Locus 3289

Sequence ID 3R_DroMel_CAF1
Location 8,817,481 – 8,817,681
Length 200
Max. P 0.999963
window5305 window5306 window5307 window5308 window5309

overview

Window 5

Location 8,817,481 – 8,817,601
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.17
Mean single sequence MFE -38.08
Consensus MFE -34.16
Energy contribution -34.76
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.90
SVM decision value 4.01
SVM RNA-class probability 0.999756
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8817481 120 + 27905053
UAAAUCAUCUCCGAUGAAUUGGAAUAAACGGAGCCAUGGUUUUCCGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACCCCGGUC
.........(((((....))))).....(((.(...((((((((.((((((...((((.(((((....)))))))))...((((......)))).))))))...)))))))).))))... ( -37.90)
>DroSec_CAF1 237458 120 + 1
UAAAUCAUCUCCGAUGAAUUGGAAUAAACGGAGCCAUGGUUUUCGGUUGAGAACGUCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUUUGGACCUCGGCAAAGAAAAUCACACCGGUC
.........(((((....))))).....(((.(...((((((((.((((((...(..(((((((....)))))))..)..((((......)))).))))))...))))))))).)))... ( -35.80)
>DroSim_CAF1 255750 120 + 1
UAAAUCAUCUCCGAUGAAUUGGAAUAAACGGAGCCAUGGUUUUCGGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUUUUCUGGACCUCGGCAAAGAAAAUCACACCGGUC
.........(((((....))))).....(((.(...((((((((.((((((...((((.(((((....)))))))))...((((......)))).))))))...))))))))).)))... ( -39.90)
>DroEre_CAF1 257525 120 + 1
UAAAUCAUCUCUGAUGAAUUGGAAAAAACGGAGCCAUGGUUUUCAGUUGAGAAAGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUC
....(((((...)))))...........(((((...((((((((.((((((...((((.(((((....)))))))))...((((......)))).))))))...)))))))))))))... ( -41.90)
>DroYak_CAF1 250654 120 + 1
UAAAUCAUCUCCGAUGAAUUUGAAUAAACAGAGCCAUGGUUUUCCGUUGAAAAAGGCUUGCUGGUUUUCCAGCAGCCUACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUC
..........((((((..((((......))))..)))(((((((.(((((...(((((.(((((....))))))))))..((((......))))..)))))...)))))))....))).. ( -34.90)
>consensus
UAAAUCAUCUCCGAUGAAUUGGAAUAAACGGAGCCAUGGUUUUCCGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACACCGGUC
....(((((...)))))...........(((.(...((((((((.((((((...((((.(((((....)))))))))...((((......)))).))))))...))))))))).)))... (-34.16 = -34.76 +   0.60)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,817,481 – 8,817,601
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.17
Mean single sequence MFE -37.90
Consensus MFE -31.78
Energy contribution -31.50
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -1.59
Structure conservation index 0.84
SVM decision value 0.68
SVM RNA-class probability 0.820654
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8817481 120 - 27905053
GACCGGGGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACGGAAAACCAUGGCUCCGUUUAUUCCAAUUCAUCGGAGAUGAUUUA
((((..((..(......)..))..))))..((.(((((((((((((((((((....))))).))))......((((((..........)))))))))))).)))).))............ ( -42.40)
>DroSec_CAF1 237458 120 - 1
GACCGGUGUGAUUUUCUUUGCCGAGGUCCAAAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGACGUUCUCAACCGAAAACCAUGGCUCCGUUUAUUCCAAUUCAUCGGAGAUGAUUUA
..((((((.....((((((((....))...))))))((((((((((((((((....))))))....(((.((....)).))).........))))))))))...)))))).......... ( -32.60)
>DroSim_CAF1 255750 120 - 1
GACCGGUGUGAUUUUCUUUGCCGAGGUCCAGAAAAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACCGAAAACCAUGGCUCCGUUUAUUCCAAUUCAUCGGAGAUGAUUUA
..((((((...((((((..((....))..)))))).((((((((((((((((....))))))(((((((.((....)).)))...))))..))))))))))...)))))).......... ( -39.30)
>DroEre_CAF1 257525 120 - 1
GACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCUUUCUCAACUGAAAACCAUGGCUCCGUUUUUUCCAAUUCAUCAGAGAUGAUUUA
...((((((.(((((((..((....))..)))))(((.(((.((((((((((....))))).)))))..))).))).......)).))))))...........(((((...))))).... ( -38.70)
>DroYak_CAF1 250654 120 - 1
GACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUAGGCUGCUGGAAAACCAGCAAGCCUUUUUCAACGGAAAACCAUGGCUCUGUUUAUUCAAAUUCAUCGGAGAUGAUUUA
((((...(..(......)..)...))))..((((((..((((((((((((((....))))).)))))(((((....))))).....))))..))).)))....(((((...))))).... ( -36.50)
>consensus
GACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACCGAAAACCAUGGCUCCGUUUAUUCCAAUUCAUCGGAGAUGAUUUA
((((...(..(......)..)...)))).....((..(((((.(((((((((....))))).)))).(((......))).......)))))..))........(((((...))))).... (-31.78 = -31.50 +  -0.28)

alignment

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secondary structure

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Window 7

Location 8,817,521 – 8,817,641
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -48.82
Consensus MFE -45.04
Energy contribution -45.24
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -3.09
Structure conservation index 0.92
SVM decision value 4.93
SVM RNA-class probability 0.999963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8817521 120 + 27905053
UUUCCGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACCCCGGUCCGCGGAUCGUAUUUAUGCAUUGUGGACUGGGUGGACGGAC
..(((((((((...((((.(((((....)))))))))...((((......)))).))))))........((((((.(((((((((..(((....)))..)))))))))))))))..))). ( -50.30)
>DroSec_CAF1 237498 120 + 1
UUUCGGUUGAGAACGUCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUUUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUACUUGUGCAUCGUGGACUGGGUGGACGGAC
.((((((((((...(..(((((((....)))))))..)..((((......)))).))))))........((((.(((((((((((...(((....))).))))))))))))))).)))). ( -48.00)
>DroSim_CAF1 255790 120 + 1
UUUCGGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUUUUCUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUAUUUGUGCAUCGUGGACUGGGUGGACGGAC
.((((((((((...((((.(((((....)))))))))...((((......)))).))))))........((((.(((((((((((...(((....))).))))))))))))))).)))). ( -51.20)
>DroEre_CAF1 257565 120 + 1
UUUCAGUUGAGAAAGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUCAGCGGAUCGUACUUAUGUAUCGUGGACUGGGUGGACGGAC
.(((.((((((...((((.(((((....)))))))))...((((......)))).))))))........((((.((((((.(((....((((....))))))).))))))))))..))). ( -43.90)
>DroYak_CAF1 250694 120 + 1
UUUCCGUUGAAAAAGGCUUGCUGGUUUUCCAGCAGCCUACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUCCGCGGAUCGUACUUAUGCAUCGUGGACUGGGUGGACGGAC
..((((((((...(((((.(((((....))))))))))..((((......))))..)))))........((((.(((((((((((..(((....)))..)))))))))))))))..))). ( -50.70)
>consensus
UUUCCGUUGAGAACGGCUUGCUGGUUUUCCAGCAGCCCACUCCACUCUUCUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUACUUAUGCAUCGUGGACUGGGUGGACGGAC
((((.((((((...((((.(((((....)))))))))...((((......)))).))))))...)))).((((.(((((((((((..(((....)))..)))))))))))))))...... (-45.04 = -45.24 +   0.20)

alignment

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secondary structure

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Window 8

Location 8,817,521 – 8,817,641
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.50
Mean single sequence MFE -42.37
Consensus MFE -33.96
Energy contribution -34.56
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value 0.60
SVM RNA-class probability 0.796619
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8817521 120 - 27905053
GUCCGUCCACCCAGUCCACAAUGCAUAAAUACGAUCCGCGGACCGGGGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACGGAAA
.(((((.....((.(((((...((.............))(((((..((..(......)..))..)))))......))))).))(((((((((....))))).)))).......))))).. ( -48.62)
>DroSec_CAF1 237498 120 - 1
GUCCGUCCACCCAGUCCACGAUGCACAAGUACGAUCCGCGGACCGGUGUGAUUUUCUUUGCCGAGGUCCAAAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGACGUUCUCAACCGAAA
(..((((..((((.(((((...((.............))(((((...(..(......)..)...)))))......))))).)))).((((((....)))))).))))..).......... ( -43.22)
>DroSim_CAF1 255790 120 - 1
GUCCGUCCACCCAGUCCACGAUGCACAAAUACGAUCCGCGGACCGGUGUGAUUUUCUUUGCCGAGGUCCAGAAAAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACCGAAA
(..((....((((.(((((....((((....((.((....)).)).)))).((((((..((....))..))))))))))).)))).((((((....))))))...))..).......... ( -38.80)
>DroEre_CAF1 257565 120 - 1
GUCCGUCCACCCAGUCCACGAUACAUAAGUACGAUCCGCUGACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCUUUCUCAACUGAAA
....(((((((((.((..((.(((....))))).....((((((...(..(......)..)...))).)))..)).))).))))))((((((....)))))).....(((......))). ( -36.60)
>DroYak_CAF1 250694 120 - 1
GUCCGUCCACCCAGUCCACGAUGCAUAAGUACGAUCCGCGGACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUAGGCUGCUGGAAAACCAGCAAGCCUUUUUCAACGGAAA
.(((((.(((((.((((.((...(........)...)).)))).)).))).((((((..((....))..)))))).(((((.((((((((((....))))).))))).)))))))))).. ( -44.60)
>consensus
GUCCGUCCACCCAGUCCACGAUGCAUAAGUACGAUCCGCGGACCGGAGUGAUUUUCUUUGCCGAGGUCCAGAAGAGUGGAGUGGGCUGCUGGAAAACCAGCAAGCCGUUCUCAACCGAAA
.........((((.(((((...((.............))(((((...(..(......)..)...)))))......))))).)))).((((((....)))))).................. (-33.96 = -34.56 +   0.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,817,561 – 8,817,681
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.33
Mean single sequence MFE -41.19
Consensus MFE -36.65
Energy contribution -36.69
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -1.26
Structure conservation index 0.89
SVM decision value 0.37
SVM RNA-class probability 0.709751
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8817561 120 + 27905053
UCCACUCUUCUGGACCUCGGCAAAGAAAAUCACCCCGGUCCGCGGAUCGUAUUUAUGCAUUGUGGACUGGGUGGACGGACCACGAGUUCCCAGAAGAUGGAAGUCGUCUCCAUGAUCAGA
((((.((((((((..((((..............((((((((((((..(((....)))..))))))))))))(((.....)))))))...)))))))))))).(((((....))))).... ( -44.50)
>DroSec_CAF1 237538 120 + 1
UCCACUCUUUUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUACUUGUGCAUCGUGGACUGGGUGGACGGACCACGAGUUCCCAGUCGCCGGAAGUCAUCUCCAUGAUCAGA
((((......))))..(((((.........(((.(((((((((((...(((....))).))))))))))))))((((((.(....).)))..))))))))..(((((....))))).... ( -40.10)
>DroSim_CAF1 255830 120 + 1
UCCACUUUUCUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUAUUUGUGCAUCGUGGACUGGGUGGACGGACCACGAGUUCCCAGUCGCCGGAAGUCAUCUCCAUGAUCAGA
........(((((((.(((((.........(((.(((((((((((...(((....))).))))))))))))))((((((.(....).)))..))))))))..)))(((.....))))))) ( -40.90)
>DroEre_CAF1 257605 120 + 1
UCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUCAGCGGAUCGUACUUAUGUAUCGUGGACUGGGUGGACGGACCACGAGUUCCCAGAAGCUGGAAGUCGUCUCCAUGAUCAGA
((((..(((((((..((((..........((((.((((((.(((....((((....))))))).))))))))))........))))...))))))).)))).(((((....))))).... ( -37.57)
>DroYak_CAF1 250734 120 + 1
UCCACUCUUCUGGACCUCGGCAAAGAAAAUCACUCCGGUCCGCGGAUCGUACUUAUGCAUCGUGGACUGGGUGGACGGACCACGAGUUCCCAGAAGCUGGAAGUCGUCUCCAUGAUCAGA
((((..(((((((..((((..........((((.(((((((((((..(((....)))..)))))))))))))))........))))...))))))).)))).(((((....))))).... ( -42.87)
>consensus
UCCACUCUUCUGGACCUCGGCAAAGAAAAUCACACCGGUCCGCGGAUCGUACUUAUGCAUCGUGGACUGGGUGGACGGACCACGAGUUCCCAGAAGCUGGAAGUCGUCUCCAUGAUCAGA
(((...(((((((..((((..........((((.(((((((((((..(((....)))..)))))))))))))))........))))...)))))))..))).(((((....))))).... (-36.65 = -36.69 +   0.04)

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 10:57:37 2006