Locus 3527

Sequence ID	2L_DroMel_CAF1
Location	10,291,687 – 10,291,827
Length	140
Max. P	0.768624

overview

Window 9

Location	10,291,687 – 10,291,788
Length	101
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	90.16
Mean single sequence MFE	-16.19
Consensus MFE	-11.92
Energy contribution	-12.26
Covariance contribution	0.34
Combinations/Pair	1.12
Mean z-score	-2.30
Structure conservation index	0.74
SVM decision value	0.02
SVM RNA-class probability	0.545853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10291687 101 + 22407834
UUGAAAAUCAACAACAUAAGCAUAUGUACAUCGAUAUGUACCGAUAUACACAUAC----ACAUAUGCAUGUAUGUAAUCACUUUUUCAAUUACACUUGAUACUUU
(((((((......(((((.((((((((.......(((((....))))).......----))))))))...))))).......)))))))................ ( -17.46)
>DroSim_CAF1 6079 105 + 1
UUGAAAAUCAACAACAUAAGCAUAUGUACAUCGAUAUGUACCGAUAUCCAAGUACACAUACAUAUGCACGUAUAUAAUCACUUUUUCAAUUACACUUGAUACAUU
(((((((............(((((((((.((((........))))......(....).)))))))))..((........)).)))))))................ ( -15.00)
>DroYak_CAF1 9294 105 + 1
UUGAAAAUCAACAAAAUAAACAUAUGUACAUCGAUAUGUACCGAUAUACACGUACCCAUACAUGUGCAUGUAUGUAAUCACUUUUUUAAUUUCACUUGAUACUUU
.(((((...................((((((....))))))..(((((((.((((........)))).)))))))..............)))))........... ( -16.10)
>consensus
UUGAAAAUCAACAACAUAAGCAUAUGUACAUCGAUAUGUACCGAUAUACACGUAC_CAUACAUAUGCAUGUAUGUAAUCACUUUUUCAAUUACACUUGAUACUUU
(((((((........(((.(((((((((.....((.((((......)))).)).....)))))))))...))).........)))))))................ (-11.92 = -12.26 +   0.34)

alignment

secondary structure

dotplot

Window 0

Location	10,291,687 – 10,291,788
Length	101
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	90.16
Mean single sequence MFE	-29.43
Consensus MFE	-19.60
Energy contribution	-20.83
Covariance contribution	1.23
Combinations/Pair	1.11
Mean z-score	-4.09
Structure conservation index	0.67
SVM decision value	0.52
SVM RNA-class probability	0.768624
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10291687 101 - 22407834
AAAGUAUCAAGUGUAAUUGAAAAAGUGAUUACAUACAUGCAUAUGU----GUAUGUGUAUAUCGGUACAUAUCGAUGUACAUAUGCUUAUGUUGUUGAUUUUCAA
...(.(((((((((((((........)))))))).((.(((((...----((((((((((((((((....)))))))))))))))).))))))))))))...).. ( -31.90)
>DroSim_CAF1 6079 105 - 1
AAUGUAUCAAGUGUAAUUGAAAAAGUGAUUAUAUACGUGCAUAUGUAUGUGUACUUGGAUAUCGGUACAUAUCGAUGUACAUAUGCUUAUGUUGUUGAUUUUCAA
..((.(((((((((((((........))))))))....(((((.((((((((((.(.(((((......))))).).)))))))))).)))))..)))))...)). ( -28.10)
>DroYak_CAF1 9294 105 - 1
AAAGUAUCAAGUGAAAUUAAAAAAGUGAUUACAUACAUGCACAUGUAUGGGUACGUGUAUAUCGGUACAUAUCGAUGUACAUAUGUUUAUUUUGUUGAUUUUCAA
...........(((((((((.(((((((...(((((((....))))))).....((((((((((((....))))))))))))....))))))).)))).))))). ( -28.30)
>consensus
AAAGUAUCAAGUGUAAUUGAAAAAGUGAUUACAUACAUGCAUAUGUAUG_GUACGUGUAUAUCGGUACAUAUCGAUGUACAUAUGCUUAUGUUGUUGAUUUUCAA
...(.((((((((((((((......))))))))).(((((....))))).(((.((((((((((((....)))))))))))).)))........)))))...).. (-19.60 = -20.83 +   1.23)

alignment

secondary structure

dotplot

Window 1

Location	10,291,712 – 10,291,827
Length	115
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.02
Mean single sequence MFE	-27.77
Consensus MFE	-20.38
Energy contribution	-20.50
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-2.01
Structure conservation index	0.73
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10291712 115 - 22407834
GUAAAACGGGAUACCCAUCG-UUAUUAUCAUGUGCAAGAAAAAGUAUCAAGUGUAAUUGAAAAAGUGAUUACAUACAUGCAUAUGU----GUAUGUGUAUAUCGGUACAUAUCGAUGUAC
.......((....))(((((-.(((((((((((((...............((((((((........))))))))(((((((....)----)))))))))))).)))).))).)))))... ( -27.50)
>DroSim_CAF1 6104 120 - 1
GUACAACGAGACACCCAUCGGUUAUUAUCAUGUGCAAGAAAAUGUAUCAAGUGUAAUUGAAAAAGUGAUUAUAUACGUGCAUAUGUAUGUGUACUUGGAUAUCGGUACAUAUCGAUGUAC
((((..((((.(((...((((((((......(((((......))))).....))))))))....)))....(((((((((....)))))))))))))...((((((....)))))))))) ( -29.10)
>DroYak_CAF1 9319 119 - 1
GUAAAACGGGACAUCCUUCG-UUUUUAUCAUUUGCAAGAAAAAGUAUCAAGUGAAAUUAAAAAAGUGAUUACAUACAUGCACAUGUAUGGGUACGUGUAUAUCGGUACAUAUCGAUGUAC
..((((((((......))))-))))..(((((((.............)))))))..........(((....(((((((....)))))))..)))..((((((((((....)))))))))) ( -26.72)
>consensus
GUAAAACGGGACACCCAUCG_UUAUUAUCAUGUGCAAGAAAAAGUAUCAAGUGUAAUUGAAAAAGUGAUUACAUACAUGCAUAUGUAUG_GUACGUGUAUAUCGGUACAUAUCGAUGUAC
(((...(((........)))........((((((((.((.......))..(((((((((......)))))))))...))))))))......)))..((((((((((....)))))))))) (-20.38 = -20.50 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:40 2006