Locus 4825

Sequence ID 3R_DroMel_CAF1
Location 12,614,850 – 12,615,004
Length 154
Max. P 0.991613
window7907 window7908 window7909 window7910

overview

Window 7

Location 12,614,850 – 12,614,964
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.08
Mean single sequence MFE -50.28
Consensus MFE -34.29
Energy contribution -34.97
Covariance contribution 0.67
Combinations/Pair 1.33
Mean z-score -3.60
Structure conservation index 0.68
SVM decision value 2.28
SVM RNA-class probability 0.991613
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12614850 114 + 27905053
ACUUUCUAACACGGGAUCCCACAGAAAGUGAGCGGGAAGUGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUCGCCU
(((((((.....((....))..)))))))..((((......(((((((((.(((.((..((((((..((((......))))...))))))..))))).))))))))).)))).. ( -52.90)
>DroPse_CAF1 101880 114 + 1
GGCAACUGAUGCUCGAGGGAACGAGAAGCGAACUAGCACUCCAGCAGAACAUUAUGCUCGGAUUCAAGCGCAGAAAGACGAGGCGCAGCUUGUGCCGGGCCUCGUCUUUGACCA
(((..(((.((((.(((..........((......))..(((((((........)))).)))))).)))))))(((((((((((.(.((....)).).)))))))))))).)). ( -44.20)
>DroSec_CAF1 97307 114 + 1
ACCUUCUCACACGGGAUCCCACAGAAAGUGAGCGGGAAGUGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUUCGAAGAAGUCUGGCGCGAUCCUUGGCGAUUGCCU
.(((.(((((..((....)).......))))).))).....(((((((((.(((.((..((((((..(.((......)).)...))))))..))))).)))))))))....... ( -47.90)
>DroSim_CAF1 97873 114 + 1
ACCUUCUCACGCGGGAACCCACAGAAAGUGAGCGGGAAGUCCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUUGCCU
.(((.((((((.((....)).).....))))).))).....(((((((((.(((.((..((((((..((((......))))...))))))..))))).)))))))))....... ( -53.90)
>DroEre_CAF1 96752 114 + 1
ACCAUCUGACGCGGGAACCCACUGAAAGUGAGCGGGAAGUGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGACGAAGUCUGGCGCGUUCCUUGGCGCUCUCCG
.........(((((....))((.....))..)))(((.(.((((((((((.(((.((..((((((..((((......))))...))))))..))))).)))))))))).)))). ( -56.50)
>DroYak_CAF1 97187 114 + 1
ACCAUCUGACCCGGGAUCCCACAGACAGUGAGCGGGAAGUGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAGGUACGACGAAGUCUGGCGCGCUGCUUGGCGGUCUCCA
.......((((.....((((.(.........).)))).....((((((.(.(((.((..((((((..((((......))))...))))))..))))).).)))))))))).... ( -46.30)
>consensus
ACCAUCUGACGCGGGAUCCCACAGAAAGUGAGCGGGAAGUGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUCGCCU
............((....))..............((.....(((((((((.(((.((((((((((..((((......))))...))))))))))))).)))))))))....)). (-34.29 = -34.97 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,614,850 – 12,614,964
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.08
Mean single sequence MFE -45.68
Consensus MFE -30.42
Energy contribution -30.18
Covariance contribution -0.24
Combinations/Pair 1.50
Mean z-score -2.50
Structure conservation index 0.67
SVM decision value 1.96
SVM RNA-class probability 0.984090
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12614850 114 - 27905053
AGGCGAUCGCCAAGGAUCGCGCCAGACUUCUUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCACUUCCCGCUCACUUUCUGUGGGAUCCCGUGUUAGAAAGU
.((.((.(((((((((((((((..(.((((...((((......))))..)))).)..)).)))))))))))))....))))....(((((((((((....)))...)))))))) ( -48.20)
>DroPse_CAF1 101880 114 - 1
UGGUCAAAGACGAGGCCCGGCACAAGCUGCGCCUCGUCUUUCUGCGCUUGAAUCCGAGCAUAAUGUUCUGCUGGAGUGCUAGUUCGCUUCUCGUUCCCUCGAGCAUCAGUUGCC
.(((.(((((((((((.((((....)))).)))))))))))(((.((((((....((((.....))))....((((((......))))))........))))))..)))..))) ( -42.70)
>DroSec_CAF1 97307 114 - 1
AGGCAAUCGCCAAGGAUCGCGCCAGACUUCUUCGAACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCACUUCCCGCUCACUUUCUGUGGGAUCCCGUGUGAGAAGGU
..((..((((((((((((((((..(.((((...(.((......)).)..)))).)..)).))))))))))))((((.((((((.........))))))....))))..))..)) ( -43.80)
>DroSim_CAF1 97873 114 - 1
AGGCAAUCGCCAAGGAUCGCGCCAGACUUCUUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGGACUUCCCGCUCACUUUCUGUGGGUUCCCGCGUGAGAAGGU
......((((((((((((((((..(.((((...((((......))))..)))).)..)).))))))))))))))....((..(((((.....((((....)))))))))..)). ( -49.90)
>DroEre_CAF1 96752 114 - 1
CGGAGAGCGCCAAGGAACGCGCCAGACUUCGUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCACUUCCCGCUCACUUUCAGUGGGUUCCCGCGUCAGAUGGU
(((.((((((((((((.(((((..(.(((((..((((......)))).))))).)..)).))).))))))))))....((((((.......)))))).)))))........... ( -48.40)
>DroYak_CAF1 97187 114 - 1
UGGAGACCGCCAAGCAGCGCGCCAGACUUCGUCGUACCUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCACUUCCCGCUCACUGUCUGUGGGAUCCCGGGUCAGAUGGU
....((((((((((.(.(((((..(.(((((..((((......)))).))))).)..)).))).).)))))).....((((((.........)))))).....))))....... ( -41.10)
>consensus
AGGCGAUCGCCAAGGAUCGCGCCAGACUUCGUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCACUUCCCGCUCACUUUCUGUGGGAUCCCGCGUCAGAAGGU
.((.((.(((((((((.(((((..(.((((...((((......))))..)))).)..)).))).)))))))))...)).))....(((((((((((....))))...))))))) (-30.42 = -30.18 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,614,889 – 12,615,004
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 78.72
Mean single sequence MFE -45.58
Consensus MFE -32.65
Energy contribution -33.93
Covariance contribution 1.28
Combinations/Pair 1.29
Mean z-score -2.57
Structure conservation index 0.72
SVM decision value 1.68
SVM RNA-class probability 0.971871
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12614889 115 + 27905053
UGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUCGCCUUGCUCCAAAAGCUGUGUGGUGCCCUGAUCUUUAUUUUCUA
...((((((((.(((.((..((((((..((((......))))...))))))..))))).))))))))(((((....((.(((.........))).))..)))))........... ( -48.50)
>DroPse_CAF1 101919 115 + 1
UCCAGCAGAACAUUAUGCUCGGAUUCAAGCGCAGAAAGACGAGGCGCAGCUUGUGCCGGGCCUCGUCUUUGACCAUCAUGCAGACACUCAGCGGGUCCACGGUCUUUGUCUUCUA
(((((((........)))).)))...(((.(((((((((((((((.(.((....)).).)))))))))))(((((((.(((.(.....).))))))....)))).)))))))... ( -39.10)
>DroSec_CAF1 97346 115 + 1
UGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUUCGAAGAAGUCUGGCGCGAUCCUUGGCGAUUGCCUUGCUCCAAAAGCUGUGUGGUGCCCUGAUCUUUAUCUUCUA
..(((((((((.(((.((..((((((..(.((......)).)...))))))..))))).)))))))))((..(...(((.....)))...)..)).................... ( -42.20)
>DroSim_CAF1 97912 115 + 1
UCCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUUGCCUUGCUCCAAAAGAUGUGUGGUGCCCUGAUCGUUAUCUUCUA
...((((((((.(((.((..((((((..((((......))))...))))))..))))).))))))))(((((....((.(((.........))).))..)))))........... ( -46.20)
>DroEre_CAF1 96791 115 + 1
UGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGACGAAGUCUGGCGCGUUCCUUGGCGCUCUCCGUGCUCCAGAAGCUGUGUGGUGCCCUGGUCUUCAUCCUUUA
.((((((((((.(((.((..((((((..((((......))))...))))))..))))).))))))))))...(((.((.(((.(.....).))).))..)))............. ( -52.00)
>DroYak_CAF1 97226 115 + 1
UGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAGGUACGACGAAGUCUGGCGCGCUGCUUGGCGGUCUCCAUGCUCCAGAAGCUGUGUGGUGCCCUGGUGUUCAUCUUCUA
.((((((.(((((((.((..((((((..((((......))))...))))))..))(((((..((((.(((......))))))).))).))))))).)).)))))).......... ( -45.50)
>consensus
UGCGCCAAGGACCGCUGCUGGGCUUCAAGUACAAGAAAGUACGAAGAAGUCUGGCGCGAUCCUUGGCGAUCGCCUUGCUCCAAAAGCUGUGUGGUGCCCUGAUCUUUAUCUUCUA
..(((((((((.(((.((((((((((..((((......))))...))))))))))))).)))))))))........((.(((.........))).)).................. (-32.65 = -33.93 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,614,889 – 12,615,004
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 78.72
Mean single sequence MFE -41.28
Consensus MFE -25.73
Energy contribution -25.85
Covariance contribution 0.12
Combinations/Pair 1.40
Mean z-score -1.99
Structure conservation index 0.62
SVM decision value 0.95
SVM RNA-class probability 0.888175
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12614889 115 - 27905053
UAGAAAAUAAAGAUCAGGGCACCACACAGCUUUUGGAGCAAGGCGAUCGCCAAGGAUCGCGCCAGACUUCUUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCA
...........((((.((...)).....(((((......)))))))))((((((((((((((..(.((((...((((......))))..)))).)..)).))))))))))))... ( -43.10)
>DroPse_CAF1 101919 115 - 1
UAGAAGACAAAGACCGUGGACCCGCUGAGUGUCUGCAUGAUGGUCAAAGACGAGGCCCGGCACAAGCUGCGCCUCGUCUUUCUGCGCUUGAAUCCGAGCAUAAUGUUCUGCUGGA
(((.(((((..(((((..(((.(.....).)))..).....))))(((((((((((.((((....)))).)))))))))))....(((((....)))))....)).))).))).. ( -44.20)
>DroSec_CAF1 97346 115 - 1
UAGAAGAUAAAGAUCAGGGCACCACACAGCUUUUGGAGCAAGGCAAUCGCCAAGGAUCGCGCCAGACUUCUUCGAACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCA
.....(((....)))...((........(((((......)))))....((((((((((((((..(.((((...(.((......)).)..)))).)..)).)))))))))))))). ( -36.70)
>DroSim_CAF1 97912 115 - 1
UAGAAGAUAACGAUCAGGGCACCACACAUCUUUUGGAGCAAGGCAAUCGCCAAGGAUCGCGCCAGACUUCUUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGGA
.....(((....)))...((.(((.........))).)).......((((((((((((((((..(.((((...((((......))))..)))).)..)).)))))))))))))). ( -41.60)
>DroEre_CAF1 96791 115 - 1
UAAAGGAUGAAGACCAGGGCACCACACAGCUUCUGGAGCACGGAGAGCGCCAAGGAACGCGCCAGACUUCGUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCA
.............(((((((........)).)))))..........((((((((((.(((((..(.(((((..((((......)))).))))).)..)).))).)))))))))). ( -45.20)
>DroYak_CAF1 97226 115 - 1
UAGAAGAUGAACACCAGGGCACCACACAGCUUCUGGAGCAUGGAGACCGCCAAGCAGCGCGCCAGACUUCGUCGUACCUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCA
.............(((((((........)).))))).((..(....).((((((.(.(((((..(.(((((..((((......)))).))))).)..)).))).).)))))))). ( -36.90)
>consensus
UAGAAGAUAAAGACCAGGGCACCACACAGCUUCUGGAGCAAGGCGAUCGCCAAGGAUCGCGCCAGACUUCGUCGUACUUUCUUGUACUUGAAGCCCAGCAGCGGUCCUUGGCGCA
.............((...((.(((.........))).))..))....(((((((((.(((((..(.((((...((((......))))..)))).)..)).))).))))))))).. (-25.73 = -25.85 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:48 2006