Locus 1098

Sequence ID 3R_DroMel_CAF1
Location 3,316,859 – 3,317,007
Length 148
Max. P 0.860960
window1796 window1797 window1798

overview

Window 6

Location 3,316,859 – 3,316,974
Length 115
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -23.48
Consensus MFE -14.35
Energy contribution -14.22
Covariance contribution -0.13
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.61
SVM decision value 0.50
SVM RNA-class probability 0.758605
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3316859 115 + 27905053
AAAAUAAAAAGUGUU----UCAUCACAUUUUUUGUAAUAUUUAUAAAUCAAGCACUUCUGCAACACUAUUUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUU
...(((((((((((.----.....)))))))))))...............(((((((((((..((((........))))..((.((((((((....)))))))))).))))))).)))) ( -33.70)
>DroSec_CAF1 10961 114 + 1
UAAAAAAAAU-UUUU----UCAUCACAUUUUUUGUAAUAUCUAUAAAUCAAGCACUUCUUCAAAACUAUUUUCCCAAUGCACACGCAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUU
..........-....----...........((((((.....))))))...(((((((((...................((.((.((((((((....)))))))))).))))))).)))) ( -19.40)
>DroSim_CAF1 4271 115 + 1
UAAAUAAAAUAUGUU----UCAUCAAAUUUUUUGUUAUAUUUAUAAAUCAAGCACUUCUUUAAAACUAUUUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUU
((((((.((((.(((----(....))))....)))).)))))).......(((((((((.....(((........)))((.((.((((((((....)))))))))).))))))).)))) ( -20.90)
>DroYak_CAF1 4432 105 + 1
-AAAUAGAAGUCACUGGACUGCUU-AAGUUUUUUUAAUAUUU------------CUUCUUCACAAAUAUUUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGUUGGGCAGAAGCUAUU
-.(((((...((((((((((....-.)))......(((((((------------.........)))))))...)))))((.(...(((((((....)))))))...))).))..))))) ( -19.90)
>consensus
UAAAUAAAAU_UGUU____UCAUCAAAUUUUUUGUAAUAUUUAUAAAUCAAGCACUUCUUCAAAACUAUUUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUU
....................................................................((((((((((....))((((((((....)))))))))))).))))...... (-14.35 = -14.22 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,316,859 – 3,316,974
Length 115
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 80.63
Mean single sequence MFE -24.23
Consensus MFE -18.17
Energy contribution -18.54
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.75
SVM decision value 0.83
SVM RNA-class probability 0.860960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3316859 115 - 27905053
AACAGCUUCUGCCCAGCAUGCAUACAAAUGCAUACGUGUGCACUGGGAAAAUAGUGUUGCAGAAGUGCUUGAUUUAUAAAUAUUACAAAAAAUGUGAUGA----AACACUUUUUAUUUU
...........(((((..(((((((..........)))))))))))).(((.(((((((((....)))............(((((((.....))))))).----)))))).)))..... ( -27.50)
>DroSec_CAF1 10961 114 - 1
AACAGCUUCUGCCCAGCAUGCAUACAAAUGCAUGCGUGUGCAUUGGGAAAAUAGUUUUGAAGAAGUGCUUGAUUUAUAGAUAUUACAAAAAAUGUGAUGA----AAAA-AUUUUUUUUA
....((((((((.((((((((((....)))))))).)).)).(..(((......)))..)))))))..............(((((((.....))))))).----....-.......... ( -25.80)
>DroSim_CAF1 4271 115 - 1
AACAGCUUCUGCCCAGCAUGCAUACAAAUGCAUACGUGUGCACUGGGAAAAUAGUUUUAAAGAAGUGCUUGAUUUAUAAAUAUAACAAAAAAUUUGAUGA----AACAUAUUUUAUUUA
...........(((((..(((((((..........))))))))))))((((((((((((..(((....(((..((((....)))))))....)))..)))----))).))))))..... ( -22.10)
>DroYak_CAF1 4432 105 - 1
AAUAGCUUCUGCCCAACAUGCAUACAAAUGCAUACGUGUGCACUGGGAAAAUAUUUGUGAAGAAG------------AAAUAUUAAAAAAACUU-AAGCAGUCCAGUGACUUCUAUUU-
....((((..(((((...(((((((..........))))))).))))..(((((((.(.....).------------))))))).......)..-))))((((....)))).......- ( -21.50)
>consensus
AACAGCUUCUGCCCAGCAUGCAUACAAAUGCAUACGUGUGCACUGGGAAAAUAGUUUUGAAGAAGUGCUUGAUUUAUAAAUAUUACAAAAAAUGUGAUGA____AACA_AUUUUAUUUA
....((((((.(((((..(((((((..........)))))))))))).............))))))..................................................... (-18.17 = -18.54 +   0.37)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,316,895 – 3,317,007
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.63
Mean single sequence MFE -25.02
Consensus MFE -16.16
Energy contribution -15.50
Covariance contribution -0.66
Combinations/Pair 1.26
Mean z-score -1.44
Structure conservation index 0.65
SVM decision value 0.17
SVM RNA-class probability 0.617138
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3316895 112 + 27905053
UUAUAAAUCAAGCACUUCUGCAACACUAU-UUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUUGCAAAACCA-------AGACGCGAGACCUCAAAACACAGA
..........(((((((((((..((((..-......))))..((.((((((((....)))))))))).))))))).)))).........-------...(....)............... ( -27.60)
>DroSec_CAF1 10996 112 + 1
CUAUAAAUCAAGCACUUCUUCAAAACUAU-UUUCCCAAUGCACACGCAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUUGCAAAACCA-------AGACGCGAGACCUCAAAACACAGA
...........((((..(((((((....)-))......(((.((.((((((((....)))))))))).)))))))..).))).......-------...(....)............... ( -21.90)
>DroSim_CAF1 4307 112 + 1
UUAUAAAUCAAGCACUUCUUUAAAACUAU-UUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUGUUGCAAAACCA-------AGACGCGAGACCUCAAAACACAGA
.......((..((...............(-(((((((((....))((((((((....)))))))))))).))))((....)).......-------....))..)).............. ( -21.10)
>DroEre_CAF1 4361 100 + 1
UU------------CUUGCUCAAAAAUAU-UUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUAUUGCAAAACCA-------AGACGCGAGACCUCAAAACAGAGA
.(------------(((((((.......(-(((((((((....))((((((((....)))))))))))).))))((....)).......-------.)).)))))).(((......))). ( -28.70)
>DroYak_CAF1 4470 100 + 1
UU------------CUUCUUCACAAAUAU-UUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGUUGGGCAGAAGCUAUUGCAAAACCA-------AGGCGCGAGACCUCAAAACAGGGA
..------------...............-..((((.((((....((((((....)))))).(((..(((....)))...)))......-------..))))((....))......)))) ( -23.30)
>DroAna_CAF1 3800 99 + 1
---------------------AGAUCGAUUUCUCGAAGUGCAUAGACAUGCAUUUGUAUGCAUGUGAGGCAGAAGGUAUUGCAACACCACGACGCGAGACGCGAGACCUCAAAACACAGA
---------------------...((((....)))).(((.....((((((((....))))))))(((((....(((........)))....((((...)))).).))))....)))... ( -27.50)
>consensus
UU____________CUUCUUCAAAACUAU_UUUCCCAGUGCACACGUAUGCAUUUGUAUGCAUGCUGGGCAGAAGCUAUUGCAAAACCA_______AGACGCGAGACCUCAAAACACAGA
..............................((((....(((.((.((((((((....)))))))))).)))...((....))....................)))).............. (-16.16 = -15.50 +  -0.66)

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 10:00:51 2006