Locus 362

Sequence ID	3R_DroMel_CAF1
Location	1,398,190 – 1,398,382
Length	192
Max. P	0.958958

overview

Window 3

Location	1,398,190 – 1,398,302
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	75.04
Mean single sequence MFE	-28.12
Consensus MFE	-12.79
Energy contribution	-14.10
Covariance contribution	1.31
Combinations/Pair	1.08
Mean z-score	-2.82
Structure conservation index	0.45
SVM decision value	1.50
SVM RNA-class probability	0.958958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1398190 112 - 27905053
GCAUGGCUACAUGCAUACGUAUGUAUGUACACACAUAUAUGUAAAUACGCGGAAGGAGUGUGUUUAAACAUACAUAAUGCACACAAGUGGGCUCGCAGGUA--------CAUAAUGCAAU
(((((....)))))....((((.(((((((..(((....)))......((((.....((((((....)))))).....((.((....)).))))))..)))--------))))))))... ( -30.50)
>DroSec_CAF1 3024 97 - 1
GCAUGGCUACAUACACACGUAUGUA------------UAUGUAAAUACGCGGAACGAGUGUGUUUAAACAUACACA-UACAUUCA--UGGGCUCGUAGGUA--------CAUAAUGCAAU
((((...(((((((....)))))))------------((((((..((((.((..(((((((((............)-))))))).--.)..))))))..))--------))))))))... ( -28.10)
>DroSim_CAF1 3084 97 - 1
GCAUGGCUACAUACACACGUAUGCA------------UAUGUAAAUUCGCGGAACGAGUGUGUUUAAACAUACACA-UACAUACA--AUGGCUCGUAGGUA--------CAUAAUGCAAU
((((((((((((((....)))))..------------((((((...(((.....)))((((((....))))))...-))))))..--.))))).((....)--------)...))))... ( -21.50)
>DroYak_CAF1 3023 102 - 1
GCAUGGGUA--UGCAUACAUAUACA------------UAUGUAAAAACGCGGACCGAGUGUGUUUUUAUAUA----UUGCACACAAGUGCGCUCGUAGAUAUGUACAUAUAUAAUGCAAU
((((..(((--((..(((((((..(------------((((((((((((((.......))))))))))))))----).((((....))))........))))))))))))...))))... ( -32.40)
>consensus
GCAUGGCUACAUACACACGUAUGCA____________UAUGUAAAUACGCGGAACGAGUGUGUUUAAACAUACACA_UACACACA__UGGGCUCGUAGGUA________CAUAAUGCAAU
((((...(((((((....)))))))............(((((((((((((.......))))))))..))))).........................................))))... (-12.79 = -14.10 +   1.31)

alignment

secondary structure

dotplot

Window 4

Location	1,398,262 – 1,398,382
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.26
Mean single sequence MFE	-27.41
Consensus MFE	-19.16
Energy contribution	-20.73
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.594277
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1398262 120 - 27905053
UUCCCCUUUUGGCGGCGCACAUCCGAGCACAAAAACCCCAUCUGCUUGGCUGCACUGAUCUAGAUCUAGACUAUCUUUUAGCAUGGCUACAUGCAUACGUAUGUAUGUACACACAUAUAU
....((....))(((.(((...(((((((.............))))))).))).))).((((....))))..........(((((....)))))......((((((((....)))))))) ( -28.42)
>DroSec_CAF1 3093 108 - 1
UUCCCCUUUUGGCGGCGCACAUCCGAGCACAAAAACCCCAUGUGCUUGGCUGCACUGAUCUAGAUCUAGACUAUCUGUUAGCAUGGCUACAUACACACGUAUGUA------------UAU
....((..(((((((.(((...(((((((((.........))))))))).))).....((((....))))....)))))))...)).(((((((....)))))))------------... ( -29.60)
>DroSim_CAF1 3153 108 - 1
UUCCCCUUUUGGCGGCGCACAUCCGAGCACAAAAACCCCAUGUGCUUGGCUGCACUGAUCUAGAUCUAGACUAUCUGUUAGCAUGGCUACAUACACACGUAUGCA------------UAU
.........((((.(((((...(((((((((.........))))))))).))).....((((....))))..........))...))))(((((....)))))..------------... ( -26.90)
>DroYak_CAF1 3099 105 - 1
UUCCCCU-UUGGCGGCGCACGUCGAAACACAAAAACCUUAUGUGCUUGGAUGCACUGAUCUAGAUCUAGACUAUCUUUUAGCAUGGGUA--UGCAUACAUAUACA------------UAU
......(-((((((.....)))))))............((((((..((.(((((...(((((...(((((......)))))..))))).--))))).))..))))------------)). ( -24.70)
>consensus
UUCCCCUUUUGGCGGCGCACAUCCGAGCACAAAAACCCCAUGUGCUUGGCUGCACUGAUCUAGAUCUAGACUAUCUGUUAGCAUGGCUACAUACACACGUAUGCA____________UAU
....((....))(((.(((...(((((((((.........))))))))).))).))).((((....))))..........(((((....))))).......................... (-19.16 = -20.73 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:24 2006