Locus 459

Sequence ID 3R_DroMel_CAF1
Location 1,736,367 – 1,736,588
Length 221
Max. P 0.997975
window743 window744 window745 window746 window747

overview

Window 3

Location 1,736,367 – 1,736,459
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.67
Mean single sequence MFE -30.55
Consensus MFE -24.98
Energy contribution -25.15
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.36
Structure conservation index 0.82
SVM decision value 0.91
SVM RNA-class probability 0.879117
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1736367 92 + 27905053
-------------UCGUUC-----CACUCG-------UUCGCAC---UGUGUACAUUUGACCCGAAGUGCAUUGGUCAUCACGUGUGGCCAUGUGUCUGCAUUUGAGUGCACUUUGGUCA
-------------..((..-----(((...-------.......---.))).))...(((((.((((((((((((((((.....))))))((((....))))...))))))))))))))) ( -28.40)
>DroVir_CAF1 52916 102 + 1
-------------CCAGGU-----GGGUGGUUGGUCCCUUGCACAUUUGAGAACAUUUGACCUGAAGUGCAUUGGUCAUCACGUGUGGCCAUGAGUCUGCAUUUGAGUGCACUUUGGUCA
-------------....(.-----.((.((.....))))..)...............(((((.((((((((((((((((.....))))))(((......)))...))))))))))))))) ( -31.70)
>DroEre_CAF1 44334 92 + 1
-------------UCGUUC-----CACUCG-------UUUGCAC---UGUGUACAUUUGACCCGAAGUGCAUUGGUCAUCACGUGUGGCCAUGUGUCUGCAUUUGAGUGCACUUUGGUCA
-------------..((..-----(((...-------.......---.))).))...(((((.((((((((((((((((.....))))))((((....))))...))))))))))))))) ( -28.40)
>DroWil_CAF1 40404 106 + 1
AGCCUCCUUACUGCUCUUA-----CAGUCU-------CUCGUAUG--UUUGCACAUUUGACCCGAAGUGCAUUGGUCAUCACGUGUGGCCAUGUGUCUGCAUUUGAGUGCACUUUGGUGA
.........((((......-----))))..-------.(((.(((--(....)))).)))(((((((((((((((((((.....))))))((((....))))...)))))))))))).). ( -29.50)
>DroMoj_CAF1 48680 102 + 1
-------------GCAGCU-----GGGUGGCUGGUGCCUUGCACAUUUAAGAACAUUUGACCUGAAGUGCAUUGGUCAUCACGUGUGGCCAUGAGUCUGCAUUUGAGUGCACUUUGGUCA
-------------.(((((-----....)))))((((...)))).............(((((.((((((((((((((((.....))))))(((......)))...))))))))))))))) ( -35.30)
>DroAna_CAF1 41251 97 + 1
-------------ACGUUCUCGUCGACUCG-------UUCGCAC---UGUGCACAUUUGACCCGAAGUGCAUUGGUCAUCACGUGUGGCCAUGUGUCUGCAUUUGAGUGCACUUUGGUCA
-------------........(((((...(-------(.(((..---.))).))..)))))((((((((((((((((((.....))))))((((....))))...))))))))))))... ( -30.00)
>consensus
_____________CCGUUC_____CACUCG_______CUCGCAC___UGUGAACAUUUGACCCGAAGUGCAUUGGUCAUCACGUGUGGCCAUGUGUCUGCAUUUGAGUGCACUUUGGUCA
.........................................................(((((.((((((((((((((((.....))))))(((......)))...))))))))))))))) (-24.98 = -25.15 +   0.17) 

alignment

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secondary structure

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Window 4

Location 1,736,367 – 1,736,459
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.67
Mean single sequence MFE -23.74
Consensus MFE -19.30
Energy contribution -19.47
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -0.75
Structure conservation index 0.81
SVM decision value -0.05
SVM RNA-class probability 0.510385
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1736367 92 - 27905053
UGACCAAAGUGCACUCAAAUGCAGACACAUGGCCACACGUGAUGACCAAUGCACUUCGGGUCAAAUGUACACA---GUGCGAA-------CGAGUG-----GAACGA-------------
(((((.(((((((........((..(((.((....)).))).)).....)))))))..)))))..(((.(((.---((....)-------)..)))-----..))).------------- ( -22.92)
>DroVir_CAF1 52916 102 - 1
UGACCAAAGUGCACUCAAAUGCAGACUCAUGGCCACACGUGAUGACCAAUGCACUUCAGGUCAAAUGUUCUCAAAUGUGCAAGGGACCAACCACCC-----ACCUGG-------------
(((((.((((((((((....).))..(((((......))))).......)))))))..)))))..(((.(......).))).(((........)))-----......------------- ( -23.60)
>DroEre_CAF1 44334 92 - 1
UGACCAAAGUGCACUCAAAUGCAGACACAUGGCCACACGUGAUGACCAAUGCACUUCGGGUCAAAUGUACACA---GUGCAAA-------CGAGUG-----GAACGA-------------
(((((.(((((((........((..(((.((....)).))).)).....)))))))..)))))..(((.(((.---((....)-------)..)))-----..))).------------- ( -22.92)
>DroWil_CAF1 40404 106 - 1
UCACCAAAGUGCACUCAAAUGCAGACACAUGGCCACACGUGAUGACCAAUGCACUUCGGGUCAAAUGUGCAAA--CAUACGAG-------AGACUG-----UAAGAGCAGUAAGGAGGCU
...((.(((((((........((..(((.((....)).))).)).....))))))).))(((..((((....)--))).....-------..((((-----(....))))).....))). ( -23.92)
>DroMoj_CAF1 48680 102 - 1
UGACCAAAGUGCACUCAAAUGCAGACUCAUGGCCACACGUGAUGACCAAUGCACUUCAGGUCAAAUGUUCUUAAAUGUGCAAGGCACCAGCCACCC-----AGCUGC-------------
(((((.((((((((((....).))..(((((......))))).......)))))))..))))).............((((...))))((((.....-----.)))).------------- ( -25.60)
>DroAna_CAF1 41251 97 - 1
UGACCAAAGUGCACUCAAAUGCAGACACAUGGCCACACGUGAUGACCAAUGCACUUCGGGUCAAAUGUGCACA---GUGCGAA-------CGAGUCGACGAGAACGU-------------
.(((.....((((((....((((.((((.((....)).))).(((((...........)))))..).)))).)---)))))..-------...)))...........------------- ( -23.50)
>consensus
UGACCAAAGUGCACUCAAAUGCAGACACAUGGCCACACGUGAUGACCAAUGCACUUCGGGUCAAAUGUACACA___GUGCAAA_______CGACUC_____GAACGA_____________
(((((.((((((((((....).))...((((......))))........)))))))..)))))..(((((......)))))....................................... (-19.30 = -19.47 +   0.17) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,736,459 – 1,736,558
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -34.98
Consensus MFE -29.85
Energy contribution -29.80
Covariance contribution -0.05
Combinations/Pair 1.17
Mean z-score -1.49
Structure conservation index 0.85
SVM decision value 0.00
SVM RNA-class probability 0.535157
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1736459 99 + 27905053
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG
.(((((......((.(((((.(((((.......))))).))))).))............(((((.(((((.(....)))))).)))))...)))))... ( -37.90)
>DroPse_CAF1 39022 97 + 1
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCUCUCGCUGCCAACAAAGUUGCCUUAGCCACGACGUAUG--UGAGCGAGGGUUGACUGACG
............((((..((((((((.......))))(((((((((..((((...((.((....)).))...)).))--..))))))))).)))))))) ( -28.20)
>DroSim_CAF1 46795 99 + 1
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCCCUCGCUACCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG
.(((((..........((((.(((((.......))))).))))................(((((.(((((.(....)))))).)))))...)))))... ( -37.60)
>DroEre_CAF1 44426 99 + 1
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGACUGAUU
............((.(((((.(((((.......))))).))))).)).......((((((((((.(((((.(....)))))).)))))..))))).... ( -38.50)
>DroYak_CAF1 45653 99 + 1
GCAAUUAUUUUACGUCGAGGUCGCAUUAGAGGUGUGCGCCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUU
.(((((......((.(((((.(((((.......))))).))))).))............(((((.(((((.(....)))))).)))))...)))))... ( -39.50)
>DroPer_CAF1 39556 97 + 1
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCUCUCGCUGCCAACAAAGUUGCCUUAGCCACGACGUAUG--UGAGCGAGGGUUGACUGACG
............((((..((((((((.......))))(((((((((..((((...((.((....)).))...)).))--..))))))))).)))))))) ( -28.20)
>consensus
GCAAUUAUUUUACGUUGAGGUCGCAUUAGAGGUGUGCGCCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGACUGAUG
............((((((((.(((((.......))))).))))...........(((((((((.((((((.(....))))).)).)))).))))))))) (-29.85 = -29.80 +  -0.05) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,736,497 – 1,736,588
Length 91
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 86.03
Mean single sequence MFE -37.92
Consensus MFE -30.32
Energy contribution -30.72
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -3.25
Structure conservation index 0.80
SVM decision value 2.97
SVM RNA-class probability 0.997975
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1736497 91 + 27905053
CCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG------GUU-CGAUGAAUGACCAUUGACGAAAUGAUA
(((((((((((((..........)))))((((.(....)))))))))))))(((.(..(((------(((-........))))))..))))....... ( -39.10)
>DroSec_CAF1 45666 91 + 1
CCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG------GUU-CGAUGGAUGACCGUUGACGAAUAGAUA
(((((((((((((..........)))))((((.(....)))))))))))))(((.(..(((------(((-........))))))..))))....... ( -38.70)
>DroSim_CAF1 46833 91 + 1
CCCUCGCUACCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG------GUU-CGAUGGAUGACCAUUGACGCAAAGAUA
.....((.((((.(((.....(((((.(((((.(....)))))).))))).....))).))------))(-((((((....))))))).))....... ( -35.90)
>DroEre_CAF1 44464 98 + 1
CCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGACUGAUUCGAAUGGCACAAAUGGCUGUCCAUUGACGAGCAGAUA
(((((((((((((..........)))))((((.(....)))))))))))))....(((.(((((((((.(((......))))))))..)))))))... ( -40.10)
>DroYak_CAF1 45691 98 + 1
CCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUUAGAACGCGAAGAAUGGAUGUCCAUUGUCGAAAAGACA
(((((((((((((..........)))))((((.(....)))))))))))))................(((..(((((....))))).)))........ ( -35.80)
>consensus
CCCUCGCUGCCAACAAAGUUGCCUUGGCCAGGACGAAAGCCUGGGCGAGGGUCGAUUGAUG______GUU_CGAUGGAUGACCAUUGACGAAAAGAUA
(((((((((((((..........)))))((((.(....)))))))))))))....................((((((....))))))........... (-30.32 = -30.72 +   0.40) 

alignment

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secondary structure

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dotplot

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Window 7

Location 1,736,497 – 1,736,588
Length 91
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 86.03
Mean single sequence MFE -31.22
Consensus MFE -26.62
Energy contribution -26.50
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.97
Structure conservation index 0.85
SVM decision value 1.28
SVM RNA-class probability 0.939357
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1736497 91 - 27905053
UAUCAUUUCGUCAAUGGUCAUUCAUCG-AAC------CAUCAAUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGCAGCGAGGG
.......(((...((((((.......)-.))------)))....)))(((((((.(((((....).))))((((((....))....)))).))))))) ( -30.80)
>DroSec_CAF1 45666 91 - 1
UAUCUAUUCGUCAACGGUCAUCCAUCG-AAC------CAUCAAUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGCAGCGAGGG
...............((....)).(((-(..------......))))(((((((.(((((....).))))((((((....))....)))).))))))) ( -29.00)
>DroSim_CAF1 46833 91 - 1
UAUCUUUGCGUCAAUGGUCAUCCAUCG-AAC------CAUCAAUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGUAGCGAGGG
...((((((.((.((((....)))).)-)((------((.(((.....(((.(.((((((....).))))).).))).....))).)))).)))))). ( -29.40)
>DroEre_CAF1 44464 98 - 1
UAUCUGCUCGUCAAUGGACAGCCAUUUGUGCCAUUCGAAUCAGUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGCAGCGAGGG
..((.(((..(((((((((((....)))).))))).))...))).))(((((((.(((((....).))))((((((....))....)))).))))))) ( -35.40)
>DroYak_CAF1 45691 98 - 1
UGUCUUUUCGACAAUGGACAUCCAUUCUUCGCGUUCUAAUCAAUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGCAGCGAGGG
.(((.....)))(((((....))))).....................(((((((.(((((....).))))((((((....))....)))).))))))) ( -31.50)
>consensus
UAUCUUUUCGUCAAUGGUCAUCCAUCG_AAC______CAUCAAUCGACCCUCGCCCAGGCUUUCGUCCUGGCCAAGGCAACUUUGUUGGCAGCGAGGG
.............((((....))))......................(((((((.(((((....).))))((((((....))....)))).))))))) (-26.62 = -26.50 +  -0.12) 

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 09:43:45 2006