Locus 10216

Sequence ID 3R_DroMel_CAF1
Location 27,401,045 – 27,401,193
Length 148
Max. P 0.850763
window16268 window16269 window16270

overview

Window 8

Location 27,401,045 – 27,401,165
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -40.89
Consensus MFE -22.58
Energy contribution -23.37
Covariance contribution 0.78
Combinations/Pair 1.25
Mean z-score -2.16
Structure conservation index 0.55
SVM decision value 0.79
SVM RNA-class probability 0.850763
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27401045 120 + 27905053
AAUCUGACGGUGCGCAGCACGGACCAGGACGUGGCGGAGCUGAUAACGGCGGCCAUUGGAUAAGACAGCGAGCCAUGCAGGAACCUCCUUUGGUUCCUGCGUGCUGUGAACGUAAUCUGA
......(((...((((((((..........(((((((.((((....))))..)).(((.......)))...)))))(((((((((......)))))))))))))))))..)))....... ( -51.10)
>DroVir_CAF1 3122 120 + 1
AAUCUAACCGUGCGUAGCACAGAUCAGGAUGUGGCCGAGCUCAUAACGGCAGCCAUCGGAUAAACCUACGCGCCAUGCAGAGACUUAAUAGGAUCUCUGCGUGCUCUGCAAAUACUAUGA
.........((((((((.....(((..((((..((((.........))))...)))).)))....))))))))((((((((((((.....)).))))))))))................. ( -40.40)
>DroGri_CAF1 3378 120 + 1
AAUCUGACAGUGCGUAGCACGGAUCAGGAUGUGGCCGAGCUCAUAACGGCAGCCAUCGGAUAAGAUUGCGAGCCAUGCAGAGAUCUCGUUGGGUUUCUGCGUGCCAUGAAUAUGAUAUGA
..(((((..((((...))))...)))))..(((((............(((.((.(((......))).))..)))((((((((((((....)))))))))))))))))............. ( -40.50)
>DroWil_CAF1 2823 120 + 1
AAUCUAACUGUGCGAAGCACAGAUCAAGAUGUAGCAGAGGUUAUAACGGCGGCCAUUGGAUAAGACAGCGAGCCAUGCAGAAAUCUUGUUGGUUUUCUGCGUGCAAUUAACAAAAUAUAA
.......((((((...)))))).....(.((((((....)))))).).((((((.(((.......))).).)))(((((((((.((....)).)))))))))))................ ( -31.10)
>DroMoj_CAF1 3257 120 + 1
AAUUUAACCGUGCGAAGCACAGAUCAGGAUGUGGCCGAGCUAAUAACGGCAGCGAUCGGAUAAAAUUGCGCACCAUGCAGAGACCUAAUCGUACAGCUGCGUACUCUGCAUAUAUUAUGA
.........(((((........(((..(((((.((((.........)))).)).))).))).......))))).((((((((.......((((....))))..))))))))......... ( -31.06)
>DroAna_CAF1 3210 120 + 1
AACCUGACCGUGCGCAGCACAGAUCAGGAUGUGGCGGAGCUAAUAACGGCGGCCAUCGGAUAAGACAGCGCGCCAUGCAGGAAUCUGAUAUGGUUCCUGCGUGCUGCCAACAUAAUCUGA
..((((((.((((...)))).).)))))(((((((((.((.......((((((..((......))..)).))))..(((((((((......))))))))))).))))).))))....... ( -51.20)
>consensus
AAUCUAACCGUGCGAAGCACAGAUCAGGAUGUGGCCGAGCUAAUAACGGCAGCCAUCGGAUAAGACAGCGAGCCAUGCAGAAACCUAAUUGGGUUUCUGCGUGCUAUGAACAUAAUAUGA
.((((((..((((...))))...........((((...(((......))).))))))))))............((((((((((.(......).))))))))))................. (-22.58 = -23.37 +   0.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 27,401,045 – 27,401,165
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.78
Mean single sequence MFE -36.94
Consensus MFE -24.05
Energy contribution -23.80
Covariance contribution -0.25
Combinations/Pair 1.39
Mean z-score -1.59
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.772620
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27401045 120 - 27905053
UCAGAUUACGUUCACAGCACGCAGGAACCAAAGGAGGUUCCUGCAUGGCUCGCUGUCUUAUCCAAUGGCCGCCGUUAUCAGCUCCGCCACGUCCUGGUCCGUGCUGCGCACCGUCAGAUU
...(((...((.(.(((((((((((((((......)))))))))(((((..(((((........))))).)))))..........((((.....))))..)))))).).)).)))..... ( -41.60)
>DroVir_CAF1 3122 120 - 1
UCAUAGUAUUUGCAGAGCACGCAGAGAUCCUAUUAAGUCUCUGCAUGGCGCGUAGGUUUAUCCGAUGGCUGCCGUUAUGAGCUCGGCCACAUCCUGAUCUGUGCUACGCACGGUUAGAUU
...........((.((((..((((((((........))))))))((((((.((.((.....))....)))))))).....)))).))......((((.((((((...))))))))))... ( -40.20)
>DroGri_CAF1 3378 120 - 1
UCAUAUCAUAUUCAUGGCACGCAGAAACCCAACGAGAUCUCUGCAUGGCUCGCAAUCUUAUCCGAUGGCUGCCGUUAUGAGCUCGGCCACAUCCUGAUCCGUGCUACGCACUGUCAGAUU
..........((((((((..(((((..............)))))..(((..((.(((......))).)).)))))))))))............(((((..((((...)))).)))))... ( -30.44)
>DroWil_CAF1 2823 120 - 1
UUAUAUUUUGUUAAUUGCACGCAGAAAACCAACAAGAUUUCUGCAUGGCUCGCUGUCUUAUCCAAUGGCCGCCGUUAUAACCUCUGCUACAUCUUGAUCUGUGCUUCGCACAGUUAGAUU
................(((.(((((((.(......).)))))))(((((..(((((........))))).))))).........)))...((((....((((((...))))))..)))). ( -28.60)
>DroMoj_CAF1 3257 120 - 1
UCAUAAUAUAUGCAGAGUACGCAGCUGUACGAUUAGGUCUCUGCAUGGUGCGCAAUUUUAUCCGAUCGCUGCCGUUAUUAGCUCGGCCACAUCCUGAUCUGUGCUUCGCACGGUUAAAUU
...((((.(((((((((((((....)))))(((...)))))))))))(((((.........((((..((((.......)))))))).((((........))))...))))).)))).... ( -29.10)
>DroAna_CAF1 3210 120 - 1
UCAGAUUAUGUUGGCAGCACGCAGGAACCAUAUCAGAUUCCUGCAUGGCGCGCUGUCUUAUCCGAUGGCCGCCGUUAUUAGCUCCGCCACAUCCUGAUCUGUGCUGCGCACGGUCAGGUU
.......((((.((((((..(((((((.(......).)))))))((((((.((((((......)))))))))))).....)))..)))))))(((((.((((((...))))))))))).. ( -51.70)
>consensus
UCAUAUUAUGUUCACAGCACGCAGAAACCCAAUGAGAUCUCUGCAUGGCGCGCAGUCUUAUCCGAUGGCCGCCGUUAUGAGCUCGGCCACAUCCUGAUCUGUGCUACGCACGGUCAGAUU
................((..(((((((..........)))))))(((((..((..((......))..)).)))))..........))......((((.((((((...))))))))))... (-24.05 = -23.80 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 27,401,085 – 27,401,193
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 81.12
Mean single sequence MFE -28.93
Consensus MFE -24.65
Energy contribution -24.48
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -1.67
Structure conservation index 0.85
SVM decision value 0.71
SVM RNA-class probability 0.829189
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27401085 108 + 27905053
UGAUAACGGCGGCCAUUGGAUAAGACAGCGAGCCAUGCAGGAACCUCCUUUGGUUCCUGCGUGCUGUGAACGUAAUCUGAACUCCCUACGAAACUACGAAACAGAAAG
.....(((((((((.(((.......))).).)))(((((((((((......))))))))))))))))...((((............)))).................. ( -33.90)
>DroPse_CAF1 3227 103 + 1
UAAUAACAGCGGCCAUCGGAUAAGACAGCGAGCCAUGCAGGAAUCUCGUCUGGUUUCUGCGUGCCGUCAAUAUAAUCUAAACA-ACACA---ACUAU-AAAGAGAAAA
........(((((....((....(....)...))(((((((((((......))))))))))))))))................-.....---.....-.......... ( -22.30)
>DroEre_CAF1 3278 102 + 1
UCAUAACGGCGGCCAUCGGAUAAGACAGCGAGCCAUGCAGGAACCUCAUUUGGUUUUUGCGUGCUGUCAACGUAAUCUGAACUGC------AACUGCGAAACAGAAAG
........((((...((((((..((((((.....(((((((((((......)))))))))))))))))......)))))).))))------..(((.....))).... ( -32.30)
>DroYak_CAF1 2840 96 + 1
UCAUAACGGCGGCCAUCGGAUAAGACAGCGAGCCAUGCAGGAACCUCGUUUGGUUUUUGCGUGCUGUCAACGUAAUCUGAAC------------UACGAAACAGAAAG
.......(((.((..((......))..))..)))(((((((((((......))))))))))).((((...((((........------------))))..)))).... ( -28.50)
>DroAna_CAF1 3250 105 + 1
UAAUAACGGCGGCCAUCGGAUAAGACAGCGCGCCAUGCAGGAAUCUGAUAUGGUUCCUGCGUGCUGCCAACAUAAUCUGAGCAUCCACUGAA---ACGAAACAGAGAG
......(((.((...((((((......(.(((.((((((((((((......)))))))))))).))))......))))))....)).)))..---............. ( -34.30)
>DroPer_CAF1 2566 107 + 1
UAAUAACAGCGGCCAUCGGAUAAGACAGCGAGCCAUGCAGGAAUCUCGUCUGGUUUCUGCGUGCCGUCAAUAUAAUCUAAACAAACACAAAUACUAU-AAAGAGAAAN
........(((((....((....(....)...))(((((((((((......))))))))))))))))..............................-.......... ( -22.30)
>consensus
UAAUAACGGCGGCCAUCGGAUAAGACAGCGAGCCAUGCAGGAACCUCGUUUGGUUUCUGCGUGCUGUCAACAUAAUCUGAACA_CCAC___AACUACGAAACAGAAAG
.....((((((((..(((..........))))))(((((((((((......))))))))))))))))......................................... (-24.65 = -24.48 +  -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 13:51:39 2006