Locus 3663

Sequence ID 3R_DroMel_CAF1
Location 9,915,863 – 9,915,996
Length 133
Max. P 0.853759
window5883 window5884 window5885

overview

Window 3

Location 9,915,863 – 9,915,969
Length 106
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.60
Mean single sequence MFE -25.75
Consensus MFE -13.32
Energy contribution -12.80
Covariance contribution -0.52
Combinations/Pair 1.39
Mean z-score -2.00
Structure conservation index 0.52
SVM decision value 0.07
SVM RNA-class probability 0.566619
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9915863 106 + 27905053
ACGUUUGU----UAUAUGGCAUCAGGU-UGUCUAU-AUGUGUGUGUUCAU--AUGAAUGCAAUUUGCAUUUUAAGCACCCUUGUUUGUUUGAGCCACACAAAAAUGAUUUGCAA
..((..((----(((..((((......-))))...-.((((((.(((((.--..((((((.....))))))((((((....))))))..)))))))))))...)))))..)).. ( -28.00)
>DroPse_CAF1 143325 102 + 1
AUGGGUAA----UGAUUUGCUUAUGA------UAUAAUCUG-CUAUUGACUUGUCAAUGCAAUUUGCAUUUUAAGUA-UCGAAUGUGUCUAAGCCAAACAGAAAUGAUUGGCAA
((((((((----....))))))))((------((((.((((-(.(((((....))))))))...(((.......)))-..)).))))))...(((((.((....)).))))).. ( -26.90)
>DroSec_CAF1 118783 104 + 1
ACGUAUGU----UAUAUGGCAUCUGGU-UGUCUAU-AUGU--GUGUUCAU--UUGAAUGCAAUUUGCAUUUUAAGCACUCUUGUUUGUUUGGGCCACACAAAAAUGAUUUGCUA
..(((.((----(((..((((......-))))...-.(((--(((..(..--..((((((.....))))))((((((........)))))))..))))))...))))).))).. ( -23.90)
>DroSim_CAF1 122812 104 + 1
ACGCUUGU----UAUAUGGCAUCAGGU-UGUCUAU-AUGU--GUGUUCAU--UUGAAUGCAAUUUGCAUUUUAAGCACUCUUGUUUGUUUGGGCCACACAAAAAUGAUUUGCAA
..((..((----(((..((((......-))))...-.(((--(((..(..--..((((((.....))))))((((((........)))))))..))))))...)))))..)).. ( -25.70)
>DroEre_CAF1 124214 104 + 1
UCGUUUGU----UAUAUGGCAUCAGGUUUGUCUAU-AUGU--GAGUUCAU--AUGAAUGCA-UUUGCAUUUUAAGCACUCUUGUUUGUUUGGGCCACACAAAAAUGAUUUGUAA
((((((..----((((.((((.......)))))))-)(((--(.(((((.--..((((((.-...))))))((((((....))))))..)))))))))...))))))....... ( -21.90)
>DroYak_CAF1 123244 109 + 1
UAGUUUGUGUACUGUAUGGCAGCAAGUUUUUCUAC-AUGU--GUGUUCAU--AUGAAUGCAAUUUGCAUUUCAAGCACUCUUGUUUGCUUGGGCCACACAAAAAUGAUUUGCAA
((((......)))).......(((((((.......-.(((--(((..(..--..((((((.....))))))((((((........)))))))..)))))).....))))))).. ( -28.12)
>consensus
ACGUUUGU____UAUAUGGCAUCAGGU_UGUCUAU_AUGU__GUGUUCAU__AUGAAUGCAAUUUGCAUUUUAAGCACUCUUGUUUGUUUGGGCCACACAAAAAUGAUUUGCAA
................((((......................(((((((....)))))))..........(((((((........))))))))))).................. (-13.32 = -12.80 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,915,863 – 9,915,969
Length 106
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 79.60
Mean single sequence MFE -19.74
Consensus MFE -12.27
Energy contribution -12.06
Covariance contribution -0.22
Combinations/Pair 1.29
Mean z-score -2.03
Structure conservation index 0.62
SVM decision value 0.80
SVM RNA-class probability 0.853759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9915863 106 - 27905053
UUGCAAAUCAUUUUUGUGUGGCUCAAACAAACAAGGGUGCUUAAAAUGCAAAUUGCAUUCAU--AUGAACACACACAU-AUAGACA-ACCUGAUGCCAUAUA----ACAAACGU
.............((((((((((((.........((((((..............))))))((--(((........)))-)).....-...))).))))))))----)....... ( -20.84)
>DroPse_CAF1 143325 102 - 1
UUGCCAAUCAUUUCUGUUUGGCUUAGACACAUUCGA-UACUUAAAAUGCAAAUUGCAUUGACAAGUCAAUAG-CAGAUUAUA------UCAUAAGCAAAUCA----UUACCCAU
..(((((.((....)).)))))............((-(.((((..(((.((.(((((((((....))))).)-))).)).))------)..))))...))).----........ ( -17.20)
>DroSec_CAF1 118783 104 - 1
UAGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAA--AUGAACAC--ACAU-AUAGACA-ACCAGAUGCCAUAUA----ACAUACGU
.............(((((((((............((((((..............))))))..--(((.....--.)))-.......-.......))))))))----)....... ( -17.24)
>DroSim_CAF1 122812 104 - 1
UUGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAA--AUGAACAC--ACAU-AUAGACA-ACCUGAUGCCAUAUA----ACAAGCGU
.............(((((((((............((((((..............))))))..--........--....-.(((...-..)))..))))))))----)....... ( -17.44)
>DroEre_CAF1 124214 104 - 1
UUACAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAA-UGCAUUCAU--AUGAACUC--ACAU-AUAGACAAACCUGAUGCCAUAUA----ACAAACGA
.............(((((((((............((((((............-.))))))((--(((.....--.)))-)).............))))))))----)....... ( -19.72)
>DroYak_CAF1 123244 109 - 1
UUGCAAAUCAUUUUUGUGUGGCCCAAGCAAACAAGAGUGCUUGAAAUGCAAAUUGCAUUCAU--AUGAACAC--ACAU-GUAGAAAAACUUGCUGCCAUACAGUACACAAACUA
.............(((((((((.((((((........))))))....((((.((...(((((--(((.....--.)))-)).))).)).)))).)))))))))........... ( -26.00)
>consensus
UUGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAU__AUGAACAC__ACAU_AUAGACA_ACCUGAUGCCAUAUA____ACAAACGU
..............((((((((............((((((..............))))))....(((........)))................))))))))............ (-12.27 = -12.06 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,915,892 – 9,915,996
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -22.73
Consensus MFE -14.55
Energy contribution -13.55
Covariance contribution -0.99
Combinations/Pair 1.42
Mean z-score -1.96
Structure conservation index 0.64
SVM decision value 0.45
SVM RNA-class probability 0.739402
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9915892 104 - 27905053
CGCGAAGUCU-------------GGAGACCAUAAAAAGUUUUGCAAAUCAUUUUUGUGUGGCUCAAACAAACAAGGGUGCUUAAAAUGCAAAUUGCAUUCAU--AUGAACACACACAU-A
.((((((.((-------------(....).......))))))))..........((((((((((..........))))......(((((.....)))))...--.......)))))).-. ( -18.61)
>DroPse_CAF1 143349 118 - 1
CAUAAAGUCUCAAGAGCCAACCAGAAGCUCGUAGAAAAUGUUGCCAAUCAUUUCUGUUUGGCUUAGACACAUUCGA-UACUUAAAAUGCAAAUUGCAUUGACAAGUCAAUAG-CAGAUUA
......((((...(((((((.((((((...((((......))))......)))))).)))))))))))........-...............(((((((((....))))).)-))).... ( -26.30)
>DroSec_CAF1 118812 102 - 1
CGCGAAGUCU-------------GGAGCCCAUAAAAAGUUUAGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAA--AUGAACAC--ACAU-A
......((.(-------------((.(((((((((((.............)))))))).)))))).))......((((((..............))))))..--........--....-. ( -22.86)
>DroSim_CAF1 122841 102 - 1
CGCGAAGUCU-------------GGAGUCCAUAAAAAGUUUUGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAA--AUGAACAC--ACAU-A
......((.(-------------((.(((((((((((.............)))))))).)))))).))......((((((..............))))))..--........--....-. ( -20.16)
>DroEre_CAF1 124244 101 - 1
UGCAAAGUCU-------------GGAGCCCAUAAAAAGCUUUACAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAA-UGCAUUCAU--AUGAACUC--ACAU-A
......((.(-------------((.(((((((((((.............)))))))).)))))).))......((((......(((((...-.)))))...--....))))--....-. ( -24.64)
>DroYak_CAF1 123278 102 - 1
CGCAAAGUCU-------------GGAGCCCAUAAAAAGUUUUGCAAAUCAUUUUUGUGUGGCCCAAGCAAACAAGAGUGCUUGAAAUGCAAAUUGCAUUCAU--AUGAACAC--ACAU-G
.((((((.((-------------.............))))))))..........((((((...((((((........)))))).(((((.....)))))...--.....)))--))).-. ( -23.82)
>consensus
CGCAAAGUCU_____________GGAGCCCAUAAAAAGUUUUGCAAAUCAUUUUUGUGUGGCCCAAACAAACAAGAGUGCUUAAAAUGCAAAUUGCAUUCAU__AUGAACAC__ACAU_A
.((((..................((.(((((((((((.............)))))))).))))).............(((.......)))..)))).((((....))))........... (-14.55 = -13.55 +  -0.99)

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 11:06:52 2006