Locus 8125

Sequence ID	X_DroMel_CAF1
Location	20,205,584 – 20,205,742
Length	158
Max. P	0.900351

overview

Window 9

Location	20,205,584 – 20,205,677
Length	93
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	70.25
Mean single sequence MFE	-43.38
Consensus MFE	-16.69
Energy contribution	-18.09
Covariance contribution	1.40
Combinations/Pair	1.40
Mean z-score	-1.81
Structure conservation index	0.38
SVM decision value	0.40
SVM RNA-class probability	0.721314
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20205584 93 + 22224390
CGG---AUCCAGUGGCCAGGGUGCUGGGUCCAGCCAGACCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGAGUAGGAGGGGGUGGAGGUGCCAG
.((---((((((((.(....)))))))))))..(((..((.((((((((((.(((((....)))))---------.)))...))))))).)).)))......... ( -40.40)
>DroGri_CAF1 16284 96 + 1
CGAAUAAUCCGGUGG---------CGGCUCCAGCUGCGUAACCACACCAGCAGCAGUCGCAGCAGAUGUGGCUGGAGCUGGUGCUGGUGGCGGCUGUGGUGCGAG
..............(---------((.(..(((((((...(((((((((((..((((((((.....))))))))..))))))).)))).)))))))..))))... ( -48.90)
>DroSec_CAF1 33807 93 + 1
CGG---AUCCAGUGGCCAAGGUGCUGGGUCCAGCCAGCCCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGUGUAGGAGGGGGUGGAGGUGCCAG
.((---((((((((.(....))))))))))).(((.((((.((((((((.(((((((....)))))---------...)).)))))))).))))...)))..... ( -47.60)
>DroSim_CAF1 33464 93 + 1
CGG---AUCCAGUGGCCAAGGUGCUGGGUCCAGCCAGCCCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGUGUAGGAGGGGGUGGAGGUGCCAG
.((---((((((((.(....))))))))))).(((.((((.((((((((.(((((((....)))))---------...)).)))))))).))))...)))..... ( -47.60)
>DroEre_CAF1 22025 81 + 1
UGG---AUCCAGUGGCCAGGGUGCUGGCACCAGCCAGUCCGCUGCUGCACCACCAGUUUCCGCGGG---------AGUAGGG------------GGAGUUGCCAG
(((---.(((.(..((.((.(..(((((....)))))..).))))..)....((..((((....))---------))..)).------------)))....))). ( -32.40)
>consensus
CGG___AUCCAGUGGCCAAGGUGCUGGGUCCAGCCAGCCCGCUUCUGCAGCACCAGUCUCCGCUGG_________AGUUGGUGUAGGAGGGGGUGGAGGUGCCAG
............((((...((.(((((......)))))))((((((((.........((((((.............)).)))).........)))))))))))). (-16.69 = -18.09 +   1.40)

alignment

secondary structure

dotplot

Window 0

Location	20,205,616 – 20,205,712
Length	96
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	66.96
Mean single sequence MFE	-42.48
Consensus MFE	-18.32
Energy contribution	-20.07
Covariance contribution	1.75
Combinations/Pair	1.32
Mean z-score	-1.97
Structure conservation index	0.43
SVM decision value	1.01
SVM RNA-class probability	0.900351
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20205616 96 + 22224390
AGACCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGAGUAGGAGGGGGUGGAGGUGCCAGUGGA---GCAGCGGCAGGAGCAGGCUCCGCAGCAGGAU
...((((((((.(.((.((((.((((...))---------)))))).)).)..))))))))...(((..(((((---((....((....))..))))))).))).... ( -38.70)
>DroGri_CAF1 16310 94 + 1
GCGUAACCACACCAGCAGCAGUCGCAGCAGAUGUGGCUGGAGCUGGUGCUGGUGGCGGCUGUGGUGCGAGUAGCUUGGUAACGGCUUGAUGA----------CU----
.(((.(((((((((((..((((((((.....))))))))..))))))).)))).)))(((((...((.....))......))))).......----------..---- ( -42.10)
>DroSec_CAF1 33839 96 + 1
AGCCCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGA---GCAGCGGCAGGAGCGGGCUCCGCAGCAGGAU
.((((((((((((.(((((((.((((...))---------))))))))).............(.((((....).---))).).))))))))))))(((......))). ( -47.30)
>DroSim_CAF1 33496 96 + 1
AGCCCGCUUCUGCAGCACCAGUCUCCGCUGG---------AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGA---GCAGCGGCAGGAGCAGGCUCCGCAGCAGGAU
.((((.((((((((.(((((((....)))))---------...)).)))))))).)))).....(((..(((((---((....((....))..))))))).))).... ( -45.30)
>DroEre_CAF1 22057 84 + 1
AGUCCGCUGCUGCACCACCAGUUUCCGCGGG---------AGUAGGG------------GGAGUUGCCAGUGUA---GCAGCGGUAGGAGCGAGCUCCGCGGCAGGAU
.((((((((((((((...((..((((.(...---------....).)------------)))..))...)))))---))))).((.((((....))))...)).)))) ( -39.00)
>consensus
AGCCCGCUUCUGCAGCACCAGUCUCCGCUGG_________AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGA___GCAGCGGCAGGAGCAGGCUCCGCAGCAGGAU
.(((.((((((((.((......((((((.............................)))))).(((..........))))).)))))))).)))(((......))). (-18.32 = -20.07 +   1.75)

alignment

secondary structure

dotplot

Window 1

Location	20,205,616 – 20,205,712
Length	96
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	66.96
Mean single sequence MFE	-33.40
Consensus MFE	-13.18
Energy contribution	-14.53
Covariance contribution	1.35
Combinations/Pair	1.33
Mean z-score	-1.88
Structure conservation index	0.39
SVM decision value	0.49
SVM RNA-class probability	0.757785
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20205616 96 - 22224390
AUCCUGCUGCGGAGCCUGCUCCUGCCGCUGC---UCCACUGGCACCUCCACCCCCUCCUACUCCAACU---------CCAGCGGAGACUGGUGCUGCAGAAGCGGUCU
(((((.(((((((((..((.......)).))---)))...((((((........((((..........---------.....))))...)))))))))).)).))).. ( -29.86)
>DroGri_CAF1 16310 94 - 1
----AG----------UCAUCAAGCCGUUACCAAGCUACUCGCACCACAGCCGCCACCAGCACCAGCUCCAGCCACAUCUGCUGCGACUGCUGCUGGUGUGGUUACGC
----..----------.........(((.((((.((.....))...........((((((((.(((.((((((.......)))).))))).)))))))))))).))). ( -32.20)
>DroSec_CAF1 33839 96 - 1
AUCCUGCUGCGGAGCCCGCUCCUGCCGCUGC---UCCACUGGCACCUCCACCCCCUCCUACACCAACU---------CCAGCGGAGACUGGUGCUGCAGAAGCGGGCU
.(((......)))(((((((.((((((((.(---(((.((((..........................---------)))).))))...))))..)))).))))))). ( -37.67)
>DroSim_CAF1 33496 96 - 1
AUCCUGCUGCGGAGCCUGCUCCUGCCGCUGC---UCCACUGGCACCUCCACCCCCUCCUACACCAACU---------CCAGCGGAGACUGGUGCUGCAGAAGCGGGCU
.(((......)))(((((((.((((((((.(---(((.((((..........................---------)))).))))...))))..)))).))))))). ( -35.47)
>DroEre_CAF1 22057 84 - 1
AUCCUGCCGCGGAGCUCGCUCCUACCGCUGC---UACACUGGCAACUCC------------CCCUACU---------CCCGCGGAAACUGGUGGUGCAGCAGCGGACU
..........((((....))))..(((((((---(.(((((....)...------------.......---------.(((.(....)))).)))).))))))))... ( -31.80)
>consensus
AUCCUGCUGCGGAGCCUGCUCCUGCCGCUGC___UCCACUGGCACCUCCACCCCCUCCUACACCAACU_________CCAGCGGAGACUGGUGCUGCAGAAGCGGGCU
.(((......)))..(((((.((((.((......(((.((((...................................)))).))).......)).)))).)))))... (-13.18 = -14.53 +   1.35)

alignment

secondary structure

dotplot

Window 2

Location	20,205,647 – 20,205,742
Length	95
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	84.69
Mean single sequence MFE	-35.15
Consensus MFE	-28.49
Energy contribution	-29.05
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.81
SVM decision value	0.05
SVM RNA-class probability	0.558368
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20205647 95 + 22224390
AGUUGGAGUAGGAGGGGGUGGAGGUGCCAGUGGAGCAGCGGCAGGAGCAGGCUCCGCAGCAGGAUCUGGAUCGG------GAUCAGGUUCCGGAUCAGCAG
................(((......))).(((((((....((....))..))))))).((..((((((((((..------.....)).)))))))).)).. ( -32.50)
>DroSec_CAF1 33870 95 + 1
AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGAGCAGCGGCAGGAGCGGGCUCCGCAGCAGGAUCUGGAUCCG------GAUCAGGUUCCGGAUCAGCAG
.((((((...(((...(((......))).(((((((.((.......))..))))))).((..((((((....))------))))..)))))..)))))).. ( -38.20)
>DroSim_CAF1 33527 95 + 1
AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGAGCAGCGGCAGGAGCAGGCUCCGCAGCAGGAUCUGGAUCCG------GAUCAGGUUCCGGAUCAGCAG
.((((((...(((...(((......))).(((((((....((....))..))))))).((..((((((....))------))))..)))))..)))))).. ( -37.40)
>DroEre_CAF1 22088 89 + 1
AGUAGGG------------GGAGUUGCCAGUGUAGCAGCGGUAGGAGCGAGCUCCGCGGCAGGAUCUGGAUCCGGAUGCGGAUCAGGUUCCACAUCAGCAG
.......------------.....(((..((((....((.((.((((....)))))).)).(((.((.((((((....)))))).)).)))))))..))). ( -32.50)
>consensus
AGUUGGUGUAGGAGGGGGUGGAGGUGCCAGUGGAGCAGCGGCAGGAGCAGGCUCCGCAGCAGGAUCUGGAUCCG______GAUCAGGUUCCGGAUCAGCAG
...................((.....)).(((((((.((.......))..))))))).((..((((((((.((............)).)))))))).)).. (-28.49 = -29.05 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	20,205,647 – 20,205,742
Length	95
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	84.69
Mean single sequence MFE	-26.98
Consensus MFE	-19.76
Energy contribution	-20.33
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.73
SVM decision value	0.92
SVM RNA-class probability	0.882936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20205647 95 - 22224390
CUGCUGAUCCGGAACCUGAUC------CCGAUCCAGAUCCUGCUGCGGAGCCUGCUCCUGCCGCUGCUCCACUGGCACCUCCACCCCCUCCUACUCCAACU
(((..((((.(((......))------).)))))))....(((((.(((((..((.......)).))))).).))))........................ ( -23.10)
>DroSec_CAF1 33870 95 - 1
CUGCUGAUCCGGAACCUGAUC------CGGAUCCAGAUCCUGCUGCGGAGCCCGCUCCUGCCGCUGCUCCACUGGCACCUCCACCCCCUCCUACACCAACU
(((..((((((((......))------)))))))))....(((((.(((((..((....))....))))).).))))........................ ( -28.40)
>DroSim_CAF1 33527 95 - 1
CUGCUGAUCCGGAACCUGAUC------CGGAUCCAGAUCCUGCUGCGGAGCCUGCUCCUGCCGCUGCUCCACUGGCACCUCCACCCCCUCCUACACCAACU
(((..((((((((......))------)))))))))....(((((.(((((..((.......)).))))).).))))........................ ( -29.20)
>DroEre_CAF1 22088 89 - 1
CUGCUGAUGUGGAACCUGAUCCGCAUCCGGAUCCAGAUCCUGCCGCGGAGCUCGCUCCUACCGCUGCUACACUGGCAACUCC------------CCCUACU
.((((..((((((.(..((((((....))))))..).))).((.((((((.......)).)))).)).)))..)))).....------------....... ( -27.20)
>consensus
CUGCUGAUCCGGAACCUGAUC______CGGAUCCAGAUCCUGCUGCGGAGCCCGCUCCUGCCGCUGCUCCACUGGCACCUCCACCCCCUCCUACACCAACU
.....((((.(((.((............)).))).)))).(((((.(((((..((.......)).))))).).))))........................ (-19.76 = -20.33 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:18 2006