Locus 5752

Sequence ID 3L_DroMel_CAF1
Location 15,629,400 – 15,629,672
Length 272
Max. P 0.958344
window9123 window9124 window9125 window9126 window9127

overview

Window 3

Location 15,629,400 – 15,629,518
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.84
Mean single sequence MFE -24.55
Consensus MFE -21.99
Energy contribution -22.05
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.90
SVM decision value 1.49
SVM RNA-class probability 0.958344
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15629400 118 + 23771897
ACCGGAGCAACCCGAUUCCAAAAAUCCAAAAAUCCAGAGAUCCAUA--GAUCCAGAGUAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAU
.(((((((((...(.((((.................(.((((....--)))))...((..(((......)))..)))))).).(((((....)))))...........)))))))))... ( -24.70)
>DroSec_CAF1 51628 118 + 1
ACCGGAGCAACCCGACUUCAAAAAUCCCAAAAUCCAGAGAUCCAUA--GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAU
.(((((((((.(((......................(.((((....--))))).........((((...))))..))).....(((((....)))))...........)))))))))... ( -23.20)
>DroSim_CAF1 52637 118 + 1
ACCGGAGCAACCCGACUCCAAAAAUCCAAAAAUCCUAAGAUCCAUA--GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAU
...((((........))))...........................--..((((((((((..((((...))))..........(((((....)))))...........)))))))))).. ( -24.20)
>DroYak_CAF1 56196 120 + 1
ACCGAAGCAACCCGACUCCAAAAAUCCACAGAUCUAAAAAUCCAUAGAGAUCCAGAGUAAAGCAGCCAGGCUGAACGGAAGCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAU
.(((((((((....................(((((............)))))..((((((..((((...))))..(....).....))))))................)))))))))... ( -26.10)
>consensus
ACCGGAGCAACCCGACUCCAAAAAUCCAAAAAUCCAAAGAUCCAUA__GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAU
.(((((((((.(((........................((((......))))..........((((...))))..))).....(((((....)))))...........)))))))))... (-21.99 = -22.05 +   0.06)

alignment

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secondary structure

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Window 4

Location 15,629,400 – 15,629,518
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.84
Mean single sequence MFE -34.44
Consensus MFE -26.56
Energy contribution -26.50
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.77
SVM decision value -0.04
SVM RNA-class probability 0.514772
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15629400 118 - 23771897
AUUCCAAAGCAAUUUUGAUGUUGACAUUGAGUAAUGUUGGUUCCGUUCAGCCUGGCUGCUUUACUCUGGAUC--UAUGGAUCUCUGGAUUUUUGGAUUUUUGGAAUCGGGUUGCUCCGGU
...((..((((((((..(((....)))..)).....((((((((((..(((......)))..))...(((((--((..((((....))))..)))))))..))))))))))))))..)). ( -30.90)
>DroSec_CAF1 51628 118 - 1
AUUCCAAAGCAAUUUUGAUGUUGACAUUGAGUAAUGUUGGUUCCGUUCAGCCUGGCUGCUUUGCUCUGGAUC--UAUGGAUCUCUGGAUUUUGGGAUUUUUGAAGUCGGGUUGCUCCGGU
...((((......((..(((....)))..)).....))))..(((..((((((((((......(((..((((--((........))))))..)))........))))))))))...))). ( -33.14)
>DroSim_CAF1 52637 118 - 1
AUUCCAAAGCAAUUUUGAUGUUGACAUUGAGUAAUGUUGGUUCCGUUCAGCCUGGCUGCUUUGCUCUGGAUC--UAUGGAUCUUAGGAUUUUUGGAUUUUUGGAGUCGGGUUGCUCCGGU
...((((......((..(((....)))..)).....))))..(((..((((((((((.(........(((((--((..((((....))))..)))))))..).))))))))))...))). ( -34.40)
>DroYak_CAF1 56196 120 - 1
AUUCCAAAGCAAUUUUGAUGUUGACAUUGAGUAAUGUUGCUUCCGUUCAGCCUGGCUGCUUUACUCUGGAUCUCUAUGGAUUUUUAGAUCUGUGGAUUUUUGGAGUCGGGUUGCUUCGGU
......(((((((((..(((....)))..))....)))))))(((..(((((((........((((..((..((((((((((....))))))))))..))..)))))))))))...))). ( -39.30)
>consensus
AUUCCAAAGCAAUUUUGAUGUUGACAUUGAGUAAUGUUGGUUCCGUUCAGCCUGGCUGCUUUACUCUGGAUC__UAUGGAUCUCUGGAUUUUUGGAUUUUUGGAGUCGGGUUGCUCCGGU
...((((......((..(((....)))..)).....))))..(((..((((((((((.(....((..(((((......)))))..))(((....)))....).))))))))))...))). (-26.56 = -26.50 +  -0.06)

alignment

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secondary structure

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Window 5

Location 15,629,440 – 15,629,558
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.18
Mean single sequence MFE -25.23
Consensus MFE -24.15
Energy contribution -23.90
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.96
SVM decision value 1.09
SVM RNA-class probability 0.914008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15629440 118 + 23771897
UCCAUA--GAUCCAGAGUAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAAC
..(((.--.(((((((((((..((((...))))..........(((((....)))))...........))))))))).))..)))..............(((((.......))))).... ( -23.50)
>DroSec_CAF1 51668 118 + 1
UCCAUA--GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAAC
..(((.--.(((((((((((..((((...))))..........(((((....)))))...........))))))))).))..)))..............(((((.......))))).... ( -25.50)
>DroSim_CAF1 52677 118 + 1
UCCAUA--GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAAC
..(((.--.(((((((((((..((((...))))..........(((((....)))))...........))))))))).))..)))..............(((((.......))))).... ( -25.50)
>DroYak_CAF1 56236 120 + 1
UCCAUAGAGAUCCAGAGUAAAGCAGCCAGGCUGAACGGAAGCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAAC
..(((.(((.((((((((((.((..((.(......)))..)).(((((....)))))...........)))))))))).))))))..............(((((.......))))).... ( -26.40)
>consensus
UCCAUA__GAUCCAGAGCAAAGCAGCCAGGCUGAACGGAACCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAAC
..........((((((((((..((((...))))..........(((((....)))))...........)))))))))).....................(((((.......))))).... (-24.15 = -23.90 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,629,478 – 15,629,598
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -21.60
Consensus MFE -21.60
Energy contribution -21.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 1.00
SVM decision value 0.16
SVM RNA-class probability 0.613238
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15629478 120 + 23771897
CCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAACUAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAA
........(((((..(((.........(((((...(((((..(((....)))..)))))(((((.......)))))........)))))...((((.......))))))))))))..... ( -21.60)
>DroSec_CAF1 51706 120 + 1
CCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAACUAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAA
........(((((..(((.........(((((...(((((..(((....)))..)))))(((((.......)))))........)))))...((((.......))))))))))))..... ( -21.60)
>DroSim_CAF1 52715 120 + 1
CCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAACUAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAA
........(((((..(((.........(((((...(((((..(((....)))..)))))(((((.......)))))........)))))...((((.......))))))))))))..... ( -21.60)
>DroYak_CAF1 56276 120 + 1
GCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAACUAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAA
........(((((..(((.........(((((...(((((..(((....)))..)))))(((((.......)))))........)))))...((((.......))))))))))))..... ( -21.60)
>consensus
CCAACAUUACUCAAUGUCAACAUCAAAAUUGCUUUGGAAUUCAUGCAUUCAUUUAUUUCGCCUUCAACAAAAAGGCAAACUAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAA
........(((((..(((.........(((((...(((((..(((....)))..)))))(((((.......)))))........)))))...((((.......))))))))))))..... (-21.60 = -21.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,629,558 – 15,629,672
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.31
Mean single sequence MFE -33.98
Consensus MFE -32.54
Energy contribution -32.60
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.96
SVM decision value 1.28
SVM RNA-class probability 0.939496
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15629558 114 + 23771897
UAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAAUUCGGGGGAAUCGGAAUCUCCGGGGUCCUUAAAUAGCUGAACAGCCGUUUGGGAAUGAGAAUGGGAACGG------GAAC
...(.(.........(((((((((((((((((((((...(((..((((..((((.....))))..))))..)))))))...))))))....)))))))))))(....)).------)... ( -32.70)
>DroSec_CAF1 51786 120 + 1
UAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAAUUCGGGGGAAUCGGAAUCUCCGGGGUCCUUAAAUAGCUGAACAGCCGGUUGGGAAUGGGAAUGGGAACGGGAAUGGGAAC
...(.((........(((..((((..((((((.......(((..((((..((((.....))))..))))..))).(((....)))))))))..))))..)))(....).....)).)... ( -35.10)
>DroSim_CAF1 52795 114 + 1
UAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAAUUCGGGGGAAUCGGAAUCUCCGGGGUCCUUAAAUAGCUGAACAGCCGGUUGGGAAUGGGAAUGGGAACGG------GAAC
...(.(.........(((..((((..((((((.......(((..((((..((((.....))))..))))..))).(((....)))))))))..))))..)))(....)).------)... ( -34.40)
>DroYak_CAF1 56356 104 + 1
UAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAAUUCGGGGGAAUCGGAAUCUCCGGGGUCCUUAAAUAGCUGAACAGCCGGUUGGGAAUGGGAAUGG----------------
...............(((..((((..((((((.......(((..((((..((((.....))))..))))..))).(((....)))))))))..))))..)))..---------------- ( -33.70)
>consensus
UAACGCAGUAUAGAAAUUUUCAUUUUCGGCUGAGUUUUAAUUCGGGGGAAUCGGAAUCUCCGGGGUCCUUAAAUAGCUGAACAGCCGGUUGGGAAUGGGAAUGGGAACGG______GAAC
...............(((((((((..((((((.......(((..((((..((((.....))))..))))..))).(((....)))))))))..))))))))).................. (-32.54 = -32.60 +   0.06)

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 11:58:50 2006