Locus 5987

Sequence ID 2L_DroMel_CAF1
Location 16,869,951 – 16,870,103
Length 152
Max. P 0.938842
window9510 window9511 window9512 window9513 window9514

overview

Window 0

Location 16,869,951 – 16,870,044
Length 93
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 83.38
Mean single sequence MFE -27.68
Consensus MFE -20.52
Energy contribution -20.38
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.735354
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16869951 93 + 22407834
CACAC---CACACAUGGGUAUAACGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG-------CUGUUUGUUGGCCAACUGUCAACGUCUUGUAA
.((.(---((....)))))........((((.((((((.((((((((..(((((((....))))-------)))......)))))...))))))))))))).. ( -26.60)
>DroSec_CAF1 9379 92 + 1
CACACCACCACACAUGGGUAAAGCGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAA
.((.(((.......)))))........((((.((((((.((((((((..(((((((....))))-------)))----..)))))...))))))))))))).. ( -28.60)
>DroSim_CAF1 11815 92 + 1
CACACCACCACACAUGGGUAAAGCGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAA
.((.(((.......)))))........((((.((((((.((((((((..(((((((....))))-------)))----..)))))...))))))))))))).. ( -28.60)
>DroEre_CAF1 41610 83 + 1
CA--------CACAUGGCCA-AACGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAA
..--------..........-......((((.((((((.((((((((..(((((((....))))-------)))----..)))))...))))))))))))).. ( -26.80)
>DroYak_CAF1 4708 83 + 1
CA--------CACAUGGGAA-AACGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAA
..--------..........-......((((.((((((.((((((((..(((((((....))))-------)))----..)))))...))))))))))))).. ( -26.80)
>DroPer_CAF1 34445 93 + 1
UAUACUACAAUAU------AUAACCAGAUAAUGACGUUUGAUUGGCCUUUGGCAAGGCCGUUUUAGCCUGUCGG----UUGGCCAAAUGUCAACGUCUUGUAA
.............------...((.((((..(((((((((.(..(((...((((.(((.......)))))))))----)..).)))))))))..)))).)).. ( -28.70)
>consensus
CACAC___CACACAUGGGUA_AACGAAAUAAUGACGUUUGAUUGGCCUUCGGCAAGGCCGUUUG_______CUG____UUGGCCAACUGUCAACGUCUUGUAA
...........................((((.((((((.((((((((..((((...))))....................)))))...))))))))))))).. (-20.52 = -20.38 +  -0.14)

alignment

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secondary structure

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Window 1

Location 16,869,951 – 16,870,044
Length 93
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -26.80
Consensus MFE -19.61
Energy contribution -20.32
Covariance contribution 0.71
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.73
SVM decision value 0.36
SVM RNA-class probability 0.705521
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16869951 93 - 22407834
UUACAAGACGUUGACAGUUGGCCAACAAACAG-------CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGUUAUACCCAUGUGUG---GUGUG
......((((((....(((((((..(.....)-------....((((...))))..)))))))..))))))..........(((((((....).)---))))) ( -26.50)
>DroSec_CAF1 9379 92 - 1
UUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGCUUUACCCAUGUGUGGUGGUGUG
......((((((....(((((((..----(.(-------(((......)))).)..)))))))..)))))).......(((.((((((....).))))).))) ( -29.30)
>DroSim_CAF1 11815 92 - 1
UUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGCUUUACCCAUGUGUGGUGGUGUG
......((((((....(((((((..----(.(-------(((......)))).)..)))))))..)))))).......(((.((((((....).))))).))) ( -29.30)
>DroEre_CAF1 41610 83 - 1
UUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGUU-UGGCCAUGUG--------UG
.............(((..(((((..----...-------.....((((((....))))))....(((((.........))))-))))))..))--------). ( -24.20)
>DroYak_CAF1 4708 83 - 1
UUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGUU-UUCCCAUGUG--------UG
......((((((....(((((((..----(.(-------(((......)))).)..)))))))..))))))...........-..........--------.. ( -23.70)
>DroPer_CAF1 34445 93 - 1
UUACAAGACGUUGACAUUUGGCCAA----CCGACAGGCUAAAACGGCCUUGCCAAAGGCCAAUCAAACGUCAUUAUCUGGUUAU------AUAUUGUAGUAUA
((((((((((((((..(((((((..----......)))))))..((((((....))))))..)).))))))..((......)).------...)))))).... ( -27.80)
>consensus
UUACAAGACGUUGACAGUUGGCCAA____CAG_______CAAACGGCCUUGCCGAAGGCCAAUCAAACGUCAUUAUUUCGUU_UACCCAUGUGUG___GUGUG
......((((((....(((((((........((.....))...((((...))))..)))))))..))))))................................ (-19.61 = -20.32 +   0.71)

alignment

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secondary structure

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Window 2

Location 16,869,985 – 16,870,075
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 82.62
Mean single sequence MFE -24.55
Consensus MFE -13.45
Energy contribution -13.95
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.55
SVM decision value -0.05
SVM RNA-class probability 0.506870
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16869985 90 + 22407834
UUGAUUGGC-----CUUCGGCAAGGCCGUUUG-------CUGUUUGUUGGCCAACUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAGCAAUUUUUU
......(((-----(((....))))))..(((-------(((..((((((((((.......................))))))))))..).)))))...... ( -27.40)
>DroVir_CAF1 23181 87 + 1
UUGAUUGGCUCGACCUUGACCAAGAGAAU----------CCG----UUGGCCAU-CGUCAACGACUUGUAAAAUUUAUUGGCCAAUAUUCAGGCAAAUUUCU
....((((.(((....)))))))((((..----------.((----(((((...-.))))))).................(((........)))...)))). ( -18.10)
>DroPse_CAF1 32317 93 + 1
UUGAUUGGC-----CUUUGGCAAGGCCGUUUUAGCCUGUCGG----UUGGCCAAAUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAAGAAUUUUUU
...((((((-----(..(((((.(((.......))))))))(----(((((.....)))))).................)))))))................ ( -25.50)
>DroSec_CAF1 9416 86 + 1
UUGAUUGGC-----CUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAGCAAUUUUAU
......(((-----(((....))))))(((((-------.((----((((((((.......................))))))))))..)))))........ ( -25.40)
>DroYak_CAF1 4736 84 + 1
UUGAUUGGC-----CUUCGGCAAGGCCGUUUG-------CUG----UUGGCCAACUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAGCAAUUUU--
......(((-----(((....))))))(((((-------.((----((((((((.......................))))))))))..)))))......-- ( -25.40)
>DroPer_CAF1 34476 93 + 1
UUGAUUGGC-----CUUUGGCAAGGCCGUUUUAGCCUGUCGG----UUGGCCAAAUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAAGAAUUUUUU
...((((((-----(..(((((.(((.......))))))))(----(((((.....)))))).................)))))))................ ( -25.50)
>consensus
UUGAUUGGC_____CUUCGGCAAGGCCGUUUG_______CUG____UUGGCCAACUGUCAACGUCUUGUAAAAUUUAUUGGCCAAUAUUCAAGCAAUUUUUU
...((((((..........(((((((....................(((((.....))))).)))))))...........))))))................ (-13.45 = -13.95 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,869,985 – 16,870,075
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 82.62
Mean single sequence MFE -23.20
Consensus MFE -12.27
Energy contribution -12.19
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.94
Structure conservation index 0.53
SVM decision value 0.32
SVM RNA-class probability 0.687707
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16869985 90 - 22407834
AAAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAACAAACAG-------CAAACGGCCUUGCCGAAG-----GCCAAUCAA
......(((((......(((((((((.......((.....)).....))))))))).....))-------)))..((((((....)))-----)))...... ( -25.80)
>DroVir_CAF1 23181 87 - 1
AGAAAUUUGCCUGAAUAUUGGCCAAUAAAUUUUACAAGUCGUUGACG-AUGGCCAA----CGG----------AUUCUCUUGGUCAAGGUCGAGCCAAUCAA
.((..((.(((.((((.((((((((......))....((((....))-))))))))----...----------))))....))).))..))........... ( -18.70)
>DroPse_CAF1 32317 93 - 1
AAAAAAUUCUUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAUUUGGCCAA----CCGACAGGCUAAAACGGCCUUGCCAAAG-----GCCAAUCAA
..........((((...((((((((........((.....))......))))))))----((....)).......((((((....)))-----)))..)))) ( -22.84)
>DroSec_CAF1 9416 86 - 1
AUAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAG-----GCCAAUCAA
......(((((.(....(((((((((.......((.....)).....)))))))))----)))-------)))..((((((....)))-----)))...... ( -24.50)
>DroYak_CAF1 4736 84 - 1
--AAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA----CAG-------CAAACGGCCUUGCCGAAG-----GCCAAUCAA
--....(((((.(....(((((((((.......((.....)).....)))))))))----)))-------)))..((((((....)))-----)))...... ( -24.50)
>DroPer_CAF1 34476 93 - 1
AAAAAAUUCUUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAUUUGGCCAA----CCGACAGGCUAAAACGGCCUUGCCAAAG-----GCCAAUCAA
..........((((...((((((((........((.....))......))))))))----((....)).......((((((....)))-----)))..)))) ( -22.84)
>consensus
AAAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA____CAG_______CAAACGGCCUUGCCGAAG_____GCCAAUCAA
...........(((...((((((((........((.....))......))))))))...................(((...)))..............))). (-12.27 = -12.19 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,870,012 – 16,870,103
Length 91
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 79.23
Mean single sequence MFE -17.01
Consensus MFE -11.31
Energy contribution -11.95
Covariance contribution 0.64
Combinations/Pair 1.11
Mean z-score -2.25
Structure conservation index 0.66
SVM decision value 1.27
SVM RNA-class probability 0.938842
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16870012 91 - 22407834
AAAAAGCGAUGAACUCGAA--------AUGAAAAAAAAAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAACAAACAG-------
...(((((((.........--------..............))))))).....(((((((((.......((.....)).....))))))))).......------- ( -16.10)
>DroPse_CAF1 32344 100 - 1
AAAAAGAGA--GACUGAGAGGGAGACAUUCAAAAACAAAAAAUUCUUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAUUUGGCCAA----CCGACAGGCU
.........--..(((...((.....(((((((............))))))).((((((((........((.....))......))))))))----))..)))... ( -18.44)
>DroSec_CAF1 9443 87 - 1
AAAAAGCGAUGAACUCAAA--------AUGAAAAAAAUAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA----CAG-------
...(((((((.........--------..............))))))).....(((((((((.......((.....)).....)))))))))----...------- ( -16.10)
>DroEre_CAF1 41665 82 - 1
AAAAAGCGAUGAACUGAAC--------AUAAAA-----AAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA----CAG-------
...(((((((.........--------......-----...))))))).....(((((((((.......((.....)).....)))))))))----...------- ( -16.37)
>DroYak_CAF1 4763 83 - 1
AAAAAGCAAUGAACUUAAA--------AUAAAAA----AAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA----CAG-------
...(((((((.........--------.......----...))))))).....(((((((((.......((.....)).....)))))))))----...------- ( -16.61)
>DroPer_CAF1 34503 100 - 1
AAAAAGAGA--GACUGAGAGGGAGACAUUCAAAAACAAAAAAUUCUUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAUUUGGCCAA----CCGACAGGCU
.........--..(((...((.....(((((((............))))))).((((((((........((.....))......))))))))----))..)))... ( -18.44)
>consensus
AAAAAGCGAUGAACUGAAA________AUAAAAAA_AAAAAAUUGCUUGAAUAUUGGCCAAUAAAUUUUACAAGACGUUGACAGUUGGCCAA____CAG_______
...(((((((...............................))))))).....(((((((((.......((.....)).....))))))))).............. (-11.31 = -11.95 +   0.64)

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 11:58:16 2006