Locus 988

Sequence ID	3R_DroMel_CAF1
Location	3,167,848 – 3,168,008
Length	160
Max. P	0.949254

overview

Window 8

Location	3,167,848 – 3,167,968
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-41.52
Consensus MFE	-41.38
Energy contribution	-41.38
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.95
Structure conservation index	1.00
SVM decision value	1.39
SVM RNA-class probability	0.949254
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3167848 120 + 27905053
GUAGAAGUCAGCAAUUAUCUAAAAAGCGAGCAGCGGCGACAUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUU
.((((.(........).))))....((.((((((((.(((((((((((((...........(((((....))))).)))))).)))((.....))....)))))))))))).))...... ( -41.20)
>DroSec_CAF1 15927 120 + 1
GUAGAAGUCAGCAAUUAUCUAAAAAGCGAGCAGCGGCGACAUCCUGCGAAAAGGAUAACAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUU
.((((.(........).))))....((.((((((((.(((((((((((((..(.....)..(((((....))))).)))))).)))((.....))....)))))))))))).))...... ( -42.40)
>DroSim_CAF1 18691 120 + 1
GUAGAAGUCAGCAAUUAUCUAAAAAGCGAGCAGCGGCGACAUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUU
.((((.(........).))))....((.((((((((.(((((((((((((...........(((((....))))).)))))).)))((.....))....)))))))))))).))...... ( -41.20)
>DroEre_CAF1 7587 119 + 1
GUAGAAGUCAGCAAUUAUCUAAAAAGCGAGCAGCGGCGACAUCCUGCGAA-AGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUU
.((((.(........).))))....((.((((((((.(((((((((((((-..........(((((....))))).)))))).)))((.....))....)))))))))))).))...... ( -41.30)
>consensus
GUAGAAGUCAGCAAUUAUCUAAAAAGCGAGCAGCGGCGACAUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUU
.((((.(........).))))....((.((((((((.(((((((((((((...........(((((....))))).)))))).)))((.....))....)))))))))))).))...... (-41.38 = -41.38 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	3,167,848 – 3,167,968
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-35.12
Consensus MFE	-35.08
Energy contribution	-35.08
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	1.00
SVM decision value	0.48
SVM RNA-class probability	0.754575
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3167848 120 - 27905053
AAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAUGUCGCCGCUGCUCGCUUUUUAGAUAAUUGCUGACUUCUAC
......((.(((((((((((.((........))))))..((....(((((....)))))....((((((......))))))..))))))))).))....((((............)))). ( -35.10)
>DroSec_CAF1 15927 120 - 1
AAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUGUUAUCCUUUUCGCAGGAUGUCGCCGCUGCUCGCUUUUUAGAUAAUUGCUGACUUCUAC
......((.(((((((((((.((........))))))..((....(((((....)))))..(.((((((......)))))).)))))))))).))....((((............)))). ( -35.40)
>DroSim_CAF1 18691 120 - 1
AAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAUGUCGCCGCUGCUCGCUUUUUAGAUAAUUGCUGACUUCUAC
......((.(((((((((((.((........))))))..((....(((((....)))))....((((((......))))))..))))))))).))....((((............)))). ( -35.10)
>DroEre_CAF1 7587 119 - 1
AAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCU-UUCGCAGGAUGUCGCCGCUGCUCGCUUUUUAGAUAAUUGCUGACUUCUAC
......((.(((((((((((.((........))))))..((....(((((....)))))....((((((-.....))))))..))))))))).))....((((............)))). ( -34.90)
>consensus
AAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAUGUCGCCGCUGCUCGCUUUUUAGAUAAUUGCUGACUUCUAC
......((.(((((((((((.((........))))))..((....(((((....)))))....((((((......))))))..))))))))).))....((((............)))). (-35.08 = -35.08 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	3,167,888 – 3,168,008
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.60
Mean single sequence MFE	-30.75
Consensus MFE	-29.30
Energy contribution	-29.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.95
SVM decision value	0.28
SVM RNA-class probability	0.666323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3167888 120 + 27905053
AUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUUACACAGAAACAUUUCCAAACAGAAAUAGGCAGAAAGAAGA
...((((.............(((..((.(((((((....(((((..((.....))..))))).....)))))))...))..)))......(((((......)))))..))))........ ( -31.70)
>DroSec_CAF1 15967 115 + 1
AUCCUGCGAAAAGGAUAACAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUUACACAGAAACAUUUCCAAACAU-----GGCAGAAAGAAGA
(((((......)))))....(((..((.(((((((....(((((..((.....))..))))).....)))))))...))..))).......((((((....)-----)).)))....... ( -30.50)
>DroSim_CAF1 18731 115 + 1
AUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUUACACAGAAACAUUUCCAAACAU-----GGCAGAAAGAAGA
(((((......)))))....(((..((.(((((((....(((((..((.....))..))))).....)))))))...))..))).......((((((....)-----)).)))....... ( -30.50)
>DroEre_CAF1 7627 114 + 1
AUCCUGCGAA-AGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUUACACAGAAACAUUUCCAAACAU-----GGCAGAAAGAAGA
(((((.....-)))))....(((..((.(((((((....(((((..((.....))..))))).....)))))))...))..))).......((((((....)-----)).)))....... ( -30.30)
>consensus
AUCCUGCGAAAAGGAUAAUAGUGCUGAGGCCAGCAAUUUGCACGGACCAAUUUGGAAUGUGUCCCGCUGCUGGCAUAUUUACACAGAAACAUUUCCAAACAU_____GGCAGAAAGAAGA
...((((.............(((..((.(((((((....(((((..((.....))..))))).....)))))))...))..))).(((....))).............))))........ (-29.30 = -29.30 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	3,167,888 – 3,168,008
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.60
Mean single sequence MFE	-33.10
Consensus MFE	-31.90
Energy contribution	-31.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.96
SVM decision value	1.33
SVM RNA-class probability	0.942395
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3167888 120 - 27905053
UCUUCUUUCUGCCUAUUUCUGUUUGGAAAUGUUUCUGUGUAAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAU
......((((((.(((((((....))))))).....((((......((((((((((((((.((........)))))).)))....)))))))....)))).............)))))). ( -35.10)
>DroSec_CAF1 15967 115 - 1
UCUUCUUUCUGCC-----AUGUUUGGAAAUGUUUCUGUGUAAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUGUUAUCCUUUUCGCAGGAU
......(((((((-----(....))((((.((..(.((((......((((((((((((((.((........)))))).)))....)))))))....)))).)..))...)))))))))). ( -32.60)
>DroSim_CAF1 18731 115 - 1
UCUUCUUUCUGCC-----AUGUUUGGAAAUGUUUCUGUGUAAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAU
......((((((.-----......(((...((....((((......((((((((((((((.((........)))))).)))....)))))))....)))).))..))).....)))))). ( -32.20)
>DroEre_CAF1 7627 114 - 1
UCUUCUUUCUGCC-----AUGUUUGGAAAUGUUUCUGUGUAAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCU-UUCGCAGGAU
......(((((((-----(....))((((.(.....((((......((((((((((((((.((........)))))).)))....)))))))....))))......).)-))))))))). ( -32.50)
>consensus
UCUUCUUUCUGCC_____AUGUUUGGAAAUGUUUCUGUGUAAAUAUGCCAGCAGCGGGACACAUUCCAAAUUGGUCCGUGCAAAUUGCUGGCCUCAGCACUAUUAUCCUUUUCGCAGGAU
......((((((............((((....))))((((......((((((((((((((.((........)))))).)))....)))))))....)))).............)))))). (-31.90 = -31.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:43 2006