Locus 6168

Sequence ID	3L_DroMel_CAF1
Location	16,349,631 – 16,349,731
Length	100
Max. P	0.996486

overview

Window 2

Location	16,349,631 – 16,349,731
Length	100
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	77.92
Mean single sequence MFE	-37.16
Consensus MFE	-22.70
Energy contribution	-25.02
Covariance contribution	2.32
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.61
SVM decision value	1.30
SVM RNA-class probability	0.939269
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16349631 100 + 23771897
GGGCAACCGCCGCACGGCAGAGAUAUUCGCCAGAUAUCAGCGGGAGCUAUAGCCCAUAGCCCUAUAGGCUAUAGCU---------UUUGCUAAGGCCGCUGCCGGAGGA
((....)).((...((((((.((((((.....))))))((((((((((((((((.(((....))).))))))))))---------)))))).......))))))..)). ( -49.20)
>DroSec_CAF1 32452 88 + 1
GGGCAACCGCCGCACGGCAGAGA----CGCCAGAUAUCGGCGGGAGCUAUGGG--------CUAUAGGCUAUAGCU---------UUUGCUAAGGCCGCUACCUGAGGA
((....))(((....(((.....----.))).......((((((((((((((.--------(....).))))))))---------))))))..)))............. ( -35.20)
>DroSim_CAF1 36024 92 + 1
GGGCAACCGCCGCACGGCAGAGAUAUUCGCCAGAUAUCGGCGGGAGCUAUGGG--------CUAUAGGCUAUAGCU---------UUUGCUAAGGCCGCUACCAGAGGA
((....))......((((...((((((.....))))))((((((((((((((.--------(....).))))))))---------))))))...))))........... ( -36.10)
>DroEre_CAF1 32373 101 + 1
GGGCAACCAGCAAACGGCAGAGAUAUUCGCCAGAUAUCGUCGGGGGCCAUAGGCAAUA--------GGCUAUAGCUUUCAUAGAUUUUGCUAAGGCCGCUGCCGGAGGA
((....))......((((((.((((((.....))))))((((..(((.((((.(....--------).)))).)))..).(((......))).)))..))))))..... ( -34.50)
>DroYak_CAF1 38671 108 + 1
GGGCAACCAGCGAACGGUAGAGAUAUUCGCCAGAUAUAGACGGGGACCAUAGGCUAUAGC-CUAUAGACUAUAGCUUUCAUAGAUUUAGCUAAGGCCGCUGCCGGUGGA
((....))......((((((.(.....)(((.....(((..(....).((((((....))-))))...)))(((((...........))))).)))..))))))..... ( -30.80)
>consensus
GGGCAACCGCCGCACGGCAGAGAUAUUCGCCAGAUAUCGGCGGGAGCUAUAGGC_AUA___CUAUAGGCUAUAGCU_________UUUGCUAAGGCCGCUGCCGGAGGA
((....)).((...((((((.....((((((.......))))))......................((((.((((.............)))).)))).))))))..)). (-22.70 = -25.02 +   2.32)

alignment

secondary structure

dotplot

Window 3

Location	16,349,631 – 16,349,731
Length	100
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	77.92
Mean single sequence MFE	-36.14
Consensus MFE	-25.92
Energy contribution	-25.80
Covariance contribution	-0.12
Combinations/Pair	1.22
Mean z-score	-2.67
Structure conservation index	0.72
SVM decision value	2.70
SVM RNA-class probability	0.996486
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16349631 100 - 23771897
UCCUCCGGCAGCGGCCUUAGCAAA---------AGCUAUAGCCUAUAGGGCUAUGGGCUAUAGCUCCCGCUGAUAUCUGGCGAAUAUCUCUGCCGUGCGGCGGUUGCCC
......((((((.((((((((...---------((((((((((((((....))))))))))))))...))))).....((((........))))....))).)))))). ( -49.20)
>DroSec_CAF1 32452 88 - 1
UCCUCAGGUAGCGGCCUUAGCAAA---------AGCUAUAGCCUAUAG--------CCCAUAGCUCCCGCCGAUAUCUGGCG----UCUCUGCCGUGCGGCGGUUGCCC
......(((((((((..((((...---------.))))..)))....(--------((((..((...(((((.....)))))----.....))..)).))).)))))). ( -35.00)
>DroSim_CAF1 36024 92 - 1
UCCUCUGGUAGCGGCCUUAGCAAA---------AGCUAUAGCCUAUAG--------CCCAUAGCUCCCGCCGAUAUCUGGCGAAUAUCUCUGCCGUGCGGCGGUUGCCC
......(((((((((..((((...---------.))))..)))....(--------((((..((...(((((.....))))).........))..)).))).)))))). ( -32.40)
>DroEre_CAF1 32373 101 - 1
UCCUCCGGCAGCGGCCUUAGCAAAAUCUAUGAAAGCUAUAGCC--------UAUUGCCUAUGGCCCCCGACGAUAUCUGGCGAAUAUCUCUGCCGUUUGCUGGUUGCCC
......(((((((((..((((.............))))..)))--------....((..(((((....((.((((((....).))))))).)))))..))..)))))). ( -29.62)
>DroYak_CAF1 38671 108 - 1
UCCACCGGCAGCGGCCUUAGCUAAAUCUAUGAAAGCUAUAGUCUAUAG-GCUAUAGCCUAUGGUCCCCGUCUAUAUCUGGCGAAUAUCUCUACCGUUCGCUGGUUGCCC
......((((((((...(((((...........)))))..(.((((((-((....)))))))).).))))......(..((((((.........))))))..).)))). ( -34.50)
>consensus
UCCUCCGGCAGCGGCCUUAGCAAA_________AGCUAUAGCCUAUAG___UAU_GCCUAUAGCUCCCGCCGAUAUCUGGCGAAUAUCUCUGCCGUGCGGCGGUUGCCC
......(((((((((..((((.............))))..)))........................(((((.....(((((........)))))..))))))))))). (-25.92 = -25.80 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:45 2006