Locus 2291

Sequence ID 2R_DroMel_CAF1
Location 8,437,130 – 8,437,317
Length 187
Max. P 0.720347
window3765 window3766 window3767

overview

Window 5

Location 8,437,130 – 8,437,247
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.41
Mean single sequence MFE -42.98
Consensus MFE -27.81
Energy contribution -29.45
Covariance contribution 1.64
Combinations/Pair 1.22
Mean z-score -1.99
Structure conservation index 0.65
SVM decision value 0.21
SVM RNA-class probability 0.635991
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8437130 117 + 20766785
AUCAGCU---GCUGGGUAGUAAGGAAUUGGCACCGAGGUUCAAACGCAACUUGAUCACCACGAACCAGGAUGCGGUGGAGAACUUGCAAAUGCGCCCGGCAGCCAACUCCUUGCUCUUCC
.......---...(((.((((((((.(((((.(((.(((.((...((((.((..(((((.((........)).)))))..)).))))...)).))))))..))))).))))))))..))) ( -40.10)
>DroVir_CAF1 6947 120 + 1
AUCAGCUGAUGCUGGGCGGCAAGGAGUUGGCGCCGCGCUUUAAACGCAAUCUGAUCACCACCAAUCAGGAUUCGGUUGAGAAUCUGCAAAUGCGCCCGGCGGCCAACUCGUUGCUGUUCC
.(((((....)))))(((((((.(((((((((((((((.......(((..(((((........)))))(((((......))))))))....))))..))).)))))))).)))))))... ( -54.00)
>DroPse_CAF1 25583 117 + 1
AUCAGCU---GCUGGGCAGCAAGGAGCUAGCGCCGCGUUUCAAGCGCAAUUUGAUCACCACGAACCAGGAUGCGGUGGAAAACUUGCAAAUGCGCCCGGCGGCCAACUCCUUGCUUUUCC
....(((---(((((((.(((((...(((.(((.((((.....))))..........((........))..))).)))....)))))......))))))))))................. ( -40.30)
>DroGri_CAF1 313 117 + 1
AUCAGAUGCUCCU---UGGCAAAGAGUUGGCGCCGCGUUUCAAGCGCAAUAUGAUCACAGCGAAUCAGGAUUCGGUUGAGAAUCUGCAGAUGCGUCCGGCAGCCAACUCGUUGCUGUUCC
.............---.(((((.(((((((((((((((.....))))............(((.(((.((((((......))))))...))).)))..))).)))))))).)))))..... ( -42.80)
>DroWil_CAF1 267 117 + 1
AUCAGCU---GCUGGGCAGUAAGGAGUUAGCACCGCGAUUCAAGCGCAAUUUGAUCACCACAAAUCAGGAUGCAGUGGAGAAUUUGCAAAUGCGCCCGGCGGCCAACUCCUUGCUCUUCC
....(((---(((((((.(((.((.(....).))(((((((..(((((.((((((........)))))).))).))...))).))))...)))))))))))))................. ( -37.30)
>DroMoj_CAF1 299 120 + 1
AUCAAAUGAUGCUGGGCGGCAAGGAGUUGGCGCCACGUUUCAAGCGCAACUUGAUAUCGACCAAUCAGGAUUCGGUUGAGAAUCUGCAAAUGCGUCCAGCAGCUAAUUCGUUGCUGUUCC
.............(((((((((.((((((((((....((((((.((...((((((........))))))...)).))))))....))...(((.....))))))))))).))))))))). ( -43.40)
>consensus
AUCAGCU___GCUGGGCAGCAAGGAGUUGGCGCCGCGUUUCAAGCGCAAUUUGAUCACCACGAAUCAGGAUGCGGUGGAGAAUCUGCAAAUGCGCCCGGCAGCCAACUCCUUGCUGUUCC
.(((((....)))))..(((((.((((((((((((.(......(((((.((((((........)))))).....(..(.....)..)...)))))))))).)))))))).)))))..... (-27.81 = -29.45 +   1.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,437,130 – 8,437,247
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.41
Mean single sequence MFE -43.75
Consensus MFE -30.49
Energy contribution -30.52
Covariance contribution 0.03
Combinations/Pair 1.32
Mean z-score -1.99
Structure conservation index 0.70
SVM decision value 0.40
SVM RNA-class probability 0.720347
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8437130 117 - 20766785
GGAAGAGCAAGGAGUUGGCUGCCGGGCGCAUUUGCAAGUUCUCCACCGCAUCCUGGUUCGUGGUGAUCAAGUUGCGUUUGAACCUCGGUGCCAAUUCCUUACUACCCAGC---AGCUGAU
((...((.(((((((((((.((((((..((..(((((.((...((((((..........))))))...)).)))))..))..)).))))))))))))))).))..))...---....... ( -47.60)
>DroVir_CAF1 6947 120 - 1
GGAACAGCAACGAGUUGGCCGCCGGGCGCAUUUGCAGAUUCUCAACCGAAUCCUGAUUGGUGGUGAUCAGAUUGCGUUUAAAGCGCGGCGCCAACUCCUUGCCGCCCAGCAUCAGCUGAU
((....((((.((((((((.((((.((.....(((((((((......)))))((((((......))))))..))))......)).)))))))))))).))))..))((((....)))).. ( -51.90)
>DroPse_CAF1 25583 117 - 1
GGAAAAGCAAGGAGUUGGCCGCCGGGCGCAUUUGCAAGUUUUCCACCGCAUCCUGGUUCGUGGUGAUCAAAUUGCGCUUGAAACGCGGCGCUAGCUCCUUGCUGCCCAGC---AGCUGAU
((...((((((((((((((.((((.(..((..(((((......((((((..........))))))......)))))..))...).))))))))))))))))))..))...---....... ( -52.00)
>DroGri_CAF1 313 117 - 1
GGAACAGCAACGAGUUGGCUGCCGGACGCAUCUGCAGAUUCUCAACCGAAUCCUGAUUCGCUGUGAUCAUAUUGCGCUUGAAACGCGGCGCCAACUCUUUGCCA---AGGAGCAUCUGAU
......((((.((((((((.(((((...((..(((((((..(((..(((((....)))))...)))..)).)))))..))...).)))))))))))).))))..---............. ( -38.30)
>DroWil_CAF1 267 117 - 1
GGAAGAGCAAGGAGUUGGCCGCCGGGCGCAUUUGCAAAUUCUCCACUGCAUCCUGAUUUGUGGUGAUCAAAUUGCGCUUGAAUCGCGGUGCUAACUCCUUACUGCCCAGC---AGCUGAU
.....((((((((((((((.((((((..((..(((((......(((..((........))..)))......)))))..))..)).)))))))))))))))..(((...))---))))... ( -42.20)
>DroMoj_CAF1 299 120 - 1
GGAACAGCAACGAAUUAGCUGCUGGACGCAUUUGCAGAUUCUCAACCGAAUCCUGAUUGGUCGAUAUCAAGUUGCGCUUGAAACGUGGCGCCAACUCCUUGCCGCCCAGCAUCAUUUGAU
....(((((.(......).)))))((.((.....(((((((......)))).)))..(((.((.((...(((((((((........)))).)))))...)).)).))))).))....... ( -30.50)
>consensus
GGAACAGCAACGAGUUGGCCGCCGGGCGCAUUUGCAAAUUCUCAACCGAAUCCUGAUUCGUGGUGAUCAAAUUGCGCUUGAAACGCGGCGCCAACUCCUUGCCGCCCAGC___AGCUGAU
......((((.((((((((.(((((...((..(((((..((.((((.............)))).)).....)))))..))...).)))))))))))).))))....((((....)))).. (-30.49 = -30.52 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,437,207 – 8,437,317
Length 110
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.52
Mean single sequence MFE -43.20
Consensus MFE -28.74
Energy contribution -28.10
Covariance contribution -0.64
Combinations/Pair 1.39
Mean z-score -1.25
Structure conservation index 0.67
SVM decision value 0.02
SVM RNA-class probability 0.545185
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8437207 110 - 20766785
CUGCCGC---UGCUAUUGGGCGGUGUUGACAUGGGCAACGUAGCCGGAAACUUUUGGUUCUGGGAGGCCGCUCGGAAGAGCAAGGAGUUGGCUGCCGGGCGCAUUUGCAAGUU
.((((((---((((....))))))).....(((.((...(((((((...((((((((((......))))((((....)))).)))))))))))))...)).)))..))).... ( -42.60)
>DroVir_CAF1 7027 110 - 1
CUGGAGU---UGCCGCUGGGCGGCGUCGAGAUGGGCAGCGUGGCCGGGAAUUUUUGAUUCUGUGAGGCGGCACGGAACAGCAACGAGUUGGCCGCCGGGCGCAUUUGCAGAUU
(((.((.---(((.(((.((((((((((((((.(((......))).)....)))))))((((((......)))))).((((.....)))))))))).)))))).)).)))... ( -45.20)
>DroWil_CAF1 344 113 - 1
UUGCUGCCGCCACCAUUUGGUGGUGUCGAUAUAGGCAAGUUUGCUGGGAAUUUUUGAUUUUGCGAUGCCGCUCGGAAGAGCAAGGAGUUGGCCGCCGGGCGCAUUUGCAAAUU
.(((.(((((((((....))))))((((((...((((...((((...(((((...))))).))))))))((((....)))).....)))))).....)))))).......... ( -40.90)
>DroMoj_CAF1 379 110 - 1
CUGCUGU---UGCCGCUGGGCGGCGUCGAAAUGGGCAGCGUGGCCGGGAAUUUCUGAUUCUGCGAGGCGGCACGGAACAGCAACGAAUUAGCUGCUGGACGCAUUUGCAGAUU
((((...---(((((((..((((.((((((((.(((......)))....))))).))).))))..)))))))((...(((((.(......).)))))..)).....))))... ( -43.40)
>DroAna_CAF1 331 110 - 1
UUGCUGU---UGCUGUUCGGCGGCGUGGAUAUGGGCAGCGUGGCUGGGAACUUUUGGUUCUGGGAGGCCGCUCGGAAGAGCAAGGAGUUGGCUGCCGGGCGCAUCUGCAAGUU
((((...---(((.((((((((((.........(((.......((.(((((.....))))).))..)))((((....)))).........)))))))))))))...))))... ( -48.60)
>DroPer_CAF1 23895 105 - 1
-----GC---UGCUGUUGGGUGGCGUCGACAUGGGCAACGUGGCUGGGAACUUCUGGUUUUGGUUGGCCGCUCGGAAAAGCAAGGAGUUGGCCGCCGGGCGCAUUUGCAAGUU
-----((---(((.(((.((((((..((((..((.((((..(((..((....))..)))...)))).))(((......))).....)))))))))).))))))...))..... ( -38.50)
>consensus
CUGCUGC___UGCCGUUGGGCGGCGUCGACAUGGGCAACGUGGCCGGGAACUUUUGAUUCUGGGAGGCCGCUCGGAAGAGCAAGGAGUUGGCCGCCGGGCGCAUUUGCAAAUU
.....((...(((.(((.((((((.........(((......)))...(((((((..(((((((......))))))).....))))))).)))))).))))))...))..... (-28.74 = -28.10 +  -0.64)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:54 2006