Locus 8160

Sequence ID	3L_DroMel_CAF1
Location	21,506,322 – 21,506,482
Length	160
Max. P	0.942627

overview

Window 8

Location	21,506,322 – 21,506,442
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-28.93
Consensus MFE	-27.78
Energy contribution	-27.89
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.96
SVM decision value	0.42
SVM RNA-class probability	0.730302
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21506322 120 + 23771897
AAAUUCCAACCAGUAGCAAAUUUCCUUUUAAGAAGGAAUUUAGGGAGCUGGAAAAUAUAGAUUUGCCCGAACUACGAGAGGCAAUACAUGACUUUCAGGCACGAUUGGAGUGCAUGAAAA
.........(((((..(....(((((((...))))))).....)..)))))...........((((((.........).)))))........(((((.((((.......)))).))))). ( -27.60)
>DroSec_CAF1 11763 120 + 1
AAAUUCCAACCAGUAGCAAAUUUCCUUUUAAGAAGGAAUUUAUGGAGCUGGAAAAUAUAGAUUUGCCCGAACUACGAGAGGCAAUUCAUGACUUUCAGGCACGAUUGGAGUGUAUGAAAA
.........(((((..((((.(((((((...))))))).)).))..)))))........((.((((((.........).))))).)).....(((((.((((.......)))).))))). ( -29.60)
>DroSim_CAF1 11629 120 + 1
AAAUUCCAACCAGUAGCAAAUUUCCUUUUAAGAAGGAAUUUAUGGAGCUGGAAAAUAUAGAUUUGCCCGAACUACGAGAGGCAAUUCAUGACUUUCAGGCACGAUUGGAGUGUAUGAAAA
.........(((((..((((.(((((((...))))))).)).))..)))))........((.((((((.........).))))).)).....(((((.((((.......)))).))))). ( -29.60)
>consensus
AAAUUCCAACCAGUAGCAAAUUUCCUUUUAAGAAGGAAUUUAUGGAGCUGGAAAAUAUAGAUUUGCCCGAACUACGAGAGGCAAUUCAUGACUUUCAGGCACGAUUGGAGUGUAUGAAAA
.........(((((.......(((((((...)))))))........)))))........((.((((((.........).))))).)).....(((((.((((.......)))).))))). (-27.78 = -27.89 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	21,506,322 – 21,506,442
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-28.63
Consensus MFE	-26.93
Energy contribution	-27.27
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.94
SVM decision value	1.33
SVM RNA-class probability	0.942627
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21506322 120 - 23771897
UUUUCAUGCACUCCAAUCGUGCCUGAAAGUCAUGUAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCCUAAAUUCCUUCUUAAAAGGAAAUUUGCUACUGGUUGGAAUUU
((((((.((((.......)))).)))))).......((((((..........)))))).........((((((((...((((((((((.....)))).)))))).....))))))))... ( -28.90)
>DroSec_CAF1 11763 120 - 1
UUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUAAAUUCCUUCUUAAAAGGAAAUUUGCUACUGGUUGGAAUUU
.(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...........((((((((...((((((((((.....)))).)))))).....))))))))... ( -28.50)
>DroSim_CAF1 11629 120 - 1
UUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUAAAUUCCUUCUUAAAAGGAAAUUUGCUACUGGUUGGAAUUU
.(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...........((((((((...((((((((((.....)))).)))))).....))))))))... ( -28.50)
>consensus
UUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUAAAUUCCUUCUUAAAAGGAAAUUUGCUACUGGUUGGAAUUU
.(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...........((((((((...((((((((((.....)))).)))))).....))))))))... (-26.93 = -27.27 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	21,506,362 – 21,506,482
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.28
Mean single sequence MFE	-25.80
Consensus MFE	-21.57
Energy contribution	-22.57
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.47
Structure conservation index	0.84
SVM decision value	0.57
SVM RNA-class probability	0.785198
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21506362 120 - 23771897
UUCACUAAUUUAAAAGAGUGUUUUACCUCGGAGUUUACACUUUUCAUGCACUCCAAUCGUGCCUGAAAGUCAUGUAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCCUA
...............(((.(.....))))((((((((((.((((((.((((.......)))).))))))...))))((((((..........)))))).............))))))... ( -26.30)
>DroSec_CAF1 11803 117 - 1
UUAACUAUUUUU---UAGUGCUUCACCUCGGAGUUUACACUUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUA
...((((.....---))))..........((((((......(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...............))))))... ( -24.50)
>DroSim_CAF1 11669 117 - 1
UUCACUAUUUUU---UAGUGCUUCACCUCGGAGUUUACACUUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUA
..(((((.....---))))).........((((((......(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...............))))))... ( -26.60)
>consensus
UUCACUAUUUUU___UAGUGCUUCACCUCGGAGUUUACACUUUUCAUACACUCCAAUCGUGCCUGAAAGUCAUGAAUUGCCUCUCGUAGUUCGGGCAAAUCUAUAUUUUCCAGCUCCAUA
..(((((........))))).........((((((......(((((..(((.......)))..)))))(((.((((((((.....)))))))))))...............))))))... (-21.57 = -22.57 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:54 2006