Locus 7760

Sequence ID 3L_DroMel_CAF1
Location 20,705,208 – 20,705,356
Length 148
Max. P 0.770670
window12637 window12638 window12639

overview

Window 7

Location 20,705,208 – 20,705,321
Length 113
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -29.14
Consensus MFE -20.15
Energy contribution -20.59
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 0.39
SVM RNA-class probability 0.716003
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20705208 113 - 23771897
UGCUAGCAGCUGAUGCAUCAGCUGCUAAGAUUCCAUGCGCGCAUCUCGUGAGUAGGACAC-AAUUUAAAUGUAUCAAGUAAUUUGUAAAAAUAUCUACAGAUCUGACUGUUAAA----
(((((((((((((....))))))))))....(((.(((.(((.....))).))))))...-.........)))...(((.(((((((........)))))))...)))......---- ( -29.20)
>DroSec_CAF1 1872 113 - 1
UGCUACCAGCUGAUGCGUCAGCUGCUGAGAUUCCAUGCGCGCACCUCGUGAGUCAGGCAC-AAUUUAAAUAUAUCAAGCAAUUUGUGAAAAUAUUUACAGAUCUGACUGUUAAA----
..((..(((((((....)))))))...))........((((.....))))((((((((..-................)).(((((((((....)))))))))))))))......---- ( -26.07)
>DroSim_CAF1 1859 113 - 1
UGCUAGCAGCUGAUGCAUCAGCUGCUGAGAUUCCAUGCGCGCAUCUCGUGAGUCAGGCAC-AAUUUAAAUAUAUCAAGCAAUUUGUGAAAAUAUCUACAUAUCUGACUGUUAAA----
....(((((((((....)))))))))(((((.((....).).)))))...((((((.(((-((...................)))))...((((....))))))))))......---- ( -27.51)
>DroEre_CAF1 27436 118 - 1
UGCUAGCAGCUGAUGCGUCAGCUGCUGUGAUUUCACGCGCCCAUCUCGUGAGUCACGCAUGAACUUGAAUAAAGCCAUCAAUUUAUAAGCAGAUAUUUUGUUCUGACUGUUAAAAAUA
(((.(((((((((....)))))))))((((((.((((.(.....).)))))))))))))(((.(((.....)))...))).((((..((((((........)))).))..)))).... ( -33.80)
>consensus
UGCUAGCAGCUGAUGCAUCAGCUGCUGAGAUUCCAUGCGCGCAUCUCGUGAGUCAGGCAC_AAUUUAAAUAUAUCAAGCAAUUUGUAAAAAUAUCUACAGAUCUGACUGUUAAA____
...((((((((((....))))))))))......((((.(.....).))))((((((((...................)).(((((((........))))))))))))).......... (-20.15 = -20.59 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,705,244 – 20,705,356
Length 112
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 85.04
Mean single sequence MFE -35.95
Consensus MFE -27.80
Energy contribution -27.93
Covariance contribution 0.13
Combinations/Pair 1.19
Mean z-score -1.59
Structure conservation index 0.77
SVM decision value 0.23
SVM RNA-class probability 0.646067
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20705244 112 + 23771897
CUUGAUACAUUUAAAUU-GUGUCCUACUCACGAGAUGCGCGCAUGGAAUCUUAGCAGCUGAUGCAUCAGCUGCUAGCACUGAAUUUCACGACGAGUUGGCAACACAAAGCCGA
...((((((.......)-)))))..((((.....(((....)))(((((((((((((((((....)))))))))))....).))))).....))))((((........)))). ( -31.40)
>DroSec_CAF1 1908 112 + 1
CUUGAUAUAUUUAAAUU-GUGCCUGACUCACGAGGUGCGCGCAUGGAAUCUCAGCAGCUGACGCAUCAGCUGGUAGCACUGAAUUUCUCGCCGAGUUGGCAGCACGAACCCGA
...............((-(((((..((((.((((((((..((.(((....))).(((((((....))))))))).)))).......))))..))))..)..))))))...... ( -34.21)
>DroSim_CAF1 1895 112 + 1
CUUGAUAUAUUUAAAUU-GUGCCUGACUCACGAGAUGCGCGCAUGGAAUCUCAGCAGCUGAUGCAUCAGCUGCUAGCACUGAAUUUCUCGCAGAGUUGGCAGCACGAAACCGA
...............((-(((((..((((.(((((..((.((...(.....)(((((((((....))))))))).)).).)....)))))..))))..)..))))))...... ( -36.50)
>DroEre_CAF1 27476 113 + 1
AUGGCUUUAUUCAAGUUCAUGCGUGACUCACGAGAUGGGCGCGUGAAAUCACAGCAGCUGACGCAUCAGCUGCUAGCACUGAAUUCUUCGCCGAGUUGGCAGCACCGCGCUGA
.((((...(((((.((((((.((((...))))..))))))(((((....)))(((((((((....))))))))).))..))))).....))))......((((.....)))). ( -41.70)
>consensus
CUUGAUAUAUUUAAAUU_GUGCCUGACUCACGAGAUGCGCGCAUGGAAUCUCAGCAGCUGACGCAUCAGCUGCUAGCACUGAAUUUCUCGCCGAGUUGGCAGCACGAAGCCGA
..................(((((((((((.(((((((....)))........(((((((((....)))))))))............))))..)))))))..))))........ (-27.80 = -27.93 +   0.13)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,705,244 – 20,705,356
Length 112
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 85.04
Mean single sequence MFE -36.92
Consensus MFE -29.55
Energy contribution -30.18
Covariance contribution 0.63
Combinations/Pair 1.13
Mean z-score -1.74
Structure conservation index 0.80
SVM decision value 0.53
SVM RNA-class probability 0.770670
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20705244 112 - 23771897
UCGGCUUUGUGUUGCCAACUCGUCGUGAAAUUCAGUGCUAGCAGCUGAUGCAUCAGCUGCUAAGAUUCCAUGCGCGCAUCUCGUGAGUAGGACAC-AAUUUAAAUGUAUCAAG
......((((((..((.(((((.((.((......((((((((((((((....)))))))))).(....)..))))...)).))))))).))))))-))............... ( -34.90)
>DroSec_CAF1 1908 112 - 1
UCGGGUUCGUGCUGCCAACUCGGCGAGAAAUUCAGUGCUACCAGCUGAUGCGUCAGCUGCUGAGAUUCCAUGCGCGCACCUCGUGAGUCAGGCAC-AAUUUAAAUAUAUCAAG
..((((.(((((.(((.....)))(.(((.(((((......(((((((....)))))))))))).))))..))))).)))).(((.......)))-................. ( -33.80)
>DroSim_CAF1 1895 112 - 1
UCGGUUUCGUGCUGCCAACUCUGCGAGAAAUUCAGUGCUAGCAGCUGAUGCAUCAGCUGCUGAGAUUCCAUGCGCGCAUCUCGUGAGUCAGGCAC-AAUUUAAAUAUAUCAAG
........(((((....((((.((((((......((((((((((((((....)))))))))).(....)..))))...))))))))))..)))))-................. ( -38.60)
>DroEre_CAF1 27476 113 - 1
UCAGCGCGGUGCUGCCAACUCGGCGAAGAAUUCAGUGCUAGCAGCUGAUGCGUCAGCUGCUGUGAUUUCACGCGCCCAUCUCGUGAGUCACGCAUGAACUUGAAUAAAGCCAU
.((((.....)))).......(((.....(((((((((.(((((((((....)))))))))((((((.((((.(.....).)))))))))))))).....)))))...))).. ( -40.40)
>consensus
UCGGCUUCGUGCUGCCAACUCGGCGAGAAAUUCAGUGCUAGCAGCUGAUGCAUCAGCUGCUGAGAUUCCAUGCGCGCAUCUCGUGAGUCAGGCAC_AAUUUAAAUAUAUCAAG
........(((((....(((((.(((((......((((((((((((((....)))))))))).(....)..))))...))))))))))..))))).................. (-29.55 = -30.18 +   0.63)

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 12:56:18 2006