Locus 3874

Sequence ID 2R_DroMel_CAF1
Location 12,823,316 – 12,823,452
Length 136
Max. P 0.961841
window6256 window6257 window6258 window6259

overview

Window 6

Location 12,823,316 – 12,823,427
Length 111
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 81.27
Mean single sequence MFE -20.36
Consensus MFE -14.52
Energy contribution -14.96
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.97
Structure conservation index 0.71
SVM decision value 0.85
SVM RNA-class probability 0.865445
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12823316 111 + 20766785
---AUUCAUGCAUUUUAGU-UUCAAAUUACUUUUAUUAUUCGAAUAAAA-AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGUGCAGAUUUCGGCGCCACCUCAGCACAUCU
---.....((((((((((.-..........(((((((.....)))))))-..((((.....))))......)))))))....(((((((.(....).)))))))....)))..... ( -21.20)
>DroSec_CAF1 167302 93 + 1
---UUUCAUGCAUUUUAGU-UUCAA------------------AUAAAA-AAUGCCAAAUUGGUAAUUUCUUAAAAAUUUAUGUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCU
---.....(((........-.....------------------......-..((((.....)))).................(((((((.(....).)))))))....)))..... ( -20.40)
>DroSim_CAF1 172615 93 + 1
---UUUCAUGCAUUUUAGU-UUCAA------------------AUAAAA-AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGCGCAGAAUUCGGCGCCACCUCAGCACAUCU
---.....(((........-.....------------------......-..((((.....)))).................(((((((.(....).)))))))....)))..... ( -20.40)
>DroEre_CAF1 170195 97 + 1
CAGUAUCAC-CAUUUUAUUAUUCAA------------------AUAAAACAAUGCCGGAUUGGUAAUUUCUUUGAAAAUUAUUUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCU
.........-..(((((((.....)------------------))))))...(((.((...((((((((......))))))))((((((.(....).))))))))...)))..... ( -17.10)
>DroYak_CAF1 175162 97 + 1
CAGCAUUAU-CCUUUUAUUAUUCAA------------------AUAAAGGAAUGCCAAACUGGUAAUUUCUUUGAACAUUAUUCGGCGCAGAUUUCGGCGCCACCUCAGCACAUCU
..((.....-...............------------------.((((((((((((.....))).)))))))))..........(((((.(....).)))))......))...... ( -22.70)
>consensus
___UUUCAUGCAUUUUAGU_UUCAA__________________AUAAAA_AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCU
....................................................((((.....)))).................(((((((.(....).)))))))............ (-14.52 = -14.96 +   0.44)

alignment

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secondary structure

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Window 7

Location 12,823,316 – 12,823,427
Length 111
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 81.27
Mean single sequence MFE -22.44
Consensus MFE -16.28
Energy contribution -16.76
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.70
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.709404
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12823316 111 - 20766785
AGAUGUGCUGAGGUGGCGCCGAAAUCUGCACCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU-UUUUAUUCGAAUAAUAAAAGUAAUUUGAA-ACUAAAAUGCAUGAAU---
............((((.((.(....).)).)))).((((((...((....))...))))))(((((-((...(((((((.((....)).)))))))-...)))))))......--- ( -20.50)
>DroSec_CAF1 167302 93 - 1
AGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCACAUAAAUUUUUAAGAAAUUACCAAUUUGGCAUU-UUUUAU------------------UUGAA-ACUAAAAUGCAUGAAA---
............(((((((.(....).))))))).((((((..(((....)))..))))))(((((-((....------------------.....-...)))))))......--- ( -22.30)
>DroSim_CAF1 172615 93 - 1
AGAUGUGCUGAGGUGGCGCCGAAUUCUGCGCCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU-UUUUAU------------------UUGAA-ACUAAAAUGCAUGAAA---
....((((..(((((((((.(....).))))))).....(((((((((((...((.....))...)-)))..)------------------)))))-))).....))))....--- ( -21.60)
>DroEre_CAF1 170195 97 - 1
AGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCAAAUAAUUUUCAAAGAAAUUACCAAUCCGGCAUUGUUUUAU------------------UUGAAUAAUAAAAUG-GUGAUACUG
......((((.((((((((.(....).)))))...(((((((....)))))))...)))))))((..((((((------------------(.....)))))))..-))....... ( -24.10)
>DroYak_CAF1 175162 97 - 1
AGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCGAAUAAUGUUCAAAGAAAUUACCAGUUUGGCAUUCCUUUAU------------------UUGAAUAAUAAAAGG-AUAAUGCUG
......((((....(((((.(....).)))))((((...))))...........))))..(((((((((((((------------------(.....))).)))))-)..))))). ( -23.70)
>consensus
AGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU_UUUUAU__________________UUGAA_ACUAAAAUGCAUGAAA___
....(((((((((((((((.(....).)))))))..........((....)).....))))))))................................................... (-16.28 = -16.76 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,823,352 – 12,823,452
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 92.62
Mean single sequence MFE -21.38
Consensus MFE -18.92
Energy contribution -19.36
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.88
SVM decision value 0.97
SVM RNA-class probability 0.892713
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12823352 100 + 20766785
CGAAUAAAA-AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGUGCAGAUUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
.((......-..((((.....)))).................(((((((.(....).))))))).))(((..((((..(((....)))..))))...))). ( -20.00)
>DroSec_CAF1 167323 97 + 1
---AUAAAA-AAUGCCAAAUUGGUAAUUUCUUAAAAAUUUAUGUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
---......-..((((.....)))).................(((((((.(....).)))))))...(((..((((..(((....)))..))))...))). ( -21.70)
>DroSim_CAF1 172636 97 + 1
---AUAAAA-AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGCGCAGAAUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
---......-..((((.....)))).................(((((((.(....).)))))))...(((..((((..(((....)))..))))...))). ( -21.70)
>DroEre_CAF1 170219 98 + 1
---AUAAAACAAUGCCGGAUUGGUAAUUUCUUUGAAAAUUAUUUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
---.........(((.((...((((((((......))))))))((((((.(....).))))))))...)))........((((((((....))))).))). ( -19.00)
>DroYak_CAF1 175186 98 + 1
---AUAAAGGAAUGCCAAACUGGUAAUUUCUUUGAACAUUAUUCGGCGCAGAUUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
---.((((((((((((.....))).)))))))))..........(((((.(....).))))).....(((..((((..(((....)))..))))...))). ( -24.50)
>consensus
___AUAAAA_AAUGCCAAAUUGGUAAUUUCUUUAAAAUUUAUGUGGCGCAGAUUUCGGCGCCACCUCAGCACAUCUCUCAGCAAAUUGUUAGAUUUCGCUU
............((((.....)))).................(((((((.(....).)))))))...(((..((((..(((....)))..))))...))). (-18.92 = -19.36 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,823,352 – 12,823,452
Length 100
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 92.62
Mean single sequence MFE -25.24
Consensus MFE -20.80
Energy contribution -21.12
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.82
SVM decision value 1.53
SVM RNA-class probability 0.961841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12823352 100 - 20766785
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAAUCUGCACCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU-UUUUAUUCG
.((((((.........))))))..((((.((((..((((((.((.(....).)).))))...((((((...)))))).....))..)))).-))))..... ( -21.10)
>DroSec_CAF1 167323 97 - 1
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCACAUAAAUUUUUAAGAAAUUACCAAUUUGGCAUU-UUUUAU---
.((((((.........))))))(((((((((......(((((((.(....).))))))).((((((..(((....)))..)))))))))))-))))..--- ( -27.90)
>DroSim_CAF1 172636 97 - 1
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAUUCUGCGCCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU-UUUUAU---
.((((((.........))))))..((((.((((..(((((((((.(....).)))))))...((((((...)))))).....))..)))).-))))..--- ( -26.50)
>DroEre_CAF1 170219 98 - 1
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCAAAUAAUUUUCAAAGAAAUUACCAAUCCGGCAUUGUUUUAU---
.((((((.........))))))..(((((((((((.((((((((.(....).)))))...(((((((....)))))))...)))))))).))))))..--- ( -24.80)
>DroYak_CAF1 175186 98 - 1
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCGAAUAAUGUUCAAAGAAAUUACCAGUUUGGCAUUCCUUUAU---
.((((((.........)))))).((((..((((..(((((((((.(....).)))))((((...)))).........)))...)..))))..))))..--- ( -25.90)
>consensus
AAGCGAAAUCUAACAAUUUGCUGAGAGAUGUGCUGAGGUGGCGCCGAAAUCUGCGCCACAUAAAUUUUAAAGAAAUUACCAAUUUGGCAUU_UUUUAU___
.((((((.........)))))).((((..(((((((((((((((.(....).)))))))..........((....)).....))))))))..))))..... (-20.80 = -21.12 +   0.32)

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 11:06:11 2006