Locus 4169

Sequence ID 2R_DroMel_CAF1
Location 13,718,359 – 13,718,482
Length 123
Max. P 0.976573
window6704 window6705 window6706

overview

Window 4

Location 13,718,359 – 13,718,449
Length 90
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 91.42
Mean single sequence MFE -23.62
Consensus MFE -19.20
Energy contribution -19.44
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.65
Structure conservation index 0.81
SVM decision value 0.72
SVM RNA-class probability 0.831222
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13718359 90 + 20766785
GUUGGGGCAAAUGGAAAAGCUGCAACUGCAUAUGCAACGCCAGCA-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUG
((((.(((..........))).))))(((....)))..(((.(((-((((......)))...)))).(((.......)))...)))..... ( -24.20)
>DroSec_CAF1 19518 84 + 1
GUUGGGGCAAAUGGAAAAGCUGCAAC------UGCAACGCCAGCG-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUG
((((..((((((....(((.((((..------(((.......)))-..)))).)))....)))))).(((.......)))..))))..... ( -22.40)
>DroSim_CAF1 21867 90 + 1
GUUGGGGCAAAUGGAAAAGCUGCAACUGCAACUGCAACGCAAGCA-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUG
((((..((...((.....((((((((((....((((.(....)..-..))))....)))...)))))))....))...))..))))..... ( -24.50)
>DroEre_CAF1 19200 84 + 1
GUUGGGGCAAAUGGAAAAGCUGCAAC------UGCAACACCAGCA-ACUGCAACUUCAGCAUCUGCAACCACACAACGGCAACGGCAACUG
(((((((((.(((...(((.((((..------(((.......)))-..)))).)))...))).)))..))......((....)).)))).. ( -21.40)
>DroYak_CAF1 20278 85 + 1
GUUGGGGCAAAUGGAAAAGCUGCAAC------UGCAACACCAGCAAACUGCAUCUUCAGAAGUUGCAGCCACACAACGGCAACGGCAACUG
((((..((...((.....((((((((------(((.......))...(((......))).)))))))))....))...))..))))..... ( -25.60)
>consensus
GUUGGGGCAAAUGGAAAAGCUGCAAC______UGCAACGCCAGCA_ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUG
((((..((...((.....(((((((.......(((.......)))..(((......)))...)))))))....))...))..))))..... (-19.20 = -19.44 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,718,359 – 13,718,449
Length 90
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 91.42
Mean single sequence MFE -28.38
Consensus MFE -21.36
Energy contribution -21.64
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.65
Structure conservation index 0.75
SVM decision value 0.08
SVM RNA-class probability 0.574853
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13718359 90 - 20766785
CAGUUGCCGUUGCCGUUGUGUGGCUGCAAAUUCUGAAGUUGCAGU-UGCUGGCGUUGCAUAUGCAGUUGCAGCUUUUCCAUUUGCCCCAAC
..((((.....((((.....)))).((((((...(((((((((..-(((..((...))....)))..)))))))))...))))))..)))) ( -29.20)
>DroSec_CAF1 19518 84 - 1
CAGUUGCCGUUGCCGUUGUGUGGCUGCAAAUUCUGAAGUUGCAGU-CGCUGGCGUUGCA------GUUGCAGCUUUUCCAUUUGCCCCAAC
.((((((..(((((((((.((((((((((.........)))))))-))))))))..)))------)..))))))................. ( -29.00)
>DroSim_CAF1 21867 90 - 1
CAGUUGCCGUUGCCGUUGUGUGGCUGCAAAUUCUGAAGUUGCAGU-UGCUUGCGUUGCAGUUGCAGUUGCAGCUUUUCCAUUUGCCCCAAC
..((((.....((((.....)))).((((((...(((((((((..-(((..((......)).)))..)))))))))...))))))..)))) ( -30.00)
>DroEre_CAF1 19200 84 - 1
CAGUUGCCGUUGCCGUUGUGUGGUUGCAGAUGCUGAAGUUGCAGU-UGCUGGUGUUGCA------GUUGCAGCUUUUCCAUUUGCCCCAAC
(((..((....))..)))..(((..(((((((..(((((((((..-(((.......)))------..)))))))))..))))))).))).. ( -31.20)
>DroYak_CAF1 20278 85 - 1
CAGUUGCCGUUGCCGUUGUGUGGCUGCAACUUCUGAAGAUGCAGUUUGCUGGUGUUGCA------GUUGCAGCUUUUCCAUUUGCCCCAAC
.((((((.((..(......)..)).)))))).........((((.....(((.(((((.------...)))))....))).))))...... ( -22.50)
>consensus
CAGUUGCCGUUGCCGUUGUGUGGCUGCAAAUUCUGAAGUUGCAGU_UGCUGGCGUUGCA______GUUGCAGCUUUUCCAUUUGCCCCAAC
..((((.....((((.....)))).((((((...((((((((((..(((.......))).......))))))))))...))))))..)))) (-21.36 = -21.64 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,718,375 – 13,718,482
Length 107
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 91.71
Mean single sequence MFE -32.73
Consensus MFE -27.38
Energy contribution -28.12
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.84
SVM decision value 1.77
SVM RNA-class probability 0.976573
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13718375 107 + 20766785
AAGCUGCAACUGCAUAUGCAACGCCAGCA-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUGGCGAUAAGCAGCUCGGGAAAACUGAGAAGCCAA
..(((((...(((....))).((((((..-.((((((.........))))))........((....))....))))))....)))))((((.....))))........ ( -34.90)
>DroSec_CAF1 19534 101 + 1
AAGCUGCAAC------UGCAACGCCAGCG-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUGGCGAUAAGCAGCUCGGGAAAACUGAGAAACCGA
..(((((...------.))..((((((.(-.((((((.........)))))).)......((....))....))))))...)))..(((((.....)))))....... ( -31.40)
>DroSim_CAF1 21883 107 + 1
AAGCUGCAACUGCAACUGCAACGCAAGCA-ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUGGCGAUAAGCAGCUCGGGAAAACUGAGAAGCCGA
..((((((((((....((((.(....)..-..))))....)))...))))))).......((((..((.(....).))........(((((.....)))))..)))). ( -32.10)
>DroYak_CAF1 20294 102 + 1
AAGCUGCAAC------UGCAACACCAGCAAACUGCAUCUUCAGAAGUUGCAGCCACACAACGGCAACGGCAACUGGCGAUAAGCAGCUCGGGAAAACUGAGAAGCCGC
..((((((((------(((.......))...(((......))).))))))))).......((((..((.(....).))........(((((.....)))))..)))). ( -32.50)
>consensus
AAGCUGCAAC______UGCAACGCCAGCA_ACUGCAACUUCAGAAUUUGCAGCCACACAACGGCAACGGCAACUGGCGAUAAGCAGCUCGGGAAAACUGAGAAGCCGA
..((((((........)))..((((((....((((((.........))))))........((....))....))))))...)))..(((((.....)))))....... (-27.38 = -28.12 +   0.75)

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 11:13:25 2006