Locus 1441

Sequence ID 2R_DroMel_CAF1
Location 5,521,269 – 5,521,424
Length 155
Max. P 0.924544
window2461 window2462 window2463 window2464

overview

Window 1

Location 5,521,269 – 5,521,367
Length 98
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 80.36
Mean single sequence MFE -18.10
Consensus MFE -13.01
Energy contribution -13.07
Covariance contribution 0.06
Combinations/Pair 1.23
Mean z-score -1.11
Structure conservation index 0.72
SVM decision value -0.03
SVM RNA-class probability 0.519948
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5521269 98 - 20766785
CACCACCACCUGCAUCUAU----GUACACCUGCGGCUGCAGUAAAAAUGACAUUAAAAUGAAAGUCAUAU-----GCACAUGGUUAACUCGCCA-CGCAUAACCAAGC
.........(((((....(----(((....))))..)))))......((((.((......)).))))(((-----((...((((......))))-.)))))....... ( -16.60)
>DroSec_CAF1 44425 102 - 1
CACCACCACCUGCUCCUAUGUAUGUCCACCUGCAGCUGCAGUAAAAGUGACAUUAAAAUGGAAGUCAUAU-----GCACAUGGUUAACUCGCCA-CGCAUAACCAAGU
...........(((.((((..(((((.((((((....)))).....)))))))....)))).)))..(((-----((...((((......))))-.)))))....... ( -20.70)
>DroSim_CAF1 21716 102 - 1
CACCACCACCUGCACCUAUGUAUGUACACCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAU-----GCACAUGGUUAACUCGCCA-CGCAUAACCAAGC
.........(((((....((((.(....).))))..)))))......((((.((......)).))))(((-----((...((((......))))-.)))))....... ( -18.30)
>DroEre_CAF1 21453 82 - 1
CACCACCACCUGCA--------------A------CUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAU-----GCACAUGGUUAACUCGCUA-CGCAUAACCAAGC
.........((((.--------------.------..))))......((((.((......)).))))(((-----((...((((......))))-.)))))....... ( -12.60)
>DroWil_CAF1 28161 91 - 1
------GUCCUGCA-----------GCACCUGCAGUUGCAGUAAAAAUGGCAUUAAAAUGAAAGUCAUAUAUGCAGCACAUGGUUAACUUUUCAGCGCAUAACUAAGC
------...(((((-----------((.......))))))).....(((((.((......)).))))).(((((.((....((....)).....)))))))....... ( -18.00)
>DroYak_CAF1 21938 88 - 1
CACCACCACCUGCA--------------GCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAU-----GCACAUGGUUAACUCGCCA-CGCAUAACCAAGC
.........(((((--------------((....)))))))......((((.((......)).))))(((-----((...((((......))))-.)))))....... ( -22.40)
>consensus
CACCACCACCUGCA____________CACCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAU_____GCACAUGGUUAACUCGCCA_CGCAUAACCAAGC
..........(((................((((....)))).....(((((.((......)).))))).......)))..((((((....((....)).))))))... (-13.01 = -13.07 +   0.06)

alignment

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secondary structure

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Window 2

Location 5,521,299 – 5,521,405
Length 106
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 84.14
Mean single sequence MFE -31.52
Consensus MFE -25.76
Energy contribution -26.56
Covariance contribution 0.80
Combinations/Pair 1.19
Mean z-score -1.73
Structure conservation index 0.82
SVM decision value 0.50
SVM RNA-class probability 0.758785
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5521299 106 + 20766785
GCAUAUGACUUUCAUUUUAAUGUCAUUUUUACUGCAGCCGCAGGUGUAC----AUAGAUGCAGGUGGUGGUGAAAGGUGAAAGCACCUAACCGCACCCACCCACCGUCGA
(((((((((............))))).....((((....))))......----....)))).(((((.((((..(((((....))))).....))))...)))))..... ( -32.30)
>DroSec_CAF1 44455 110 + 1
GCAUAUGACUUCCAUUUUAAUGUCACUUUUACUGCAGCUGCAGGUGGACAUACAUAGGAGCAGGUGGUGGUGAAAGGUGAAGGCACCUAACCGCACCCACCCACCGUCGA
.....((((((((......(((((.......((((....))))...))))).....))))..(((((.((((..(((((....))))).....))))...))))))))). ( -35.20)
>DroSim_CAF1 21746 110 + 1
GCAUAUGACUUCCAUUUUAAUGUCAUUUUUACUGCAGCUGCAGGUGUACAUACAUAGGUGCAGGUGGUGGUGAAAGGUGAAGGCGCCUAACCGCACCCACCCACCGUCGA
.....((((..........(((((((.....((((....))))))).)))).....((((..(((((..(((..(((((....)))))...)))..))))))))))))). ( -34.10)
>DroEre_CAF1 21483 90 + 1
GCAUAUGACUUCCAUUUUAAUGUCAUUUUUACUGCAG------U--------------UGCAGGUGGUGGUGAAAGGUGAAAGCACCUAACCGCAUCCACCCAUCGUCAU
....(((((......................((((..------.--------------.))))(.(((((((..(((((....))))).....)).))))))...))))) ( -24.70)
>DroYak_CAF1 21968 96 + 1
GCAUAUGACUUCCAUUUUAAUGUCAUUUUUACUGCAGCUGCAGC--------------UGCAGGUGGUGGUGAAAGGUGAAAGCACCUAACCGCGCCCACCCAUCGUCAC
.....((((......................(((((((....))--------------)))))(.(((((((..(((((....))))).....)).))))))...)))). ( -31.30)
>consensus
GCAUAUGACUUCCAUUUUAAUGUCAUUUUUACUGCAGCUGCAGGUG_AC____AUAG_UGCAGGUGGUGGUGAAAGGUGAAAGCACCUAACCGCACCCACCCACCGUCGA
(((((((((............))))).....((((....))))..............)))).(((((.((((..(((((....))))).....))))...)))))..... (-25.76 = -26.56 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,521,299 – 5,521,405
Length 106
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 84.14
Mean single sequence MFE -31.58
Consensus MFE -23.38
Energy contribution -24.66
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -1.51
Structure conservation index 0.74
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5521299 106 - 20766785
UCGACGGUGGGUGGGUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCAUCUAU----GUACACCUGCGGCUGCAGUAAAAAUGACAUUAAAAUGAAAGUCAUAUGC
..(((.(..(((((.((..(..(((((....)))))..)..)))))))..)......----......((((....))))......................)))...... ( -30.30)
>DroSec_CAF1 44455 110 - 1
UCGACGGUGGGUGGGUGCGGUUAGGUGCCUUCACCUUUCACCACCACCUGCUCCUAUGUAUGUCCACCUGCAGCUGCAGUAAAAGUGACAUUAAAAUGGAAGUCAUAUGC
..(((((..(((((.((..(..(((((....)))))..)..)))))))..)).((((..(((((.((((((....)))).....)))))))....))))..)))...... ( -37.70)
>DroSim_CAF1 21746 110 - 1
UCGACGGUGGGUGGGUGCGGUUAGGCGCCUUCACCUUUCACCACCACCUGCACCUAUGUAUGUACACCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAUGC
..((((((((..(((((.(((.....)))..)))))....))))).((.......((((........((((....))))........))))......))..)))...... ( -31.61)
>DroEre_CAF1 21483 90 - 1
AUGACGAUGGGUGGAUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA--------------A------CUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAUGC
(((((...((((((.((..(..(((((....)))))..)..))))))))((.--------------.------..))........................))))).... ( -25.40)
>DroYak_CAF1 21968 96 - 1
GUGACGAUGGGUGGGCGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA--------------GCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAUGC
(((((....(((((.....(..(((((....)))))..).)))))..(((((--------------((....)))))))......................))))).... ( -32.90)
>consensus
UCGACGGUGGGUGGGUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA_CUAU____GU_CACCUGCAGCUGCAGUAAAAAUGACAUUAAAAUGGAAGUCAUAUGC
......((((((((.((..(..(((((....)))))..)..))))))))))................((((....)))).....(((((.((......)).))))).... (-23.38 = -24.66 +   1.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,521,333 – 5,521,424
Length 91
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 81.36
Mean single sequence MFE -36.90
Consensus MFE -27.18
Energy contribution -27.82
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.74
SVM decision value 1.16
SVM RNA-class probability 0.924544
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5521333 91 - 20766785
CCACUGUGGGUGGCCAACGUCGACGGUGGGUGGGUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCAUCUAU----GUACACCUGCGGCUG
...(((..((((..((.((....))(..(((((.((..(..(((((....)))))..)..)))))))..).....)----)..))))..)))... ( -38.20)
>DroSec_CAF1 44489 95 - 1
CCACUGUGGGUGGCCAUCGUCGACGGUGGGUGGGUGCGGUUAGGUGCCUUCACCUUUCACCACCACCUGCUCCUAUGUAUGUCCACCUGCAGCUG
...(((..(((((.((((((.(..((..(((((.((..(..(((((....)))))..)..)))))))..)).).))).))).)))))..)))... ( -43.30)
>DroSim_CAF1 21780 95 - 1
CCACUGUGGGUGGCCAUCGUCGACGGUGGGUGGGUGCGGUUAGGCGCCUUCACCUUUCACCACCACCUGCACCUAUGUAUGUACACCUGCAGCUG
...(((..((((.((((((....))))))(((((((((((.(((........))).........))).)))))))).......))))..)))... ( -37.70)
>DroEre_CAF1 21517 75 - 1
CCACUGUGGGUGGCCAUGGAUGACGAUGGGUGGAUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA--------------A------CUG
....((..(((((...(((.(((....(((((((.(((......))).))))))).)))))))))))..))--------------.------... ( -29.50)
>DroYak_CAF1 22002 81 - 1
CCACUGUGGGUGGCCAUGGGUGACGAUGGGUGGGCGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA--------------GCUGCAGCUG
.(((((..(((((.....(((((....((((((((((......)))))..))))).))))).)))))..))--------------).))...... ( -35.80)
>consensus
CCACUGUGGGUGGCCAUCGUCGACGGUGGGUGGGUGCGGUUAGGUGCUUUCACCUUUCACCACCACCUGCA_CUAU____GU_CACCUGCAGCUG
.....(..(((((((((((....))))))........(((.(((((....)))))...))).)))))..)......................... (-27.18 = -27.82 +   0.64)

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 10:04:57 2006