Locus 6582

Sequence ID	2L_DroMel_CAF1
Location	18,506,906 – 18,507,034
Length	128
Max. P	0.742159

overview

Window 7

Location	18,506,906 – 18,506,996
Length	90
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	92.27
Mean single sequence MFE	-18.77
Consensus MFE	-15.50
Energy contribution	-16.88
Covariance contribution	1.38
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.83
SVM decision value	0.45
SVM RNA-class probability	0.742159
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18506906 90 + 22407834
UAAACAUUAUAAAACUUGCAUGAUGUUCAGGAAUUGUACGAUGUCUGGAAAUUAACACCUUAAUGAUGGUAU-AAUGGGAGACAUACCAUA
....((((((..........((((.(((((..(((....)))..))))).))))..(((........)))))-))))(....)........ ( -15.20)
>DroSec_CAF1 27285 90 + 1
UAAACAUUAUAAAACUUGCAUGAUAUGCAGCA-UUUUACGAUGUCUGGAAAUUAACACCUGAAUGAUGGUAUUAAUGGGAGACCUACCAUA
...((((..(((((.((((((...))))))..-)))))..)))).(((..(((((.(((........))).)))))((....))..))).. ( -20.80)
>DroSim_CAF1 26479 90 + 1
UAAACAUUAUAAAACUUGCAUGAUAUGCAGGA-UUUUACGAUGUCUGGAAAUGAACACCUUAAUGAUGGUAUUAAUGGGAGACCUACCAUA
...((((..((((((((((((...))))))).-)))))..)))).(((........(((........)))......((....))..))).. ( -22.50)
>DroYak_CAF1 27355 90 + 1
AAAACAUAAUAAAACUUGCAUGAUGUGCAGAA-UUUUACGAUGUCUGGAAAUUAAGACCUGAAUGAUGGUAUUAAUGGGAGACUUACCAUA
...((((..(((((.((((((...))))))..-)))))..)))).(((..(((((.(((........))).)))))((....))..))).. ( -16.60)
>consensus
UAAACAUUAUAAAACUUGCAUGAUAUGCAGGA_UUUUACGAUGUCUGGAAAUUAACACCUGAAUGAUGGUAUUAAUGGGAGACCUACCAUA
...((((..((((((((((((...)))))))..)))))..)))).(((..(((((.(((........))).)))))((....))..))).. (-15.50 = -16.88 +   1.38)

alignment

secondary structure

dotplot

Window 8

Location	18,506,906 – 18,506,996
Length	90
Sequences	4
Columns	91
Reading direction	reverse
Mean pairwise identity	92.27
Mean single sequence MFE	-18.55
Consensus MFE	-13.52
Energy contribution	-14.78
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.73
SVM decision value	0.24
SVM RNA-class probability	0.646632
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18506906 90 - 22407834
UAUGGUAUGUCUCCCAUU-AUACCAUCAUUAAGGUGUUAAUUUCCAGACAUCGUACAAUUCCUGAACAUCAUGCAAGUUUUAUAAUGUUUA
.((((((((........)-)))))))......((((((........))))))..........(((((((.(((.......))).))))))) ( -15.60)
>DroSec_CAF1 27285 90 - 1
UAUGGUAGGUCUCCCAUUAAUACCAUCAUUCAGGUGUUAAUUUCCAGACAUCGUAAAA-UGCUGCAUAUCAUGCAAGUUUUAUAAUGUUUA
...((..((....))(((((((((........)))))))))..))((((((..(((((-(..(((((...))))).))))))..)))))). ( -23.30)
>DroSim_CAF1 26479 90 - 1
UAUGGUAGGUCUCCCAUUAAUACCAUCAUUAAGGUGUUCAUUUCCAGACAUCGUAAAA-UCCUGCAUAUCAUGCAAGUUUUAUAAUGUUUA
.((((........)))).((((((........)))))).......((((((..(((((-(..(((((...))))).))))))..)))))). ( -18.80)
>DroYak_CAF1 27355 90 - 1
UAUGGUAAGUCUCCCAUUAAUACCAUCAUUCAGGUCUUAAUUUCCAGACAUCGUAAAA-UUCUGCACAUCAUGCAAGUUUUAUUAUGUUUU
..(((........)))((((.(((........))).)))).....((((((.((((((-((.((((.....)))))))))))).)))))). ( -16.50)
>consensus
UAUGGUAGGUCUCCCAUUAAUACCAUCAUUAAGGUGUUAAUUUCCAGACAUCGUAAAA_UCCUGCACAUCAUGCAAGUUUUAUAAUGUUUA
..(((........)))((((((((........)))))))).....((((((..(((((....((((.....))))..)))))..)))))). (-13.52 = -14.78 +   1.25)

alignment

secondary structure

dotplot

Window 9

Location	18,506,941 – 18,507,034
Length	93
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.93
Mean single sequence MFE	-24.36
Consensus MFE	-9.42
Energy contribution	-11.14
Covariance contribution	1.72
Combinations/Pair	1.24
Mean z-score	-1.78
Structure conservation index	0.39
SVM decision value	0.28
SVM RNA-class probability	0.664630
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18506941 93 - 22407834
UGAAGUGGACCAGAAAGCUUGUUA--GCUUACCCGCCUUAUAUGGUAUGUCU---------CCCAUU-AUACCAUCAUUAAGGUGUUAA--------------UUUCCAGACAU-CGUAC
.....((((.....(((((....)--))))...(((((((.((((((((...---------.....)-)))))))...)))))))....--------------..)))).....-..... ( -24.70)
>DroPse_CAF1 32456 117 - 1
UAGCCAUAGCC--AUAGCUUUAUACGGUUUACGCCUCAUAUAUG-UAUGUAUGUUAGUGUGGCUUUUACCACCAUAAUAAAGGUGCCUAGACUCUGGCCUGUUUGGCUAGACAUUCGAGU
.((((..((((--.((......)).)))).((((..((((((..-..))))))...)))))))).....((((........))))....((.(((((((.....)))))))...)).... ( -29.40)
>DroSec_CAF1 27319 94 - 1
CGAAGUGGACCAGAAAGCUUGUUA--GCUUACCCGCCUUAUAUGGUAGGUCU---------CCCAUUAAUACCAUCAUUCAGGUGUUAA--------------UUUCCAGACAU-CGUAA
(((.(((((((...(((((....)--))))....(((......))).)))))---------...(((((((((........))))))))--------------)......)).)-))... ( -24.60)
>DroSim_CAF1 26513 94 - 1
CGAAGUGGACCAGAAAGCUUGUUA--GCUUACCCGCCUUGUAUGGUAGGUCU---------CCCAUUAAUACCAUCAUUAAGGUGUUCA--------------UUUCCAGACAU-CGUAA
.(((((((((....(((((....)--))))....((((((.((((((.....---------........))))))...)))))))))))--------------)))).......-..... ( -25.12)
>DroYak_CAF1 27389 94 - 1
UGAAGUGGACCAGAAAGCUUGUCA--GCUUACCCACCUUAUAUGGUAAGUCU---------CCCAUUAAUACCAUCAUUCAGGUCUUAA--------------UUUCCAGACAU-CGUAA
(((.((((....(.(((((....)--)))).))))).)))((((((..((((---------...(((((.(((........))).))))--------------)....))))))-)))). ( -18.00)
>consensus
UGAAGUGGACCAGAAAGCUUGUUA__GCUUACCCGCCUUAUAUGGUAGGUCU_________CCCAUUAAUACCAUCAUUAAGGUGUUAA______________UUUCCAGACAU_CGUAA
...(((((......((((........))))(((.(((......))).)))............)))))((((((........))))))................................. ( -9.42 = -11.14 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:43 2006