Locus 6233

Sequence ID	X_DroMel_CAF1
Location	15,833,988 – 15,834,125
Length	137
Max. P	0.950520

overview

Window 2

Location	15,833,988 – 15,834,108
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.59
Mean single sequence MFE	-24.57
Consensus MFE	-17.02
Energy contribution	-18.78
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.69
SVM decision value	0.22
SVM RNA-class probability	0.641612
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15833988 120 + 22224390
UUUGGACGCCAACUGCCAUUUGACGUUGGUAAUGCACUAAUAAAUUUUAAACAAUAUCGAAAGCAAAACCAUUUUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAG
......(((.((((((((........))))..........................((((((.........)))))).......)))).)))((((((((((....))))))).)))... ( -27.60)
>DroSec_CAF1 6178 94 + 1
UUCGGACGCCAACU------------------------ACUAAAUUAUAAACAAUAUCGAAAGCAA-ACCAU-UUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAG
..............------------------------........................((((-((((.-.........)).))))))(((((((((((....))))))).)))).. ( -22.10)
>DroEre_CAF1 6868 114 + 1
UUCCGACGCCAUCUGUCAUUUGCCG---AAAAUACAC---AAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUUUAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAG
....((((.....))))........---.........---......................(((((..((..(.....)..))..)))))(((((((((((....))))))).)))).. ( -22.40)
>DroYak_CAF1 6070 114 + 1
UGCGAACGCCAUCUGCCAUUUGACG---AUAAUGCAC---UAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUCUAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAG
.((((((......(((..(((((..---(((((....---...)))))........))))).)))........((........))))))))(((((((((((....))))))).)))).. ( -26.20)
>consensus
UUCGGACGCCAACUGCCAUUUGACG___AUAAUGCAC___UAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAG
..............................................................(((((..((...........))..)))))(((((((((((....))))))).)))).. (-17.02 = -18.78 +   1.75)

alignment

secondary structure

dotplot

Window 3

Location	15,834,028 – 15,834,125
Length	97
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-23.00
Consensus MFE	-19.67
Energy contribution	-21.43
Covariance contribution	1.75
Combinations/Pair	1.04
Mean z-score	-2.77
Structure conservation index	0.86
SVM decision value	1.40
SVM RNA-class probability	0.950520
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15834028 97 + 22224390
UAAAUUUUAAACAAUAUCGAAAGCAAAACCAUUUUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAGUGUAUUAUAGGUUAUUU
..........(((.........(((((..((..(.....)..))..)))))(((((((((((....))))))).))))..))).............. ( -20.50)
>DroSec_CAF1 6194 95 + 1
UAAAUUAUAAACAAUAUCGAAAGCAA-ACCAU-UUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAGUGUAUUAUAGGUUAUUU
....(((((((((.........((((-((((.-.........)).))))))(((((((((((....))))))).))))..))).))))))....... ( -25.20)
>DroEre_CAF1 6902 97 + 1
AAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUUUAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAGUGUAUUAUAAGUUACUU
....(((((((((.........(((((..((..(.....)..))..)))))(((((((((((....))))))).))))..))).))))))....... ( -23.20)
>DroYak_CAF1 6104 97 + 1
UAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUCUAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAGUGUAUUAUAAGUUACUU
....(((((((((.........(((((..((...........))..)))))(((((((((((....))))))).))))..))).))))))....... ( -23.10)
>consensus
UAAAUUAUAAACAAUAUCAAAAGCAAAACCAUUUUGAAUAUCUGAGUUUGCGGCUAUACGGAGUAAUCCGUGUAAGCUAGUGUAUUAUAAGUUACUU
....(((((((((.........(((((..((...........))..)))))(((((((((((....))))))).))))..))).))))))....... (-19.67 = -21.43 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:54 2006