Locus 2385

Sequence ID 3R_DroMel_CAF1
Location 6,740,892 – 6,741,038
Length 146
Max. P 0.974952
window3852 window3853 window3854 window3855

overview

Window 2

Location 6,740,892 – 6,741,002
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.42
Mean single sequence MFE -29.80
Consensus MFE -25.81
Energy contribution -25.88
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.12
Structure conservation index 0.87
SVM decision value 1.24
SVM RNA-class probability 0.935103
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740892 110 + 27905053
UUUGGCUUCAAACAGGUGGGCGCCACAAUUACUAAAUGUUGCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAGAGGCAAUGGCAAAGG----------
....(((((......((((...))))..........(.(((((((((..((((((((((.........)))))..))))).))))))))).)..)))))...........---------- ( -29.20)
>DroSec_CAF1 5672 113 + 1
UUUGGCUUCAAACAGGUGGGCGCCACAAUUACUAAAUGUUGCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC-------AA
..((((((((......)))).)))).............(((((((((..((((((((((.........)))))..))))).))))))))).((....((....))....))-------.. ( -28.50)
>DroSim_CAF1 10005 113 + 1
UUUGGCUUCAAACAGGUGGGCGCCACAAUUACUAAAUGUUGCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC-------AA
..((((((((......)))).)))).............(((((((((..((((((((((.........)))))..))))).))))))))).((....((....))....))-------.. ( -28.50)
>DroYak_CAF1 208 120 + 1
UUUGGCUUCAAACAGGUGGGCGCCACAAUUACUAAAUGUUGCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAGCGCAAAGGCAACAGCAAGAGCGAAAUCAAA
.(((..(((......((((...))))...........((((((((((..((((((((((.........)))))..))))).))))))))))((....((....))....)))))..))). ( -33.00)
>consensus
UUUGGCUUCAAACAGGUGGGCGCCACAAUUACUAAAUGUUGCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC_______AA
..((((((((......)))).)))).............(((((((((..((((((((((.........)))))..))))).))))))))).((....((....))....))......... (-25.81 = -25.88 +   0.06)

alignment

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secondary structure

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Window 3

Location 6,740,892 – 6,741,002
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -30.27
Consensus MFE -27.51
Energy contribution -27.57
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.91
SVM decision value 1.49
SVM RNA-class probability 0.958897
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740892 110 - 27905053
----------CCUUUGCCAUUGCCUCUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGCAACAUUUAGUAAUUGUGGCGCCCACCUGUUUGAAGCCAAA
----------.....(((((.....(((..(((((((((((((((..(((((.........)))))))))).))))))))))....))).....)))))..................... ( -29.00)
>DroSec_CAF1 5672 113 - 1
UU-------GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGCAACAUUUAGUAAUUGUGGCGCCCACCUGUUUGAAGCCAAA
..-------..(((..(.(((((...((..(((((((((((((((..(((((.........)))))))))).))))))))))))....))))).)..))).................... ( -30.50)
>DroSim_CAF1 10005 113 - 1
UU-------GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGCAACAUUUAGUAAUUGUGGCGCCCACCUGUUUGAAGCCAAA
..-------..(((..(.(((((...((..(((((((((((((((..(((((.........)))))))))).))))))))))))....))))).)..))).................... ( -30.50)
>DroYak_CAF1 208 120 - 1
UUUGAUUUCGCUCUUGCUGUUGCCUUUGCGCUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGCAACAUUUAGUAAUUGUGGCGCCCACCUGUUUGAAGCCAAA
.(((..(((((....)).((..(..((((..((((((((((((((..(((((.........)))))))))).))))))))).......))))..)..))............)))..))). ( -31.10)
>consensus
UU_______GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGCAACAUUUAGUAAUUGUGGCGCCCACCUGUUUGAAGCCAAA
...............((.(((((.......(((((((((((((((..(((((.........)))))))))).))))))))))......))))).))(((...((......))..)))... (-27.51 = -27.57 +   0.06)

alignment

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secondary structure

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Window 4

Location 6,740,932 – 6,741,038
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -27.73
Consensus MFE -22.67
Energy contribution -22.30
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -2.63
Structure conservation index 0.82
SVM decision value 1.68
SVM RNA-class probability 0.971982
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740932 106 + 27905053
GCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAGAGGCAAUGGCAAAGG------------CAAAAGCAAAAGCA--CAGAGGAGCCCAAAGCGUUGAA
(((((((..((((((((((.........)))))..))))).)))))))((.((...(((..((((....(------------(....))....)).--)).....)))....)).))... ( -25.70)
>DroSec_CAF1 5712 113 + 1
GCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC-------AACUCAAAAGCAAAAGCACACAGAGGAGCCCAAAGCGUUGAA
(((((((..((((((((((.........)))))..))))).)))))))..........((((.((...(((-------..(((....((....)).....)))..)))....)))))).. ( -29.80)
>DroSim_CAF1 10045 111 + 1
GCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC-------AAGGCAAAAGCAAAAGCA--CAGAGGAGCCCAAAGCGUUGAA
(((((((..((((((((((.........)))))..))))).)))))))........(....)..(((((..-------..(((....((....)).--(....).))).....))))).. ( -25.90)
>DroYak_CAF1 248 118 + 1
GCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAGCGCAAAGGCAACAGCAAGAGCGAAAUCAAAAGCAAAAGCAAAAGCA--CCGAGGAGCCCAAAGCGUUGAA
(((((((..((((((((((.........)))))..))))).)))))))(((((...(((..(.((....))..........((....)).......--....)..)))....)))))... ( -29.50)
>consensus
GCUGCAGCAGCUUUUAAAUCAAAUGAAUAUUUAUUAAAGCACUGCAGCAAGGCAAAGGCAACAGCAACGGC_______AA_GCAAAAGCAAAAGCA__CAGAGGAGCCCAAAGCGUUGAA
(((((((..((((((((((.........)))))..))))).)))))))...((....))..((((......................((....))..........((.....)))))).. (-22.67 = -22.30 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,740,932 – 6,741,038
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -30.00
Consensus MFE -25.20
Energy contribution -25.45
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.51
Structure conservation index 0.84
SVM decision value 1.74
SVM RNA-class probability 0.974952
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6740932 106 - 27905053
UUCAACGCUUUGGGCUCCUCUG--UGCUUUUGCUUUUG------------CCUUUGCCAUUGCCUCUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGC
......((...((((.....((--.((....((....)------------)....))))..))))..))...(((((((((((((..(((((.........)))))))))).)))))))) ( -27.70)
>DroSec_CAF1 5712 113 - 1
UUCAACGCUUUGGGCUCCUCUGUGUGCUUUUGCUUUUGAGUU-------GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGC
..((((((....(((..(((.....((....))....)))..-------)))...)).))))..........(((((((((((((..(((((.........)))))))))).)))))))) ( -32.30)
>DroSim_CAF1 10045 111 - 1
UUCAACGCUUUGGGCUCCUCUG--UGCUUUUGCUUUUGCCUU-------GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGC
..((((((...((((.......--.((....))....)))).-------).)))))................(((((((((((((..(((((.........)))))))))).)))))))) ( -28.20)
>DroYak_CAF1 248 118 - 1
UUCAACGCUUUGGGCUCCUCGG--UGCUUUUGCUUUUGCUUUUGAUUUCGCUCUUGCUGUUGCCUUUGCGCUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGC
.....(((...((((....(((--(((....))....((..........))....))))..))))..)))..(((((((((((((..(((((.........)))))))))).)))))))) ( -31.80)
>consensus
UUCAACGCUUUGGGCUCCUCUG__UGCUUUUGCUUUUGC_UU_______GCCGUUGCUGUUGCCUUUGCCUUGCUGCAGUGCUUUAAUAAAUAUUCAUUUGAUUUAAAAGCUGCUGCAGC
......((...((((..........((....))................((....))....))))..))...(((((((((((((..(((((.........)))))))))).)))))))) (-25.20 = -25.45 +   0.25)

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 10:34:08 2006