Locus 5522

Sequence ID 3L_DroMel_CAF1
Location 15,163,548 – 15,163,661
Length 113
Max. P 0.861987
window8723 window8724

overview

Window 3

Location 15,163,548 – 15,163,661
Length 113
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.08
Mean single sequence MFE -37.13
Consensus MFE -26.73
Energy contribution -27.30
Covariance contribution 0.57
Combinations/Pair 1.26
Mean z-score -1.64
Structure conservation index 0.72
SVM decision value 0.83
SVM RNA-class probability 0.861987
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15163548 113 + 23771897
GAGUCAAGUGUCUGAGUACGAGACACUCGAGUGACGUUGAGCCGGCCUACUGGUGGGUAGAUGUCGGUCAAUAGCUAUAUGUCCGGCGAACAUAUGUGCGUUGUAGACCCUGA
.(.((.(((((((.......))))))).)).)((((((..(((.(((....))).))).))))))((((.((((((((((((.......)))))))...))))).)))).... ( -39.90)
>DroSec_CAF1 53249 113 + 1
GAGUCAAGUGCCUGAGUACGAGACACUCGAGUGACGUUGAGCCGGCCUACUGGUGGGUAGAUGUCGGUCAAUAGCUAUAUGUCCGGCGAACAUAUGUGCGUUGUAGACCUUGA
..(((..((((....))))..)))..((((..((((((..(((.(((....))).))).))))))((((.((((((((((((.......)))))))...))))).)))))))) ( -37.90)
>DroSim_CAF1 54530 112 + 1
GAGUCAAGUGUCUGAGUACGAGACACUCGAGUGACGUUGAGCCGGCCUACUGGUGGGUAGAUGUCGGUCAAUAGCUAUAUGUCCGGCGAACAUAUGUGCGUC-AAGACCUUGA
...(((((.((((((((.......))))((.(((((((..(((.(((....))).))).))))))).))....(((((((((.......))))))).))...-.))))))))) ( -39.80)
>DroEre_CAF1 54287 106 + 1
GAGUCAAGUGUCUC------AGACACUCGAGUGACGUUGAGCCGGCCUACUGGUGGGUAGAUGUCGGUCAAUGGUUAUGUGUCCGCUGGACAUAUGUGCGUUG-GGACCUUGA
...(((((.(((((------((.(((..((.(((((((..(((.(((....))).))).))))))).)).......((((((((...)))))))))))..)))-))))))))) ( -45.70)
>DroYak_CAF1 54595 106 + 1
GAGUCAAGUGCCUG------AGACACUCGAGUGACGUUGAGUCGGCCUACUGGUGGGUAGAUGUCGGUCACUGGUAAUGUGUCCGAUGAACAUAUGUGCGUUG-GGACCUUGA
...(((((..((..------.(((((.(.((((((.....(((.(((((....))))).)))....)))))).)....)))))(((((.((....)).)))))-))..))))) ( -36.60)
>DroAna_CAF1 49507 87 + 1
GAGUGGACUGUUU-----UGAGAUACUCAAGUGACGUUGAGCUGGUCUACUGGUGGGCCGAUGUCUG-----------AUGUCUCUCUAAU---------UUA-CGACCUUGU
(((.((((...((-----((((...)))))).(((((((.(((..((....))..))))))))))..-----------..)))))))....---------...-......... ( -22.90)
>consensus
GAGUCAAGUGUCUG____CGAGACACUCGAGUGACGUUGAGCCGGCCUACUGGUGGGUAGAUGUCGGUCAAUAGCUAUAUGUCCGGCGAACAUAUGUGCGUUG_AGACCUUGA
.(.((.(((((((.......))))))).)).)((((((..(((.(((....))).))).))))))((((....(((((((((.......))))))).))......)))).... (-26.73 = -27.30 +   0.57)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 15,163,548 – 15,163,661
Length 113
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.08
Mean single sequence MFE -27.32
Consensus MFE -17.01
Energy contribution -17.43
Covariance contribution 0.42
Combinations/Pair 1.25
Mean z-score -1.51
Structure conservation index 0.62
SVM decision value 0.19
SVM RNA-class probability 0.625438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15163548 113 - 23771897
UCAGGGUCUACAACGCACAUAUGUUCGCCGGACAUAUAGCUAUUGACCGACAUCUACCCACCAGUAGGCCGGCUCAACGUCACUCGAGUGUCUCGUACUCAGACACUUGACUC
....(((((((...((..(((((((.....))))))).))....((......)).........)))))))(((.....)))..((((((((((.......))))))))))... ( -31.60)
>DroSec_CAF1 53249 113 - 1
UCAAGGUCUACAACGCACAUAUGUUCGCCGGACAUAUAGCUAUUGACCGACAUCUACCCACCAGUAGGCCGGCUCAACGUCACUCGAGUGUCUCGUACUCAGGCACUUGACUC
....(((((((...((..(((((((.....))))))).))....((......)).........)))))))(((.....)))..((((((((((.......))))))))))... ( -31.20)
>DroSim_CAF1 54530 112 - 1
UCAAGGUCUU-GACGCACAUAUGUUCGCCGGACAUAUAGCUAUUGACCGACAUCUACCCACCAGUAGGCCGGCUCAACGUCACUCGAGUGUCUCGUACUCAGACACUUGACUC
((((((((((-(((((..(((((((.....))))))).))..(((((((...(((((......))))).))).)))).))))...(((((.....))))))))).)))))... ( -34.00)
>DroEre_CAF1 54287 106 - 1
UCAAGGUCC-CAACGCACAUAUGUCCAGCGGACACAUAACCAUUGACCGACAUCUACCCACCAGUAGGCCGGCUCAACGUCACUCGAGUGUCU------GAGACACUUGACUC
((((((((.-((.(((...........)))(((((.......(((((((...(((((......))))).))).))))((.....)).))))))------).))).)))))... ( -28.10)
>DroYak_CAF1 54595 106 - 1
UCAAGGUCC-CAACGCACAUAUGUUCAUCGGACACAUUACCAGUGACCGACAUCUACCCACCAGUAGGCCGACUCAACGUCACUCGAGUGUCU------CAGGCACUUGACUC
....(((..-.................((((.(((.......))).))))...((((......)))))))(((.....)))..((((((((..------...))))))))... ( -25.80)
>DroAna_CAF1 49507 87 - 1
ACAAGGUCG-UAA---------AUUAGAGAGACAU-----------CAGACAUCGGCCCACCAGUAGACCAGCUCAACGUCACUUGAGUAUCUCA-----AAACAGUCCACUC
....((((.-...---------....((......)-----------).......((....))....)))).((((((......))))))......-----............. ( -13.20)
>consensus
UCAAGGUCU_CAACGCACAUAUGUUCGCCGGACAUAUAGCUAUUGACCGACAUCUACCCACCAGUAGGCCGGCUCAACGUCACUCGAGUGUCUCG____CAGACACUUGACUC
....((((.............((((.....))))....................(((......)))))))(((.....)))..((((((((((.......))))))))))... (-17.01 = -17.43 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:18 2006