Locus 4786

Sequence ID 3R_DroMel_CAF1
Location 12,516,307 – 12,516,428
Length 121
Max. P 0.829825
window7852 window7853 window7854

overview

Window 2

Location 12,516,307 – 12,516,403
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.48
Mean single sequence MFE -31.63
Consensus MFE -19.58
Energy contribution -19.83
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.62
SVM decision value 0.49
SVM RNA-class probability 0.758389
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12516307 96 + 27905053
UAAAGCAACA--CGCGGCGCAACAUGCA---------------------ACGUGCAACAUGCAACAUGCGAGUUGGCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGGCUGCGGA-CUG
..........--((((((.((((.((((---------------------...(((.....)))...)))).)))).((((...((((((.......))))))..))))))))))..-... ( -34.00)
>DroPse_CAF1 3601 112 + 1
UAAAGCAACA--CGCGGUGCAACAUGCAGCGUGCAGCAUGCAGCAGGCAGCAUGCAGCAUGCACCAUGCGAGCUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGG-----GA-CUG
...(((....--((((((((.....)).((((((.((((((........)))))).)))))))))..))).))).(((((...((((((.......))))))..)))))-----..-... ( -42.70)
>DroSec_CAF1 5338 96 + 1
UAAAGCAACA--CGCGGCGCAACAUGCA---------------------AAGUGCAACAUGCAACAUGCGAGUUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGGCUUUGGA-CUG
((((((....--.((((.(((((.((((---------------------...(((.....)))...)))).)))))..)))).((((((.......))))))......))))))..-... ( -31.30)
>DroYak_CAF1 2180 96 + 1
UAAAGCAACA--CGCGGCGCAACAUGCA---------------------ACGUGCAACAUGCAACAUGCGAGCUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGGCUAUGCA-AUG
....(((...--.((..((((...((((---------------------..........))))...)))).)).((((((...((((((.......))))))..))))))..))).-... ( -30.70)
>DroAna_CAF1 6275 92 + 1
UAAAGCAACACACGCGGUGCAACAUG----------------------------CAACAUGCAACAUGCGAGCUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGGAAAUGGGAAAG
.............((..((((...((----------------------------(.....)))...)))).))..(((((...((((((.......))))))..)))))........... ( -22.50)
>DroPer_CAF1 7587 91 + 1
UAAAGCAACA--CGCGGUGCAACAUGCA---------------------GCAUGCAGCAUGCAACAUGCGAGCUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGG-----AA-AUG
...(((....--((((.((((...(((.---------------------....)))...))))...)))).))).(((((...((((((.......))))))..)))))-----..-... ( -28.60)
>consensus
UAAAGCAACA__CGCGGCGCAACAUGCA_____________________ACGUGCAACAUGCAACAUGCGAGCUGCCAUUGCACGUUCCGGGAAUAGGAAUGGAAAUGGCU_UGGA_AUG
............((((..(((...((((........................))))...)))....)))).....(((((...((((((.......))))))..)))))........... (-19.58 = -19.83 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,516,307 – 12,516,403
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.48
Mean single sequence MFE -30.39
Consensus MFE -21.19
Energy contribution -21.05
Covariance contribution -0.14
Combinations/Pair 1.11
Mean z-score -2.11
Structure conservation index 0.70
SVM decision value 0.71
SVM RNA-class probability 0.829825
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12516307 96 - 27905053
CAG-UCCGCAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGCCAACUCGCAUGUUGCAUGUUGCACGU---------------------UGCAUGUUGCGCCGCG--UGUUGCUUUA
(((-..(((.((((.......(((.......)))((((((((((.((((..((.....))..))))..)))---------------------))))))))).)).)))--..)))..... ( -29.40)
>DroPse_CAF1 3601 112 - 1
CAG-UC-----CCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGGUGCAUGCUGCAUGCUGCCUGCUGCAUGCUGCACGCUGCAUGUUGCACCGCG--UGUUGCUUUA
...-..-----.((((.((.((((.......)))).).).))))(((((.(((..((((((....((((((.((.(((........))).)).)))))))))))))))--.))))).... ( -41.70)
>DroSec_CAF1 5338 96 - 1
CAG-UCCAAAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAACUCGCAUGUUGCAUGUUGCACUU---------------------UGCAUGUUGCGCCGCG--UGUUGCUUUA
...-...(((((........((((.......)))).(((((((((((((......))))).))))))))..---------------------.((((((......)))--))).))))). ( -27.20)
>DroYak_CAF1 2180 96 - 1
CAU-UGCAUAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGUUGCAUGUUGCACGU---------------------UGCAUGUUGCGCCGCG--UGUUGCUUUA
(((-(((((..((..................))...))))))))(((((.(((.(((.((((((.......---------------------.)))))).)))..)))--.))))).... ( -31.27)
>DroAna_CAF1 6275 92 - 1
CUUUCCCAUUUCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGUUGCAUGUUG----------------------------CAUGUUGCACCGCGUGUGUUGCUUUA
...............................(.((((((((((((((((......))))).)))))----------------------------)))))).)...(((.....))).... ( -23.80)
>DroPer_CAF1 7587 91 - 1
CAU-UU-----CCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGUUGCAUGCUGCAUGC---------------------UGCAUGUUGCACCGCG--UGUUGCUUUA
...-..-----.((((.((.((((.......)))).).).))))(((((.(((.(((.((((((.......---------------------.)))))).)))..)))--.))))).... ( -29.00)
>consensus
CAG_UCCA_AGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGUUGCAUGUUGCACGU_____________________UGCAUGUUGCACCGCG__UGUUGCUUUA
............((((.((.((((.......)))).).).))))(((((.(((.(((.((((((.............................)))))).)))..)))...))))).... (-21.19 = -21.05 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,516,333 – 12,516,428
Length 95
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 84.28
Mean single sequence MFE -22.40
Consensus MFE -17.97
Energy contribution -18.38
Covariance contribution 0.42
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.80
SVM decision value -0.02
SVM RNA-class probability 0.525503
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12516333 95 - 27905053
CCAUUCCAGUU-----CCCAAUCCCAGCCCCAGUCCGCAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGCCAACUCGCAUGUUGCAUGUUGCACGU---------
...........-----..........((........))............(((.......)))(((((((((..((((......))))...)))))))))--------- ( -17.60)
>DroPse_CAF1 3639 104 - 1
GGGUUCAAGUUGCAGUCCCAGUGCCAGUCCCAGUC-----CCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGGUGCAUGCUGCAUGCUGCCUGCUG
((((...(((((((((....(..(((...(.(((.-----(((((.((.((((.......)))).).).)))))..))).)..)))..)..)))))).))))))).... ( -29.50)
>DroSec_CAF1 5364 95 - 1
CCAUUCCAGUU-----CCCAAUCCCAGCCGCAGUCCAAAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAACUCGCAUGUUGCAUGUUGCACUU---------
........(((-----(((.......)..((........))...................)))))(((((((((((((......))))).))))))))..--------- ( -20.70)
>DroSim_CAF1 5461 95 - 1
CCAUUCCAGUU-----CCCAAUCCCAGCCCCAGUCCACAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAACUCGCAUGUUGCAUGUUGCACGU---------
...........-----..................................(((.......)))(((((((((((((((......))))).))))))))))--------- ( -21.40)
>DroEre_CAF1 2960 90 - 1
-----CCAGUU-----CCCAAUUCCAGCUCCAUUCCACAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAACUCGCAUGUUGCAUGUUGCACGU---------
-----......-----..........(((.........))).........(((.......)))(((((((((((((((......))))).))))))))))--------- ( -21.60)
>DroYak_CAF1 2206 95 - 1
CCAUUCCAGUU-----CCCAACUCCAGCCCCAUUGCAUAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAGCUCGCAUGUUGCAUGUUGCACGU---------
........(((-----((........((......))((((............))))....)))))(((((((((((((......))))).))))))))..--------- ( -23.60)
>consensus
CCAUUCCAGUU_____CCCAAUCCCAGCCCCAGUCCACAGCCAUUUCCAUUCCUAUUCCCGGAACGUGCAAUGGCAACUCGCAUGUUGCAUGUUGCACGU_________
.................................................((((.......))))((((((((((((((......))))).))))))))).......... (-17.97 = -18.38 +   0.42)

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 11:38:54 2006