Locus 6975

Sequence ID	3L_DroMel_CAF1
Location	18,823,367 – 18,823,510
Length	143
Max. P	0.991518

overview

Window 1

Location	18,823,367 – 18,823,470
Length	103
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	83.06
Mean single sequence MFE	-33.60
Consensus MFE	-25.91
Energy contribution	-27.47
Covariance contribution	1.56
Combinations/Pair	1.06
Mean z-score	-4.73
Structure conservation index	0.77
SVM decision value	2.15
SVM RNA-class probability	0.989058
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18823367 103 + 23771897
U-----------------AUAAAAACUAUAUUUAAUUAGCCUCGUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAAUUUAGGGACGUUUUGAGCAAAGUCUUGAAUAAGAGGCUA
.-----------------..................(((((((.((((..(.(((....(((.((((((((.(((((.......)))))))))))))))).))).)..)))).))))))) ( -36.60)
>DroSec_CAF1 30657 120 + 1
UUCCUUUUUUGUUAUAGAAUAAAAACUAUAUUUAAUUAGCCUCUUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAACUUAGGAACAUUAUGACCACUGUCUUGAAUAAGAGGCUG
.....((((((((....))))))))...........((((((((((((..(...((((((((......))...((((.......)))))))))).(((....))))..)))))))))))) ( -30.00)
>DroSim_CAF1 31755 120 + 1
UUCCUUUUUUGUUAGAGAAUAAAAACUAUAUUUAAUUAGCCUCUUAUUUGACACUGAUGUACAUCAAAGCGAUUCCUUUUAUUUAAGGACGUAAUGACCACAGUCUUGAAUAAGAGGCUA
.....((((((((....))))))))...........((((((((((((..(.((((.((..(((....(((..(((((......)))))))).)))..)))))).)..)))))))))))) ( -34.20)
>consensus
UUCCUUUUUUGUUA_AGAAUAAAAACUAUAUUUAAUUAGCCUCUUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAAUUUAGGGACGUUAUGACCACAGUCUUGAAUAAGAGGCUA
....................................((((((((((((..(.((((.((....(((.((((.(((((.......))))))))).))).)))))).)..)))))))))))) (-25.91 = -27.47 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	18,823,367 – 18,823,470
Length	103
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.06
Mean single sequence MFE	-29.63
Consensus MFE	-19.71
Energy contribution	-20.60
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-3.79
Structure conservation index	0.67
SVM decision value	2.09
SVM RNA-class probability	0.987754
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18823367 103 - 23771897
UAGCCUCUUAUUCAAGACUUUGCUCAAAACGUCCCUAAAUUAAAGGAAUCGCUUUGAUGCACAUCAGUGUCAAAUACGAGGCUAAUUAAAUAUAGUUUUUAU-----------------A
(((((((.((((..(.(((.((((((((.((..(((.......)))...)).))))).)))....))).)..)))).)))))))..................-----------------. ( -25.00)
>DroSec_CAF1 30657 120 - 1
CAGCCUCUUAUUCAAGACAGUGGUCAUAAUGUUCCUAAGUUAAAGGAAUCGCUUUGAUGCACAUCAGUGUCAAAUAAGAGGCUAAUUAAAUAUAGUUUUUAUUCUAUAACAAAAAAGGAA
.(((((((((((...((((.((((......((((((.......)))))).((......))..)))).)))).))))))))))).......(((((........)))))............ ( -32.90)
>DroSim_CAF1 31755 120 - 1
UAGCCUCUUAUUCAAGACUGUGGUCAUUACGUCCUUAAAUAAAAGGAAUCGCUUUGAUGUACAUCAGUGUCAAAUAAGAGGCUAAUUAAAUAUAGUUUUUAUUCUCUAACAAAAAAGGAA
((((((((((((..(.((((((..((((((((((((......)))))..))...)))))..)).)))).)..)))))))))))).................................... ( -31.00)
>consensus
UAGCCUCUUAUUCAAGACUGUGGUCAUAACGUCCCUAAAUUAAAGGAAUCGCUUUGAUGCACAUCAGUGUCAAAUAAGAGGCUAAUUAAAUAUAGUUUUUAUUCU_UAACAAAAAAGGAA
((((((((((((..(.((((((...........(((.......)))....((......)).)).)))).)..)))))))))))).................................... (-19.71 = -20.60 +   0.89)

alignment

secondary structure

dotplot

Window 3

Location	18,823,390 – 18,823,510
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.98
Mean single sequence MFE	-29.03
Consensus MFE	-21.74
Energy contribution	-23.63
Covariance contribution	1.89
Combinations/Pair	1.06
Mean z-score	-3.09
Structure conservation index	0.75
SVM decision value	2.27
SVM RNA-class probability	0.991518
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18823390 120 + 23771897
CUCGUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAAUUUAGGGACGUUUUGAGCAAAGUCUUGAAUAAGAGGCUAAUUAAAGCUGUGCCUAAUUAAAGUGUAUAUUCAACACUAA
(((.((((..(.(((....(((.((((((((.(((((.......)))))))))))))))).))).)..)))).)))(((......))).............(((((.......))))).. ( -33.60)
>DroSec_CAF1 30697 104 + 1
CUCUUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAACUUAGGAACAUUAUGACCACUGUCUUGAAUAAGAGGCUGAU----------------UAAAGUGUAUAUUCUGCACUAA
((((((((..(...((((((((......))...((((.......)))))))))).(((....))))..))))))))......----------------...((((((.....)))))).. ( -24.80)
>DroSim_CAF1 31795 104 + 1
CUCUUAUUUGACACUGAUGUACAUCAAAGCGAUUCCUUUUAUUUAAGGACGUAAUGACCACAGUCUUGAAUAAGAGGCUAAU----------------UAAAGUGUAUAUUCUGCACUAA
((((((((..(.((((.((..(((....(((..(((((......)))))))).)))..)))))).)..))))))))......----------------...((((((.....)))))).. ( -28.70)
>consensus
CUCUUAUUUGACACUGAUGUGCAUCAAAGCGAUUCCUUUAAUUUAGGGACGUUAUGACCACAGUCUUGAAUAAGAGGCUAAU________________UAAAGUGUAUAUUCUGCACUAA
((((((((..(.((((.((....(((.((((.(((((.......))))))))).))).)))))).)..)))))))).........................((((((.....)))))).. (-21.74 = -23.63 +   1.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:33 2006