Locus 6335

Sequence ID	2R_DroMel_CAF1
Location	19,854,702 – 19,854,827
Length	125
Max. P	0.990222

overview

Window 3

Location	19,854,702 – 19,854,799
Length	97
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	87.86
Mean single sequence MFE	-23.00
Consensus MFE	-20.08
Energy contribution	-21.08
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.87
SVM decision value	0.66
SVM RNA-class probability	0.815464
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19854702 97 + 20766785
AUCGACACCUACUCAGAACCAGC------------AUCUGAAUCAGAAUCCGAAUGCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCG
.......................------------(((((((((.((.(((((...((....))..))))).))....(((......)))......))))))))).... ( -24.20)
>DroSec_CAF1 96702 97 + 1
AUCGACACCUACUCAGAAGCAGC------------AUCAGCAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCG
...............((.((...------------....)).)).(((((.(((((.((((((((.(((.........)))......)))))))).))))).))))).. ( -23.80)
>DroSim_CAF1 73584 97 + 1
AUCGACACCUACUCAGAAGCAGC------------AUCAGAAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCG
.......................------------....(((((.(((((.((.(((((((.....(((.........)))....))))))).)).))))).))))).. ( -24.60)
>DroEre_CAF1 98489 109 + 1
AUCGACACCUACUCAGAACCAGACGCAGACGCAGACUCAGACUCAGAAUCAGAAUCCGAUUUUGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCG
...........(((..........((....)).((.((.((.((((((((.......)))))))).)).)).)).....)))......(((((((.......))))))) ( -24.20)
>DroYak_CAF1 96520 109 + 1
AUCGACACCUACUCAGAACCAGAACCAGAACCAGAAGCAGCAUCAGAAUCAGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUACGAUUCAGAUUCCG
.............................................(((((.(((((.(((((((...)))))))....(((......)))......))))).))))).. ( -18.20)
>consensus
AUCGACACCUACUCAGAACCAGC____________AUCAGAAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCG
.......................................(((((.(((((.((.(((((((.....(((.........)))....))))))).)).))))).))))).. (-20.08 = -21.08 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	19,854,702 – 19,854,799
Length	97
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	87.86
Mean single sequence MFE	-32.25
Consensus MFE	-23.13
Energy contribution	-23.93
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.36
Structure conservation index	0.72
SVM decision value	0.86
SVM RNA-class probability	0.869232
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19854702 97 - 20766785
CGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGCAUUCGGAUUCUGAUUCAGAU------------GCUGGUUCUGAGUAGGUGUCGAU
((((((((((((((((.((.((..........)).)).))))))))(((......)))))))))))(((((((.------------......))))))).......... ( -30.80)
>DroSec_CAF1 96702 97 - 1
CGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUGCUGAU------------GCUGCUUCUGAGUAGGUGUCGAU
((((((((((((((((...(((......))).))))).((((((.....)))))))))))))))))....((((------------((((((....)))).)))))).. ( -32.90)
>DroSim_CAF1 73584 97 - 1
CGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUUCUGAU------------GCUGCUUCUGAGUAGGUGUCGAU
.((((((.(((((.((.(((((((....(((.((.......))..)))))))))).)).))))).))))))(((------------((((((....)))).)))))... ( -33.50)
>DroEre_CAF1 98489 109 - 1
CGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCAAAAUCGGAUUCUGAUUCUGAGUCUGAGUCUGCGUCUGCGUCUGGUUCUGAGUAGGUGUCGAU
..(((((.((((((((...(((......))).)))))))).)))))....((((((((.......))))))))(((.((..((((.((.......))))))..)).))) ( -37.00)
>DroYak_CAF1 96520 109 - 1
CGGAAUCUGAAUCGUAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCUGAUUCUGAUGCUGCUUCUGGUUCUGGUUCUGGUUCUGAGUAGGUGUCGAU
(((((((.(((.((...............))))).)))))))..((((.((((((.......)))))).((((((..((..((......))..))))))))...)))). ( -27.06)
>consensus
CGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUUCUGAU____________GCUGGUUCUGAGUAGGUGUCGAU
(((((((.((((.(((..........))).)))).)))))))..((((.(((..(((((((..(.........................)..))))))).))).)))). (-23.13 = -23.93 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	19,854,725 – 19,854,827
Length	102
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	95.13
Mean single sequence MFE	-27.58
Consensus MFE	-22.34
Energy contribution	-22.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.81
SVM decision value	1.06
SVM RNA-class probability	0.908185
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19854725 102 + 20766785
-AUCUGAAUCAGAAUCCGAAUGCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCGCUUUCGGACCGUGUCAAUUGUUUGCAUU
-.((((...)))).((((((.(((...((((((((((.((....(((......))))).)))))))).))...))).))))))..(((.(((....)))))). ( -30.90)
>DroSec_CAF1 96725 102 + 1
-AUCAGCAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCGCUUUCGGACCGUGUCAAUUGUUUGCAUU
-....(((.(((((((.((.(((((((.....(((.........)))....))))))).)).))))).(((((((....))))....)))...))..)))... ( -27.30)
>DroSim_CAF1 73607 102 + 1
-AUCAGAAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCGCUUUCGGACCGUGUCAAUUGUUUGCAUU
-....(((((.(((((.((.(((((((.....(((.........)))....))))))).)).))))).)))))......(((((.((....)).))))).... ( -26.60)
>DroEre_CAF1 98523 103 + 1
ACUCAGACUCAGAAUCAGAAUCCGAUUUUGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCGCAUUCGGACCGUGUCAAUUGUUUGCAUU
.....(((.(.(((((.((.(((((((.....(((.........)))....))))))).)).)))))....((((....))))..).)))............. ( -27.20)
>DroYak_CAF1 96554 103 + 1
AAGCAGCAUCAGAAUCAGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUACGAUUCAGAUUCCGCUUUCGGACCGUGUCAAUUGUUUGCAUU
..((((((...(((((.((.((((((.....)))))).))....(((......)))......))))).(((((((....))))....)))...)).))))... ( -25.90)
>consensus
_AUCAGAAUCAGAAUCCGAAUCCGAUUUCGAAUCGGAAUCAGAACGAGAAUAAUCGGAAUCCGAUUCAGAUUCCGCUUUCGGACCGUGUCAAUUGUUUGCAUU
...........(((((.((.(((((((.....(((.........)))....))))))).)).)))))....((((....))))..(((.(((....)))))). (-22.34 = -22.74 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	19,854,725 – 19,854,827
Length	102
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	95.13
Mean single sequence MFE	-30.22
Consensus MFE	-24.84
Energy contribution	-25.64
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.82
SVM decision value	2.20
SVM RNA-class probability	0.990222
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19854725 102 - 20766785
AAUGCAAACAAUUGACACGGUCCGAAAGCGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGCAUUCGGAUUCUGAUUCAGAU-
...........((((((..(((((((.((((..((.((((((((.((.((..........)).)).))))))))))..)))).)))))))..))..))))..- ( -33.70)
>DroSec_CAF1 96725 102 - 1
AAUGCAAACAAUUGACACGGUCCGAAAGCGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUGCUGAU-
...(((..(....).((..(((((((..(((((((((...))))))))).................((((((.....)))))))))))))..)).)))....- ( -30.50)
>DroSim_CAF1 73607 102 - 1
AAUGCAAACAAUUGACACGGUCCGAAAGCGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUUCUGAU-
...............((..(((.(((..(((((((((...)))))))))...........(((((.((((((.....)))))).)))))))).)))..))..- ( -31.00)
>DroEre_CAF1 98523 103 - 1
AAUGCAAACAAUUGACACGGUCCGAAUGCGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCAAAAUCGGAUUCUGAUUCUGAGUCUGAGU
.................(((..(((...(((((((((...))))))))).......)))..)))((((.((((((.((((((...)))))).)))))).)))) ( -30.10)
>DroYak_CAF1 96554 103 - 1
AAUGCAAACAAUUGACACGGUCCGAAAGCGGAAUCUGAAUCGUAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCUGAUUCUGAUGCUGCUU
.........................((((((.(((.((((((...(((((((....(((.((.......))..))))))))))...)))))).))).)))))) ( -25.80)
>consensus
AAUGCAAACAAUUGACACGGUCCGAAAGCGGAAUCUGAAUCGGAUUCCGAUUAUUCUCGUUCUGAUUCCGAUUCGAAAUCGGAUUCGGAUUCUGAUUCUGAU_
...............((..(((((((..(((((((((...))))))))).................((((((.....)))))))))))))..))......... (-24.84 = -25.64 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:36 2006