Locus 2696

Sequence ID 2R_DroMel_CAF1
Location 9,508,010 – 9,508,168
Length 158
Max. P 0.981715
window4442 window4443 window4444 window4445

overview

Window 2

Location 9,508,010 – 9,508,129
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.88
Mean single sequence MFE -26.34
Consensus MFE -20.84
Energy contribution -21.16
Covariance contribution 0.32
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.79
SVM decision value 0.58
SVM RNA-class probability 0.788808
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9508010 119 + 20766785
GGUAAGUAAGUUAAGUCUCUUAUCGCCUAAUUAGUUUAUAGCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUCAUAUGCCUUUU-UUUCUCU
((((.(((((..(((((.((((.(((..((((((...........))))))..))))))).)))))))))).....((((((.(........).))))))....))))....-....... ( -21.80)
>DroSec_CAF1 5023 120 + 1
GGUAAGUAAGUUAACGCUCUUAUCGCCUAAUUAGUUUAUAGCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUACUUCGGGUUUUGAUAUGCCUUUUUUUUCACU
((((.(((((....(((((....(((..((((((...........))))))..))).)))))....)))))...((((((((.(........).))))))))..))))............ ( -25.60)
>DroSim_CAF1 5022 119 + 1
GGUAAGUAAGUUAACGCUCUUAUCGCCUAAUUAGUUUAUAGCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAUAUGCCUUUU-UUUCUCU
((((.(((((....(((((....(((..((((((...........))))))..))).)))))....)))))...((((((((.(........).))))))))..))))....-....... ( -25.60)
>DroEre_CAF1 5047 116 + 1
GGUAAGUAAGCUAAUGCUCUUAUCGCCUAAUUAGUUAAUAGCGUUUUAUUUUUGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAAAUGCCUUU--UUU--CU
((((((..(((....)))))))))(((((....(..(((((....)))))..)...)))))........(((((((((((((.(........).)))))))))))))....--...--.. ( -30.10)
>DroYak_CAF1 4986 117 + 1
GGUAAGUAAGUUAACGCUCUUAUCGCCUAAUUAGUUUAUAGCGUUUUAUUUUCUUGUGGGUGGCUUUUCGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAAAUGCCUUUU-UUU--CU
((((((...(....)...))))))(((((...((...((((....))))...))..)))))........(((((((((((((.(........).))))))))))))).....-...--.. ( -28.60)
>consensus
GGUAAGUAAGUUAACGCUCUUAUCGCCUAAUUAGUUUAUAGCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAUAUGCCUUUU_UUUC_CU
((((((..(((....)))))))))(((((...........(((.........))).)))))........((((.((((((((.(........).)))))))).))))............. (-20.84 = -21.16 +   0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,508,010 – 9,508,129
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.88
Mean single sequence MFE -21.33
Consensus MFE -17.30
Energy contribution -17.50
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.81
SVM decision value 1.89
SVM RNA-class probability 0.981715
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9508010 119 - 20766785
AGAGAAA-AAAAGGCAUAUGAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGCUAUAAACUAAUUAGGCGAUAAGAGACUUAACUUACUUACC
.(((...-.....((((.(.((((((.(........).)))))).).))))..........................((((............))))........)))............ ( -14.50)
>DroSec_CAF1 5023 120 - 1
AGUGAAAAAAAAGGCAUAUCAAAACCCGAAGUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGCUAUAAACUAAUUAGGCGAUAAGAGCGUUAACUUACUUACC
(((((........((((.((((((((.(........).)))))))).))))........................((((((.....((....))........))))))...))))).... ( -22.12)
>DroSim_CAF1 5022 119 - 1
AGAGAAA-AAAAGGCAUAUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGCUAUAAACUAAUUAGGCGAUAAGAGCGUUAACUUACUUACC
.(((...-.....((((.((((((((.(........).)))))))).))))........................((((((.....((....))........))))))..)))....... ( -21.02)
>DroEre_CAF1 5047 116 - 1
AG--AAA--AAAGGCAUUUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACAAAAAUAAAACGCUAUUAACUAAUUAGGCGAUAAGAGCAUUAGCUUACUUACC
..--...--.((((((((((((((((.(........).)))))))))))))..........................((((............))))....((((....)))).)))... ( -24.70)
>DroYak_CAF1 4986 117 - 1
AG--AAA-AAAAGGCAUUUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCGAAAAGCCACCCACAAGAAAAUAAAACGCUAUAAACUAAUUAGGCGAUAAGAGCGUUAACUUACUUACC
..--...-..((((((((((((((((.(........).)))))))))))))........................((((((.....((....))........))))))..)))....... ( -24.32)
>consensus
AG_GAAA_AAAAGGCAUAUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGCUAUAAACUAAUUAGGCGAUAAGAGCGUUAACUUACUUACC
..........(((((((.((((((((.(........).)))))))).))))..........................((((............)))).................)))... (-17.30 = -17.50 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,508,050 – 9,508,168
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.59
Mean single sequence MFE -27.11
Consensus MFE -21.96
Energy contribution -22.24
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.46
Structure conservation index 0.81
SVM decision value 0.17
SVM RNA-class probability 0.618766
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9508050 118 + 20766785
GCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUCAUAUGCCUUUU-UUUCUCUUCUC-AUGUUGAUAAGACCUUGAAGCGCUUUUCGUGUAGA
(((((((((...((((((((..((.....))...))((((((.(........).))))))))))))......-....((((.((-.....)).))))..)))))))))............ ( -21.90)
>DroSec_CAF1 5063 119 + 1
GCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUACUUCGGGUUUUGAUAUGCCUUUUUUUUCACUUCUC-AUGUUGAUAGGACCUUGAAGCGCUUUUCGUGUAGA
((((((((((((((((.((((((......((((.((((((((.(........).)))))))).))))........))))))..)-)))......))))..))))))))............ ( -29.04)
>DroSim_CAF1 5062 119 + 1
GCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAUAUGCCUUUU-UUUCUCUUCUCUAUGUUGAUAAGACCUUGAAGCGCUUUUCGUGUAGA
(((.....((((((...((..........((((.((((((((.(........).)))))))).)))).....-....((((.((......)).)))))).))))))......)))..... ( -27.00)
>DroEre_CAF1 5087 115 + 1
GCGUUUUAUUUUUGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAAAUGCCUUU--UUU--CUUCUG-AUGUUGAUAAGACCUUGAAGCGCUUUUCGUGUAGA
..........((((..((((.(((.....(((((((((((((.(........).)))))))))))))....--...--((((..-..(((.....)))...)))).))).))))..)))) ( -28.80)
>DroYak_CAF1 5026 116 + 1
GCGUUUUAUUUUCUUGUGGGUGGCUUUUCGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAAAUGCCUUUU-UUU--CUUGUG-AUGUUGAUAAGACCUUGAAGUGCUUUUCGUGUAGA
...........(((..((((.(((.(((((((((((((((((.(........).))))))))))))).....-..(--(((((.-......))))))....)))).))).))))...))) ( -28.80)
>consensus
GCGUUUUAGUUUCGUGUGGGUGGCUUUUUGCAUUUCAAAACCAGUUCUAUUUCGGGUUUUGAUAUGCCUUUU_UUUC_CUUCUC_AUGUUGAUAAGACCUUGAAGCGCUUUUCGUGUAGA
((((((((.........((((........((((.((((((((.(........).)))))))).))))...........(((.((......)).)))))))))))))))............ (-21.96 = -22.24 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,508,050 – 9,508,168
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.59
Mean single sequence MFE -20.66
Consensus MFE -15.78
Energy contribution -16.02
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.14
Structure conservation index 0.76
SVM decision value 0.69
SVM RNA-class probability 0.824176
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9508050 118 - 20766785
UCUACACGAAAAGCGCUUCAAGGUCUUAUCAACAU-GAGAAGAGAAA-AAAAGGCAUAUGAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGC
............(((.(((....((((((....))-))))...))).-.....((((.(.((((((.(........).)))))).).))))..........................))) ( -16.40)
>DroSec_CAF1 5063 119 - 1
UCUACACGAAAAGCGCUUCAAGGUCCUAUCAACAU-GAGAAGUGAAAAAAAAGGCAUAUCAAAACCCGAAGUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGC
......((.....((((((...((.......))..-..)))))).........((((.((((((((.(........).)))))))).))))...............))............ ( -20.90)
>DroSim_CAF1 5062 119 - 1
UCUACACGAAAAGCGCUUCAAGGUCUUAUCAACAUAGAGAAGAGAAA-AAAAGGCAUAUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGC
............(.((((.....((((.((........)).))))..-.....((((.((((((((.(........).)))))))).))))...)))))..................... ( -20.40)
>DroEre_CAF1 5087 115 - 1
UCUACACGAAAAGCGCUUCAAGGUCUUAUCAACAU-CAGAAG--AAA--AAAGGCAUUUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACAAAAAUAAAACGC
............(((((((...((.......))..-..))))--...--....(((((((((((((.(........).)))))))))))))..........................))) ( -21.80)
>DroYak_CAF1 5026 116 - 1
UCUACACGAAAAGCACUUCAAGGUCUUAUCAACAU-CACAAG--AAA-AAAAGGCAUUUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCGAAAAGCCACCCACAAGAAAAUAAAACGC
(((....(((......)))..((.(((.((....(-(....)--)..-.....(((((((((((((.(........).))))))))))))))).))))).......)))........... ( -23.80)
>consensus
UCUACACGAAAAGCGCUUCAAGGUCUUAUCAACAU_GAGAAG_GAAA_AAAAGGCAUAUCAAAACCCGAAAUAGAACUGGUUUUGAAAUGCAAAAAGCCACCCACACGAAACUAAAACGC
.......((.(((.(((....)))))).)).......................((((.((((((((.(........).)))))))).))))............................. (-15.78 = -16.02 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:44 2006