Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_234 ID=scaffold_234-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: 9116
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1787 original size:44 final size:44
Alignment explanation
Indices: 1716--2244 Score: 244
Period size: 44 Copynumber: 12.2 Consensus size: 44
1706 ACTTGATGCG
* * * *
1716 ATCTGCTCTACTACAACTTCAGAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGAT-TATCGACTTCA
* *
1760 ATTTGCTCCACTACAACTTCAGGGAGATAGGATTATCGACTTCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
* * **
1804 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCTTCTTCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTAT-CGACTTCA
* * *** * * * **
1848 GTCTGCCCCACTGTTACTTCAGGGGGATAAAACT-T-GTTTTCCCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTT--CA
* * ** * *
1892 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCT-GA-TGCG
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
** * * ** * *
1933 ATCCACTCTACTGCAACTTCAGATAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGAT-TATCGACTTCA
* * *
1977 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
** * ** *
2021 ATCTGCTCCACTGTAACTTTAGGGAGATAAGATT-TGCTTCTTCG
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTAT-CGACTTCA
* * * **
2065 ATCTGC-CCTACTGCAACTTCAGGGGGATAAGACT-T-GTTTTATCA
1 ATCTGCTCC-ACTACAACTTCAGGGAGATAAGATTATCG-ACT-TCA
* * * * ** * *
2109 GTCTGGTCCATTACAACTTCAGAGAGATAAGA-CCT-GA-TGCG
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
** * * * * *
2150 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGAT-TATCGACTTCA
** * * *
2194 ATCCACTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
2238 ATCTGCT
1 ATCTGCT
2245 TCTTTACACT
Statistics
Matches: 366, Mismatches: 100, Indels: 38
0.73 0.20 0.08
Matches are distributed among these distances:
41 53 0.14
42 4 0.01
43 20 0.05
44 287 0.78
45 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
Found at i:2086 original size:217 final size:217
Alignment explanation
Indices: 1703--2244 Score: 861
Period size: 217 Copynumber: 2.5 Consensus size: 217
1693 TCTAGTCGGC
* ** * **
1703 AAGACTTGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATTTGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
*
1768 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
** *
1833 AGATTTGCTTCTTCAGTCTGCCCCACTGTTACTTCAGGGGGATAAAACTTGTTTTCCCAGTCTGC
131 AGATTTGCTTCTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAAACTTGTTTTACCAGTCTGC
* *
1898 TCCACTGCAACTTCAGGGAGAT
196 TCCACTACAACTTCAGAGAGAT
*
1920 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGATAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
1985 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTTAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
* * *
2050 AGATTTGCTTCTTC-GATCTGCCCTACTGCAACTTCAGGGGGATAAGACTTGTTTTATCAGTCTG
131 AGATTTGCTTCTTCAG-TCTGCCCCACTGCAACTTCAGGGGGATAAAACTTGTTTTACCAGTCTG
* *
2114 GTCCATTACAACTTCAGAGAGAT
195 CTCCACTACAACTTCAGAGAGAT
*
2137 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCACTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
*
2202 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCT
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCT
2245 TCTTTACACT
Statistics
Matches: 300, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
216 1 0.00
217 299 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (217 bp):
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
AGATTTGCTTCTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAAACTTGTTTTACCAGTCTGC
TCCACTACAACTTCAGAGAGAT
Found at i:3771 original size:7 final size:7
Alignment explanation
Indices: 3742--3799 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
3732 CCTTAGCCTC
3742 TTCATTT
1 TTCATTT
3749 TT-ACTTT
1 TTCA-TTT
*
3756 TCCACTTT
1 TTCA-TTT
3764 TTCATTT
1 TTCATTT
3771 TTCATTT
1 TTCATTT
3778 TTCA-TT
1 TTCATTT
3784 TTCATTT
1 TTCATTT
3791 TTCATTT
1 TTCATTT
3798 TT
1 TT
3800 TGACTCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
6 7 0.15
7 31 0.67
8 8 0.17
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
TTCATTT
Found at i:3785 original size:13 final size:14
Alignment explanation
Indices: 3742--3798 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 14
3732 CCTTAGCCTC
3742 TTCATTTTT-ACTT
1 TTCATTTTTCACTT
*
3755 TTCCACTTTTTCATTT
1 TT-CA-TTTTTCACTT
3771 TTCATTTTTCA-TT
1 TTCATTTTTCACTT
3784 TTCATTTTTCA-TT
1 TTCATTTTTCACTT
3797 TT
1 TT
3799 TTGACTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
13 19 0.47
14 9 0.22
15 7 0.17
16 5 0.12
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
TTCATTTTTCACTT
Found at i:3787 original size:20 final size:20
Alignment explanation
Indices: 3762--3799 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3752 CTTTTCCACT
3762 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
3782 TTTTCATTTTTCATTTTT
1 TTTTCATTTTTCATTTTT
3800 TGACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:4690 original size:7 final size:7
Alignment explanation
Indices: 4678--4711 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4668 CCATCTAGAT
4678 TTTTTTC
1 TTTTTTC
4685 TTTTTTC
1 TTTTTTC
4692 TTCTTTTC
1 TT-TTTTC
*
4700 TTCTTTC
1 TTTTTTC
4707 TTTTT
1 TTTTT
4712 CTCTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:4728 original size:6 final size:6
Alignment explanation
Indices: 4719--4753 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
4709 TTTCTCTCAT
*
4719 TTTTTA TTTTGA TTTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TTTT
4754 TTTTGAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74
Consensus pattern (6 bp):
TTTTGA
Found at i:4754 original size:13 final size:13
Alignment explanation
Indices: 4717--4753 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
4707 TTTTTCTCTC
*
4717 ATTTTTTATTTTG
1 ATTTTTGATTTTG
4730 ATTTTTGATTTTG
1 ATTTTTGATTTTG
4743 A-TTTTGATTTT
1 ATTTTTGATTTT
4754 TTTTGAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (13 bp):
ATTTTTGATTTTG
Done.