Locus 4382

Sequence ID 3L_DroMel_CAF1
Location 12,856,140 – 12,856,270
Length 130
Max. P 0.946221
window6784 window6785 window6786

overview

Window 4

Location 12,856,140 – 12,856,240
Length 100
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 95.86
Mean single sequence MFE -18.63
Consensus MFE -18.15
Energy contribution -17.93
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.71
Structure conservation index 0.97
SVM decision value 0.53
SVM RNA-class probability 0.769993
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12856140 100 + 23771897
AAAUUUCCUUGCGUUCAGCGAAGAGUAAAACCGCACCGAACAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAA----AAAACGAA-AAC
...(((((..((((((.(((...........)))...))))...........((((((((......))))).)))..)).)))))....----........-... ( -18.20)
>DroSec_CAF1 94446 104 + 1
AAAUUUCCUUGCGUUCAGCGAAGAGUAAAACCGCACCGAACAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGGAAAAA-AGAAAACGAAAAAC
...(((((((..((((.(((...........)))...)))).........((((((((((......))))))..))))...)))))))..-.............. ( -19.50)
>DroSim_CAF1 95951 105 + 1
AAAUUUCCUUGCGUUCAGCGAAGAGUAAAACCGCACCGAACAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAAAAAAAAAACGAAAAAC
...(((((..((((((.(((...........)))...))))...........((((((((......))))).)))..)).))))).................... ( -18.20)
>consensus
AAAUUUCCUUGCGUUCAGCGAAGAGUAAAACCGCACCGAACAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAAA_A_AAAACGAAAAAC
...(((((..((((((.(((...........)))...))))...........((((((((......))))).)))..)).))))).................... (-18.15 = -17.93 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,856,140 – 12,856,240
Length 100
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 95.86
Mean single sequence MFE -25.03
Consensus MFE -24.99
Energy contribution -24.77
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 1.00
SVM decision value 1.36
SVM RNA-class probability 0.946221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12856140 100 - 23771897
GUU-UUCGUUUU----UUUUUCUCCAGCAGGGCCAUAUUUAAAUGAAUAUGCCUGAGAUUUUUUGUUCGGUGCGGUUUUACUCUUCGCUGAACGCAAGGAAAUUU
(((-(((.....----....((((.....((((.((((((....))))))))))))))......((((((((.((.......)).))))))))....)))))).. ( -24.50)
>DroSec_CAF1 94446 104 - 1
GUUUUUCGUUUUCU-UUUUUCCUCCAGCAGGGCCAUAUUUAAAUGAAUAUGCCUGAGAUUUUUUGUUCGGUGCGGUUUUACUCUUCGCUGAACGCAAGGAAAUUU
..............-..((((((...((.((((.((((((....))))))))))..........((((((((.((.......)).)))))))))).))))))... ( -26.70)
>DroSim_CAF1 95951 105 - 1
GUUUUUCGUUUUUUUUUUUUUCUCCAGCAGGGCCAUAUUUAAAUGAAUAUGCCUGAGAUUUUUUGUUCGGUGCGGUUUUACUCUUCGCUGAACGCAAGGAAAUUU
......................(((.((.((((.((((((....))))))))))..........((((((((.((.......)).))))))))))..)))..... ( -23.90)
>consensus
GUUUUUCGUUUU_U_UUUUUUCUCCAGCAGGGCCAUAUUUAAAUGAAUAUGCCUGAGAUUUUUUGUUCGGUGCGGUUUUACUCUUCGCUGAACGCAAGGAAAUUU
.................((((((...((.((((.((((((....))))))))))..........((((((((.((.......)).)))))))))).))))))... (-24.99 = -24.77 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,856,180 – 12,856,270
Length 90
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -13.77
Consensus MFE -13.62
Energy contribution -13.40
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.33
Structure conservation index 0.99
SVM decision value -0.02
SVM RNA-class probability 0.521925
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12856180 90 + 23771897
CAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAA----AAAACGAA-AACUGAGAAAAAAGCUUAAAAAAUGCCUUGGUU
.......((((.((((...((((......))))...)))).))))....----........-(((..((......((.........))))..))) ( -13.80)
>DroSec_CAF1 94486 94 + 1
CAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGGAAAAA-AGAAAACGAAAAACUGAGAAAAAAGCUUAAAAAAUGCCUUGGUU
(((....((((((.((((((......))))))..(((.....))).....-.............)))))).....((.........)).)))... ( -13.70)
>DroSim_CAF1 95991 95 + 1
CAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAAAAAAAAAACGAAAAACUGAGAAAAAAGCUUAAAAAAUGCCUUGGUU
.......((((.((((...((((......))))...)))).)))).................(((..((......((.........))))..))) ( -13.80)
>consensus
CAAAAAAUCUCAGGCAUAUUCAUUUAAAUAUGGCCCUGCUGGAGAAAAAA_A_AAAACGAAAAACUGAGAAAAAAGCUUAAAAAAUGCCUUGGUU
.......((((.((((...((((......))))...)))).)))).................(((..((......((.........))))..))) (-13.62 = -13.40 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:08 2006