Locus 2005

Sequence ID 2R_DroMel_CAF1
Location 7,549,720 – 7,549,862
Length 142
Max. P 0.999592
window3311 window3312 window3313 window3314

overview

Window 1

Location 7,549,720 – 7,549,830
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.63
Mean single sequence MFE -24.20
Consensus MFE -16.41
Energy contribution -16.47
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -2.38
Structure conservation index 0.68
SVM decision value 3.76
SVM RNA-class probability 0.999592
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7549720 110 + 20766785
UUUGUUUCUAACUUUUUUCUUUUCAAUUUCAAAGUCGCUCUUAGGAGGGCUAAAACUAAUUU----------GAAUAUUGAUAACAAAUGAACUAUCGAUAAGAGGCCGUCGAUAGUUCA
((((((................((((((((((((((.(((....))))))).........))----------))).))))).))))))((((((((((((........)))))))))))) ( -26.63)
>DroSim_CAF1 8257 109 + 1
UUUGUUUCAAACUUUUUCAU-UUCAAUUUUAAAGUCGCUCUUAGAAGGGCUAAAACAAAUUU----------GAAUAUAGAUAACAAAAGGGCUAUCGAUAAGAGACCGUCGAUAGUUCA
((((((((..(((((.....-.........))))).(((((....)))))............----------.......)).)))))).(((((((((((........))))))))))). ( -23.54)
>DroEre_CAF1 10913 103 + 1
-----------------GCUUUUCAAUUUUAAAGUGAUUCAUAUAAGGGUUAAAACAAAUUUGAGUCCAGCUGAAUUCUGGUAACCAAUGAACUAUCGAUAAGAGGUCGUCGAUAGUUCA
-----------------(((((........)))))............(((((...((...((.((.....)).))...)).)))))..((((((((((((........)))))))))))) ( -24.60)
>DroYak_CAF1 8027 91 + 1
-----------------UGUCUUCAAUUUUAAAGUGGAUAAUAUAAGGGUUAAAUCAAA------------UGAAUUCUGAUAGCCAAUGAACUAUCGAUAAAAGGCUGUCGAUAGUUCA
-----------------(((((.............))))).......(((((..(((..------------.......))))))))..(((((((((((((......))))))))))))) ( -22.02)
>consensus
_________________UCUUUUCAAUUUUAAAGUCGCUCAUAGAAGGGCUAAAACAAAUUU__________GAAUACUGAUAACAAAUGAACUAUCGAUAAGAGGCCGUCGAUAGUUCA
..................................((((((......)))))).....................................(((((((((((........))))))))))). (-16.41 = -16.47 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,549,720 – 7,549,830
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.63
Mean single sequence MFE -20.21
Consensus MFE -11.44
Energy contribution -11.75
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.57
SVM decision value 1.44
SVM RNA-class probability 0.954008
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7549720 110 - 20766785
UGAACUAUCGACGGCCUCUUAUCGAUAGUUCAUUUGUUAUCAAUAUUC----------AAAUUAGUUUUAGCCCUCCUAAGAGCGACUUUGAAAUUGAAAAGAAAAAAGUUAGAAACAAA
(((((((((((..(....)..)))))))))))(((.((.(((((.(((----------(((...(((((((.....)).)))))...))))))))))).)).)))............... ( -25.20)
>DroSim_CAF1 8257 109 - 1
UGAACUAUCGACGGUCUCUUAUCGAUAGCCCUUUUGUUAUCUAUAUUC----------AAAUUUGUUUUAGCCCUUCUAAGAGCGACUUUAAAAUUGAA-AUGAAAAAGUUUGAAACAAA
....(((((((..(....)..)))))))....................----------...(((((((((((.((....)).))((((((.........-.....))))))))))))))) ( -16.24)
>DroEre_CAF1 10913 103 - 1
UGAACUAUCGACGACCUCUUAUCGAUAGUUCAUUGGUUACCAGAAUUCAGCUGGACUCAAAUUUGUUUUAACCCUUAUAUGAAUCACUUUAAAAUUGAAAAGC-----------------
(((((((((((..(....)..)))))))))))..(((((((((.......))))((........))..)))))..............................----------------- ( -21.50)
>DroYak_CAF1 8027 91 - 1
UGAACUAUCGACAGCCUUUUAUCGAUAGUUCAUUGGCUAUCAGAAUUCA------------UUUGAUUUAACCCUUAUAUUAUCCACUUUAAAAUUGAAGACA-----------------
(((((((((((..........)))))))))))..((..((((((.....------------))))))....)).............(((((....)))))...----------------- ( -17.90)
>consensus
UGAACUAUCGACGGCCUCUUAUCGAUAGUUCAUUGGUUAUCAAAAUUC__________AAAUUUGUUUUAACCCUUAUAAGAGCCACUUUAAAAUUGAAAAGA_________________
.((((((((((..(....)..))))))))))......................................................................................... (-11.44 = -11.75 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,549,760 – 7,549,862
Length 102
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 81.19
Mean single sequence MFE -23.90
Consensus MFE -17.60
Energy contribution -16.64
Covariance contribution -0.96
Combinations/Pair 1.35
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.83
SVM RNA-class probability 0.861474
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7549760 102 + 20766785
UUAGGAGGGCUAAAACUAAUUU----------GAAUAUUGAUAACAAAUGAACUAUCGAUAAGAGGCCGUCGAUAGUUCACGGUGCAACAUCAACUCUCCCAUCACUAGUUC
...((((((...........((----------((...(((...((...((((((((((((........))))))))))))..)).)))..))))))))))............ ( -26.10)
>DroSec_CAF1 8035 102 + 1
UUAGAAGGGCUAAAGCAAAUUU----------GAAUAUUGAUAACAAAUGUGCUAUCGAUAAGAGGCCGUCGAUAGUUCGCAGUACAACAUCAACUCUCCCAUCACUAGUUA
...((.((((....))......----------.....(((((......((((((((((((........)))))))))..))).......))))).....)).))........ ( -19.02)
>DroSim_CAF1 8296 102 + 1
UUAGAAGGGCUAAAACAAAUUU----------GAAUAUAGAUAACAAAAGGGCUAUCGAUAAGAGACCGUCGAUAGUUCACAGUGCAACAUCAACUCUCCCAUCACUAGUUC
...((.(((.............----------.................(((((((((((........)))))))))))..(((.........)))..))).))........ ( -19.10)
>DroEre_CAF1 10936 112 + 1
AUAUAAGGGUUAAAACAAAUUUGAGUCCAGCUGAAUUCUGGUAACCAAUGAACUAUCGAUAAGAGGUCGUCGAUAGUUCAGGAUGCAACAUUAAUUCUUCCAUCACUAGUUC
....(((((((((..((...((.((.....)).))...))(((.((..((((((((((((........)))))))))))))).)))....)))))))))............. ( -26.00)
>DroYak_CAF1 8050 100 + 1
AUAUAAGGGUUAAAUCAAA------------UGAAUUCUGAUAGCCAAUGAACUAUCGAUAAAAGGCUGUCGAUAGUUCAGGGUGCAACAUCAAUUGUCCCACCACUAGUUC
.......(((((..(((..------------.......))))))))..(((((((((((((......))))))))))))).((((..(((.....)))..))))........ ( -29.30)
>consensus
UUAGAAGGGCUAAAACAAAUUU__________GAAUAUUGAUAACAAAUGAACUAUCGAUAAGAGGCCGUCGAUAGUUCACGGUGCAACAUCAACUCUCCCAUCACUAGUUC
......(((........................................(((((((((((........)))))))))))..(((.........)))..)))........... (-17.60 = -16.64 +  -0.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,549,760 – 7,549,862
Length 102
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 81.19
Mean single sequence MFE -25.98
Consensus MFE -16.36
Energy contribution -18.08
Covariance contribution 1.72
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.63
SVM decision value 0.35
SVM RNA-class probability 0.698259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7549760 102 - 20766785
GAACUAGUGAUGGGAGAGUUGAUGUUGCACCGUGAACUAUCGACGGCCUCUUAUCGAUAGUUCAUUUGUUAUCAAUAUUC----------AAAUUAGUUUUAGCCCUCCUAA
((((((((.....(((.(((((((..(((..((((((((((((..(....)..)))))))))))).)))))))))).)))----------..))))))))............ ( -30.10)
>DroSec_CAF1 8035 102 - 1
UAACUAGUGAUGGGAGAGUUGAUGUUGUACUGCGAACUAUCGACGGCCUCUUAUCGAUAGCACAUUUGUUAUCAAUAUUC----------AAAUUUGCUUUAGCCCUUCUAA
...((((.((((((((.((((((((((.....)))..)))))))...))))))))(((((((....))))))).......----------.........))))......... ( -23.80)
>DroSim_CAF1 8296 102 - 1
GAACUAGUGAUGGGAGAGUUGAUGUUGCACUGUGAACUAUCGACGGUCUCUUAUCGAUAGCCCUUUUGUUAUCUAUAUUC----------AAAUUUGUUUUAGCCCUUCUAA
((((.(((((((((((((((((((((........))).))))))..)))))))))((((((......)))))).......----------..))).))))............ ( -22.90)
>DroEre_CAF1 10936 112 - 1
GAACUAGUGAUGGAAGAAUUAAUGUUGCAUCCUGAACUAUCGACGACCUCUUAUCGAUAGUUCAUUGGUUACCAGAAUUCAGCUGGACUCAAAUUUGUUUUAACCCUUAUAU
.(((((((((((.((.(.....).)).))))..((((((((((..(....)..))))))))))))))))).((((.......)))).......................... ( -26.40)
>DroYak_CAF1 8050 100 - 1
GAACUAGUGGUGGGACAAUUGAUGUUGCACCCUGAACUAUCGACAGCCUUUUAUCGAUAGUUCAUUGGCUAUCAGAAUUCA------------UUUGAUUUAACCCUUAUAU
.....((.((((.((((.....)))).))))))((((((((((..........))))))))))...((..((((((.....------------))))))....))....... ( -26.70)
>consensus
GAACUAGUGAUGGGAGAGUUGAUGUUGCACCGUGAACUAUCGACGGCCUCUUAUCGAUAGUUCAUUUGUUAUCAAUAUUC__________AAAUUUGUUUUAGCCCUUCUAA
((((((.(((((((((.(((((((((........))).))))))...))))))))).))))))................................................. (-16.36 = -18.08 +   1.72)

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 10:18:36 2006