Locus 66

Sequence ID 4_DroMel_CAF1
Location 523,607 – 523,857
Length 250
Max. P 0.982435
window100 window101 window102 window103 window104 window105

overview

Window 0

Location 523,607 – 523,701
Length 94
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 80.15
Mean single sequence MFE -15.30
Consensus MFE -13.92
Energy contribution -13.70
Covariance contribution -0.22
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.91
SVM decision value 1.63
SVM RNA-class probability 0.968828
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523607 94 - 1281640
CAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCACUUUAUCACUGUACAUACAUAUAUGGCUCCAGUUUUUUGAAAGAAUGAU
.((((..(((((((.((.......)).))))))).))))......((((...((((..((((....))))....))))......))))...... ( -18.60)
>DroSec_CAF1 29914 74 - 1
CAGUCAGUUGGCGACACAAAAGUAGUUUUGCCAAGGACUUUACCACCUUAUAA--------------------CCACUUUUUUUAAAUAAUGAU
.((((..(((((((.((.......)).))))))).))))..............--------------------..................... ( -13.50)
>DroSim_CAF1 30764 74 - 1
CAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCACCUUAUAA--------------------CCACUUUUUUUAAAUAAUGAU
.((((..(((((((.((.......)).))))))).))))..............--------------------..................... ( -13.80)
>consensus
CAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCACCUUAUAA____________________CCACUUUUUUUAAAUAAUGAU
.((((..(((((((.((.......)).))))))).))))....................................................... (-13.92 = -13.70 +  -0.22) 

alignment

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secondary structure

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Window 1

Location 523,634 – 523,741
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.34
Mean single sequence MFE -32.12
Consensus MFE -22.75
Energy contribution -22.75
Covariance contribution 0.00
Combinations/Pair 1.14
Mean z-score -2.34
Structure conservation index 0.71
SVM decision value 1.91
SVM RNA-class probability 0.982435
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523634 107 + 1281640
AUAUGUAUGUACAGUGAUAAAG-------------UGGUAAAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACUGGU
....................((-------------(((((.((((.(((((((.((.......)).)))))))..))))...(((((((((.......))))))..))).)))))))... ( -31.50)
>DroSec_CAF1 29935 93 + 1
--------------UUAUAAGG-------------UGGUAAAGUCCUUGGCAAAACUACUUUUGUGUCGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGU
--------------......((-------------(((((.((((.(((((...((.......))...)))))..))))...(((((((((.......))))))..))).)))))))... ( -31.20)
>DroSim_CAF1 30785 93 + 1
--------------UUAUAAGG-------------UGGUAAAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGU
--------------......((-------------(((((.((((.(((((((.((.......)).)))))))..))))...(((((((((.......))))))..))).)))))))... ( -34.10)
>DroYak_CAF1 37747 104 + 1
--------------UCA--AGAUCGGACCUAUUCACGAUCGAGUCCUUGGCGAAACCACUUUUGUGUUGCCAACUGGCUGCAGUAGGUCGAUCACCUUUCGACUGUCACCUGCCACUGGU
--------------...--.(((((((.....)).))))).......((((((...(((....)))))))))((..(..((((..((((((.......)))))).....))))..)..)) ( -31.70)
>consensus
______________UUAUAAGG_____________UGGUAAAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGU
...................................((((..((((.(((((((.((.......)).)))))))..))))((.(((((((((.......))))))..)))..)).)))).. (-22.75 = -22.75 +   0.00) 

alignment

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secondary structure

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Window 2

Location 523,634 – 523,741
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.34
Mean single sequence MFE -29.50
Consensus MFE -22.91
Energy contribution -23.10
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.78
SVM decision value 0.58
SVM RNA-class probability 0.788860
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523634 107 - 1281640
ACCAGUGGCAGGUGACAGUCGAAAGGUGAUCGACCCACAGCAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCA-------------CUUUAUCACUGUACAUACAUAU
..((((((.(((((...(((((.......))))).......((((..(((((((.((.......)).))))))).))))....))-------------)))..))))))........... ( -29.30)
>DroSec_CAF1 29935 93 - 1
ACCGGUGGCAGGUGACAGUCGAAAGGUGAUCGACCCACAGCAGUCAGUUGGCGACACAAAAGUAGUUUUGCCAAGGACUUUACCA-------------CCUUAUAA--------------
...(((((...(((...(((((.......))))).)))...((((..(((((((.((.......)).))))))).))))...)))-------------))......-------------- ( -29.30)
>DroSim_CAF1 30785 93 - 1
ACCGGUGGCAGGUGACAGUCGAAAGGUGAUCGACCCACAGCAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCA-------------CCUUAUAA--------------
...(((((...(((...(((((.......))))).)))...((((..(((((((.((.......)).))))))).))))...)))-------------))......-------------- ( -29.60)
>DroYak_CAF1 37747 104 - 1
ACCAGUGGCAGGUGACAGUCGAAAGGUGAUCGACCUACUGCAGCCAGUUGGCAACACAAAAGUGGUUUCGCCAAGGACUCGAUCGUGAAUAGGUCCGAUCU--UGA--------------
(((..((((.(....).))))...)))((((((((((.....(((....)))..(((.....(((.....)))..((.....)))))..))))).))))).--...-------------- ( -29.80)
>consensus
ACCAGUGGCAGGUGACAGUCGAAAGGUGAUCGACCCACAGCAGUCAGUUGGCAACACAAAAGUAGUUUUGCCAAGGACUUUACCA_____________CCUUAUAA______________
....((((..(....).(((((.......)))))))))...((((..(((((((.((.......)).))))))).))))......................................... (-22.91 = -23.10 +   0.19) 

alignment

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secondary structure

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dotplot

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Window 3

Location 523,661 – 523,777
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.25
Mean single sequence MFE -30.57
Consensus MFE -28.44
Energy contribution -28.62
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.94
Structure conservation index 0.93
SVM decision value 1.47
SVM RNA-class probability 0.956648
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523661 116 + 1281640
AAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACUGGUCACGGCAAUUUCACCCGCAUACACCUGUAUACAU----AU
.((((.(((((((.((.......)).)))))))..))))((((((((((((.......))))))...(((.......)))))))))..........(.((((....)))).)..----.. ( -33.70)
>DroSec_CAF1 29948 120 + 1
AAGUCCUUGGCAAAACUACUUUUGUGUCGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGUCACGGCAAUUACACCCGCAUACACCUAUAUACAUACUUAU
.((((.(((((...((.......))...)))))..))))((((((((((((.......))))))...(((.......))))))))).................................. ( -28.50)
>DroSim_CAF1 30798 120 + 1
AAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGUCACGGCAAUUACACCCGCAUACACCUAUAUACAUACUUAU
.((((.(((((((.((.......)).)))))))..))))((((((((((((.......))))))...(((.......))))))))).................................. ( -31.40)
>DroYak_CAF1 37771 108 + 1
GAGUCCUUGGCGAAACCACUUUUGUGUUGCCAACUGGCUGCAGUAGGUCGAUCACCUUUCGACUGUCACCUGCCACUGGUCACGGCAAUUACACCCGCAUACAUGUAU------------
.........(((....(((....)))(((((.((..(..((((..((((((.......)))))).....))))..)..))...))))).......)))..........------------ ( -28.70)
>consensus
AAGUCCUUGGCAAAACUACUUUUGUGUUGCCAACUGACUGCUGUGGGUCGAUCACCUUUCGACUGUCACCUGCCACCGGUCACGGCAAUUACACCCGCAUACACCUAUAUACAU____AU
.((((.(((((((.((.......)).)))))))..))))...(((((((((.......))))((((.(((.......))).))))........)))))...................... (-28.44 = -28.62 +   0.19) 

alignment

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secondary structure

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Window 4

Location 523,741 – 523,857
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.03
Mean single sequence MFE -23.40
Consensus MFE -15.06
Energy contribution -16.50
Covariance contribution 1.44
Combinations/Pair 1.21
Mean z-score -1.88
Structure conservation index 0.64
SVM decision value 0.18
SVM RNA-class probability 0.621577
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523741 116 + 1281640
CACGGCAAUUUCACCCGCAUACACCUGUAUACAU----AUGUACAUAAACUGGCACAUCAGGGUUUUUACUUAAUUGGGUUCUUUUUAAGCCUUGCUGUUGCCUGCCGGCUUCUCCCUAA
..(((((..................((((((...----.))))))......((((((.((((((((..((((....)))).......)))))))).)).)))))))))............ ( -27.80)
>DroSec_CAF1 30028 120 + 1
CACGGCAAUUACACCCGCAUACACCUAUAUACAUACUUAUAUACAUACACUGGCACAUCUCGGUUUUUACUUAAUUGGGUUCUUUUUAAGCCUUGCUGUUGCCUGCCGUCUUCUCCCUAA
.((((((..................((((((......))))))........((((((.(..(((((..((((....)))).......)))))..).)).))))))))))........... ( -21.10)
>DroSim_CAF1 30878 120 + 1
CACGGCAAUUACACCCGCAUACACCUAUAUACAUACUUAUAUACAUACACUGGCACAUCUCGGUUUUUACUUAAUUGGGUUCUUUUUAAGCCUUGCUGUUGCCUGCCGUCUUCUCCCUAA
.((((((..................((((((......))))))........((((((.(..(((((..((((....)))).......)))))..).)).))))))))))........... ( -21.10)
>DroYak_CAF1 37851 108 + 1
CACGGCAAUUACACCCGCAUACAUGUAU------------AUACAUACACUUGCACAUCGGGGUUUUAACUUAAUUGGGUUCUUUUUGAACCUUAAGGUUUCCUGUCGUCUACUCCCUAA
.(((((..........(((....(((((------------....)))))..)))......(((....(((((....((((((.....))))))..))))).))))))))........... ( -23.60)
>consensus
CACGGCAAUUACACCCGCAUACACCUAUAUACAU____AUAUACAUACACUGGCACAUCUCGGUUUUUACUUAAUUGGGUUCUUUUUAAGCCUUGCUGUUGCCUGCCGUCUUCUCCCUAA
..(((((..................((((((......))))))........((((((.((((((((..((((....)))).......)))))))).)).)))))))))............ (-15.06 = -16.50 +   1.44) 

alignment

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secondary structure

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dotplot

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Window 5

Location 523,741 – 523,857
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.03
Mean single sequence MFE -31.42
Consensus MFE -18.64
Energy contribution -19.70
Covariance contribution 1.06
Combinations/Pair 1.16
Mean z-score -2.34
Structure conservation index 0.59
SVM decision value 0.11
SVM RNA-class probability 0.590084
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 523741 116 - 1281640
UUAGGGAGAAGCCGGCAGGCAACAGCAAGGCUUAAAAAGAACCCAAUUAAGUAAAAACCCUGAUGUGCCAGUUUAUGUACAU----AUGUAUACAGGUGUAUGCGGGUGAAAUUGCCGUG
...(((..(((((.((.(....).))..)))))........)))......((((..((((..((((((........))))))----..((((((....))))))))))....)))).... ( -31.50)
>DroSec_CAF1 30028 120 - 1
UUAGGGAGAAGACGGCAGGCAACAGCAAGGCUUAAAAAGAACCCAAUUAAGUAAAAACCGAGAUGUGCCAGUGUAUGUAUAUAAGUAUGUAUAUAGGUGUAUGCGGGUGUAAUUGCCGUG
...........(((((((...(((.....((((((...........)))))).....(((..(((..((.((((((((((....)))))))))).))..))).))).)))..))))))). ( -33.10)
>DroSim_CAF1 30878 120 - 1
UUAGGGAGAAGACGGCAGGCAACAGCAAGGCUUAAAAAGAACCCAAUUAAGUAAAAACCGAGAUGUGCCAGUGUAUGUAUAUAAGUAUGUAUAUAGGUGUAUGCGGGUGUAAUUGCCGUG
...........(((((((...(((.....((((((...........)))))).....(((..(((..((.((((((((((....)))))))))).))..))).))).)))..))))))). ( -33.10)
>DroYak_CAF1 37851 108 - 1
UUAGGGAGUAGACGACAGGAAACCUUAAGGUUCAAAAAGAACCCAAUUAAGUUAAAACCCCGAUGUGCAAGUGUAUGUAU------------AUACAUGUAUGCGGGUGUAAUUGCCGUG
...((.(((....(((.(....).....(((((.....))))).......)))...((((((.((((((.(((((....)------------)))).)))))))))).)).))).))... ( -28.00)
>consensus
UUAGGGAGAAGACGGCAGGCAACAGCAAGGCUUAAAAAGAACCCAAUUAAGUAAAAACCCAGAUGUGCCAGUGUAUGUAUAU____AUGUAUAUAGGUGUAUGCGGGUGUAAUUGCCGUG
...........(((((((((....))..............((((..................((((((........))))))......((((((....))))))))))....))))))). (-18.64 = -19.70 +   1.06) 

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 09:33:18 2006