Locus 3582

Sequence ID 3L_DroMel_CAF1
Location 10,542,044 – 10,542,187
Length 143
Max. P 0.749942
window5584 window5585 window5586

overview

Window 4

Location 10,542,044 – 10,542,155
Length 111
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 73.94
Mean single sequence MFE -45.33
Consensus MFE -27.21
Energy contribution -28.60
Covariance contribution 1.39
Combinations/Pair 1.11
Mean z-score -1.47
Structure conservation index 0.60
SVM decision value 0.47
SVM RNA-class probability 0.749942
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10542044 111 + 23771897
U-CCGUUUCUUUUUUCUC-UUUU--GAACAUGCAGCACAUGGUGCAGGCGGGCGUAGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGU
.-(((((.(((..(((..-....--)))....(((....((((((.(((((.((.(((((((.....))))))).)).))(((...))))))))))))....)))))).))))). ( -48.00)
>DroVir_CAF1 469219 106 + 1
---CCUUUGU-----CUGCCUCU-CUCAUUUGCAGCACAUGGUGCAGGCUGGCGUGGCGCCUUUUCCAGGCGCACCAGCUGGCUAUGCCGCAGCACCUGGACCGGCCGCUGCAGC
---.......-----........-.....(((((((....(((((.((((((....((((((.....)))))).))))))(((...)))...))))).((.....))))))))). ( -44.60)
>DroPse_CAF1 454141 107 + 1
U-CCGUCUCUCUUU-----AUCU--AUCCAUACAGCACAUGGUGCAGGCUGGCGUGGCGCCAUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCUCCAGGGCAGGCAGCAGCGGC
.-((((........-----....--.........((((...)))).((((((((..(((((.......)))))..).))))))).(((.((((((....))).))).))))))). ( -44.50)
>DroGri_CAF1 432488 103 + 1
---CUUUUCC-----CCG-UUCUCAUCAUUUACAGCACAUGGUGCAGACUGGAGUG---CCGUUUUCGGGCGCCCCGGCUGCCUAUGCGGCCGCACCAGGACCGGCGGCUGCGGC
---.......-----((.-...................((((.((((.((((.(((---((.......))))).))))))))))))((((((((..........)))))))))). ( -41.60)
>DroSim_CAF1 429788 111 + 1
U-CCGUUUCUUUUUUCUC-UUCU--GAACAUGCAGCACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGU
.-(((((.((((.(((..-..((--(......))).....(((((.(((((.((..((((((.....))))))..)).))(((...))))))))))))))....)))).))))). ( -48.70)
>DroAna_CAF1 415566 106 + 1
UGACAUUUUUUUUGU-------C--CAAAAUGCAGCACAUGGUGCAGGCGGGCGUAGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCUCCAGGUCCGGCAGCAGCAGC
.((((.......)))-------)--.....(((.((....(((..((.(((.((.(((((((.....))))))).)).))).))..)))((((.........)))).)).))).. ( -44.60)
>consensus
U_CCGUUUCUUUUU_CU__UUCU__GAACAUGCAGCACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCAGGUCCGGCAGCAGCGGC
..............................(((.((.(.((((((.(((.(((((((((((.......)))((....))..)))))))))))))))))......)..)).))).. (-27.21 = -28.60 +   1.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,542,044 – 10,542,155
Length 111
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 73.94
Mean single sequence MFE -43.83
Consensus MFE -27.16
Energy contribution -28.13
Covariance contribution 0.98
Combinations/Pair 1.16
Mean z-score -1.18
Structure conservation index 0.62
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10542044 111 - 23771897
ACCGCUGCUCCAGGAUUCGGUGCGGCGGCAUAGCCGGCCGGAGCGCCCGGAAAAGGCGCUACGCCCGCCUGCACCAUGUGCUGCAUGUUC--AAAA-GAGAAAAAAGAAACGG-A
.(((...((.(((.((..(((((((((((...)))((.((.((((((.......)))))).)).))))).)))))..)).)))....(((--....-..)))...))...)))-. ( -42.10)
>DroVir_CAF1 469219 106 - 1
GCUGCAGCGGCCGGUCCAGGUGCUGCGGCAUAGCCAGCUGGUGCGCCUGGAAAAGGCGCCACGCCAGCCUGCACCAUGUGCUGCAAAUGAG-AGAGGCAG-----ACAAAGG---
(((((((((.((......)))))))))))...((..((((((((((((.....))))))...))))))..)).((...((((((...(...-.)..))))-----.))..))--- ( -51.00)
>DroPse_CAF1 454141 107 - 1
GCCGCUGCUGCCUGCCCUGGAGCGGCGGCAUAGCCGGCCGGAGCGCCCGGAAAUGGCGCCACGCCAGCCUGCACCAUGUGCUGUAUGGAU--AGAU-----AAAGAGAGACGG-A
(((((((((.((......)))))))))))...((.(((.((.(((((.......)))))....)).))).)).(((((.....)))))..--....-----............-. ( -45.30)
>DroGri_CAF1 432488 103 - 1
GCCGCAGCCGCCGGUCCUGGUGCGGCCGCAUAGGCAGCCGGGGCGCCCGAAAACGG---CACUCCAGUCUGCACCAUGUGCUGUAAAUGAUGAGAA-CGG-----GGAAAAG---
((((....((...((((((((...(((.....))).))))))))...))....)))---).((((..(((.((.(((.........))).))))).-.))-----)).....--- ( -37.30)
>DroSim_CAF1 429788 111 - 1
ACCGCUGCUCCAGGAUUCGGUGCGGCGGCAUAGCCGGCCGGAGCGCCCGGAAAAGGCGCCACGCCCGCCUGCACCAUGUGCUGCAUGUUC--AGAA-GAGAAAAAAGAAACGG-A
.(((...((.(((.((..(((((((((((...)))((.((..(((((.......)))))..)).))))).)))))..)).)))....(((--....-..)))...))...)))-. ( -41.80)
>DroAna_CAF1 415566 106 - 1
GCUGCUGCUGCCGGACCUGGAGCGGCGGCAUAGCCGGCCGGAGCGCCCGGAAAAGGCGCUACGCCCGCCUGCACCAUGUGCUGCAUUUUG--G-------ACAAAAAAAAUGUCA
(((((((((.(((....))))))))))))...((.(((...((((((.......))))))..))).))..((((...)))).(((((((.--.-------......))))))).. ( -45.50)
>consensus
GCCGCUGCUGCCGGACCUGGUGCGGCGGCAUAGCCGGCCGGAGCGCCCGGAAAAGGCGCCACGCCAGCCUGCACCAUGUGCUGCAUGUUA__AGAA__AG_AAAAAGAAACGG_A
..((((.(..........).))))((((((((((.(((.((.(((((.......)))))....)).))).))....))))))))............................... (-27.16 = -28.13 +   0.98)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,542,076 – 10,542,187
Length 111
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 85.12
Mean single sequence MFE -60.52
Consensus MFE -44.42
Energy contribution -46.33
Covariance contribution 1.92
Combinations/Pair 1.09
Mean z-score -2.23
Structure conservation index 0.73
SVM decision value 0.07
SVM RNA-class probability 0.570738
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10542076 111 + 23771897
ACAUGGUGCAGGCGGGCGUAGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCGGCCGCCGC-------CCAACAACAGC
...((((((.(((((.((.(((((((.....))))))).)).))(((...)))))))))))).....(((.((.((((((((((...)))))))))).))-------)))........ ( -59.90)
>DroSec_CAF1 421545 111 + 1
ACAUGGUGCAGGCGGGCGUGGCGCCUUUCCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCGGCCGCCGC-------CCAACAGCAGC
...((((((.(((((.((..((((((.....))))))..)).))(((...)))))))))))).....(((.((.((((((((((...)))))))))).))-------)))........ ( -60.50)
>DroSim_CAF1 429820 111 + 1
ACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCGGCCGCCGC-------CCAACAACAGC
...((((((.(((((.((..((((((.....))))))..)).))(((...)))))))))))).....(((.((.((((((((((...)))))))))).))-------)))........ ( -60.50)
>DroEre_CAF1 430475 111 + 1
ACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCUCCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCGGCCGCCGC-------CCAACAGCAGC
...((.((..(((((.((..((((((.....))))))..)).))(((...(((((.((((((.....)))))).(((((....))))).))))).)))))-------)...)).)).. ( -61.20)
>DroYak_CAF1 430761 111 + 1
ACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCUCCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCCGCCGCCGC-------CCAACAGCAGC
...(((.((.(((((.((..((((((.....))))))..)(((((((...(((((.((((((.....)))))).)))))....))))..)))))))))))-------)))........ ( -61.30)
>DroMoj_CAF1 539142 100 + 1
ACAUGGUGCAGGCUGGCGUGGCGCCGUUUCCAGGCGCACCAGCCGGCUAUCCUGCCGCGCCAGGACCAGCGGCAGCGGCCGC---------------UGCUGGUGCGCCCACAGC---
...(((.((.((((((....(((((.......))))).))))))(((......)))(((((((...(((((((....)))))---------------))))))))))))))....--- ( -59.70)
>consensus
ACAUGGUGCAGGCGGGCGUGGCGCCUUUUCCGGGCGCUCCGGCCGGCUAUGCCGCCGCACCGAAUCCUGGAGCAGCGGUUGUUGCCGCAGCGGCCGCCGC_______CCAACAGCAGC
...((((((.(((.((...(((((((.....))))))))).)))(((......))))))))).........((.((((((((((...)))))))))).)).................. (-44.42 = -46.33 +   1.92)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:31 2006