Locus 9239

Sequence ID	3R_DroMel_CAF1
Location	24,635,351 – 24,635,511
Length	160
Max. P	0.978565

overview

Window 8

Location	24,635,351 – 24,635,471
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.08
Mean single sequence MFE	-40.38
Consensus MFE	-32.14
Energy contribution	-32.20
Covariance contribution	0.06
Combinations/Pair	1.18
Mean z-score	-1.41
Structure conservation index	0.80
SVM decision value	0.01
SVM RNA-class probability	0.540572
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24635351 120 + 27905053
CUGUGUGUAUGUUGGAGUGCUGCUUAAGCUUCGAAUUGCUGAUGAAGCUCUUGUCGCACACUGUGCACGCGAAUGGUCGCUGCUCAAGAUGCACCAAGUUGUGGACCUUGAGACAGCGCU
.(((((((((...((.((((.((...(((((((.........)))))))...)).)))).)))))))))))...((.(((((((((((.(.(((......))).).)))))).))))))) ( -45.40)
>DroVir_CAF1 131767 120 + 1
CUGUAUGAAUGUUCGAGUGCUGUUUCAGCUUCGAGUUGCUAAUGAAGCUCUUGUCGCACACGGUGCAGGCAAAUGGACGCUGCUCCAGAUGCACCAAGUUAUGCACCUUUAGGCAGCGUU
((((.((..((((((.((((..(...(((((((.........)))))))...)..)))).))).)))..)).))))((((((((..((.((((........)))).))...)))))))). ( -37.10)
>DroSim_CAF1 118219 120 + 1
CUGUAUGUAUGUUGGAGUGCUGCUUCAGCUUCGAAUUGCUGAUGAAGCUCUUGUCACACACUGUGCACGCGAAUGGUCGCUGCUCAAGAUGCACCAAGUUGUGGACCUUAAGACAGCGCU
..........(((((((.(((...(((((........)))))...))).)))(((.(((((((((((.((((....))))..(....).)))))..)).))))))).......))))... ( -34.50)
>DroMoj_CAF1 137955 120 + 1
CCGUAUGAAUGUUCGAGUGUUGUUUCAGCUUCGAAUUGCUGAUGAAGCUCUUGUCGCACACGGUACAAGCAAACGGACGCUGCUCCAAGUGCACCAGAUUGUGCACCUUCAGGCAGCGUU
((((.((..((((((.((((..(...(((((((.........)))))))...)..)))).))).)))..)).))))((((((((..((((((((......))))).)))..)))))))). ( -44.50)
>consensus
CUGUAUGAAUGUUCGAGUGCUGCUUCAGCUUCGAAUUGCUGAUGAAGCUCUUGUCGCACACGGUGCACGCAAAUGGACGCUGCUCAAGAUGCACCAAGUUGUGCACCUUAAGACAGCGCU
((((.((..((((((.((((.((...(((((((.........)))))))...)).)))).))).)))..)).)))).(((((((.(((.(((((......))))).))).)).))))).. (-32.14 = -32.20 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	24,635,351 – 24,635,471
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.08
Mean single sequence MFE	-40.23
Consensus MFE	-33.25
Energy contribution	-34.75
Covariance contribution	1.50
Combinations/Pair	1.16
Mean z-score	-2.54
Structure conservation index	0.83
SVM decision value	1.82
SVM RNA-class probability	0.978565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24635351 120 - 27905053
AGCGCUGUCUCAAGGUCCACAACUUGGUGCAUCUUGAGCAGCGACCAUUCGCGUGCACAGUGUGCGACAAGAGCUUCAUCAGCAAUUCGAAGCUUAAGCAGCACUCCAACAUACACACAG
.((((((.((((((((.(((......))).))))))))))((((....))))))))...(.((((..(..(((((((...........)))))))..)..)))).).............. ( -39.10)
>DroVir_CAF1 131767 120 - 1
AACGCUGCCUAAAGGUGCAUAACUUGGUGCAUCUGGAGCAGCGUCCAUUUGCCUGCACCGUGUGCGACAAGAGCUUCAUUAGCAACUCGAAGCUGAAACAGCACUCGAACAUUCAUACAG
.(((((((((..((((((((......)))))))))).)))))))..............((.((((......((((((...........))))))......)))).))............. ( -37.80)
>DroSim_CAF1 118219 120 - 1
AGCGCUGUCUUAAGGUCCACAACUUGGUGCAUCUUGAGCAGCGACCAUUCGCGUGCACAGUGUGUGACAAGAGCUUCAUCAGCAAUUCGAAGCUGAAGCAGCACUCCAACAUACAUACAG
.((((((.((((((((.(((......))).))))))))))((((....))))))))...((((((....((.(((.(.(((((........))))).).))).))...))))))...... ( -41.10)
>DroMoj_CAF1 137955 120 - 1
AACGCUGCCUGAAGGUGCACAAUCUGGUGCACUUGGAGCAGCGUCCGUUUGCUUGUACCGUGUGCGACAAGAGCUUCAUCAGCAAUUCGAAGCUGAAACAACACUCGAACAUUCAUACGG
.(((((((((..((((((((......)))))))))).)))))))((((.((..(((.(.((((((.......))....(((((........)))))....))))..).)))..)).)))) ( -42.90)
>consensus
AACGCUGCCUAAAGGUCCACAACUUGGUGCAUCUGGAGCAGCGACCAUUCGCGUGCACAGUGUGCGACAAGAGCUUCAUCAGCAAUUCGAAGCUGAAACAGCACUCCAACAUACAUACAG
..(((((.((((((((((((......))))))))))))))))).......(..((...((.((((......((((((...........))))))......)))).))..))..)...... (-33.25 = -34.75 +   1.50)

alignment

secondary structure

dotplot

Window 0

Location	24,635,391 – 24,635,511
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.22
Mean single sequence MFE	-41.58
Consensus MFE	-29.24
Energy contribution	-31.43
Covariance contribution	2.19
Combinations/Pair	1.11
Mean z-score	-2.09
Structure conservation index	0.70
SVM decision value	0.62
SVM RNA-class probability	0.803204
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24635391 120 + 27905053
GAUGAAGCUCUUGUCGCACACUGUGCACGCGAAUGGUCGCUGCUCAAGAUGCACCAAGUUGUGGACCUUGAGACAGCGCUCCGUUUUGUACAUCUUGCCGCACUUUUCGCAACGAUAGGA
........((((((((((...((((((...((((((.(((((((((((.(.(((......))).).)))))).)))))..))))))))))))...))).((.......))...))))))) ( -42.60)
>DroVir_CAF1 131807 120 + 1
AAUGAAGCUCUUGUCGCACACGGUGCAGGCAAAUGGACGCUGCUCCAGAUGCACCAAGUUAUGCACCUUUAGGCAGCGUUCGGUUUUGUACAUUUUGCCGCAUUUCUCGCAGCGAUAGGA
........(((((((((...((((((.(((((((((((((((((..((.((((........)))).))...)))))))))))((.....))..))))))))))....))..))))))))) ( -44.10)
>DroSim_CAF1 118259 120 + 1
GAUGAAGCUCUUGUCACACACUGUGCACGCGAAUGGUCGCUGCUCAAGAUGCACCAAGUUGUGGACCUUAAGACAGCGCUCCGUUUUGUACAUCUUGCCGCACUUUUCGCAACGAUAGGA
........(((((((......((((((...((((((.(((((((.(((.(.(((......))).).))).)).)))))..)))))))))))).......((.......))...))))))) ( -33.40)
>DroMoj_CAF1 137995 120 + 1
GAUGAAGCUCUUGUCGCACACGGUACAAGCAAACGGACGCUGCUCCAAGUGCACCAGAUUGUGCACCUUCAGGCAGCGUUCGGUUUUGUACAUUUUGCCGCAUUUCUCACAGCGAUAAGA
........((((((((((....(((((((....(((((((((((..((((((((......))))).)))..)))))))))))..)))))))....))).((..........))))))))) ( -46.20)
>consensus
GAUGAAGCUCUUGUCGCACACGGUGCACGCAAAUGGACGCUGCUCAAGAUGCACCAAGUUGUGCACCUUAAGACAGCGCUCCGUUUUGUACAUCUUGCCGCACUUCUCGCAACGAUAGGA
........(((((((((.....(((((...((((((((((((((.(((.(((((......))))).))).)).)))))))).)))))))))........((.......)).))))))))) (-29.24 = -31.43 +   2.19)

alignment

secondary structure

dotplot

Window 1

Location	24,635,391 – 24,635,511
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-40.05
Consensus MFE	-34.06
Energy contribution	-34.62
Covariance contribution	0.56
Combinations/Pair	1.27
Mean z-score	-1.62
Structure conservation index	0.85
SVM decision value	0.46
SVM RNA-class probability	0.745539
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24635391 120 - 27905053
UCCUAUCGUUGCGAAAAGUGCGGCAAGAUGUACAAAACGGAGCGCUGUCUCAAGGUCCACAACUUGGUGCAUCUUGAGCAGCGACCAUUCGCGUGCACAGUGUGCGACAAGAGCUUCAUC
.......((((((.....))))))..............(((((((((.((((((((.(((......))).))))))))))))......(((((..(...)..))))).....)))))... ( -42.00)
>DroVir_CAF1 131807 120 - 1
UCCUAUCGCUGCGAGAAAUGCGGCAAAAUGUACAAAACCGAACGCUGCCUAAAGGUGCAUAACUUGGUGCAUCUGGAGCAGCGUCCAUUUGCCUGCACCGUGUGCGACAAGAGCUUCAUU
.....((((((((.(...(((((((((..((.....)).(.(((((((((..((((((((......)))))))))).))))))).).)))))).)))))))).))))............. ( -39.30)
>DroSim_CAF1 118259 120 - 1
UCCUAUCGUUGCGAAAAGUGCGGCAAGAUGUACAAAACGGAGCGCUGUCUUAAGGUCCACAACUUGGUGCAUCUUGAGCAGCGACCAUUCGCGUGCACAGUGUGUGACAAGAGCUUCAUC
.......((((((((..(((((......))))).....((..(((((.((((((((.(((......))).))))))))))))).)).)))))((.(((.....)))))...)))...... ( -38.00)
>DroMoj_CAF1 137995 120 - 1
UCUUAUCGCUGUGAGAAAUGCGGCAAAAUGUACAAAACCGAACGCUGCCUGAAGGUGCACAAUCUGGUGCACUUGGAGCAGCGUCCGUUUGCUUGUACCGUGUGCGACAAGAGCUUCAUC
((((.(((((((.......))))).....((((((((.((.(((((((((..((((((((......)))))))))).))))))).)).))..)))))).......)).))))........ ( -40.90)
>consensus
UCCUAUCGCUGCGAAAAAUGCGGCAAAAUGUACAAAACCGAACGCUGCCUAAAGGUCCACAACUUGGUGCAUCUGGAGCAGCGACCAUUCGCGUGCACAGUGUGCGACAAGAGCUUCAUC
.......((((((((..(((((......)))))......(.((((((.((((((((((((......)))))))))))))))))).).))))).(((((...))))).....)))...... (-34.06 = -34.62 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:36 2006