Locus 5264

Sequence ID 3R_DroMel_CAF1
Location 13,728,663 – 13,728,792
Length 129
Max. P 0.967216
window8591 window8592 window8593

overview

Window 1

Location 13,728,663 – 13,728,756
Length 93
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 74.57
Mean single sequence MFE -27.82
Consensus MFE -15.34
Energy contribution -16.23
Covariance contribution 0.89
Combinations/Pair 1.20
Mean z-score -1.55
Structure conservation index 0.55
SVM decision value 0.17
SVM RNA-class probability 0.616443
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13728663 93 + 27905053
AAAUGACAGAAGGAGUUGAGUGGG-----------------------GGCGGUAAGCGGUGGGCGGUAUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUA
..............((((.(..((-----------------------..(((((((((.((.((.......)).))...)))))))).)...))..)((((....)))).-.)))). ( -28.30)
>DroPse_CAF1 2545 87 + 1
AAAUGACAGCAGCUGGAGUGCG-------------------------GAAGGGGAGUGUUGGG-----GAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCAGGCAAUA
........((.((...((((((-------------------------.(((.((.((((((..-----......)))))).....)).....))).))))))...))....)).... ( -24.40)
>DroSec_CAF1 1898 116 + 1
AAAUGACAGAAGGAGUUGUGUGGGCGGUGCGGGGAGAUGGCGGAUUGGGCGGUAAGCGGUGGGCGGUGUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUA
..............((((..(.((((.((((((......((.......))((((((((.((.((.......)).))...)))))))).....))))))))))...)..))-)).... ( -37.60)
>DroEre_CAF1 1543 91 + 1
AAAUGACAGAAGGAGUUGUGUG-------------------------GGCGGUGGGCGGUGGGCGGUGUAUGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUA
..............((((..(.-------------------------(((((..((.....(((((.(((((.....)))))))))).....))..).))))...)..))-)).... ( -29.50)
>DroAna_CAF1 1854 86 + 1
AAAUGGUAGGGGAAUUUUUGGG---------------------------UGGU---UUCGGGGUGCUGCAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUA
...(((((((((((((......---------------------------.)))---)))...(((.(((....))).))).))))))).....((((((((....)))).-)))).. ( -24.90)
>DroPer_CAF1 2469 87 + 1
AAAUGACAGCAGCUGGAGAGGG-------------------------GGAGGGGAGUGUUGGG-----GAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCAGGCAAUA
........((.((.((.....(-------------------------(.(((...((((((..-----......)))))).))).)).....)).))((((....))))..)).... ( -22.20)
>consensus
AAAUGACAGAAGGAGUUGUGUG_________________________GGCGGUGAGCGGUGGGCGGUGUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA_GCAAUA
..................................................((((((((.((.((.......)).))...))))))))......((((((((....))))..)))).. (-15.34 = -16.23 +   0.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,728,687 – 13,728,792
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.48
Mean single sequence MFE -33.38
Consensus MFE -24.37
Energy contribution -24.90
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -1.39
Structure conservation index 0.73
SVM decision value -0.00
SVM RNA-class probability 0.531431
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13728687 105 + 27905053
----------GGCGGUAAGCGGUGGGCGGUAUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCACUG----
----------(((((((((((.((.((.......)).))...))))))))......((((((((....)))).-))))......................)))((.....))....---- ( -32.90)
>DroSec_CAF1 1938 112 + 1
CGGAU---UGGGCGGUAAGCGGUGGGCGGUGUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCACUG----
.((.(---(((..((((((((.((.((.......)).))...))))))))......((((((((....)))).-))))................))))...))((.....))....---- ( -34.70)
>DroEre_CAF1 1565 105 + 1
----------GGCGGUGGGCGGUGGGCGGUGUAUGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCACUG----
----------.((((((...(((((((((.(((((.....))))))))))......((((((((....)))).-))))..............))))...))))))...........---- ( -37.60)
>DroYak_CAF1 1684 115 + 1
GUAAGCGGUGGGUGGUAGGCGGUGGGCGGUGUAAGUGCAACAUAGUUGCCAGAAACUUGCGCGCUAAUGUGUA-GCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCACUG----
((((((((((((((((..((.....)).(((((((((((((...))))).....))))))))((((.....))-))..............))))))...))))))...))))....---- ( -35.50)
>DroAna_CAF1 1876 100 + 1
------------UGGU---UUCGGGGUGCUGCAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA-GCAAUAAAAAAUUGGAAUCACCCAGAACGGCAUGUUGCACAG----
------------.(((---........)))....((((((((((((..........((((((((....)))).-)))).......((((......))))...))))))))))))..---- ( -32.70)
>DroPer_CAF1 2491 105 + 1
----------GGAGGGGAGUGUUGGG-----GAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCAGGCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCAUACUUGU
----------.............(((-----...(((((((((((............((((((....))))))(((........................)))))))))))))).))).. ( -26.86)
>consensus
__________GGCGGUAAGCGGUGGGCGGUGUAAGUGCAACAUGCUUGCCAGAAACUUGCGCGCUAAUGUGCA_GCAAUAAAAAAUUUAAAUCACCAAGCGCCGCAUGUUGCACUG____
..................................(((((((((((..((.((...)).))(((((...(((.....(((.....))).....)))..))))).)))))))))))...... (-24.37 = -24.90 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,728,687 – 13,728,792
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.48
Mean single sequence MFE -31.38
Consensus MFE -29.59
Energy contribution -29.82
Covariance contribution 0.22
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.94
SVM decision value 1.61
SVM RNA-class probability 0.967216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13728687 105 - 27905053
----CAGUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGC-UGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACUUAUACCGCCCACCGCUUACCGCC----------
----.((((((((((((.(((((..(((.....(((.....)))..-..)))...)))))((.((...)).))..)))))))))))).............((.....)).---------- ( -33.80)
>DroSec_CAF1 1938 112 - 1
----CAGUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGC-UGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACUUACACCGCCCACCGCUUACCGCCCA---AUCCG
----.((((((((((((.(((((..(((.....(((.....)))..-..)))...)))))((.((...)).))..)))))))))))).............((.....))...---..... ( -33.80)
>DroEre_CAF1 1565 105 - 1
----CAGUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGC-UGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACAUACACCGCCCACCGCCCACCGCC----------
----..(((((((((((.(((((..(((.....(((.....)))..-..)))...)))))((.((...)).))..)))))))))))........................---------- ( -33.40)
>DroYak_CAF1 1684 115 - 1
----CAGUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGC-UACACAUUAGCGCGCAAGUUUCUGGCAACUAUGUUGCACUUACACCGCCCACCGCCUACCACCCACCGCUUAC
----.(((((((((((((.((((..(((.....(((.....)))..-..)))...)))))))........(....).))))))))))................................. ( -27.20)
>DroAna_CAF1 1876 100 - 1
----CUGUGCAACAUGCCGUUCUGGGUGAUUCCAAUUUUUUAUUGC-UGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACUUGCAGCACCCCGAA---ACCA------------
----..(((((((((((.....((((....))))........((((-(((......))((....))....))))))))))))))))...............---....------------ ( -30.10)
>DroPer_CAF1 2491 105 - 1
ACAAGUAUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGCCUGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACUUC-----CCCAACACUCCCCUCC----------
.......((((((((((.(((((..(((.....(((.....))).....)))...)))))((.((...)).))..))))))))))....-----................---------- ( -30.00)
>consensus
____CAGUGCAACAUGCGGCGCUUGGUGAUUUAAAUUUUUUAUUGC_UGCACAUUAGCGCGCAAGUUUCUGGCAAGCAUGUUGCACUUACACCGCCCACCGCUUACCGCC__________
......(((((((((((.(((((..(((.....(((.....))).....)))...)))))((.((...)).))..))))))))))).................................. (-29.59 = -29.82 +   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 11:50:37 2006