Locus 4250

Sequence ID 2R_DroMel_CAF1
Location 14,030,467 – 14,030,736
Length 269
Max. P 0.980419
window6821 window6822 window6823 window6824 window6825 window6826

overview

Window 1

Location 14,030,467 – 14,030,582
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.20
Mean single sequence MFE -41.10
Consensus MFE -35.19
Energy contribution -35.50
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -3.29
Structure conservation index 0.86
SVM decision value 1.84
SVM RNA-class probability 0.979703
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030467 115 + 20766785
AUAAA-----AUGCAUUGGGGCUGGCAAUGGCAUUGGCCGAGGGGAUGUUUUGGGCCAAAAAAGCUCCAACCCACCCCAACGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAA
.....-----.....((((.((.((((.((((.((((((..((((.((..((((((.......)).))))..))))))...(....)....))))))..)))).)))))).))))..... ( -38.50)
>DroSim_CAF1 60549 115 + 1
AUAAA-----AUGCAUUGGGGCUGGCAAUGGCAUUGGCCGAGGGGAUGUUUUGGGCCAAAAAAGCUCCAACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAA
.....-----.....((((.((.((((.((((.(((((((((((((.(..((((((.......)).))))..)))))).))(....)....))))))..)))).)))))).))))..... ( -39.50)
>DroEre_CAF1 63780 114 + 1
AUAAA----AAAGCAUUGGGGCUGGCAAUGGCAUUGGCCGAGGGGAUGUUUUGGGCCAA-AAAGCUC-UACCAUCCCCAUCGACCUCAACAGGCCAGCAGUUGAUGCUGUGCCAAAAAAA
.....----..(((((..(.((((((..((.....((.((((((((((....((((...-...))))-...))))))).))).))....)).))))))..)..)))))............ ( -45.40)
>DroYak_CAF1 62416 118 + 1
AUAAAGAAGAAAGCAUUGGGGCUGGCAAUGGCAUUGGCCGAGGGGAUGUUUUGGGCCAAAAAAGCUC-AACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAA-AAU
........(..(((......)))..)..((((..((((((((((((.(..((((((.......))))-))..)))))).))(....)....)))))(((((....)))))))))..-... ( -41.00)
>consensus
AUAAA_____AAGCAUUGGGGCUGGCAAUGGCAUUGGCCGAGGGGAUGUUUUGGGCCAAAAAAGCUC_AACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAA
...............((((.((.((((.((((.((((((..(((((.(.((.((((.......)))).)).).)))))...(....)....))))))..)))).)))))).))))..... (-35.19 = -35.50 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,030,467 – 14,030,582
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.20
Mean single sequence MFE -43.05
Consensus MFE -36.92
Energy contribution -38.17
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -3.34
Structure conservation index 0.86
SVM decision value 1.86
SVM RNA-class probability 0.980419
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030467 115 - 20766785
UUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGUUGGGGUGGGUUGGAGCUUUUUUGGCCCAAAACAUCCCCUCGGCCAAUGCCAUUGCCAGCCCCAAUGCAU-----UUUAU
......(((((..((((((((.........)))))(((((..((((((..((((.(((.....)))))))..))))))..)))))..)))...)))))((......))..-----..... ( -44.80)
>DroSim_CAF1 60549 115 - 1
UUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUUGGAGCUUUUUUGGCCCAAAACAUCCCCUCGGCCAAUGCCAUUGCCAGCCCCAAUGCAU-----UUUAU
......(((((..((((((((.........)))))((((((.((((((..((((.(((.....)))))))..).)))))))))))..)))...)))))((......))..-----..... ( -44.70)
>DroEre_CAF1 63780 114 - 1
UUUUUUUGGCACAGCAUCAACUGCUGGCCUGUUGAGGUCGAUGGGGAUGGUA-GAGCUUU-UUGGCCCAAAACAUCCCCUCGGCCAAUGCCAUUGCCAGCCCCAAUGCUUU----UUUAU
............(((((.....((((((..((...((((((.(((((((...-(.(((..-..))).)....)))))))))))))...))....))))))....)))))..----..... ( -41.50)
>DroYak_CAF1 62416 118 - 1
AUU-UUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUU-GAGCUUUUUUGGCCCAAAACAUCCCCUCGGCCAAUGCCAUUGCCAGCCCCAAUGCUUUCUUCUUUAU
...-.((((((..((((((((.........)))))((((((.((((((..((-(.(((.....))).)))..).)))))))))))..)))...))))))..................... ( -41.20)
>consensus
UUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUU_GAGCUUUUUUGGCCCAAAACAUCCCCUCGGCCAAUGCCAUUGCCAGCCCCAAUGCAU_____UUUAU
......(((((..((((((((.........)))))((((((.(((((...((((.(((.....)))))))....)))))))))))..)))...)))))((......))............ (-36.92 = -38.17 +   1.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,030,502 – 14,030,622
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.83
Mean single sequence MFE -41.45
Consensus MFE -34.41
Energy contribution -34.73
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -3.06
Structure conservation index 0.83
SVM decision value 1.14
SVM RNA-class probability 0.920719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030502 120 + 20766785
AGGGGAUGUUUUGGGCCAAAAAAGCUCCAACCCACCCCAACGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAAUAGUGGGAAGCACAAGGAAUUGAACUUUGUGCCCCGUCUG
.((((.((..((((((.......)).))))..))))))...(((.......(((..(((((....))))))))...........(((..((((((((.......)))))))))))))).. ( -42.10)
>DroSim_CAF1 60584 119 + 1
AGGGGAUGUUUUGGGCCAAAAAAGCUCCAACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAAUAGUGGGAAGCACAAGGAAUUGAACUUUGUGC-CCGUCUG
.(((((.(..((((((.......)).))))..))))))...(((.......(((..(((((....))))))))............((..((((((((.......))))))))-))))).. ( -39.00)
>DroEre_CAF1 63816 117 + 1
AGGGGAUGUUUUGGGCCAA-AAAGCUC-UACCAUCCCCAUCGACCUCAACAGGCCAGCAGUUGAUGCUGUGCCAAAAAAAUAGUGGGAAGCACAAGGAAUUGAACUUUGUGC-CCGCCUG
.(((((((....((((...-...))))-...))))))).............((((((((.....))))).))).........((((...((((((((.......))))))))-))))... ( -44.90)
>DroYak_CAF1 62456 117 + 1
AGGGGAUGUUUUGGGCCAAAAAAGCUC-AACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAA-AAUUAGUGGGUAGCACAAGGAAUUGAACUUUGUGC-CCGUCUG
.(((((.(..((((((.......))))-))..))))))...(((.......(((..(((((....))))))))...-........((..((((((((.......))))))))-))))).. ( -39.80)
>consensus
AGGGGAUGUUUUGGGCCAAAAAAGCUC_AACCCUCCCCAUCGACCUCAACAGGCCAACAGUUGAUGCUGUGCCAAAAAAAUAGUGGGAAGCACAAGGAAUUGAACUUUGUGC_CCGUCUG
.(((((.(.((.((((.......)))).)).).))))).............(((..(((((....)))))))).......((((((...((((((((.......)))))))).))).))) (-34.41 = -34.73 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,030,502 – 14,030,622
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.83
Mean single sequence MFE -41.67
Consensus MFE -34.88
Energy contribution -35.50
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.84
SVM decision value 0.95
SVM RNA-class probability 0.888338
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030502 120 - 20766785
CAGACGGGGCACAAAGUUCAAUUCCUUGUGCUUCCCACUAUUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGUUGGGGUGGGUUGGAGCUUUUUUGGCCCAAAACAUCCCCU
..((((((((((((.(.......).))))))..)))...........(((.(((((.....)))))))).......)))...((((((..((((.(((.....)))))))..)))))).. ( -44.00)
>DroSim_CAF1 60584 119 - 1
CAGACGG-GCACAAAGUUCAAUUCCUUGUGCUUCCCACUAUUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUUGGAGCUUUUUUGGCCCAAAACAUCCCCU
..(((((-((((((.(.......).))))))))..............(((.(((((.....)))))))).......)))...((((((..((((.(((.....)))))))..).))))). ( -40.10)
>DroEre_CAF1 63816 117 - 1
CAGGCGG-GCACAAAGUUCAAUUCCUUGUGCUUCCCACUAUUUUUUUGGCACAGCAUCAACUGCUGGCCUGUUGAGGUCGAUGGGGAUGGUA-GAGCUUU-UUGGCCCAAAACAUCCCCU
..((..(-((((((.(.......).)))))))..)).(.(((((...(((.(((((.....))))))))....))))).)..(((((((...-(.(((..-..))).)....))))))). ( -40.80)
>DroYak_CAF1 62456 117 - 1
CAGACGG-GCACAAAGUUCAAUUCCUUGUGCUACCCACUAAUU-UUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUU-GAGCUUUUUUGGCCCAAAACAUCCCCU
.....((-((..((((((((((.((((((((((..........-..))))))........((((((((((....)))))))))).)))))))-)))))))....))))............ ( -41.80)
>consensus
CAGACGG_GCACAAAGUUCAAUUCCUUGUGCUUCCCACUAUUUUUUUGGCACAGCAUCAACUGUUGGCCUGUUGAGGUCGAUGGGGAGGGUU_GAGCUUUUUUGGCCCAAAACAUCCCCU
..(((((.((((((.(.......).))))))...))...........(((.(((((.....)))))))).......)))...(((((...((((.(((.....)))))))....))))). (-34.88 = -35.50 +   0.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,030,582 – 14,030,696
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.42
Mean single sequence MFE -29.47
Consensus MFE -21.20
Energy contribution -21.43
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.72
SVM decision value -0.00
SVM RNA-class probability 0.531399
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030582 114 + 20766785
UAGUGGGAAGCACAAGGAAUUGAACUUUGUGCCCCGUCUGAUUGCACUUCGCUUCUUCCCUUCUCUA------UGUGUCUCUCUCGCACACUCUGUAGCCAUCUCUCUCGCUCUAGGGUG
(((.(((((((((((((.......)))))))).......((..((.....)).)))))))....)))------((((.......))))(((((((.(((..........))).))))))) ( -29.40)
>DroSim_CAF1 60664 113 + 1
UAGUGGGAAGCACAAGGAAUUGAACUUUGUGC-CCGUCUGAUUGCACUUCGCUUCCUCCCUUCUCUC------UCCGUCUCUCUCACACCCUAUGUAGCCAUCUCACUCGCUCUAGGGUG
.((.((((((....(((((.((((....((((-..........)))))))).)))))..)))))).)------)............(((((((.(.(((..........))))))))))) ( -28.70)
>DroEre_CAF1 63894 119 + 1
UAGUGGGAAGCACAAGGAAUUGAACUUUGUGC-CCGCCUGAUUGCACUUCUCUUCCCCCUCUCACCCCCUCCCGCCCUCUCUUUCCCACACUCUAUAGCCGUCUCUCUCGCUCUAGGGUG
..(((((((((((((((.......))))))))-..((......)).....................................)))))))((((((.(((..........))).)))))). ( -30.30)
>consensus
UAGUGGGAAGCACAAGGAAUUGAACUUUGUGC_CCGUCUGAUUGCACUUCGCUUCCUCCCUUCUCUC______UCCGUCUCUCUCACACACUCUGUAGCCAUCUCUCUCGCUCUAGGGUG
..((((((.((((((((.......))))))))...((......))....................................)))))).(((((((.(((..........))).))))))) (-21.20 = -21.43 +   0.23)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,030,622 – 14,030,736
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.00
Mean single sequence MFE -34.48
Consensus MFE -20.44
Energy contribution -19.33
Covariance contribution -1.10
Combinations/Pair 1.18
Mean z-score -2.26
Structure conservation index 0.59
SVM decision value 0.17
SVM RNA-class probability 0.616286
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14030622 114 - 20766785
UGUACAUAUAAGCCCAUUGUACAUAUCUAACUUUCGCUCUCACCCUAGAGCGAGAGAGAUGGCUACAGAGUGUGCGAGAGAGACACA------UAGAGAAGGGAAGAAGCGAAGUGCAAU
(((((.......(((.(((((..(((((..((((((((((......)))))))))))))))..))))).((((.(....)..)))).------.......)))..........))))).. ( -35.23)
>DroSim_CAF1 60703 110 - 1
UGU----AUAAGCCCAUUGUACAUAUCCAACUUUCGCUCUCACCCUAGAGCGAGUGAGAUGGCUACAUAGGGUGUGAGAGAGACGGA------GAGAGAAGGGAGGAAGCGAAGUGCAAU
(((----((((.....)))))))..(((..(((((.(((((((((((.(((.(......).)))...))))))((.......)).))------))).)))))..))).((.....))... ( -35.80)
>DroEre_CAF1 63933 116 - 1
UGU----AUAAGCCCAUUGUACAUAUUCAACUUUCGCUCUCACCCUAGAGCGAGAGAGACGGCUAUAGAGUGUGGGAAAGAGAGGGCGGGAGGGGGUGAGAGGGGGAAGAGAAGUGCAAU
...----........(((((((...(((...(..(.((((((((((....(....)...(.(((......(......)......))).)...)))))))))).)..)...)))))))))) ( -32.40)
>consensus
UGU____AUAAGCCCAUUGUACAUAUCCAACUUUCGCUCUCACCCUAGAGCGAGAGAGAUGGCUACAGAGUGUGCGAGAGAGACGGA______GAGAGAAGGGAGGAAGCGAAGUGCAAU
...............(((((((...(((..((((((((((......)))))..........((........))........................)))))..)))......))))))) (-20.44 = -19.33 +  -1.10)

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 11:15:20 2006