Locus 188

Sequence ID	3R_DroMel_CAF1
Location	847,621 – 847,837
Length	216
Max. P	0.924223

overview

Window 5

Location	847,621 – 847,739
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.31
Mean single sequence MFE	-30.17
Consensus MFE	-22.24
Energy contribution	-21.43
Covariance contribution	-0.81
Combinations/Pair	1.23
Mean z-score	-1.48
Structure conservation index	0.74
SVM decision value	0.03
SVM RNA-class probability	0.548082
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 847621 118 - 27905053
--AUACAUACGUACUACAACCCAGACUCGCCGAUUCUUCGCCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCAUAACGAGGUCCGAACUAUCCGCACUGUGCUCCAGUCCGCC
--........((((....((((((((..(.(((....))).)...))))))))......((...(((.((((..((((.....))))..)))))))....))...))))........... ( -31.20)
>DroSec_CAF1 23291 120 - 1
ACAUACAUACAUACUGCAGCCCAGACUCGCCGAUUCUUCACCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCAUAACGAGGUCCAAACUAUCCGCACUAUGCCACAGCCCACC
.........((((.(((.(((.((((((((.((.....(((((......)))))..)).))..)))))).))).((((.....)))).............))).))))............ ( -31.60)
>DroSim_CAF1 22539 120 - 1
ACAUACAUACAUACUACAGCCCAGACUCGCCGAUUCUUCACCCUUGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCAUAACGAGGUCCAAACUAUCCGCACUAUGCCACAGCCCACC
..................(((.((((((((.((.....(((((......)))))..)).))..)))))).)))....(((((....((..........))....)))))........... ( -28.90)
>DroEre_CAF1 24351 108 - 1
ACGUAC--UCGUACUACCACCCAGACUCGCCGGCUCCUCGUCUUUGUCUGGGUGUUUCAGCCGGAGUCUCGGUAUGCGCAUAACGAGCUUCAAACUAUCC----------ACAGCCCACC
..(((.--...)))...(((((((((.....(((.....)))...)))))))))........((((.((((.(((....))).)))))))).........----------.......... ( -29.00)
>consensus
ACAUACAUACAUACUACAACCCAGACUCGCCGAUUCUUCACCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCAUAACGAGGUCCAAACUAUCCGCACUAUGCCACAGCCCACC
..................(((.((((((((.((.....(((((......)))))..)).))..)))))).))).((((.....))))................................. (-22.24 = -21.43 +  -0.81)

alignment

secondary structure

dotplot

Window 6

Location	847,661 – 847,773
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.22
Mean single sequence MFE	-43.20
Consensus MFE	-30.51
Energy contribution	-31.45
Covariance contribution	0.94
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.71
SVM decision value	0.70
SVM RNA-class probability	0.825547
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 847661 112 + 27905053
UGCGAAUACCGAGACUCUGGCUGAAACACCCAGACGAGGGCGAAGAAUCGGCGAGUCUGGGUUGUAGUACGUAUGUAU--------GGUGGAUUCGGCACAAGUGUGCUAUGUACAGCUC
.((....(((.((((((..(((((..(.(((......))).).....))))))))))).)))....(((((((.((((--------.(((.......)))....))))))))))).)).. ( -36.40)
>DroSec_CAF1 23331 120 + 1
UGCGAAUACCGAGACUCUGGCUGAAACACCCAGACGAGGGUGAAGAAUCGGCGAGUCUGGGCUGCAGUAUGUAUGUAUGUAUGUGAGGUGGAUUCGGCACAAGUGUGCUGUGUACAGCUC
.((((((.((.((((((..(((((..(((((......))))).....))))))))))).))(..(..(((((((....)))))))..)..)))))(((((....))))).......)).. ( -43.50)
>DroSim_CAF1 22579 120 + 1
UGCGAAUACCGAGACUCUGGCUGAAACACCCAGACAAGGGUGAAGAAUCGGCGAGUCUGGGCUGUAGUAUGUAUGUAUGUAUGUGAGGUGGAUUCGGCACAAGUGUGCUAUGUACAGCUC
.((..(((((.((((((..(((((..(((((......))))).....))))))))))).)).))).(((((((.(((..(.((((.((.....))..)))).)..)))))))))).)).. ( -42.20)
>DroEre_CAF1 24381 118 + 1
UGCGCAUACCGAGACUCCGGCUGAAACACCCAGACAAAGACGAGGAGCCGGCGAGUCUGGGUGGUAGUACGA--GUACGUAUGUACGCUGGAUUCGGCACAAGUGUGCUAUGUGCAGCUC
((((((((.((((..((((((.....(((((((((...(.((......)).)..)))))))))((((((((.--...))))).)))))))))))))((((....)))))))))))).... ( -50.70)
>consensus
UGCGAAUACCGAGACUCUGGCUGAAACACCCAGACAAGGGCGAAGAAUCGGCGAGUCUGGGCUGUAGUACGUAUGUAUGUAUGUGAGGUGGAUUCGGCACAAGUGUGCUAUGUACAGCUC
........((.((((((..(((((..(((((......))))).....)))))))))))))((((((((((....)))).................(((((....)))))...)))))).. (-30.51 = -31.45 +   0.94)

alignment

secondary structure

dotplot

Window 7

Location	847,661 – 847,773
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-34.50
Consensus MFE	-28.91
Energy contribution	-27.85
Covariance contribution	-1.06
Combinations/Pair	1.21
Mean z-score	-2.05
Structure conservation index	0.84
SVM decision value	1.16
SVM RNA-class probability	0.924223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 847661 112 - 27905053
GAGCUGUACAUAGCACACUUGUGCCGAAUCCACC--------AUACAUACGUACUACAACCCAGACUCGCCGAUUCUUCGCCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCA
..((.((((...((((....)))).(....)...--------........))))....(((.((((((((.((.....(((((......)))))..)).))..)))))).)))....)). ( -32.10)
>DroSec_CAF1 23331 120 - 1
GAGCUGUACACAGCACACUUGUGCCGAAUCCACCUCACAUACAUACAUACAUACUGCAGCCCAGACUCGCCGAUUCUUCACCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCA
(((.((....(.((((....)))).)....)).)))...................((.(((.((((((((.((.....(((((......)))))..)).))..)))))).)))....)). ( -32.50)
>DroSim_CAF1 22579 120 - 1
GAGCUGUACAUAGCACACUUGUGCCGAAUCCACCUCACAUACAUACAUACAUACUACAGCCCAGACUCGCCGAUUCUUCACCCUUGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCA
..((((((....((((....)))).((.......))..................))))))((((((((((.((.....(((((......)))))..)).))..)))))).))........ ( -32.30)
>DroEre_CAF1 24381 118 - 1
GAGCUGCACAUAGCACACUUGUGCCGAAUCCAGCGUACAUACGUAC--UCGUACUACCACCCAGACUCGCCGGCUCCUCGUCUUUGUCUGGGUGUUUCAGCCGGAGUCUCGGUAUGCGCA
.....((.((((((((....))))(((.(((.((((((....))))--.........(((((((((.....(((.....)))...))))))))).....)).)))...))).)))).)). ( -41.10)
>consensus
GAGCUGUACAUAGCACACUUGUGCCGAAUCCACCUCACAUACAUACAUACAUACUACAACCCAGACUCGCCGAUUCUUCACCCUCGUCUGGGUGUUUCAGCCAGAGUCUCGGUAUUCGCA
..((........((((....))))..................................(((.((((((((.((.....(((((......)))))..)).))..)))))).)))....)). (-28.91 = -27.85 +  -1.06)

alignment

secondary structure

dotplot

Window 8

Location	847,739 – 847,837
Length	98
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.20
Mean single sequence MFE	-33.52
Consensus MFE	-26.34
Energy contribution	-27.90
Covariance contribution	1.56
Combinations/Pair	1.06
Mean z-score	-1.86
Structure conservation index	0.79
SVM decision value	0.70
SVM RNA-class probability	0.825803
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 847739 98 - 27905053
UUCUACACACCUAUGGG----------------UAGGAGCACUGCCUCAUUUGUUUGAGCAAGUGCCGGCAAACGACCUCGAGCUGUACAUAGCACACUUGUGCCGAAUCCACC------
........(((....))----------------).((((((((..((((......))))..)))))(((((..((....)).((((....)))).......)))))..)))...------ ( -29.20)
>DroSec_CAF1 23411 120 - 1
UUCUACACACCUAUGGGUAUACAUAUAACUUGGUAGGAGCACUGCCUCAUUUGUUUGAGCAAGUGCCGGCAAACGACCUCGAGCUGUACACAGCACACUUGUGCCGAAUCCACCUCACAU
........(((....))).............(((.((((((((..((((......))))..)))))(((((..((....)).((((....)))).......)))))..))))))...... ( -35.00)
>DroSim_CAF1 22659 120 - 1
UUCUACACACCUAUGGGUAUACAUAUACCUUGGUAGGAGCACUGCCUCAUUUGUUUGAGCAAGUGCCGGCAAACGACCUCGAGCUGUACAUAGCACACUUGUGCCGAAUCCACCUCACAU
........(((...((((((....)))))).))).((((((((..((((......))))..)))))(((((..((....)).((((....)))).......)))))..)))......... ( -35.90)
>DroEre_CAF1 24459 116 - 1
UUCCCCAUACCUAUGGGUAU----AUACCUUGGUGGGUGCUCUGCCCCAUUUGUUUGAGCAAGUGCCGGCAAACGACCUCGAGCUGCACAUAGCACACUUGUGCCGAAUCCAGCGUACAU
.......((((...((((..----..)))).)))).((((..((((.(((((((....)))))))..))))..((....)).((((......((((....))))......)))))))).. ( -34.00)
>consensus
UUCUACACACCUAUGGGUAU____AUACCUUGGUAGGAGCACUGCCUCAUUUGUUUGAGCAAGUGCCGGCAAACGACCUCGAGCUGUACAUAGCACACUUGUGCCGAAUCCACCUCACAU
.........(((((((((((....))))))..))))).(((((..((((......))))..)))))(((((..((....)).((((....)))).......))))).............. (-26.34 = -27.90 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:41 2006