Locus 2396

Sequence ID 3R_DroMel_CAF1
Location 6,748,163 – 6,748,472
Length 309
Max. P 0.999253
window3876 window3877 window3878 window3879 window3880 window3881 window3882 window3883

overview

Window 6

Location 6,748,163 – 6,748,278
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.33
Mean single sequence MFE -23.18
Consensus MFE -19.81
Energy contribution -19.62
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.57
Structure conservation index 0.85
SVM decision value 1.35
SVM RNA-class probability 0.944558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748163 115 + 27905053
UUAACUUUUCAUUGCCUAGUAGGGCAAACACAAUUAGGGGCCAUCCACAAAACUAAAA-AA--AAAA--AUCGAAUAGUAGUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUU
...(((.(((.((((((....)))))).........(((....)))............-..--....--...))).)))...............(.(((((....))))).)........ ( -19.90)
>DroSec_CAF1 12408 114 + 1
UUAACUUUUCAUUGCCUAGUAGGGCAAACACAAUUAGGGGCCACCCCCAAAACUAAAA-AA--AAAAACAUCGAAUA---GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUU
...(((.(((.((((((....)))))).........((((....))))..........-..--.........))).)---))............(.(((((....))))).)........ ( -24.80)
>DroSim_CAF1 16721 116 + 1
UUAACUUUUCAUUGCCUAGUAGGGCAAACACAAUUAGGGGCCACCCCCAAAACUAAAA-AAAAAAAAACAUCGAAUA---GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUU
...(((.(((.((((((....)))))).........((((....))))..........-.............))).)---))............(.(((((....))))).)........ ( -24.80)
>DroYak_CAF1 8529 117 + 1
UUAACUUUUCAUUGCCUAGUAGGGCAAACACAAUUAGGGGCCACCCGCGAAACUAAACUAAAAAAAAACAUCGAAUA---GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUU
...(((.(((.((((((....)))))).........(((....)))..........................))).)---))............(.(((((....))))).)........ ( -23.20)
>consensus
UUAACUUUUCAUUGCCUAGUAGGGCAAACACAAUUAGGGGCCACCCCCAAAACUAAAA_AA__AAAAACAUCGAAUA___GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUU
....(((((..((((((....)))))).........(((....)))............................................))))).(((((....))))).......... (-19.81 = -19.62 +  -0.19)

alignment

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secondary structure

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Window 7

Location 6,748,238 – 6,748,358
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -34.08
Consensus MFE -32.14
Energy contribution -32.45
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -3.55
Structure conservation index 0.94
SVM decision value 1.95
SVM RNA-class probability 0.983715
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748238 120 + 27905053
GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUUUACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGAACAGUUUUCCUU
((((((.((.......(((((....)))))....)).))))))..........(((.(((.((.....(((((((.......)))))))..((((((....))))))....)).)))))) ( -33.50)
>DroSec_CAF1 12482 120 + 1
GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUUUACGGCGACUAUAGAACGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUU
((((((.((.......(((((....)))))....)).))))))........((((((...........(((((((.......)))))))((((((((....))))))))..))))))... ( -34.70)
>DroSim_CAF1 16797 120 + 1
GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUUUACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUU
((((((.((.......(((((....)))))....)).))))))........((((((...........(((((((.......)))))))((((((((....))))))))..))))))... ( -34.70)
>DroYak_CAF1 8606 116 + 1
GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUUUACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUGAGUUUU----
((((((.((.......(((((....)))))....)).)))))).........(((((...........(((((((.......)))))))((((((((....))))))))..)))))---- ( -33.40)
>consensus
GUAAAAAGACAAAAGGCAGGGGAAACUUUGACAAUUAUUUUACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUU
((((((.((.......(((((....)))))....)).)))))).........(((((...........(((((((.......)))))))((((((((....))))))))..))))).... (-32.14 = -32.45 +   0.31)

alignment

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secondary structure

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Window 8

Location 6,748,238 – 6,748,358
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.39
Mean single sequence MFE -27.19
Consensus MFE -24.85
Energy contribution -25.16
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.45
Structure conservation index 0.91
SVM decision value 1.39
SVM RNA-class probability 0.948886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748238 120 - 27905053
AAGGAAAACUGUUCUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUAAAAUAAUUGUCAAAGUUUCCCCUGCCUUUUGUCUUUUUAC
(((((........((((((....))))))..(((........(((((((((..((((((...((((....)).))..)))))).....)))))))))......))).....))))).... ( -25.34)
>DroSec_CAF1 12482 120 - 1
AAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGUUCUAUAGUCGCCGUAAAAUAAUUGUCAAAGUUUCCCCUGCCUUUUGUCUUUUUAC
..((((((...((((((((....))))))))(((........(((((((((..((((((...((.........))..)))))).....)))))))))......)))........)))))) ( -27.84)
>DroSim_CAF1 16797 120 - 1
AAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUAAAAUAAUUGUCAAAGUUUCCCCUGCCUUUUGUCUUUUUAC
..((((((...((((((((....))))))))(((........(((((((((..((((((...((((....)).))..)))))).....)))))))))......)))........)))))) ( -28.84)
>DroYak_CAF1 8606 116 - 1
----AAAACUCAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUAAAAUAAUUGUCAAAGUUUCCCCUGCCUUUUGUCUUUUUAC
----.......((((((((....))))))))(((........(((((((((..((((((...((((....)).))..)))))).....)))))))))......))).............. ( -26.74)
>consensus
AAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUAAAAUAAUUGUCAAAGUUUCCCCUGCCUUUUGUCUUUUUAC
...........((((((((....))))))))(((........(((((((((..((((((...((((....)).))..)))))).....)))))))))......))).............. (-24.85 = -25.16 +   0.31)

alignment

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secondary structure

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Window 9

Location 6,748,278 – 6,748,392
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.15
Mean single sequence MFE -31.98
Consensus MFE -24.12
Energy contribution -24.25
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -3.01
Structure conservation index 0.75
SVM decision value 2.34
SVM RNA-class probability 0.992650
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748278 114 + 27905053
UACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGAACAGUUUUCCUUUCUUCCC------UCUCCACAGGAAAAACCCCUUUUUUUU
...((.((....((((.(((.((.....(((((((.......)))))))..((((((....))))))....)).)))..))))....------)).))..(((.......)))....... ( -29.60)
>DroSec_CAF1 12522 118 + 1
UACGGCGACUAUAGAACGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUU
...(((((...((((((...........(((((((.......)))))))((((((((....))))))))..))))))..)))))....(((..........)))...........--... ( -32.40)
>DroSim_CAF1 16837 118 + 1
UACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUU
...(((((...((((((...........(((((((.......)))))))((((((((....))))))))..))))))..)))))....(((..........)))...........--... ( -32.40)
>DroYak_CAF1 8646 104 + 1
UACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUGAGUUUU----------------CCACCCCCUGGAAAACCCCCUAGUUUUG
...........((((((...........(((((((.......)))))))((((((((....))))))))..(((((----------------(((.....))))))))......)))))) ( -33.50)
>consensus
UACGGCGACUAUAGAGCGAAUGCAAAAAGGCCAAAGUUAAUAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCC_____CCACCCACCGGAAAAACCCCUUU__UUU
...((.(.....(((((...........(((((((.......)))))))((((((((....))))))))..)))))...................((....)).....).))........ (-24.12 = -24.25 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,748,278 – 6,748,392
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.15
Mean single sequence MFE -38.70
Consensus MFE -26.61
Energy contribution -27.61
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -2.86
Structure conservation index 0.69
SVM decision value 1.80
SVM RNA-class probability 0.977988
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748278 114 - 27905053
AAAAAAAAGGGGUUUUUCCUGUGGAGA------GGGAAGAAAGGAAAACUGUUCUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUA
..........(((.....((((((((.------..(((...(((((.......((((((....))))))..(((((((.......))))))))))))...))).))))))))..)))... ( -32.30)
>DroSec_CAF1 12522 118 - 1
AAA--AAAGGGGUUUUUCCGGUGGGUGGGGGAUGGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGUUCUAUAGUCGCCGUA
...--....(((....)))........((.(((.((((((((((((((...((((((((....))))))))(((((((.......))))))).)))))).))))))))...))).))... ( -44.00)
>DroSim_CAF1 16837 118 - 1
AAA--AAAGGGGUUUUUCCGGUGGGUGGGGGAUGGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUA
...--....(((....)))....(((((...((((((.((((((((((...((((((((....))))))))(((((((.......))))))).)))))).))))))))))..)))))... ( -43.50)
>DroYak_CAF1 8646 104 - 1
CAAAACUAGGGGGUUUUCCAGGGGGUGG----------------AAAACUCAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUA
........((.(..(....((.(((((.----------------((((...((((((((....))))))))(((((((.......))))))).)))).))))).))....)..).))... ( -35.00)
>consensus
AAA__AAAGGGGUUUUUCCGGUGGGUGG_____GGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUAUUAACUUUGGCCUUUUUGCAUUCGCUCUAUAGUCGCCGUA
........((.(.......((((((((........................((((((((....))))))))(((((((.......)))))))......)))))))).......).))... (-26.61 = -27.61 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,748,318 – 6,748,432
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.82
Mean single sequence MFE -34.98
Consensus MFE -24.62
Energy contribution -24.88
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -3.47
Structure conservation index 0.70
SVM decision value 3.46
SVM RNA-class probability 0.999253
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748318 114 + 27905053
UAUUUGGCCAACUGGACAAUGGUCCAGAACAGUUUUCCUUUCUUCCC------UCUCCACAGGAAAAACCCCUUUUUUUUCGGGGACACCAGCCCACCGGCUGACUUUCCUUCAGUUUCG
...((((....((((((....))))))....................------.......((((((..((((.........))))....(((((....)))))..))))))))))..... ( -29.00)
>DroSec_CAF1 12562 115 + 1
UAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUUCGGGGACACCAGCCCACCGGCUGACUUU---UCAGUUUCG
.....(((.((((((((....))))))))............((((((......(.......)((((((.....))--))))))))))....)))....((((((....---))))))... ( -32.30)
>DroSim_CAF1 16877 115 + 1
UAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUUCGGGGACACCAGCCCACCGGCUGACUUU---CCAGUUUCG
...((((..((((((((....))))))))............((((((......(.......)((((((.....))--))))))))))..(((((....))))).....---))))..... ( -33.70)
>DroYak_CAF1 8686 101 + 1
UAUUUGGCCAACUGGACAAUGGUCCAGUUGAGUUUU----------------CCACCCCCUGGAAAACCCCCUAGUUUUGGGGGGUCACCAGCCCAACGGCUGACUUU---CCAGUUUGG
.....((((((((((((....))))))))).)))..----------------(((....(((((((((((((((....))))))))...(((((....)))))..)))---))))..))) ( -44.90)
>consensus
UAUUUGGCCAACUGGACAAUGGUCCAGUUCAGUUUUACUUCGUCCCC_____CCACCCACCGGAAAAACCCCUUU__UUUCGGGGACACCAGCCCACCGGCUGACUUU___CCAGUUUCG
...((((..((((((((....)))))))).(((...................................((((.........))))....(((((....)))))))).....))))..... (-24.62 = -24.88 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,748,318 – 6,748,432
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.82
Mean single sequence MFE -40.03
Consensus MFE -25.75
Energy contribution -26.62
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -2.76
Structure conservation index 0.64
SVM decision value 2.13
SVM RNA-class probability 0.988644
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748318 114 - 27905053
CGAAACUGAAGGAAAGUCAGCCGGUGGGCUGGUGUCCCCGAAAAAAAAGGGGUUUUUCCUGUGGAGA------GGGAAGAAAGGAAAACUGUUCUGGACCAUUGUCCAGUUGGCCAAAUA
.....(((.(((((((((((((....))))))...((((.........)))).))))))).)))...------.((..((.((.....))...((((((....))))))))..))..... ( -32.60)
>DroSec_CAF1 12562 115 - 1
CGAAACUGA---AAAGUCAGCCGGUGGGCUGGUGUCCCCGAAA--AAAGGGGUUUUUCCGGUGGGUGGGGGAUGGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUA
....(((..---..)))..((((((..(((..((((((((...--........((..(((.....)))..)))))))))).)))...))).((((((((....)))))))))))...... ( -38.80)
>DroSim_CAF1 16877 115 - 1
CGAAACUGG---AAAGUCAGCCGGUGGGCUGGUGUCCCCGAAA--AAAGGGGUUUUUCCGGUGGGUGGGGGAUGGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUA
....(((((---((((((((((....))))))...((((....--...)))).))))))))).(((......((....))...........((((((((....)))))))).)))..... ( -41.90)
>DroYak_CAF1 8686 101 - 1
CCAAACUGG---AAAGUCAGCCGUUGGGCUGGUGACCCCCCAAAACUAGGGGGUUUUCCAGGGGGUGG----------------AAAACUCAACUGGACCAUUGUCCAGUUGGCCAAAUA
((...((((---((..((((((....)))))).(((((((........))))))))))))).)).(((----------------.....((((((((((....))))))))))))).... ( -46.80)
>consensus
CGAAACUGA___AAAGUCAGCCGGUGGGCUGGUGUCCCCGAAA__AAAGGGGUUUUUCCGGUGGGUGG_____GGGGACGAAGUAAAACUGAACUGGACCAUUGUCCAGUUGGCCAAAUA
...................(((.....(((((...((((.........)))).....))))).............................((((((((....)))))))))))...... (-25.75 = -26.62 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,748,358 – 6,748,472
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.09
Mean single sequence MFE -37.02
Consensus MFE -30.11
Energy contribution -30.18
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.81
SVM decision value 0.02
SVM RNA-class probability 0.545971
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6748358 114 + 27905053
UCUUCCC------UCUCCACAGGAAAAACCCCUUUUUUUUCGGGGACACCAGCCCACCGGCUGACUUUCCUUCAGUUUCGUGGGACACAUGGCUUCGGAGCGAACUAGAGUAAUGUCGUG
.......------..(((((((((((..((((.........))))....(((((....)))))..))))))........)))))((((((.((((..(......)..)))).)))).)). ( -31.30)
>DroSec_CAF1 12602 115 + 1
CGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUUCGGGGACACCAGCCCACCGGCUGACUUU---UCAGUUUCGUGGGACACAUGGCUUCGGAGCGAACUAGAGUAAUGUCGUG
.((((((.........((.(((((((((....)))--))))))))....(((((....))))).....---........).)))))((((.((((..(......)..)))).)))).... ( -34.90)
>DroSim_CAF1 16917 115 + 1
CGUCCCCAUCCCCCACCCACCGGAAAAACCCCUUU--UUUCGGGGACACCAGCCCACCGGCUGACUUU---CCAGUUUCGUGGGACACAUGGCUUCGGAGCGAACUAGAGUAAUGUCGUG
...........(((((..((.(((((..((((...--....))))....(((((....)))))..)))---)).))...)))))((((((.((((..(......)..)))).)))).)). ( -36.50)
>DroYak_CAF1 8722 105 + 1
------------CCACCCCCUGGAAAACCCCCUAGUUUUGGGGGGUCACCAGCCCAACGGCUGACUUU---CCAGUUUGGUGGGACACAUGGCUUCGGAGCGAACUAGAGUAAUGUCGUG
------------(((((..(((((((((((((((....))))))))...(((((....)))))..)))---))))...)))))((((....((((..(......)..))))..))))... ( -45.40)
>consensus
CGUCCCC_____CCACCCACCGGAAAAACCCCUUU__UUUCGGGGACACCAGCCCACCGGCUGACUUU___CCAGUUUCGUGGGACACAUGGCUUCGGAGCGAACUAGAGUAAUGUCGUG
...............(((((..((....((((.........))))....(((((....)))))............))..)))))((((((.((((..(......)..)))).)))).)). (-30.11 = -30.18 +   0.06)

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 10:34:34 2006