Locus 3021

Sequence ID 3R_DroMel_CAF1
Location 8,073,228 – 8,073,388
Length 160
Max. P 0.962661
window4859 window4860 window4861 window4862

overview

Window 9

Location 8,073,228 – 8,073,319
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.54
Mean single sequence MFE -31.68
Consensus MFE -21.16
Energy contribution -20.97
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -1.82
Structure conservation index 0.67
SVM decision value 1.31
SVM RNA-class probability 0.940673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8073228 91 + 27905053
UUGUGUUUGACAAAGUUGCGAAACAAGAUGUUAACCCCGGGGGUUGACUCCA---------------GAAUGAAGGCAGGGAUGCAGCAGCAUCUUGAGAAAAGAU--------------
((((.....)))).(((((.......((.((((((((...))))))))))..---------------........(((....))).)))))(((((.....)))))-------------- ( -23.40)
>DroPse_CAF1 19166 119 + 1
UUGUGUUUGACAAAGUUGCGCAACAAGAUGUUAACCCCGAGGGUUGACAUCUGUACUCCGUACAACGUGGUGGA-GUGGGGACGCAACAGCAUCUUGAGAAAAGAUCUCAGAGAUCUCUG
((((.....)))).(((((((..(.((((((((((((...))))))))))))..((((((..........))))-)))..).))))))((.(((((((((.....))))).))))))... ( -41.20)
>DroEre_CAF1 17773 91 + 1
UUGUGUUUGACAAAGUUGCGAAACAAGAUGUUAACCCCGGGGGUUGACUCCA---------------UGGUGGAGGCAGGGAUGCAGCAGCAUCUUGAGAAAAGAU--------------
((((.....))))..........(((((((((..(((((((((....)))).---------------))).))..(((....)))...))))))))).........-------------- ( -25.20)
>DroYak_CAF1 18172 91 + 1
UUGUGUUUGACAAAGUUGCGAAACAAGAUGUUAACCCCGAGGGUUGACUCCG---------------AAGUGGAGGCAGGGAUGCAGCAGCAUCUUGAGAAAAGAU--------------
((((.....)))).(((((...........(((((((...)))))))((((.---------------....))))(((....))).)))))(((((.....)))))-------------- ( -24.40)
>DroAna_CAF1 24855 105 + 1
UUGUGUCUGACAAAGUUGCGAAACAAGAUGUUAACCCCGGGGGUUGACUUUU---------------CGUUGGACUUAGGGAUGCAGCAGCAUCUUGAGAAAAGAUCUCGGUGAUCUGUG
....(((..((...(((....)))..((.((((((((...))))))))...)---------------)))..)))...(((((((....)))))))......(((((.....)))))... ( -33.40)
>DroPer_CAF1 19282 119 + 1
UUGUGUUUGACAAAGUUGCGCAACAAGAUGUUAACCCCGAGGGUUGACAUCUGUACUCCGUACAGCGUGGUGGA-GUGGGGACGCAACAGCAUCUUGAGAAAAGAUCUCAGAGAUCUCUG
((((((((..((..(..((((....((((((((((((...))))))))))))((((...)))).))))..)...-.)).))))))))(((.(((((((((.....))))).))))..))) ( -42.50)
>consensus
UUGUGUUUGACAAAGUUGCGAAACAAGAUGUUAACCCCGAGGGUUGACUCCU_______________UGGUGGAGGCAGGGAUGCAGCAGCAUCUUGAGAAAAGAU______________
((((.....)))).(((((..........((((((((...))))))))...........................(((....))).)))))(((((.....))))).............. (-21.16 = -20.97 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,073,228 – 8,073,319
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.54
Mean single sequence MFE -25.82
Consensus MFE -16.24
Energy contribution -16.22
Covariance contribution -0.03
Combinations/Pair 1.10
Mean z-score -2.10
Structure conservation index 0.63
SVM decision value 1.54
SVM RNA-class probability 0.962661
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8073228 91 - 27905053
--------------AUCUUUUCUCAAGAUGCUGCUGCAUCCCUGCCUUCAUUC---------------UGGAGUCAACCCCCGGGGUUAACAUCUUGUUUCGCAACUUUGUCAAACACAA
--------------............(((((....)))))....((.......---------------.)).((.(((((...))))).))....(((((.(((....))).)))))... ( -17.70)
>DroPse_CAF1 19166 119 - 1
CAGAGAUCUCUGAGAUCUUUUCUCAAGAUGCUGUUGCGUCCCCAC-UCCACCACGUUGUACGGAGUACAGAUGUCAACCCUCGGGGUUAACAUCUUGUUGCGCAACUUUGUCAAACACAA
.(((((((.....)))))))......((((..(((((((..(.((-(((............)))))..((((((.(((((...))))).)))))).)..)))))))..))))........ ( -36.90)
>DroEre_CAF1 17773 91 - 1
--------------AUCUUUUCUCAAGAUGCUGCUGCAUCCCUGCCUCCACCA---------------UGGAGUCAACCCCCGGGGUUAACAUCUUGUUUCGCAACUUUGUCAAACACAA
--------------............(((((....)))))...(.((((....---------------.)))).)(((((...))))).......(((((.(((....))).)))))... ( -20.10)
>DroYak_CAF1 18172 91 - 1
--------------AUCUUUUCUCAAGAUGCUGCUGCAUCCCUGCCUCCACUU---------------CGGAGUCAACCCUCGGGGUUAACAUCUUGUUUCGCAACUUUGUCAAACACAA
--------------............(((((....)))))...(.((((....---------------.)))).)(((((...))))).......(((((.(((....))).)))))... ( -19.80)
>DroAna_CAF1 24855 105 - 1
CACAGAUCACCGAGAUCUUUUCUCAAGAUGCUGCUGCAUCCCUAAGUCCAACG---------------AAAAGUCAACCCCCGGGGUUAACAUCUUGUUUCGCAACUUUGUCAGACACAA
...........((((.....))))..(((((....))))).....(((..(((---------------((..((.(((((...))))).))...(((.....))).)))))..))).... ( -23.50)
>DroPer_CAF1 19282 119 - 1
CAGAGAUCUCUGAGAUCUUUUCUCAAGAUGCUGUUGCGUCCCCAC-UCCACCACGCUGUACGGAGUACAGAUGUCAACCCUCGGGGUUAACAUCUUGUUGCGCAACUUUGUCAAACACAA
.(((((((.....)))))))......((((..(((((((..(.((-(((............)))))..((((((.(((((...))))).)))))).)..)))))))..))))........ ( -36.90)
>consensus
______________AUCUUUUCUCAAGAUGCUGCUGCAUCCCUACCUCCACCA_______________AGAAGUCAACCCCCGGGGUUAACAUCUUGUUUCGCAACUUUGUCAAACACAA
..........................(((((....)))))................................((.(((((...))))).))....(((((.(((....))).)))))... (-16.24 = -16.22 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,073,293 – 8,073,388
Length 95
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 80.16
Mean single sequence MFE -29.65
Consensus MFE -18.48
Energy contribution -18.32
Covariance contribution -0.16
Combinations/Pair 1.10
Mean z-score -1.67
Structure conservation index 0.62
SVM decision value 0.26
SVM RNA-class probability 0.658662
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8073293 95 + 27905053
GAUGCAGCAGCAUCUUGAGAAAAGAU---------------CAGCAGCUGCCCUU-GUCGCAGUGAGAUCACCGAAAACUGACAUUUGACCAUUGGUCAAAGGGUUGACCA--
...(((((.(((((((.....)))))---------------..)).)))))....-(((...(((....)))........(((.(((((((...)))))))..))))))..-- ( -26.20)
>DroPse_CAF1 19245 109 + 1
GACGCAACAGCAUCUUGAGAAAAGAUCUCAGAGAUCUCUGACAGCAGCUGCCCUCCGAAAGAGAGAGAGUUCG----GUUAACAUUUGACCAUUGGUCAAAGGGUUGACCAGA
((.((..(((((((((.....))))).(((((....))))).....))))..((((....).)))...))))(----((((((.(((((((...)))))))..)))))))... ( -36.20)
>DroSec_CAF1 19339 95 + 1
GAUGCAGCAGCAUCUUGAGAAAAGAU---------------CAGCAGCUGCCCUU-GUCGCAGUGAGAUCAACGAAAACUGACAUUUGACCACUGGUCAAAGGGUUGACCA--
(((((....))))).........(((---------------(....(((((....-...)))))..))))..........(((.(((((((...)))))))..))).....-- ( -25.20)
>DroEre_CAF1 17838 95 + 1
GAUGCAGCAGCAUCUUGAGAAAAGAU---------------CAGCAGCUGCCCUU-GUCGCAGUGAGAUCACCGAGAACUGACAUUUGACCAUUGGUCAAAGGGUUGACCA--
...(((((.(((((((.....)))))---------------..)).)))))....-(((((.((.((.((.....)).)).)).(((((((...)))))))..).))))..-- ( -26.20)
>DroYak_CAF1 18237 95 + 1
GAUGCAGCAGCAUCUUGAGAAAAGAU---------------CAGCAGCUGCCCUU-GUCGCAGUGAGAUCACCGAAAACUGACAUUUGACCAUUGGUCAAAGGGUUGGCCA--
(((((....))))).........(((---------------(....(((((....-...)))))..))))........(..((.(((((((...)))))))..))..)...-- ( -27.90)
>DroPer_CAF1 19361 109 + 1
GACGCAACAGCAUCUUGAGAAAAGAUCUCAGAGAUCUCUGACAGCAGCUGCCCUCCGAAAGAGAGAGAGUUCG----GUUAACAUUUGACCAUUGGUCAAAGGGUUGACCAGA
((.((..(((((((((.....))))).(((((....))))).....))))..((((....).)))...))))(----((((((.(((((((...)))))))..)))))))... ( -36.20)
>consensus
GAUGCAGCAGCAUCUUGAGAAAAGAU_______________CAGCAGCUGCCCUU_GUCGCAGUGAGAUCACCGAAAACUGACAUUUGACCAUUGGUCAAAGGGUUGACCA__
(((((....))))).................................(.((((.........(((....)))............(((((((...))))))))))).)...... (-18.48 = -18.32 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,073,293 – 8,073,388
Length 95
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.16
Mean single sequence MFE -30.05
Consensus MFE -18.86
Energy contribution -19.14
Covariance contribution 0.28
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.63
SVM decision value 0.50
SVM RNA-class probability 0.758617
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8073293 95 - 27905053
--UGGUCAACCCUUUGACCAAUGGUCAAAUGUCAGUUUUCGGUGAUCUCACUGCGAC-AAGGGCAGCUGCUG---------------AUCUUUUCUCAAGAUGCUGCUGCAUC
--........(((((((((...)))))).((((......(((((....))))).)))-))))(((((.((..---------------(((((.....))))))).)))))... ( -28.30)
>DroPse_CAF1 19245 109 - 1
UCUGGUCAACCCUUUGACCAAUGGUCAAAUGUUAAC----CGAACUCUCUCUCUUUCGGAGGGCAGCUGCUGUCAGAGAUCUCUGAGAUCUUUUCUCAAGAUGCUGUUGCGUC
...(((.(((..(((((((...))))))).))).))----)((..((((((((.....)))(((((...))))))))))..))(((((.....))))).(((((....))))) ( -34.00)
>DroSec_CAF1 19339 95 - 1
--UGGUCAACCCUUUGACCAGUGGUCAAAUGUCAGUUUUCGUUGAUCUCACUGCGAC-AAGGGCAGCUGCUG---------------AUCUUUUCUCAAGAUGCUGCUGCAUC
--(((((((....)))))))(.((((((.((........)))))))).)........-....(((((.((..---------------(((((.....))))))).)))))... ( -26.70)
>DroEre_CAF1 17838 95 - 1
--UGGUCAACCCUUUGACCAAUGGUCAAAUGUCAGUUCUCGGUGAUCUCACUGCGAC-AAGGGCAGCUGCUG---------------AUCUUUUCUCAAGAUGCUGCUGCAUC
--(((((((....)))))))..(((((..((((...((.(((((....))))).)).-...)))).....))---------------))).........(((((....))))) ( -28.60)
>DroYak_CAF1 18237 95 - 1
--UGGCCAACCCUUUGACCAAUGGUCAAAUGUCAGUUUUCGGUGAUCUCACUGCGAC-AAGGGCAGCUGCUG---------------AUCUUUUCUCAAGAUGCUGCUGCAUC
--...((.....(((((((...)))))))((((......(((((....))))).)))-).))(((((.((..---------------(((((.....))))))).)))))... ( -28.70)
>DroPer_CAF1 19361 109 - 1
UCUGGUCAACCCUUUGACCAAUGGUCAAAUGUUAAC----CGAACUCUCUCUCUUUCGGAGGGCAGCUGCUGUCAGAGAUCUCUGAGAUCUUUUCUCAAGAUGCUGUUGCGUC
...(((.(((..(((((((...))))))).))).))----)((..((((((((.....)))(((((...))))))))))..))(((((.....))))).(((((....))))) ( -34.00)
>consensus
__UGGUCAACCCUUUGACCAAUGGUCAAAUGUCAGUUUUCGGUGAUCUCACUGCGAC_AAGGGCAGCUGCUG_______________AUCUUUUCUCAAGAUGCUGCUGCAUC
..........(((((((((...)))))............(((((....))))).....))))(((((.((.................(((((.....))))))).)))))... (-18.86 = -19.14 +   0.28)

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 10:50:23 2006