Locus 3534

Sequence ID	2L_DroMel_CAF1
Location	10,317,954 – 10,318,070
Length	116
Max. P	0.955601

overview

Window 8

Location	10,317,954 – 10,318,070
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.87
Mean single sequence MFE	-32.87
Consensus MFE	-22.67
Energy contribution	-23.32
Covariance contribution	0.64
Combinations/Pair	1.29
Mean z-score	-2.66
Structure conservation index	0.69
SVM decision value	1.46
SVM RNA-class probability	0.955601
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10317954 116 + 22407834
CUUCUUCUUCCUCAUCCUCGGCGUGGGCGUGGAAUUCGAUUCCCGUUCCGCCGAUAGGGAAGAUC---UAUAGCGAUCGUUUGUGGGUC-UCUCCUCAUAUCUUAAUCUUACAUUAUUUU
.................((((((.(((((.(((((...)))))))))))))))).(((..(((((---((((((....).)))))))))-)..)))........................ ( -36.40)
>DroSec_CAF1 3703 116 + 1
CUUCUUCUUCCUCAUCCUCGGCGUGGGCGUGGAAUUCGAUUCCCGUUCCGCCGAUAUGGAAGAUC---UAUUGCGAUCGUUUGUAGGUC-UCUCCUCAUACCUUAAUCUUACAUUAUUUU
.................((((((.(((((.(((((...))))))))))))))))...((((((((---(((.((....))..)))))))-).)))......................... ( -33.90)
>DroSim_CAF1 2483 116 + 1
CUUCUUCUUCCUCAUCCUCGGCGUGGGCGUGGAAUUCGAUUCCCGUUCCGCCGAUAUGGAAGAUC---UAUAGCGAUCGUUUGUAGGUC-UCUCCUCAUAUCUUAAUCUUACAUUAUUGU
.................((((((.(((((.(((((...))))))))))))))))...((((((((---((((((....).)))))))))-).)))......................... ( -34.40)
>DroEre_CAF1 2643 110 + 1
CUUCUUCUUCCUCAUCCUCGGCGUGGGCGUAGAAUUUGAUUCCCGUUCCGUCGAUAUGGAAGAUC---UGUUGCGAUCGUUUGUGGGUC-UCUCACCAUAU------CUUACAUUAUUUU
.....((((((..(((..(((..((((.((........)).))))..)))..)))..))))))..---..........((.(((((...-.....))))).------...))........ ( -27.80)
>DroYak_CAF1 2589 110 + 1
CUUCUUCUUCCGCAUCCUCGGCGUGGGCGUGGAAUUUGAUUCCCGUUCCGCCGAUAUGGAAGAUC---UAUAGCGUUCGCUUGUGGGUC-UCUCACGAUAU------CUUACAUUAUUUU
.............(((.((((((.(((((.(((((...))))))))))))))))..((..(((((---((((((....)).))))))))-)..)).)))..------............. ( -36.50)
>DroAna_CAF1 2101 110 + 1
UUUCUUCUUCCUCAUCCUAGGUGUGGGUGUAGCAUUGGAGUCUUGCUCCUCUGACAUGGAUAAUGCCAUAAUGCGACCGAAACCACACCGACUCCGAAUAAC------UGGC----CUUU
...................(((((((.((..(((((((((.....))))......((((......)))))))))...))...)))))))....(((......------))).----.... ( -28.20)
>consensus
CUUCUUCUUCCUCAUCCUCGGCGUGGGCGUGGAAUUCGAUUCCCGUUCCGCCGAUAUGGAAGAUC___UAUAGCGAUCGUUUGUAGGUC_UCUCCUCAUAUC_____CUUACAUUAUUUU
.....((((((......((((((.(((((.(((((...))))))))))))))))...))))))..................((((((....................))))))....... (-22.67 = -23.32 +   0.64)

alignment

secondary structure

dotplot

Window 9

Location	10,317,954 – 10,318,070
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.87
Mean single sequence MFE	-28.66
Consensus MFE	-18.58
Energy contribution	-18.52
Covariance contribution	-0.05
Combinations/Pair	1.19
Mean z-score	-1.32
Structure conservation index	0.65
SVM decision value	-0.02
SVM RNA-class probability	0.522346
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10317954 116 - 22407834
AAAAUAAUGUAAGAUUAAGAUAUGAGGAGA-GACCCACAAACGAUCGCUAUA---GAUCUUCCCUAUCGGCGGAACGGGAAUCGAAUUCCACGCCCACGCCGAGGAUGAGGAAGAAGAAG
.......((((.((((......((.((...-..)))).....))))..))))---..(((((((..(((((((..(((((((...))))).))..).))))))....).))))))..... ( -28.80)
>DroSec_CAF1 3703 116 - 1
AAAAUAAUGUAAGAUUAAGGUAUGAGGAGA-GACCUACAAACGAUCGCAAUA---GAUCUUCCAUAUCGGCGGAACGGGAAUCGAAUUCCACGCCCACGCCGAGGAUGAGGAAGAAGAAG
............((((...((.(((((...-..))).)).))))))......---..((((((...(((((((..(((((((...))))).))..).))))))......))))))..... ( -29.20)
>DroSim_CAF1 2483 116 - 1
ACAAUAAUGUAAGAUUAAGAUAUGAGGAGA-GACCUACAAACGAUCGCUAUA---GAUCUUCCAUAUCGGCGGAACGGGAAUCGAAUUCCACGCCCACGCCGAGGAUGAGGAAGAAGAAG
.......((((.((((........(((...-..)))......))))..))))---..((((((...(((((((..(((((((...))))).))..).))))))......))))))..... ( -28.54)
>DroEre_CAF1 2643 110 - 1
AAAAUAAUGUAAG------AUAUGGUGAGA-GACCCACAAACGAUCGCAACA---GAUCUUCCAUAUCGACGGAACGGGAAUCAAAUUCUACGCCCACGCCGAGGAUGAGGAAGAAGAAG
.......(((..(------((...(((...-....))).....)))...)))---..((((((.((((..(((...(((..............)))...)))..)))).))))))..... ( -24.44)
>DroYak_CAF1 2589 110 - 1
AAAAUAAUGUAAG------AUAUCGUGAGA-GACCCACAAGCGAACGCUAUA---GAUCUUCCAUAUCGGCGGAACGGGAAUCAAAUUCCACGCCCACGCCGAGGAUGCGGAAGAAGAAG
.......(((...------...((....))-.....)))(((....)))...---..((((((...(((((((..(((((((...))))).))..).))))))......))))))..... ( -30.00)
>DroAna_CAF1 2101 110 - 1
AAAG----GCCA------GUUAUUCGGAGUCGGUGUGGUUUCGGUCGCAUUAUGGCAUUAUCCAUGUCAGAGGAGCAAGACUCCAAUGCUACACCCACACCUAGGAUGAGGAAGAAGAAA
....----.((.------.((((((......(((((((.....((.(((((.((((((.....))))))..((((.....))))))))).))..)))))))..))))))))......... ( -31.00)
>consensus
AAAAUAAUGUAAG_____GAUAUGAGGAGA_GACCCACAAACGAUCGCAAUA___GAUCUUCCAUAUCGGCGGAACGGGAAUCGAAUUCCACGCCCACGCCGAGGAUGAGGAAGAAGAAG
.........................................................((((((.((((..(((...(((..............)))...)))..)))).))))))..... (-18.58 = -18.52 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:48 2006