Locus 1900

Sequence ID 3L_DroMel_CAF1
Location 5,323,669 – 5,323,775
Length 106
Max. P 0.831220
window2956 window2957

overview

Window 6

Location 5,323,669 – 5,323,775
Length 106
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.89
Mean single sequence MFE -31.75
Consensus MFE -18.62
Energy contribution -19.91
Covariance contribution 1.28
Combinations/Pair 1.24
Mean z-score -2.41
Structure conservation index 0.59
SVM decision value 0.72
SVM RNA-class probability 0.831220
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5323669 106 + 23771897
AAUUCCGAACGCCACAUGUGGCAUUAAGUGGAA-UAUAGAG-GCAUGUCGAUCACCG-------AACGUGCCACGUGUGUUAUUCAGGAAAUAAUGCCAUCAUUAGCAUAUUGGA
...(((((..((...(((((((((((....(((-((..(.(-((((((((.....))-------.))))))).)......)))))......)))))))).)))..))...))))) ( -31.00)
>DroSec_CAF1 70940 104 + 1
AAUUCCGAACACCACAUGUGGCAUUAAGUGGAA-U--AGAG-GCUUGUCUAUCACCG-------AACGUGCCACGUGUGUUAUUCCGGAAAUAAUGCCAUCAUUAGCGUAUUGGA
..(((((.....((((((((((((....(((.(-(--(((.-.....)))))..)))-------...))))))))))))......))))).(((((((.......).)))))).. ( -32.90)
>DroSim_CAF1 72902 104 + 1
AAUUCCGAACGCCACAUGUGGCAUUAAGUGGAA-U--AGAG-GCUUGUCGAUCACCG-------AACGUGCCACGUGUGUUAUUCCGGAAAUAAUGCCAUCAUUAGCGUAUUGGA
...(((((((((...(((((((((((..(((((-(--((.(-((.(((((.....))-------.))).))).......))))))))....)))))))).)))..)))).))))) ( -33.80)
>DroEre_CAF1 70881 105 + 1
AAUUCCGAAUGCCACAUGUGGCAUUAAGUAGAA-U--AGAGAGCUAUUCGAUCACUG-------AACGCGCCACGUGUGUUAUUAAGGAAAUAAUUCCAUUAUAAGCGUAUUGGA
...(((((((((((((((((((....(((.(((-(--((....))))))....))).-------.....)))))))))).......((((....)))).......)))).))))) ( -33.90)
>DroYak_CAF1 79454 105 + 1
AAUUCCAAACGCCACAUGUGGCAUUAACUAGAA-U--AGAGUGCUUUUCGAUCACUG-------AACGUGCCACGUGUGUUAUGCAGGAAAUAAUGCCAUUAUUAGCGUAUUGGA
...(((((((((((((((((((((....(((..-.--.(((.....))).....)))-------...))))))))))))....(((........)))........)))).))))) ( -32.00)
>DroAna_CAF1 69990 112 + 1
AAUUCGUAGCGCCAAAUGUGGCAUUUGAUGAAAAUGUGGGG-GCUCGACGAUCGGUGUCUUCUUCACGUGCCACGUGAGUGAUCCAGGAAAUAAAUAUAU--UCAAUAUAGUGAA
..(((....(((...(((((((((.(((.........((((-(((((.....))).)))))).))).)))))))))..))).....)))..........(--(((......)))) ( -26.90)
>consensus
AAUUCCGAACGCCACAUGUGGCAUUAAGUGGAA_U__AGAG_GCUUGUCGAUCACCG_______AACGUGCCACGUGUGUUAUUCAGGAAAUAAUGCCAUCAUUAGCGUAUUGGA
...(((((((((((((((((((((..............((...........))..............)))))))))))).......((........)).......)))).))))) (-18.62 = -19.91 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,323,669 – 5,323,775
Length 106
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.89
Mean single sequence MFE -28.65
Consensus MFE -14.93
Energy contribution -16.05
Covariance contribution 1.12
Combinations/Pair 1.27
Mean z-score -2.30
Structure conservation index 0.52
SVM decision value 0.22
SVM RNA-class probability 0.638490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5323669 106 - 23771897
UCCAAUAUGCUAAUGAUGGCAUUAUUUCCUGAAUAACACACGUGGCACGUU-------CGGUGAUCGACAUGC-CUCUAUA-UUCCACUUAAUGCCACAUGUGGCGUUCGGAAUU
(((...(((((((((.((((((((......(((((((....))((((.((.-------((.....)))).)))-)....))-)))....))))))))))).))))))..)))... ( -30.40)
>DroSec_CAF1 70940 104 - 1
UCCAAUACGCUAAUGAUGGCAUUAUUUCCGGAAUAACACACGUGGCACGUU-------CGGUGAUAGACAAGC-CUCU--A-UUCCACUUAAUGCCACAUGUGGUGUUCGGAAUU
........((((....)))).....(((((((....((((.((((((....-------..(..(((((.....-.)))--)-)..)......)))))).))))...))))))).. ( -32.80)
>DroSim_CAF1 72902 104 - 1
UCCAAUACGCUAAUGAUGGCAUUAUUUCCGGAAUAACACACGUGGCACGUU-------CGGUGAUCGACAAGC-CUCU--A-UUCCACUUAAUGCCACAUGUGGCGUUCGGAAUU
(((...(((((((((.((((((((.....((((((((....))(((..((.-------((.....))))..))-)..)--)-))))...))))))))))).))))))..)))... ( -32.90)
>DroEre_CAF1 70881 105 - 1
UCCAAUACGCUUAUAAUGGAAUUAUUUCCUUAAUAACACACGUGGCGCGUU-------CAGUGAUCGAAUAGCUCUCU--A-UUCUACUUAAUGCCACAUGUGGCAUUCGGAAUU
(((.....(.((((...((((....))))...))))).((((((..(((((-------.((((...((((((....))--)-))))))).)))))..))))))......)))... ( -27.20)
>DroYak_CAF1 79454 105 - 1
UCCAAUACGCUAAUAAUGGCAUUAUUUCCUGCAUAACACACGUGGCACGUU-------CAGUGAUCGAAAAGCACUCU--A-UUCUAGUUAAUGCCACAUGUGGCGUUUGGAAUU
(((((.((((((....((((((((.....(((...((....)).)))....-------.((((.........))))..--.-.......))))))))....)))))))))))... ( -28.20)
>DroAna_CAF1 69990 112 - 1
UUCACUAUAUUGA--AUAUAUUUAUUUCCUGGAUCACUCACGUGGCACGUGAAGAAGACACCGAUCGUCGAGC-CCCCACAUUUUCAUCAAAUGCCACAUUUGGCGCUACGAAUU
....(((....((--(((....)))))..)))........((((((..(((((((.(((.......)))(...-...)...))))))).....((((....)))))))))).... ( -20.40)
>consensus
UCCAAUACGCUAAUGAUGGCAUUAUUUCCUGAAUAACACACGUGGCACGUU_______CAGUGAUCGACAAGC_CUCU__A_UUCCACUUAAUGCCACAUGUGGCGUUCGGAAUU
........((((....)))).....((((.((((..((((.((((((.............................................)))))).))))..)))))))).. (-14.93 = -16.05 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:25 2006