Locus 6610

Sequence ID 2R_DroMel_CAF1
Location 20,702,640 – 20,702,800
Length 160
Max. P 0.848243
window10518 window10519 window10520

overview

Window 8

Location 20,702,640 – 20,702,760
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -27.12
Consensus MFE -27.16
Energy contribution -27.04
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.24
Structure conservation index 1.00
SVM decision value 0.65
SVM RNA-class probability 0.810270
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20702640 120 + 20766785
GUGCUAUAAAUCAUAUAUAAAUGUAAACUUGAUGAUUUUGCGUUAUAAACAGUGAACUUUUUGUUUAGGUAAAAAUUGCUCUGUUUAUGUUGCGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((.(((((.....(((((((.((((((((((((((.....)))))((((.....))))))))))))).))))))).))))).)))(((.....))).. ( -24.40)
>DroSec_CAF1 136241 120 + 1
GUGCUAUAAAUCAUAUAUAAAUGUUAACUUGAUGAUUUUGCGUUAUAAACAGUGAACUUUUUGUUUAGGUAAAAAUUGCUCUGUUUAUGUUGCGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((((((((.....(((((((.((((((((((((((.....)))))((((.....))))))))))))).))))))).)))))))))(((.....))).. ( -28.30)
>DroSim_CAF1 139876 120 + 1
GUGCUAUAAAUCAUAUAUAAAUGUUAACUUGAUGAUUUUGCGUUAUAAACAGUGAACUUUUUGUUUAGGUAAAAAUUGCUCUGUUUAUGUUGCGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((((((((.....(((((((.((((((((((((((.....)))))((((.....))))))))))))).))))))).)))))))))(((.....))).. ( -28.30)
>DroEre_CAF1 176936 120 + 1
GUGCUAUAAAUCAUAUAUAAAUGUUAACUUGAUGAUUUUGCGUUAUAAACAGCGAACUUUUUGUUUAGGUAAAAACUGCUCUGUUUAUGUUGUGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((((((((.....(((..((.(((((((((.(...((((((......))))))...).))))))))).))..))).)))))))))(((.....))).. ( -26.30)
>DroYak_CAF1 141691 120 + 1
GUGCUAUAAAUCAUAUAUAAAUGUUAACUUGAUGAUUUUGCGUUAUAAACAGUGAACUUUUUGUUUAUGUAAAAACUGCUCUGUUUAUAUUGCGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((((((((.....(((((((.(((((((((.(...((((((......))))))...).))))))))).))))))).)))))))))(((.....))).. ( -28.30)
>consensus
GUGCUAUAAAUCAUAUAUAAAUGUUAACUUGAUGAUUUUGCGUUAUAAACAGUGAACUUUUUGUUUAGGUAAAAAUUGCUCUGUUUAUGUUGCGGGGAAAGUUAAUAGGGUCCAGCCCAC
.....................(((((((((.....(((((((.(((((((((.(...((((((......))))))...).))))))))).))))))).)))))))))(((.....))).. (-27.16 = -27.04 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,702,640 – 20,702,760
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -19.21
Consensus MFE -18.39
Energy contribution -17.99
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.20
Structure conservation index 0.96
SVM decision value 0.26
SVM RNA-class probability 0.657803
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20702640 120 - 20766785
GUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACGCAAAAUCAUCAAGUUUACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))...((((((((.(.(((((((.........)))))))).))))))))...((.(((((((.................)))))))...)).. ( -19.03)
>DroSec_CAF1 136241 120 - 1
GUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACGCAAAAUCAUCAAGUUAACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))...((((((((.(.(((((((.........)))))))).))))))))...((.(((((((.................)))))))...)).. ( -19.03)
>DroSim_CAF1 139876 120 - 1
GUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACGCAAAAUCAUCAAGUUAACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))...((((((((.(.(((((((.........)))))))).))))))))...((.(((((((.................)))))))...)).. ( -19.03)
>DroEre_CAF1 176936 120 - 1
GUGGGCUGGACCCUAUUAACUUUCCCCACAACAUAAACAGAGCAGUUUUUACCUAAACAAAAAGUUCGCUGUUUAUAACGCAAAAUCAUCAAGUUAACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))...((((((((.(.(.(((((........))))).).).))))))))...((.(((((((.................)))))))...)).. ( -19.23)
>DroYak_CAF1 141691 120 - 1
GUGGGCUGGACCCUAUUAACUUUCCCCGCAAUAUAAACAGAGCAGUUUUUACAUAAACAAAAAGUUCACUGUUUAUAACGCAAAAUCAUCAAGUUAACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))..(((((((((.(.(.(((((........))))).).).)))))))))..((.(((((((.................)))))))...)).. ( -19.73)
>consensus
GUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACGCAAAAUCAUCAAGUUAACAUUUAUAUAUGAUUUAUAGCAC
(((((..((..........))...)))))...((((((((.(.(((((((.........)))))))).))))))))...((.(((((((.................)))))))...)).. (-18.39 = -17.99 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,702,680 – 20,702,800
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -25.52
Consensus MFE -23.92
Energy contribution -23.92
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -1.33
Structure conservation index 0.94
SVM decision value 0.78
SVM RNA-class probability 0.848243
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20702680 120 - 20766785
UUUUGUUUUUCUAGUUCGUAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACG
.............((((((.((....))....)))))).((((((..((..........))...))))))..((((((((.(.(((((((.........)))))))).)))))))).... ( -26.40)
>DroSec_CAF1 136281 120 - 1
UUUUGUUUUUCUUGUUCGUAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACG
............(((((((.((....))....)))))))((((((..((..........))...))))))..((((((((.(.(((((((.........)))))))).)))))))).... ( -26.90)
>DroSim_CAF1 139916 120 - 1
UUUUGUUUUUCUAUUUCGUAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACG
..............(((((.((....))....)))))..((((((..((..........))...))))))..((((((((.(.(((((((.........)))))))).)))))))).... ( -22.50)
>DroEre_CAF1 176976 120 - 1
UUUUGUUUUUCUAGUUCGAAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCACAACAUAAACAGAGCAGUUUUUACCUAAACAAAAAGUUCGCUGUUUAUAACG
.............(((((..((....)).....))))).((((((..((..........))...))))))..((((((((.(.(.(((((........))))).).).)))))))).... ( -24.70)
>DroYak_CAF1 141731 119 - 1
-UUUGUUUUUCUAGUUCGUAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCGCAAUAUAAACAGAGCAGUUUUUACAUAAACAAAAAGUUCACUGUUUAUAACG
-............((((((.((....))....)))))).((((((..((..........))...)))))).(((((((((.(.(.(((((........))))).).).)))))))))... ( -27.10)
>consensus
UUUUGUUUUUCUAGUUCGUAAGGAAACUGUUAACGGACAUGUGGGCUGGACCCUAUUAACUUUCCCCGCAACAUAAACAGAGCAAUUUUUACCUAAACAAAAAGUUCACUGUUUAUAACG
.............((((((.((....))....)))))).((((((..((..........))...))))))..((((((((.(.(((((((.........)))))))).)))))))).... (-23.92 = -23.92 +  -0.00)

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 12:15:02 2006