Locus 4630

Sequence ID 2R_DroMel_CAF1
Location 15,146,760 – 15,146,961
Length 201
Max. P 0.999962
window7433 window7434 window7435 window7436 window7437 window7438 window7439

overview

Window 3

Location 15,146,760 – 15,146,867
Length 107
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.13
Mean single sequence MFE -33.08
Consensus MFE -20.87
Energy contribution -21.27
Covariance contribution 0.39
Combinations/Pair 1.21
Mean z-score -2.14
Structure conservation index 0.63
SVM decision value 1.30
SVM RNA-class probability 0.939457
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146760 107 + 20766785
ACGUCGUAAUGAGAAAAUGAGAGCUGUAUUAUUUUUGUACUGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGUAGUGCGGCGCGAGUUUU
.((.(((...............(((((((..((((..((.......))..))))..)))))))(((((.((((((((.....)))).))))))))))))))...... ( -33.50)
>DroVir_CAF1 183578 81 + 1
AAUUCGUACUGAGAAAAUGAGCGGCGUGCU---------------------CUGCAGUAAAAAACCACAUUUGCCACAUAGUGUGCGAACAGUACAGCAUGU-----
.....((((((.......((((.....)))---------------------).................((((((((...))).))))))))))).......----- ( -18.90)
>DroSec_CAF1 118970 107 + 1
ACGUCGUAAUGAGAAAAUGAGAGCGGUAUUAUUUUUGUAGUGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUC
......................((((((((((....)))))))).((((....))))....(((((((.((((((((.....)))).)))))))))))))....... ( -37.40)
>DroSim_CAF1 104022 107 + 1
ACGUCGUAAUGAGAAAAUGAGAGCGGUAUUAUUUUUGUAGUGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUU
......................((((((((((....)))))))).((((....))))....(((((((.((((((((.....)))).)))))))))))))....... ( -37.40)
>DroEre_CAF1 122796 106 + 1
-CGUCGUAAUGAGAAAAUGAGAGCUGUAUUAUUUUUGUAGUGCUUUAGUGAGAGCAAUACAGUCGCACAUGCUGCGCAGUGUGUGCGAGCAGUACGGCGUUAGUUUU
-(((((((.((.((((((((........))))))))(((.((((((....)))))).)))..(((((((((((....))))))))))).)).)))))))........ ( -37.40)
>DroYak_CAF1 124800 107 + 1
ACGUCGUAAUGAGAAAAUGAGAGCCGUGUUAUUUUUGUAGUACUUUAGUGAGAGCGAUACAGUCGCACAUGCUGCGCAGUGUGUGCGAGCAGUGCGGCGCUAGUUUU
.............(((((.((.((((..((....(((((...((((....))))...)))))(((((((((((....)))))))))))..))..)))).)).))))) ( -33.90)
>consensus
ACGUCGUAAUGAGAAAAUGAGAGCCGUAUUAUUUUUGUAGUGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUU
.(((((((.((..............(((((.((((..(.........)..)))).)))))..(((((((((........))))))))).)).)))))))........ (-20.87 = -21.27 +   0.39)

alignment

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secondary structure

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Window 4

Location 15,146,760 – 15,146,867
Length 107
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 78.13
Mean single sequence MFE -24.05
Consensus MFE -14.95
Energy contribution -16.20
Covariance contribution 1.25
Combinations/Pair 1.23
Mean z-score -2.09
Structure conservation index 0.62
SVM decision value 1.19
SVM RNA-class probability 0.928814
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146760 107 - 20766785
AAAACUCGCGCCGCACUACUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCAGUACAAAAAUAAUACAGCUCUCAUUUUCUCAUUACGACGU
.......((..(((((..((((((.....)))).))...)))))..(((((.(((........))).)))))...........))...................... ( -21.70)
>DroVir_CAF1 183578 81 - 1
-----ACAUGCUGUACUGUUCGCACACUAUGUGGCAAAUGUGGUUUUUUACUGCAG---------------------AGCACGCCGCUCAUUUUCUCAGUACGAAUU
-----......(((((((...((.(((...)))))...((..((.....))..))(---------------------(((.....)))).......))))))).... ( -21.10)
>DroSec_CAF1 118970 107 - 1
GAAACUUGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCACUACAAAAAUAAUACCGCUCUCAUUUUCUCAUUACGACGU
((((...(((.(((((((((((((.....)))).)))).)))))..((((..(((........)))..))))..........)))......))))............ ( -25.90)
>DroSim_CAF1 104022 107 - 1
AAAACUUGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCACUACAAAAAUAAUACCGCUCUCAUUUUCUCAUUACGACGU
.......(((.(((((((((((((.....)))).)))).)))))..((((..(((........)))..))))..........)))...................... ( -25.60)
>DroEre_CAF1 122796 106 - 1
AAAACUAACGCCGUACUGCUCGCACACACUGCGCAGCAUGUGCGACUGUAUUGCUCUCACUAAAGCACUACAAAAAUAAUACAGCUCUCAUUUUCUCAUUACGACG-
.........(((((((((((((((.....)))).)))).)))))..((((.((((........)))).))))...........)).....................- ( -24.30)
>DroYak_CAF1 124800 107 - 1
AAAACUAGCGCCGCACUGCUCGCACACACUGCGCAGCAUGUGCGACUGUAUCGCUCUCACUAAAGUACUACAAAAAUAACACGGCUCUCAUUUUCUCAUUACGACGU
((((..((.(((((((((((((((.....)))).)))).))))...((((..(((........)))..))))..........))).))..))))............. ( -25.70)
>consensus
AAAACUAGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCACUACAAAAAUAAUACAGCUCUCAUUUUCUCAUUACGACGU
.........(((((((((((((((.....)))).)))).)))))..((((..(((........)))..))))...........))...................... (-14.95 = -16.20 +   1.25)

alignment

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secondary structure

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Window 5

Location 15,146,800 – 15,146,895
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 88.75
Mean single sequence MFE -39.98
Consensus MFE -34.94
Energy contribution -34.66
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -3.77
Structure conservation index 0.87
SVM decision value 4.42
SVM RNA-class probability 0.999894
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146800 95 + 20766785
UGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGUAGUGCGGCGCGAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAA
....((((((((((((.....(((((((.((((((((.....)))).)))))))))))((((((.....)))))).....)))))).)))))).. ( -41.00)
>DroSec_CAF1 119010 95 + 1
UGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUCGCGCUUGUAAUGCUGCUCUGCACAGAAA
....((((((((((((.....(((((((.((((((((.....)))).)))))))))))((((((.....)))))).....)))))).)))))).. ( -43.30)
>DroSim_CAF1 104062 95 + 1
UGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAA
....((((((((((((.....(((((((.((((((((.....)))).)))))))))))((((((.....)))))).....)))))).)))))).. ( -43.30)
>DroEre_CAF1 122835 87 + 1
UGCUUUAGUGAGAGCAAUACAGUCGCACAUGCUGCGCAGUGUGUGCGAGCAGUACGGCGUUAGUUUUGCGCUUGUAAUGCUGCUCUG--------
..........((((((......(((((((((((....)))))))))))(((.((((((((.......)))).)))).))))))))).-------- ( -36.50)
>DroYak_CAF1 124840 85 + 1
UACUUUAGUGAGAGCGAUACAGUCGCACAUGCUGCGCAGUGUGUGCGAGCAGUGCGGCGCUAGUUUUGCGCUUGUAAUGCUGCUC----------
.........(((((((.(((((.(((((.((((((((.....)))).)))))))))((((.......))))))))).)))).)))---------- ( -35.80)
>consensus
UGCCUUUGUGAGAGCGAUACAGUCGCACAUGCUGCGCAAUGUGUGCGAGCAGUGCGGCGCAAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAA
.........(((((((.(((((.(((((.((((((((.....)))).)))))))))((((.......))))))))).)))).))).......... (-34.94 = -34.66 +  -0.28)

alignment

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secondary structure

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Window 6

Location 15,146,800 – 15,146,895
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 88.75
Mean single sequence MFE -34.88
Consensus MFE -31.98
Energy contribution -32.22
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -4.11
Structure conservation index 0.92
SVM decision value 4.93
SVM RNA-class probability 0.999962
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146800 95 - 20766785
UUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUCGCGCCGCACUACUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCA
....((((.(((((.....((((.((((.......))))(((((..((((((.....)))).))...)))))..))))..)))))))))...... ( -32.00)
>DroSec_CAF1 119010 95 - 1
UUUCUGUGCAGAGCAGCAUUACAAGCGCGAAACUUGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCA
....((((.(((((.....((((.((((((...))))))(((((((((((((.....)))).)))).)))))..))))..)))))))))...... ( -38.30)
>DroSim_CAF1 104062 95 - 1
UUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUUGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCA
....((((.(((((.....((((.(((((.....)))))(((((((((((((.....)))).)))).)))))..))))..)))))))))...... ( -38.60)
>DroEre_CAF1 122835 87 - 1
--------CAGAGCAGCAUUACAAGCGCAAAACUAACGCCGUACUGCUCGCACACACUGCGCAGCAUGUGCGACUGUAUUGCUCUCACUAAAGCA
--------..(((.((((.((((.(((.........)))(((((((((((((.....)))).)))).)))))..)))).)))))))......... ( -30.80)
>DroYak_CAF1 124840 85 - 1
----------GAGCAGCAUUACAAGCGCAAAACUAGCGCCGCACUGCUCGCACACACUGCGCAGCAUGUGCGACUGUAUCGCUCUCACUAAAGUA
----------(((.(((..((((.((((.......))))(((((((((((((.....)))).)))).)))))..))))..))))))......... ( -34.70)
>consensus
UUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUAGCGCCGCACUGCUCGCACACAUUGCGCAGCAUGUGCGACUGUAUCGCUCUCACAAAGGCA
..........(((.(((..((((.((((.......))))(((((((((((((.....)))).)))).)))))..))))..))))))......... (-31.98 = -32.22 +   0.24)

alignment

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secondary structure

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Window 7

Location 15,146,839 – 15,146,935
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 93.66
Mean single sequence MFE -32.27
Consensus MFE -28.15
Energy contribution -27.93
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.87
SVM decision value 0.77
SVM RNA-class probability 0.846316
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146839 96 + 20766785
UGUGUGCGAGUAGUGCGGCGCGAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAAUCGAAGAGAGGUUUGUUUC
..(((((((((((((((((((((...)))))).)))...))))))).)))))(((((.(((.((((.....))))..((.....)))))..))))) ( -30.70)
>DroSec_CAF1 119049 92 + 1
UGUGUGCGAGCAGUGCGGCGCAAGUUUCGCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUUGUAAAAGAGUUACAUUCGAAGAGAGGU----UUC
..(((((((((((((((((((.......)))).)))...))))))).)))))((((((.(((......((((...))))...))).)))----))) ( -33.10)
>DroSim_CAF1 104101 92 + 1
UGUGUGCGAGCAGUGCGGCGCAAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAUUCGAAGAGAGGU----UUC
..((((((((((((((((((((.....))))).)))...))))))).)))))((((((.((.((((.....))))......))...)))----))) ( -33.00)
>consensus
UGUGUGCGAGCAGUGCGGCGCAAGUUUUGCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAUUCGAAGAGAGGU____UUC
..(((((((((((((((((((.......)))).)))...))))))).)))))(.((((.((......)))))).)..................... (-28.15 = -27.93 +  -0.22)

alignment

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secondary structure

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Window 8

Location 15,146,839 – 15,146,935
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 93.66
Mean single sequence MFE -22.47
Consensus MFE -19.27
Energy contribution -19.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.86
SVM decision value -0.04
SVM RNA-class probability 0.511148
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146839 96 - 20766785
GAAACAAACCUCUCUUCGAUUGUAACUCUUUUACCAGCAGUUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUCGCGCCGCACUACUCGCACACA
(((((.....((.....))..((((.....)))).....)))))(((((.(((.((........((((.......))))....)).)))))))).. ( -17.20)
>DroSec_CAF1 119049 92 - 1
GAA----ACCUCUCUUCGAAUGUAACUCUUUUACAAGCAGUUUCUGUGCAGAGCAGCAUUACAAGCGCGAAACUUGCGCCGCACUGCUCGCACACA
(((----((.((.....)).(((((.....)))))....)))))(((((.((((((........((((((...))))))....))))))))))).. ( -25.90)
>DroSim_CAF1 104101 92 - 1
GAA----ACCUCUCUUCGAAUGUAACUCUUUUACCAGCAGUUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUUGCGCCGCACUGCUCGCACACA
(((----((.((.....))..((((.....)))).....)))))(((((.((((((........(((((.....)))))....))))))))))).. ( -24.30)
>consensus
GAA____ACCUCUCUUCGAAUGUAACUCUUUUACCAGCAGUUUCUGUGCAGAGCAGCAUUACAAGCGCAAAACUUGCGCCGCACUGCUCGCACACA
.....................(.((((((......)).)))).)(((((.((((((........((((.......))))....))))))))))).. (-19.27 = -19.60 +   0.33)

alignment

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secondary structure

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Window 9

Location 15,146,867 – 15,146,961
Length 94
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 95.68
Mean single sequence MFE -25.20
Consensus MFE -23.67
Energy contribution -24.33
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.94
SVM decision value 0.25
SVM RNA-class probability 0.652785
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15146867 94 + 20766785
GCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAAUCGAAGAGAGGUUUGUUUCUCUUUUGCUUUCUCGCGCACAUCUCA
((((......(((......)))(((......)))(((((((((..((((((.......)).))))..)))))))))......))))........ ( -26.00)
>DroSec_CAF1 119077 90 + 1
GCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUUGUAAAAGAGUUACAUUCGAAGAGAGGU----UUCUCUUUUGCUUUCUCGCGCACAUCUCA
((((......(((......))).(((((......(((((((((..((.(((.....)))))----..)))))))))))))).))))........ ( -24.10)
>DroSim_CAF1 104129 90 + 1
GCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAUUCGAAGAGAGGU----UUCUCUUUUGCUUUCUCGCGCACAUCUCA
((((......(((......)))(((......)))(((((((((..((.(((.....)))))----..)))))))))......))))........ ( -25.50)
>consensus
GCGCUUGUAAUGCUGCUCUGCACAGAAACUGCUGGUAAAAGAGUUACAUUCGAAGAGAGGU____UUCUCUUUUGCUUUCUCGCGCACAUCUCA
((((.((.((((..(((((...(((......))).....)))))..))))))((((((((......))))))))........))))........ (-23.67 = -24.33 +   0.67)

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 11:25:08 2006