Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019989.1 Corchorus olitorius cultivar O-4 contig20022, 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: 27978
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:6930 original size:24 final size:23
Alignment explanation
Indices: 6899--6944 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
6889 AACGGAGGAA
6899 AAATATACTAGCAAAAGAAAAGT
1 AAATATACTAGCAAAAGAAAAGT
* *
6922 AAATGATACTAGCTAAAGGAAAG
1 AAAT-ATACTAGCAAAAGAAAAG
6945 GGGTGAGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (23 bp):
AAATATACTAGCAAAAGAAAAGT
Found at i:7319 original size:16 final size:16
Alignment explanation
Indices: 7288--7354 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
7278 TCTTTTTCGG
*
7288 GTATGAACTG-TTTTT
1 GTATGAAATGTTTTTT
7303 GTATGAAATGTTTTTT
1 GTATGAAATGTTTTTT
* *
7319 GGGTATGAACTATTTTTT
1 --GTATGAAATGTTTTTT
7337 GTATGAAATGTTTTTT
1 GTATGAAATGTTTTTT
7353 GT
1 GT
7355 TTTTTTTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
15 9 0.20
16 21 0.48
18 14 0.32
ACGTcount: A:0.22, C:0.03, G:0.21, T:0.54
Consensus pattern (16 bp):
GTATGAAATGTTTTTT
Found at i:7323 original size:33 final size:34
Alignment explanation
Indices: 7280--7353 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
7270 GACTCTGTTC
*
7280 TTTTTCGGGTATGAACT-GTTTTTGTATGAAATG
1 TTTTTTGGGTATGAACTAGTTTTTGTATGAAATG
*
7313 TTTTTTGGGTATGAACTATTTTTTGTATGAAATG
1 TTTTTTGGGTATGAACTAGTTTTTGTATGAAATG
7347 TTTTTTG
1 TTTTTTG
7354 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 16 0.42
34 22 0.58
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.54
Consensus pattern (34 bp):
TTTTTTGGGTATGAACTAGTTTTTGTATGAAATG
Found at i:7857 original size:2 final size:2
Alignment explanation
Indices: 7850--7885 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7840 ATCACCTTCC
7850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7886 GAAACGTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7952 original size:36 final size:36
Alignment explanation
Indices: 7903--7974 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
7893 CCTTGCCTTG
7903 CCTTCACAAATTAAGCTTTTGCCCAAATATAAGTTA
1 CCTTCACAAATTAAGCTTTTGCCCAAATATAAGTTA
*
7939 CCTTCACAGATTAAGCTTTTGCCCAAATATAAGTTA
1 CCTTCACAAATTAAGCTTTTGCCCAAATATAAGTTA
7975 AACAACATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
CCTTCACAAATTAAGCTTTTGCCCAAATATAAGTTA
Found at i:8034 original size:9 final size:8
Alignment explanation
Indices: 8013--8042 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8003 GCAATCTGGA
*
8013 CTTTTCTT
1 CTTTTTTT
8021 CTTTTTTT
1 CTTTTTTT
8029 CTTTTTTT
1 CTTTTTTT
8037 CTTTTT
1 CTTTTT
8043 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
CTTTTTTT
Found at i:8821 original size:39 final size:38
Alignment explanation
Indices: 8763--8893 Score: 163
Period size: 39 Copynumber: 3.4 Consensus size: 38
8753 TGAAACGGAA
*
8763 ACCTAAGCAGGTTTTCTTAAACGAAAATTCTAAATAGAG
1 ACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAATA-AG
* * *
8802 ACCTAAGCAGGTTTGCTTAAATGGAAATTCTAAACAAG
1 ACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAATAAG
* * *
8840 AACCTAAGCAGGTTTGATTAAACAAAAATTCTGAATAAGG
1 -ACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAATAA-G
*
8880 ACCTAATCAGGTTT
1 ACCTAAGCAGGTTT
8894 AATCAATCGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.03
39 76 0.96
40 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (38 bp):
ACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAATAAG
Found at i:20358 original size:39 final size:39
Alignment explanation
Indices: 20304--20381 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
20294 TTCATCTTAT
*
20304 TCACCTTTCTCTTCTCATAGCTTGACAATAACACAAAAA
1 TCACCTTTCTCTTCTCATAGCTTGACAAGAACACAAAAA
*
20343 TCACCTTTCTCTTCTCATGGCTTGACAAGAACACAAAAA
1 TCACCTTTCTCTTCTCATAGCTTGACAAGAACACAAAAA
20382 ATAACAGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.29
Consensus pattern (39 bp):
TCACCTTTCTCTTCTCATAGCTTGACAAGAACACAAAAA
Found at i:21022 original size:113 final size:114
Alignment explanation
Indices: 20890--21433 Score: 841
Period size: 113 Copynumber: 4.8 Consensus size: 114
20880 TCTGTGCAAA
**
20890 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCAAGAAATG
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
20955 CAAATTGGGTAAAAATG-AGACTAAAATATAGCGGCGTTTCTACCCAAG
66 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
* * * **
21003 ACGCCGCTAAATGGGGGCGTTT-AAGTCTTACAACGCCGTCATAATCAAATTTTTTT--GGGAAA
1 ACGCCGCTAAATGGGGGCGTTTGAGGT-TAAAAACGCCGTCAT-ATTTAATTTTTTTCCGGGAAA
* *
21065 TACAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCTTTTCTACCCAAG
64 TGCAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
21116 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATA-TTAATTTTTTTCCGGGAAATG
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
21180 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
66 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
* * * *
21229 ACGCCGCTAAATGGGGGCGTCTGAGGTTTACAACGCCGTCATATTGAAATTTTTTT--GGGAAAT
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATT-TAATTTTTTTCCGGGAAAT
* *
21292 ACAAATTGGGTAAAAATGAAGAGTAAAATATAGCGGCGTTTCTACCCAAG
65 GCAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
* *
21342 ACGCCGCTAAATGGGAGCGTTTGAGCTTAAAAACGCCGTCATATTTAATTTTTTTTTCCGGGAAA
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAA--TTTTTTTCCGGGAAA
21407 TGCAAATTGGGTAAAAATGAAGACTAA
64 TGCAAATTGGGTAAAAATGAAGACTAA
21434 TTCCTCGGCG
Statistics
Matches: 389, Mismatches: 30, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
111 9 0.02
112 28 0.07
113 290 0.75
114 22 0.06
115 9 0.02
116 31 0.08
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (114 bp):
ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAG
Found at i:21263 original size:226 final size:227
Alignment explanation
Indices: 20890--21433 Score: 950
Period size: 226 Copynumber: 2.4 Consensus size: 227
20880 TCTGTGCAAA
**
20890 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCAAGAAATG
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
20955 CAAATTGGGTAAAAATG-AGACTAAAATATAGCGGCGTTTCTACCCAAGACGCCGCTAAATGGGG
66 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAGACGCCGCTAAATGGGG
*
21019 GCGTTTAAGTCTTACAACGCCGTCATAATCAAATTTTTTTGGGAAATACAAATTGGGTAAAAATG
131 GCGTTGAAGTCTTACAACGCCGTCATAATCAAATTTTTTTGGGAAATACAAATTGGGTAAAAATG
*
21084 AAGACTAAAATATAGCGGCTTTTCTACCCAAG
196 AAGACTAAAATATAGCGGCGTTTCTACCCAAG
21116 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATA-TTAATTTTTTTCCGGGAAATG
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
21180 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAGACGCCGCTAAATGGGG
66 CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAGACGCCGCTAAATGGGG
* * *
21245 GCGTCTGAGGT-TTACAACGCCGTCATATTGAAATTTTTTTGGGAAATACAAATTGGGTAAAAAT
131 GCGT-TGAAGTCTTACAACGCCGTCATAATCAAATTTTTTTGGGAAATACAAATTGGGTAAAAAT
*
21309 GAAGAGTAAAATATAGCGGCGTTTCTACCCAAG
195 GAAGACTAAAATATAGCGGCGTTTCTACCCAAG
* *
21342 ACGCCGCTAAATGGGAGCGTTTGAGCTTAAAAACGCCGTCATATTTAATTTTTTTTTCCGGGAAA
1 ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAA--TTTTTTTCCGGGAAA
21407 TGCAAATTGGGTAAAAATGAAGACTAA
64 TGCAAATTGGGTAAAAATGAAGACTAA
21434 TTCCTCGGCG
Statistics
Matches: 303, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
225 36 0.12
226 217 0.72
227 8 0.03
229 42 0.14
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (227 bp):
ACGCCGCTAAATGGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAATTTTTTTCCGGGAAATG
CAAATTGGGTAAAAATGAAGACTAAAATATAGCGGCGTTTCTACCCAAGACGCCGCTAAATGGGG
GCGTTGAAGTCTTACAACGCCGTCATAATCAAATTTTTTTGGGAAATACAAATTGGGTAAAAATG
AAGACTAAAATATAGCGGCGTTTCTACCCAAG
Found at i:23479 original size:32 final size:32
Alignment explanation
Indices: 23441--23567 Score: 148
Period size: 33 Copynumber: 3.9 Consensus size: 32
23431 GAAAAAACCA
* *
23441 AAATAGCGGCG-TTTCTGTATAGAAACGCCATT
1 AAATAGCGGCGTTTTATGTA-AGAAACGCCACT
* * *
23473 AAATAGCGTCGTTTTTTGTACGGAAACGCCACT
1 AAATAGCGGCGTTTTATGTA-AGAAACGCCACT
*
23506 AAATAGCGACGTTTTATGTAAGGAAACGCCACT
1 AAATAGCGGCGTTTTATGTAA-GAAACGCCACT
*
23539 AAATAGCGGCGTTTTATGTACGGAAACGC
1 AAATAGCGGCGTTTTATGTA-AGAAACGC
23568 TGCTATCTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
32 10 0.12
33 72 0.88
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (32 bp):
AAATAGCGGCGTTTTATGTAAGAAACGCCACT
Found at i:23509 original size:33 final size:33
Alignment explanation
Indices: 23462--23567 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
23452 TTTCTGTATA
* * *
23462 GAAACGCCATTAAATAGCGTCGTTTTTTGTACG
1 GAAACGCCACTAAATAGCGACGTTTTATGTACG
*
23495 GAAACGCCACTAAATAGCGACGTTTTATGTAAG
1 GAAACGCCACTAAATAGCGACGTTTTATGTACG
*
23528 GAAACGCCACTAAATAGCGGCGTTTTATGTACG
1 GAAACGCCACTAAATAGCGACGTTTTATGTACG
23561 GAAACGC
1 GAAACGC
23568 TGCTATCTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (33 bp):
GAAACGCCACTAAATAGCGACGTTTTATGTACG
Found at i:23535 original size:66 final size:65
Alignment explanation
Indices: 23441--23567 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 65
23431 GAAAAAACCA
* * * * *
23441 AAATAGCGGCGTTTCTGTATAGAAACGCCATTAAATAGCGTCGTTTTTTGTACGGAAACGCCACT
1 AAATAGCGACGTTTATGTATAGAAACGCCACTAAATAGCGGCGTTTTATGTACGGAAACGCCACT
23506 AAATAGCGACGTTTTATGTA-AGGAAACGCCACTAAATAGCGGCGTTTTATGTACGGAAACGC
1 AAATAGCGACG-TTTATGTATA-GAAACGCCACTAAATAGCGGCGTTTTATGTACGGAAACGC
23568 TGCTATCTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 11 0.20
66 44 0.80
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (65 bp):
AAATAGCGACGTTTATGTATAGAAACGCCACTAAATAGCGGCGTTTTATGTACGGAAACGCCACT
Done.