Locus 5782

Sequence ID 3R_DroMel_CAF1
Location 15,076,832 – 15,077,027
Length 195
Max. P 0.920237
window9473 window9474 window9475 window9476

overview

Window 3

Location 15,076,832 – 15,076,930
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.29
Mean single sequence MFE -29.85
Consensus MFE -17.44
Energy contribution -17.42
Covariance contribution -0.03
Combinations/Pair 1.09
Mean z-score -1.67
Structure conservation index 0.58
SVM decision value -0.03
SVM RNA-class probability 0.520531
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15076832 98 + 27905053
CACAGAA----UAUGCGCAAGACAUUGAUUUUCGCCAGGUAAUGAGGCAACUCAUUAAUCAUUU-UUUCGUUGCG----------------CACUGGCUGGGGGAUUAUGUUGCU-GUUG
.((((((----(((((....).)).(((((..((((((.(((((((....))))))).......-....(.....----------------).)))))..)..))))))))).))-)).. ( -27.80)
>DroVir_CAF1 4040 97 + 1
CAGAGCA----UAUGCGC--GACAUUGAUUUUCGCCAAGUAAUGAGGCAACUCAUUAAUCAUUUUUUUAGUUGUG----------------CAUCGGCUGGGGGAUUAUGUUGCC-GGCG
.......----.((((((--(((.(((........))).(((((((....)))))))............))))))----------------)))..(((((.((......)).))-))). ( -30.00)
>DroGri_CAF1 4335 112 + 1
CACAGAA----UAUGUGC--GACAUUGAUUUUCGUAAAGUAAUGAGGCAACUCAUUAAUCAUUU-UUUAGUUGUGUAUGUGUGUAAAAAUUCAUCGUCAGGGGGAUUAUGUUGCU-AGCA
.(((...----..)))((--(((((.((((..(......(((((((....))))))).......-.....(((((.(((.((......)).))))).))))..))))))))))).-.... ( -25.60)
>DroEre_CAF1 1581 98 + 1
CACGGAA----UAUGCGCAAGACAUUGAUUUUCGCCAGGUAAUGAGGCAACUCAUUAAUCAUUU-UUUCGUUGCG----------------CACUGGCUGGGGGAUUAUGUUGCU-UUUG
.......----.....(((..((((.((((..((((((.(((((((....))))))).......-....(.....----------------).)))))..)..))))))))))).-.... ( -26.60)
>DroMoj_CAF1 3977 102 + 1
GGGCGCAGUGCAAUGCGC--GACAUUGAUUUUCGCGAAGUAAUGAGGCAACUCAUUAAUCAUUUUUUUAGCUGUG----------------CAUCGGCUGGGGGAUUAUGCUGCCCGGCA
..(((((((......(((--((.........)))))...(((((((....)))))))............))))))----------------)....((((((((......)).)))))). ( -37.90)
>DroAna_CAF1 51 98 + 1
CGCAGAA----UAUGCGCAAGACAUUGAUUUUCGCCAGGUAAUGAGGCAACUCAUUAAUCAUUU-UUUCGUUGAG----------------CUCUGGCUGGGGGAUUAUGUUGCA-GUUG
.(((...----..)))(((..((((.((((..((((((((((((((....))))))).(((...-......))).----------------.))))))..)..))))))))))).-.... ( -31.20)
>consensus
CACAGAA____UAUGCGC__GACAUUGAUUUUCGCCAAGUAAUGAGGCAACUCAUUAAUCAUUU_UUUAGUUGUG________________CACCGGCUGGGGGAUUAUGUUGCU_GGCG
................((..(((((.((((..(......(((((((....)))))))............((((.....................))))..)..)))))))))))...... (-17.44 = -17.42 +  -0.03)

alignment

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secondary structure

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Window 4

Location 15,076,868 – 15,076,959
Length 91
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 82.73
Mean single sequence MFE -30.48
Consensus MFE -21.15
Energy contribution -21.39
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -2.21
Structure conservation index 0.69
SVM decision value 1.13
SVM RNA-class probability 0.920237
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15076868 91 + 27905053
AAUGAGGCAACUCAUUAAUCAUUUUUUCGUUGCGCACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAA----CCG-------G
((((((....))))))............(((((.((.((((.((.(..((.((((((....))))))))..).))))))..))))))----)..-------. ( -30.90)
>DroSec_CAF1 2035 91 + 1
AAUGAGGCAACUCAUUAAUCAUUUUUUCGUUGCGCACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAA----CCG-------G
((((((....))))))............(((((.((.((((.((.(..((.((((((....))))))))..).))))))..))))))----)..-------. ( -30.90)
>DroEre_CAF1 1617 98 + 1
AAUGAGGCAACUCAUUAAUCAUUUUUUCGUUGCGCACUGGCUGGGGGAUUAUGUUGCUUUUGCAACAAGCACACCGGCAACUCGCAA----CUGGCAACUGG
((((((....))))))............((((((.....(((((.(..((.((((((....))))))))..).)))))....)))))----).(....)... ( -34.00)
>DroAna_CAF1 87 86 + 1
AAUGAGGCAACUCAUUAAUCAUUUUUUCGUUGAGCUCUGGCUGGGGGAUUAUGUUGCAGUUGCAAG-------CCGGUG--UGUCGAUGUGCCU-------G
((((((....))))))...........((((((((.((((((..(.((((.......)))).).))-------)))).)--).)))))).....-------. ( -26.10)
>consensus
AAUGAGGCAACUCAUUAAUCAUUUUUUCGUUGCGCACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAA____CCG_______G
((((((....)))))).............((((......(((((.......((((((....))))))......))))).....))))............... (-21.15 = -21.39 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,076,902 – 15,076,992
Length 90
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 78.52
Mean single sequence MFE -31.50
Consensus MFE -19.70
Energy contribution -20.53
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.63
SVM decision value 0.40
SVM RNA-class probability 0.719362
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15076902 90 + 27905053
CACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAACCG-------GCAACCGGCAACGAGCAACGUGCAACAGUUGCUG
.....(((((((.....((((((....))))))......))(((....)))..)))-------))...((....))((((((........)))))). ( -34.40)
>DroSec_CAF1 2069 72 + 1
CACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAACCG-------GC--------------AACGUGCAACAGUU----
(((..(((((((.....((((((....))))))......))(((....)))..)))-------))--------------...)))........---- ( -25.20)
>DroEre_CAF1 1651 97 + 1
CACUGGCUGGGGGAUUAUGUUGCUUUUGCAACAAGCACACCGGCAACUCGCAACUGGCAACUGGCGACCGGCUACGAGCAACGUGCAACAGUUGCCG
.....(((((.(..((.((((((....))))))))..).)))))...........(((((((((((....((.....))....)))..)))))))). ( -34.90)
>consensus
CACUGGCUGGGGGAUUAUGUUGCUGUUGCAACAAGCACACCGCCAACUGGCAACCG_______GC_ACCGGC_ACGAGCAACGUGCAACAGUUGC_G
....(((((........((((((....)))))).((((...(((....))).................((....))......))))..))))).... (-19.70 = -20.53 +   0.83)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,076,930 – 15,077,027
Length 97
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 79.34
Mean single sequence MFE -33.17
Consensus MFE -21.63
Energy contribution -22.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.65
SVM decision value 1.00
SVM RNA-class probability 0.898463
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15076930 97 + 27905053
CAACAAGCACACCGCCAACUGGCAACCG-------GCAACCGGCAACGAGCAACGUGCAACAGUUGCUGCUGCCUCUGACGGAAUGCUGGCAACAUGUUGAGCG
(((((((((..(((.((...((((..((-------(((((((....)).((.....))....))))))).))))..)).)))..))))(....).))))).... ( -35.60)
>DroSec_CAF1 2097 77 + 1
CAACAAGCACACCGCCAACUGGCAACCG-------GC--------------AACGUGCAACAGUU------GCCUCUGACGGAAUGCUGGCAACAUGUUGAGCG
(((((((((..(((((....)))....(-------((--------------(((........)))------)))......))..))))(....).))))).... ( -27.20)
>DroEre_CAF1 1679 104 + 1
CAACAAGCACACCGGCAACUCGCAACUGGCAACUGGCGACCGGCUACGAGCAACGUGCAACAGUUGCCGCUGCCUCUGACGGAAUGCUGGCAACAUGUUGAGCG
(((((.((((..(((....((((....(....)..)))))))((.....))...))))....((((((((..((......))...)).)))))).))))).... ( -36.70)
>consensus
CAACAAGCACACCGCCAACUGGCAACCG_______GC_ACCGGC_ACGAGCAACGUGCAACAGUUGC_GCUGCCUCUGACGGAAUGCUGGCAACAUGUUGAGCG
(((((((((..(((.((...(((.................((....)).(((((........)))))....)))..)).)))..))))(....).))))).... (-21.63 = -22.30 +   0.67)

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 12:04:39 2006