Locus 4216

Sequence ID 3R_DroMel_CAF1
Location 11,359,684 – 11,359,924
Length 240
Max. P 0.999790
window6807 window6808 window6809 window6810 window6811

overview

Window 7

Location 11,359,684 – 11,359,804
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -43.20
Consensus MFE -38.94
Energy contribution -39.90
Covariance contribution 0.96
Combinations/Pair 1.05
Mean z-score -1.17
Structure conservation index 0.90
SVM decision value 0.08
SVM RNA-class probability 0.572320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359684 120 - 27905053
GGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCCAGGACACCAUCGCCAAUGUGCUGAACCUCAAGUCCAACGA
((((((((........))))))))((((.....))))((((((.((((((((((((.....)))).(((((.(((.....)))...)))))......))))...))))))))))...... ( -44.50)
>DroSec_CAF1 107232 120 - 1
GGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCCAGGACACCAUCGCCAAUGUGCUGAACCUCAAGUCCAACGA
((((((((........))))))))((((.....))))((((((.((((((((((((.....)))).(((((.(((.....)))...)))))......))))...))))))))))...... ( -44.50)
>DroSim_CAF1 98014 120 - 1
GGAACCGCAGACAACAGUGGUUCUGCCUUUCGAGGGCGGCUUGCAGGUGUACACUGCCACCCAGUGGAUGGACCUAACCCAGGACACCAUCGCCAAUGUGCUGAACCUCAAGUCCAACGA
((((((((........))))))))((((.....))))((((((.((((...(((((.....)))))(((((.(((.....)))...))))).............))))))))))...... ( -42.10)
>DroEre_CAF1 94662 120 - 1
GGAACCGCAGACGACAGUGGUUCUGCCCUUCGAGGGCGGCCUGCAGGUCUACUCGGCCACUCAGUGGAUGGACCUCACCCAGGACACCAUCGCGAAUGUGCUGAACCUCAAGUCCAACGA
((((((((........))))))))((((.....))))(((.((.((((....(((((((.((.(((.((((.(((.....)))...))))))))).)).))))))))))).)))...... ( -42.80)
>DroYak_CAF1 97337 120 - 1
GGAACCGCAGACAACCGUGGUUGUGCCCUUCGAGGGCGGCCUGCAGGUGUACUCGGCCACCCAGUGGAUGGACCUAACCCAGGACACCAUCGCCAAUGUGCUGAACCUCAAGUCCAACGA
(((...(((((((((....)))))((((.....))))...))))((((((((..((((((...)))(((((.(((.....)))...))))))))...))))...))))....)))..... ( -42.10)
>consensus
GGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCCAGGACACCAUCGCCAAUGUGCUGAACCUCAAGUCCAACGA
((((((((........))))))))((((.....))))((((((.(((((((((..(((((...)))(((((.(((.....)))...)))))))...)))))...))))))))))...... (-38.94 = -39.90 +   0.96)

alignment

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secondary structure

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Window 8

Location 11,359,724 – 11,359,844
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -46.04
Consensus MFE -38.52
Energy contribution -38.72
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.68
SVM RNA-class probability 0.822180
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359724 120 - 27905053
CCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAUGGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCC
..(((((((((((........)))))).(((((.......((((((((........)))))))).......(..((((((.(((....))).))))))..).))))).))).))...... ( -45.70)
>DroSec_CAF1 107272 120 - 1
CCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAUGGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCC
..(((((((((((........)))))).(((((.......((((((((........)))))))).......(..((((((.(((....))).))))))..).))))).))).))...... ( -45.70)
>DroSim_CAF1 98054 120 - 1
CCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAUGGAACCGCAGACAACAGUGGUUCUGCCUUUCGAGGGCGGCUUGCAGGUGUACACUGCCACCCAGUGGAUGGACCUAACCC
..(((((((((((........)))))).(((((.......((((((((........))))))))((((.....))))((...((((.......))))...))))))).))).))...... ( -43.90)
>DroEre_CAF1 94702 120 - 1
CCGGUCAGCUGGAUAUGGGACUGCAGUACCACUACUACAUGGAACCGCAGACGACAGUGGUUCUGCCCUUCGAGGGCGGCCUGCAGGUCUACUCGGCCACUCAGUGGAUGGACCUCACCC
((((....))))....(((..(((((..((..........((((((((........))))))))((((.....)))))).)))))((((((.((.((......)).))))))))...))) ( -46.50)
>DroYak_CAF1 97377 120 - 1
CCGGUCAGCUGGAUAUGGGUCUGCAGUACCACUACUACAUGGAACCGCAGACAACCGUGGUUGUGCCCUUCGAGGGCGGCCUGCAGGUGUACUCGGCCACCCAGUGGAUGGACCUAACCC
..((((.(((((....((((((((.((.(((........))).)).))))))..))((((((((((((.....)))))(((....))).....)))))))))))).....))))...... ( -48.40)
>consensus
CCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAUGGAACCGCAGACAACAGUGGUUCUGCCCUUCGAGGGCGGCUUGCAGGUGUACGCUGCCACCCAGUGGAUGGACCUAACCC
..(((((((((((........)))))).(((((.......((((((((........))))))))((((.....))))((...(((((....).))))...))))))).))).))...... (-38.52 = -38.72 +   0.20)

alignment

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secondary structure

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Window 9

Location 11,359,764 – 11,359,884
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -52.58
Consensus MFE -46.46
Energy contribution -47.18
Covariance contribution 0.72
Combinations/Pair 1.05
Mean z-score -2.94
Structure conservation index 0.88
SVM decision value 4.08
SVM RNA-class probability 0.999790
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359764 120 + 27905053
GCCGCCCUCGAAGGGCAGAACCACUGUUGUCUGCGGUUCCAUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCAAAGGGUUCCUCCAGCUGGAGGACAUC
.((((((.....))))((.(((((((....(((((......)))))))))))).)))).((((....(((((((....((((((((((........)))))))))))))))))))))... ( -53.30)
>DroSec_CAF1 107312 120 + 1
GCCGCCCUCGAAGGGCAGAACCACUGUUGUCUGCGGUUCCAUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAGGGUUCCUCUAGCUGGAGGACCUC
.((((((.....))))((.(((((((....(((((......)))))))))))).)))).((((....(((((((....((((((((((........)))))))))))))))))))))... ( -50.70)
>DroSim_CAF1 98094 120 + 1
GCCGCCCUCGAAAGGCAGAACCACUGUUGUCUGCGGUUCCAUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAAGGUUCCUCUAGCUGGAGGACCUC
...((((((....(((...(((((((....(((((......))))))))))))((((((........))))))..))).)))).))..........((((.(((((....))))))))). ( -43.90)
>DroEre_CAF1 94742 120 + 1
GCCGCCCUCGAAGGGCAGAACCACUGUCGUCUGCGGUUCCAUGUAGUAGUGGUACUGCAGUCCCAUAUCCAGCUGACCGGAGGAGCUCACAUCGAAGGGUUCCUCCAGCUGGAGGACAUC
...((((.....))))........(((((.(((((((.((((......)))).))))))).).....(((((((....((((((((((........))))))))))))))))).)))).. ( -56.30)
>DroYak_CAF1 97417 120 + 1
GCCGCCCUCGAAGGGCACAACCACGGUUGUCUGCGGUUCCAUGUAGUAGUGGUACUGCAGACCCAUAUCCAGCUGACCGGAGGAGCUCACGUCGAAGGGUUCCUCCAGCUGGAGCACAUC
((.((((.....))))........((..(((((((((.((((......)))).)))))))))))...(((((((....((((((((((........)))))))))))))))))))..... ( -58.70)
>consensus
GCCGCCCUCGAAGGGCAGAACCACUGUUGUCUGCGGUUCCAUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAGGGUUCCUCCAGCUGGAGGACAUC
...((((.....))))((.(((((((....(((((......)))))))))))).))...((((....(((((((....((((((((((........)))))))))))))))))))))... (-46.46 = -47.18 +   0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,359,804 – 11,359,924
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -49.18
Consensus MFE -42.32
Energy contribution -42.60
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -2.69
Structure conservation index 0.86
SVM decision value 3.46
SVM RNA-class probability 0.999253
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359804 120 + 27905053
AUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCAAAGGGUUCCUCCAGCUGGAGGACAUCGAUGGUGGACUUGAUGGGCUGCUCCAACCGCUUGUUAUUG
.......((((((..(((((((((((.(((((((....((((((((((........)))))))))))))))))(..(((.....)))..)...)))))..))))))))))))........ ( -51.60)
>DroSec_CAF1 107352 120 + 1
AUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAGGGUUCCUCUAGCUGGAGGACCUCGAUGGUGGACUUGAUGGGCUGCUCCAACCGCUUGUUAUUG
.......((((((..(((((((((((.(((..(..((..(((((((((........)))))))))..))..)...(((.....))))))....)))))..))))))))))))........ ( -49.80)
>DroSim_CAF1 98134 120 + 1
AUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAAGGUUCCUCUAGCUGGAGGACCUCGAUGGUGGACUUGAUGGGCUGCUCCAACCGCUUGUUAUUG
.......((((((..(((((((((((....((((.((((((((.......(((....)))((((((....))))))))))..)))).))))..)))))..))))))))))))........ ( -47.60)
>DroEre_CAF1 94782 120 + 1
AUGUAGUAGUGGUACUGCAGUCCCAUAUCCAGCUGACCGGAGGAGCUCACAUCGAAGGGUUCCUCCAGCUGGAGGACAUCGAUGGAGGACUUGACGGGUUGCUGGAACCGCUUGUUGUUU
.......((((((.((((((.(((...(((((((....((((((((((........)))))))))))))))))(..(.((....)))..).....))))))).)).))))))........ ( -47.40)
>DroYak_CAF1 97457 120 + 1
AUGUAGUAGUGGUACUGCAGACCCAUAUCCAGCUGACCGGAGGAGCUCACGUCGAAGGGUUCCUCCAGCUGGAGCACAUCGAUGGUGGACUUGAUGGCUUGCUCCAACCGCUUGCUGUUG
...((((((((((...((((.......(((((((....((((((((((........)))))))))))))))))((.((((((.(.....)))))))))))))....))))).)))))... ( -49.50)
>consensus
AUGUAGUAGUGGUACUGGAGUCCCAUAUCCAGUUGGCCGGAGGAGCUCACAUCGAAGGGUUCCUCCAGCUGGAGGACAUCGAUGGUGGACUUGAUGGGCUGCUCCAACCGCUUGUUAUUG
.......((((((..(((((((((...(((((((....((((((((((........))))))))))))))))).....((((.(.....))))).)))..))))))))))))........ (-42.32 = -42.60 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,359,804 – 11,359,924
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -41.54
Consensus MFE -34.58
Energy contribution -35.62
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -2.70
Structure conservation index 0.83
SVM decision value 2.93
SVM RNA-class probability 0.997793
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11359804 120 - 27905053
CAAUAACAAGCGGUUGGAGCAGCCCAUCAAGUCCACCAUCGAUGUCCUCCAGCUGGAGGAACCCUUUGAUGUGAGCUCCUCCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAU
...........((((((((.(((((((((((((.......))).((((((....)))))).....)))))).).))).)))))))).((((((........))))))............. ( -42.20)
>DroSec_CAF1 107352 120 - 1
CAAUAACAAGCGGUUGGAGCAGCCCAUCAAGUCCACCAUCGAGGUCCUCCAGCUAGAGGAACCCUUCGAUGUGAGCUCCUCCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAU
........((.((((((((...(((((..((..(((.((((((((((((......)))))...))))))))))..))..(((((....))))).))))).)))))..))).))....... ( -42.60)
>DroSim_CAF1 98134 120 - 1
CAAUAACAAGCGGUUGGAGCAGCCCAUCAAGUCCACCAUCGAGGUCCUCCAGCUAGAGGAACCUUUCGAUGUGAGCUCCUCCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAU
........((.((((((((...(((((..((..(((.((((((((((((......)))).)))..))))))))..))..(((((....))))).))))).)))))..))).))....... ( -42.00)
>DroEre_CAF1 94782 120 - 1
AAACAACAAGCGGUUCCAGCAACCCGUCAAGUCCUCCAUCGAUGUCCUCCAGCUGGAGGAACCCUUCGAUGUGAGCUCCUCCGGUCAGCUGGAUAUGGGACUGCAGUACCACUACUACAU
.........(((((((((............(..(((((((((..((((((....)))))).....)))))).)))..).(((((....)))))..)))))))))((((....)))).... ( -43.50)
>DroYak_CAF1 97457 120 - 1
CAACAGCAAGCGGUUGGAGCAAGCCAUCAAGUCCACCAUCGAUGUGCUCCAGCUGGAGGAACCCUUCGACGUGAGCUCCUCCGGUCAGCUGGAUAUGGGUCUGCAGUACCACUACUACAU
.....((...(((((((((((...((((............)))))))))))))))..(((.(((...(((....).)).(((((....)))))...))))))))((((....)))).... ( -37.40)
>consensus
CAAUAACAAGCGGUUGGAGCAGCCCAUCAAGUCCACCAUCGAUGUCCUCCAGCUGGAGGAACCCUUCGAUGUGAGCUCCUCCGGCCAACUGGAUAUGGGACUCCAGUACCACUACUACAU
........((.((((((((...(((((..((..(((.(((((..((((((....)))))).....))))))))..))..(((((....))))).))))).)))))..))).))....... (-34.58 = -35.62 +   1.04)

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 11:22:04 2006