Locus 2701

Sequence ID	2L_DroMel_CAF1
Location	7,564,919 – 7,565,053
Length	134
Max. P	0.999004

overview

Window 3

Location	7,564,919 – 7,565,014
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	90.17
Mean single sequence MFE	-23.20
Consensus MFE	-20.58
Energy contribution	-20.66
Covariance contribution	0.08
Combinations/Pair	1.17
Mean z-score	-2.45
Structure conservation index	0.89
SVM decision value	3.32
SVM RNA-class probability	0.999004
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7564919 95 + 22407834
CGGCACGGAAAAUCACCACAGGCCUAUGCUCCGGUCCCUAUUUCCUUUUCUACACUGAAAUAAAUAAGCGCCGAGAGCGCAUCCUAAAAACUUUA
.(((..((.......))....)))...((((((((.(.(((((...((((......)))).))))).).)))).))))................. ( -21.50)
>DroSec_CAF1 64656 91 + 1
CGGCACGGAAAAUCACCACAGGCCUAUGCUCCGGUCCCUAUUUCCUUUCCAACACUGCAAUAAAUAGGCACCGAGAGCGCAUCCUAAAAAC----
.(((..((.......))....)))...((((((((.(((((((...((.((....)).)).))))))).)))).)))).............---- ( -23.70)
>DroSim_CAF1 69351 91 + 1
CGGCACGGAAAAUCACCACAGGCCUAUGCUCCGGUCCCUAUUUCCUUUCCAACACUGAAAUUAAUAGGCACCGAGAGCGCAUCCUAAAAAC----
.(((..((.......))....)))...((((((((.((((((...((((.......))))..)))))).)))).)))).............---- ( -25.50)
>DroEre_CAF1 63766 95 + 1
CGGCACGGAAAAUCACCGCAGGCCUAUGCUACAGUCCCUAUUUCCUUUCCUACACUGAAACAAAUAGGCACUGAGAGUGCAUCCCAAGAACUUUA
..((((((.......))(((......)))..((((.(((((((..((((.......)))).))))))).))))...))))............... ( -21.10)
>DroYak_CAF1 66037 95 + 1
CGGCACGGAAAAUCACCACAGGCCUAUGCUCCGGUCCCUAUUUCCUUUGCUACACUGAAAUAAAUAGGCACUGAGAGCGCAUCCUGAAAACUUUU
......((.......)).((((....(((((((((.(((((((..(((........)))..))))))).)))).)))))...))))......... ( -24.20)
>consensus
CGGCACGGAAAAUCACCACAGGCCUAUGCUCCGGUCCCUAUUUCCUUUCCUACACUGAAAUAAAUAGGCACCGAGAGCGCAUCCUAAAAACUUU_
.(((..((.......))....)))...((((((((.(((((((..(((........)))..))))))).)))).))))................. (-20.58 = -20.66 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	7,564,941 – 7,565,053
Length	112
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	78.25
Mean single sequence MFE	-22.71
Consensus MFE	-15.78
Energy contribution	-15.86
Covariance contribution	0.08
Combinations/Pair	1.22
Mean z-score	-2.72
Structure conservation index	0.69
SVM decision value	2.70
SVM RNA-class probability	0.996466
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7564941 112 + 22407834
CCUAUGCUCCGGUCCCUAUUUCCUUUUCUACACUGAAAUAAAUAAGCGCCGAGAGCGCAUCCUAAAAACUUUACGC-AAAUAGCCUUUCUCAAACUUGGAAGCGAACUACACA
.....((((((((.(.(((((...((((......)))).))))).).)))).))))((.(((............((-.....)).............))).)).......... ( -22.71)
>DroSec_CAF1 64678 93 + 1
CCUAUGCUCCGGUCCCUAUUUCCUUUCCAACACUGCAAUAAAUAGGCACCGAGAGCGCAUCCUAAAAAC--------------------UCAAACUUGAAAGCGAACUACACA
.....((((((((.(((((((...((.((....)).)).))))))).)))).)))).............--------------------........................ ( -18.90)
>DroSim_CAF1 69373 93 + 1
CCUAUGCUCCGGUCCCUAUUUCCUUUCCAACACUGAAAUUAAUAGGCACCGAGAGCGCAUCCUAAAAAC--------------------UCAAACCUGGAAGCGAACUACACA
.....((((((((.((((((...((((.......))))..)))))).)))).))))((.(((.......--------------------........))).)).......... ( -25.76)
>DroEre_CAF1 63788 113 + 1
CCUAUGCUACAGUCCCUAUUUCCUUUCCUACACUGAAACAAAUAGGCACUGAGAGUGCAUCCCAAGAACUUUAAGCCAAGUAGCCCUACUCAAACUUGGAACCGAGCUAUAUA
.....(((.((((.(((((((..((((.......)))).))))))).))))(((((...........)))))...((((((............)))))).....)))...... ( -21.20)
>DroYak_CAF1 66059 113 + 1
CCUAUGCUCCGGUCCCUAUUUCCUUUGCUACACUGAAAUAAAUAGGCACUGAGAGCGCAUCCUGAAAACUUUUAGCGAAAUAGUCUUUCUCUAAAUUGUAUCCGAGCUACAUA
.....((((((((.(((((((..(((........)))..))))))).)))).))))((.((..((.....(((((.((((.....)))).))))).....)).))))...... ( -25.00)
>consensus
CCUAUGCUCCGGUCCCUAUUUCCUUUCCUACACUGAAAUAAAUAGGCACCGAGAGCGCAUCCUAAAAACUUU__GC_AA_UAG_C_U_CUCAAACUUGGAAGCGAACUACACA
.....((((((((.(((((((..(((........)))..))))))).)))).))))......................................................... (-15.78 = -15.86 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:02 2006