Locus 7003

Sequence ID X_DroMel_CAF1
Location 17,543,924 – 17,544,164
Length 240
Max. P 0.968997
window11437 window11438 window11439 window11440 window11441 window11442

overview

Window 7

Location 17,543,924 – 17,544,044
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -31.15
Consensus MFE -22.36
Energy contribution -22.43
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -1.42
Structure conservation index 0.72
SVM decision value -0.03
SVM RNA-class probability 0.517963
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17543924 120 + 22224390
CUUAGCCAAGACGCGAACCCAUACAGGUGCGUGUUACCCAGACAGCAACCGACACAGAAGUACCGCAUUUCGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGC
.........((((((.(((......))).)))))).........((..........(((((.....)))))((((((...........))))))..((((((((.....)))))))).)) ( -31.60)
>DroSec_CAF1 36041 120 + 1
UUUAGCGAAGAUGCGAACCCACACAGAUGCGUUUAUCCCAGACAUCAACCGACACAGAAGUGCCGCAUUUUGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGC
....(((((((((...(((.(((.((((((((((.....)))).......(.(((....))).)))))))))).)))..)))))))..........((((((((.....)))))))).)) ( -33.30)
>DroSim_CAF1 25554 120 + 1
UUUAGCGAAGACGCGAACCCACACAGAUGCGUUUAUCCCAGACAUCAACCGACACAGAAGUGCCGCAUUUUGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGC
....(((....)))...........(((((((((.....)))).......(.(((....))).))))))((((((((...........))))))))((((((((.....))))))))... ( -31.20)
>DroYak_CAF1 32861 117 + 1
GUUAGCUAAGACACGAACCGAAACAAGUGCACCUUCCCCAGACAGCAACCGAUAUAGAAAUAGCACAUUUCGUUGGUA---UUUUCAUACCAACAAUUGGCGCGAAAGCCGUGCCAAAGC
....(((............((((...((((..((.....)).............((....)))))).))))(((((((---(....))))))))..((((((((.....))))))))))) ( -28.50)
>consensus
UUUAGCGAAGACGCGAACCCACACAGAUGCGUUUAUCCCAGACAGCAACCGACACAGAAGUACCGCAUUUCGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGC
....((..................((((((((((.....)))).......(.(((....))).))))))).((((((...........))))))..((((((((.....)))))))).)) (-22.36 = -22.43 +   0.06)

alignment

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secondary structure

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Window 8

Location 17,543,924 – 17,544,044
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -41.68
Consensus MFE -30.80
Energy contribution -30.80
Covariance contribution 0.00
Combinations/Pair 1.29
Mean z-score -2.25
Structure conservation index 0.74
SVM decision value 0.96
SVM RNA-class probability 0.890133
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17543924 120 - 22224390
GCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACGAAAUGCGGUACUUCUGUGUCGGUUGCUGUCUGGGUAACACGCACCUGUAUGGGUUCGCGUCUUGGCUAAG
((.(((((((((...(((((....((((((((((.......))))))))))..))))).....)))))))))..))....(((.(((.((((((((....))))..)))).))).))).. ( -40.70)
>DroSec_CAF1 36041 120 - 1
GCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUCUGGGAUAAACGCAUCUGUGUGGGUUCGCAUCUUCGCUAAA
((.(((((.((.....)).)))))((((((((((.......))))))))))...))(((((....)))))(((.(((((...((((..((((....))))..)))))))))...)))... ( -41.60)
>DroSim_CAF1 25554 120 - 1
GCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUCUGGGAUAAACGCAUCUGUGUGGGUUCGCGUCUUCGCUAAA
((.(((((.((.....)).)))))((((((((((.......))))))))))...))(((((....)))))(((.(((((...((((..((((....))))..)))))))))...)))... ( -41.20)
>DroYak_CAF1 32861 117 - 1
GCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUAUGAAAA---UACCAACGAAAUGUGCUAUUUCUAUAUCGGUUGCUGUCUGGGGAAGGUGCACUUGUUUCGGUUCGUGUCUUAGCUAAC
(((..((((((((....))(((....((((((((....)---)))))))(((((((((..(((((....(((...)))....)))))...))))..)))))))).))))))..))).... ( -43.20)
>consensus
GCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUCUGGGAAAAACGCACCUGUGUGGGUUCGCGUCUUCGCUAAA
...((((((((((..((..((...((((((((((.......))))))))))...))(((((....)))))))..))))).((.((..(((((....)))))...)).)).....))))). (-30.80 = -30.80 +   0.00)

alignment

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secondary structure

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Window 9

Location 17,543,964 – 17,544,084
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -35.85
Consensus MFE -30.02
Energy contribution -29.65
Covariance contribution -0.37
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.84
SVM decision value 0.87
SVM RNA-class probability 0.869790
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17543964 120 + 22224390
GACAGCAACCGACACAGAAGUACCGCAUUUCGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGCAGAGAUGCGAUAAAGAAGAGGAGUGCAGAGAGGCGGCAGU
....((..((.((......))...(((((((((((((...........))))))..((((((((.....)))))))).(((....)))...........))))))).....))..))... ( -36.50)
>DroSec_CAF1 36081 120 + 1
GACAUCAACCGACACAGAAGUGCCGCAUUUUGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGCAGAGAUGCGAUAAAGAAGAGGAGUGCAGAGAGGCGGCAGU
....................((((((.((((....(((((.(((((..........((((((((.....)))))))).(((....)))......)))))..))))).)))).)))))).. ( -36.90)
>DroSim_CAF1 25594 120 + 1
GACAUCAACCGACACAGAAGUGCCGCAUUUUGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGCAGAGAUGCGAUAAAGAAGAGGAGUGCAGAGAGGCGGCAGU
....................((((((.((((....(((((.(((((..........((((((((.....)))))))).(((....)))......)))))..))))).)))).)))))).. ( -36.90)
>DroYak_CAF1 32901 112 + 1
GACAGCAACCGAUAUAGAAAUAGCACAUUUCGUUGGUA---UUUUCAUACCAACAAUUGGCGCGAAAGCCGUGCCAAAGCGGAGAUGCGAUUAAGAAGAGGCGCGCAGA-----GGCAGU
....((..(((.....(((((.....)))))(((((((---(....))))))))..((((((((.....))))))))..)))...((((.((......))...))))..-----.))... ( -33.10)
>consensus
GACAGCAACCGACACAGAAGUACCGCAUUUCGUUGGUAUUAUUUUCACACCAACAAUUGGCGCGAAAGCCGUGCCAAAGCAGAGAUGCGAUAAAGAAGAGGAGUGCAGAGAGGCGGCAGU
........((..(((....))).((((((((((((((...........))))))..((((((((.....))))))))....))))))))..........))...((.........))... (-30.02 = -29.65 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,543,964 – 17,544,084
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -34.84
Consensus MFE -30.61
Energy contribution -29.68
Covariance contribution -0.94
Combinations/Pair 1.20
Mean z-score -2.25
Structure conservation index 0.88
SVM decision value 1.63
SVM RNA-class probability 0.968997
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17543964 120 - 22224390
ACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACGAAAUGCGGUACUUCUGUGUCGGUUGCUGUC
((.((.(((.....((((..........((((((((.((....(((((.((.....)).)))))..((((((((.......)))))))))).)))))))).....)))).))).)).)). ( -35.66)
>DroSec_CAF1 36081 120 - 1
ACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUC
.(.(((((......))................((((.......(((((.((.....)).)))))((((((((((.......)))))))))).))))(((((....)))))))).)..... ( -35.30)
>DroSim_CAF1 25594 120 - 1
ACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUC
.(.(((((......))................((((.......(((((.((.....)).)))))((((((((((.......)))))))))).))))(((((....)))))))).)..... ( -35.30)
>DroYak_CAF1 32901 112 - 1
ACUGCC-----UCUGCGCGCCUCUUCUUAAUCGCAUCUCCGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUAUGAAAA---UACCAACGAAAUGUGCUAUUUCUAUAUCGGUUGCUGUC
...((.-----...))(((((...........((......))..(((((((((......)))..((((((((((....)---)))))))))...))))))..........)).))).... ( -33.10)
>consensus
ACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAUAAUACCAACAAAAUGCGGCACUUCUGUGUCGGUUGAUGUC
.(.(((..........................((((.......(((((.((.....)).)))))((((((((((.......)))))))))).))))(((((....)))))))).)..... (-30.61 = -29.68 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,544,004 – 17,544,124
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -36.52
Consensus MFE -34.05
Energy contribution -34.62
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.75
Structure conservation index 0.93
SVM decision value 0.94
SVM RNA-class probability 0.886092
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17544004 120 - 22224390
CGCCGCGCUUGUGUGCGAUUCCACUGGUGUUUCUCCACAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAU
.((((.(((.(((((((((......(((((((......)))).)))((......)).............)))))))....))...))).))))((((((((((.....)))))))))).. ( -37.60)
>DroSec_CAF1 36121 120 - 1
CGCCGCGCUUGUGUGUGAUUCCACUGGUGUUUCUCCGCAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAU
.((((.(((.(((((((((......((.......))(((((..(....)..))))).............)))))))....))...))).))))((((((((((.....)))))))))).. ( -37.80)
>DroSim_CAF1 25634 120 - 1
CGCCGCGCUUGUGUGUGAUUCCACUGGUGUUUCUCCGCAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAU
.((((.(((.(((((((((......((.......))(((((..(....)..))))).............)))))))....))...))).))))((((((((((.....)))))))))).. ( -37.80)
>DroYak_CAF1 32939 114 - 1
CGCCGCGCUUGUGUGCGACUCCGCUGGUGUUUCUCCACAGACUGCC-----UCUGCGCGCCUCUUCUUAAUCGCAUCUCCGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUAUGAAAA-
.((((.(((.((((((((.......(((((.......((((.....-----)))).))))).........)))))....)))...))).))))(((((..(((.....)))..))))).- ( -32.89)
>consensus
CGCCGCGCUUGUGUGCGAUUCCACUGGUGUUUCUCCACAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCUGCUUUGGCACGGCUUUCGCGCCAAUUGUUGGUGUGAAAAU
.((((.(((.(((((((((......((.((......(((((..........))))))).))........)))))))....))...))).))))((((((((((.....)))))))))).. (-34.05 = -34.62 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,544,044 – 17,544,164
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -32.02
Consensus MFE -27.97
Energy contribution -28.34
Covariance contribution 0.37
Combinations/Pair 1.10
Mean z-score -1.91
Structure conservation index 0.87
SVM decision value 0.82
SVM RNA-class probability 0.859347
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17544044 120 - 22224390
AACCCGCGGUCUGGAUUUUCACACACGUCCGCUUUCGAAUCGCCGCGCUUGUGUGCGAUUCCACUGGUGUUUCUCCACAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCU
.....((((((((((...((.((((((..(((............)))..)))))).)).)))....(((......)))))))))).((......))........................ ( -30.20)
>DroSec_CAF1 36161 120 - 1
AACCCGCGGCCUGGAUUUUCACACACGUCCGCUUUCGAAUCGCCGCGCUUGUGUGUGAUUCCACUGGUGUUUCUCCGCAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCU
.....((((((((((...(((((((((..(((............)))..))))))))).))))..)))........(((((..(....)..)))))...............)))...... ( -35.40)
>DroSim_CAF1 25674 120 - 1
AACCCGCGGCCUGGAUUUUCACACACGUCCGCUUUCGAAUCGCCGCGCUUGUGUGUGAUUCCACUGGUGUUUCUCCGCAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCU
.....((((((((((...(((((((((..(((............)))..))))))))).))))..)))........(((((..(....)..)))))...............)))...... ( -35.40)
>DroYak_CAF1 32978 115 - 1
AACCCGCGGCCUGGAUUUUCACACACGUCCGCUUUCGAAUCGCCGCGCUUGUGUGCGACUCCGCUGGUGUUUCUCCACAGACUGCC-----UCUGCGCGCCUCUUCUUAAUCGCAUCUCC
.....((((...(((...((.((((((..(((............)))..)))))).)).)))((.(((((((......)))).)))-----...))..............))))...... ( -27.10)
>consensus
AACCCGCGGCCUGGAUUUUCACACACGUCCGCUUUCGAAUCGCCGCGCUUGUGUGCGAUUCCACUGGUGUUUCUCCACAGACUGCCGCCUCUCUGCACUCCUCUUCUUUAUCGCAUCUCU
.....(((((.((((...(((((((((..(((............)))..))))))))).))))(((.((......)))))...))))).....(((................)))..... (-27.97 = -28.34 +   0.37)

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 12:27:50 2006