Locus 5681

Sequence ID	3L_DroMel_CAF1
Location	15,564,653 – 15,564,790
Length	137
Max. P	0.784580

overview

Window 4

Location	15,564,653 – 15,564,751
Length	98
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	86.17
Mean single sequence MFE	-24.38
Consensus MFE	-18.56
Energy contribution	-18.56
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.74
Structure conservation index	0.76
SVM decision value	0.36
SVM RNA-class probability	0.704932
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15564653 98 + 23771897
--CCCCCACUUCACCCCCCCUC-CCCCCAUCGACUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUG-UUGUGU
--.........(((.....(((-.((((((((.....))).......(((((..(((((((........)))))))..)))))))))).)))...-..))). ( -24.70)
>DroSec_CAF1 27034 92 + 1
--CCCCCACUUCGCC-------CCCCCCAUCGUCUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUG-UUGUUU
--.............-------.....((((.((((((.(.......(((((..(((((((........)))))))..)))))).))))))))))-...... ( -22.31)
>DroSim_CAF1 27501 99 + 1
--CCCCCACUUCGACCCCCAUCCCCCCCAUCGUCUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUG-UUGUUU
--..........(((...(((((.(((((...((....)).......(((((..(((((((........)))))))..)))))))))).).))))-..))). ( -23.90)
>DroEre_CAF1 27323 86 + 1
AGCCCCCACUUCG-------------CCAUCUCCUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUGGUUG---
............(-------------(((((((((((..........(((((..(((((((........)))))))..))))).)))).))))))))..--- ( -27.90)
>DroYak_CAF1 47571 85 + 1
AGCCCCCACUUCG-------------CCAUCUCCUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUG-UUG---
.............-------------.((((((((((..........(((((..(((((((........)))))))..))))).)))).))))))-...--- ( -23.10)
>consensus
__CCCCCACUUCG_C________CCCCCAUCGCCUCCUGAAUUUAUUGUUGGAUCUUGAAGUUUUCACUUUUUAAGCGCCAGCUGGGGAGAGAUG_UUGU_U
...(((((.....................((.......)).......(((((..(((((((........)))))))..)))))))))).............. (-18.56 = -18.56 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	15,564,690 – 15,564,790
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	94.22
Mean single sequence MFE	-10.28
Consensus MFE	-9.62
Energy contribution	-10.02
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.94
SVM decision value	0.57
SVM RNA-class probability	0.784580
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15564690 100 - 23771897
AAUCAAUUAAUGCUUUUUAAAAGCAACACUCGCAGCACA-ACACAA-CAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
.(((......(((((.....))))).((((((((((...-......-............))).))).......))))..........)))............ ( -11.21)
>DroSec_CAF1 27065 101 - 1
AAUCAAUUAAUGCUUUUUAAAAGCAACACUCGCACAACACAAACAA-CAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
..........(((((.....))))).....................-............(.(((..(((...((((....)))).)))..))).)....... ( -10.50)
>DroSim_CAF1 27539 101 - 1
AAUCAAUUAAUGCUUUUUAAAAGCAACACUCGCACAACACAAACAA-CAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
..........(((((.....))))).....................-............(.(((..(((...((((....)))).)))..))).)....... ( -10.50)
>DroEre_CAF1 27350 94 - 1
AAUCAAUUAAUGCU--UUAAAAGCAACACUCGCA--ACA----CAACCAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
..........((((--.....)))).........--...----................(.(((..(((...((((....)))).)))..))).)....... (  -9.60)
>DroYak_CAF1 47598 93 - 1
AAUCAAUUAAUGCU--UUAAAAGCAACACUCGCA--ACA----CAA-CAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
..........((((--.....)))).........--...----...-............(.(((..(((...((((....)))).)))..))).)....... (  -9.60)
>consensus
AAUCAAUUAAUGCUUUUUAAAAGCAACACUCGCA__ACA_A_ACAA_CAUCUCUCCCCAGCUGGCGCUUAAAAAGUGAAAACUUCAAGAUCCAACAAUAAAU
..........(((((.....)))))..................................(.(((..(((...((((....)))).)))..))).)....... ( -9.62 = -10.02 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:29 2006