Locus 911

Sequence ID 2R_DroMel_CAF1
Location 4,054,927 – 4,055,162
Length 235
Max. P 0.701166
window1604 window1605 window1606 window1607 window1608

overview

Window 4

Location 4,054,927 – 4,055,044
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.19
Mean single sequence MFE -23.30
Consensus MFE -19.50
Energy contribution -19.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.32
SVM RNA-class probability 0.687844
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4054927 117 + 20766785
CUUUUUUCCGC---UGCUGGCAAGUUGCCAUUGUCCGAUUACAUUCUGCCAAGCUGGCAUUCCAUUCCGGCACCAGCUGCUCCUCAUUCCCGCCCCCAUCCAUACACGUACCUCCACCAU
.........((---.(((((.....((((.......((......))((((.....)))).........))))))))).))........................................ ( -21.90)
>DroSim_CAF1 43713 117 + 1
CUUUUUUACGCUGCUGCUGGCAAGUUGCCAUUGUCCGAUUACAUUUUGCCAAGCUGGCAUUCCAUUCCGGCACCAGCUGCUCCUCAUUCCCGCCCCUAUCCAUACACACACCUCCAC---
.........((.((((.(((((((.((..(((....)))..)).))))))).(((((.(......))))))..)))).)).....................................--- ( -23.90)
>DroEre_CAF1 37570 116 + 1
CUU-UUUCCGC---UGCUGGCAAGUUGCCAUUGUCCGACUACAUUCUGCCAAGCUGGCAUUCCAUUCCGGCACCAGCUGCUCCUCAUUCCCGGCCACAUCCAGGCACACACCUCCACCGC
...-.....((---.(((((.....((((..(((......)))...((((.....)))).........))))))))).))............(((.......)))............... ( -25.50)
>DroYak_CAF1 41037 113 + 1
CUUUUUUCCGC---UGCUGGCAAGUUGCCAUUGUCCGAUUACAUUCUGCCAAGCUGGCAUUCCAUUCCGGCACCAGCUGCUCCUCAUACCCGUCCAUAUCAACAC----ACAUACACCUC
.........((---.(((((.....((((.......((......))((((.....)))).........))))))))).)).........................----........... ( -21.90)
>consensus
CUUUUUUCCGC___UGCUGGCAAGUUGCCAUUGUCCGAUUACAUUCUGCCAAGCUGGCAUUCCAUUCCGGCACCAGCUGCUCCUCAUUCCCGCCCACAUCCAUACACACACCUCCACC_C
.........((....(((((.....((((..(((......)))...((((.....)))).........))))))))).))........................................ (-19.50 = -19.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,055,004 – 4,055,122
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.22
Mean single sequence MFE -24.17
Consensus MFE -11.20
Energy contribution -12.45
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.46
SVM decision value 0.35
SVM RNA-class probability 0.701166
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4055004 118 + 20766785
UCCUCAUUCCCGCCCCCAUCCAUACACGUACCUCCACCAUCGCCACCAUCC--UCAGCCGUAUCCAUGCCCAUAUCCAGGCGAGUAUGCCCCACCCAAAAGGGCAGCAUAAAAACGGGGC
...........(((((.......................(((((.......--...((.........)).........))))).((((((((........)))..))))).....))))) ( -24.41)
>DroSim_CAF1 43793 105 + 1
UCCUCAUUCCCGCCCCUAUCCAUACACACACCUCCAC------------CC--UCAGCCGUAUCCAUGCCCAUAUCCACGCCAGUAUGCC-CACCCAAAAGGGCAGCAUAAAAACGGGGC
...........(((((.....((((............------------..--......))))..((((........((....)).((((-(........)))))))))......))))) ( -20.65)
>DroEre_CAF1 37646 117 + 1
UCCUCAUUCCCGGCCACAUCCAGGCACACACCUCCACCGCCACCACCACCCCAUAGCCCGUAUCUAUUCUCAUAUCCAGGCCAGUA--CC-CGCCCAAAAGGGCAGCAUAAAAACGGGGC
.......((((((((.......(((.............)))...........((((.......))))...........))))....--..-.((((....))))...........)))). ( -25.22)
>DroYak_CAF1 41114 107 + 1
UCCUCAUACCCGUCCAUAUCAACAC----ACAUACACCUCCACCC--------UUACCCGUAUCUAUGGCCAUAUCCAGGCCAGUAUGCC-CACCCAAAAGGGCAGCAUAAAAACGGGGC
.........................----................--------...(((((.....(((((.......)))))((.((((-(........)))))))......))))).. ( -26.40)
>consensus
UCCUCAUUCCCGCCCACAUCCAUACACACACCUCCACC_CCACCA____CC__UCACCCGUAUCCAUGCCCAUAUCCAGGCCAGUAUGCC_CACCCAAAAGGGCAGCAUAAAAACGGGGC
........((((............................................(((((((........))))...)))...(((((....(((....)))..)))))....)))).. (-11.20 = -12.45 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,055,004 – 4,055,122
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.22
Mean single sequence MFE -39.55
Consensus MFE -22.62
Energy contribution -23.75
Covariance contribution 1.12
Combinations/Pair 1.21
Mean z-score -1.83
Structure conservation index 0.57
SVM decision value -0.04
SVM RNA-class probability 0.515113
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4055004 118 - 20766785
GCCCCGUUUUUAUGCUGCCCUUUUGGGUGGGGCAUACUCGCCUGGAUAUGGGCAUGGAUACGGCUGA--GGAUGGUGGCGAUGGUGGAGGUACGUGUAUGGAUGGGGGCGGGAAUGAGGA
..(((((((((((.((((((.((..((((((.....))))))..))...)))))...((((((((..--..((.((....)).))...))).)))))..).)))))))))))........ ( -42.50)
>DroSim_CAF1 43793 105 - 1
GCCCCGUUUUUAUGCUGCCCUUUUGGGUG-GGCAUACUGGCGUGGAUAUGGGCAUGGAUACGGCUGA--GG------------GUGGAGGUGUGUGUAUGGAUAGGGGCGGGAAUGAGGA
((((((((..(((((..(((....)))..-).))))..)))...........((((.(((((.((..--..------------....)).))))).))))....)))))........... ( -37.50)
>DroEre_CAF1 37646 117 - 1
GCCCCGUUUUUAUGCUGCCCUUUUGGGCG-GG--UACUGGCCUGGAUAUGAGAAUAGAUACGGGCUAUGGGGUGGUGGUGGCGGUGGAGGUGUGUGCCUGGAUGUGGCCGGGAAUGAGGA
(((((((.......((((((....)))))-).--....((((((..(((....)))....)))))))))))))..((((.(((....((((....))))...))).)))).......... ( -43.40)
>DroYak_CAF1 41114 107 - 1
GCCCCGUUUUUAUGCUGCCCUUUUGGGUG-GGCAUACUGGCCUGGAUAUGGCCAUAGAUACGGGUAA--------GGGUGGAGGUGUAUGU----GUGUUGAUAUGGACGGGUAUGAGGA
((((((..(((((.((((((........)-))))...(((((.......))))).......).))))--------)..))).)))((((.(----((.(......).))).))))..... ( -34.80)
>consensus
GCCCCGUUUUUAUGCUGCCCUUUUGGGUG_GGCAUACUGGCCUGGAUAUGGGCAUAGAUACGGCUGA__GG____UGGUGG_GGUGGAGGUGUGUGUAUGGAUAGGGGCGGGAAUGAGGA
..((((((((((((((((((....))))..)))....(((((((..(((....)))....)))))))..................................)))))))))))........ (-22.62 = -23.75 +   1.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,055,044 – 4,055,162
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.13
Mean single sequence MFE -31.37
Consensus MFE -22.15
Energy contribution -23.65
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.71
SVM decision value 0.01
SVM RNA-class probability 0.538380
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4055044 118 + 20766785
CGCCACCAUCC--UCAGCCGUAUCCAUGCCCAUAUCCAGGCGAGUAUGCCCCACCCAAAAGGGCAGCAUAAAAACGGGGCAUCAUAAAAAAAUGGCGUCAAUUGGCGACGCGUUAGCCUG
(((((......--...(((((.....((((........)))).(.(((((((.(((....)))..(........)))))))))........)))))......)))))..((....))... ( -34.06)
>DroSim_CAF1 43830 108 + 1
---------CC--UCAGCCGUAUCCAUGCCCAUAUCCACGCCAGUAUGCC-CACCCAAAAGGGCAGCAUAAAAACGGGGCAUCAUAAAAAAAUGGCGUCAAUUGGCGACGCGUUAGCCUG
---------..--....((((....((((........((....)).((((-(........)))))))))....))))(((..(((......)))(((((.......)))))....))).. ( -29.20)
>DroEre_CAF1 37686 117 + 1
CACCACCACCCCAUAGCCCGUAUCUAUUCUCAUAUCCAGGCCAGUA--CC-CGCCCAAAAGGGCAGCAUAAAAACGGGGCAUCAUAAAAAAAUGGCGUCAAUUGGCGACGCGUUAGCCUG
....................................(((((..((.--((-(((((....)))).(........))))))..............(((((.......)))))....))))) ( -26.70)
>DroYak_CAF1 41150 111 + 1
CACCC--------UUACCCGUAUCUAUGGCCAUAUCCAGGCCAGUAUGCC-CACCCAAAAGGGCAGCAUAAAAACGGGGCAUCAUAAAAAAAUGGCGUCAAUUGGCGACGCGUUAGCCUG
.....--------....((((.....(((((.......)))))((.((((-(........)))))))......))))(((..(((......)))(((((.......)))))....))).. ( -35.50)
>consensus
CACCA____CC__UCACCCGUAUCCAUGCCCAUAUCCAGGCCAGUAUGCC_CACCCAAAAGGGCAGCAUAAAAACGGGGCAUCAUAAAAAAAUGGCGUCAAUUGGCGACGCGUUAGCCUG
.................((((.(.(((((.........(((......)))...(((....)))..))))).).))))(((..(((......)))(((((.......)))))....))).. (-22.15 = -23.65 +   1.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,055,044 – 4,055,162
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.13
Mean single sequence MFE -40.30
Consensus MFE -31.85
Energy contribution -32.23
Covariance contribution 0.37
Combinations/Pair 1.10
Mean z-score -1.36
Structure conservation index 0.79
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4055044 118 - 20766785
CAGGCUAACGCGUCGCCAAUUGACGCCAUUUUUUUAUGAUGCCCCGUUUUUAUGCUGCCCUUUUGGGUGGGGCAUACUCGCCUGGAUAUGGGCAUGGAUACGGCUGA--GGAUGGUGGCG
.........((((((.....))))))..............((((((((((((.(((((((.((..((((((.....))))))..))...))))..(....)))))))--)))))).))). ( -46.50)
>DroSim_CAF1 43830 108 - 1
CAGGCUAACGCGUCGCCAAUUGACGCCAUUUUUUUAUGAUGCCCCGUUUUUAUGCUGCCCUUUUGGGUG-GGCAUACUGGCGUGGAUAUGGGCAUGGAUACGGCUGA--GG---------
(((.(....((((((.....))))))..........(.((((((((((..(((((..(((....)))..-).))))..)))).......)))))).)....).))).--..--------- ( -36.71)
>DroEre_CAF1 37686 117 - 1
CAGGCUAACGCGUCGCCAAUUGACGCCAUUUUUUUAUGAUGCCCCGUUUUUAUGCUGCCCUUUUGGGCG-GG--UACUGGCCUGGAUAUGAGAAUAGAUACGGGCUAUGGGGUGGUGGUG
...((((.(((((((.....))))))..............(((((((.......((((((....)))))-).--....((((((..(((....)))....)))))))))))))).)))). ( -41.30)
>DroYak_CAF1 41150 111 - 1
CAGGCUAACGCGUCGCCAAUUGACGCCAUUUUUUUAUGAUGCCCCGUUUUUAUGCUGCCCUUUUGGGUG-GGCAUACUGGCCUGGAUAUGGCCAUAGAUACGGGUAA--------GGGUG
..(((....((((((.....))))))(((......)))..)))((((.(((((.(..(((....)))..-).......((((.......))))))))).))))....--------..... ( -36.70)
>consensus
CAGGCUAACGCGUCGCCAAUUGACGCCAUUUUUUUAUGAUGCCCCGUUUUUAUGCUGCCCUUUUGGGUG_GGCAUACUGGCCUGGAUAUGGGCAUAGAUACGGCUGA__GG____UGGUG
..(((....((((((.....))))))(((......)))..)))((((.((((((((((((....))))..(((......)))........)))))))).))))................. (-31.85 = -32.23 +   0.37)

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 09:51:07 2006