Locus 3250

Sequence ID	2R_DroMel_CAF1
Location	11,103,528 – 11,103,669
Length	141
Max. P	0.997258

overview

Window 4

Location	11,103,528 – 11,103,635
Length	107
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	74.04
Mean single sequence MFE	-31.16
Consensus MFE	-17.27
Energy contribution	-19.31
Covariance contribution	2.04
Combinations/Pair	1.12
Mean z-score	-2.55
Structure conservation index	0.55
SVM decision value	2.83
SVM RNA-class probability	0.997258
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11103528 107 + 20766785
CAACGUAACGUCAGACAAAUUAUCACGUUACACUCGAGUGCGUGAGGCGGG-----CAACUAU------CUGCCUUUCGCUUGCCUCAUCCUGUUGCCGCCCCCCCAUACCAUCGCCC
(((((((((((.............)))))))....(((.(((.((((((((-----......)------))))))).)))....))).....))))...................... ( -27.62)
>DroGri_CAF1 23494 94 + 1
GUGCGACAAGUCAGACAAAUUAUCACGUUACAGUCGAGUGCGUGAGGCGUGUGGCACAACUAA------CGUGC---CGCAUGCCCCACCCAAC---------------CAGUCAGUC
....((....)).(((......((((((.((......))))))))((((((((((((......------.))))---)))))))).........---------------..))).... ( -34.90)
>DroSec_CAF1 15757 106 + 1
CAACGUAACGUCAGACAAAUUAUCACGUUACACUCGAGUGCGUGAGGCAGG-----CAACUAU------CUGCCUCUCGCUUGCCUCAUCCUGUUGCAGC-CCCUCAUCCCACCACCC
(((((((((((.............)))))))....(((.(((.((((((((-----......)------))))))).)))....))).....))))....-................. ( -30.82)
>DroEre_CAF1 16125 98 + 1
CAACGUAACGUCAGACAAAUUAUCACGUUACACUCGAGUGCGUGAGGCGGG-----CAACUAU------CUGCCUCUCGCUUGCCUCAUCCUGUUGCAACGAGCCC---------UUC
....(((((((.............))))))).((((...(((.((((((((-----......)------))))))).)))((((..(.....)..))))))))...---------... ( -32.02)
>DroYak_CAF1 16897 103 + 1
CAACGUAACGUCAGACAAAUUAUCACGUUACACUCGAGUGCGUGAGGCGGG-----CAACUAUCUGUAUCUGCCUCUCGCUUGCCUCAUCCUGUUGCCGCCCCCCC----------CA
(((((((((((.............)))))))....(((.(((.((((((((-----..((.....)).)))))))).)))....))).....))))..........----------.. ( -30.42)
>consensus
CAACGUAACGUCAGACAAAUUAUCACGUUACACUCGAGUGCGUGAGGCGGG_____CAACUAU______CUGCCUCUCGCUUGCCUCAUCCUGUUGCAGC_CCCCC___C___C_CCC
(((((((((((.............)))))))....(((.(((.(((((((...................))))))).)))....))).....))))...................... (-17.27 = -19.31 +   2.04)

alignment

secondary structure

dotplot

Window 5

Location	11,103,568 – 11,103,669
Length	101
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	79.71
Mean single sequence MFE	-23.73
Consensus MFE	-20.19
Energy contribution	-20.00
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.85
SVM decision value	0.85
SVM RNA-class probability	0.865258
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11103568 101 + 20766785
CGUGAGGCGGGCAACUAU------CUGCCUUUCGCUUGCCUCAUCCUGUUGCCGCCCCCCCAUACCAUCGCCCAACGCCCACCGCCC--UCCUGGCACGCCCCCUUUUC
.(((((((((((......------.........)))))))))))...((((..((..............)).)))).......(((.--....)))............. ( -22.30)
>DroSec_CAF1 15797 100 + 1
CGUGAGGCAGGCAACUAU------CUGCCUCUCGCUUGCCUCAUCCUGUUGCAGC-CCCUCAUCCCACCACCCUACGCCCACCGCCC--UUCUGGCACGCCCCCUUUUC
.(((.((((((((.....------.)))))...(((.((..(.....)..)))))-....................)))))).(((.--....)))............. ( -23.10)
>DroEre_CAF1 16165 94 + 1
CGUGAGGCGGGCAACUAU------CUGCCUCUCGCUUGCCUCAUCCUGUUGCAACGAGCCC---------UUCCCCGCCCACCGCCCACCGCUGGCACGCCCCCUUUCC
.(((.((((((((.....------.)))).((((.((((..(.....)..))))))))...---------.....))))))).(((.......)))............. ( -27.90)
>DroYak_CAF1 16937 97 + 1
CGUGAGGCGGGCAACUAUCUGUAUCUGCCUCUCGCUUGCCUCAUCCUGUUGCCGCCCCCCC----------CACCCUCCCACCGCCC--CUCUGGCACGCCCCCUUUCC
.....((((((((((....((.....((.....))......))....))))))........----------............(((.--....))).))))........ ( -21.60)
>consensus
CGUGAGGCGGGCAACUAU______CUGCCUCUCGCUUGCCUCAUCCUGUUGCAGCCCCCCC_________CCCCACGCCCACCGCCC__CUCUGGCACGCCCCCUUUCC
.(((((((((((.....................))))))))))).......................................(((.......)))............. (-20.19 = -20.00 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:03 2006