Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019744.1 Corchorus olitorius cultivar O-4 contig19777, 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: 24808
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:5163 original size:33 final size:33
Alignment explanation
Indices: 5121--5183 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
5111 TAACCTAAAT
5121 TGAACATAGCCTACATAGGAGGGATATAAAAGA
1 TGAACATAGCCTACATAGGAGGGATATAAAAGA
*
5154 TGAACATAGCCTACATAGGATGGATATAAA
1 TGAACATAGCCTACATAGGAGGGATATAAA
5184 GGCATGGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (33 bp):
TGAACATAGCCTACATAGGAGGGATATAAAAGA
Found at i:16140 original size:30 final size:30
Alignment explanation
Indices: 16104--16168 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
16094 TTATTTTTAA
** *
16104 TAATATTTATTGTATATTAAATCAATA-TTC
1 TAATATTTATTACATATT-AATAAATATTTC
16134 TAATATTTATTACATATTAATAAATATTTC
1 TAATATTTATTACATATTAATAAATATTTC
16164 TAATA
1 TAATA
16169 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (30 bp):
TAATATTTATTACATATTAATAAATATTTC
Found at i:16847 original size:28 final size:28
Alignment explanation
Indices: 16807--16863 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
16797 GGAGTAATCT
16807 ATTAGTTTTAGATCCTAAAGTTAAGATA
1 ATTAGTTTTAGATCCTAAAGTTAAGATA
16835 ATTAGTTTTAGATCCTAAAGTTAAGATA
1 ATTAGTTTTAGATCCTAAAGTTAAGATA
16863 A
1 A
16864 GGAGATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
ATTAGTTTTAGATCCTAAAGTTAAGATA
Found at i:19918 original size:52 final size:52
Alignment explanation
Indices: 19856--19958 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
19846 ATAATTTGAT
* * *
19856 ACTTTTACTAGATCAGATGGTTATAACGTATGAAAATTATGAAAAGCCTGAA
1 ACTTTTACTAGATCAGATAGTTATAAAGTATGAAAATAATGAAAAGCCTGAA
*
19908 ACTTTTACTAGATCAGATAGTTATAAAGTATGAAAATAATGAAAAGTCTGA
1 ACTTTTACTAGATCAGATAGTTATAAAGTATGAAAATAATGAAAAGCCTGA
19959 TTAAGACTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (52 bp):
ACTTTTACTAGATCAGATAGTTATAAAGTATGAAAATAATGAAAAGCCTGAA
Found at i:22694 original size:22 final size:22
Alignment explanation
Indices: 22669--22729 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
22659 CATAGGTAAA
** *
22669 TTATCAATCTTTCATAACGTGG
1 TTATCAAAATTTCATAACGTAG
* *
22691 TTATCAAAATTTAATAAGGTAG
1 TTATCAAAATTTCATAACGTAG
22713 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
22730 AAATATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAACGTAG
Found at i:23266 original size:5 final size:5
Alignment explanation
Indices: 23256--23280 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23246 GGAAGTGATC
23256 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
23281 GAAAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:23653 original size:15 final size:17
Alignment explanation
Indices: 23633--23670 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
23623 CGTTCAAATG
23633 TCGGGTC-A-TTTGGGT
1 TCGGGTCAATTTTGGGT
23648 TCGGGTCAATTTTGGGT
1 TCGGGTCAATTTTGGGT
23665 T-GGGTC
1 TCGGGTC
23671 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.08, C:0.13, G:0.39, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTTTGGGT
Found at i:24702 original size:32 final size:31
Alignment explanation
Indices: 24659--24766 Score: 87
Period size: 32 Copynumber: 3.4 Consensus size: 31
24649 TAACACTAAT
* *
24659 TTAAACTAATTAATGAAAATTAATTATTAAA
1 TTAAACAAATTAATGAAAATTAAATATTAAA
**
24690 TTATTTCAAATTAA--AACTAATTAAATATTAAA
1 TTA-AACAAATTAATGAA--AATTAAATATTAAA
* * *
24722 TTAAACAAATT-ATGAAAATGCAAGCTTTTAAA
1 TTAAACAAATTAATGAAAAT-TAA-ATATTAAA
24754 TTAAACAAATTAA
1 TTAAACAAATTAA
24767 AATATGTTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
30 6 0.10
31 11 0.18
32 42 0.70
33 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (31 bp):
TTAAACAAATTAATGAAAATTAAATATTAAA
Done.