Locus 2050

Sequence ID 3R_DroMel_CAF1
Location 5,814,824 – 5,814,936
Length 112
Max. P 0.998582
window3356 window3357

overview

Window 6

Location 5,814,824 – 5,814,936
Length 112
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 86.62
Mean single sequence MFE -40.83
Consensus MFE -31.12
Energy contribution -30.04
Covariance contribution -1.08
Combinations/Pair 1.23
Mean z-score -4.31
Structure conservation index 0.76
SVM decision value 3.15
SVM RNA-class probability 0.998582
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5814824 112 + 27905053
AAUCGGAGGUGCUGCAGAAAUCACUUUGCUUGGAAUUCACAUUGAUGUACGUAAGAAUUCA---UCACGAAGUGGUUUCUGUGUUGCCUCCGAUUGAAAGCAGA-AUAUUCAAAUG
(((((((((((..(((((((((((((((....((((((................)))))).---...)))))))))))))))..))))))))))).........-........... ( -43.19)
>DroSec_CAF1 106299 115 + 1
AAUCGGAGGUGCUGCAGAAAUCACUUUGCUGGGAAUUCACAUUGAUGUACGUAAGAAUUCAUCAUCACUGAGUGGUUUUUUUGUUGCCUCCGUUUGAAAGCAGA-AUAUUCAAACG
....((((((...(((((((((((((((.(((((((((................)))))).))).))..))))))))))..))).))))))(((((((......-...))))))). ( -33.29)
>DroSim_CAF1 107105 112 + 1
AAUCGGAGGUGCGGCAGAAAUCACUUUGCUGGGAAUUCACAUUGAUGUACGUAAGAAUUCA---UCACUGAGUGGUUUUUGUGUUGCCUCCGUUUGAAAGCAGA-AUAUUCAAACG
....(((((((..(((((((((((((.(.(((((((((................)))))).---)))).)))))))))))))..)))))))(((((((......-...))))))). ( -38.49)
>DroEre_CAF1 103328 108 + 1
----GGAGGUGGUGCAGAAAUCCCUUUGCUCGGAAUUUACGUUGAUGUACGCAAGAAUUCG---UCACGAAGUGAUUUCUGUGCCGCCUCCGCUUGAAAGCAGA-AUAUUCAAACG
----((((((((..((((((((.(((((..((((.(((.(((......)))..))).))))---...))))).))))))))..))))))))(((....)))...-........... ( -45.10)
>DroYak_CAF1 92352 113 + 1
AAUCGGCGGUGGUGCAGAAAUCACUUAGCUCUGAAUUUACAUUGAUGUACGUAAGAAUUCG---UCACGAAGUGAUUUGUGUGCCGCCGCCGCUUAAAAGCAGAAAUAUUUAAACG
..((((((((((..((.(((((((((.....((((((((((....))))(....)))))))---.....))))))))).))..))))))))(((....))).))............ ( -44.10)
>consensus
AAUCGGAGGUGCUGCAGAAAUCACUUUGCUCGGAAUUCACAUUGAUGUACGUAAGAAUUCA___UCACGAAGUGGUUUCUGUGUUGCCUCCGCUUGAAAGCAGA_AUAUUCAAACG
...((((((((.((((((((((((((......((((((..((........))..)))))).........)))))))))))))).)))))))).(((((..........)))))... (-31.12 = -30.04 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,814,824 – 5,814,936
Length 112
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 86.62
Mean single sequence MFE -32.80
Consensus MFE -22.90
Energy contribution -22.74
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -3.47
Structure conservation index 0.70
SVM decision value 1.98
SVM RNA-class probability 0.984494
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5814824 112 - 27905053
CAUUUGAAUAU-UCUGCUUUCAAUCGGAGGCAACACAGAAACCACUUCGUGA---UGAAUUCUUACGUACAUCAAUGUGAAUUCCAAGCAAAGUGAUUUCUGCAGCACCUCCGAUU
...........-.........(((((((((.....((((((.(((((.((..---.((((((..((((......))))))))))...)).))))).)))))).....))))))))) ( -34.10)
>DroSec_CAF1 106299 115 - 1
CGUUUGAAUAU-UCUGCUUUCAAACGGAGGCAACAAAAAAACCACUCAGUGAUGAUGAAUUCUUACGUACAUCAAUGUGAAUUCCCAGCAAAGUGAUUUCUGCAGCACCUCCGAUU
.(((((((...-......)))))))(((((............(((....((((((((........))).)))))..)))......(((.(((....)))))).....))))).... ( -26.20)
>DroSim_CAF1 107105 112 - 1
CGUUUGAAUAU-UCUGCUUUCAAACGGAGGCAACACAAAAACCACUCAGUGA---UGAAUUCUUACGUACAUCAAUGUGAAUUCCCAGCAAAGUGAUUUCUGCCGCACCUCCGAUU
.(((((((...-......)))))))(((((.....((.(((.((((..((..---.((((((..((((......))))))))))...))..)))).))).)).....))))).... ( -28.00)
>DroEre_CAF1 103328 108 - 1
CGUUUGAAUAU-UCUGCUUUCAAGCGGAGGCGGCACAGAAAUCACUUCGUGA---CGAAUUCUUGCGUACAUCAACGUAAAUUCCGAGCAAAGGGAUUUCUGCACCACCUCC----
.(((((((...-......)))))))(((((.((..((((((((.(((.((..---.(((((..(((((......))))))))))...)).))).))))))))..)).)))))---- ( -39.20)
>DroYak_CAF1 92352 113 - 1
CGUUUAAAUAUUUCUGCUUUUAAGCGGCGGCGGCACACAAAUCACUUCGUGA---CGAAUUCUUACGUACAUCAAUGUAAAUUCAGAGCUAAGUGAUUUCUGCACCACCGCCGAUU
.(((((((..........)))))))(((((.((..((.(((((((((.((..---.(((((..(((((......))))))))))...)).))))))))).))..)).))))).... ( -36.50)
>consensus
CGUUUGAAUAU_UCUGCUUUCAAACGGAGGCAACACAAAAACCACUUCGUGA___UGAAUUCUUACGUACAUCAAUGUGAAUUCCCAGCAAAGUGAUUUCUGCAGCACCUCCGAUU
.(((((((..........)))))))(((((.....((.(((.(((((.((......((((..((((((......))))))))))...)).))))).))).)).....))))).... (-22.90 = -22.74 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:10 2006