Locus 365

Sequence ID 2L_DroMel_CAF1
Location 1,154,445 – 1,154,560
Length 115
Max. P 0.999555
window574 window575 window576 window577

overview

Window 4

Location 1,154,445 – 1,154,537
Length 92
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 79.16
Mean single sequence MFE -31.76
Consensus MFE -20.67
Energy contribution -21.11
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -2.84
Structure conservation index 0.65
SVM decision value 2.63
SVM RNA-class probability 0.995912
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1154445 92 + 22407834
AAUUCAAAGCGGGGCUGGGAAUGCAGGGGUCGACCUGUUCUGGUUUCAGCUUAACUAUAUGGAUAUUUUGGGCG---------UGAAACCAAAACAGGAUC
.((((..(((...)))..))))...........((((((.((((((((((((((..(((....))).)))))).---------)))))))).))))))... ( -29.60)
>DroSec_CAF1 47961 92 + 1
AAUUCAAAGCGUUGCAGGGAAUGCAGGGGACGACCUGUUCUGGUUUCAGCUUAACUAGAUGGAUAUCUUGGGCG---------UGAAACCAGAACAGGAUC
.........(.(((((.....))))).).....((((((((((((((((((((...((((....))))))))).---------)))))))))))))))... ( -38.10)
>DroSim_CAF1 43005 92 + 1
AAUUCAAAGCGGGGCUGGGAAUGCAAGGAUCGAUCUGUUCUGGUUUCAGCUUAACUAGAUUGAUAUCUUGGGCG---------UGAAACCAGAACAGGAUC
.((((..(((...)))..)))).....((((...(((((((((((((((((((...((((....))))))))).---------)))))))))))))))))) ( -35.00)
>DroEre_CAF1 41643 100 + 1
AGUUCAAAGCGUGGCAGGGAAUGCAGG-GUCAGCCUGCUCUGGUUUCAACUAAACUGGAUGGAUAUCUUGGGCGCAGUUGCAGUGAAACCAGAACAGGGUC
........((((........))))...-.....((((.((((((((((....((((((..((....))....).)))))....)))))))))).))))... ( -32.20)
>DroYak_CAF1 42767 85 + 1
AGUUCAAGCAGUGGCAGGGAAUGCAGG-GUCAGCCUGCUCUGGUUUCAACUAAACUUAGACCAGAACU---------------UGAAACCAGAACAGGAUC
.((((.....((..((((....(((((-.....)))))((((((((...........)))))))).))---------------))..))..))))...... ( -23.90)
>consensus
AAUUCAAAGCGUGGCAGGGAAUGCAGGGGUCGACCUGUUCUGGUUUCAGCUUAACUAGAUGGAUAUCUUGGGCG_________UGAAACCAGAACAGGAUC
.............((.......)).........(((((((((((((((...................................)))))))))))))))... (-20.67 = -21.11 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,154,445 – 1,154,537
Length 92
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 79.16
Mean single sequence MFE -29.27
Consensus MFE -20.79
Energy contribution -20.59
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -3.77
Structure conservation index 0.71
SVM decision value 3.72
SVM RNA-class probability 0.999555
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1154445 92 - 22407834
GAUCCUGUUUUGGUUUCA---------CGCCCAAAAUAUCCAUAUAGUUAAGCUGAAACCAGAACAGGUCGACCCCUGCAUUCCCAGCCCCGCUUUGAAUU
((.(((((((((((((((---------.((......(((....))).....))))))))))))))))))).........((((..(((...)))..)))). ( -26.70)
>DroSec_CAF1 47961 92 - 1
GAUCCUGUUCUGGUUUCA---------CGCCCAAGAUAUCCAUCUAGUUAAGCUGAAACCAGAACAGGUCGUCCCCUGCAUUCCCUGCAACGCUUUGAAUU
((.(((((((((((((((---------.((.(.((((....)))).)....)))))))))))))))))))......((((.....))))............ ( -31.80)
>DroSim_CAF1 43005 92 - 1
GAUCCUGUUCUGGUUUCA---------CGCCCAAGAUAUCAAUCUAGUUAAGCUGAAACCAGAACAGAUCGAUCCUUGCAUUCCCAGCCCCGCUUUGAAUU
((((.(((((((((((((---------.((.(.((((....)))).)....))))))))))))))))))).........((((..(((...)))..)))). ( -29.30)
>DroEre_CAF1 41643 100 - 1
GACCCUGUUCUGGUUUCACUGCAACUGCGCCCAAGAUAUCCAUCCAGUUUAGUUGAAACCAGAGCAGGCUGAC-CCUGCAUUCCCUGCCACGCUUUGAACU
...((((((((((((((((((.(((((.................)))))))).))))))))))))))).....-...(((.....)))............. ( -30.63)
>DroYak_CAF1 42767 85 - 1
GAUCCUGUUCUGGUUUCA---------------AGUUCUGGUCUAAGUUUAGUUGAAACCAGAGCAGGCUGAC-CCUGCAUUCCCUGCCACUGCUUGAACU
...(((((((((((((((---------------(.(.((......))...).)))))))))))))))).....-...(((.....)))............. ( -27.90)
>consensus
GAUCCUGUUCUGGUUUCA_________CGCCCAAGAUAUCCAUCUAGUUAAGCUGAAACCAGAACAGGUCGACCCCUGCAUUCCCUGCCACGCUUUGAAUU
...(((((((((((((((...................................))))))))))))))).........((.......))............. (-20.79 = -20.59 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,154,469 – 1,154,560
Length 91
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -29.79
Consensus MFE -19.59
Energy contribution -20.03
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -2.64
Structure conservation index 0.66
SVM decision value 2.01
SVM RNA-class probability 0.985622
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1154469 91 + 22407834
AGGGGUCGACCUGUUCUGGUUUCAGCUUAACUAUAUGGAUAUUUUGGGCG---------UGAAACCAAAACAGGAUCUUGGGUAAGCAUACAUGUCGUUC
.((.((.((((((((.((((((((((((((..(((....))).)))))).---------)))))))).)))))).))....(((....))))).)).... ( -26.00)
>DroSec_CAF1 47985 91 + 1
AGGGGACGACCUGUUCUGGUUUCAGCUUAACUAGAUGGAUAUCUUGGGCG---------UGAAACCAGAACAGGAUCUUGGCUAAGCAUACAUGUCGUUC
...((((((((((((((((((((((((((...((((....))))))))).---------)))))))))))))))......((...)).......)))))) ( -36.70)
>DroSim_CAF1 43029 91 + 1
AAGGAUCGAUCUGUUCUGGUUUCAGCUUAACUAGAUUGAUAUCUUGGGCG---------UGAAACCAGAACAGGAUCUUGGCUAAGCAUACAUGUCGUUC
.((((((...(((((((((((((((((((...((((....))))))))).---------))))))))))))))))))))(((...........))).... ( -34.60)
>DroEre_CAF1 41667 99 + 1
AGG-GUCAGCCUGCUCUGGUUUCAACUAAACUGGAUGGAUAUCUUGGGCGCAGUUGCAGUGAAACCAGAACAGGGUCUGGAGUAAGCAUACAUGUCGUUC
...-.((((((((.((((((((((....((((((..((....))....).)))))....)))))))))).))))..)))).(((....)))......... ( -30.30)
>DroYak_CAF1 42791 84 + 1
AGG-GUCAGCCUGCUCUGGUUUCAACUAAACUUAGACCAGAACU---------------UGAAACCAGAACAGGAUCUUGAGUAAGCAUACAUGUCAUUC
..(-.(((.((((.(((((((((((..................)---------------)))))))))).))))....))).)................. ( -21.37)
>consensus
AGGGGUCGACCUGUUCUGGUUUCAGCUUAACUAGAUGGAUAUCUUGGGCG_________UGAAACCAGAACAGGAUCUUGGGUAAGCAUACAUGUCGUUC
.........(((((((((((((((...................................))))))))))))))).......................... (-19.59 = -20.03 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,154,469 – 1,154,560
Length 91
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -28.73
Consensus MFE -20.63
Energy contribution -20.43
Covariance contribution -0.20
Combinations/Pair 1.13
Mean z-score -3.56
Structure conservation index 0.72
SVM decision value 3.37
SVM RNA-class probability 0.999099
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1154469 91 - 22407834
GAACGACAUGUAUGCUUACCCAAGAUCCUGUUUUGGUUUCA---------CGCCCAAAAUAUCCAUAUAGUUAAGCUGAAACCAGAACAGGUCGACCCCU
...((((..(((....)))........((((((((((((((---------.((......(((....))).....))))))))))))))))))))...... ( -26.00)
>DroSec_CAF1 47985 91 - 1
GAACGACAUGUAUGCUUAGCCAAGAUCCUGUUCUGGUUUCA---------CGCCCAAGAUAUCCAUCUAGUUAAGCUGAAACCAGAACAGGUCGUCCCCU
....(((......((...))...((.(((((((((((((((---------.((.(.((((....)))).)....)))))))))))))))))))))).... ( -30.90)
>DroSim_CAF1 43029 91 - 1
GAACGACAUGUAUGCUUAGCCAAGAUCCUGUUCUGGUUUCA---------CGCCCAAGAUAUCAAUCUAGUUAAGCUGAAACCAGAACAGAUCGAUCCUU
.......................((((.(((((((((((((---------.((.(.((((....)))).)....)))))))))))))))))))....... ( -27.50)
>DroEre_CAF1 41667 99 - 1
GAACGACAUGUAUGCUUACUCCAGACCCUGUUCUGGUUUCACUGCAACUGCGCCCAAGAUAUCCAUCCAGUUUAGUUGAAACCAGAGCAGGCUGAC-CCU
.........(((....)))..(((..((((((((((((((((((.(((((.................)))))))).))))))))))))))))))..-... ( -31.93)
>DroYak_CAF1 42791 84 - 1
GAAUGACAUGUAUGCUUACUCAAGAUCCUGUUCUGGUUUCA---------------AGUUCUGGUCUAAGUUUAGUUGAAACCAGAGCAGGCUGAC-CCU
...(((...(((....))))))....(((((((((((((((---------------(.(.((......))...).)))))))))))))))).....-... ( -27.30)
>consensus
GAACGACAUGUAUGCUUACCCAAGAUCCUGUUCUGGUUUCA_________CGCCCAAGAUAUCCAUCUAGUUAAGCUGAAACCAGAACAGGUCGACCCCU
..........................(((((((((((((((...................................)))))))))))))))......... (-20.63 = -20.43 +  -0.20)

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 09:34:03 2006