Locus 3507

Sequence ID 3R_DroMel_CAF1
Location 9,480,952 – 9,481,128
Length 176
Max. P 0.898327
window5631 window5632 window5633 window5634 window5635

overview

Window 1

Location 9,480,952 – 9,481,054
Length 102
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 82.27
Mean single sequence MFE -38.27
Consensus MFE -27.69
Energy contribution -28.00
Covariance contribution 0.31
Combinations/Pair 1.31
Mean z-score -1.92
Structure conservation index 0.72
SVM decision value 0.46
SVM RNA-class probability 0.746962
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9480952 102 + 27905053
UGUUGGCUUGGGUGCCAUCGGAAUUACAUAGUGGGCCCAGCCGUUAGUGAAUGCCGAUGGCGGCAGGACGGAUUGGGCCAGAUAGGGAUUGUAGUUGGGAUU---
..(..(((..(((.((((((......)......((((((((((((......(((((....))))).))))).))))))).))).)).)))..)))..)....--- ( -38.60)
>DroVir_CAF1 152121 99 + 1
UGUUG---UUGGAAUUGUCGGUGCCACAUAUGAGGCCCAGCCAUUAAAGAAUGCCGAUGGUGGUAACGACGUUUGAGCCUGAUACGGAUUAUAGUUCGGAUU---
.((((---(((..((..((((.(((........))))).(.((((....)))).)))..))..)))))))((((((((.((((....))))..)))))))).--- ( -26.50)
>DroSec_CAF1 110540 102 + 1
UGUUGGCUUGGAUGCCAUCGGAAUCACAUAGUGGGCCCAGCCGUUGGUGAAUGCCGAUGGCGGCAGAACGGACUGGGCCAGAUAGCGAUUGUAGUUGGGAUU---
......((..(.(((.((((..(((.(.....)((((((((((((......(((((....))))).))))).))))))).)))..)))).))).)..))...--- ( -39.40)
>DroSim_CAF1 100512 102 + 1
UGUUGGCUUGGAUGCCAUCGGAAUCACAUAGUGGGCCCAGCCGUUGGUGAAUGCCGAUGGCGGCAGAACGGACUGGGCCAGAUAGGGAUGGUAGUUGGGAUU---
......((..(.(((((((.....(((...)))((((((((((((......(((((....))))).))))).))))))).......))))))).)..))...--- ( -43.60)
>DroEre_CAF1 118093 102 + 1
UGUGGGCUUGGGUGCCACCGGAGUCACAUAGUGGGCCCAGCCGUGAGUGAAGGCUGAUGGCGGCAGGACGGACUGGGCCAGGUAGGGAUUGUAGUUGGCGUU---
.((.((((..(((.(((((.....(((...)))(((((((((((........((((....))))...)))).))))))).))).)).)))..)))).))...--- ( -39.30)
>DroYak_CAF1 112421 105 + 1
UGUUGGCUUGGGUGCCACCGGAGUCACAUAGUGGGCCCAGCCAUGAGUGAAUGCCGAUGGCGGCAGGACGGACUGGGCCAGGUAGGGAUUGUAGUUGGCAUUGCU
(((..(((..(((.(((((.....(((...)))(((((((((....((...(((((....)))))..)))).))))))).))).)).)))..)))..)))..... ( -42.20)
>consensus
UGUUGGCUUGGGUGCCAUCGGAAUCACAUAGUGGGCCCAGCCGUUAGUGAAUGCCGAUGGCGGCAGGACGGACUGGGCCAGAUAGGGAUUGUAGUUGGGAUU___
..(..(((..(((.((((((......)......(((((((((((.......(((((....)))))..)))).))))))).))).)).)))..)))..)....... (-27.69 = -28.00 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,480,952 – 9,481,054
Length 102
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -29.34
Consensus MFE -20.93
Energy contribution -23.02
Covariance contribution 2.08
Combinations/Pair 1.10
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 1.00
SVM RNA-class probability 0.898327
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9480952 102 - 27905053
---AAUCCCAACUACAAUCCCUAUCUGGCCCAAUCCGUCCUGCCGCCAUCGGCAUUCACUAACGGCUGGGCCCACUAUGUAAUUCCGAUGGCACCCAAGCCAACA
---.......................((((((..((((..(((((....))))).......)))).))))))..............(.((((......)))).). ( -26.70)
>DroVir_CAF1 152121 99 - 1
---AAUCCGAACUAUAAUCCGUAUCAGGCUCAAACGUCGUUACCACCAUCGGCAUUCUUUAAUGGCUGGGCCUCAUAUGUGGCACCGACAAUUCCAA---CAACA
---..............(((((((.(((((((...(((((((((......)).......)))))))))))))).))))).))...............---..... ( -18.91)
>DroSec_CAF1 110540 102 - 1
---AAUCCCAACUACAAUCGCUAUCUGGCCCAGUCCGUUCUGCCGCCAUCGGCAUUCACCAACGGCUGGGCCCACUAUGUGAUUCCGAUGGCAUCCAAGCCAACA
---............((((((.....(((((((.(((((.(((((....)))))......))))))))))))......))))))..(.((((......)))).). ( -37.50)
>DroSim_CAF1 100512 102 - 1
---AAUCCCAACUACCAUCCCUAUCUGGCCCAGUCCGUUCUGCCGCCAUCGGCAUUCACCAACGGCUGGGCCCACUAUGUGAUUCCGAUGGCAUCCAAGCCAACA
---...........(((((.......(((((((.(((((.(((((....)))))......))))))))))))(((...))).....))))).............. ( -33.00)
>DroEre_CAF1 118093 102 - 1
---AACGCCAACUACAAUCCCUACCUGGCCCAGUCCGUCCUGCCGCCAUCAGCCUUCACUCACGGCUGGGCCCACUAUGUGACUCCGGUGGCACCCAAGCCCACA
---...(((.................(((((((.((((..((..((.....))...))...)))))))))))(((...))).....)))(((......))).... ( -28.00)
>DroYak_CAF1 112421 105 - 1
AGCAAUGCCAACUACAAUCCCUACCUGGCCCAGUCCGUCCUGCCGCCAUCGGCAUUCACUCAUGGCUGGGCCCACUAUGUGACUCCGGUGGCACCCAAGCCAACA
......(((.................(((((((.((((..(((((....))))).......)))))))))))(((...))).....)))(((......))).... ( -31.90)
>consensus
___AAUCCCAACUACAAUCCCUAUCUGGCCCAGUCCGUCCUGCCGCCAUCGGCAUUCACUAACGGCUGGGCCCACUAUGUGACUCCGAUGGCACCCAAGCCAACA
..........................(((((((.((((..(((((....))))).......)))))))))))..............(.((((......)))).). (-20.93 = -23.02 +   2.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,480,978 – 9,481,088
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -38.72
Consensus MFE -25.92
Energy contribution -27.09
Covariance contribution 1.17
Combinations/Pair 1.34
Mean z-score -1.27
Structure conservation index 0.67
SVM decision value 0.03
SVM RNA-class probability 0.548244
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9480978 110 + 27905053
CAUAGUGGGCCCAGCCGUUAGUGAAUGCCGAUGGCGGCAGGACGGAUUGGGCCAGAUAGGGAUUGUAGUUGGGAUUGUUGUAAUUGUAGCUAUCAGCAGUGGCCGGCUGG
.......((((((((((((......(((((....))))).))))).)))))))............(((((((.(((((((.............)))))))..))))))). ( -40.92)
>DroVir_CAF1 152144 107 + 1
CAUAUGAGGCCCAGCCAUUAAAGAAUGCCGAUGGUGGUAACGACGUUUGAGCCUGAUACGGAUUAUAGUUCGGAUU---AUAGACUAAGUUAUCCAUAAUGGUCGGCUGG
..........(((((((((....)))((((...((((((((...(((((....((((.(((((....))))).)))---))))))...)))).))))..)))).)))))) ( -26.90)
>DroSec_CAF1 110566 110 + 1
CAUAGUGGGCCCAGCCGUUGGUGAAUGCCGAUGGCGGCAGAACGGACUGGGCCAGAUAGCGAUUGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAGCGGUGGCCGGCUGG
....((.((((((((((((......(((((....))))).))))).))))))).....)).....(((((((.(((((((((((....)))).)))))))..))))))). ( -45.80)
>DroSim_CAF1 100538 110 + 1
CAUAGUGGGCCCAGCCGUUGGUGAAUGCCGAUGGCGGCAGAACGGACUGGGCCAGAUAGGGAUGGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAGCGGUGGCCGGCUGG
..((((.((((..((((((((((..(((.(((.(((((((..(.((((..((((........)))))))).)..))))))).))))))..)))))))))))))).)))). ( -47.60)
>DroEre_CAF1 118119 110 + 1
CAUAGUGGGCCCAGCCGUGAGUGAAGGCUGAUGGCGGCAGGACGGACUGGGCCAGGUAGGGAUUGUAGUUGGCGUUGUUGUAGUUGUAGCUAUCCAAAGUGGGCGGCUGG
..((((.(.(((((((((.(((....))).)))))((((.(((.(((.(.(((((.((.......)).))))).).)))...))).).)))........))))).)))). ( -37.20)
>DroAna_CAF1 106158 110 + 1
CAUACGAGGCCCAGCCGUUAAUGAAGGCCGAUGGCGGGAGGACGGUCUGCGCCAGGUAGGGAUUGUAGGUGCUGCUGCUGUAGUUGUAGCUAUCCAGGGAGGCCGGUUGC
..(((((..(((.((((((......)))...((((((((......))).)))))))).))).)))))((((((((.((....)).)))))..((....)).)))...... ( -33.90)
>consensus
CAUAGUGGGCCCAGCCGUUAGUGAAUGCCGAUGGCGGCAGGACGGACUGGGCCAGAUAGGGAUUGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAACAGUGGCCGGCUGG
.......((((((((((((......(((((....))))).))))).)))))))............(((((((.......(((((....))))).........))))))). (-25.92 = -27.09 +   1.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,480,978 – 9,481,088
Length 110
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -28.86
Consensus MFE -15.71
Energy contribution -17.60
Covariance contribution 1.89
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.54
SVM decision value 0.47
SVM RNA-class probability 0.748958
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9480978 110 - 27905053
CCAGCCGGCCACUGCUGAUAGCUACAAUUACAACAAUCCCAACUACAAUCCCUAUCUGGCCCAAUCCGUCCUGCCGCCAUCGGCAUUCACUAACGGCUGGGCCCACUAUG
(((((((((((.....(((((..............................))))))))))..........(((((....))))).........)))))).......... ( -27.81)
>DroVir_CAF1 152144 107 - 1
CCAGCCGACCAUUAUGGAUAACUUAGUCUAU---AAUCCGAACUAUAAUCCGUAUCAGGCUCAAACGUCGUUACCACCAUCGGCAUUCUUUAAUGGCUGGGCCUCAUAUG
((((((((((..(((((((....(((((...---.....).))))..)))))))...)).))....((((..........))))..........)))))).......... ( -27.00)
>DroSec_CAF1 110566 110 - 1
CCAGCCGGCCACCGCUGAUAGCUACAACUACAACAAUCCCAACUACAAUCGCUAUCUGGCCCAGUCCGUUCUGCCGCCAUCGGCAUUCACCAACGGCUGGGCCCACUAUG
..(((.(....).)))((((((............................)))))).(((((((.(((((.(((((....)))))......))))))))))))....... ( -34.39)
>DroSim_CAF1 100538 110 - 1
CCAGCCGGCCACCGCUGAUAGCUACAACUACAACAAUCCCAACUACCAUCCCUAUCUGGCCCAGUCCGUUCUGCCGCCAUCGGCAUUCACCAACGGCUGGGCCCACUAUG
.((((.(....).))))........................................(((((((.(((((.(((((....)))))......))))))))))))....... ( -32.10)
>DroEre_CAF1 118119 110 - 1
CCAGCCGCCCACUUUGGAUAGCUACAACUACAACAACGCCAACUACAAUCCCUACCUGGCCCAGUCCGUCCUGCCGCCAUCAGCCUUCACUCACGGCUGGGCCCACUAUG
..(((..((......))...)))..................................(((((((.((((..((..((.....))...))...)))))))))))....... ( -24.20)
>DroAna_CAF1 106158 110 - 1
GCAACCGGCCUCCCUGGAUAGCUACAACUACAGCAGCAGCACCUACAAUCCCUACCUGGCGCAGACCGUCCUCCCGCCAUCGGCCUUCAUUAACGGCUGGGCCUCGUAUG
((..((((.....))))...(((........))).))...............(((..(((.(((.((((......(((...)))........))))))).)))..))).. ( -27.64)
>consensus
CCAGCCGGCCACCGCGGAUAGCUACAACUACAACAAUCCCAACUACAAUCCCUAUCUGGCCCAGUCCGUCCUGCCGCCAUCGGCAUUCACUAACGGCUGGGCCCACUAUG
.........................................................(((((((.((((..(((((....))))).......)))))))))))....... (-15.71 = -17.60 +   1.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,481,018 – 9,481,128
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.76
Mean single sequence MFE -40.75
Consensus MFE -29.12
Energy contribution -28.02
Covariance contribution -1.10
Combinations/Pair 1.48
Mean z-score -1.31
Structure conservation index 0.71
SVM decision value 0.57
SVM RNA-class probability 0.786759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9481018 110 + 27905053
GACGGAUUGGGCCAGAUAGGGAUUGUAGUUGGGAUUGUUGUAAUUGUAGCUAUCAGCAGUGGCCGGCUGGGGCGGAAUGUAGCCGGCUCGAACCGAGCUAAAUAUGGGGA
..(((.(((((((............(((((((.(((((((.............)))))))..))))))).(((........)))))))))).)))............... ( -33.92)
>DroPse_CAF1 113828 107 + 1
GCUUGACUGUGCCAAAAACGGAUUGAAGUGUGGAUUGUAGCAGUU---UCUGUCCAUCACGGCUGGCUGCGGCGGCACGUAGCCGGCGCGGGCCGCACCGCCCAUGGGAA
((..((((((.(((...((........)).)))......))))))---...))((((....((((((((((......))))))))))..((((......))))))))... ( -40.80)
>DroSec_CAF1 110606 110 + 1
AACGGACUGGGCCAGAUAGCGAUUGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAGCGGUGGCCGGCUGGGGCGGAAUGUAGCCGGCUCGGACCGAGCUGGAAAUGGGGA
..(((.(((((((............(((((((.(((((((((((....)))).)))))))..))))))).(((........)))))))))).)))............... ( -38.80)
>DroSim_CAF1 100578 110 + 1
AACGGACUGGGCCAGAUAGGGAUGGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAGCGGUGGCCGGCUGGGGCGGAAUGUAGCCGGCUCGGACCGAGCUGGAAAUGGGGU
......((.(.((((.......(((((((((.(((((...))))).))))))))).(((((((((((((.(......).)))))))))...))))..))))...).)).. ( -40.80)
>DroEre_CAF1 118159 110 + 1
GACGGACUGGGCCAGGUAGGGAUUGUAGUUGGCGUUGUUGUAGUUGUAGCUAUCCAAAGUGGGCGGCUGGGGCGGAAUGUAGCCGGCCCGGAUCGAGCUGGAAACGGGGA
..(((.(((((((.......(((....)))(((...(((...(((.(((((..((.....))..))))).)))..)))...)))))))))).)))..(((....)))... ( -41.00)
>DroAna_CAF1 106198 110 + 1
GACGGUCUGCGCCAGGUAGGGAUUGUAGGUGCUGCUGCUGUAGUUGUAGCUAUCCAGGGAGGCCGGUUGCGGCGGAAUGUAGCCGGCGCGGGCGGCUCCGCCCACGGGGA
..(.(((((((((.(((..((((.((....(((((....)))))....)).))))......)))(((((((......)))))))))))))))).)(((((....))))). ( -49.20)
>consensus
GACGGACUGGGCCAGAUAGGGAUUGUAGUUGGGAUUGUUGUAGUUGUAGCUAUCAACGGUGGCCGGCUGGGGCGGAAUGUAGCCGGCUCGGACCGAGCUGGAAAUGGGGA
..(((.(((((((...........(((((((.(((((...))))).)))))))...........(((((.(......).)))))))))))).)))..(((....)))... (-29.12 = -28.02 +  -1.10)

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 11:02:50 2006