Locus 6196

Sequence ID 3R_DroMel_CAF1
Location 16,190,166 – 16,190,326
Length 160
Max. P 0.999241
window10096 window10097 window10098

overview

Window 6

Location 16,190,166 – 16,190,286
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.67
Mean single sequence MFE -33.76
Consensus MFE -31.18
Energy contribution -31.78
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.92
SVM decision value 0.64
SVM RNA-class probability 0.809988
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190166 120 + 27905053
GGCUCAGCGGUAAUCCCACUUACAUCAAGAUGAAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAACAUAGAAUAGAGAAUAGAGUGCUUGGCGCAUUGC
...(((((((((.((...(((.....)))..)).)))))))))(((((((..(((.(((....(....)(((....))).....................))).)))..))))))).... ( -32.80)
>DroSec_CAF1 19365 120 + 1
GGCUCAGCGGUAAUCCCACUUACAUCAAGAUGGAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAACAUAGAAUAGAGAAUAGAGUGCUUGGCGCAUUGC
...(((((((((.(((..(((.....)))..))))))))))))(((((((..(((.(((....(....)(((....))).....................))).)))..))))))).... ( -35.40)
>DroSim_CAF1 12928 120 + 1
GGCUCAGCGGUAAUCCCACUUACAUCAAGAUGGAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAACAUAGAAUAGAGAAUAGAGUGCUUGGCGCAUUGC
...(((((((((.(((..(((.....)))..))))))))))))(((((((..(((.(((....(....)(((....))).....................))).)))..))))))).... ( -35.40)
>DroEre_CAF1 18725 120 + 1
GGCUCAGCCGUAAUCCCACUUACAUCAAGAUGGAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAACAUAGAAUAGAGAACAGGGCGCUUGGCGCAUUGC
...(((((.(((.(((..(((.....)))..)))))).)))))(((((((....((((.....(....)(((....)))........................))))..))))))).... ( -29.50)
>DroYak_CAF1 20065 120 + 1
GGCUCAGCCGUAAUCCCACUUACAUCAAGAUGGAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAGCAUAGAAUAGAGAAUAGAGCGCUUGGCGCAUUGC
...(((((.(((.(((..(((.....)))..)))))).)))))((((((.((((((((((.(((((.......)))))....))))))))))...(((.........))))))))).... ( -35.70)
>consensus
GGCUCAGCGGUAAUCCCACUUACAUCAAGAUGGAUGCCGCUGAUGCGCCAUUUAUGCUGAAAUCGAAAGGAUAUCGAUCACAUUAACAUAGAAUAGAGAAUAGAGUGCUUGGCGCAUUGC
...(((((((((.(((..(((.....)))..))))))))))))((((((.((((((.(((.(((((.......)))))....))).))))))...(((.........))))))))).... (-31.18 = -31.78 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,190,166 – 16,190,286
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.67
Mean single sequence MFE -36.10
Consensus MFE -35.18
Energy contribution -35.26
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -2.17
Structure conservation index 0.97
SVM decision value 3.46
SVM RNA-class probability 0.999241
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190166 120 - 27905053
GCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUUCAUCUUGAUGUAAGUGGGAUUACCGCUGAGCC
((..(((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))(((((((...((..((((...))))...))...))))))))). ( -35.10)
>DroSec_CAF1 19365 120 - 1
GCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUCCAUCUUGAUGUAAGUGGGAUUACCGCUGAGCC
((..(((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))(((((((.((((..((((...))))..))))..))))))))). ( -37.80)
>DroSim_CAF1 12928 120 - 1
GCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUCCAUCUUGAUGUAAGUGGGAUUACCGCUGAGCC
((..(((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))(((((((.((((..((((...))))..))))..))))))))). ( -37.80)
>DroEre_CAF1 18725 120 - 1
GCAAUGCGCCAAGCGCCCUGUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUCCAUCUUGAUGUAAGUGGGAUUACGGCUGAGCC
((..((((((((((.....)))........(((((...((.((((((.......)))))).)))))))..)))))))(((((.(.((((..((((...))))..))))..).))))))). ( -34.50)
>DroYak_CAF1 20065 120 - 1
GCAAUGCGCCAAGCGCUCUAUUCUCUAUUCUAUGCUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUCCAUCUUGAUGUAAGUGGGAUUACGGCUGAGCC
((..(((((((((....))...........((((((.....((((((.......))))))..))))))..)))))))(((((.(.((((..((((...))))..))))..).))))))). ( -35.30)
>consensus
GCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCAGCGGCAUCCAUCUUGAUGUAAGUGGGAUUACCGCUGAGCC
((..(((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))(((((((.((((..((((...))))..))))..))))))))). (-35.18 = -35.26 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,190,206 – 16,190,326
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.50
Mean single sequence MFE -23.06
Consensus MFE -22.98
Energy contribution -22.82
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.42
Structure conservation index 1.00
SVM decision value 1.08
SVM RNA-class probability 0.911684
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190206 120 - 27905053
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))((((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))).. ( -22.50)
>DroSec_CAF1 19405 120 - 1
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))((((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))).. ( -22.50)
>DroSim_CAF1 12968 120 - 1
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))((((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))).. ( -22.50)
>DroEre_CAF1 18765 120 - 1
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCGCCCUGUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))(((((((((((.....)))........(((((...((.((((((.......)))))).)))))))..)))))))).. ( -23.50)
>DroYak_CAF1 20105 120 - 1
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCGCUCUAUUCUCUAUUCUAUGCUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))((((((((((....))...........((((((.....((((((.......))))))..))))))..)))))))).. ( -24.30)
>consensus
UUAACAAUCUAGUAUCUGUAGCUCUAUGCAAAUCAAAUCUGCAAUGCGCCAAGCACUCUAUUCUCUAUUCUAUGUUAAUGUGAUCGAUAUCCUUUCGAUUUCAGCAUAAAUGGCGCAUCA
..........................((((.........))))((((((((((....))...........(((((...((.((((((.......)))))).)))))))..)))))))).. (-22.98 = -22.82 +  -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 12:15:08 2006