Locus 6113

Sequence ID 2R_DroMel_CAF1
Location 19,235,851 – 19,236,150
Length 299
Max. P 0.999902
window9787 window9788 window9789 window9790 window9791

overview

Window 7

Location 19,235,851 – 19,235,971
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.16
Mean single sequence MFE -35.93
Consensus MFE -19.19
Energy contribution -20.12
Covariance contribution 0.94
Combinations/Pair 1.18
Mean z-score -1.87
Structure conservation index 0.53
SVM decision value 0.97
SVM RNA-class probability 0.891549
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19235851 120 - 20766785
UUCUGGCACUCGCUUCCCGCCACCAAUGGCUGGCUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCUUUUCAAUAAAGAUUUUAGCUGCAAUCAGGACCUUUUUGCAUCUGCAGGUGCA
.....((((..((..((.((((....)))).))(((((((((((((...)))))))).(((((...((((.....))))......))))).)))))...............))..)))). ( -41.00)
>DroSim_CAF1 25285 110 - 1
UUCUGGCACUCGGCUCCC-------AUGGCU--CUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCCUUUCAAUAAAGAUUUGAGCUGCAAUCAGGAUAU-UUUGCAUCUGCAGGUGCA
(((((((.(.(((...((-------((((((--.....))))))))...))).)))..(((((.......((((.......)))))))))...)))))...-..((((((....)))))) ( -38.61)
>DroEre_CAF1 26385 101 - 1
UUCUGUUC--------CCACCAUCAAUG--------GUGGCCAUGGCUACUGGGGCUCGCAGCCACCUUU--AGUAAAGAUUUAAGCUGCAAUCAGUAUAU-UUCGCAUGGGCAGGUGCG
.(((((..--------((((((....))--------))))(((((((((..(((((.....))).))..)--)))...((..((.((((....)))).)).-.)).)))))))))).... ( -35.40)
>DroYak_CAF1 26456 91 - 1
UUCUGGCA------------CAUCAAUGGC----CGGUGGUCAUGGCUACUGUG----GCAGCCACCUGU--AAUAAGGAUUUAUGCUGCAAUCAAGAUGC-UUUG------CAGCUGCA
...((((.------------((....))((----(((((((....))))))..)----)).))))(((..--....)))......(((((((.........-.)))------)))).... ( -28.70)
>consensus
UUCUGGCA________CC__CAUCAAUGGC____UGGUGGCCAUGGCUACCGUGGCUCGCAGCCACCUUU__AAUAAAGAUUUAAGCUGCAAUCAGGAUAU_UUUGCAUCUGCAGGUGCA
(((((.............................(((((((....)))))))......(((((......................)))))...)))))......(((((......))))) (-19.19 = -20.12 +   0.94)

alignment

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secondary structure

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Window 8

Location 19,235,891 – 19,236,010
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.83
Mean single sequence MFE -39.30
Consensus MFE -26.40
Energy contribution -25.63
Covariance contribution -0.77
Combinations/Pair 1.22
Mean z-score -2.44
Structure conservation index 0.67
SVM decision value 4.46
SVM RNA-class probability 0.999902
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19235891 119 - 20766785
UACAACAA-UUGCUUGAUGUUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGCUUCCCGCCACCAAUGGCUGGCUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCUUUUCAAUAAAGA
.......(-(((......(..((((.((((..((((((....))))))..(((..((.((((....)))).))..((((((....)))))))))))))))))..)......))))..... ( -42.10)
>DroSim_CAF1 25324 110 - 1
UGCGGCAA-UUGCUUGAUGCUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCGGCUCCC-------AUGGCU--CUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCCUUUCAAUAAAGA
(((((((.-..((.....))..))))((((..((((((....))))))(.(((...((-------((((((--.....))))))))...))).))))))))................... ( -45.20)
>DroYak_CAF1 26489 92 - 1
---AGCAAUUUGCUUGAUGUU---CCGAGUUUUGCUGGAUUUCUGGCA------------CAUCAAUGGC----CGGUGGUCAUGGCUACUGUG----GCAGCCACCUGU--AAUAAGGA
---(((((...(((((.....---.))))).))))).(((..(((((.------------((....))))----)))..))).(((((.(....----).)))))(((..--....))). ( -30.60)
>consensus
U_CAGCAA_UUGCUUGAUGUUCUGCCGAGCUCUGCCAGAUUUCUGGCACUCG__UCCC__CA_CAAUGGCU__CUGGUGGCCAUGGCUACCGUGGCUCGCAGCCCCCUUUUCAAUAAAGA
...........(((((.........)))))..((((((....))))))...................((((....((((((....))))))((.....))))))................ (-26.40 = -25.63 +  -0.77)

alignment

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secondary structure

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Window 9

Location 19,235,931 – 19,236,046
Length 115
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 74.93
Mean single sequence MFE -32.04
Consensus MFE -17.99
Energy contribution -19.33
Covariance contribution 1.34
Combinations/Pair 1.14
Mean z-score -1.78
Structure conservation index 0.56
SVM decision value 0.09
SVM RNA-class probability 0.578833
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19235931 115 + 20766785
CCACCAGCCAGCCAUUGGUGGCGGGAAGCGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAACAUCAAGCAA-UUGUUGUACCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAU
.((((((.......))))))((((((......((((((....))))))((((((((....(((.(((....-))).)))(((....)))))))))))......))))))....... ( -41.00)
>DroSim_CAF1 25364 106 + 1
CCACCAG--AGCCAU-------GGGAGCCGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAGCAUCAAGCAA-UUGCCGCACCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAU
......(--..((((-------(((.((((((((((((....)))))...)))))))...((..(((....-)))..)).)))).)))..)(((((.....))))).......... ( -38.50)
>DroYak_CAF1 26523 93 + 1
CCACCG----GCCAUUGAUG------------UGCCAGAAAUCCAGCAAAACUCGG---AACAUCAAGCAAAUUGCU----CCGUAGGUCCGAACUUAUUAAAUUCCGCAUUUCAA
....((----(((.((((((------------(.((((.............)).))---.)))))))((.....)).----.....)).)))........................ ( -16.62)
>consensus
CCACCAG__AGCCAUUG_UG__GGGA__CGAGUGCCAGAAAUCUGGCAGAGCUCGGCAGAACAUCAAGCAA_UUGCUG_ACCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAU
..........((....................((((((....))))))((((((((...(((....(((.....)))......)))...))))))))..........))....... (-17.99 = -19.33 +   1.34)

alignment

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secondary structure

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Window 0

Location 19,236,010 – 19,236,122
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 97.02
Mean single sequence MFE -37.62
Consensus MFE -35.77
Energy contribution -35.33
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.99
Structure conservation index 0.95
SVM decision value 0.74
SVM RNA-class probability 0.838484
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19236010 112 + 20766785
CCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAUUAUGAGUGCAUUGCCUCAUAGAGAGCUUCAUGCGGCUAUGUUGGCUUUGGGCUCAGACGCUCGGAUGGAAGUACUU
....((.((((((((.......................(((((.((..(((.(((((...((.....))..)))))..)))..)).)))))...)))))))).))....... ( -35.77)
>DroSec_CAF1 26893 112 + 1
CCCGUUGGUCCGAGCUUAUUAAAUUCCGCAUUUCAUUAUGAGUGCAUUGCCUCAUAGAGAGCUCCAUGCGGCUAUGUUGGCUUUGGGCUCAGACGCUCGGAUGGAUGUACUC
..((((.((((((((.....((((.....)))).....(((((.((..(((.(((((...((.....))..)))))..)))..)).)))))...)))))))).))))..... ( -41.40)
>DroSim_CAF1 25434 112 + 1
CCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAUUAUGAGUGCAUUGCCUCAUAGAGAGCUCCAUGCGGCUAUGUUGGCUUUGGGCCCAGACGCUCGGAUGGAAGUACUU
....((.((((((((..........(((((((((.(((((((.((...))))))))).)))....))))))....((((((.....)))..))))))))))).))....... ( -35.70)
>consensus
CCCGUUGGUCCGAGUUUAUUAAAUUCCGCAUUUCAUUAUGAGUGCAUUGCCUCAUAGAGAGCUCCAUGCGGCUAUGUUGGCUUUGGGCUCAGACGCUCGGAUGGAAGUACUU
....((.((((((((..........(((((((((.(((((((.((...))))))))).)))....))))))....((((((.....)))..))))))))))).))....... (-35.77 = -35.33 +  -0.44)

alignment

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secondary structure

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Window 1

Location 19,236,046 – 19,236,150
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 96.79
Mean single sequence MFE -30.87
Consensus MFE -29.08
Energy contribution -29.42
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.94
SVM decision value 0.06
SVM RNA-class probability 0.563832
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19236046 104 - 20766785
ACUUUGGCUCUCAGCAACAGGCGUGCCAAAGUACUUCCAUCCGAGCGUCUGAGCCCAAAGCCAACAUAGCCGCAUGAAGCUCUCUAUGAGGCAAUGCACUCAUA
((((((((.....((.....))..)))))))).................((((..((..(((..(((((..((.....))...))))).)))..))..)))).. ( -26.10)
>DroSec_CAF1 26929 104 - 1
ACUUUGGCUCUCAGCAACAGGCGUGCCCGAGUACAUCCAUCCGAGCGUCUGAGCCCAAAGCCAACAUAGCCGCAUGGAGCUCUCUAUGAGGCAAUGCACUCAUA
...((((((....((..(((((((...((..(......)..)).))))))).))....))))))(((.(((.((((((....)))))).))).)))........ ( -32.70)
>DroSim_CAF1 25470 104 - 1
ACUUUGGCUCUCAGCAACAGGCGUGCCAAAGUACUUCCAUCCGAGCGUCUGGGCCCAAAGCCAACAUAGCCGCAUGGAGCUCUCUAUGAGGCAAUGCACUCAUA
((((((((.....((.....))..))))))))..........(((.((...(((.....)))......(((.((((((....)))))).)))...)).)))... ( -33.80)
>consensus
ACUUUGGCUCUCAGCAACAGGCGUGCCAAAGUACUUCCAUCCGAGCGUCUGAGCCCAAAGCCAACAUAGCCGCAUGGAGCUCUCUAUGAGGCAAUGCACUCAUA
...((((((....((..(((((((....................))))))).))....))))))(((.(((.((((((....)))))).))).)))........ (-29.08 = -29.42 +   0.33)

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 12:03:07 2006