Locus 7188

Sequence ID 3R_DroMel_CAF1
Location 18,957,610 – 18,957,787
Length 177
Max. P 0.958496
window11628 window11629 window11630 window11631 window11632 window11633

overview

Window 8

Location 18,957,610 – 18,957,728
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 91.20
Mean single sequence MFE -23.07
Consensus MFE -22.82
Energy contribution -22.60
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.23
Structure conservation index 0.99
SVM decision value 0.23
SVM RNA-class probability 0.644399
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957610 118 + 27905053
AAAAAAAACAUGAACAUGAAGAAAAUGAAGUAUGAAAAAGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAA
........((((..(((.......)))...))))..................((((.....))))(((((..........)))))((((((((..(..(....)..).)))))))).. ( -24.40)
>DroSec_CAF1 69039 105 + 1
-------------ACAUGAAGGAAAUGAAGUAUGAAAGAGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAA
-------------.....(((..(((.((((........(....)(..((((.........))))..)......)))).)))..)))((((((..(..(....)..).)))))).... ( -22.40)
>DroSim_CAF1 70185 105 + 1
-------------ACAUGAAGGAAAUGAAGUAUGAAAGAGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAA
-------------.....(((..(((.((((........(....)(..((((.........))))..)......)))).)))..)))((((((..(..(....)..).)))))).... ( -22.40)
>consensus
_____________ACAUGAAGGAAAUGAAGUAUGAAAGAGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAA
..................((((.(((.((((........(....)(..((((.........))))..)......)))).))).))))((((((..(..(....)..).)))))).... (-22.82 = -22.60 +  -0.22)

alignment

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secondary structure

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Window 9

Location 18,957,610 – 18,957,728
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 91.20
Mean single sequence MFE -18.06
Consensus MFE -17.79
Energy contribution -17.79
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.28
Structure conservation index 0.99
SVM decision value 0.27
SVM RNA-class probability 0.661365
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957610 118 - 27905053
UUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCUUUUUCAUACUUCAUUUUCUUCAUGUUCAUGUUUUUUUU
..((((((((...............))))))))((.(((.((((......(((((((...........)))).)))...........)))).))).)).................... ( -18.59)
>DroSec_CAF1 69039 105 - 1
UUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCUCUUUCAUACUUCAUUUCCUUCAUGU-------------
((((((((((...............)))))))))).(((.((((......(((((((...........)))).)))...........)))).)))..........------------- ( -17.79)
>DroSim_CAF1 70185 105 - 1
UUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCUCUUUCAUACUUCAUUUCCUUCAUGU-------------
((((((((((...............)))))))))).(((.((((......(((((((...........)))).)))...........)))).)))..........------------- ( -17.79)
>consensus
UUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCUCUUUCAUACUUCAUUUCCUUCAUGU_____________
((((((((((...............)))))))))).(((.((((......(((((((...........)))).)))...........)))).)))....................... (-17.79 = -17.79 +  -0.00)

alignment

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secondary structure

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Window 0

Location 18,957,648 – 18,957,757
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.42
Mean single sequence MFE -35.20
Consensus MFE -24.71
Energy contribution -26.23
Covariance contribution 1.52
Combinations/Pair 1.19
Mean z-score -2.11
Structure conservation index 0.70
SVM decision value 0.55
SVM RNA-class probability 0.776931
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957648 109 + 27905053
AGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUC-----------GGUCUUUGGGGCAGUU
..(..(((((((..(((((.((((((((((((..........)))))((((((((..(..(....)..).))))))))))).))))..)))))-----------..)))))))..).... ( -39.20)
>DroSec_CAF1 69064 109 + 1
AGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUC-----------GGUCUUUGGGGCAGUU
..(..(((((((..(((((.((((((((((((..........)))))((((((((..(..(....)..).))))))))))).))))..)))))-----------..)))))))..).... ( -39.20)
>DroSim_CAF1 70210 109 + 1
AGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUC-----------GGUCUUUGGGGCAGUU
..(..(((((((..(((((.((((((((((((..........)))))((((((((..(..(....)..).))))))))))).))))..)))))-----------..)))))))..).... ( -39.20)
>DroEre_CAF1 69220 109 + 1
AAGAACCAAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUC-----------GGUCUUUGGGGCAGUU
..(..(((((((..(((((.((((((((((((..........)))))((((((((..(..(....)..).))))))))))).))))..)))))-----------..)))))))..).... ( -39.70)
>DroAna_CAF1 71268 106 + 1
-----------AAAG-AAGGAAAUCUUGGCGAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGGUCGUAU--GGAGCAUUUUCCUCUCUCUUGUUAUUUGGUGUUUGGGGCAGUU
-----------.(((-(......))))(((((..........)))))(((.((((..(..(.((((.((......--((((....)))).....)).)))).)..)....)))).))).. ( -18.70)
>consensus
AGGAACCGAAGAGAGAGAGCAAAUCUUGGCAAGAAAACUUAAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUC___________GGUCUUUGGGGCAGUU
..(..((((((((((.(((.((((((((((((..........)))))((((((((..(..(....)..).))))))))))).)))).)))))).............)))))))..).... (-24.71 = -26.23 +   1.52)

alignment

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secondary structure

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Window 1

Location 18,957,648 – 18,957,757
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.42
Mean single sequence MFE -26.39
Consensus MFE -17.12
Energy contribution -17.48
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -2.06
Structure conservation index 0.65
SVM decision value 0.09
SVM RNA-class probability 0.578192
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957648 109 - 27905053
AACUGCCCCAAAGACC-----------GAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCU
............((((-----------((..(((....((((((((((((...............)))))))))).....(((((((......)))))))))....)))..))))))... ( -28.46)
>DroSec_CAF1 69064 109 - 1
AACUGCCCCAAAGACC-----------GAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCU
............((((-----------((..(((....((((((((((((...............)))))))))).....(((((((......)))))))))....)))..))))))... ( -28.46)
>DroSim_CAF1 70210 109 - 1
AACUGCCCCAAAGACC-----------GAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCU
............((((-----------((..(((....((((((((((((...............)))))))))).....(((((((......)))))))))....)))..))))))... ( -28.46)
>DroEre_CAF1 69220 109 - 1
AACUGCCCCAAAGACC-----------GAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUUGGUUCUU
....(..(((((((..-----------(((((((((((..((((((((((...............)))))))))).......))))))).((........))))))..)))))))..).. ( -31.66)
>DroAna_CAF1 71268 106 - 1
AACUGCCCCAAACACCAAAUAACAAGAGAGAGGAAAAUGCUCC--AUACGACCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUCGCCAAGAUUUCCUU-CUUU-----------
........................(((((.((((((..(((..--........)))...........(((.(((((......)))))...)))....)))))))-))))----------- ( -14.90)
>consensus
AACUGCCCCAAAGACC___________GAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUUAAGUUUUCUUGCCAAGAUUUGCUCUCUCUCUUCGGUUCCU
...........................(((((((.(((..((((((((((...............))))))))))..)))...))))))).............................. (-17.12 = -17.48 +   0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,957,688 – 18,957,787
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 99.19
Mean single sequence MFE -31.60
Consensus MFE -30.30
Energy contribution -30.50
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.96
SVM decision value 1.49
SVM RNA-class probability 0.958496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957688 99 + 27905053
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUCGGUCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......((((((((..(..(....)..).)))))))).((((....((......((((((..(((.........)))..)))))).....)).)))). ( -31.80)
>DroSec_CAF1 69104 99 + 1
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUCGGUCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......((((((((..(..(....)..).)))))))).((((....((......((((((..(((.........)))..)))))).....)).)))). ( -31.80)
>DroSim_CAF1 70250 99 + 1
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUCGGUCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......((((((((..(..(....)..).)))))))).((((....((......((((((..(((.........)))..)))))).....)).)))). ( -31.80)
>DroEre_CAF1 69260 99 + 1
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUCGGUCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......((((((((..(..(....)..).)))))))).((((....((......((((((..(((.........)))..)))))).....)).)))). ( -31.80)
>DroYak_CAF1 71376 99 + 1
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAACGGGCCAAAAGCAUUUUCUUCUCGGCCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......(((((((((.(..(....)..)))))))))).((((....((......((((.(..(((.........)))..)))))......)).)))). ( -30.80)
>consensus
AAUUGUCUUGGCCCGUUUUGGUUGGCUGAUCGGGCCAAAAGCAUUUUCUUCUCGGUCUUUGGGGCAGUUUCGUUAUGUUUCGGGGAAAACUGGUUGCUG
.......((((((((..(..(....)..).)))))))).((((....((......((((((..(((.........)))..)))))).....)).)))). (-30.30 = -30.50 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,957,688 – 18,957,787
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 99.19
Mean single sequence MFE -20.50
Consensus MFE -19.46
Energy contribution -19.46
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.95
SVM decision value 1.21
SVM RNA-class probability 0.931444
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957688 99 - 27905053
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGACCGAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUU
.......(((((((..............))))))).....................((.((((((((((...............))))))))))))... ( -19.30)
>DroSec_CAF1 69104 99 - 1
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGACCGAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUU
.......(((((((..............))))))).....................((.((((((((((...............))))))))))))... ( -19.30)
>DroSim_CAF1 70250 99 - 1
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGACCGAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUU
.......(((((((..............))))))).....................((.((((((((((...............))))))))))))... ( -19.30)
>DroEre_CAF1 69260 99 - 1
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGACCGAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUU
.......(((((((..............))))))).....................((.((((((((((...............))))))))))))... ( -19.30)
>DroYak_CAF1 71376 99 - 1
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGGCCGAGAAGAAAAUGCUUUUGGCCCGUUCAGCCAACCAAAACGGGCCAAGACAAUU
..(((....(((((....))))).........(.(((.....))).).........)))((((((((((((...........))))))))))))..... ( -25.30)
>consensus
CAGCAACCAGUUUUCCCCGAAACAUAACGAAACUGCCCCAAAGACCGAGAAGAAAAUGCUUUUGGCCCGAUCAGCCAACCAAAACGGGCCAAGACAAUU
.......(((((((..............))))))).....................((.((((((((((...............))))))))))))... (-19.46 = -19.46 +   0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:41 2006