Locus 1064

Sequence ID X_DroMel_CAF1
Location 3,108,054 – 3,108,186
Length 132
Max. P 0.999996
window1726 window1727 window1728 window1729

overview

Window 6

Location 3,108,054 – 3,108,173
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 63.53
Mean single sequence MFE -25.80
Consensus MFE -13.40
Energy contribution -15.40
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.52
SVM decision value 4.19
SVM RNA-class probability 0.999830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3108054 119 + 22224390
UGUUCGUUUUUUUUUUUUUUUUUGUAGGGUUGCGUUCGUGCGAAUUAUGUCAAUUGGGAUGCAAUGGUUCGAAAGUACAUAAUGACUUGGCAUUUUGCCAAGAGCCC-CCAAUUGCAUAA
....................((((((.((......)).))))))(((((.((((((((..((.(((...(....)..))).....((((((.....)))))).)).)-)))))))))))) ( -35.00)
>DroSec_CAF1 67178 91 + 1
----------UUUCGUUUUUUUUUUAAGGUUGCGUUCGUGCGAACUAUGUCAAUU------------------AGUACAUAAUGACUUGGCAUUUUGCCAAGAGCAA-CCAAUUGCAUAC
----------.................((((((((((....))))((((((....------------------.).)))))....((((((.....)))))).))))-)).......... ( -25.30)
>DroYak_CAF1 72087 94 + 1
UU------------------UUUUCCACUUUAC------GCGUAUUAUGUCAAUUAGGAAGCAAUGAUUCGAAAAUACAUAAUUACUUGGCAUUUUGCCAAGACC--CCCAAUUGCAUAC
..------------------.............------(((((((...(((((((........))))).)).))))).......((((((.....))))))...--.......)).... ( -17.10)
>consensus
U_________UUU__UUUUUUUUUUAAGGUUGCGUUCGUGCGAAUUAUGUCAAUU_GGA_GCAAUG_UUCGAAAGUACAUAAUGACUUGGCAUUUUGCCAAGAGC___CCAAUUGCAUAC
.....................................(((((((((((((......((((......))))......)))))))..((((((.....))))))..........)))))).. (-13.40 = -15.40 +   2.00)

alignment

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secondary structure

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Window 7

Location 3,108,054 – 3,108,173
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 63.53
Mean single sequence MFE -24.97
Consensus MFE -13.74
Energy contribution -13.30
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -3.21
Structure conservation index 0.55
SVM decision value 6.08
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3108054 119 - 22224390
UUAUGCAAUUGG-GGGCUCUUGGCAAAAUGCCAAGUCAUUAUGUACUUUCGAACCAUUGCAUCCCAAUUGACAUAAUUCGCACGAACGCAACCCUACAAAAAAAAAAAAAAAAACGAACA
((((((((((((-((((.((((((.....))))))......((......)).......)).))))))))).)))))...((......))............................... ( -26.90)
>DroSec_CAF1 67178 91 - 1
GUAUGCAAUUGG-UUGCUCUUGGCAAAAUGCCAAGUCAUUAUGUACU------------------AAUUGACAUAGUUCGCACGAACGCAACCUUAAAAAAAAAACGAAA----------
..........((-((((.((((((.....))))))....(((((...------------------.....)))))((((....)))))))))).................---------- ( -24.30)
>DroYak_CAF1 72087 94 - 1
GUAUGCAAUUGGG--GGUCUUGGCAAAAUGCCAAGUAAUUAUGUAUUUUCGAAUCAUUGCUUCCUAAUUGACAUAAUACGC------GUAAAGUGGAAAA------------------AA
.((((((((((((--((.((((((.....)))))).......(((............))))))))))))).))))...(((------.....))).....------------------.. ( -23.70)
>consensus
GUAUGCAAUUGG___GCUCUUGGCAAAAUGCCAAGUCAUUAUGUACUUUCGAA_CAUUGC_UCC_AAUUGACAUAAUUCGCACGAACGCAACCUUAAAAAAAAAA__AAA_________A
...(((............((((((.....))))))..(((((((..........................)))))))..........))).............................. (-13.74 = -13.30 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,108,094 – 3,108,186
Length 92
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 74.46
Mean single sequence MFE -20.96
Consensus MFE -11.95
Energy contribution -12.45
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.69
Structure conservation index 0.57
SVM decision value 2.87
SVM RNA-class probability 0.997513
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3108094 92 + 22224390
CGAAUUAUGUCAAUUGGGAUGCAAUGGUUCGAAAGUACAUAAUGACUUGGCAUUUUGCCAAGAGCCC-CCAAUUGCAUAAAUGUGCAUAAAUU
....(((((.((((((((..((.(((...(....)..))).....((((((.....)))))).)).)-))))))))))))............. ( -30.20)
>DroSec_CAF1 67208 74 + 1
CGAACUAUGUCAAUU------------------AGUACAUAAUGACUUGGCAUUUUGCCAAGAGCAA-CCAAUUGCAUACAUGUGCAUAAAUU
...............------------------.((((((.....((((((.....)))))).((((-....))))....))))))....... ( -19.10)
>DroEre_CAF1 67753 78 + 1
CGAAUUAUGACAAUUAGGAAGCAAUGAUUCGA---------------UGGCAUUUCGCCAAGAGCCCCCAAAUUGCAUACAUGUGCAUAAAUU
((((((((...............)))))))).---------------((((.....)))).............(((((....)))))...... ( -15.26)
>DroYak_CAF1 72103 91 + 1
CGUAUUAUGUCAAUUAGGAAGCAAUGAUUCGAAAAUACAUAAUUACUUGGCAUUUUGCCAAGACC--CCCAAUUGCAUACAUGUGCAUAAAUU
.((((((((.(((((.((.....((((((....))).))).....((((((.....))))))...--)).)))))))))...))))....... ( -19.30)
>consensus
CGAAUUAUGUCAAUUAGGAAGCAAUGAUUCGA_AGUACAUAAUGACUUGGCAUUUUGCCAAGAGCCC_CCAAUUGCAUACAUGUGCAUAAAUU
.............................................((((((.....))))))...........(((((....)))))...... (-11.95 = -12.45 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,108,094 – 3,108,186
Length 92
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 74.46
Mean single sequence MFE -21.07
Consensus MFE -12.45
Energy contribution -15.20
Covariance contribution 2.75
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.59
SVM decision value 2.10
SVM RNA-class probability 0.988037
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3108094 92 - 22224390
AAUUUAUGCACAUUUAUGCAAUUGG-GGGCUCUUGGCAAAAUGCCAAGUCAUUAUGUACUUUCGAACCAUUGCAUCCCAAUUGACAUAAUUCG
.............((((((((((((-((((.((((((.....))))))......((......)).......)).))))))))).))))).... ( -25.60)
>DroSec_CAF1 67208 74 - 1
AAUUUAUGCACAUGUAUGCAAUUGG-UUGCUCUUGGCAAAAUGCCAAGUCAUUAUGUACU------------------AAUUGACAUAGUUCG
..............(((((((((((-(.((.((((((.....)))))).......)))))------------------))))).))))..... ( -18.70)
>DroEre_CAF1 67753 78 - 1
AAUUUAUGCACAUGUAUGCAAUUUGGGGGCUCUUGGCGAAAUGCCA---------------UCGAAUCAUUGCUUCCUAAUUGUCAUAAUUCG
..............(((((((((.((((((((.((((.....))))---------------..))......)))))).))))).))))..... ( -18.60)
>DroYak_CAF1 72103 91 - 1
AAUUUAUGCACAUGUAUGCAAUUGGG--GGUCUUGGCAAAAUGCCAAGUAAUUAUGUAUUUUCGAAUCAUUGCUUCCUAAUUGACAUAAUACG
..............((((((((((((--((.((((((.....)))))).......(((............))))))))))))).))))..... ( -21.40)
>consensus
AAUUUAUGCACAUGUAUGCAAUUGG_GGGCUCUUGGCAAAAUGCCAAGUCAUUAUGUACU_UCGAAUCAUUGCUUCCUAAUUGACAUAAUUCG
..............(((((((((((((.((.((((((.....)))))).......................)).))))))))).))))..... (-12.45 = -15.20 +   2.75)

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 10:00:44 2006