Locus 4299

Sequence ID 3L_DroMel_CAF1
Location 12,608,961 – 12,609,063
Length 102
Max. P 0.952578
window6652 window6653

overview

Window 2

Location 12,608,961 – 12,609,063
Length 102
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 89.84
Mean single sequence MFE -25.37
Consensus MFE -20.90
Energy contribution -21.98
Covariance contribution 1.08
Combinations/Pair 1.00
Mean z-score -3.00
Structure conservation index 0.82
SVM decision value 1.42
SVM RNA-class probability 0.952578
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12608961 102 + 23771897
GAACUCAUUUAUUCGCAUUUUUUC--CCCAUGCUUU---UUUGCUGCUCUUUUGGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....(((((((((....--.....((...---...)).(((.....))))))))))))(((((..((((((....))))))..))))).)))))...... ( -26.70)
>DroSec_CAF1 96827 102 + 1
GAACUCAUUUAUUCGCAUUUUUUC--CCCCGGCUUU---UUUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....(((((((((....--....(((...---...)))((.......)))))))))))(((((..((((((....))))))..))))).)))))...... ( -27.70)
>DroSim_CAF1 99712 102 + 1
GAACUCAUUUAUUCGCAUUUUUUC--CCCCGGCUUU---UUUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....(((((((((....--....(((...---...)))((.......)))))))))))(((((..((((((....))))))..))))).)))))...... ( -27.70)
>DroEre_CAF1 99981 99 + 1
GAACUCAUUUAUUCGCAUUUUUU---GCCCUGCUU----UCUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUU-UCCGCCAUCAUUUUGAGUGAUGUC
..(((((....(((((((((...---.....((..----...)).((.......)))))))))))(((((..(((((.....-)))))..))))).)))))...... ( -25.20)
>DroYak_CAF1 100755 107 + 1
GAACUCAUUUAUUCGCAUUUUUUUGGCCCCUGCUUUUUUUUUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....(((((((((....(((....)))...........((.......)))))))))))(((((..((((((....))))))..))))).)))))...... ( -25.60)
>DroAna_CAF1 93836 90 + 1
GAACUCAUUUAUUCGCAUUUUUUC--UUCUCGUUUU---UUU---------UUUG---UUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....((((((.......--..........---...---------....---.))))))(((((..((((((....))))))..))))).)))))...... ( -19.31)
>consensus
GAACUCAUUUAUUCGCAUUUUUUC__CCCCUGCUUU___UUUGCUGCUCUUUUUGCAAAUGCGAAAAUGAAUGUGGAAACUUUUCCGCCAUCAUUUUGAGUGAUGUC
..(((((....((((((((............((.........))(((.......)))))))))))(((((..((((((....))))))..))))).)))))...... (-20.90 = -21.98 +   1.08)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 12,608,961 – 12,609,063
Length 102
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 89.84
Mean single sequence MFE -21.83
Consensus MFE -17.96
Energy contribution -19.17
Covariance contribution 1.21
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.82
SVM decision value 0.45
SVM RNA-class probability 0.740481
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12608961 102 - 23771897
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCCAAAAGAGCAGCAAA---AAAGCAUGGG--GAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)((((((((((((((((.((......((......---...))....)--)...))))))))..)))))))).. ( -24.00)
>DroSec_CAF1 96827 102 - 1
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAAA---AAAGCCGGGG--GAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)((((((((((((((((((.......)).((...---...)).....--....))))))))..)))))))).. ( -22.90)
>DroSim_CAF1 99712 102 - 1
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAAA---AAAGCCGGGG--GAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)((((((((((((((((((.......)).((...---...)).....--....))))))))..)))))))).. ( -22.90)
>DroEre_CAF1 99981 99 - 1
GACAUCACUCAAAAUGAUGGCGGA-AAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAGA----AAGCAGGGC---AAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.(((-.....))).)((((((((((((((((((.......)).((...----..)).....---...))))))))..)))))))).. ( -22.70)
>DroYak_CAF1 100755 107 - 1
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAAAAAAAAAGCAGGGGCCAAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)((((((((((((((((((.......)).((.........))...........))))))))..)))))))).. ( -22.80)
>DroAna_CAF1 93836 90 - 1
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAA---CAAA---------AAA---AAAACGAGAA--GAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)(((((((((((((.---....---------...---..........--.......)))))..)))))))).. ( -15.71)
>consensus
GACAUCACUCAAAAUGAUGGCGGAAAAGUUUCCACAUUCAUUUUCGCAUUUGCAAAAAGAGCAGCAAA___AAAGCAGGGG__GAAAAAAUGCGAAUAAAUGAGUUC
..(((((.......)))))(.((((....)))).)((((((((((((((((((.......)).((.........))...........))))))))..)))))))).. (-17.96 = -19.17 +   1.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:59 2006