Locus 3475

Sequence ID 2L_DroMel_CAF1
Location 10,112,962 – 10,113,089
Length 127
Max. P 0.993507
window5494 window5495 window5496 window5497

overview

Window 4

Location 10,112,962 – 10,113,064
Length 102
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 78.67
Mean single sequence MFE -28.35
Consensus MFE -17.68
Energy contribution -18.77
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.62
SVM decision value 1.59
SVM RNA-class probability 0.965736
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10112962 102 + 22407834
AUUCGC--CAUAAAUAACCGCACGGGGCCAAAUUAAAUUUAUGCUACUUAACUGCGAGGGCGUGGCGACACGCCCACAUACAU----ACAUUGCAACAGUCGGCAAAU-----
....((--(........((....))(((.............(((.........))).(((((((....)))))))........----...........))))))....----- ( -27.60)
>DroSec_CAF1 39250 87 + 1
AUUCGC--CAUAAAUAACCGCACCGGGCCAAAUUAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGAU-------------------GCACAU-----
....((--.........(((((...(((..............))).......)))))(((((((....)))))))........-------------------))....----- ( -23.94)
>DroSim_CAF1 42710 87 + 1
AUUCGC--CAUAAAUAACCGCACCGGGCCAAAUUAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGUU-------------------GCACAU-----
....((--.((......(((((...(((..............))).......)))))(((((((....))))))).....)).-------------------))....----- ( -23.94)
>DroEre_CAF1 37875 97 + 1
AUUCAC--CAUAAAUAACCGCACCGAGCCAAAUUAAAUUUAUGCCACUUUACUGCGGGGGCGUGCCAACACGCCCACAUAGCUG---------CAACAGUCGGCAGAU-----
......--.........(((((..(((....((.......))....)))...)))))(((((((....)))))))......(((---------(........))))..----- ( -25.40)
>DroYak_CAF1 39493 111 + 1
AUUCGC--CAUAAAUAACCGCACCGAGCCAAAUUAAAUUUAUGCCACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGUUGCAACCAUUGCAACAGUCGGCAGAUGCCAC
....((--(........(((((..(((....((.......))....)))...)))))(((((((....))))))).....((((((.....))))))....)))......... ( -34.50)
>DroAna_CAF1 42538 99 + 1
AGUGGCCGCAUAAAUAGCAACACCGAAACAAAUUAAAUUUAUGCUACUUUACUGCAUGGGCGUGGUGACACGCCCAUAAUGGUG---------CAACUGUCGGCAAAU-----
....((((.....((((...(((((.................((.........))(((((((((....)))))))))..)))))---------...))))))))....----- ( -34.70)
>consensus
AUUCGC__CAUAAAUAACCGCACCGAGCCAAAUUAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGAU__________CAACAGUCGGCAAAU_____
.................(((((..(((....((.......))....)))...)))))(((((((....)))))))...................................... (-17.68 = -18.77 +   1.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,112,962 – 10,113,064
Length 102
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 78.67
Mean single sequence MFE -30.57
Consensus MFE -19.69
Energy contribution -19.38
Covariance contribution -0.30
Combinations/Pair 1.15
Mean z-score -1.51
Structure conservation index 0.64
SVM decision value 0.38
SVM RNA-class probability 0.713719
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10112962 102 - 22407834
-----AUUUGCCGACUGUUGCAAUGU----AUGUAUGUGGGCGUGUCGCCACGCCCUCGCAGUUAAGUAGCAUAAAUUUAAUUUGGCCCCGUGCGGUUAUUUAUG--GCGAAU
-----(((((((((((((((((....----.)))).(.(((((((....))))))).)))))))(((((((.(((((...)))))((.....)).)))))))..)--)))))) ( -32.10)
>DroSec_CAF1 39250 87 - 1
-----AUGUGC-------------------AUCUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUAAUUUGGCCCGGUGCGGUUAUUUAUG--GCGAAU
-----...(((-------------------........(((((((....)))))))(((((.(......((.(((((...)))))))..).))))).........--)))... ( -23.10)
>DroSim_CAF1 42710 87 - 1
-----AUGUGC-------------------AACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUAAUUUGGCCCGGUGCGGUUAUUUAUG--GCGAAU
-----.(((((-------------------.(((.((((((((((....)))))))..)))....))).))))).........(((((......)))))......--...... ( -25.50)
>DroEre_CAF1 37875 97 - 1
-----AUCUGCCGACUGUUG---------CAGCUAUGUGGGCGUGUUGGCACGCCCCCGCAGUAAAGUGGCAUAAAUUUAAUUUGGCUCGGUGCGGUUAUUUAUG--GUGAAU
-----....((((((((...---------.(((((...(((((((....)))))))((((......)))).............))))))))).))))........--...... ( -30.60)
>DroYak_CAF1 39493 111 - 1
GUGGCAUCUGCCGACUGUUGCAAUGGUUGCAACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUGGCAUAAAUUUAAUUUGGCUCGGUGCGGUUAUUUAUG--GCGAAU
...(((((.(((((..((((((.....))))))((((.(((((((....)))))))((((......))))))))........)))))..))))).((((....))--)).... ( -39.30)
>DroAna_CAF1 42538 99 - 1
-----AUUUGCCGACAGUUG---------CACCAUUAUGGGCGUGUCACCACGCCCAUGCAGUAAAGUAGCAUAAAUUUAAUUUGUUUCGGUGUUGCUAUUUAUGCGGCCACU
-----....((((..(((.(---------((((..((((((((((....)))))))))).......(.((((...........)))).)))))).))).......)))).... ( -32.80)
>consensus
_____AUCUGCCGACUGUUG__________AACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUAAUUUGGCCCGGUGCGGUUAUUUAUG__GCGAAU
......................................(((((((....))))))).(((.((.(((((((.(((((...)))))((.....)).)))))))))...)))... (-19.69 = -19.38 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,112,993 – 10,113,089
Length 96
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 75.71
Mean single sequence MFE -31.18
Consensus MFE -21.66
Energy contribution -21.72
Covariance contribution 0.06
Combinations/Pair 1.24
Mean z-score -3.24
Structure conservation index 0.69
SVM decision value 2.40
SVM RNA-class probability 0.993507
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10112993 96 + 22407834
UAAAUUUAUGCUACUUAACUGCGAGGGCGUGGCGACACGCCCACAUACAU----ACAUUGCAACAGUCGGCAAAU-------------------GCCACAUGCAAACCGGCGGAAAAUA
..................((((..(((((((....)))))))........----...(((((...((.(((....-------------------))))).)))))....))))...... ( -31.60)
>DroSec_CAF1 39281 80 + 1
UAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGAU-------------------GCACAU-------------------GCCACAUGCAAACCGGCG-AAAAUA
...((((.((((......(((.(.(((((((....))))))).).))).(-------------------(((...-------------------......))))....))))-.)))). ( -22.60)
>DroSim_CAF1 42741 80 + 1
UAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGUU-------------------GCACAU-------------------GCCACAUGCAAACCGGCG-AAAAUA
...((((.((((.......((((.(((((((....))))))).....((.-------------------((....-------------------)).)).))))....))))-.)))). ( -23.30)
>DroEre_CAF1 37906 90 + 1
UAAAUUUAUGCCACUUUACUGCGGGGGCGUGCCAACACGCCCACAUAGCUG---------CAACAGUCGGCAGAU-------------------GCCACAUGCAAGCCGGCG-AAAAUA
...((((.((((............(((((((....))))))).....((((---------((...((.(((....-------------------))))).))).))).))))-.)))). ( -31.40)
>DroYak_CAF1 39524 118 + 1
UAAAUUUAUGCCACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGUUGCAACCAUUGCAACAGUCGGCAGAUGCCACACAUACCCACAGAUGCCACAUGCAAACCGGCG-AAAAUA
...((((.((((......(((.(((((((((....))))))).....((((((.....)))))).((.(((....)))))......)).))).(((.....)))....))))-.)))). ( -41.90)
>DroAna_CAF1 42571 90 + 1
UAAAUUUAUGCUACUUUACUGCAUGGGCGUGGUGACACGCCCAUAAUGGUG---------CAACUGUCGGCAAAU-------------------GCCACAUGCGAACUGGCA-GAAAUA
...((((.(((((.((((((..(((((((((....)))))))))...)))(---------((..(((.(((....-------------------)))))))))))).)))))-.)))). ( -36.30)
>consensus
UAAAUUUAUGCUACUUUACUGCGGGGGCGUGUCGACACGCCCACAUAGAU__________CAACAGUCGGCAAAU___________________GCCACAUGCAAACCGGCG_AAAAUA
....(((.((((.......((((.(((((((....)))))))..........................(((.......................)))...))))....)))).)))... (-21.66 = -21.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,112,993 – 10,113,089
Length 96
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 75.71
Mean single sequence MFE -32.68
Consensus MFE -20.49
Energy contribution -20.85
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -2.53
Structure conservation index 0.63
SVM decision value 2.21
SVM RNA-class probability 0.990396
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10112993 96 - 22407834
UAUUUUCCGCCGGUUUGCAUGUGGC-------------------AUUUGCCGACUGUUGCAAUGU----AUGUAUGUGGGCGUGUCGCCACGCCCUCGCAGUUAAGUAGCAUAAAUUUA
........((.(((.(((.....))-------------------)...)))((((((((((....----.)))).(.(((((((....))))))).))))))).....))......... ( -28.90)
>DroSec_CAF1 39281 80 - 1
UAUUUU-CGCCGGUUUGCAUGUGGC-------------------AUGUGC-------------------AUCUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUA
......-.((.(.(((((.((((((-------------------(((...-------------------...)))).(((((((....))))))))))))))))).).))......... ( -27.40)
>DroSim_CAF1 42741 80 - 1
UAUUUU-CGCCGGUUUGCAUGUGGC-------------------AUGUGC-------------------AACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUA
......-.((.(.(((((.((((((-------------------(((...-------------------...)))).(((((((....))))))))))))))))).).))......... ( -27.40)
>DroEre_CAF1 37906 90 - 1
UAUUUU-CGCCGGCUUGCAUGUGGC-------------------AUCUGCCGACUGUUG---------CAGCUAUGUGGGCGUGUUGGCACGCCCCCGCAGUAAAGUGGCAUAAAUUUA
......-.(((((((.(((.(((((-------------------....))).))...))---------))))).((((((((((....)))))))..))).......)))......... ( -34.30)
>DroYak_CAF1 39524 118 - 1
UAUUUU-CGCCGGUUUGCAUGUGGCAUCUGUGGGUAUGUGUGGCAUCUGCCGACUGUUGCAAUGGUUGCAACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUGGCAUAAAUUUA
......-.((((.(((((.....))..(((((((..((((((((((..(((.((.((((((.....))))))...)).)))))))).)))))..))))))).))).))))......... ( -48.20)
>DroAna_CAF1 42571 90 - 1
UAUUUC-UGCCAGUUCGCAUGUGGC-------------------AUUUGCCGACAGUUG---------CACCAUUAUGGGCGUGUCACCACGCCCAUGCAGUAAAGUAGCAUAAAUUUA
((((((-(((......(((((((((-------------------....))).)))..))---------)......(((((((((....)))))))))))))..)))))........... ( -29.90)
>consensus
UAUUUU_CGCCGGUUUGCAUGUGGC___________________AUCUGCCGACUGUUG__________AACUAUGUGGGCGUGUCGACACGCCCCCGCAGUAAAGUAGCAUAAAUUUA
........((.(.(((((.(((((.............................(....)..................(((((((....))))))))))))))))).).))......... (-20.49 = -20.85 +   0.36)

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 10:53:25 2006