Locus 2275

Sequence ID 3L_DroMel_CAF1
Location 6,367,609 – 6,367,746
Length 137
Max. P 0.986005
window3514 window3515 window3516 window3517

overview

Window 4

Location 6,367,609 – 6,367,709
Length 100
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 75.83
Mean single sequence MFE -29.97
Consensus MFE -17.34
Energy contribution -18.70
Covariance contribution 1.36
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.58
SVM decision value 1.42
SVM RNA-class probability 0.952368
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6367609 100 + 23771897
AGGGGCCGUACCCCAUUGAUCUCACACUAAAGCUGCUCGAUCAAGGC---UGCGAAUAGAUUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGC
.((((.....)))).(((((((((..(((..((.(((.......)))---.))...)))......----((((((......)))))).))))))))).......... ( -31.30)
>DroSec_CAF1 132035 100 + 1
AGGGGCCGUACCCCAUUGAUCUCACACUAAAGCUGUUCGAUCAAGGC---UGCGAAUAGAAUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGC
.((((.....)))).(((((((((........(((((((........---..)))))))......----((((((......)))))).))))))))).......... ( -31.70)
>DroSim_CAF1 138748 100 + 1
AGGGGCCGUACCCCAUUGAUCUCACACUAAAGCUGCUCGAUCAAGGC---UGCGAAUAGAUUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGC
.((((.....)))).(((((((((..(((..((.(((.......)))---.))...)))......----((((((......)))))).))))))))).......... ( -31.30)
>DroEre_CAF1 136460 83 + 1
AGGGGCCGAACCCCAUUGAUCUCGUACUAAAGCUGCUC--------------------GAUUGCG----AGAUCGUUUAACCGAUCUAAGAGAUCAGCUAGAAUUGC
.((((.....)))).((((((((..........(((..--------------------....)))----((((((......))))))..)))))))).......... ( -26.40)
>DroYak_CAF1 144515 100 + 1
AGGGGCCGAACCCCAUUGAUCUCACACUAAAGCUGCACGUUCCAGUC---UCCGCACAGAUUUCG----AGAUCGUUUAACCGAUCUAAGAGAUCAACUAGAAUUGC
.((((.....)))).((((((((..............((....((((---(......))))).))----((((((......))))))..)))))))).......... ( -26.80)
>DroAna_CAF1 134381 98 + 1
GGGGGCUGGAAACCGUUGAUCUCGGCCCGGAGCUCCCCAAACAAGUCGGUUGGGUUGCGUUUUCGAAGCAGAUCGGCUGGCCGA---------UCAACAAAAAUUGC
..((........))(((((..((((((.((......)).....((((((((..(((.((....)).))).))))))))))))))---------)))))......... ( -32.30)
>consensus
AGGGGCCGUACCCCAUUGAUCUCACACUAAAGCUGCUCGAUCAAGGC___UGCGAAUAGAUUUCG____AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGC
.((((.....)))).((((((((...................................(....).....((((((......))))))..)))))))).......... (-17.34 = -18.70 +   1.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,367,609 – 6,367,709
Length 100
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 75.83
Mean single sequence MFE -32.22
Consensus MFE -20.44
Energy contribution -21.72
Covariance contribution 1.28
Combinations/Pair 1.18
Mean z-score -2.37
Structure conservation index 0.63
SVM decision value 2.03
SVM RNA-class probability 0.986005
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6367609 100 - 23771897
GCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAAUCUAUUCGCA---GCCUUGAUCGAGCAGCUUUAGUGUGAGAUCAAUGGGGUACGGCCCCU
.........(((((((((((((((((......))))).----......(((...((.---(((......).)).))..)))))))))))))))((((.....)))). ( -33.10)
>DroSec_CAF1 132035 100 - 1
GCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAUUCUAUUCGCA---GCCUUGAUCGAACAGCUUUAGUGUGAGAUCAAUGGGGUACGGCCCCU
.........(((((((((((((((((......)))))(----(((..((........---.....))))))..........))))))))))))((((.....)))). ( -31.52)
>DroSim_CAF1 138748 100 - 1
GCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAAUCUAUUCGCA---GCCUUGAUCGAGCAGCUUUAGUGUGAGAUCAAUGGGGUACGGCCCCU
.........(((((((((((((((((......))))).----......(((...((.---(((......).)).))..)))))))))))))))((((.....)))). ( -33.10)
>DroEre_CAF1 136460 83 - 1
GCAAUUCUAGCUGAUCUCUUAGAUCGGUUAAACGAUCU----CGCAAUC--------------------GAGCAGCUUUAGUACGAGAUCAAUGGGGUUCGGCCCCU
.......(((((((((.....)))))))))...(((((----(((....--------------------..)).((....))..))))))...((((.....)))). ( -28.40)
>DroYak_CAF1 144515 100 - 1
GCAAUUCUAGUUGAUCUCUUAGAUCGGUUAAACGAUCU----CGAAAUCUGUGCGGA---GACUGGAACGUGCAGCUUUAGUGUGAGAUCAAUGGGGUUCGGCCCCU
.........(((((((((..((((((......))))))----..(((.(((..((..---........))..))).))).....)))))))))((((.....)))). ( -35.50)
>DroAna_CAF1 134381 98 - 1
GCAAUUUUUGUUGA---------UCGGCCAGCCGAUCUGCUUCGAAAACGCAACCCAACCGACUUGUUUGGGGAGCUCCGGGCCGAGAUCAACGGUUUCCAGCCCCC
....((((((..((---------((((....)))))).....)))))).((..(((((.(.....).)))))..))...((((.(((((.....)))))..)))).. ( -31.70)
>consensus
GCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU____CGAAAUCUAUUCGCA___GCCUUGAUCGAGCAGCUUUAGUGUGAGAUCAAUGGGGUACGGCCCCU
.........(((((((((..((((((......)))))).................................(((.......))))))))))))((((.....)))). (-20.44 = -21.72 +   1.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,367,642 – 6,367,746
Length 104
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 76.25
Mean single sequence MFE -27.65
Consensus MFE -13.09
Energy contribution -15.95
Covariance contribution 2.86
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.47
SVM decision value 1.14
SVM RNA-class probability 0.921010
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6367642 104 + 23771897
UGCUCGAUCAAGGC---UGCGAAUAGAUUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGCUACCAAUUCGGGGCA-GUUUAGUUAAUUAACCGAACCA
...(((....((((---(((.....(((((((----((((((......)))))).)))))))..((.((((((....)))))).)))))-)))).(((....)))))).... ( -29.70)
>DroSec_CAF1 132068 104 + 1
UGUUCGAUCAAGGC---UGCGAAUAGAAUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGCUACCAAUUCGGGGCA-GUUUAGUUAAUUAACCGAACCA
.(((((....((((---(((.....((.((((----((((((......)))))).)))).))..((.((((((....)))))).)))))-)))).(((....)))))))).. ( -29.10)
>DroSim_CAF1 138781 104 + 1
UGCUCGAUCAAGGC---UGCGAAUAGAUUUCG----AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGCUACCAAUUCGGGGCA-GUUUAGUUAAUUAACCGAACCA
...(((....((((---(((.....(((((((----((((((......)))))).)))))))..((.((((((....)))))).)))))-)))).(((....)))))).... ( -29.70)
>DroEre_CAF1 136493 86 + 1
UGCUC--------------------GAUUGCG----AGAUCGUUUAACCGAUCUAAGAGAUCAGCUAGAAUUGCCACCGAUUCG-GGCA-GUUUAGUUAAUUAACCGAACCA
(((((--------------------((((...----((((((......))))))....)))).....((((((....)))))))-))))-(((..(((....)))..))).. ( -24.80)
>DroYak_CAF1 144548 104 + 1
UGCACGUUCCAGUC---UCCGCACAGAUUUCG----AGAUCGUUUAACCGAUCUAAGAGAUCAACUAGAAUUGCUACCAAUUCGUGGCA-GUUUAGUUAAUUAACCAAACCA
(((((......)).---...)))..((((((.----((((((......))))))..))))))(((((((.(((((((......))))))-)))))))).............. ( -27.00)
>DroAna_CAF1 134414 103 + 1
UCCCCAAACAAGUCGGUUGGGUUGCGUUUUCGAAGCAGAUCGGCUGGCCGA---------UCAACAAAAAUUGCUACCAAUUCCGCUUAGGCCUAAUUAACCAACAAAACCA
...........((..((((((((.((....))((((.((((((....))))---------))......(((((....)))))..)))).))))))))..))........... ( -25.60)
>consensus
UGCUCGAUCAAGGC___UGCGAAUAGAUUUCG____AGAUCGUUUAUCCGAUCUAUGAGAUCAACUAGAAUUGCUACCAAUUCGGGGCA_GUUUAGUUAAUUAACCGAACCA
(((((....................((((((.....((((((......))))))..)))))).....((((((....)))))).))))).((((.(((....))).)))).. (-13.09 = -15.95 +   2.86)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,367,642 – 6,367,746
Length 104
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 76.25
Mean single sequence MFE -27.65
Consensus MFE -14.86
Energy contribution -16.92
Covariance contribution 2.06
Combinations/Pair 1.24
Mean z-score -1.79
Structure conservation index 0.54
SVM decision value 0.42
SVM RNA-class probability 0.727933
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6367642 104 - 23771897
UGGUUCGGUUAAUUAACUAAAC-UGCCCCGAAUUGGUAGCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAAUCUAUUCGCA---GCCUUGAUCGAGCA
..((((((((((.........(-(((...((((((....)))))).....(((.((..((((((......))))))----.)).))).....)))---)..)))))))))). ( -28.00)
>DroSec_CAF1 132068 104 - 1
UGGUUCGGUUAAUUAACUAAAC-UGCCCCGAAUUGGUAGCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAUUCUAUUCGCA---GCCUUGAUCGAACA
..((((((((((.........(-((((.......)))))........((((.......((((((......))))))----(((((...)))))))---)).)))))))))). ( -27.20)
>DroSim_CAF1 138781 104 - 1
UGGUUCGGUUAAUUAACUAAAC-UGCCCCGAAUUGGUAGCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU----CGAAAUCUAUUCGCA---GCCUUGAUCGAGCA
..((((((((((.........(-(((...((((((....)))))).....(((.((..((((((......))))))----.)).))).....)))---)..)))))))))). ( -28.00)
>DroEre_CAF1 136493 86 - 1
UGGUUCGGUUAAUUAACUAAAC-UGCC-CGAAUCGGUGGCAAUUCUAGCUGAUCUCUUAGAUCGGUUAAACGAUCU----CGCAAUC--------------------GAGCA
..((((((((............-((((-(......).))))....(((((((((.....)))))))))........----...))))--------------------)))). ( -24.50)
>DroYak_CAF1 144548 104 - 1
UGGUUUGGUUAAUUAACUAAAC-UGCCACGAAUUGGUAGCAAUUCUAGUUGAUCUCUUAGAUCGGUUAAACGAUCU----CGAAAUCUGUGCGGA---GACUGGAACGUGCA
.(((((((((....))))))))-)((((.....)))).(((.((((((((........((((((......))))))----.....(((....)))---))))))))..))). ( -30.60)
>DroAna_CAF1 134414 103 - 1
UGGUUUUGUUGGUUAAUUAGGCCUAAGCGGAAUUGGUAGCAAUUUUUGUUGA---------UCGGCCAGCCGAUCUGCUUCGAAAACGCAACCCAACCGACUUGUUUGGGGA
.(((((.(((....))).)))))...(((...((((.((((.........((---------((((....))))))))))))))...)))..(((((.(.....).))))).. ( -27.60)
>consensus
UGGUUCGGUUAAUUAACUAAAC_UGCCCCGAAUUGGUAGCAAUUCUAGUUGAUCUCAUAGAUCGGAUAAACGAUCU____CGAAAUCUAUUCGCA___GCCUUGAUCGAGCA
..(((((((((((((((((..........((((((....)))))))))))))......((((((......)))))).........................)))))))))). (-14.86 = -16.92 +   2.06)

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 10:28:26 2006