Locus 2609

Sequence ID 3R_DroMel_CAF1
Location 7,054,468 – 7,054,646
Length 178
Max. P 0.946032
window4246 window4247 window4248 window4249 window4250

overview

Window 6

Location 7,054,468 – 7,054,566
Length 98
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 85.39
Mean single sequence MFE -43.62
Consensus MFE -34.67
Energy contribution -35.45
Covariance contribution 0.78
Combinations/Pair 1.22
Mean z-score -2.88
Structure conservation index 0.79
SVM decision value 0.94
SVM RNA-class probability 0.887002
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7054468 98 + 27905053
AUAGUGAAAGGAAUCGG---CAGCUGCUUCAAGUGUGGGUGUGGCCAGUGUGCUGCCCACACCGCUGGCCGAGUGAAAGACCUCGAAGGAGGUCUGCAGUG
...((........((((---((((.((.....))...(((((((.(((....))).)))))))))).))))).....(((((((....))))))))).... ( -42.80)
>DroSec_CAF1 4079 98 + 1
AUAGUGAAAGGAAUCGG---CAGAUGCUUCCAGUGUGGGUGUGGCCAGUGUGCUGCCCACACCGCUGGCCGAGUGAAAGACCUCGAAGGAGGUCUGCAGUG
...((........((((---(.((....))((((...(((((((.(((....))).)))))))))))))))).....(((((((....))))))))).... ( -42.00)
>DroSim_CAF1 5452 98 + 1
AUAGUGAAAGGAAUCGG---CAGCUGCUUCCAGUGUGGGUGUGGCCAGUGUGCUGCCCACACCGCUGGCCGAGUGAAAGACCUCGAAGGAGGUCUGCAGUG
.................---..(((((..(((((...(((((((.(((....))).)))))))))))).........(((((((....)))))))))))). ( -43.10)
>DroEre_CAF1 1939 98 + 1
GUAGUGGAAAGAGUCGG---CAGCUGCUUCCAGCGUGGGUGUGGCCAGUGUGCUGCACACACCGCUGGCCGAAUGGAAGACCUCGAAUGAGGUCUGCAGUG
...((.((.....)).)---).(((((..((((((((.(((..((......))..))).)).)))))).........(((((((....)))))))))))). ( -41.60)
>DroYak_CAF1 1938 98 + 1
GUAGUGGAAGGAGUCUG---CACCUGCUUCCAGUGUAGGUGUGGCCAGCGUGCUGCCUACACCGCUGGCCGAAUGAAAGACCUCGAAGGAGGUCUGCAGUG
..............(((---(((((((.......)))))).(((((((((((.......)).)))))))))......(((((((....))))))))))).. ( -43.80)
>DroAna_CAF1 1966 101 + 1
GUAGGCGAAGGAUUCGCCUCCAGCCGCUUCCAUGCCAGGCGUAGCCAGGGCAGUGCCCACAUUGGUGGCGGAGUGAAAGACCUCGAAAGAGGUCUGCAACG
(.((((((.....)))))).)..(((((.(((.....((((..((....))..)))).....))).))))).((...(((((((....)))))))...)). ( -48.40)
>consensus
AUAGUGAAAGGAAUCGG___CAGCUGCUUCCAGUGUGGGUGUGGCCAGUGUGCUGCCCACACCGCUGGCCGAGUGAAAGACCUCGAAGGAGGUCUGCAGUG
......................(((((..(((((...(((((((.(((....))).)))))))))))).........(((((((....)))))))))))). (-34.67 = -35.45 +   0.78)

alignment

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secondary structure

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Window 7

Location 7,054,468 – 7,054,566
Length 98
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 85.39
Mean single sequence MFE -38.82
Consensus MFE -31.15
Energy contribution -31.98
Covariance contribution 0.84
Combinations/Pair 1.16
Mean z-score -3.40
Structure conservation index 0.80
SVM decision value 1.36
SVM RNA-class probability 0.946032
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7054468 98 - 27905053
CACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCACACUUGAAGCAGCUG---CCGAUUCCUUUCACUAU
......(((((((....))))))).....(((((.((((((((((.(((....))).)))))))((....)).....))))---))))............. ( -38.70)
>DroSec_CAF1 4079 98 - 1
CACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCACACUGGAAGCAUCUG---CCGAUUCCUUUCACUAU
......(((((((....))))))).....(((((..(.(((((((.(((....))).))))))))....((....))...)---))))............. ( -35.60)
>DroSim_CAF1 5452 98 - 1
CACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCACACUGGAAGCAGCUG---CCGAUUCCUUUCACUAU
......(((((((....))))))).....(((((.((((((((((.(((....))).))))))).....((....))))))---))))............. ( -40.40)
>DroEre_CAF1 1939 98 - 1
CACUGCAGACCUCAUUCGAGGUCUUCCAUUCGGCCAGCGGUGUGUGCAGCACACUGGCCACACCCACGCUGGAAGCAGCUG---CCGACUCUUUCCACUAC
......(((((((....))))))).....(((((..(.((((((..(((....)))..)))))))..((((....)))).)---))))............. ( -37.10)
>DroYak_CAF1 1938 98 - 1
CACUGCAGACCUCCUUCGAGGUCUUUCAUUCGGCCAGCGGUGUAGGCAGCACGCUGGCCACACCUACACUGGAAGCAGGUG---CAGACUCCUUCCACUAC
..(((((((((((....))))))........((((((((.(((.....))))))))))).........(((....))).))---))).............. ( -39.10)
>DroAna_CAF1 1966 101 - 1
CGUUGCAGACCUCUUUCGAGGUCUUUCACUCCGCCACCAAUGUGGGCACUGCCCUGGCUACGCCUGGCAUGGAAGCGGCUGGAGGCGAAUCCUUCGCCUAC
.((((((((((((....))))))).....((((((((....)).)))..((((..(((...))).)))).))).)))))...((((((.....)))))).. ( -42.00)
>consensus
CACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCACACUGGAAGCAGCUG___CCGAUUCCUUCCACUAC
..(((((((((((....))))))).........((((.(((((((.(((....))).)))))))....))))..))))....................... (-31.15 = -31.98 +   0.84)

alignment

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secondary structure

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Window 8

Location 7,054,500 – 7,054,606
Length 106
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 89.37
Mean single sequence MFE -43.35
Consensus MFE -32.00
Energy contribution -32.62
Covariance contribution 0.61
Combinations/Pair 1.18
Mean z-score -3.04
Structure conservation index 0.74
SVM decision value -0.04
SVM RNA-class probability 0.514067
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7054500 106 - 27905053
UCACUGCAGCUGCUGGAUGAGAAGGAGCAGGAGAUUAAGACACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCA
........(((((((..(((((....((((............)))).((((((....)))))))))))..))).))))(((((((.(((....))).))))))).. ( -48.10)
>DroSec_CAF1 4111 106 - 1
UCACUGCAGCUGCUGGACGAGAAGGAGCAGGAGAUCAAGACACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCA
...........(((((.((((.....((((............))))(((((((....)))))))....)))).)))))(((((((.(((....))).))))))).. ( -49.10)
>DroSim_CAF1 5484 106 - 1
UCACUGCAGCUGCUGGACGAGAAGGAGCAGGAGAUCAAGACACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCA
...........(((((.((((.....((((............))))(((((((....)))))))....)))).)))))(((((((.(((....))).))))))).. ( -49.10)
>DroEre_CAF1 1971 106 - 1
UCACUGCAGCUUCUUGAUGAGAAAGAGCAGGAGAUCAAGACACUGCAGACCUCAUUCGAGGUCUUCCAUUCGGCCAGCGGUGUGUGCAGCACACUGGCCACACCCA
....(((((..(((((((...............)))))))..)))))((((((....))))))........((((((..((((.....)))).))))))....... ( -39.56)
>DroYak_CAF1 1970 106 - 1
UCACUGCAGCUUCUUGAUGAGAAGGAGCAGGAGAUCAAGACACUGCAGACCUCCUUCGAGGUCUUUCAUUCGGCCAGCGGUGUAGGCAGCACGCUGGCCACACCUA
....(((((..(((((((...............)))))))..)))))((((((....))))))........((((((((.(((.....)))))))))))....... ( -42.26)
>DroAna_CAF1 2001 106 - 1
UCCCUCCAGCUUCUUGACGAAAAAGAGCAGGAGAUCAAAACGUUGCAGACCUCUUUCGAGGUCUUUCACUCCGCCACCAAUGUGGGCACUGCCCUGGCUACGCCUG
...((((.(((.(((.......)))))).))))...........(((((((((....)))))))........((((.......((((...))))))))...))... ( -32.01)
>consensus
UCACUGCAGCUGCUGGACGAGAAGGAGCAGGAGAUCAAGACACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCAGCGGUGUGGGCAGCACACUGGCCACACCCA
........(((......((((.....((((............))))(((((((....)))))))....))))...)))(((((((.(((....))).))))))).. (-32.00 = -32.62 +   0.61)

alignment

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secondary structure

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Window 9

Location 7,054,530 – 7,054,646
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -44.75
Consensus MFE -26.40
Energy contribution -27.10
Covariance contribution 0.70
Combinations/Pair 1.33
Mean z-score -2.74
Structure conservation index 0.59
SVM decision value 0.42
SVM RNA-class probability 0.728883
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7054530 116 + 27905053
---UGGCCGAGUGAAAGACCUCGAAGGAGGUCUGCAGUGUCUUAAUCUCCUGCUCCUUCUCAUCCAGCAGCUGCAGUGACCUCUGGCGCUGCUUCUGCAGUAGCUGUUCCAGCUCGUUC
---(((..(((.((.(((((((....)))))))((((.(.........)))))))...)))..)))((((..((((((.((...))))))))..)))).(.(((((...)))))).... ( -44.20)
>DroVir_CAF1 2014 116 + 1
---UGGGCUUGUGAAACACCUCGAAGGAGGUUUGCAGCGUCUUAAUCUCCUGCUCCUUCUCGUCGAGCAACUGUAAUGAACGCUGCCGCUGCUUUUGGAGCAGCUGCUCCAGCUCGUUA
---.((((..(((....(((((....)))))..(((((((..........(((((.........)))))..........))))))))))......((((((....)))))))))).... ( -42.05)
>DroPse_CAF1 1991 119 + 1
CACCGGCUGUAUGAAAUACCUCAAAUGAGGUCUGCAGCGUCUUGAUCUCCUGCUCCUUCUCGUCGAGAAGCUGCAGGGAUCGCUGUCGCUGCUUCUGCAGCAGCUGCUCCAGCUCGUUG
((.((((((((.(((..(((((....)))))..((((((.(.(((((.(((((..((((((...))))))..))))))))))..).)))))))))))))))(((((...))))))).)) ( -55.10)
>DroGri_CAF1 2235 116 + 1
---UGGGCUUGUGAAACACUUCGAAGGAGGUUUGCAAUGUUUUAAUCUCCUGCUCCUUCUCGUCGAGCAGCUGCAGCGAUCGUUGCCGCUGCUUCUGCAGCAACUGUUCCAGCUCAUUC
---((((((.(.(((.((..((((((((((...(((..............))).))))))..))))((((..((((((........))))))..))))......))))))))))))... ( -38.94)
>DroMoj_CAF1 1988 116 + 1
---UUGGCUUGUGGAACACCUCGAAGGAGGUCUGCAACGUUUUAAUCUCCUGCUCCUUCUCGUCGAGCAGUUGGAGUGAACGCUGCCGCUGUUUUUGCAGCAACUGCUCCAGCUCGUUC
---..((((.(..(...(((((....)))))..(((.(((((...(((.((((((.........))))))..)))..))))).))).(((((....)))))..)..)...))))..... ( -39.60)
>DroAna_CAF1 2031 116 + 1
---UGGCGGAGUGAAAGACCUCGAAAGAGGUCUGCAACGUUUUGAUCUCCUGCUCUUUUUCGUCAAGAAGCUGGAGGGAUCGCUGGCGCUGCUUCUGCAGCAACUGCUCCAGUUCGUUG
---.((((((.((..(((((((....)))))))(((..(((.(((((.(((.(.((((((....))))))..).))))))))..)))(((((....)))))...)))..)).)))))). ( -48.60)
>consensus
___UGGCCGUGUGAAACACCUCGAAGGAGGUCUGCAACGUCUUAAUCUCCUGCUCCUUCUCGUCGAGCAGCUGCAGUGAUCGCUGCCGCUGCUUCUGCAGCAACUGCUCCAGCUCGUUC
.....(((.........(((((....)))))((((((............((((((.........))))))))))))........)))(((((....)))))(((((...)))))..... (-26.40 = -27.10 +   0.70)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,054,530 – 7,054,646
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -43.21
Consensus MFE -23.80
Energy contribution -23.89
Covariance contribution 0.09
Combinations/Pair 1.24
Mean z-score -2.73
Structure conservation index 0.55
SVM decision value 0.23
SVM RNA-class probability 0.643058
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7054530 116 - 27905053
GAACGAGCUGGAACAGCUACUGCAGAAGCAGCGCCAGAGGUCACUGCAGCUGCUGGAUGAGAAGGAGCAGGAGAUUAAGACACUGCAGACCUCCUUCGAGGUCUUUCACUCGGCCA---
(..((((.((((.((((..((((((..((..(....)..))..))))))..))))...........((((............))))(((((((....)))))))))))))))..).--- ( -42.10)
>DroVir_CAF1 2014 116 - 1
UAACGAGCUGGAGCAGCUGCUCCAAAAGCAGCGGCAGCGUUCAUUACAGUUGCUCGACGAGAAGGAGCAGGAGAUUAAGACGCUGCAAACCUCCUUCGAGGUGUUUCACAAGCCCA---
....(.((((((((.((((((.....)))))).((((((((........((((((.........))))))........))))))))..(((((....))))))))))...))).).--- ( -41.49)
>DroPse_CAF1 1991 119 - 1
CAACGAGCUGGAGCAGCUGCUGCAGAAGCAGCGACAGCGAUCCCUGCAGCUUCUCGACGAGAAGGAGCAGGAGAUCAAGACGCUGCAGACCUCAUUUGAGGUAUUUCAUACAGCCGGUG
...((.((((..(((((((((((....)))))).....(((((((((..((((((...))))))..))))).)))).....)))))..(((((....)))))........))))))... ( -55.30)
>DroGri_CAF1 2235 116 - 1
GAAUGAGCUGGAACAGUUGCUGCAGAAGCAGCGGCAACGAUCGCUGCAGCUGCUCGACGAGAAGGAGCAGGAGAUUAAAACAUUGCAAACCUCCUUCGAAGUGUUUCACAAGCCCA---
...((.(((((((((((((..((((..(((((((......)))))))..)))).))))..(((((((...(..((......))..)....)))))))....))))))...))).))--- ( -39.00)
>DroMoj_CAF1 1988 116 - 1
GAACGAGCUGGAGCAGUUGCUGCAAAAACAGCGGCAGCGUUCACUCCAACUGCUCGACGAGAAGGAGCAGGAGAUUAAAACGUUGCAGACCUCCUUCGAGGUGUUCCACAAGCCAA---
....(.((((((((...(((((......)))))((((((((..((((...(((((.........))))))))).....))))))))..(((((....))))))))))...))))..--- ( -40.60)
>DroAna_CAF1 2031 116 - 1
CAACGAACUGGAGCAGUUGCUGCAGAAGCAGCGCCAGCGAUCCCUCCAGCUUCUUGACGAAAAAGAGCAGGAGAUCAAAACGUUGCAGACCUCUUUCGAGGUCUUUCACUCCGCCA---
(((((..((((....((((((.....)))))).)))).((((..(((.(((.(((.......)))))).)))))))....))))).(((((((....)))))))............--- ( -40.80)
>consensus
GAACGAGCUGGAGCAGCUGCUGCAGAAGCAGCGGCAGCGAUCACUGCAGCUGCUCGACGAGAAGGAGCAGGAGAUUAAAACGCUGCAGACCUCCUUCGAGGUGUUUCACAAGCCCA___
........(((((..((((((.....))))))(.(((((.......(..((((((.........))))))..).......))))))..(((((....))))).)))))........... (-23.80 = -23.89 +   0.09)

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 10:40:27 2006