Locus 4568

Sequence ID 2R_DroMel_CAF1
Location 14,931,445 – 14,931,577
Length 132
Max. P 0.999933
window7317 window7318 window7319 window7320

overview

Window 7

Location 14,931,445 – 14,931,540
Length 95
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 77.32
Mean single sequence MFE -38.82
Consensus MFE -33.32
Energy contribution -32.44
Covariance contribution -0.88
Combinations/Pair 1.23
Mean z-score -2.53
Structure conservation index 0.86
SVM decision value 3.38
SVM RNA-class probability 0.999114
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14931445 95 + 20766785
GCCGCGUGGAAACAUUUC-CCGGCCGGCAAAUCGU----AUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCAUCAAAAU--------UGCAUGGCAA
((((((.((((....)))-)))..)))).......----.(((((((((((((..............)))))))))))))((((((....--------)).))))... ( -38.54)
>DroYak_CAF1 17830 95 + 1
GCCGCGUGGAAGCAUUUC-CCGGCCGGCAAACCGUAUGUAUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCA----AAU--------UGCAUGGCAA
((((((.((((....)))-)))..)))).....((((((((((((((((((((..............)))))))))))))...----...--------))))).)).. ( -37.94)
>DroAna_CAF1 17627 105 + 1
GUCGCGUGGAAACAUUUCUCCGGCCGGCAUACUCUGU---UCGGUGGCGCCACCAUUCUGUCCUUUUAUGGCGCCACCGGCCGCCCAAAUAAUAGCCUGGCAUGGCAA
...(((((....)))......((((((((.....)))---).((((((((((................))))))))))))))))..........(((......))).. ( -39.99)
>consensus
GCCGCGUGGAAACAUUUC_CCGGCCGGCAAACCGU_U__AUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCA_C_AAAU________UGCAUGGCAA
((((((((....)))......((.(((....)))......(((((((((((((..............))))))))))))))).................))..))).. (-33.32 = -32.44 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,931,445 – 14,931,540
Length 95
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 77.32
Mean single sequence MFE -40.35
Consensus MFE -30.57
Energy contribution -30.47
Covariance contribution -0.10
Combinations/Pair 1.18
Mean z-score -2.30
Structure conservation index 0.76
SVM decision value 2.58
SVM RNA-class probability 0.995486
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14931445 95 - 20766785
UUGCCAUGCA--------AUUUUGAUGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAU----ACGAUUUGCCGGCCGG-GAAAUGUUUCCACGCGGC
..(((..(((--------(..(((...(((((.((((((((...((......)).)))))))).)))))----.))).))))..((..(-(((....))))..))))) ( -38.00)
>DroYak_CAF1 17830 95 - 1
UUGCCAUGCA--------AUU----UGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAUACAUACGGUUUGCCGGCCGG-GAAAUGCUUCCACGCGGC
..(((..((.--------...----((((((((((((((((...((......)).))))))))(((.........)))..))))))))(-(((....))))..))))) ( -39.80)
>DroAna_CAF1 17627 105 - 1
UUGCCAUGCCAGGCUAUUAUUUGGGCGGCCGGUGGCGCCAUAAAAGGACAGAAUGGUGGCGCCACCGA---ACAGAGUAUGCCGGCCGGAGAAAUGUUUCCACGCGAC
((((...(((.(((...(((((....(..((((((((((((..............)))))))))))).---.).))))).)))))).(((((....)))))..)))). ( -43.24)
>consensus
UUGCCAUGCA________AUUU_G_UGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAU__A_ACGGUUUGCCGGCCGG_GAAAUGUUUCCACGCGGC
......(((................((((((((((((((((...((......)).))))))))(((.........)))..))))))))(.(((....))))..))).. (-30.57 = -30.47 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,931,479 – 14,931,577
Length 98
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 75.16
Mean single sequence MFE -33.82
Consensus MFE -30.42
Energy contribution -29.87
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -2.87
Structure conservation index 0.90
SVM decision value 4.64
SVM RNA-class probability 0.999933
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14931479 98 + 20766785
-AUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCAUCAAAAU--------UGCAUGGCAACACG---ACGAUAAUGAAAAUGCCGGCCACGAAAAGGAAA
-.(((((((((((((..............)))))))))))))((.(((..((--------(((.((....)).)---.))))..)))......((....))....))... ( -33.34)
>DroYak_CAF1 17867 95 + 1
UAUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCA----AAU--------UGCAUGGCAACACG---AUGGUAAUGAAAAUGCCGGCCACAAAAAUGAAA
..(((((((((((((..............)))))))))))))((.----.((--------((..((....))))---))((((.(....))))))).............. ( -31.64)
>DroAna_CAF1 17664 102 + 1
--UCGGUGGCGCCACCAUUCUGUCCUUUUAUGGCGCCACCGGCCGCCCAAAUAAUAGCCUGGCAUGGCAACACACGAAUGGUAAUGAAAAUGCCGGCAACGAAA------
--.(((((((((((................)))))))))))(((............(((......)))...........((((.(....)))))))).......------ ( -36.49)
>consensus
_AUUGGUGGCGCCACCAUUCCGGCAUUUUGUGGCGCCGCCAACCA_C_AAAU________UGCAUGGCAACACG___AUGGUAAUGAAAAUGCCGGCCACGAAAA_GAAA
..(((((((((((((..............)))))))))))))...................((.(((((.....................)))))))............. (-30.42 = -29.87 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,931,479 – 14,931,577
Length 98
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 75.16
Mean single sequence MFE -36.42
Consensus MFE -28.44
Energy contribution -28.89
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -2.56
Structure conservation index 0.78
SVM decision value 4.03
SVM RNA-class probability 0.999766
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14931479 98 - 20766785
UUUCCUUUUCGUGGCCGGCAUUUUCAUUAUCGU---CGUGUUGCCAUGCA--------AUUUUGAUGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAU-
..............((((((((((......(((---(((...(((((.((--------....)))))))..))))))....))))))))))..(((((....)))))..- ( -35.70)
>DroYak_CAF1 17867 95 - 1
UUUCAUUUUUGUGGCCGGCAUUUUCAUUACCAU---CGUGUUGCCAUGCA--------AUU----UGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAUA
..((((....))))((((((((((.........---.(((((((((.((.--------...----..)))))))))))...))))))))))..(((((....)))))... ( -33.52)
>DroAna_CAF1 17664 102 - 1
------UUUCGUUGCCGGCAUUUUCAUUACCAUUCGUGUGUUGCCAUGCCAGGCUAUUAUUUGGGCGGCCGGUGGCGCCAUAAAAGGACAGAAUGGUGGCGCCACCGA--
------....((((((((((....(((........)))...))))....((((......))))))))))((((((((((((..............)))))))))))).-- ( -40.04)
>consensus
UUUC_UUUUCGUGGCCGGCAUUUUCAUUACCAU___CGUGUUGCCAUGCA________AUUU_G_UGGUUGGCGGCGCCACAAAAUGCCGGAAUGGUGGCGCCACCAAU_
.........((((((.(((((................)))))))))))...................(((((.((((((((...((......)).)))))))).))))). (-28.44 = -28.89 +   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 11:23:15 2006