Locus 1334

Sequence ID 3L_DroMel_CAF1
Location 3,866,849 – 3,866,989
Length 140
Max. P 0.962315
window2079 window2080 window2081 window2082

overview

Window 9

Location 3,866,849 – 3,866,952
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.75
Mean single sequence MFE -26.30
Consensus MFE -19.39
Energy contribution -20.20
Covariance contribution 0.81
Combinations/Pair 1.10
Mean z-score -2.04
Structure conservation index 0.74
SVM decision value 1.06
SVM RNA-class probability 0.907957
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3866849 103 + 23771897
AACCGA-UCAUUUUCCAUA---------------UCAUUUUCACAACCGUUUUCACGCAGAUUCACGCCCCCAAAAAAGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC-CAUGAU
......-...........(---------------((((.....(((((........((........))..........((((((((.....))))))))........))))).-.))))) ( -22.00)
>DroSec_CAF1 65942 117 + 1
AACCGA-UCAUUUUCCAUAUCCAUAUGUAUAUUAUCAUUUUCACAACCGUUUUCACGCUGAUUCACGCCCACAA-AAGGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC-CAUGAU
.....(-((((....((((....))))................(((((........((........))......-..(((((((((.....))))))))).......))))).-.))))) ( -27.00)
>DroEre_CAF1 68234 118 + 1
AACCGAAACCUCUUCCACAUGUACGAGUAUAUUCUCAUUUUCACAACCGUUUUCACGCCGAUUCACGCCCACAA-AUGGGCCACUCUAUUAGAGUGGACCGCCGCUAGGUUGC-CGUGAU
...............(((......(((......))).......(((((((....))((.(..((..(((((...-.)))))(((((.....)))))))...).))..))))).-.))).. ( -27.40)
>DroYak_CAF1 68383 114 + 1
AACCGA-UCAUCUUCCAUAUAU----GUAUAUUCCCAUAUUCACAAUCGUUUUCACGCUGAUUCACGCCCACAA-AGAGUCCACUCUAUUAGAGUGGACCACCGUUAGGCUGAAGGUGAU
.....(-((((((((...((((----(........)))))..........................(((.....-...((((((((.....))))))))........))).))))))))) ( -28.79)
>consensus
AACCGA_UCAUCUUCCAUAU_U____GUAUAUUCUCAUUUUCACAACCGUUUUCACGCUGAUUCACGCCCACAA_AAAGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC_CAUGAU
..................................((((.....(((((........((........)).........(((((((((.....))))))))).......)))))...)))). (-19.39 = -20.20 +   0.81)

alignment

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secondary structure

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Window 0

Location 3,866,849 – 3,866,952
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.75
Mean single sequence MFE -35.38
Consensus MFE -25.58
Energy contribution -26.20
Covariance contribution 0.62
Combinations/Pair 1.13
Mean z-score -2.31
Structure conservation index 0.72
SVM decision value 1.54
SVM RNA-class probability 0.962315
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3866849 103 - 23771897
AUCAUG-GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACUUUUUUGGGGGCGUGAAUCUGCGUGAAAACGGUUGUGAAAAUGA---------------UAUGGAAAAUGA-UCGGUU
.(((((-.(..(((((..(.(((((((((.....))))))))))..)))))).))))).(((.(((....)))((..(....)..)---------------)..)))......-...... ( -31.50)
>DroSec_CAF1 65942 117 - 1
AUCAUG-GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACCUU-UUGUGGGCGUGAAUCAGCGUGAAAACGGUUGUGAAAAUGAUAAUAUACAUAUGGAUAUGGAAAAUGA-UCGGUU
.(((..-((..((((.....(((((((((.....)))))))))..-...))))..........(((....)))))..)))...((((......((((....)))).......)-)))... ( -34.82)
>DroEre_CAF1 68234 118 - 1
AUCACG-GCAACCUAGCGGCGGUCCACUCUAAUAGAGUGGCCCAU-UUGUGGGCGUGAAUCGGCGUGAAAACGGUUGUGAAAAUGAGAAUAUACUCGUACAUGUGGAAGAGGUUUCGGUU
.(((((-((((((..(((.((((.(((((.....)))))(((((.-...)))))....)))).)))......))))))....(((((......)))))...))))).............. ( -37.90)
>DroYak_CAF1 68383 114 - 1
AUCACCUUCAGCCUAACGGUGGUCCACUCUAAUAGAGUGGACUCU-UUGUGGGCGUGAAUCAGCGUGAAAACGAUUGUGAAUAUGGGAAUAUAC----AUAUAUGGAAGAUGA-UCGGUU
((((.((((.(((((.(((.(((((((((.....)))))))))..-)))))))).....(((.(((....)))....)))(((((........)----))))...)))).)))-)..... ( -37.30)
>consensus
AUCACG_GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACCUU_UUGUGGGCGUGAAUCAGCGUGAAAACGGUUGUGAAAAUGAGAAUAUAC____A_AUAUGGAAAAUGA_UCGGUU
.((((..((((((.......(((((((((.....))))))))).........((((......))))......))))))....)))).................................. (-25.58 = -26.20 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,866,873 – 3,866,989
Length 116
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.48
Mean single sequence MFE -30.37
Consensus MFE -21.23
Energy contribution -21.85
Covariance contribution 0.62
Combinations/Pair 1.11
Mean z-score -2.31
Structure conservation index 0.70
SVM decision value 0.46
SVM RNA-class probability 0.745595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3866873 116 + 23771897
UCACAACCGUUUUCACGCAGAUUCACGCCCCCAAAAAAGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC-CAUGAUCUGAUCUCACUCAUUUUCCCAGGCCCAAAGCUAUAAA
.................((((((...((..........((((((((.....)))))))).(((....))).))-...))))))..................(((.....)))..... ( -24.70)
>DroSec_CAF1 65981 115 + 1
UCACAACCGUUUUCACGCUGAUUCACGCCCACAA-AAGGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC-CAUGAUCUGAUCUCACUCAUUUUCCCAGGCCCAAAGCUGUAAA
................(((.......(((.....-..(((((((((.....)))))))))(..((((((((..-...))))))))..).............)))....)))...... ( -29.60)
>DroEre_CAF1 68274 113 + 1
UCACAACCGUUUUCACGCCGAUUCACGCCCACAA-AUGGGCCACUCUAUUAGAGUGGACCGCCGCUAGGUUGC-CGUGAUCGG--CUCACCCAUUUUCCCAGGCCCAAAGCCAUAUA
................((((((.((((((((...-.)))))(((((.....)))))((((.......))))..-.))))))))--)...............(((.....)))..... ( -35.90)
>DroYak_CAF1 68418 114 + 1
UCACAAUCGUUUUCACGCUGAUUCACGCCCACAA-AGAGUCCACUCUAUUAGAGUGGACCACCGUUAGGCUGAAGGUGAUCUG--CUCACCCAUUUUCCCAGGCCCAAAGCUAUAUA
........(((((...(((..((((.(((.....-...((((((((.....))))))))........)))))))(((((....--.)))))..........)))..)))))...... ( -31.29)
>consensus
UCACAACCGUUUUCACGCUGAUUCACGCCCACAA_AAAGUCCACUCUAUUAGAGUGGACCGCCGUUAGGUUGC_CAUGAUCUG__CUCACCCAUUUUCCCAGGCCCAAAGCUAUAAA
...(((((........((........)).........(((((((((.....))))))))).......))))).............................(((.....)))..... (-21.23 = -21.85 +   0.62)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,866,873 – 3,866,989
Length 116
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 89.48
Mean single sequence MFE -40.55
Consensus MFE -33.85
Energy contribution -33.47
Covariance contribution -0.38
Combinations/Pair 1.12
Mean z-score -2.37
Structure conservation index 0.83
SVM decision value 1.53
SVM RNA-class probability 0.962002
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3866873 116 - 23771897
UUUAUAGCUUUGGGCCUGGGAAAAUGAGUGAGAUCAGAUCAUG-GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACUUUUUUGGGGGCGUGAAUCUGCGUGAAAACGGUUGUGA
.(((((((((((.(((...(...((((.((....))..)))).-.)..(((((..(.(((((((((.....))))))))))..)))))))).))))....(((....)))))))))) ( -36.70)
>DroSec_CAF1 65981 115 - 1
UUUACAGCUUUGGGCCUGGGAAAAUGAGUGAGAUCAGAUCAUG-GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACCUU-UUGUGGGCGUGAAUCAGCGUGAAAACGGUUGUGA
.(((((((((((.(((((.((((.((.((((.......)))).-.)).((....)).(((((((((.....)))))))))))-)).))))).))))....(((....)))))))))) ( -42.10)
>DroEre_CAF1 68274 113 - 1
UAUAUGGCUUUGGGCCUGGGAAAAUGGGUGAG--CCGAUCACG-GCAACCUAGCGGCGGUCCACUCUAAUAGAGUGGCCCAU-UUGUGGGCGUGAAUCGGCGUGAAAACGGUUGUGA
..((..(((....(((((......)))))..(--(((((((((-((..((....))..)))(((((.....)))))(((((.-...)))))))).))))))((....)))))..)). ( -43.40)
>DroYak_CAF1 68418 114 - 1
UAUAUAGCUUUGGGCCUGGGAAAAUGGGUGAG--CAGAUCACCUUCAGCCUAACGGUGGUCCACUCUAAUAGAGUGGACUCU-UUGUGGGCGUGAAUCAGCGUGAAAACGAUUGUGA
........((((.(((((((.....((((((.--....))))))....))).((((.(((((((((.....)))))))))..-)))))))).)))).((((((....))).)))... ( -40.00)
>consensus
UAUAUAGCUUUGGGCCUGGGAAAAUGAGUGAG__CAGAUCACG_GCAACCUAACGGCGGUCCACUCUAAUAGAGUGGACCUU_UUGUGGGCGUGAAUCAGCGUGAAAACGGUUGUGA
..((((((((((.(((((((.......((((.......))))......)))......(((((((((.....))))))))).......)))).))))....(((....))))))))). (-33.85 = -33.47 +  -0.38)

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 10:05:02 2006