Locus 1159

Sequence ID 2R_DroMel_CAF1
Location 4,613,329 – 4,613,449
Length 120
Max. P 0.823492
window2034 window2035

overview

Window 4

Location 4,613,329 – 4,613,449
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.89
Mean single sequence MFE -37.63
Consensus MFE -22.07
Energy contribution -23.52
Covariance contribution 1.45
Combinations/Pair 1.28
Mean z-score -1.78
Structure conservation index 0.59
SVM decision value 0.69
SVM RNA-class probability 0.823492
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4613329 120 + 20766785
UGAACUCCGAAAAUGAGAACUUGCCAUUGGCACAGCACUGUUUUAUUCAGGCUGUAGUGCUGGAAAAAAAGUGCUACACAGCGUGGACCAAUCUCGGAGUUCUCUAUAUUAAACUGAAUG
.(((((((((.....((..((((((...)))).))..))......((((.(((((((..((........))..))..))))).))))......))))))))).................. ( -36.00)
>DroVir_CAF1 3408 120 + 1
UGCACGCCGCCAACGAGAAUCUGCCUGUGGCGCAGCAUUGUUUCAUUCAGGCAGUUGUGCUGGAUCGAAAAUCCUACACGGCCUGGACAAAUCUGGGUGUGCUGUACAUCAAGCUGAACG
.((((((((((.........((((((((((.((......)).)))..)))))))..(((..((((.....))))..))))))..(((....))).))))))).................. ( -38.20)
>DroGri_CAF1 3373 120 + 1
UGUACUCCGCCAGCGAGAAUCUGCCCAUGGCGCAGCAUUGUUUAAUUCAGGCACUGAUGCUGGACCGCAAAUCCUACACAGCAUGGACGAACCUGGGUGUGCUGUACAUAAAGCUGGGCA
........((((((........(((...)))(((((((......(((((((...(.((((((................)))))).).....)))))))))))))).......))).))). ( -34.69)
>DroEre_CAF1 3111 120 + 1
UGCACUCCGAAUAUGAAAACUUGUCAUUGGCACAGCACUGUUUUAUUCAAGCUGUGGAGCUCGAAAGAAAGUGCUACACAGCGUGGACCAAUCUCGGAGUGCUCUAUAUUAAACUAAAUG
.(((((((((...(((.......)))((((.(((....)))....((((.((((((.(((((....))....))).)))))).))))))))..))))))))).................. ( -37.70)
>DroYak_CAF1 3064 120 + 1
UGCACUCCGAAUAUGAGAACUUGCCAUUGGCCCAGCACUGUUUUAUUCAGGCUGUGGAACUAGAAAGAAAGUGCUACACAGCGUGGACCAAUCUCGGAGUGCUUUAUAUUAAACUAAAAG
.(((((((((.....(((((.(((..........)))..))))).((((.((((((..(((........)))....)))))).))))......))))))))).................. ( -36.60)
>DroAna_CAF1 3084 120 + 1
UGCACUCGGAUCACGAAAACUUGCCGUUGGCCCAGCACUGUUUCAUACAGGCCGUGGAGCUGGAACGAAAGUGUUUCACGGCCUGGACGAACCUCGGGGUUCUGUACGUAAAAAUAGACA
(((..(((.....)))......(((...)))...)))((((((....(((((((((((((....((....)))))))))))))))...(((((....))))).........))))))... ( -42.60)
>consensus
UGCACUCCGAAAACGAGAACUUGCCAUUGGCACAGCACUGUUUUAUUCAGGCUGUGGAGCUGGAAAGAAAGUGCUACACAGCGUGGACCAAUCUCGGAGUGCUGUACAUUAAACUAAACG
.(((((((((............(((...)))..............((((.((((((..(((........)))....)))))).))))......))))))))).................. (-22.07 = -23.52 +   1.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,613,329 – 4,613,449
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.89
Mean single sequence MFE -38.12
Consensus MFE -17.06
Energy contribution -17.84
Covariance contribution 0.78
Combinations/Pair 1.32
Mean z-score -2.07
Structure conservation index 0.45
SVM decision value 0.21
SVM RNA-class probability 0.635497
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4613329 120 - 20766785
CAUUCAGUUUAAUAUAGAGAACUCCGAGAUUGGUCCACGCUGUGUAGCACUUUUUUUCCAGCACUACAGCCUGAAUAAAACAGUGCUGUGCCAAUGGCAAGUUCUCAUUUUCGGAGUUCA
..................(((((((((((.(((..(..((((..(((((((.((((..((((......).)))...)))).)))))))..)....)))..)..).)).))))))))))). ( -37.80)
>DroVir_CAF1 3408 120 - 1
CGUUCAGCUUGAUGUACAGCACACCCAGAUUUGUCCAGGCCGUGUAGGAUUUUCGAUCCAGCACAACUGCCUGAAUGAAACAAUGCUGCGCCACAGGCAGAUUCUCGUUGGCGGCGUGCA
.((.((......)).)).((((.....(.((..(.(((((.((((.(((((...))))).))))....))))).)..)).)...((((((((...))).(.....)....))))))))). ( -36.70)
>DroGri_CAF1 3373 120 - 1
UGCCCAGCUUUAUGUACAGCACACCCAGGUUCGUCCAUGCUGUGUAGGAUUUGCGGUCCAGCAUCAGUGCCUGAAUUAAACAAUGCUGCGCCAUGGGCAGAUUCUCGCUGGCGGAGUACA
.(((.(((......(((((((......((.....)).))))))).((((((((((((.((((((..((...........)).)))))).)))....))))))))).))))))........ ( -35.30)
>DroEre_CAF1 3111 120 - 1
CAUUUAGUUUAAUAUAGAGCACUCCGAGAUUGGUCCACGCUGUGUAGCACUUUCUUUCGAGCUCCACAGCUUGAAUAAAACAGUGCUGUGCCAAUGACAAGUUUUCAUAUUCGGAGUGCA
..................((((((((((.............(..(((((((((..((((((((....))))))))..))..)))))))..)..((((.......)))).)))))))))). ( -40.40)
>DroYak_CAF1 3064 120 - 1
CUUUUAGUUUAAUAUAAAGCACUCCGAGAUUGGUCCACGCUGUGUAGCACUUUCUUUCUAGUUCCACAGCCUGAAUAAAACAGUGCUGGGCCAAUGGCAAGUUCUCAUAUUCGGAGUGCA
..................((((((((((((((((((((((((((.(((............))).))))))(((.......))).).))))))))).....(....)...)))))))))). ( -39.60)
>DroAna_CAF1 3084 120 - 1
UGUCUAUUUUUACGUACAGAACCCCGAGGUUCGUCCAGGCCGUGAAACACUUUCGUUCCAGCUCCACGGCCUGUAUGAAACAGUGCUGGGCCAACGGCAAGUUUUCGUGAUCCGAGUGCA
.............((((.(((((....)))))...(((((((((....................)))))))))(((((((...(((((......)))))...)))))))......)))). ( -38.95)
>consensus
CGUUCAGUUUAAUAUACAGCACUCCGAGAUUGGUCCACGCUGUGUAGCACUUUCGUUCCAGCACCACAGCCUGAAUAAAACAGUGCUGCGCCAAUGGCAAGUUCUCAUUUUCGGAGUGCA
..................((((.((((((((.(((......((((((((((....(((..(((....)))..)))......))))))))))....))).)))).......)))).)))). (-17.06 = -17.84 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:56 2006