Locus 4

Sequence ID 2L_DroMel_CAF1
Location 16,654 – 16,838
Length 184
Max. P 0.962505
window4 window5 window6 window7 window8

overview

Window 4

Location 16,654 – 16,758
Length 104
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 85.80
Mean single sequence MFE -34.88
Consensus MFE -24.82
Energy contribution -27.93
Covariance contribution 3.11
Combinations/Pair 1.03
Mean z-score -3.34
Structure conservation index 0.71
SVM decision value 1.37
SVM RNA-class probability 0.947051
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16654 104 + 22407834
UCAACAAA-GCUUCAGGUACCUCCUCAUAUUUGGCACCGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAACCUUUUU-UAUGCGGUGCUUUGU
........-((((...((((.((((..(((.((....)).)))..))))))))...........))))...(((((((((((........-..))))))))))).. ( -28.44)
>DroSec_CAF1 4811 104 + 1
-CCGCAAUGUCUGUGCGUACCUGCCCAUAUUUGGCACAGCAUAGAAGGAGAGCACAAAAU-AACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGU
-..((....(((((((.....((((.......))))..)))))))......)).......-..........((((((((((((((.....)))))))))))))).. ( -37.50)
>DroSim_CAF1 4916 105 + 1
-CCGCAAUGUCUGUGCGUACCUGCGCAUAUUUGGCACAGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUGUGU
-..(((...(((((((.....(((.((....)))))..))))))).....))).............(((....((((((((((((.....)))))))))))).))) ( -38.70)
>consensus
_CCGCAAUGUCUGUGCGUACCUGCCCAUAUUUGGCACAGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGU
...((......((((((......))))))((((((((..(......)..)))).))))........))...((((((((((((((.....)))))))))))))).. (-24.82 = -27.93 +   3.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,654 – 16,758
Length 104
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 85.80
Mean single sequence MFE -33.17
Consensus MFE -25.45
Energy contribution -27.90
Covariance contribution 2.45
Combinations/Pair 1.09
Mean z-score -2.56
Structure conservation index 0.77
SVM decision value 0.92
SVM RNA-class probability 0.881516
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16654 104 - 22407834
ACAAAGCACCGCAUA-AAAAAGGUUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCGGUGCCAAAUAUGAGGAGGUACCUGAAGC-UUUGUUGA
((((((((((.....-.....)))...((((((((....(((((....((((.(((((.(......).))))))))).)))))))))))))....))-)))))... ( -32.70)
>DroSec_CAF1 4811 104 - 1
ACAAAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUU-AUUUUGUGCUCUCCUUCUAUGCUGUGCCAAAUAUGGGCAGGUACGCACAGACAUUGCGG-
..(((((((((.((((.....)))).)))))))))(((((((((.-..((((.((.(..(......)..).)))))).)))))))))..((((.......)))).- ( -34.40)
>DroSim_CAF1 4916 105 - 1
ACACAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCUGUGCCAAAUAUGCGCAGGUACGCACAGACAUUGCGG-
....(((((((.((((.....)))).)))))))..(((((.(((....((((.((((..(......)..)))))))).))).)))))..((((.......)))).- ( -32.40)
>consensus
ACAAAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCUGUGCCAAAUAUGAGCAGGUACGCACAGACAUUGCGG_
..(((((((((.((((.....)))).)))))))))(((((((((....((((.((((..(......)..)))))))).)))))))))..((((.......)))).. (-25.45 = -27.90 +   2.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,679 – 16,798
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.50
Mean single sequence MFE -41.40
Consensus MFE -31.89
Energy contribution -33.67
Covariance contribution 1.78
Combinations/Pair 1.03
Mean z-score -3.99
Structure conservation index 0.77
SVM decision value 1.06
SVM RNA-class probability 0.908751
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16679 119 + 22407834
AUAUUUGGCACCGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAACCUUUUU-UAUGCGGUGCUUUGUGGCGCGAGUCUACAAAAUACUGUGUGUGUAUGCGGUUUAC
.........((((((((.(.(.((((......(((..((.((...(((((((((((........-..)))))))))))...)).))..)))......)))).)...).)))))))).... ( -39.40)
>DroSec_CAF1 4836 117 + 1
AUAUUUGGCACAGCAUAGAAGGAGAGCACAAAAU-AACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGUGGCGCGAGUCUAAAAAAUACUGUG--UUGAUGCGGCGUAC
.(((.(.(((((((((((..(.......).....-..((.((...((((((((((((((.....))))))))))))))...)).)).............)))))--))).))).).))). ( -42.30)
>DroSim_CAF1 4941 118 + 1
AUAUUUGGCACAGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUGUGUGGCGCGAGUCUAAAAAAUACUGUG--UUGAUGCGGCGUAC
.(((.(.(((((((((((..(.......)...(((..((.((.....((((((((((((.....)))))))))))).....)).))..)))........)))))--))).))).).))). ( -42.50)
>consensus
AUAUUUGGCACAGCAUAGAAGGAGUGCACAAAAGAAACGAGCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGUGGCGCGAGUCUAAAAAAUACUGUG__UUGAUGCGGCGUAC
...((((((((..(......)..)))).))))....(((.(((..((((((((((((((.....))))))))))))))..(((....)))....................)))..))).. (-31.89 = -33.67 +   1.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,679 – 16,798
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.50
Mean single sequence MFE -30.10
Consensus MFE -23.99
Energy contribution -26.10
Covariance contribution 2.11
Combinations/Pair 1.03
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 0.11
SVM RNA-class probability 0.589394
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16679 119 - 22407834
GUAAACCGCAUACACACACAGUAUUUUGUAGACUCGCGCCACAAAGCACCGCAUA-AAAAAGGUUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCGGUGCCAAAUAU
....((((((((........((((.....(((..((.((...(((((((((....-..........)))))))))...)).))..)))...))))........))))))))......... ( -32.53)
>DroSec_CAF1 4836 117 - 1
GUACGCCGCAUCAA--CACAGUAUUUUUUAGACUCGCGCCACAAAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUU-AUUUUGUGCUCUCCUUCUAUGCUGUGCCAAAUAU
(((((..((((...--...(((((..........((.((...(((((((((.((((.....)))).)))))))))...)).))..-.....)))))........)))))))))....... ( -28.67)
>DroSim_CAF1 4941 118 - 1
GUACGCCGCAUCAA--CACAGUAUUUUUUAGACUCGCGCCACACAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCUGUGCCAAAUAU
(((((..((((...--....((((.....(((..((.((.....(((((((.((((.....)))).))))))).....)).))..)))...)))).........)))))))))....... ( -29.09)
>consensus
GUACGCCGCAUCAA__CACAGUAUUUUUUAGACUCGCGCCACAAAGCACCGCAUCAAGAAAUGAUACGGUGCUUUUUUGCUCGUUUCUUUUGUGCACUCCUUCUAUGCUGUGCCAAAUAU
...(((.((((.........((((.....(((..((.((...(((((((((.((((.....)))).)))))))))...)).))..)))...)))).........)))).)))........ (-23.99 = -26.10 +   2.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,719 – 16,838
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -38.33
Consensus MFE -34.08
Energy contribution -35.41
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.93
Structure conservation index 0.89
SVM decision value 1.54
SVM RNA-class probability 0.962505
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16719 119 + 22407834
GCAAAAAAGCACCGUAACCUUUUU-UAUGCGGUGCUUUGUGGCGCGAGUCUACAAAAUACUGUGUGUGUAUGCGGUUUACUUGUAGUUGCGGUGGAAAAAAUUUACCUAAAUGUUAAUGC
((...(((((((((((........-..)))))))))))...))((((..((((((...(((((((....)))))))....))))))))))((((((.....))))))............. ( -37.60)
>DroSec_CAF1 4875 118 + 1
GCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGUGGCGCGAGUCUAAAAAAUACUGUG--UUGAUGCGGCGUACUUGUAGUUGCGGUGGACAAAAUUUACCUAAAUGUAAAUGC
((...((((((((((((((.....))))))))))))))...))((..(((((.......((((.--.....))))((((........)))).)))))...((((((......)))))))) ( -39.30)
>DroSim_CAF1 4981 118 + 1
GCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUGUGUGGCGCGAGUCUAAAAAAUACUGUG--UUGAUGCGGCGUACUUGUAGUUGCGGUGGACAAAAUUUACCUAAAUGUAAAUGC
(((....((((((((((((.....)))))))))))).)))(((....)))............((--((.(((((((.........))))).)).))))..((((((......)))))).. ( -38.10)
>consensus
GCAAAAAAGCACCGUAUCAUUUCUUGAUGCGGUGCUUUGUGGCGCGAGUCUAAAAAAUACUGUG__UUGAUGCGGCGUACUUGUAGUUGCGGUGGACAAAAUUUACCUAAAUGUAAAUGC
(((..((((((((((((((.....))))))))))))))(..((((((((.......(..((((........))))..))))))).))..)((((((.....))))))..........))) (-34.08 = -35.41 +   1.33)

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 09:23:03 2006