Locus 7748

Sequence ID X_DroMel_CAF1
Location 19,270,784 – 19,271,059
Length 275
Max. P 0.990595
window12716 window12717 window12718 window12719 window12720

overview

Window 6

Location 19,270,784 – 19,270,874
Length 90
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 88.42
Mean single sequence MFE -33.80
Consensus MFE -31.53
Energy contribution -31.20
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -2.34
Structure conservation index 0.93
SVM decision value 1.59
SVM RNA-class probability 0.966381
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19270784 90 + 22224390
UUGCUUGCUAUACGAUAGUAGACUGCAUCUAUUCGUGUGGCAGAAAGGCGCAGAACUGGAGACAGGUGUCCCGGUUGAGUGCACACCCA------U
....(((((((((((..(((((.....))))))))))))))))....((((..((((((.(((....)))))))))..)))).......------. ( -34.70)
>DroSim_CAF1 61823 96 + 1
UUGCAUGCUAUACGAUAGUAGACUGCAUCUAUUCGUGUGGCAGAAAGGCGCAGAACUGGAGACAGGUGUCCUGGUUGAGUGCACACCCAUACCCAU
.....((((((((((..(((((.....))))))))))))))).....((((..(((..(.(((....))))..)))..)))).............. ( -31.70)
>DroEre_CAF1 54191 91 + 1
AUGCAGGCUACACGACAGUAGACUGCAUCUAUCCGUGUGGCAGA-AGGCGCAGAGCUGGAGACAGGUGUCCUGGUUGAGUGCACACCCACAC----
((((((.((((......)))).))))))......((((((....-..((((..(((..(.(((....))))..)))..))))....))))))---- ( -35.00)
>consensus
UUGCAUGCUAUACGAUAGUAGACUGCAUCUAUUCGUGUGGCAGAAAGGCGCAGAACUGGAGACAGGUGUCCUGGUUGAGUGCACACCCA_AC___U
......(((((((((..(((((.....))))))))))))))......((((..((((((.(((....)))))))))..)))).............. (-31.53 = -31.20 +  -0.33)

alignment

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secondary structure

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Window 7

Location 19,270,874 – 19,270,991
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.94
Mean single sequence MFE -42.65
Consensus MFE -37.70
Energy contribution -38.26
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.88
SVM decision value 0.64
SVM RNA-class probability 0.808524
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19270874 117 - 22224390
UCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUCAACG---UUAGUGGAUGUGGAUGUAGAUGUGGAUGUGGAU
....((((......))))..(..((((..((.((((((((((....(((((((....)))))))(((((..(((.........)---)).))))).)))))))))).))..))))..).. ( -45.90)
>DroSim_CAF1 61919 117 - 1
UCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUCAACG---UCAGUGGAUGUGGAUGUGGAUGUGGAAGUGGAU
....((.....))...((((((((....)))))))).....((((.(((((((....)))))))((((((...(...(((.(((---((....))))).)))...).)))))).)))).. ( -44.60)
>DroEre_CAF1 54282 114 - 1
UCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCACUCGCCGCACAGGAAUCACGCUUCUUGUCCACGCAGCAAAGUCAACG---UCAGUGGAUGUGGAUGUGGAUGUGGAUGUG---
............((((((((((((....)))))))).....(((((((((((......))))))(((((........(((.(((---((....))))).))))))))))))).))))--- ( -38.30)
>DroYak_CAF1 58365 120 - 1
UCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUCAACGUCGUCAGUGGAUGUGGAUGUGGAUGAGGAUGUGGAU
............((((((((((((....)))))))).((((((((((((((((....)))))))((((((...((..(.(......).)..))..))))))))))).))))..))))... ( -41.80)
>consensus
UCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUCAACG___UCAGUGGAUGUGGAUGUGGAUGUGGAUGUGGAU
....((((......))))....(((((..((.((((((((((....(((((((....)))))))(((((........(....).......))))).)))))))))).))..))))).... (-37.70 = -38.26 +   0.56)

alignment

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secondary structure

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Window 8

Location 19,270,911 – 19,271,028
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.97
Mean single sequence MFE -43.50
Consensus MFE -33.86
Energy contribution -33.48
Covariance contribution -0.38
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 0.78
SVM decision value 0.23
SVM RNA-class probability 0.645470
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19270911 117 + 22224390
GACUUUGCUGCGUGGACAAGAAGCGUGCUUCCUGUGCGGCGAAUGCAGCUGCAAAUGCAACUGCUGUGCUGUCAGCUAGAAAACUACAACGCGAC---UCCUCCGCGAUUCAGUCAAGGA
..((((((((((((((..((..((((.((..(((.((((((...((((.(((....))).))))..)))))))))..)).........))))..)---)..))))))...))).))))). ( -45.00)
>DroSim_CAF1 61956 117 + 1
GACUUUGCUGCGUGGACAAGAAGCGUGCUUCCUGUGCGGCGAAUGCAGCUGCAAAUGCAACUGCUGUGCUGUCAGCUAGAAAACUACAACGCGAC---UCCUCCUCGACUCGGUGAAGGA
..(((..(((((.(((..((..((((.((..(((.((((((...((((.(((....))).))))..)))))))))..)).........))))..)---)..))).))...)))..))).. ( -42.50)
>DroEre_CAF1 54316 117 + 1
GACUUUGCUGCGUGGACAAGAAGCGUGAUUCCUGUGCGGCGAGUGCAGCUGCAAAUGCAACUGCUGUGCUGUCAGCUAGAAAACUACAUCGCGAC---UUCUCCCCGACUCAGUCAAGGA
..((((((((.((((...(((((((((((..(((.((((((...((((.(((....))).))))..))))))))).(((....))).)))))).)---))))..)).)).))).))))). ( -43.50)
>DroYak_CAF1 58405 120 + 1
GACUUUGCUGCGUGGACAAGAAGCGUGCUUCCUGUGCGGCGAAUGCAGCUGCAAAUGCAACUGCUGUGCUGUCAGCUAGAAAACUACAUCGCGAGGAGGAGUCCUCGACUCAGUCAGGGA
..((((((((.((((....((((....))))(((.((((((...((((.(((....))).))))..)))))))))........))))....((((((....))))))...))).))))). ( -43.00)
>consensus
GACUUUGCUGCGUGGACAAGAAGCGUGCUUCCUGUGCGGCGAAUGCAGCUGCAAAUGCAACUGCUGUGCUGUCAGCUAGAAAACUACAACGCGAC___UCCUCCUCGACUCAGUCAAGGA
..(((..(((((.(((.......((((....(((.((((((...((((.(((....))).))))..))))))))).(((....)))...))))........))).))...)))..))).. (-33.86 = -33.48 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,270,911 – 19,271,028
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.97
Mean single sequence MFE -42.55
Consensus MFE -37.24
Energy contribution -38.92
Covariance contribution 1.69
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.88
SVM decision value 1.06
SVM RNA-class probability 0.909263
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19270911 117 - 22224390
UCCUUGACUGAAUCGCGGAGGA---GUCGCGUUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUC
..(((..(((....((((.(((---...(.(((((((((....)))).))))).).((((((((....)))))))).))).))))((((((((....)))))))).....)))..))).. ( -45.10)
>DroSim_CAF1 61956 117 - 1
UCCUUCACCGAGUCGAGGAGGA---GUCGCGUUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUC
(((((.((...)).)))))(((---((.(((((((((((....)))).)))))...((((((((....))))))))....)).)).(((((((....))))))))))............. ( -41.50)
>DroEre_CAF1 54316 117 - 1
UCCUUGACUGAGUCGGGGAGAA---GUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCACUCGCCGCACAGGAAUCACGCUUCUUGUCCACGCAGCAAAGUC
..(((..(((.((.((.(((..---((.((....(((((....)))))...)))).((((((((....)))))))).))).))(.(((((((......))))))).))).)))..))).. ( -39.80)
>DroYak_CAF1 58405 120 - 1
UCCCUGACUGAGUCGAGGACUCCUCCUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUC
.....((((((((.(((((....)))))((....(((((....)))))...))...((((((((....))))))))))))((.((((((((((....))))))))....)).))..)))) ( -43.80)
>consensus
UCCUUGACUGAGUCGAGGAGGA___GUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUCGCCGCACAGGAAGCACGCUUCUUGUCCACGCAGCAAAGUC
((((((((...)))))))).........(.(((((((((....)))).))))).).((((((((....))))))))....((.((((((((((....))))))))....)).))...... (-37.24 = -38.92 +   1.69)

alignment

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secondary structure

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Window 0

Location 19,270,951 – 19,271,059
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.15
Mean single sequence MFE -36.70
Consensus MFE -25.36
Energy contribution -27.05
Covariance contribution 1.69
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.69
SVM decision value 2.22
SVM RNA-class probability 0.990595
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19270951 108 - 22224390
AAGGAGCCA---------AAGGAGCCAAAGGAGCACCGGUUCCUUGACUGAAUCGCGGAGGA---GUCGCGUUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUC
((((((((.---------..((.(((....).)).))))))))))(((((...(((((....---.)))))...))))).....((.....))...((((((((....)))))))).... ( -39.30)
>DroSim_CAF1 61996 90 - 1
---------------------------AAGGAGCACUAGUUCCUUCACCGAGUCGAGGAGGA---GUCGCGUUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUC
---------------------------(((((((....)))))))...(((.((......))---.))).(((((((((....)))).)))))...((((((((....)))))))).... ( -33.40)
>DroEre_CAF1 54356 90 - 1
AA---------------------------GGAGUACGGAUUCCUUGACUGAGUCGGGGAGAA---GUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCACUC
..---------------------------.((((.....(((((((((...)))))))))..---((.((....(((((....)))))...)))).((((((((....)))))))))))) ( -32.30)
>DroYak_CAF1 58445 120 - 1
AAGGAGCCAGAGGAGCAAAAGGAGUCAAAGGAGCACGGAUUCCCUGACUGAGUCGAGGACUCCUCCUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUC
.........((((((.....((((((...(.....).))))))......(((((...)))))))))))((....(((((....)))))...))...((((((((....)))))))).... ( -41.80)
>consensus
AA_________________________AAGGAGCACGGAUUCCUUGACUGAGUCGAGGAGGA___GUCGCGAUGUAGUUUUCUAGCUGACAGCACAGCAGUUGCAUUUGCAGCUGCAUUC
.......................................(((((((((...)))))))))........(.(((((((((....)))).))))).).((((((((....)))))))).... (-25.36 = -27.05 +   1.69)

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 12:46:41 2006