Locus 5600

Sequence ID 2R_DroMel_CAF1
Location 17,868,966 – 17,869,227
Length 261
Max. P 0.999068
window8968 window8969 window8970 window8971

overview

Window 8

Location 17,868,966 – 17,869,082
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -22.58
Consensus MFE -17.38
Energy contribution -18.18
Covariance contribution 0.80
Combinations/Pair 1.07
Mean z-score -1.61
Structure conservation index 0.77
SVM decision value 0.18
SVM RNA-class probability 0.619334
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17868966 116 + 20766785
AGAAAAUAACUUAU----UUGCAUAGUAAAACGGGCAAUUGAAUGCCUUGAGAAUCCAAACAAUCGACAAACAAAGAACCCGUCUUGCUAUUCAUUUAUGGAAGUAUCCAUAUUUUCAGC
.(((((((...((.----.((.(((((((.(((((...((((.((..(((......))).)).))))(.......)..))))).))))))).))..))((((....)))))))))))... ( -24.60)
>DroSec_CAF1 33832 116 + 1
AGAAAAUAUCUUAU----UUGCAUAGUAAAACGGGCAAUUGAAUGCCUUGAGAACCCAAACAAUCGACAAACAAAGAACCCGUUUUGCUAUUCAUUUAUGGAAGUAUCCACAUUUCCAGC
...........((.----.((.(((((((((((((...((((.((..(((......))).)).))))(.......)..))))))))))))).))..))(((((((......))))))).. ( -26.00)
>DroSim_CAF1 34183 116 + 1
AGAAAAUAUCUUAU----UUGCAUAGUAAAACGGGCAAUUGAAUGCCUUGAGAACCCAAACAAUCGACAAACAAAGAACCCGUCUUGCUAUUCAUUUAUGGAAGUAUCCACAUUUCCAGC
...........((.----.((.(((((((.(((((...((((.((..(((......))).)).))))(.......)..))))).))))))).))..))(((((((......))))))).. ( -22.50)
>DroEre_CAF1 36259 120 + 1
AGAAAACAUCUUACAUAUUUACAUAAUAAAACGGGCAAUUGAAUGCCUUGAGAGCCCAAACAAUCGACAAACAAAGAACCCGUUUUGCUAUUCAUUUAUGGAAGUAUCCACAUUUUCAGC
.(((((................(((.(((((((((...(((..((..((((..(......)..))))))..)))....))))))))).))).......((((....))))..)))))... ( -17.30)
>DroYak_CAF1 32687 116 + 1
UAGAAAUAUCUUGC----UUACUUAAUAAAAGGGGCAAUUGAAUGCCUUGAGAGGCCAAACAAUCGACAAACAAAGAACCUGUUUUGCUAUUCAUUUAUGGAAGUAUCCACAUUUUCAGC
..((((.....((.----.(((((.(((((.((((((......))))))(((.(((.(((((.((..........))...))))).))).))).)))))..)))))..))...))))... ( -22.50)
>consensus
AGAAAAUAUCUUAU____UUGCAUAGUAAAACGGGCAAUUGAAUGCCUUGAGAACCCAAACAAUCGACAAACAAAGAACCCGUUUUGCUAUUCAUUUAUGGAAGUAUCCACAUUUUCAGC
......................(((((((((((((...((((.((..(((......))).)).))))(.......)..))))))))))))).......(((((((......))))))).. (-17.38 = -18.18 +   0.80)

alignment

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secondary structure

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Window 9

Location 17,868,966 – 17,869,082
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.58
Mean single sequence MFE -29.74
Consensus MFE -28.16
Energy contribution -27.60
Covariance contribution -0.56
Combinations/Pair 1.21
Mean z-score -2.05
Structure conservation index 0.95
SVM decision value 3.35
SVM RNA-class probability 0.999068
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17868966 116 - 20766785
GCUGAAAAUAUGGAUACUUCCAUAAAUGAAUAGCAAGACGGGUUCUUUGUUUGUCGAUUGUUUGGAUUCUCAAGGCAUUCAAUUGCCCGUUUUACUAUGCAA----AUAAGUUAUUUUCU
...(((((((((((....))))))..((.((((.(((((((((...(((..((((....(........)....))))..)))..))))))))).)))).)).----........))))). ( -32.10)
>DroSec_CAF1 33832 116 - 1
GCUGGAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACGGGUUCUUUGUUUGUCGAUUGUUUGGGUUCUCAAGGCAUUCAAUUGCCCGUUUUACUAUGCAA----AUAAGAUAUUUUCU
...(((((((((((....))).....((.((((.(((((((((...(((..((((....(........)....))))..)))..))))))))).)))).)).----.....)))))))). ( -31.80)
>DroSim_CAF1 34183 116 - 1
GCUGGAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAGACGGGUUCUUUGUUUGUCGAUUGUUUGGGUUCUCAAGGCAUUCAAUUGCCCGUUUUACUAUGCAA----AUAAGAUAUUUUCU
...(((((((((((....))).....((.((((.(((((((((...(((..((((....(........)....))))..)))..))))))))).)))).)).----.....)))))))). ( -31.90)
>DroEre_CAF1 36259 120 - 1
GCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACGGGUUCUUUGUUUGUCGAUUGUUUGGGCUCUCAAGGCAUUCAAUUGCCCGUUUUAUUAUGUAAAUAUGUAAGAUGUUUUCU
...(((((((((((....)))))......((((.(((((((((...(((..((((((..((....))..))..))))..)))..))))))))).))))...............)))))). ( -29.80)
>DroYak_CAF1 32687 116 - 1
GCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACAGGUUCUUUGUUUGUCGAUUGUUUGGCCUCUCAAGGCAUUCAAUUGCCCCUUUUAUUAAGUAA----GCAAGAUAUUUCUA
(((.....((((((....))))))((((((..((.((((((.....))))))...(((((....((((....))))...)))))))....)))))).....)----)).(((....))). ( -23.10)
>consensus
GCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACGGGUUCUUUGUUUGUCGAUUGUUUGGGUUCUCAAGGCAUUCAAUUGCCCGUUUUACUAUGCAA____AUAAGAUAUUUUCU
...(((((((((((....)))))...((.((((.(((((((((...(((..((((....(........)....))))..)))..))))))))).)))).))............)))))). (-28.16 = -27.60 +  -0.56)

alignment

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secondary structure

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Window 0

Location 17,869,042 – 17,869,154
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.41
Mean single sequence MFE -27.75
Consensus MFE -25.47
Energy contribution -24.95
Covariance contribution -0.52
Combinations/Pair 1.13
Mean z-score -1.80
Structure conservation index 0.92
SVM decision value 2.27
SVM RNA-class probability 0.991563
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17869042 112 - 20766785
AGAGCUUUCAGCUGGAAUGUUUGCUGGCAAGUG--------UACGUAAAUUAAAACAAGAGCCGCAAUCAAGUGUUCAUGGCUGAAAAUAUGGAUACUUCCAUAAAUGAAUAGCAAGACG
...((((((((((((((..((((.((((...((--------(............)))...))))....))))..))).))))))))).((((((....))))))........))...... ( -30.30)
>DroSec_CAF1 33908 112 - 1
AGAGCUUUCAGCCGGAAUGUUUUCUCGCAAGUG--------UACGUAAAUUAAAACAAGAGCUGCAAUCAAGUGUUCAUGGCUGGAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACG
...((((((((((((((..(((....(((.((.--------...((........))....)))))....)))..))).))))))))).((((((....))))))........))...... ( -28.50)
>DroSim_CAF1 34259 112 - 1
AGAGCUUUCAGCUGGAAUGUUUGCUCGCAAGUG--------UACGUAAAUUAAAACAAGAGCCGCAAUCAAGUGUUCAUGGCUGGAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAGACG
...((((((((((((((..((((...((..((.--------...((........))....)).))...))))..))).))))))))).((((((....))))))........))...... ( -26.00)
>DroEre_CAF1 36339 112 - 1
AGAGCUUUCAGCUGGAAUGUUUGUUCGAAAGUG--------UACGCAAAUUAAAACAAGAGCCGCAAUCAAGUGUUCAUGGCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACG
...((((((((((((((..((((..(....)((--------(..((..............)).)))..))))..))).))))))))).((((((....))))))........))...... ( -26.24)
>DroYak_CAF1 32763 120 - 1
AGAGCUUGCAGCCGAAAUGUUUGUUCGGAAGUACACAUACAUACGUAAAUUAAAACAAGAGCCGCAAUCAAGUGUUCAUGGCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACA
...(((..((((((..((((.(((.(....)...))).))))................((((.((......)))))).))))))....((((((....)))))).......)))...... ( -27.70)
>consensus
AGAGCUUUCAGCUGGAAUGUUUGCUCGCAAGUG________UACGUAAAUUAAAACAAGAGCCGCAAUCAAGUGUUCAUGGCUGAAAAUGUGGAUACUUCCAUAAAUGAAUAGCAAAACG
...(((((((((((...(((((........(((........)))........))))).((((.((......)))))).))))))))).((((((....))))))........))...... (-25.47 = -24.95 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,869,121 – 17,869,227
Length 106
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 89.43
Mean single sequence MFE -21.56
Consensus MFE -16.62
Energy contribution -16.94
Covariance contribution 0.32
Combinations/Pair 1.21
Mean z-score -1.62
Structure conservation index 0.77
SVM decision value 0.26
SVM RNA-class probability 0.655625
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17869121 106 + 20766785
-------CACUUGCCAGCAAACAUUCCAGCUGAAAGCUCUUUAAGCUGGAAAAACAAACAAAAAUCAGGCGGAUAAACGGACUUUAAAUUUUUUGAAUACGCAGCAAGGCAAA
-------..(((((..((.....((((((((.(((....))).)))))))).......((((((..((.((......))..))......)))))).....)).)))))..... ( -24.60)
>DroSec_CAF1 33987 106 + 1
-------CACUUGCGAGAAAACAUUCCGGCUGAAAGCUCUUUAAGCUGGAAAAACAAACAACAAUCAGACGGAUAAACGGACUUUAAAUUUUUUGAAUACGCAGCAUGGCAAA
-------...(((((........((((((((.(((....))).))))))))...((((........((.((......))..))........))))....)))))......... ( -19.09)
>DroSim_CAF1 34338 106 + 1
-------CACUUGCGAGCAAACAUUCCAGCUGAAAGCUCUUUAAGCUGGAAAAACAAACAAAAAUCAGACGGAUAAACGGACUUUAAAUUUUUUGAAUACGCAGCAUGGCAAA
-------...((((.(((.....((((((((.(((....))).)))))))).......((((((..((.((......))..))......))))))........)).).)))). ( -22.20)
>DroEre_CAF1 36418 106 + 1
-------CACUUUCGAACAAACAUUCCAGCUGAAAGCUCUUUAAGCUGGGAAGACAAACAAAAAUCAGACGGUAAAACGGACUUUAAAUUUUUUGAAUACGCAGAAAGGCAAA
-------..(((((.........((((((((.(((....))).)))))))).......((((((......(((.......)))......))))))........)))))..... ( -20.40)
>DroYak_CAF1 32843 113 + 1
GUAUGUGUACUUCCGAACAAACAUUUCGGCUGCAAGCUCUUUAAGCUGGAAAAACAAACAAAAAUCAGAGGAAUAAACGGACCUUAAAUUUUUUGAAUACGCAGCAGGGCAAA
.....((..((..((((.......))))(((((.((((.....))))...........((((((...((((..........))))....)))))).....)))))))..)).. ( -21.50)
>consensus
_______CACUUGCGAGCAAACAUUCCAGCUGAAAGCUCUUUAAGCUGGAAAAACAAACAAAAAUCAGACGGAUAAACGGACUUUAAAUUUUUUGAAUACGCAGCAAGGCAAA
.........(((((.........((((((((.(((....))).)))))))).......((((((.....((......))..........))))))........)))))..... (-16.62 = -16.94 +   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 11:49:37 2006