Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023533.1 Corchorus olitorius cultivar O-4 contig23566, 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: 9527
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1711 original size:40 final size:40
Alignment explanation
Indices: 1642--1830 Score: 218
Period size: 41 Copynumber: 4.6 Consensus size: 40
1632 TTCTTCTTCA
* * *
1642 ATTTGCTCCTTGATTGATGTTGATGTCTTTTAATTGGTTCG
1 ATTTACTCC-TGATTGATGTTAATATCTTTTAATTGGTTCG
*
1683 ATTTACTCCTAATTGATGTTAATATCTTTTAATTGGTTCG
1 ATTTACTCCTGATTGATGTTAATATCTTTTAATTGGTTCG
* *
1723 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
1 ATTT-ACTCCTGATTGATGTTAATATCTTTTAATTGGTTCG
* * * *
1764 ATTTGCTCCCTGATTGAGGTTATTATCTTTTTAATTGATTCG
1 ATTTACT-CCTGATTGATGTTAATATC-TTTTAATTGGTTCG
*
1806 ATTT-CGTCCTTGATTGAGGTTAATA
1 ATTTAC-TCC-TGATTGATGTTAATA
1831 CTTACTATTT
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
40 33 0.25
41 65 0.50
42 32 0.25
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (40 bp):
ATTTACTCCTGATTGATGTTAATATCTTTTAATTGGTTCG
Found at i:1739 original size:81 final size:83
Alignment explanation
Indices: 1642--1809 Score: 241
Period size: 81 Copynumber: 2.0 Consensus size: 83
1632 TTCTTCTTCA
* * * * *
1642 ATTTGCTCCTTGATTGATGTTGATGTCTTTTAATTGGTTCGATTTACT-CCTAATTGATGTTAAT
1 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCGATTTACTCCCTAATTGAGGTTAAT
*
1706 ATC-TTTTAATTGGTTCG
66 ATCTTTTTAATTGATTCG
* * *
1723 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCGATTTGCTCCCTGATTGAGGTTATT
1 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCGATTTACTCCCTAATTGAGGTTAAT
1788 ATCTTTTTAATTGATTCG
66 ATCTTTTTAATTGATTCG
1806 ATTT
1 ATTT
1810 CGTCCTTGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
81 43 0.57
82 16 0.21
83 17 0.22
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.50
Consensus pattern (83 bp):
ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCGATTTACTCCCTAATTGAGGTTAAT
ATCTTTTTAATTGATTCG
Found at i:1751 original size:41 final size:41
Alignment explanation
Indices: 1642--1809 Score: 221
Period size: 41 Copynumber: 4.1 Consensus size: 41
1632 TTCTTCTTCA
* * * *
1642 ATTTGCTCCTTGATTGATGTTGATGTCTTTTAATTGGTTCG
1 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
* * *
1683 ATTT-ACTCCTAATTGATGTTAATATCTTTTAATTGGTTCG
1 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
1723 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
1 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
* * * *
1764 ATTTGCTCCCTGATTGAGGTTATTATCTTTTTAATTGATTCG
1 ATTTGCCCCCTGATTGATGTTAATATC-TTTTAATTGGTTCG
1806 ATTT
1 ATTT
1810 CGTCCTTGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 33 0.30
41 61 0.55
42 17 0.15
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.50
Consensus pattern (41 bp):
ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCG
Found at i:1851 original size:83 final size:82
Alignment explanation
Indices: 1642--1851 Score: 201
Period size: 83 Copynumber: 2.6 Consensus size: 82
1632 TTCTTCTTCA
* * * * * * * * * *
1642 ATTTGCTCCTTGATTGATGTTGATGTCTTTTAATTGGTTCGATTTACT-CCTAATTGATGTTAAT
1 ATTTGCCCCCTGATTGAGGTTAATATCTTCTAATTGGTTCAATTTGCTCCCTGATTGAGGTTAAT
*
1706 ATCTTTTAATTGGTTCG
66 ATCTTTTAATTGATTCG
* * * *
1723 ATTTGCCCCCTGATTGATGTTAATATCTTTTAATTGGTTCGATTTGCTCCCTGATTGAGGTTATT
1 ATTTGCCCCCTGATTGAGGTTAATATCTTCTAATTGGTTCAATTTGCTCCCTGATTGAGGTTAAT
1788 ATCTTTTTAATTGATTCG
66 ATC-TTTTAATTGATTCG
* * * *
1806 ATTT-CGTCCTTGATTGAGGTTAATA-CTTACTATTTGTTTCAATTTG
1 ATTTGC-CCCCTGATTGAGGTTAATATCTT-CTAATTGGTTCAATTTG
1852 ACTCTTGAAA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
81 43 0.39
82 20 0.18
83 46 0.42
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.50
Consensus pattern (82 bp):
ATTTGCCCCCTGATTGAGGTTAATATCTTCTAATTGGTTCAATTTGCTCCCTGATTGAGGTTAAT
ATCTTTTAATTGATTCG
Found at i:2769 original size:21 final size:21
Alignment explanation
Indices: 2744--2788 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2734 TTAGAGGTAG
*
2744 AAAAAGGGAAAAAATCCAAAA
1 AAAAAGAGAAAAAATCCAAAA
* *
2765 AAAAAGAGAAAAAATTCAGAA
1 AAAAAGAGAAAAAATCCAAAA
2786 AAA
1 AAA
2789 TTAAAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAAAGAGAAAAAATCCAAAA
Found at i:6358 original size:19 final size:18
Alignment explanation
Indices: 6325--6360 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6315 TCGAGATAAT
6325 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
6343 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
6361 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.