Locus 4132

Sequence ID 2L_DroMel_CAF1
Location 11,884,709 – 11,884,830
Length 121
Max. P 0.937240
window6519 window6520 window6521

overview

Window 9

Location 11,884,709 – 11,884,817
Length 108
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 76.53
Mean single sequence MFE -33.70
Consensus MFE -19.02
Energy contribution -19.05
Covariance contribution 0.03
Combinations/Pair 1.33
Mean z-score -2.12
Structure conservation index 0.56
SVM decision value 1.26
SVM RNA-class probability 0.937240
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11884709 108 - 22407834
GGUAAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGAAAGGAAAGAG--GAGAGAGGUGGAG----ACACUUGGUCCAG
......(((((.(((((...((((((......)))))).)))(((((((.....)))))))..)))))))...........(--((...(((((...----.)))))..))).. ( -39.40)
>DroSec_CAF1 107486 108 - 1
GGUGAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCGGUUGCCGGAAAGGAAAGAG--GAGAGAGGUGGCG----ACACUUGGUCCAG
......(((((.(((((...((((((......)))))).)))(((((((.....)))))))..)))))))...........(--((...(((((...----.)))))..))).. ( -37.70)
>DroSim_CAF1 73053 108 - 1
GGUGAACGGCAAGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGUAAGGAAAGAG--GAGAGAGGUGGCG----ACAAUUGGUCCAG
......((((((..(((...((((((......)))))).)))(((((((.....)))))))...))))))...........(--((..((..((...----.)).))..))).. ( -35.30)
>DroEre_CAF1 78841 111 - 1
GGUGAACGACACGCGCAUUUGUCAUCAUUAAGGGUGGUUUGCAGGACUAAAAAUUAGUCCUCGGCUGCCGGAAAGGAAAGUG--GAGACCG-GGCAGGGGUAUCCUUGGUCCAG
(((...(..((((((((....(((((......)))))..)))(((((((.....)))))))..))..((.....))...)))--..))))(-(((((((....)))).)))).. ( -33.50)
>DroYak_CAF1 75353 101 - 1
GGUGG---------GCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCACUUGCCGGAAAGGAGAGAGAGGAGAGAGGGGCAG----ACCCUUGGUCCAG
.....---------(((...((((((......)))))).))).(((((.........(((((.((..((.....))..)).)))))..(((((....----.)))))))))).. ( -38.40)
>DroAna_CAF1 82492 83 - 1
GGC-AAUG----GCGCAUUUGUCAUCAUUAAGAAUGGUUUGCCGAGCUAAAAAUUAGUCUACAGAUGCCGGG----------------------GCC----CGUUAUGUUCCAC
(((-..((----((..((((((....(((((...((((((...))))))....)))))..))))))))))..----------------------)))----............. ( -17.90)
>consensus
GGUGAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGAAAGGAAAGAG__GAGAGAGGUGGAG____ACACUUGGUCCAG
(((((.........(((...((((((......)))))).)))(((((((.....)))))))...)))))............................................. (-19.02 = -19.05 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,884,740 – 11,884,830
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.29
Mean single sequence MFE -20.57
Consensus MFE -14.14
Energy contribution -14.25
Covariance contribution 0.11
Combinations/Pair 1.18
Mean z-score -1.69
Structure conservation index 0.69
SVM decision value 0.74
SVM RNA-class probability 0.839021
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11884740 90 + 22407834
UCCUUUCCGGCAACUGAGGACUAAUUUUUAGUCCUGCAAGCCAUCCUUAAUGAUGACAAAUGCGCGUGCCGUUUACCGCCC----------ACAACCUUC--
.......(((((....(((((((.....)))))))(((.(.((((......)))).)...)))...)))))..........----------.........-- ( -21.10)
>DroSec_CAF1 107517 92 + 1
UCCUUUCCGGCAACCGAGGACUAAUUUUUAGUCCUGCAAGCCAUCCUUAAUGAUGACAAAUGCGCGUGCCGUUCACCGCCC----------ACAGCCUCCAC
........(((.....(((((((.....)))))))....(.((((......)))).)....(((.(((.....))))))..----------...)))..... ( -21.60)
>DroSim_CAF1 73084 90 + 1
UCCUUACCGGCAACUGAGGACUAAUUUUUAGUCCUGCAAGCCAUCCUUAAUGAUGACAAAUGCGCUUGCCGUUCACCGCCC----------ACAGCCUCC--
........(((.....(((((((.....)))))))((((((((((......))))........))))))............----------...)))...-- ( -23.20)
>DroEre_CAF1 78875 89 + 1
UCCUUUCCGGCAGCCGAGGACUAAUUUUUAGUCCUGCAAACCACCCUUAAUGAUGACAAAUGCGCGUGUCGUUCACCGCCC----------ACAGCCUC---
........(((.((..(((((((.....)))))))))........................(((.(((.....))))))..----------...)))..--- ( -21.90)
>DroYak_CAF1 75386 81 + 1
UCCUUUCCGGCAAGUGAGGACUAAUUUUUAGUCCUGCAAGCCAUCCUUAAUGAUGACAAAUGC---------CCACCGCCC----------ACAGCCACC--
........(((..((((((((((.....)))))))(((.(.((((......)))).)...)))---------........)----------)).)))...-- ( -19.60)
>DroAna_CAF1 82508 88 + 1
-----CCCGGCAUCUGUAGACUAAUUUUUAGCUCGGCAAACCAUUCUUAAUGAUGACAAAUGCGC----CAUU-GCCACCCUAGCUCCUAAACAGGAG----
-----...((((......(((((.....))).))(((.......((........)).......))----)..)-))).......(((((....)))))---- ( -16.04)
>consensus
UCCUUUCCGGCAACUGAGGACUAAUUUUUAGUCCUGCAAGCCAUCCUUAAUGAUGACAAAUGCGCGUGCCGUUCACCGCCC__________ACAGCCUCC__
........(((.....(((((((.....)))))))(((...((((......)))).....)))..............)))...................... (-14.14 = -14.25 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,884,740 – 11,884,830
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.29
Mean single sequence MFE -28.40
Consensus MFE -21.25
Energy contribution -21.03
Covariance contribution -0.22
Combinations/Pair 1.29
Mean z-score -1.73
Structure conservation index 0.75
SVM decision value 0.96
SVM RNA-class probability 0.889831
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11884740 90 - 22407834
--GAAGGUUGU----------GGGCGGUAAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGAAAGGA
--.........----------..........(((((.(((((...((((((......)))))).)))(((((((.....)))))))..)))))))....... ( -28.70)
>DroSec_CAF1 107517 92 - 1
GUGGAGGCUGU----------GGGCGGUGAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCGGUUGCCGGAAAGGA
.(((..(((((----------(.((.(....).)).)))(((...((((((......)))))).)))(((((((.....))))))).)))..)))....... ( -32.50)
>DroSim_CAF1 73084 90 - 1
--GGAGGCUGU----------GGGCGGUGAACGGCAAGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGUAAGGA
--....((((.----------...))))...((((((..(((...((((((......)))))).)))(((((((.....)))))))...))))))....... ( -32.10)
>DroEre_CAF1 78875 89 - 1
---GAGGCUGU----------GGGCGGUGAACGACACGCGCAUUUGUCAUCAUUAAGGGUGGUUUGCAGGACUAAAAAUUAGUCCUCGGCUGCCGGAAAGGA
---(((((.((----------(.(((((.....)).))).)))..))).))......((..(((.(.(((((((.....)))))))))))..))........ ( -28.90)
>DroYak_CAF1 75386 81 - 1
--GGUGGCUGU----------GGGCGGUGG---------GCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCACUUGCCGGAAAGGA
--.....((.(----------.(((((((.---------(((...((((((......)))))).)))(((((((.....)))))))))).)))).)...)). ( -28.80)
>DroAna_CAF1 82508 88 - 1
----CUCCUGUUUAGGAGCUAGGGUGGC-AAUG----GCGCAUUUGUCAUCAUUAAGAAUGGUUUGCCGAGCUAAAAAUUAGUCUACAGAUGCCGGG-----
----(((((....)))))....((((((-((..----......))))))))........((((......(((((.....))).))......))))..----- ( -19.40)
>consensus
__GGAGGCUGU__________GGGCGGUGAACGGCACGCGCAUUUGUCAUCAUUAAGGAUGGCUUGCAGGACUAAAAAUUAGUCCUCAGUUGCCGGAAAGGA
......................(((((............(((...((((((......)))))).)))(((((((.....)))))))...)))))........ (-21.25 = -21.03 +  -0.22)

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 11:10:21 2006