Locus 8498

Sequence ID 3R_DroMel_CAF1
Location 22,692,839 – 22,692,936
Length 97
Max. P 0.934900
window13669 window13670

overview

Window 9

Location 22,692,839 – 22,692,936
Length 97
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -33.92
Consensus MFE -22.58
Energy contribution -23.58
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.67
SVM decision value -0.05
SVM RNA-class probability 0.505577
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22692839 97 + 27905053
AGCGGCAGCGCAUCUCGCUUUUCCCACUGCGCGUGCCCCCCGCGAAUUAAAUAUUGAUGCGG-----GGAUUGC-GGAGACGCGGACAACAAAGUGCACGCA-A
.((((.((((.....)))).......))))((((((.((((((((((.....)))..)))))-----)).((((-(....)))))..........)))))).-. ( -37.30)
>DroSec_CAF1 140377 88 + 1
AGCGGCAGCGCAGCUCGCUUUUCGCACUGCGCGUGCCCCCCGCGAAUUAAAUAUUGAUGC---------------GAAGACGCGGACAACACAGUGCACGCG-A
.((((((((((((...((.....)).))))))(((....(((((..((..((....))..---------------.))..)))))....)))..))).))).-. ( -30.50)
>DroSim_CAF1 142563 88 + 1
AGCGGCAGCGCAGCUCGCUUUUCGCACUGCGCGUGCCCCCCGCGAAUUAAAUAUUGAUGC---------------GGAGACGCGGACAACACAGUGCACGCA-A
.((((((((((((...((.....)).))))))(((....(((((.((((.....)))).)---------------(....)))))....)))..))).))).-. ( -31.70)
>DroYak_CAF1 146295 99 + 1
AGCGGCAGCGCAGCUUGCUAUUCGCACUGCGCGUGCCCCCCGCGAAUUAAAUAUUGAUGCGUAUUCCGAAUUGCGGGAGACGC-----ACACAGUGCACUCGAA
.((((((((((((..(((.....))))))))).))))...............((((.(((((.(((((.....))))).))))-----)..))))))....... ( -36.20)
>consensus
AGCGGCAGCGCAGCUCGCUUUUCGCACUGCGCGUGCCCCCCGCGAAUUAAAUAUUGAUGC_______________GGAGACGCGGACAACACAGUGCACGCA_A
.((((((((((((...((.....)).)))))).))))..((((..((((.....)))).................(....)))))..........))....... (-22.58 = -23.58 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 22,692,839 – 22,692,936
Length 97
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -39.09
Consensus MFE -28.22
Energy contribution -30.22
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.72
SVM decision value 1.24
SVM RNA-class probability 0.934900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22692839 97 - 27905053
U-UGCGUGCACUUUGUUGUCCGCGUCUCC-GCAAUCC-----CCGCAUCAAUAUUUAAUUCGCGGGGGGCACGCGCAGUGGGAAAAGCGAGAUGCGCUGCCGCU
.-.((((((............(((....)-))..(((-----((((...............)))))))))))))..(((((....((((.....)))).))))) ( -37.66)
>DroSec_CAF1 140377 88 - 1
U-CGCGUGCACUGUGUUGUCCGCGUCUUC---------------GCAUCAAUAUUUAAUUCGCGGGGGGCACGCGCAGUGCGAAAAGCGAGCUGCGCUGCCGCU
.-.(((.(((..(((((.((((((.....---------------................)))))).)))))(((((((.((.....)).))))))))))))). ( -38.80)
>DroSim_CAF1 142563 88 - 1
U-UGCGUGCACUGUGUUGUCCGCGUCUCC---------------GCAUCAAUAUUUAAUUCGCGGGGGGCACGCGCAGUGCGAAAAGCGAGCUGCGCUGCCGCU
.-.(((.(((..(((((.((((((.....---------------................)))))).)))))(((((((.((.....)).))))))))))))). ( -38.50)
>DroYak_CAF1 146295 99 - 1
UUCGAGUGCACUGUGU-----GCGUCUCCCGCAAUUCGGAAUACGCAUCAAUAUUUAAUUCGCGGGGGGCACGCGCAGUGCGAAUAGCAAGCUGCGCUGCCGCU
......((((((((((-----(.(((((((((((((..(((((........))))))))).))))))))).)))))))))))...(((..((......)).))) ( -41.40)
>consensus
U_CGCGUGCACUGUGUUGUCCGCGUCUCC_______________GCAUCAAUAUUUAAUUCGCGGGGGGCACGCGCAGUGCGAAAAGCGAGCUGCGCUGCCGCU
...(((.(((..(((((.((((((....................................)))))).)))))(((((((((.....))..))))))))))))). (-28.22 = -30.22 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:46 2006