Locus 5145

Sequence ID	X_DroMel_CAF1
Location	13,420,945 – 13,421,084
Length	139
Max. P	0.996618

overview

Window 5

Location	13,420,945 – 13,421,054
Length	109
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	68.97
Mean single sequence MFE	-25.58
Consensus MFE	-8.73
Energy contribution	-10.46
Covariance contribution	1.72
Combinations/Pair	1.12
Mean z-score	-2.63
Structure conservation index	0.34
SVM decision value	2.14
SVM RNA-class probability	0.988898
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13420945 109 - 22224390
AACCGCACAAUGUGCACGCCAUCAACCAUACA-----UAGAUGGC-GCCACCAAGCGAC---CAUCAAACCCACAUCAUCAUUGUGAUCAAUGAUAUUCCUUUCAGUUUCAUGGCUUC
....((((...))))..(((((.(((......-----..((((((-((......))).)---))))...........(((((((....)))))))..........)))..)))))... ( -29.40)
>DroGri_CAF1 6986 96 - 1
GCAAGCUAAACGUGCCCCAAACCAACCAAAUGCAUCUUAUAUCCCAGGCAUGGAGCCAA---CG--------------UCAUUAUCAACG-UGGUUAUCAAUAUGGUUGCUU----GU
((((((....((((((..............................)))))).(((((.---((--------------(........)))-)))))............))))----)) ( -20.51)
>DroSec_CAF1 16569 95 - 1
AAACGCACAAUGUGCACGCCAUCAACCAUACA-----UAGAUGGC-GCCACCAAGCGAC---CA--------------UCAUUGUGAUCAAUGGUAUUCCUUUCAGUUUCAUGGCUUU
....((((...))))..(((((.(((..((((-----..((((((-((......))).)---))--------------))..))))......((....)).....)))..)))))... ( -25.80)
>DroSim_CAF1 15843 95 - 1
AAACGCACAAUGUGCACGCCAUCAACCAUACA-----UAGAUGGC-GCCACCAAGCGAC---CA--------------UCAUUGUGAUCAAUGGUAUUCCUUACAGUUUCAUGGCUUU
....((((...))))..((((((.........-----..))))))-((((..((((...---..--------------.(((((....)))))(((.....))).))))..))))... ( -26.50)
>DroEre_CAF1 11370 101 - 1
AAGCGCACAAAGUGCGUACUAUC--------A-----CAGAUGGC-GCCACCAAGCGAC---CAUCAAACCCACAUCAUCAUUGUGAUCAAUGGUAUUCCUUUCAGUUUUAUGGCUUU
((((((((...))))(((((((.--------.-----..((((((-((......))).)---)))).....((((.......))))....)))))))................)))). ( -26.20)
>DroYak_CAF1 26216 108 - 1
AAGCGCACAAUGUGCAUACUAUCAACC----A-----UAGAUGGC-GCCAGCAAGCGAACCACAUCAAACCCACAUCAUCAUUGUGAUCAAUGGUGUUCCUUUCAGUUUCAUGGCUUU
..((((.....))))...(((((....----.-----..))))).-((((..(((((((..((((((....((((.......)))).....))))))....))).))))..))))... ( -25.10)
>consensus
AAACGCACAAUGUGCACGCCAUCAACCAUACA_____UAGAUGGC_GCCACCAAGCGAC___CA______________UCAUUGUGAUCAAUGGUAUUCCUUUCAGUUUCAUGGCUUU
....((((...))))...(((((................)))))..((((..(((((.....)...............((((((....))))))...........))))..))))... ( -8.73 = -10.46 +   1.72)

alignment

secondary structure

dotplot

Window 6

Location	13,420,985 – 13,421,084
Length	99
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	72.90
Mean single sequence MFE	-17.34
Consensus MFE	-11.98
Energy contribution	-11.90
Covariance contribution	-0.08
Combinations/Pair	1.13
Mean z-score	-2.28
Structure conservation index	0.69
SVM decision value	2.72
SVM RNA-class probability	0.996618
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13420985 99 - 22224390
CA----ACAGAACUUUAUAGUUUUUCCCAUUUUUAACCGCACAAUGUGCACGCCAUCAACCAUACAUAGAUGGCGCCACCAAGCGAC---CAUCAAACCCACAUCA
..----..((((((....))))))..............((((...))))...................((((((((......))).)---))))............ ( -18.00)
>DroSec_CAF1 16609 84 - 1
CA----AGAGA-UUUUAUAGUUUUUCCCAUCUUUAAACGCACAAUGUGCACGCCAUCAACCAUACAUAGAUGGCGCCACCAAGCGAC---CA--------------
..----(((((-(...............))))))...(((.....(((..(((((((...........))))))).)))...)))..---..-------------- ( -16.96)
>DroSim_CAF1 15883 84 - 1
CA----AGAGA-UUUUAUAGUUUUUCCCAUCUUUAAACGCACAAUGUGCACGCCAUCAACCAUACAUAGAUGGCGCCACCAAGCGAC---CA--------------
..----(((((-(...............))))))...(((.....(((..(((((((...........))))))).)))...)))..---..-------------- ( -16.96)
>DroEre_CAF1 11410 94 - 1
AAAAAUGCAGAACAUCAAAGUUUUUC-CAUCUAUAAGCGCACAAAGUGCGUACUAUC--------ACAGAUGGCGCCACCAAGCGAC---CAUCAAACCCACAUCA
....(((.(((((......)))))..-)))......((((((...))))))......--------...((((((((......))).)---))))............ ( -20.70)
>DroYak_CAF1 26256 102 - 1
AAAGAAGCAGAACAUCAUAGUUUUUCCCAACAUUAAGCGCACAAUGUGCAUACUAUCAACC----AUAGAUGGCGCCAGCAAGCGAACCACAUCAAACCCACAUCA
......((....((((...(((......))).....((((.....))))............----...))))((....))..))...................... ( -14.10)
>consensus
CA____ACAGAACUUUAUAGUUUUUCCCAUCUUUAAACGCACAAUGUGCACGCCAUCAACCAUACAUAGAUGGCGCCACCAAGCGAC___CAUCAAACCCACAUCA
...................((((...............((((...)))).(((((((...........))))))).....))))...................... (-11.98 = -11.90 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:02 2006