Locus 5338

Sequence ID 2L_DroMel_CAF1
Location 15,117,940 – 15,118,077
Length 137
Max. P 0.658983
window8476 window8477 window8478

overview

Window 6

Location 15,117,940 – 15,118,039
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 77.63
Mean single sequence MFE -14.66
Consensus MFE -11.86
Energy contribution -12.66
Covariance contribution 0.80
Combinations/Pair 1.20
Mean z-score -1.15
Structure conservation index 0.81
SVM decision value 0.26
SVM RNA-class probability 0.658983
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15117940 99 - 22407834
GCUAGCUAGCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAAAAAACCACCUACCCACCUACCCCGCAUCCACCACC
(((((....)))))..(((((.((((.(....).)))).)))))....................................................... ( -16.70)
>DroSec_CAF1 62732 82 - 1
GCUA----GCUAGCGAGCAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG----CAACCU--------ACCC-CCAUCCACCACC
(((.----...)))..(((((.((((.(....).)))).)))))....................----......--------....-............ ( -11.70)
>DroSim_CAF1 60419 82 - 1
GCUA----GCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG----CAACCU--------ACCC-CCAUCCACCACC
(((.----...)))..(((((.((((.(....).)))).)))))....................----......--------....-............ ( -11.40)
>DroEre_CAF1 63741 85 - 1
GCUGGCUAGCUAGCAAGCGGGCUAGACCUGUCGCUCUGUCCUGUAAA-CCAGCCAAAGGGAAAU-----CACCCA-------CCCA-CCAGCCACCACC
(((((...(((.(...(((((.((((.(....).)))).)))))...-).)))....(((....-----..))).-------....-)))))....... ( -23.30)
>DroYak_CAF1 77673 80 - 1
GCUAGCUAGCGAGCGA---GGCUAGACCUGUCGUUCUGUCCUGCAAAUCCACCCAAA---AAAC-----CACCUA-------CCUA-CCACCCACCACC
(((....)))..((.(---((.((((.(....).)))).))))).............---....-----......-------....-............ ( -10.20)
>consensus
GCUAGCUAGCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG____CCACCUA_______ACCC_CCAUCCACCACC
(((((....)))))..(((((.((((.(....).)))).)))))....................................................... (-11.86 = -12.66 +   0.80)

alignment

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secondary structure

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Window 7

Location 15,117,959 – 15,118,077
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 84.02
Mean single sequence MFE -30.14
Consensus MFE -20.32
Energy contribution -21.60
Covariance contribution 1.28
Combinations/Pair 1.09
Mean z-score -1.64
Structure conservation index 0.67
SVM decision value -0.04
SVM RNA-class probability 0.513758
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15117959 118 + 22407834
GUGGGUAGGUGGUUUUUUUUUUUUUUGGUUGGUUUUACAGGACAGAACGACAGGUCUAGCCUGUUCGCUAGCUAGCUAGCUAGUUUGUGUGUUGCAGAAAUUUACUGUAAAAUACAAU
.....(((.((((............((((((((...(((((..(((.(....).)))..)))))..)))))))))))).)))..((((((.((((((.......)))))).)))))). ( -32.20)
>DroSec_CAF1 62748 104 + 1
------AGGUUG----CUUUUUUUUUGGUUGGUUUUACAGGACAGAACGACAGGUCUAGCCUGCUCGCUAGC----UAGCUAGUUUGUGUGUUGCACAAAUUUACUGUAAAAUACAAU
------......----...........(((((((((((((.......(((((((.....)))).)))((((.----...))))((((((.....))))))....))))))))).)))) ( -27.00)
>DroSim_CAF1 60435 104 + 1
------AGGUUG----CUUUUUUUUUGGUUGGUUUUACAGGACAGAACGACAGGUCUAGCCUGUUCGCUAGC----UAGCUAGUUUGUGUGUUGCACAAAUUUACUGUAAAAUACAAU
------......----...........(((((((((((((........((((((.....)))))).(((((.----...)))))(((((.....))))).....))))))))).)))) ( -27.20)
>DroEre_CAF1 63757 107 + 1
-----UGGGUG-----AUUUCCCUUUGGCUGG-UUUACAGGACAGAGCGACAGGUCUAGCCCGCUUGCUAGCUAGCCAGCUAGUUUGUGUGCUGCAGAAAUUUACUGUAAAAUACAAU
-----.(((..-----....))).((((((((-((..(.((...(((((...((.....))))))).)).)..)))))))))).((((((..(((((.......)))))..)))))). ( -35.80)
>DroYak_CAF1 77689 102 + 1
-----UAGGUG-----GUUU---UUUGGGUGGAUUUGCAGGACAGAACGACAGGUCUAGCC---UCGCUCGCUAGCUAGCUAGUUUGUGUGUUGCAGCAAUUUACUGUAAAAUACAAU
-----(((.((-----((..---...((.((((((((..(.......)..)))))))).))---......)))).)))......((((((.((((((.......)))))).)))))). ( -28.50)
>consensus
_____UAGGUGG____CUUUUUUUUUGGUUGGUUUUACAGGACAGAACGACAGGUCUAGCCUGCUCGCUAGCUAGCUAGCUAGUUUGUGUGUUGCAGAAAUUUACUGUAAAAUACAAU
......................(((((.(((......)))..))))).((((((.....)))).))((((((......))))))((((((.((((((.......)))))).)))))). (-20.32 = -21.60 +   1.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,117,959 – 15,118,077
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 84.02
Mean single sequence MFE -22.04
Consensus MFE -14.52
Energy contribution -15.04
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.79
Structure conservation index 0.66
SVM decision value 0.09
SVM RNA-class probability 0.578150
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15117959 118 - 22407834
AUUGUAUUUUACAGUAAAUUUCUGCAACACACAAACUAGCUAGCUAGCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAAAAAACCACCUACCCAC
......((((((((.....................((((((....))))))(((.((((.....))))))).......))))))))................................ ( -20.80)
>DroSec_CAF1 62748 104 - 1
AUUGUAUUUUACAGUAAAUUUGUGCAACACACAAACUAGCUA----GCUAGCGAGCAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG----CAACCU------
......((((((((....((((((.....))))))((((((.----(((....))).))))))...............))))))))................----......------ ( -23.00)
>DroSim_CAF1 60435 104 - 1
AUUGUAUUUUACAGUAAAUUUGUGCAACACACAAACUAGCUA----GCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG----CAACCU------
......((((((((....((((((.....))))))((((...----.))))(((.((((.....))))))).......))))))))................----......------ ( -20.80)
>DroEre_CAF1 63757 107 - 1
AUUGUAUUUUACAGUAAAUUUCUGCAGCACACAAACUAGCUGGCUAGCUAGCAAGCGGGCUAGACCUGUCGCUCUGUCCUGUAAA-CCAGCCAAAGGGAAAU-----CACCCA-----
.......(((((((.........((((..((((..((((((.(((.(....).))).))))))...))).)..)))).)))))))-.........(((....-----..))).----- ( -26.20)
>DroYak_CAF1 77689 102 - 1
AUUGUAUUUUACAGUAAAUUGCUGCAACACACAAACUAGCUAGCUAGCGAGCGA---GGCUAGACCUGUCGUUCUGUCCUGCAAAUCCACCCAAA---AAAC-----CACCUA-----
((((((...))))))...((((.(((..(((((..((((((.(((....)))..---))))))...))).))..)))...))))...........---....-----......----- ( -19.40)
>consensus
AUUGUAUUUUACAGUAAAUUUCUGCAACACACAAACUAGCUAGCUAGCUAGCGAACAGGCUAGACCUGUCGUUCUGUCCUGUAAAACCAACCAAAAAAAAAG____CCACCUA_____
((((((...)))))).......((((..(((....(((((......)))))(((.((((.....)))))))...)))..))))................................... (-14.52 = -15.04 +   0.52)

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 11:41:43 2006