Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024873.1 Corchorus olitorius cultivar O-4 contig24906, 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: 13787
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4474 original size:50 final size:50
Alignment explanation
Indices: 4410--4510 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
4400 TAAAATGCCC
*
4410 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
**
4460 TTTGAAAATTGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
4510 T
1 T
4511 ATAAAACTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
Found at i:4806 original size:6 final size:6
Alignment explanation
Indices: 4795--4853 Score: 66
Period size: 6 Copynumber: 9.2 Consensus size: 6
4785 TTTCTTCATT
4795 TTTTCA TTTTCA TTTTCA TTTTCA TTTTTTCA -TTTCA TTTTTTCA TTTTTCA
1 TTTTCA TTTTCA TTTTCA TTTTCA --TTTTCA TTTTCA --TTTTCA -TTTTCA
4847 TTTTCA T
1 TTTTCA T
4854 CATTTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.10
6 25 0.52
7 7 0.15
8 11 0.23
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:4853 original size:13 final size:14
Alignment explanation
Indices: 4789--4850 Score: 94
Period size: 13 Copynumber: 4.6 Consensus size: 14
4779 GTTTCTTTTC
4789 TTCATTTTTTCATT
1 TTCATTTTTTCATT
4803 TTCA--TTTTCATT
1 TTCATTTTTTCATT
4815 TTCATTTTTTCA-T
1 TTCATTTTTTCATT
4828 TTCATTTTTTCATTT
1 TTCATTTTTTCA-TT
4843 TTCATTTT
1 TTCATTTT
4851 CATCATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.27
13 13 0.30
14 10 0.23
15 9 0.20
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCATTTTTTCATT
Found at i:4863 original size:20 final size:18
Alignment explanation
Indices: 4789--4864 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 18
4779 GTTTCTTTTC
4789 TTCATTTTTTCATTTTCATT
1 TTCATTTTTT--TTTTCATT
4809 TTCATTTTCATTTTTTCA-T
1 TTCATTTT--TTTTTTCATT
4828 TTCATTTTTTCATTTTTCATT
1 TTCA-TTTTT--TTTTTCATT
4849 TTCATCATTTTTTTTT
1 TTCAT--TTTTTTTTT
4865 TTGCATGCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
20 31 0.65
21 5 0.10
22 6 0.12
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCATTTTTTTTTTCATT
Found at i:5208 original size:13 final size:13
Alignment explanation
Indices: 5159--5212 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
5149 CTTATACCTT
*
5159 TTTCAATTTTCAGT
1 TTTCAATTTTCA-C
5173 TTTCAATTTTCAC
1 TTTCAATTTTCAC
*
5186 TTTC-ACTTTCAC
1 TTTCAATTTTCAC
5198 TTTCAATTTTCAC
1 TTTCAATTTTCAC
5211 TT
1 TT
5213 CTCTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.31
13 13 0.36
14 12 0.33
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTCAATTTTCAC
Found at i:6152 original size:75 final size:75
Alignment explanation
Indices: 6050--6201 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
6040 TGAATTCAAC
* * * * * *
6050 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCATCTTT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
6115 CCTTTGCTCA
66 CCTTTGCTCA
*
6125 CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
6190 CCTTTGCTCA
66 CCTTTGCTCA
6200 CA
1 CA
6202 GTACAGATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.37
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
CCTTTGCTCA
Found at i:11142 original size:34 final size:34
Alignment explanation
Indices: 10994--11158 Score: 170
Period size: 34 Copynumber: 4.6 Consensus size: 34
10984 AATGTTTTTG
* *
10994 ATGGGAACTTTCCCACTTTGAAAACT-AAAGCTGAAA
1 ATGGGAACTTTCCCAATTTGAAAACTAAAACCT---A
* *
11030 ATGACGGGAACTTTCCCTAAATTGAAAACTAAAACCTG
1 AT---GGGAACTTTCCC-AATTTGAAAACTAAAACCTA
* * * *
11068 GTGAGAACTTTCCCAATTTGAAAACTTAAAAACTTG
1 ATGGGAACTTTCCCAATTTGAAAAC-T-AAAACCTA
11104 ATGGGAACTTTCCCAATTTGAAAACTAAAACCTA
1 ATGGGAACTTTCCCAATTTGAAAACTAAAACCTA
11138 ATGGGAACTTTCCCAATTTGA
1 ATGGGAACTTTCCCAATTTGA
11159 CTTTTGAGTT
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
34 37 0.34
35 13 0.12
36 32 0.29
38 1 0.01
39 12 0.11
40 10 0.09
41 5 0.05
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (34 bp):
ATGGGAACTTTCCCAATTTGAAAACTAAAACCTA
Found at i:11146 original size:70 final size:71
Alignment explanation
Indices: 10994--11158 Score: 208
Period size: 70 Copynumber: 2.3 Consensus size: 71
10984 AATGTTTTTG
*
10994 ATGGGAACTTTCCCACTTTGAAAACTAAAGCTGAAAATGACGGGAACTTTCCCTAAATTGAAAAC
1 ATGGGAACTTTCCCAATTTGAAAACTAAA---GAAAATGACGGGAACTTTCCCTAAATTGAAAAC
*
11059 TAAAACCTG
63 TAAAACCTA
* * ** * *
11068 GTGAGAACTTTCCCAATTTGAAAACTTAAA-AACTTGATGGGAACTTTCCC-AATTTGAAAACTA
1 ATGGGAACTTTCCCAATTTGAAAAC-TAAAGAAAATGACGGGAACTTTCCCTAAATTGAAAACTA
11131 AAACCTA
65 AAACCTA
11138 ATGGGAACTTTCCCAATTTGA
1 ATGGGAACTTTCCCAATTTGA
11159 CTTTTGAGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
70 37 0.46
71 17 0.21
74 22 0.28
75 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (71 bp):
ATGGGAACTTTCCCAATTTGAAAACTAAAGAAAATGACGGGAACTTTCCCTAAATTGAAAACTAA
AACCTA
Found at i:12056 original size:56 final size:56
Alignment explanation
Indices: 11966--12079 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
11956 TATCTGTTTC
11966 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
* **
12022 CTTTCACACAATAAATGTTATAATAAATCTTATCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
12078 CT
1 CT
12080 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTAACTCTACTTAATTATT
Found at i:12203 original size:42 final size:42
Alignment explanation
Indices: 12144--12224 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
12134 TAAGGATCGG
12144 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
12186 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
12225 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.