Locus 1148

Sequence ID 2R_DroMel_CAF1
Location 4,576,326 – 4,576,453
Length 127
Max. P 0.893155
window2018 window2019 window2020

overview

Window 8

Location 4,576,326 – 4,576,423
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 94.16
Mean single sequence MFE -17.10
Consensus MFE -14.17
Energy contribution -14.48
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -2.42
Structure conservation index 0.83
SVM decision value 0.97
SVM RNA-class probability 0.893155
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4576326 97 + 20766785
UCCCCAUUCUCCAUCUGCAUCAUCCAUCCUCCGGCGAACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACACGGCUGCAAUCAGCAGCAUCCACA
................................((...........(((((((....)))))))............(((((.....)))))..))... ( -15.20)
>DroSec_CAF1 7771 97 + 1
UCCCCAUUCCCCAUCUGCAUCAUCCAUCCUCCGGCGAACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUUCACA
...............(((.((..............(((....)))(((((((....)))))))......)).)))(((((.....)))))....... ( -17.60)
>DroSim_CAF1 8068 97 + 1
UCCCCAUUCCCCAUCUGCAUCAUCCAUCCUCCGGCGAACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUUCACA
...............(((.((..............(((....)))(((((((....)))))))......)).)))(((((.....)))))....... ( -17.60)
>DroEre_CAF1 14706 96 + 1
UUCCCAUUGCCCAUCUCCAUUACCCAUCCUCCGGCGAACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUG-CAUCAGCGGCAUCCACA
......(((((.....................)))))........(((((((....)))))))......((.((.((((-...)))).)).)).... ( -18.00)
>consensus
UCCCCAUUCCCCAUCUGCAUCAUCCAUCCUCCGGCGAACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUCCACA
.................................(((.........(((((((....)))))))........))).(((((.....)))))....... (-14.17 = -14.48 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,576,363 – 4,576,453
Length 90
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 87.37
Mean single sequence MFE -16.66
Consensus MFE -14.14
Energy contribution -14.02
Covariance contribution -0.12
Combinations/Pair 1.13
Mean z-score -1.66
Structure conservation index 0.85
SVM decision value 0.68
SVM RNA-class probability 0.821808
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4576363 90 + 20766785
ACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACACGGCUGCAAUCAGCAGCAUCCACAUA------CACGCGAAAAAAUAUAUAGAAAUAUGCU
.....((((((((((....)))))))............(((((.....))))).........------.....)))......((((....)))).. ( -16.50)
>DroSec_CAF1 7808 84 + 1
ACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUUCACAUA------CAGGCGAAAAAAUAG------AUAUGCU
...((((((((((((....)))))))........(((.(((((.....))))).....(...------..))))........)------).))).. ( -17.10)
>DroSim_CAF1 8105 84 + 1
ACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUUCACAUA------CAGACGAAAAAAUAG------AUAUGCU
.....((((((((((....)))))))............(((((.....))))).........------.....))).......------....... ( -15.30)
>DroEre_CAF1 14743 88 + 1
ACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUG-CAUCAGCGGCAUCCACAUACGAGUACAGGCGAAG-AAUAG------UUAUGCU
....(((((((((((....)))))))........(((.((((-(....)))))....((......))....)))..)-)))..------....... ( -18.80)
>DroYak_CAF1 14700 83 + 1
AGACAUUCAUUGUCAAUUUUGACAAUCAACAAGACACGGCUGCCAUCAGCAGCAUCCACAUA------CAGGCGAGA-AAUAG------AUAUGGU
...((((((((((((....)))))))..........(((((((.....)))))..((.....------..))))...-....)------).))).. ( -15.60)
>consensus
ACACAUUCAUUGUCAAUUUUGACAAUCAACAAGACGCGGCUGCAAUCAGCAGCAUCCACAUA______CAGGCGAAAAAAUAG______AUAUGCU
.....((((((((((....)))))))............(((((.....)))))....................))).................... (-14.14 = -14.02 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,576,363 – 4,576,453
Length 90
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 87.37
Mean single sequence MFE -22.46
Consensus MFE -19.10
Energy contribution -19.66
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.85
SVM decision value 0.89
SVM RNA-class probability 0.875929
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4576363 90 - 20766785
AGCAUAUUUCUAUAUAUUUUUUCGCGUG------UAUGUGGAUGCUGCUGAUUGCAGCCGUGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUGU
.((((...(((((((((..........)------)))))))).(((((.....))))).))))...(((.(((((((....))))))).))).... ( -24.90)
>DroSec_CAF1 7808 84 - 1
AGCAUAU------CUAUUUUUUCGCCUG------UAUGUGAAUGCUGCUGAUUGCAGCCGCGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUGU
.((....------.......(((((...------...))))).(((((.....))))).)).....(((.(((((((....))))))).))).... ( -22.40)
>DroSim_CAF1 8105 84 - 1
AGCAUAU------CUAUUUUUUCGUCUG------UAUGUGAAUGCUGCUGAUUGCAGCCGCGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUGU
.((((((------..((......))..)------)))))....(((((.....)))))((((((((((..(((.....)))..)))).).))))). ( -21.40)
>DroEre_CAF1 14743 88 - 1
AGCAUAA------CUAUU-CUUCGCCUGUACUCGUAUGUGGAUGCCGCUGAUG-CAGCCGCGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUGU
.(((((.------.....-(.......)......)))))((((((.((((...-)))).)))))).(((.(((((((....))))))).))).... ( -22.60)
>DroYak_CAF1 14700 83 - 1
ACCAUAU------CUAUU-UCUCGCCUG------UAUGUGGAUGCUGCUGAUGGCAGCCGUGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUCU
.((((((------(....-........)------.))))))..(((((.....)))))........(((.(((((((....))))))).))).... ( -21.00)
>consensus
AGCAUAU______CUAUUUUUUCGCCUG______UAUGUGGAUGCUGCUGAUUGCAGCCGCGUCUUGUUGAUUGUCAAAAUUGACAAUGAAUGUGU
.((((..................................((((((.((((....)))).)))))).(((.(((((((....))))))).))))))) (-19.10 = -19.66 +   0.56)

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 09:57:41 2006