Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012373.1 Corchorus olitorius cultivar O-4 contig12406, 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: 29149
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1840 original size:13 final size:13
Alignment explanation
Indices: 1822--1867 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1812 TGGAGAATGA
1822 TCTAGTTGGAAGG
1 TCTAGTTGGAAGG
*
1835 TCTAGTAT-AAGAGG
1 TCTAGT-TGGA-AGG
1849 TCTAGTTGGAAGG
1 TCTAGTTGGAAGG
1862 TCTAGT
1 TCTAGT
1868 ATAAGAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (13 bp):
TCTAGTTGGAAGG
Found at i:1851 original size:14 final size:14
Alignment explanation
Indices: 1832--1873 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1822 TCTAGTTGGA
1832 AGGTCTAGTATAAG
1 AGGTCTAGTATAAG
*
1846 AGGTCTAGT-T-GG
1 AGGTCTAGTATAAG
1858 AAGGTCTAGTATAAG
1 -AGGTCTAGTATAAG
1873 A
1 A
1874 ATGGTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 11 0.48
15 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (14 bp):
AGGTCTAGTATAAG
Found at i:1860 original size:27 final size:27
Alignment explanation
Indices: 1822--1873 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1812 TGGAGAATGA
1822 TCTAGTTGGAAGGTCTAGTATAAGAGG
1 TCTAGTTGGAAGGTCTAGTATAAGAGG
1849 TCTAGTTGGAAGGTCTAGTATAAGA
1 TCTAGTTGGAAGGTCTAGTATAAGA
1874 ATGGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (27 bp):
TCTAGTTGGAAGGTCTAGTATAAGAGG
Found at i:5949 original size:25 final size:25
Alignment explanation
Indices: 5911--5962 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5901 AAATGCAATC
5911 TCATAGAAAGACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
*
5936 TCATAGAAATACACCTTTTCATGTT
1 TCATAGAAAGACACCTTTTCATGTT
5961 TC
1 TC
5963 CGCAGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (25 bp):
TCATAGAAAGACACCTTTTCATGTT
Found at i:9868 original size:25 final size:25
Alignment explanation
Indices: 9830--9881 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
9820 AGATGCAATC
9830 TCATAGAAAGACACATTTTCATGTT
1 TCATAGAAAGACACATTTTCATGTT
* *
9855 TCATAGAAATACACCTTTTCATGTT
1 TCATAGAAAGACACATTTTCATGTT
9880 TC
1 TC
9882 CGCAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (25 bp):
TCATAGAAAGACACATTTTCATGTT
Found at i:11696 original size:21 final size:21
Alignment explanation
Indices: 11670--11710 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11660 CTTTCTCTAT
*
11670 TTTGAGACAAAATTCATCCTA
1 TTTGAGACAAAATGCATCCTA
*
11691 TTTGAGACAGAATGCATCCT
1 TTTGAGACAAAATGCATCCT
11711 GCAGGTAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (21 bp):
TTTGAGACAAAATGCATCCTA
Found at i:16820 original size:3 final size:3
Alignment explanation
Indices: 16814--16893 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
16804 AAAAAAGTAC
16814 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16862 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16894 AGGAAGGACG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19058 original size:11 final size:11
Alignment explanation
Indices: 19044--19107 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
19034 GTTTCTGAAA
19044 TCAGTCTGATT
1 TCAGTCTGATT
**
19055 TCAGTTTCTGAAA
1 TCAG--TCTGATT
19068 TCAGTCTGATT
1 TCAGTCTGATT
**
19079 TCAGTTTCTGAAA
1 TCAG--TCTGATT
19092 TCAGTCTGATT
1 TCAGTCTGATT
19103 TCAGT
1 TCAGT
19108 TTCTGAAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 23 0.56
13 18 0.44
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (11 bp):
TCAGTCTGATT
Found at i:19062 original size:24 final size:24
Alignment explanation
Indices: 19033--19128 Score: 176
Period size: 24 Copynumber: 4.0 Consensus size: 24
19023 TGTTGTTTGT
19033 AGTTTCTGAAATCAGTCTGATTTC
1 AGTTTCTGAAATCAGTCTGATTTC
19057 AGTTTCTGAAATCAGTCTGATTTC
1 AGTTTCTGAAATCAGTCTGATTTC
19081 AGTTTCTGAAATCAGTCTGATTTC
1 AGTTTCTGAAATCAGTCTGATTTC
19105 AGTTTCTGAAATCAGTTCT-ATTTC
1 AGTTTCTGAAATCAG-TCTGATTTC
19129 CATTATTTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
24 68 0.96
25 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.43
Consensus pattern (24 bp):
AGTTTCTGAAATCAGTCTGATTTC
Found at i:19071 original size:13 final size:13
Alignment explanation
Indices: 19033--19121 Score: 82
Period size: 13 Copynumber: 7.3 Consensus size: 13
19023 TGTTGTTTGT
19033 AGTTTCTGAAATC
1 AGTTTCTGAAATC
**
19046 AG--TCTGATTTC
1 AGTTTCTGAAATC
19057 AGTTTCTGAAATC
1 AGTTTCTGAAATC
**
19070 AG--TCTGATTTC
1 AGTTTCTGAAATC
19081 AGTTTCTGAAATC
1 AGTTTCTGAAATC
**
19094 AG--TCTGATTTC
1 AGTTTCTGAAATC
19105 AGTTTCTGAAATC
1 AGTTTCTGAAATC
19118 AGTT
1 AGTT
19122 CTATTTCCAT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
11 27 0.47
13 31 0.53
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (13 bp):
AGTTTCTGAAATC
Found at i:27028 original size:33 final size:33
Alignment explanation
Indices: 26986--27049 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
26976 TGGCTTACGG
26986 ACTATGACTTGAGGGCACAATGATAAATTAAGA
1 ACTATGACTTGAGGGCACAATGATAAATTAAGA
* *
27019 ACTATGACTTGAGGGCATAATGATCAATTAA
1 ACTATGACTTGAGGGCACAATGATAAATTAA
27050 TAAATTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (33 bp):
ACTATGACTTGAGGGCACAATGATAAATTAAGA
Found at i:27642 original size:14 final size:14
Alignment explanation
Indices: 27623--27652 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27613 AAATACTCTT
*
27623 TATTTGACTAATTA
1 TATTTGACAAATTA
27637 TATTTGACAAATTA
1 TATTTGACAAATTA
27651 TA
1 TA
27653 CAATACACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TATTTGACAAATTA
Found at i:28010 original size:202 final size:203
Alignment explanation
Indices: 27633--28045 Score: 699
Period size: 203 Copynumber: 2.0 Consensus size: 203
27623 TATTTGACTA
27633 ATTATA-TTTGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCAGGTCC
1 ATTATATTTTGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCAGGTCC
* *
27697 TGAAAGGTGACATGTGTCATCTAGGGACTAAATTGAAATATTTAAATCTTAATTAATTCAAAAAA
66 TCAAAGGTGACATGTGTCATCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAA
* *
27762 TGGATATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACTGCCGGTGTATCAAAT
131 TGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAAT
27827 AATTACCC
196 AATTACCC
* * *
27835 ATTATATTTTGGCAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTTC
1 ATTATATTTTGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCAGGTCC
* * *
27900 TCAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATT-AAAAAA
66 TCAAAGGTGACATGTGTCATCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAA
27964 TGGACATGTGTCAACTCCACTAA-CCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAA
131 TGGACATGTGTCAACTCCAC-AACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAA
28028 TAATTACCC
195 TAATTACCC
28037 -TTATATTTT
1 ATTATATTTT
28046 TCCTCACTTT
Statistics
Matches: 199, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
201 9 0.05
202 80 0.40
203 110 0.55
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (203 bp):
ATTATATTTTGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCAGGTCC
TCAAAGGTGACATGTGTCATCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAA
TGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAAT
AATTACCC
Found at i:28172 original size:22 final size:22
Alignment explanation
Indices: 28136--28178 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28126 AAGCCTCCAA
28136 ATTTGGGCTACAAAGCAACTAAC
1 ATTTGGGCTACAAAG-AACTAAC
*
28159 ATTTGGGCT-GAAAGAACTAA
1 ATTTGGGCTACAAAGAACTAA
28179 TCATGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 9 0.47
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (22 bp):
ATTTGGGCTACAAAGAACTAAC
Done.