Locus 4456

Sequence ID 2R_DroMel_CAF1
Location 14,649,620 – 14,649,759
Length 139
Max. P 1.000000
window7118 window7119 window7120 window7121

overview

Window 8

Location 14,649,620 – 14,649,726
Length 106
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 67.54
Mean single sequence MFE -27.31
Consensus MFE -17.54
Energy contribution -16.66
Covariance contribution -0.88
Combinations/Pair 1.21
Mean z-score -3.75
Structure conservation index 0.64
SVM decision value 7.47
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14649620 106 + 20766785
GUUUGCAAAUCAAACUCAUGCAUAGCUUGAGCGAACAAAGCUUAAUAG-CCCUUGCAGAAUAACUACACAUUCAUUUUAAGAAGCCC-----------AUUGUAUUCUGCAAGGGCAA
(((((((...........)))).)))((((((.......))))))..(-(((((((((((((........(((.......)))....-----------....)))))))))))))).. ( -34.89)
>DroEre_CAF1 4394 101 + 1
GGUUAUAAAUCGAAAUCAUGGCAAGCUU------AUAA----------ACCCUUGUAGAAUAACUA-ACAUUAACAUUAAGUAGCCCGUAGUGCUACAAAAGUAUUCUGCAAGGGCAA
.(((((...........)))))......------....----------.(((((((((((((.((.-...(((....)))(((((.......)))))...)))))))))))))))... ( -24.10)
>DroYak_CAF1 4381 106 + 1
GGUUGUAAACCGAAAUCAUGCACAGUUUCAGCAAACAA----------ACUCUUGCAGAAUGACUA-ACAUUAACAUUAAGUAGCUUAUAG-ACCAUAAAAGUAUUCUGCAAGAGCAA
(((.....)))(((((........))))).........----------.(((((((((((((.((.-..........((((...))))...-........)))))))))))))))... ( -22.95)
>consensus
GGUUGUAAAUCGAAAUCAUGCAAAGCUU_AGC_AACAA__________ACCCUUGCAGAAUAACUA_ACAUUAACAUUAAGUAGCCC_UAG__C_A_AAAAGUAUUCUGCAAGGGCAA
.................................................(((((((((((((.(.....................................))))))))))))))... (-17.54 = -16.66 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,649,620 – 14,649,726
Length 106
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 67.54
Mean single sequence MFE -31.50
Consensus MFE -16.55
Energy contribution -16.67
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -3.73
Structure conservation index 0.53
SVM decision value 5.49
SVM RNA-class probability 0.999988
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14649620 106 - 20766785
UUGCCCUUGCAGAAUACAAU-----------GGGCUUCUUAAAAUGAAUGUGUAGUUAUUCUGCAAGGG-CUAUUAAGCUUUGUUCGCUCAAGCUAUGCAUGAGUUUGAUUUGCAAAC
..((((((((((((((...(-----------(.(((((.......))).)).))..)))))))))))))-).((((((((((((..((....))...))).)))))))))........ ( -37.80)
>DroEre_CAF1 4394 101 - 1
UUGCCCUUGCAGAAUACUUUUGUAGCACUACGGGCUACUUAAUGUUAAUGU-UAGUUAUUCUACAAGGGU----------UUAU------AAGCUUGCCAUGAUUUCGAUUUAUAACC
..(((((((.((((((.....(((((.(....))))))(((((......))-))).)))))).)))))))----------((((------(((.(((.........)))))))))).. ( -25.10)
>DroYak_CAF1 4381 106 - 1
UUGCUCUUGCAGAAUACUUUUAUGGU-CUAUAAGCUACUUAAUGUUAAUGU-UAGUCAUUCUGCAAGAGU----------UUGUUUGCUGAAACUGUGCAUGAUUUCGGUUUACAACC
..((((((((((((((((..(((...-...((((...))))......))).-.))).)))))))))))))----------((((..((((((((.......).)))))))..)))).. ( -31.60)
>consensus
UUGCCCUUGCAGAAUACUUUU_U_G__CUA_GGGCUACUUAAUGUUAAUGU_UAGUUAUUCUGCAAGGGU__________UUGUU_GCU_AAGCUAUGCAUGAUUUCGAUUUACAACC
..((((((((((((((((.............(((...))).............))).)))))))))))))................................................ (-16.55 = -16.67 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,649,658 – 14,649,759
Length 101
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 67.01
Mean single sequence MFE -28.39
Consensus MFE -19.59
Energy contribution -19.99
Covariance contribution 0.40
Combinations/Pair 1.17
Mean z-score -3.42
Structure conservation index 0.69
SVM decision value 3.46
SVM RNA-class probability 0.999253
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14649658 101 + 20766785
AGCUUAAUAG-CCCUUGCAGAAUAACUACACAUUCAUUUUAAGAAGCCC-----------AUUGUAUUCUGCAAGGGCAAAAGUAUUCUGGUAACGUACCGUUGCAGCUGCUC
((((.....(-(((((((((((((........(((.......)))....-----------....))))))))))))))............((((((...)))))))))).... ( -35.09)
>DroSec_CAF1 4420 83 + 1
AGCCUGAUAAUCCCUUGCAGAAUAACUACA------------------------------ACAGUAUUCUGCAAAGGCAAUCGUAUGUUGGGAACGUACCGUUGCAGCUGCUC
(((.........(.((((((((((.((...------------------------------..)))))))))))).)(((((.((((((.....)))))).))))).))).... ( -25.70)
>DroSim_CAF1 4277 83 + 1
AGCCUAAUAAUCCCUUGCAGGAUAACUACA------------------------------AAAGUAUUCUGCAAAGGCAAUCGUAUGUUGGGAACGUACCGUUGCAGCUGCUC
(((.........(.((((((((((.((...------------------------------..)))))))))))).)(((((.((((((.....)))))).))))).))).... ( -25.40)
>DroEre_CAF1 4426 102 + 1
----------ACCCUUGUAGAAUAACUA-ACAUUAACAUUAAGUAGCCCGUAGUGCUACAAAAGUAUUCUGCAAGGGCAAAAGUAUGCUAGGAACUUACCGUUGCAGCUGCUC
----------.(((((((((((((.((.-...(((....)))(((((.......)))))...)))))))))))))))....((((.(((.(.(((.....))).)))))))). ( -31.10)
>DroYak_CAF1 4419 101 + 1
----------ACUCUUGCAGAAUGACUA-ACAUUAACAUUAAGUAGCUUAUAG-ACCAUAAAAGUAUUCUGCAAGAGCAAAAAUAUGCUAGGAACGUACCGUUGCAGCUGCUC
----------.(((((((((((((.((.-..........((((...))))...-........))))))))))))))).........(((.(.((((...)))).))))..... ( -24.65)
>consensus
AGC_U_AUA_ACCCUUGCAGAAUAACUACACAUU_A__UUAAG_AGC_____________AAAGUAUUCUGCAAGGGCAAAAGUAUGCUGGGAACGUACCGUUGCAGCUGCUC
............((((((((((((.((...................................))))))))))))))((((..(((((.......)))))..))))........ (-19.59 = -19.99 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,649,658 – 14,649,759
Length 101
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 67.01
Mean single sequence MFE -28.16
Consensus MFE -18.37
Energy contribution -18.21
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -2.55
Structure conservation index 0.65
SVM decision value 3.05
SVM RNA-class probability 0.998248
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14649658 101 - 20766785
GAGCAGCUGCAACGGUACGUUACCAGAAUACUUUUGCCCUUGCAGAAUACAAU-----------GGGCUUCUUAAAAUGAAUGUGUAGUUAUUCUGCAAGGG-CUAUUAAGCU
....((((.....((((...))))...........((((((((((((((...(-----------(.(((((.......))).)).))..)))))))))))))-).....)))) ( -34.50)
>DroSec_CAF1 4420 83 - 1
GAGCAGCUGCAACGGUACGUUCCCAACAUACGAUUGCCUUUGCAGAAUACUGU------------------------------UGUAGUUAUUCUGCAAGGGAUUAUCAGGCU
....((((......(((.((.....)).)))(((..((((((((((((((((.------------------------------..))).)))))))))))))...))).)))) ( -26.20)
>DroSim_CAF1 4277 83 - 1
GAGCAGCUGCAACGGUACGUUCCCAACAUACGAUUGCCUUUGCAGAAUACUUU------------------------------UGUAGUUAUCCUGCAAGGGAUUAUUAGGCU
.(((..((((((.(((((((.........)))..)))).))))))....((((------------------------------(((((.....)))))))))........))) ( -24.60)
>DroEre_CAF1 4426 102 - 1
GAGCAGCUGCAACGGUAAGUUCCUAGCAUACUUUUGCCCUUGCAGAAUACUUUUGUAGCACUACGGGCUACUUAAUGUUAAUGU-UAGUUAUUCUACAAGGGU----------
.....((((.(((.....))).).)))........(((((((.((((((.....(((((.(....))))))(((((......))-))).)))))).)))))))---------- ( -28.60)
>DroYak_CAF1 4419 101 - 1
GAGCAGCUGCAACGGUACGUUCCUAGCAUAUUUUUGCUCUUGCAGAAUACUUUUAUGGU-CUAUAAGCUACUUAAUGUUAAUGU-UAGUCAUUCUGCAAGAGU----------
.....((((.((((...)))).).)))........((((((((((((((((..(((...-...((((...))))......))).-.))).)))))))))))))---------- ( -26.90)
>consensus
GAGCAGCUGCAACGGUACGUUCCCAGCAUACUUUUGCCCUUGCAGAAUACUUU_____________GCU_CUUAA__U_AAUGUGUAGUUAUUCUGCAAGGGA_UAU_A_GCU
........((((..(((.((.....)).)))..))))((((((((((((((...................................))).)))))))))))............ (-18.37 = -18.21 +  -0.16)

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 11:20:05 2006