Locus 3504

Sequence ID 3L_DroMel_CAF1
Location 10,282,685 – 10,282,814
Length 129
Max. P 0.990473
window5470 window5471 window5472

overview

Window 0

Location 10,282,685 – 10,282,776
Length 91
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 79.40
Mean single sequence MFE -15.52
Consensus MFE -9.05
Energy contribution -9.58
Covariance contribution 0.53
Combinations/Pair 1.19
Mean z-score -1.81
Structure conservation index 0.58
SVM decision value 0.32
SVM RNA-class probability 0.687424
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10282685 91 + 23771897
AUACAUCGAUCACAACACACGC---------CGGCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA--UUUU-----GUUUUUUUUUUGCACUCGCAAAUUCUUU
....................((---------.((..((((((((........))))))))..)).)).--....-----........(((((....)))))...... ( -15.50)
>DroSec_CAF1 157697 93 + 1
AUACAUCGAUCACAACACACGC---------CGGCUAAUUUGCAUAAAUUUUUGCAAAA-AACCCGCA--UUUCUUU--UUUUUUUUUUUGCACGCGCAAAUUCUUU
....................((---------.((....((((((........)))))).-..)).)).--.......--........(((((....)))))...... ( -13.30)
>DroSim_CAF1 163788 89 + 1
AUGCAUCGAUCACAACACACGC---------CGGCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA--UUUCUUU--U-----UUUUUGCACGCGCAAAUUCUUU
....................((---------.((..((((((((........))))))))..)).)).--.......--.-----..(((((....)))))...... ( -15.50)
>DroEre_CAF1 168090 97 + 1
AUACAUCGAUCACAACACACGC---------CGGCUAAUUUGCAUAAAUU-UUGCGAAUUUACUCGCUAUUUUCUUUUUUUUUUUUUUUUGCACGCGCAAAUUCUUU
....................((---------.((..((((((((......-.))))))))..)).))....................(((((....)))))...... ( -14.70)
>DroYak_CAF1 165864 87 + 1
AUACAUCGAUCAGAACACACGC---------CGGCUAAUUUGCAUAAAUUUUUGCGAGUUUACUCGCU-----------UUUUUUUAUUUGCACGCGCAAAUUCUUU
...........((((.....((---------.((..((((((((........))))))))..)).)).-----------........(((((....))))))))).. ( -16.10)
>DroAna_CAF1 169733 94 + 1
AUACAUCGAUCACAACACACACACACACUGGCAGCUAAUUUGCAUAAAUUUUUGCAAUUUCGUUGGAG-------------UUUUUUGUUGGUUGUGCAAAUUUUUU
..........((((((.((.(((...(((..((((.((.(((((........))))).)).)))).))-------------)....))))))))))).......... ( -18.00)
>consensus
AUACAUCGAUCACAACACACGC_________CGGCUAAUUUGCAUAAAUUUUUGCGAAUUUACUCGCA__UUUC_____UUUUUUUUUUUGCACGCGCAAAUUCUUU
...............................(((..((((((((........))))))))...))).....................(((((....)))))...... ( -9.05 =  -9.58 +   0.53)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,282,709 – 10,282,814
Length 105
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.93
Mean single sequence MFE -20.85
Consensus MFE -10.85
Energy contribution -11.02
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.52
SVM decision value 1.92
SVM RNA-class probability 0.982597
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10282709 105 + 23771897
GCUAAUUUGCAUAAAUUUUU--GCGAAUUUACUCGCAUUUU---GUUUUUUUUUUGCACUCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCG
(((((((((((((((....(--((((......)))))....---........(((((....)))))...))))))))))))..)))(((.....)))............. ( -24.10)
>DroVir_CAF1 189926 90 + 1
GCUAAUUUGCAUAAAUUGUUUGGCAGUU-U-----------UU-UUUUUUUUUUUG-----GCAAAC--CUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCC
((((((((((((((...(((((.(((..-.-----------..-.........)))-----.)))))--.)))))))))))..)))(((.....)))............. ( -20.14)
>DroPse_CAF1 170981 82 + 1
GCUAAUUUGCAUAUUUUUUU--------------------C---UUUUUUUUUUUG-----GCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUGCA
((.((((((((((....(((--------------------(---(..........)-----).))).....))))))))))....((((.....)))).........)). ( -12.80)
>DroSec_CAF1 157721 107 + 1
GCUAAUUUGCAUAAAUUUUU--GCAAAA-AACCCGCAUUUCUUUUUUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCG
(((((((((((((((....(--((....-.....)))...............(((((....)))))...))))))))))))..)))(((.....)))............. ( -19.30)
>DroYak_CAF1 165888 101 + 1
GCUAAUUUGCAUAAAUUUUU--GCGAGUUUACUCGCU-------UUUUUUUAUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCG
(((((((((((((((.....--(((((....))))).-------.......((((((....))))))..))))))))))))..)))(((.....)))............. ( -26.80)
>DroAna_CAF1 169766 99 + 1
GCUAAUUUGCAUAAAUUUUU--GCAAUUUCGUUGGAG---------UUUUUUGUUGGUUGUGCAAAUUUUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCG
(((((((((((((((..(((--(((...(((......---------........)))...))))))...))))))))))))..)))(((.....)))............. ( -21.94)
>consensus
GCUAAUUUGCAUAAAUUUUU__GCAAAU_UACUCGC________UUUUUUUUUUUGCACGCGCAAAUUCUUUAUGCAAAUUCAAGUGCAUUAUUUGCAAAUCAUGUUCCG
((......))...................................................((((((.....(((((........))))).))))))............. (-10.85 = -11.02 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,282,709 – 10,282,814
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.93
Mean single sequence MFE -20.38
Consensus MFE -13.30
Energy contribution -13.47
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.32
Structure conservation index 0.65
SVM decision value 2.22
SVM RNA-class probability 0.990473
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10282709 105 - 23771897
CGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGAGUGCAAAAAAAAAAC---AAAAUGCGAGUAAAUUCGC--AAAAAUUUAUGCAAAUUAGC
.......(((((((((.....((((((((.((((.......))))...))))))))..........---....((((((....)))))--)........))))))))).. ( -26.70)
>DroVir_CAF1 189926 90 - 1
GGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAG--GUUUGC-----CAAAAAAAAAAA-AA-----------A-AACUGCCAAACAAUUUAUGCAAAUUAGC
............((((.....))))....(((((((((((.--(((((.-----((..........-..-----------.-...)).)))))...)))))))))))... ( -16.79)
>DroPse_CAF1 170981 82 - 1
UGCAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGC-----CAAAAAAAAAAA---G--------------------AAAAAAAUAUGCAAAUUAGC
.......(((((((((....(((((........)))))......(((..-----....))).....---.--------------------.........))))))))).. ( -11.60)
>DroSec_CAF1 157721 107 - 1
CGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAAAAAAGAAAUGCGGGUU-UUUUGC--AAAAAUUUAUGCAAAUUAGC
............((((.....))))....((((((((((((...(((((((.((((.................)))).)).-....))--)))..))))))))))))... ( -22.53)
>DroYak_CAF1 165888 101 - 1
CGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAUAAAAAAA-------AGCGAGUAAACUCGC--AAAAAUUUAUGCAAAUUAGC
............((((.....))))....((((((((((((..((((((....)))))).......-------.(((((....)))))--.....))))))))))))... ( -27.60)
>DroAna_CAF1 169766 99 - 1
CGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAAAAUUUGCACAACCAACAAAAAA---------CUCCAACGAAAUUGC--AAAAAUUUAUGCAAAUUAGC
............((((.....))))....((((((((((((...((((((..............---------............)))--)))..))))))))))))... ( -17.07)
>consensus
CGGAACAUGAUUUGCAAAUAAUGCACUUGAAUUUGCAUAAAGAAUUUGCGCGUGCAAAAAAAAAAA________GCGAGUA_AAUUGC__AAAAAUUUAUGCAAAUUAGC
.......(((((((((....(((((........)))))......((((......)))).........................................))))))))).. (-13.30 = -13.47 +   0.17)

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 10:59:45 2006