Locus 6246

Sequence ID	3L_DroMel_CAF1
Location	16,614,599 – 16,614,746
Length	147
Max. P	0.995281

overview

Window 5

Location	16,614,599 – 16,614,712
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	88.79
Mean single sequence MFE	-30.30
Consensus MFE	-27.04
Energy contribution	-28.85
Covariance contribution	1.81
Combinations/Pair	1.09
Mean z-score	-2.90
Structure conservation index	0.89
SVM decision value	2.56
SVM RNA-class probability	0.995281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16614599 113 + 23771897
UAGGAAAACAGUUCUCCAGUAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCAAGUAUCGCAAACUGUGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUG
.((((...(((..((((.(.((((........))))).........(((((...(((...((((((((.....))))))))...)))...))))))))).))).))))..... ( -28.70)
>DroSim_CAF1 21880 113 + 1
UAGGAAAACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCGAGUAUCGCAUACUGUGUGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUG
.((((...(((..((((.(.((((........))))).........(((((...(((.(..((((((((...))))))))..).)))...))))))))).))).))))..... ( -28.80)
>DroEre_CAF1 22643 113 + 1
UUGGAAAACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAGAUUGCCUGUCGUUUGAGUAUCGCAUACAGAGCGAUAUUUACACUAAAGGCAGGAGUCUGAUCCUUCUUG
..(((...(((..((((..................((......)).(((((...((.((((((((((.......)))))))))).))...))))))))).))).)))...... ( -31.20)
>DroYak_CAF1 22822 113 + 1
CUGGAAAACAGUUUUCCAGCAAAUCAAAUUCUAUUUCAACCAAGAAUGCCCGACGUUUGAUUAUCGCAUACAAAGCGAUAUUGAAACUUUAGGCAGGAGUCUGAUCCUUCUUG
(((((((.....))))))).....................((((((((((..(.((((.(.((((((.......)))))).).)))).)..))))(((......))))))))) ( -32.50)
>consensus
UAGGAAAACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCGAGUAUCGCAUACAGAGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUG
..(((...(((..((((.(.((((........))))).........(((((...(((((((((((((.......)))))))))))))...))))))))).))).)))...... (-27.04 = -28.85 +   1.81)

alignment

secondary structure

dotplot

Window 6

Location	16,614,599 – 16,614,712
Length	113
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	88.79
Mean single sequence MFE	-31.18
Consensus MFE	-27.67
Energy contribution	-28.18
Covariance contribution	0.50
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.89
SVM decision value	1.35
SVM RNA-class probability	0.944991
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16614599 113 - 23771897
CAAGAAGGAUCAGACUCCUGCCUUCAGUUUGGAUAUCGCACAGUUUGCGAUACUUGAACGACAGGCAUUUUUGGUUGAAAUUGAAUUUGAUUUACUGGAGAACUGUUUUCCUA
.....((((.(((.(((((((((...(((..(.(((((((.....))))))).)..)))...))))).....(((..((......))..)))....))))..)))...)))). ( -34.00)
>DroSim_CAF1 21880 113 - 1
CAAGAAGGAUCAGACUCCUGCCUUCAGUUUGGAUAUCACACAGUAUGCGAUACUCGAACGACAGGCAUUUUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUUUUCCUA
.....((((.(((.(((((((((...(((((..((((.((.....)).))))..)))))...))))).....(((..(((((......))))))))))))..)))...)))). ( -31.20)
>DroEre_CAF1 22643 113 - 1
CAAGAAGGAUCAGACUCCUGCCUUUAGUGUAAAUAUCGCUCUGUAUGCGAUACUCAAACGACAGGCAAUCUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUUUUCCAA
......(((.(((.(((((((((...((.....((((((.......)))))).....))...))))).....(((..(((((......))))))))))))..)))...))).. ( -28.30)
>DroYak_CAF1 22822 113 - 1
CAAGAAGGAUCAGACUCCUGCCUAAAGUUUCAAUAUCGCUUUGUAUGCGAUAAUCAAACGUCGGGCAUUCUUGGUUGAAAUAGAAUUUGAUUUGCUGGAAAACUGUUUUCCAG
(((((((((......)))(((((...((((.(.((((((.......)))))).).))))...)))))))))))((..((......))..))...(((((((.....))))))) ( -31.20)
>consensus
CAAGAAGGAUCAGACUCCUGCCUUCAGUUUGAAUAUCGCACAGUAUGCGAUACUCAAACGACAGGCAUUCUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUUUUCCAA
......(((.(((.(((((((((...((((((.((((((.......)))))).))))))...))))).....(((..((......))..)))....))))..)))...))).. (-27.67 = -28.18 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	16,614,639 – 16,614,746
Length	107
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	72.49
Mean single sequence MFE	-27.37
Consensus MFE	-8.39
Energy contribution	-9.97
Covariance contribution	1.59
Combinations/Pair	1.16
Mean z-score	-2.08
Structure conservation index	0.31
SVM decision value	0.07
SVM RNA-class probability	0.568845
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16614639 107 + 23771897
CAAAAAUGCCUGUC--GUUCAAGUAUCGCAAACUGUGCGAUAUCCAAACUGAAGGCAGG-----AGUCUGAUCCUUCUUGAGAAUUU-UAACUAAAAUUGGGAGGCAACACAAAA
......(((((.((--(.....((((((((.....)))))))).....((.((((.(((-----(......)))))))).)).....-..........))).)))))........ ( -28.80)
>DroPse_CAF1 24259 99 + 1
------CGCCUAUUCUGCCUGAAUAUCU-AUAU---CCCUUAGAUACACUAGAGGGGGGUACAGCGUGU----GUUCUUGAGAAUUUCUAACUA-ACUUAGGAGGCAACACAA-A
------.(((((((((.(..((((((((-.(((---(((((((.....)))...))))))).))...))----))))..)))))).(((((...-..))))))))).......-. ( -23.50)
>DroSim_CAF1 21920 107 + 1
CAAAAAUGCCUGUC--GUUCGAGUAUCGCAUACUGUGUGAUAUCCAAACUGAAGGCAGG-----AGUCUGAUCCUUCUUGAGAAUUU-UAACUAAAAUUGGGAGGCAACACAAAA
......(((((.((--(...(..((((((((...))))))))..)...((.((((.(((-----(......)))))))).)).....-..........))).)))))........ ( -28.70)
>DroEre_CAF1 22683 107 + 1
CAAGAUUGCCUGUC--GUUUGAGUAUCGCAUACAGAGCGAUAUUUACACUAAAGGCAGG-----AGUCUGAUCCUUCUUGAGAAUUU-UAACUAAAAUUGGGAGGCAACACAAAA
..(((((.((((((--((.((((((((((.......)))))))))).))....))))))-----)))))...((((((....(((((-(....)))))))))))).......... ( -30.30)
>DroYak_CAF1 22862 107 + 1
CAAGAAUGCCCGAC--GUUUGAUUAUCGCAUACAAAGCGAUAUUGAAACUUUAGGCAGG-----AGUCUGAUCCUUCUUGAGAAUUU-UAACUAAAAUUGGGAGGCAACACAAAA
((((((((((..(.--((((.(.((((((.......)))))).).)))).)..))))((-----(......)))))))))..(((((-(....))))))....(....)...... ( -27.90)
>DroPer_CAF1 35145 99 + 1
------CGCCUAUUCUGCCUGAAUAUCU-AUAU---CCCUUAGAUACACUAGAGGGGGGUACAGCGUGU----GUUCAUGAGAAUUUCUAACUA-ACUUAGGAGGCAACACAA-A
------.(((((((((.(.(((((((((-.(((---(((((((.....)))...))))))).))...))----))))).)))))).(((((...-..))))))))).......-. ( -25.00)
>consensus
CAA_AAUGCCUGUC__GUUUGAGUAUCGCAUAC_G_GCGAUAUAUAAACUAAAGGCAGG_____AGUCUGAUCCUUCUUGAGAAUUU_UAACUAAAAUUGGGAGGCAACACAAAA
......(((((............((((((.......))))))..........)))))................((((((((................)))))))).......... ( -8.39 =  -9.97 +   1.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:40 2006