Locus 403

Sequence ID 3R_DroMel_CAF1
Location 1,494,409 – 1,494,526
Length 117
Max. P 0.657618
window659 window660

overview

Window 9

Location 1,494,409 – 1,494,526
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.91
Mean single sequence MFE -37.20
Consensus MFE -25.75
Energy contribution -26.12
Covariance contribution 0.37
Combinations/Pair 1.35
Mean z-score -1.50
Structure conservation index 0.69
SVM decision value 0.10
SVM RNA-class probability 0.584777
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1494409 117 + 27905053
UUAGAUACGGAUUUGCCGGACUUGAUCGU---CGGCAGCGACACGGAGAUUUGCAUUUUGGCCAGCGGCUUGAGGUACAAGCUGUGCGGCAAGUAAAAAGGAAUGCAGUCUGCCACAUUU
........(...((((((.((......))---))))))...)..(((((((.(((((((.(((.((((((((.....))))))))..))).........)))))))))))).))...... ( -38.30)
>DroVir_CAF1 3532 120 + 1
UUGGAAACGGAUUUUCCGGUUUUGAUUUUUUCGGGCAAUGCAACUGAUAUUUGCAUUUUUGCCAACGGCUUGAGGUACAAACUGUGCGGCAGAUACAGCGGCGUGCAGUCCGCAACAUUU
(..(((.(((.....))).)))..)......(((((.((((..(((.(((((((.(((..(((...)))..)))((((.....)))).))))))))))..))))...)))))........ ( -37.40)
>DroGri_CAF1 3341 120 + 1
UUUGAUACGGAUUUGCCGGUUUUGAUUUUUUCGGGCAAUGCAACUGAUAUUUGCAUUUUGGCCAACGGCUUGAGGUACAAGCUGUGCGGCAAAUAGAGCGGCGUGCAAUCCGCCACAUUU
..........((((((((..............((.((((((((.......))))))..)).)).((((((((.....)))))))).))))))))...(.((((.......)))).).... ( -37.90)
>DroWil_CAF1 2997 117 + 1
UUUGAAACAGAUUUGCCAGACUUAAUUGU---CGGCAAUGCAACGGAGAUUUGCAUUUUAGCCAAUGGCUUAAGAUAUAGGCUGUGAGGCAGAUACAGCGGAGUGCAGUCUGACACAUUU
.......((((((((((.(((......))---))))))((((.((...((((((....(((((.(((........))).)))))....))))))....))...)))))))))........ ( -35.20)
>DroMoj_CAF1 3145 120 + 1
UUUGAUACGGAUUUGCCGGUUUUGAUUUUUUCGGGCAAUGCAACUGAUAUUUGCAUUUUUGCCAAAGGCUUGAGGUACAAGCUGUGCGGCAAAUAAAGCGGUGUGCAGUCCGCAACAUUU
..........((((((((...............((((((((((.......))))))...))))...((((((.....))))))...))))))))...((((........))))....... ( -35.30)
>DroAna_CAF1 2928 117 + 1
UUGGAUACGGAUUUGCCGGAUUUAAUAGG---CGGCAGCGAGACGGAGAUUUGCAUUUUUGCCACAGGCUUGAGAUACAAGCUGUGCGGCAGGUACAGUGGCGUGCAGUCCGUGACAUUU
.....((((((((((((..........))---))((((((((.......)))))......(((((.((((((.....))))))((((.....)))).))))).)))))))))))...... ( -39.10)
>consensus
UUUGAUACGGAUUUGCCGGAUUUGAUUGU___CGGCAAUGCAACGGAGAUUUGCAUUUUUGCCAACGGCUUGAGGUACAAGCUGUGCGGCAAAUACAGCGGCGUGCAGUCCGCCACAUUU
.......(((((((((((...............((((((((((.......)))))))...))).((((((((.....)))))))).)))))).....((.....)).)))))........ (-25.75 = -26.12 +   0.37) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,494,409 – 1,494,526
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.91
Mean single sequence MFE -30.97
Consensus MFE -19.11
Energy contribution -20.17
Covariance contribution 1.06
Combinations/Pair 1.22
Mean z-score -2.07
Structure conservation index 0.62
SVM decision value 0.26
SVM RNA-class probability 0.657618
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1494409 117 - 27905053
AAAUGUGGCAGACUGCAUUCCUUUUUACUUGCCGCACAGCUUGUACCUCAAGCCGCUGGCCAAAAUGCAAAUCUCCGUGUCGCUGCCG---ACGAUCAAGUCCGGCAAAUCCGUAUCUAA
..(..(((.(((.((((((...........(((((...(((((.....))))).)).)))...))))))..))))))..)...(((((---((......)).)))))............. ( -28.64)
>DroVir_CAF1 3532 120 - 1
AAAUGUUGCGGACUGCACGCCGCUGUAUCUGCCGCACAGUUUGUACCUCAAGCCGUUGGCAAAAAUGCAAAUAUCAGUUGCAUUGCCCGAAAAAAUCAAAACCGGAAAAUCCGUUUCCAA
..(((..((((........))))..))).(((((.((.(((((.....))))).)))))))..(((((((.......)))))))...................(((((.....))))).. ( -27.70)
>DroGri_CAF1 3341 120 - 1
AAAUGUGGCGGAUUGCACGCCGCUCUAUUUGCCGCACAGCUUGUACCUCAAGCCGUUGGCCAAAAUGCAAAUAUCAGUUGCAUUGCCCGAAAAAAUCAAAACCGGCAAAUCCGUAUCAAA
....((((((.......))))))...((((((((.((.(((((.....))))).)).(((...(((((((.......))))))))))...............)))))))).......... ( -35.50)
>DroWil_CAF1 2997 117 - 1
AAAUGUGUCAGACUGCACUCCGCUGUAUCUGCCUCACAGCCUAUAUCUUAAGCCAUUGGCUAAAAUGCAAAUCUCCGUUGCAUUGCCG---ACAAUUAAGUCUGGCAAAUCUGUUUCAAA
.....(((((((((.......(((((.........)))))...............(((((...(((((((.......)))))))))))---)......)))))))))............. ( -29.10)
>DroMoj_CAF1 3145 120 - 1
AAAUGUUGCGGACUGCACACCGCUUUAUUUGCCGCACAGCUUGUACCUCAAGCCUUUGGCAAAAAUGCAAAUAUCAGUUGCAUUGCCCGAAAAAAUCAAAACCGGCAAAUCCGUAUCAAA
...((.((((((..((.....))....(((((((....(((((.....))))).(((((....(((((((.......)))))))..)))))...........))))))))))))).)).. ( -34.00)
>DroAna_CAF1 2928 117 - 1
AAAUGUCACGGACUGCACGCCACUGUACCUGCCGCACAGCUUGUAUCUCAAGCCUGUGGCAAAAAUGCAAAUCUCCGUCUCGCUGCCG---CCUAUUAAAUCCGGCAAAUCCGUAUCCAA
.......(((((..(((((....((((..(((((((..(((((.....))))).)))))))....))))......)))...))(((((---...........)))))..)))))...... ( -30.90)
>consensus
AAAUGUGGCGGACUGCACGCCGCUGUAUCUGCCGCACAGCUUGUACCUCAAGCCGUUGGCAAAAAUGCAAAUAUCAGUUGCAUUGCCC___AAAAUCAAAACCGGCAAAUCCGUAUCAAA
.......(((((..((.....))......(((((....(((((.....)))))....(((...(((((((.......))))))))))...............)))))..)))))...... (-19.11 = -20.17 +   1.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:20 2006