Locus 5344

Sequence ID X_DroMel_CAF1
Location 13,930,855 – 13,931,249
Length 394
Max. P 0.984441
window8659 window8660 window8661 window8662 window8663 window8664 window8665

overview

Window 9

Location 13,930,855 – 13,930,967
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.62
Mean single sequence MFE -38.74
Consensus MFE -31.55
Energy contribution -32.39
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.77
Structure conservation index 0.81
SVM decision value 0.77
SVM RNA-class probability 0.845073
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930855 112 - 22224390
GUUGUGCAGCGGAUGCAGAGAGGCAG-AGGGUGGCGGAGGUGGUGCUGCGUCAGUAGCAACGCCUUCGCAUCAACCAGGACACCAGGACAAGAAUUCGAAAA----AA---AAGGGAAUU
.((((.(..(...(((......))).-.)(((((((((((((.((((((....)))))).))))))))).((......)))))).).)))).(((((.....----..---....))))) ( -37.80)
>DroSec_CAF1 10903 111 - 1
GUGGUGCAGCGGAUGCAGAGGGGCAG-GGGGUGGCGGAGGUGGUGCUGCGUCAAUAGCAACGCCUUCGCAUCAACCAGGACACC--GACAAGAACUCGAAAAA---AA---AAGGGAAUU
(((((((......(((......)))(-(..(..(((((((((.(((((......))))).)))))))))..)..))..).))))--.)).....(((......---..---..))).... ( -35.50)
>DroSim_CAF1 13501 110 - 1
GUGGUGCAGCGGAUGCAGAGGGGCAG-GGGGUGGCGGAGGUGGUGCUGCGUCAGUAGCAACGCCUUCGCAUCAACCAGGACACC--GACAAGAACUCGAAAA----AA---AAGGGAAUU
(((((((......(((......)))(-(..(..(((((((((.((((((....)))))).)))))))))..)..))..).))))--.)).....(((.....----..---..))).... ( -40.00)
>DroEre_CAF1 12636 112 - 1
UUGGUGCAGCGGUUGCAGAGGGGC--GGGGGCGGCGGUGGUGUUGCUGCGUCAGGAGCAACGCCUUCGCAUCAACCAGGACACC--CGCAAGAACUCCAAAA----AAAGGAAGGGCAAC
...........(((((......((--(((....((((.(((((((((.(....).))))))))).)))).((......))..))--)))......(((....----...)))...))))) ( -40.80)
>DroYak_CAF1 13001 118 - 1
GUGAUGCAGCGGAUGCAGAGGGUCAGGGGGGUGGCGGCGGUGGUGCUGCGUCAGUAGCAACGCCUUCGCAUCAACCAGGACACC--CACAAGAACUCAAAAAAAAAAAAAGAAGGGAAUU
(((.((((.....))))..(((((..((..(..((((.((((.((((((....)))))).)))).))))..)..))..))).))--)))............................... ( -39.60)
>consensus
GUGGUGCAGCGGAUGCAGAGGGGCAG_GGGGUGGCGGAGGUGGUGCUGCGUCAGUAGCAACGCCUUCGCAUCAACCAGGACACC__GACAAGAACUCGAAAA____AA___AAGGGAAUU
....((((.....))))(((.........(((((((((((((.((((((....)))))).))))))))).((......))))))..........)))....................... (-31.55 = -32.39 +   0.84)

alignment

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secondary structure

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Window 0

Location 13,930,928 – 13,931,027
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 79.38
Mean single sequence MFE -27.96
Consensus MFE -18.87
Energy contribution -20.40
Covariance contribution 1.53
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.67
SVM decision value 0.72
SVM RNA-class probability 0.831672
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930928 99 + 22224390
CCUCCGCCACCCUCUGCCUCUCUGCAUCCGCUGCACAACUGGGUGGCCUGGCCUGGGCUCGCCUAAACUGCCCCUCGCUGACCACCCUGCCACGUUGCC
.......................(((..((..(((.....((((((.(.(((..((((...........))))...)))).)))))))))..)).))). ( -26.00)
>DroSec_CAF1 10975 83 + 1
CCUCCGCCACCCCCUGCCCCUCUGCAUCCGCUGCACCACUGGGUGGCCUG----------GCCUAAGCCGCCCCUCCCUGGCCACCAUGCCCC------
.....(((((((..((......((((.....)))).))..))))))).((----------(((................))))).........------ ( -23.09)
>DroSim_CAF1 13572 88 + 1
CCUCCGCCACCCCCUGCCCCUCUGCAUCCGCUGCACCACUGGGUGGCCUGGCCUGGGCUGGCCUAAGCCGCCCCUCCCUGGCCACCAU-----------
.....(((((((..((......((((.....)))).))..))))))).(((((.((((.(((....)))))))......)))))....----------- ( -34.80)
>consensus
CCUCCGCCACCCCCUGCCCCUCUGCAUCCGCUGCACCACUGGGUGGCCUGGCCUGGGCU_GCCUAAGCCGCCCCUCCCUGGCCACCAUGCC_C______
.....((((.............((((.....)))).....(((((((..((((......))))...))))))).....))))................. (-18.87 = -20.40 +   1.53)

alignment

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secondary structure

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Window 1

Location 13,930,928 – 13,931,027
Length 99
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 79.38
Mean single sequence MFE -37.53
Consensus MFE -24.61
Energy contribution -24.83
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -1.76
Structure conservation index 0.66
SVM decision value 0.36
SVM RNA-class probability 0.704309
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930928 99 - 22224390
GGCAACGUGGCAGGGUGGUCAGCGAGGGGCAGUUUAGGCGAGCCCAGGCCAGGCCACCCAGUUGUGCAGCGGAUGCAGAGAGGCAGAGGGUGGCGGAGG
.....(((.((.((((((((.((...((((.((....))..))))..))..))))))))..((.((((.....)))).)).........)).))).... ( -38.00)
>DroSec_CAF1 10975 83 - 1
------GGGGCAUGGUGGCCAGGGAGGGGCGGCUUAGGC----------CAGGCCACCCAGUGGUGCAGCGGAUGCAGAGGGGCAGGGGGUGGCGGAGG
------..(((..(((.(((.......))).)))...))----------)..(((((((..((.(.(.((....))...).).))..)))))))..... ( -34.30)
>DroSim_CAF1 13572 88 - 1
-----------AUGGUGGCCAGGGAGGGGCGGCUUAGGCCAGCCCAGGCCAGGCCACCCAGUGGUGCAGCGGAUGCAGAGGGGCAGGGGGUGGCGGAGG
-----------....(((((.(((..((.(......).))..))).))))).(((((((..((.(.(.((....))...).).))..)))))))..... ( -40.30)
>consensus
______G_GGCAUGGUGGCCAGGGAGGGGCGGCUUAGGC_AGCCCAGGCCAGGCCACCCAGUGGUGCAGCGGAUGCAGAGGGGCAGGGGGUGGCGGAGG
.............(((.(((.......))).)))..(((........)))..(((((((.((......))...(((......)))..)))))))..... (-24.61 = -24.83 +   0.23)

alignment

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secondary structure

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Window 2

Location 13,930,967 – 13,931,067
Length 100
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 78.91
Mean single sequence MFE -38.83
Consensus MFE -25.85
Energy contribution -27.63
Covariance contribution 1.78
Combinations/Pair 1.05
Mean z-score -2.47
Structure conservation index 0.67
SVM decision value 1.97
SVM RNA-class probability 0.984441
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930967 100 + 22224390
UGGGUGGCCUGGCCUGGGCUCGCCUAAACUGCCCCUCGCUGACCACCCUGCCACGUUGCCACGAGAGUCAGCAACUCCACUGGCGACUCCAAGCCAUCCG
.(((((((.(((...((((...........))))....................(((((((...((((.....))))...))))))).))).))))))). ( -36.90)
>DroSec_CAF1 11014 84 + 1
UGGGUGGCCUG----------GCCUAAGCCGCCCCUCCCUGGCCACCAUGCCCC------GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCG
((((((((..(----------((....)))))).(((((.(((......)))..------))))).(((((........))))).......))))).... ( -34.00)
>DroSim_CAF1 13611 89 + 1
UGGGUGGCCUGGCCUGGGCUGGCCUAAGCCGCCCCUCCCUGGCCACCAU-----------GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCG
..(((((((.((...((((.(((....)))))))...)).)))))))..-----------.((((.(((((........)))))..)))).......... ( -45.60)
>consensus
UGGGUGGCCUGGCCUGGGCU_GCCUAAGCCGCCCCUCCCUGGCCACCAUGCC_C______GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCG
..(((((((......((((...........))))......)))))))..............((((.(((((........)))))..)))).......... (-25.85 = -27.63 +   1.78)

alignment

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secondary structure

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Window 3

Location 13,930,967 – 13,931,067
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 78.91
Mean single sequence MFE -45.30
Consensus MFE -28.38
Energy contribution -28.83
Covariance contribution 0.45
Combinations/Pair 1.20
Mean z-score -1.97
Structure conservation index 0.63
SVM decision value 0.64
SVM RNA-class probability 0.807438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930967 100 - 22224390
CGGAUGGCUUGGAGUCGCCAGUGGAGUUGCUGACUCUCGUGGCAACGUGGCAGGGUGGUCAGCGAGGGGCAGUUUAGGCGAGCCCAGGCCAGGCCACCCA
.((.((((((((..((((((.((...(((((((((..(.((.(.....).)).)..)))))))))....)).)...)))))..))))))))..))..... ( -45.10)
>DroSec_CAF1 11014 84 - 1
CGGAUGGGUUGGAGUCGCCAGUGGAGUUGCUGGCUCUCCC------GGGGCAUGGUGGCCAGGGAGGGGCGGCUUAGGC----------CAGGCCACCCA
.((.(((.((((((((((((((......)))).(((((((------..(((......))).)))))))))))))....)----------))).))).)). ( -42.70)
>DroSim_CAF1 13611 89 - 1
CGGAUGGGUUGGAGUCGCCAGUGGAGUUGCUGGCUCUCCC-----------AUGGUGGCCAGGGAGGGGCGGCUUAGGCCAGCCCAGGCCAGGCCACCCA
...(((((..(((...((((((......))))))))))))-----------))(((((((..((..(((((((....))).))))...)).))))))).. ( -48.10)
>consensus
CGGAUGGGUUGGAGUCGCCAGUGGAGUUGCUGGCUCUCCC______G_GGCAUGGUGGCCAGGGAGGGGCGGCUUAGGC_AGCCCAGGCCAGGCCACCCA
.........(((.((.(((.........((((.(((((((........(((......))).))))))).))))...(((........))).))).))))) (-28.38 = -28.83 +   0.45)

alignment

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secondary structure

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Window 4

Location 13,931,027 – 13,931,147
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -45.42
Consensus MFE -34.09
Energy contribution -34.77
Covariance contribution 0.69
Combinations/Pair 1.16
Mean z-score -1.66
Structure conservation index 0.75
SVM decision value 0.32
SVM RNA-class probability 0.686755
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931027 120 + 22224390
ACGAGAGUCAGCAACUCCACUGGCGACUCCAAGCCAUCCGGAUUCAGCCCAUACGACGCAUGCACAGAGCCAUCGUUGGAGUGGCAUGUGUGGCAAGUGUCAUGGGUGGUGAUCUCAGCA
..((((.(((.(...(((..((((........))))...)))....((((((..(((((.((((((.((((((.......))))).).))).))).)))))))))))).))))))).... ( -45.30)
>DroSec_CAF1 11058 120 + 1
GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCGGCUUCAGCCCAUACGACGCAUGCACAGAGCCAUCGUUUGAGUGGCAUGUGUGGCAAAUGUCAUGGGUGGGGAUCUCUGCA
.((((.(((((........)))))..))))..((((((((((....))).....((((..((((((.((((((.......))))).).))).)))..))))..))))))).......... ( -49.20)
>DroSim_CAF1 13660 120 + 1
GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCGGCUUCAGCCCAUACGACGCAUGCACAGAGCCAUCGUUGGAGUGGCAUGUGUGGCAAGUGUCAUGGGUGGGGAUCUCUGCA
.((((.(((((........)))))..))))..((((((((((....))).....(((((.((((((.((((((.......))))).).))).))).)))))..))))))).......... ( -53.10)
>DroYak_CAF1 13175 108 + 1
GGGAAGGCGAGCAACUCCAGUGGCGACUCCAACCCAUACGGAUUCAGCCCAAACGACGCAUGCACAGAGCCAUCGCUGGAGUGGCAUGUGUUCCG------------GGGGAUUUUAGCA
.((((.(((.((.(((((((((((((.(((.........))).)).((.........)).........)))...)))))))).)).))).)))).------------............. ( -34.10)
>consensus
GGGAGAGCCAGCAACUCCACUGGCGACUCCAACCCAUCCGGAUUCAGCCCAUACGACGCAUGCACAGAGCCAUCGUUGGAGUGGCAUGUGUGGCAAGUGUCAUGGGUGGGGAUCUCAGCA
..(((((((((........)))))........(((((((((......))....(.((((((((.((...(((....)))..)))))))))).)..........)))))))..)))).... (-34.09 = -34.77 +   0.69)

alignment

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secondary structure

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Window 5

Location 13,931,147 – 13,931,249
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -29.86
Consensus MFE -21.94
Energy contribution -22.08
Covariance contribution 0.14
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.73
SVM decision value 1.27
SVM RNA-class probability 0.939077
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931147 102 - 22224390
-GUGCGCCCUGUGCACCCUGCAGCUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGCGGAACUCCCCCUC-----------------UCCAUCCCC
-((((((...)))))).((((((((((((.....))))).....).))))))....((((((......))))))....((.((....)).))..-----------------......... ( -28.90)
>DroSec_CAF1 11178 101 - 1
-GUGCGCCCUGUGCACCCUGCAGCUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGCGGAACC--CCCUGCA---------------CCCA-CCCC
-((((((...))))))..(((((.((.((((..(((((.........)))))....((((((......))))))....)))).))..--..)))))---------------....-.... ( -30.70)
>DroSim_CAF1 13780 100 - 1
NNNNNNNNNNNNNNNNCCUGCAGCUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGCGGAACC--CCCUC-----------------UCCA-GCCC
.................((((((((((((.....))))).....).))))))....((((((......))))))....((((((...--.....-----------------))).-))). ( -25.10)
>DroEre_CAF1 12852 111 - 1
-GUGCGCCCUGUGCACCCUGCAAGUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGUGGCAGC--CCCUCCACCCC-----GCACUUGCCA-CACA
-((((((...))))))...((((((.(((....(((((.........)))))....((((((......))))))....(((((.((.--..))))))).)-----))))))))..-.... ( -35.30)
>DroYak_CAF1 13283 116 - 1
-GUGCGCCCUGUGCACCCUGCAGCUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGCGGAAUC--CCCUCUCCCCCCCCUCCCCCUCUCCA-CCCC
-((((((...)))))).((((((((((((.....))))).....).))))))....((((((......))))))....((.(((...--.....)))))................-.... ( -29.30)
>consensus
_GUGCGCCCUGUGCACCCUGCAGCUUGCGCCUAUUGCAAUAUAUGCCUGCAGAUUGGUCAGUUCAAACACUGACAUCCGGCGGAACC__CCCUC_________________UCCA_CCCC
.((((((...))))))((.((.....))(((..(((((.........)))))....((((((......))))))....)))))..................................... (-21.94 = -22.08 +   0.14)

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 11:45:36 2006