Locus 2270

Sequence ID X_DroMel_CAF1
Location 6,152,426 – 6,152,577
Length 151
Max. P 0.992305
window3677 window3678 window3679 window3680

overview

Window 7

Location 6,152,426 – 6,152,537
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.21
Mean single sequence MFE -35.17
Consensus MFE -27.84
Energy contribution -27.71
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.43
SVM RNA-class probability 0.733022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6152426 111 + 22224390
AAGUGGAAGUGGCAGUGGCAGUAGAAGUGGAGCAACAACAGCAA---------UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUA
..(((...((((((.((((.......((......))..((....---------))))))))))))..((.((((.(.((((........))))(((....)))..).)))).)))))... ( -34.50)
>DroSec_CAF1 5636 111 + 1
AAUUGGAAGCGGCAUUGGCAGUAGAUGUGGAGCAACAACAGCAU---------UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUA
........((.((.((.(((.....))).)))).......((((---------(((((.(((((((....))))))).)))........(((.(((....)))..))).))))))))... ( -38.60)
>DroEre_CAF1 3379 114 + 1
AAGUGGAAGU------GGCAGUAGAAGUGGAGCAACAGCAACAGCAACUGCGAUGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUA
........((------.(((((.(...((..((....))..)).).))))).)).(((.(((((((....))))))).)))..(((.(.(((.(((....)))..)))....).)))... ( -38.60)
>DroYak_CAF1 2980 105 + 1
AAGUGGAAGU------GGCAGUAGAAGUGGAGCAACAACAGCAG---------UGGCCAUGCCACAACACUGUGGCACGGCAAGUGGAGGCCAAAAGACCCUUGAGGCAUAAUGCGCAUA
(((.((...(------(((.......((......)).....((.---------(.(((.(((((((....))))))).))).).))...)))).....)))))...((.....))..... ( -29.00)
>consensus
AAGUGGAAGU______GGCAGUAGAAGUGGAGCAACAACAGCAG_________UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUA
........((.......((............)).......)).............(((.(((((((....))))))).)))..(((.(.(((.(((....)))..)))....).)))... (-27.84 = -27.71 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,152,426 – 6,152,537
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.21
Mean single sequence MFE -32.38
Consensus MFE -29.29
Energy contribution -29.10
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.90
SVM decision value 1.49
SVM RNA-class probability 0.958395
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6152426 111 - 22224390
UAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA---------UUGCUGUUGUUGCUCCACUUCUACUGCCACUGCCACUUCCACUU
..((.(((....(((.....))).....(((........(((((((((((....)))))))))))..---------..((.......))............)))..)))))......... ( -30.50)
>DroSec_CAF1 5636 111 - 1
UAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA---------AUGCUGUUGUUGCUCCACAUCUACUGCCAAUGCCGCUUCCAAUU
...(((((((..(((.....))).....(((........(((((((((((....)))))))))))..---------..((.......))............))))))).)))........ ( -34.10)
>DroEre_CAF1 3379 114 - 1
UAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCAUCGCAGUUGCUGUUGCUGUUGCUCCACUUCUACUGCC------ACUUCCACUU
...(((((...(((.....(((((....)))))......(((((((((((....)))))))))))....)))..)))((..((....))..))........)).------.......... ( -35.00)
>DroYak_CAF1 2980 105 - 1
UAUGCGCAUUAUGCCUCAAGGGUCUUUUGGCCUCCACUUGCCGUGCCACAGUGUUGUGGCAUGGCCA---------CUGCUGUUGUUGCUCCACUUCUACUGCC------ACUUCCACUU
...(((((....((.....(((((....)))))......((((((((((......))))))))))..---------..))...)).)))...............------.......... ( -29.90)
>consensus
UAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA_________CUGCUGUUGUUGCUCCACUUCUACUGCC______ACUUCCACUU
.....(((....((..((.(((((....)))))......(((((((((((....)))))))))))............))..))...)))............................... (-29.29 = -29.10 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,152,466 – 6,152,577
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.21
Mean single sequence MFE -48.20
Consensus MFE -46.51
Energy contribution -46.33
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.34
Structure conservation index 0.96
SVM decision value 2.32
SVM RNA-class probability 0.992305
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6152466 111 + 22224390
GCAA---------UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUAUCGUUCGGUUGGCCAACCUGGCCACUGGGUCGUCCACAUC
....---------..(((.(((((((....))))))).)))..(((((((((..((((((..(((.((.......))...)))...))))((((.....)))).)).)))).)))))... ( -47.00)
>DroSec_CAF1 5676 111 + 1
GCAU---------UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUAUCGUUCGGUUGGCCAACCUGGCCACUGGGUCGUCCGCAUC
((((---------(((((.(((((((....))))))).)))........(((.(((....)))..))).))))))((....((((((((.((((.....)))))))))).))...))... ( -47.20)
>DroEre_CAF1 3413 120 + 1
ACAGCAACUGCGAUGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUAUCGUUCGGUUGGCCAACCUGGCCACUGGGUCGUCCACGUC
...((....))....(((.(((((((....))))))).)))..(((((((((..((((((..(((.((.......))...)))...))))((((.....)))).)).)))).)))))... ( -48.50)
>DroYak_CAF1 3014 111 + 1
GCAG---------UGGCCAUGCCACAACACUGUGGCACGGCAAGUGGAGGCCAAAAGACCCUUGAGGCAUAAUGCGCAUAUCGUUGGGUUGGCCAACCUGGCCACUGGGUCGUCCACGUC
....---------..(((.(((((((....))))))).)))..(((((((((....(((((.(((.((.......))...)))..)))))((((.....))))....)))).)))))... ( -50.10)
>consensus
GCAG_________UGGCCAUGCCACAACAGUGUGGCACGGCAAGUGGAGGCCGAAGGACCCUUGAGGCAUAAUGCGCAUAUCGUUCGGUUGGCCAACCUGGCCACUGGGUCGUCCACAUC
...............(((.(((((((....))))))).)))..(((((((((....((((..(((.((.......))...)))...))))((((.....))))....)))).)))))... (-46.51 = -46.33 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,152,466 – 6,152,577
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.21
Mean single sequence MFE -45.42
Consensus MFE -43.61
Energy contribution -43.68
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.96
SVM decision value 1.06
SVM RNA-class probability 0.908303
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6152466 111 - 22224390
GAUGUGGACGACCCAGUGGCCAGGUUGGCCAACCGAACGAUAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA---------UUGC
...(((((.(((((..(((((.....)))))..............((.....)).....)))))(....)..)))))..(((((((((((....)))))))))))..---------.... ( -45.80)
>DroSec_CAF1 5676 111 - 1
GAUGCGGACGACCCAGUGGCCAGGUUGGCCAACCGAACGAUAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA---------AUGC
((.((.((.(((((..(((((.....)))))..............((.....)).....)))))..)).)).)).....(((((((((((....)))))))))))..---------.... ( -44.40)
>DroEre_CAF1 3413 120 - 1
GACGUGGACGACCCAGUGGCCAGGUUGGCCAACCGAACGAUAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCAUCGCAGUUGCUGU
...(((((.(((((..(((((.....)))))..............((.....)).....)))))(....)..)))))..(((((((((((....)))))))))))....((....))... ( -47.20)
>DroYak_CAF1 3014 111 - 1
GACGUGGACGACCCAGUGGCCAGGUUGGCCAACCCAACGAUAUGCGCAUUAUGCCUCAAGGGUCUUUUGGCCUCCACUUGCCGUGCCACAGUGUUGUGGCAUGGCCA---------CUGC
..((....))...((((((((.((..(((((((((...((...(((.....))).))..))))....))))).)).......(((((((......))))))))))))---------))). ( -44.30)
>consensus
GACGUGGACGACCCAGUGGCCAGGUUGGCCAACCGAACGAUAUGCGCAUUAUGCCUCAAGGGUCCUUCGGCCUCCACUUGCCGUGCCACACUGUUGUGGCAUGGCCA_________CUGC
...(((((.(((((..(((((.....)))))..............((.....)).....)))))(....)..)))))..(((((((((((....)))))))))))............... (-43.61 = -43.68 +   0.06)

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 10:30:18 2006