Locus 8305

Sequence ID 3L_DroMel_CAF1
Location 21,748,744 – 21,748,904
Length 160
Max. P 0.984450
window13593 window13594 window13595 window13596

overview

Window 3

Location 21,748,744 – 21,748,864
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.53
Mean single sequence MFE -27.45
Consensus MFE -27.25
Energy contribution -27.12
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.59
Structure conservation index 0.99
SVM decision value 0.44
SVM RNA-class probability 0.736014
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21748744 120 + 23771897
AUAAUUCAUUUGUGACAAUUGUGAGAAACUGUAGAGAUGCGAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCGAAAUCGAA
.....((((((.............((((.((((....)))).))))((((((((.(....).))))))))...))))))..((((((((..(((((..........))))))))))))). ( -28.00)
>DroSec_CAF1 34007 120 + 1
AGAAUUCAUUUGUGACAAUUGUGAGAAACUGUAGAGAUGCGAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAA
.....((((((.............((((.((((....)))).))))((((((((.(....).))))))))...))))))..(((((((...(((((..........))))).))))))). ( -27.70)
>DroSim_CAF1 35891 120 + 1
AGAAUUCAUUUGUGACAAUUGUGAGAAACUGUAGAGAUGCGAUUUCGCACAUUUAGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAA
.....((((((.............((((.((((....)))).))))((((((((.(....).))))))))...))))))..(((((((...(((((..........))))).))))))). ( -27.70)
>DroEre_CAF1 16526 119 + 1
AUAACUCAUUUGUGACA-UUGUGAGAAACUGUUGGGAUGCGAUUUCGCACAUUUCGUAGACAAAAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAA
.....((((((......-......((((.(((......))).))))((((((((.(....).))))))))...))))))..(((((((...(((((..........))))).))))))). ( -26.40)
>consensus
AGAAUUCAUUUGUGACAAUUGUGAGAAACUGUAGAGAUGCGAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAA
.....((((((.............((((.((((....)))).))))((((((((.(....).))))))))...))))))..((((((((..(((((..........))))))))))))). (-27.25 = -27.12 +  -0.12)

alignment

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secondary structure

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Window 4

Location 21,748,744 – 21,748,864
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.53
Mean single sequence MFE -28.23
Consensus MFE -26.88
Energy contribution -27.62
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.95
SVM decision value 1.97
SVM RNA-class probability 0.984450
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21748744 120 - 23771897
UUCGAUUUCGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUCGCAUCUCUACAGUUUCUCACAAUUGUCACAAAUGAAUUAU
((((((((.((((((........))))))...)))))))).(((((((((((((((.(((....))).)))))))))...........((((((......))))))...))))))..... ( -28.00)
>DroSec_CAF1 34007 120 - 1
UUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUCGCAUCUCUACAGUUUCUCACAAUUGUCACAAAUGAAUUCU
(((((((((((((((........))))))..))))))))).(((((((((((((((.(((....))).)))))))))...........((((((......))))))...))))))..... ( -29.00)
>DroSim_CAF1 35891 120 - 1
UUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACUAAAUGUGCGAAAUCGCAUCUCUACAGUUUCUCACAAUUGUCACAAAUGAAUUCU
(((((((((((((((........))))))..))))))))).(((((((((((((((...(....)...)))))))))...........((((((......))))))...))))))..... ( -26.00)
>DroEre_CAF1 16526 119 - 1
UUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUUUUGUCUACGAAAUGUGCGAAAUCGCAUCCCAACAGUUUCUCACAA-UGUCACAAAUGAGUUAU
(((((((((((((((........))))))..))))))))).((((((...((((((((((....))))))))))(((((.(........).)))))......-......))))))..... ( -29.90)
>consensus
UUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUCGCAUCUCUACAGUUUCUCACAAUUGUCACAAAUGAAUUAU
(((((((((((((((........))))))..))))))))).(((((((((((((((.(((....))).)))))))))...........((((((......))))))...))))))..... (-26.88 = -27.62 +   0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,748,784 – 21,748,904
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -24.70
Consensus MFE -23.65
Energy contribution -23.77
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -2.49
Structure conservation index 0.96
SVM decision value 1.46
SVM RNA-class probability 0.955560
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21748784 120 + 23771897
GAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCGAAAUCGAAAACAUUAUUACUGUAAUUAAAAUUCAAUUCGAAAAAAUAA
..((((((((((((.(....).))))))))....((((...((((((((..(((((..........)))))))))))))...))))........................))))...... ( -23.30)
>DroSec_CAF1 34047 120 + 1
GAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAAAACAUUAUUACUGUAAUUAAAAUUCAAUUCGGUAAAUUAA
......((((((((.(....).))))))))....((((...(((((((...(((((..........))))).)))))))...)))).((((((.((((.......))))))))))..... ( -25.20)
>DroSim_CAF1 35931 120 + 1
GAUUUCGCACAUUUAGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAAAACAUUAUUACUGUAAUUAAAAUUCAAUUCGGUAAAUUAA
......((((((((.(....).))))))))....((((...(((((((...(((((..........))))).)))))))...)))).((((((.((((.......))))))))))..... ( -25.20)
>DroEre_CAF1 16565 120 + 1
GAUUUCGCACAUUUCGUAGACAAAAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAAAACAUUAUUACUGUAAUUAAAAUUCAAUUCGGUAAAUUAA
......((((((((.(....).))))))))....((((...(((((((...(((((..........))))).)))))))...)))).((((((.((((.......))))))))))..... ( -25.10)
>consensus
GAUUUCGCACAUUUCGUAGACAAGAUGUGCAAAAAAUGAUCUCGAUUUUGGGCUUUACUUUUACACAAAGCAAAAUCGAAAACAUUAUUACUGUAAUUAAAAUUCAAUUCGGUAAAUUAA
......((((((((.(....).))))))))....((((...((((((((..(((((..........)))))))))))))...)))).((((((.((((.......))))))))))..... (-23.65 = -23.77 +   0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,748,784 – 21,748,904
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -29.90
Consensus MFE -27.99
Energy contribution -28.55
Covariance contribution 0.56
Combinations/Pair 1.02
Mean z-score -3.43
Structure conservation index 0.94
SVM decision value 1.56
SVM RNA-class probability 0.964235
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21748784 120 - 23771897
UUAUUUUUUCGAAUUGAAUUUUAAUUACAGUAAUAAUGUUUUCGAUUUCGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUC
..................................((((.(((((((((.((((((........))))))...))))))))).))))((((((((((.(((....))).)))))))))).. ( -27.60)
>DroSec_CAF1 34047 120 - 1
UUAAUUUACCGAAUUGAAUUUUAAUUACAGUAAUAAUGUUUUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUC
.....((((.(((((((...)))))).).)))).((((.((((((((((((((((........))))))..)))))))))).))))((((((((((.(((....))).)))))))))).. ( -30.50)
>DroSim_CAF1 35931 120 - 1
UUAAUUUACCGAAUUGAAUUUUAAUUACAGUAAUAAUGUUUUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACUAAAUGUGCGAAAUC
.....((((.(((((((...)))))).).)))).((((.((((((((((((((((........))))))..)))))))))).))))((((((((((...(....)...)))))))))).. ( -27.50)
>DroEre_CAF1 16565 120 - 1
UUAAUUUACCGAAUUGAAUUUUAAUUACAGUAAUAAUGUUUUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUUUUGUCUACGAAAUGUGCGAAAUC
.....((((.(((((((...)))))).).)))).((((.((((((((((((((((........))))))..)))))))))).))))((((((((((((((....)))))))))))))).. ( -34.00)
>consensus
UUAAUUUACCGAAUUGAAUUUUAAUUACAGUAAUAAUGUUUUCGAUUUUGCUUUGUGUAAAAGUAAAGCCCAAAAUCGAGAUCAUUUUUUGCACAUCUUGUCUACGAAAUGUGCGAAAUC
.....((((.(((((((...)))))).).)))).((((.((((((((((((((((........))))))..)))))))))).))))((((((((((.(((....))).)))))))))).. (-27.99 = -28.55 +   0.56)

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 13:12:10 2006