Locus 9343

Sequence ID 3R_DroMel_CAF1
Location 24,825,399 – 24,825,527
Length 128
Max. P 0.811339
window14952 window14953 window14954

overview

Window 2

Location 24,825,399 – 24,825,513
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.94
Mean single sequence MFE -34.89
Consensus MFE -19.70
Energy contribution -20.28
Covariance contribution 0.58
Combinations/Pair 1.18
Mean z-score -1.62
Structure conservation index 0.56
SVM decision value 0.54
SVM RNA-class probability 0.775239
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24825399 114 + 27905053
---ACC-G-CUGGGUGUUGCAUUUCACACCAAUUGA-GAAGCUUUUACACCACUCGCGCUUGGCUCGGCGCUCACUCAGUCGGAUGAGUGACGAAAGCAGCGCACUGCAAUCCAAUGACA
---...-(-(.((((((.((.(((((.......)))-)).))....)))))....(((((..(((...((.(((((((......)))))))))..)))))))).).))............ ( -37.50)
>DroPse_CAF1 37583 117 + 1
AGUAUU-G-CAGCGUGUUGCAUUUCACACCAAUUGA-GAAGCUUUUACACUGCUUGCGCCUGGCUCGGCGCUCACUCAGUCGAAUGAAUGACGAAAGCAACGCAGUGCAAUGAAAUGGGA
..((((-(-((..(((((((.((((........(((-(((((.........))))(((((......)))))...))))((((......)))))))))))))))..)))))))........ ( -40.50)
>DroWil_CAF1 35010 90 + 1
---GUA-G-AGUCGUGUUGCAUUUCACACCAAUUGAAGGGGCUUUUCCAA------CGCUUGGCUCGGCGCUCACUCAUUCGUAUGAAUGACGAAAGCGUC-------------------
---...-(-((((((((((.......(.((.......))).......)))------)))..)))))((((((..(((((((....)))))).)..))))))------------------- ( -26.54)
>DroMoj_CAF1 71140 102 + 1
---GCCAACUAGCAUGUUGCAUUUCACACCAAUUGG-GGGAAUUUUCACC------CGCUUGGCUCGGCGCUCACUCAAUCGUAUGAAUGACGAAAGCAUUGCGAGGU--------GAGG
---(((.....((.....))........((((.(((-(.((....)).))------)).))))...))).((((((...(((((...(((.(....))))))))))))--------))). ( -32.20)
>DroAna_CAF1 36164 114 + 1
---GCA-G-UGGCGUGUUGCAUUUCACACCAAUUGA-GGAGCUUUUACACCACUCGCGCUUGAGUCGGCGCUCACUCAGUCGAAUGAAUGACGAAAGCAACGCAAUGCAAUCCAAUGACA
---(((-.-....(((((((.((((........(((-(((((.......(((((((....))))).)).)))).))))((((......)))))))))))))))..)))............ ( -32.10)
>DroPer_CAF1 38137 117 + 1
AGUAUU-G-CAGCGUGUUGCAUUUCACACCAAUUGA-GAAGCUUUUACACUGCUUGCGCCUGGCUCGGCGCUCACUCAGUCGAAUGAAUGACGAAAGCAACGCAGUGCAAUGAAAUGGGA
..((((-(-((..(((((((.((((........(((-(((((.........))))(((((......)))))...))))((((......)))))))))))))))..)))))))........ ( -40.50)
>consensus
___ACA_G_CAGCGUGUUGCAUUUCACACCAAUUGA_GAAGCUUUUACAC__CU_GCGCUUGGCUCGGCGCUCACUCAGUCGAAUGAAUGACGAAAGCAACGCAAUGCAAU__AAUGAGA
.............(((((((.((((..............................(((((......)))))(((.(((......))).))).)))))))))))................. (-19.70 = -20.28 +   0.58)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,825,399 – 24,825,513
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.94
Mean single sequence MFE -35.10
Consensus MFE -20.50
Energy contribution -22.10
Covariance contribution 1.60
Combinations/Pair 1.30
Mean z-score -1.60
Structure conservation index 0.58
SVM decision value 0.65
SVM RNA-class probability 0.811339
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24825399 114 - 27905053
UGUCAUUGGAUUGCAGUGCGCUGCUUUCGUCACUCAUCCGACUGAGUGAGCGCCGAGCCAAGCGCGAGUGGUGUAAAAGCUUC-UCAAUUGGUGUGAAAUGCAACACCCAG-C-GGU---
.........(((((...(((((((((.(((((((((......))))))).))..))))..)))))(((.(((......))).)-))....(((((........)))))..)-)-)))--- ( -37.80)
>DroPse_CAF1 37583 117 - 1
UCCCAUUUCAUUGCACUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGAGCCAGGCGCAAGCAGUGUAAAAGCUUC-UCAAUUGGUGUGAAAUGCAACACGCUG-C-AAUACU
.........((((((.((.(((((((((.(((((((......)))))))(((((((...((((....))(((......))).)-)...))))))))))).))))).)).))-)-)))... ( -38.90)
>DroWil_CAF1 35010 90 - 1
-------------------GACGCUUUCGUCAUUCAUACGAAUGAGUGAGCGCCGAGCCAAGCG------UUGGAAAAGCCCCUUCAAUUGGUGUGAAAUGCAACACGACU-C-UAC---
-------------------...((((((.((((((((....))))))))(((((((...(((.(------((.....)))..)))...))))))))))).)).........-.-...--- ( -22.50)
>DroMoj_CAF1 71140 102 - 1
CCUC--------ACCUCGCAAUGCUUUCGUCAUUCAUACGAUUGAGUGAGCGCCGAGCCAAGCG------GGUGAAAAUUCCC-CCAAUUGGUGUGAAAUGCAACAUGCUAGUUGGC---
..((--------(((.(((...((((.(((((((((......))))))).))..))))...)))------)))))........-((((((((((((........)))))))))))).--- ( -38.30)
>DroAna_CAF1 36164 114 - 1
UGUCAUUGGAUUGCAUUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGACUCAAGCGCGAGUGGUGUAAAAGCUCC-UCAAUUGGUGUGAAAUGCAACACGCCA-C-UGC---
.......(((..((.(((((..((((...(((((((......)))))))((((........))))))))..)))))..)))))-.....(((((((........)))))))-.-...--- ( -34.20)
>DroPer_CAF1 38137 117 - 1
UCCCAUUUCAUUGCACUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGAGCCAGGCGCAAGCAGUGUAAAAGCUUC-UCAAUUGGUGUGAAAUGCAACACGCUG-C-AAUACU
.........((((((.((.(((((((((.(((((((......)))))))(((((((...((((....))(((......))).)-)...))))))))))).))))).)).))-)-)))... ( -38.90)
>consensus
UCUCAUU__AUUGCACUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGAGCCAAGCGC_AG__GUGUAAAAGCUCC_UCAAUUGGUGUGAAAUGCAACACGCUG_C_AAC___
..........(((((((((..(((((((((((((((......)))))))....)))...)))))...)))))))))..............((((((........)))))).......... (-20.50 = -22.10 +   1.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,825,433 – 24,825,527
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.04
Mean single sequence MFE -33.28
Consensus MFE -25.50
Energy contribution -24.33
Covariance contribution -1.16
Combinations/Pair 1.22
Mean z-score -0.68
Structure conservation index 0.77
SVM decision value 0.16
SVM RNA-class probability 0.614397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24825433 94 - 27905053
------------------------GAAUCCCCGC--CUUCUGUCAUUGGAUUGCAGUGCGCUGCUUUCGUCACUCAUCCGACUGAGUGAGCGCCGAGCCAAGCGCGAGUGGUGUAAAAGC
------------------------........((--..(((......)))..))..(((((..(((...(((((((......)))))))((((........)))))))..)))))..... ( -30.40)
>DroPse_CAF1 37620 117 - 1
CAG-CACCGCACCGCCCAGCGCACC--UCUCUGCCUCGCCUCCCAUUUCAUUGCACUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGAGCCAGGCGCAAGCAGUGUAAAAGC
..(-(...((........))(((..--....)))...))...........(((((((((..........(((((((......)))))))(((((......)))))..))))))))).... ( -36.30)
>DroSec_CAF1 41340 94 - 1
------------------------GAAUCCCCGC--CUUCUGUCAUUGGAUUGCAGUGCGCUGCUUUCGUCACUCAUCCGACUGAGUGAGCGCCAAGCCAAGCGCGAGUGGUGUAAAAGC
------------------------........((--..(((......)))..))..(((((..(((...(((((((......)))))))((((........)))))))..)))))..... ( -30.40)
>DroSim_CAF1 43542 93 - 1
------------------------G-AUCCCCGC--UUUCUGUCAUUGGAUUGCAGUGCGCUGCUUUCGUCACUCAUCCGACUGAGUGAGCGCCGAGCCAAGCGCGAGUGGUGUAAAAGC
------------------------.-....((((--((.(((.((......))))).(((((((((.(((((((((......))))))).))..))))..)))))))))))......... ( -31.60)
>DroAna_CAF1 36198 117 - 1
CACCAACCCCACCGACCAACCCGUCACCCACCG---CGGCUGUCAUUGGAUUGCAUUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGACUCAAGCGCGAGUGGUGUAAAAGC
.............(((......)))...(((((---(.((.(((....))).)).(((((((....(((.(.(((((((....))))))).).)))....)))))))))))))....... ( -33.30)
>DroPer_CAF1 38174 115 - 1
CAG-CACCGCACCG--CAGCGCACC--UCUCUGCCUCGCCUCCCAUUUCAUUGCACUGCGUUGCUUUCGUCAUUCAUUCGACUGAGUGAGCGCCGAGCCAGGCGCAAGCAGUGUAAAAGC
..(-(...((...(--(((.(....--.).))))...))...........(((((((((..........(((((((......)))))))(((((......)))))..)))))))))..)) ( -37.70)
>consensus
________________________C_AUCCCCGC__CGUCUGUCAUUGGAUUGCAGUGCGCUGCUUUCGUCACUCAUCCGACUGAGUGAGCGCCGAGCCAAGCGCGAGUGGUGUAAAAGC
....................................................((..((((((((((...(((((((......)))))))((((........))))))))))))))...)) (-25.50 = -24.33 +  -1.16)

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 13:32:16 2006