Locus 1701

Sequence ID 2R_DroMel_CAF1
Location 6,435,196 – 6,435,323
Length 127
Max. P 0.927417
window2839 window2840 window2841

overview

Window 9

Location 6,435,196 – 6,435,309
Length 113
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.35
Mean single sequence MFE -32.48
Consensus MFE -18.92
Energy contribution -19.95
Covariance contribution 1.03
Combinations/Pair 1.22
Mean z-score -2.74
Structure conservation index 0.58
SVM decision value 1.18
SVM RNA-class probability 0.927417
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6435196 113 + 20766785
GUA---CGAACCGCAAGUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUAGGCCCUGAGGCAAAAACUUUACUGCCAAAGUGCCGUAAAUUGGCAGCUC-GCAGUUGCUU-UU
...---......((((.((......((((...)))).((((((((((...((((.(((.((..((((..........))))..)).))))))))))))))))).-.)).))))..-.. ( -32.10)
>DroVir_CAF1 4609 108 + 1
UCA---CAAGCCGCAGCUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUUCGC----CGGCA-AAACUCUACGGCAAAAGUGCCGUAAAUUGGCAGA-A-GCUGUUUUUAUUU
...---......((((((.......((((...))))...((((((((.........(.----...).-......(((((((....))))))).)))))))).-)-)))))........ ( -26.30)
>DroPse_CAF1 8799 112 + 1
GCGGGAGACACCGCAAGUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUAG----CAAGGCAAAAACUUUACGGCCAAAGCGCCGUAAAUUGGCAGCAA-GGAGUUAUUG-UU
((((......)))).(((((((((.((((...))))..(((((((((........(----(...)).......(((((((......))))))))))))))))..-))))))))).-.. ( -37.40)
>DroMoj_CAF1 9011 107 + 1
ACA---GAAGCCACAGCUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUUCGC----CGGCA-AAACUCUACAGCAAAAGUGCCGUAAAUUGGCAGU-G-GCUGUUUACG-UU
...---..((((((.((((......((((...))))..((((.(((((...)))).).----)))).-........)))).....(((((.....)))))))-)-))).......-.. ( -27.60)
>DroAna_CAF1 9527 113 + 1
GGG---ACUACCGCAAGUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUAGGCA-AGAGGCAAAAACUUUACGGCCAAAGUGCCGUAAAUUGGCAGCUCCGAAGUUGUUU-CU
((.---....))(.(((..(((((.((((...)))).((((((((((.........((.-....)).......(((((((......)))))))))))))))))..)))))..)))-). ( -32.40)
>DroPer_CAF1 9042 112 + 1
GCGGGAGACACCGCAAGUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUAG----CAAGGCAAAAACUUUGCGGCCAAAGUGCCGUAAAUUGGCAGCAA-GGAGUUAUUG-UU
((((......)))).(((((((((.((((...))))..(((((((((........(----(((((......))))))(((......)))....)))))))))..-))))))))).-.. ( -39.10)
>consensus
GCA___GAAACCGCAAGUGACUUUAGUGAAAUUUACAAGCUGUCAAUAAUUUAUAGGC____AGGCAAAAACUUUACGGCCAAAGUGCCGUAAAUUGGCAGC_A_GCAGUUAUUG_UU
...............((((((....((((...))))..(((((((((.........((......))........((((((......)))))).)))))))))......)))))).... (-18.92 = -19.95 +   1.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,435,232 – 6,435,323
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 74.15
Mean single sequence MFE -21.85
Consensus MFE -13.45
Energy contribution -14.32
Covariance contribution 0.86
Combinations/Pair 1.06
Mean z-score -1.55
Structure conservation index 0.62
SVM decision value 0.77
SVM RNA-class probability 0.847532
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6435232 91 + 20766785
CUGUCAAUAAUUUAUAGGCCCUGAGGCAAAAACUUUACUGCCAAAGUGCCGUAAAUUGGCAGCUC-GCAGUUGCUU-UUGUGGUUCUAUGUCA
............(((((..((.((((((........(((((...(((((((.....))))).)).-))))))))))-)...))..)))))... ( -25.00)
>DroVir_CAF1 4645 83 + 1
CUGUCAAUAAUUUAUUCGC----CGGCA-AAACUCUACGGCAAAAGUGCCGUAAAUUGGCAGA-A-GCUGUUUUUAUUUGUUGUUGU---GGU
...............((((----(((((-((.....(((((.....(((((.....)))))..-.-))))).....)))))))..))---)). ( -18.80)
>DroPse_CAF1 8838 76 + 1
CUGUCAAUAAUUUAUAG----CAAGGCAAAAACUUUACGGCCAAAGCGCCGUAAAUUGGCAGCAA-GGAGUUAUUG-UUGUG-----------
....(((((((((...(----(...((...((.((((((((......)))))))))).)).))..-.)))))))))-.....----------- ( -20.80)
>DroMoj_CAF1 9047 82 + 1
CUGUCAAUAAUUUAUUCGC----CGGCA-AAACUCUACAGCAAAAGUGCCGUAAAUUGGCAGU-G-GCUGUUUACG-UUGUUGUUGU---UGU
....((((((.........----(((((-(......(((((...(.(((((.....))))).)-.-))))).....-))))))))))---)). ( -21.10)
>DroAna_CAF1 9563 91 + 1
CUGUCAAUAAUUUAUAGGCA-AGAGGCAAAAACUUUACGGCCAAAGUGCCGUAAAUUGGCAGCUCCGAAGUUGUUU-CUGUGGCGGUGUCUGC
((((((.((((((((.((((-...(((............)))....))))))))))))((((((....))))))..-...))))))....... ( -24.10)
>DroPer_CAF1 9081 76 + 1
CUGUCAAUAAUUUAUAG----CAAGGCAAAAACUUUGCGGCCAAAGUGCCGUAAAUUGGCAGCAA-GGAGUUAUUG-UUGUG-----------
.......((((((((.(----(((((......))))))(((......)))))))))))(((((((-.......)))-)))).----------- ( -21.30)
>consensus
CUGUCAAUAAUUUAUAGGC____AGGCAAAAACUUUACGGCCAAAGUGCCGUAAAUUGGCAGC_A_GCAGUUAUUG_UUGUGGUUGU___UG_
((((((((.........((......))........((((((......)))))).))))))))............................... (-13.45 = -14.32 +   0.86)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,435,232 – 6,435,323
Length 91
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 74.15
Mean single sequence MFE -17.22
Consensus MFE -10.83
Energy contribution -10.83
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.18
Structure conservation index 0.63
SVM decision value 0.02
SVM RNA-class probability 0.544430
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6435232 91 - 20766785
UGACAUAGAACCACAA-AAGCAACUGC-GAGCUGCCAAUUUACGGCACUUUGGCAGUAAAGUUUUUGCCUCAGGGCCUAUAAAUUAUUGACAG
....((((..((.(((-((((.(((((-(((.((((.......)))))))..)))))...))))))).....))..))))............. ( -22.30)
>DroVir_CAF1 4645 83 - 1
ACC---ACAACAACAAAUAAAAACAGC-U-UCUGCCAAUUUACGGCACUUUUGCCGUAGAGUUU-UGCCG----GCGAAUAAAUUAUUGACAG
...---...................((-(-...((...(((((((((....)))))))))....-.)).)----))................. ( -15.70)
>DroPse_CAF1 8838 76 - 1
-----------CACAA-CAAUAACUCC-UUGCUGCCAAUUUACGGCGCUUUGGCCGUAAAGUUUUUGCCUUG----CUAUAAAUUAUUGACAG
-----------.....-((((((....-..((.((...((((((((......))))))))......))...)----)......)))))).... ( -17.10)
>DroMoj_CAF1 9047 82 - 1
ACA---ACAACAACAA-CGUAAACAGC-C-ACUGCCAAUUUACGGCACUUUUGCUGUAGAGUUU-UGCCG----GCGAAUAAAUUAUUGACAG
...---..........-........((-(-...((...(((((((((....)))))))))....-.)).)----))................. ( -15.40)
>DroAna_CAF1 9563 91 - 1
GCAGACACCGCCACAG-AAACAACUUCGGAGCUGCCAAUUUACGGCACUUUGGCCGUAAAGUUUUUGCCUCU-UGCCUAUAAAUUAUUGACAG
(((((.((.((..(.(-((.....))))..))......((((((((......)))))))))).)))))....-.................... ( -18.50)
>DroPer_CAF1 9081 76 - 1
-----------CACAA-CAAUAACUCC-UUGCUGCCAAUUUACGGCACUUUGGCCGCAAAGUUUUUGCCUUG----CUAUAAAUUAUUGACAG
-----------.....-((((((..((-..(.((((.......)))).)..))..((((.((....)).)))----)......)))))).... ( -14.30)
>consensus
_CA___ACAACCACAA_CAAAAACUGC_U_GCUGCCAAUUUACGGCACUUUGGCCGUAAAGUUUUUGCCU____GCCUAUAAAUUAUUGACAG
...............................(((.(((((((((((......))))))))((....))..................))).))) (-10.83 = -10.83 +   0.00)

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 10:11:07 2006