Locus 7403

Sequence ID 3R_DroMel_CAF1
Location 19,685,178 – 19,685,320
Length 142
Max. P 0.985697
window11965 window11966 window11967

overview

Window 5

Location 19,685,178 – 19,685,281
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.70
Mean single sequence MFE -29.15
Consensus MFE -28.30
Energy contribution -28.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.97
SVM decision value 2.02
SVM RNA-class probability 0.985697
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19685178 103 + 27905053
---------------AUUA-UAAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-G
---------------....-.....(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))....-. ( -28.30)
>DroSec_CAF1 52403 103 + 1
---------------AUUA-UAAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-G
---------------....-.....(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))....-. ( -28.30)
>DroWil_CAF1 98784 105 + 1
---------------AUUAAUUAAGGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAAUG
---------------.........((((((((.((((....))))..))))))))..............((.(((.((((((.......)))))))))..(((.....))).))...... ( -29.70)
>DroYak_CAF1 53209 103 + 1
---------------AUUA-UUAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-G
---------------....-.....(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))....-. ( -28.30)
>DroAna_CAF1 57272 103 + 1
---------------AUUA-UUUAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-G
---------------....-.....(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))....-. ( -28.30)
>DroPer_CAF1 75091 118 + 1
AAUGGUUCGAUAUUUAUUA-UUUAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGCA-G
..((((..((((.....))-))...(((((((.((((....))))..))))))).))))..........((..((.((((((.......))))))))((.(((.....))).)).)).-. ( -32.00)
>consensus
_______________AUUA_UUAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG_G
.........................(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))...... (-28.30 = -28.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,685,178 – 19,685,281
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.70
Mean single sequence MFE -31.03
Consensus MFE -30.90
Energy contribution -30.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.03
Structure conservation index 1.00
SVM decision value 1.17
SVM RNA-class probability 0.925304
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19685178 103 - 27905053
C-CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUUA-UAAU---------------
.-...(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))........-....--------------- ( -30.90)
>DroSec_CAF1 52403 103 - 1
C-CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUUA-UAAU---------------
.-...(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))........-....--------------- ( -30.90)
>DroWil_CAF1 98784 105 - 1
CAUUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACCUUAAUUAAU---------------
......((.(((.....))).(((((((((((....).)))))).))))))...(((((...(((...(((((.(((((....)))))))))))))..)))))..--------------- ( -31.30)
>DroYak_CAF1 53209 103 - 1
C-CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUAA-UAAU---------------
.-...(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))........-....--------------- ( -30.90)
>DroAna_CAF1 57272 103 - 1
C-CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUAAA-UAAU---------------
.-...(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))........-....--------------- ( -30.90)
>DroPer_CAF1 75091 118 - 1
C-UGCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUAAA-UAAUAAAUAUCGAACCAUU
.-.((.((..((...(((.(.(((((((((((....).)))))).))))).).))....))..)).))(((((.(((((....)))))))))).......-................... ( -31.30)
>consensus
C_CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUAA_UAAU_______________
.....(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))............................ (-30.90 = -30.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,685,202 – 19,685,320
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.04
Mean single sequence MFE -33.38
Consensus MFE -29.50
Energy contribution -29.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.88
SVM decision value 0.60
SVM RNA-class probability 0.794634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19685202 118 + 27905053
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-GUGCAAUGGCCAAGCCUCACUCCGGAGGAAC-CGCCUUCGU
..(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).)-)...))))))............((((((...-..)))))). ( -33.60)
>DroPse_CAF1 73406 119 + 1
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAA-GUGCAAUGGCCAAGCCUCACUCCGGAGGAACACGCCUUGGU
..(((......))).(((((.........((((((.((((((.......))))))))((.(((.....))).))....-))))...(((....((((......)))).....)))))))) ( -33.70)
>DroWil_CAF1 98809 119 + 1
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAAUGUGCAAUGGCCAAGCCUCACUCCGGAGGAAC-CGCCUUCGU
..(((((((..((((.................(((.((((((.......)))))))))..(((.....)))))))))))).))...(((....((((......))))...-.)))..... ( -32.10)
>DroYak_CAF1 53233 118 + 1
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-GUGCAAUGGCCAAGCCUCACUCCGGAGGAAC-CGCCUUCGU
..(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).)-)...))))))............((((((...-..)))))). ( -33.60)
>DroAna_CAF1 57296 118 + 1
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAG-GUGCAAUGGCCAAGCCUCACUCCGGAGGAAC-CGCCUUCGU
..(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).)-)...))))))............((((((...-..)))))). ( -33.60)
>DroPer_CAF1 75130 119 + 1
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGCA-GUGCAAUGGCCAAGCCUCACUCCGGAGGAACACGCCUUGGU
..(((......))).(((((.........((((((.((((((.......))))))))((.(((.....))).))....-))))...(((....((((......)))).....)))))))) ( -33.70)
>consensus
ACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAA_GUGCAAUGGCCAAGCCUCACUCCGGAGGAAC_CGCCUUCGU
..(((......)))...............((((((.((((((.......))))))))((.(((.....))).)).....))))...(((....((((......)))).....)))..... (-29.50 = -29.50 +   0.00)

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 12:45:05 2006