Locus 3787

Sequence ID 3R_DroMel_CAF1
Location 10,269,231 – 10,269,359
Length 128
Max. P 0.862582
window6076 window6077 window6078

overview

Window 6

Location 10,269,231 – 10,269,325
Length 94
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 82.36
Mean single sequence MFE -17.80
Consensus MFE -11.55
Energy contribution -11.63
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.74
Structure conservation index 0.65
SVM decision value 0.05
SVM RNA-class probability 0.556926
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10269231 94 - 27905053
GUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUACGGCCUAUUGACACUCAUGUCAUAAAUUUC-GUACAAUUU-UCGCAGUUA-----
((((...((((....(((((((((.......))))))))).)))).........(((((....)))))........-)))).....-.........----- ( -16.60)
>DroPse_CAF1 136464 87 - 1
G--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGUGGCCUAUUGACACUUGUCCCAUAAAUUUG-UUGCUAU---UCGCAA--------
(--(..(((((....(((((((((.......))))))))).)))))..)).....(((....)))...........-((((...---..))))-------- ( -17.00)
>DroEre_CAF1 127311 94 - 1
GUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUGCGGCCUAUUGACACUCUUGUCAUAAAUUUC-GUACAAUAU-UCGCAUUUA-----
((((..(((((....(((((((((.......))))))))).)))))........(((((....)))))........-)))).....-.........----- ( -18.80)
>DroWil_CAF1 141645 97 - 1
G--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGCGGCCCAUUGACACU--UGCCAUAAAUUUUUGUUUUGUUUGUCGAAUUUGUUAUU
(--(..(((((....(((((((((.......))))))))).)))))..))...((((((..--.((...((((....)))).)).)))))).......... ( -18.30)
>DroYak_CAF1 134406 94 - 1
GUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUACGGCCUAUUGACACUCUUGUCAUAAAUUUC-GUACAAUUC-GUACAUUUA-----
((((...((((....(((((((((.......))))))))).))))((((.....(((((....)))))......))-)).......-)))).....----- ( -19.10)
>DroPer_CAF1 139222 87 - 1
G--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGUGGCCUAUUGACACUUGUCCCAUAAAUUUG-UUGCUAU---UCGCAA--------
(--(..(((((....(((((((((.......))))))))).)))))..)).....(((....)))...........-((((...---..))))-------- ( -17.00)
>consensus
G__UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGCGGCCUAUUGACACUCGUGCCAUAAAUUUC_GUACAAUUU_UCGCAUUUA_____
......(((((....(((((((((.......))))))))).)))))....................................................... (-11.55 = -11.63 +   0.08)

alignment

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secondary structure

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Window 7

Location 10,269,252 – 10,269,359
Length 107
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.45
Mean single sequence MFE -17.00
Consensus MFE -12.44
Energy contribution -12.17
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -1.11
Structure conservation index 0.73
SVM decision value 0.24
SVM RNA-class probability 0.648542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10269252 107 + 27905053
AUUUAUGACAUGAGUGUCAAUAGGCCGUAGCACAUAAAUGCUGUUAAUUAACAUUUAUUGUUUGCUGAUAUACUACA---CAAUGAGAUAAAUAGAAGAAAA-AAAAAACG
((((((..(((..((((.....(((...((((.(((((((.((.....)).))))))))))).)))........)))---).)))..)))))).........-........ ( -15.22)
>DroPse_CAF1 136480 102 + 1
AUUUAUGGGACAAGUGUCAAUAGGCCACAGCACAUAAAUGUUGUUAAUUAACAUUUAUUGUUUGCUGAUA--CUACAACAACAGAAAAUAAGCAAAA----A---AAAAAA
.(((((..(((....))).)))))...(((((.((((((((((.....))))))))))....)))))...--.........................----.---...... ( -17.00)
>DroEre_CAF1 127332 101 + 1
AUUUAUGACAAGAGUGUCAAUAGGCCGCAGCACAUAAAUGCUGUUAAUUAACAUUUAUUGUUUGCUGAUAUACUACA---CAAUAAGAUAGGCAGGA----A---AAAACG
.....(((((....)))))....(((((((((......)))))).........((((((((..(........)...)---)))))))...)))....----.---...... ( -19.50)
>DroWil_CAF1 141673 85 + 1
AUUUAUGGCA--AGUGUCAAUGGGCCGCAGCACAUAAAUGUUGUUAAUUAACAUUUAUUGUUUGCUGAUA--CUAUGGU---------------GGA----A-A-AAAAU-
.((((((((.--.((....))..))).(((((.((((((((((.....))))))))))....)))))...--.....))---------------)))----.-.-.....- ( -19.70)
>DroYak_CAF1 134427 104 + 1
AUUUAUGACAAGAGUGUCAAUAGGCCGUAGCACAUAAAUGCUGUUAAUUAACAUUUAUUGUUUGCUGAUAUACUACA---CAAUAAGAUAAAUAGAA----AAAAAAAACG
((((((((((....))))..(((....(((((.(((((((.((.....)).)))))))....))))).....)))..---.......))))))....----.......... ( -13.60)
>DroPer_CAF1 139238 97 + 1
AUUUAUGGGACAAGUGUCAAUAGGCCACAGCACAUAAAUGUUGUUAAUUAACAUUUAUUGUUUGCUGAUA--CUACAACAACAGAAAAUAUGCAAAA----A---A-----
.(((((..(((....))).)))))...(((((.((((((((((.....))))))))))....)))))...--.........................----.---.----- ( -17.00)
>consensus
AUUUAUGACAAGAGUGUCAAUAGGCCGCAGCACAUAAAUGCUGUUAAUUAACAUUUAUUGUUUGCUGAUA__CUACA___CAAUAAGAUAAGCAGAA____A___AAAACG
.....(((((....))))).(((....(((((.((((....((((....))))....)))).))))).....))).................................... (-12.44 = -12.17 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,269,252 – 10,269,359
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.45
Mean single sequence MFE -17.58
Consensus MFE -12.32
Energy contribution -12.43
Covariance contribution 0.11
Combinations/Pair 1.11
Mean z-score -1.60
Structure conservation index 0.70
SVM decision value 0.83
SVM RNA-class probability 0.862582
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10269252 107 - 27905053
CGUUUUUU-UUUUCUUCUAUUUAUCUCAUUG---UGUAGUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUACGGCCUAUUGACACUCAUGUCAUAAAU
........-.........((((((..(((.(---(((((((..((((((....(((((((((.......))))))))).))))..))..)))).))))..)))..)))))) ( -17.90)
>DroPse_CAF1 136480 102 - 1
UUUUUU---U----UUUUGCUUAUUUUCUGUUGUUGUAG--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGUGGCCUAUUGACACUUGUCCCAUAAAU
......---.----..............((((...((((--...(((((....(((((((((.......))))))))).)))))....)))).)))).............. ( -17.20)
>DroEre_CAF1 127332 101 - 1
CGUUUU---U----UCCUGCCUAUCUUAUUG---UGUAGUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUGCGGCCUAUUGACACUCUUGUCAUAAAU
......---.----....(((....((((((---(...((......))..)))))))...........((((((....)))))).)))....(((((....)))))..... ( -19.90)
>DroWil_CAF1 141673 85 - 1
-AUUUU-U-U----UCC---------------ACCAUAG--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGCGGCCCAUUGACACU--UGCCAUAAAU
-.....-.-.----...---------------.......--...(((((....(((((((((.......))))))))).))))).(((...........--.)))...... ( -15.40)
>DroYak_CAF1 134427 104 - 1
CGUUUUUUUU----UUCUAUUUAUCUUAUUG---UGUAGUAUAUCAGCAAACAAUAAAUGUUAAUUAACAGCAUUUAUGUGCUACGGCCUAUUGACACUCUUGUCAUAAAU
..........----....((((((..((..(---(((((((..((((((....(((((((((.......))))))))).))))..))..)))).))))...))..)))))) ( -16.00)
>DroPer_CAF1 139238 97 - 1
-----U---U----UUUUGCAUAUUUUCUGUUGUUGUAG--UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGUGGCCUAUUGACACUUGUCCCAUAAAU
-----.---.----....((((......((((((((...--...)))).))))(((((((((.......)))))))))))))(((((......(((....))))))))... ( -19.10)
>consensus
CGUUUU___U____UUCUGCUUAUCUUAUUG___UGUAG__UAUCAGCAAACAAUAAAUGUUAAUUAACAACAUUUAUGUGCUGCGGCCUAUUGACACUCGUGCCAUAAAU
...................................((((.....(((((....(((((((((.......))))))))).)))))....))))................... (-12.32 = -12.43 +   0.11)

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 11:10:11 2006