Locus 3043

Sequence ID 2R_DroMel_CAF1
Location 10,496,849 – 10,496,987
Length 138
Max. P 0.999843
window5010 window5011 window5012 window5013

overview

Window 0

Location 10,496,849 – 10,496,949
Length 100
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 82.34
Mean single sequence MFE -32.50
Consensus MFE -22.88
Energy contribution -24.28
Covariance contribution 1.40
Combinations/Pair 1.22
Mean z-score -3.09
Structure conservation index 0.70
SVM decision value 2.47
SVM RNA-class probability 0.994317
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10496849 100 + 20766785
CUAUCACCUGCUCUUCUUUGCAGUGCAGUUUUUGUUGGUACAGUGCAUACCCGAUUCGGUGAAUUGUGAAGACCGAG--GGUAUCCACUGUACCAAAGUGAU
..(((((((((.((.......)).))))......(((((((((((.((((((...(((((...........))))))--))))).))))))))))).))))) ( -40.80)
>DroSec_CAF1 10210 100 + 1
CUAUCACCUGUUCUUCUUUGCAGUGCAGUUUUUGUUGUUACAGUGCUUACUCGAUUCGGUGAAUUGUGUAGACCGAG--GGUGUUCACUGUACCAAAGUGAU
..(((((((((........))))...........(((.(((((((..(((((...(((((...........))))))--))))..))))))).))).))))) ( -27.80)
>DroSim_CAF1 10178 100 + 1
CUAUCACCUGUUCUUCUUUGCAGUGCAGUUUUUGUUGGUACAGUGAUUACUCGAUUCGGUGAAUUGUAUAGACCGAG--GGUGUUUACUGUACCAAAGUGAU
..(((((((((........))))...........((((((((((((.(((((...(((((...........))))))--)))).)))))))))))).))))) ( -33.70)
>DroEre_CAF1 10403 99 + 1
CUAUCGGCUGUUCUCCUAUACAGUGCAGUUUUUGUUGGUACAGUGCUUACUCGGUACGGUGAAUUGUGAAGCCCAAGGGGGUGUUCACUGUACCAAAG---U
......(((((...((...((((........)))).)).)))))........((((((((((((......((((....))))))))))))))))....---. ( -32.20)
>DroYak_CAF1 10523 86 + 1
CUAUCGCCUGUUCUGCUAUGCAGUGCAGUUUUU-UUGGUACAGUGCUUACCGGCUAGGGUGAAUUG---------------UGUUCACUGUACCAAAUUUAU
.......((((.((((...)))).))))....(-(((((((((((.(((((......)))))....---------------....))))))))))))..... ( -28.00)
>consensus
CUAUCACCUGUUCUUCUUUGCAGUGCAGUUUUUGUUGGUACAGUGCUUACUCGAUUCGGUGAAUUGUGAAGACCGAG__GGUGUUCACUGUACCAAAGUGAU
....((.((((........)))))).........(((((((((((..((((...((((((...........))))))..))))..)))))))))))...... (-22.88 = -24.28 +   1.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,496,849 – 10,496,949
Length 100
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 82.34
Mean single sequence MFE -28.23
Consensus MFE -16.55
Energy contribution -17.83
Covariance contribution 1.28
Combinations/Pair 1.05
Mean z-score -3.54
Structure conservation index 0.59
SVM decision value 2.41
SVM RNA-class probability 0.993605
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10496849 100 - 20766785
AUCACUUUGGUACAGUGGAUACC--CUCGGUCUUCACAAUUCACCGAAUCGGGUAUGCACUGUACCAACAAAAACUGCACUGCAAAGAAGAGCAGGUGAUAG
(((((.(((((((((((.(((((--((((((...........)))))...)))))).)))))))))))......((((.((.......)).))))))))).. ( -44.20)
>DroSec_CAF1 10210 100 - 1
AUCACUUUGGUACAGUGAACACC--CUCGGUCUACACAAUUCACCGAAUCGAGUAAGCACUGUAACAACAAAAACUGCACUGCAAAGAAGAACAGGUGAUAG
(((((((((.(((((((......--(((((((.............).))))))....)))))))....))))..(((..((.......))..)))))))).. ( -22.12)
>DroSim_CAF1 10178 100 - 1
AUCACUUUGGUACAGUAAACACC--CUCGGUCUAUACAAUUCACCGAAUCGAGUAAUCACUGUACCAACAAAAACUGCACUGCAAAGAAGAACAGGUGAUAG
(((((.((((((((((.......--.(((((...........)))))...((....))))))))))))......(((..((.......))..)))))))).. ( -27.10)
>DroEre_CAF1 10403 99 - 1
A---CUUUGGUACAGUGAACACCCCCUUGGGCUUCACAAUUCACCGUACCGAGUAAGCACUGUACCAACAAAAACUGCACUGUAUAGGAGAACAGCCGAUAG
.---..(((((((((((....(((....))).......((((........))))...)))))))))))...........((((...((.......)).)))) ( -23.40)
>DroYak_CAF1 10523 86 - 1
AUAAAUUUGGUACAGUGAACA---------------CAAUUCACCCUAGCCGGUAAGCACUGUACCAA-AAAAACUGCACUGCAUAGCAGAACAGGCGAUAG
.....((((((((((((....---------------......(((......)))...)))))))))))-)....(((..((((...))))..)))....... ( -24.32)
>consensus
AUCACUUUGGUACAGUGAACACC__CUCGGUCUACACAAUUCACCGAAUCGAGUAAGCACUGUACCAACAAAAACUGCACUGCAAAGAAGAACAGGUGAUAG
......(((((((((((.........((((.............))))..........)))))))))))......(((..((.......))..)))....... (-16.55 = -17.83 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,496,876 – 10,496,987
Length 111
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 75.38
Mean single sequence MFE -31.24
Consensus MFE -19.22
Energy contribution -21.18
Covariance contribution 1.96
Combinations/Pair 1.14
Mean z-score -3.14
Structure conservation index 0.62
SVM decision value 3.83
SVM RNA-class probability 0.999644
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10496876 111 + 20766785
GUUUUUGUUGGUACAGUGCAUACCCGAUUCGGUGAAUUGUGAAGACCGAG--GGUAUCCACUGUACCAAAGUGAUAAAUGUGCACCUAGAUUUUCAUAC-AAAAA-UAUGUUUAC
((((((((((((((((((.((((((...(((((...........))))))--))))).))))))))))..((((.((((.((....)).))))))))))-)))))-)........ ( -38.00)
>DroSec_CAF1 10237 112 + 1
GUUUUUGUUGUUACAGUGCUUACUCGAUUCGGUGAAUUGUGUAGACCGAG--GGUGUUCACUGUACCAAAGUGAUAAUUGUGCCCCCAGAUUUUCAUAC-AAAAAUUAUGUUUAC
((((((((((.(((((((..(((((...(((((...........))))))--))))..))))))).))..((((.((((.........)))).))))))-))))))......... ( -26.90)
>DroSim_CAF1 10205 112 + 1
GUUUUUGUUGGUACAGUGAUUACUCGAUUCGGUGAAUUGUAUAGACCGAG--GGUGUUUACUGUACCAAAGUGAUAAUUGUGCACCUAGAUUUUCAUAC-AAAAAUUAUGUUUAC
(((((((((((((((((((.(((((...(((((...........))))))--)))).)))))))))))..((((.((((.........)))).))))))-))))))......... ( -32.80)
>DroEre_CAF1 10430 99 + 1
GUUUUUGUUGGUACAGUGCUUACUCGGUACGGUGAAUUGUGAAGCCCAAGGGGGUGUUCACUGUACCAAAG---UAAAUCUG----------UUCAUCAAAAA---UGUGUUAAC
(((((((.(((.((((...(((((.((((((((((((......((((....))))))))))))))))..))---)))..)))----------)))).))))))---)........ ( -35.90)
>DroYak_CAF1 10550 90 + 1
GUUUUU-UUGGUACAGUGCUUACCGGCUAGGGUGAAUUG---------------UGUUCACUGUACCAAAUUUAUAAAUGUGA--UUUGAUUUUCAUGU-AAA---UCUCUU---
.....(-(((((((((((.(((((......)))))....---------------....)))))))))))).......((((((--........))))))-...---......--- ( -22.60)
>consensus
GUUUUUGUUGGUACAGUGCUUACUCGAUUCGGUGAAUUGUGAAGACCGAG__GGUGUUCACUGUACCAAAGUGAUAAAUGUGC_CCUAGAUUUUCAUAC_AAAAA_UAUGUUUAC
.......(((((((((((..((((...((((((...........))))))..))))..))))))))))).............................................. (-19.22 = -21.18 +   1.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,496,876 – 10,496,987
Length 111
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 75.38
Mean single sequence MFE -25.43
Consensus MFE -14.67
Energy contribution -15.95
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -3.45
Structure conservation index 0.58
SVM decision value 4.23
SVM RNA-class probability 0.999843
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10496876 111 - 20766785
GUAAACAUA-UUUUU-GUAUGAAAAUCUAGGUGCACAUUUAUCACUUUGGUACAGUGGAUACC--CUCGGUCUUCACAAUUCACCGAAUCGGGUAUGCACUGUACCAACAAAAAC
.........-(((((-((..........(((((.........)))))((((((((((.(((((--((((((...........)))))...)))))).))))))))))))))))). ( -37.40)
>DroSec_CAF1 10237 112 - 1
GUAAACAUAAUUUUU-GUAUGAAAAUCUGGGGGCACAAUUAUCACUUUGGUACAGUGAACACC--CUCGGUCUACACAAUUCACCGAAUCGAGUAAGCACUGUAACAACAAAAAC
..........(((((-((.((.....(..(((............)))..)(((((((......--(((((((.............).))))))....))))))).))))))))). ( -20.02)
>DroSim_CAF1 10205 112 - 1
GUAAACAUAAUUUUU-GUAUGAAAAUCUAGGUGCACAAUUAUCACUUUGGUACAGUAAACACC--CUCGGUCUAUACAAUUCACCGAAUCGAGUAAUCACUGUACCAACAAAAAC
..........(((((-((..........(((((.........)))))(((((((((.......--.(((((...........)))))...((....)))))))))))))))))). ( -24.50)
>DroEre_CAF1 10430 99 - 1
GUUAACACA---UUUUUGAUGAA----------CAGAUUUA---CUUUGGUACAGUGAACACCCCCUUGGGCUUCACAAUUCACCGUACCGAGUAAGCACUGUACCAACAAAAAC
.........---((((((.((.(----------(((.((((---(((.(((((.(((((..(((....)))........))))).))))))))))))..))))..)).)))))). ( -25.30)
>DroYak_CAF1 10550 90 - 1
---AAGAGA---UUU-ACAUGAAAAUCAAA--UCACAUUUAUAAAUUUGGUACAGUGAACA---------------CAAUUCACCCUAGCCGGUAAGCACUGUACCAA-AAAAAC
---....((---(((-......)))))...--.............((((((((((((....---------------......(((......)))...)))))))))))-)..... ( -19.92)
>consensus
GUAAACAUA_UUUUU_GUAUGAAAAUCUAGG_GCACAUUUAUCACUUUGGUACAGUGAACACC__CUCGGUCUACACAAUUCACCGAAUCGAGUAAGCACUGUACCAACAAAAAC
..............................................(((((((((((.........((((.............))))..........)))))))))))....... (-14.67 = -15.95 +   1.28)

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 10:45:53 2006