Locus 9109

Sequence ID 3R_DroMel_CAF1
Location 24,316,282 – 24,316,395
Length 113
Max. P 0.799272
window14576 window14577 window14578

overview

Window 6

Location 24,316,282 – 24,316,381
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.70
Mean single sequence MFE -22.82
Consensus MFE -12.68
Energy contribution -12.82
Covariance contribution 0.14
Combinations/Pair 1.11
Mean z-score -1.80
Structure conservation index 0.56
SVM decision value 0.04
SVM RNA-class probability 0.553883
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24316282 99 + 27905053
-------C-------CCGAUCCUGGUGCACA------GAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCG
-------.-------(((....(((((((..------(((.......(((............))).(((((((.((((-((....)))))).)))))))))).))).))))....))).. ( -22.80)
>DroVir_CAF1 118288 100 + 1
-------GUUUUUUCGGGAUCCUG-----CA------UAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGA--AUUUUUAUUUUUAAUCGGAUUUCAUGCUGCCAUCAACGGCG
-------........(((......-----..------...)))....(((..........(((((.(((((((((((--((....)))))).)))))))....))))).........))) ( -20.41)
>DroPse_CAF1 146541 104 + 1
---------------CAGGUCUUGCAGAAGAGAGAACGAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGUG
---------------..(((..(((.((((((.(......).)))))))))..........((((.(((((((.((((-((....)))))).)))))))....))))))).......... ( -23.30)
>DroWil_CAF1 110054 109 + 1
GUUUUUUGACGGCGAUGGGUCCUG-----CA------UAACCCUUUUCGCACAUAAAUUACAGCACAUCCGAUAAGAAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUGCCAUCAACGGCG
((..((((...((((.((((....-----..------..))))...))))...))))..))((((.(((((((.(((((.......))))).)))))))....))))(((......))). ( -30.90)
>DroAna_CAF1 140582 85 + 1
----------------------------GCA------GAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCG
----------------------------(((------(((.......(((............))).(((((((.((((-((....)))))).)))))))))).)))..((......)).. ( -16.20)
>DroPer_CAF1 146583 104 + 1
---------------UAGGUCUUGCAGAAGAGAGAACGAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGUG
---------------..(((..(((.((((((.(......).)))))))))..........((((.(((((((.((((-((....)))))).)))))))....))))))).......... ( -23.30)
>consensus
_______________CAGGUCCUG____ACA______GAACCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAA_AUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCG
.............................................................((((.((((((((((((........))))).)))))))....))))(((......))). (-12.68 = -12.82 +   0.14)

alignment

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secondary structure

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Window 7

Location 24,316,282 – 24,316,381
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.70
Mean single sequence MFE -25.66
Consensus MFE -17.10
Energy contribution -17.21
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value 0.52
SVM RNA-class probability 0.766615
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24316282 99 - 27905053
CGCCGUUGAUGGUAGCAUGAAAUCCGAUUAAAAAUAAAAAU-UUCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUC------UGUGCACCAGGAUCGG-------G-------
..(((....((((.((((((((((((((...((((....))-))...)))))))((((..........))))........)))------.))))))))....)))-------.------- ( -28.40)
>DroVir_CAF1 118288 100 - 1
CGCCGUUGAUGGCAGCAUGAAAUCCGAUUAAAAAUAAAAAU--UCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUA------UG-----CAGGAUCCCGAAAAAAC-------
((((((.(((.(((((.....(((((((.............--....)))))))..))))).))).))).)))....(((((.------..-----...))))).........------- ( -25.13)
>DroPse_CAF1 146541 104 - 1
CACCGUUGAUGGUAGCAUGAAAUCCGAUUAAAAAUAAAAAU-UUCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUCGUUCUCUCUUCUGCAAGACCUG---------------
..........(((.(((....(((((((...((((....))-))...)))))))((((..........))))(((.((((......)))).))))))...)))..--------------- ( -22.80)
>DroWil_CAF1 110054 109 - 1
CGCCGUUGAUGGCAGCAUGAAAUCCGAUUAAAAAUAAAAAUUUUCUUAUCGGAUGUGCUGUAAUUUAUGUGCGAAAAGGGUUA------UG-----CAGGACCCAUCGCCGUCAAAAAAC
.....(((((((((((((...(((((((..(((((....)))))...)))))))))))))).........((((...(((((.------..-----...))))).))))))))))..... ( -35.00)
>DroAna_CAF1 140582 85 - 1
CGCCGUUGAUGGUAGCAUGAAAUCCGAUUAAAAAUAAAAAU-UUCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUC------UGC----------------------------
((((((.(((..((((.....(((((((...((((....))-))...)))))))..))))..))).))).)))..........------...---------------------------- ( -19.80)
>DroPer_CAF1 146583 104 - 1
CACCGUUGAUGGUAGCAUGAAAUCCGAUUAAAAAUAAAAAU-UUCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUCGUUCUCUCUUCUGCAAGACCUA---------------
..........(((.(((....(((((((...((((....))-))...)))))))((((..........))))(((.((((......)))).))))))...)))..--------------- ( -22.80)
>consensus
CGCCGUUGAUGGUAGCAUGAAAUCCGAUUAAAAAUAAAAAU_UUCUUAUCGGAUGCGCUGUAAUUUAUGUGCGAAAAGGGUUC______UGU____CAGGACCCA_______________
((((((.(((..((((.....(((((((...................)))))))..))))..))).))).)))............................................... (-17.10 = -17.21 +   0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,316,302 – 24,316,395
Length 93
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.43
Mean single sequence MFE -26.65
Consensus MFE -15.06
Energy contribution -15.17
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -3.49
Structure conservation index 0.56
SVM decision value 0.61
SVM RNA-class probability 0.799272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24316302 93 + 27905053
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCGCCGU---A------CUCCGU---------UGU
.....................((((.(((((((.((((((....)))))).)))))))....)))).....((((((.(....---.------).))))---------)). ( -20.80)
>DroVir_CAF1 118310 98 + 1
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUGCCAUCAACGGCGCCAG---CGU----CAGCGUCAGCGCC-----
....................(((((.(((((((((((-((....)))))).)))))))....)))))........(((((..(---((.----...)))..)))))----- ( -28.20)
>DroPse_CAF1 146566 102 + 1
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGUGGCGCCACCAUCUCGCGCCUU---------UGU
......................(((((((((((.((((((....)))))).))))))).....((((((......))))))...........))))...---------... ( -28.30)
>DroGri_CAF1 120217 94 + 1
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGA-AUUUUUAUUUUUAAUCGGAUUUCAUGCUGCCAUCAACGGCGCCAG---CGC----CAGCGUCGA---------
.......(((..........(((((.(((((((((((-((....)))))).)))))))....)))))........((((....---)))----).)))....--------- ( -27.10)
>DroAna_CAF1 140588 103 + 1
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCGCCAC---CAU----CGCCGUUG-UGUCCUUGU
........((((.........((((.(((((((.((((((....)))))).)))))))....))))......(((((((....---...----))))))))-)))...... ( -27.20)
>DroPer_CAF1 146608 102 + 1
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGUGGCGCCACCAUCUCGCGCCUU---------UGU
......................(((((((((((.((((((....)))))).))))))).....((((((......))))))...........))))...---------... ( -28.30)
>consensus
CCCUUUUCGCACAUAAAUUACAGCGCAUCCGAUAAGAAAUUUUUAUUUUUAAUCGGAUUUCAUGCUACCAUCAACGGCGCCAC___CAU____CGCCGU_________UGU
.......(((...........((((.(((((((.((((((....)))))).)))))))....))))..........)))................................ (-15.06 = -15.17 +   0.11)

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 13:26:47 2006