Locus 1701

Sequence ID 3L_DroMel_CAF1
Location 4,963,242 – 4,963,406
Length 164
Max. P 0.773607
window2625 window2626

overview

Window 5

Location 4,963,242 – 4,963,332
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 72.70
Mean single sequence MFE -15.50
Consensus MFE -8.81
Energy contribution -9.01
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.57
SVM decision value 0.24
SVM RNA-class probability 0.648590
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4963242 90 + 23771897
UUCUGGAUCUGGAUACACUCAUAUAUCCAUCUCGCUGUGUGUAUGCGGCUCUGUCAGCCUAGCGACCCAGCCCCGAAAAAAACCCAACCC
(((.((...((((((........))))))....((((.(.((.(((((((.....))))..)))))))))))).)))............. ( -20.90)
>DroSec_CAF1 184022 71 + 1
-----GAUCUGGAUACACUCAUAUAUCCAUCUCGCUGUGU------------GUCAGCCUAGCGACCCAACCCCGAA--AAACCCUACCC
-----....((((((........))))))..((((((.((------------....)).))))))............--........... ( -12.90)
>DroSim_CAF1 203197 76 + 1
UUCUGGAUCUGGAUACACUCAUAUAUCCAUCUCGCUGUGU------------GUCAGCCUAGCGACCCAGCCCCGAA--AAACCCUACCC
..((((...((((((........))))))..((((((.((------------....)).)))))).)))).......--........... ( -17.70)
>DroEre_CAF1 185132 73 + 1
CUCUGGAUCUGGAUACACUCAUAUAUCCAUCUCGCUGUAUG--UGCGGCUCUGUCAGCCC---CG-AAAAA-----------CCCUACCC
..(((((..((((((........))))))..))(((((...--.))))).....)))...---..-.....-----------........ ( -13.90)
>DroYak_CAF1 190605 74 + 1
UUCUGGUGCUGGAUACACUCAUAUAUCCAUCUCGCUGU--------------GUCAGCCUAGCCAAAAAGACCCCAU--ACCCCAUACCC
...((((..((((((........))))))....((((.--------------..))))...))))............--........... ( -12.10)
>consensus
UUCUGGAUCUGGAUACACUCAUAUAUCCAUCUCGCUGUGU____________GUCAGCCUAGCGACCCAGCCCCGAA__AAACCCUACCC
.....((..((((((........))))))..))((((.................))))................................ ( -8.81 =  -9.01 +   0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 6

Location 4,963,300 – 4,963,406
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.13
Mean single sequence MFE -23.57
Consensus MFE -21.26
Energy contribution -21.65
Covariance contribution 0.39
Combinations/Pair 1.09
Mean z-score -1.39
Structure conservation index 0.90
SVM decision value 0.54
SVM RNA-class probability 0.773607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4963300 106 + 23771897
--------CUAGCGACCCAGCCCCGAAAAAAACCCAACCC---CAUACUGACAUCCACCGCAUU-UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG--
--------...((......))...................---.....((((((..........-.))))))...(.((((((((((..((.(((.....))))))))))))))).).-- ( -25.10)
>DroPse_CAF1 236229 108 + 1
CCACAUCUCUGGCUACUCAU------------CCGUACUCCUUCCUCCUCAUCUCCACCGCAUUUUGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUCUCUGAC
..........((.(((....------------..)))..)).......(((.......(((.....)))..........((((((((..((.(((.....)))))))))))))...))). ( -19.30)
>DroSec_CAF1 184063 104 + 1
--------CUAGCGACCCAACCCCGAA--AAACCCUACCC---CAUACUGACAUCCACCGCAUU-UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG--
--------...................--...........---.....((((((..........-.))))))...(.((((((((((..((.(((.....))))))))))))))).).-- ( -23.90)
>DroSim_CAF1 203243 104 + 1
--------CUAGCGACCCAGCCCCGAA--AAACCCUACCC---CAUACUGACAUCCACCGCAUU-UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG--
--------...((......))......--...........---.....((((((..........-.))))))...(.((((((((((..((.(((.....))))))))))))))).).-- ( -25.10)
>DroEre_CAF1 185188 91 + 1
--------CC---CG-AAAAA-----------CCCUACCC---CGCACUGACAUCCACCGCAUU-UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG--
--------..---..-.....-----------........---.(((.((((((..........-.))))))..)))((((((((((..((.(((.....)))))))))))))))...-- ( -24.10)
>DroYak_CAF1 190649 104 + 1
--------CUAGCCAAAAAGACCCCAU--ACCCCAUACCC---CCUACUGACAUCCACCGCAUU-UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG--
--------...................--...........---.....((((((..........-.))))))...(.((((((((((..((.(((.....))))))))))))))).).-- ( -23.90)
>consensus
________CUAGCGACCCAGCCCCGAA__AAACCCUACCC___CAUACUGACAUCCACCGCAUU_UGUGUCAUUUGUUUAGCUGUCAUUGCCGGCGUAUUGCCGCUGACAGCUAACCG__
................................................((((((............))))))...(.((((((((((..((.(((.....))))))))))))))).)... (-21.26 = -21.65 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:02 2006