Locus 4162

Sequence ID 3R_DroMel_CAF1
Location 11,326,695 – 11,326,942
Length 247
Max. P 0.967928
window6674 window6675 window6676

overview

Window 4

Location 11,326,695 – 11,326,810
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -30.54
Consensus MFE -26.78
Energy contribution -26.74
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.88
SVM decision value 1.62
SVM RNA-class probability 0.967928
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11326695 115 - 27905053
-----GCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAGUGAAAUAUGAUUGAAAGUGUAAAUACAUAUUUCAUUGGCAUGGGAAUCAA
-----.(((.(((((.((.........)).)))))......(((((..(....).)))))...((((.((((((((((((((.........))).))))))))))))))))))....... ( -32.10)
>DroSec_CAF1 65879 115 - 1
-----UCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAGUGAAAUAUGAUUGAAAGUGUAAAUAGAUAUUUCAUUGGCCUGGGAAUCAA
-----(((..(((((.((.........)).)))))......(((((..(....).)))))....(((.((((((((((.(((.........)))..)))))))))))))...)))..... ( -27.80)
>DroSim_CAF1 64041 115 - 1
-----GCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAGUGAAAUAUGAUUGAAAGUGUAAAUAGAUAUUUCAUUGGCCUGGGAAUCAA
-----(((...((((.((.........)).))))((((...(((((..(....).)))))...)))).((((((((((.(((.........)))..)))))))))))))........... ( -28.10)
>DroEre_CAF1 61300 120 - 1
CGAUGGCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAAUGAAAUAUGAUUGAAAGUGUAAAUAGAUAUUUCAUUGGCAUGGCAAUCAA
.(((.((((.(((((.((.........)).)))))......(((((..(....).)))))...((((.((((((((((.(((.........)))..)))))))))))))))))).))).. ( -35.40)
>DroYak_CAF1 63088 120 - 1
CGAUGGCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAAUGAAAUAUGAUUGAAAGUGUAAAUAGACAUUUCAUUGGCAUGGGAAUCAA
.(((..(((.(((((.((.........)).)))))......(((((..(....).)))))...((((.((((((((...(((.........)))....)))))))))))))))..))).. ( -29.30)
>consensus
_____GCCAACUGCCUGCUAAUUGAGUGCUGGCAGACAUAAUGUUUUCGGAAACUGAGCAAACUGUCGAGUGAAAUAUGAUUGAAAGUGUAAAUAGAUAUUUCAUUGGCAUGGGAAUCAA
......(((.(((((.((.........)).)))))......(((((..(....).)))))....(((.((((((((((.(((.........)))..))))))))))))).)))....... (-26.78 = -26.74 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,326,810 – 11,326,902
Length 92
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 83.58
Mean single sequence MFE -28.55
Consensus MFE -20.23
Energy contribution -21.73
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 1.03
SVM RNA-class probability 0.903846
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11326810 92 + 27905053
---GACCAUCGA------------CCAGAACCAGGACGCAGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUUUUGGUUAAUUGAAAGCAAAC
---..(.((..(------------(((((((..((((.......(((.......)))(((((....)))))........)))).))))))))..)).)......... ( -25.90)
>DroSec_CAF1 65994 92 + 1
---GACCAUCGA------------CCAGAACCAGGACGUUGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUUUUGGUUAAUUGAAAGCAAAC
---..(.((..(------------(((((((..(((((((((((((....((......))....))))))))))))).......))))))))..)).)......... ( -28.90)
>DroSim_CAF1 64156 92 + 1
---GACCAUCGA------------CCAGAACCAGGACGUUGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCUAGUCCAGUUUUGGUUAAUUGAAAGCAAAC
---..(.((..(------------((((((((((((((((((((((....((......))....)))))))))))))).)....))))))))..)).)......... ( -30.60)
>DroEre_CAF1 61420 99 + 1
UGAGACCAUAGACCAGAACCAGAACCAGAACCAGGACGCACCA--------CGACUGCGUCCAAUUGGGCGAUGUCCAAGUCCAGUUUUGGUUAAUUGAAAGCAAAC
..........(((((((((..((..........(((((((...--------....)))))))..((((((...)))))).))..))))))))).............. ( -28.80)
>consensus
___GACCAUCGA____________CCAGAACCAGGACGCAGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUUUUGGUUAAUUGAAAGCAAAC
........................(((((((..(((((((((........)))))..(((((....)))))........)))).)))))))................ (-20.23 = -21.73 +   1.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,326,823 – 11,326,942
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.46
Mean single sequence MFE -32.82
Consensus MFE -26.03
Energy contribution -26.43
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.79
SVM decision value 1.24
SVM RNA-class probability 0.934862
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11326823 119 + 27905053
AACCAGGACGCAGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUU-UUGGUUAAUUGAAAGCAAACAAAACAAAACGCAGCGGAAAUGCUGCUCAAACACGCUAGA
((((((((((.(((...........))).)))))((((((((.........))))))))-.)))))........................((((((....)))))).............. ( -30.80)
>DroSec_CAF1 66007 119 + 1
AACCAGGACGUUGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUU-UUGGUUAAUUGAAAGCAAACAAAACAAAACGCAGCGGAAAUGCUGCUCAAACACGCUAGA
.....(((((((((((((....((......))....))))))))))))).(((...(((-(((.....(((....)))......))))))((((((....))))))........)))... ( -35.50)
>DroSim_CAF1 64169 119 + 1
AACCAGGACGUUGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCUAGUCCAGUU-UUGGUUAAUUGAAAGCAAACAAAACAAAACGCAGCGGAAAUGCUGCUCAAACACGCUAGA
.((.((((((((((((((....((......))....)))))))))))))).))...(((-(((.....(((....)))......))))))((((((....)))))).............. ( -36.30)
>DroEre_CAF1 61448 111 + 1
AACCAGGACGCACCA--------CGACUGCGUCCAAUUGGGCGAUGUCCAAGUCCAGUU-UUGGUUAAUUGAAAGCAAACAAAACAGAGCGCUGCGGAAAUGCUGCUCAAACACGCUAGG
((((((((((((...--------....)))))))((((((((.........))))))))-.)))))....................(((((..(((....))))))))............ ( -32.60)
>DroYak_CAF1 63248 109 + 1
AACCAGGACGUAGUC--------CGU---AGUCCAAUUGGGCGAUGUCCAAGUCCAGUUUUUGGUUAAUUGAAAGCAAACAAAACAAAACGCAGCGGAAAUGCUGCUCAAACACGCUAGA
.....((((((.(((--------((.---........))))).)))))).(((...(((((..(....)..)))))..............((((((....))))))........)))... ( -28.90)
>consensus
AACCAGGACGUAGUCCGAGCCCACAACUCCGUCCAAUUGGGCGAUGUCCAAGUCCAGUU_UUGGUUAAUUGAAAGCAAACAAAACAAAACGCAGCGGAAAUGCUGCUCAAACACGCUAGA
((((((((((...................)))))((((((((.........))))))))..)))))........................((((((....)))))).............. (-26.03 = -26.43 +   0.40)

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 11:19:55 2006