Locus 3873

Sequence ID 3R_DroMel_CAF1
Location 10,532,330 – 10,532,483
Length 153
Max. P 0.999547
window6203 window6204 window6205 window6206

overview

Window 3

Location 10,532,330 – 10,532,446
Length 116
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 88.82
Mean single sequence MFE -37.28
Consensus MFE -25.34
Energy contribution -25.90
Covariance contribution 0.56
Combinations/Pair 1.15
Mean z-score -2.84
Structure conservation index 0.68
SVM decision value 0.72
SVM RNA-class probability 0.833122
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10532330 116 + 27905053
---AUGGCAUCUUACAUGUGGUGCCUAUGCCUUUGAGAAGAACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
---..((((((........))))))(((((....(((((((.....)))))))((((((....))).))).....((.((((((((....).))))))).)).....)))))....... ( -41.20)
>DroSec_CAF1 7593 108 + 1
---AAGGCAUCUUACAUGUUG--------CGUUUGAGAAGAACCUAUUUUCUUGGCCGUUUCUGUGCGCUCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
---...(((...((((.(..(--------((.(..((((((.....))))))..).)))..))))).........((.((((((((....).))))))).))....))).......... ( -31.80)
>DroSim_CAF1 6132 116 + 1
---AAGGCAUCUUACAUGAUGUGCUUAUGCCUUUGAGAAGAACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
---...(((((......)))))..((((((....(((((((.....)))))))((((((....))).))).....((.((((((((....).))))))).)).....))))))...... ( -38.10)
>DroEre_CAF1 7301 114 + 1
----AGGCAUCUAACAUGU-GUGCUUGUGCCUUUGAGAAGAACCUAUUUUCGUGGCCGCUCCUGUGCGCCCACGAUCGUGGCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
----((((((...((....-))....)))))).((...(((..((((..((((((.(((......))).))))))..))))(((((....).))))........))).))......... ( -36.40)
>DroYak_CAF1 6409 119 + 1
UUAAAGGAAUCAAACAUUUAGUGUUUGUGCCUUGGAAAAGAACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGGCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
...((((...(((((((...)))))))..))))..............(((((((.((((((.((.(((.((((....)))).)))))...)))))).)))))))............... ( -38.90)
>consensus
___AAGGCAUCUUACAUGUUGUGCUUAUGCCUUUGAGAAGAACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAA
.........................(((((....(((((.......))))).(((.(((......))).)))...((.((((((((....).))))))).)).....)))))....... (-25.34 = -25.90 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,532,330 – 10,532,446
Length 116
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 88.82
Mean single sequence MFE -37.38
Consensus MFE -26.22
Energy contribution -27.06
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.70
SVM decision value 0.75
SVM RNA-class probability 0.842128
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10532330 116 - 27905053
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUUCUUCUCAAAGGCAUAGGCACCACAUGUAAGAUGCCAU---
.......(((((...(((((((.((((((((...(((..(((....)))..)))..)))))))).))))))).......(((....))))))))((((.(........).))))..--- ( -40.40)
>DroSec_CAF1 7593 108 - 1
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGAGCGCACAGAAACGGCCAAGAAAAUAGGUUCUUCUCAAACG--------CAACAUGUAAGAUGCCUU---
..........(((....((.((((((((.....)))))))).)).(((..(((...((((..((((.........)))).))))....))--------).))).......)))...--- ( -24.60)
>DroSim_CAF1 6132 116 - 1
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUUCUUCUCAAAGGCAUAAGCACAUCAUGUAAGAUGCCUU---
...............(((((((.((((((((...(((..(((....)))..)))..)))))))).)))))))..............(((((((..(((.....)))...)))))))--- ( -39.60)
>DroEre_CAF1 7301 114 - 1
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGCCACGAUCGUGGGCGCACAGGAGCGGCCACGAAAAUAGGUUCUUCUCAAAGGCACAAGCAC-ACAUGUUAGAUGCCU----
...............((((.((.((((((((...(((.((((....)))).)))..)))))))).)).))))...............((((((.((((.-...)))).).)))))---- ( -39.40)
>DroYak_CAF1 6409 119 - 1
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGCCACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUUCUUUUCCAAGGCACAAACACUAAAUGUUUGAUUCCUUUAA
.........(((...(((((((.((((((((...(((.((((....)))).)))..)))))))).)))))))...((.......))...)))((((((.....)))))).......... ( -42.90)
>consensus
UUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUUCUUCUCAAAGGCACAAGCACAACAUGUAAGAUGCCUU___
...............(((((((.((((((((...(((..(((....)))..)))..)))))))).)))))))...(((...(((.......................))).)))..... (-26.22 = -27.06 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,532,367 – 10,532,483
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 97.41
Mean single sequence MFE -35.90
Consensus MFE -32.40
Energy contribution -32.48
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.94
Structure conservation index 0.90
SVM decision value 3.71
SVM RNA-class probability 0.999547
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10532367 116 + 27905053
AACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAUUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
..............(((((.((((((((.......((.((((((((....).))))))).))....))))))...(((((.((.(((....))).))))))).)).)))))..... ( -35.20)
>DroSec_CAF1 7622 116 + 1
AACCUAUUUUCUUGGCCGUUUCUGUGCGCUCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAUUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
................((((.((((((........((.((((((((....).))))))).))......((((((......(((.(((....))).))))))))))))))).)))). ( -32.80)
>DroSim_CAF1 6169 116 + 1
AACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAAUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
..............(((((.((((((((.......((.((((((((....).))))))).))....)))))).....((((((.(((....))).))))))..)).)))))..... ( -37.90)
>DroEre_CAF1 7336 116 + 1
AACCUAUUUUCGUGGCCGCUCCUGUGCGCCCACGAUCGUGGCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAUUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
..........(((.(((((.(((((((..((((....))))(((((....).))))...........)))))...(((((.((.(((....))).))))))).)).))))).))). ( -39.00)
>DroYak_CAF1 6449 116 + 1
AACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGGCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAUUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
.......(((((((.((((((.((.(((.((((....)))).)))))...)))))).)))))))....((((((......(((.(((....))).)))))))))..(((....))) ( -34.60)
>consensus
AACCUAUUUUCUUGGCCGCUCCUGUGCGCCCACAAUCGUGUCCGCCGAAAGAGCGGACAAGAAAUCUGCAUAAAUUAAAUUAUAUUGUAAACAAAAUAUUUAUGGCGCGGCGACGU
..............(((((.((((((((.......((.((((((((....).))))))).))....))))))...((((.(((.(((....))).))))))).)).)))))..... (-32.40 = -32.48 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,532,367 – 10,532,483
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 97.41
Mean single sequence MFE -37.20
Consensus MFE -32.20
Energy contribution -33.00
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.73
Structure conservation index 0.87
SVM decision value 2.78
SVM RNA-class probability 0.996992
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10532367 116 - 27905053
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAAUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUU
.....(((..((.(((((((..((((.......))))..).))))))))...(((((((.((((((((...(((..(((....)))..)))..)))))))).)))))))...))). ( -37.50)
>DroSec_CAF1 7622 116 - 1
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAAUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGAGCGCACAGAAACGGCCAAGAAAAUAGGUU
.(((..(.(((((((((.(((.(((....))).)))..................((.((((((((.....)))))))).))))))).))))...)..)))(((.........))). ( -29.20)
>DroSim_CAF1 6169 116 - 1
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAUUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUU
.....((((((....((((((.(((....))).)))))).......)))...(((((((.((((((((...(((..(((....)))..)))..)))))))).)))))))...))). ( -38.50)
>DroEre_CAF1 7336 116 - 1
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAAUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGCCACGAUCGUGGGCGCACAGGAGCGGCCACGAAAAUAGGUU
.....(((..((.(((((((..((((.......))))..).))))))))...((((.((.((((((((...(((.((((....)))).)))..)))))))).)).))))...))). ( -38.80)
>DroYak_CAF1 6449 116 - 1
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAAUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGCCACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUU
.....(((..((.(((((((..((((.......))))..).))))))))...(((((((.((((((((...(((.((((....)))).)))..)))))))).)))))))...))). ( -42.00)
>consensus
ACGUCGCCGCGCCAUAAAUAUUUUGUUUACAAUAUAAUUUAAUUUAUGCAGAUUUCUUGUCCGCUCUUUCGGCGGACACGAUUGUGGGCGCACAGGAGCGGCCAAGAAAAUAGGUU
.....(((..((.((((((...((((.......))))....))))))))...(((((((.((((((((...(((..(((....)))..)))..)))))))).)))))))...))). (-32.20 = -33.00 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:13 2006