Locus 5330

Sequence ID X_DroMel_CAF1
Location 13,916,731 – 13,916,918
Length 187
Max. P 0.754195
window8629 window8630 window8631 window8632

overview

Window 9

Location 13,916,731 – 13,916,838
Length 107
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -35.58
Consensus MFE -19.15
Energy contribution -20.40
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -2.45
Structure conservation index 0.54
SVM decision value 0.48
SVM RNA-class probability 0.754195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13916731 107 + 22224390
AAUCCAAGAGCUAGCUAACUGCAGCUCAAGAGCGCUGCCAAAGAGAGCGCCACUUAG--GCACUGAUUGAGAGAGCAAUCUGGCACGAUGCGAGAGCGGGAGCUUAAAA
..(((..(((((.((.....))))))).....((.(((((.....((.(((.....)--)).))(((((......)))))))))))).(((....))))))........ ( -35.10)
>DroSec_CAF1 17055 107 + 1
AAUCCAAGAGCUCCCAAACUGCAGCUCAAGAGCGCUGCAAAAGAGAGCGCGACUUAG--GCACUGAUUGGGAGAACAAUCUGGCACGUUGCGAGAGCGGGAGCUUAAAA
.......((((((((.((((((.((..(((.(((((.(......))))))..)))..--)).(.(((((......))))).)))).)))((....)))))))))).... ( -42.70)
>DroEre_CAF1 12948 105 + 1
AAUCCAAGAGCUCGCUCGCUGCAGCUCAAGAGCGCUGGAAAAGAGAGCCCGACUCAG--AGACGGAUUGAGAGUAG-AACUAGCACGUUGCGAGCGCGAGAGUU-UAAA
.......((((((((((((.((.(((....)))(((((....(......)..(((((--.......))))).....-..)))))..)).))))))....)))))-)... ( -29.60)
>DroYak_CAF1 27740 109 + 1
AAUCCGAGAGCUCGCAAGCUGCAGCUCAAGAGCGCUGAAAAAGAGAGCUCAACUCAGGCACACGGAUUGCGAGUGCAAACUGCUACGUUGCGAGCAUAAGAGCUUCAAA
.........(((((((((..((((.....((((.((.....))...)))).......((((.((.....)).))))...))))..).)))))))).............. ( -34.90)
>consensus
AAUCCAAGAGCUCGCAAACUGCAGCUCAAGAGCGCUGCAAAAGAGAGCGCGACUCAG__ACACGGAUUGAGAGAACAAACUGGCACGUUGCGAGAGCGAGAGCUUAAAA
.......((((((....((((((((......(((((.........))))).................((..(((....)))..)).))))).)))....)))))).... (-19.15 = -20.40 +   1.25)

alignment

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secondary structure

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Window 0

Location 13,916,760 – 13,916,878
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.03
Mean single sequence MFE -42.15
Consensus MFE -25.31
Energy contribution -25.25
Covariance contribution -0.06
Combinations/Pair 1.23
Mean z-score -2.03
Structure conservation index 0.60
SVM decision value 0.16
SVM RNA-class probability 0.611479
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13916760 118 + 22224390
GAGCGCUGCCAAAGAGAGCGCCACUUAG--GCACUGAUUGAGAGAGCAAUCUGGCACGAUGCGAGAGCGGGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGC
..((((((((..(((..(((((.....)--)).....((....))))..))).((.((((((..(((..(((((((............))))))).)))..))))))..)).)))))))) ( -46.10)
>DroSec_CAF1 17084 118 + 1
GAGCGCUGCAAAAGAGAGCGCGACUUAG--GCACUGAUUGGGAGAACAAUCUGGCACGUUGCGAGAGCGGGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGC
..(((((((......(((.(.(((((..--((...(((((......)))))..)).(((((((.((((....))))....))))).))))))).).)))..((......))..))))))) ( -42.90)
>DroEre_CAF1 12977 116 + 1
GAGCGCUGGAAAAGAGAGCCCGACUCAG--AGACGGAUUGAGAGUAG-AACUAGCACGUUGCGAGCGCGAGAGUU-UAAAUGCAAUCGCAGUCUCACUCAAGCGUCGCAGCGGGCAGCGC
..((((((.....(..((....((((.(--(......))..))))..-..))..).((((((((.(((..((((.-....(((....))).....))))..)))))))))))..)))))) ( -41.60)
>DroYak_CAF1 27769 120 + 1
GAGCGCUGAAAAAGAGAGCUCAACUCAGGCACACGGAUUGCGAGUGCAAACUGCUACGUUGCGAGCAUAAGAGCUUCAAAUGCAAUCGAAGUUUCACUCAGGCGUCGCAGCAGGCAGCGC
((((.((.....))...)))).......((((.((.....)).))))...(((((..(((((((((....(((((((..........))))))).......)).))))))).)))))... ( -38.00)
>consensus
GAGCGCUGCAAAAGAGAGCGCGACUCAG__ACACGGAUUGAGAGAACAAACUGGCACGUUGCGAGAGCGAGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGC
..(((((((......(((.....)))............((..(((....)))..)).(((((((...(((..((.......))..)))..((((.....)))).)))))))..))))))) (-25.31 = -25.25 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,916,760 – 13,916,878
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.03
Mean single sequence MFE -41.13
Consensus MFE -23.36
Energy contribution -23.80
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -2.28
Structure conservation index 0.57
SVM decision value 0.11
SVM RNA-class probability 0.589796
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13916760 118 - 22224390
GCGCUGCCUGCUGCGACGCUUGAGUGAAACUUCGAUUGCAUUUUAAGCUCCCGCUCUCGCAUCGUGCCAGAUUGCUCUCUCAAUCAGUGC--CUAAGUGGCGCUCUCUUUGGCAGCGCUC
((((((((.((.((((.((..(((((...(((.((......)).)))....)))))..)).))))))..(((((......)))))(((((--(.....))))))......)))))))).. ( -44.90)
>DroSec_CAF1 17084 118 - 1
GCGCUGCCUGCUGCGACGCUUGAGUGAAACUUCGAUUGCAUUUUAAGCUCCCGCUCUCGCAACGUGCCAGAUUGUUCUCCCAAUCAGUGC--CUAAGUCGCGCUCUCUUUUGCAGCGCUC
(((((((..((.(((((((..(((((...(((.((......)).)))....)))))..))...(..(..(((((......))))).)..)--....)))))))........))))))).. ( -37.80)
>DroEre_CAF1 12977 116 - 1
GCGCUGCCCGCUGCGACGCUUGAGUGAGACUGCGAUUGCAUUUA-AACUCUCGCGCUCGCAACGUGCUAGUU-CUACUCUCAAUCCGUCU--CUGAGUCGGGCUCUCUUUUCCAGCGCUC
(((((((.((.((((((((..((((..((.(((....))).)).-.))))..))).))))).)).)).((((-(.((((...........--..)))).))))).........))))).. ( -40.62)
>DroYak_CAF1 27769 120 - 1
GCGCUGCCUGCUGCGACGCCUGAGUGAAACUUCGAUUGCAUUUGAAGCUCUUAUGCUCGCAACGUAGCAGUUUGCACUCGCAAUCCGUGUGCCUGAGUUGAGCUCUCUUUUUCAGCGCUC
((((((.((((((((..((..(((((.((((((((......))))))...)).)))))))..))))))))...((((.((.....)).))))..(((.....))).......)))))).. ( -41.20)
>consensus
GCGCUGCCUGCUGCGACGCUUGAGUGAAACUUCGAUUGCAUUUUAAGCUCCCGCGCUCGCAACGUGCCAGAUUGCACUCUCAAUCAGUGC__CUAAGUCGCGCUCUCUUUUGCAGCGCUC
(((((((.((.((((((((..((((.....................))))..))).))))).))......................((((.........))))........))))))).. (-23.36 = -23.80 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,916,798 – 13,916,918
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.83
Mean single sequence MFE -42.15
Consensus MFE -27.01
Energy contribution -31.20
Covariance contribution 4.19
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.64
SVM decision value 0.42
SVM RNA-class probability 0.730541
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13916798 120 + 22224390
AGAGAGCAAUCUGGCACGAUGCGAGAGCGGGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGCAGUCGGCGUUGCAGCUCAAAGAGAACUGUGUCGCAAAAGA
.(((.((......)).(((((((.((((....))))....))).))))........)))..(((.(((((...(((((((.....)))))))..(((...)))..))))).)))...... ( -40.30)
>DroSec_CAF1 17122 120 + 1
GGAGAACAAUCUGGCACGUUGCGAGAGCGGGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGCAGCCGGCGUUGCAGCUGAAAGAGAACUGUGACGCGAAAGA
.(((..(..(((.((.....)).)))..)(((((((............))))))).)))..(((((((((((((((((((.....)))))))..)))........)))))))))...... ( -40.80)
>DroEre_CAF1 13015 118 + 1
AGAGUAG-AACUAGCACGUUGCGAGCGCGAGAGUU-UAAAUGCAAUCGCAGUCUCACUCAAGCGUCGCAGCGGGCAGCGCAGCCGGCGUUGCAGCUCGAAGAGAACAGAUUCGCGAAAGA
.((((..-........((((((((.(((..((((.-....(((....))).....))))..))))))))))).(((((((.....))))))).))))................(....). ( -44.40)
>DroYak_CAF1 27809 120 + 1
CGAGUGCAAACUGCUACGUUGCGAGCAUAAGAGCUUCAAAUGCAAUCGAAGUUUCACUCAGGCGUCGCAGCAGGCAGCGCAGCCGGCGUUGCAGCUCAAAGAGAACUGUUUCGCCAAAGA
.(((((.(((((....((((((((((......)))).....)))).)).)))))))))).((((..((((...(((((((.....)))))))..(((...)))..))))..))))..... ( -43.10)
>consensus
AGAGAACAAACUGGCACGUUGCGAGAGCGAGAGCUUAAAAUGCAAUCGAAGUUUCACUCAAGCGUCGCAGCAGGCAGCGCAGCCGGCGUUGCAGCUCAAAGAGAACUGUGUCGCGAAAGA
.(((((.(((((.....((((((.((((....))))....))))))...))))))))))..(((.(((((...(((((((.....)))))))..(((...)))..))))).)))...... (-27.01 = -31.20 +   4.19)

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 11:45:07 2006