Locus 7700

Sequence ID	3L_DroMel_CAF1
Location	20,601,130 – 20,601,278
Length	148
Max. P	0.846541

overview

Window 9

Location	20,601,130 – 20,601,238
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.73
Mean single sequence MFE	-23.38
Consensus MFE	-19.41
Energy contribution	-19.17
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.83
SVM decision value	0.77
SVM RNA-class probability	0.846541
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20601130 108 - 23771897
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUCUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAGCAAA
...((((((((((........))).((((((------------(....)))))))))))))).....((...(((....(((((((.................)))).))).)))))... ( -23.63)
>DroSec_CAF1 45975 108 - 1
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUUUGGCAGCCAUGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAGCAAA
((((.((((((((.......(((((((((((------------(....)))))))..)))))....)))..............((....))........))))).))))........... ( -23.10)
>DroAna_CAF1 68138 120 - 1
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCAGCACAGCACACAGCCUCUGACGGCCGAGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAACAAA
...((((((((((............((((.....))))...(((...)))..)))))))))).........((((....(((((((.................)))).))).)))).... ( -22.33)
>DroSim_CAF1 40751 108 - 1
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUUUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAGCAAA
...((((((((((........))).((((((------------(....)))))))))))))).....((...(((....(((((((.................)))).))).)))))... ( -23.63)
>DroEre_CAF1 38460 108 - 1
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUCUGGCGGCCAAGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAACAAA
((((.(((((.......((((((.(((((((------------(((...))))))..)))).))))))...............((....))........))))).))))........... ( -24.20)
>consensus
UUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC____________GCCUCUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUACAUAGUAAUAACAAUAAUAACAAAUACUAAUGGUGAGCAAA
...((((((((((.........((....)).............(((...))))))))))))).........((((....(((((((.................)))).))).)))).... (-19.41 = -19.17 +  -0.24)

alignment

secondary structure

dotplot

Window 0

Location	20,601,170 – 20,601,278
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.13
Mean single sequence MFE	-33.96
Consensus MFE	-27.40
Energy contribution	-27.64
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-1.62
Structure conservation index	0.81
SVM decision value	0.58
SVM RNA-class probability	0.789371
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20601170 108 - 23771897
AGUCCGAGGAGGCCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUCUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUAC
.(..((((...(((.(((.((((.....)))))))))).....((((((((((........))).((((((------------(....))))))))))))))))))..)........... ( -34.30)
>DroSec_CAF1 46015 108 - 1
AGUCCGAGGAGGCCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUUUGGCAGCCAUGCUUCUUGAGCAAUUCAAAUAC
.(..((((((((((.(((.((((.....))))))))))............(((........))).((((((------------(....)))))))....)))))))..)........... ( -32.50)
>DroAna_CAF1 68178 117 - 1
---ACGCGGAGGUCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCAGCACAGCACACAGCCUCUGACGGCCGAGCUUCUUGAGCAAUUCAAAUAC
---.((.((((.((.(((.((((.....)))))))(((.(((((((.((((((........))).((((.....))))...))).))))))).))))).)))).)).............. ( -34.80)
>DroSim_CAF1 40791 108 - 1
AGUCCGAGGAGGCCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUUUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUAC
.(..((((...(((.(((.((((.....)))))))))).....((((((((((........))).((((((------------(....))))))))))))))))))..)........... ( -34.30)
>DroEre_CAF1 38500 108 - 1
AGUCCGAGGAGGCCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC------------GCCUCUGGCGGCCAAGCUUCUUGAGCAAUUCAAAUAC
.(..((((...(((.(((.((((.....)))))))))).....((((((((((........)))....(((------------(((...)))))))))))))))))..)........... ( -33.90)
>consensus
AGUCCGAGGAGGCCUAGAACAAAGUGCAUUUGUCUGGCAGUUAGAGUUUGGCUAAUUUUUAAGCAGCUGCC____________GCCUCUGGCAGCCAAGCUUCUUGAGCAAUUCAAAUAC
.(..((((...(((.(((.((((.....)))))))))).....((((((((((.........((....)).............(((...)))))))))))))))))..)........... (-27.40 = -27.64 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:17 2006