Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_221 ID=scaffold_221-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9205
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Found at i:1651 original size:44 final size:44
Alignment explanation
Indices: 1593--2109 Score: 191
Period size: 44 Copynumber: 11.9 Consensus size: 44
1583 TACTCTATTG
* * * *
1593 CAACTTTAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTA
1 CAACTTCAGGGAGATAAGATCTATTATTTCAATCTGCTCCACTA
* *** *
1637 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCTACTA
1 CAACTTCAGGGAGATAAGATCTAT-TATTTCAATCTGCTCCACTA
* *** * * **
1681 CAAGC-TCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACCG
1 CAA-CTTCAGGGAGATAAGATCTATTAT-TTCAATCTGCTCCACTA
* * * * * *
1726 CAACTTCAGAGG-GATAAGACCTGCTTA-CTCAGTCTGCTCCGCTG
1 CAACTTCAG-GGAGATAAGATCT-ATTATTTCAATCTGCTCCACTA
* * * * * * * *
1770 TAACTTCAGGGAGATAAGA-C-CTGA-TGCTATCTACTCTACTG
1 CAACTTCAGGGAGATAAGATCTATTATTTCAATCTGCTCCACTA
* * *
1811 TAACTTCAGAGAGATAAGATCTATTATTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATCTATTATTTCAATCTGCTCCACTA
* ***
1855 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATCTAT-TATTTCAATCTGCTCCACTA
* * * *** * * **
1899 CAACCTCA-GGATATAAGATTTGCCATCTTCGATCTGCCCCACCG
1 CAACTTCAGGGAGATAAGATCTATTAT-TTCAATCTGCTCCACTA
* * * * * * * * *
1943 CAACTTTAGGGGGATAAGACCTGCTTA-CTCAGTCTCCTCCGCTG
1 CAACTTCAGGGAGATAAGATCT-ATTATTTCAATCTGCTCCACTA
* * * * * ** * *
1987 CAACTTTAGGGAGATAAGA-C-CTGA-TGCGATCCACTCTACTG
1 CAACTTCAGGGAGATAAGATCTATTATTTCAATCTGCTCCACTA
* **
2028 CAACTTCAGAGAGATAAGATCTATTACTTT-AATCCACTCCACTA
1 CAACTTCAGGGAGATAAGATCTATTA-TTTCAATCTGCTCCACTA
* * *
2072 CAACTTCAGGGAGATAGGAT-TATCGACTTCAATCTGCT
1 CAACTTCAGGGAGATAAGATCTAT-TATTTCAATCTGCT
2110 TCCTTACTCT
Statistics
Matches: 343, Mismatches: 108, Indels: 44
0.69 0.22 0.09
Matches are distributed among these distances:
41 60 0.17
42 2 0.01
43 28 0.08
44 210 0.61
45 39 0.11
46 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATCTATTATTTCAATCTGCTCCACTA
Found at i:2025 original size:217 final size:218
Alignment explanation
Indices: 1496--2109 Score: 1005
Period size: 217 Copynumber: 2.8 Consensus size: 218
1486 CTGTTGTCAG
* * * * ** *
1496 TCTGCCCCACTGCAACTGCAGGGGGATAAGACTTGCTTTCTCAGTCTGCTCCATTGCAACCTCAG
1 TCTGCCCCACCGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTCAG
* *
1561 GGAGATAAGACCTGATGCGATCTACTCTATTGCAACTTTAGAGAGATAAGATCTATTATTTTAAT
66 GGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAAT
* *
1626 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCTACTACAAGCTCAGG
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAGG
1691 GAGATAAGATTTGCCATCTTCGA
196 GAGATAAGATTTGCCATCTTCGA
* *
1714 TCTGCCCCACCGCAACTTCAGAGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGTAACTTCAG
1 TCTGCCCCACCGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTCAG
* *
1779 GGAGATAAGACCTGATGCTATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAAT
66 GGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAAT
*
1844 CTGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCA-G
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAGG
*
1908 GATATAAGATTTGCCATCTTCGA
196 GAGATAAGATTTGCCATCTTCGA
* * *
1931 TCTGCCCCACCGCAACTTTAGGGGGATAAGACCTGCTTACTCAGTCTCCTCCGCTGCAACTTTAG
1 TCTGCCCCACCGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTCAG
* *
1996 GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
66 GGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAAT
* *
2061 CCACTCCACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCT
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCT
2110 TCCTTACTCT
Statistics
Matches: 367, Mismatches: 29, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
217 190 0.52
218 177 0.48
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (218 bp):
TCTGCCCCACCGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTCAG
GGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAAT
CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAGG
GAGATAAGATTTGCCATCTTCGA
Found at i:2157 original size:49 final size:49
Alignment explanation
Indices: 2085--2183 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
2075 CTTCAGGGAG
*
2085 ATAGGATTATCGACTTCAATCTGCTTCCTTACTCTTGAAGATAAGATTC
1 ATAGGATTATCGACTTCAATCTGCTTCCTTACTCTTAAAGATAAGATTC
2134 ATAGGATTATCGACTTCAATCTGCTTCCTTACTCTTAAAGATAAGATTC
1 ATAGGATTATCGACTTCAATCTGCTTCCTTACTCTTAAAGATAAGATTC
2183 A
1 A
2184 CCGTCTTCGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (49 bp):
ATAGGATTATCGACTTCAATCTGCTTCCTTACTCTTAAAGATAAGATTC
Found at i:2430 original size:128 final size:127
Alignment explanation
Indices: 2151--2635 Score: 727
Period size: 128 Copynumber: 3.8 Consensus size: 127
2141 TATCGACTTC
* * *
2151 AATCTGCTTCCTTACTCTTAAAGATAAGATTCACCGTCTTCGATCTACTCCGCTATTGTTTAGGG
1 AATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
* **
2216 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAATGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTT--TAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* *
2280 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGG
1 AATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
* *
2345 AGAGAAGATCTGTAATTTCTAACCTATTCCACTGCTGACTAGGGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTT-TAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * **
2408 AATCTACTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTCGATCTGTTCCGCTATTGCTTAGGG
1 AATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
* * *
2473 AGTCAAGATCTATTATTTTCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTTT-AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
*
2536 AATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
1 AATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
* * **
2601 AGTCAAGATCTGTTATCTTTAACCTGCTCCACTGC
66 AGACAAGATCTGTAAT-TTTAACCTATTCCACTGC
2636 AACCGAGGAA
Statistics
Matches: 329, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
127 1 0.00
128 248 0.75
129 80 0.24
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (127 bp):
AATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGATCTACTCCGCTATTGCTTAGGG
AGACAAGATCTGTAATTTTAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
Found at i:3968 original size:13 final size:14
Alignment explanation
Indices: 3939--3975 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
3929 GGTCTCTCCA
*
3939 TTTCTTTTTTCATT
1 TTTCATTTTTCATT
3953 TTTCATTTTTCA-T
1 TTTCATTTTTCATT
3966 TTTCATTTTT
1 TTTCATTTTT
3976 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCATTTTTCATT
Found at i:3976 original size:14 final size:14
Alignment explanation
Indices: 3939--3982 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3929 GGTCTCTCCA
3939 TTTC-TTTTTTCATT
1 TTTCATTTTTTCA-T
3953 TTTCA-TTTTTCAT
1 TTTCATTTTTTCAT
*
3966 TTTCATTTTTTTAT
1 TTTCATTTTTTCAT
3980 TTT
1 TTT
3983 TTTCTGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCATTTTTTCAT
Found at i:3984 original size:7 final size:7
Alignment explanation
Indices: 3939--3975 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
3929 GGTCTCTCCA
*
3939 TTTCTTT
1 TTTCATT
3946 TTTCATT
1 TTTCATT
3953 TTTCATT
1 TTTCATT
3960 TTTCA-T
1 TTTCATT
3966 TTTCATT
1 TTTCATT
3973 TTT
1 TTT
3976 TTATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCATT
Found at i:4836 original size:6 final size:6
Alignment explanation
Indices: 4834--4905 Score: 90
Period size: 6 Copynumber: 11.7 Consensus size: 6
4824 CATTTTTATT
* ** *
4834 TTTTGA CTTTGA TTTTGA TTTTTTCT TTTTGC TTTTGA TTTTGA TTTTGA
1 TTTTGA TTTTGA TTTTGA --TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
4884 TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTT
4906 TTTTCTTCCC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 53 0.93
8 4 0.07
ACGTcount: A:0.12, C:0.04, G:0.14, T:0.69
Consensus pattern (6 bp):
TTTTGA
Done.