Locus 2377

Sequence ID 3L_DroMel_CAF1
Location 6,674,604 – 6,674,734
Length 130
Max. P 0.993431
window3663 window3664 window3665 window3666

overview

Window 3

Location 6,674,604 – 6,674,705
Length 101
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 90.65
Mean single sequence MFE -23.70
Consensus MFE -19.14
Energy contribution -19.45
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.81
SVM decision value 0.82
SVM RNA-class probability 0.859942
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6674604 101 + 23771897
CGGCGGACACACUCGAAUGCCUUAUAUCUAAAGCUUGUUUUGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUAU----AU
.(((((.(......)..(((((.((((.((....(((...(((((((.((.......)).)))))))...))))).)))))))))))))).........----.. ( -22.70)
>DroEre_CAF1 63310 105 + 1
CGGCGGACACACUCGAAUGCCUUAUAUCUAAAGCUUGUUUUGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUACAAGUAU
.((((..(......)..))))...........((((((..(((((((.((.......)).))))))).........(((((((.....)))))))..)))))).. ( -25.80)
>DroYak_CAF1 60285 101 + 1
CGGCGGACACACUCGAAUGCCUUAUAUCUAAAGCUUGUUUCGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUA----UAU
.((((((((((((((((.((.(((....))).))....)))))))...))))...............((((.((....)).)))))))))........----... ( -24.10)
>DroAna_CAF1 58067 96 + 1
CGGCGGACACACUCGAAUGCUUCAUAUCUAAAGCUUGUUUCGGGUUUUGUGUUUCAAAUUAUACCCAUACGA----AUGUAGGUAU-ACCUAUAUAUAU----GU
....(((((((((((((.((((........))))....)))))))...))))))...........((((...----(((((((...-.))))))).)))----). ( -22.20)
>consensus
CGGCGGACACACUCGAAUGCCUUAUAUCUAAAGCUUGUUUCGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUAU____AU
.((((((((((((((((.((.(((....))).))....)))))))...))))..........(((.(((........))).))).)))))............... (-19.14 = -19.45 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,674,604 – 6,674,705
Length 101
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 90.65
Mean single sequence MFE -27.79
Consensus MFE -24.48
Energy contribution -24.92
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -2.98
Structure conservation index 0.88
SVM decision value 2.40
SVM RNA-class probability 0.993431
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6674604 101 - 23771897
AU----AUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAGCUUUAGAUAUAAGGCAUUCGAGUGUGUCCGCCG
..----.........(((((....(((((((.(((...(((((((.............)))))))...)))((((((....))))))....))))))).))))). ( -29.62)
>DroEre_CAF1 63310 105 - 1
AUACUUGUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAGCUUUAGAUAUAAGGCAUUCGAGUGUGUCCGCCG
...............(((((....(((((((.(((...(((((((.............)))))))...)))((((((....))))))....))))))).))))). ( -29.62)
>DroYak_CAF1 60285 101 - 1
AUA----UAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCGAAACAAGCUUUAGAUAUAAGGCAUUCGAGUGUGUCCGCCG
...----........(((((....(((((((.(((...(((((((.............)))))))...)))((((((....))))))....))))))).))))). ( -28.92)
>DroAna_CAF1 58067 96 - 1
AC----AUAUAUAUAGGU-AUACCUACAU----UCGUAUGGGUAUAAUUUGAAACACAAAACCCGAAACAAGCUUUAGAUAUGAAGCAUUCGAGUGUGUCCGCCG
..----.........(((-..((..((((----(((..(((((....((((.....)))))))))......((((((....))))))...)))))))))..))). ( -23.00)
>consensus
AU____AUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAGCUUUAGAUAUAAGGCAUUCGAGUGUGUCCGCCG
...............(((((....(((((((.......(((((((.............)))))))......((((((....))))))....))))))).))))). (-24.48 = -24.92 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,674,637 – 6,674,734
Length 97
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 75.80
Mean single sequence MFE -18.10
Consensus MFE -14.10
Energy contribution -14.35
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.78
SVM decision value 1.99
SVM RNA-class probability 0.984939
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6674637 97 + 23771897
CUUGUUUUGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUAU----AUACAUAUACAUAUUU-AGUUUAUAUGCCUUU
..((...(((((((.((.......)).)))))))...))(((.(((((((.....))))))).)))----...((((((.((....-.)).))))))..... ( -18.90)
>DroEre_CAF1 63343 93 + 1
CUUGUUUUGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUACAAGUAUGU-------UAUAU-AGUUUAUAUGC-UUC
.(((...(((((((.((.......)).)))))))...)))...(((((((.....)))))))....((((((((-------.....-.....))))))-)). ( -20.60)
>DroYak_CAF1 60318 84 + 1
CUUGUUUCGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUA----UAUAC-------UAUA------UAUAUAG-UUU
........((((((.((.......)).)))))).((((.((....)).))))....(((((((((----((...-------))))------)))))))-... ( -17.80)
>DroAna_CAF1 58100 93 + 1
CUUGUUUCGGGUUUUGUGUUUCAAAUUAUACCCAUACGA----AUGUAGGUAU-ACCUAUAUAUAU----GUUCUUUUAUGUGUCCCUAUUGAUGUGCCUUU
.((((...((((((((.....))))....))))..))))----....((((((-(.(...((((((----(......))))))).......).))))))).. ( -15.10)
>consensus
CUUGUUUCGGGUUUUGUGUUUCAAAUUAAACCCAUACCAAUAAAUGUAGGUACCGCCUAUAUAUAU____AUAC_______UAUAU_AGUUUAUAUGC_UUU
........((((((.((.......)).))))))..........(((((((.....)))))))........................................ (-14.10 = -14.35 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,674,637 – 6,674,734
Length 97
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 75.80
Mean single sequence MFE -16.77
Consensus MFE -8.92
Energy contribution -8.92
Covariance contribution -0.00
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.53
SVM decision value 0.25
SVM RNA-class probability 0.654471
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6674637 97 - 23771897
AAAGGCAUAUAAACU-AAAUAUGUAUAUGUAU----AUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAG
..(((..(((...((-(.((((((((....))----)))))).)))...)))))).......(((...(((((((.............)))))))...))). ( -18.12)
>DroEre_CAF1 63343 93 - 1
GAA-GCAUAUAAACU-AUAUA-------ACAUACUUGUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAG
...-.........((-(((((-------(((....))).)))))))...(((((..........)))))((((((.............))))))........ ( -17.22)
>DroYak_CAF1 60318 84 - 1
AAA-CUAUAUA------UAUA-------GUAUA----UAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCGAAACAAG
...-(((((((------((((-------...))----)))))))))...(((((..........)))))((((((.............))))))........ ( -18.92)
>DroAna_CAF1 58100 93 - 1
AAAGGCACAUCAAUAGGGACACAUAAAAGAAC----AUAUAUAUAGGU-AUACCUACAU----UCGUAUGGGUAUAAUUUGAAACACAAAACCCGAAACAAG
...............(((..............----...........(-(((((((...----.....)))))))).((((.....)))).)))........ ( -12.80)
>consensus
AAA_GCAUAUAAACU_AUAUA_______GUAU____AUAUAUAUAGGCGGUACCUACAUUUAUUGGUAUGGGUUUAAUUUGAAACACAAAACCCAAAACAAG
...........................................((((.....))))............(((((((.............)))))))....... ( -8.92 =  -8.92 +  -0.00)

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 10:30:48 2006