Locus 5185

Sequence ID	3R_DroMel_CAF1
Location	13,587,617 – 13,587,714
Length	97
Max. P	0.686449

overview

Window 6

Location	13,587,617 – 13,587,714
Length	97
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	70.91
Mean single sequence MFE	-33.78
Consensus MFE	-15.97
Energy contribution	-18.08
Covariance contribution	2.11
Combinations/Pair	1.21
Mean z-score	-1.68
Structure conservation index	0.47
SVM decision value	0.32
SVM RNA-class probability	0.686449
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13587617 97 + 27905053
CUGGAACCGGGCGAUGGGUGAAGGUGAAGGGUUUUCUGC-CAGAGGG---UCCUCUUUGAGGGUCCUCCAG--AAGAAGGGUCCUCCCCGUCGCUAUGUUUAC
...((((..(((((((((.((.((.......(((((((.-..((((.---.((((...))))..)))))))--)))).....)))))))))))))..)))).. ( -43.80)
>DroSec_CAF1 37110 91 + 1
CUGGAACCGGGCG-------AAGGUGAAGGGUUUUCAGCCCAGAGGG---UCCUCCAUGAGGGUCCUCCAG--AAGAUGGGUCCUCCCCGUCGCACUGUUUAC
(((((...(((((-------((..(.....)..))).))))...((.---.((((...))))..)))))))--..((((((.....))))))........... ( -36.50)
>DroSim_CAF1 29251 91 + 1
CUGGAACCGGGCG-------AAGGUGAAGGGUUUUCUGCCCAGAGGG---UCCUCUGUGAGGGUCCUCCAG--AAGAAGGGUCCUCCCCGUCGCGCUGUUUAC
...((((.(.(((-------(.((.(..((((.....)))).((((.---.((((((.(((....))))))--)....))..))))))).)))).).)))).. ( -39.20)
>DroEre_CAF1 27764 93 + 1
CUG-AAGCGGCUG-------GAGGUGAAGGGUU-CCUGC-CGGAGGACCCUCCUCAACGAGGGUCCUCCAGAAGAGAAGGGUCCUCCCCGUCGCACUGUUUAC
...-..(((((.(-------((((.....(((.-...))-)(((((((((((......))))))))))).............)))))..)))))......... ( -43.70)
>DroYak_CAF1 28086 88 + 1
CUG-AACCGGUUG-------AAGGUGAAGGGUU-CCUGA-CGGAGGG---UCCUCAAUGAUGGUCCUCCAG--GAGAAAGGUCCUCCCCGUCGCACUGUUUAC
.((-(((.(((((-------(.((.(.((((((-(((..-.((((((---.((........))))))))))--))).....)))).))).))).)))))))). ( -26.90)
>DroPer_CAF1 41109 73 + 1
CU------GCCAG-------GAACUAAAGGGU--CCUGA-AGAGGCC---UCCUCUCUCGUCUCCCCCCU-----------CUCUCUCUCCCUCUCUGUUUAC
..------.....-------((((...((((.--...((-(((((..---.................)))-----------)).))...))))....)))).. ( -12.61)
>consensus
CUG_AACCGGGCG_______AAGGUGAAGGGUU_CCUGC_CAGAGGG___UCCUCUAUGAGGGUCCUCCAG__AAGAAGGGUCCUCCCCGUCGCACUGUUUAC
.......................((((.(((...........((((.....))))...((((..(((.(......).)))..))))))).))))......... (-15.97 = -18.08 +   2.11)

alignment

secondary structure

dotplot

Window 7

Location	13,587,617 – 13,587,714
Length	97
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	70.91
Mean single sequence MFE	-31.65
Consensus MFE	-13.84
Energy contribution	-15.82
Covariance contribution	1.98
Combinations/Pair	1.22
Mean z-score	-1.73
Structure conservation index	0.44
SVM decision value	0.21
SVM RNA-class probability	0.635706
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13587617 97 - 27905053
GUAAACAUAGCGACGGGGAGGACCCUUCUU--CUGGAGGACCCUCAAAGAGGA---CCCUCUG-GCAGAAAACCCUUCACCUUCACCCAUCGCCCGGUUCCAG
...(((...((((.(((((((....((((.--(..((((..((((...)))).---.))))..-).))))...))))........))).))))...))).... ( -31.40)
>DroSec_CAF1 37110 91 - 1
GUAAACAGUGCGACGGGGAGGACCCAUCUU--CUGGAGGACCCUCAUGGAGGA---CCCUCUGGGCUGAAAACCCUUCACCUU-------CGCCCGGUUCCAG
...(((.(.((((.(((((((.....((.(--(..((((..((((...)))).---.))))..))..))....))))).)).)-------))).).))).... ( -31.60)
>DroSim_CAF1 29251 91 - 1
GUAAACAGCGCGACGGGGAGGACCCUUCUU--CUGGAGGACCCUCACAGAGGA---CCCUCUGGGCAGAAAACCCUUCACCUU-------CGCCCGGUUCCAG
...(((.(.((((.(((((((....(((((--(..((((..((((...)))).---.))))..)).))))...))))).)).)-------))).).))).... ( -34.40)
>DroEre_CAF1 27764 93 - 1
GUAAACAGUGCGACGGGGAGGACCCUUCUCUUCUGGAGGACCCUCGUUGAGGAGGGUCCUCCG-GCAGG-AACCCUUCACCUC-------CAGCCGCUU-CAG
.........(((.(..(((((.......(((((((((((((((((......))))))))))))-).)))-)........))))-------).).)))..-... ( -43.36)
>DroYak_CAF1 28086 88 - 1
GUAAACAGUGCGACGGGGAGGACCUUUCUC--CUGGAGGACCAUCAUUGAGGA---CCCUCCG-UCAGG-AACCCUUCACCUU-------CAACCGGUU-CAG
...........(((((((.((.((((....--.(((....))).....)))).---)))))))-))..(-((((.........-------.....))))-).. ( -26.84)
>DroPer_CAF1 41109 73 - 1
GUAAACAGAGAGGGAGAGAGAG-----------AGGGGGGAGACGAGAGAGGA---GGCCUCU-UCAGG--ACCCUUUAGUUC-------CUGGC------AG
.......(...(((((....((-----------((((.(....)((.(((((.---..)))))-))...--.))))))..)))-------))..)------.. ( -22.30)
>consensus
GUAAACAGUGCGACGGGGAGGACCCUUCUU__CUGGAGGACCCUCAUAGAGGA___CCCUCCG_GCAGA_AACCCUUCACCUU_______CGCCCGGUU_CAG
...........((.(((((((..(((((......)))))..))))...((((.....))))...........))).))......................... (-13.84 = -15.82 +   1.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:35 2006