Locus 4685

Sequence ID 2L_DroMel_CAF1
Location 13,467,126 – 13,467,250
Length 124
Max. P 0.990113
window7402 window7403 window7404 window7405

overview

Window 2

Location 13,467,126 – 13,467,228
Length 102
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 89.30
Mean single sequence MFE -37.56
Consensus MFE -26.78
Energy contribution -26.78
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -3.55
Structure conservation index 0.71
SVM decision value 1.74
SVM RNA-class probability 0.974797
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467126 102 + 22407834
GAUUUCGCGUUCGUGUUUCGGAUUUC-------AGUUUACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUA
......(((((((.....(((((..(-------((...((((((..------.......((((((((....)))))))).)))))))))...)))))..))))).))........ ( -32.20)
>DroSec_CAF1 66632 102 + 1
GAUUUCGCGUUCGUGUUUCGGAUUUC-------GGUUUACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUA
......(((((((.....(((((..(-------((..((((((...------.....)))(((((((....)))))))))).)))...)))))......))))).))........ ( -34.50)
>DroSim_CAF1 67852 102 + 1
GAUUUCGCGUUCGUGUUUCGGAUUUC-------GGUUUACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUA
......(((((((.....(((((..(-------((..((((((...------.....)))(((((((....)))))))))).)))...)))))......))))).))........ ( -34.50)
>DroEre_CAF1 71179 109 + 1
GAUUCCGCGUUCGUGUUUCGGAUUUCGGAUUACGGAUUCCGGAUUC------CGGAAUCCGGACAUAUACCUGUGUCCGCAUCCGUUUGUCCGUCCGCUCGGACUGCAUAAUUUA
......(((((((.((..(((((..(((((...(((((((((...)------))))))))(((((((....)))))))..)))))...)))))...)).))))).))........ ( -48.80)
>DroYak_CAF1 67874 115 + 1
GAUUCCGCGUUCGUGUUUCGUGUUUCGGAUUUCGGUUUACGGAUUCGUUUUACGGAUUCCGGACAUAUACCUGUGUCCGUAUCCGUUUGUCCGUCCGUUCGGACUGCAUAAUUUA
((.((((...(((...((((.....))))...)))....)))).)).....((((((..((((((((....)))))))).))))))..(((((......)))))........... ( -37.80)
>consensus
GAUUUCGCGUUCGUGUUUCGGAUUUC_______GGUUUACGGAUUC______CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUA
((...(((....)))..))((((.................((((((.......))))))((((((((....)))))))).))))((..(((((......))))).))........ (-26.78 = -26.78 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,467,126 – 13,467,228
Length 102
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 89.30
Mean single sequence MFE -32.36
Consensus MFE -24.88
Energy contribution -25.04
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.92
Structure conservation index 0.77
SVM decision value 2.12
SVM RNA-class probability 0.988514
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467126 102 - 22407834
UAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUAAACU-------GAAAUCCGAAACACGAACGCGAAAUC
.......(((.(((((......)))))...(((((.((((((........))))))...((((------(..........))-------))))))))..........)))..... ( -28.10)
>DroSec_CAF1 66632 102 - 1
UAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUAAACC-------GAAAUCCGAAACACGAACGCGAAAUC
.......(((.(((((......)))))...(((((.((((((........))))))...((((------(..........))-------))))))))..........)))..... ( -30.30)
>DroSim_CAF1 67852 102 - 1
UAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUAAACC-------GAAAUCCGAAACACGAACGCGAAAUC
.......(((.(((((......)))))...(((((.((((((........))))))...((((------(..........))-------))))))))..........)))..... ( -30.30)
>DroEre_CAF1 71179 109 - 1
UAAAUUAUGCAGUCCGAGCGGACGGACAAACGGAUGCGGACACAGGUAUAUGUCCGGAUUCCG------GAAUCCGGAAUCCGUAAUCCGAAAUCCGAAACACGAACGCGGAAUC
.......(((.((((....))))(((....((((((((((((........)))))((((((((------(...))))))))))).)))))...)))...........)))..... ( -41.50)
>DroYak_CAF1 67874 115 - 1
UAAAUUAUGCAGUCCGAACGGACGGACAAACGGAUACGGACACAGGUAUAUGUCCGGAAUCCGUAAAACGAAUCCGUAAACCGAAAUCCGAAACACGAAACACGAACGCGGAAUC
...........(((((......)))))..((((((.((((((........))))))..)))))).....((.(((((....((.....)).....((.....))...))))).)) ( -31.60)
>consensus
UAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG______GAAUCCGUAAACC_______GAAAUCCGAAACACGAACGCGAAAUC
.......(((.(((((......)))))...(((((..(((((........)))))(((.((........)).))).................)))))..........)))..... (-24.88 = -25.04 +   0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,467,156 – 13,467,250
Length 94
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 92.95
Mean single sequence MFE -31.20
Consensus MFE -24.27
Energy contribution -24.67
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.78
SVM decision value 0.58
SVM RNA-class probability 0.789602
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467156 94 + 22407834
UACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUAGCAGGCCGUUAGUGCAAACCCG
...((((..------((.((..((((((((....)))))))).)).))...))))(..(...(((.((((........)))).)))...)..)....... ( -28.70)
>DroSec_CAF1 66662 94 + 1
UACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUAGCAGGCCGUUAGUGCAAGCCCG
...((((..------((.((..((((((((....)))))))).)).))...))))(..(...(((.((((........)))).)))...)..)....... ( -28.70)
>DroSim_CAF1 67882 94 + 1
UACGGAUUC------CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUAGCAGGCCGUUAGUGCAAGCCCG
...((((..------((.((..((((((((....)))))))).)).))...))))(..(...(((.((((........)))).)))...)..)....... ( -28.70)
>DroEre_CAF1 71216 94 + 1
UCCGGAUUC------CGGAAUCCGGACAUAUACCUGUGUCCGCAUCCGUUUGUCCGUCCGCUCGGACUGCAUAAUUUAGCAGGCCUUUAGUGCAAGCCCA
..(((((..------((((...((((((((....))))))))..))))...)))))..((((.((.((((........)))).))...))))........ ( -32.40)
>DroYak_CAF1 67911 100 + 1
UACGGAUUCGUUUUACGGAUUCCGGACAUAUACCUGUGUCCGUAUCCGUUUGUCCGUCCGUUCGGACUGCAUAAUUUAGCAGGCCGUUAGUGGAAGCCCG
..(((((.......((((((..((((((((....)))))))).))))))..)))))((((..(((.((((........)))).)))....))))...... ( -37.50)
>consensus
UACGGAUUC______CGAAUUCCGGACAUAUACCUGUGUCCGUAUCCGUCUGUCCGUCCGUUCGGACUGCAUAAUUUAGCAGGCCGUUAGUGCAAGCCCG
.((((((...............((((((((....)))))))).))))))..(((((......)))))(((........)))(((...........))).. (-24.27 = -24.67 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,467,156 – 13,467,250
Length 94
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 92.95
Mean single sequence MFE -32.76
Consensus MFE -27.86
Energy contribution -27.90
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.85
SVM decision value 2.20
SVM RNA-class probability 0.990113
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467156 94 - 22407834
CGGGUUUGCACUAACGGCCUGCUAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUA
(((((((((.(....))).(((........)))(((((......)))))...(((((.((((((........))))))..)))))------))))))).. ( -31.50)
>DroSec_CAF1 66662 94 - 1
CGGGCUUGCACUAACGGCCUGCUAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUA
(((((..((.(....))).(((........)))))))).....(((((....(((((.((((((........))))))..)))))------...))))). ( -31.40)
>DroSim_CAF1 67882 94 - 1
CGGGCUUGCACUAACGGCCUGCUAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG------GAAUCCGUA
(((((..((.(....))).(((........)))))))).....(((((....(((((.((((((........))))))..)))))------...))))). ( -31.40)
>DroEre_CAF1 71216 94 - 1
UGGGCUUGCACUAAAGGCCUGCUAAAUUAUGCAGUCCGAGCGGACGGACAAACGGAUGCGGACACAGGUAUAUGUCCGGAUUCCG------GAAUCCGGA
.((((((.......))))))((........)).((((....))))(((....(((((.((((((........)))))).).))))------...)))... ( -33.80)
>DroYak_CAF1 67911 100 - 1
CGGGCUUCCACUAACGGCCUGCUAAAUUAUGCAGUCCGAACGGACGGACAAACGGAUACGGACACAGGUAUAUGUCCGGAAUCCGUAAAACGAAUCCGUA
.((....)).....(((.((((........)))).))).(((((((.....((((((.((((((........))))))..))))))....))..))))). ( -35.70)
>consensus
CGGGCUUGCACUAACGGCCUGCUAAAUUAUGCAGUCCGAACGGACGGACAGACGGAUACGGACACAGGUAUAUGUCCGGAAUUCG______GAAUCCGUA
.(((((.........)))))((........)).(((((......)))))..((((((.((((((........))))))(....).........)))))). (-27.86 = -27.90 +   0.04)

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 11:24:33 2006