Locus 8877

Sequence ID	3R_DroMel_CAF1
Location	23,814,912 – 23,815,111
Length	199
Max. P	0.944653

overview

Window 5

Location	23,814,912 – 23,815,016
Length	104
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	66.82
Mean single sequence MFE	-29.10
Consensus MFE	-6.28
Energy contribution	-7.36
Covariance contribution	1.08
Combinations/Pair	1.35
Mean z-score	-2.32
Structure conservation index	0.22
SVM decision value	0.66
SVM RNA-class probability	0.815088
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23814912 104 + 27905053
AAUGCAAUUCUUUCUCUCCCAUCUUACGCUUCGCUGAGCUGGUGAGAAU---UCUU---AGGG---------AAAAGAUAGAGAGAGGGGAGAGAAAGAAGAGAGUCGAAGAAUGAGGU
.......(((((((((((((.((((.(.((((.(((((..(((....))---))))---)).)---------)..))...).)))).)))))))))))))................... ( -32.20)
>DroSec_CAF1 20123 81 + 1
GCUGCAAUUCUUUC---------UUACGCUUCGCUGAGCUGGUGAGAAU---UCUC---AGGG---------AAAAGACAGAGAGAGGGGAGAGAA-------------AGAAUGU-GU
...(((((((((((---------((.(.((((.(((..((..((((...---.)))---)...---------...)).)))...)))).).)))))-------------))))).)-)) ( -23.90)
>DroSim_CAF1 20178 101 + 1
GCUGCAAUUCUUUC--UCCCAUCUUACGCUUCGCUGAGCUGGUGAGAAU---UCUC---AGGG---------AAAAGACAGAGAGAGGGGAGAGAAGGAAGAGAGUCCAAGAAUGA-GU
(((.((.(((((((--(((..((((...((((.(((((..(((....))---))))---)).)---------)..))...))))..))))))))))(((......))).....)))-)) ( -29.50)
>DroYak_CAF1 20669 91 + 1
ACUGCAAUUUCUGC--UCUCAUCUUACGCUUCGCUGAGCUGCUGAGAAA---ACUC---AGAG---------AAAAGAGA-----------GAGAGAGAAGAGAGUCGAAGAAUGAGGU
(((.((.((((.((--((((.((((.(..(((.((...((.(((((...---.)))---))))---------...)).))-----------).).)))).)))))).))))..)).))) ( -27.00)
>DroAna_CAF1 20894 111 + 1
GCUGCACUUUUUGC--UCUCACCUUACGCUUGGUUGGGUGUGUGAGAAAAACGCUCGAGAGGGCACAUUAAUGAAAAACAGAGAGAGGUGCGC--UCGGAGAGAG---AAGAACGG-AA
...(((((((((..--((((((...((((((....)))))))))))).....((((....))))..................))))))))).(--((.....)))---........-.. ( -32.90)
>consensus
GCUGCAAUUCUUUC__UCCCAUCUUACGCUUCGCUGAGCUGGUGAGAAU___UCUC___AGGG_________AAAAGACAGAGAGAGGGGAGAGAAAGAAGAGAGUC_AAGAAUGA_GU
.......(((((((.......((((((((((....))))..))))))......(((....)))..........................)))))))....................... ( -6.28 =  -7.36 +   1.08)

alignment

secondary structure

dotplot

Window 6

Location	23,814,912 – 23,815,016
Length	104
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	66.82
Mean single sequence MFE	-22.60
Consensus MFE	-5.26
Energy contribution	-6.40
Covariance contribution	1.14
Combinations/Pair	1.17
Mean z-score	-2.34
Structure conservation index	0.23
SVM decision value	0.80
SVM RNA-class probability	0.854412
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23814912 104 - 27905053
ACCUCAUUCUUCGACUCUCUUCUUUCUCUCCCCUCUCUCUAUCUUUU---------CCCU---AAGA---AUUCUCACCAGCUCAGCGAAGCGUAAGAUGGGAGAGAAAGAAUUGCAUU
...................(((((((((((((.(((..(..((((..---------....---))))---..........(((......))))..))).)))))))))))))....... ( -28.60)
>DroSec_CAF1 20123 81 - 1
AC-ACAUUCU-------------UUCUCUCCCCUCUCUCUGUCUUUU---------CCCU---GAGA---AUUCUCACCAGCUCAGCGAAGCGUAA---------GAAAGAAUUGCAGC
.(-(.(((((-------------((((..(..((.((.(((......---------...(---(((.---...))))......))).)))).)..)---------)))))))))).... ( -14.16)
>DroSim_CAF1 20178 101 - 1
AC-UCAUUCUUGGACUCUCUUCCUUCUCUCCCCUCUCUCUGUCUUUU---------CCCU---GAGA---AUUCUCACCAGCUCAGCGAAGCGUAAGAUGGGA--GAAAGAAUUGCAGC
..-..(((((((((......)))...((((((.(((..(.((...((---------(.((---(((.---...........))))).))))))..))).))))--))))))))...... ( -24.50)
>DroYak_CAF1 20669 91 - 1
ACCUCAUUCUUCGACUCUCUUCUCUCUC-----------UCUCUUUU---------CUCU---GAGU---UUUCUCAGCAGCUCAGCGAAGCGUAAGAUGAGA--GCAGAAAUUGCAGU
........((.(((...(((.(((((((-----------(..(.(((---------(.((---((((---(........))))))).)))).)..))).))))--).)))..))).)). ( -24.30)
>DroAna_CAF1 20894 111 - 1
UU-CCGUUCUU---CUCUCUCCGA--GCGCACCUCUCUCUGUUUUUCAUUAAUGUGCCCUCUCGAGCGUUUUUCUCACACACCCAACCAAGCGUAAGGUGAGA--GCAAAAAGUGCAGC
..-..((.(((---(((((.((((--(.((((.......((.....)).....)))).)))....((((((.................))))))..)).))))--)....))).))... ( -21.43)
>consensus
AC_UCAUUCUU_GACUCUCUUCUUUCUCUCCCCUCUCUCUGUCUUUU_________CCCU___GAGA___AUUCUCACCAGCUCAGCGAAGCGUAAGAUGAGA__GAAAGAAUUGCAGC
.....((((((....((((.((.........................................(((.......)))....(((......)))....)).))))....))))))...... ( -5.26 =  -6.40 +   1.14)

alignment

secondary structure

dotplot

Window 7

Location	23,814,977 – 23,815,086
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	73.01
Mean single sequence MFE	-29.20
Consensus MFE	-10.01
Energy contribution	-10.20
Covariance contribution	0.19
Combinations/Pair	1.07
Mean z-score	-2.26
Structure conservation index	0.34
SVM decision value	0.77
SVM RNA-class probability	0.847444
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23814977 109 + 27905053
GAGAGAGGGGAGAGAAAGAAGAGAGUCGAAGAAUGAGGUAACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCAUUCUUCAAUCAGA-U
....((..((((((..((..((((((.(.((((((.......((.((....))))..(((((.....))))).)))))).)))))).)..-----))...))))))..))...-. ( -30.70)
>DroSec_CAF1 20179 95 + 1
GAGAGAGGGGAGAGAA-------------AGAAUGU-GUGACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCUUUCUUCAAUCAGA-C
((..((((..((((..-------------(((((((-(.((.((.((....))))..(((((.....)))))....))))))))))....-----)).))..))))..))...-. ( -30.50)
>DroSim_CAF1 20241 108 + 1
GAGAGAGGGGAGAGAAGGAAGAGAGUCCAAGAAUGA-GUGACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCUUUCUUCAAUCAGA-C
..((..((((((((.((....(((((...((((((.-.....((.((....))))..(((((.....))))).))))))..)))))....-----)).))))))))..))...-. ( -34.00)
>DroEre_CAF1 20691 103 + 1
CAGA-------GAGAAAGAAGAGAGUCGAAGAAUGAGGUGACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAU-----CUGCCUUCUUCAAUCCGAGA
..((-------..(((.((((..((..(.(((((((((((..((.((....))))..(((((.....))))).)).))).)))))).)..-----))..)))))))..))..... ( -28.30)
>DroYak_CAF1 20732 91 + 1
-----------GAGAGAGAAGAGAGUCGAAGAAUGAGGUGACAGCAUGUGAGCGCAAAGAGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGUCAUCGCC--------C
-----------......((.((.(((.(.((((((.(....)((.(((((.((((............))))))))).)).)))))).).)-----)).)).))...--------. ( -27.90)
>DroAna_CAF1 20972 105 + 1
GAGAGAGGUGCGC--UCGGAGAGAG---AAGAACGG-AAGAUAGCACGUGAGUAGAAGGUGCAAAGAGCUCAAAAUUCUACAUUCUACAAAGUAUCUGUAUCUUUUUAU---G-U
.((((((((((.(--((.....)))---.(((((..-..)...........((((((.(.((.....)).)....)))))).))))...........))))))))))..---.-. ( -23.80)
>consensus
GAGAGAGGGGAGAGAAAGAAGAGAGUCGAAGAAUGA_GUGACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA_____CUGCAUUCUUCAAUCAGA_C
.............................((((((........((((.(.......).))))..((((.......)))).))))))............................. (-10.01 = -10.20 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	23,815,016 – 23,815,111
Length	95
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	68.00
Mean single sequence MFE	-24.52
Consensus MFE	-9.27
Energy contribution	-10.46
Covariance contribution	1.19
Combinations/Pair	1.05
Mean z-score	-2.16
Structure conservation index	0.38
SVM decision value	1.35
SVM RNA-class probability	0.944653
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23815016 95 + 27905053
AACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCAUUCUUCAAUCAGA-UUUGUAGAAUUGUACAUGGACG---------------UACA
........(((.(((((.(((((.....)))))......((((((((((((-----(((.(((....)))))).-.)))))))).))))..))))).---------------))). ( -27.10)
>DroSec_CAF1 20204 110 + 1
GACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCUUUCUUCAAUCAGA-CUUGUAGAAUUGUACAUGUACGUAGCAAUUGCGAUUUUACA
....((((((........(((((.....)))))((((..((((((((((((-----(((.((.....)).))).-.)))))))).)))).)))))))).))............... ( -27.10)
>DroSim_CAF1 20279 107 + 1
GACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGCUUUCUUCAAUCAGA-CUUGUAGAAUUGUGCUUGUACG---CAAUUGUGAUUUUACA
.(((((((((((((....(((((.....)))))..)))).))(((((((((-----(((.((.....)).))).-.))))))))).)))).))).((---(....)))........ ( -27.50)
>DroEre_CAF1 20723 82 + 1
GACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAU-----CUGCCUUCUUCAAUCCGAGAUUGUAGAAUGU-----------------------------
...((.((....))))..(((((.....)))))((((((((((.(((....-----.((.......)).....))).))))))))))----------------------------- ( -24.80)
>DroYak_CAF1 20760 74 + 1
GACAGCAUGUGAGCGCAAAGAGCAAAGAGCGCCACAUUCUACAUUCUACAA-----CUGUCAUCGCC--------CUUGUAGAGUUA-----------------------------
...((.(((((.((((............))))))))).))..(((((((((-----..((....)).--------.)))))))))..----------------------------- ( -20.60)
>DroAna_CAF1 21005 100 + 1
GAUAGCACGUGAGUAGAAGGUGCAAAGAGCUCAAAAUUCUACAUUCUACAAAGUAUCUGUAUCUUUUUAU---G-UAUCAAGAAGUGUAGAU--ACGUAA--AG--------UACA
........(((.((((((.(.((.....)).)....))))))..........(((((((((.((((((..---.-....)))))))))))))--))....--..--------))). ( -20.00)
>consensus
GACAGCACGUGAGUCUAAGGUGCAAAGAGCGCCACAUUCUACAUUCUACAA_____CUGCAUUCUUCAAUCAGA_CUUGUAGAAUUGUACAU__ACG_______________UACA
........((((((....(((((.....)))))..)))).))((((((((...........................))))))))............................... ( -9.27 = -10.46 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:51 2006