Locus 2815

Sequence ID 2L_DroMel_CAF1
Location 8,034,959 – 8,035,129
Length 170
Max. P 0.916504
window4474 window4475 window4476 window4477

overview

Window 4

Location 8,034,959 – 8,035,066
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 78.52
Mean single sequence MFE -24.22
Consensus MFE -16.80
Energy contribution -16.43
Covariance contribution -0.37
Combinations/Pair 1.19
Mean z-score -1.58
Structure conservation index 0.69
SVM decision value 0.11
SVM RNA-class probability 0.590236
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8034959 107 + 22407834
AAAUAAUAUGUAUAUCAAUAGCUAAGCACACAGCUAUUCAGCUGACCUGCAACGUUGGAGCGUGGGUGCUGACCACUUCCCCUCCAUUGUUGGUUUUAUGUUUUUUA
(((.((((((...((((((((....(((..(((((....)))))...))).....(((((.(..((((.....))))..).)))))))))))))..)))))).))). ( -29.10)
>DroSec_CAF1 2649 96 + 1
U---------CAUAUCAAUAACUAAGCA--CAGCUAUUCAACUGACCUGCAACGUUGGAGCGUGGGUGCUGACCACUUCCCCUCUAUUGUUGGUUUUAUGUUAUUUU
.---------......((((((.((((.--(((........))).....(((((.(((((.(..((((.....))))..).))))).)))))))))...)))))).. ( -22.60)
>DroSim_CAF1 2653 98 + 1
U---------CAUAUCAAUAACUAAGCACACAGCUAUUCAACUGACCUGCAACGUUGGAGCGUGGGUGCUGACCACUUCCCCUCCAUUGUUGGUUUUAUGUUAUUUU
.---------......((((((.((((...(((........))).....(((((.(((((.(..((((.....))))..).))))).)))))))))...)))))).. ( -24.90)
>DroYak_CAF1 2894 98 + 1
ACAUAAUACACAUAUCAAUCACUAAGCAGGCUGCUAUUUGACUGACCAGAAACGUAGAAGCGUGGGUGCUGCCCACUUCCCCUCCAUUUUUUGUGGU---------U
................((((((...((...((((..((((......))))...))))..))(((((.....)))))................)))))---------) ( -20.30)
>consensus
A_________CAUAUCAAUAACUAAGCACACAGCUAUUCAACUGACCUGCAACGUUGGAGCGUGGGUGCUGACCACUUCCCCUCCAUUGUUGGUUUUAUGUUAUUUU
...................(((..(((.....)))..............(((((.(((((.(..((((.....))))..).))))).))))))))............ (-16.80 = -16.43 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,034,959 – 8,035,066
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 78.52
Mean single sequence MFE -26.32
Consensus MFE -19.74
Energy contribution -19.30
Covariance contribution -0.44
Combinations/Pair 1.17
Mean z-score -1.66
Structure conservation index 0.75
SVM decision value 0.52
SVM RNA-class probability 0.769030
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8034959 107 - 22407834
UAAAAAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGCUGAAUAGCUGUGUGCUUAGCUAUUGAUAUACAUAUUAUUU
.......((....(((..(((((..((((..((((.......)))).))))..)))))..)))....))((((((((......))))))))................ ( -26.60)
>DroSec_CAF1 2649 96 - 1
AAAAUAACAUAAAACCAACAAUAGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGUUGAAUAGCUG--UGCUUAGUUAUUGAUAUG---------A
.......((((..(((..((((...((((..((((.......)))).))))...))))..)))....(.((((((((--....)))))))).)))))---------. ( -21.70)
>DroSim_CAF1 2653 98 - 1
AAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGUUGAAUAGCUGUGUGCUUAGUUAUUGAUAUG---------A
.......((((..(((..(((((..((((..((((.......)))).))))..)))))..)))....(.((((((((......)))))))).)))))---------. ( -26.30)
>DroYak_CAF1 2894 98 - 1
A---------ACCACAAAAAAUGGAGGGGAAGUGGGCAGCACCCACGCUUCUACGUUUCUGGUCAGUCAAAUAGCAGCCUGCUUAGUGAUUGAUAUGUGUAUUAUGU
.---------..((((..(((((.(((((..(((((.....))))).))))).)))))...((((((((...(((.....)))...)))))))).))))........ ( -30.70)
>consensus
AAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGUUGAAUAGCUGUGUGCUUAGUUAUUGAUAUG_________A
..................(((((..((((..((((.......)))).))))..)))))...((((((.(...(((.....)))...).))))))............. (-19.74 = -19.30 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,034,999 – 8,035,106
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 85.51
Mean single sequence MFE -20.50
Consensus MFE -17.69
Energy contribution -17.38
Covariance contribution -0.31
Combinations/Pair 1.11
Mean z-score -1.41
Structure conservation index 0.86
SVM decision value 0.07
SVM RNA-class probability 0.570292
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8034999 107 - 22407834
CCAGAAGUAUAACUAUGACGCCCCUGCAAAAAAUAAAAAAUAAAAAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGC
...............(((....(((((((.........................(((....))).((((..((((.......)))).))))....)))))))))).. ( -22.30)
>DroSec_CAF1 2678 107 - 1
CCAGAAGUAUAACUAUGACGCCCCAGCAAAAAAUAUAAAAAAAAUAACAUAAAACCAACAAUAGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGU
...............((((.(..((((...........................((.........))(((.((((.......))))..)))...))))..))))).. ( -17.30)
>DroSim_CAF1 2684 107 - 1
CCAGAAGUAUAACUAUGACGCCCCAGCAAAAAUAAUAAAAAAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGU
...............((((((....))...............................(((((..((((..((((.......)))).))))..)))))...)))).. ( -20.10)
>DroYak_CAF1 2934 97 - 1
UCAGAACUAAAACUAUGACGCCCCUGCAAAAUAAA-AAAAA---------ACCACAAAAAAUGGAGGGGAAGUGGGCAGCACCCACGCUUCUACGUUUCUGGUCAGU
((((((..............(((((.((.......-.....---------...........)).)))))..(((((.....)))))..........))))))..... ( -22.30)
>consensus
CCAGAAGUAUAACUAUGACGCCCCAGCAAAAAAAAUAAAAAAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGUCAGCACCCACGCUCCAACGUUGCAGGUCAGU
...............((((((....))...............................(((((..((((..((((.......)))).))))..)))))...)))).. (-17.69 = -17.38 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,035,030 – 8,035,129
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 85.52
Mean single sequence MFE -18.45
Consensus MFE -15.97
Energy contribution -16.54
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.87
SVM decision value 1.11
SVM RNA-class probability 0.916504
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8035030 99 - 22407834
UACUCUAACUGGCUAACUUUGUGCCAGAAGUAUAACUAUGACGCCCCUGCAAAAAAUAAAAAAUAAAAAACAUAAAACCAACAAUGGAGGGGAAGUGGU
((((....(((((.........))))).))))..(((((....(((((.((.................................)).)))))..))))) ( -20.81)
>DroSec_CAF1 2709 99 - 1
UAUUCUAACUGGCUAACUUUUUGCCAGAAGUAUAACUAUGACGCCCCAGCAAAAAAUAUAAAAAAAAUAACAUAAAACCAACAAUAGAGGGGAAGUGGU
........(((((.........))))).......(((((....((((.........................................))))..))))) ( -16.48)
>DroSim_CAF1 2715 99 - 1
UAUUCUAACUGGCUAACUUUUUGCCAGAAGUAUAACUAUGACGCCCCAGCAAAAAUAAUAAAAAAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGU
........(((((.........))))).......(((((....((((...........((.......))........(((....))).))))..))))) ( -18.30)
>DroYak_CAF1 2965 89 - 1
UACUCUAACUGGCUAACUUUGUGUCAGAACUAAAACUAUGACGCCCCUGCAAAAUAAA-AAAAA---------ACCACAAAAAAUGGAGGGGAAGUGGG
........(((((.........)))))........((((....(((((.((.......-.....---------...........)).)))))..)))). ( -18.20)
>consensus
UACUCUAACUGGCUAACUUUGUGCCAGAAGUAUAACUAUGACGCCCCAGCAAAAAAAAUAAAAAAAAUAACAUAAAACCAACAAUGGAGGGGAAGUGGU
........(((((.........)))))........((((....(((((.((.................................)).)))))..)))). (-15.97 = -16.54 +   0.56)

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 10:36:57 2006