Locus 8169

Sequence ID	3L_DroMel_CAF1
Location	21,514,868 – 21,515,053
Length	185
Max. P	0.988536

overview

Window 4

Location	21,514,868 – 21,514,973
Length	105
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	91.23
Mean single sequence MFE	-46.10
Consensus MFE	-44.27
Energy contribution	-44.17
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.85
Structure conservation index	0.96
SVM decision value	0.98
SVM RNA-class probability	0.893449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21514868 105 - 23771897
UGUUACUCCUCGUGAGAGGAGAGGGCCAGGGUGAUGGCCCAGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGCCGCCUCGAUGGCUC---------AAAUGGCAAAG
(((((((((((....)))))).((((((((((....)))).(((((..(.....(((((..(.....)..).)))).)..)))))...))))))---------...)))))... ( -44.40)
>DroSec_CAF1 19988 114 - 1
UGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGUGGCCGCCUCGAUGGCUCAAAUGGCUCAAAUGGCAAAG
.....((((((....)))))).((((((((((....))))((((((..(....((((((..(.....)..).))))))..))))))..)))))).....(((.....))).... ( -48.00)
>DroSim_CAF1 20098 114 - 1
UGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGCCGCCUCGAUGGCUCAAAUGGCUCAAAUGGCAAAG
.....((((((....)))))).((((((((((....))))((((((..(.....(((((..(.....)..).)))).)..))))))..)))))).....(((.....))).... ( -45.90)
>consensus
UGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGCCGCCUCGAUGGCUCAAAUGGCUCAAAUGGCAAAG
(((((((((((....)))))).((((((((((....))))((((((..(.....(((((..(.....)..).)))).)..))))))..))))))............)))))... (-44.27 = -44.17 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	21,514,893 – 21,515,013
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.66
Mean single sequence MFE	-52.60
Consensus MFE	-50.43
Energy contribution	-50.77
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.65
Structure conservation index	0.96
SVM decision value	2.12
SVM RNA-class probability	0.988536
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21514893 120 + 23771897
GCCGCAACUCCAGUCUCUCCAGGUCGUACAUGAUCGCCCUGGGCCAUCACCCUGGCCCUCUCCUCUCACGAGGAGUAACAGAAGAUGGGGUUGGAGAUGGGCAGGAGGUGGGCCGCGGCA
(((((...(((.((((((((((((((....)))))(((((((((((......)))))).((((((....))))))...........)))))))))))..))).)))((....))))))). ( -57.80)
>DroSec_CAF1 20022 108 + 1
GCCACAACUCCAGUCUCUCCAGGUCGUACAUGAUCGCCCCGGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA------------UGGGCAGGAGGUGGGCCGCGGCA
(((.(...((((...(((((.(((((....)))))((((.((((((......)))))).((((((....))))))..........------------.)))).)))))))))..).))). ( -47.30)
>DroSim_CAF1 20132 108 + 1
GCCGCAACUCCAGUCUCUCCAGGUCGUACAUGAUCGCCCCGGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA------------UGGGCAGGAGGUGGGCCGCGGCA
(((((...((((...(((((.(((((....)))))((((.((((((......)))))).((((((....))))))..........------------.)))).)))))))))..))))). ( -52.70)
>consensus
GCCGCAACUCCAGUCUCUCCAGGUCGUACAUGAUCGCCCCGGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA____________UGGGCAGGAGGUGGGCCGCGGCA
(((((...((((...(((((.(((((....)))))((((.((((((......)))))).((((((....)))))).......................)))).)))))))))..))))). (-50.43 = -50.77 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	21,514,893 – 21,515,013
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.66
Mean single sequence MFE	-53.50
Consensus MFE	-53.72
Energy contribution	-53.50
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.98
Structure conservation index	1.00
SVM decision value	1.89
SVM RNA-class probability	0.981534
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21514893 120 - 23771897
UGCCGCGGCCCACCUCCUGCCCAUCUCCAACCCCAUCUUCUGUUACUCCUCGUGAGAGGAGAGGGCCAGGGUGAUGGCCCAGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGC
.((((((((((((((((.((((.......................((((((....)))))).((((((......)))))).))))(.((......)).).)))).)..))).)))))))) ( -56.80)
>DroSec_CAF1 20022 108 - 1
UGCCGCGGCCCACCUCCUGCCCA------------UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGUGGC
.((((((((((((((((.((((.------------..........((((((....)))))).((((((......)))))).))))(.((......)).).)))).)..))).)))))))) ( -50.90)
>DroSim_CAF1 20132 108 - 1
UGCCGCGGCCCACCUCCUGCCCA------------UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGC
.((((((((((((((((.((((.------------..........((((((....)))))).((((((......)))))).))))(.((......)).).)))).)..))).)))))))) ( -52.80)
>consensus
UGCCGCGGCCCACCUCCUGCCCA____________UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCCGGGGCGAUCAUGUACGACCUGGAGAGACUGGAGUUGCGGC
.((((((((((((((((.((((.......................((((((....)))))).((((((......)))))).))))(.((......)).).)))).)..))).)))))))) (-53.72 = -53.50 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	21,514,933 – 21,515,053
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.23
Mean single sequence MFE	-53.06
Consensus MFE	-51.09
Energy contribution	-50.87
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.96
SVM decision value	1.26
SVM RNA-class probability	0.936750
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21514933 120 + 23771897
GGGCCAUCACCCUGGCCCUCUCCUCUCACGAGGAGUAACAGAAGAUGGGGUUGGAGAUGGGCAGGAGGUGGGCCGCGGCACAGGCGUUGCGUCUGGCACGGGCUAGUGGCCAUAAUUCUC
.((((((((((((.(((((((((.(((((.....))..((.....)))))..))))).)))).)).))))((((.((((.((((((...)))))))).)))))).))))))......... ( -55.30)
>DroSec_CAF1 20062 108 + 1
GGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA------------UGGGCAGGAGGUGGGCCGCGGCACAGGCGUUGGGUCUGGCACGGGCUAGUGGCCAUAAUUCUC
.((((((.((((.(((((((((((.((((................------------)))).)))))).)))))...((.(((((.....)))))))..))))..))))))......... ( -51.59)
>DroSim_CAF1 20172 108 + 1
GGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA------------UGGGCAGGAGGUGGGCCGCGGCACAGGCGUUGCGUCUGGCACGGGCUAGUGGCCAUAAUUCUC
.((((((.((((.(((((((((((.((((................------------)))).)))))).)))))...((.((((((...))))))))..))))..))))))......... ( -52.29)
>consensus
GGGCCAUCGCCCUGGCCCUCUCCUCUCCAGAGGAGCAACAGAAGA____________UGGGCAGGAGGUGGGCCGCGGCACAGGCGUUGCGUCUGGCACGGGCUAGUGGCCAUAAUUCUC
.((((((((((((.((((.((((((....))))))...(....)..............)))).)).))))((((.((((.(((((.....))))))).)))))).))))))......... (-51.09 = -50.87 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	21,514,933 – 21,515,053
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-45.23
Consensus MFE	-43.49
Energy contribution	-43.27
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.22
Structure conservation index	0.96
SVM decision value	0.07
SVM RNA-class probability	0.569731
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21514933 120 - 23771897
GAGAAUUAUGGCCACUAGCCCGUGCCAGACGCAACGCCUGUGCCGCGGCCCACCUCCUGCCCAUCUCCAACCCCAUCUUCUGUUACUCCUCGUGAGAGGAGAGGGCCAGGGUGAUGGCCC
.........(((((...(((((.(((((.((...)).))).)))).))).(((((...((((......(((..........))).((((((....)))))).))))..))))).))))). ( -47.90)
>DroSec_CAF1 20062 108 - 1
GAGAAUUAUGGCCACUAGCCCGUGCCAGACCCAACGCCUGUGCCGCGGCCCACCUCCUGCCCA------------UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCC
.........(((((...(((((((((((.........))).).)))(((((..(((((...((------------........))((((...))))))))).))))).))))..))))). ( -43.30)
>DroSim_CAF1 20172 108 - 1
GAGAAUUAUGGCCACUAGCCCGUGCCAGACGCAACGCCUGUGCCGCGGCCCACCUCCUGCCCA------------UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCC
.........(((((...(((((((((((.((...)).))).).)))(((((..(((((...((------------........))((((...))))))))).))))).))))..))))). ( -44.50)
>consensus
GAGAAUUAUGGCCACUAGCCCGUGCCAGACGCAACGCCUGUGCCGCGGCCCACCUCCUGCCCA____________UCUUCUGUUGCUCCUCUGGAGAGGAGAGGGCCAGGGCGAUGGCCC
.........(((((...(((((((((((.(.....).))).).)))(((((..(....)..........................((((((....)))))).))))).))))..))))). (-43.49 = -43.27 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:19 2006