Locus 7744

Sequence ID	3R_DroMel_CAF1
Location	20,785,473 – 20,785,830
Length	357
Max. P	0.969285

overview

Window 6

Location	20,785,473 – 20,785,590
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.38
Mean single sequence MFE	-31.31
Consensus MFE	-29.99
Energy contribution	-29.77
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.48
Structure conservation index	0.96
SVM decision value	1.64
SVM RNA-class probability	0.969285
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20785473 117 - 27905053
AUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCGAGCAGCUCCCCACUUUCCGGGCACACCUC---CCCCAACCCCCUCUUUACAGGCCAAACAUACAAAUUAGAGCAAAUUCA
(((((((((((((((.((((....))))......((((.(((...))).)))).....)))).......---.........(((......))).............)))))))))))... ( -31.80)
>DroSec_CAF1 1260 116 - 1
AUUUGCUCUGAGCCCAGGCAAAAAUGUCAGCUGUGUGGCGAGCAGCUCCCCACUUUCCGGGCACACCUC---CCCC-CCUCCCGCUUUACAGACCAAACAUACAAAUUAGAGCAAAUACA
(((((((((((((....))....((((...((((((((.(((...))).))))....((((........---....-...))))....)))).....)))).....)))))))))))... ( -31.66)
>DroSim_CAF1 1243 119 - 1
AUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCGAGCAGCUCCCCACUUUCCGGGCACACCUCCUUCCCC-CCUCCCGCUUUACAGACCAAACAUACAAAUUAGAGCAAAUACA
(((((((((((((....))....((((...((((((((.(((...))).))))....((((...............-...))))....)))).....)))).....)))))))))))... ( -30.47)
>consensus
AUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCGAGCAGCUCCCCACUUUCCGGGCACACCUC___CCCC_CCUCCCGCUUUACAGACCAAACAUACAAAUUAGAGCAAAUACA
(((((((((((((((.((((....))))......((((.(((...))).)))).....)))).............................(......).......)))))))))))... (-29.99 = -29.77 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	20,785,550 – 20,785,670
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-47.60
Consensus MFE	-44.52
Energy contribution	-44.85
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.94
SVM decision value	0.30
SVM RNA-class probability	0.676766
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20785550 120 - 27905053
GGCAGCGAAUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGACGCGUUCUAAUUAGCCAUGCCAGGCACAUUUUGGUAUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCG
((((((....(((((..((((((((((.....).)))))))).)...)))))......))..)))).(.(((((.(((..((((((.(((....))))))..)))..)))..))))).). ( -43.60)
>DroSec_CAF1 1336 120 - 1
GGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGUAUUUGCUCUGAGCCCAGGCAAAAAUGUCAGCUGUGUGGCG
(((....((...(((.(((((((((((.....).)))))))).)))))...)).....)))..(((..((((((((.(..((((((.(((....))))))..)))..)))))))))))). ( -48.90)
>DroSim_CAF1 1322 120 - 1
GGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGUAUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCG
(((....((...(((.(((((((((((.....).)))))))).)))))...)).....)))..(((..((((((((.(..((((((.(((....))))))..)))..)))))))))))). ( -50.30)
>consensus
GGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGUAUUUGCUCUGGGCCCAGGCAAAAAUGUCAGCUGUGUGGCG
(((.......(((((.(((((((((((.....).)))))))).).).)))))......)))..(((..((((((((.(..((((((.(((....))))))..)))..)))))))))))). (-44.52 = -44.85 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	20,785,590 – 20,785,710
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-39.37
Consensus MFE	-37.59
Energy contribution	-36.93
Covariance contribution	-0.66
Combinations/Pair	1.08
Mean z-score	-1.51
Structure conservation index	0.95
SVM decision value	0.02
SVM RNA-class probability	0.544939
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20785590 120 + 27905053
ACCAAAAUGUGCCUGGCAUGGCUAAUUAGAACGCGUCUAAGUGCGAGCAGUCAGUCGCACUCGCUCGCUCAUUCGCUGCCACGCAUGCGCAGAUACAUUUGUAUCUUUGUAUCUUCGGGC
..........(((((((.((((...(((((.....)))))(.((((((((((....).))).)))))).).......)))).))(((((.((((((....)))))).)))))...))))) ( -40.90)
>DroSec_CAF1 1376 120 + 1
ACCAAACUGUGCCUGGCAUGGCUAAUUAGAACGCGGCUAAGUGCGAGCAGUCAGUCGCACUCGCUCGCUCACUCGUCGCCACGCAUGCGCAGAUACAUUUGUAUCUUCGUAUCUUCCGGC
.((.....((((.((((.(((((...........))))).(.((((((((((....).))).)))))).).......)))).))))(((.((((((....)))))).))).......)). ( -39.40)
>DroSim_CAF1 1362 120 + 1
ACCAAACUGUGCCUGGCAUGGCUAAUUAGAACGCGGCUAAGUGCGAGCAGUCAGUCGCACUCGCUCGCUCACUCGUCGCCACGCAUGCGCAGAUACAUUUGUAUCUUUGUAUCUUCCGGC
.((.....((((.((((.(((((...........))))).(.((((((((((....).))).)))))).).......)))).))))(((.((((((....)))))).))).......)). ( -37.80)
>consensus
ACCAAACUGUGCCUGGCAUGGCUAAUUAGAACGCGGCUAAGUGCGAGCAGUCAGUCGCACUCGCUCGCUCACUCGUCGCCACGCAUGCGCAGAUACAUUUGUAUCUUUGUAUCUUCCGGC
.((.....((((.((((..(((...((((.......))))(.((((((((((....).))).)))))).)....))))))).))))(((.((((((....)))))).))).......)). (-37.59 = -36.93 +  -0.66)

alignment

secondary structure

dotplot

Window 9

Location	20,785,590 – 20,785,710
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-45.77
Consensus MFE	-42.59
Energy contribution	-42.92
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.93
SVM decision value	1.20
SVM RNA-class probability	0.929780
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20785590 120 - 27905053
GCCCGAAGAUACAAAGAUACAAAUGUAUCUGCGCAUGCGUGGCAGCGAAUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGACGCGUUCUAAUUAGCCAUGCCAGGCACAUUUUGGU
..((((((......((((((....))))))(.((..(((((((.......(((((..((((((((((.....).)))))))).)...)))))......)))))))...)).).)))))). ( -43.02)
>DroSec_CAF1 1376 120 - 1
GCCGGAAGAUACGAAGAUACAAAUGUAUCUGCGCAUGCGUGGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGU
((((((......(.((((((....)))))).)((..(((((((....((...(((.(((((((((((.....).)))))))).)))))...)).....)))))))...))....)))))) ( -47.30)
>DroSim_CAF1 1362 120 - 1
GCCGGAAGAUACAAAGAUACAAAUGUAUCUGCGCAUGCGUGGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGU
((((((........((((((....))))))(.((..(((((((....((...(((.(((((((((((.....).)))))))).)))))...)).....)))))))...)).)..)))))) ( -47.00)
>consensus
GCCGGAAGAUACAAAGAUACAAAUGUAUCUGCGCAUGCGUGGCGACGAGUGAGCGAGCGAGUGCGACUGACUGCUCGCACUUAGCCGCGUUCUAAUUAGCCAUGCCAGGCACAGUUUGGU
((((((........((((((....))))))(.((..(((((((.......(((((.(((((((((((.....).)))))))).).).)))))......)))))))...)).)..)))))) (-42.59 = -42.92 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	20,785,710 – 20,785,830
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-31.17
Consensus MFE	-31.10
Energy contribution	-31.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	1.00
SVM decision value	0.53
SVM RNA-class probability	0.772747
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20785710 120 - 27905053
GACAAAUGUUGUCAAGCAUUUGGCGAAAAAUUGGCAAAUAGAUUCGCGCAUAAGGGGCCGCACAAAACAAAGAACAUUCGCCAAGUGCGCGUGGGUCAAGAAAGAAGUCAAGUCAAGUCA
..((((((((....))))))))..((....(((((.....(((((((((....(....)((((.....................)))))))))))))..((......))..))))).)). ( -31.10)
>DroSec_CAF1 1496 120 - 1
GACAAAUGUUGUCAAGCAUUUGGCGAAAAAUUGGCAAAUAGAUUCGCGCAUAAGGGGCCGCACAAAACAAAGAACGUUCGCCAAGUGCGCGUGGGUCAAGAAAGAAGUCAAGUCAAGUCA
..((((((((....))))))))..((....(((((.....(((((((((.((...(((.(.((............)).))))...)).)))))))))..((......))..))))).)). ( -31.20)
>DroSim_CAF1 1482 120 - 1
GACAAAUGUUGUCAAGCAUUUGGCGAAAAAUUGGCAAAUAGAUUCGCGCAUAAGGGGCCGCACAAAACAAAGAACGUUCGCCAAGUGCGCGUGGGUCAAGAAAGAAGUCAAGUCAAGUCA
..((((((((....))))))))..((....(((((.....(((((((((.((...(((.(.((............)).))))...)).)))))))))..((......))..))))).)). ( -31.20)
>consensus
GACAAAUGUUGUCAAGCAUUUGGCGAAAAAUUGGCAAAUAGAUUCGCGCAUAAGGGGCCGCACAAAACAAAGAACGUUCGCCAAGUGCGCGUGGGUCAAGAAAGAAGUCAAGUCAAGUCA
..((((((((....))))))))..((....(((((.....(((((((((....(....)((((.....................)))))))))))))..((......))..))))).)). (-31.10 = -31.10 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:37 2006