Locus 4358

Sequence ID	2L_DroMel_CAF1
Location	12,516,504 – 12,516,599
Length	95
Max. P	0.982722

overview

Window 1

Location	12,516,504 – 12,516,599
Length	95
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.12
Mean single sequence MFE	-43.87
Consensus MFE	-28.06
Energy contribution	-28.25
Covariance contribution	0.20
Combinations/Pair	1.17
Mean z-score	-2.04
Structure conservation index	0.64
SVM decision value	1.40
SVM RNA-class probability	0.950208
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12516504 95 + 22407834
GCACCACCGGC---------UGCAUCACCGCAUGUUGCAGCCGCCGCAACGGCGGCAAAAACGCUGGCACAUUCCAGCGGUGAUCGUGGUC------UACGAUCACCGGA
......(((((---------((((.((.....)).)))))))(((((....)))))......(((((......)))))((((((((((...------)))))))))))). ( -48.70)
>DroSec_CAF1 89218 95 + 1
GCACCACCAGC---------UGCACCACCGCAAGUUGCAGCCGCCGCAACGGCAGCAAAAACGGUGGCACAUUCCAGCGGAGAUCGUGGUC------UGCGAUCGCCGGA
......((.((---------((..((((((....((((.((((......)))).))))...)))))).......))))((.((((((....------.)))))).)))). ( -39.30)
>DroSim_CAF1 92342 95 + 1
GCACCACCAGC---------UGCACCACCGCAAGUUGCAGCCGCCGCAACGGCGGCAAAAACGGUGGCACAUUCCAGCGGAGAUCGGGGUC------UGCGAUCGCCGGA
......((.((---------((..(((((((.....)).(((((((...)))))))......))))).......))))((.(((((.....------..))))).)))). ( -40.40)
>DroEre_CAF1 87070 107 + 1
GCGCCAC---CUGCACCACCUGCACCACCGCAAGUUGCAGCGGCCGCGACGGCGGCAAACACGGUGGCACAUUCCAGCGGAGAUCGGGAUCUGCACUUGCGGUCGCCGGA
(.(((((---(((((..((.(((......))).))))))...(((((....)))))......)))))).).((((...)))).((((((.((((....)))))).)))). ( -42.80)
>DroYak_CAF1 90789 107 + 1
GCACCACCAGCUGCAUCAGUUGCACCACCGCAAGUGGCAGCCGCAGCGACGGCGGCAAACACGGUGGCGCAUUCCAGAGGAGAUCGGGU--UGCGGAUGCGGUUGCU-GA
....((.((((((((((.......(((((((.....)).(((((.......)))))......)))))((((..((.((.....))))..--)))))))))))))).)-). ( -46.60)
>DroAna_CAF1 88685 92 + 1
GGGC--UCUGU---------UGCACCACCGGAUGUGGCUGCCGCAGCCACGGCGGCAAGAACGGUGGCACACUCCAGCGGCGAUCGUGGCC------UUCGAUCGCCGG-
((((--.....---------.)).((((((..(...(((((((......)))))))..)..))))))......))..(((((((((.....------..))))))))).- ( -45.40)
>consensus
GCACCACCAGC_________UGCACCACCGCAAGUUGCAGCCGCCGCAACGGCGGCAAAAACGGUGGCACAUUCCAGCGGAGAUCGGGGUC______UGCGAUCGCCGGA
....................((..((((((....((((.((((......)))).))))...))))))..))......(((.(((((.............))))).))).. (-28.06 = -28.25 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	12,516,504 – 12,516,599
Length	95
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.12
Mean single sequence MFE	-48.67
Consensus MFE	-35.06
Energy contribution	-36.67
Covariance contribution	1.61
Combinations/Pair	1.10
Mean z-score	-2.44
Structure conservation index	0.72
SVM decision value	1.92
SVM RNA-class probability	0.982722
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12516504 95 - 22407834
UCCGGUGAUCGUA------GACCACGAUCACCGCUGGAAUGUGCCAGCGUUUUUGCCGCCGUUGCGGCGGCUGCAACAUGCGGUGAUGCA---------GCCGGUGGUGC
...(((((((((.------....)))))))))(((((......)))))......((((((((((((...(((((.....)))))..))))---------).))))))).. ( -48.60)
>DroSec_CAF1 89218 95 - 1
UCCGGCGAUCGCA------GACCACGAUCUCCGCUGGAAUGUGCCACCGUUUUUGCUGCCGUUGCGGCGGCUGCAACUUGCGGUGGUGCA---------GCUGGUGGUGC
....(((((((..------.....))))).((((..(..((..(((((((..((((.(((((....))))).))))...)))))))..))---------.)..)))).)) ( -47.50)
>DroSim_CAF1 92342 95 - 1
UCCGGCGAUCGCA------GACCCCGAUCUCCGCUGGAAUGUGCCACCGUUUUUGCCGCCGUUGCGGCGGCUGCAACUUGCGGUGGUGCA---------GCUGGUGGUGC
....(((((((..------.....))))).((((..(..((..(((((((..((((.(((((....))))).))))...)))))))..))---------.)..)))).)) ( -47.10)
>DroEre_CAF1 87070 107 - 1
UCCGGCGACCGCAAGUGCAGAUCCCGAUCUCCGCUGGAAUGUGCCACCGUGUUUGCCGCCGUCGCGGCCGCUGCAACUUGCGGUGGUGCAGGUGGUGCAG---GUGGCGC
(((((((...((....))((((....)))).)))))))..((((((((.(((..((((((...(((.(((((((.....)))))))))).))))))))))---))))))) ( -57.30)
>DroYak_CAF1 90789 107 - 1
UC-AGCAACCGCAUCCGCA--ACCCGAUCUCCUCUGGAAUGCGCCACCGUGUUUGCCGCCGUCGCUGCGGCUGCCACUUGCGGUGGUGCAACUGAUGCAGCUGGUGGUGC
..-.(((.((((..(.(((--.((.((.....)).))..((((((((((((...((.(((((....))))).))....)))))))))))).....))).)...))))))) ( -44.60)
>DroAna_CAF1 88685 92 - 1
-CCGGCGAUCGAA------GGCCACGAUCGCCGCUGGAGUGUGCCACCGUUCUUGCCGCCGUGGCUGCGGCAGCCACAUCCGGUGGUGCA---------ACAGA--GCCC
-.(((((((((..------.....)))))))))(((...((..((((((.....((.(((((....))))).))......))))))..))---------.))).--.... ( -46.90)
>consensus
UCCGGCGAUCGCA______GACCACGAUCUCCGCUGGAAUGUGCCACCGUUUUUGCCGCCGUUGCGGCGGCUGCAACUUGCGGUGGUGCA_________GCUGGUGGUGC
(((((((((((.............)))))...)))))).(((((((((((..((((.(((((....))))).))))...))))))))))).................... (-35.06 = -36.67 +   1.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:50 2006