Locus 8090

Sequence ID 3L_DroMel_CAF1
Location 21,279,113 – 21,279,273
Length 160
Max. P 0.991827
window13219 window13220 window13221 window13222

overview

Window 9

Location 21,279,113 – 21,279,233
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -42.43
Consensus MFE -41.84
Energy contribution -40.15
Covariance contribution -1.69
Combinations/Pair 1.21
Mean z-score -1.92
Structure conservation index 0.99
SVM decision value 1.77
SVM RNA-class probability 0.976649
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21279113 120 + 23771897
GGAAAAACCCCAUUCAGAAGAGUACUGGUUCCAGCGUUAAUCUGAUCAUCCGGGUUUUCCUGGUCGCCAUGUGCCUGCAGAGGUAUUUCCCCCUCUGCAGCAUCUGGUGUGCUGGAUGGU
((((((.(((...(((((..((..(((....)))..))..)))))......))))))))).((((((((.((((.((((((((........)))))))))))).))))).)))....... ( -49.00)
>DroSec_CAF1 37355 120 + 1
GGAAAAACCCCAUUCAGAAGGGUACUGGUUCCAGCGUUUAUUUGAGCAUCCGGGUUUUCCUGGUCGCCCUUUGCCUGCAGAGGUAUUUCCCCUUCUGCAGCAUCUGGUGUGCUGAAAGGU
......(((.....((((((((..(((....)))...........((..(((((....)))))..))((((((....))))))......))))))))((((((.....))))))...))) ( -41.00)
>DroSim_CAF1 39618 120 + 1
GGAAAAACCCCAUUCAGAAGGGUACUGGUUCCAGCGUUUAUUUGAUCGUCCGGGUUUUCCUGGUCGCCCUGUGCCUGCAGAGGUAUUUCCCCUUCUGCAGCAUCUGGUGUGCUGGAAGGU
......((((.........)))).....((((((((...........(.(((((....))))).)(((..((((.((((((((........))))))))))))..))).))))))))... ( -44.30)
>DroEre_CAF1 38594 120 + 1
GGAAAAACACCAUUCAGAAGAGUACUGGUUCCAGCGUUUAUCUGAUCAUCCCUGUUUUCCUGGUCGCCUUGGGACUCUGGAGGUAUUUUGCCCUCUACAUCUUCUGGUGUGCUGGAUGGU
........(((((((((.((((((((...(((((.((((...((((((............)))))).....)))).)))))))))))))......((((((....))))))))))))))) ( -35.40)
>consensus
GGAAAAACCCCAUUCAGAAGAGUACUGGUUCCAGCGUUUAUCUGAUCAUCCGGGUUUUCCUGGUCGCCCUGUGCCUGCAGAGGUAUUUCCCCCUCUGCAGCAUCUGGUGUGCUGGAAGGU
((((((.(((...(((((..((..(((....)))..))..)))))......))))))))).(((((((..((((.((((((((........))))))))))))..)))).)))....... (-41.84 = -40.15 +  -1.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,279,113 – 21,279,233
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -39.68
Consensus MFE -31.52
Energy contribution -32.40
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.36
Structure conservation index 0.79
SVM decision value 1.23
SVM RNA-class probability 0.933686
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21279113 120 - 23771897
ACCAUCCAGCACACCAGAUGCUGCAGAGGGGGAAAUACCUCUGCAGGCACAUGGCGACCAGGAAAACCCGGAUGAUCAGAUUAACGCUGGAACCAGUACUCUUCUGAAUGGGGUUUUUCC
...........(.(((..(((((((((((........)))))))).)))..))).)....(((((((((.(....(((((.....((((....)))).....))))).).))))))))). ( -45.60)
>DroSec_CAF1 37355 120 - 1
ACCUUUCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCAAAGGGCGACCAGGAAAACCCGGAUGCUCAAAUAAACGCUGGAACCAGUACCCUUCUGAAUGGGGUUUUUCC
.(((((((((((....).)))))..)))))(((((.(((((..((((....(((((.((.((....)).)).)))))........((((....)))).....))))...))))).))))) ( -41.40)
>DroSim_CAF1 39618 120 - 1
ACCUUCCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCACAGGGCGACCAGGAAAACCCGGACGAUCAAAUAAACGCUGGAACCAGUACCCUUCUGAAUGGGGUUUUUCC
.(((((((((((....).)))))..)))))(((((.(((((..((((...((((((.((.((....)).)).))...........((((....)))).))))))))...))))).))))) ( -41.90)
>DroEre_CAF1 38594 120 - 1
ACCAUCCAGCACACCAGAAGAUGUAGAGGGCAAAAUACCUCCAGAGUCCCAAGGCGACCAGGAAAACAGGGAUGAUCAGAUAAACGCUGGAACCAGUACUCUUCUGAAUGGUGUUUUUCC
..........((((((.........((((........))))....(((((..((...)).(.....).)))))..(((((.....((((....)))).....))))).))))))...... ( -29.80)
>consensus
ACCAUCCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCACAGGGCGACCAGGAAAACCCGGAUGAUCAAAUAAACGCUGGAACCAGUACCCUUCUGAAUGGGGUUUUUCC
...........(.((...(((((((((((........)))))))).)))...)).)....(((((((((.(....(((((.....((((....)))).....))))).).))))))))). (-31.52 = -32.40 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,279,153 – 21,279,273
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.14
Mean single sequence MFE -45.52
Consensus MFE -42.76
Energy contribution -42.45
Covariance contribution -0.31
Combinations/Pair 1.15
Mean z-score -2.39
Structure conservation index 0.94
SVM decision value 2.29
SVM RNA-class probability 0.991827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21279153 120 + 23771897
UCUGAUCAUCCGGGUUUUCCUGGUCGCCAUGUGCCUGCAGAGGUAUUUCCCCCUCUGCAGCAUCUGGUGUGCUGGAUGGUGAGGACAUCAUGGUGGGCUCACAUGUUACCAGCUCCACUU
.........(((((....))))).(((((.((((.((((((((........)))))))))))).))))).(((((...(((((..(((....)))..)))))......)))))....... ( -51.70)
>DroSec_CAF1 37395 120 + 1
UUUGAGCAUCCGGGUUUUCCUGGUCGCCCUUUGCCUGCAGAGGUAUUUCCCCUUCUGCAGCAUCUGGUGUGCUGAAAGGUGAGGACAUCAUGGUGGGCUCACAUGUUACCAGCUCCACUU
...((((..(((((....))))).((((...(((.((((((((........)))))))))))...))))((.(((...(((((..(((....)))..)))))...))).))))))..... ( -44.80)
>DroSim_CAF1 39658 120 + 1
UUUGAUCGUCCGGGUUUUCCUGGUCGCCCUGUGCCUGCAGAGGUAUUUCCCCUUCUGCAGCAUCUGGUGUGCUGGAAGGUGAGGACAUCAUGGUGGGCUCACAUGUUACCAGCUCCACUU
..((((.((((..(..((((.(((((((..((((.((((((((........))))))))))))..)))).)))))))..)..)))))))).((((((((...........))).))))). ( -48.10)
>DroEre_CAF1 38634 120 + 1
UCUGAUCAUCCCUGUUUUCCUGGUCGCCUUGGGACUCUGGAGGUAUUUUGCCCUCUACAUCUUCUGGUGUGCUGGAUGGUGAGGACAUCAUGGUGGGCUCACAGGUUACCAGCUCCACCU
(((.(((((((..........(((((((..((((...((((((........))))))..))))..)))).)))))))))).))).......((((((((...........))).))))). ( -37.50)
>consensus
UCUGAUCAUCCGGGUUUUCCUGGUCGCCCUGUGCCUGCAGAGGUAUUUCCCCCUCUGCAGCAUCUGGUGUGCUGGAAGGUGAGGACAUCAUGGUGGGCUCACAUGUUACCAGCUCCACUU
.........(((((....))))).((((..((((.((((((((........))))))))))))..)))).(((((...(((((..(((....)))..)))))......)))))....... (-42.76 = -42.45 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,279,153 – 21,279,273
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.14
Mean single sequence MFE -39.85
Consensus MFE -32.21
Energy contribution -32.52
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.81
SVM decision value 0.88
SVM RNA-class probability 0.872434
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21279153 120 - 23771897
AAGUGGAGCUGGUAACAUGUGAGCCCACCAUGAUGUCCUCACCAUCCAGCACACCAGAUGCUGCAGAGGGGGAAAUACCUCUGCAGGCACAUGGCGACCAGGAAAACCCGGAUGAUCAGA
........(((((.....(((((..((......))..)))))(((((....(.(((..(((((((((((........)))))))).)))..))).)....((.....)))))))))))). ( -43.80)
>DroSec_CAF1 37395 120 - 1
AAGUGGAGCUGGUAACAUGUGAGCCCACCAUGAUGUCCUCACCUUUCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCAAAGGGCGACCAGGAAAACCCGGAUGCUCAAA
..(((..(((((......(((((..((......))..)))))...))))).)))....(((((((((.((.......)))))))).)))..(((((.((.((....)).)).)))))... ( -40.80)
>DroSim_CAF1 39658 120 - 1
AAGUGGAGCUGGUAACAUGUGAGCCCACCAUGAUGUCCUCACCUUCCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCACAGGGCGACCAGGAAAACCCGGACGAUCAAA
..((((.(((.(.......).)))))))..((((((((.....((((...........(((((((((.((.......)))))))).)))..((....)).)))).....)))).)))).. ( -39.40)
>DroEre_CAF1 38634 120 - 1
AGGUGGAGCUGGUAACCUGUGAGCCCACCAUGAUGUCCUCACCAUCCAGCACACCAGAAGAUGUAGAGGGCAAAAUACCUCCAGAGUCCCAAGGCGACCAGGAAAACAGGGAUGAUCAGA
.((((..(((((......(((((..((......))..)))))...))))).))))....(((...((((........))))....(((((..((...)).(.....).))))).)))... ( -35.40)
>consensus
AAGUGGAGCUGGUAACAUGUGAGCCCACCAUGAUGUCCUCACCAUCCAGCACACCAGAUGCUGCAGAAGGGGAAAUACCUCUGCAGGCACAGGGCGACCAGGAAAACCCGGAUGAUCAAA
...(((.(((((......(((((..((......))..)))))...))))).(.((...(((((((((((........)))))))).)))...)).).))).................... (-32.21 = -32.52 +   0.31)

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 13:06:00 2006