Locus 4916

Sequence ID 3R_DroMel_CAF1
Location 12,906,975 – 12,907,158
Length 183
Max. P 0.999999
window8044 window8045 window8046 window8047 window8048

overview

Window 4

Location 12,906,975 – 12,907,078
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.94
Mean single sequence MFE -31.00
Consensus MFE -12.98
Energy contribution -13.10
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -3.94
Structure conservation index 0.42
SVM decision value 1.46
SVM RNA-class probability 0.956059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12906975 103 + 27905053
AUAACAGUGAUAAUUCCGCAUAAAAGAGGGCUUGGCUAUAAAUACAUG---------UGUGCCACACAC--UCACACACU------CGCAUCUGCAUGGCAAACCUCGCAAAAACAUUCA
......(((.......)))......((((.....(((((.......((---------((((........--.))))))..------.((....)))))))...))))............. ( -20.20)
>DroEre_CAF1 24196 109 + 1
ACAAUACCGAUGAUUCCCCAUCAAAGAGGGCUUGCCUAUAAAUGCAUACUGUAUGUGUGUAC-AUACAUGUGUGCAAACA------UGCAUCUGCAUGGCAAGCCUCGCAAAAACA----
........((((......))))...((((.((((((......((((((((((((((....))-))))).)))))))...(------(((....)))))))))))))).........---- ( -41.40)
>DroYak_CAF1 25237 105 + 1
ACAAAAGUGAUGAUUU-UCAUCAAAGAGGGCUUGGCUAUAAAUACAUA---------UGUAC-AUACAUGUGUGCGCACACUAAUGUGCAUCUGCAUGGCAAACCUCGCAAAAACA----
.......(((((....-.)))))..((((.....(((((...((((((---------(((..-..))))))))).(((((....)))))......)))))...)))).........---- ( -31.40)
>consensus
ACAAAAGUGAUGAUUCCCCAUCAAAGAGGGCUUGGCUAUAAAUACAUA_________UGUAC_AUACAUGUGUGCACACA______UGCAUCUGCAUGGCAAACCUCGCAAAAACA____
........((((......))))...((((..(((.((((..................(((((.........)))))...........((....))))))))).))))............. (-12.98 = -13.10 +   0.12)

alignment

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secondary structure

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Window 5

Location 12,907,015 – 12,907,118
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.12
Mean single sequence MFE -25.23
Consensus MFE -13.77
Energy contribution -13.00
Covariance contribution -0.77
Combinations/Pair 1.24
Mean z-score -3.56
Structure conservation index 0.55
SVM decision value 5.21
SVM RNA-class probability 0.999979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12907015 103 + 27905053
AAUACAUG---------UGUGCCACACAC--UCACACACU------CGCAUCUGCAUGGCAAACCUCGCAAAAACAUUCAUUCUCUUCAUUUCUCAUUUUUGCAGUCUUUCGCUGCAAUU
......((---------((((........--.))))))..------......(((..((....))..))).............................(((((((.....))))))).. ( -16.90)
>DroEre_CAF1 24236 97 + 1
AAUGCAUACUGUAUGUGUGUAC-AUACAUGUGUGCAAACA------UGCAUCUGCAUGGCAAGCCUCGCAAAAACA----------------CUCAUUUUUGCAGUCUUUCGCUGCAGUU
..((((((((((((((....))-))))).)))))))..((------(((....)))))(((.((...(((((((..----------------....))))))).(.....)))))).... ( -32.40)
>DroYak_CAF1 25276 94 + 1
AAUACAUA---------UGUAC-AUACAUGUGUGCGCACACUAAUGUGCAUCUGCAUGGCAAACCUCGCAAAAACA----------------CUUAUUUUUGCAGUCUUUCGCUGCAAUU
..((((((---------(((..-..))))))))).(((((....)))))...(((..((....))..)))......----------------.......(((((((.....))))))).. ( -26.40)
>consensus
AAUACAUA_________UGUAC_AUACAUGUGUGCACACA______UGCAUCUGCAUGGCAAACCUCGCAAAAACA________________CUCAUUUUUGCAGUCUUUCGCUGCAAUU
.................(((((.........)))))................(((..((....))..))).............................(((((((.....))))))).. (-13.77 = -13.00 +  -0.77)

alignment

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secondary structure

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Window 6

Location 12,907,015 – 12,907,118
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.12
Mean single sequence MFE -32.00
Consensus MFE -20.10
Energy contribution -20.33
Covariance contribution 0.23
Combinations/Pair 1.17
Mean z-score -3.91
Structure conservation index 0.63
SVM decision value 6.74
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12907015 103 - 27905053
AAUUGCAGCGAAAGACUGCAAAAAUGAGAAAUGAAGAGAAUGAAUGUUUUUGCGAGGUUUGCCAUGCAGAUGCG------AGUGUGUGA--GUGUGUGGCACA---------CAUGUAUU
..(((((((....).))))))..............((((((....))))))(((.((....)).))).((((((------.((((((.(--.....).)))))---------).)))))) ( -28.90)
>DroEre_CAF1 24236 97 - 1
AACUGCAGCGAAAGACUGCAAAAAUGAG----------------UGUUUUUGCGAGGCUUGCCAUGCAGAUGCA------UGUUUGCACACAUGUAU-GUACACACAUACAGUAUGCAUU
...((((((....).))))).......(----------------(((.((((((.((....)).)))))).)))------)...((((.((.(((((-((....))))))))).)))).. ( -34.30)
>DroYak_CAF1 25276 94 - 1
AAUUGCAGCGAAAGACUGCAAAAAUAAG----------------UGUUUUUGCGAGGUUUGCCAUGCAGAUGCACAUUAGUGUGCGCACACAUGUAU-GUACA---------UAUGUAUU
..(((((((....).))))))......(----------------(((.((((((.((....)).)))))).))))....(((((((.((....)).)-)))))---------)....... ( -32.80)
>consensus
AAUUGCAGCGAAAGACUGCAAAAAUGAG________________UGUUUUUGCGAGGUUUGCCAUGCAGAUGCA______UGUGUGCACACAUGUAU_GUACA_________UAUGUAUU
..(((((((....).)))))).......................(((.((((((.((....)).)))))).))).......((((..((....))...)))).................. (-20.10 = -20.33 +   0.23)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,907,044 – 12,907,158
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -22.80
Consensus MFE -17.57
Energy contribution -17.13
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.77
SVM decision value 1.44
SVM RNA-class probability 0.953766
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12907044 114 + 27905053
------CGCAUCUGCAUGGCAAACCUCGCAAAAACAUUCAUUCUCUUCAUUUCUCAUUUUUGCAGUCUUUCGCUGCAAUUGUGUGCAUUAUUUUUUAUGUAUUUUGCGCAGCAUCGUUCG
------((.((((((..((....))..((((((.....................(((..(((((((.....)))))))..)))(((((........))))))))))))))).)))).... ( -25.70)
>DroEre_CAF1 24275 96 + 1
------UGCAUCUGCAUGGCAAGCCUCGCAAAAACA----------------CUCAUUUUUGCAGUCUUUCGCUGCAGUUGUGUUUAUUAUUUUUUAUGUAUU-U-UGCAGCAUCGUUCG
------((((..((((((((.......))..(((((----------------(......(((((((.....)))))))..)))))).........))))))..-.-)))).......... ( -21.70)
>DroYak_CAF1 25306 102 + 1
CUAAUGUGCAUCUGCAUGGCAAACCUCGCAAAAACA----------------CUUAUUUUUGCAGUCUUUCGCUGCAAUUGUGUUCAUUAUUU-UUAUGUAUUUU-UGCAACAUCGUUUG
...(((((((..((((((((.......))...((((----------------(......(((((((.....)))))))..)))))........-.))))))....-))).))))...... ( -21.00)
>consensus
______UGCAUCUGCAUGGCAAACCUCGCAAAAACA________________CUCAUUUUUGCAGUCUUUCGCUGCAAUUGUGUUCAUUAUUUUUUAUGUAUUUU_UGCAGCAUCGUUCG
.......((...(((..((....))..)))........................(((..(((((((.....)))))))..)))........................))........... (-17.57 = -17.13 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,907,044 – 12,907,158
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -25.80
Consensus MFE -20.11
Energy contribution -20.00
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -2.99
Structure conservation index 0.78
SVM decision value 2.92
SVM RNA-class probability 0.997750
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12907044 114 - 27905053
CGAACGAUGCUGCGCAAAAUACAUAAAAAAUAAUGCACACAAUUGCAGCGAAAGACUGCAAAAAUGAGAAAUGAAGAGAAUGAAUGUUUUUGCGAGGUUUGCCAUGCAGAUGCG------
....((...((((((((((.((((..................(((((((....).))))))...(.(....).).........))))))))))..((....))..))))...))------ ( -27.10)
>DroEre_CAF1 24275 96 - 1
CGAACGAUGCUGCA-A-AAUACAUAAAAAAUAAUAAACACAACUGCAGCGAAAGACUGCAAAAAUGAG----------------UGUUUUUGCGAGGCUUGCCAUGCAGAUGCA------
...........(((-.-..................(((((...((((((....).))))).......)----------------))))((((((.((....)).))))))))).------ ( -22.30)
>DroYak_CAF1 25306 102 - 1
CAAACGAUGUUGCA-AAAAUACAUAA-AAAUAAUGAACACAAUUGCAGCGAAAGACUGCAAAAAUAAG----------------UGUUUUUGCGAGGUUUGCCAUGCAGAUGCACAUUAG
.....(((((((((-(((((((....-......((....)).(((((((....).))))))......)----------------))))))))))).((((((...))))))...)))).. ( -28.00)
>consensus
CGAACGAUGCUGCA_AAAAUACAUAAAAAAUAAUGAACACAAUUGCAGCGAAAGACUGCAAAAAUGAG________________UGUUUUUGCGAGGUUUGCCAUGCAGAUGCA______
..........((((............................(((((((....).))))))...........................((((((.((....)).))))))))))...... (-20.11 = -20.00 +  -0.11)

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 11:41:58 2006