Locus 616

Sequence ID 3R_DroMel_CAF1
Location 2,285,564 – 2,285,690
Length 126
Max. P 0.972863
window978 window979 window980 window981

overview

Window 8

Location 2,285,564 – 2,285,661
Length 97
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 91.05
Mean single sequence MFE -29.35
Consensus MFE -24.28
Energy contribution -25.70
Covariance contribution 1.42
Combinations/Pair 1.08
Mean z-score -2.47
Structure conservation index 0.83
SVM decision value 0.92
SVM RNA-class probability 0.881523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2285564 97 + 27905053
UGGGAAAGUCGGGACUUGACUCAUCACGCAAGUCCCGCCACCUUUUU-UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUU
..((((....((((((((.(.......)))))))))(((((......-.)))))...(((.(((((..(....)..))))).)))....))))..... ( -33.40)
>DroSec_CAF1 22093 98 + 1
UGGGAAAGUCGGGACUUGACUCAUCACGCAAGUCCCGCCACCUUUUUCUGUGGCUAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUU
..((((....((((((((.(.......)))))))))(((((........)))))...(((.(((((..(....)..))))).)))....))))..... ( -33.20)
>DroSim_CAF1 22539 98 + 1
UGGGAAAGUCGGGACUUGACUCAUCACGCAAGUCCCGCCACCUUUUUCUGUGGCUAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUU
..((((....((((((((.(.......)))))))))(((((........)))))...(((.(((((..(....)..))))).)))....))))..... ( -33.20)
>DroEre_CAF1 22213 97 + 1
UGGGAAAGUCGGCACUUGACUCAUCACGCAAGUCCCGCCACCUUUUU-UGUGGCACACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUU
..((((....((.(((((.(.......)))))).))(((((......-.)))))...(((.(((((..(....)..))))).)))....))))..... ( -26.60)
>DroYak_CAF1 21537 97 + 1
UGGGAAAGUCGGGACUUGACUCAUCACGCAAGUCCCGCCACCUUUUU-UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUACCGCGUU
.((.......((((((((.(.......)))))))))(((((......-.)))))...(((.(((((..(....)..))))).)))......))..... ( -31.30)
>DroAna_CAF1 21649 93 + 1
--CAACAG-CCAGACUUGACUCAUCACGGAUGCCCCGCCACCUUUU--UGUGGCAAACAAAUCAGUAAAUUUACGAGCUGAAUUGCAAAUUCUUUCCA
--...(((-((.((.(((.........((.....))(((((.....--.)))))...))).)).(((....)))).)))).................. ( -18.40)
>consensus
UGGGAAAGUCGGGACUUGACUCAUCACGCAAGUCCCGCCACCUUUUU_UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUU
.((((.....((((((((..........))))))))(((((........)))))...(((.(((((..(....)..))))).)))....))))..... (-24.28 = -25.70 +   1.42)

alignment

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secondary structure

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Window 9

Location 2,285,564 – 2,285,661
Length 97
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 91.05
Mean single sequence MFE -33.13
Consensus MFE -28.20
Energy contribution -28.98
Covariance contribution 0.78
Combinations/Pair 1.14
Mean z-score -2.67
Structure conservation index 0.85
SVM decision value 1.70
SVM RNA-class probability 0.972863
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2285564 97 - 27905053
AACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA-AAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUCCCGACUUUCCCA
...(.((((...((((.(((((..(....)..))))).))))..(((((.-......)))))(((((((((.......).))))))))....))))). ( -35.70)
>DroSec_CAF1 22093 98 - 1
AACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUAGCCACAGAAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUCCCGACUUUCCCA
...(.((((...((((.(((((..(....)..))))).))))..(((((........)))))(((((((((.......).))))))))....))))). ( -36.20)
>DroSim_CAF1 22539 98 - 1
AACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUAGCCACAGAAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUCCCGACUUUCCCA
...(.((((...((((.(((((..(....)..))))).))))..(((((........)))))(((((((((.......).))))))))....))))). ( -36.20)
>DroEre_CAF1 22213 97 - 1
AACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUGUGCCACA-AAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUGCCGACUUUCCCA
...(.((((...((((.(((((..(....)..))))).))))..(((((.-......)))))((.((((((.......).))))).))....))))). ( -31.60)
>DroYak_CAF1 21537 97 - 1
AACGCGGUAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA-AAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUCCCGACUUUCCCA
...(.((((...((((.(((((..(....)..))))).)))).)))).).-.....((.((((((((((((.......).))))))))).))...)). ( -35.40)
>DroAna_CAF1 21649 93 - 1
UGGAAAGAAUUUGCAAUUCAGCUCGUAAAUUUACUGAUUUGUUUGCCACA--AAAAGGUGGCGGGGCAUCCGUGAUGAGUCAAGUCUGG-CUGUUG--
.(((..((((.....)))).((((.((((((....))))))..((((((.--.....)))))))))).)))......(((((....)))-))....-- ( -23.70)
>consensus
AACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA_AAAAAGGUGGCGGGACUUGCGUGAUGAGUCAAGUCCCGACUUUCCCA
.....((((...((((.(((((..(....)..))))).))))..(((((........)))))(((((((((.......).))))))))....)))).. (-28.20 = -28.98 +   0.78)

alignment

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secondary structure

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Window 0

Location 2,285,597 – 2,285,690
Length 93
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -26.23
Consensus MFE -16.16
Energy contribution -16.18
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -2.39
Structure conservation index 0.62
SVM decision value 1.05
SVM RNA-class probability 0.907619
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2285597 93 + 27905053
CCCGCCACCUUUUU-UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUUGG------AAAAUCCCAACGAC-UUCUUGCUUACGA----
...(((((......-.))))).......(((((..(....)..)))))...((((......((((((------......))))))..-...))))......---- ( -26.40)
>DroSec_CAF1 22126 94 + 1
CCCGCCACCUUUUUCUGUGGCUAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUUGG------AAAAUCCCAACGAC-UUCUUGCUUACGA----
...(((((........))))).......(((((..(....)..)))))...((((......((((((------......))))))..-...))))......---- ( -26.20)
>DroSim_CAF1 22572 94 + 1
CCCGCCACCUUUUUCUGUGGCUAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUUGG------AAAAUCCCAACGAC-UUCUUGCUUACGA----
...(((((........))))).......(((((..(....)..)))))...((((......((((((------......))))))..-...))))......---- ( -26.20)
>DroEre_CAF1 22246 88 + 1
CCCGCCACCUUUUU-UGUGGCACACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUUGGCAUCGGAAAAUCUUA--GGAAUC-U-------------
.(((((((......-.)))))...(((.(((((..(....)..))))).)))....(((((.(....)..))))).......--))....-.------------- ( -21.70)
>DroYak_CAF1 21570 98 + 1
CCCGCCACCUUUUU-UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUACCGCGUUGGCAUCGGAAAGUCUUU--GACGUUCUUGCUUACGA----
...(((((......-.)))))...(((.(((((..(....)..))))).))).........(((.((((..((((.(((...--))).)))))))).))).---- ( -27.30)
>DroAna_CAF1 21679 102 + 1
CCCGCCACCUUUU--UGUGGCAAACAAAUCAGUAAAUUUACGAGCUGAAUUGCAAAUUCUUUCCAGGCAUUGGCAAAUCUUUGAGAG-GGUUUGCAUACGAGACG
...(((((.....--.))))).......(((((..........)))))..(((((((((((((.(((.(((....)))))).)))))-))))))))......... ( -29.60)
>consensus
CCCGCCACCUUUUU_UGUGGCAAACAAAUCAGCAAGUUUACGAGCUGAAUUGCAAAUUCCGCGUUGG______AAAAUCCCAACGAC_UUCUUGCUUACGA____
.(((((((........)))))...(((.(((((..(....)..))))).))).............))...................................... (-16.16 = -16.18 +   0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,285,597 – 2,285,690
Length 93
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -26.08
Consensus MFE -19.24
Energy contribution -19.27
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -1.19
Structure conservation index 0.74
SVM decision value 0.17
SVM RNA-class probability 0.615141
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2285597 93 - 27905053
----UCGUAAGCAAGAA-GUCGUUGGGAUUUU------CCAACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA-AAAAAGGUGGCGGG
----......(((((..-(.(((((((....)------)))))))....)))))...(((((..(....)..))))).....(((((((.-......))))))). ( -28.00)
>DroSec_CAF1 22126 94 - 1
----UCGUAAGCAAGAA-GUCGUUGGGAUUUU------CCAACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUAGCCACAGAAAAAGGUGGCGGG
----......(((((..-(.(((((((....)------)))))))....)))))...(((((..(....)..))))).......(((((........)))))... ( -27.80)
>DroSim_CAF1 22572 94 - 1
----UCGUAAGCAAGAA-GUCGUUGGGAUUUU------CCAACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUAGCCACAGAAAAAGGUGGCGGG
----......(((((..-(.(((((((....)------)))))))....)))))...(((((..(....)..))))).......(((((........)))))... ( -27.80)
>DroEre_CAF1 22246 88 - 1
-------------A-GAUUCC--UAAGAUUUUCCGAUGCCAACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUGUGCCACA-AAAAAGGUGGCGGG
-------------.-....((--.......(((((.((....)))))))...((((.(((((..(....)..))))).))))..(((((.-......))))))). ( -24.80)
>DroYak_CAF1 21570 98 - 1
----UCGUAAGCAAGAACGUC--AAAGACUUUCCGAUGCCAACGCGGUAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA-AAAAAGGUGGCGGG
----..........(((.(((--...))).))).((((((.....)))))).((((.(((((..(....)..))))).))))(((((((.-......))))))). ( -25.90)
>DroAna_CAF1 21679 102 - 1
CGUCUCGUAUGCAAACC-CUCUCAAAGAUUUGCCAAUGCCUGGAAAGAAUUUGCAAUUCAGCUCGUAAAUUUACUGAUUUGUUUGCCACA--AAAAGGUGGCGGG
...............((-(......((((((.(((.....)))...))))))((((.((((............)))).))))..(((((.--.....)))))))) ( -22.20)
>consensus
____UCGUAAGCAAGAA_GUCGUUAAGAUUUU______CCAACGCGGAAUUUGCAAUUCAGCUCGUAAACUUGCUGAUUUGUUUGCCACA_AAAAAGGUGGCGGG
......................................((............((((.(((((..(....)..))))).))))..(((((........))))))). (-19.24 = -19.27 +   0.03)

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 09:47:33 2006