Locus 8672

Sequence ID 3R_DroMel_CAF1
Location 23,159,767 – 23,160,047
Length 280
Max. P 0.968403
window13926 window13927 window13928 window13929

overview

Window 6

Location 23,159,767 – 23,159,887
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -28.64
Consensus MFE -24.14
Energy contribution -24.03
Covariance contribution -0.10
Combinations/Pair 1.15
Mean z-score -2.45
Structure conservation index 0.84
SVM decision value 0.57
SVM RNA-class probability 0.784671
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23159767 120 + 27905053
AAGAAAAACCAGGCAAAAAAGUGAACAAUUUAAACUUUUGUAUGAAUAUAAAAGGGGGGCUGUGUGGGAAAUUAAAGCGCUGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGGCGAAAG
........((((.(....................((((((((....))))))))((((((.((((...........)))).)))..((((........)))).)))).))))........ ( -28.70)
>DroSec_CAF1 9830 120 + 1
ACGAAAAACCAGGCAAAAAAGUGAACAAUUUAAACUUUUAUAUGUAUAUAAAAGGGGGGCUACGUAGGAAAUUAAAGCGCUGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGUCGAAAG
.(((....((((.(....................((((((((....))))))))((((((..(((...........)))..)))..((((........)))).)))).)))).))).... ( -29.80)
>DroSim_CAF1 15136 120 + 1
AAGAAAAACCAGGCAAAAAAGUGAACAAUUUAAACUUUUGUAUGAAUAAAUAAGGGGGGCUAUGCAGGAAAUUAAAGCGCUGCCAAGAUGUUUAAUAUCAUCACCUGGUUGGGUCGAAAG
..((..(((((((........((((((.......(((((((........))))))).(((..(((...........)))..)))....)))))).........)))))))...))..... ( -27.43)
>consensus
AAGAAAAACCAGGCAAAAAAGUGAACAAUUUAAACUUUUGUAUGAAUAUAAAAGGGGGGCUAUGUAGGAAAUUAAAGCGCUGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGUCGAAAG
........((((.(....................((((((((....))))))))((((((..(((...........)))..)))..((((........)))).)))).))))........ (-24.14 = -24.03 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 23,159,847 – 23,159,967
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -33.86
Consensus MFE -32.40
Energy contribution -32.96
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.60
Structure conservation index 0.96
SVM decision value 1.63
SVM RNA-class probability 0.968403
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23159847 120 + 27905053
UGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGGCGAAAGAUCUAAAAUAAUUUUAUUUGCCACACAUUACCGCAGACAUGCUGGACUCCAUCCGCCAUUCUCGUCCUGCGAGUUGAACA
........(((((((..........((((.((((((((.((............)).))))))........(((((....))).)).......))))))..((((.....))))))))))) ( -26.30)
>DroSec_CAF1 9910 120 + 1
UGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGUCGAAAGAUCUAAAAUAAUUUUAUUUGCCACACAUUACGGCAGACAUGCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUUGAACA
((((..((((........))))...((((((((((....))))))(((((....)))))))))........))))(((.((((((((................)))))))).)))..... ( -37.49)
>DroSim_CAF1 15216 120 + 1
UGCCAAGAUGUUUAAUAUCAUCACCUGGUUGGGUCGAAAGAUCUAAAAUAAUUUUAUUUGCCACACAUUACGGCAGACAUGCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUCGAACA
((((..((((........))))...((((((((((....))))))(((((....)))))))))........))))(((.((((((((................)))))))).)))..... ( -37.79)
>consensus
UGCCAAGAUGUUUAAUAUCAUCACCUGGCUGGGUCGAAAGAUCUAAAAUAAUUUUAUUUGCCACACAUUACGGCAGACAUGCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUUGAACA
((((..((((........))))...((((((((((....))))))(((((....)))))))))........))))(((.((((((((................)))))))).)))..... (-32.40 = -32.96 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 23,159,927 – 23,160,047
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -31.63
Consensus MFE -30.36
Energy contribution -30.47
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.96
SVM decision value 0.01
SVM RNA-class probability 0.540324
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23159927 120 + 27905053
GCUGGACUCCAUCCGCCAUUCUCGUCCUGCGAGUUGAACAAAACUUUUUACGCAUAGCCAGGACUCGCAGCGCAUUUUAGCUAAAAGCAUUUCAUUGCUGUUAACUAUUUUUGAUGGCGU
...(((.....)))((((((...((.(((((((((..........................))))))))).))....(((.(((.((((......)))).))).))).....)))))).. ( -30.87)
>DroSec_CAF1 9990 120 + 1
GCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUUGAACAAAACUUUUUACGCAUAGCCAGGACUCGCAGCGCAUUUUAGCUAAAAGCAUUUCAACGCUGUUAACUAUUUUUGAUGGCGU
...(((.....)))((((((...((((((.(((((......))))).....((...))))))))..((((((.......((.....)).......))))))...........)))))).. ( -30.44)
>DroSim_CAF1 15296 120 + 1
GCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUCGAACAAAACUUUUUACGCAUAGCCAGGACUCGCAGCGCAUUUUAGCUAAAAGCAUUUCAAUGCUGUUAACUAUUUUUGAUGGCGU
...(((.....)))((((((...((.(((((((((..........................))))))))).))....(((.(((.(((((....))))).))).))).....)))))).. ( -33.57)
>consensus
GCAGGACACCAUCCGCCAUUCUCGUCCUGCGAGUUGAACAAAACUUUUUACGCAUAGCCAGGACUCGCAGCGCAUUUUAGCUAAAAGCAUUUCAAUGCUGUUAACUAUUUUUGAUGGCGU
...(((.....)))((((((...((.(((((((((..........................))))))))).))....(((.(((.((((......)))).))).))).....)))))).. (-30.36 = -30.47 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 23,159,927 – 23,160,047
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -38.30
Consensus MFE -36.71
Energy contribution -36.93
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.96
SVM decision value 1.32
SVM RNA-class probability 0.941450
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23159927 120 - 27905053
ACGCCAUCAAAAAUAGUUAACAGCAAUGAAAUGCUUUUAGCUAAAAUGCGCUGCGAGUCCUGGCUAUGCGUAAAAAGUUUUGUUCAACUCGCAGGACGAGAAUGGCGGAUGGAGUCCAGC
..((((((.....(((((((.((((......)))).))))))).......((((((((...(((...((.......))...)))..)))))))).....).)))))((((...))))... ( -35.80)
>DroSec_CAF1 9990 120 - 1
ACGCCAUCAAAAAUAGUUAACAGCGUUGAAAUGCUUUUAGCUAAAAUGCGCUGCGAGUCCUGGCUAUGCGUAAAAAGUUUUGUUCAACUCGCAGGACGAGAAUGGCGGAUGGUGUCCUGC
((((((((.....(((((((.(((((....))))).))))))).....((((.(..((((((((...))......((((......))))..))))))..)...))))))))))))..... ( -38.30)
>DroSim_CAF1 15296 120 - 1
ACGCCAUCAAAAAUAGUUAACAGCAUUGAAAUGCUUUUAGCUAAAAUGCGCUGCGAGUCCUGGCUAUGCGUAAAAAGUUUUGUUCGACUCGCAGGACGAGAAUGGCGGAUGGUGUCCUGC
((((((((.....(((((((.(((((....))))).))))))).......(((((((((..(((...((.......))...))).))))))))).............))))))))..... ( -40.80)
>consensus
ACGCCAUCAAAAAUAGUUAACAGCAUUGAAAUGCUUUUAGCUAAAAUGCGCUGCGAGUCCUGGCUAUGCGUAAAAAGUUUUGUUCAACUCGCAGGACGAGAAUGGCGGAUGGUGUCCUGC
((((((((.....(((((((.(((((....))))).))))))).....((((.(..((((((((...))......((((......))))..))))))..)...))))))))))))..... (-36.71 = -36.93 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:55 2006