Locus 3308

Sequence ID 3R_DroMel_CAF1
Location 8,870,014 – 8,870,139
Length 125
Max. P 0.870617
window5336 window5337

overview

Window 6

Location 8,870,014 – 8,870,110
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 80.23
Mean single sequence MFE -31.72
Consensus MFE -19.02
Energy contribution -19.80
Covariance contribution 0.78
Combinations/Pair 1.31
Mean z-score -2.32
Structure conservation index 0.60
SVM decision value 0.87
SVM RNA-class probability 0.870617
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8870014 96 + 27905053
AAAGAGGGCG---------GCAAGAAGAAAGGAGGCGUGGGAAAGUCCAUUGGUUGCGACAUUUUCAAUGACGCCGCCAUGGAAAACGCCUACUAUGUCUGCCAU
.........(---------(((.((....((.((((((.......(((((.(((.(((.(((.....))).))).))))))))..)))))).))...)))))).. ( -33.60)
>DroVir_CAF1 1860 105 + 1
AAGGAAGGCGUUGGUGGCACUAAGAAAAAAGGUGGUGUGGGCAAGUCCAUCGGCUGUGAUAUAUUUAAUGAUGCCGCAAUGGAAAAUGCCUACUAUGUGUGCCAC
.............(((((((................(((((((..(((((((((..(((.....))).....))))..)))))...))))))).....))))))) ( -31.80)
>DroGri_CAF1 1813 105 + 1
AAGGAAGGCGCCGGUGGCAGCAAGAAAAAGGCUGGCGUUGGCAAGUCCAUUGGCUGUGAUAUAUUCAAUGAUGCAGCCAUGGAUAAUGCCUACUAUGUGUGUCAC
..((.(((((((..((.((((.........)))).))..)))..((((((.(((((((.(((.....))).)))))))))))))...)))).))........... ( -41.30)
>DroWil_CAF1 8705 105 + 1
AAAGAGGGCGGCGGAGGUGGUAAGAAAAAAGGAGGCGUGGGCAAGUCCAUUGGAUGUGAUAUUUUUAACGAUGCUGCCAUGGAAAAUGCCUACUAUGUGUGCCAU
.........((((.(.((((((........((.(((((.(.((.((((...)))).))..........).))))).))..((......)))))))).).)))).. ( -26.90)
>DroMoj_CAF1 1995 102 + 1
AAGGAAGGCAUUAGUGGC---AAGAAAAAAGGGGGCGUUGGCAAGUCCAUUGGCUGUGAUAUAUUCAAUGAUGCAGCAAUGGAGAAUGCUUACUAUGUAUGCCAC
......((((((((((((---(............((....))...(((((((.(((((.(((.....))).))))))))))))...))).)))))...))))).. ( -28.80)
>DroAna_CAF1 6340 99 + 1
AAAGAGGGCG------GUGGCAAGAAGAAAGGGGGCGUGGGAAAAUCCAUUGGAUGUGAUAUCUUCAAUGAUGCUGCCAUGGAAAACGCCUACUAUGUGUGCCAU
..........------((((((...(.(.((..(((((.......(((((.((....(.((((......)))))..)))))))..)))))..)).).).)))))) ( -27.90)
>consensus
AAAGAAGGCG__GGUGGC_GCAAGAAAAAAGGAGGCGUGGGCAAGUCCAUUGGCUGUGAUAUAUUCAAUGAUGCAGCCAUGGAAAAUGCCUACUAUGUGUGCCAC
......((((....................(....)(((((((..(((((.(((.(((.(((.....))).))).))))))))...)))))))......)))).. (-19.02 = -19.80 +   0.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,870,030 – 8,870,139
Length 109
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.99
Mean single sequence MFE -29.87
Consensus MFE -20.61
Energy contribution -20.00
Covariance contribution -0.61
Combinations/Pair 1.31
Mean z-score -1.37
Structure conservation index 0.69
SVM decision value 0.39
SVM RNA-class probability 0.716857
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8870030 109 + 27905053
AGAAAGGAGGCGUGGGAAAGUCCAUUGGUUGCGACAUUUUCAAUGACGCCGCCAUGGAAAACGCCUACUAUGUCUGCCAUAAUGUUCAGGUAAGUCAUUACU--UAAA---GUA---
.....(((((((((((....(((((.(((.(((.(((.....))).))).)))))))).....)))))...)))).)).........((((((....)))))--)...---...--- ( -31.80)
>DroVir_CAF1 1885 112 + 1
AAAAAGGUGGUGUGGGCAAGUCCAUCGGCUGUGAUAUAUUUAAUGAUGCCGCAAUGGAAAAUGCCUACUAUGUGUGCCACAAUGUGCAGGUGGGAUAUCAAC--AGAA---AUAAAU
.....(.(((((((((((..(((((((((..(((.....))).....))))..)))))...))))).((((.((..(......)..)).)))).)))))).)--....---...... ( -31.90)
>DroEre_CAF1 6141 105 + 1
AGAAAGGGGGCGUGGGAAAGUCCAUUGGUUGCGACAUUUUCAAUGACGCCGCCAUGGAAAACGCCUACUAUGUGUGCCACAAUGUUCAGGUAAGUUAAUAUU--UA-------G---
.(((((..(((((.......(((((.(((.(((.(((.....))).))).))))))))..)))))..)).((((...))))...)))...............--..-------.--- ( -28.60)
>DroWil_CAF1 8730 106 + 1
AAAAAGGAGGCGUGGGCAAGUCCAUUGGAUGUGAUAUUUUUAACGAUGCUGCCAUGGAAAAUGCCUACUAUGUGUGCCAUAAUGUUCAGGUGAGAAAAUGUU--CAUU---------
........((((((((((..(((((.((....(.((((......)))))..)))))))...))))))).......)))..((((..((..(....)..))..--))))--------- ( -23.51)
>DroYak_CAF1 5520 114 + 1
AGAAAGGGGGCGUGGGAAAGUCCAUUGGUUGCGACAUUUUCAACGACGCCGCCAUGGAAAAUGCCUACUACGUCUGCCACAAUGUGCAGGUGGGUUAAAAUUAUUAAUGCCCUA---
......((((((((((....(((((.(((.(((.............))).)))))))).....)))))..(..(((((.....).))))..)................))))).--- ( -38.02)
>DroAna_CAF1 6359 103 + 1
AGAAAGGGGGCGUGGGAAAAUCCAUUGGAUGUGAUAUCUUCAAUGAUGCUGCCAUGGAAAACGCCUACUAUGUGUGCCAUAAUGUACAGGUGAGUUUUUAAU--U------------
.....(((((((((((....(((((.((....(.((((......)))))..))))))).....)))))(((.(((((......))))).))).))))))...--.------------ ( -25.40)
>consensus
AGAAAGGGGGCGUGGGAAAGUCCAUUGGUUGCGACAUUUUCAAUGACGCCGCCAUGGAAAACGCCUACUAUGUGUGCCACAAUGUUCAGGUGAGUUAAUAUU__UAA______A___
....((.((((((.......(((((.(((.(((.(((.....))).))).))))))))..)))))).)).....((((..........))))......................... (-20.61 = -20.00 +  -0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:05 2006