Locus 2850

Sequence ID 3L_DroMel_CAF1
Location 8,139,396 – 8,139,511
Length 115
Max. P 0.955826
window4453 window4454 window4455

overview

Window 3

Location 8,139,396 – 8,139,492
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.53
Mean single sequence MFE -28.35
Consensus MFE -18.10
Energy contribution -18.08
Covariance contribution -0.03
Combinations/Pair 1.18
Mean z-score -1.69
Structure conservation index 0.64
SVM decision value 0.80
SVM RNA-class probability 0.853066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8139396 96 + 23771897
-----CAA-----GCUCU-G-GGGCU------CUGC--ACGUGUUGCCGCGUUUGAAGUUGAUGCAAAAGUUGUAAAAAAAUUCGCAUCAAUUUUAGUUUUAUACUCAAGAGCAGA----
-----...-----(((((-(-((...------..((--(((((....))))).((((((((((((.((..((.....))..)).))))))))))))))......))).)))))...---- ( -28.10)
>DroVir_CAF1 36741 97 + 1
-----CG-------AGCU-GCUA--G------CUGC--ACGUGUUGCCGCGUUUGGAGUUGAUGCAAAAGUUAGAAAAAAUUUCGCAUCAAUUUUAGUUUUAUACUCAAGAGCAGGUCGA
-----((-------(.((-(((.--(------(.((--(.....))).))..(((((((((((((..(((((......))))).))))))))))))).............))))).))). ( -31.10)
>DroGri_CAF1 37186 106 + 1
-----CGAUCUGUGAGCU-GCGAGUG------CUGC--ACGUGUUGCCGCGUUUGGAGUUGAUGCAAAAGUUAGAAAAAAUUUCGCAUCAAUUUUUGUUUUAUACUCAAGAGCAGGUCGA
-----((((((((...((-..(((((------..((--(((((....)))))..(((((((((((..(((((......))))).))))))))))).))....))))).)).)))))))). ( -33.80)
>DroWil_CAF1 44699 98 + 1
-----UCU-----GCACUCU-GGUCU------CUGCACACGUGUUGCCGCGUUUGAAGUUGAUGCAAAAGUUAGAA-AAAAUUCGCAUCAAUUUUAGUUUUAUACUCAAGAGCAGC----
-----.((-----((.((..-(((..------..((..(((((....))))).((((((((((((...((((....-..)))).)))))))))))))).....)))..)).)))).---- ( -24.40)
>DroAna_CAF1 72279 98 + 1
CUGAGCUG-----GCGUU-G-GAGCU------CUGC--ACGUGUUGCCGCGUUUGAAGUUGAUACAAAAGUUGUAAAAAAAUUCGCAUCAAUUUUAGUUUUAUACUCG---GUUCG----
..((((((-----(.(((-(-((((.------....--(((((....))))).((((((((((.(.((..((.....))..)).).)))))))))))))))).)))))---)))).---- ( -22.40)
>DroPer_CAF1 39096 102 + 1
-----CUG-----GAGCU-G-GAGCGUCUGGGGUGC--ACGUGUGGCCGCGUUUGAAGUUGAUGCAAAAGUUAGACAAAAAUUCGCAUCAAUUUUAGUUUUAUACUCGAGAGCGCG----
-----...-----.....-.-..((((((.(((((.--(((((....)))))(((((((((((((...................))))))))))))).....))))).))).))).---- ( -30.31)
>consensus
_____CGA_____GAGCU_G_GAGCG______CUGC__ACGUGUUGCCGCGUUUGAAGUUGAUGCAAAAGUUAGAAAAAAAUUCGCAUCAAUUUUAGUUUUAUACUCAAGAGCAGG____
................................((((..(((((....)))))(((((((((((((...................)))))))))))))..............))))..... (-18.10 = -18.08 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,139,396 – 8,139,492
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.53
Mean single sequence MFE -24.31
Consensus MFE -15.48
Energy contribution -15.78
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.64
SVM decision value 1.46
SVM RNA-class probability 0.955826
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8139396 96 - 23771897
----UCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUUUACAACUUUUGCAUCAACUUCAAACGCGGCAACACGU--GCAG------AGCCC-C-AGAGC-----UUG-----
----...(((((.(.((............((((((((((.............))))))))))..((..(((.(....).)))--...)------))).)-.-)))))-----...----- ( -23.72)
>DroVir_CAF1 36741 97 - 1
UCGACCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAAUUUUUUCUAACUUUUGCAUCAACUCCAAACGCGGCAACACGU--GCAG------C--UAGC-AGCU-------CG-----
.(((.(((((....(((............(((((((((((.((.....)).)))))))))))......(((.(....).)))--...)------)--))))-)).)-------))----- ( -25.40)
>DroGri_CAF1 37186 106 - 1
UCGACCUGCUCUUGAGUAUAAAACAAAAAUUGAUGCGAAAUUUUUUCUAACUUUUGCAUCAACUCCAAACGCGGCAACACGU--GCAG------CACUCGC-AGCUCACAGAUCG-----
..((.((((....((((............(((((((((((.((.....)).)))))))))))........((.(((.....)--)).)------)))))))-)).))........----- ( -26.30)
>DroWil_CAF1 44699 98 - 1
----GCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUU-UUCUAACUUUUGCAUCAACUUCAAACGCGGCAACACGUGUGCAG------AGACC-AGAGUGC-----AGA-----
----.((((.(((..((............((((((((((..((-....))..))))))))))(((...(((((......)))))...)------)))).-.))).))-----)).----- ( -28.70)
>DroAna_CAF1 72279 98 - 1
----CGAAC---CGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUUUACAACUUUUGUAUCAACUUCAAACGCGGCAACACGU--GCAG------AGCUC-C-AACGC-----CAGCUCAG
----.(((.---..(((.....)))....((((((((((.............)))))))))).)))..(((.(....).)))--...(------((((.-.-.....-----.))))).. ( -20.02)
>DroPer_CAF1 39096 102 - 1
----CGCGCUCUCGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUGUCUAACUUUUGCAUCAACUUCAAACGCGGCCACACGU--GCACCCCAGACGCUC-C-AGCUC-----CAG-----
----.(((.(((.(.((............((((((((((..((.....))..)))))))))).......((((......)))--).)).).))))))..-.-.....-----...----- ( -21.70)
>consensus
____CCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUUUCUAACUUUUGCAUCAACUUCAAACGCGGCAACACGU__GCAG______AGCUC_C_AGCGC_____CAG_____
.....((((....................((((((((((..((.....))..))))))))))......(((.(....).)))..))))................................ (-15.48 = -15.78 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,139,416 – 8,139,511
Length 95
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.69
Mean single sequence MFE -25.00
Consensus MFE -13.87
Energy contribution -13.87
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.55
SVM decision value 1.07
SVM RNA-class probability 0.911041
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8139416 95 - 23771897
GAGUCCA---ACG----AGCC-----AGCGC----UCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUUUACAACUUUUGCAUCAACUUCAAACGCGGCAACAC
.......---...----.(((-----.((((----((.......))))............((((((((((.............))))))))))........)))))..... ( -21.82)
>DroVir_CAF1 36758 97 - 1
-UGGUA----ACG----GCGC-----CGCGCUCGACCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAAUUUUUUCUAACUUUUGCAUCAACUCCAAACGCGGCAACAC
-.....----...----..((-----(((((((((.......))))))............(((((((((((.((.....)).)))))))))))........)))))..... ( -27.60)
>DroPse_CAF1 46005 98 - 1
GACCCCG---GAC----AACCCCG--AGCAA----CGCGCUCUCGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUGUCUAACUUUUGCAUCAACUUCAAACGCGGCCACAC
.....((---(..----....)))--.....----((((......(((.....)))....((((((((((..((.....))..)))))))))).......))))....... ( -19.90)
>DroWil_CAF1 44722 103 - 1
GACCAAG---CGGCGGCAACAUCGGCGGCUG----GCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUU-UUCUAACUUUUGCAUCAACUUCAAACGCGGCAACAC
.......---((((.((.......)).))))----(((((..((((((.....)).....((((((((((..((-....))..))))))))))..))))..)))))..... ( -29.20)
>DroMoj_CAF1 37695 102 - 1
GUGGCAAACGACG----CCGC-----CGCGCUCGACCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAAUUUUUUCUAACUUUUGCAUCAACUCCAAACGCGGCAACAC
..(((.......)----))((-----(((((((((.......))))))............(((((((((((.((.....)).)))))))))))........)))))..... ( -31.60)
>DroPer_CAF1 39122 98 - 1
GACCCCG---GAC----AACCCCG--AGCAA----CGCGCUCUCGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUGUCUAACUUUUGCAUCAACUUCAAACGCGGCCACAC
.....((---(..----....)))--.....----((((......(((.....)))....((((((((((..((.....))..)))))))))).......))))....... ( -19.90)
>consensus
GACCCAG___ACG____AACC_____AGCGC____CCUGCUCUUGAGUAUAAAACUAAAAUUGAUGCGAAUUUUUUUCUAACUUUUGCAUCAACUUCAAACGCGGCAACAC
...........................((.........(((....)))............((((((((((..((.....))..))))))))))........))(....).. (-13.87 = -13.87 +  -0.00)

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 10:43:20 2006