Locus 3629

Sequence ID 3L_DroMel_CAF1
Location 10,679,638 – 10,679,871
Length 233
Max. P 0.849267
window5658 window5659 window5660 window5661

overview

Window 8

Location 10,679,638 – 10,679,744
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 95.47
Mean single sequence MFE -30.13
Consensus MFE -27.44
Energy contribution -27.68
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.35
Structure conservation index 0.91
SVM decision value 0.78
SVM RNA-class probability 0.849267
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10679638 106 - 23771897
UGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAUACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCAACAUUCGUAGAAUGGGUUAGAUCCGUCUGCAAC
..(((((...(((((.(((.(((...((((((....((......))(((..............)))))))))...)))))).)))))((......)).)))))... ( -29.74)
>DroSec_CAF1 14075 106 - 1
UGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAACACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCAACAGCCGUAGAAUGGGAUAGAUCCGUCUGCAGC
..(((((...(((((..(((..((((.(.((((.(.......).)))).)...)))))))....(((((.......))))).)))))(((....))).)))))... ( -30.90)
>DroSim_CAF1 14723 106 - 1
UGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAACACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCAACAGCCGUAGAAUGGGAUAGAUCCGUCUGCAGC
..(((((...(((((..(((..((((.(.((((.(.......).)))).)...)))))))....(((((.......))))).)))))(((....))).)))))... ( -30.90)
>DroEre_CAF1 14650 106 - 1
UGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAACACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCUACAUCCGUAGAAUGGGAAAGAUCCGUCUGCAGC
..(((((...(((((.(((.......((((((..(....)..(((..(((........)))..)))))))))......))).)))))(((....))).)))))... ( -30.52)
>DroYak_CAF1 26022 106 - 1
UGGCAGGUAACAUUCAACGCAAUUUCGCAGCCAACACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCAACAUCCGUAGAAUGGUAAGGAUCCGUCUGCGGC
..(((((...(((((.(((((.((((.((((((.(.......).))))))...)))).))....((....))......))).)))))....(....).)))))... ( -28.60)
>consensus
UGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAACACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCGGCAGCAACAUCCGUAGAAUGGGAUAGAUCCGUCUGCAGC
..(((((...(((((.(((.......((((((..(....)..(((..(((........)))..)))))))))......))).)))))((......)).)))))... (-27.44 = -27.68 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,679,673 – 10,679,768
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.84
Mean single sequence MFE -30.19
Consensus MFE -22.36
Energy contribution -22.78
Covariance contribution 0.42
Combinations/Pair 1.12
Mean z-score -2.64
Structure conservation index 0.74
SVM decision value 0.03
SVM RNA-class probability 0.551069
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10679673 95 + 23771897
CUGC-CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU--------AUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACAC--ACAUACACGCU--------------
((((-((((..............)))..((.....))--------...))))).......((((.(.((((..((((((....))))))....--)))).))))).-------------- ( -26.14)
>DroSec_CAF1 14110 95 + 1
CUGC-CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU--------GUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGGCAC--ACAAACACGCA--------------
....-((((...............((((((.......--------))))))))))....(((((....(((..((((((....))))))..))--).....)))))-------------- ( -30.56)
>DroSim_CAF1 14758 95 + 1
CUGC-CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU--------GUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACAC--ACAUACACGCA--------------
....-((((...............((((((.......--------))))))))))....(((((.(.((((..((((((....))))))....--)))).))))))-------------- ( -30.56)
>DroEre_CAF1 14685 95 + 1
CUGC-CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU--------GUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACAC--ACAUACACGCA--------------
....-((((...............((((((.......--------))))))))))....(((((.(.((((..((((((....))))))....--)))).))))))-------------- ( -30.56)
>DroYak_CAF1 26057 97 + 1
CUGC-CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU--------GUUGGCUGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACACACACAUACACGCA--------------
....-..........((((...((((((((.......--------)))))))).)))).(((((((..(((..((((((....))))))..)))..))...)))))-------------- ( -31.70)
>DroAna_CAF1 14323 118 + 1
GUGCACUUUUCCCACUUUCUUUUUCCUGGCUUCUUGUGCUGUCCUGUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACAC--ACACACACACACGCAAAAAGGAUCU
.......................((((.........(((((.((....)))))))...((((((((..(((..((((((....))))))..))--)..)).....))))))..))))... ( -31.60)
>consensus
CUGC_CGCUUUCCACUUUCUUUCAGCCAGCUUCUUGU________GUUGGCAGCGAAAUUGCGUUGAAUGUUACCUGCCAUUUGGCAGGACAC__ACAUACACGCA______________
...................((((.((((((...............))))))...))))..((((.(.((((..((((((....))))))......)))).)))))............... (-22.36 = -22.78 +   0.42)

alignment

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secondary structure

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Window 0

Location 10,679,673 – 10,679,768
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.84
Mean single sequence MFE -33.34
Consensus MFE -24.26
Energy contribution -24.88
Covariance contribution 0.61
Combinations/Pair 1.12
Mean z-score -2.70
Structure conservation index 0.73
SVM decision value -0.05
SVM RNA-class probability 0.509559
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10679673 95 - 23771897
--------------AGCGUGUAUGU--GUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAU--------ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG-GCAG
--------------.((((..((((--....((((((....))))))..))))...)))).......(((((...--------.((......))(((..............))))-)))) ( -31.14)
>DroSec_CAF1 14110 95 - 1
--------------UGCGUGUUUGU--GUGCCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAC--------ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG-GCAG
--------------(((((....((--((..((((((....))))))..))))...)))))......(((((..(--------....)..(((..(((........)))..))))-)))) ( -33.50)
>DroSim_CAF1 14758 95 - 1
--------------UGCGUGUAUGU--GUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAC--------ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG-GCAG
--------------(((((..((((--....((((((....))))))..))))...)))))......(((((..(--------....)..(((..(((........)))..))))-)))) ( -32.60)
>DroEre_CAF1 14685 95 - 1
--------------UGCGUGUAUGU--GUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAC--------ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG-GCAG
--------------(((((..((((--....((((((....))))))..))))...)))))......(((((..(--------....)..(((..(((........)))..))))-)))) ( -32.60)
>DroYak_CAF1 26057 97 - 1
--------------UGCGUGUAUGUGUGUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCAGCCAAC--------ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG-GCAG
--------------(((((....((((....((((((....))))))..))))...))))).((((.((((((.(--------.......).))))))...))))((.(....).-)).. ( -35.20)
>DroAna_CAF1 14323 118 - 1
AGAUCCUUUUUGCGUGUGUGUGUGU--GUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAACAGGACAGCACAAGAAGCCAGGAAAAAGAAAGUGGGAAAAGUGCAC
...((((..((((((.((...((((--....((((((....))))))..)))).))))))))....((((((....)).))))..........))))........(((.(.....).))) ( -35.00)
>consensus
______________UGCGUGUAUGU__GUGUCCUGCCAAAUGGCAGGUAACAUUCAACGCAAUUUCGCUGCCAAC________ACAAGAAGCUGGCUGAAAGAAAGUGGAAAGCG_GCAG
..............(((((..((((......((((((....))))))..))))...))))).(((((((((((...................))))........)))))))......... (-24.26 = -24.88 +   0.61)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,679,768 – 10,679,871
Length 103
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 85.60
Mean single sequence MFE -34.48
Consensus MFE -22.18
Energy contribution -22.50
Covariance contribution 0.32
Combinations/Pair 1.08
Mean z-score -2.36
Structure conservation index 0.64
SVM decision value 0.49
SVM RNA-class probability 0.758126
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10679768 103 + 23771897
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCAUC------UUCCUUCCAUCCUCUCCUCUCCACCAGUCGAGUAUUAAGUAAAUGUUUGGGGCCUGUAGGA
.(((.(((((((((.........))))))))).)))......------..............(((((.((.((((.((..(((...)))..)).))))))...).)))) ( -26.30)
>DroSec_CAF1 14205 100 + 1
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCAUC------GGCCUCCACUCCUCUCGUCUCCGCCAGUCGAGUAUUAAGUAAAUGUU-GGGGCC--UAGGA
.(((.(((((((((.........))))))))).))).((...------((((((.((....((((.((.....)).))))............)).-))))))--..)). ( -35.09)
>DroSim_CAF1 14853 100 + 1
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCAUC------GGCCUCCGCUCCUCUCGUCUCCGCCAGUCGAGUAUUAAGUAAAUGUU-GGGGCC--UAGGA
.(((.(((((((((.........))))))))).))).((...------((((((.((....((((.((.....)).))))............)).-))))))--..)). ( -35.39)
>DroEre_CAF1 14780 105 + 1
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCUCUUGCUCUGGGC-UCCUUCCCCUCGACUCCUCCAGUCGAGUAUUGAGUAAAUGUU-GGGGCC--UAGGA
.(((.(((((((((.........))))))))).))).........(((((((-(((.....(((((((.....)))))))((((.....))))..-))))))--)))). ( -43.60)
>DroYak_CAF1 26154 93 + 1
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCUCC-------------ACUUCGCUCGACUCCUCCACUCGAGUAUUGAGUAAAUGUU-GGGGCC--UAGGA
.(((.(((((((((.........))))))))).))).((((.-------------((((..(((.((((........))))...)))..)).)).-))))..--..... ( -32.00)
>consensus
GGGUCCAGGAUCCCUUUUAACCCGGGAUUCUGCACCACCAUC______GGCCUCCACUCCUCUCGUCUCCGCCAGUCGAGUAUUAAGUAAAUGUU_GGGGCC__UAGGA
.(((.(((((((((.........))))))))).)))....................((((.((((.((.....)).))))((((.....))))...))))......... (-22.18 = -22.50 +   0.32)

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 11:02:43 2006