Locus 5309

Sequence ID	3L_DroMel_CAF1
Location	14,669,521 – 14,669,813
Length	292
Max. P	0.931605

overview

Window 2

Location	14,669,521 – 14,669,641
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.72
Mean single sequence MFE	-26.30
Consensus MFE	-24.95
Energy contribution	-24.82
Covariance contribution	-0.14
Combinations/Pair	1.03
Mean z-score	-1.20
Structure conservation index	0.95
SVM decision value	1.21
SVM RNA-class probability	0.931605
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14669521 120 - 23771897
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCAAUCCCAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
......((((....).)))((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... ( -26.70)
>DroSec_CAF1 19287 120 - 1
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCAAUCCCAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
......((((....).)))((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... ( -26.70)
>DroSim_CAF1 20141 120 - 1
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCAAUCCCAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
......((((....).)))((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... ( -26.70)
>DroEre_CAF1 19772 120 - 1
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCGAUCACAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
......((((....).)))((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... ( -26.70)
>DroYak_CAF1 20019 120 - 1
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCGAUCCCAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
......((((....).)))((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... ( -26.70)
>DroAna_CAF1 16892 120 - 1
AUCAUUCAACUGACGCUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUUCGAUCCCCACACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUCC
...................((((((((..((((...(((....)))...)))).......((..(((..........(......).(((((....))))))))..)).)))))))).... ( -24.30)
>consensus
AUCAUUGCACGAACGUUGCUAAGCCGACUAUGCAAAUUGAAGUCAAGAGGCAUUAAGUCCAAUCCCAAAACUAAAACGCUACUCCAUGACACAAUUGUCAGGGUUUUAUCGGCUUAUUUC
...................((((((((((((((...(((....)))...))))..))))............((((((......((.(((((....)))))))))))))..)))))).... (-24.95 = -24.82 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	14,669,641 – 14,669,737
Length	96
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	90.36
Mean single sequence MFE	-16.86
Consensus MFE	-14.18
Energy contribution	-13.66
Covariance contribution	-0.52
Combinations/Pair	1.13
Mean z-score	-1.56
Structure conservation index	0.84
SVM decision value	0.71
SVM RNA-class probability	0.828761
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14669641 96 - 23771897
UCAUCGGUUUAACUUUUCUUCCGUUUCCUCCGAC----CGGAAAAAGCUCUUCCUUAGCUGUCAACUGGUAAAUGCCGAAUUCUAUCAAUUUGUCAUUCA
....(((...(((.........)))....)))((----(((....((((.......)))).....))))).((((.((((((.....)))))).)))).. ( -15.50)
>DroSec_CAF1 19407 96 - 1
UCAUCGGUUUAACUUUUCUUCCGUUUCCUCCGAC----CGGAAAAAGCUUUUCCUUAGCUGUCAACUGCUAAAUGCCGAAUUCUAUCAAUUCGUCAUUCA
...((((...(((.........)))....)))).----.(((((.....))))).((((........))))((((.((((((.....)))))).)))).. ( -17.70)
>DroSim_CAF1 20261 96 - 1
UCAUCGGUUUAACUUUUCUUCCGUUUCCUCCGAC----CGGAAAAUGCUUUUCCUUAGCUGUCAACUGCUAAAUGCCGAAUUCUAUCAAUUCGUCAUUCA
...((((...(((.........)))....)))).----.(((((.....))))).((((........))))((((.((((((.....)))))).)))).. ( -17.70)
>DroEre_CAF1 19892 95 - 1
UCAUCAGUUUAACUUUCCCUCCGUUUCCUCCGUC----CGGAA-AAGCUUUUCCUUAGCUGUCAACUGGUAAGUGCCGAAUUCUAUCAAUUUGUCAUUCA
..(((((((..............(((((......----.))))-)((((.......))))...))))))).((((.((((((.....)))))).)))).. ( -16.20)
>DroYak_CAF1 20139 97 - 1
GCAUCAGUUUAA--UUCCUUCCGCUUUCUCCGUCUCACCGGAA-AAGCUUUUCCCUAGCUGUCAACUGCUAAGUGCCGAAUUCUAUCAAUUUGUCAUUCA
((((........--........(((((.((((......)))))-)))).......((((........)))).))))((((((.....))))))....... ( -17.20)
>consensus
UCAUCGGUUUAACUUUUCUUCCGUUUCCUCCGAC____CGGAAAAAGCUUUUCCUUAGCUGUCAACUGCUAAAUGCCGAAUUCUAUCAAUUUGUCAUUCA
....(((((...................((((......))))...((((.......))))...)))))...((((.((((((.....)))))).)))).. (-14.18 = -13.66 +  -0.52)

alignment

secondary structure

dotplot

Window 4

Location	14,669,716 – 14,669,813
Length	97
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	82.85
Mean single sequence MFE	-14.70
Consensus MFE	-9.18
Energy contribution	-9.46
Covariance contribution	0.28
Combinations/Pair	1.32
Mean z-score	-2.03
Structure conservation index	0.62
SVM decision value	0.39
SVM RNA-class probability	0.716208
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14669716 97 - 23771897
UAGGCAAAUGAAAAGUCCUUUUUAACCGGCACGAUAAUUAAAUCAUGCUCAAACAGAAUU-UGAACUGAAAUCUCCAUCAUCGGUUUAACUUUUCUUC
.........(((((((...........((((.(((......))).))))...........-((((((((...........)))))))))))))))... ( -16.40)
>DroSec_CAF1 19482 97 - 1
UAAGCAAAUGAAAAAUUUUAUUUAACCGGUAUGAUAAAUAAAUCAUGCUCAAACAGAAUU-UGAACUGAAAUCUGCAUCAUCGGUUUAACUUUUCUUC
(((((..((((................((((((((......))))))))....((((.((-(.....))).))))..))))..))))).......... ( -17.00)
>DroSim_CAF1 20336 97 - 1
UAAGCAAAUGAAAAAUCUUAUUUAACCGGUACGAUAAUUAAAUCAUGCUCAAACAGAAUU-UGAACUGAAAUCUCCAUCAUCGGUUUAACUUUUCUUC
..(((((((((......)))))).........(((......)))..))).....((((.(-((((((((...........)))))))))...)))).. ( -11.70)
>DroEre_CAF1 19966 97 - 1
UAAACAAAUGAAAUAUCAUAUUAAACCAUCAUGAUAAUUAAAUCGUGCUCAAACAGAAUU-UCAACUGAAAUCGCCAUCAUCAGUUUAACUUUCCCUC
(((((..((((..................((((((......))))))........((.((-((....))))))....))))..))))).......... ( -11.60)
>DroYak_CAF1 20217 84 - 1
UAAACAAA------------UUUAACCAUCACGAUAAUUAAAUGGUGCUCAAAGAGAAUUCUCAACUGAAAUCUCCAGCAUCAGUUUAA--UUCCUUC
........------------...............((((((((((((((....((((.(((......))).)))).))))))).)))))--))..... ( -16.80)
>consensus
UAAGCAAAUGAAAAAUCUUAUUUAACCGGCACGAUAAUUAAAUCAUGCUCAAACAGAAUU_UGAACUGAAAUCUCCAUCAUCGGUUUAACUUUUCUUC
...........................((((((((......))))))))......(((...((((((((...........))))))))...))).... ( -9.18 =  -9.46 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:57 2006