Locus 5765

Sequence ID	3L_DroMel_CAF1
Location	15,635,988 – 15,636,148
Length	160
Max. P	0.950883

overview

Window 5

Location	15,635,988 – 15,636,108
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-41.45
Consensus MFE	-33.39
Energy contribution	-34.45
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-1.97
Structure conservation index	0.81
SVM decision value	0.25
SVM RNA-class probability	0.654660
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15635988 120 - 23771897
CAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGGACAAGGGGCAAUGCAGCACAGGUCGCGAUUGUACACUAAG
........((.(((((((((..(((((((.....))((((....))))...)))))(((((((....)))))))..........)))))..(((.((....)).)))......)))).)) ( -43.10)
>DroSec_CAF1 58096 120 - 1
CAAAAUCACUAAGUGGACCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGGACAAGGGGCAAUACAGCACAGGUCGCGAUUGUACACUCAG
........((.((((..(((..(((((((.....))((((....))))...)))))(((((((....)))))))..........)))(((((...((.......)).))))).)))).)) ( -38.90)
>DroSim_CAF1 59063 120 - 1
CAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGUUCAAUGAUCAUCAGGACAAGGGGCACUCCAGCACAGGUCGCGAUUGUACACUCAG
........((.(((((((((..(((((((.....))((((....))))...)))))(((((((....)))))))..........)))))((....((.......))....)).)))).)) ( -41.70)
>DroYak_CAF1 63009 116 - 1
CAAAAUCACUAAGUGGCCCUGAGUGCCGCAGGUAG---CCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCGGGACAAGGG-CCAUCCAGCACAGGUCGCGAUUGUACACUUAG
........(((((((..((((((((((.(.....(---((....)))..).)))))(((((((....))))))).)))))((((..(-(...((......))..))..)))).))))))) ( -42.10)
>consensus
CAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGGACAAGGGGCAAUCCAGCACAGGUCGCGAUUGUACACUCAG
........((.(((((((((..(((((.(......(((((....)))))).)))))(((((((....)))))))..........)))))......((.......)).......)))).)) (-33.39 = -34.45 +   1.06)

alignment

secondary structure

dotplot

Window 6

Location	15,636,028 – 15,636,148
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-42.17
Consensus MFE	-38.85
Energy contribution	-39.35
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.92
SVM decision value	1.41
SVM RNA-class probability	0.950883
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15636028 120 + 23771897
CCUGAUGAUCAUUGAUCAAUGAUCGUGCCUCCUGCCGUCUGGCAGCUACCUGCGGCACUCGGGGCCACUUAGUGAUUUUGGCCGUUGUUUGUUGACCUGGCCAAACAGCUGCCACUACUU
(((((.(((((((....)))))))(((((...((((....))))((.....)))))))))))).......((((....((((.((((((((..........)))))))).)))).)))). ( -43.80)
>DroSec_CAF1 58136 120 + 1
CCUGAUGAUCAUUGAUCAAUGAUCGUGCCUCCUGCCGUCUGGCAGCUACCUGCGGCACUCGGGUCCACUUAGUGAUUUUGGCCGUUGUUUGUUGACCAUGCCAAACAGCUGCCACUACUU
(((((.(((((((....)))))))(((((...((((....))))((.....)))))))))))).......((((....((((.((((((((..........)))))))).)))).)))). ( -43.10)
>DroSim_CAF1 59103 120 + 1
CCUGAUGAUCAUUGAACAAUGAUCGUGCCUCCUGCCGUCUGGCAGCUACCUGCGGCACUCGGGGCCACUUAGUGAUUUUGGCCGUUGUUUGUUGACCAGGCCAAACAGCUGCCACUACUU
(((((.(((((((....)))))))(((((...((((....))))((.....))))))))))))......((((...(((((((...(((....)))..)))))))..))))......... ( -43.80)
>DroYak_CAF1 63048 117 + 1
CCCGAUGAUCAUUGAUCAAUGAUCGUGCCUCCUGCCGUCUGG---CUACCUGCGGCACUCAGGGCCACUUAGUGAUUUUGGCCGUUGUUUGUUGACCAGGCCAAACAGCUGCCACUACUU
....(((((((((....)))))))))((((..((((((..((---...)).))))))....))))....((((...(((((((...(((....)))..)))))))..))))......... ( -38.00)
>consensus
CCUGAUGAUCAUUGAUCAAUGAUCGUGCCUCCUGCCGUCUGGCAGCUACCUGCGGCACUCGGGGCCACUUAGUGAUUUUGGCCGUUGUUUGUUGACCAGGCCAAACAGCUGCCACUACUU
....(((((((((....)))))))))(((((.((((((..((......)).))))))...))))).....((((....((((.((((((((..........)))))))).)))).)))). (-38.85 = -39.35 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	15,636,028 – 15,636,148
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-41.92
Consensus MFE	-37.55
Energy contribution	-38.05
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.90
SVM decision value	0.75
SVM RNA-class probability	0.841395
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15636028 120 - 23771897
AAGUAGUGGCAGCUGUUUGGCCAGGUCAACAAACAACGGCCAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGG
..((..((((((((((((((((..((......))...)))))))........(((((.......)))))...))))))))).)).((.....))..(((((((....)))))))...... ( -43.10)
>DroSec_CAF1 58136 120 - 1
AAGUAGUGGCAGCUGUUUGGCAUGGUCAACAAACAACGGCCAAAAUCACUAAGUGGACCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGG
.....(((.(.((((((((((((((((..........)))))......(((.((((((....)).))))...))).)))))))))))....).)))(((((((....)))))))...... ( -40.50)
>DroSim_CAF1 59103 120 - 1
AAGUAGUGGCAGCUGUUUGGCCUGGUCAACAAACAACGGCCAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGUUCAAUGAUCAUCAGG
..((..((((((((((((((((..((......))...)))))))........(((((.......)))))...))))))))).)).((.....))..(((((((....)))))))...... ( -43.10)
>DroYak_CAF1 63048 117 - 1
AAGUAGUGGCAGCUGUUUGGCCUGGUCAACAAACAACGGCCAAAAUCACUAAGUGGCCCUGAGUGCCGCAGGUAG---CCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCGGG
.....(((.(.((((((((((.(((((..........)))))..........(((((.......))))).....)---)))))))))....).)))(((((((....)))))))...... ( -41.00)
>consensus
AAGUAGUGGCAGCUGUUUGGCCUGGUCAACAAACAACGGCCAAAAUCACUAAGUGGCCCCGAGUGCCGCAGGUAGCUGCCAGACGGCAGGAGGCACGAUCAUUGAUCAAUGAUCAUCAGG
.....(((.(.((((((((((..((((..........))))...........(((((.......)))))........))))))))))....).)))(((((((....)))))))...... (-37.55 = -38.05 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:19 2006