Locus 9954

Sequence ID	3R_DroMel_CAF1
Location	26,679,422 – 26,679,621
Length	199
Max. P	0.990497

overview

Window 1

Location	26,679,422 – 26,679,541
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.88
Mean single sequence MFE	-49.10
Consensus MFE	-44.80
Energy contribution	-45.52
Covariance contribution	0.72
Combinations/Pair	1.08
Mean z-score	-1.43
Structure conservation index	0.91
SVM decision value	1.14
SVM RNA-class probability	0.921069
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26679422 119 + 27905053
CGGCAAGUUCUACCGAGGAUUUAGCC-AACAGCUCAAUCCUGACAGGAAGCGGCAGCCCGAACUCCUCGGCCUCUGCUGAAUCCAGGGGUCUUCUGGAGUCGGGAAAAGUGGCGGCCAUG
.(((...((((....((((((.(((.-....))).))))))....))))((.((..(((((.((((..((((((((.......))))))))....)))))))))....)).)).)))... ( -49.10)
>DroSec_CAF1 269961 119 + 1
CGGCAAGUUCUACCGAGGAUUUGGCC-AACAGCUCAAUCCUGACAGGAAGCGGCAGCCCGAACUCCUCGGCCUCUGCUGAAUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUG
.(((...((((....((((((.(((.-....))).))))))....))))((.((..(((((.((((..((((((((.......))))))))....)))))))))....)).)).)))... ( -49.10)
>DroSim_CAF1 266733 119 + 1
CGGCAAGUUCUACCGAGGAUUUGGCC-AACAGCUCGAUCCUGACCGGAAGCGGCAGCCCGAACUCCUCGGCCUCUGCUGAAUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUG
.(((........(((((((((.(((.-....))).))))))...)))..((.((..(((((.((((..((((((((.......))))))))....)))))))))....)).)).)))... ( -50.90)
>DroEre_CAF1 285851 120 + 1
CGGCCAGUUCUACAGAGGAUUUGGCGGAACAGCUCGAUCCUGACCGGAAGCGGCAGCCCGAACUCUUCGGCCUCUGCGGAAUCCAAGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUG
.((((..((((....((((((.(((......))).))))))....))))((.((..(((((.((((..((((..((.(....)))..))))....)))))))))....)).))))))... ( -48.00)
>DroYak_CAF1 275045 119 + 1
CGGCCAGCUCUACUGAGGAUUUGGCG-AACAGCUCCAUCCUGACCGGAAGCGGCAGCCCGAACUCCUCGGCCUCGGCUGAAUCCAAGGGUCUUCUGGAGUCGGGUAAGGUGGCUGCGAUG
((((((.((......(((((..(((.-....)))..)))))(.(((....)))).((((((.(((((((((....)))))(((....))).....)))))))))).)).))))))..... ( -48.40)
>consensus
CGGCAAGUUCUACCGAGGAUUUGGCC_AACAGCUCAAUCCUGACCGGAAGCGGCAGCCCGAACUCCUCGGCCUCUGCUGAAUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUG
.(((...((((....((((((.(((......))).))))))....))))((.((..(((((.((((..((((((((.......))))))))....)))))))))....)).)).)))... (-44.80 = -45.52 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	26,679,501 – 26,679,621
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-45.90
Consensus MFE	-40.28
Energy contribution	-40.88
Covariance contribution	0.60
Combinations/Pair	1.05
Mean z-score	-1.97
Structure conservation index	0.88
SVM decision value	2.22
SVM RNA-class probability	0.990497
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26679501 120 + 27905053
AUCCAGGGGUCUUCUGGAGUCGGGAAAAGUGGCGGCCAUGCACAACGAUGCCCGGAGUGCGCUGCACAACUACAUCCAGAGGACCCAUCCCUCGCAGCCCAUGCGAUUCCAGACGCUCUU
....((((((..(((((((((.(((..(((.(((((...((((..((.....))..)))))))))...)))...))).((((.......))))(((.....)))))))))))).)))))) ( -47.10)
>DroSec_CAF1 270040 120 + 1
AUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUGCACAACGAUGCCCGGAGUGCGCUGCACAACUACAUCCAGAGGACCCAUCCCUCGCAGCCCAUGCGAUUCCAGACCCUCUU
.....(((((((...((((((.(((..(((.(((((...((((..((.....))..)))))))))...)))...))).((((.......))))(((.....))))))))))))))))... ( -47.20)
>DroSim_CAF1 266812 120 + 1
AUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUGCACAACGAUGCCCGAAGUGCGCUGCACAACUACAUCCAGAGGACCCAUCCCUCGCAGCCCAUGCGAUUCCAGACCCUCUU
.....(((((((...((((((.(((..(((.(((((...((((..((.....))..)))))))))...)))...))).((((.......))))(((.....))))))))))))))))... ( -46.40)
>DroEre_CAF1 285931 120 + 1
AUCCAAGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUGCACAACGAUGCCCGGAGUGCGCUGCACAACUACAUCCAGAGGACCCAUCCCGCGCAGCCCAUGCGAUUCCAGACCCUCUU
.....(((((((...((((((((((..(((.(((((...((((..((.....))..)))))))))...)))...(((...)))....))))..(((.....))))))))))))))))... ( -46.40)
>DroYak_CAF1 275124 120 + 1
AUCCAAGGGUCUUCUGGAGUCGGGUAAGGUGGCUGCGAUGCACAACGAUGCCCGGAGUGCGCUGCACAACUACAUCCAGAGAACGCAUCCCACGCAGCCCAUGCGAUUCCAGACGCUGUU
....((.(((..((((((((((.((...(.(((((((..(((......)))..((..(((((((............)))....))))..)).)))))))))).)))))))))).))).)) ( -42.40)
>consensus
AUCCAGGGGUCUCCUGGAGUCGGGAAAAGUGGCGGCCAUGCACAACGAUGCCCGGAGUGCGCUGCACAACUACAUCCAGAGGACCCAUCCCUCGCAGCCCAUGCGAUUCCAGACCCUCUU
.....(((((((...((((((((((..(((.(((((...((((..((.....))..)))))))))...)))...(((...)))....))))..(((.....))))))))))))))))... (-40.28 = -40.88 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:35 2006