Locus 3427

Sequence ID 3R_DroMel_CAF1
Location 9,303,655 – 9,303,852
Length 197
Max. P 0.991277
window5497 window5498 window5499 window5500 window5501 window5502

overview

Window 7

Location 9,303,655 – 9,303,759
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 81.95
Mean single sequence MFE -38.82
Consensus MFE -27.50
Energy contribution -27.81
Covariance contribution 0.31
Combinations/Pair 1.19
Mean z-score -1.93
Structure conservation index 0.71
SVM decision value 0.50
SVM RNA-class probability 0.759647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303655 104 + 27905053
CAACUCAAGGAGCUGCCCUCGUUGGGCAGUAAAACUGGCGCCCAACAG-----AGGAUGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAACGGAAUGCGAGGUAG
...(((..((.(((((((.....))))))).....(((((((((((((-----.(.....).)))))))))))))))....((.((.....))..)).....))).... ( -41.20)
>DroPse_CAF1 72467 105 + 1
UAACUUUGCAAGCGGCCCUCGG-GGGCCGUAAAACUGCCGGCAAACAGCGUAGGGGCAGGCAUUUCUGGGUGGCGUCAUGACCAUCAAUAUGAACGGAAUGCCAGG---
...((((((..(((((((....-)))))))......((.(.....).))))))))...((((((((..(((((........))))).........))))))))...--- ( -37.10)
>DroSim_CAF1 76157 104 + 1
CAACUCAAGGAGCUGCCCUCGUUGGGCAGUAAAACUGGCGCCCAACAG-----AGGAUGGCAUUGUUGGGCGGCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAG
...(((..((.(((((((.....))))))).....((.((((((((((-----.(.....).)))))))))).))))....((.((.....))..)).....))).... ( -40.90)
>DroEre_CAF1 75664 104 + 1
CAACUCAAGGAGCUGCCCUCGCCGGGCAGUAAAACUGGCGCCCAACAG-----AGGAUGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUUG
...(((..((.(((((((.....))))))).....(((((((((((((-----.(.....).)))))))))))))))....((.((.....))..)).....))).... ( -42.20)
>DroYak_CAF1 75585 104 + 1
CAACUGAAGGAGCUGCCCUCGCUGGGCAGUACAACUGGCGCCCAACAG-----AGGACGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAG
........((.(((((((.....))))))).....(((((((((((((-----.(.....).)))))))))))))))...(((.((.....))((.....))..))).. ( -40.40)
>DroPer_CAF1 75663 105 + 1
UAACUUUGCAAACGGCCCUCGG-GGUCCGUAAAACUGCCGGCAAACAGCGUAGGGGCAGGCAUUUCUGGGUGGCGUCAUGACCAUCAAUAUGAACGGAAUGCCAGG---
...((((((..(((((((...)-)).))))......((.(.....).))))))))...((((((((..(((((........))))).........))))))))...--- ( -31.10)
>consensus
CAACUCAAGGAGCUGCCCUCGCUGGGCAGUAAAACUGGCGCCCAACAG_____AGGAUGGCAUUGUUGGGCGGCACCAUGACCAUCAAUAUGAACGGAAUGCGAGGUAG
...........(((((((.....))))))).....(((((((((((((..............))))))))))))).(((..((.((.....))..)).)))........ (-27.50 = -27.81 +   0.31)

alignment

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secondary structure

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Window 8

Location 9,303,690 – 9,303,797
Length 107
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.23
Mean single sequence MFE -36.12
Consensus MFE -21.04
Energy contribution -21.46
Covariance contribution 0.42
Combinations/Pair 1.26
Mean z-score -2.61
Structure conservation index 0.58
SVM decision value 1.39
SVM RNA-class probability 0.949340
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303690 107 + 27905053
UGGCGCCCAA------CAGAGGAUGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAACGGAAUGCGAGGUAGGAGACCGAUGGUGGAUGGUAGAUGGAGAAUGAAGGGCA
((((((((((------(((.(.....).)))))))))))))((((.((((((..(((.(.(((..(.(......).)..))).).)))))))))..))))............. ( -39.00)
>DroSec_CAF1 74846 107 + 1
UGGCGCCCAA------CAGAGGAUGGCAUUGUUGGGCGGCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAGGAGACCGAUGGUGGAUGGUAGGAGGAGAAUGAAGGGCA
.(.(((((((------(((.(.....).)))))))))).)(((((.((((((.......((.....))..(((.....))))))))).).))))................... ( -36.60)
>DroSim_CAF1 76192 107 + 1
UGGCGCCCAA------CAGAGGAUGGCAUUGUUGGGCGGCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAGGAGACCGAUGGUGGAUGGUAGGUGGAGAAUGAAGGGCA
((.(((((((------(((.(.....).)))))))))).))((((.((((((.((.....(((..(.(......).)..)))...)).))))))..))))............. ( -37.50)
>DroEre_CAF1 75699 93 + 1
UGGCGCCCAA------CAGAGGAUGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUUGGAGACCG-------GUGGUGGAU-------GGAGGGCA
((((((((((------(((.(.....).)))))))))))))((((.((((((.......((.....))..((((...)))))-------))))).).)-------))...... ( -37.30)
>DroYak_CAF1 75620 100 + 1
UGGCGCCCAA------CAGAGGACGGCAUUGUUGGGCGUCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAGGAGACCGAUGGUUGGUGGUAGAU-------GGAGGGCA
((((((((((------(((.(.....).)))))))))))))((((.(((((((((.....(((..(.(......).)..)))...)))))))))..))-------))...... ( -42.60)
>DroAna_CAF1 73689 94 + 1
UCCCUACCGAAUAGCUCAGAGGCCGGCAUUGUUGGGAGGCGCCAGGACCAUCAAUAUGACCAGAAUCCAAGGUGGGGGACG-AAGGC-GAUGGUUG-----------------
((((((((.....(((....))).(((((.(((((..(((.....).)).)))))))).)).........))))))))...-.....-........----------------- ( -23.70)
>consensus
UGGCGCCCAA______CAGAGGAUGGCAUUGUUGGGCGGCACCAUGACCAUCAAUAUGAGCGGAAUGCGAGGUAGGAGACCGAUGGUGGAUGGUAGAU_______GAAGGGCA
((((((((((......((.....))......)))))))))).....((((((........(((..(.(......).)..)))......))))))................... (-21.04 = -21.46 +   0.42)

alignment

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secondary structure

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Window 9

Location 9,303,690 – 9,303,797
Length 107
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.23
Mean single sequence MFE -28.80
Consensus MFE -16.91
Energy contribution -18.42
Covariance contribution 1.50
Combinations/Pair 1.20
Mean z-score -3.03
Structure conservation index 0.59
SVM decision value 1.79
SVM RNA-class probability 0.977269
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303690 107 - 27905053
UGCCCUUCAUUCUCCAUCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGUUCAUAUUGAUGGUCAUGGUGACGCCCAACAAUGCCAUCCUCUG------UUGGGCGCCA
..................((((((..(((((((((.....)))..((.....)).......)))))).)))))).(((((((((..(.....)..))------)))))))... ( -28.70)
>DroSec_CAF1 74846 107 - 1
UGCCCUUCAUUCUCCUCCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGCCGCCCAACAAUGCCAUCCUCUG------UUGGGCGCCA
..................((((((..(((((((((.....)))..((.....)).......)))))).)))))).(((((((((..(.....)..))------)))))))... ( -30.70)
>DroSim_CAF1 76192 107 - 1
UGCCCUUCAUUCUCCACCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGCCGCCCAACAAUGCCAUCCUCUG------UUGGGCGCCA
..................((((((..(((((((((.....)))..((.....)).......)))))).)))))).(((((((((..(.....)..))------)))))))... ( -30.70)
>DroEre_CAF1 75699 93 - 1
UGCCCUCC-------AUCCACCAC-------CGGUCUCCAACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGCCCAACAAUGCCAUCCUCUG------UUGGGCGCCA
.(((..((-------(((......-------.(((.....)))..((.....)).......)))))....)))(.(((((((((..(.....)..))------))))))).). ( -26.50)
>DroYak_CAF1 75620 100 - 1
UGCCCUCC-------AUCUACCACCAACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGCCCAACAAUGCCGUCCUCUG------UUGGGCGCCA
........-------......((((((((((((((.....)))..((.....)).......))))))..))))).(((((((((..(.....)..))------)))))))... ( -32.40)
>DroAna_CAF1 73689 94 - 1
-----------------CAACCAUC-GCCUU-CGUCCCCCACCUUGGAUUCUGGUCAUAUUGAUGGUCCUGGCGCCUCCCAACAAUGCCGGCCUCUGAGCUAUUCGGUAGGGA
-----------------..((((((-(((..-.((((........))))...)))......)))))).((((((...........))))))((((((((...))))).))).. ( -23.80)
>consensus
UGCCCUUC_______AUCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGCCCAACAAUGCCAUCCUCUG______UUGGGCGCCA
..................(((((...(((((((((.....)))..((.....)).......))))))..))))).(((((((......((.....))......)))))))... (-16.91 = -18.42 +   1.50)

alignment

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secondary structure

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Window 0

Location 9,303,719 – 9,303,828
Length 109
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.60
Mean single sequence MFE -29.78
Consensus MFE -18.30
Energy contribution -20.33
Covariance contribution 2.03
Combinations/Pair 1.17
Mean z-score -1.68
Structure conservation index 0.61
SVM decision value 0.31
SVM RNA-class probability 0.680737
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303719 109 - 27905053
GCACGGUCUG-UCAGCUGGCCACAUGGCCAUCUGCCCUUCAUUCUCCAUCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGUUCAUAUUGAUGGUCAUGGUGACGC
.....(((..-.(((.(((((....))))).))).................(((((..(((((((((.....)))..((.....)).......)))))).)))))))).. ( -27.80)
>DroSec_CAF1 74875 109 - 1
GCAGGGUCUG-UCAGCUGGCCAGAUGGCCAUCUGCCCUUCAUUCUCCUCCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGCCGC
((((((....-.(((.(((((....))))).)))))))............((((((..(((((((((.....)))..((.....)).......)))))).))))))..)) ( -33.00)
>DroSim_CAF1 76221 109 - 1
GCAGGGUCUG-UCAGCUGGCCAGAUGGCCAUCUGCCCUUCAUUCUCCACCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGCCGC
((((((....-.(((.(((((....))))).)))))))............((((((..(((((((((.....)))..((.....)).......)))))).))))))..)) ( -33.00)
>DroEre_CAF1 75728 95 - 1
GCAGUGUCUG-UCAGCUGGCCAGAUGGCCAACUGCCCUCC-------AUCCACCAC-------CGGUCUCCAACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGC
...(((((..-.(((.(((((....))))).))).((.((-------(((......-------.(((.....)))..((.....)).......)))))....)).))))) ( -27.00)
>DroYak_CAF1 75649 102 - 1
GCAGUGUCUG-UCAGCUGGCCAGAUGGCCAACUGCCCUCC-------AUCUACCACCAACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGC
...(((((..-.(((.(((((....))))).)))......-------.......(((((((((((((.....)))..((.....)).......))))))..))))))))) ( -31.90)
>DroAna_CAF1 73724 91 - 1
GCUGAGUCUGGCCAUCUGGCCAUUUGGUCAUC-----------------CAACCAUC-GCCUU-CGUCCCCCACCUUGGAUUCUGGUCAUAUUGAUGGUCCUGGCGCCUC
........(((((....)))))...(((...(-----------------((((((((-(((..-.((((........))))...)))......))))))..))).))).. ( -26.00)
>consensus
GCAGGGUCUG_UCAGCUGGCCAGAUGGCCAUCUGCCCUUC_______AUCUACCAUCCACCAUCGGUCUCCUACCUCGCAUUCCGCUCAUAUUGAUGGUCAUGGUGACGC
............(((.(((((....))))).)))................(((((...(((((((((.....)))..((.....)).......))))))..))))).... (-18.30 = -20.33 +   2.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,303,759 – 9,303,852
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 81.89
Mean single sequence MFE -40.48
Consensus MFE -21.16
Energy contribution -20.88
Covariance contribution -0.28
Combinations/Pair 1.05
Mean z-score -3.27
Structure conservation index 0.52
SVM decision value 1.98
SVM RNA-class probability 0.984587
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303759 93 + 27905053
GAGACCGAUGGUGGAUGGUAGAUGGAGAAUGAAGGGCAGAUGGCCAUGUGGCCAGCUGACAGACCGUGCUCCUCCUUCCUUCCAAACGGCAGC
..(.(((....((((.((.((..((((.(((....((((.(((((....))))).))).)....))).))))..)).)).))))..))))... ( -34.60)
>DroSec_CAF1 74915 91 + 1
GAGACCGAUGGUGGAUGGUAGGAGGAGAAUGAAGGGCAGAUGGCCAUCUGGCCAGCUGACAGACCCUGCUCCUCCUUCCAC--CAACGGCAGC
..(.(((.(((((((....((((((((.....(((((((.(((((....))))).))).....)))).)))))))))))))--)).))))... ( -48.20)
>DroSim_CAF1 76261 91 + 1
GAGACCGAUGGUGGAUGGUAGGUGGAGAAUGAAGGGCAGAUGGCCAUCUGGCCAGCUGACAGACCCUGCUCCUCCUUCCAC--CAACGGCAGC
..(.(((.(((((((....(((.((((.....(((((((.(((((....))))).))).....)))).)))).))))))))--)).))))... ( -44.00)
>DroEre_CAF1 75768 77 + 1
GAGACCG-------GUGGUGGAU-------GGAGGGCAGUUGGCCAUCUGGCCAGCUGACAGACACUGCUCCUCCUCCCUC--CAACGGCUGC
.((.(((-------.(((.((..-------(((((((((((((((....))))))))).(((...))).))))))..)).)--)).))))).. ( -40.00)
>DroYak_CAF1 75689 84 + 1
GAGACCGAUGGUUGGUGGUAGAU-------GGAGGGCAGUUGGCCAUCUGGCCAGCUGACAGACACUGCUCCUCCUCCCCA--UAACGUCUGC
......((((..(((.((..((.-------((((..(((((((((....))))))))).(((...)))))))))..)))))--...))))... ( -35.60)
>consensus
GAGACCGAUGGUGGAUGGUAGAUGGAGAAUGAAGGGCAGAUGGCCAUCUGGCCAGCUGACAGACCCUGCUCCUCCUUCCAC__CAACGGCAGC
...((((........))))...........(((((((((.(((((....))))).))).(((...)))....))))))............... (-21.16 = -20.88 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,303,759 – 9,303,852
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 81.89
Mean single sequence MFE -38.58
Consensus MFE -22.62
Energy contribution -22.10
Covariance contribution -0.52
Combinations/Pair 1.10
Mean z-score -3.26
Structure conservation index 0.59
SVM decision value 2.26
SVM RNA-class probability 0.991277
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9303759 93 - 27905053
GCUGCCGUUUGGAAGGAAGGAGGAGCACGGUCUGUCAGCUGGCCACAUGGCCAUCUGCCCUUCAUUCUCCAUCUACCAUCCACCAUCGGUCUC
...((((..((((.((.((..((((...((...(.(((.(((((....))))).))))...))...))))..)).)).))))....))))... ( -32.80)
>DroSec_CAF1 74915 91 - 1
GCUGCCGUUG--GUGGAAGGAGGAGCAGGGUCUGUCAGCUGGCCAGAUGGCCAUCUGCCCUUCAUUCUCCUCCUACCAUCCACCAUCGGUCUC
...((((.((--(((((((((((((.((((.....(((.(((((....))))).))))))).....))))))))....))))))).))))... ( -46.90)
>DroSim_CAF1 76261 91 - 1
GCUGCCGUUG--GUGGAAGGAGGAGCAGGGUCUGUCAGCUGGCCAGAUGGCCAUCUGCCCUUCAUUCUCCACCUACCAUCCACCAUCGGUCUC
...((((.((--((((((((.((((.((((.....(((.(((((....))))).))))))).....)))).)))....))))))).))))... ( -42.00)
>DroEre_CAF1 75768 77 - 1
GCAGCCGUUG--GAGGGAGGAGGAGCAGUGUCUGUCAGCUGGCCAGAUGGCCAACUGCCCUCC-------AUCCACCAC-------CGGUCUC
...((((.((--(.((..(((((.(((((((......))(((((....)))))))))))))))-------..)).))).-------))))... ( -39.30)
>DroYak_CAF1 75689 84 - 1
GCAGACGUUA--UGGGGAGGAGGAGCAGUGUCUGUCAGCUGGCCAGAUGGCCAACUGCCCUCC-------AUCUACCACCAACCAUCGGUCUC
..(((((((.--(((((((((((.(((((((......))(((((....)))))))))))))))-------.))).)))..))).....)))). ( -31.90)
>consensus
GCUGCCGUUG__GAGGAAGGAGGAGCAGGGUCUGUCAGCUGGCCAGAUGGCCAUCUGCCCUUCAUUCUCCAUCUACCAUCCACCAUCGGUCUC
..................(((((.(((((((......))(((((....)))))))))))))))...........(((..........)))... (-22.62 = -22.10 +  -0.52)

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 11:00:45 2006