Locus 9678

Sequence ID 3R_DroMel_CAF1
Location 25,605,285 – 25,605,423
Length 138
Max. P 0.850374
window15464 window15465 window15466

overview

Window 4

Location 25,605,285 – 25,605,383
Length 98
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.50
Mean single sequence MFE -29.83
Consensus MFE -18.45
Energy contribution -19.40
Covariance contribution 0.95
Combinations/Pair 1.29
Mean z-score -1.33
Structure conservation index 0.62
SVM decision value -0.00
SVM RNA-class probability 0.531066
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25605285 98 + 27905053
CCCGGCUGGCGCCCACAAGUAGAUCGUGCU----------CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUAUCGAACAAGCCA
...((((.(((((...(((..((.((((..----------...)))).)))))..)))...(((......)))))((((((((....))))))))........)))). ( -27.80)
>DroVir_CAF1 43003 101 + 1
AACGAUUGGCGGCCUGCUGCAGAUACUCG-GCACGAGUCUCGCCCUGCA------GCGCUCGCAACUGAUUGAUCAGCAUGCUCUCGGGCACAUUGUCGAAGAGGCCG
.........(((((((((((((..(((((-...)))))......)))))------))..((((((((((....))))..((((....))))..))).)))..)))))) ( -35.70)
>DroSec_CAF1 32282 98 + 1
CCCGGCUGGCGCCCUCCAGGAGAUCGCGCU----------CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCA
...(((((((........(((((......)----------))))...((.....)))))...........(((.(((((((((....))))))))))))....)))). ( -31.90)
>DroSim_CAF1 33091 98 + 1
CCCGGCUGGCGCCCUCCAGGAGAUCGCGCU----------CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACGUGCUCUCGGGCAUGUUGUCGAACAAGCCA
...(((((((........(((((......)----------))))...((.....)))))...........(((.(((((((((....))))))))))))....)))). ( -31.50)
>DroEre_CAF1 33250 98 + 1
CCUGGCUGGCGCACUGCAGCAGAUCCCGCU----------CCCCACGCUCCUUUAAGCCAUUCAAUAUCUUGAGCAACAUGCUCUCGGGCAUGUUAUCGAACAAUCCA
..(((((((.((...(.(((.......)))----------.)....)).))....))))).........((((..((((((((....)))))))).))))........ ( -24.40)
>DroYak_CAF1 34384 98 + 1
CCUGGCUGGCGCCCUGCAGCAGAUCCCGCU----------CCCCACGCUCCUUCAAACCAUUCAAUAUCUUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCA
..(((..((((..(((...)))....))))----------..))).(((..(((.......((((....))))((((((((((....)))))))))).)))..))).. ( -27.70)
>consensus
CCCGGCUGGCGCCCUCCAGCAGAUCCCGCU__________CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCA
...(((((((((.(((...)))...)))))........................................(((.(((((((((....))))))))))))....)))). (-18.45 = -19.40 +   0.95)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,605,315 – 25,605,423
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 83.27
Mean single sequence MFE -43.77
Consensus MFE -31.17
Energy contribution -33.53
Covariance contribution 2.36
Combinations/Pair 1.16
Mean z-score -2.93
Structure conservation index 0.71
SVM decision value 0.79
SVM RNA-class probability 0.850374
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25605315 108 + 27905053
CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUAUCGAACAAGCCAUCGGUGGCCAGGAGCACCAGGUCACCGGGUAGUAGGGAGU
((((..(((((....(((..((((......)))).((((((((....)))))))).........)))..((((((((.((....)).)))))))))).)))..)))). ( -42.90)
>DroVir_CAF1 43042 102 + 1
CGCCCUGCA------GCGCUCGCAACUGAUUGAUCAGCAUGCUCUCGGGCACAUUGUCGAAGAGGCCGUCCGUGGCCAGCAGUACAAGAUCGCCCGGCUGUAGUGGCA
.((((((((------((....(((.((((....))))..)))...(((((...(((((.....(((((....)))))....).))))....)))))))))))).))). ( -43.60)
>DroSec_CAF1 32312 108 + 1
CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCAUCGGUGGCCAGGAGCACCAGGUCGCCGGGUAGUAGGGAGU
((((..(((((....(((...(((......)))((((((((((....)))))))))).......)))..((((((((.((....)).)))))))))).)))..)))). ( -46.10)
>DroSim_CAF1 33121 108 + 1
CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACGUGCUCUCGGGCAUGUUGUCGAACAAGCCAUCGGUGGCCAGGAGCACCAGGUCGCCGGGUAGUAGGGAGU
((((..(((((....(((...(((......)))((((((((((....)))))))))).......)))..((((((((.((....)).)))))))))).)))..)))). ( -45.70)
>DroEre_CAF1 33280 108 + 1
CCCCACGCUCCUUUAAGCCAUUCAAUAUCUUGAGCAACAUGCUCUCGGGCAUGUUAUCGAACAAUCCAUCGGUGGCCAGGAGCACCAGGUCGCCCGGCAGCAAGGAGU
......(((((((...(((..........((((..((((((((....)))))))).))))..........(((((((.((....)).))))))).)))...))))))) ( -41.20)
>DroYak_CAF1 34414 108 + 1
CCCCACGCUCCUUCAAACCAUUCAAUAUCUUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCAUCGGUGGCCAGGAGCACCAGGUCGCCCGGCAGCAAGGAGU
......((((((((...............((((.(((((((((....)))))))))))))....(((...(((((((.((....)).))))))).))).).))))))) ( -43.10)
>consensus
CUCCACGCUCCUUUAGGCCAUUCAAUAUACUGAGCAACAUGCUCUCGGGCAUGUUGUCGAACAAGCCAUCGGUGGCCAGGAGCACCAGGUCGCCCGGCAGUAGGGAGU
......(((((((...(((...........(((.(((((((((....))))))))))))...........(((((((.((....)).))))))).)))...))))))) (-31.17 = -33.53 +   2.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,605,315 – 25,605,423
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 83.27
Mean single sequence MFE -42.37
Consensus MFE -27.43
Energy contribution -28.80
Covariance contribution 1.37
Combinations/Pair 1.20
Mean z-score -1.95
Structure conservation index 0.65
SVM decision value -0.03
SVM RNA-class probability 0.518771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25605315 108 - 27905053
ACUCCCUACUACCCGGUGACCUGGUGCUCCUGGCCACCGAUGGCUUGUUCGAUAACAUGCCCGAGAGCAUGUUGCUCAGUAUAUUGAAUGGCCUAAAGGAGCGUGGAG
.(((((....(((.(....)..)))(((((((((((.(((((((.((((....)))).)))...((((.....)))).....))))..)))))...))))))).)))) ( -40.10)
>DroVir_CAF1 43042 102 - 1
UGCCACUACAGCCGGGCGAUCUUGUACUGCUGGCCACGGACGGCCUCUUCGACAAUGUGCCCGAGAGCAUGCUGAUCAAUCAGUUGCGAGCGC------UGCAGGGCG
.(((.((.((((((((((...((((......((((......))))......))))..))))))...(((.(((((....))))))))....))------)).))))). ( -43.30)
>DroSec_CAF1 32312 108 - 1
ACUCCCUACUACCCGGCGACCUGGUGCUCCUGGCCACCGAUGGCUUGUUCGACAACAUGCCCGAGAGCAUGUUGCUCAGUAUAUUGAAUGGCCUAAAGGAGCGUGGAG
.(((((....(((.((...)).)))(((((((((((.(((((..(((...(.((((((((......))))))))).)))..)))))..)))))...))))))).)))) ( -40.50)
>DroSim_CAF1 33121 108 - 1
ACUCCCUACUACCCGGCGACCUGGUGCUCCUGGCCACCGAUGGCUUGUUCGACAACAUGCCCGAGAGCACGUUGCUCAGUAUAUUGAAUGGCCUAAAGGAGCGUGGAG
.(((((....(((.((...)).)))(((((((((((.(((((((.((((....)))).)))...((((.....)))).....))))..)))))...))))))).)))) ( -39.80)
>DroEre_CAF1 33280 108 - 1
ACUCCUUGCUGCCGGGCGACCUGGUGCUCCUGGCCACCGAUGGAUUGUUCGAUAACAUGCCCGAGAGCAUGUUGCUCAAGAUAUUGAAUGGCUUAAAGGAGCGUGGGG
...(((..(.((((((...))))))(((((((((((.(((((..(((...(.((((((((......))))))))).)))..)))))..)))))...)))))))..))) ( -44.80)
>DroYak_CAF1 34414 108 - 1
ACUCCUUGCUGCCGGGCGACCUGGUGCUCCUGGCCACCGAUGGCUUGUUCGACAACAUGCCCGAGAGCAUGUUGCUCAAGAUAUUGAAUGGUUUGAAGGAGCGUGGGG
...(((..(.((((((...))))))((((((.((((.(((((.((((...(.((((((((......))))))))).)))).)))))..))))....)))))))..))) ( -45.70)
>consensus
ACUCCCUACUACCCGGCGACCUGGUGCUCCUGGCCACCGAUGGCUUGUUCGACAACAUGCCCGAGAGCAUGUUGCUCAAUAUAUUGAAUGGCCUAAAGGAGCGUGGAG
.((((.....(((.((...)).)))(((((((((((.(((((((.((((....)))).)))...((((.....)))).....))))..)))))...))))))..)))) (-27.43 = -28.80 +   1.37)

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 13:39:42 2006