 109 + 1
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACCGCGCAGCCGCAGCAGCAGAAGCUGCAUUUGCUGAGGUAGCUGAAGAAGCCGCGUCAGAAGCCCA
..((((........(((((((((.(((.((....)).)))))...)).)))))...(((((....))))).....((((.(..(((.....)))..).))))...)))) ( -39.80)
>consensus
GGUGGGAAAGAGAAGGCUGGCCGACAAAUGUAGACAGUUGCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCA
..((((........(((((....((....))...)))))....(((((((((..(((((((...(((.......)))...))))))).....)))))).)))...)))) (-32.08 = -33.68 +   1.60)

alignment

secondary structure

dotplot

Window 3

Location	11,069,373 – 11,069,482
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-38.16
Consensus MFE	-31.28
Energy contribution	-31.68
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-2.80
Structure conservation index	0.82
SVM decision value	2.73
SVM RNA-class probability	0.996659
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11069373 109 - 22407834
UGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((((.(((((((((((.(..(((((..(((((....)))))....)))))..).))))))(((((....)))))........)))))..)))))............. ( -37.70)
>DroSec_CAF1 58010 109 - 1
UGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((((.(((((((((((.(..(((((..(((((....)))))....)))))..).))))))(((((....)))))........)))))..)))))............. ( -37.70)
>DroSim_CAF1 58196 109 - 1
UGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((((.(((((((((((.(..(((((..(((((....)))))....)))))..).))))))(((((....)))))........)))))..)))))............. ( -37.70)
>DroEre_CAF1 60822 104 - 1
UGGCCUUCUGACGCGGCUUCUUCAGCAACCUU-----CUGCUGCUGCGGCUGCUGCGGCUGCGCAGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((...(((((((((((.(..(((((.....-----.)))))..).))))))(((((((....))))))).............)))))...))).............. ( -38.40)
>DroYak_CAF1 60854 109 - 1
UGGGCUUCUGACGCGGCUUCUUCAGCUACCUCAGCAAAUGCAGCUUCUGCUGCUGCGGCUGCGCGGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((((...(.(((((((.(....(((.....)))....(((((....))))).).))))))))((((((((.((....)).))).))))))))))............. ( -39.30)
>consensus
UGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGCAACUGUCUACAUUUGUCGGCCAGCCUUCUCUUUCCCACC
.(((((.(((((((((((.(..((((......(((.......)))...))))..).))))))(((((....)))))........)))))..)))))............. (-31.28 = -31.68 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	11,069,412 – 11,069,517
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.35
Mean single sequence MFE	-40.76
Consensus MFE	-29.76
Energy contribution	-31.20
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.73
SVM decision value	0.87
SVM RNA-class probability	0.871820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11069412 105 + 22407834
GCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAAGCUGAGGAG
....(((((....)))))((((...(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...)))))..))))..... ( -39.50)
>DroSec_CAF1 58049 104 + 1
GCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAUGCUGAGG-G
....(((((....)))))(((((..(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...))))).)))))...-. ( -42.10)
>DroSim_CAF1 58235 105 + 1
GCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAGACUGAGGGG
((..(((((((((..(((((((...(((.......)))...))))))).....)))))).)))..))((.....(((...(((........)))..)))...)). ( -39.20)
>DroEre_CAF1 60861 99 + 1
GCGACUGCGCAGCCGCAGCAGCCGCAGCAGCAG-----AAGGUUGCUGAAGAAGCCGCGUCAGAAGGCCAGAAAGGUGGGAGCGAGAAGGAGCUAGGCUGCUG-C
(((....)))....(((((((((.(((((((..-----...)))))))....((((((..(.....(((.....))).)..))).......))).))))))))-) ( -39.21)
>DroYak_CAF1 60893 103 + 1
GCGACCGCGCAGCCGCAGCAGCAGAAGCUGCAUUUGCUGAGGUAGCUGAAGAAGCCGCGUCAGAAGCCCAGA-AGGUGGGAGCGAGAAGGGGCUGAGCUGCUG-C
(((.(.((.(((((.(.(((((....))))).((((((((.(..(((.....)))..).)).....((((..-...))))))))))..).))))).)).).))-) ( -43.80)
>consensus
GCGACUGCGCAGCCGCAGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAAGCUGAGG_G
((..(((((((((..(((((((...(((.......)))...))))))).....)))))).)))..)).......(((...(((........)))..)))...... (-29.76 = -31.20 +   1.44)

alignment

secondary structure

dotplot

Window 5

Location	11,069,412 – 11,069,517
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	88.35
Mean single sequence MFE	-33.58
Consensus MFE	-25.38
Energy contribution	-25.78
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-1.84
Structure conservation index	0.76
SVM decision value	0.50
SVM RNA-class probability	0.759963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11069412 105 - 22407834
CUCCUCAGCUUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGC
.....((((..(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))...))))..((((((....)))))) ( -32.30)
>DroSec_CAF1 58049 104 - 1
C-CCUCAGCAUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGC
.-...(((((.(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))..)))))..((((((....)))))) ( -32.80)
>DroSim_CAF1 58235 105 - 1
CCCCUCAGUCUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGC
...........(((........))).(((......)))((..(((.(((((((.(..(((((..(((((....)))))....)))))..).))))))))))..)) ( -31.50)
>DroEre_CAF1 60861 99 - 1
G-CAGCAGCCUAGCUCCUUCUCGCUCCCACCUUUCUGGCCUUCUGACGCGGCUUCUUCAGCAACCUU-----CUGCUGCUGCGGCUGCUGCGGCUGCGCAGUCGC
(-((((((((.(((........))).(((......))).........(((((......((((.....-----.))))))))))))))))))((((....)))).. ( -35.90)
>DroYak_CAF1 60893 103 - 1
G-CAGCAGCUCAGCCCCUUCUCGCUCCCACCU-UCUGGGCUUCUGACGCGGCUUCUUCAGCUACCUCAGCAAAUGCAGCUUCUGCUGCUGCGGCUGCGCGGUCGC
(-(.((.((.(((((.......((.((((...-..))))....(((.(..(((.....)))..).)))))....(((((.......)))))))))).)).)).)) ( -35.40)
>consensus
C_CCUCAGCCUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCUGCGGCUGCGCAGUCGC
...........(((........)))((((......))))...(((.(((((((.(..((((......(((.......)))...))))..).)))))))))).... (-25.38 = -25.78 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:22 2006