Locus 9801

Sequence ID 3R_DroMel_CAF1
Location 26,039,297 – 26,039,483
Length 186
Max. P 0.893586
window15651 window15652 window15653

overview

Window 1

Location 26,039,297 – 26,039,405
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 85.79
Mean single sequence MFE -24.63
Consensus MFE -20.26
Energy contribution -19.86
Covariance contribution -0.40
Combinations/Pair 1.17
Mean z-score -1.92
Structure conservation index 0.82
SVM decision value 0.98
SVM RNA-class probability 0.893586
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26039297 108 + 27905053
GAAAA----UCGA-AAUUAAUAAUUCAUUUUGUUUAGUUUUGAAGGGAAUCCAUACGAUUUUUUUUCCCAGCUUCCUAAGCCAACCAGCCUCUGAGUUUCCCAGGCUGAUGGC
.....----((((-(((((((((......))).)))))))))).(((((...............)))))..........((((..((((((..(.....)..)))))).)))) ( -26.26)
>DroSec_CAF1 32158 109 + 1
GAAAA----UCCAAAAUAAAUAAUUCAUUUUGUUUAGCUUAGAAGGGAAUCCAUACGAUUUUCUUUCCCAGCUUCCUAAGCCAACCAGCCUCUGUGUUUCCCAGGCUGAUGGC
.....----.......(((((((......)))))))(((..((((..((((.....))))..))))...))).......((((..((((((..(.....)..)))))).)))) ( -26.20)
>DroSim_CAF1 33543 108 + 1
GAAAA----UCGA-GUUUAAUAAUUCAUUUCAUUUAGUUUAGAAGGGAAUCCAUACGAUUUUCUUUCCCAGCUUCCUAAGCCAACCAGCCUCUGUGUUUCCCAGGCUGAUGGC
((((.----..((-(((....))))).))))....((((..((((..((((.....))))..))))...))))......((((..((((((..(.....)..)))))).)))) ( -24.60)
>DroEre_CAF1 37358 110 + 1
GAAAAUACGUCCA-AAUUAGUAUUGUAUUUC--UUAAUUUAGAAAGAAAUUCUUACGAUUUUCUUGCCCAGCUUCCUAAGCCAACCAGCCUCCGAAUUUCCCAGGCUGAUGGC
((((((.(((...-....((.(((...((((--(......)))))..))).)).)))))))))................((((..((((((..(.....)..)))))).)))) ( -21.10)
>DroYak_CAF1 32925 106 + 1
GAAAA----CCCA-AAUAAAUAUUUUAUUUC--GUAGCUUAGAAAGGAAUCCUUACGAUUUUCUUUCCCAGCUUCCUGAGCCAACCAGCCUCCGAACUUCCCAGGCUGAUGGC
.....----....-...............((--(.((((..((((((((..(....)..))))))))..))))...)))((((..((((((..(.....)..)))))).)))) ( -25.00)
>consensus
GAAAA____UCCA_AAUUAAUAAUUCAUUUC_UUUAGUUUAGAAGGGAAUCCAUACGAUUUUCUUUCCCAGCUUCCUAAGCCAACCAGCCUCUGAGUUUCCCAGGCUGAUGGC
...................................((((..((((((((..(....)..))))))))..))))......((((..((((((..(.....)..)))))).)))) (-20.26 = -19.86 +  -0.40)

alignment

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secondary structure

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Window 2

Location 26,039,297 – 26,039,405
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -31.16
Consensus MFE -21.20
Energy contribution -21.44
Covariance contribution 0.24
Combinations/Pair 1.13
Mean z-score -2.47
Structure conservation index 0.68
SVM decision value 0.89
SVM RNA-class probability 0.875117
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26039297 108 - 27905053
GCCAUCAGCCUGGGAAACUCAGAGGCUGGUUGGCUUAGGAAGCUGGGAAAAAAAAUCGUAUGGAUUCCCUUCAAAACUAAACAAAAUGAAUUAUUAAUU-UCGA----UUUUC
(((((((((((((....))...))))))).))))((((......(((((...............))))).......))))......((((........)-))).----..... ( -27.08)
>DroSec_CAF1 32158 109 - 1
GCCAUCAGCCUGGGAAACACAGAGGCUGGUUGGCUUAGGAAGCUGGGAAAGAAAAUCGUAUGGAUUCCCUUCUAAGCUAAACAAAAUGAAUUAUUUAUUUUGGA----UUUUC
(((((((((((.(....)....))))))).))))((((....))))....(((((((((.((((......)))).))....((((((((.....))))))))))----))))) ( -34.40)
>DroSim_CAF1 33543 108 - 1
GCCAUCAGCCUGGGAAACACAGAGGCUGGUUGGCUUAGGAAGCUGGGAAAGAAAAUCGUAUGGAUUCCCUUCUAAACUAAAUGAAAUGAAUUAUUAAAC-UCGA----UUUUC
(((((((((((.(....)....))))))).))))((((....))))....((((((((....(((((..(((..........)))..))))).......-.)))----))))) ( -30.50)
>DroEre_CAF1 37358 110 - 1
GCCAUCAGCCUGGGAAAUUCGGAGGCUGGUUGGCUUAGGAAGCUGGGCAAGAAAAUCGUAAGAAUUUCUUUCUAAAUUAA--GAAAUACAAUACUAAUU-UGGACGUAUUUUC
.(.((((((((..(.....)..)))))))).)((((((....))))))((((((.((....)).))))))(((((((((.--............)))))-))))......... ( -30.72)
>DroYak_CAF1 32925 106 - 1
GCCAUCAGCCUGGGAAGUUCGGAGGCUGGUUGGCUCAGGAAGCUGGGAAAGAAAAUCGUAAGGAUUCCUUUCUAAGCUAC--GAAAUAAAAUAUUUAUU-UGGG----UUUUC
(((((((((((..(.....)..))))))).))))......((((.((((((.((.((....)).)).)))))).)))).(--.((((((.....)))))-).).----..... ( -33.10)
>consensus
GCCAUCAGCCUGGGAAACUCAGAGGCUGGUUGGCUUAGGAAGCUGGGAAAGAAAAUCGUAUGGAUUCCCUUCUAAACUAAA_GAAAUGAAUUAUUAAUU_UGGA____UUUUC
(((((((((((..(.....)..))))))).))))((((..((..(((((...............)))))..))...))))................................. (-21.20 = -21.44 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,039,365 – 26,039,483
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.10
Mean single sequence MFE -34.67
Consensus MFE -27.21
Energy contribution -27.93
Covariance contribution 0.73
Combinations/Pair 1.21
Mean z-score -1.92
Structure conservation index 0.78
SVM decision value 0.32
SVM RNA-class probability 0.685113
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26039365 118 - 27905053
UUUCUU--UCAAUCCGAUCGUAAGCCAACAAUCUCGUCAUGAACUUCAACAAGAUCUUCGUCUUUGUGGCACUCAUCCUGGCCAUCAGCCUGGGAAACUCAGAGGCUGGUUGGCUUAGGA
......--.........((.(((((((((.........(((((..((.....))..)))))....(((((.(.......))))))((((((((....))...))))))))))))))).)) ( -36.70)
>DroSec_CAF1 32227 118 - 1
UUUCUU--GCAAUCCGGUCGUAAGCCAACAAUCUCGUCAUGAACUUCAACAAGAUCUUCGUCUUCGUGGCCCUCAUCCUGGCCAUCAGCCUGGGAAACACAGAGGCUGGUUGGCUUAGGA
......--.........((.(((((((((.........(((((..((.....))..)))))....((((((........))))))((((((.(....)....))))))))))))))).)) ( -38.80)
>DroSim_CAF1 33611 118 - 1
UUUCUU--UCAAUCCAGUCGUAAGCCAACAAUCUCGUCAUGAACUUCAACAAGAUCUUCGUCUUCGUGGCCCUCAUCCUGGCCAUCAGCCUGGGAAACACAGAGGCUGGUUGGCUUAGGA
......--.........((.(((((((((.........(((((..((.....))..)))))....((((((........))))))((((((.(....)....))))))))))))))).)) ( -38.80)
>DroEre_CAF1 37428 118 - 1
UUCCUA--UCAAUCCGGUAACAAGCCGACAAUCCCGUCAUGAACUUCAACAAGAUCUUCGUCUUCGUGGCCCUCAUCCUGGCCAUCAGCCUGGGAAAUUCGGAGGCUGGUUGGCUUAGGA
.(((((--((((.(((((......((((...(((((...(((......(((((((....))))).))((((........)))).)))...)))))...))))..)))))))))..))))) ( -36.90)
>DroYak_CAF1 32991 118 - 1
CUCCUC--UCAAUUCAAUAAUAAGCCAACAAUCUAGACAUGAACUUCAACAAGAUCUUCGUCUUCGUGGCUCUCAUCUUGGCCAUCAGCCUGGGAAGUUCGGAGGCUGGUUGGCUCAGGA
......--..............(((((.......((((..(((..((.....))..)))))))...)))))....((((((((((((((((..(.....)..))))))).)))).))))) ( -33.60)
>DroAna_CAF1 33989 115 - 1
UUACUUUCUGAAUCAA-----AGAAAAAUAUUCCCAUCAUGAACUUCAACAAGAUCUUCGUCUUCGUCGCCAUUAUCCUGGCCAUUAGCUUGGGACAGACCGAAGCAGGUUGGCUGAAAA
....(((((.......-----))))).....(((((..(((((..((.....))..))))).......((((......))))........)))))(((.((((......))))))).... ( -23.20)
>consensus
UUUCUU__UCAAUCCAGUCGUAAGCCAACAAUCUCGUCAUGAACUUCAACAAGAUCUUCGUCUUCGUGGCCCUCAUCCUGGCCAUCAGCCUGGGAAACACAGAGGCUGGUUGGCUUAGGA
....................(((((((((.........(((((..((.....))..)))))....((((((........))))))((((((..(.....)..)))))))))))))))... (-27.21 = -27.93 +   0.73)

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 13:42:29 2006