Locus 6508

Sequence ID	3L_DroMel_CAF1
Location	17,264,776 – 17,264,895
Length	119
Max. P	0.894888

overview

Window 8

Location	17,264,776 – 17,264,895
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.03
Mean single sequence MFE	-19.55
Consensus MFE	-17.54
Energy contribution	-18.34
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.90
SVM decision value	0.27
SVM RNA-class probability	0.663649
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17264776 119 + 23771897
AG-CUCAAGACAAAGUAUAAAUACUCACUGAAAUGUGAGUCAAAAUCUUAUCGAGUGGCAAACAAAAAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
..-.....((..(((.......((((((......))))))......))).))..(((((...................((......))..(((((........)))))...))))).... ( -21.32)
>DroSec_CAF1 148306 119 + 1
AG-CUUAAGACAAAGUAUAAAUACUCACUGAAAUGUGAGUCAAAAUCUUAUCGAGUGGCAAACAAAAAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
.(-(((......))))......((((((......))))))..............(((((...................((......))..(((((........)))))...))))).... ( -21.80)
>DroSim_CAF1 143340 119 + 1
AG-CUUAAGACAAAGUAUAAAUACUCACUGAAAUGUGAGUCAAAAUCUUAUCGAGUGGCAAACAAAAAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
.(-(((......))))......((((((......))))))..............(((((...................((......))..(((((........)))))...))))).... ( -21.80)
>DroEre_CAF1 151361 115 + 1
AAUAGUAAGACAAAGUAUAAAUACUC-CUGAAAUGCGAGCCAAAAUCUUAUCGAGAGGCAAA----AAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
..........((.((((....)))).-.))...((((.((.....(((((((....).....----..))))))................(((((........)))))...))))))... ( -14.71)
>DroYak_CAF1 155826 115 + 1
AG-CCUAAGACAAAGUAUAAAUACUC-CUGAAAUGUGAGUCGGAAUCUUAUCGAGUGGCAAA---AAAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
..-..(((((...((((....)))).-((((........))))..)))))....(((((...---.............((......))..(((((........)))))...))))).... ( -18.10)
>consensus
AG_CUUAAGACAAAGUAUAAAUACUCACUGAAAUGUGAGUCAAAAUCUUAUCGAGUGGCAAACAAAAAAUGAGAGAAGCGACAAAACGAAUGACAAAUUUUAAUGUCAAUAGCCGCAGAC
........((..(((.......((((((......))))))......))).))..(((((...................((......))..(((((........)))))...))))).... (-17.54 = -18.34 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	17,264,776 – 17,264,895
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.03
Mean single sequence MFE	-21.91
Consensus MFE	-19.74
Energy contribution	-19.98
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.41
Structure conservation index	0.90
SVM decision value	0.98
SVM RNA-class probability	0.894888
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17264776 119 - 23771897
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUUUUUGUUUGCCACUCGAUAAGAUUUUGACUCACAUUUCAGUGAGUAUUUAUACUUUGUCUUGAG-CU
......((((...((((.((((((((.....(((....((.((......((.....))...)).)).)))..))))))))((((((......))))))..........))))...))-)) ( -23.00)
>DroSec_CAF1 148306 119 - 1
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUUUUUGUUUGCCACUCGAUAAGAUUUUGACUCACAUUUCAGUGAGUAUUUAUACUUUGUCUUAAG-CU
......((((...((((.((((((((.....(((....((.((......((.....))...)).)).)))..))))))))((((((......))))))..........))))...))-)) ( -21.90)
>DroSim_CAF1 143340 119 - 1
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUUUUUGUUUGCCACUCGAUAAGAUUUUGACUCACAUUUCAGUGAGUAUUUAUACUUUGUCUUAAG-CU
......((((...((((.((((((((.....(((....((.((......((.....))...)).)).)))..))))))))((((((......))))))..........))))...))-)) ( -21.90)
>DroEre_CAF1 151361 115 - 1
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUU----UUUGCCUCUCGAUAAGAUUUUGGCUCGCAUUUCAG-GAGUAUUUAUACUUUGUCUUACUAUU
...((((((((.(((((........)))))...(((((((((.......((...----..)).....)))))))))..)))).)))).....(-(((((....))))))........... ( -22.20)
>DroYak_CAF1 155826 115 - 1
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUUU---UUUGCCACUCGAUAAGAUUCCGACUCACAUUUCAG-GAGUAUUUAUACUUUGUCUUAGG-CU
....(((((...(((((........)))))........)))))............---...(((....((((((......((((.(......)-))))........))))))...))-). ( -20.54)
>consensus
GUCUGCGGCUAUUGACAUUAAAAUUUGUCAUUCGUUUUGUCGCUUCUCUCAUUUUUUGUUUGCCACUCGAUAAGAUUUUGACUCACAUUUCAGUGAGUAUUUAUACUUUGUCUUAAG_CU
....(((((...(((((........)))))........))))).........................((((((......((((((......))))))........))))))........ (-19.74 = -19.98 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:57 2006