Locus 649

Sequence ID 3L_DroMel_CAF1
Location 1,929,667 – 1,929,784
Length 117
Max. P 0.779006
window991 window992 window993

overview

Window 1

Location 1,929,667 – 1,929,765
Length 98
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -30.51
Consensus MFE -21.95
Energy contribution -22.12
Covariance contribution 0.17
Combinations/Pair 1.25
Mean z-score -1.77
Structure conservation index 0.72
SVM decision value 0.55
SVM RNA-class probability 0.779006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1929667 98 - 23771897
AAUACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACGAUUGAGACCCCCACUGCCACUCCUGAC----ACGAAUA---------GUCAGGA
....(((....(((((((((((.(((((((...))))))).)).)).)))))))....)))................(((((((----.......---------))))))) ( -31.70)
>DroSec_CAF1 51797 107 - 1
AAUACAAAUACCGCCACACCACAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCACUGCCACUCCUGAC----ACGAAUAGCCCAUCUAGUCAGGA
......(((.((((((.((....)).)))))).))).......((((.((((.(...........).)))).)))).(((((((----..((........))..))))))) ( -30.30)
>DroSim_CAF1 52209 107 - 1
AAUACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCACUGCCACUCCUGAC----ACGAAUAGCCCAUCUAGUCAGGA
....(((....(((((((((((.(((((((...))))))).)).)).)))))))....)))................(((((((----..((........))..))))))) ( -31.30)
>DroEre_CAF1 53688 107 - 1
AAAACGAAUACCGCCACACCGCAGUUUAACGGCGUUAAACAGCUGGUUGUGGCGACAAUUGAGACUCCUACUGCCACACCGGAC----ACAGACAAAUCAUCUAGUCAGGA
..........((((((((((((.(((((((...))))))).)).)).))))))(((...(((...........((.....))..----.........)))....))).)). ( -28.35)
>DroYak_CAF1 53232 107 - 1
AAAACGAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACUCCCACUGCCACUCCUGAC----ACAGAUAACUCAUCUAGUCAAGA
......(((.((((((.((....)).)))))).))).......((((.((((.((..........)))))).)))).((.((((----..((((.....)))).)))).)) ( -27.20)
>DroAna_CAF1 55925 108 - 1
--AUCAAAUGCCAGCACACCACAGCUUUGCGGGGCAAAGCAUCUGGUUGUGGCCACAAUAGAGACUCCAAGGCCAACUCCUGACGAACAGGAAGAGA-GUGCUAGUAAAGA
--......(((.(((((((((..(((((((...)))))))...))))..(((((................)))))..(((((.....))))).....-))))).))).... ( -34.19)
>consensus
AAAACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCACUGCCACUCCUGAC____ACGAAUAGC_CAUCUAGUCAGGA
...........((((((((((..(((((((...)))))))...))).))))))).......................(((((((....................))))))) (-21.95 = -22.12 +   0.17) 

alignment

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secondary structure

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Window 2

Location 1,929,694 – 1,929,784
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 81.93
Mean single sequence MFE -29.13
Consensus MFE -21.16
Energy contribution -21.97
Covariance contribution 0.81
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.73
SVM decision value 0.01
SVM RNA-class probability 0.536357
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1929694 90 + 23771897
GUGGGGGUCUCAAUCGUCGCCACAACCAGCUGUUUAACUCCGCCAAACUGCGGUGUGGCGGUAUUUGUAUUGUCCGCAGGACGAACGAAC
((((.((.(......))).)))).....(((((...((.((((......)))).)).))))).(((((.((((((...))))))))))). ( -28.30)
>DroSec_CAF1 51833 90 + 1
GUGGGGGUCUCAAUUGUCGCCACAACCAGCUGUUUAACUCCGCCAAACUGUGGUGUGGCGGUAUUUGUAUUGUCCGCAGGACGAACGAAC
(((((.(...(((.(..(((((((.(((.(.((((.........)))).)))))))))))..).)))...).)))))............. ( -28.70)
>DroSim_CAF1 52245 90 + 1
GUGGGGGUCUCAAUUGUCGCCACAACCAGCUGUUUAACUCCGCCAAACUGCGGUGUGGCGGUAUUUGUAUUGUCCGCAGGACGAACGAAC
(((((.(...(((.(..(((((((.((.((.((((.........)))).)))))))))))..).)))...).)))))............. ( -30.20)
>DroEre_CAF1 53724 90 + 1
GUAGGAGUCUCAAUUGUCGCCACAACCAGCUGUUUAACGCCGUUAAACUGCGGUGUGGCGGUAUUCGUUUUGUCCGCAGGACGAACGAAG
..............(..(((((((.((.((.(((((((...))))))).)))))))))))..)(((((((.((((...))))))))))). ( -34.50)
>DroYak_CAF1 53268 90 + 1
GUGGGAGUCUCAAUUGUCGCCACAACCAGCUGUUUAACUCCGCCAAACUGCGGUGUGGCGGUAUUCGUUUUGUCCGUAGGACGAACGAAC
.((((...))))..(..(((((((.((.((.((((.........)))).)))))))))))..)(((((((.((((...))))))))))). ( -29.90)
>DroAna_CAF1 55964 69 + 1
CUUGGAGUCUCUAUUGUGGCCACAACCAGAUGCUUUGCCCCGCAAAGCUGUGGUGUGCUGGCAUUUGAU---------------------
.(((..(((.(....).)))..))).((((((((..((((((((....))))).).)).))))))))..--------------------- ( -23.20)
>consensus
GUGGGAGUCUCAAUUGUCGCCACAACCAGCUGUUUAACUCCGCCAAACUGCGGUGUGGCGGUAUUUGUAUUGUCCGCAGGACGAACGAAC
..............((((((((((.((.((.((((.........)))).))))))))))))))(((((.((((((...))))))))))). (-21.16 = -21.97 +   0.81) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,929,694 – 1,929,784
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 81.93
Mean single sequence MFE -27.50
Consensus MFE -22.95
Energy contribution -22.50
Covariance contribution -0.45
Combinations/Pair 1.27
Mean z-score -1.59
Structure conservation index 0.83
SVM decision value 0.47
SVM RNA-class probability 0.747871
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1929694 90 - 23771897
GUUCGUUCGUCCUGCGGACAAUACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACGAUUGAGACCCCCAC
.((((.((((((...))))...........(((((((((((.(((((((...))))))).)).)).)))))))..)).))))........ ( -29.00)
>DroSec_CAF1 51833 90 - 1
GUUCGUUCGUCCUGCGGACAAUACAAAUACCGCCACACCACAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCAC
((((((.......))))))....(((....(((((((((((.(((((((...))))))).).))).)))))))....))).......... ( -27.00)
>DroSim_CAF1 52245 90 - 1
GUUCGUUCGUCCUGCGGACAAUACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCAC
((((((.......))))))....(((....(((((((((((.(((((((...))))))).)).)).)))))))....))).......... ( -28.50)
>DroEre_CAF1 53724 90 - 1
CUUCGUUCGUCCUGCGGACAAAACGAAUACCGCCACACCGCAGUUUAACGGCGUUAAACAGCUGGUUGUGGCGACAAUUGAGACUCCUAC
.((((((.((((...))))..))))))...(((((((((((.(((((((...))))))).)).)).)))))))................. ( -30.30)
>DroYak_CAF1 53268 90 - 1
GUUCGUUCGUCCUACGGACAAAACGAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACUCCCAC
(((((((.((((...))))..)))))))..(((((((((((.(((((((...))))))).)).)).)))))))................. ( -31.30)
>DroAna_CAF1 55964 69 - 1
---------------------AUCAAAUGCCAGCACACCACAGCUUUGCGGGGCAAAGCAUCUGGUUGUGGCCACAAUAGAGACUCCAAG
---------------------.......((((.((.((((..(((((((...)))))))...)))))))))).................. ( -18.90)
>consensus
GUUCGUUCGUCCUGCGGACAAAACAAAUACCGCCACACCGCAGUUUGGCGGAGUUAAACAGCUGGUUGUGGCGACAAUUGAGACCCCCAC
....(((((.....)))))...........((((((((((..(((((((...)))))))...))).)))))))................. (-22.95 = -22.50 +  -0.45) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:37 2006