Locus 46

Sequence ID	3R_DroMel_CAF1
Location	304,357 – 304,510
Length	153
Max. P	0.914275

overview

Window 2

Location	304,357 – 304,471
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.16
Mean single sequence MFE	-35.13
Consensus MFE	-23.38
Energy contribution	-22.50
Covariance contribution	-0.88
Combinations/Pair	1.32
Mean z-score	-1.73
Structure conservation index	0.67
SVM decision value	1.09
SVM RNA-class probability	0.914275
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 304357 114 - 27905053
CGCGAGUGUGUAUUUGUGGCCGUGCACAA----GUGCAUUUGUGUGUGUGCACUCGGGAUUCCUCUUCCAUUCCAAUCGCCGCUCGACCCCCCC--CCCCCCCUUCCACACCAUACCUCG
..((((.((((...(((((..(((((((.----(..(....)..).))))))).(((((((.............)))).)))............--.........)))))..)))))))) ( -30.12)
>DroSec_CAF1 39577 106 - 1
CGCGAGUGCGCAUUUGUGACCGUGCACGA----GUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCUAAUUGC-ACUC-------GC--CGCCGCCUUCUGCACUCUACCUCG
...(((((((((((((((......)))))----))))...((.(((.(((((.(..((((.........))))..).)))-)).)-------))--)).........))))))....... ( -37.10)
>DroEre_CAF1 43991 114 - 1
CGCGGGUGCGUAUUUGUGGCCGUGAACGAGUGAGUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCCAAUUGCCGCUCGCCCCCGCUUGCCCCCGCUUCCG------CCCACG
.(((((.(((.....((((..((((.((.((((((((((........))))))))((((......)))).........)))).))))..)))).))).))))).....------...... ( -42.30)
>DroYak_CAF1 43963 91 - 1
CGCGAGUGCGUAUUUGUGGCCGUGUACGA----GUGCAUUCGUAUGUGUGCACACGGAAUUCCUCUUCCAUUCCAAUUGCCGCUUGCCU-------------------------CUCUCG
((.(((.(.(((...(((((.(((((((.----((((....)))).)))))))..((((......)))).........))))).)))).-------------------------))).)) ( -31.00)
>consensus
CGCGAGUGCGUAUUUGUGGCCGUGCACGA____GUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCCAAUUGCCGCUCGCCC___CC__CCCCCCCUUCCG______ACCUCG
.((((((((((((.(..((..((((((......))))))))..).))))))))))((((......)))).........))........................................ (-23.38 = -22.50 +  -0.88)

alignment

secondary structure

dotplot

Window 3

Location	304,395 – 304,510
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.51
Mean single sequence MFE	-38.95
Consensus MFE	-31.75
Energy contribution	-31.50
Covariance contribution	-0.25
Combinations/Pair	1.12
Mean z-score	-1.77
Structure conservation index	0.82
SVM decision value	0.47
SVM RNA-class probability	0.747520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 304395 115 - 27905053
CAAAAGCGCGGGCCCUU-UACACUUGCGUUCGUUCUCCUUCGCGAGUGUGUAUUUGUGGCCGUGCACAA----GUGCAUUUGUGUGUGUGCACUCGGGAUUCCUCUUCCAUUCCAAUCGC
.......((((((((..-((((((((((............)))))))))).....).))))(((((((.----(..(....)..).)))))))..((((......))))........))) ( -40.20)
>DroSec_CAF1 39607 115 - 1
CAAAAGCGCGGGCCCUU-UACACUUGCGUUCGUUCUCCUUCGCGAGUGCGCAUUUGUGACCGUGCACGA----GUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCUAAUUGC
.....((((((......-..((((((((............))))))))(((....))).))))))..((----((((((........))))))))((((......))))........... ( -40.50)
>DroEre_CAF1 44025 120 - 1
CAAAAGCGCGGGCCCUUCUACACUUGCGUUCGUUCUCUUUCGCGGGUGCGUAUUUGUGGCCGUGAACGAGUGAGUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCCAAUUGC
....((((((((..........))))))))....(((.(((((((.((((....)))).))))))).))).((((((((........))))))))((((......))))........... ( -40.60)
>DroYak_CAF1 43978 116 - 1
UAAAAGCGCGGGCCCUUCUACACUUGCGUUCGUUCUCCUUCGCGAGUGCGUAUUUGUGGCCGUGUACGA----GUGCAUUCGUAUGUGUGCACACGGAAUUCCUCUUCCAUUCCAAUUGC
.......((((((((.....((((((((............)))))))).......).))))(((((((.----((((....)))).)))))))..((((......))))........))) ( -34.50)
>consensus
CAAAAGCGCGGGCCCUU_UACACUUGCGUUCGUUCUCCUUCGCGAGUGCGUAUUUGUGGCCGUGCACGA____GUGCAUUCGUGUGUGUGCACUCGGAAUUCCUCUUCCAUUCCAAUUGC
.....((((((.(.(.....((((((((............)))))))).......).).))))))........((((((........))))))..((((......))))........... (-31.75 = -31.50 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:14 2006