Locus 5436

Sequence ID	2R_DroMel_CAF1
Location	17,489,088 – 17,489,315
Length	227
Max. P	0.924157

overview

Window 2

Location	17,489,088 – 17,489,200
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.66
Mean single sequence MFE	-34.98
Consensus MFE	-29.11
Energy contribution	-29.92
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-2.10
Structure conservation index	0.83
SVM decision value	1.16
SVM RNA-class probability	0.924157
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17489088 112 + 20766785
ACAAAUCAAAUUUAAUCAAGCUCUCAGGAAGUCAGGCCCCCGGGCUGGAUUUGGUCAUUAAGUCUGGCCUGUGGGGCA--------CAAUACUAUCCGAUUUAACCAACCCACUGCGACU
..........................((((((...((((((((((..((((((.....))))))..))))).))))).--------....))).)))....................... ( -34.00)
>DroSec_CAF1 16904 112 + 1
ACAAAUCAAAUUUAAUCAAGCUUUCAGGAAGUCAGGCCCCCGGGAUGGAUUUGGUCAUUAAGUCUGGCCUGUGGGGCA--------CAAUACUAUCCGAUUUGCCCAACCCACUGCGAUU
.((((((............(....).((((((...(((((((((..(((((((.....)))))))..)))).))))).--------....))).)))))))))................. ( -30.00)
>DroSim_CAF1 29763 108 + 1
ACAAAUCAAAUUUAAUCAAGCUCUCAGGAAGUCAGGCCCCCGGGCUGGAUUUGGUCAUUAAGUCUGGCCUGUGGGGCA--------CAAUACUAUCCGAUUGGCCCAA----UUGCGAUU
...................(((....((((((...((((((((((..((((((.....))))))..))))).))))).--------....))).)))....)))....----........ ( -36.70)
>DroYak_CAF1 25922 120 + 1
ACAAAUCAAAUUUAAUCAAGCUCGCAGGAAGUCAUGCCCCCGGGCUGGAUUUGGUCAUUAAGUCUGGCCUGCGGGGCAGAAUGCUACAAUACUAUCCGAUUGGCCCAAACCACUCCGAUU
.......................(((.....((.(((((((((((..((((((.....))))))..))))).)))))))).))).........(((.((.(((......))).)).))). ( -39.20)
>consensus
ACAAAUCAAAUUUAAUCAAGCUCUCAGGAAGUCAGGCCCCCGGGCUGGAUUUGGUCAUUAAGUCUGGCCUGUGGGGCA________CAAUACUAUCCGAUUGGCCCAACCCACUGCGAUU
.((((((............((((....).)))...((((((((((((((((((.....))))))))))))).)))))....................))))))................. (-29.11 = -29.92 +   0.81)

alignment

secondary structure

dotplot

Window 3

Location	17,489,200 – 17,489,315
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-32.68
Consensus MFE	-25.58
Energy contribution	-26.08
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.78
SVM decision value	0.13
SVM RNA-class probability	0.596526
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17489200 115 + 20766785
GUGUUC-----CUUUCUACCCGUGUGGUUCGAUAUUCCUCGACGGCUUUUUGUAUUAAUUCCAAUUAUACGCACGACUGGGGAAUUUCCAUUUGGGUUGAAAGGAUUUUGGGUCAUUAUG
....((-----(((((.(((((.((((......((((((((.((((.....((((...........)))))).))..))))))))..)))).))))).)))))))............... ( -32.70)
>DroSec_CAF1 17016 113 + 1
--GUUC-----CUUUCUACCCGUGUGGUUCGAUAUUCCUCGACGGCUUUUUGUAUUAAUUCCAAUUAUACGCACGACUGGGGAAUUUCCAUUUGGGUUGAAAGGAUUUCGGGUCAUUAUG
--..((-----(((((.(((((.((((......((((((((.((((.....((((...........)))))).))..))))))))..)))).))))).)))))))............... ( -32.70)
>DroSim_CAF1 29871 113 + 1
--GUUC-----CUUUCUACCCGUGUGGUUCGAUAUUCCUCGACGGCUUUUUGUAUUAAUUCCAAUUAUACGCACGACUGGGGAAUUUCCAUUUGGGUUGAAAGGAUUUCGGGUCAUUAUG
--..((-----(((((.(((((.((((......((((((((.((((.....((((...........)))))).))..))))))))..)))).))))).)))))))............... ( -32.70)
>DroYak_CAF1 26042 118 + 1
--GUUCCUUUCCUUUCGCCCCGUGUGGUUCGAUAUUCCUCUACUGCUUUUUGUAUUAAUUCCAAUUAUACGCACGACUGGGGAAUUUCCAUUUGGGUUGAAAGGAUUUCGGGUCAUUAUG
--(..((..((((((((.((((.((((......(((((((..((((.....((((...........))))))).)...)))))))..)))).)))).))))))))....))..)...... ( -32.60)
>consensus
__GUUC_____CUUUCUACCCGUGUGGUUCGAUAUUCCUCGACGGCUUUUUGUAUUAAUUCCAAUUAUACGCACGACUGGGGAAUUUCCAUUUGGGUUGAAAGGAUUUCGGGUCAUUAUG
...........(((((.(((((.((((......(((((((..((((.....((((...........)))))).))...)))))))..)))).))))).)))))(((.....)))...... (-25.58 = -26.08 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:48 2006