Locus 4369

Sequence ID X_DroMel_CAF1
Location 11,487,787 – 11,487,927
Length 140
Max. P 0.922317
window7174 window7175 window7176

overview

Window 4

Location 11,487,787 – 11,487,892
Length 105
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 74.17
Mean single sequence MFE -25.11
Consensus MFE -13.67
Energy contribution -13.90
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -2.02
Structure conservation index 0.54
SVM decision value 0.61
SVM RNA-class probability 0.798651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11487787 105 + 22224390
UUAUGGGCAAACUUCCUUU-----UUUGCCAUCAUCUGGCUUU---UUAUUUCUUUGACGUCUUAUGCGAUUUUGAUGGCCAUAAAAUGUCAUGGGAUAAGGCGUCAUAAAAA
.....((((((........-----))))))......((((.((---((((..(..((((((.((((((.((....)).).))))).)))))).)..)))))).))))...... ( -27.80)
>DroSec_CAF1 22694 113 + 1
UUUUGGCCAAACUUUCUUUUUUUUUUUGCCAUCAUCUGGCUUUUUUUUAUUUCUUUGACGUCUUAUGCGACUUUGAUGGCCAUAAAAUGUCAUGGGAUAAGGCGUCAUAAAAA
.....(((...................((((.....))))......((((..(..((((((.(((((.(.((.....)))))))).)))))).)..))))))).......... ( -25.30)
>DroAna_CAF1 31116 99 + 1
AAGGGGUGGAAAUGUAUUUU----UU--------UCUGGGGGUU--UCUUCCCAUUGACGUCUUAUGAGAUUUUGAUGGCCAUAAAAUGUCAAAGGAUAAGAUGCCAUAAAAA
.............(((((((----.(--------(((.((((..--...)))).(((((((.(((((.............))))).))))))))))).)))))))........ ( -22.22)
>consensus
UUAUGGCCAAACUUUCUUUU____UUUGCCAUCAUCUGGCUUUU__UUAUUUCUUUGACGUCUUAUGCGAUUUUGAUGGCCAUAAAAUGUCAUGGGAUAAGGCGUCAUAAAAA
.......................................................((((((((((......(((.(((((........))))).)))))))))))))...... (-13.67 = -13.90 +   0.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,487,787 – 11,487,892
Length 105
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 74.17
Mean single sequence MFE -19.93
Consensus MFE -10.59
Energy contribution -12.04
Covariance contribution 1.45
Combinations/Pair 1.16
Mean z-score -2.11
Structure conservation index 0.53
SVM decision value 0.59
SVM RNA-class probability 0.790606
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11487787 105 - 22224390
UUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAAUCGCAUAAGACGUCAAAGAAAUAA---AAAGCCAGAUGAUGGCAAA-----AAAGGAAGUUUGCCCAUAA
(((((.(((((.((((((((((((....))))))...........).))))).))))).)))))...---...((((.....))))...-----...((........)).... ( -20.50)
>DroSec_CAF1 22694 113 - 1
UUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAGUCGCAUAAGACGUCAAAGAAAUAAAAAAAAGCCAGAUGAUGGCAAAAAAAAAAAGAAAGUUUGGCCAAAA
...(((((...........))))).......((((((.....(((......)))...................((((.....))))..................))))))... ( -20.60)
>DroAna_CAF1 31116 99 - 1
UUUUUAUGGCAUCUUAUCCUUUGACAUUUUAUGGCCAUCAAAAUCUCAUAAGACGUCAAUGGGAAGA--AACCCCCAGA--------AA----AAAAUACAUUUCCACCCCUU
(((((.(((..((((.(((.(((((.((((((((...........)))))))).))))).)))))))--.....))).)--------))----)).................. ( -18.70)
>consensus
UUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAAUCGCAUAAGACGUCAAAGAAAUAA__AAAAGCCAGAUGAUGGCAAA____AAAAGAAAGUUUGACCAAAA
(((((.(((((.(((((.((((((....)))))).............))))).))))).))))).........((((.....))))........................... (-10.59 = -12.04 +   1.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,487,822 – 11,487,927
Length 105
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 82.32
Mean single sequence MFE -16.97
Consensus MFE -12.04
Energy contribution -12.27
Covariance contribution 0.23
Combinations/Pair 1.21
Mean z-score -2.39
Structure conservation index 0.71
SVM decision value 1.15
SVM RNA-class probability 0.922317
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11487822 105 - 22224390
CCCCUUUUCU---CGUUUUCCCUUUAUUUUCCAGCUUAUUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAAUCGCAUAAGACGUCAAAGAAAUAA---AAA
..........---......................((((((((.(((((.((((((((((((....))))))...........).))))).))))).))))))))---... ( -16.80)
>DroSec_CAF1 22734 108 - 1
CCCCUUUUCU---CGUUUUCCCUUUUUUCCGCAUCUUAUUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAGUCGCAUAAGACGUCAAAGAAAUAAAAAAAA
..........---......................((((((((.((((........((((((....))))))........(((......))))))).))))))))...... ( -17.20)
>DroAna_CAF1 31144 108 - 1
CCCCUUUUUUUUAUGUUUUCCUUUUAUUU-UCAUCUUAUUUUUAUGGCAUCUUAUCCUUUGACAUUUUAUGGCCAUCAAAAUCUCAUAAGACGUCAAUGGGAAGA--AACC
.............................-...............((..((((.(((.(((((.((((((((...........)))))))).))))).)))))))--..)) ( -16.90)
>consensus
CCCCUUUUCU___CGUUUUCCCUUUAUUU_CCAUCUUAUUUUUAUGACGCCUUAUCCCAUGACAUUUUAUGGCCAUCAAAAUCGCAUAAGACGUCAAAGAAAUAA__AAAA
...................................((((((((.(((((.(((((.((((((....)))))).............))))).))))).))))))))...... (-12.04 = -12.27 +   0.23)

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 11:23:17 2006