Locus 4284

Sequence ID 2R_DroMel_CAF1
Location 14,086,023 – 14,086,145
Length 122
Max. P 0.858223
window6874 window6875 window6876 window6877

overview

Window 4

Location 14,086,023 – 14,086,125
Length 102
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.93
Mean single sequence MFE -27.33
Consensus MFE -16.04
Energy contribution -15.85
Covariance contribution -0.19
Combinations/Pair 1.19
Mean z-score -1.74
Structure conservation index 0.59
SVM decision value -0.02
SVM RNA-class probability 0.522867
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14086023 102 + 20766785
UGUUGGGAUCUCUAGAACU---UGC-UGCAUUUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCCUCG-C-AUUUUC
(((.((((.......(((.---((.-.(((((((........))))))).)).)))...(((((((((-(((.....--))))..)).))))))..)))).)-)-)..... ( -26.80)
>DroVir_CAF1 2089 103 + 1
UGUUGGCAU---UAAUGCUUUUGGCCGUCAUUUGAUUUAUGGCAAAUGCUUAUGUUGACAUGCCGCAAGAGCAUUUCCAGCUUAAUGAUUGCAUUCUUGCCAGCCA-----
.(((((((.---.(((((..(((((.(((....)))...(((.((((((((.(((.(.....).))).))))))))))))))....))..)))))..)))))))..----- ( -33.20)
>DroGri_CAF1 2320 97 + 1
UGUUGGCAU---UAAUGCUUUUGGCCGUCAUUUGAUUUAUGGCAAAUGCUUAUGUUGACAUGCCGCAA-AGCAUUUCCAGCUUAAUGAUUGCAUUCUUGC-----A-----
.(((((...---.((((((((((((.((((..........(((....))).....))))..)))).))-)))))).)))))........((((....)))-----)----- ( -26.96)
>DroSec_CAF1 1256 102 + 1
UGUUGGGAUCUCUAGAACU---UGC-UGCAUUUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCUUCG-C-AUUUUC
....(((.((....))..(---(((-((...........))))))...)))(((..((.(((((((((-(((.....--))))..)).))))))..))..))-)-...... ( -25.30)
>DroSim_CAF1 10925 102 + 1
UGUUGGGAUCUCUAGAACU---UGC-UGCAUUUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCCUCG-C-AUUUUC
(((.((((.......(((.---((.-.(((((((........))))))).)).)))...(((((((((-(((.....--))))..)).))))))..)))).)-)-)..... ( -26.80)
>DroYak_CAF1 11663 103 + 1
UGUUGGGAUCUGUAGAACUU--UGC-UGCAUUUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUCC--GCUUAAUGAUGGCAUUUUCUUCG-C-AUUUUC
(((..(((...(.(((.(((--(((-.(((((..((....(((....)))...))..).)))).))))-)).))).)--(((.......)))....)))..)-)-)..... ( -24.90)
>consensus
UGUUGGGAUCUCUAGAACU___UGC_UGCAUUUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA_AGCUUUUC__GCUUAAUGACGGCAUUUUCCUCG_C_AUUUUC
....(((....................(((((((........)))))))..........((((((((..(((.......)))...)).))))))....))).......... (-16.04 = -15.85 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,086,023 – 14,086,125
Length 102
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.93
Mean single sequence MFE -26.38
Consensus MFE -14.60
Energy contribution -15.27
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -2.23
Structure conservation index 0.55
SVM decision value 0.33
SVM RNA-class probability 0.691381
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14086023 102 - 20766785
GAAAAU-G-CGAGGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAAAUGCA-GCA---AGUUCUAGAGAUCCCAACA
(((..(-(-(..((...(((((((....((((--.....)))-).))))))).)).......(((((((........))))))).-)))---..))).............. ( -28.20)
>DroVir_CAF1 2089 103 - 1
-----UGGCUGGCAAGAAUGCAAUCAUUAAGCUGGAAAUGCUCUUGCGGCAUGUCAACAUAAGCAUUUGCCAUAAAUCAAAUGACGGCCAAAAGCAUUA---AUGCCAACA
-----..(.(((((..(((((.........((.(((.....))).))((((((....)))..(((((((........)))))).).)))....))))).---.))))).). ( -27.50)
>DroGri_CAF1 2320 97 - 1
-----U-----GCAAGAAUGCAAUCAUUAAGCUGGAAAUGCU-UUGCGGCAUGUCAACAUAAGCAUUUGCCAUAAAUCAAAUGACGGCCAAAAGCAUUA---AUGCCAACA
-----(-----(((....))))........(.(((.((((((-((..((((((....)))..(((((((........)))))).).))).)))))))).---...))).). ( -23.20)
>DroSec_CAF1 1256 102 - 1
GAAAAU-G-CGAAGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAAAUGCA-GCA---AGUUCUAGAGAUCCCAACA
(((..(-(-(((.....(((((((....((((--.....)))-).))))))).)).......(((((((........))))))).-)))---..))).............. ( -27.90)
>DroSim_CAF1 10925 102 - 1
GAAAAU-G-CGAGGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAAAUGCA-GCA---AGUUCUAGAGAUCCCAACA
(((..(-(-(..((...(((((((....((((--.....)))-).))))))).)).......(((((((........))))))).-)))---..))).............. ( -28.20)
>DroYak_CAF1 11663 103 - 1
GAAAAU-G-CGAAGAAAAUGCCAUCAUUAAGC--GGAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAAAUGCA-GCA--AAGUUCUACAGAUCCCAACA
......-.-.(.((((..(((...((((..((--.....))(-((((((((((((......))))..)))))))))...))))..-)))--...)))).)........... ( -23.30)
>consensus
GAAAAU_G_CGAAGAAAAUGCCAUCAUUAAGC__GAAAAGCU_UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAAAUGCA_GCA___AGUUCUAGAGAUCCCAACA
............((((..(((...((((.(((.......))).((((((((((((......))))..))))))))....))))...))).....))))............. (-14.60 = -15.27 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,086,050 – 14,086,145
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.46
Mean single sequence MFE -23.53
Consensus MFE -13.31
Energy contribution -12.73
Covariance contribution -0.58
Combinations/Pair 1.18
Mean z-score -1.71
Structure conservation index 0.57
SVM decision value 0.82
SVM RNA-class probability 0.858223
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14086050 95 + 20766785
UUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCCUCG-C-AUUUUCGUAGCAUUUUU---------CUAGCCCUC-----------
.....((((((.((((((....(..((.(((((((((-(((.....--))))..)).))))))))..)..)-)-)))))))))).......---------.........----------- ( -22.60)
>DroVir_CAF1 2117 95 + 1
UUGAUUUAUGGCAAAUGCUUAUGUUGACAUGCCGCAAGAGCAUUUCCAGCUUAAUGAUUGCAUUCUUGCCAGCCA-------GCCAUUUCUAUUUGG-------GCUGU-----------
........(((((((((((((.((((..(((((....).))))...)))).))).....))))..))))))..((-------(((...........)-------)))).----------- ( -26.30)
>DroGri_CAF1 2348 96 + 1
UUGAUUUAUGGCAAAUGCUUAUGUUGACAUGCCGCAA-AGCAUUUCCAGCUUAAUGAUUGCAUUCUUGC-----A-------ACCAUUUCUAUUUGGAUACCAGGCCAG-----------
........((((.(((((((.(((.(.....).))))-))))))(((((...((((.(((((....)))-----)-------).)))).....)))))......)))).----------- ( -24.90)
>DroSec_CAF1 1283 95 + 1
UUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCUUCG-C-AUUUUCGUAGCAUUUUU---------CUAGCCCUC-----------
.....((((((.((((((..((....))(((((((((-(((.....--))))..)).)))))).......)-)-)))))))))).......---------.........----------- ( -22.20)
>DroSim_CAF1 10952 95 + 1
UUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUUC--GCUUAAUGACGGCAUUUUCCUCG-C-AUUUUCGUAGCAUUUCU---------CUAGCCCUC-----------
.....((((((.((((((....(..((.(((((((((-(((.....--))))..)).))))))))..)..)-)-)))))))))).......---------.........----------- ( -22.60)
>DroYak_CAF1 11691 106 + 1
UUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA-AGCUUUCC--GCUUAAUGAUGGCAUUUUCUUCG-C-AUUUUCGUAGCAUUUUC---------CUCGCAUUUUCGUAGCAUUU
.....((((((.((((((..(((..((.(((((((((-(((.....--))))..)).))))))..))..))-)-......(.((.......---------)))))))))))))))..... ( -22.60)
>consensus
UUGAUUUACGGCAAAUGCCCGUGUUGACAUGCCGCAA_AGCUUUUC__GCUUAAUGACGGCAUUUUCCUCG_C_AUUUUCGUAGCAUUUCU_________CUAGCCCUC___________
......((((((....)).)))).....((((((((..(((.......)))...)).))))))......................................................... (-13.31 = -12.73 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,086,050 – 14,086,145
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.46
Mean single sequence MFE -25.12
Consensus MFE -11.03
Energy contribution -11.70
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.44
SVM decision value 0.73
SVM RNA-class probability 0.835093
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14086050 95 - 20766785
-----------GAGGGCUAG---------AAAAAUGCUACGAAAAU-G-CGAGGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAA
-----------...(((...---------..(((((((.((.....-.-)).((...(((((((....((((--.....)))-).))))))).))......))))))))))......... ( -25.60)
>DroVir_CAF1 2117 95 - 1
-----------ACAGC-------CCAAAUAGAAAUGGC-------UGGCUGGCAAGAAUGCAAUCAUUAAGCUGGAAAUGCUCUUGCGGCAUGUCAACAUAAGCAUUUGCCAUAAAUCAA
-----------.((((-------(...........)))-------))..((((((..((((.........((((.((......)).))))(((....)))..))))))))))........ ( -24.80)
>DroGri_CAF1 2348 96 - 1
-----------CUGGCCUGGUAUCCAAAUAGAAAUGGU-------U-----GCAAGAAUGCAAUCAUUAAGCUGGAAAUGCU-UUGCGGCAUGUCAACAUAAGCAUUUGCCAUAAAUCAA
-----------.(((((..((.((......))((((((-------(-----(((....))))))))))..))..)(((((((-(((..(.....)..)).))))))))))))........ ( -25.30)
>DroSec_CAF1 1283 95 - 1
-----------GAGGGCUAG---------AAAAAUGCUACGAAAAU-G-CGAAGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAA
-----------((.(((...---------.....(((.........-)-))........))).))....(((--.....)))-((((((((((((......))))..))))))))..... ( -25.59)
>DroSim_CAF1 10952 95 - 1
-----------GAGGGCUAG---------AGAAAUGCUACGAAAAU-G-CGAGGAAAAUGCCGUCAUUAAGC--GAAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAA
-----------...(((...---------..(((((((.((.....-.-)).((...(((((((....((((--.....)))-).))))))).))......))))))))))......... ( -25.60)
>DroYak_CAF1 11691 106 - 1
AAAUGCUACGAAAAUGCGAG---------GAAAAUGCUACGAAAAU-G-CGAAGAAAAUGCCAUCAUUAAGC--GGAAAGCU-UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAA
....(((.((..((((...(---------(......((.((.....-.-)).))......))..))))...)--)...)))(-((((((((((((......))))..))))))))).... ( -23.80)
>consensus
___________GAGGGCUAG_________AAAAAUGCUACGAAAAU_G_CGAAGAAAAUGCCAUCAUUAAGC__GAAAAGCU_UUGCGGCAUGUCAACACGGGCAUUUGCCGUAAAUCAA
.....................................................................(((.......))).((((((((((((......))))..))))))))..... (-11.03 = -11.70 +   0.67)

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 11:16:09 2006