Locus 2760

Sequence ID 2L_DroMel_CAF1
Location 7,782,152 – 7,782,285
Length 133
Max. P 0.954205
window4384 window4385 window4386 window4387

overview

Window 4

Location 7,782,152 – 7,782,245
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 63.82
Mean single sequence MFE -35.48
Consensus MFE -12.27
Energy contribution -10.08
Covariance contribution -2.19
Combinations/Pair 1.53
Mean z-score -1.90
Structure conservation index 0.35
SVM decision value 0.54
SVM RNA-class probability 0.774070
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7782152 93 + 22407834
--------------------------GC-GUGGCUUUGAGCAGCACAAUCGCAUCCGUGAAGUCAUCCAACAGAAGAAAGUGCUGGAGACCAUGUUGCAGCAGCACAAGAAGCUGCAAAG
--------------------------((-(((((((....((((((..((((....))))..((.((.....)).))..))))))))).))))))((((((..(....)..))))))... ( -29.90)
>DroVir_CAF1 59566 120 + 1
GAGGCGCGGCUACUCGGAGAUUGGUCCAAAGAGUUUUAGCAAUCAGCGACGUAUUCGAGAGGUGCUGCUGCAGAAAACUGUGCUAGAGAACAUGUUGUUACAGCACAAGAGAUUGCAGCG
.....(((.((.((((((......)))...((((....((.....)).....))))))))).))).(((((((.....((((((....(((.....)))..)))))).....))))))). ( -35.60)
>DroPse_CAF1 33998 120 + 1
GCGACGCGGAUUGAACGAUACUGGUGGCAAGAGUUUCCACAAUCAGCGUCGCAUUCGAGAGGUGUUGCAGCAGAAGGUCAUGCUGGAGCAAAUGCUGUUGCAGCACAAGAGACUGCAGCG
(((((((.(((((........(((..((....))..)))))))).)))))(((.((.....((((((((((((.......(((....)))....))))))))))))....)).))).)). ( -47.10)
>DroSec_CAF1 35101 93 + 1
--------------------------GC-GGGGCUUUGAGCAGCACAGCCGCAUUCGUGAAGUCAUCCAACAGAAGAAAGUGCUGGAGACCAUGUUGCAGCAGCACAAGAAGCUGCAAAG
--------------------------..-..((((.((.....)).))))(((..((((..(((.((((.((........)).))))))))))).))).(((((.......))))).... ( -29.00)
>DroYak_CAF1 29934 93 + 1
--------------------------GA-GGGGCUUUGAACAGAACAGCCGCAUCCGAGAGGUCAUUCAACAGAAGAAGGUGCUGGAGACCAUGUUGCAGCAGCACAAGAAGCUGCAAAG
--------------------------..-(.((((.(.......).)))).)........((((.((((.((........)).))))))))...(((((((..(....)..))))))).. ( -24.80)
>DroPer_CAF1 34091 120 + 1
GCGGCGCGGAUUGAACGAUACUGGUGGCAAGAGUUUCCACAAUCAGCGUCGCAUUCGAGAGGUGUUGCAGCAGAAGGUAAUGCUGGAGCAAAUGCUGUUGCAGCACAAGAGACUGCAGCG
(((((((.(((((........(((..((....))..)))))))).)))))(((.((.....((((((((((((.......(((....)))....))))))))))))....)).))).)). ( -46.50)
>consensus
__________________________GC_AGAGCUUUGACAAGCACAGUCGCAUUCGAGAGGUCAUGCAACAGAAGAAAGUGCUGGAGAACAUGUUGCAGCAGCACAAGAAACUGCAAAG
...............................((((((.............((((.......((......))........)))).........(((((...)))))...))))))...... (-12.27 = -10.08 +  -2.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,782,152 – 7,782,245
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 63.82
Mean single sequence MFE -32.12
Consensus MFE -13.04
Energy contribution -11.79
Covariance contribution -1.25
Combinations/Pair 1.50
Mean z-score -2.12
Structure conservation index 0.41
SVM decision value 1.44
SVM RNA-class probability 0.954205
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7782152 93 - 22407834
CUUUGCAGCUUCUUGUGCUGCUGCAACAUGGUCUCCAGCACUUUCUUCUGUUGGAUGACUUCACGGAUGCGAUUGUGCUGCUCAAAGCCAC-GC--------------------------
..(((((((..(....)..)))))))..((((...((((((..((.(((((.(((....))))))))...))..))))))......)))).-..-------------------------- ( -29.30)
>DroVir_CAF1 59566 120 - 1
CGCUGCAAUCUCUUGUGCUGUAACAACAUGUUCUCUAGCACAGUUUUCUGCAGCAGCACCUCUCGAAUACGUCGCUGAUUGCUAAAACUCUUUGGACCAAUCUCCGAGUAGCCGCGCCUC
.((((((.....((((((((.(((.....)))...)))))))).....)))))).........((..(((.(((..((((((((((....)))))..)))))..))))))..))...... ( -32.00)
>DroPse_CAF1 33998 120 - 1
CGCUGCAGUCUCUUGUGCUGCAACAGCAUUUGCUCCAGCAUGACCUUCUGCUGCAACACCUCUCGAAUGCGACGCUGAUUGUGGAAACUCUUGCCACCAGUAUCGUUCAAUCCGCGUCGC
.((.((((....(..(((((....(((....))).)))))..)....)))).))..............(((((((.(((((..((.(((.........))).))...))))).))))))) ( -39.60)
>DroSec_CAF1 35101 93 - 1
CUUUGCAGCUUCUUGUGCUGCUGCAACAUGGUCUCCAGCACUUUCUUCUGUUGGAUGACUUCACGAAUGCGGCUGUGCUGCUCAAAGCCCC-GC--------------------------
(((((.(((.....(..(.((((((....(((((((((((........))))))).)))).......)))))).)..).))))))))....-..-------------------------- ( -32.60)
>DroYak_CAF1 29934 93 - 1
CUUUGCAGCUUCUUGUGCUGCUGCAACAUGGUCUCCAGCACCUUCUUCUGUUGAAUGACCUCUCGGAUGCGGCUGUUCUGUUCAAAGCCCC-UC--------------------------
....(((((.......))))).(((.(..((((..(((((........)))))...)))).....).)))((((...........))))..-..-------------------------- ( -25.40)
>DroPer_CAF1 34091 120 - 1
CGCUGCAGUCUCUUGUGCUGCAACAGCAUUUGCUCCAGCAUUACCUUCUGCUGCAACACCUCUCGAAUGCGACGCUGAUUGUGGAAACUCUUGCCACCAGUAUCGUUCAAUCCGCGCCGC
.((.((((......((((((....(((....))).))))))......)))).))..............(((.(((.(((((..((.(((.........))).))...))))).))).))) ( -33.80)
>consensus
CGCUGCAGCCUCUUGUGCUGCAACAACAUGGUCUCCAGCACUUUCUUCUGCUGCAUCACCUCUCGAAUGCGACGCUGAUGGUCAAAACCCC_GC__________________________
.((.((((......((((((...............))))))......)))).)).................................................................. (-13.04 = -11.79 +  -1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,782,165 – 7,782,285
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.94
Mean single sequence MFE -40.17
Consensus MFE -20.98
Energy contribution -23.76
Covariance contribution 2.78
Combinations/Pair 1.21
Mean z-score -2.23
Structure conservation index 0.52
SVM decision value 0.91
SVM RNA-class probability 0.879523
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7782165 120 + 22407834
CAGCACAAUCGCAUCCGUGAAGUCAUCCAACAGAAGAAAGUGCUGGAGACCAUGUUGCAGCAGCACAAGAAGCUGCAAAGCGAUCGACACACCAUAGCGAUGGAUAUCCAGCGAAUGCGU
..((((.(((((...((((..(((.((((.((........)).)))))))))))(((((((..(....)..))))))).))))).)...........((.(((....))).))..))).. ( -34.00)
>DroVir_CAF1 59606 120 + 1
AAUCAGCGACGUAUUCGAGAGGUGCUGCUGCAGAAAACUGUGCUAGAGAACAUGUUGUUACAGCACAAGAGAUUGCAGCGCGACAGGCAAACGAUUGCCUCGGACAUACAGCGGAUGCGU
........(((((((((....((((((((((((.....((((((....(((.....)))..)))))).....))))))).....((((((....)))))).)).)))....))))))))) ( -40.40)
>DroPse_CAF1 34038 120 + 1
AAUCAGCGUCGCAUUCGAGAGGUGUUGCAGCAGAAGGUCAUGCUGGAGCAAAUGCUGUUGCAGCACAAGAGACUGCAGCGCGACAGGCAGACCAUAGCUCUGGACAUACAGCGGAUGCGU
.........((((((((....(((((.(((.((..((((.((((.((((....)))((((((((......).)))))))....).))))))))....))))))))))....)))))))). ( -44.00)
>DroYak_CAF1 29947 120 + 1
CAGAACAGCCGCAUCCGAGAGGUCAUUCAACAGAAGAAGGUGCUGGAGACCAUGUUGCAGCAGCACAAGAAGCUGCAAAGCGAUCGUCACACCAUAGCAAUGGACAUCCAGCGAAUGCGU
.........(((((((....))..................((((((((((...(((((.(((((.......)))))...))))).)))...((((....))))...))))))).))))). ( -36.50)
>DroMoj_CAF1 42299 120 + 1
AAUCAGCGCCGCAUUCGUGAGGUGUUGCUGCAAAAAACUGUGCUAGAGAAUAUGUUGUUACAGCACAAGAGAUUGCAGCGCGACAGGCAAACAAUUGCGCUGGAUAUACAGCGAAUGCGA
.........(((((((((...((((((((((((.....((((((.((.((....)).))..)))))).....)))))))....(((((((....)))).))))))))...))))))))). ( -42.70)
>DroPer_CAF1 34131 120 + 1
AAUCAGCGUCGCAUUCGAGAGGUGUUGCAGCAGAAGGUAAUGCUGGAGCAAAUGCUGUUGCAGCACAAGAGACUGCAGCGCGACAGGCAGACCAUAGCUCUGGACAUACAGCGGAUGCGU
.........((((((((....(((((.(((((........)))))((((...(((.((((((((......).))))))))))...((....))...))))..)))))....)))))))). ( -43.40)
>consensus
AAUCAGCGUCGCAUUCGAGAGGUGUUGCAGCAGAAGAAAGUGCUGGAGAACAUGUUGUUGCAGCACAAGAGACUGCAGCGCGACAGGCAAACCAUAGCGCUGGACAUACAGCGAAUGCGU
.........((((((((....(((((((((.........((((((.((.........)).))))))......)))))))))..................(((......))))))))))). (-20.98 = -23.76 +   2.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,782,165 – 7,782,285
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.94
Mean single sequence MFE -38.51
Consensus MFE -21.28
Energy contribution -19.81
Covariance contribution -1.47
Combinations/Pair 1.33
Mean z-score -2.08
Structure conservation index 0.55
SVM decision value 0.84
SVM RNA-class probability 0.863015
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7782165 120 - 22407834
ACGCAUUCGCUGGAUAUCCAUCGCUAUGGUGUGUCGAUCGCUUUGCAGCUUCUUGUGCUGCUGCAACAUGGUCUCCAGCACUUUCUUCUGUUGGAUGACUUCACGGAUGCGAUUGUGCUG
.((((((((((((....)))..))....(((.((((((((..(((((((..(....)..)))))))..)))))(((((((........))))))).)))..))))))))))......... ( -44.70)
>DroVir_CAF1 59606 120 - 1
ACGCAUCCGCUGUAUGUCCGAGGCAAUCGUUUGCCUGUCGCGCUGCAAUCUCUUGUGCUGUAACAACAUGUUCUCUAGCACAGUUUUCUGCAGCAGCACCUCUCGAAUACGUCGCUGAUU
....(((.(((((((...((((((((....)))))....((((((((.....((((((((.(((.....)))...)))))))).....)))))).)).....))).)))))..)).))). ( -35.90)
>DroPse_CAF1 34038 120 - 1
ACGCAUCCGCUGUAUGUCCAGAGCUAUGGUCUGCCUGUCGCGCUGCAGUCUCUUGUGCUGCAACAGCAUUUGCUCCAGCAUGACCUUCUGCUGCAACACCUCUCGAAUGCGACGCUGAUU
....(((.((.(((.(.(((......))).))))..(((((((.((((....(..(((((....(((....))).)))))..)....)))).)).....(....)...))))))).))). ( -34.30)
>DroYak_CAF1 29947 120 - 1
ACGCAUUCGCUGGAUGUCCAUUGCUAUGGUGUGACGAUCGCUUUGCAGCUUCUUGUGCUGCUGCAACAUGGUCUCCAGCACCUUCUUCUGUUGAAUGACCUCUCGGAUGCGGCUGUUCUG
.(((((((((((((.(((((((.....)))).)))(((((..(((((((..(....)..)))))))..)))))))))))....(((((....))).))......)))))))......... ( -43.50)
>DroMoj_CAF1 42299 120 - 1
UCGCAUUCGCUGUAUAUCCAGCGCAAUUGUUUGCCUGUCGCGCUGCAAUCUCUUGUGCUGUAACAACAUAUUCUCUAGCACAGUUUUUUGCAGCAACACCUCACGAAUGCGGCGCUGAUU
(((((((((.((......(((.((((....)))))))....(((((((....((((((((...............))))))))....))))))).......)))))))))))........ ( -39.16)
>DroPer_CAF1 34131 120 - 1
ACGCAUCCGCUGUAUGUCCAGAGCUAUGGUCUGCCUGUCGCGCUGCAGUCUCUUGUGCUGCAACAGCAUUUGCUCCAGCAUUACCUUCUGCUGCAACACCUCUCGAAUGCGACGCUGAUU
....(((.((.(((.(.(((......))).))))..(((((((.((((......((((((....(((....))).))))))......)))).)).....(....)...))))))).))). ( -33.50)
>consensus
ACGCAUCCGCUGUAUGUCCAGAGCUAUGGUCUGCCUGUCGCGCUGCAGUCUCUUGUGCUGCAACAACAUGUUCUCCAGCACAAUCUUCUGCUGCAACACCUCUCGAAUGCGACGCUGAUU
.(((((.((.............((.((.(.....).)).))((.((((......((((((...............))))))......)))).)).........)).)))))......... (-21.28 = -19.81 +  -1.47)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:33 2006