Locus 3518

Sequence ID	3L_DroMel_CAF1
Location	10,317,224 – 10,317,318
Length	94
Max. P	0.716857

overview

Window 3

Location	10,317,224 – 10,317,318
Length	94
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	80.19
Mean single sequence MFE	-22.49
Consensus MFE	-13.71
Energy contribution	-14.77
Covariance contribution	1.06
Combinations/Pair	1.10
Mean z-score	-1.83
Structure conservation index	0.61
SVM decision value	0.38
SVM RNA-class probability	0.711178
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10317224 94 + 23771897
CAAGUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUC-------UGGGACCAAAACCGAGUUGCAUCUCAAUUUGCUUCAACCUGCAAC-UGCAAUUC----
.......((((..((((....(((((((.............-------.((........))(((......)))..))))))).....))))..-))))....---- ( -20.70)
>DroSec_CAF1 191657 94 + 1
UAAGUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUC-------UGGGACCAAAUCCGAGUUGCAUCUCAAUUUGCUUCAACCUGCAAC-UGCGAUUC----
.......((((..((((....(((((((.......((...(-------(.(((.....))).))..)).......))))))).....))))..-))))....---- ( -20.24)
>DroSim_CAF1 197149 94 + 1
UAAGUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUC-------UGGGACCAAAACCGAGUUGCAUCUCAAUUUGCUUCAACCUGCAAC-UGCGAUUC----
.......((((..((((....(((((((.............-------.((........))(((......)))..))))))).....))))..-))))....---- ( -20.00)
>DroEre_CAF1 203423 91 + 1
CAAAUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUC-------UGGAACCAAAACCGAGUUGUAUCUCAAUUUGCUUGGAACUGCAAC-UGCGA-------
.......((((..((((....(((((((.......((((..-------((....)))))).(((......)))..))))))).....))))..-)))).------- ( -20.00)
>DroYak_CAF1 201089 95 + 1
CAAAUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUG-------UGGCACCAAAACCGAGUUGCAUCUCAAUUUGCUUUUACCUGCAACCUGCGACUU----
......(((((..((((.((((((((((.......((((((-------......)))))).(((......)))..))))))))))..))))...))).))..---- ( -25.00)
>DroMoj_CAF1 254161 101 + 1
UAAAUCGUGCAAGUACAAUAAAAGUA-AAUUAAAUGCUUUGCUUGCUG---CGCUCCUGUCGAGUUGUGUCUCAAUUUGCCACAC-CGGCAAGAGGCGGCCAGUGA
......(((....)))....((((((-.......))))))(((.((((---(.(((.(((((.((.(((.(.......).)))))-))))).)))))))).))).. ( -29.00)
>consensus
CAAAUCGUGCAAGUGCAAUAAAAGCAAAAUUAAACGUUUUC_______UGGGACCAAAACCGAGUUGCAUCUCAAUUUGCUUCAACCUGCAAC_UGCGAUUC____
.......((((..((((....(((((((.....................((........))(((......)))..))))))).....))))...))))........ (-13.71 = -14.77 +   1.06)

alignment

secondary structure

dotplot

Window 4

Location	10,317,224 – 10,317,318
Length	94
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-26.07
Consensus MFE	-15.27
Energy contribution	-16.22
Covariance contribution	0.95
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.59
SVM decision value	0.39
SVM RNA-class probability	0.716857
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10317224 94 - 23771897
----GAAUUGCA-GUUGCAGGUUGAAGCAAAUUGAGAUGCAACUCGGUUUUGGUCCCA-------GAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGACUUG
----....((((-(.(((((...(((((((((((((......)))))(((((....))-------)))..........))))))))..))))).)))))....... ( -25.50)
>DroSec_CAF1 191657 94 - 1
----GAAUCGCA-GUUGCAGGUUGAAGCAAAUUGAGAUGCAACUCGGAUUUGGUCCCA-------GAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGACUUA
----.....(((-(.(((((...((((((((...(((((...((.((((...)))).)-------)....)))))...))))))))..))))).))))........ ( -26.60)
>DroSim_CAF1 197149 94 - 1
----GAAUCGCA-GUUGCAGGUUGAAGCAAAUUGAGAUGCAACUCGGUUUUGGUCCCA-------GAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGACUUA
----.....(((-(.(((((...(((((((((((((......)))))(((((....))-------)))..........))))))))..))))).))))........ ( -25.20)
>DroEre_CAF1 203423 91 - 1
-------UCGCA-GUUGCAGUUCCAAGCAAAUUGAGAUACAACUCGGUUUUGGUUCCA-------GAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGAUUUG
-------..(((-(.((((((...((((((((((((......)))))(((((....))-------)))..........)))))))..)))))).))))........ ( -24.20)
>DroYak_CAF1 201089 95 - 1
----AAGUCGCAGGUUGCAGGUAAAAGCAAAUUGAGAUGCAACUCGGUUUUGGUGCCA-------CAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGAUUUG
----(((((((((((.((((.((((((((((.((((......))))((((((......-------)))))).......))))))))))))))))))))..))))). ( -32.00)
>DroMoj_CAF1 254161 101 - 1
UCACUGGCCGCCUCUUGCCG-GUGUGGCAAAUUGAGACACAACUCGACAGGAGCG---CAGCAAGCAAAGCAUUUAAUU-UACUUUUAUUGUACUUGCACGAUUUA
......((.((((((((.((-(((((...........))).)).)).)))))).)---).))..((((.(((..(((..-.....))).)))..))))........ ( -22.90)
>consensus
____GAAUCGCA_GUUGCAGGUUGAAGCAAAUUGAGAUGCAACUCGGUUUUGGUCCCA_______GAAAACGUUUAAUUUUGCUUUUAUUGCACUUGCACGACUUA
.........(((...(((((...((((((((..(((......)))((........)).....................))))))))..)))))..)))........ (-15.27 = -16.22 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:05 2006