Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008270.1 Corchorus olitorius cultivar O-4 contig08297, whole genome shotgun sequence
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: 11189
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1582 original size:2 final size:2
Alignment explanation
Indices: 1575--1609 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1565 TTTATTTGTA
1575 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
1610 TATTTGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1872 original size:56 final size:56
Alignment explanation
Indices: 1781--1892 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
1771 TCCGTTTCCC
* *
1781 TTCATACAATAAATGTTGTAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1837 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1893 ACAAAATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (56 bp):
TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
Found at i:2018 original size:42 final size:42
Alignment explanation
Indices: 1959--2038 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1949 AAGGATCAGA
*
1959 ATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTCTATG
1 ATTTGAGTTCAATATTTCTTAATTTACAAAGAATTTTCTATG
* *
2001 ATTTGAGTTGAATATTTCTTAATTTACAGAGAATTTTC
1 ATTTGAGTTCAATATTTCTTAATTTACAAAGAATTTTC
2039 AAGACTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (42 bp):
ATTTGAGTTCAATATTTCTTAATTTACAAAGAATTTTCTATG
Found at i:2025 original size:21 final size:21
Alignment explanation
Indices: 1958--2025 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
1948 TAAGGATCAG
* *
1958 AATTTGAGTTCAGTATTTCTT
1 AATTTGAGTTGAATATTTCTT
***
1979 AATTT-ACAAAGAAT-TTTCTAT
1 AATTTGA-GTTGAATATTTCT-T
*
2000 GATTTGAGTTGAATATTTCTT
1 AATTTGAGTTGAATATTTCTT
2021 AATTT
1 AATTT
2026 ACAGAGAATT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
AATTTGAGTTGAATATTTCTT
Found at i:2034 original size:21 final size:20
Alignment explanation
Indices: 1973--2038 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
1963 GAGTTCAGTA
*
1973 TTTCTTAATTTACAAAGAAT
1 TTTCTTAATTTACAGAGAAT
* * *
1993 TTTCTATGATTT-GAGTTGAAT
1 TTTCT-TAATTTACAG-AGAAT
2014 ATTTCTTAATTTACAGAGAAT
1 -TTTCTTAATTTACAGAGAAT
2035 TTTC
1 TTTC
2039 AAGACTTACC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 10 0.29
21 18 0.51
22 7 0.20
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTCTTAATTTACAGAGAAT
Found at i:3451 original size:3 final size:3
Alignment explanation
Indices: 3443--3477 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3433 AGCTCAGACC
*
3443 GAA GAA GAA GAA GAA GAA GAA TAA GAA GAAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA G
3478 CTGCGAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:11100 original size:30 final size:30
Alignment explanation
Indices: 11043--11101 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
11033 ATCATCTCCA
* **
11043 CCACTTCCATAGCCAGAGCCGTAGCCAGAG
1 CCACTTCCATAGCCAGACCCACAGCCAGAG
* *
11073 CCACTTCCATAGCCTGACCCACGGCCAGA
1 CCACTTCCATAGCCAGACCCACAGCCAGA
11102 ACCATTGCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.41, G:0.20, T:0.14
Consensus pattern (30 bp):
CCACTTCCATAGCCAGACCCACAGCCAGAG
Found at i:11133 original size:15 final size:15
Alignment explanation
Indices: 11109--11181 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
11099 AGAACCATTG
*
11109 CCTCCTCCACCGCCT
1 CCTCCACCACCGCCT
*
11124 CCTCCACCACCACCT
1 CCTCCACCACCGCCT
* *
11139 CCTCCACCTCCGCCC
1 CCTCCACCACCGCCT
* * *
11154 CCACCACCTCCACCT
1 CCTCCACCACCGCCT
11169 -CTACCACCACCGC
1 CCT-CCACCACCGC
11182 TTCCATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 1 0.02
15 45 0.98
ACGTcount: A:0.15, C:0.67, G:0.04, T:0.14
Consensus pattern (15 bp):
CCTCCACCACCGCCT
Found at i:11139 original size:12 final size:12
Alignment explanation
Indices: 11112--11167 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
11102 ACCATTGCCT
* *
11112 CCTCCACCGCCT
1 CCTCCACCACCA
11124 CCTCCACCACCA
1 CCTCCACCACCA
* *
11136 CCTCCTCCACCT
1 CCTCCACCACCA
* *
11148 CCGCCCCCACCA
1 CCTCCACCACCA
11160 CCTCCACC
1 CCTCCACC
11168 TCTACCACCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.14, C:0.70, G:0.04, T:0.12
Consensus pattern (12 bp):
CCTCCACCACCA
Found at i:11186 original size:21 final size:21
Alignment explanation
Indices: 11115--11179 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
11105 ATTGCCTCCT
* *
11115 CCACCGCCTCCTCCACCACCA
1 CCACCTCCACCTCCACCACCA
* * *
11136 CCTCCTCCACCTCCGCCCCCA
1 CCACCTCCACCTCCACCACCA
*
11157 CCACCTCCACCTCTACCACCA
1 CCACCTCCACCTCCACCACCA
11178 CC
1 CC
11180 GCTTCCATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.68, G:0.03, T:0.12
Consensus pattern (21 bp):
CCACCTCCACCTCCACCACCA
Done.