Locus 1761

Sequence ID 2R_DroMel_CAF1
Location 6,598,741 – 6,598,868
Length 127
Max. P 0.987359
window2932 window2933 window2934

overview

Window 2

Location 6,598,741 – 6,598,841
Length 100
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 90.86
Mean single sequence MFE -29.30
Consensus MFE -23.77
Energy contribution -24.53
Covariance contribution 0.75
Combinations/Pair 1.04
Mean z-score -3.11
Structure conservation index 0.81
SVM decision value 1.73
SVM RNA-class probability 0.974639
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6598741 100 + 20766785
--GGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCUGCCACCACCUCUCGCUGGCGAACUCAUUGCUCUC
--((((...(((.....((((((((((((....(.(((((...))))).)....))))))))))))..((((.(.......).))))))).....))))... ( -27.80)
>DroSec_CAF1 151236 95 + 1
--GGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAG-----CUUGCUGGCGAACUCAUUGCUCUC
--((((...........((((((((((((....(.(((((...))))).)....)))))))))))).((((((-----....)))))).......))))... ( -33.30)
>DroSim_CAF1 138032 95 + 1
--GGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAG-----CUUGCUGGCGAACUCAUUGCUCUC
--((((...........((((((((((((....(.(((((...))))).)....)))))))))))).((((((-----....)))))).......))))... ( -33.30)
>DroYak_CAF1 157646 93 + 1
GUGGAAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCUGCCAG---------CGGACGGACUCAUUGCUCUC
...((.(((........((((((((((((....(.(((((...))))).)....))))))))))))(((....---------)))..))).))......... ( -22.80)
>consensus
__GGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAG_____CUUGCUGGCGAACUCAUUGCUCUC
..((((...........((((((((((((....(.(((((...))))).)....)))))))))))).((((((.........)))))).......))))... (-23.77 = -24.53 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,598,741 – 6,598,841
Length 100
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 90.86
Mean single sequence MFE -32.32
Consensus MFE -28.58
Energy contribution -29.20
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.57
Structure conservation index 0.88
SVM decision value 2.08
SVM RNA-class probability 0.987359
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6598741 100 - 20766785
GAGAGCAAUGAGUUCGCCAGCGAGAGGUGGUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCC--
..((((.....))))((((.(....).))))(((((((.((((((((((...(..(((.....)))..)...)))))))))).)))..((....))))))-- ( -33.10)
>DroSec_CAF1 151236 95 - 1
GAGAGCAAUGAGUUCGCCAGCAAG-----CUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCC--
((((((.....(((((((((....-----))))))))).((((((((((...(..(((.....)))..)...)))))))))).))))))...........-- ( -36.00)
>DroSim_CAF1 138032 95 - 1
GAGAGCAAUGAGUUCGCCAGCAAG-----CUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCC--
((((((.....(((((((((....-----))))))))).((((((((((...(..(((.....)))..)...)))))))))).))))))...........-- ( -36.00)
>DroYak_CAF1 157646 93 - 1
GAGAGCAAUGAGUCCGUCCG---------CUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUUCCAC
((((((.....(((.(((..---------..))).))).((((((((((...(..(((.....)))..)...)))))))))).))))))............. ( -24.20)
>consensus
GAGAGCAAUGAGUUCGCCAGCAAG_____CUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCC__
((((((.....(((((((((.........))))))))).((((((((((...(..(((.....)))..)...)))))))))).))))))............. (-28.58 = -29.20 +   0.62)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,598,777 – 6,598,868
Length 91
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -24.48
Consensus MFE -19.71
Energy contribution -20.34
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.642468
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6598777 91 - 20766785
AUUUUGAGUGCAUUU-------UCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCGAGAGGUGGUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAU
...(..((((.....-------((((((...)))).))((((((((..(((((.(....).)))))(....)......)))).))))...))))..). ( -24.60)
>DroSec_CAF1 151272 86 - 1
AUUUUGAGUGAAUUU-------UCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCAAG-----CUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAU
...(..((((.....-------((((((...)))).))((((((((((((((((....-----))))))))).......))).))))...))))..). ( -27.81)
>DroSim_CAF1 138068 86 - 1
AUUUUGAGUGCAUUU-------UCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCAAG-----CUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAU
...(..((((.....-------((((((...)))).))((((((((((((((((....-----))))))))).......))).))))...))))..). ( -27.11)
>DroYak_CAF1 157684 89 - 1
AUUUUGAGUGCAUUUUACGUGUUCCGUGUUUUACGAGAGCAAUGAGUCCGUCCG---------CUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAU
...(..((((..........((((((((...)))).))))((((((.......(---------((....)))......))))))......))))..). ( -18.42)
>consensus
AUUUUGAGUGCAUUU_______UCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCAAG_____CUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAU
...(..((((............((((((...)))).))((((((((((((((((.........))))))))).......))).))))...))))..). (-19.71 = -20.34 +   0.63)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:33 2006