Locus 1948

Sequence ID 3L_DroMel_CAF1
Location 5,400,757 – 5,401,020
Length 263
Max. P 0.962228
window3044 window3045 window3046 window3047 window3048

overview

Window 4

Location 5,400,757 – 5,400,874
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.84
Mean single sequence MFE -26.20
Consensus MFE -22.20
Energy contribution -22.53
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.85
SVM decision value 0.10
SVM RNA-class probability 0.581328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400757 117 + 23771897
UCUGCUACAUGGACCCCAUAAUUUGUAAUUUCAACCUAAUUACUUCAAGCCCAGCCGAACGGGGAUCGGA---CCAGCUAAACAAUGUUGUCCGUAAUAAAAUGUCAAAAACCAAAGCAA
..((((...(((.((((.......((((((.......))))))(((..((...)).))).))))..((((---(.(((........)))))))).................))).)))). ( -25.30)
>DroSec_CAF1 49600 120 + 1
UCUGCUACAUGGACCCCAUAAUUUGUAAUUUCAACCUAAUUACUUCAAGCCCAGGCGAACGGGGAUAGGAACACCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAA
..((((...(((.((((.......((((((.......)))))).....((....))....))))...(((....((((........)))))))..................))).)))). ( -25.40)
>DroYak_CAF1 49619 117 + 1
UCUGCUACAUGGACCCCAUAAUUUGUAAUUUCAACCUAAUUACUUCAAGCGCAGGCGAAGGGGGCACGGA---CCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAU
..((((...(((.((((.......((((((.......)))))).....((....))...))))...((((---(.(((........)))))))).................))).)))). ( -27.90)
>consensus
UCUGCUACAUGGACCCCAUAAUUUGUAAUUUCAACCUAAUUACUUCAAGCCCAGGCGAACGGGGAUCGGA___CCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAA
..((((...(((.((((.......((((((.......)))))).....((....))....))))...(((....((((........)))))))..................))).)))). (-22.20 = -22.53 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,400,797 – 5,400,905
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.57
Mean single sequence MFE -24.20
Consensus MFE -19.42
Energy contribution -19.53
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.80
SVM decision value 0.34
SVM RNA-class probability 0.696007
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400797 108 + 23771897
UACUUCAAGCCCAGCCGAACGGGGAUCGGA---CCAGCUAAACAAUGUUGUCCGUAAUAAAAUGUCAAAAACCAAAGCAAAACGCCCAUUUCGUCUGAUUUACACA------CACAC---
...........(((.((((..(((..((((---(.(((........))))))))........(((...........))).....)))..)))).))).........------.....--- ( -20.10)
>DroSec_CAF1 49640 117 + 1
UACUUCAAGCCCAGGCGAACGGGGAUAGGAACACCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAAAACGCCCAUUUCGUCUGAUUCACACACACACACACAC---
...........((((((((..(((...((....)).(((......(((((....)))))...((........)).)))......)))..))))))))....................--- ( -21.60)
>DroYak_CAF1 49659 117 + 1
UACUUCAAGCGCAGGCGAAGGGGGCACGGA---CCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAUAACGCCCAUUUCGUCUGAAUCACACACACACACACACAAA
...........(((((((((.((((.((((---(.(((........)))))))).......((((...........))))...)))).)))))))))....................... ( -30.90)
>consensus
UACUUCAAGCCCAGGCGAACGGGGAUCGGA___CCAGCUAAACAAUGUUGUCCGCAAUAAAAUGUCAAAAACCAAAGCAAAACGCCCAUUUCGUCUGAUUCACACACACACACACAC___
...........((((((((..(((...(((....((((........)))))))((.....................))......)))..))))))))....................... (-19.42 = -19.53 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,400,874 – 5,400,980
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.93
Mean single sequence MFE -29.25
Consensus MFE -28.36
Energy contribution -27.48
Covariance contribution -0.88
Combinations/Pair 1.15
Mean z-score -1.15
Structure conservation index 0.97
SVM decision value 0.65
SVM RNA-class probability 0.811273
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400874 106 + 23771897
AACGCCCAUUUCGUCUGAUUUACACA------CACAC--------AUGAAGACCAGAAGGACACGCCCCCUCACACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGAC
........((((((.((.........------..)).--------))))))(((((.((((((((((...(((.((((.....)))).)))....)))....)))))))...)))))... ( -29.80)
>DroSec_CAF1 49720 112 + 1
AACGCCCAUUUCGUCUGAUUCACACACACACACACAC--------AUGAAGGCCAGAAGGACACGCCCCCUCGCACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGAC
..((((...(((((.((.................)).--------)))))(((..((((((((((((...(((.((((.....)))).)))....)))....)))))))))))))))).. ( -29.83)
>DroYak_CAF1 49736 120 + 1
AACGCCCAUUUCGUCUGAAUCACACACACACACACACAAAUACAUAUGAAGGCAAAAAGGAUACGCCCCCUCACACGCACAGGGCGUAUGAUUUUGGUUUUUGUGUCCUUUGCUGGUGAC
..((((...(((((.((.........................)).)))))(((((..((((((((((...(((.((((.....)))).)))....)))....)))))))))))))))).. ( -28.11)
>consensus
AACGCCCAUUUCGUCUGAUUCACACACACACACACAC________AUGAAGGCCAGAAGGACACGCCCCCUCACACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGAC
..((((......((((.................................))))..((((((((((((...(((.((((.....)))).)))....)))....)))))))))...)))).. (-28.36 = -27.48 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,400,905 – 5,401,020
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.11
Mean single sequence MFE -36.70
Consensus MFE -35.39
Energy contribution -34.07
Covariance contribution -1.32
Combinations/Pair 1.14
Mean z-score -1.96
Structure conservation index 0.96
SVM decision value 1.11
SVM RNA-class probability 0.916370
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400905 115 + 23771897
-----AUGAAGACCAGAAGGACACGCCCCCUCACACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGACAUAUGUUAAUGAUCUGGCAGCGAUUUCUGGGUCAUUUAAA
-----((((...(((((((((((((((...(((.((((.....)))).)))....)))....)))))).((((((.((((((......))).)).).)))))).)))))).))))..... ( -37.90)
>DroSec_CAF1 49757 115 + 1
-----AUGAAGGCCAGAAGGACACGCCCCCUCGCACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGACAUAUGUUAAUGAUCUGGCAGCGAUUUCUGGGUCAUUUAAA
-----((((...(((((((((((((((...(((.((((.....)))).)))....)))....)))))).((((((.((((((......))).)).).)))))).)))))).))))..... ( -36.10)
>DroYak_CAF1 49776 120 + 1
UACAUAUGAAGGCAAAAAGGAUACGCCCCCUCACACGCACAGGGCGUAUGAUUUUGGUUUUUGUGUCCUUUGCUGGUGACAUAUGUAAAUGAUCUGGCAGCGAUUUCUGUGUCAUUUAAA
.(((((((..(.((.((((((((((((...(((.((((.....)))).)))....)))....)))))))))..)).)..)))))))(((((((...((((......)))))))))))... ( -36.10)
>consensus
_____AUGAAGGCCAGAAGGACACGCCCCCUCACACGCACAGUGCGUAUGAUUUCGGUUUUUGUGUCCUUUGCUGGUGACAUAUGUUAAUGAUCUGGCAGCGAUUUCUGGGUCAUUUAAA
......((((((((.((((((((((((...(((.((((.....)))).)))....)))....)))))))))((((.((((((......))).)).).))))........)))).)))).. (-35.39 = -34.07 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,400,905 – 5,401,020
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.11
Mean single sequence MFE -34.63
Consensus MFE -31.79
Energy contribution -32.90
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -2.64
Structure conservation index 0.92
SVM decision value 1.54
SVM RNA-class probability 0.962228
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400905 115 - 23771897
UUUAAAUGACCCAGAAAUCGCUGCCAGAUCAUUAACAUAUGUCACCAGCAAAGGACACAAAAACCGAAAUCAUACGCACUGUGCGUGUGAGGGGGCGUGUCCUUCUGGUCUUCAU-----
.......((((.((((...((((...((.(((......)))))..))))...((((((.....((....((((((((.....)))))))).))...)))))))))))))).....----- ( -38.20)
>DroSec_CAF1 49757 115 - 1
UUUAAAUGACCCAGAAAUCGCUGCCAGAUCAUUAACAUAUGUCACCAGCAAAGGACACAAAAACCGAAAUCAUACGCACUGUGCGUGCGAGGGGGCGUGUCCUUCUGGCCUUCAU-----
.....((((.((((((...((((...((.(((......)))))..))))...((((((.....(((....)...(((((.....))))).))....))))))))))))...))))----- ( -33.70)
>DroYak_CAF1 49776 120 - 1
UUUAAAUGACACAGAAAUCGCUGCCAGAUCAUUUACAUAUGUCACCAGCAAAGGACACAAAAACCAAAAUCAUACGCCCUGUGCGUGUGAGGGGGCGUAUCCUUUUUGCCUUCAUAUGUA
...(((((((.(((......)))...).))))))(((((((....(((.((((((.((.....((....((((((((.....)))))))).))...)).)))))))))....))))))). ( -32.00)
>consensus
UUUAAAUGACCCAGAAAUCGCUGCCAGAUCAUUAACAUAUGUCACCAGCAAAGGACACAAAAACCGAAAUCAUACGCACUGUGCGUGUGAGGGGGCGUGUCCUUCUGGCCUUCAU_____
.....((((.((((((...((((...((.(((......)))))..))))...((((((.....((....((((((((.....)))))))).))...))))))))))))...))))..... (-31.79 = -32.90 +   1.11)

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 10:20:49 2006