Locus 1888

Sequence ID	X_DroMel_CAF1
Location	5,239,230 – 5,239,440
Length	210
Max. P	0.999917

overview

Window 6

Location	5,239,230 – 5,239,327
Length	97
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.62
Mean single sequence MFE	-16.91
Consensus MFE	-12.44
Energy contribution	-12.63
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-1.74
Structure conservation index	0.74
SVM decision value	0.48
SVM RNA-class probability	0.753896
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5239230 97 + 22224390
AACAAAUGUAUAUGAAAA-------AAAAAACA-----AAAAAUAUAAACGCGUGCUGGUUUAUGGAACAGAUUUCAUGAUGAAGAACACGCGAAUCUUUUGAAUGCAA
......(((((.......-------........-----...........((((((((...((((((((....))))))))...))..))))))..((....))))))). ( -18.10)
>DroPse_CAF1 16217 92 + 1
ACCCGA---------AAC---C---AAAAUAUAUA--UAUAUAUAUUGUCGCGUACUCGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
...(((---------((.---.---..(((((((.--...))))))).((((((..((..((((((((....))))))))....))..))))))...)))))....... ( -16.70)
>DroSec_CAF1 12411 97 + 1
AACAAAUGUAUAUGAAAA-------AAAAACCA-----AAAUAUAUAAACGCGUGCUGGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
..(((((((((((.....-------........-----..)))))))..((((((((...((((((((....))))))))...))..)))))).....))))....... ( -17.16)
>DroEre_CAF1 12457 107 + 1
AACAAAUGUAUAUGAAAACACCAAAAAAAAACAAA--AAUAAAAAUAAACGCGUGCUGGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
......(((((........................--............((((((((...((((((((....))))))))...))..))))))..((....))))))). ( -16.30)
>DroYak_CAF1 12605 102 + 1
AACAAAUGUAUAUGAAAA-------AAAAUACAAACGAAAAAAAACAAACGCGUGCUGGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
..(((((((((.(.....-------.).)))))................((((((((...((((((((....))))))))...))..)))))).....))))....... ( -16.50)
>DroPer_CAF1 8079 92 + 1
ACCCGA---------AAC---C---AAAAUAUAUA--UAUAUAUAUUGUCGCGUACUCGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
...(((---------((.---.---..(((((((.--...))))))).((((((..((..((((((((....))))))))....))..))))))...)))))....... ( -16.70)
>consensus
AACAAAUGUAUAUGAAAA_______AAAAAACA_A___AAAAAUAUAAACGCGUGCUGGUUUAUGGAACAGAUUUCAUGAUGAAGAACAUGCGAAUCUUUUGAAUGCAA
.................................................((((((((...((((((((....))))))))...))..))))))................ (-12.44 = -12.63 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	5,239,287 – 5,239,407
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-18.92
Consensus MFE	-18.69
Energy contribution	-18.50
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-1.00
Structure conservation index	0.99
SVM decision value	1.24
SVM RNA-class probability	0.935012
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5239287 120 - 22224390
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACAUUGCAUUCAAAAGAUUCGCGUGUUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..((((........)))).))))) ( -19.90)
>DroVir_CAF1 18009 120 - 1
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACAUUGCAUUUAAAAGAUUCGCAUGCUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..((((........)))).))))) ( -19.30)
>DroPse_CAF1 16269 120 - 1
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUUGCUAUCAGCCACAUUGCAUUCAAAAGAUUCGCAUGUUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..((((........)))).))))) ( -18.20)
>DroGri_CAF1 16894 120 - 1
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACAUUGCAUUUAAAAGAUUCGCAUGCUCUUCGUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..(((((.....).)))).))))) ( -19.80)
>DroMoj_CAF1 20014 120 - 1
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCCCCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACAUUGCAUUUAAUAAAUUCGCAUGUUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......))..............((((........))))...... ( -18.10)
>DroPer_CAF1 8131 120 - 1
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUUGCUAUCAGCCACAUUGCAUUCAAAAGAUUCGCAUGUUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..((((........)))).))))) ( -18.20)
>consensus
AGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACAUUGCAUUCAAAAGAUUCGCAUGUUCUUCAUCAUGAAAUCU
(((((((.(((((.......)))).(((((..........)))))................).)))))))....((......)).......(((((..((((........)))).))))) (-18.69 = -18.50 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	5,239,327 – 5,239,440
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.70
Mean single sequence MFE	-31.60
Consensus MFE	-29.52
Energy contribution	-29.85
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.93
SVM decision value	2.10
SVM RNA-class probability	0.987863
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5239327 113 + 22224390
UGUGGCUGAUAGCGAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACAA-------
((((.((((((((((((.(((.(..(((((.....(((((..........)))))....)))).)..).))).))))))))))))))))........................------- ( -31.50)
>DroVir_CAF1 18049 114 + 1
UGUGGCUGAUAGCGAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACAAA------
((((.((((((((((((.(((.(..(((((.....(((((..........)))))....)))).)..).))).)))))))))))))))).........................------ ( -31.50)
>DroPse_CAF1 16309 120 + 1
UGUGGCUGAUAGCAAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACAAACAACUA
((((.((((((((..(((((((....)))))))(((((((..........))))).))((((..(....)..)))).)))))))))))).......((((..((((.....)))).)))) ( -29.80)
>DroWil_CAF1 18382 115 + 1
UGUGGCUGAUAGCGAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUA-CAA----UAA
((((.((((((((((((.(((.(..(((((.....(((((..........)))))....)))).)..).))).)))))))))))))))).........((((....)))-)..----... ( -31.90)
>DroMoj_CAF1 20054 114 + 1
UGUGGCUGAUAGCGAUAACAUUUUUGAGUGUUGGUUUCGGGGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACCUU------
((((.((((((((((((.(((.(..(((((.....(((((((......)))))))....)))).)..).))).))))))))))))))))........(((.........)))..------ ( -35.10)
>DroPer_CAF1 8171 120 + 1
UGUGGCUGAUAGCAAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACAAACAACUA
((((.((((((((..(((((((....)))))))(((((((..........))))).))((((..(....)..)))).)))))))))))).......((((..((((.....)))).)))) ( -29.80)
>consensus
UGUGGCUGAUAGCGAUAACAUUUUUGAGUGUUGGUUUCGGUGAUAUUGUUCCGAAUACGUACUGUGGACGUGGUAUCGCUGUCAGUACAGGAAUAAUGGUGAGUUUUUAACAAA______
((((.((((((((((((.(((.(..(((((.....(((((..........)))))....)))).)..).))).))))))))))))))))............................... (-29.52 = -29.85 +   0.33)

alignment

secondary structure

dotplot

Window 9

Location	5,239,327 – 5,239,440
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.70
Mean single sequence MFE	-20.48
Consensus MFE	-20.19
Energy contribution	-19.97
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.27
Structure conservation index	0.99
SVM decision value	4.54
SVM RNA-class probability	0.999917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5239327 113 - 22224390
-------UUGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACA
-------.........................((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -20.60)
>DroVir_CAF1 18049 114 - 1
------UUUGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACA
------..........................((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -20.60)
>DroPse_CAF1 16309 120 - 1
UAGUUGUUUGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUUGCUAUCAGCCACA
.....((((.....))))..............((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -19.50)
>DroWil_CAF1 18382 115 - 1
UUA----UUG-UAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACA
...----...-.....................((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -20.60)
>DroMoj_CAF1 20054 114 - 1
------AAGGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCCCCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACA
------..(((.........))).........((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -22.10)
>DroPer_CAF1 8171 120 - 1
UAGUUGUUUGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUUGCUAUCAGCCACA
.....((((.....))))..............((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). ( -19.50)
>consensus
______UUUGUUAAAAACUCACCAUUAUUCCUGUACUGACAGCGAUACCACGUCCACAGUACGUAUUCGGAACAAUAUCACCGAAACCAACACUCAAAAAUGUUAUCGCUAUCAGCCACA
................................((.((((.(((((((.(((((.......)))).(((((..........)))))................).))))))).))))..)). (-20.19 = -19.97 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:06 2006