Locus 6107

Sequence ID 3R_DroMel_CAF1
Location 16,010,307 – 16,010,439
Length 132
Max. P 0.711776
window9956 window9957

overview

Window 6

Location 16,010,307 – 16,010,423
Length 116
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.06
Mean single sequence MFE -32.84
Consensus MFE -18.58
Energy contribution -17.92
Covariance contribution -0.66
Combinations/Pair 1.26
Mean z-score -2.03
Structure conservation index 0.57
SVM decision value 0.38
SVM RNA-class probability 0.711776
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16010307 116 + 27905053
UCCGUUGGCCGCAAAACAAAUUACGCUGCAAAUAGACAACAUUUACGUUGCCUUGGCGAUGGGUUGG-UAGGUGGGUGGGUGGCGACGAUGGUGCCGAGAAAAAUUGGCAUCAAAUA
..(((((.((((...((....(((.((((.......((((.....((((((....)))))).)))))-)))))).))..))))))))).(((((((((......))))))))).... ( -40.11)
>DroPse_CAF1 10025 116 + 1
AAUGUUGGCCGCAAAACAAAUUACGUUGCAAAUAGACAACAUUUACAUUGCCAUGGCAAUGAGAUGC-UGCUGCUCCUGUCGCUGACGAUGGUGGCAAGAAAAAUUGGCAUCAAAUA
..(((..((.((((...........))))...(((.((.(((((.((((((....))))))))))).-)))))........))..))).(((((.(((......))).))))).... ( -32.80)
>DroEre_CAF1 10206 108 + 1
UCCGUUGGCUGCAAAACAAAUUACGCUGCAAAUAGACAACAUUUACGUUGCCUUGGCGAUGGCAAGA-AGGG--------UGGCGACGCUGGUGCCGAGAAAAAUUGGCAUCAAAUA
...((((..((((.............))))......)))).....(((..((((.((....))....-))))--------..)))....(((((((((......))))))))).... ( -31.22)
>DroYak_CAF1 11307 115 + 1
UCCGUUGGCUGCAAAACAAAUUACUCUGGAAAUAGACAACAUAUUCGUUGC-UUGACGAUAGAAGAA-AAGGGGCGGCGAAGGCGACGAUGGUGGCGAGAAAAAUUGGCAUCAAAUA
..(((((.((..............((((....))))........(((((((-((.............-...))))))))))).))))).(((((.(((......))).))))).... ( -26.89)
>DroAna_CAF1 8133 117 + 1
UCUGAUGGCCGCAAAACAAAUUACGCUGCAAAUAGACAACAUUUACAUUGCCAUGGCGAUGGAAUAGAUGACUGGGAUGCCGCCAACGAUGGUGGCAAGAAAAAUUGGCAUCAAAUA
..(((((.(((((.............)))..........((((((((((((....))))))...)))))).......((((((((....)))))))).........))))))).... ( -33.22)
>DroPer_CAF1 10042 116 + 1
AAUGUUGGCCGCAAAACAAAUUACGUUGCAAAUAGACAACAUUUACAUUGCCAUGGCAAUGAGAUGG-UGCUGCUCCUGUCGCUGACGAUGGUGGCAAGAAAAAUUGGCAUCAAAUA
..(((..((.((((...........))))...(((.((.(((((.((((((....))))))))))).-)))))........))..))).(((((.(((......))).))))).... ( -32.80)
>consensus
UCCGUUGGCCGCAAAACAAAUUACGCUGCAAAUAGACAACAUUUACAUUGCCAUGGCGAUGGGAUGG_UGGGGGGGCUGUCGCCGACGAUGGUGGCAAGAAAAAUUGGCAUCAAAUA
..(((((.(.(((.............)))................((((((....))))))....................).))))).(((((.(((......))).))))).... (-18.58 = -17.92 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,010,344 – 16,010,439
Length 95
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.88
Mean single sequence MFE -28.91
Consensus MFE -16.99
Energy contribution -17.55
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.59
SVM decision value 0.32
SVM RNA-class probability 0.685209
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16010344 95 + 27905053
AACAUUUACGUUGCCUUGGCGAUGGGUUGG-UAGGUGGGUGGGUGGCGACGAUGGUGCCGAGAAAAAUUGGCAUCAAAUAUUUCACGCUAGCUUUU------
........((((((....))))))((((((-(..((((((.(....).))..(((((((((......)))))))))......)))))))))))...------ ( -30.70)
>DroSec_CAF1 26817 95 + 1
AACAUUUACGUUGCCUUAGCGAUGGUUUGG-UGGGUGUGUGAGUGGCGACGAUGGUGCCGAGAAAAAUUGGCAUCAAAUAUUUCACGCUAGCUUUU------
..((((..((((((....))))))....))-))((((((((((((....)).(((((((((......))))))))).....)))))))..)))...------ ( -29.40)
>DroSim_CAF1 10230 95 + 1
AACAUUUACGUUGCCUUGGCGAUGGUUUGG-UGGGUGUGUGGGUGGCGACGAUGGUGCCGAGAAAAAUUGGCAUCAAAUAUUUCACGCUAGCUUUU------
..((((..((((((....))))))....))-))((((((((((((....)).(((((((((......))))))))).....)))))))..)))...------ ( -30.30)
>DroEre_CAF1 10243 86 + 1
AACAUUUACGUUGCCUUGGCGAUGGCAAGA-AGGG--------UGGCGACGCUGGUGCCGAGAAAAAUUGGCAUCAAAUAUUUCACGCCAGCUUU-------
........((((((....)))))).....(-(((.--------(((((....(((((((((......))))))))).........))))).))))------- ( -29.92)
>DroYak_CAF1 11344 93 + 1
AACAUAUUCGUUGC-UUGACGAUAGAAGAA-AAGGGGCGGCGAAGGCGACGAUGGUGGCGAGAAAAAUUGGCAUCAAAUAUUUCACGCUAGCUUU-------
.......(((((..-..))))).......(-(((.((((((....)).....(((((.(((......))).))))).........))))..))))------- ( -22.70)
>DroAna_CAF1 8170 102 + 1
AACAUUUACAUUGCCAUGGCGAUGGAAUAGAUGACUGGGAUGCCGCCAACGAUGGUGGCAAGAAAAAUUGGCAUCAAAUAUUUCACGCAAGCUUUUCACCAA
..((((((((((((....))))))...))))))..(((..((((((((....)))))))).(((((....((..............))....))))).))). ( -30.44)
>consensus
AACAUUUACGUUGCCUUGGCGAUGGAAUGG_UGGGUGGGUGGGUGGCGACGAUGGUGCCGAGAAAAAUUGGCAUCAAAUAUUUCACGCUAGCUUUU______
........(((((((.............................))))))).(((((((((......))))))))).......................... (-16.99 = -17.55 +   0.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:50 2006