Locus 3184

Sequence ID 2L_DroMel_CAF1
Location 9,107,017 – 9,107,147
Length 130
Max. P 0.969242
window5057 window5058 window5059

overview

Window 7

Location 9,107,017 – 9,107,111
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.77
Mean single sequence MFE -27.98
Consensus MFE -15.87
Energy contribution -16.23
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -2.53
Structure conservation index 0.57
SVM decision value 1.64
SVM RNA-class probability 0.969242
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9107017 94 + 22407834
AAAUUUUAGCUCAUUU-UUUGGCACUAUUC-------------------------GUGCCAAAAAUUCAGUCUCUUGGCAUUAACAUGGUAAAUAUUUGCCUAGUGGUAUUACUGACAGU
..............((-((((((((.....-------------------------)))))))))).(((((....((.(((((....(((((....)))))))))).))..))))).... ( -23.80)
>DroSec_CAF1 9191 93 + 1
AAAUUUUAGCUCACGU-UUUGGCACUGUUU-------------------------GUGCCAAAAAUUCAGUCUCUUGGCAUUAACAUGGCAAAUAUUUGCCUAGUGGUAU-GCUGACAGU
........(((....(-((((((((.....-------------------------)))))))))....)))((.(..((((...((((((((....)))))..)))..))-))..).)). ( -28.70)
>DroSim_CAF1 9263 93 + 1
AAAUUUUAGCUUACGU-UUCGGCACUGUUC-------------------------GUGCCAAAAAUGCAGUCUCUUGGCAUUAACAUGGCAAAUAUUUGCCUAGUGGUAU-GCUGACAGU
.....(((((.(((..-...(((((.....-------------------------)))))...(((((.........)))))..((((((((....)))))..)))))).-))))).... ( -25.30)
>DroEre_CAF1 9354 93 + 1
AAAUUUUAGCUCGCUU-UUUGGCACUAUUC-------------------------GUGCCAGAAGCUCGGUCCCUUGGCAUUAUUCUGGUAAAUAUUUGCCUAGUGGUAU-GCUGACAGU
.....(((((..((((-((.(((((.....-------------------------))))))))))).....((((.((((.((((......))))..)))).)).))...-))))).... ( -28.20)
>DroYak_CAF1 13996 119 + 1
AAAUUUUAGCUCACUUUUUUGGCACUGUUCUGUUCUGUGGAAAAAAGCGGAGGAAGAGCGGAAAAUUCGUUCCCUUGGCAUUAAUAUGGGAAAUAUUUGCCUAGUGGUAU-GCUGACAGU
.....((((((((((.....(((.(((((((.((((((........))))))..))))))).((((...(((((.............)))))..))))))).)))))...-))))).... ( -33.92)
>consensus
AAAUUUUAGCUCACUU_UUUGGCACUGUUC_________________________GUGCCAAAAAUUCAGUCUCUUGGCAUUAACAUGGCAAAUAUUUGCCUAGUGGUAU_GCUGACAGU
.................((((((((..............................))))))))...(((((....((.(((((....(((((....)))))))))).))..))))).... (-15.87 = -16.23 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,107,017 – 9,107,111
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.77
Mean single sequence MFE -23.92
Consensus MFE -12.59
Energy contribution -12.99
Covariance contribution 0.40
Combinations/Pair 1.19
Mean z-score -2.57
Structure conservation index 0.53
SVM decision value 1.57
SVM RNA-class probability 0.964411
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9107017 94 - 22407834
ACUGUCAGUAAUACCACUAGGCAAAUAUUUACCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC-------------------------GAAUAGUGCCAAA-AAAUGAGCUAAAAUUU
....(((((.......((.(((((((((.....)))))..)))).))..))))).((((((((((-------------------------.....))))))))-)).............. ( -23.60)
>DroSec_CAF1 9191 93 - 1
ACUGUCAGC-AUACCACUAGGCAAAUAUUUGCCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC-------------------------AAACAGUGCCAAA-ACGUGAGCUAAAAUUU
.((.(..((-((...((..(((((....)))))..))..))))..).)).((.(..(((((((((-------------------------.....))))))))-)..).))......... ( -23.60)
>DroSim_CAF1 9263 93 - 1
ACUGUCAGC-AUACCACUAGGCAAAUAUUUGCCAUGUUAAUGCCAAGAGACUGCAUUUUUGGCAC-------------------------GAACAGUGCCGAA-ACGUAAGCUAAAAUUU
....((.((-((.......(((((....))))).((((..(((((((((......))))))))).-------------------------.)))))))).)).-................ ( -24.60)
>DroEre_CAF1 9354 93 - 1
ACUGUCAGC-AUACCACUAGGCAAAUAUUUACCAGAAUAAUGCCAAGGGACCGAGCUUCUGGCAC-------------------------GAAUAGUGCCAAA-AAGCGAGCUAAAAUUU
......(((-...((.((.((((..(((((....))))).)))).)))).....((((.((((((-------------------------.....))))))..-))))..)))....... ( -27.30)
>DroYak_CAF1 13996 119 - 1
ACUGUCAGC-AUACCACUAGGCAAAUAUUUCCCAUAUUAAUGCCAAGGGAACGAAUUUUCCGCUCUUCCUCCGCUUUUUUCCACAGAACAGAACAGUGCCAAAAAAGUGAGCUAAAAUUU
......(((-......((.(((((((((.....)))))..)))).))((((......))))..........(((((((((.(((...........)))..))))))))).)))....... ( -20.50)
>consensus
ACUGUCAGC_AUACCACUAGGCAAAUAUUUACCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC_________________________GAACAGUGCCAAA_AAGUGAGCUAAAAUUU
......(((..........(((((((((.....)))))..(((((((((......)))))))))................................))))..........)))....... (-12.59 = -12.99 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,107,046 – 9,107,147
Length 101
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 84.38
Mean single sequence MFE -23.30
Consensus MFE -16.80
Energy contribution -17.04
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -1.64
Structure conservation index 0.72
SVM decision value 0.09
SVM RNA-class probability 0.576368
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9107046 101 - 22407834
CCUUUUUUUUUGGCCGAUUCUCAGGCCUGCUAUAAAACUGUCAGUAAUACCACUAGGCAAAUAUUUACCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC---------------
...........((((........))))(((((.((((...(((((.......((.(((((((((.....)))))..)))).))..))))).))))))))).--------------- ( -22.50)
>DroSec_CAF1 9220 99 - 1
CCCUUU-UUUUGGUCGACUCUCAGGCCAUCUAUAAAACUGUCAGC-AUACCACUAGGCAAAUAUUUGCCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC---------------
......-...(((((........))))).................-.........(((((....))))).......(((((((((......))))))))).--------------- ( -21.60)
>DroSim_CAF1 9292 99 - 1
CCCUUU-UUUUGGCCGACUCUCAGGCCUGCUAUAAAACUGUCAGC-AUACCACUAGGCAAAUAUUUGCCAUGUUAAUGCCAAGAGACUGCAUUUUUGGCAC---------------
......-....((((........))))(((((((....))).)))-)........(((((....))))).......(((((((((......))))))))).--------------- ( -25.70)
>DroEre_CAF1 9383 100 - 1
CCCUUUUUUUUGGCCGAUUCUCAGGCCUGCUAUAAAACUGUCAGC-AUACCACUAGGCAAAUAUUUACCAGAAUAAUGCCAAGGGACCGAGCUUCUGGCAC---------------
............(((((..(((.(((((((((((....))).)))-).....((.((((..(((((....))))).)))).)))).)))))..)).)))..--------------- ( -24.30)
>DroYak_CAF1 14036 115 - 1
CCCGUUUUUUUGGCCGACUCUCAGGCCUGCUAUAAAACUGUCAGC-AUACCACUAGGCAAAUAUUUCCCAUAUUAAUGCCAAGGGAACGAAUUUUCCGCUCUUCCUCCGCUUUUUU
..(((((((((((((........))))(((((((....))).)))-)........(((((((((.....)))))..)))))))))))))........................... ( -22.40)
>consensus
CCCUUUUUUUUGGCCGACUCUCAGGCCUGCUAUAAAACUGUCAGC_AUACCACUAGGCAAAUAUUUACCAUGUUAAUGCCAAGAGACUGAAUUUUUGGCAC_______________
...........((((........))))...........((((((........)).)))).................(((((((((......)))))))))................ (-16.80 = -17.04 +   0.24)

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 10:46:21 2006