Locus 3533

Sequence ID 3R_DroMel_CAF1
Location 9,551,615 – 9,551,740
Length 125
Max. P 0.979465
window5677 window5678 window5679 window5680

overview

Window 7

Location 9,551,615 – 9,551,715
Length 100
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 85.96
Mean single sequence MFE -31.75
Consensus MFE -22.65
Energy contribution -23.99
Covariance contribution 1.34
Combinations/Pair 1.19
Mean z-score -2.79
Structure conservation index 0.71
SVM decision value 0.07
SVM RNA-class probability 0.569812
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9551615 100 + 27905053
CUCACUUUUCGCUGCAGUUCAGUGGCCGUUGCACUUGACAUAUAGCCACUG-UCAAUGCGACUAAGAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGC
............(((((((((((((((((((((.((((((.........))-))))))))))....((.....)).....)))))))).)))))))..... ( -34.60)
>DroSec_CAF1 28240 100 + 1
CUCACUUUUCGCUGCAGUUCAGUGGCCGUUGCACUUGACAUACAGUCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUAGCCAUUGAAAUUGCAACUGC
............((((((((((((((.((((((((((((.....)))...(-((.....)))...))))))))).......))))))).)))))))..... ( -32.80)
>DroSim_CAF1 28381 100 + 1
CUCACUUUUCGCUGCAGUUCAGUGGCCGUUGCACUUGACAUACAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGUCAUUGAAAUUGCAACUGC
............((((((((((((((((((.((.((((((.........))-))))(((.((.....)))))..)).))))))))))).)))))))..... ( -31.80)
>DroEre_CAF1 29984 100 + 1
CUCACUUUUCGCUGCAGUUCAGUGGCCGUUGCACUUGACAUAUAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGC
............((((((((((((((((((.((.((((((.........))-))))(((.((.....)))))..)).))))))))))).)))))))..... ( -34.50)
>DroWil_CAF1 32410 96 + 1
ACCAUUAUUUGAUGCGGUUCAGUGGCCAAUGCACUUGACACUCUGCCACUGAUUGUUGCAACUGAAACUGGAACUGGAAUUGGAAUUGGCCUUUCA-----
.(((......(.(((((.((((((((...(((....).))....))))))))...))))).)......))).....(((..((......)).))).----- ( -21.50)
>DroYak_CAF1 28665 95 + 1
CUCACUUUUCG---CAGUUCAGUGGCCGUUGCACUUGACAUGUAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACU--
..........(---((((((((((((((((.((.((((((.((....))))-))))(((.((.....)))))..)).))))))))))).))))))....-- ( -35.30)
>consensus
CUCACUUUUCGCUGCAGUUCAGUGGCCGUUGCACUUGACAUACAGCCACUG_UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGC
............((((((((((((((((((((((((........((...........))......)))))))))......))))))))).))))))..... (-22.65 = -23.99 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 9,551,615 – 9,551,715
Length 100
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 85.96
Mean single sequence MFE -33.10
Consensus MFE -24.75
Energy contribution -26.83
Covariance contribution 2.09
Combinations/Pair 1.19
Mean z-score -2.79
Structure conservation index 0.75
SVM decision value 0.37
SVM RNA-class probability 0.706657
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9551615 100 - 27905053
GCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUCUUAGUCGCAUUGA-CAGUGGCUAUAUGUCAAGUGCAACGGCCACUGAACUGCAGCGAAAAGUGAG
...((((((..((((.(((((......((((((((..(((((((.....-..))))))).......))))))))))))).)))).)))))).......... ( -36.60)
>DroSec_CAF1 28240 100 - 1
GCAGUUGCAAUUUCAAUGGCUAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGACUGUAUGUCAAGUGCAACGGCCACUGAACUGCAGCGAAAAGUGAG
...((((((..((((.(((((......(((((((((.(((((((.....-..)))))))......)))))))))))))).)))).)))))).......... ( -36.30)
>DroSim_CAF1 28381 100 - 1
GCAGUUGCAAUUUCAAUGACCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUGUAUGUCAAGUGCAACGGCCACUGAACUGCAGCGAAAAGUGAG
((((((((((((..(((....)))..)))))).................-((((((((((.(((.....)))))))))))))))))))............. ( -31.90)
>DroEre_CAF1 29984 100 - 1
GCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUAUAUGUCAAGUGCAACGGCCACUGAACUGCAGCGAAAAGUGAG
...((((((..((((.(((((......(((((((((.(((((((.....-..)))))))......)))))))))))))).)))).)))))).......... ( -37.70)
>DroWil_CAF1 32410 96 - 1
-----UGAAAGGCCAAUUCCAAUUCCAGUUCCAGUUUCAGUUGCAACAAUCAGUGGCAGAGUGUCAAGUGCAUUGGCCACUGAACCGCAUCAAAUAAUGGU
-----......((((............(((.(((......))).)))..((((((((..(((((.....))))).))))))))..............)))) ( -23.00)
>DroYak_CAF1 28665 95 - 1
--AGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUACAUGUCAAGUGCAACGGCCACUGAACUG---CGAAAAGUGAG
--..(((((..((((.(((((......(((((((((.(((((((.....-..)))))))......)))))))))))))).)))).))---)))........ ( -33.10)
>consensus
GCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA_CAGUGGCUAUAUGUCAAGUGCAACGGCCACUGAACUGCAGCGAAAAGUGAG
...((((((..((((.(((((......(((((((((.(((((((........)))))))......)))))))))))))).)))).)))))).......... (-24.75 = -26.83 +   2.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 9,551,642 – 9,551,740
Length 98
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 78.48
Mean single sequence MFE -25.15
Consensus MFE -13.70
Energy contribution -15.07
Covariance contribution 1.38
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.54
SVM decision value 0.63
SVM RNA-class probability 0.803916
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9551642 98 + 27905053
GUUGCACUUGACAUAUAGCCACUG-UCAAUGCGACUAAGAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGCAAUUGCUAUUGCAACUGCAACUGCC
((((((.((((((.........))-))))))))))....((((((..((.((((((......((((((....)))))))))))).))..))).)))... ( -30.00)
>DroSec_CAF1 28267 98 + 1
GUUGCACUUGACAUACAGUCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUAGCCAUUGAAAUUGCAACUGCAAUUGCAAUUGCAACUGCAACUGCC
((((((((((((.....)))...(-((.....)))...)))))))))(((.....)))....((((((....))))))(((.((((....)))).))). ( -30.50)
>DroSim_CAF1 28408 98 + 1
GUUGCACUUGACAUACAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGUCAUUGAAAUUGCAACUGCAAUUGCAAUUGCAACUGCAACUGCC
((((((..((((...(((.(((((-((.....)))....))))...))).....))))......((((((.(((....))).)))))).)))))).... ( -27.30)
>DroEre_CAF1 30011 98 + 1
GUUGCACUUGACAUAUAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGCAAUUGCAAGUGCAACUGCAACUACC
((((((((((.(.....((((...-(((.(((.((.....)))))..)))..))))......((((((....))))))))))))))))).......... ( -30.20)
>DroWil_CAF1 32437 80 + 1
AAUGCACUUGACACUCUGCCACUGAUUGUUGCAACUGAAACUGGAACUGGAAUUGGAAUUGGCCUUUCA-------------------UUGUGAAUGCC
...(((.((.(((....(((((..((((((.((........)).)))...)))..)...))))......-------------------.))).))))). ( -12.40)
>DroYak_CAF1 28689 80 + 1
GUUGCACUUGACAUGUAGCCACUG-UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACU------------------GCAACUGCC
((((((.((((((.((....))))-))))))))))....((((((..((.(((..(....)..))).))..)------------------)).)))... ( -20.50)
>consensus
GUUGCACUUGACAUACAGCCACUG_UCAAUGCGACUAAAAGUGCAACUGGAAUGGCCAUUGAAAUUGCAACUGCAAUUGCAAUUGCAACUGCAACUGCC
(((((((((........((...........))......))))))))).................(((((..((((((....))))))..)))))..... (-13.70 = -15.07 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,551,642 – 9,551,740
Length 98
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 78.48
Mean single sequence MFE -32.78
Consensus MFE -24.46
Energy contribution -26.43
Covariance contribution 1.97
Combinations/Pair 1.20
Mean z-score -3.73
Structure conservation index 0.75
SVM decision value 1.84
SVM RNA-class probability 0.979465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9551642 98 - 27905053
GGCAGUUGCAGUUGCAAUAGCAAUUGCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUCUUAGUCGCAUUGA-CAGUGGCUAUAUGUCAAGUGCAAC
(((.((((.(((((((((.((....)).))))))))).)))).)))......((((((((..(((((((.....-..))))))).......)))))))) ( -38.40)
>DroSec_CAF1 28267 98 - 1
GGCAGUUGCAGUUGCAAUUGCAAUUGCAGUUGCAAUUUCAAUGGCUAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGACUGUAUGUCAAGUGCAAC
(((.((((.((((((((((((....)))))))))))).)))).)))......(((((((((.(((((((.....-..)))))))......))))))))) ( -40.90)
>DroSim_CAF1 28408 98 - 1
GGCAGUUGCAGUUGCAAUUGCAAUUGCAGUUGCAAUUUCAAUGACCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUGUAUGUCAAGUGCAAC
((..((((.((((((((((((....)))))))))))).))))..))......(((((((((.(((((((.....-..)))))))......))))))))) ( -39.90)
>DroEre_CAF1 30011 98 - 1
GGUAGUUGCAGUUGCACUUGCAAUUGCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUAUAUGUCAAGUGCAAC
(((.((((.(((((((.((((....)))).))))))).)))).)))......(((((((((.(((((((.....-..)))))))......))))))))) ( -37.80)
>DroWil_CAF1 32437 80 - 1
GGCAUUCACAA-------------------UGAAAGGCCAAUUCCAAUUCCAGUUCCAGUUUCAGUUGCAACAAUCAGUGGCAGAGUGUCAAGUGCAUU
(((((((....-------------------(((((((..((((........))))))..)))))((..(........)..)).)))))))......... ( -14.70)
>DroYak_CAF1 28689 80 - 1
GGCAGUUGC------------------AGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA-CAGUGGCUACAUGUCAAGUGCAAC
(((((((((------------------....))))))......)))......(((((((((.(((((((.....-..)))))))......))))))))) ( -25.00)
>consensus
GGCAGUUGCAGUUGCAAUUGCAAUUGCAGUUGCAAUUUCAAUGGCCAUUCCAGUUGCACUUUUAGUCGCAUUGA_CAGUGGCUAUAUGUCAAGUGCAAC
.((((((((((((((....))))))))))))))...................(((((((((.(((((((........)))))))......))))))))) (-24.46 = -26.43 +   1.97)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:35 2006