Locus 8653

Sequence ID	X_DroMel_CAF1
Location	21,864,773 – 21,864,906
Length	133
Max. P	0.681161

overview

Window 1

Location	21,864,773 – 21,864,877
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.77
Mean single sequence MFE	-32.45
Consensus MFE	-27.85
Energy contribution	-26.91
Covariance contribution	-0.94
Combinations/Pair	1.21
Mean z-score	-1.68
Structure conservation index	0.86
SVM decision value	0.31
SVM RNA-class probability	0.681161
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21864773 104 + 22224390
----------UCUCUGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG------UUGCCUCUUGCGGUGAAUGUCGCAAAUGCAACUAAAAUGUUGC
----------((.((((.((((((((((.((((.((((......)))).))))......(.((....))))------))))))))))))).))...........(((((......))))) ( -32.00)
>DroVir_CAF1 27423 108 + 1
CUUG------CCAACGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGUG------CUGCCUCUUGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGC
.(((------(((.....(((((((....((((.((((......)))).)))).....(((((....)).)------))))))))).))))))..(((((....)))))........... ( -31.30)
>DroGri_CAF1 25041 108 + 1
CUUG------CAAAUGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUGCUUCUGGCG------UUGCCUCUCGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGC
.(((------(((..((..(((((((...((((.((((......)))).)))).......))))))).))(------(((((......))).))).))))))..(((((......))))) ( -33.40)
>DroWil_CAF1 26683 120 + 1
CAUACCAGCUCCAGUGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGCGACGGCAUUGCCUCUUGUGGCGAACGUCGCAAAUGCAACUAAAAUGUUGC
..(((.((..(((((((......)))...((((.((((......)))).))))...))))..)).)))((((((...(((((......))))).))))))....(((((......))))) ( -35.50)
>DroMoj_CAF1 35102 108 + 1
CUUG------CCAACGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGUG------CUGCCUCUUGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGC
.(((------(((.....(((((((....((((.((((......)))).)))).....(((((....)).)------))))))))).))))))..(((((....)))))........... ( -31.30)
>DroAna_CAF1 20895 104 + 1
----------ACUGUGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG------UUGCCUCUUGCGGUGAGCGUCGCAAAUGCAACUAAAAUGUUGC
----------....((((((((((((((.((((.((((......)))).))))......(.((....))))------)))))))).((.....)).)))))...(((((......))))) ( -31.20)
>consensus
CUUG______CCAAUGCGAAGAGGCAAUUCAUUAGCUUUAAUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG______UUGCCUCUUGUGGCGAACGUCGCAAAUGCAACUAAAAUGUUGC
..............(((((.(((((((.......(((...((..(((.......)))..))......))).......))))))))))))((((...))))....(((((......))))) (-27.85 = -26.91 +  -0.94)

alignment

secondary structure

dotplot

Window 2

Location	21,864,803 – 21,864,906
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.30
Mean single sequence MFE	-33.18
Consensus MFE	-21.53
Energy contribution	-21.37
Covariance contribution	-0.16
Combinations/Pair	1.17
Mean z-score	-2.23
Structure conservation index	0.65
SVM decision value	0.13
SVM RNA-class probability	0.600161
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21864803 103 + 22224390
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG------UUGCCUCUUGCGGUGAAUGUCGCAAAUGCAACUAAAAUGUUGCGGUUACCGUCAUUUCC---------GCCCACA-GCCACG-
.....((.(((((....((((((((((((((------(((((......))).))))))))))..(((((......)))))))..)))).)))))))---------.......-......- ( -30.90)
>DroVir_CAF1 27457 105 + 1
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGUG------CUGCCUCUUGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGCGGUUACCUCCAUUUUC---------AUUUGCUUACCACAU
...((((((((((....(((.......((((------..(((..(((..((....))..)))..(((((......)))))))))))).)))....)---------)))))))))...... ( -31.10)
>DroGri_CAF1 25075 105 + 1
AUUUAGGUAAAUGUCCUUGGUGCUUCUGGCG------UUGCCUCUCGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGCGGUUACCGCUGUUUUC---------AUUUGCUUGCCACAU
....((((((.((((...((....)).))))------))))))...(((((((.((((((....)))))..(((((..(((((....)))))...)---------))))).))))))).. ( -32.50)
>DroWil_CAF1 26723 119 + 1
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGCGACGGCAUUGCCUCUUGUGGCGAACGUCGCAAAUGCAACUAAAAUGUUGCGGUAACCGCCAUUUUCAUUUGGGCCACCCGCU-UCCAACU
.....((.....((...((((((..(((((((((...(((((......))))).))))))....(((((......)))))(((....))).....)))..))))))...)).-.)).... ( -41.90)
>DroMoj_CAF1 35136 105 + 1
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGUG------CUGCCUCUUGUGGCGAACGUUGCAAAUGCAACUAAAAUGUUGCGGUUACCUCCAUUUUC---------AUUUGCUUACCACAU
...((((((((((....(((.......((((------..(((..(((..((....))..)))..(((((......)))))))))))).)))....)---------)))))))))...... ( -31.10)
>DroAna_CAF1 20925 104 + 1
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG------UUGCCUCUUGCGGUGAGCGUCGCAAAUGCAACUAAAAUGUUGCGGUUACCAUCAUUCCC---------GCCCACU-GCCACAU
.....((((((((....((((((((((((((------(((((......))).))))))))))..(((((......)))))))..)))).))))...---------......)-))).... ( -31.60)
>consensus
AUUUAGGUAAAUGUCCUUGGUCCUUGUGGCG______UUGCCUCUUGUGGCGAACGUCGCAAAUGCAACUAAAAUGUUGCGGUUACCGCCAUUUUC_________ACCCGCU_GCCACAU
.....(((((.............((((((((......(((((......))))).)))))))).((((((......)))))).)))))................................. (-21.53 = -21.37 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	21,864,803 – 21,864,906
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.30
Mean single sequence MFE	-31.12
Consensus MFE	-20.41
Energy contribution	-19.93
Covariance contribution	-0.47
Combinations/Pair	1.22
Mean z-score	-2.06
Structure conservation index	0.66
SVM decision value	0.06
SVM RNA-class probability	0.565184
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21864803 103 - 22224390
-CGUGGC-UGUGGGC---------GGAAAUGACGGUAACCGCAACAUUUUAGUUGCAUUUGCGACAUUCACCGCAAGAGGCAA------CGCCACAAGGACCAAGGACAUUUACCUAAAU
-.(((((-(((..((---------((............)))).))).....(((((.((((((........))))))..))))------))))))........(((.......))).... ( -31.20)
>DroVir_CAF1 27457 105 - 1
AUGUGGUAAGCAAAU---------GAAAAUGGAGGUAACCGCAACAUUUUAGUUGCAUUUGCAACGUUCGCCACAAGAGGCAG------CACCACAAGGACCAAGGACAUUUACCUAAAU
.((((((..((((((---------......((......))(((((......)))))))))))...(((.(((......)))))------))))))).......(((.......))).... ( -29.30)
>DroGri_CAF1 25075 105 - 1
AUGUGGCAAGCAAAU---------GAAAACAGCGGUAACCGCAACAUUUUAGUUGCAUUUGCAACGUUCGCCACGAGAGGCAA------CGCCAGAAGCACCAAGGACAUUUACCUAAAU
.(.((((..((((((---------(......((((...))))(((......))).)))))))...(((.(((......)))))------))))).).......(((.......))).... ( -28.60)
>DroWil_CAF1 26723 119 - 1
AGUUGGA-AGCGGGUGGCCCAAAUGAAAAUGGCGGUUACCGCAACAUUUUAGUUGCAUUUGCGACGUUCGCCACAAGAGGCAAUGCCGUCGCCACAAGGACCAAGGACAUUUACCUAAAU
...(((.-....(((((((...((....))...)))))))(((((......)))))....((((((...(((......))).....))))))........)))(((.......))).... ( -34.70)
>DroMoj_CAF1 35136 105 - 1
AUGUGGUAAGCAAAU---------GAAAAUGGAGGUAACCGCAACAUUUUAGUUGCAUUUGCAACGUUCGCCACAAGAGGCAG------CACCACAAGGACCAAGGACAUUUACCUAAAU
.((((((..((((((---------......((......))(((((......)))))))))))...(((.(((......)))))------))))))).......(((.......))).... ( -29.30)
>DroAna_CAF1 20925 104 - 1
AUGUGGC-AGUGGGC---------GGGAAUGAUGGUAACCGCAACAUUUUAGUUGCAUUUGCGACGCUCACCGCAAGAGGCAA------CGCCACAAGGACCAAGGACAUUUACCUAAAU
.((((((-.((..((---------((..((....))..)))).))......(((((.((((((........))))))..))))------))))))).......(((.......))).... ( -33.60)
>consensus
AUGUGGC_AGCAAAU_________GAAAAUGGCGGUAACCGCAACAUUUUAGUUGCAUUUGCAACGUUCGCCACAAGAGGCAA______CGCCACAAGGACCAAGGACAUUUACCUAAAU
..(((((..(((((...................((...))(((((......))))).))))).......(((......))).........)))))........(((.......))).... (-20.41 = -19.93 +  -0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:29 2006