Locus 8938

Sequence ID 3R_DroMel_CAF1
Location 23,980,759 – 23,980,880
Length 121
Max. P 0.920153
window14328 window14329 window14330 window14331

overview

Window 8

Location 23,980,759 – 23,980,859
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.73
Mean single sequence MFE -18.87
Consensus MFE -15.24
Energy contribution -15.35
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.50
Structure conservation index 0.81
SVM decision value 0.88
SVM RNA-class probability 0.873915
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23980759 100 + 27905053
------------CCGCAC--------CCGCAAAGCAAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAGCUGUUAGCAUAAAUUUACGGCCCAAAAAAAAGA
------------(((...--------..(((..((....)).))).....(((....))).(((((((((((.(((((....)))))......))))))))))))))............. ( -18.00)
>DroVir_CAF1 201997 77 + 1
-----------------------------------------CAGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAA--A
-----------------------------------------..((.....(((....))).(((((((((((.(((((....)))))......)))))))))))..)).........--. ( -13.80)
>DroGri_CAF1 157450 109 + 1
----CCU---CUCUGCCCCCU----UUAGCAAAACGAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAAAA
----...---...(((.....----...)))........((((((((...)))))......(((((((((((.(((((....)))))......))))))))))).)))............ ( -18.00)
>DroWil_CAF1 227557 100 + 1
------------UACCAU--------CCGCAAAGUAAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAGAA
------------......--------.............((((((((...)))))......(((((((((((.(((((....)))))......))))))))))).)))............ ( -16.70)
>DroYak_CAF1 191652 109 + 1
UCCGCAC---AUCCGCAC--------CCGCAAAGCAAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAGCUGUUAGCAUAAAUUUACGGCCCAAAAAAAAAA
.((((((---....((..--------..))...(((......))).....)))).......(((((((((((.(((((....)))))......))))))))))).))............. ( -19.10)
>DroMoj_CAF1 206760 115 + 1
----CCUGGCCCCUGGCCCAUAGUCGUGGCCAAACGAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAA-CG
----...((((..((((((......).)))))......((..(((((...)))))..))..(((((((((((.(((((....)))))......))))))))))).))))........-.. ( -27.60)
>consensus
____________CCGCAC________CCGCAAAGCAAAUGCCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAAAA
.......................................(((........(((....))).(((((((((((.(((((....)))))......))))))))))).)))............ (-15.24 = -15.35 +   0.11)

alignment

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secondary structure

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Window 9

Location 23,980,759 – 23,980,859
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.73
Mean single sequence MFE -26.80
Consensus MFE -17.48
Energy contribution -18.15
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.65
SVM decision value 1.13
SVM RNA-class probability 0.920153
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23980759 100 - 27905053
UCUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGCUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUUGCUUUGCGG--------GUGCGG------------
.........((((((((((((((((((......(........).....))))))))))))).)))))............((((((((...))))--------))))..------------ ( -24.70)
>DroVir_CAF1 201997 77 - 1
U--UUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCUG-----------------------------------------
.--......((((((((((((((((((......(((......)))...))))))))))))).)))))............----------------------------------------- ( -18.00)
>DroGri_CAF1 157450 109 - 1
UUUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUCGUUUUGCUAA----AGGGGGCAGAG---AGG----
............(((((((((((((((......(((......)))...))))))))))))(((....)))........))).....(((((((..----....)))))))---...---- ( -26.20)
>DroWil_CAF1 227557 100 - 1
UUCUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUUACUUUGCGG--------AUGGUA------------
.........((((((((((((((((((......(((......)))...))))))))))))).))))).(((((.((((((.......)))))).--------))))).------------ ( -27.60)
>DroYak_CAF1 191652 109 - 1
UUUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGCUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUUGCUUUGCGG--------GUGCGGAU---GUGCGGA
.........((((((((((((((((((......(........).....))))))))))))).))))).....((..((.((((((((...))))--------))))...)---)..)).. ( -29.70)
>DroMoj_CAF1 206760 115 - 1
CG-UUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUCGUUUGGCCACGACUAUGGGCCAGGGGCCAGG----
..-........((((((((((((((((......(((......)))...))))))))))))((((((.(((...))).))))))...(((((((.(......))))))))))))...---- ( -34.60)
>consensus
UUUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGGCAUUUGCUUUGCGG________GUGCAG____________
............(((((((((((((((......(((......)))...))))))))))))(((....)))........)))....................................... (-17.48 = -18.15 +   0.67)

alignment

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secondary structure

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Window 0

Location 23,980,779 – 23,980,880
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 83.77
Mean single sequence MFE -16.47
Consensus MFE -13.76
Energy contribution -13.53
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.54
Structure conservation index 0.83
SVM decision value 0.17
SVM RNA-class probability 0.617763
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23980779 101 + 27905053
CCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAGCUGUUAGCAUAAAUUUACGGCCCAAAAAAAAGA-CGACAAAAAAUGGGGAA---AAUC--
(((((((...)))))......(((((((((((.(((((....)))))......))))))))))).))((((.........-..........))))...---....-- ( -15.91)
>DroVir_CAF1 201997 92 + 1
-CAGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAA--ACCAACAUAG-CU---GAG---A-----
-((((.....(((....))).(((((((((((.(((((....)))))......))))))))))).............--.........)-))---)..---.----- ( -18.30)
>DroGri_CAF1 157479 102 + 1
CCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAAAACCCACAAAAACA-G-GAA---UAUGGC
((((......(((....))).(((((((((((.(((((....)))))......)))))))))))..........................))-)-)..---...... ( -17.20)
>DroWil_CAF1 227577 104 + 1
CCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAGAA-AGAAAAAAAAUACGAAAACGAACC--
...((.....(((....))).(((((((((((.(((((....)))))......)))))))))))..))............-........................-- ( -13.60)
>DroMoj_CAF1 206796 94 + 1
CCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAA-CGCCAACAAAC-CA---GAG---C-----
.(((......(((....))).(((((((((((.(((((....)))))......))))))))))).(((.........-.))).......-))---)..---.----- ( -16.70)
>DroAna_CAF1 191064 99 + 1
CCUGCACACAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAGCUGUUAGCAUAAAUUUACGGCCCAAAAAAAAGC---ACAAAAUUGGGGAAA---AAUC--
(((((((...)))))......(((((((((((.(((((....)))))......))))))))))).))(((((........---......)))))....---....-- ( -17.14)
>consensus
CCUGCACAUAGUGUAAACACAUAAAUUUAUGCAUUUUCAAUGGAGAACUGUUAGCAUAAAUUUACGGCCCAAAAAAAAAA_CAACAAAAACU_G_GAA___AAUC__
...((.....(((....))).(((((((((((.(((((....)))))......)))))))))))..))....................................... (-13.76 = -13.53 +  -0.22)

alignment

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secondary structure

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Window 1

Location 23,980,779 – 23,980,880
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 83.77
Mean single sequence MFE -21.16
Consensus MFE -16.93
Energy contribution -17.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.80
SVM decision value 0.06
SVM RNA-class probability 0.563474
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23980779 101 - 27905053
--GAUU---UUCCCCAUUUUUUGUCG-UCUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGCUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGG
--....---...((((..........-.........))))((((((((((((((......(........).....))))))))))))(((....)))........)) ( -16.81)
>DroVir_CAF1 201997 92 - 1
-----U---CUC---AG-CUAUGUUGGU--UUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCUG-
-----.---..(---((-(((((..(((--((.....)))))((((((((((((......(((......)))...))))))))))))(((....))))))).))))- ( -22.70)
>DroGri_CAF1 157479 102 - 1
GCCAUA---UUC-C-UGUUUUUGUGGGUUUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGG
......---..(-(-(((....((((((((.......)))))((((((((((((......(((......)))...)))))))))))).......))).....))))) ( -25.70)
>DroWil_CAF1 227577 104 - 1
--GGUUCGUUUUCGUAUUUUUUUUCU-UUCUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGG
--((((((..................-.........))))))((((((((((((......(((......)))...))))))))))))(((....))).......... ( -19.13)
>DroMoj_CAF1 206796 94 - 1
-----G---CUC---UG-GUUUGUUGGCG-UUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGG
-----(---(.(---((-((.....(((.-(......).)))((((((((((((......(((......)))...))))))))))))........)))).).))... ( -22.00)
>DroAna_CAF1 191064 99 - 1
--GAUU---UUUCCCCAAUUUUGU---GCUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGCUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUGUGUGCAGG
--....---...........(((.---.(.......((((((((((((((((((......(........).....))))))))))))).)))))......)..))). ( -20.62)
>consensus
__GAUU___UUC_C_AGUUUUUGUCG_UCUUUUUUUUGGGCCGUAAAUUUAUGCUAACAGUUCUCCAUUGAAAAUGCAUAAAUUUAUGUGUUUACACUAUGUGCAGG
....................................((((((((((((((((((......(((......)))...))))))))))))).)))))............. (-16.93 = -17.27 +   0.33)

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 13:23:08 2006