Locus 3470

Sequence ID 3R_DroMel_CAF1
Location 9,374,219 – 9,374,346
Length 127
Max. P 0.934603
window5574 window5575 window5576

overview

Window 4

Location 9,374,219 – 9,374,319
Length 100
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 81.69
Mean single sequence MFE -27.50
Consensus MFE -19.18
Energy contribution -18.93
Covariance contribution -0.25
Combinations/Pair 1.35
Mean z-score -3.14
Structure conservation index 0.70
SVM decision value 1.24
SVM RNA-class probability 0.934603
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9374219 100 - 27905053
GCGUUGGCGUGCACACG---AUGAUGUGCAUGCAUGCGCUUU--CCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAAAU---AAAGGGGAAAGAAAAGCGAAAAC
((((..(((((((((..---....)))))))))..)).((((--(((.....((((((((.((....)).))))....))))---....)))))))....))...... ( -28.00)
>DroVir_CAF1 60650 86 - 1
-CGUGGGCGUGCACA------UGAUGUGCAUGCAUGCGUUUU---CUAAAUGAUUUCUAAAGAAUUUUUAUUGGGAAAAAC-------GACAAA-----AGCGAAAAC
-(((..((((((((.------....)))))))).((((((((---((.(((((.(((....)))...))))).)).)))))-------).))..-----.)))..... ( -25.40)
>DroPse_CAF1 8719 93 - 1
GCGCGGGCUUGCACA------UGAUGUGCAUGCAUGCGUUUU--CCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAAAGG--AAAAGCGAA-----AGCGAAAAC
(((((.((.(((((.------....))))).)).)))))(((--(((.........((((.((....)).))))......)))--))).((...-----.))...... ( -27.66)
>DroWil_CAF1 2590 103 - 1
AUGUGGGCGUGCACAUGCACAUGAUGUGCAUGCAUGCGUUUUUCCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGAAAAAGAGGCAAAAGCGAAA-----AGCGAAAAC
......(((((((..(((((.....))))))))))))(((((((.........(((((((.((....)).))))))).....((....))))))-----)))...... ( -30.80)
>DroMoj_CAF1 67806 87 - 1
GUGUGGGUGUGCACA------UGAUGUGCAUGCAUGCGUUUU---CUAAAUGAUUUCCAAGGAAUUUUUAUUGGGAAAAAC-------GAUGAA-----AGCGAAAAC
(((((.(((..((..------...))..))).)))))(((((---(.......(((((((..........)))))))....-------...)))-----)))...... ( -24.44)
>DroAna_CAF1 3274 90 - 1
GUGUUGGCGUGCACA------UGAUGUGCAUGCAUGCGUUUU--CCUAAAUGAUUUCCAAAGAAUUUUUAUUGGAGAGAA-----AAAGGCGAA-----AGCGAAAAC
..((..((((((((.------....))))))))..))(((((--(........(((((((.((....)).)))))))...-----....((...-----.)))))))) ( -28.70)
>consensus
GCGUGGGCGUGCACA______UGAUGUGCAUGCAUGCGUUUU__CCUAAAUGAUUUCCAAAGAAUUUUUAUUGGAAAAAAA____AAAGGCGAA_____AGCGAAAAC
(((((.(((((((((.........))))))))).)))))..............(((((((.((....)).)))))))............................... (-19.18 = -18.93 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,374,244 – 9,374,346
Length 102
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 76.22
Mean single sequence MFE -17.09
Consensus MFE -10.52
Energy contribution -10.85
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.62
SVM decision value 0.28
SVM RNA-class probability 0.664368
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9374244 102 + 27905053
UUUUCACCAAUAAAAAUUCUUUGGAAAUCAUUUAGGAAAGCGCAUGCAUGCACAUCAUCGUGUGCACGCCAACGCCC------ACGCCC-CUAC-----UGUUCCG-CCCCGCCC
......................((((........((...(((...((.(((((((....))))))).))...)))..------...)).-....-----..)))).-........ ( -20.26)
>DroPse_CAF1 8740 101 + 1
UUUUCACCAAUAAAAAUUCUUUGGAAAUCAUUUAGGAAAACGCAUGCAUGCACAUCA---UGUGCAAGCCCGCGCCC------ACACCCGCUAC-----CAGACAGACCCCUUCU
......((((..........))))..........((.....((..((.(((((....---.))))).))..))((..------......))..)-----)............... ( -16.90)
>DroEre_CAF1 4581 107 + 1
UUUUCACCAAUAAAAAUUCUUGGGAAAUCAUUUAGGAAAGCGCAUGCAUGCACAUCAUCAUGUGCACGCCAACGCCCACGCCCACGCCC-CUAC-----CGUUUCG-CCCCGCC-
......((((.........))))(((((....((((...(((...((.(((((((....))))))).))...)))....((....)).)-))).-----.))))).-.......- ( -22.80)
>DroMoj_CAF1 67822 91 + 1
UUUUUCCCAAUAAAAAUUCCUUGGAAAUCAUUUAG-AAAACGCAUGCAUGCACAUCA---UGUGCACACCCACACAC------ACACAC-A--------CAGAAAGAGCG-----
((((((((((..........))))...........-............(((((....---.)))))...........------......-.--------..))))))...----- ( -10.60)
>DroAna_CAF1 3292 102 + 1
UUCUCUCCAAUAAAAAUUCUUUGGAAAUCAUUUAGGAAAACGCAUGCAUGCACAUCA---UGUGCACGCCAACACCC------ACGCUC-CAAGCCUGCCCCUACC-AUCCAC--
.....(((((..........))))).......((((.........((.(((((....---.))))).)).......(------(.((..-...)).))..))))..-......-- ( -17.70)
>DroPer_CAF1 8681 91 + 1
UUUUCACCAAUAAAAAUUCUUUGGAAAUCAUUUAGGAAAACGCAUGCAUGCACAUCA---UGUGCAAGCCCACGCCC------ACACCCGCUCC-----CCGACA----------
......((((..........))))..........(((........((.(((((....---.))))).))....((..------......)))))-----......---------- ( -14.30)
>consensus
UUUUCACCAAUAAAAAUUCUUUGGAAAUCAUUUAGGAAAACGCAUGCAUGCACAUCA___UGUGCACGCCAACGCCC______ACACCC_CUAC_____CAGACAG_CCCC_C__
......((((..........)))).....................((.((((((......)))))).)).............................................. (-10.52 = -10.85 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,374,244 – 9,374,346
Length 102
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.22
Mean single sequence MFE -28.28
Consensus MFE -20.14
Energy contribution -19.78
Covariance contribution -0.36
Combinations/Pair 1.19
Mean z-score -1.08
Structure conservation index 0.71
SVM decision value 0.36
SVM RNA-class probability 0.703418
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9374244 102 - 27905053
GGGCGGGG-CGGAACA-----GUAG-GGGCGU------GGGCGUUGGCGUGCACACGAUGAUGUGCAUGCAUGCGCUUUCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAA
........-.((((..-----((..-(((...------((((((..(((((((((......)))))))))..)))))).)))..))...))))...................... ( -30.10)
>DroPse_CAF1 8740 101 - 1
AGAAGGGGUCUGUCUG-----GUAGCGGGUGU------GGGCGCGGGCUUGCACA---UGAUGUGCAUGCAUGCGUUUUCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAA
....(..(((.((...-----...))(((...------(((((((.((.(((((.---....))))).)).))))))).)))....)))..)....................... ( -25.70)
>DroEre_CAF1 4581 107 - 1
-GGCGGGG-CGAAACG-----GUAG-GGGCGUGGGCGUGGGCGUUGGCGUGCACAUGAUGAUGUGCAUGCAUGCGCUUUCCUAAAUGAUUUCCCAAGAAUUUUUAUUGGUGAAAA
-...((((-((..(((-----....-...)))...)))((((((..((((((((((....))))))))))..)))))).)))......((((((((.........)))).)))). ( -35.80)
>DroMoj_CAF1 67822 91 - 1
-----CGCUCUUUCUG--------U-GUGUGU------GUGUGUGGGUGUGCACA---UGAUGUGCAUGCAUGCGUUUU-CUAAAUGAUUUCCAAGGAAUUUUUAUUGGGAAAAA
-----(((......((--------(-(((..(------(((((((......))))---).)))..)))))).)))((((-((.(((((.(((....)))...))))).)))))). ( -23.30)
>DroAna_CAF1 3292 102 - 1
--GUGGAU-GGUAGGGGCAGGCUUG-GAGCGU------GGGUGUUGGCGUGCACA---UGAUGUGCAUGCAUGCGUUUUCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGAGAGAA
--......-..((((((((.((...-..)).)------)...((..((((((((.---....))))))))..))...)))))).....(((((((.((....)).)))))))... ( -28.80)
>DroPer_CAF1 8681 91 - 1
----------UGUCGG-----GGAGCGGGUGU------GGGCGUGGGCUUGCACA---UGAUGUGCAUGCAUGCGUUUUCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAA
----------....((-----..((((.((((------((((....))))((((.---....))))..)))).))))..)).......((.((((.((....)).)))).))... ( -26.00)
>consensus
__G_GGGG_CGGACCG_____GUAG_GGGCGU______GGGCGUGGGCGUGCACA___UGAUGUGCAUGCAUGCGUUUUCCUAAAUGAUUUCCAAAGAAUUUUUAUUGGUGAAAA
........................................((((..(((((((((......)))))))))..))))((((((((..((.(((....))).))...)))).)))). (-20.14 = -19.78 +  -0.36)

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 11:01:54 2006