Locus 1572

Sequence ID 2L_DroMel_CAF1
Location 4,238,711 – 4,238,833
Length 122
Max. P 0.996673
window2530 window2531 window2532

overview

Window 0

Location 4,238,711 – 4,238,801
Length 90
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 92.11
Mean single sequence MFE -23.60
Consensus MFE -20.94
Energy contribution -21.00
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.89
SVM decision value 0.76
SVM RNA-class probability 0.842350
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4238711 90 + 22407834
U------CUGCUCUUCCUUUCGUCCUUUCUCGGGCCAGUAGACGAUGUCGUCGGGGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAA
.------.((.(((((.....((((......)))).....((((....))))))))))).......((((((((....)))))))).......... ( -22.00)
>DroSec_CAF1 13808 90 + 1
U------CUGCUCUUCCUUUCGUCCUUUCUCGGGCCAGCAGACGAUGUCGUCGGGGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAA
(------(((((.........((((......)))).))))))...(((.((.(....).)).))).((((((((....)))))))).......... ( -22.20)
>DroSim_CAF1 20955 90 + 1
U------CUGCUCUUUCUUUCGUCCUUUCUCGGGCCAGCAGACGAUGUCGUCGGGGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAA
(------(((((.........((((......)))).))))))...(((.((.(....).)).))).((((((((....)))))))).......... ( -22.20)
>DroYak_CAF1 22267 93 + 1
UGCUGUCCUGCUCUUCUUUUCGUCCUUUCUUGGGCCAGAAGACGAUGUCGUCGUGGACA---ACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAA
((.(((((.((.....((((.((((......)))).))))((((....)))))))))))---.)).((((((((....)))))))).......... ( -28.00)
>consensus
U______CUGCUCUUCCUUUCGUCCUUUCUCGGGCCAGCAGACGAUGUCGUCGGGGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAA
........((.(((((.....((((......)))).....((((....))))))))))).......((((((((....)))))))).......... (-20.94 = -21.00 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,238,737 – 4,238,833
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 74.06
Mean single sequence MFE -27.58
Consensus MFE -10.87
Energy contribution -11.03
Covariance contribution 0.17
Combinations/Pair 1.11
Mean z-score -3.14
Structure conservation index 0.39
SVM decision value 2.73
SVM RNA-class probability 0.996673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4238737 96 + 22407834
------------GGCCAGU-AGACGAUGUCGUCG---GGGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAAUGCACAAAAGCAAAACAUAAAGUGGCCAAGAC
------------(((((.(-.((((....))))(---....)........((((((((....))))))))..........(((......)))........).)))))..... ( -27.00)
>DroVir_CAF1 12728 111 + 1
GCGGCAAGCGCCGGACAGC-UGAGGAUGUCGUCGUCAACGGCGACAACAAAAUGUGCUGCUAAGUAUAUUAACUCAGAAAUGCACAAGAGCUAAACAUAAAGUAGCCGGCCA
((.....))(((((.(..(-((((..((((((((....))))))))....((((((((....))))))))..)))))....((......)).............)))))).. ( -38.70)
>DroGri_CAF1 18255 106 + 1
--AGAAGGAGAAGGA-GGA-CGAAGAUGCCAUCGUCAACGGCUACAACAAAAUGUGCUGCUAAGUAUAUUAACUCAAAAAUGCACAAGAGCUAAACAUCU--GAGCUGAUUG
--.............-.((-(((.(....).)))))..(((((.((....((((((((....))))))))...........((......))........)--)))))).... ( -20.00)
>DroEre_CAF1 14249 94 + 1
------------GGCCAGAAAGACGAUGUCGUCG---GCGACA---ACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAAUGCACAAAAGCAAAACAUAAAGUGGCCAAGAC
------------(((((((.....(.(((((...---.)))))---.)..((((((((....))))))))...)).....(((......)))..........)))))..... ( -26.90)
>DroYak_CAF1 22299 93 + 1
------------GGCCAGA-AGACGAUGUCGUCG---UGGACA---ACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAAUGCACAAAAGCAAAACAUAAAGUGGCCAAGAC
------------(((((..-.((((....))))(---((....---....((((((((....))))))))..........(((......)))...)))....)))))..... ( -26.80)
>DroMoj_CAF1 12562 93 + 1
------------------C-UGUGGAUGUCGUCGUCAACGGCGACAACAAAAUGUGCUGCUAAGUAUAUUAACUCAGAAAUGCACAAGAGCUAAACAUAAAGUAGCUGGCCG
------------------.-...((.((((((((....))))))))......(((((..((.(((......))).))....)))))..(((((.........)))))..)). ( -26.10)
>consensus
____________GGCCAGA_AGACGAUGUCGUCG___ACGACAACAACAAAAUGUGCUGCUAAGCAUAUUAACUCAAAAAUGCACAAAAGCAAAACAUAAAGUAGCCAAGAC
.........................((((.((((....))))........((((((((....))))))))...........((......))...)))).............. (-10.87 = -11.03 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,238,737 – 4,238,833
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 74.06
Mean single sequence MFE -25.27
Consensus MFE -14.52
Energy contribution -14.93
Covariance contribution 0.42
Combinations/Pair 1.25
Mean z-score -1.88
Structure conservation index 0.57
SVM decision value 1.21
SVM RNA-class probability 0.930806
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4238737 96 - 22407834
GUCUUGGCCACUUUAUGUUUUGCUUUUGUGCAUUUUUGAGUUAAUAUGCUUAGCAGCACAUUUUGUUGUUGUCCC---CGACGACAUCGUCU-ACUGGCC------------
.....(((((....((((.(((((.....((((.((......)).))))..))))).))))..((((((((....---))))))))......-..)))))------------ ( -25.30)
>DroVir_CAF1 12728 111 - 1
UGGCCGGCUACUUUAUGUUUAGCUCUUGUGCAUUUCUGAGUUAAUAUACUUAGCAGCACAUUUUGUUGUCGCCGUUGACGACGACAUCCUCA-GCUGUCCGGCGCUUGCCGC
.(((.(((.......((..(((((..(((((....((((((......))))))..)))))...((((((((.......)))))))).....)-))))..))..))).))).. ( -34.50)
>DroGri_CAF1 18255 106 - 1
CAAUCAGCUC--AGAUGUUUAGCUCUUGUGCAUUUUUGAGUUAAUAUACUUAGCAGCACAUUUUGUUGUAGCCGUUGACGAUGGCAUCUUCG-UCC-UCCUUCUCCUUCU--
..........--.((((..((((...(((((....((((((......))))))..)))))....))))..((((((...)))))).....))-)).-.............-- ( -19.90)
>DroEre_CAF1 14249 94 - 1
GUCUUGGCCACUUUAUGUUUUGCUUUUGUGCAUUUUUGAGUUAAUAUGCUUAGCAGCACAUUUUGU---UGUCGC---CGACGACAUCGUCUUUCUGGCC------------
.....(((((....((((.(((((.....((((.((......)).))))..))))).))))..(((---((((..---.))))))).........)))))------------ ( -23.90)
>DroYak_CAF1 22299 93 - 1
GUCUUGGCCACUUUAUGUUUUGCUUUUGUGCAUUUUUGAGUUAAUAUGCUUAGCAGCACAUUUUGU---UGUCCA---CGACGACAUCGUCU-UCUGGCC------------
.....(((((....((((.(((((.....((((.((......)).))))..))))).))))..(((---((((..---.)))))))......-..)))))------------ ( -23.90)
>DroMoj_CAF1 12562 93 - 1
CGGCCAGCUACUUUAUGUUUAGCUCUUGUGCAUUUCUGAGUUAAUAUACUUAGCAGCACAUUUUGUUGUCGCCGUUGACGACGACAUCCACA-G------------------
.((..(((((.........)))))..(((((....((((((......))))))..)))))...((((((((.......)))))))).))...-.------------------ ( -24.10)
>consensus
GUCUCGGCCACUUUAUGUUUAGCUCUUGUGCAUUUUUGAGUUAAUAUACUUAGCAGCACAUUUUGUUGUUGCCGU___CGACGACAUCGUCU_UCUGGCC____________
.....(((.((.....))...)))..(((((....((((((......))))))..)))))...((((((((.......)))))))).......................... (-14.52 = -14.93 +   0.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:45 2006