Locus 7131

Sequence ID 3L_DroMel_CAF1
Location 19,177,657 – 19,177,895
Length 238
Max. P 0.994957
window11577 window11578 window11579 window11580

overview

Window 7

Location 19,177,657 – 19,177,777
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.06
Mean single sequence MFE -34.77
Consensus MFE -29.90
Energy contribution -29.94
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.86
SVM decision value 1.25
SVM RNA-class probability 0.935967
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19177657 120 + 23771897
GGCUAUAUUGUUGGCCGACUCCCUUGACAUUUCUAAUGGCGCAUGGCGCACAUACACCGACUGGCCAAGAGAGAUUUAUUAUCGGCUGUCAUUGUCGACGGCCAACACACACCCACACCC
((......(((((((((.(((.((((.........(((((((...)))).)))...((....)).)))).)))........(((((.......)))))))))))))).....))...... ( -37.20)
>DroSec_CAF1 6124 118 + 1
GGCUAUAUUGUUGGCCGACUCCCUUGACAUUUCUAAUGGCGCAUGGCGCACAUACACCGACUGGCCAAGAGAGAUUUAUUAUCGGCUGUCAUUGUCGACGGCCAACACACACACCCAC--
((......(((((((((.(((.((((.........(((((((...)))).)))...((....)).)))).)))........(((((.......)))))))))))))).......))..-- ( -37.02)
>DroSim_CAF1 9142 118 + 1
GGCUAUAUUGUUGGCCGACUCCCUUGACAUUUCUAAUGGCGCAUGGCGCACAUACACCGACUGGCCAAGAGAGAUUUAUUAUCGGCUGUCAUUGUCGACGGCCAACACACACACCCAC--
((......(((((((((.(((.((((.........(((((((...)))).)))...((....)).)))).)))........(((((.......)))))))))))))).......))..-- ( -37.02)
>DroEre_CAF1 8893 110 + 1
GGCUAUAUUGUUGGUCGAGUCCCUUGACAUUUCUAAUGGCGCAUAGAGCAC----ACAGACUGGCCAAGAGAGAUUUAUUAUCGGCUGUCAUUGUCGAAGGCCAACACA----CCCAG--
((......((((((((..(((....)))((((((..((((((.....)).(----(.....))))))..))))))......(((((.......))))).))))))))..----.))..-- ( -30.50)
>DroYak_CAF1 11040 114 + 1
GGCUAUAUUGUUGGCCGAGUCCCUUGACAUUUCUAAUGGCGCAUAGCGCACAUACACAGACUGGCCAAAAGAGAUUUAUUAUCGGCUGUCAUUGUCGAAGGCCAACACA----CCCAC--
((......((((((((..(((....)))((((((..((((((.....)).....((.....))))))..))))))......(((((.......))))).))))))))..----.))..-- ( -32.10)
>consensus
GGCUAUAUUGUUGGCCGACUCCCUUGACAUUUCUAAUGGCGCAUGGCGCACAUACACCGACUGGCCAAGAGAGAUUUAUUAUCGGCUGUCAUUGUCGACGGCCAACACACAC_CCCAC__
........((((((((............((((((..((((((.....)).....((.....))))))..))))))......(((((.......))))).))))))))............. (-29.90 = -29.94 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,177,657 – 19,177,777
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.06
Mean single sequence MFE -42.54
Consensus MFE -32.40
Energy contribution -34.00
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.76
SVM decision value 1.32
SVM RNA-class probability 0.942194
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19177657 120 - 23771897
GGGUGUGGGUGUGUGUUGGCCGUCGACAAUGACAGCCGAUAAUAAAUCUCUCUUGGCCAGUCGGUGUAUGUGCGCCAUGCGCCAUUAGAAAUGUCAAGGGAGUCGGCCAACAAUAUAGCC
......((.(((((((((((((.(..(..(((((...(((.....)))(((..((((((...(((((....))))).)).))))..)))..)))))..)..).)))))))).))))).)) ( -47.30)
>DroSec_CAF1 6124 118 - 1
--GUGGGUGUGUGUGUUGGCCGUCGACAAUGACAGCCGAUAAUAAAUCUCUCUUGGCCAGUCGGUGUAUGUGCGCCAUGCGCCAUUAGAAAUGUCAAGGGAGUCGGCCAACAAUAUAGCC
--..((.(((((.(((((((((.(..(..(((((...(((.....)))(((..((((((...(((((....))))).)).))))..)))..)))))..)..).)))))))))))))).)) ( -48.20)
>DroSim_CAF1 9142 118 - 1
--GUGGGUGUGUGUGUUGGCCGUCGACAAUGACAGCCGAUAAUAAAUCUCUCUUGGCCAGUCGGUGUAUGUGCGCCAUGCGCCAUUAGAAAUGUCAAGGGAGUCGGCCAACAAUAUAGCC
--..((.(((((.(((((((((.(..(..(((((...(((.....)))(((..((((((...(((((....))))).)).))))..)))..)))))..)..).)))))))))))))).)) ( -48.20)
>DroEre_CAF1 8893 110 - 1
--CUGGG----UGUGUUGGCCUUCGACAAUGACAGCCGAUAAUAAAUCUCUCUUGGCCAGUCUGU----GUGCUCUAUGCGCCAUUAGAAAUGUCAAGGGACUCGACCAACAAUAUAGCC
--..((.----(((((((....((((...........(((.....)))(((((((((...((((.----((((.....))))...))))...))))))))).))))....))))))).)) ( -32.90)
>DroYak_CAF1 11040 114 - 1
--GUGGG----UGUGUUGGCCUUCGACAAUGACAGCCGAUAAUAAAUCUCUUUUGGCCAGUCUGUGUAUGUGCGCUAUGCGCCAUUAGAAAUGUCAAGGGACUCGGCCAACAAUAUAGCC
--...((----(.((((((((.....(..(((((...(((.....)))(((..((((((....((((....))))..)).))))..)))..)))))..).....)))))))).....))) ( -36.10)
>consensus
__GUGGG_GUGUGUGUUGGCCGUCGACAAUGACAGCCGAUAAUAAAUCUCUCUUGGCCAGUCGGUGUAUGUGCGCCAUGCGCCAUUAGAAAUGUCAAGGGAGUCGGCCAACAAUAUAGCC
.............(((((((((....(..(((((...(((.....)))(((..((((((...(((((....))))).)).))))..)))..)))))..)....)))))))))........ (-32.40 = -34.00 +   1.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,177,777 – 19,177,895
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.06
Mean single sequence MFE -29.70
Consensus MFE -24.60
Energy contribution -24.64
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.83
SVM decision value 0.75
SVM RNA-class probability 0.839672
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19177777 118 + 23771897
AACAUAUAUGUA--UGUAUUUAUAUGUUUUUGGCCACCAGCAAUCAUCGCCCACCCUCCUAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGCGCGAUGGCUGCUGCUUUG
((((((((....--......)))))))).........(((((..((((((....((.....)).((.(((.(((.((((.......)))).))).)).).))))))))..)))))..... ( -30.50)
>DroSec_CAF1 6242 113 + 1
-----GGAUAUA--UGUAUUUAUAUGUUUUUGGCCACCAGCAAUCAUCGCCCACCCUCCCAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGCGCGAUGGCUGCUGCUUUG
-----(((((((--((....)))))))))........(((((..((((((....((.....)).((.(((.(((.((((.......)))).))).)).).))))))))..)))))..... ( -30.10)
>DroSim_CAF1 9260 113 + 1
-----GGAUAUA--UGUAUUUAUAUGUUUUUGGCCACCAGCAAUCAUCGCCCACCCUCCCAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGCGCGAUGGCUGGUGCUUUG
-----(((((((--((....)))))))))..(((.((((((...((((((....((.....)).((.(((.(((.((((.......)))).))).)).).)))))))))))))))))... ( -32.40)
>DroEre_CAF1 9003 109 + 1
-----AGAUAU------AUUUAUAUGUUUUUGGCCACCAGCAAUCAUCGCCCAUCCUCCGAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGCGCGAUGGCUGCUGCCUUG
-----((((((------(....)))))))..(((....((((..((((((...(((.....)))((.(((.(((.((((.......)))).))).)).).))))))))..)))))))... ( -29.90)
>DroYak_CAF1 11154 115 + 1
-----AGAUAUACUCGUAUUUAUAUGCUUUUGGCCACCAGCAAUCAUCGCCCACCCUCUCAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGUGCGAUGGCUGCUGCUUUG
-----..........((((....))))..........(((((..((((((.((..(((....)))...((.(((.((((.......)))).))).))..)).))))))..)))))..... ( -25.60)
>consensus
_____AGAUAUA__UGUAUUUAUAUGUUUUUGGCCACCAGCAAUCAUCGCCCACCCUCCCAGGAGCCGCAAAACAUUUGUUAUAAUCAAAAGUUCUGACUGCGCGAUGGCUGCUGCUUUG
.....................................(((((..((((((....((.....)).((.(((.(((.((((.......)))).))).)).).))))))))..)))))..... (-24.60 = -24.64 +   0.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,177,777 – 19,177,895
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.06
Mean single sequence MFE -33.46
Consensus MFE -30.42
Energy contribution -30.62
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.91
SVM decision value 2.53
SVM RNA-class probability 0.994957
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19177777 118 - 23771897
CAAAGCAGCAGCCAUCGCGCAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUAGGAGGGUGGGCGAUGAUUGCUGGUGGCCAAAAACAUAUAAAUACA--UACAUAUAUGUU
.....(((((..((((((.(((.((((((.((((.......)))).)))))))..(((....)))..)).))))))..))))).........((((((((......--....)))))))) ( -35.40)
>DroSec_CAF1 6242 113 - 1
CAAAGCAGCAGCCAUCGCGCAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUGGGAGGGUGGGCGAUGAUUGCUGGUGGCCAAAAACAUAUAAAUACA--UAUAUCC-----
.....(((((..((((((.(((.((((((.((((.......)))).)))))))..(((....)))..)).))))))..)))))(((........))).........--.......----- ( -32.70)
>DroSim_CAF1 9260 113 - 1
CAAAGCACCAGCCAUCGCGCAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUGGGAGGGUGGGCGAUGAUUGCUGGUGGCCAAAAACAUAUAAAUACA--UAUAUCC-----
.....(((((((((((((.(((.((((((.((((.......)))).)))))))..(((....)))..)).))))))...)))))))....................--.......----- ( -34.50)
>DroEre_CAF1 9003 109 - 1
CAAGGCAGCAGCCAUCGCGCAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUCGGAGGAUGGGCGAUGAUUGCUGGUGGCCAAAAACAUAUAAAU------AUAUCU-----
...((((.((((((((((.(((.((((((.((((.......)))).)))))))..(((....)))..)).))))))...)))).).)))..............------......----- ( -33.40)
>DroYak_CAF1 11154 115 - 1
CAAAGCAGCAGCCAUCGCACAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUGAGAGGGUGGGCGAUGAUUGCUGGUGGCCAAAAGCAUAUAAAUACGAGUAUAUCU-----
.....(((((..((((((...(.((((((.((((.......)))).)))))))..(.(((....))).).))))))..)))))...((.....))....................----- ( -31.30)
>consensus
CAAAGCAGCAGCCAUCGCGCAGUCAGAACUUUUGAUUAUAACAAAUGUUUUGCGGCUCCUGGGAGGGUGGGCGAUGAUUGCUGGUGGCCAAAAACAUAUAAAUACA__UAUAUCU_____
.....(((((..((((((.(((.((((((.((((.......)))).)))))))..(((....)))..)).))))))..)))))(((........)))....................... (-30.42 = -30.62 +   0.20)

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 12:38:50 2006