Locus 3067

Sequence ID 2L_DroMel_CAF1
Location 8,758,714 – 8,758,808
Length 94
Max. P 0.988524
window4878 window4879

overview

Window 8

Location 8,758,714 – 8,758,808
Length 94
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 76.30
Mean single sequence MFE -32.99
Consensus MFE -14.14
Energy contribution -16.58
Covariance contribution 2.44
Combinations/Pair 1.14
Mean z-score -2.50
Structure conservation index 0.43
SVM decision value 2.12
SVM RNA-class probability 0.988524
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8758714 94 + 22407834
UCUUG-UGGGCUUCUGGCGCUU-----GGCUUAAGUGCCUGGCAAGGAAGCAG--------CCAACCAACCAGGAUGCAAAAAUAUCCGAAAGGAUACGAGACAAUGG
(((((-((.((((((((.(((.-----(((......))).)))..((......--------))......)))))).)).......(((....))))))))))...... ( -32.90)
>DroPse_CAF1 82681 96 + 1
UCCGGCUUGUCUUUCCCCGACUCUGGGGGCUUAAGUGCCCCAC-------CAAACAGCCAGCCAACCAAACAG--CGAAAAAAUAUUAGAAC---UGCAAGAGAGGCG
...((((.(((.......)))....(((((......)))))..-------.....)))).(((.......(((--................)---)).......))). ( -23.03)
>DroSec_CAF1 63022 102 + 1
UCUGG-UUGGCUUCUGCCGCUU-----GGCUUAAGUGUCUGGCAAGGAAGCAGGCAACCAACCAACCAACCAGGAUGCAAAAAUAUCCGAAAGGAUACCAGACAAUGG
(((((-(((((((((...(((.-----(((......))).)))..)))))).((.......))...)))))))).........(((((....)))))(((.....))) ( -37.00)
>DroSim_CAF1 65701 102 + 1
UCUGG-UUGGCUUCUGCCGCUU-----GGCUUAAGUGCCUGGCAAGGAAGCAGGCAACCAACCAACCAACCAGGAUGCAAAAAUAUCCGAAAGGAUACGAGACAAUGG
(((((-(((((((((...(((.-----(((......))).)))..)))))).((.......))...)))))))).........(((((....)))))........... ( -38.30)
>DroYak_CAF1 65725 100 + 1
UCUGG-UUGGCUUCUGCCGCUU-----GGCUUAAGUGCCUGGCAAGGAAGCAGCCAGCC--CCAGCCAACCAGGAUGUAAAAAUAUCCGAAAAGAUGCCAGACAAUGA
..(((-((((((...((.(((.-----(((......))).)))..((......)).)).--..)))))))))((((((....)))))).................... ( -33.70)
>consensus
UCUGG_UUGGCUUCUGCCGCUU_____GGCUUAAGUGCCUGGCAAGGAAGCAGGCAACCA_CCAACCAACCAGGAUGCAAAAAUAUCCGAAAGGAUACCAGACAAUGG
(((((....((((((...(((......(((......))).)))..))))))................................(((((....))))))))))...... (-14.14 = -16.58 +   2.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,758,714 – 8,758,808
Length 94
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 76.30
Mean single sequence MFE -33.54
Consensus MFE -12.86
Energy contribution -15.98
Covariance contribution 3.12
Combinations/Pair 1.25
Mean z-score -2.08
Structure conservation index 0.38
SVM decision value 0.88
SVM RNA-class probability 0.873377
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8758714 94 - 22407834
CCAUUGUCUCGUAUCCUUUCGGAUAUUUUUGCAUCCUGGUUGGUUGG--------CUGCUUCCUUGCCAGGCACUUAAGCC-----AAGCGCCAGAAGCCCA-CAAGA
...((((...((((((....))))))....((...(((((.(.((((--------((....(((....)))......))))-----)).))))))..))..)-))).. ( -25.40)
>DroPse_CAF1 82681 96 - 1
CGCCUCUCUUGCA---GUUCUAAUAUUUUUUCG--CUGUUUGGUUGGCUGGCUGUUUG-------GUGGGGCACUUAAGCCCCCAGAGUCGGGGAAAGACAAGCCGGA
.(((..((..(((---((...((....))...)--))))..))..)))(((((.((((-------(..((((......)))))))))(((.......))).))))).. ( -31.80)
>DroSec_CAF1 63022 102 - 1
CCAUUGUCUGGUAUCCUUUCGGAUAUUUUUGCAUCCUGGUUGGUUGGUUGGUUGCCUGCUUCCUUGCCAGACACUUAAGCC-----AAGCGGCAGAAGCCAA-CCAGA
(((.(((..(((((((....)))))))...)))...)))((((((((((..(((((.((((.((((.........))))..-----))))))))).))))))-)))). ( -35.10)
>DroSim_CAF1 65701 102 - 1
CCAUUGUCUCGUAUCCUUUCGGAUAUUUUUGCAUCCUGGUUGGUUGGUUGGUUGCCUGCUUCCUUGCCAGGCACUUAAGCC-----AAGCGGCAGAAGCCAA-CCAGA
....(((...((((((....))))))....)))..((((((((((..((((.(((((((......).)))))).))))(((-----....)))...))))))-)))). ( -37.40)
>DroYak_CAF1 65725 100 - 1
UCAUUGUCUGGCAUCUUUUCGGAUAUUUUUACAUCCUGGUUGGCUGG--GGCUGGCUGCUUCCUUGCCAGGCACUUAAGCC-----AAGCGGCAGAAGCCAA-CCAGA
....(((((((.......)))))))..........((((((((((..--(.(((((.........))))).)......(((-----....)))...))))))-)))). ( -38.00)
>consensus
CCAUUGUCUCGUAUCCUUUCGGAUAUUUUUGCAUCCUGGUUGGUUGG_UGGCUGCCUGCUUCCUUGCCAGGCACUUAAGCC_____AAGCGGCAGAAGCCAA_CCAGA
..........((((((....)))))).........((((((((((......(((((.((((........(((......))).....))))))))).)))))).)))). (-12.86 = -15.98 +   3.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:30 2006