Locus 456

Sequence ID 2R_DroMel_CAF1
Location 2,610,849 – 2,610,974
Length 125
Max. P 0.973212
window870 window871 window872 window873

overview

Window 0

Location 2,610,849 – 2,610,943
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 76.35
Mean single sequence MFE -31.30
Consensus MFE -17.49
Energy contribution -18.08
Covariance contribution 0.59
Combinations/Pair 1.37
Mean z-score -2.32
Structure conservation index 0.56
SVM decision value 1.62
SVM RNA-class probability 0.967942
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2610849 94 + 20766785
ACCGCGACAAUUGUAUGUGUCUCAACUGGCCAUCAAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAU
(((((((((........))))(((.((((((((...))))))...(((..(((((((.....)))))))...))).)).)))...))).))... ( -33.20)
>DroSec_CAF1 45489 94 + 1
GCCGCGUCAAGUGUGUGUGUCUCAACUGGCCAUCGAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCAUGUAAU
(((.(((((.((...((.(((((.(((((((((...)))))).))).)))(((((((.....)))))))..))))..))))))))))....... ( -38.20)
>DroSim_CAF1 42931 94 + 1
GCCGCGUCAAGUGUGUGUGUCUCAACUGGCCAUCGAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAU
(((.(((((.((...((.(((((.(((((((((...)))))).))).)))(((((((.....)))))))..))))..))))))))))....... ( -38.20)
>DroEre_CAF1 44763 85 + 1
GCGGCGACAAGUG----UCUCGCUACUGGCCCUCAAGUGGCCGA-----CUUGGCCAAGAAAUGGCCAGCAGCCAAAGCUGAUGGGCGUGUAAU
((((.(((....)----))))))(((..(((((((..((((.(.-----((.(((((.....)))))))).))))....))).))))..))).. ( -35.00)
>DroWil_CAF1 60461 71 + 1
------CCAAGUG-----GUUUCAACUGACAAUCAAGUGGCU---UGUAGUUAG-------AGGGCCA--AGGCAAGGUUGAUGGGCGUCUAAU
------(((..((-----(((((....)).)))))..)))..---....(((((-------(.(.(((--.(((...)))..))).).)))))) ( -18.30)
>DroYak_CAF1 43177 85 + 1
GCCACGACAAGUG----CGUCUCUACUGGCUCUCAAGUGGCCAA-----CUUGGUUAGGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAU
......(((.((.----((((.....(((((......((((((.-----((.....))....))))))..))))).....)))).)).)))... ( -24.90)
>consensus
GCCGCGACAAGUG____UGUCUCAACUGGCCAUCAAGUGGCCAA_UGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAU
..........................((.((((((..(((((((......))))))).....((((.....))))....)))))).))...... (-17.49 = -18.08 +   0.59)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,610,849 – 2,610,943
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 76.35
Mean single sequence MFE -28.34
Consensus MFE -13.93
Energy contribution -15.85
Covariance contribution 1.92
Combinations/Pair 1.15
Mean z-score -2.55
Structure conservation index 0.49
SVM decision value 1.71
SVM RNA-class probability 0.973212
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2610849 94 - 20766785
AUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUUGAUGGCCAGUUGAGACACAUACAAUUGUCGCGGU
......(((...(((((..(((...(((((((.....)))))))..)))..((((((.....)))))))))))((((........))))))).. ( -34.70)
>DroSec_CAF1 45489 94 - 1
AUUACAUGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUCGAUGGCCAGUUGAGACACACACACUUGACGCGGC
.......((((...(((....)))..((((((((...(((((((......)))))))...))))))))((..((.........))..))).))) ( -32.20)
>DroSim_CAF1 42931 94 - 1
AUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUCGAUGGCCAGUUGAGACACACACACUUGACGCGGC
......(((.....(((....)))..((((((((...(((((((......)))))))...))))))))((..((.........))..))))).. ( -32.70)
>DroEre_CAF1 44763 85 - 1
AUUACACGCCCAUCAGCUUUGGCUGCUGGCCAUUUCUUGGCCAAG-----UCGGCCACUUGAGGGCCAGUAGCGAGA----CACUUGUCGCCGC
..(((..((((.((((...(((((((((((((.....))))).))-----.)))))).))))))))..)))(((.((----(....)))..))) ( -37.30)
>DroWil_CAF1 60461 71 - 1
AUUAGACGCCCAUCAACCUUGCCU--UGGCCCU-------CUAACUACA---AGCCACUUGAUUGUCAGUUGAAAC-----CACUUGG------
....((((...(((((...((.((--((.....-------.......))---)).)).))))))))).........-----.......------ (  -8.60)
>DroYak_CAF1 43177 85 - 1
AUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCCUAACCAAG-----UUGGCCACUUGAGAGCCAGUAGAGACG----CACUUGUCGUGGC
.......((((.....((((((((((((((((.............-----.))))))....)))))))).)).((((----....))))).))) ( -24.54)
>consensus
AUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCA_UUGGCCACUUGAUGGCCAGUUGAGACA____CACUUGUCGCGGC
.......(.(((((((...(((((.(((((((.....)))))))........))))).))))))).)........................... (-13.93 = -15.85 +   1.92)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,610,874 – 2,610,974
Length 100
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 82.01
Mean single sequence MFE -32.27
Consensus MFE -21.71
Energy contribution -22.43
Covariance contribution 0.73
Combinations/Pair 1.30
Mean z-score -1.85
Structure conservation index 0.67
SVM decision value 0.31
SVM RNA-class probability 0.682785
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2610874 100 + 20766785
CUGGCCAUCAAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAUUGAUUCGGAGGCACAUGAUGGUGUGGGUGGU-
...(((((((.(((.((...(((..(((((((.....)))))))...)))...((((....((......))..)))).))))).))))))).........- ( -34.80)
>DroSec_CAF1 45514 100 + 1
CUGGCCAUCGAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCAUGUAAUUGAUUCGG-GGCACAUGAUGGUGUGGGUGGUG
...(((((((.(((.((...(((..(((((((.....)))))))...)))..(((....)))..............)-).))).))))))).......... ( -36.10)
>DroSim_CAF1 42956 100 + 1
CUGGCCAUCGAGUGGCCAAGUGGAGUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAUUGAUUCGGGGGCACAUGAUGGUGUGGGUGGU-
...(((((((.(((.((...(((..(((((((.....)))))))...)))...((((....((......))..)))))).))).))))))).........- ( -36.60)
>DroEre_CAF1 44784 93 + 1
CUGGCCCUCAAGUGGCCGA-----CUUGGCCAAGAAAUGGCCAGCAGCCAAAGCUGAUGGGCGUGUAAUUGAUUCGG--GGAUGUCAUGGUGUGGGUGGU-
...((((.((.(((((...-----(((((.(((...(((.(((.((((....)))).))).)))....)))..))))--)...)))))..)).))))...- ( -32.60)
>DroYak_CAF1 43198 94 + 1
CUGGCUCUCAAGUGGCCAA-----CUUGGUUAGGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAUUGAUUCGG-GGGACAUAAUGAUGUAGGUGGU-
.(((((.......))))).-----(((((((((...(((.(((..(((....)))..))).)))....)))).))))-)..((((....)))).......- ( -21.80)
>DroAna_CAF1 44454 93 + 1
UUGGCCGUCAAGUGGCCAAGU----UAGACCAACAAUAGCCCAAAAGCCAAAGCUGAUGGGCGUCUAAUUGUUACAGAG---UUUGAUGGGCGGGGUG-UG
(((.((((((((((((..(((----(((((........(((((..(((....)))..))))))))))))))))))....---.))))))).)))....-.. ( -31.70)
>consensus
CUGGCCAUCAAGUGGCCAAGU___GUUGGCCAAGAAAUGGCCAAAAGCCAAAGCUGAUGGGCGUGUAAUUGAUUCGG_GGCACAUGAUGGUGUGGGUGGU_
...(((((((..(((((((......)))))))....(((.(((..(((....)))..))).)))....................))))))).......... (-21.71 = -22.43 +   0.73)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,610,874 – 2,610,974
Length 100
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 82.01
Mean single sequence MFE -26.71
Consensus MFE -16.95
Energy contribution -17.70
Covariance contribution 0.75
Combinations/Pair 1.16
Mean z-score -3.12
Structure conservation index 0.63
SVM decision value 1.04
SVM RNA-class probability 0.904922
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2610874 100 - 20766785
-ACCACCCACACCAUCAUGUGCCUCCGAAUCAAUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUUGAUGGCCAG
-......((((......))))..................(((.(......).)))...((((((((...(((((((......)))))))...)))))))). ( -28.90)
>DroSec_CAF1 45514 100 - 1
CACCACCCACACCAUCAUGUGCC-CCGAAUCAAUUACAUGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUCGAUGGCCAG
.......((((......))))..-...............(((.(......).)))...((((((((...(((((((......)))))))...)))))))). ( -27.90)
>DroSim_CAF1 42956 100 - 1
-ACCACCCACACCAUCAUGUGCCCCCGAAUCAAUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAACUCCACUUGGCCACUCGAUGGCCAG
-......((((......))))..................(((.(......).)))...((((((((...(((((((......)))))))...)))))))). ( -28.20)
>DroEre_CAF1 44784 93 - 1
-ACCACCCACACCAUGACAUCC--CCGAAUCAAUUACACGCCCAUCAGCUUUGGCUGCUGGCCAUUUCUUGGCCAAG-----UCGGCCACUUGAGGGCCAG
-.....................--...............((((.((((...(((((((((((((.....))))).))-----.)))))).))))))))... ( -30.30)
>DroYak_CAF1 43198 94 - 1
-ACCACCUACAUCAUUAUGUCCC-CCGAAUCAAUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCCUAACCAAG-----UUGGCCACUUGAGAGCCAG
-......................-...............((......))..(((((((((((((.............-----.))))))....))))))). ( -17.64)
>DroAna_CAF1 44454 93 - 1
CA-CACCCCGCCCAUCAAA---CUCUGUAACAAUUAGACGCCCAUCAGCUUUGGCUUUUGGGCUAUUGUUGGUCUA----ACUUGGCCACUUGACGGCCAA
..-......(((..((((.---......((((((.....(((((..(((....)))..))))).))))))((((..----....))))..)))).)))... ( -27.30)
>consensus
_ACCACCCACACCAUCAUGUGCC_CCGAAUCAAUUACACGCCCAUCAGCUUUGGCUUUUGGCCAUUUCUUGGCCAAC___ACUUGGCCACUUGAUGGCCAG
.......................................(((.(......).)))..((((((.((...(((((((......)))))))...)).)))))) (-16.95 = -17.70 +   0.75)

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 09:39:03 2006