Locus 6285

Sequence ID 3L_DroMel_CAF1
Location 16,738,516 – 16,738,742
Length 226
Max. P 0.994413
window10079 window10080 window10081

overview

Window 9

Location 16,738,516 – 16,738,618
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 63.57
Mean single sequence MFE -24.91
Consensus MFE -13.82
Energy contribution -14.57
Covariance contribution 0.75
Combinations/Pair 1.35
Mean z-score -1.52
Structure conservation index 0.55
SVM decision value 1.15
SVM RNA-class probability 0.922656
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16738516 102 - 23771897
UAGCUUUGAA--UCCUACCUGGAAAAUGUUGUCCCAUUCAGGUAGGCCGCGGAAAAUUCGCUCGUAUUUCCCUC--AACAUAUCCU----AGCAAUAUGGCACU------C----UUUUC
..((.((((.--.((((((((((.............))))))))))..(((((...)))))...........))--))(((((...----....)))))))...------.----..... ( -22.12)
>DroGri_CAF1 42841 101 - 1
UUGCCUUGCAUUGUCUACCUGGAAAAG--CGU----CUCAGGUAAG-CGUGAAA-AUUCGCCUGUAUUAUCGUUUUG-------GC----UGCCGCAUGGCAUUUUUCUUUUUCCUUUUC
.((((.(((...(..((((((((....--..)----).))))))..-)......-....(((..............)-------))----....))).)))).................. ( -24.94)
>DroSim_CAF1 50150 102 - 1
UAGCUUUGAA--UCCUACCUGGAAAAUGUUGUCCCACUCAGGUAGUCCGCGGAAAAUUCGCUCGUAUUUCCCUC--AACAUAUCCC----GGCAACAUGGCACU------C----UUUUC
..(((.....--(((.....)))..((((((((.......((....))(((((...))))).............--..........----)))))))))))...------.----..... ( -19.70)
>DroAna_CAF1 40095 99 - 1
U----GGAAA--UCCUACCUGGAAAAG--CGACCCAUUCAGGUAGGACGCGGAA-AUUUGCUCGAAUUUCCAUCCUGGCAUAUACCAUCCUGCCGUAUGGAG--------U----UUUUC
.----((...--.))......((((((--(...((((...(((((((...((((-((((....))))))))....(((......))))))))))..)))).)--------)----))))) ( -32.90)
>consensus
UAGCUUUGAA__UCCUACCUGGAAAAG__CGUCCCACUCAGGUAGGCCGCGGAA_AUUCGCUCGUAUUUCCCUC__AACAUAUCCC____UGCAACAUGGCACU______C____UUUUC
..(((.((.....((((((((((.............))))))))))..(((((...)))))..................................)).)))................... (-13.82 = -14.57 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,738,542 – 16,738,641
Length 99
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 78.50
Mean single sequence MFE -24.10
Consensus MFE -16.47
Energy contribution -16.53
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.60
Structure conservation index 0.68
SVM decision value 2.48
SVM RNA-class probability 0.994413
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16738542 99 - 23771897
--UCCCUUUCUCUACCUGAAUCCUCUAGCUUUGAAUCCUACCUGGAAAAUGUUGUCCCAUUCAGGUAGGCCGCGGAAAAUUCGCUCGUAUUUCCCUC--AACA
--........(((((((((((....((((.((...(((.....))).)).))))....)))))))))))..(((((...))))).............--.... ( -22.30)
>DroSim_CAF1 50176 101 - 1
UCUCCCUUUCUCUACCUGAAUCCUCUAGCUUUGAAUCCUACCUGGAAAAUGUUGUCCCACUCAGGUAGUCCGCGGAAAAUUCGCUCGUAUUUCCCUC--AACA
...........((((((((......((((.((...(((.....))).)).))))......))))))))...(((((...))))).............--.... ( -19.00)
>DroAna_CAF1 40123 92 - 1
UCUUUCUUUUUCUACCUGG----UCU----GGAAAUCCUACCUGGAAAAG--CGACCCAUUCAGGUAGGACGCGGAA-AUUUGCUCGAAUUUCCAUCCUGGCA
..................(----((.----(((..(((((((((((....--.......)))))))))))...((((-((((....)))))))).))).))). ( -31.00)
>consensus
UCUCCCUUUCUCUACCUGAAUCCUCUAGCUUUGAAUCCUACCUGGAAAAUGUUGUCCCAUUCAGGUAGGCCGCGGAAAAUUCGCUCGUAUUUCCCUC__AACA
...........((((((((......((((......(((.....)))....))))......))))))))...(((((...)))))................... (-16.47 = -16.53 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,738,641 – 16,738,742
Length 101
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 76.72
Mean single sequence MFE -28.77
Consensus MFE -21.75
Energy contribution -22.53
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -1.59
Structure conservation index 0.76
SVM decision value 1.02
SVM RNA-class probability 0.901440
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16738641 101 - 23771897
CAGAAAUUCCUAACCUAAAGGACAAGCAGCUGAUCCUGGCAAAUGGCAACGCCGGCUGCUCGCUCUCCUUUUGUCCUUGCACAAUUGCUUGAGGGUUUCCC-------------
..(((((.(((......(((((((((.((..((..(.((((..((((...))))..)))).).))..)))))))))))(((....)))...))))))))..------------- ( -28.50)
>DroSim_CAF1 51037 113 - 1
CAGAAAUUCCUAACCCAAAGGACAAGCAGCUGAUCCUGGCAAAUGGCAACGCCGGCUGCUCGCUCUCCU-UUGUCCUUGCACAAUUGCUUGAGGGUUUCCCUCGCACUCUCCCU
.(((...........((((((((.((((((((....((.(....).))....)))))))).)...))))-)))............(((..(((((...)))))))).))).... ( -30.30)
>DroAna_CAF1 40218 100 - 1
-----CUUUCGGACC-GAAGGAUCUGCAGCUGAUCCUGGCAAAUGUCAAAGCCGGCUGCUCUC-CUCCA-UUGUCCUUGCACAAUCACUUAAGGGUUUUCCUUUCUCU------
-----.....((((.-(.((((...(((((((....((((....))))....)))))))..))-)).).-..))))..............(((((....)))))....------ ( -27.50)
>consensus
CAGAAAUUCCUAACC_AAAGGACAAGCAGCUGAUCCUGGCAAAUGGCAACGCCGGCUGCUCGCUCUCCU_UUGUCCUUGCACAAUUGCUUGAGGGUUUCCCU__C_CU______
...........(((((.(((((((((((((((....((.(....).))....))))))))...........)))))))((......))....)))))................. (-21.75 = -22.53 +   0.78)

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 12:14:41 2006