Locus 6252

Sequence ID	3L_DroMel_CAF1
Location	16,648,124 – 16,648,217
Length	93
Max. P	0.875014

overview

Window 5

Location	16,648,124 – 16,648,217
Length	93
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-23.24
Consensus MFE	-13.62
Energy contribution	-13.78
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-2.10
Structure conservation index	0.59
SVM decision value	0.89
SVM RNA-class probability	0.875014
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16648124 93 + 23771897
UGACCAGCACCAUCGAGAUGGAUGGUA------AUGGUACGACUCGCUAUAUGGUACAUUGCUAUAUGCUAUA-----UAUGCUUUAAUGGUAUAAUAGUGUAA
..((((..((((((......)))))).------.))))..........(((((((.....)))))))(((((.-----((((((.....))))))))))).... ( -26.10)
>DroSec_CAF1 21120 89 + 1
UUUCC---ACCAUCGAGAUGGAUGGUA------AUGGUACGACUCGCUAUAUGGUAGA-UGCUAUAUGCUAUA-----UAUGCUUUAAUGGUAUAAUAGUGUAA
.....---((((((......)))))).------.(((((..(((........)))...-)))))((((((((.-----((((((.....)))))))))))))). ( -21.20)
>DroSim_CAF1 19811 82 + 1
UGACC---ACCAUCGAGAUGGAUGGUA------AUGGUACGACUCGCUAUAUGGU--------AUAUGGUAUA-----UAUGCUUUAAUGGUAUAAUAGUGUAA
..(((---((((((......)))))).------(((((.......)))))..)))--------.((((.(((.-----((((((.....))))))))).)))). ( -18.70)
>DroEre_CAF1 21244 84 + 1
UGACC---ACCAUCGAGAUGGAUGGUA------AUGGUACGGCUCGCUAUAUGGUAUA-UGUU-------AUAUAGUAUAUGCUAUAAUGGCAUAAUGGUG---
..(((---((((((......)))))).------............(((((((((((((-((..-------......)))))))))).))))).....))).--- ( -25.10)
>DroYak_CAF1 22207 97 + 1
UGACC---ACCAUCGAGAUGGAUGGUAAUGGUAAUGGUACGGCUCGCUAUAUGGUAUA-UGGAAUAUAGUAUAUAGUAUUUGCUAUAAUGGCAUAAUGGUG---
..(((---((((((......)))))).(((.((....((..((..((((((((.((((-(...))))).))))))))....))..)).)).)))...))).--- ( -25.10)
>consensus
UGACC___ACCAUCGAGAUGGAUGGUA______AUGGUACGACUCGCUAUAUGGUAUA_UGCUAUAUGCUAUA_____UAUGCUUUAAUGGUAUAAUAGUGUAA
..(((...((((((......)))))).......(((((.......)))))..))).......................((((((.....))))))......... (-13.62 = -13.78 +   0.16)

alignment

secondary structure

dotplot

Window 6

Location	16,648,124 – 16,648,217
Length	93
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	79.21
Mean single sequence MFE	-15.12
Consensus MFE	-8.12
Energy contribution	-8.16
Covariance contribution	0.04
Combinations/Pair	1.08
Mean z-score	-1.86
Structure conservation index	0.54
SVM decision value	0.09
SVM RNA-class probability	0.578915
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16648124 93 - 23771897
UUACACUAUUAUACCAUUAAAGCAUA-----UAUAGCAUAUAGCAAUGUACCAUAUAGCGAGUCGUACCAU------UACCAUCCAUCUCGAUGGUGCUGGUCA
.....................((.((-----(((.((((......))))...))))))).....(.((((.------(((((((......))))))).))))). ( -19.20)
>DroSec_CAF1 21120 89 - 1
UUACACUAUUAUACCAUUAAAGCAUA-----UAUAGCAUAUAGCA-UCUACCAUAUAGCGAGUCGUACCAU------UACCAUCCAUCUCGAUGGU---GGAAA
.....................((.((-----(((...))))))).-((((((((....((((.........------..........)))))))))---))).. ( -14.11)
>DroSim_CAF1 19811 82 - 1
UUACACUAUUAUACCAUUAAAGCAUA-----UAUACCAUAU--------ACCAUAUAGCGAGUCGUACCAU------UACCAUCCAUCUCGAUGGU---GGUCA
...........(((.(((...((.((-----(((.......--------...))))))).))).)))..((------(((((((......))))))---))).. ( -13.20)
>DroEre_CAF1 21244 84 - 1
---CACCAUUAUGCCAUUAUAGCAUAUACUAUAU-------AACA-UAUACCAUAUAGCGAGCCGUACCAU------UACCAUCCAUCUCGAUGGU---GGUCA
---......(((((.......)))))..((((((-------....-......))))))...........((------(((((((......))))))---))).. ( -14.30)
>DroYak_CAF1 22207 97 - 1
---CACCAUUAUGCCAUUAUAGCAAAUACUAUAUACUAUAUUCCA-UAUACCAUAUAGCGAGCCGUACCAUUACCAUUACCAUCCAUCUCGAUGGU---GGUCA
---.........(((..((..((.....((((((..(((((...)-))))..))))))...))..))...........((((((......))))))---))).. ( -14.80)
>consensus
UUACACUAUUAUACCAUUAAAGCAUA_____UAUACCAUAUAGCA_UAUACCAUAUAGCGAGUCGUACCAU______UACCAUCCAUCUCGAUGGU___GGUCA
............(((..........................................(((...)))............((((((......))))))...))).. ( -8.12 =  -8.16 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:49 2006