Locus 2795

Sequence ID	2R_DroMel_CAF1
Location	9,737,455 – 9,737,595
Length	140
Max. P	0.995677

overview

Window 5

Location	9,737,455 – 9,737,562
Length	107
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	82.09
Mean single sequence MFE	-35.40
Consensus MFE	-24.96
Energy contribution	-26.27
Covariance contribution	1.31
Combinations/Pair	1.06
Mean z-score	-2.48
Structure conservation index	0.71
SVM decision value	1.74
SVM RNA-class probability	0.974904
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9737455 107 + 20766785
UUUGCUUAGCAGCUCGUUUCGGGGUCGA-------AUCGAAAUCGGAAUCAGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGAUUGGAAACAGUGCCCGAAACGGAGAGAUGGG
....((((....(((((((((((....(-------(((..((((.((((.((((((.......)))))).)))).))))..))))(....)....)))))))).)))...)))) ( -34.90)
>DroSec_CAF1 6428 113 + 1
UUUGCUUAGCAGCUCGUUUCGGGGUCGAGUU-GGAAUCGGAAUCGAAAUCGGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGUUUGGAAACAGUGCCCGAAUCGGAGAGAUGGG
.((((...))))((((((((....((((.((-.((((..(((((..(((((....)).)))..)))))..)))).))(((((((((....))).)))))).)))).)))))))) ( -34.20)
>DroSim_CAF1 6491 113 + 1
UUUGCUUAGCAGCUCGUUUCGGGGUCGAAUC-GGAAUCGAAAUCGGAAUCGGAAUCGUAUUGAGAUUUGUAUUCGGAUUGGGUUUGGAAACAGUGCCCGAAACGGAGAGAUGGG
.((((...))))((((((((.....((((((-..((((((..(((....)))..))).)))..))))))..((((..(((((((((....))).))))))..)))))))))))) ( -35.00)
>DroYak_CAF1 6356 104 + 1
----------AGCUCGCUUCGGGGUUGAAUCCGGAAUCUGAAUCUGAAUCGGAAUCUGAAUCAGAAUCAGAAUCGUAUUCGGAUUGGAAACAGAGCCCGAAACGGAGAGAUGGG
----------..((((.((((((.((.((((((((.(((((.(((((.((((...)))).))))).)))))......))))))))(....).)).)))))).).)))....... ( -37.50)
>consensus
UUUGCUUAGCAGCUCGUUUCGGGGUCGAAUC_GGAAUCGAAAUCGGAAUCGGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGAUUGGAAACAGUGCCCGAAACGGAGAGAUGGG
............(((((((((((.((((........))))((((.((((..(((((.......)))))..)))).))))....(((....)))..)))))))).)))....... (-24.96 = -26.27 +   1.31)

alignment

secondary structure

dotplot

Window 6

Location	9,737,455 – 9,737,562
Length	107
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	82.09
Mean single sequence MFE	-27.18
Consensus MFE	-17.26
Energy contribution	-18.95
Covariance contribution	1.69
Combinations/Pair	1.07
Mean z-score	-3.46
Structure conservation index	0.64
SVM decision value	2.60
SVM RNA-class probability	0.995677
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9737455 107 - 20766785
CCCAUCUCUCCGUUUCGGGCACUGUUUCCAAUCCCAAUCCGAAUAAAAAUCUCAAUACGAUUCUGAUUCCGAUUUCGAU-------UCGACCCCGAAACGAGCUGCUAAGCAAA
..........(((((((((....(((...((((..((((.((((...((((.......))))...)))).))))..)))-------).)))))))))))).(((....)))... ( -26.40)
>DroSec_CAF1 6428 113 - 1
CCCAUCUCUCCGAUUCGGGCACUGUUUCCAAACCCAAUCCGAAUAAAAAUCUCAAUACGAUUCCGAUUUCGAUUCCGAUUCC-AACUCGACCCCGAAACGAGCUGCUAAGCAAA
..........((.((((((....(((....)))..((((.((((..(((((.............)))))..)))).))))..-........)))))).)).(((....)))... ( -19.82)
>DroSim_CAF1 6491 113 - 1
CCCAUCUCUCCGUUUCGGGCACUGUUUCCAAACCCAAUCCGAAUACAAAUCUCAAUACGAUUCCGAUUCCGAUUUCGAUUCC-GAUUCGACCCCGAAACGAGCUGCUAAGCAAA
..........(((((((((................((((.((((...((((.......))))...)))).))))((((....-...)))).))))))))).(((....)))... ( -27.00)
>DroYak_CAF1 6356 104 - 1
CCCAUCUCUCCGUUUCGGGCUCUGUUUCCAAUCCGAAUACGAUUCUGAUUCUGAUUCAGAUUCCGAUUCAGAUUCAGAUUCCGGAUUCAACCCCGAAGCGAGCU----------
..........(((((((((....(((...((((((.....((.(((((.(((((.((.......)).))))).))))).)))))))).))))))))))))....---------- ( -35.50)
>consensus
CCCAUCUCUCCGUUUCGGGCACUGUUUCCAAACCCAAUCCGAAUAAAAAUCUCAAUACGAUUCCGAUUCCGAUUCCGAUUCC_GAUUCGACCCCGAAACGAGCUGCUAAGCAAA
..........(((((((((................((((.((((...((((.......))))...)))).)))).(((........)))..))))))))).(((....)))... (-17.26 = -18.95 +   1.69)

alignment

secondary structure

dotplot

Window 7

Location	9,737,486 – 9,737,595
Length	109
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	84.38
Mean single sequence MFE	-31.35
Consensus MFE	-18.69
Energy contribution	-20.50
Covariance contribution	1.81
Combinations/Pair	1.04
Mean z-score	-2.37
Structure conservation index	0.60
SVM decision value	0.46
SVM RNA-class probability	0.744142
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9737486 109 + 20766785
GAAAUCGGAAUCAGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGAUUGGAAACAGUGCCCGAAACGGAGAGAUGGGAUGUGGAUG------UGGAAACUGGGCUGCGUCAUGAGG
..((((.((((.((((((.......)))))).)))).))))(((((((....)))).)))...............((((..(...------.(....)....)..))))...... ( -33.00)
>DroSec_CAF1 6465 103 + 1
GGAAUCGAAAUCGGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGUUUGGAAACAGUGCCCGAAUCGGAGAGAUGGGAUG------------UGGAAACUGGGCUGCGUCAUGAGG
((((((..(((((....)).)))..))))))..(((((.(((((((((....))).)))))).))))).......((((------------..(........)..))))...... ( -28.00)
>DroSim_CAF1 6528 109 + 1
GAAAUCGGAAUCGGAAUCGUAUUGAGAUUUGUAUUCGGAUUGGGUUUGGAAACAGUGCCCGAAACGGAGAGAUGGGAUGUGGCUG------UGGAAACUGGGCUGCGUCAUGAGG
....(((...((.(((((.......)))))...((((..(((((((((....))).))))))..))))))..)))((((..(((.------.(....)..)))..))))...... ( -36.10)
>DroYak_CAF1 6384 115 + 1
UGAAUCUGAAUCGGAAUCUGAAUCAGAAUCAGAAUCGUAUUCGGAUUGGAAACAGAGCCCGAAACGGAGAGAUGGGAUGUGGAUGUUGAUGUGAAAAGUGGGCUGCGUCAUGAGG
(((.(((((.((((...)))).))))).)))...((((.(((((.(((....)))...)))))))))........(((((....(((.((.......)).))).)))))...... ( -28.30)
>consensus
GAAAUCGGAAUCGGAAUCGUAUUGAGAUUUUUAUUCGGAUUGGGAUUGGAAACAGUGCCCGAAACGGAGAGAUGGGAUGUGGAUG______UGGAAACUGGGCUGCGUCAUGAGG
.........(((.(((((.......)))))...((((..(((((((((....))).))))))..))))..)))..(((((((....................)))))))...... (-18.69 = -20.50 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:41 2006