Locus 2811

Sequence ID 2L_DroMel_CAF1
Location 8,004,258 – 8,004,426
Length 168
Max. P 0.925497
window4467 window4468 window4469

overview

Window 7

Location 8,004,258 – 8,004,360
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.24
Mean single sequence MFE -29.54
Consensus MFE -21.11
Energy contribution -21.99
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -2.21
Structure conservation index 0.71
SVM decision value 1.17
SVM RNA-class probability 0.925497
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8004258 102 - 22407834
GCUGAU-UAUUAGCGGGUAACAUGUUUCGUUUAACGGAACAGCUGUUCAU-UUAG---------------UCGGCAGUUAUCGCUUAAGCCGCAUGUUAUCGAUAUCUUCAAU-UAUUUU
(((((.-..))))).((((((((((...((((((((((((.((((.....-....---------------.)))).))).))).)))))).))))))))))............-...... ( -26.60)
>DroSec_CAF1 4880 102 - 1
GCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGCACAGCUGUUCAU-UUAG---------------UCGGCAGUUAUCGGUUAAGCCGCAUGUUAUCGAUAUCUUCAAU-UAUUUU
.(((((-....)))))(((((((((...(((((((.(...(((((((...-....---------------..)))))))..).))))))).))))))))).............-...... ( -25.90)
>DroSim_CAF1 4829 102 - 1
GCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGAACAGCUGUUCAU-UUAG---------------ACGGCAGUUAUCGGUUAAGCCGCAUGCUAUCGAUAUCUUCAAU-UAUUUU
(((((.-..(((((.((((((.(((..(((((((..((((....))))..-))))---------------)))))))))))).)))))...))).))................-...... ( -28.90)
>DroEre_CAF1 4742 104 - 1
GCUGUUCUUUUAGCGGGUAACAUGCAUCGCUUAACGGAACAGCUGUUACU-UCAG---------------UCGGCCGUUAUCGGUUAAGCCGCAUGUUAUCGAUACCCGGAAUUUAUUUU
((((......)))).((((((((((...(((((((.((((.((((.....-....---------------.)))).))..)).))))))).))))))))))................... ( -33.40)
>DroYak_CAF1 4928 120 - 1
GCUUUUUUUUUAACGGGUAACAUGCAUCGUUUAACGGAACAGCUGUUAUUUUCAGUUACAGAACUGCUGUUCGGCUGUUAUGGGCAAAGCCGCAUGUUAUCGAUAACCGAAAUUUAUUUG
...............((((((((((.........((.((((((((..((...(((((....)))))..)).)))))))).))(((...)))))))))))))................... ( -32.90)
>consensus
GCUGUU_UAUUAACGGGUAACAUGCUUCGUUUAACGGAACAGCUGUUCAU_UUAG_______________UCGGCAGUUAUCGGUUAAGCCGCAUGUUAUCGAUAUCUUCAAU_UAUUUU
...............((((((((((...(((((((.((((.((((..........................)))).))..)).))))))).))))))))))................... (-21.11 = -21.99 +   0.88)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,004,297 – 8,004,400
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.74
Mean single sequence MFE -32.70
Consensus MFE -19.71
Energy contribution -19.99
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -2.28
Structure conservation index 0.60
SVM decision value 1.07
SVM RNA-class probability 0.909808
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8004297 103 - 22407834
AAUCAACCGGUUGCGGUUAAAAGCUCUGUUAAACGGAGAUGCUGAU-UAUUAGCGGGUAACAUGUUUCGUUUAACGGAACAGCUGUUCAU-UUAG---------------UCGGCAGUUA
....(((((....))))).....(((((.....))))).(((((((-((..(((((......(((((((.....))))))).)))))...-.)))---------------)))))).... ( -31.30)
>DroSec_CAF1 4919 103 - 1
AAUCAACCGGUUGCGAUUAAAAGCUCUGUUAAAUUGAGAAGCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGCACAGCUGUUCAU-UUAG---------------UCGGCAGUUA
..........((((((((((((((((((((((((...(((((((((-.(((....))))))).))))))))))))))...)))).....)-))))---------------)).))))... ( -25.50)
>DroSim_CAF1 4868 103 - 1
AAUCAACCGGGUGCGGUUAAAAGCUCUGUUAAAUGGAGAAGCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGAACAGCUGUUCAU-UUAG---------------ACGGCAGUUA
....(((((....)))))...((((((((((((((((..(((((((-(...(((((((.....)).))))).....)))))))).)))))-)).)---------------)))).)))). ( -33.00)
>DroEre_CAF1 4782 103 - 1
AGCCAACCGGUUGCGGUUAACUGCUCUGUUAGGU-AAGACGCUGUUCUUUUAGCGGGUAACAUGCAUCGCUUAACGGAACAGCUGUUACU-UCAG---------------UCGGCCGUUA
((((....))))(((((..((((.......((((-((.(.((((((((.(((((((((.....)).)))).))).))))))))).)))))-))))---------------)..))))).. ( -37.61)
>DroYak_CAF1 4968 120 - 1
AAACAACCGGUUGCGGUUAACUGCGCUGUUAAGCGUAGAUGCUUUUUUUUUAACGGGUAACAUGCAUCGUUUAACGGAACAGCUGUUAUUUUCAGUUACAGAACUGCUGUUCGGCUGUUA
.((((.((((..((((((..(((..(((((((((...(((((.....................))))))))))))))..)))((((.((.....)).))))))))))...)))).)))). ( -36.10)
>consensus
AAUCAACCGGUUGCGGUUAAAAGCUCUGUUAAAUGGAGAAGCUGUU_UAUUAACGGGUAACAUGCUUCGUUUAACGGAACAGCUGUUCAU_UUAG_______________UCGGCAGUUA
....(((((....)))))....(.((((((((((...(((((((((............)))).))))))))))))))).).((((..........................))))..... (-19.71 = -19.99 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,004,321 – 8,004,426
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -27.64
Consensus MFE -21.40
Energy contribution -21.44
Covariance contribution 0.04
Combinations/Pair 1.29
Mean z-score -1.80
Structure conservation index 0.77
SVM decision value 0.86
SVM RNA-class probability 0.867756
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8004321 105 - 22407834
-------------UCAUUUAAAUUUAAA-AAACAACCGCCAAUCAACCGGUUGCGGUUAAAAGCUCUGUUAAACGGAGAUGCUGAU-UAUUAGCGGGUAACAUGUUUCGUUUAACGGAAC
-------------...............-....((((((.((((....))))))))))......((((((((((((((.((((((.-..)))))).........)))))))))))))).. ( -29.50)
>DroSec_CAF1 4943 105 - 1
-------------UCAUUGAAAUUUUAA-AAACAACCGCCAAUCAACCGGUUGCGAUUAAAAGCUCUGUUAAAUUGAGAAGCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGCAC
-------------.........((((((-...((((((.........))))))...))))))(((..(((((((...(((((((((-.(((....))))))).))))))))))))))).. ( -22.70)
>DroSim_CAF1 4892 105 - 1
-------------UCAUUUAAAUUUUAA-AAACAACCGCCAAUCAACCGGGUGCGGUUAAAAGCUCUGUUAAAUGGAGAAGCUGUU-UAUUAACGGGUAACAUGCUUCGUUUAACGGAAC
-------------...............-....((((((...((....))..))))))......((((((((((((((.(.(((((-....))))).)......)))))))))))))).. ( -26.90)
>DroEre_CAF1 4806 119 - 1
CUGCCGGUACACCACAUUUAAAUUUAAAUAAACAACCGCCAGCCAACCGGUUGCGGUUAACUGCUCUGUUAGGU-AAGACGCUGUUCUUUUAGCGGGUAACAUGCAUCGCUUAACGGAAC
..((.((....))....................((((((.((((....))))))))))....))((((((((((-....(((((......))))).((.....))...)))))))))).. ( -33.00)
>DroYak_CAF1 5008 120 - 1
UUAUUAGUACACCACAUUUAAAUUGAAAUAAAGAACCGCCAAACAACCGGUUGCGGUUAACUGCGCUGUUAAGCGUAGAUGCUUUUUUUUUAACGGGUAACAUGCAUCGUUUAACGGAAC
...........((...........((((.((((((((((..(((.....)))))))))..(((((((....)))))))...)))).)))).(((((((.....)).)))))....))... ( -26.10)
>consensus
_____________UCAUUUAAAUUUAAA_AAACAACCGCCAAUCAACCGGUUGCGGUUAAAAGCUCUGUUAAAUGGAGAAGCUGUU_UAUUAACGGGUAACAUGCUUCGUUUAACGGAAC
.................................((((((.((((....)))))))))).......(((((((((...(((((((((............)))).))))))))))))))... (-21.40 = -21.44 +   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 10:36:50 2006