Locus 6740

Sequence ID 3R_DroMel_CAF1
Location 17,760,790 – 17,760,911
Length 121
Max. P 0.968871
window10945 window10946 window10947 window10948

overview

Window 5

Location 17,760,790 – 17,760,885
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -23.58
Consensus MFE -18.68
Energy contribution -19.36
Covariance contribution 0.68
Combinations/Pair 1.13
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.62
SVM RNA-class probability 0.801800
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17760790 95 + 27905053
UAGGCGUCAGAAUGGACGGAAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGUCCCGAUUAACAGC
.((((((((((((.((.((.....)))).)))))))))))).(((((..(((.(((...((.........))....))).)))..)).....))) ( -26.70)
>DroSec_CAF1 49411 89 + 1
UAGGCGUCUGAAUGUACGGAAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUGAAAACCAACACUUAAGGCACCUGAGGACCCGAU------C
..((((((.((((....((.....))...)))).))))))(((..((((.(..((....((.........))))..).))))..))).------. ( -21.30)
>DroSim_CAF1 49829 89 + 1
UAGGCGUUUGAAUGUACGGAAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------C
.((((((..((((....((.....))...))))..)))))).(((((.((....)).............((....)))))))......------. ( -18.90)
>DroEre_CAF1 52126 89 + 1
UAAGCGCCAGAAUGCACGGAAAUACCUCCAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------C
.....(((((((((...((.....))..)))))))))((((((...(((....................)))....))))))......------. ( -25.75)
>DroYak_CAF1 53015 89 + 1
UAAGCGCCAGAAUGCACGGAAAUACCUGAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------A
.....((((((((.((.((.....)))).))))))))((((((...(((....................)))....))))))......------. ( -25.25)
>consensus
UAGGCGUCAGAAUGCACGGAAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU______C
.((((((((((((....((.....))...)))))))))))).(((((.((....)).............((....)))))))............. (-18.68 = -19.36 +   0.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,760,790 – 17,760,885
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 91.58
Mean single sequence MFE -30.22
Consensus MFE -23.64
Energy contribution -24.12
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.78
SVM decision value 0.01
SVM RNA-class probability 0.537427
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17760790 95 - 27905053
GCUGUUAAUCGGGACCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUUCCGUCCAUUCUGACGCCUA
.(((...(((((((((...((..(.....)..)))))))))))..)))......(((((.((((((.((((.....)).)).)))))).))))). ( -31.70)
>DroSec_CAF1 49411 89 - 1
G------AUCGGGUCCUCAGGUGCCUUAAGUGUUGGUUUUCAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUUCCGUACAUUCAGACGCCUA
(------(.((((.(((((((((((((........((((((......)))))))))))))).....)))))....)))).....))......... ( -25.80)
>DroSim_CAF1 49829 89 - 1
G------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUUCCGUACAUUCAAACGCCUA
.------....((((....((((((((...(.((((........)))).)...))))))))....(((((((((....)))).)))))..)))). ( -26.50)
>DroEre_CAF1 52126 89 - 1
G------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUGGAGGUAUUUCCGUGCAUUCUGGCGCUUA
.------.((..(((.(((((.(((.........)))))))).)))..))....(((((((((((((.(((.....)).).))))))))))))). ( -34.60)
>DroYak_CAF1 53015 89 - 1
U------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUCAGGUAUUUCCGUGCAUUCUGGCGCUUA
.------.((..(((.(((((.(((.........)))))))).)))..))....((((((((((((.((((.....)).)).)))))))))))). ( -32.50)
>consensus
G______AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUUCCGUACAUUCUGACGCCUA
.........((((((((((((((((((...(.((((........)))).)...)))))))).....))))))...))))................ (-23.64 = -24.12 +   0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,760,809 – 17,760,911
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 94.79
Mean single sequence MFE -18.95
Consensus MFE -17.47
Energy contribution -17.55
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.54
Structure conservation index 0.92
SVM decision value 1.63
SVM RNA-class probability 0.968871
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17760809 102 + 27905053
AAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGUCCCGAUUAACAGCCGUUAACAGCCAUUUUUUGGCCACAA
....((((((.....((.((((.......((..........)).......)))).))))))))...(.(((((....)))))).((((.....))))..... ( -19.64)
>DroSec_CAF1 49430 95 + 1
AAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUGAAAACCAACACUUAAGGCACCUGAGGACCCGAU------CCGUUAACAGCCAUUU-UUGGCCACAA
.....(((((.....((.((((.......((..........)).......)))).))))))).......------.........((((...-.))))..... ( -17.64)
>DroSim_CAF1 49848 95 + 1
AAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------CCGUUAACAGCCAUUU-UUGGCCACAA
............((.((.((((((...(((....................)))....)))))))).)).------.........((((...-.))))..... ( -19.15)
>DroEre_CAF1 52145 95 + 1
AAAUACCUCCAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------CCGUUAACAGCCAUUU-UUGGCCACAA
............((.((.((((((...(((....................)))....)))))))).)).------.........((((...-.))))..... ( -19.15)
>DroYak_CAF1 53034 95 + 1
AAAUACCUGAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU------ACGUUAACAGCCAUUU-UUGGCCACAA
............((.((.((((((...(((....................)))....)))))))).)).------.........((((...-.))))..... ( -19.15)
>consensus
AAAUACCUCAAUUCUGGCGCCUCGCUUCCUGACAUCAAAACCAACACUUAAGGCACCUGAGGCCCCGAU______CCGUUAACAGCCAUUU_UUGGCCACAA
..............(((.((((((...(((....................)))....)))))).))).................((((.....))))..... (-17.47 = -17.55 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,760,809 – 17,760,911
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 94.79
Mean single sequence MFE -28.68
Consensus MFE -26.72
Energy contribution -27.20
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.08
Structure conservation index 0.93
SVM decision value 0.04
SVM RNA-class probability 0.555202
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17760809 102 - 27905053
UUGUGGCCAAAAAAUGGCUGUUAACGGCUGUUAAUCGGGACCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUU
......((....((((((((....)))))))).....))((((((((((((((...(.((((........)))).)...)))))))).....)))))).... ( -32.00)
>DroSec_CAF1 49430 95 - 1
UUGUGGCCAA-AAAUGGCUGUUAACGG------AUCGGGUCCUCAGGUGCCUUAAGUGUUGGUUUUCAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUU
..(..((((.-...))))..)......------...(((((((((((((((((........((((((......)))))))))))))).....))))).)))) ( -27.60)
>DroSim_CAF1 49848 95 - 1
UUGUGGCCAA-AAAUGGCUGUUAACGG------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUU
..(..((((.-...))))..)......------......((((((((((((((...(.((((........)))).)...)))))))).....)))))).... ( -29.30)
>DroEre_CAF1 52145 95 - 1
UUGUGGCCAA-AAAUGGCUGUUAACGG------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUGGAGGUAUUU
.((.((((..-...((((((....)))------.))).)))).))((((((((...(.((((........)))).)...))))))))............... ( -28.10)
>DroYak_CAF1 53034 95 - 1
UUGUGGCCAA-AAAUGGCUGUUAACGU------AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUCAGGUAUUU
..(..((((.-...))))..)....((------(((..((..((.((((((((...(.((((........)))).)...)))))))).))..)).))))).. ( -26.40)
>consensus
UUGUGGCCAA_AAAUGGCUGUUAACGG______AUCGGGGCCUCAGGUGCCUUAAGUGUUGGUUUUGAUGUCAGGAAGCGAGGCGCCAGAAUUGAGGUAUUU
..(..((((.....))))..)..................((((((((((((((...(.((((........)))).)...)))))))).....)))))).... (-26.72 = -27.20 +   0.48)

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 12:28:48 2006