Locus 9480

Sequence ID 3R_DroMel_CAF1
Location 25,088,727 – 25,088,877
Length 150
Max. P 0.640292
window15181 window15182

overview

Window 1

Location 25,088,727 – 25,088,817
Length 90
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 84.35
Mean single sequence MFE -26.97
Consensus MFE -20.95
Energy contribution -21.95
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.78
SVM decision value 0.11
SVM RNA-class probability 0.588340
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25088727 90 - 27905053
AUGGGCUGGAUCGGCGGACACUCCUUUUAGGAGUCCGUA------AACCCUCUAAAU---AAAACAAG------------AAAACCUUU-UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....((((((..(((.....))))))))).------............---........------------.........-..((((.....))))))))))) ( -25.90)
>DroSec_CAF1 17811 90 - 1
AUGGGCUGGAUCGGCGGACACUCCUUUUAGGAGUCCGUA------AACCCUCUAAAU---AAAACAAG------------GAAACCUUU-UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....((((((..(((.....))))))))).------............---.......(------------....)....-..((((.....))))))))))) ( -26.30)
>DroSim_CAF1 17931 90 - 1
AUGGGCUGGAUCGGCGGACACUCCUUUUAGAAGUCCGUA------AAACCUCUAAAU---AAAACAAG------------GAAACCUUU-UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....((((((..((......)).)))))).------............---.......(------------....)....-..((((.....))))))))))) ( -22.80)
>DroEre_CAF1 18192 93 - 1
AUGGGCUGGAUCGGCGGACACUCCUUUUAGGAGUCCGUA------AACCCUCUAAAU---AAAACAAAAAAAA---------AACCUUU-UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....((((((..(((.....))))))))).------............---.............---------.......-..((((.....))))))))))) ( -25.90)
>DroYak_CAF1 18380 102 - 1
AUGGGCUGGAUCGGCGGACACUCCUUUUAGGAGACCGUA------AACCCUCUAAAU---AAAACAAAAAAAAAAAAGAGAAAACCUUU-UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....((((...((((.....)))).)))).------....((((....---................)))).........-..((((.....))))))))))) ( -24.85)
>DroAna_CAF1 22759 103 - 1
AUGGGCUGGAUCGGCGGACACUCCUUUCAGCAGAGCGGAGUGCGAGGGCCUCAGGAUCCGAAAACAAAAGG---------GAAGCCUUUAUCCCGCUCCCAGUGGCAGCUCA
.((((((((((((((...((((((.(((....))).)))))).....)))....))))).......(((((---------....)))))...((((.....)))).)))))) ( -36.10)
>consensus
AUGGGCUGGAUCGGCGGACACUCCUUUUAGGAGUCCGUA______AACCCUCUAAAU___AAAACAAA____________GAAACCUUU_UCCCGCUCUCAGUGGCAGCUCA
.(((((((.....(((((..((((.....)))))))))......................................................((((.....))))))))))) (-20.95 = -21.95 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,088,781 – 25,088,877
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.67
Mean single sequence MFE -21.30
Consensus MFE -10.70
Energy contribution -10.15
Covariance contribution -0.55
Combinations/Pair 1.13
Mean z-score -2.04
Structure conservation index 0.50
SVM decision value 0.22
SVM RNA-class probability 0.640292
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25088781 96 + 27905053
---GGACUCCUAAA-AGGAGUGUCCGCCGAUCCAGCCCAUAAUUAACUAUUCAAACAAUGGGCAC--------GCACAAAGGGAUCAGCAAUCAAAUACGCAUACA----CA--------
---(((((((....-.)))..))))((.(((((.((((((.................)))))).(--------.......)))))).)).................----..-------- ( -26.03)
>DroVir_CAF1 25195 106 + 1
ACGGCUUGACUCAA-AGGAGUGUACGCCGAUCCAACCCAUAAUUAACUAUUCAAACAAUAGAGAGAUGCGUGCCUACAA-AGGAUCGGCAAUCAAAUACGCAAACA----CA--------
...((...((((..-..))))....((((((((.............(((((.....)))))........((....))..-.))))))))..........)).....----..-------- ( -23.00)
>DroPse_CAF1 22488 102 + 1
---GGU---CUGAAAAGGAGUGUCCGCUGAUCCAACCCAUAAUUAACUAUUCAAACAAUAGGCAU--------AUACAAAAGGAUCUGCAAUCAAAUACACACACA----CACACGGAAC
---..(---(((....((.....))((.(((((.............(((((.....)))))....--------........))))).)).................----....)))).. ( -16.31)
>DroYak_CAF1 18446 96 + 1
---GGUCUCCUAAA-AGGAGUGUCCGCCGAUCCAGCCCAUAAUUAACUAUUCAAACAAUGGGCAC--------GCACAAAGGGAUCAGCAAUCAAAUACGCAUACA----CA--------
---((.((((....-.))))...))((.(((((.((((((.................)))))).(--------.......)))))).)).................----..-------- ( -25.53)
>DroAna_CAF1 22826 96 + 1
---GCUCUGCUGAA-AGGAGUGUCCGCCGAUCCAGCCCAUAAUUAACUAUUCAAACAAUAGGCAC--------ACACAAAGGGAUCAGCAAUCAAACACAUAUACA----UG--------
---(((((......-.)))))....((.(((((.............(((((.....)))))....--------........))))).)).................----..-------- ( -16.51)
>DroPer_CAF1 21976 105 + 1
---GGU---CUGAA-AGGAGUGUCCGCUGAUCCAACCCAUAAUUAACUAUUCAAACAAUAGGCAU--------AUACAAAAGGAUCUGCAAUCAAAUACACACACACAGACACACGGAAC
---.((---(((..-.((.....))((.(((((.............(((((.....)))))....--------........))))).)).................)))))......... ( -20.41)
>consensus
___GGUCU_CUGAA_AGGAGUGUCCGCCGAUCCAACCCAUAAUUAACUAUUCAAACAAUAGGCAC________ACACAAAAGGAUCAGCAAUCAAAUACACAUACA____CA________
................((.....))((.(((((.............(((((.....))))).............(.....)))))).))............................... (-10.70 = -10.15 +  -0.55)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:37 2006