Locus 1307

Sequence ID 3L_DroMel_CAF1
Location 3,802,522 – 3,802,653
Length 131
Max. P 0.932307
window2044 window2045 window2046 window2047

overview

Window 4

Location 3,802,522 – 3,802,613
Length 91
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 88.45
Mean single sequence MFE -23.33
Consensus MFE -19.66
Energy contribution -21.10
Covariance contribution 1.44
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.84
SVM decision value 0.93
SVM RNA-class probability 0.884681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3802522 91 + 23771897
GAUGUGAACAUAAUAAUAUUAGUG--CGCUUAUUAUUACUAUUGCAACAUUUUCGGUUUUUGCAGCCGCCGGUUGCGGUUGCAUUUUAAAGUG
..((..(...((((((((..((..--..))))))))))...)..)).((((((..(....(((((((((.....))))))))).)..)))))) ( -23.40)
>DroSec_CAF1 2381 91 + 1
GAUGUGAACUUAAUAAUAUUAGUG--CGCUUAUUAUUACUAUUGCAACAUUUACGGAUCUUGCAGCCGCCGGUUGCGGUUGCAUUUUUAAGUG
..((..(...((((((((..((..--..))))))))))...)..)).((((((..((...(((((((((.....)))))))))))..)))))) ( -24.20)
>DroSim_CAF1 2347 91 + 1
GAUGUGAACUUAAUAAUAUAAGUG--UGCUUAUUAUUACUAUUGCAACAUUUACGGAUUUUGCAGCCGCCGGUUGCGGUUGCAUUUUUAAGUG
.......((((((.(((.((((((--(((..............)).)))))))........((((((((.....))))))))))).)))))). ( -24.54)
>DroEre_CAF1 2615 91 + 1
GAUGUGGAUUUGAAAUUAUUAGUG--CGCUUAUUAUAACGAUUGCAACAUUUUCGGUUUUUGCAGCCGCCGGUUGCGGUUGCAUUUUUAAGUG
........................--((((((......((((((((((.....(((((.....)))))...))))))))))......)))))) ( -21.40)
>DroYak_CAF1 2637 93 + 1
GAUGUGGAUUGUAAAUGAAUAGUGUGUGCUUAUUACUAUAAUUGCAACAUUUUCGGUUUUUGCAGCCGCCGGUUGCGGUUGCAUUUUAAAGUG
........((((((....((((((.........))))))..))))))((((((..(....(((((((((.....))))))))).)..)))))) ( -23.10)
>consensus
GAUGUGAACUUAAUAAUAUUAGUG__CGCUUAUUAUUACUAUUGCAACAUUUUCGGUUUUUGCAGCCGCCGGUUGCGGUUGCAUUUUUAAGUG
..((..(...((((((((..(((....)))))))))))...)..)).((((((.((....(((((((((.....))))))))).)).)))))) (-19.66 = -21.10 +   1.44)

alignment

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secondary structure

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Window 5

Location 3,802,522 – 3,802,613
Length 91
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 88.45
Mean single sequence MFE -18.12
Consensus MFE -13.28
Energy contribution -13.52
Covariance contribution 0.24
Combinations/Pair 1.07
Mean z-score -2.55
Structure conservation index 0.73
SVM decision value 1.22
SVM RNA-class probability 0.932307
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3802522 91 - 23771897
CACUUUAAAAUGCAACCGCAACCGGCGGCUGCAAAAACCGAAAAUGUUGCAAUAGUAAUAAUAAGCG--CACUAAUAUUAUUAUGUUCACAUC
..........((((.((((.....)))).))))..........((((.(((.((((((((.((....--...)).)))))))))))..)))). ( -18.10)
>DroSec_CAF1 2381 91 - 1
CACUUAAAAAUGCAACCGCAACCGGCGGCUGCAAGAUCCGUAAAUGUUGCAAUAGUAAUAAUAAGCG--CACUAAUAUUAUUAAGUUCACAUC
.((((((...((((.((((.....)))).)))).....(((...((((((....))))))....)))--...........))))))....... ( -19.50)
>DroSim_CAF1 2347 91 - 1
CACUUAAAAAUGCAACCGCAACCGGCGGCUGCAAAAUCCGUAAAUGUUGCAAUAGUAAUAAUAAGCA--CACUUAUAUUAUUAAGUUCACAUC
.((((((...((((.((((.....)))).))))...........((((((....))))))(((((..--..)))))....))))))....... ( -19.60)
>DroEre_CAF1 2615 91 - 1
CACUUAAAAAUGCAACCGCAACCGGCGGCUGCAAAAACCGAAAAUGUUGCAAUCGUUAUAAUAAGCG--CACUAAUAAUUUCAAAUCCACAUC
..........((((.((((.....)))).))))......((((.(((((....((((......))))--...))))).))))........... ( -18.00)
>DroYak_CAF1 2637 93 - 1
CACUUUAAAAUGCAACCGCAACCGGCGGCUGCAAAAACCGAAAAUGUUGCAAUUAUAGUAAUAAGCACACACUAUUCAUUUACAAUCCACAUC
..........((((.((((.....)))).))))......(((..((((((..((((....))))))).)))...)))................ ( -15.40)
>consensus
CACUUAAAAAUGCAACCGCAACCGGCGGCUGCAAAAACCGAAAAUGUUGCAAUAGUAAUAAUAAGCG__CACUAAUAUUAUUAAGUUCACAUC
..........((((.((((.....)))).))))...........((((((....))))))................................. (-13.28 = -13.52 +   0.24)

alignment

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secondary structure

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Window 6

Location 3,802,559 – 3,802,653
Length 94
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.87
Mean single sequence MFE -25.83
Consensus MFE -13.32
Energy contribution -15.35
Covariance contribution 2.03
Combinations/Pair 1.07
Mean z-score -2.34
Structure conservation index 0.52
SVM decision value 1.07
SVM RNA-class probability 0.909906
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3802559 94 + 23771897
UAUUGCAACAUUU------UCGGUUUUUGCAGCCGCCGG---UUGCGGUUGC-------AUUUUAAAGUGCACUACAUACGCACACACACACAUGUGCACAUACAAAUUU
...((((.(((..------........(((((((((...---..))))))))-------).......((((.........))))........)))))))........... ( -24.70)
>DroSec_CAF1 2418 88 + 1
UAUUGCAACAUUU------ACGGAUCUUGCAGCCGCCGG---UUGCGGUUGC-------AUUUUUAAGUGCACUACAUA------CACACACAUGUGCACAUACAAAUUU
.............------........(((((((((...---..))))))))-------).......((((((......------.........)))))).......... ( -24.26)
>DroSim_CAF1 2384 88 + 1
UAUUGCAACAUUU------ACGGAUUUUGCAGCCGCCGG---UUGCGGUUGC-------AUUUUUAAGUGCACUACAUA------CACACACAUGUGCACAUACAAAUUU
.............------........(((((((((...---..))))))))-------).......((((((......------.........)))))).......... ( -24.26)
>DroEre_CAF1 2652 86 + 1
GAUUGCAACAUUU------UCGGUUUUUGCAGCCGCCGG---UUGCGGUUGC-------AUUUUUAAGUGCACUGCGUA------CACACACAUGU--ACAUACAUAUUU
....(((.(((((------........(((((((((...---..))))))))-------).....)))))...)))(((------((......)))--)).......... ( -24.02)
>DroYak_CAF1 2676 88 + 1
AAUUGCAACAUUU------UCGGUUUUUGCAGCCGCCGG---UUGCGGUUGC-------AUUUUAAAGUGCACUACAUA------CACACACAUGUGCACAUACAUAUUU
.............------........(((((((((...---..))))))))-------).......((((((......------.........)))))).......... ( -24.26)
>DroAna_CAF1 2675 101 + 1
AAAGGCAGCGUUUGGGUCGCCGGUUCUUCCGGGAGUCGGAAUUGGCGGAGACACGGGAGAUUCUGGAGCGCCGGCUGUA------C-CACACAUGU--ACUUACAUAUGU
...(((.((((((((((((((((((((..(....)..)))))))))(....)......)))))..))))))..)))...------.-.(((.((((--....)))).))) ( -33.50)
>consensus
UAUUGCAACAUUU______UCGGUUUUUGCAGCCGCCGG___UUGCGGUUGC_______AUUUUUAAGUGCACUACAUA______CACACACAUGUGCACAUACAAAUUU
............................((((((((........))))))))...............((((((.....................)))))).......... (-13.32 = -15.35 +   2.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,802,559 – 3,802,653
Length 94
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.87
Mean single sequence MFE -25.30
Consensus MFE -14.03
Energy contribution -15.62
Covariance contribution 1.59
Combinations/Pair 1.22
Mean z-score -1.97
Structure conservation index 0.55
SVM decision value 0.66
SVM RNA-class probability 0.814241
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3802559 94 - 23771897
AAAUUUGUAUGUGCACAUGUGUGUGUGUGCGUAUGUAGUGCACUUUAAAAU-------GCAACCGCAA---CCGGCGGCUGCAAAAACCGA------AAAUGUUGCAAUA
......(((((..(((((....)))))..)))))....(((.........(-------(((.((((..---...)))).))))..(((...------....))))))... ( -27.30)
>DroSec_CAF1 2418 88 - 1
AAAUUUGUAUGUGCACAUGUGUGUG------UAUGUAGUGCACUUAAAAAU-------GCAACCGCAA---CCGGCGGCUGCAAGAUCCGU------AAAUGUUGCAAUA
....(((((.(((((((((((....------))))).)))))).......(-------(((.((((..---...)))).))))........------......))))).. ( -24.30)
>DroSim_CAF1 2384 88 - 1
AAAUUUGUAUGUGCACAUGUGUGUG------UAUGUAGUGCACUUAAAAAU-------GCAACCGCAA---CCGGCGGCUGCAAAAUCCGU------AAAUGUUGCAAUA
....(((((.(((((((((((....------))))).)))))).......(-------(((.((((..---...)))).))))........------......))))).. ( -24.30)
>DroEre_CAF1 2652 86 - 1
AAAUAUGUAUGU--ACAUGUGUGUG------UACGCAGUGCACUUAAAAAU-------GCAACCGCAA---CCGGCGGCUGCAAAAACCGA------AAAUGUUGCAAUC
.....(((((((--((.(((((...------.))))))))))........(-------(((.((((..---...)))).))))........------......))))... ( -23.10)
>DroYak_CAF1 2676 88 - 1
AAAUAUGUAUGUGCACAUGUGUGUG------UAUGUAGUGCACUUUAAAAU-------GCAACCGCAA---CCGGCGGCUGCAAAAACCGA------AAAUGUUGCAAUU
.....((((.(((((((((((....------))))).)))))).......(-------(((.((((..---...)))).))))........------......))))... ( -23.70)
>DroAna_CAF1 2675 101 - 1
ACAUAUGUAAGU--ACAUGUGUG-G------UACAGCCGGCGCUCCAGAAUCUCCCGUGUCUCCGCCAAUUCCGACUCCCGGAAGAACCGGCGACCCAAACGCUGCCUUU
((((((((....--))))))))(-(------..((((.(((((.............)))))..((((..(((((.....))))).....))))........))))))... ( -29.12)
>consensus
AAAUAUGUAUGUGCACAUGUGUGUG______UAUGUAGUGCACUUAAAAAU_______GCAACCGCAA___CCGGCGGCUGCAAAAACCGA______AAAUGUUGCAAUA
.....((((.((((((.((((((........))))))))))))...............(((.((((........)))).))).....................))))... (-14.03 = -15.62 +   1.59)

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 10:04:28 2006