Locus 790

Sequence ID 3R_DroMel_CAF1
Location 2,707,599 – 2,707,724
Length 125
Max. P 0.765523
window1258 window1259 window1260

overview

Window 8

Location 2,707,599 – 2,707,702
Length 103
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -29.26
Consensus MFE -21.54
Energy contribution -21.98
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.74
SVM decision value 0.17
SVM RNA-class probability 0.617650
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2707599 103 - 27905053
--CACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCACUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGCACCGAAAAAAAAUAUAUCGUAAGCAUGAAUA---------
--...((((..(((-((....))))).((.(((((.....(((((..(((....)))..)))))....))))))).......................))))....--------- ( -29.50)
>DroSec_CAF1 17984 113 - 1
ACCACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGCACAGAAAAC-AAUUUUUCUAAAUCAUGAAUAUUUAAAUUA
.....(((((((((-((....))))).((.(((((.....(((((..(((....)))..)))))....)))))))..((((((.-...))))))..))))))............. ( -31.90)
>DroSim_CAF1 19063 113 - 1
ACCACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGCACCGAAAAC-AAUUUUUCUAAAUCAUGAAUAUUUAAAUUA
.....(((((((((-((....))))).((.(((((.....(((((..(((....)))..)))))....)))))))...(((((.-...)))))...))))))............. ( -30.80)
>DroEre_CAF1 18863 107 - 1
--CACCAUGAUGCCCAUGCCAAUGGCCGCCAUACGCACAAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGCACCGGAAAA-AAUAUUUCGAAGGCAUGACUAUUUA-----
--......((((..((((((.((((...))))..(((((.(((((..(((....)))..)))))......)))))..(((((..-....)))))..))))))..))))..----- ( -31.40)
>DroYak_CAF1 18731 109 - 1
ACCACCAUGAUGCCAAUGCCAAUGGCCGCCAUACGCACAAUUGUGUGUGCGUGAGUAUCUGCAGAAGCCGUGACACCGGGAAAA-AAUAUUUCGAAAACAUAAAUAUUUA-----
.....((((..((...(((.....(((((((((((((....)))))))).))).))....)))...))))))....((..(...-....)..))................----- ( -22.70)
>consensus
ACCACCAUGAUGCC_AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGCACCGAAAAA_AAUAUUUCGAAAGCAUGAAUAUUUA_____
.....((((.......(((..(((((.((.....))....(((((..(((....)))..)))))..)))))..)))..((((.......)))).....))))............. (-21.54 = -21.98 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,707,630 – 2,707,724
Length 94
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 88.75
Mean single sequence MFE -43.60
Consensus MFE -32.96
Energy contribution -33.40
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.76
SVM decision value 0.51
SVM RNA-class probability 0.765523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2707630 94 + 27905053
GCACACGGCUUCUGCGGAUACUCACGCACUCACAGUGGUGCGUAUGGCGGCCAUUGGCAU-GGCAUCAUGGUG-----------GUGCCAUGAUGGUGGUGC---CGUU
....(((((...(((.(.(((.(((.(((.....)))))).)))).)))((((((..(((-((((((.....)-----------))))))))..))))))))---))). ( -41.90)
>DroSec_CAF1 18023 105 + 1
GCACACGGCUUCUGCGGAUACUCACGCACUCACAAUGGUGCGUAUGGCGGCCAUUGGCAU-GGCAUCAUGGUGGUGCUCCGGUGGUGCCAUGGUGGUGGUGC---CGUU
.....(.((....)).)......(((((((......)))))))((((((.((((((.(((-((((((((..(((....)))))))))))))).)))))))))---))). ( -47.00)
>DroSim_CAF1 19102 108 + 1
GCACACGGCUUCUGCGGAUACUCACGCACUCACAAUGGUGCGUAUGGCGGCCAUUGGCAU-GGCAUCAUGGUGGUGCUCCGGUGGUGCCAUGGUGGUGGUGCCGCCGUU
....(((((..............(((((((......)))))))..((((.((((((.(((-((((((((..(((....)))))))))))))).))))))))))))))). ( -51.40)
>DroEre_CAF1 18897 95 + 1
GCACACGGCUUCUGCGGAUACUCACGCACUCACAAUUGUGCGUAUGGCGGCCAUUGGCAUGGGCAUCAUGGUG-----------GUGGCAUGGUGGUGGUGC---UGUU
((((((.(((..(((.....(..((((((........))))))..)((.(((((..((....))...))))).-----------)).))).))).)).))))---.... ( -34.10)
>consensus
GCACACGGCUUCUGCGGAUACUCACGCACUCACAAUGGUGCGUAUGGCGGCCAUUGGCAU_GGCAUCAUGGUG___________GUGCCAUGGUGGUGGUGC___CGUU
((((((.(((...((.(...(..((((((........))))))..).).))....))).....((((((((((.(((....))).)))))))))))).))))....... (-32.96 = -33.40 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,707,630 – 2,707,724
Length 94
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 88.75
Mean single sequence MFE -34.71
Consensus MFE -25.75
Energy contribution -25.82
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.74
SVM decision value 0.31
SVM RNA-class probability 0.684665
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2707630 94 - 27905053
AACG---GCACCACCAUCAUGGCAC-----------CACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCACUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGC
...(---((......(((((((...-----------..)))))))(((-((....))))).)))...(((((..(((((..(((....)))..))))).....))))). ( -37.90)
>DroSec_CAF1 18023 105 - 1
AACG---GCACCACCACCAUGGCACCACCGGAGCACCACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGC
...(---((.(((....(((((((.((..((.......)).)).))))-)))....)))..)))...(((((..(((((..(((....)))..))))).....))))). ( -35.50)
>DroSim_CAF1 19102 108 - 1
AACGGCGGCACCACCACCAUGGCACCACCGGAGCACCACCAUGAUGCC-AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGC
...((((((........(((((((.((..((.......)).)).))))-)))......))))))...(((((..(((((..(((....)))..))))).....))))). ( -41.14)
>DroEre_CAF1 18897 95 - 1
AACA---GCACCACCACCAUGCCAC-----------CACCAUGAUGCCCAUGCCAAUGGCCGCCAUACGCACAAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGC
....---.............((((.-----------...((((.....))))....))))...((((((.....(((((..(((....)))..)))))....)))))). ( -24.30)
>consensus
AACG___GCACCACCACCAUGGCAC___________CACCAUGAUGCC_AUGCCAAUGGCCGCCAUACGCACCAUUGUGAGUGCGUGAGUAUCCGCAGAAGCCGUGUGC
.......((((...((.(((((................))))).)).........(((((.((.....))....(((((..(((....)))..)))))..))))))))) (-25.75 = -25.82 +   0.06)

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 09:52:12 2006