Locus 8407

Sequence ID X_DroMel_CAF1
Location 20,881,545 – 20,881,694
Length 149
Max. P 0.997324
window13804 window13805 window13806 window13807

overview

Window 4

Location 20,881,545 – 20,881,656
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.43
Mean single sequence MFE -40.02
Consensus MFE -31.21
Energy contribution -32.27
Covariance contribution 1.06
Combinations/Pair 1.17
Mean z-score -2.57
Structure conservation index 0.78
SVM decision value 1.74
SVM RNA-class probability 0.974732
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20881545 111 + 22224390
ACUUGGAGAGCCGUCGAAAGACAUAUGCGUCAGCAUCAGCUGUCCAAUGUGGCAAUCAUUCGACAGAAGAGGGCGAUGUGGCCAACACAC---------CCACACCACCCUCUUUCGUCU
(((((((.(((.(((....)))..((((....))))..))).))))).))...........(((..(((((((.(.(((((.........---------))))).).)))))))..))). ( -44.80)
>DroSec_CAF1 1495 111 + 1
ACUUGGAGAGCCGUCGAACGACAUCUGCGUCAGCAUCAGCUGUCCCAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC---------CCACACCACCCUCUUCCGCCC
..(((((..((((((....)))...((.(.((((....)))).).))...))).....)))))..((((((((.(.(((((.........---------))))).).))))))))..... ( -39.10)
>DroSim_CAF1 2292 111 + 1
ACUUGGAGAGCCGUCGAACGACAUCUGCGUCAGCAUCAGCUGUCCCAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC---------CCACACCACCCUCUUCCGCCC
..(((((..((((((....)))...((.(.((((....)))).).))...))).....)))))..((((((((.(.(((((.........---------))))).).))))))))..... ( -39.10)
>DroYak_CAF1 2389 120 + 1
ACAUGGAGUGUCGCUGAAAGACAUCUGCGUCAGCGUCUGCUGUCCAAUGUGGCAUUGAUCCAACAGAAGAGGGCGACAUGAUCAACACCACGACAUGGUCAACACCACCCUCUUCCGCCC
((((((((((.((((((.((....))...)))))).).))..))).))))(((..((......))((((((((.(...((((((...........))))))....).)))))))).))). ( -37.10)
>consensus
ACUUGGAGAGCCGUCGAAAGACAUCUGCGUCAGCAUCAGCUGUCCAAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC_________CCACACCACCCUCUUCCGCCC
..(((((..((((((....)))......(.((((....)))).)......))).....)))))..((((((((.(.(((((..................))))).).))))))))..... (-31.21 = -32.27 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,881,545 – 20,881,656
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.43
Mean single sequence MFE -51.65
Consensus MFE -42.37
Energy contribution -42.49
Covariance contribution 0.13
Combinations/Pair 1.18
Mean z-score -3.59
Structure conservation index 0.82
SVM decision value 2.84
SVM RNA-class probability 0.997324
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20881545 111 - 22224390
AGACGAAAGAGGGUGGUGUGG---------GUGUGUUGGCCACAUCGCCCUCUUCUGUCGAAUGAUUGCCACAUUGGACAGCUGAUGCUGACGCAUAUGUCUUUCGACGGCUCUCCAAGU
.((((.(((((((((((((((---------.(.....).))))))))))))))).))))..............(((((.((((.((((....))))..(((....))))))).))))).. ( -49.10)
>DroSec_CAF1 1495 111 - 1
GGGCGGAAGAGGGUGGUGUGG---------GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACAGCUGAUGCUGACGCAGAUGUCGUUCGACGGCUCUCCAAGU
.((((((((((((((((((((---------.........))))))))))))))))))))(((.....(((...((.(.((((....)))).).))...(((....))))))..))).... ( -56.60)
>DroSim_CAF1 2292 111 - 1
GGGCGGAAGAGGGUGGUGUGG---------GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACAGCUGAUGCUGACGCAGAUGUCGUUCGACGGCUCUCCAAGU
.((((((((((((((((((((---------.........))))))))))))))))))))(((.....(((...((.(.((((....)))).).))...(((....))))))..))).... ( -56.60)
>DroYak_CAF1 2389 120 - 1
GGGCGGAAGAGGGUGGUGUUGACCAUGUCGUGGUGUUGAUCAUGUCGCCCUCUUCUGUUGGAUCAAUGCCACAUUGGACAGCAGACGCUGACGCAGAUGUCUUUCAGCGACACUCCAUGU
.((((((((((((((((....)))..(.((((((....)))))).))))))))))))))(((((((((...)))))).((((....)))).(((.((......)).)))....))).... ( -44.30)
>consensus
GGGCGGAAGAGGGUGGUGUGG_________GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACAGCUGAUGCUGACGCAGAUGUCGUUCGACGGCUCUCCAAGU
.((((((((((((((((((((..................))))))))))))))))))))(((.....(((........((((....))))........(((....))))))..))).... (-42.37 = -42.49 +   0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,881,585 – 20,881,694
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.34
Mean single sequence MFE -28.73
Consensus MFE -20.27
Energy contribution -21.65
Covariance contribution 1.38
Combinations/Pair 1.09
Mean z-score -2.12
Structure conservation index 0.71
SVM decision value 0.83
SVM RNA-class probability 0.860762
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20881585 109 + 22224390
UGUCCAAUGUGGCAAUCAUUCGACAGAAGAGGGCGAUGUGGCCAACACAC---------CCACACCACCCUCUUUCGUCUC--ACAGUACCGCCUCCUUUUCCACACCCACCCACGCGCC
.......(((((.........(((..(((((((.(.(((((.........---------))))).).)))))))..)))..--...(.....)........))))).............. ( -27.40)
>DroSec_CAF1 1535 109 + 1
UGUCCCAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC---------CCACACCACCCUCUUCCGCCCC--CCAGUACCGCCUCCUUUUCCCCACCCACCCACGCGCC
........((((.((((....(.(.((((((((.(.(((((.........---------))))).).)))))))).))...--.)))).))))........................... ( -28.00)
>DroSim_CAF1 2332 110 + 1
UGUCCCAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC---------CCACACCACCCUCUUCCGCCCCC-CCGGUACCGCCUCCUUUUCCACACCCACCCACGCGCC
.......(((((....((..((...((((((((.(.(((((.........---------))))).).)))))))).(((...-..)))..))..)).....))))).............. ( -29.80)
>DroYak_CAF1 2429 119 + 1
UGUCCAAUGUGGCAUUGAUCCAACAGAAGAGGGCGACAUGAUCAACACCACGACAUGGUCAACACCACCCUCUUCCGCCCCCCCCAGAGCCGCC-CCUUUGCCACACCCACCCACGCGCC
.......(((((((..(........((((((((.(...((((((...........))))))....).)))))))).((.(......).))....-.)..))))))).............. ( -29.70)
>consensus
UGUCCAAUGUGGCAUUGAUCCGACAGAAGAGGGCGAUGUGGUCAACACAC_________CCACACCACCCUCUUCCGCCCC__CCAGUACCGCCUCCUUUUCCACACCCACCCACGCGCC
........((((.((((........((((((((.(.(((((..................))))).).)))))))).........)))).))))........................... (-20.27 = -21.65 +   1.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,881,585 – 20,881,694
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.34
Mean single sequence MFE -47.65
Consensus MFE -38.86
Energy contribution -38.55
Covariance contribution -0.31
Combinations/Pair 1.23
Mean z-score -3.06
Structure conservation index 0.82
SVM decision value 2.48
SVM RNA-class probability 0.994483
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20881585 109 - 22224390
GGCGCGUGGGUGGGUGUGGAAAAGGAGGCGGUACUGU--GAGACGAAAGAGGGUGGUGUGG---------GUGUGUUGGCCACAUCGCCCUCUUCUGUCGAAUGAUUGCCACAUUGGACA
.((((.(....).)))).........((((((...((--..((((.(((((((((((((((---------.(.....).))))))))))))))).))))..)).)))))).......... ( -44.40)
>DroSec_CAF1 1535 109 - 1
GGCGCGUGGGUGGGUGGGGAAAAGGAGGCGGUACUGG--GGGGCGGAAGAGGGUGGUGUGG---------GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACA
..(.((((....((((..((.....((......))..--..((((((((((((((((((((---------.........))))))))))))))))))))...))..)))).)))).)... ( -48.80)
>DroSim_CAF1 2332 110 - 1
GGCGCGUGGGUGGGUGUGGAAAAGGAGGCGGUACCGG-GGGGGCGGAAGAGGGUGGUGUGG---------GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACA
..(.((((....(((((.((........((....)).-...((((((((((((((((((((---------.........))))))))))))))))))))...)).))))).)))).)... ( -50.40)
>DroYak_CAF1 2429 119 - 1
GGCGCGUGGGUGGGUGUGGCAAAGG-GGCGGCUCUGGGGGGGGCGGAAGAGGGUGGUGUUGACCAUGUCGUGGUGUUGAUCAUGUCGCCCUCUUCUGUUGGAUCAAUGCCACAUUGGACA
..(((....)))(((((((((..((-..((((...(((((((((((......(((((....)))))..((((((....))))))))))))))))).))))..))..)))))))))..... ( -47.00)
>consensus
GGCGCGUGGGUGGGUGUGGAAAAGGAGGCGGUACUGG__GGGGCGGAAGAGGGUGGUGUGG_________GUGUGUUGACCACAUCGCCCUCUUCUGUCGGAUCAAUGCCACAUGGGACA
.....((((...(((((.(.........).)))))......((((((((((((((((((((..................)))))))))))))))))))).........))))........ (-38.86 = -38.55 +  -0.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:11 2006