Locus 6056

Sequence ID 3L_DroMel_CAF1
Location 16,122,353 – 16,122,551
Length 198
Max. P 0.984524
window9701 window9702 window9703 window9704

overview

Window 1

Location 16,122,353 – 16,122,472
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -24.40
Consensus MFE -24.19
Energy contribution -23.97
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.99
SVM decision value 0.35
SVM RNA-class probability 0.700768
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16122353 119 + 23771897
CACCUCCACCUUCACCUCC-CCCUGCCGCCUGUCUACGGGCAUUAUCAGCAGACAUAUAGUUUGGUUCCAUUUGUAAUCGCUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUC
...............(((.-.......(((((....))))).......(((.......(((((((.....((((.(((((.....)))))))))...))))))).....))).))).... ( -23.80)
>DroSec_CAF1 8056 119 + 1
CACCUCCACCCUCACCUCC-CCCUGCCGCCUGUCUACGGGCAUUAUCAGCAGACAUAUAGUUUGGUUCCAUUUGUAAUCGCUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUC
..........(((......-.......(((((....))))).......(((.......(((((((.....((((.(((((.....)))))))))...))))))).....))).))).... ( -24.70)
>DroSim_CAF1 7368 120 + 1
CACCUCCACCCUCACCUCCCCCCUGCCGCCUGUCUACGGGCAUUAUCAGCAGACAUAUAGUUUGGUUCCAUUUGUAAUCGCUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUC
..........(((..............(((((....))))).......(((.......(((((((.....((((.(((((.....)))))))))...))))))).....))).))).... ( -24.70)
>consensus
CACCUCCACCCUCACCUCC_CCCUGCCGCCUGUCUACGGGCAUUAUCAGCAGACAUAUAGUUUGGUUCCAUUUGUAAUCGCUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUC
..........(((..............(((((....))))).......(((.......(((((((.....((((.(((((.....)))))))))...))))))).....))).))).... (-24.19 = -23.97 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,122,392 – 16,122,512
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -31.77
Consensus MFE -30.03
Energy contribution -30.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.95
SVM decision value 0.28
SVM RNA-class probability 0.667447
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16122392 120 - 23771897
AAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCUGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAGCGAUUACAAAUGGAACCAAACUAUAUGUCUGCUGAUAAUG
..((.((.((.((((((...(....).((((.((((((.(....).)))))))))).((((((....))))))......)))))).)).)).))...........((((....))))... ( -34.40)
>DroSec_CAF1 8095 120 - 1
AAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAUUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAGCGAUUACAAAUGGAACCAAACUAUAUGUCUGCUGAUAAUG
..((.((.((.((((((...(....).((((.((((...(....)...)))))))).((((((....))))))......)))))).)).)).))...........((((....))))... ( -30.40)
>DroSim_CAF1 7408 120 - 1
AAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAGCGAUUACAAAUGGAACCAAACUAUAUGUCUGCUGAUAAUG
..((.((.((.((((((...(....).((((.((((.(.(....).).)))))))).((((((....))))))......)))))).)).)).))...........((((....))))... ( -30.50)
>consensus
AAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAGCGAUUACAAAUGGAACCAAACUAUAUGUCUGCUGAUAAUG
..((.((.((.((((((...(....).((((.((((...(....)...)))))))).((((((....))))))......)))))).)).)).))...........((((....))))... (-30.03 = -30.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,122,432 – 16,122,551
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -35.66
Consensus MFE -33.21
Energy contribution -33.10
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -3.56
Structure conservation index 0.93
SVM decision value 1.98
SVM RNA-class probability 0.984524
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16122432 119 + 23771897
CUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUCCACAGCACGUGUGCGUUUCCAUUGCGAUUCCAUAUCGAUUCGCAAUGGAAUCAGACAUUA-AAACUGACACACAGUAUAU
...................((((((........)))))).........(((((...(((((((((((.((......)).)))))))))))((((......-...)))))))))....... ( -31.20)
>DroSec_CAF1 8135 120 + 1
CUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUCCAAUGCACGUGUGCGUUUCCAUUGCGAUUCCAUAUCGAUUCGCGAUGGAAUCGGACAUAAAAAACUGACACACGGUAUAU
.....((((((.(....).))).)))..((((((.((.((........((((.((.(((((((((((.((......)).))))))))))).)).))))........)).)).)))))).. ( -36.49)
>DroSim_CAF1 7448 120 + 1
CUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUCCACUGCACGUGUGCGUUUCCAUUGCGAUUCCAUAUCGAUUCGCGAUGGAAGCGGACAUAAAAAACUGACACACAGUAUAU
...((((..((((......((((((........)))))).........((((.((((((((((((((.((......)).)))))))))))))).))))......))))....)))).... ( -39.30)
>consensus
CUCAUUGAUUCAGAAUUCCGAACUCACAAUGCCGAGUUUCCACUGCACGUGUGCGUUUCCAUUGCGAUUCCAUAUCGAUUCGCGAUGGAAUCGGACAUAAAAAACUGACACACAGUAUAU
...((((..((((......((((((........)))))).........((((.((.(((((((((((.((......)).))))))))))).)).))))......))))....)))).... (-33.21 = -33.10 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,122,432 – 16,122,551
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -38.67
Consensus MFE -33.22
Energy contribution -33.00
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.71
Structure conservation index 0.86
SVM decision value 0.86
SVM RNA-class probability 0.868515
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16122432 119 - 23771897
AUAUACUGUGUGUCAGUUU-UAAUGUCUGAUUCCAUUGCGAAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCUGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAG
......((((((((((...-......))))(((((((((((.((......)).))))))))))).)))))).((((((.(....).))))))..(((.(((((....))))))))..... ( -43.40)
>DroSec_CAF1 8135 120 - 1
AUAUACCGUGUGUCAGUUUUUUAUGUCCGAUUCCAUCGCGAAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAUUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAG
......(((...((((.........(((((((((((.((((.((......)).)))).))))))((.((((.((((...(....)...)))))))).)))))))...))))....))).. ( -36.80)
>DroSim_CAF1 7448 120 - 1
AUAUACUGUGUGUCAGUUUUUUAUGUCCGCUUCCAUCGCGAAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAG
...(((...(((((((((.......(((((((((((.((((.((......)).)))).))))))..(((....))).))))))))).))))).))).((((((....))))))....... ( -35.81)
>consensus
AUAUACUGUGUGUCAGUUUUUUAUGUCCGAUUCCAUCGCGAAUCGAUAUGGAAUCGCAAUGGAAACGCACACGUGCAGUGGAAACUCGGCAUUGUGAGUUCGGAAUUCUGAAUCAAUGAG
......(((((((((........))...(.((((((.((((.((......)).)))).)))))).))))))))(((...(....)...)))(..(..((((((....))))))..)..). (-33.22 = -33.00 +  -0.22)

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 12:08:28 2006