Locus 6190

Sequence ID 3R_DroMel_CAF1
Location 16,186,420 – 16,186,537
Length 117
Max. P 0.963567
window10086 window10087 window10088

overview

Window 6

Location 16,186,420 – 16,186,514
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.51
Mean single sequence MFE -41.37
Consensus MFE -28.95
Energy contribution -28.82
Covariance contribution -0.14
Combinations/Pair 1.19
Mean z-score -4.58
Structure conservation index 0.70
SVM decision value 1.55
SVM RNA-class probability 0.963567
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16186420 94 + 27905053
UUAUGCC---------------------GUGUGUGGCCCAGA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUU
...(((.---------------------..((((((((((((----((......)))))..((((((((((.....))))))))))))))))))).))-).((((((.......)))))) ( -42.50)
>DroPse_CAF1 15220 118 + 1
UCAUAGCAGAGAUGACGGGGCCAUUCCAGUUUUUGCCUCUCGGGUCGUUUAAAUCCUCUUUUGGCCUAGUGUCA--CAUUUGGCCAGGGUCACAUGGCCAAAACGCGCAGUUAUUGCAUU
.....(((...(((((.((((((....((..((((((.....))).....)))..))....)))))).((((..--..((((((((.(....).))))))))..)))).))))))))... ( -34.60)
>DroSec_CAF1 15643 94 + 1
UUAUGCC---------------------GUGUGUGGCCCAGA----GGCUAAGUCCUCUUUUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCACU
...(((.---------------------..((((((((((((----((......)))))..((((((((((.....))))))))))))))))))).))-)......(((.....)))... ( -41.80)
>DroSim_CAF1 9199 94 + 1
UUAUGCC---------------------GUGUGUGGCCCAGA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUU
...(((.---------------------..((((((((((((----((......)))))..((((((((((.....))))))))))))))))))).))-).((((((.......)))))) ( -42.50)
>DroEre_CAF1 14894 94 + 1
UUAUGGC---------------------GUGUGUGGCCCAGA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUU
.....((---------------------(.((((((((((((----((......)))))..((((((((((.....))))))))))))))))))))))-..((((((.......)))))) ( -42.30)
>DroYak_CAF1 16301 94 + 1
UUAUGGC---------------------GUGUGUGGCCCAGA----GGCUAAGUCCUCUUAUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUCGC-AAAAUGCGCAAUUAUUGCAUU
.....((---------------------(.((((((((((((----((......)))))..((((((((((.....))))))))))))))))))))))-..((((((.......)))))) ( -44.50)
>consensus
UUAUGCC_____________________GUGUGUGGCCCAGA____GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC_AAAAUGCGCAAUUAUUGCAUU
............................(((((((((((.......((......)).....((((((((((.....)))))))))))))))))).)))........((((...))))... (-28.95 = -28.82 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,186,420 – 16,186,514
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.51
Mean single sequence MFE -32.13
Consensus MFE -19.81
Energy contribution -19.98
Covariance contribution 0.17
Combinations/Pair 1.21
Mean z-score -2.47
Structure conservation index 0.62
SVM decision value 0.07
SVM RNA-class probability 0.567865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16186420 94 - 27905053
AAUGCAAUAAUUGCGCAUUUU-GCAAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAGAAGAGGACUUAGCC----UCUGGGCCACACAC---------------------GGCAUAA
...(((.....)))(((((..-..)))))..((((((((((.((.....)).)))))))).(((((......))----)))))(((......---------------------))).... ( -33.30)
>DroPse_CAF1 15220 118 - 1
AAUGCAAUAACUGCGCGUUUUGGCCAUGUGACCCUGGCCAAAUG--UGACACUAGGCCAAAAGAGGAUUUAAACGACCCGAGAGGCAAAAACUGGAAUGGCCCCGUCAUCUCUGCUAUGA
...(((.....)))((..((((((((........)))))))).(--((((....(((((.....(........)...((....))............)))))..)))))....))..... ( -29.40)
>DroSec_CAF1 15643 94 - 1
AGUGCAAUAAUUGCGCAUUUU-GCAAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAAAAGAGGACUUAGCC----UCUGGGCCACACAC---------------------GGCAUAA
.(((((.....)))))....(-((..((.(.((((((((((.((.....)).)))))))..(((((......))----)))))).).))...---------------------.)))... ( -33.00)
>DroSim_CAF1 9199 94 - 1
AAUGCAAUAAUUGCGCAUUUU-GCAAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAGAAGAGGACUUAGCC----UCUGGGCCACACAC---------------------GGCAUAA
...(((.....)))(((((..-..)))))..((((((((((.((.....)).)))))))).(((((......))----)))))(((......---------------------))).... ( -33.30)
>DroEre_CAF1 14894 94 - 1
AAUGCAAUAAUUGCGCAUUUU-GCAAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAGAAGAGGACUUAGCC----UCUGGGCCACACAC---------------------GCCAUAA
...(((.....)))(((((..-..))))).....((((.....(((((.....(((((...(((((......))----))).))))))))))---------------------))))... ( -31.70)
>DroYak_CAF1 16301 94 - 1
AAUGCAAUAAUUGCGCAUUUU-GCGAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAUAAGAGGACUUAGCC----UCUGGGCCACACAC---------------------GCCAUAA
...(((.....)))(((((..-..))))).....((((.....(((((.....(((((...(((((......))----))).))))))))))---------------------))))... ( -32.10)
>consensus
AAUGCAAUAAUUGCGCAUUUU_GCAAUGCGACCCUGGCCAAAUGUGUGACACUUGGCCAGAAGAGGACUUAGCC____UCUGGGCCACACAC_____________________GCCAUAA
...(((.....)))(((((.....))))).....(((((((.((.....)).))))))).....((.(((((.......))))))).................................. (-19.81 = -19.98 +   0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,186,439 – 16,186,537
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.08
Mean single sequence MFE -42.93
Consensus MFE -32.16
Energy contribution -32.30
Covariance contribution 0.14
Combinations/Pair 1.14
Mean z-score -3.35
Structure conservation index 0.75
SVM decision value 0.76
SVM RNA-class probability 0.843839
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16186439 98 + 27905053
GA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUUUGUGGCGCGUGGCAG-------GCGGCAUU----------
((----((......)))).((((((((((((.....))))))))))))(((((.((((-...((((((...((.......))..)))))).))))-------)))))...---------- ( -45.40)
>DroPse_CAF1 15260 111 + 1
CGGGUCGUUUAAAUCCUCUUUUGGCCUAGUGUCA--CAUUUGGCCAGGGUCACAUGGCCAAAACGCGCAGUUAUUGCAUUUGCGGCGCGUGGCGC-------GUGGCAGUCAGGCAGUCA
.((((.......)))).......(((((.(((((--(.((((((((.(....).))))))))((((((.((..........)).)))))).....-------)))))).).))))..... ( -41.20)
>DroSec_CAF1 15662 98 + 1
GA----GGCUAAGUCCUCUUUUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCACUUGUGGCGCGUGGCAG-------GCGGCAUU----------
((----((......)))).((((((((((((.....))))))))))))(((((.((((-...((((((...((.......))..)))))).))))-------)))))...---------- ( -42.90)
>DroSim_CAF1 9218 98 + 1
GA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUUUGUGGCGCGUGGCAG-------GCGGCAUU----------
((----((......)))).((((((((((((.....))))))))))))(((((.((((-...((((((...((.......))..)))))).))))-------)))))...---------- ( -45.40)
>DroEre_CAF1 14913 105 + 1
GA----GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC-AAAAUGCGCAAUUAUUGCAUUUGUGGCGCGUGGCAGGCGGCAGGCGGCAUU----------
..----.(((..(((....((((((((((((.....))))))))))))(((((.((((-...((((((...((.......))..)))))).))))))))).))))))...---------- ( -45.60)
>DroYak_CAF1 16320 98 + 1
GA----GGCUAAGUCCUCUUAUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUCGC-AAAAUGCGCAAUUAUUGCAUUUGUGGCGCGUGGCAG-------ACGGCAUU----------
..----.(((..(((......((((((((((.....))))))))))..(((((..(((-.(((((((.......)))))))...))).))))).)-------)))))...---------- ( -37.10)
>consensus
GA____GGCUAAGUCCUCUUCUGGCCAAGUGUCACACAUUUGGCCAGGGUCGCAUUGC_AAAAUGCGCAAUUAUUGCAUUUGUGGCGCGUGGCAG_______GCGGCAUU__________
...................((((((((((((.....))))))))))))(((((.((((....((((((.((..........)).)))))).)))).......)))))............. (-32.16 = -32.30 +   0.14)

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 12:14:58 2006