Locus 6854

Sequence ID 3R_DroMel_CAF1
Location 18,137,579 – 18,137,717
Length 138
Max. P 0.991920
window11122 window11123 window11124

overview

Window 2

Location 18,137,579 – 18,137,679
Length 100
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.28
Mean single sequence MFE -32.28
Consensus MFE -14.90
Energy contribution -15.30
Covariance contribution 0.39
Combinations/Pair 1.31
Mean z-score -2.61
Structure conservation index 0.46
SVM decision value 0.05
SVM RNA-class probability 0.557953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18137579 100 + 27905053
ACAAUUUCUAUAAGUGAGUGGUAUGUGGUUUCUGUUAUCCUGUAUAUUCGGUCUAAGCAGCAGCGAUGCUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGU
.((....((((......))))....))........((((((....(((((((((((((((((....))))))))).))))))))....))))))...... ( -35.10)
>DroSec_CAF1 166176 97 + 1
ACAAUUUCUAUAAGUGAGUGAUGUGUGGUUUUUGUUAUCCUGUAUAUUCGGUCUAAGCAGCAGCG---CUGCUUAGGGCCGAAUCCUAGGGAUGCUUUGU
((((...(((((.((.....)).)))))...))))((((((....((((((((((((((((...)---))))))).))))))))....))))))...... ( -33.30)
>DroSim_CAF1 171079 97 + 1
ACAAUUUCUAUAAGUGAGUGGUGUGUGGUUUUUGUUAUCCUGUAUAUUCGGUCUAAGCAGCAGCG---CUGCUUAGGGCCGAAUCCUAGGGAUGCUUUGU
((((...(((((..(.....)..)))))...))))((((((....((((((((((((((((...)---))))))).))))))))....))))))...... ( -32.30)
>DroEre_CAF1 177819 94 + 1
ACAAUUUCUAUAAGUGAGU-AUGU--GUCUUCUGUAUUCCUGGGUAUUGGUACUAAGCAGCAGCG---CUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGU
(((..(((.......))).-.)))--.......(((((((((((..((((..(((((((((...)---))))))))..))))..)))))))))))..... ( -38.80)
>DroYak_CAF1 175113 96 + 1
ACAAUUUCUAUAAGUGAGU-AUGUGUGUUUUCUGUUAUCCUGCAUAUUGGUACUAAGCAGCAGCG---CUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGU
(((..(((.......))).-...))).........((((((.....((((..(((((((((...)---))))))))..))))......))))))...... ( -27.30)
>DroPer_CAF1 194206 89 + 1
--AAUGCCUGUG----UGUUGAUUGGGGGUUCGAUUGUUUAG--CGUCGAUCUUAAGCAGCAGCG---CUGCUUAGGGCCGUGUCCUAGGGAUGCUUCGU
--....((((..----.......))))((((((((((.....--...))))).((((((((...)---))))))))))))((((((...))))))..... ( -26.90)
>consensus
ACAAUUUCUAUAAGUGAGUGAUGUGUGGUUUCUGUUAUCCUGUAUAUUCGGUCUAAGCAGCAGCG___CUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGU
...................................((((((........(.(((((((((........))))))))).).........))))))...... (-14.90 = -15.30 +   0.39)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,137,579 – 18,137,679
Length 100
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.28
Mean single sequence MFE -23.37
Consensus MFE -11.77
Energy contribution -11.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.50
SVM decision value 0.24
SVM RNA-class probability 0.647054
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18137579 100 - 27905053
ACGAAGCAUCCCUAGGAUUCGGCCCUAAGCAGCAUCGCUGCUGCUUAGACCGAAUAUACAGGAUAACAGAAACCACAUACCACUCACUUAUAGAAAUUGU
.......((((.....((((((..((((((((((....)))))))))).)))))).....)))).................................... ( -27.80)
>DroSec_CAF1 166176 97 - 1
ACAAAGCAUCCCUAGGAUUCGGCCCUAAGCAG---CGCUGCUGCUUAGACCGAAUAUACAGGAUAACAAAAACCACACAUCACUCACUUAUAGAAAUUGU
.......((((.....((((((..((((((((---(...))))))))).)))))).....)))).................................... ( -25.30)
>DroSim_CAF1 171079 97 - 1
ACAAAGCAUCCCUAGGAUUCGGCCCUAAGCAG---CGCUGCUGCUUAGACCGAAUAUACAGGAUAACAAAAACCACACACCACUCACUUAUAGAAAUUGU
.......((((.....((((((..((((((((---(...))))))))).)))))).....)))).................................... ( -25.30)
>DroEre_CAF1 177819 94 - 1
ACGAAGCAUCCCUAGGAUUCGGCCCUAAGCAG---CGCUGCUGCUUAGUACCAAUACCCAGGAAUACAGAAGAC--ACAU-ACUCACUUAUAGAAAUUGU
..........(((.(((((.((..((((((((---(...)))))))))..))))).)).)))............--....-................... ( -22.90)
>DroYak_CAF1 175113 96 - 1
ACGAAGCAUCCCUAGGAUUCGGCCCUAAGCAG---CGCUGCUGCUUAGUACCAAUAUGCAGGAUAACAGAAAACACACAU-ACUCACUUAUAGAAAUUGU
.....((((((...)))...((..((((((((---(...)))))))))..))....))).....................-................... ( -20.60)
>DroPer_CAF1 194206 89 - 1
ACGAAGCAUCCCUAGGACACGGCCCUAAGCAG---CGCUGCUGCUUAAGAUCGACG--CUAAACAAUCGAACCCCCAAUCAACA----CACAGGCAUU--
.((((((.(((...)))..((..(.(((((((---(...)))))))).)..))..)--))......)))...............----..........-- ( -18.30)
>consensus
ACGAAGCAUCCCUAGGAUUCGGCCCUAAGCAG___CGCUGCUGCUUAGAACCAAUAUACAGGAUAACAGAAACCACACACCACUCACUUAUAGAAAUUGU
...((((.....((((.......))))(((((.....)))))))))...................................................... (-11.77 = -11.77 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,137,610 – 18,137,717
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.27
Mean single sequence MFE -38.57
Consensus MFE -26.36
Energy contribution -26.45
Covariance contribution 0.09
Combinations/Pair 1.22
Mean z-score -2.27
Structure conservation index 0.68
SVM decision value 2.30
SVM RNA-class probability 0.991920
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18137610 107 + 27905053
---CUGUUAUCCUGU-----A--UAUUCGG-UCUAAGCAGCAGCGAUGCUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGUAUAGUUAUUGAGCGGCAUCUCGUUCACAUGAGUGUGUG--
---....((((((..-----.--.((((((-(((((((((((....))))))))).))))))))....)))))).....((((.(((((((((((....))))))).)))).))))..-- ( -43.50)
>DroPse_CAF1 168390 104 + 1
---CGAUUGUUUAG---------CGUUGAU-CUUAAGCAGCAGCG---CUGCUUAGGGCCGUGUCCUAGGGAUGCUUCGUGUAGUUGUUCAGCGGCAUCUCGUUGACGUGGGCAUGGGCC
---.(((((.....---------...))))-).((((((((...)---)))))))((.((((((((..((((((((.(.((........))).))))))))(....)..)))))))).)) ( -39.40)
>DroEre_CAF1 177847 104 + 1
---CUGUAUUCCUGG-----G--UAUUGGU-ACUAAGCAGCAGCG---CUGCUUAGGGCCGAAUCCUAGGGAUGCUUCGUAUAAUUAUUGAGCGGCAUCUCGUUCACAUGGGUGUGGG--
---..((((((((((-----(--..((((.-.(((((((((...)---))))))))..))))..)))))))))))..(.((((.(((((((((((....))))))).)))).)))).)-- ( -46.50)
>DroWil_CAF1 183791 109 + 1
UAAUCGUUGUCUUAA-----AUGUGUAAAU-CUUAUGCAGCAUCA---AUGCUGAUGGCCGUAUCCUAGGGAUGCUUUGUAUAAUUGUUCAAUGGCAUCUCGUUGACAUGGGUGUGGG--
....((((......)-----))).......-(((((((..(((((---....))))).((((.((...(((((((((((.((....)).))).))))))))...)).)))))))))))-- ( -26.00)
>DroAna_CAF1 161496 110 + 1
---AAUGUAUCCGAUAUCUGA--UAUCAAGACUUAAGCAGCUGCG---CUGCUUAGGGCCGUAUCCUAGGGAUGCUUUGUGUAAUUAUUUAAGGGCAUUUCGGUCACGUGGGUGUGGG--
---.......((.((((((..--........((((((((((...)---)))))))))..(((..((..(..(((((((.............)))))))..)))..))).)))))).))-- ( -34.52)
>DroPer_CAF1 194231 104 + 1
---CGAUUGUUUAG---------CGUCGAU-CUUAAGCAGCAGCG---CUGCUUAGGGCCGUGUCCUAGGGAUGCUUCGUGUAGUUGUUCAGCGGCAUCUCGUUGACGUGGGCAUGGGCC
---.(((((.....---------...))))-).((((((((...)---)))))))((.((((((((..((((((((.(.((........))).))))))))(....)..)))))))).)) ( -41.50)
>consensus
___CGGUUGUCCUG______A__UAUUGAU_CUUAAGCAGCAGCG___CUGCUUAGGGCCGUAUCCUAGGGAUGCUUCGUAUAAUUAUUCAGCGGCAUCUCGUUCACAUGGGUGUGGG__
...............................(((((((((........))))))))).((((((((..((((((((.(.............).))))))))(....)..))))))))... (-26.36 = -26.45 +   0.09)

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 12:31:35 2006