Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016871.1 Corchorus olitorius cultivar O-4 contig16904, 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: 3734
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Found at i:1500 original size:8 final size:8
Alignment explanation
Indices: 1487--1517 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1477 CCTAAACTGC
1487 AAAAAATA
1 AAAAAATA
1495 AAAAAATAA
1 AAAAAAT-A
1504 AAAAAATA
1 AAAAAATA
1512 AAAAAA
1 AAAAAA
1518 ATCAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:1524 original size:8 final size:9
Alignment explanation
Indices: 1487--1525 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
1477 CCTAAACTGC
1487 AAAAAAT-A
1 AAAAAATAA
1495 AAAAAATAA
1 AAAAAATAA
1504 AAAAAATAA
1 AAAAAATAA
1513 AAAAAATCAA
1 AAAAAAT-AA
1523 AAA
1 AAA
1526 GAAAAAGCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 7 0.24
9 17 0.59
10 5 0.17
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1751 original size:47 final size:47
Alignment explanation
Indices: 1656--1773 Score: 159
Period size: 47 Copynumber: 2.5 Consensus size: 47
1646 TCAAGAATCT
* * * *
1656 GATGCAGAGGTAGAGGGCGAT-ATATAATCAACCCCGCCAAGAAGCC
1 GATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAAAAACC
1702 GATGCAGAGGTAGAGGGCGATAAAAAAATCAGA-CCCGCCAAAAAACC
1 GATGCAGAGGTAGAGGGCGATAAAAAAATCA-ACCCCGCCAAAAAACC
* *
1749 GATGCAGTGGTAGAAGGCGATAAAA
1 GATGCAGAGGTAGAGGGCGATAAAA
1774 GGCCGATGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
46 21 0.33
47 42 0.66
48 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.12
Consensus pattern (47 bp):
GATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAAAAACC
Found at i:1773 original size:29 final size:29
Alignment explanation
Indices: 1741--1804 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1731 CAGACCCGCC
*
1741 AAAAAACCGATGCAGTGGTAGAAGGCGAT
1 AAAAAACCGATGCAGAGGTAGAAGGCGAT
** *
1770 AAAAGGCCGATGCAGAGGTAGAGGGCGAT
1 AAAAAACCGATGCAGAGGTAGAAGGCGAT
1799 AAAAAA
1 AAAAAA
1805 ATCAATCCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.33, T:0.11
Consensus pattern (29 bp):
AAAAAACCGATGCAGAGGTAGAAGGCGAT
Found at i:1839 original size:47 final size:45
Alignment explanation
Indices: 1770--1991 Score: 243
Period size: 46 Copynumber: 4.7 Consensus size: 45
1760 AGAAGGCGAT
*
1770 AAAAGGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAATCCCGCC
1 AAAA-GCCGATGCAGAGGTAGAGGGCGATAAAAAAATC-ACCCCGCC
* *
1817 AAAAGGCCGATGCAGAGGTAGAGAGGTAGAGGGTGATAAAAGATCACCCCGCC
1 AAAA-GCCGATGCAGAGGTAGAG-GG-CGA---T-A-AAAAAATCACCCCGCC
* * *
1870 AAGAAGCCGATGTAGAGGTAGAGGGCGATAAAAAATTAACCCCGCC
1 AA-AAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCACCCCGCC
*
1916 AAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAGCCCTGCC
1 AA-AAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCA-CCCCGCC
1963 ---AGCCGATGCAGAGGTAGAGGGCGATAAAA
1 AAAAGCCGATGCAGAGGTAGAGGGCGATAAAA
1992 GGCCGATGCA
Statistics
Matches: 154, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
43 29 0.19
46 49 0.32
47 30 0.19
48 3 0.02
49 2 0.01
51 2 0.01
52 3 0.02
53 27 0.18
54 9 0.06
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.11
Consensus pattern (45 bp):
AAAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCACCCCGCC
Found at i:2006 original size:29 final size:29
Alignment explanation
Indices: 1964--2021 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1954 AGCCCTGCCA
1964 GCCGATGCAGAGGTAGAGGGCGATAAAAG
1 GCCGATGCAGAGGTAGAGGGCGATAAAAG
*
1993 GCCGATGCAGAGGTAGAGGGTGATAAAAG
1 GCCGATGCAGAGGTAGAGGGCGATAAAAG
2022 ATTACCCCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.41, T:0.12
Consensus pattern (29 bp):
GCCGATGCAGAGGTAGAGGGCGATAAAAG
Found at i:2023 original size:163 final size:167
Alignment explanation
Indices: 1838--2158 Score: 517
Period size: 163 Copynumber: 1.9 Consensus size: 167
1828 GCAGAGGTAG
1838 AGAGGTAGAGGGTGATAAAAGATCACCCCGCCAAGAAGCCGATGTAG-AGGTAGAGGGCGAT-AA
1 AGAGGTAGAGGGTGATAAAAGATCACCCCGCCAAGAAGCCGATGT-GTAGGTAGAGGGCGATAAA
* * *
1901 AAAATTAACCCC-GCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAGCCCTGCC-A
65 AAAATCAACCCCTGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAA
1964 -GCCGATGCAGAGGTAGAGGGCGATAAAAGGCCGATGC
130 TGCCGATGCAGAGGTAGAGGGCGATAAAAGGCCGATGC
* *
2001 AGAGGTAGAGGGTGATAAAAGATTACCCCGCGAAGAAGCCGATGTGTAGGTAGAGGGCGATAAAA
1 AGAGGTAGAGGGTGATAAAAGATCACCCCGCCAAGAAGCCGATGTGTAGGTAGAGGGCGATAAAA
*
2066 AAATCAACCCCTGCTAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAG
66 AAATCAACCCCTGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCC-A-
*
2131 ATGCCGATGCAGAGGTAGAGGGTGATAA
129 ATGCCGATGCAGAGGTAGAGGGCGATAA
2159 TTAATCAACC
Statistics
Matches: 144, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
162 1 0.01
163 57 0.40
164 13 0.09
165 47 0.33
168 1 0.01
169 25 0.17
ACGTcount: A:0.37, C:0.19, G:0.31, T:0.13
Consensus pattern (167 bp):
AGAGGTAGAGGGTGATAAAAGATCACCCCGCCAAGAAGCCGATGTGTAGGTAGAGGGCGATAAAA
AAATCAACCCCTGCCAAGAAGCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAT
GCCGATGCAGAGGTAGAGGGCGATAAAAGGCCGATGC
Found at i:2139 original size:47 final size:47
Alignment explanation
Indices: 1993--2158 Score: 221
Period size: 48 Copynumber: 3.6 Consensus size: 47
1983 GCGATAAAAG
* * * *
1993 GCCGATGCAGAGGTAGAGGGTGAT-AAAAGAT-TACCCCGCGAAGAA
1 GCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAA
* *
2038 GCCGATG-TGTAGGTAGAGGGCGATAAAAAAATCAACCCCTGCTAAGAA
1 GCCGATGCAG-AGGTAGAGGGCGATAAAAAAATCAACCCC-GCCAAGAA
*
2086 GCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAT
1 GCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAA
*
2133 GCCGATGCAGAGGTAGAGGGTGATAA
1 GCCGATGCAGAGGTAGAGGGCGATAA
2159 TTAATCAACC
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
44 1 0.01
45 20 0.19
46 6 0.06
47 36 0.34
48 43 0.40
49 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.14
Consensus pattern (47 bp):
GCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAA
Found at i:2158 original size:95 final size:92
Alignment explanation
Indices: 1993--2171 Score: 234
Period size: 95 Copynumber: 1.9 Consensus size: 92
1983 GCGATAAAAG
* * * * *
1993 GCCGATGCAGAGGTAGAGGGTGATAAAAGATTACCCCGCGAAGAAGCCGATGTGTAGGTAGAGGG
1 GCCGATGCAGAGGTAGAGGGCGATAAAAAATAACCCCGCCAAGAAGCCGATGAGTAGGTAGAGGG
2058 CGATAAAAAAATCAACCCCTGCTAAGAA
66 CGAT-AAAAAATCAACCCCTGCTAAGAA
*
2086 GCCGATGCAGAGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGATGCCGATGCAG-AGGTAGA
1 GCCGATGCAGAGGTAGAGGGCGAT-AAAAAAT-AACCCCGCCAAGAAGCCGATG-AGTAGGTAGA
* **
2150 GGGTGATAATTAATCAACCCCT
63 GGGCGATAAAAAATCAACCCCT
2172 CCATTCCACA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 23 0.31
94 19 0.26
95 31 0.42
96 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.29, T:0.15
Consensus pattern (92 bp):
GCCGATGCAGAGGTAGAGGGCGATAAAAAATAACCCCGCCAAGAAGCCGATGAGTAGGTAGAGGG
CGATAAAAAATCAACCCCTGCTAAGAA
Found at i:2233 original size:39 final size:39
Alignment explanation
Indices: 2169--2277 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
2159 TTAATCAACC
*
2169 CCTCCATTCCACAAAATTGAAGGAAAAGGTGCCATTCCA
1 CCTCCATTCCACAAAGTTGAAGGAAAAGGTGCCATTCCA
*
2208 CCTCCATTCCACAAAGTTGATGGAAAAGGTGCCATTCCA
1 CCTCCATTCCACAAAGTTGAAGGAAAAGGTGCCATTCCA
* * *
2247 CCGCTATTCCACAAAGCTTGAAGCAAAAGGT
1 CCTCCATTCCACAAAG-TTGAAGGAAAAGGT
2278 AGAGGGCGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 51 0.81
40 12 0.19
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (39 bp):
CCTCCATTCCACAAAGTTGAAGGAAAAGGTGCCATTCCA
Found at i:2395 original size:46 final size:46
Alignment explanation
Indices: 2325--2456 Score: 223
Period size: 44 Copynumber: 2.9 Consensus size: 46
2315 ATACAGAAGC
2325 CGATGCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGT
1 CGATGCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGT
*
2371 CGATGCAGAGGTAGAGGGCGATAAATAATCAACCCCGCC-A-AAGT
1 CGATGCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGT
* *
2415 CGATGCAGAGGTAGAGGGTAATAAATAATCAACGCCGCCAAT
1 CGATGCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAAT
2457 GTTGAAAGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
44 40 0.50
45 2 0.03
46 38 0.47
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (46 bp):
CGATGCAGAGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGT
Done.