Locus 5652

Sequence ID 3R_DroMel_CAF1
Location 14,835,818 – 14,836,018
Length 200
Max. P 0.970558
window9229 window9230 window9231 window9232 window9233

overview

Window 9

Location 14,835,818 – 14,835,938
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.93
Mean single sequence MFE -33.73
Consensus MFE -27.73
Energy contribution -28.73
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.73
Structure conservation index 0.82
SVM decision value 1.10
SVM RNA-class probability 0.914769
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835818 120 + 27905053
CGACAACUUGGAUCCCUGUUCAAUAGGUUGCCAAACUUGUUUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGUCGACUGUCGACUGUCGCCAGCUAUCCUCAUUUUUUGUUU
.(((((((.((...(((((...)))))((((((((.....))))))))........))))))))).....((((((((........)))))))).......................... ( -35.80)
>DroSec_CAF1 14034 101 + 1
CGACAACUUGGAUCCCUGUUCAAUAGGUUGCCAAACUUGUUUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGAC--------------UGUCGCCAGCUAUCCUGGUUUU-----U
.(((((((.((...(((((...)))))((((((((.....))))))))........))))))))).....(((....)--------------))..(((((.....)))))...-----. ( -29.10)
>DroSim_CAF1 14169 108 + 1
CGACAACUUGGAUCCCUGUUCAAUAGGUUGCCAAACUUGUUUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGU-------CGACUGUCGCCAGCUAUCCUGGUUUU-----U
.(((((((.((...(((((...)))))((((((((.....))))))))........))))))))).....((((((.....-------))))))..(((((.....)))))...-----. ( -36.30)
>consensus
CGACAACUUGGAUCCCUGUUCAAUAGGUUGCCAAACUUGUUUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGU_______CGACUGUCGCCAGCUAUCCUGGUUUU_____U
.(((((((.((...(((((...)))))((((((((.....))))))))........))))))))).......(.((((.((((.....)))).)))).)..................... (-27.73 = -28.73 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,835,818 – 14,835,938
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.93
Mean single sequence MFE -36.50
Consensus MFE -32.07
Energy contribution -33.07
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.88
SVM decision value 1.44
SVM RNA-class probability 0.954169
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835818 120 - 27905053
AAACAAAAAAUGAGGAUAGCUGGCGACAGUCGACAGUCGACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAAACAAGUUUGGCAACCUAUUGAACAGGGAUCCAAGUUGUCG
..............(((((((.....((((((((........))))))))(((((((((((....)))))).((((((((.....))))))))(((.......)))))))).))))))). ( -40.40)
>DroSec_CAF1 14034 101 - 1
A-----AAAACCAGGAUAGCUGGCGACA--------------GUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAAACAAGUUUGGCAACCUAUUGAACAGGGAUCCAAGUUGUCG
.-----....((((....((((....))--------------))...))))....((((((.(((.((((((((((((((.....))))))))......)))))).)..))..)))))). ( -32.70)
>DroSim_CAF1 14169 108 - 1
A-----AAAACCAGGAUAGCUGGCGACAGUCG-------ACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAAACAAGUUUGGCAACCUAUUGAACAGGGAUCCAAGUUGUCG
.-----........(((((((.....((((((-------.....))))))(((((((((((....)))))).((((((((.....))))))))(((.......)))))))).))))))). ( -36.40)
>consensus
A_____AAAACCAGGAUAGCUGGCGACAGUCG_______ACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAAACAAGUUUGGCAACCUAUUGAACAGGGAUCCAAGUUGUCG
..............(((((((((((((.((((.....)))).)))).)).(((((((((((....)))))).((((((((.....))))))))(((.......)))))))).))))))). (-32.07 = -33.07 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,835,858 – 14,835,978
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.21
Mean single sequence MFE -29.70
Consensus MFE -21.83
Energy contribution -23.50
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -3.50
Structure conservation index 0.74
SVM decision value 1.47
SVM RNA-class probability 0.956502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835858 120 + 27905053
UUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGUCGACUGUCGACUGUCGCCAGCUAUCCUCAUUUUUUGUUUUUUUCUCAUCUUUGUUUUUGCCAGCUGCAAUCGACUUUUA
.(((((((((((((.((.(((.(.((.((.((((((.....))))))..)).)).)))).))......((.....))..............)))))))))))))................ ( -31.60)
>DroSec_CAF1 14074 101 + 1
UUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGAC--------------UGUCGCCAGCUAUCCUGGUUUU-----UUUUUCUCAUUUUUGUUUUUGCCAGCUCCAAUCGACUUUUA
.(((((((((((((.(.((((((.(.......).))))--------------)).)(((((.....)))))...-----............)))))))))))))................ ( -27.40)
>DroSim_CAF1 14209 108 + 1
UUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGU-------CGACUGUCGCCAGCUAUCCUGGUUUU-----UUUUUCACAUUUUUGUUUUUGCCAGCUCCAAUCGACUUUUA
.(((((((((((((.(.((((((.((.((......)).)).-------)))))).)(((((.....)))))...-----............)))))))))))))................ ( -30.10)
>consensus
UUUGGCAAAAACAACGCCGGUUGUCAAUCCCAGUCGACUGU_______CGACUGUCGCCAGCUAUCCUGGUUUU_____UUUUUCUCAUUUUUGUUUUUGCCAGCUCCAAUCGACUUUUA
.(((((((((((((....(..((.......))..)(((.((((.....)))).)))(((((.....)))))....................)))))))))))))................ (-21.83 = -23.50 +   1.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,835,858 – 14,835,978
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.21
Mean single sequence MFE -33.74
Consensus MFE -25.75
Energy contribution -26.87
Covariance contribution 1.11
Combinations/Pair 1.04
Mean z-score -3.86
Structure conservation index 0.76
SVM decision value 1.66
SVM RNA-class probability 0.970558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835858 120 - 27905053
UAAAAGUCGAUUGCAGCUGGCAAAAACAAAGAUGAGAAAAAAACAAAAAAUGAGGAUAGCUGGCGACAGUCGACAGUCGACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAA
.................((((((((((((..............((.....))......(((((...(((((..((((((.....)))))).)))))....))))).)))))))))))).. ( -37.20)
>DroSec_CAF1 14074 101 - 1
UAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGAGAAAAA-----AAAACCAGGAUAGCUGGCGACA--------------GUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAA
....(((((((((..((..((....................-----............))..))..))--------------)))))))((.(..((((((....))))))..).))... ( -31.75)
>DroSim_CAF1 14209 108 - 1
UAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGUGAAAAA-----AAAACCAGGAUAGCUGGCGACAGUCG-------ACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAA
.....((((((((..((..((.............(....).-----............))..))..))))))-------)).......(((.(..((((((....))))))..).))).. ( -32.27)
>consensus
UAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGAGAAAAA_____AAAACCAGGAUAGCUGGCGACAGUCG_______ACAGUCGACUGGGAUUGACAACCGGCGUUGUUUUUGCCAAA
.................((((((((((((.....................((((.....))))((((.((((.....)))).)))).((((.........))))..)))))))))))).. (-25.75 = -26.87 +   1.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,835,898 – 14,836,018
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -21.98
Consensus MFE -19.65
Energy contribution -19.65
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.89
SVM decision value 1.14
SVM RNA-class probability 0.921975
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835898 120 - 27905053
UAAAAGUCAUUUUAUUAAGAAGCAGUCGACAGAAUGGAGCUAAAAGUCGAUUGCAGCUGGCAAAAACAAAGAUGAGAAAAAAACAAAAAAUGAGGAUAGCUGGCGACAGUCGACAGUCGA
.........................(((((((.......))....((((((((..((..((.....((....)).........((.....))......))..))..)))))))).))))) ( -25.30)
>DroSec_CAF1 14112 103 - 1
UAAAAGUCAUUUUAUUAAGAAGCAGUCGACAGAAUGGAGCUAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGAGAAAAA-----AAAACCAGGAUAGCUGGCGACA------------
.....(((..............((((((((...............))))))))..((..((....................-----............))..))))).------------ ( -20.11)
>DroSim_CAF1 14249 108 - 1
UAAAAGUCAUUUUAUUAAGAAGCAGUCGACAGAAUGGAGCUAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGUGAAAAA-----AAAACCAGGAUAGCUGGCGACAGUCG-------A
.....(((..............((((((((...............))))))))..((..((.............(....).-----............))..))))).....-------. ( -20.53)
>consensus
UAAAAGUCAUUUUAUUAAGAAGCAGUCGACAGAAUGGAGCUAAAAGUCGAUUGGAGCUGGCAAAAACAAAAAUGAGAAAAA_____AAAACCAGGAUAGCUGGCGACAGUCG_______A
.....(((..............((((((((...............))))))))..((..((.....................................))..)))))............. (-19.65 = -19.65 +   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 12:00:44 2006