Locus 1172

Sequence ID 2L_DroMel_CAF1
Location 3,213,776 – 3,213,925
Length 149
Max. P 0.949115
window1900 window1901 window1902

overview

Window 0

Location 3,213,776 – 3,213,887
Length 111
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 92.51
Mean single sequence MFE -28.07
Consensus MFE -21.55
Energy contribution -22.15
Covariance contribution 0.60
Combinations/Pair 1.15
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value 0.49
SVM RNA-class probability 0.754893
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3213776 111 + 22407834
CAAAGGGCGGCACGGCAAAAA-AAAAAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAACAAGUCCAGGCGAGAAGUUGGGAGUGUGU----GUGCGGCCGGGAAGG
.....(((.((((((((....-............(((((((.....((....((.((((((.....))))))))....))....))))))).))).)----)))).)))....... ( -28.13)
>DroSec_CAF1 47917 110 + 1
CAAAGGGCGGCACGGCAAAAA--AAAAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAGCAAGUCCAGGCGAGAAGUUGAGAGUGUGU----GUGCGGCAGGGAAGG
......((.((((((((....--...........(((((((.....((....((.((((((.....))))))))....))....))))))).))).)----)))).))........ ( -25.79)
>DroSim_CAF1 46346 109 + 1
CAAAGGGCGGCACGGCAAAAA---AAAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAACAAGUCCAGGCGAGAAGUUGAGAGUGUGU----GUGCGGCCGGGAAGG
.....(((.((((((((....---..........(((((((.....((....((.((((((.....))))))))....))....))))))).))).)----)))).)))....... ( -29.16)
>DroEre_CAF1 44502 109 + 1
CAAAGGGCGGCACGGCGCAAA-AAAGAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAACAAGUCCAGGCGAGAAGUUGAAAGUGUGUGC------GGCCGGGAAGG
.....(((.(((((.(((...-......((....))(((((.....((....((.((((((.....))))))))....))....)))))..))))))))------.)))....... ( -27.30)
>DroYak_CAF1 43093 116 + 1
CAAAGGGCGGCACGGCAAAAAAAAAAAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAACAAGUCCAGGCGAGCAGUUGAGAGUGUGUGCGUGUGUGGCCGGGAAGG
.....(((.((((((((.................(((((((.....((....((.((((((.....))))))))....))....))))))).....))).))))).)))....... ( -29.95)
>consensus
CAAAGGGCGGCACGGCAAAAA_AAAAAAGAAAAAUCUCAACCAAACCGAACAGAACUUGUUUAUGAAACAAGUCCAGGCGAGAAGUUGAGAGUGUGU____GUGCGGCCGGGAAGG
.....(((.((((.(((.................(((((((.....((....((.((((((.....))))))))....))....)))))))...)))....)))).)))....... (-21.55 = -22.15 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,213,776 – 3,213,887
Length 111
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 92.51
Mean single sequence MFE -27.35
Consensus MFE -20.76
Energy contribution -22.20
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -2.62
Structure conservation index 0.76
SVM decision value 1.33
SVM RNA-class probability 0.943122
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3213776 111 - 22407834
CCUUCCCGGCCGCAC----ACACACUCCCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUUUUU-UUUUUGCCGUGCCGCCCUUUG
.......(((.((((----.........(((((..(((...(((((((((.....)))))))))....)))...)))))(((....))).....-........)))).)))..... ( -28.00)
>DroSec_CAF1 47917 110 - 1
CCUUCCCUGCCGCAC----ACACACUCUCAACUUCUCGCCUGGACUUGCUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUUUU--UUUUUGCCGUGCCGCCCUUUG
........((.((((----......((((((((....(((.((((..((((.......))))...)))))))..)))))))).....(.....--.....)..)))).))...... ( -23.10)
>DroSim_CAF1 46346 109 - 1
CCUUCCCGGCCGCAC----ACACACUCUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUUU---UUUUUGCCGUGCCGCCCUUUG
.......(((.((((----......((((((((..(((...(((((((((.....)))))))))....)))...)))))))).....(....---.....)..)))).)))..... ( -29.80)
>DroEre_CAF1 44502 109 - 1
CCUUCCCGGCC------GCACACACUUUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUCUUU-UUUGCGCCGUGCCGCCCUUUG
.......(((.------((((......((((((..(((...(((((((((.....)))))))))....)))...))))))((....))......-........)))).)))..... ( -28.80)
>DroYak_CAF1 43093 116 - 1
CCUUCCCGGCCACACACGCACACACUCUCAACUGCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUUUUUUUUUUUGCCGUGCCGCCCUUUG
.......(((..(((..(((.....(((((((((((.((..(((((((((.....))))))))).))..)))..)))))))).................))).)))..)))..... ( -27.05)
>consensus
CCUUCCCGGCCGCAC____ACACACUCUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGAGAUUUUUCUUUUUU_UUUUUGCCGUGCCGCCCUUUG
.......(((.((((..........((((((((..(((...(((((((((.....)))))))))....)))...)))))))).....(............)..)))).)))..... (-20.76 = -22.20 +   1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,213,811 – 3,213,925
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.05
Mean single sequence MFE -27.38
Consensus MFE -22.62
Energy contribution -23.98
Covariance contribution 1.36
Combinations/Pair 1.06
Mean z-score -2.05
Structure conservation index 0.83
SVM decision value 1.39
SVM RNA-class probability 0.949115
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3213811 114 - 22407834
UUUUUAUAUA--AUUUUUCUGAGUGUUCAAGUGUCACCGCCCUUCCCGGCCGCAC----ACACACUCCCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
..........--........((((((....((((..(((.......)))..))))----..)))))).(((((..(((...(((((((((.....)))))))))....)))...))))). ( -29.00)
>DroSec_CAF1 47951 114 - 1
UCUCUCUAUA--AUUUCUCUGAGUGUUCAAGUGUCACCGCCCUUCCCUGCCGCAC----ACACACUCUCAACUUCUCGCCUGGACUUGCUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
..........--........((((((....((((....((........)).))))----..))))))((((((....(((.((((..((((.......))))...)))))))..)))))) ( -23.00)
>DroSim_CAF1 46379 114 - 1
UCUCUCUAUA--AUUUUUCUGAGUGUUGAAGUGUCACCGCCCUUCCCGGCCGCAC----ACACACUCUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
..........--........((((((....((((..(((.......)))..))))----..))))))((((((..(((...(((((((((.....)))))))))....)))...)))))) ( -30.00)
>DroEre_CAF1 44537 110 - 1
----UAUAUAAUAUUUCUCUGAGUGUUCUAGUGUCACCGCCCUUCCCGGCC------GCACACACUUUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
----................((((((....((((..(((.......)))..------))))))))))((((((..(((...(((((((((.....)))))))))....)))...)))))) ( -27.20)
>DroYak_CAF1 43129 106 - 1
--------------UUCUCUCAGUGUUGAAGUGUCACCGCCCUUCCCGGCCACACACGCACACACUCUCAACUGCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
--------------.......(((((....((((....(((......)))...))))....))))).(((((((((.((..(((((((((.....))))))))).))..)))..)))))) ( -27.70)
>consensus
U_U_UAUAUA__AUUUCUCUGAGUGUUCAAGUGUCACCGCCCUUCCCGGCCGCAC____ACACACUCUCAACUUCUCGCCUGGACUUGUUUCAUAAACAAGUUCUGUUCGGUUUGGUUGA
....................((((((....((((....(((......))).))))......))))))((((((..(((...(((((((((.....)))))))))....)))...)))))) (-22.62 = -23.98 +   1.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:26 2006