Locus 2961

Sequence ID X_DroMel_CAF1
Location 7,901,933 – 7,902,150
Length 217
Max. P 0.992357
window4857 window4858 window4859 window4860 window4861

overview

Window 7

Location 7,901,933 – 7,902,030
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -26.30
Consensus MFE -26.52
Energy contribution -26.30
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.68
Structure conservation index 1.01
SVM decision value 2.32
SVM RNA-class probability 0.992357
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7901933 97 + 22224390
UCACAGAGAGCAACACCAAAAAAAAAAUAAAAAGAUGAGCCAGGAGCGGCGCUCUCAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACA
...................................((((((....(.(((((((((..((((......)))).....)))))))))))))))).... ( -27.50)
>DroSec_CAF1 2550 91 + 1
UCACAGAGAGCAACACCAAAAAAA------AAAGAUGAGCCAGGAGCGGCGCUCUUAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACA
........................------.....((((((....(.(((((((((..((((......)))).....)))))))))))))))).... ( -25.70)
>DroSim_CAF1 5664 91 + 1
UCACAGAGAGCAACACCAAAAAAA------AAAGAUGAGCCAGGAGCGGCGCUCUUAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACA
........................------.....((((((....(.(((((((((..((((......)))).....)))))))))))))))).... ( -25.70)
>consensus
UCACAGAGAGCAACACCAAAAAAA______AAAGAUGAGCCAGGAGCGGCGCUCUUAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACA
...................................((((((....(.(((((((((..((((......)))).....)))))))))))))))).... (-26.52 = -26.30 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,901,933 – 7,902,030
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -27.53
Consensus MFE -26.20
Energy contribution -26.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.95
SVM decision value 0.18
SVM RNA-class probability 0.621050
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7901933 97 - 22224390
UGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUGAGAGCGCCGCUCCUGGCUCAUCUUUUUAUUUUUUUUUUGGUGUUGCUCUCUGUGA
...(((((((((((((((((.....((((......))))..))))))))).....)))))))).................................. ( -30.20)
>DroSec_CAF1 2550 91 - 1
UGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUCCUGGCUCAUCUUU------UUUUUUUGGUGUUGCUCUCUGUGA
...((((((((((((((((....(.((((......)))).).)))))))).....))))))))....------........................ ( -26.20)
>DroSim_CAF1 5664 91 - 1
UGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUCCUGGCUCAUCUUU------UUUUUUUGGUGUUGCUCUCUGUGA
...((((((((((((((((....(.((((......)))).).)))))))).....))))))))....------........................ ( -26.20)
>consensus
UGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUCCUGGCUCAUCUUU______UUUUUUUGGUGUUGCUCUCUGUGA
...((((((((((((((((......((((......))))...)))))))).....)))))))).................................. (-26.20 = -26.20 +  -0.00)

alignment

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secondary structure

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Window 9

Location 7,901,954 – 7,902,070
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.77
Mean single sequence MFE -34.92
Consensus MFE -33.12
Energy contribution -33.12
Covariance contribution 0.00
Combinations/Pair 1.04
Mean z-score -2.16
Structure conservation index 0.95
SVM decision value 1.76
SVM RNA-class probability 0.976186
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7901954 116 + 22224390
AAAAAAUAAAAAGAUGAGCCAG----GAGCGGCGCUCUCAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACAUACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUU
..............((((((..----..(.(((((((((..((((......)))).....))))))))))))))))...............((((((.((........)).)))).)).. ( -36.30)
>DroSec_CAF1 2571 110 + 1
AAA------AAAGAUGAGCCAG----GAGCGGCGCUCUUAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACAUACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUU
...------.....((((((..----..(.(((((((((..((((......)))).....))))))))))))))))...............((((((.((........)).)))).)).. ( -34.50)
>DroSim_CAF1 5685 110 + 1
AAA------AAAGAUGAGCCAG----GAGCGGCGCUCUUAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACAUACACGCAUAUGCAGACCGCACAAUAGAGCUGUCUCGCUU
...------.....((((((..----..(.(((((((((..((((......)))).....))))))))))))))))...............((((((.((........)).)))).)).. ( -34.20)
>DroYak_CAF1 5745 114 + 1
AAA------AAAGAUGAGCCAGAGUGAAGCGGCGCUCUCAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACAUACACGCAUACGCAUACCGCACAAUAGAGCUGUCUCGCUU
...------.(((.((((.(((.((((.(((((((((((..((((......)))).....)))))))))..))))))........((....))................))).))))))) ( -34.70)
>consensus
AAA______AAAGAUGAGCCAG____GAGCGGCGCUCUCAUUUUCUAGUUCGAAAUUCGAGAGAGCGCCCGGCUCACACAUACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUU
..............((((((.(.......)(((((((((..((((......)))).....))))))))).))))))...............((((((.((........)).)))).)).. (-33.12 = -33.12 +   0.00)

alignment

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secondary structure

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Window 0

Location 7,901,954 – 7,902,070
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.77
Mean single sequence MFE -38.90
Consensus MFE -36.66
Energy contribution -37.23
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.91
Structure conservation index 0.94
SVM decision value 1.29
SVM RNA-class probability 0.938108
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7901954 116 - 22224390
AAGCGAGACAGCUCUAUUGUGCGGUCUGCGUAUGCGUGUAUGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUGAGAGCGCCGCUC----CUGGCUCAUCUUUUUAUUUUUU
.....((((.((.(....).)).))))((((((....))))))(((((((((((((((((.....((((......))))..)))))))))....----.))))))))............. ( -40.70)
>DroSec_CAF1 2571 110 - 1
AAGCGAGACAGCUCUAUUGUGCGGUCUGCGUAUGCGUGUAUGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUC----CUGGCUCAUCUUU------UUU
.....((((.((.(....).)).))))((((((....))))))((((((((((((((((....(.((((......)))).).))))))))....----.))))))))....------... ( -36.70)
>DroSim_CAF1 5685 110 - 1
AAGCGAGACAGCUCUAUUGUGCGGUCUGCAUAUGCGUGUAUGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUC----CUGGCUCAUCUUU------UUU
.(((.((..(((.........((((..(((((((....)))))))..))))((((((((....(.((((......)))).).))))))))))).----)).))).......------... ( -38.30)
>DroYak_CAF1 5745 114 - 1
AAGCGAGACAGCUCUAUUGUGCGGUAUGCGUAUGCGUGUAUGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUGAGAGCGCCGCUUCACUCUGGCUCAUCUUU------UUU
.(((.(((..((.(....).)).(((((((....)))))))(((.((((..(((((((((.....((((......))))..))))))))))))))))))).))).......------... ( -39.90)
>consensus
AAGCGAGACAGCUCUAUUGUGCGGUCUGCGUAUGCGUGUAUGUGUGAGCCGGGCGCUCUCUCGAAUUUCGAACUAGAAAAUAAGAGCGCCGCUC____CUGGCUCAUCUUU______UUU
.....((((.((.(....).)).))))((((((....))))))(((((((((((((((((.....((((......))))..))))))))).........))))))))............. (-36.66 = -37.23 +   0.56)

alignment

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secondary structure

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Window 1

Location 7,902,030 – 7,902,150
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -29.66
Consensus MFE -29.29
Energy contribution -29.41
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.99
SVM decision value 1.22
SVM RNA-class probability 0.932526
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7902030 120 + 22224390
UACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUUGCACUUGAGGAAACAGAACAAGCAAAGCAGGCAAAUGGCGCACGCUAAACGCUGCAAAAUACGUUUAGUAAACCUUAAAA
.....(((..((.((((.((........)).))))))..)))..((((((..((.((((.......((((.(...((((....))))...))))).......)))).))...)))))).. ( -29.34)
>DroSec_CAF1 2641 120 + 1
UACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUUGCACUUGAGGAAACAGAGCAAGCAAAGCAGGCAAAUGGCGCACGCUAAACGCUGCAAAAUACGUUUUGUAAACCUUAAAA
.....(((..((.((((.((........)).))))))..)))..((((((..(((((((.......((((.(...((((....))))...))))).......)))))))...)))))).. ( -33.14)
>DroSim_CAF1 5755 120 + 1
UACACGCAUAUGCAGACCGCACAAUAGAGCUGUCUCGCUUGCACUUAAGGAAACAGAGCAAGCAAAGCAGGCAAAUGGCGCACGCUAAACGCUGCAAAAUACGUUUUGUAAACCUUAAAA
.....(((...((((((.((........)).)))).)).)))..((((((..(((((((.......((((.(...((((....))))...))))).......)))))))...)))))).. ( -32.54)
>DroYak_CAF1 5819 120 + 1
UACACGCAUACGCAUACCGCACAAUAGAGCUGUCUCGCUUGCACUUGAGGAUAAAGAGCAACCAAAGCAGGCAAAUGGCGCACGCUUAACGCUGCAAAAUAUGUUUUUUAAACCUAAAAA
.....(((..((...((.((........)).))..))..))).....(((.(((((((((......((((.(....(((....)))....)))))......)))))))))..)))..... ( -23.60)
>consensus
UACACGCAUACGCAGACCGCACAAUAGAGCUGUCUCGCUUGCACUUGAGGAAACAGAGCAAGCAAAGCAGGCAAAUGGCGCACGCUAAACGCUGCAAAAUACGUUUUGUAAACCUUAAAA
.....(((..((.((((.((........)).))))))..)))..((((((..(((((((.......((((.(...((((....))))...))))).......)))))))...)))))).. (-29.29 = -29.41 +   0.12)

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 10:47:49 2006