Locus 4540

Sequence ID 3R_DroMel_CAF1
Location 12,042,533 – 12,042,699
Length 166
Max. P 0.986419
window7413 window7414 window7415 window7416

overview

Window 3

Location 12,042,533 – 12,042,634
Length 101
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -37.12
Consensus MFE -31.96
Energy contribution -32.40
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.97
Structure conservation index 0.86
SVM decision value 0.56
SVM RNA-class probability 0.781150
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12042533 101 - 27905053
GUGCUGCUGUACAUGUGUGCGUGUGUGU--GUGUACUGUUUGUUAGUAUGUAUUUGGGUCACAUGCAUACACGCACGGGGCCACAGACAGCCGCCAACAAGGA
(.((((((((...(.(((((((((((((--(((((((....((........))...))).))))))))))))))))).)...)))).))))).((.....)). ( -38.80)
>DroSec_CAF1 13867 103 - 1
GUGCUGCUGUACAUGUGUGCGAGUGUGUGGGUGUGCUGUUUGUUAGUAUGUAUUUGGGUCACAUGCAUACACGCACGGGGCCACAGACAGCCGCCAACAAGGA
.....(((((((....)))).))).(((.((((.(((((((((..((((((((.((...)).))))))))..((.....)).))))))))))))).))).... ( -35.10)
>DroSim_CAF1 13772 101 - 1
GUGCUGCUGUACAUGUGUGCGAGUGUGU--GUGUGCUGUUUGUUAGUAUGUAUUUGGGUCAUAUGCAUACGCGCACGGGGCCACAGACAGCCGCCAACAAGGA
(.((.(((((...((((.((..((((((--((((((.........(((((.........)))))))))))))))))...)))))).))))).)))........ ( -38.10)
>DroYak_CAF1 13333 101 - 1
GUGCUGCUGUACAUGUGUGUUUGCGUGU--GUGUGCUGUUUGUUAGUAUGUAUUUGGGUCACAUGCAUACACGCACGGGGCCACAGACAGCCGCCAACAAGGA
(.((.(((((...((((.((((.(((((--((((((((.....))))((((((.((...)).))))))))))))))))))))))).))))).)))........ ( -36.50)
>consensus
GUGCUGCUGUACAUGUGUGCGAGUGUGU__GUGUGCUGUUUGUUAGUAUGUAUUUGGGUCACAUGCAUACACGCACGGGGCCACAGACAGCCGCCAACAAGGA
(.((((((((...(.(((((((((((((..(..(((((.....)))))..)...((.....)).))))))))))))).)...)))).))))).((.....)). (-31.96 = -32.40 +   0.44)

alignment

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secondary structure

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Window 4

Location 12,042,568 – 12,042,671
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 95.99
Mean single sequence MFE -12.93
Consensus MFE -11.24
Energy contribution -11.50
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.87
SVM decision value 0.55
SVM RNA-class probability 0.777693
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12042568 103 + 27905053
AUGCAUGUGACCCAAAUACAUACUAACAAACAGUACAC--ACACACACGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACA
.((((((((...........((((.......))))...--...........))))))))...................(((((.............))))).... ( -13.83)
>DroSec_CAF1 13902 105 + 1
AUGCAUGUGACCCAAAUACAUACUAACAAACAGCACACCCACACACUCGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACA
.((((((((.......((.....)).......((..............)).))))))))...................(((((.............))))).... ( -12.96)
>DroSim_CAF1 13807 103 + 1
AUGCAUAUGACCCAAAUACAUACUAACAAACAGCACAC--ACACACUCGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACA
..((((((((......................((....--........))....(((.(((((.................))))).)))))))))..))...... ( -10.73)
>DroYak_CAF1 13368 103 + 1
AUGCAUGUGACCCAAAUACAUACUAACAAACAGCACAC--ACACGCAAACACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACA
.((((((((.......((.....)).......((....--....)).....))))))))...................(((((.............))))).... ( -14.22)
>consensus
AUGCAUGUGACCCAAAUACAUACUAACAAACAGCACAC__ACACACACGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACA
.((((((((..........................................))))))))...................(((((.............))))).... (-11.24 = -11.50 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,042,604 – 12,042,699
Length 95
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 85.70
Mean single sequence MFE -23.36
Consensus MFE -15.58
Energy contribution -15.30
Covariance contribution -0.28
Combinations/Pair 1.18
Mean z-score -3.69
Structure conservation index 0.67
SVM decision value 2.04
SVM RNA-class probability 0.986419
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12042604 95 + 27905053
AC--ACACACACGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACACUUGGCCUGCCACAUGUCAAAGUGCGUC
..--......((((((((((((...((((..((((.......(((((.............))))).....)))).)))).))))))....)))))). ( -26.52)
>DroSec_CAF1 13938 97 + 1
ACCCACACACUCGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACACUUGGCCUGCCACAUGUCAAAGUGCGUC
...........(((((((((((...((((..((((.......(((((.............))))).....)))).)))).))))))....))))).. ( -25.12)
>DroSim_CAF1 13843 95 + 1
AC--ACACACUCGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACACUUGGCCUGCCACAUGUCAAAGUGCGUC
..--.......(((((((((((...((((..((((.......(((((.............))))).....)))).)))).))))))....))))).. ( -25.12)
>DroYak_CAF1 13404 95 + 1
AC--ACACGCAAACACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACACUUGGCCUGCCACUUGUCAAAGUGCGUC
..--..(((((.....(((.((...((((..((((.......(((((.............))))).....)))).)))).)).))).....))))). ( -21.32)
>DroAna_CAF1 12489 72 + 1
------------------GCGCACAGC-------ACACACAAUGCCUGUUCAUUCAUAUGAGCCAAACACUUGGCCUGCCACAUGUCAAAGUGCGUC
------------------((((((.((-------(.......)))..((((((....))))))...(((..(((....)))..)))....)))))). ( -18.70)
>consensus
AC__ACACACACGCACACAUGUACAGCAGCACCAACACACAAUGGCUGUUCAUUCAUAUAAGCCAAACACUUGGCCUGCCACAUGUCAAAGUGCGUC
..................((((((..................(((((.............))))).(((..(((....)))..)))....)))))). (-15.58 = -15.30 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,042,604 – 12,042,699
Length 95
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 85.70
Mean single sequence MFE -30.07
Consensus MFE -20.32
Energy contribution -21.88
Covariance contribution 1.56
Combinations/Pair 1.10
Mean z-score -2.06
Structure conservation index 0.68
SVM decision value 0.36
SVM RNA-class probability 0.706409
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12042604 95 - 27905053
GACGCACUUUGACAUGUGGCAGGCCAAGUGUUUGGCUUAUAUGAAUGAACAGCCAUUGUGUGUUGGUGCUGCUGUACAUGUGUGCGUGUGUGU--GU
.((((((....(((((((((((((((((..(.(((((.............)))))..)..).))))).)))))..))))))))))))......--.. ( -31.32)
>DroSec_CAF1 13938 97 - 1
GACGCACUUUGACAUGUGGCAGGCCAAGUGUUUGGCUUAUAUGAAUGAACAGCCAUUGUGUGUUGGUGCUGCUGUACAUGUGUGCGAGUGUGUGGGU
.((((((((..(((((((((((((((((..(.(((((.............)))))..)..).))))).)))))..))))))....)))))))).... ( -32.52)
>DroSim_CAF1 13843 95 - 1
GACGCACUUUGACAUGUGGCAGGCCAAGUGUUUGGCUUAUAUGAAUGAACAGCCAUUGUGUGUUGGUGCUGCUGUACAUGUGUGCGAGUGUGU--GU
.((((((((..(((((((((((((((((..(.(((((.............)))))..)..).))))).)))))..))))))....))))))))--.. ( -32.52)
>DroYak_CAF1 13404 95 - 1
GACGCACUUUGACAAGUGGCAGGCCAAGUGUUUGGCUUAUAUGAAUGAACAGCCAUUGUGUGUUGGUGCUGCUGUACAUGUGUGUUUGCGUGU--GU
...(((((...((((((((((((((((....)))))))...((......)))))))).)))...))))).....(((((((......))))))--). ( -29.80)
>DroAna_CAF1 12489 72 - 1
GACGCACUUUGACAUGUGGCAGGCCAAGUGUUUGGCUCAUAUGAAUGAACAGGCAUUGUGUGU-------GCUGUGCGC------------------
..(((((...(((((.(((....))).))))).(((.(((((.((((......))))))))).-------)))))))).------------------ ( -24.20)
>consensus
GACGCACUUUGACAUGUGGCAGGCCAAGUGUUUGGCUUAUAUGAAUGAACAGCCAUUGUGUGUUGGUGCUGCUGUACAUGUGUGCGAGUGUGU__GU
..(((((..(((((.((((((((((((....))))))(((((.((((......)))))))))....))))))))).))...)))))........... (-20.32 = -21.88 +   1.56)

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 11:31:51 2006