Locus 9522

Sequence ID	3R_DroMel_CAF1
Location	25,163,873 – 25,163,968
Length	95
Max. P	0.991805

overview

Window 5

Location	25,163,873 – 25,163,968
Length	95
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	77.59
Mean single sequence MFE	-33.18
Consensus MFE	-15.04
Energy contribution	-16.57
Covariance contribution	1.53
Combinations/Pair	1.05
Mean z-score	-2.32
Structure conservation index	0.45
SVM decision value	0.66
SVM RNA-class probability	0.813324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25163873 95 + 27905053
AAG-UUGGCAAGUGGACAAAGAGCGCCGGCUAAUUAGCCA---G--CUCGCUCAAUGGCCAAUUGCCACGCAAAAUCAGCCAAG-GGUGGCGGCA-A------CGACAA
..(-(((((((.(((.((..((((((.((((....)))).---)--)..))))..)).))).)))))).))....((.((((..-..))))(...-.------)))... ( -35.00)
>DroVir_CAF1 26015 97 + 1
GAGUCCGGAAAGUGGACAAAAAGCGCCGGCUAAUUAGC--CUCG--CUCGCUCAAUGGCCAAUUGCCACGCAA-AUCAGCGACAGGCUGACUGCC-U------CUGUCG
..(((((.....))))).....(((..(((...(((((--((.(--.(((((...((((.....)))).....-...)))))))))))))..)))-.------.))).. ( -30.00)
>DroEre_CAF1 23467 95 + 1
AAG-UUGGCAAGUGGACAAAGAGCGCCGGCUAAUUAGCCA---G--CUCGCUCAAUGGCCAAUUGCCACGCAAAAUCAGCCAAG-GGUGGCGACU-G------CGACAA
...-.((((((.(((.((..((((((.((((....)))).---)--)..))))..)).))).))))))((((...((.((((..-..)))))).)-)------)).... ( -37.10)
>DroWil_CAF1 98400 91 + 1
GGC-UGUGGAUGUGGACAAAAGGCACUGGCUAAUUAGCCA---GUGUUCGCUCAAUGGCCAAUUGCCAUGCAAAAUCAGCGAAG-GACGACGACA-A------------
...-(((.(...((..(.....(((((((((....)))))---))))(((((..(((((.....)))))........))))).)-..)).).)))-.------------ ( -29.50)
>DroYak_CAF1 23012 101 + 1
AAG-UUGGCCAGUGGACAAAGAGCGGCGGCUAAUUAGCCA---G--CUCGCUCAAUGGCCAAUUGCCACGCAAAAUCAGCCAAG-GGUGGCGACU-ACGACUACGACAA
.((-((((((((....)...(((((((((((....)))).---)--).)))))..)))))))))(((((.(............)-.)))))....-............. ( -38.40)
>DroAna_CAF1 20725 94 + 1
--U-GUGCCAAGUGGACAAAGAGCGCCGGCUAAUUAGCCA---G--UUCGCUCAAUGGCCAAUUGCCACGCAAAAUCAGCCAAG-GGUAGCGACAGG------CGACGA
--(-((.((....)))))....(((((((((....)))).---(--(.(((((..((((...((((...)))).....))))..-.).)))))).))------)).).. ( -29.10)
>consensus
AAG_UUGGCAAGUGGACAAAGAGCGCCGGCUAAUUAGCCA___G__CUCGCUCAAUGGCCAAUUGCCACGCAAAAUCAGCCAAG_GGUGGCGACA_A______CGACAA
......(((((.(((.((..(((((..((((....)))).........)))))..)).))).)))))..((.......))............................. (-15.04 = -16.57 +   1.53)

alignment

secondary structure

dotplot

Window 6

Location	25,163,873 – 25,163,968
Length	95
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	77.59
Mean single sequence MFE	-37.50
Consensus MFE	-22.99
Energy contribution	-23.97
Covariance contribution	0.98
Combinations/Pair	1.28
Mean z-score	-3.13
Structure conservation index	0.61
SVM decision value	2.29
SVM RNA-class probability	0.991805
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25163873 95 - 27905053
UUGUCG------U-UGCCGCCACC-CUUGGCUGAUUUUGCGUGGCAAUUGGCCAUUGAGCGAG--C---UGGCUAAUUAGCCGGCGCUCUUUGUCCACUUGCCAA-CUU
....((------(-..(.((((..-..)))).).....)))((((((.(((.((..((((..(--(---(((((....)))))))))))..)).))).)))))).-... ( -39.30)
>DroVir_CAF1 26015 97 - 1
CGACAG------A-GGCAGUCAGCCUGUCGCUGAU-UUGCGUGGCAAUUGGCCAUUGAGCGAG--CGAG--GCUAAUUAGCCGGCGCUUUUUGUCCACUUUCCGGACUC
....((------(-((((((((((.....))))))-).((.((((((((((((.(((......--))))--))))))).)))))))))))).((((.......)))).. ( -36.60)
>DroEre_CAF1 23467 95 - 1
UUGUCG------C-AGUCGCCACC-CUUGGCUGAUUUUGCGUGGCAAUUGGCCAUUGAGCGAG--C---UGGCUAAUUAGCCGGCGCUCUUUGUCCACUUGCCAA-CUU
....((------(-((((((((..-..)))).)))..))))((((((.(((.((..((((..(--(---(((((....)))))))))))..)).))).)))))).-... ( -43.90)
>DroWil_CAF1 98400 91 - 1
------------U-UGUCGUCGUC-CUUCGCUGAUUUUGCAUGGCAAUUGGCCAUUGAGCGAACAC---UGGCUAAUUAGCCAGUGCCUUUUGUCCACAUCCACA-GCC
------------.-..........-....((((..((((((((((.....)))))...)))))(((---(((((....)))))))).................))-)). ( -28.00)
>DroYak_CAF1 23012 101 - 1
UUGUCGUAGUCGU-AGUCGCCACC-CUUGGCUGAUUUUGCGUGGCAAUUGGCCAUUGAGCGAG--C---UGGCUAAUUAGCCGCCGCUCUUUGUCCACUGGCCAA-CUU
....(((((....-((((((((..-..)))).)))))))))((((...(((.((..(((((.(--(---.((((....)))))))))))..)).)))...)))).-... ( -39.20)
>DroAna_CAF1 20725 94 - 1
UCGUCG------CCUGUCGCUACC-CUUGGCUGAUUUUGCGUGGCAAUUGGCCAUUGAGCGAA--C---UGGCUAAUUAGCCGGCGCUCUUUGUCCACUUGGCAC-A--
.....(------(..(((((((..-..)))).)))...))(((.(((.(((.((..(((((..--(---(((((....)))))))))))..)).))).))).)))-.-- ( -38.00)
>consensus
UUGUCG______U_UGUCGCCACC_CUUGGCUGAUUUUGCGUGGCAAUUGGCCAUUGAGCGAG__C___UGGCUAAUUAGCCGGCGCUCUUUGUCCACUUGCCAA_CUU
..................((((.....))))..........((((((.(((.((..(((((........(((((....))))).)))))..)).))).))))))..... (-22.99 = -23.97 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:24 2006