Locus 6201

Sequence ID	2L_DroMel_CAF1
Location	17,289,576 – 17,289,738
Length	162
Max. P	0.995843

overview

Window 9

Location	17,289,576 – 17,289,686
Length	110
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	90.25
Mean single sequence MFE	-39.80
Consensus MFE	-31.60
Energy contribution	-33.40
Covariance contribution	1.80
Combinations/Pair	1.06
Mean z-score	-1.64
Structure conservation index	0.79
SVM decision value	0.50
SVM RNA-class probability	0.759451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17289576 110 + 22407834
AGGAUAUGUCCU---------CCUUCACUUGUUCCUCCACGCGAUGAUGACGUUGCGAUGUUGUGUCCUGUUGCGAGGUGAAGAUGAUGAUGAUCAUCAACAUCAUGAUGAUGGAGAUA
((((....))))---------.............(((((((..((((((((.((((((((........)))))))).))...((((((....))))))..))))))..)).)))))... ( -31.90)
>DroSec_CAF1 139641 119 + 1
AGGAGAUGUCCUCAUUGCUCUCCUCCACUUGUUCCUCCACGCGAUGAUGACGUUGCGAUGUUGUGACCCGUUGCGAGGUGAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUA
((((((.((.......))))))))..........((((((((.((((((((.((((((((........)))))))).))......((((.....))))..)))))).))).)))))... ( -42.10)
>DroSim_CAF1 132794 119 + 1
AGGAGAUGUCCUCAUUGCUCUCCUCCACUUGUUCCUCCACGCGAUGAUGACGUUGCGAUGUUGUGCCCCGUUGCGAGGUGAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUA
((((((.((.......))))))))..........((((((((.((((((((.((((((((........)))))))).))......((((.....))))..)))))).))).)))))... ( -42.10)
>DroEre_CAF1 127868 119 + 1
AGGAGAUGUCCUCCAUGCUCUCCUCCACUGGCUGCUCCACGCGAUGAUGGCGUUCCGAUGUUGUGCCCUGUUGCGAGGUGAAGAUGAUGAUGAUCAUCAACCUCACGGUGAUGGAGAUA
.((((.....))))....(((((..(((((((.((....(((((((.(((....))).)))))))....)).))(((((...((((((....)))))).))))).)))))..))))).. ( -45.10)
>DroYak_CAF1 130695 119 + 1
AGGAGAUGUCCUCAUUGCUCUCCUCCACUUGUUUCUCCACGCGAUGAUGACGUUCCGAUGUUGUGCACUGUUGCGAGGUGGAGACGAUGAUGAUCAUCAACAUCACGGUGAUGGAGAUA
..(((.....))).....(((((..((((.((((((((.((((((..(((((.........))).))..)))))).)).))))))((((.((.....)).))))..))))..))))).. ( -37.80)
>consensus
AGGAGAUGUCCUCAUUGCUCUCCUCCACUUGUUCCUCCACGCGAUGAUGACGUUGCGAUGUUGUGCCCUGUUGCGAGGUGAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUA
((((((.((.......))))))))..........((((((((.((((((((.((((((((........)))))))).))......((((.....))))..)))))).))).)))))... (-31.60 = -33.40 +   1.80)

alignment

secondary structure

dotplot

Window 0

Location	17,289,607 – 17,289,725
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	95.34
Mean single sequence MFE	-31.56
Consensus MFE	-27.02
Energy contribution	-27.10
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-1.67
Structure conservation index	0.86
SVM decision value	1.12
SVM RNA-class probability	0.918500
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17289607 118 - 22407834
GCUGAAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCAUCAUGAUGUUGAUGAUCAUCAUCAUCUUCACCUCGCAACAGGACACAACAUCGCAACGUCAUCAUCGC
((((..((((((((...))))))))..)))).....................((((((((((((((....))))))....(((......)))............))))))))...... ( -27.10)
>DroSec_CAF1 139681 118 - 1
GCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUCACCUCGCAACGGGUCACAACAUCGCAACGUCAUCAUCGC
(((((.((((((((...)))))))).))))).......................(((((((.(((((.....((.........)).....))))))))))))................ ( -30.70)
>DroSim_CAF1 132834 118 - 1
GCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUCACCUCGCAACGGGGCACAACAUCGCAACGUCAUCAUCGC
(((((.((((((((...)))))))).))))).....................((((((((((((((....))))))....(((((...)))))...........))))))))...... ( -32.50)
>DroEre_CAF1 127908 118 - 1
GCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCGUGAGGUUGAUGAUCAUCAUCAUCUUCACCUCGCAACAGGGCACAACAUCGGAACGCCAUCAUCGC
(((((.((((((((...)))))))).)))))...((((((......))....(((((((.((((((....))))))...)))))))....))))........((....))........ ( -36.60)
>DroYak_CAF1 130735 118 - 1
GCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCGUGAUGUUGAUGAUCAUCAUCGUCUCCACCUCGCAACAGUGCACAACAUCGGAACGUCAUCAUCGC
(((((.((((((((...)))))))).))))).....................((((((.(((((.((.................(((....))).(......))).))))).)))))) ( -30.90)
>consensus
GCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUCACCUCGCAACAGGGCACAACAUCGCAACGUCAUCAUCGC
(((((.((((((((...)))))))).))))).....................((((((((((((((....))))))....(((......)))............))))))))...... (-27.02 = -27.10 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	17,289,646 – 17,289,738
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	96.96
Mean single sequence MFE	-25.64
Consensus MFE	-24.34
Energy contribution	-23.98
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-1.34
Structure conservation index	0.95
SVM decision value	0.89
SVM RNA-class probability	0.874618
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17289646 92 + 22407834
GAAGAUGAUGAUGAUCAUCAACAUCAUGAUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUUCAGCUGCAGUUUUCCUG
...((((.((((....)))).))))........(((((.....(((..((.((.(((((((.....))))))).)).)))))...))))).. ( -23.50)
>DroSec_CAF1 139720 92 + 1
GAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUCCAGCUGCAGUUUUCCUG
....((.((((((........)))))).))...(((((.....(((..((.((.(((((((.....))))))).)).)))))...))))).. ( -26.40)
>DroSim_CAF1 132873 92 + 1
GAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUCCAGCUGCAGUUUUCCUG
....((.((((((........)))))).))...(((((.....(((..((.((.(((((((.....))))))).)).)))))...))))).. ( -26.40)
>DroEre_CAF1 127947 92 + 1
GAAGAUGAUGAUGAUCAUCAACCUCACGGUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUCCAGCUGCAGUUUUCCUG
...((((((....)))))).(((....)))...(((((.....(((..((.((.(((((((.....))))))).)).)))))...))))).. ( -26.20)
>DroYak_CAF1 130774 92 + 1
GGAGACGAUGAUGAUCAUCAACAUCACGGUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUCCAGCUGCAGUUUUCCUG
((((((((((.....))))..((((.....)))).........(((..((.((.(((((((.....))))))).)).))))).))))))... ( -25.70)
>consensus
GAAGACGAUGAUGAUCAUCAACAUCAUGGUGAUGGAGAUAUAGGCGAUGCCGGCAAACAGUCAACAACUGUUUUCCAGCUGCAGUUUUCCUG
((((((((((.....))))..((((.....)))).........(((..((.((.(((((((.....))))))).)).))))).))))))... (-24.34 = -23.98 +  -0.36)

alignment

secondary structure

dotplot

Window 2

Location	17,289,646 – 17,289,738
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	96.96
Mean single sequence MFE	-25.26
Consensus MFE	-23.58
Energy contribution	-23.74
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.94
Structure conservation index	0.93
SVM decision value	2.62
SVM RNA-class probability	0.995843
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17289646 92 - 22407834
CAGGAAAACUGCAGCUGAAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCAUCAUGAUGUUGAUGAUCAUCAUCAUCUUC
..(((.....((.((((..((((((((...))))))))..))))...)).......)))........((((.((((....)))).))))... ( -22.50)
>DroSec_CAF1 139720 92 - 1
CAGGAAAACUGCAGCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUC
..(((.....((.(((((.((((((((...)))))))).)))))...)).......)))........((((.((((....)))).))))... ( -25.10)
>DroSim_CAF1 132873 92 - 1
CAGGAAAACUGCAGCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUC
..(((.....((.(((((.((((((((...)))))))).)))))...)).......)))........((((.((((....)))).))))... ( -25.10)
>DroEre_CAF1 127947 92 - 1
CAGGAAAACUGCAGCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCGUGAGGUUGAUGAUCAUCAUCAUCUUC
(((.....)))..(((((.((((((((...)))))))).)))))..............(((((((....)).)))))............... ( -28.30)
>DroYak_CAF1 130774 92 - 1
CAGGAAAACUGCAGCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCGUGAUGUUGAUGAUCAUCAUCGUCUCC
..(((.....((.(((((.((((((((...)))))))).)))))...)).......)))......(.((((.((((....)))).)))).). ( -25.30)
>consensus
CAGGAAAACUGCAGCUGGAAAACAGUUGUUGACUGUUUGCCGGCAUCGCCUAUAUCUCCAUCACCAUGAUGUUGAUGAUCAUCAUCGUCUUC
(((.....)))..(((((.((((((((...)))))))).)))))..............((((.....))))..((((((....))))))... (-23.58 = -23.74 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:06 2006