Locus 5081

Sequence ID	2R_DroMel_CAF1
Location	16,508,882 – 16,508,989
Length	107
Max. P	0.860036

overview

Window 2

Location	16,508,882 – 16,508,989
Length	107
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.45
Mean single sequence MFE	-34.59
Consensus MFE	-21.21
Energy contribution	-22.47
Covariance contribution	1.25
Combinations/Pair	1.30
Mean z-score	-1.59
Structure conservation index	0.61
SVM decision value	0.20
SVM RNA-class probability	0.630662
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16508882 107 + 20766785
AG---GAGGAGGCGGGCUCGACGGAUCUGAACCAAAAUUUCGAGAAGAUACCCUGCAAAGAGGAGUUCCUGUGCCUCGAG---GAGGAAGAGGAGGACUUUCUCGACGAUG---CG
.(---(.(((..((.......))..)))...))......((((((((...((((....)).))..(((((.(.((((...---)))).).)))))...)))))))).....---.. ( -27.60)
>DroVir_CAF1 11766 106 + 1
-G---AAUGAGGCAGCCGCUAUCGAUUUAAAUCAAAACUUUGAGAAGAUUCUCUGCAAGGAGGAGUUUAUGUGCCUCGAU---GAG---GAGGAUGACUUCCUCGAUGAUGACGCC
-.---..(((((((.......(((((....)))....((((((((......))).)))))..)).......))))))).(---(((---((((....))))))))........... ( -27.74)
>DroPse_CAF1 11767 113 + 1
AGGAAGAGGAGGCCGGUUCUACAGAUCUGAACCAGAAUUUCGAGAAAAUCCUUUGCAAAGAGGAGUUUCUGGGCCUCGACGACGAGGAGGAGGAGGAAUUCCUCCAUGAUG---CG
........(((((((((((.........))))).........(((((.((((((....)))))).))))).))))))(.((.((.(((((((......))))))).)).))---). ( -42.20)
>DroEre_CAF1 6070 107 + 1
AG---GAGGAGGCGGGUUCAACGGAUCUGAACCAGAAUUUCGAGAAGAUCCCCUGCAAAGAGGAGUUUAUGUGCCUCGAG---GAGGAGGAGGAGGACUUUCUCGACGAUG---CA
..---......(((((((((.......))))))......((((((((.(((((((((.(((....))).))).((((...---...))))))).))).))))))))...))---). ( -33.10)
>DroAna_CAF1 5771 107 + 1
AG---GAUGAGGCUGGAUCGACUGAUCUGAACCAGAACUUUGAAAAGAUUCUCUGCAAGGAGGAGUUCCUGUGCCUCGAG---GAGGAGGAGGAGGACUUCCUCAAUGAUG---UA
..---..((((((.(((.(..((..((((...)))).(((((...((.....)).)))))))..).)))...))))))..---...(((((((....))))))).......---.. ( -32.70)
>DroPer_CAF1 11704 113 + 1
AGGAAGACGAGGCCGGUUCUACAGAUCUGAACCAGAAUUUCGAGAAAAUCCUUUGCAAAGAGGAGUUUCUGGGCCUCGACGACGAGGAGGAGGAGGAAUUCCUCCAUGAUG---CG
.......((((((((((((.........))))).........(((((.((((((....)))))).))))).))))))).......(((((((......)))))))......---.. ( -44.20)
>consensus
AG___GAGGAGGCCGGUUCUACAGAUCUGAACCAGAAUUUCGAGAAGAUCCUCUGCAAAGAGGAGUUUCUGUGCCUCGAG___GAGGAGGAGGAGGACUUCCUCGAUGAUG___CG
........((((((((.((.........)).))........((((...((((((....)))))).))))..))))))......(((((((.......)))))))............ (-21.21 = -22.47 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	16,508,882 – 16,508,989
Length	107
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.45
Mean single sequence MFE	-30.09
Consensus MFE	-16.61
Energy contribution	-17.12
Covariance contribution	0.50
Combinations/Pair	1.26
Mean z-score	-2.31
Structure conservation index	0.55
SVM decision value	0.82
SVM RNA-class probability	0.860036
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16508882 107 - 20766785
CG---CAUCGUCGAGAAAGUCCUCCUCUUCCUC---CUCGAGGCACAGGAACUCCUCUUUGCAGGGUAUCUUCUCGAAAUUUUGGUUCAGAUCCGUCGAGCCCGCCUCCUC---CU
.(---(....(((((((.....((((...((((---...))))...))))((.(((......)))))...)))))))......(((((.((....))))))).))......---.. ( -26.30)
>DroVir_CAF1 11766 106 - 1
GGCGUCAUCAUCGAGGAAGUCAUCCUC---CUC---AUCGAGGCACAUAAACUCCUCCUUGCAGAGAAUCUUCUCAAAGUUUUGAUUUAAAUCGAUAGCGGCUGCCUCAUU---C-
((((((...(((((..((((((.((((---...---...))))....................((((....)))).......))))))...)))))...))).))).....---.- ( -25.00)
>DroPse_CAF1 11767 113 - 1
CG---CAUCAUGGAGGAAUUCCUCCUCCUCCUCGUCGUCGAGGCCCAGAAACUCCUCUUUGCAAAGGAUUUUCUCGAAAUUCUGGUUCAGAUCUGUAGAACCGGCCUCCUCUUCCU
..---......((((((.....))))))........(..((((((.(((((.((((........)))).))))).........(((((.........)))))))))))..)..... ( -34.70)
>DroEre_CAF1 6070 107 - 1
UG---CAUCGUCGAGAAAGUCCUCCUCCUCCUC---CUCGAGGCACAUAAACUCCUCUUUGCAGGGGAUCUUCUCGAAAUUCUGGUUCAGAUCCGUUGAACCCGCCUCCUC---CU
.(---(....(((((((..(((.(((.(((...---...)))(((..............)))))))))..)))))))......(((((((.....))))))).))......---.. ( -29.54)
>DroAna_CAF1 5771 107 - 1
UA---CAUCAUUGAGGAAGUCCUCCUCCUCCUC---CUCGAGGCACAGGAACUCCUCCUUGCAGAGAAUCUUUUCAAAGUUCUGGUUCAGAUCAGUCGAUCCAGCCUCAUC---CU
..---...((..(((((..((((...((((...---...))))...))))..)))))..))...((((.(((....)))))))((((..((((....)))).)))).....---.. ( -27.30)
>DroPer_CAF1 11704 113 - 1
CG---CAUCAUGGAGGAAUUCCUCCUCCUCCUCGUCGUCGAGGCCCAGAAACUCCUCUUUGCAAAGGAUUUUCUCGAAAUUCUGGUUCAGAUCUGUAGAACCGGCCUCGUCUUCCU
..---......((((((.....))))))........(.(((((((.(((((.((((........)))).))))).........(((((.........)))))))))))).)..... ( -37.70)
>consensus
CG___CAUCAUCGAGGAAGUCCUCCUCCUCCUC___CUCGAGGCACAGAAACUCCUCUUUGCAGAGGAUCUUCUCGAAAUUCUGGUUCAGAUCCGUAGAACCCGCCUCCUC___CU
............(((((.....)))))............(((((...................((((....))))........(((((.........))))).)))))........ (-16.61 = -17.12 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:02 2006