Locus 8034

Sequence ID 3R_DroMel_CAF1
Location 21,586,687 – 21,586,825
Length 138
Max. P 0.992917
window12933 window12934 window12935

overview

Window 3

Location 21,586,687 – 21,586,799
Length 112
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 83.56
Mean single sequence MFE -24.73
Consensus MFE -12.04
Energy contribution -11.92
Covariance contribution -0.12
Combinations/Pair 1.17
Mean z-score -2.73
Structure conservation index 0.49
SVM decision value 0.40
SVM RNA-class probability 0.722025
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21586687 112 + 27905053
UUAAUUUAAAA-AUACGUUUUGUUAUUUUAUACUCAA-GUUGGGCAAAUAUCCCCUGAGAAAGAAAAAGAAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGCGAACCAACAA
........(((-(((........))))))........-((((((((((((((.(((..............))).(((((((....)))))))...)))))))))...))))).. ( -27.34)
>DroSec_CAF1 75358 103 + 1
UUAAUUUAAAA-AUACUUUUUGUUAUUUUAUACUCAA-GGUGGGCAAAUAUCCCCCGAGAAAGCAAAAGAAGGACUCAAGUGCUAACUUGAGAAUG---------AACCAACAA
...........-.......(((((..(((((.(((((-((.(((........)))).....((((...((.....))...))))..)))))).)))---------))..))))) ( -20.00)
>DroSim_CAF1 70617 103 + 1
UUAAUUUAAAA-AUACUUUUUGUUAUUUUAUACUCAA-GGUGGGCAAAUAUCCCCCGAGAAAGCAAAAGAAGGAUUCAAGUGCUAACUUGAGAAUG---------AACCAACAA
...........-.......(((((..(((((.(((((-(...((((...((((..(............)..)))).....))))..)))))).)))---------))..))))) ( -21.30)
>DroEre_CAF1 65828 112 + 1
UUAACAUAUAA-AUAAUUUUUGUUAUUUUGUACUCAA-AGUGGGCAAAACUGCACAGAGAAGGCAAAAUGAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGCAAAUCAAAUA
..(((((....-.......((.(((((((((.(((..-.(..(......)..)...)))...))))))))).))(((((((....)))))))....)))))............. ( -25.50)
>DroYak_CAF1 69897 114 + 1
UUAAUUUAUAAAAUACUUUUUGUUAUUUUGUACUCAAAAGUGGACAGAUGUCCACAGAGAAAGCAAAAUAAGAACUCAAGUGCUAACUUGAGAAUGAUGUUUGCAAAUCAAAGA
...................((.(((((((((.(((....((((((....)))))).)))...))))))))).))(((((((....)))))))..((((........)))).... ( -29.50)
>consensus
UUAAUUUAAAA_AUACUUUUUGUUAUUUUAUACUCAA_GGUGGGCAAAUAUCCCCAGAGAAAGCAAAAGAAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGC_AACCAACAA
.................(((((((.((((..(((....)))(((......)))...)))).)))))))......(((((((....)))))))...................... (-12.04 = -11.92 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,586,720 – 21,586,825
Length 105
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 78.12
Mean single sequence MFE -25.02
Consensus MFE -13.84
Energy contribution -13.08
Covariance contribution -0.76
Combinations/Pair 1.33
Mean z-score -2.70
Structure conservation index 0.55
SVM decision value 2.36
SVM RNA-class probability 0.992917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21586720 105 + 27905053
CAA-GUUGGGCAAAUAUCCCCUGAGAAAGAAAAAGAAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGCGAACCAACAAAGGUUAUAUAGGG------------UAAUCGCACAAAG
...-((((((((((((((.(((..............))).(((((((....)))))))...)))))))))...)))))...((((((.....)------------)))))........ ( -30.54)
>DroSec_CAF1 75391 96 + 1
CAA-GGUGGGCAAAUAUCCCCCGAGAAAGCAAAAGAAGGACUCAAGUGCUAACUUGAGAAUG---------AACCAACAAAGGUUAUAUAGGG------------UAAUCGCACAAAG
...-((.(((.......)))))......((..........(((((((....)))))))....---------..........((((((.....)------------)))))))...... ( -21.20)
>DroSim_CAF1 70650 96 + 1
CAA-GGUGGGCAAAUAUCCCCCGAGAAAGCAAAAGAAGGAUUCAAGUGCUAACUUGAGAAUG---------AACCAACAAAGGUUAUAUAGGG------------UAAUCGCACAAAG
...-((.(((.......)))))......((..........(((((((....)))))))....---------..........((((((.....)------------)))))))...... ( -18.70)
>DroEre_CAF1 65861 117 + 1
CAA-AGUGGGCAAAACUGCACAGAGAAGGCAAAAUGAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGCAAAUCAAAUAAGGUUAUAUAGGGUUUUCAGACAGAUAAUUGCACAAAA
...-.(..(......)..).........((((........(((((((....))))))).....((((((.(((((..(((......)))..))))).)))))).....))))...... ( -25.40)
>DroYak_CAF1 69931 118 + 1
CAAAAGUGGACAGAUGUCCACAGAGAAAGCAAAAUAAGAACUCAAGUGCUAACUUGAGAAUGAUGUUUGCAAAUCAAAGAAGAUUAUAUAGGUGUUUUAAAAAGUUAAUUGCACAAAG
.....((((((....)))))).......(((((.......(((((((....))))))).......))))).((((......))))......((((.((((....))))..)))).... ( -29.24)
>consensus
CAA_GGUGGGCAAAUAUCCCCAGAGAAAGCAAAAGAAGGACUCAAGUGCUAACUUGAGAAUGAUGUUUGC_AACCAACAAAGGUUAUAUAGGG____________UAAUCGCACAAAG
.....(((.(..............................(((((((....))))))).............((((......))))........................).))).... (-13.84 = -13.08 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,586,720 – 21,586,825
Length 105
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 78.12
Mean single sequence MFE -20.42
Consensus MFE -11.26
Energy contribution -11.42
Covariance contribution 0.16
Combinations/Pair 1.26
Mean z-score -1.79
Structure conservation index 0.55
SVM decision value 0.11
SVM RNA-class probability 0.588077
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21586720 105 - 27905053
CUUUGUGCGAUUA------------CCCUAUAUAACCUUUGUUGGUUCGCAAACAUCAUUCUCAAGUUAGCACUUGAGUCCUUCUUUUUCUUUCUCAGGGGAUAUUUGCCCAAC-UUG
..(((.((((.((------------((((....((((......)))).............(((((((....)))))))...................)))).)).)))).))).-... ( -21.70)
>DroSec_CAF1 75391 96 - 1
CUUUGUGCGAUUA------------CCCUAUAUAACCUUUGUUGGUU---------CAUUCUCAAGUUAGCACUUGAGUCCUUCUUUUGCUUUCUCGGGGGAUAUUUGCCCACC-UUG
...((.((((.((------------((((....((((......))))---------....(((((((....)))))))...................)))).)).)))).))..-... ( -20.90)
>DroSim_CAF1 70650 96 - 1
CUUUGUGCGAUUA------------CCCUAUAUAACCUUUGUUGGUU---------CAUUCUCAAGUUAGCACUUGAAUCCUUCUUUUGCUUUCUCGGGGGAUAUUUGCCCACC-UUG
...((.((((.((------------((((....((((......))))---------......(.((..((((...((.....))...))))..)).))))).)).)))).))..-... ( -18.70)
>DroEre_CAF1 65861 117 - 1
UUUUGUGCAAUUAUCUGUCUGAAAACCCUAUAUAACCUUAUUUGAUUUGCAAACAUCAUUCUCAAGUUAGCACUUGAGUCCUCAUUUUGCCUUCUCUGUGCAGUUUUGCCCACU-UUG
...((.((((....((((..((.......(((......)))..((...(((((.......(((((((....))))))).......)))))..))))...))))..)))).))..-... ( -18.44)
>DroYak_CAF1 69931 118 - 1
CUUUGUGCAAUUAACUUUUUAAAACACCUAUAUAAUCUUCUUUGAUUUGCAAACAUCAUUCUCAAGUUAGCACUUGAGUUCUUAUUUUGCUUUCUCUGUGGACAUCUGUCCACUUUUG
.................................((((......)))).(((((.......(((((((....))))))).......))))).......((((((....))))))..... ( -22.34)
>consensus
CUUUGUGCGAUUA____________CCCUAUAUAACCUUUGUUGGUU_GCAAACAUCAUUCUCAAGUUAGCACUUGAGUCCUUCUUUUGCUUUCUCGGGGGAUAUUUGCCCACC_UUG
...((.((((.......................((((......)))).............(((((((....)))))))((((((............))))))...)))).))...... (-11.26 = -11.42 +   0.16)

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 13:00:57 2006