Locus 3618

Sequence ID 3R_DroMel_CAF1
Location 9,766,086 – 9,766,226
Length 140
Max. P 0.807727
window5826 window5827

overview

Window 6

Location 9,766,086 – 9,766,187
Length 101
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 88.52
Mean single sequence MFE -22.58
Consensus MFE -16.80
Energy contribution -17.64
Covariance contribution 0.84
Combinations/Pair 1.05
Mean z-score -1.72
Structure conservation index 0.74
SVM decision value 0.23
SVM RNA-class probability 0.646042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9766086 101 - 27905053
GGCAGUGGUAGCCGGGCCAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGAACAAAAAAAAAAAAAAACAACAAGAG-GGGGAAAAUGGUUGUUGGUAAAU
(((.......)))..(((..(((((.(((......))))))))..((((....))))..........((((((.....-..........))))))))).... ( -23.36)
>DroSec_CAF1 89341 95 - 1
GGCAGUGGUAGCUGGGCCAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGAACAAAAA-----AAAAACAACAAGAG-G-GGAAAAUGAUUGUUGGUAAAU
.((.(((((......(((((....)))))......))))).))..((((....))))..-----.....((((((..(-.-......)..))))))...... ( -23.50)
>DroSim_CAF1 89765 96 - 1
GGCAGUGGUAGCCGGGCCAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGAACAAAAAA----AAAAACAACAAGAG-G-GGAAAAUGGUUGUUGGUAAAU
(((.......)))..(((..(((((.(((......))))))))..((((....))))...----...((((((.....-.-........))))))))).... ( -23.44)
>DroEre_CAF1 92792 90 - 1
GGCAGUGGUAGCCGGGCAAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGCG--AAAA-----AAAAA---CAGAGG-G-GGAAAAUGGUUGUCGGUAAAU
(((.......))).(((((.(((((.(((......))))))))..((((....--....-----.....---))))..-.-.........)))))....... ( -19.02)
>DroYak_CAF1 92382 91 - 1
GGCAGUGGUAGCCGGGCCAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGCG--AACA-----AAAAA---CGAAGGGG-GGAAAAUGGUUGUUGGUAAAU
...(.(..(((((((.(((((((..((((......))))....))))))).).--....-----.....---(....)..-......))))))..).).... ( -23.60)
>consensus
GGCAGUGGUAGCCGGGCCAAGUCAUUGGCAAUCGAGCCAUGGCGAUUUGGGAACAAAAA_____AAAAACAACAAGAG_G_GGAAAAUGGUUGUUGGUAAAU
(((..((((......)))).)))((..(((((((.((....))..((((....))))..............................)))))))..)).... (-16.80 = -17.64 +   0.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,766,125 – 9,766,226
Length 101
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 84.58
Mean single sequence MFE -34.12
Consensus MFE -23.37
Energy contribution -23.77
Covariance contribution 0.39
Combinations/Pair 1.27
Mean z-score -3.42
Structure conservation index 0.69
SVM decision value 0.64
SVM RNA-class probability 0.807727
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9766125 101 - 27905053
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG-GCUGGCAGUGGUAGCCGGGCCAAGUCAUUGGCAA--UCGAGCCAUGGCGAUUUGGGAACAAAAAAAA
....((((((....(((((..(((.....)))..))-)))(((.......))).))))))(((((.(((..--....))))))))..((((....))))..... ( -36.50)
>DroSec_CAF1 89377 98 - 1
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG-GCUGGCAGUGGUAGCUGGGCCAAGUCAUUGGCAA--UCGAGCCAUGGCGAUUUGGGAACAAAAA---
....((((((....(((((..(((.....)))..))-)))..((((....))))))))))(((((.(((..--....))))))))..((((....))))..--- ( -35.90)
>DroSim_CAF1 89801 99 - 1
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG-GCUGGCAGUGGUAGCCGGGCCAAGUCAUUGGCAA--UCGAGCCAUGGCGAUUUGGGAACAAAAAA--
....((((((....(((((..(((.....)))..))-)))(((.......))).))))))(((((.(((..--....))))))))..((((....))))...-- ( -36.50)
>DroEre_CAF1 92825 96 - 1
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG-GCUGGCAGUGGUAGCCGGGCAAAGUCAUUGGCAA--UCGAGCCAUGGCGAUUUGGGCG--AAAA---
....(((.(((....((((.(((...((((.(((((-(((.((..(((...))).))..))))))))..))--))..))).))))....))).))--)...--- ( -33.00)
>DroYak_CAF1 92416 96 - 1
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG-GCUGGCAGUGGUAGCCGGGCCAAGUCAUUGGCAA--UCGAGCCAUGGCGAUUUGGGCG--AACA---
....(((.(((....((((.(((...((((.(((((-((((((..(((...))).))).))))))))..))--))..))).))))....))).))--)...--- ( -37.10)
>DroMoj_CAF1 85564 86 - 1
AUUAUUGGCAAUAAAGCCAAGGUGUGGAUUAUAGUUGGCUGGUAGCUU-AGCCAGU--UGGCCACUGCGAAUAUCGAGUGAUGGAGAUG---------------
....(((((......))))).............((..((((((.....-.))))))--..))((((.((.....)))))).........--------------- ( -25.70)
>consensus
AUUAUUGGCCAUAAAGCCAAGGUGUGGAUUAUAGUG_GCUGGCAGUGGUAGCCGGGCCAAGUCAUUGGCAA__UCGAGCCAUGGCGAUUUGGGAA__AAAA___
........(((....((((.((..(((...........(((((.......)))))(((((....)))))....)))..)).))))....)))............ (-23.37 = -23.77 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:54 2006