Locus 5273

Sequence ID	3R_DroMel_CAF1
Location	13,758,464 – 13,758,654
Length	190
Max. P	0.999500

overview

Window 3

Location	13,758,464 – 13,758,563
Length	99
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	68.62
Mean single sequence MFE	-23.94
Consensus MFE	-13.52
Energy contribution	-14.48
Covariance contribution	0.96
Combinations/Pair	1.28
Mean z-score	-2.89
Structure conservation index	0.56
SVM decision value	3.66
SVM RNA-class probability	0.999500
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13758464 99 + 27905053
GGGUGCAUAUAUAUAAAAUUUGCAUAGGUACCUAAAAGUAUGCAACAAUAUAUA--------GUUG----GCCC-----AUUUUUUGUUGCAUACUUUUACACACCUCUCGAAUU--U
..(((((.............)))))((((...((((((((((((((((......--------....----....-----.....))))))))))))))))...))))........--. ( -26.23)
>DroSec_CAF1 31063 116 + 1
AAUUGCAUAUUUAUAUAAUUUGUAUAGAUAUUUAAACGUAUUCAACCAUACAUUUAAGCCAAUUUGAGAGGCACACACACUUUUUCGUUGAAUACUUUUACACACCUCUCGAAUU--U
....((((((((((((.....))))))))))(((((.((((......)))).))))))).(((((((((((............(((...)))............)))))))))))--. ( -21.45)
>DroSim_CAF1 30038 116 + 1
AAUUGCAUAUUUAUAUCAUUUGUAUAGAUAUCUGAACGUAUGCAACAAUACAUUCAAGCCAAUUUGAGAGAAACACACACUUUUUCGUUGCAUACUUUUACACACCUCUCGAAUU--U
......((((((((((.....)))))))))).((((.(((((((((.......(((((....)))))((((((.......))))))))))))))).))))...............--. ( -23.00)
>DroEre_CAF1 29926 99 + 1
AACUGCAUAUUUUUAUCAUUUCUGUGGGGACCUAAAAGUAAGCAACAAGAAAUGUAAG-------------------CGCUAUUUUGCUGCAUACUUUUGCACACCUCUAAACAUAAU
.........................((((...((((((((.(((.(((((...((...-------------------.))..))))).))).))))))))....)))).......... ( -17.10)
>DroYak_CAF1 31816 118 + 1
AAUUGGCUAUUUAUAUCAUGUCUAUGGGUAGCUAAAAGUAUGCAACAAUAUAUGUAAGCCGUUUGAAUAGACCCACACGCUCUGUUGUUGCAUACUUUUACACAUCUUUAAGCAUAAU
....(((((((((((.......)))))))))))(((((((((((((((((......(((.((.((........)).))))).)))))))))))))))))................... ( -31.90)
>consensus
AAUUGCAUAUUUAUAUCAUUUGUAUAGGUACCUAAAAGUAUGCAACAAUACAUGUAAGCC__UUUGA_AGACACACACACUUUUUUGUUGCAUACUUUUACACACCUCUCGAAUU__U
......(((((((((.......))))))))).((((((((((((((((....................................)))))))))))))))).................. (-13.52 = -14.48 +   0.96)

alignment

secondary structure

dotplot

Window 4

Location	13,758,464 – 13,758,563
Length	99
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	68.62
Mean single sequence MFE	-26.37
Consensus MFE	-16.44
Energy contribution	-17.32
Covariance contribution	0.88
Combinations/Pair	1.24
Mean z-score	-2.55
Structure conservation index	0.62
SVM decision value	3.16
SVM RNA-class probability	0.998622
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13758464 99 - 27905053
A--AAUUCGAGAGGUGUGUAAAAGUAUGCAACAAAAAAU-----GGGC----CAAC--------UAUAUAUUGUUGCAUACUUUUAGGUACCUAUGCAAAUUUUAUAUAUAUGCACCC
.--........(((((..((((((((((((((((.(.((-----((..----...)--------))).).))))))))))))))))..))))).((((.((.......)).))))... ( -32.70)
>DroSec_CAF1 31063 116 - 1
A--AAUUCGAGAGGUGUGUAAAAGUAUUCAACGAAAAAGUGUGUGUGCCUCUCAAAUUGGCUUAAAUGUAUGGUUGAAUACGUUUAAAUAUCUAUACAAAUUAUAUAAAUAUGCAAUU
.--((((.((((((((..((......(((...)))......))..)))))))).)))).((((((((((((......))))))))))((((.((((.......)))).)))))).... ( -24.20)
>DroSim_CAF1 30038 116 - 1
A--AAUUCGAGAGGUGUGUAAAAGUAUGCAACGAAAAAGUGUGUGUUUCUCUCAAAUUGGCUUGAAUGUAUUGUUGCAUACGUUCAGAUAUCUAUACAAAUGAUAUAAAUAUGCAAUU
.--((((.((((((((((((....))))))((......)).......)))))).)))).((((((((((((......))))))))))(((((.........)))))......)).... ( -22.50)
>DroEre_CAF1 29926 99 - 1
AUUAUGUUUAGAGGUGUGCAAAAGUAUGCAGCAAAAUAGCG-------------------CUUACAUUUCUUGUUGCUUACUUUUAGGUCCCCACAGAAAUGAUAAAAAUAUGCAGUU
..(((((((...((.(..(.((((((.(((((((.......-------------------..........))))))).))))))...)..))).((....))....)))))))..... ( -19.23)
>DroYak_CAF1 31816 118 - 1
AUUAUGCUUAAAGAUGUGUAAAAGUAUGCAACAACAGAGCGUGUGGGUCUAUUCAAACGGCUUACAUAUAUUGUUGCAUACUUUUAGCUACCCAUAGACAUGAUAUAAAUAGCCAAUU
((((((((.......((.((((((((((((((((...(..(((((((((.........))))))))).).)))))))))))))))))).......)).)))))).............. ( -33.24)
>consensus
A__AAUUCGAGAGGUGUGUAAAAGUAUGCAACAAAAAAGCGUGUGGGCCU_UCAAA__GGCUUAAAUAUAUUGUUGCAUACUUUUAGAUACCUAUACAAAUGAUAUAAAUAUGCAAUU
............(((((.((((((((((((((((....................................)))))))))))))))).))))).......................... (-16.44 = -17.32 +   0.88)

alignment

secondary structure

dotplot

Window 5

Location	13,758,502 – 13,758,601
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	72.33
Mean single sequence MFE	-28.77
Consensus MFE	-10.77
Energy contribution	-11.65
Covariance contribution	0.87
Combinations/Pair	1.22
Mean z-score	-2.73
Structure conservation index	0.37
SVM decision value	0.55
SVM RNA-class probability	0.778980
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13758502 99 - 27905053
AGUUGUGUAUCUAAU--CAUUGAAUAUUGCGGUUUUAAGUA--AAUUCGAGAGGUGUGUAAAAGUAUGCAACAAAAAAU-----GGGC----CAAC--------UAUAUAUUGUUGCAUA
..(((..(((((...--..((((((.((((........)))--))))))).)))))..)))...((((((((((.(.((-----((..----...)--------))).).)))))))))) ( -25.90)
>DroSec_CAF1 31101 118 - 1
AGUUGUAUACCUAAUACCAAUAAGUAUUGGGUUUUUAAGUA--AAUUCGAGAGGUGUGUAAAAGUAUUCAACGAAAAAGUGUGUGUGCCUCUCAAAUUGGCUUAAAUGUAUGGUUGAAUA
((..(((((((((((((......))))))))..(((((((.--((((.((((((((..((......(((...)))......))..)))))))).)))).))))))))))))..))..... ( -32.60)
>DroSim_CAF1 30076 118 - 1
AGUUGUAUACCUAAUACCAUUGAGUAUUGGGUUUUUAAGUA--AAUUCGAGAGGUGUGUAAAAGUAUGCAACGAAAAAGUGUGUGUUUCUCUCAAAUUGGCUUGAAUGUAUUGUUGCAUA
........(((((((((......)))))))))..((((((.--((((.((((((((((((....))))))((......)).......)))))).)))).))))))(((((....))))). ( -28.50)
>DroYak_CAF1 31854 118 - 1
AGUUGUUAACCUAAA--UAUUAAAUAUUAGGGGUCUCAAUAUUAUGCUUAAAGAUGUGUAAAAGUAUGCAACAACAGAGCGUGUGGGUCUAUUCAAACGGCUUACAUAUAUUGUUGCAUA
.((((....(((.((--(((...))))).)))....)))).((((((........))))))...((((((((((...(..(((((((((.........))))))))).).)))))))))) ( -28.10)
>consensus
AGUUGUAUACCUAAU__CAUUAAAUAUUGGGGUUUUAAGUA__AAUUCGAGAGGUGUGUAAAAGUAUGCAACAAAAAAGUGUGUGGGCCUCUCAAAUUGGCUUAAAUAUAUUGUUGCAUA
.........((((((((......)))))))).................................((((((((((....................................)))))))))) (-10.77 = -11.65 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	13,758,563 – 13,758,654
Length	91
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	80.41
Mean single sequence MFE	-18.56
Consensus MFE	-12.28
Energy contribution	-12.84
Covariance contribution	0.56
Combinations/Pair	1.13
Mean z-score	-1.72
Structure conservation index	0.66
SVM decision value	0.26
SVM RNA-class probability	0.657004
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13758563 91 + 27905053
ACUUAAAACCGCAAUAUUCAAUG--AUUAGAUACACAACUUGAGGCACAUUUUUCUCUGUGUACAACUGUGGUUAUAUCCACGUGUAUACGUG
......(((((((....((....--....))((((((....((((........))))))))))....))))))).....(((((....))))) ( -17.80)
>DroSec_CAF1 31179 93 + 1
ACUUAAAAACCCAAUACUUAUUGGUAUUAGGUAUACAACUAAAUGCACAUUUUUCCCUGUGUACAACUGUGGUUAUAUCCACGUGUAUACGUG
............((((((....))))))..(((((((......((((((........)))))).....((((......)))).)))))))... ( -21.40)
>DroSim_CAF1 30154 93 + 1
ACUUAAAAACCCAAUACUCAAUGGUAUUAGGUAUACAACUUAAUGCACAUUUUUCCCUGUGUACAACUGUGGUUACAUCCACGUGUAUACGUG
...................(((((((((((((.....))))))))).)))).......(((((((...((((......)))).)))))))... ( -23.40)
>DroEre_CAF1 30025 80 + 1
A-----------ACUAUUUAGUA--UUCAGGUAAACAACUCAAAGCACAUUUUUCACUGUGUACCACUGUGGCUAUAUCCACGUGUAUACGUG
.-----------........((.--((.((........)).)).))........(((.((((((.((.((((......))))))))))))))) ( -13.70)
>DroYak_CAF1 31934 91 + 1
AUUGAGACCCCUAAUAUUUAAUA--UUUAGGUUAACAACUCAAGGCACAUUUCUCACUGUGUACAACUGCGGUUAUAUCCACGUGUAUACGUG
.(((((...(((((.........--.))))).......)))))...........(((.(((((((...(.((......)).).)))))))))) ( -16.50)
>consensus
ACUUAAAAACCCAAUAUUUAAUG__AUUAGGUAAACAACUCAAGGCACAUUUUUCACUGUGUACAACUGUGGUUAUAUCCACGUGUAUACGUG
..............................((((((........(((((........)))))......((((......))))))))))..... (-12.28 = -12.84 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:49 2006