Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013426.1 Corchorus capsularis cultivar CVL-1 contig13447, 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: 14247
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:772 original size:19 final size:19
Alignment explanation
Indices: 720--777 Score: 72
Period size: 17 Copynumber: 3.3 Consensus size: 19
710 TTCATGAGAA
720 GAGAGT-TCATAATAATT-
1 GAGAGTATCATAATAATTG
*
737 G-GAGTATTAT-A-AATTG
1 GAGAGTATCATAATAATTG
753 GAGAGTATCATAATAATTG
1 GAGAGTATCATAATAATTG
772 GAGAGT
1 GAGAGT
778 TCTTCAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 12 0.35
18 1 0.03
19 11 0.32
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (19 bp):
GAGAGTATCATAATAATTG
Found at i:1676 original size:109 final size:109
Alignment explanation
Indices: 1485--1703 Score: 420
Period size: 109 Copynumber: 2.0 Consensus size: 109
1475 TGACGACAAT
* *
1485 TTTATAAAATGACTTAACTATCCCTATTGATTTGCTCTTCAATTCATGAGAAGAGAGGGTTAGAC
1 TTTATAAAATGACTTAACTATCCCTACTGATTTGCTCTACAATTCATGAGAAGAGAGGGTTAGAC
1550 CCTCTTTTTGTCATTTGACTGGTTATTCTTAATATTTTGTATAA
66 CCTCTTTTTGTCATTTGACTGGTTATTCTTAATATTTTGTATAA
1594 TTTATAAAATGACTTAACTATCCCTACTGATTTGCTCTACAATTCATGAGAAGAGAGGGTTAGAC
1 TTTATAAAATGACTTAACTATCCCTACTGATTTGCTCTACAATTCATGAGAAGAGAGGGTTAGAC
1659 CCTCTTTTTGTCATTTGACTGGTTATTCTTAATATTTTGTATAA
66 CCTCTTTTTGTCATTTGACTGGTTATTCTTAATATTTTGTATAA
1703 T
1 T
1704 AATAATATAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (109 bp):
TTTATAAAATGACTTAACTATCCCTACTGATTTGCTCTACAATTCATGAGAAGAGAGGGTTAGAC
CCTCTTTTTGTCATTTGACTGGTTATTCTTAATATTTTGTATAA
Found at i:1726 original size:33 final size:33
Alignment explanation
Indices: 1688--1792 Score: 110
Period size: 33 Copynumber: 3.1 Consensus size: 33
1678 TGGTTATTCT
*
1688 TAATATTTTGTATAATAATAATATA-ATAATGTA
1 TAATATTTAGTATAAT-ATAATATATATAATGTA
*
1721 TAATATAATATAATATAATATAATAATAATATAATGTA
1 TAATAT--T-TAGTATAATATAAT-AT-ATATAATGTA
1759 TAATA--TAGTATAATATAATA-ATATAATGTA
1 TAATATTTAGTATAATATAATATATATAATGTA
1789 TAAT
1 TAAT
1793 GTTGTTACTG
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
30 14 0.22
32 1 0.02
33 19 0.30
35 6 0.10
36 9 0.14
37 1 0.02
38 13 0.21
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (33 bp):
TAATATTTAGTATAATATAATATATATAATGTA
Found at i:1744 original size:38 final size:38
Alignment explanation
Indices: 1702--1794 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
1692 ATTTTGTATA
1702 ATAATAATATAATAATGTATAATATAATATAATATAAT
1 ATAATAATATAATAATGTATAATATAATATAATATAAT
*
1740 ATAATAATA-ATATAATGTATAATATAGTATAATATAAT
1 ATAATAATATA-ATAATGTATAATATAATATAATATAAT
*
1778 A-ATATAATGT-ATAATGT
1 ATA-ATAATATAATAATGT
1795 TGTTACTGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
37 9 0.18
38 41 0.82
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (38 bp):
ATAATAATATAATAATGTATAATATAATATAATATAAT
Found at i:1781 original size:30 final size:30
Alignment explanation
Indices: 1698--1792 Score: 113
Period size: 30 Copynumber: 3.0 Consensus size: 30
1688 TAATATTTTG
1698 TATAATAATAATATAATAATGTATAA--TATAA
1 TATAAT-ATAATATAATAA--TATAATGTATAA
1729 TATAATATAATATAATAATAATATAATGTATAA
1 TATAATAT-A-AT-ATAATAATATAATGTATAA
*
1762 TATAGTATAATATAATAATATAATGTATAA
1 TATAATATAATATAATAATATAATGTATAA
1792 T
1 T
1793 GTTGTTACTG
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
30 22 0.38
31 14 0.24
32 3 0.05
33 19 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (30 bp):
TATAATATAATATAATAATATAATGTATAA
Found at i:1785 original size:5 final size:5
Alignment explanation
Indices: 1698--1778 Score: 92
Period size: 5 Copynumber: 15.4 Consensus size: 5
1688 TAATATTTTG
*
1698 TATAA TAATAA TATAA TA-ATG TATAA TATAA TATAA TATAA TATAA TAATAA
1 TATAA T-ATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA
*
1750 TATAA TGTATAA TATAG TATAA TATAA TA
1 TATAA --TATAA TATAA TATAA TATAA TA
1779 ATATAATGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 1 0.02
5 49 0.74
6 11 0.17
7 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:5775 original size:16 final size:16
Alignment explanation
Indices: 5754--5787 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5744 CATATGAGGG
5754 TAATTCTTAGAACACA
1 TAATTCTTAGAACACA
5770 TAATTCTTAGAACACA
1 TAATTCTTAGAACACA
5786 TA
1 TA
5788 TGTGTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (16 bp):
TAATTCTTAGAACACA
Found at i:10840 original size:1 final size:1
Alignment explanation
Indices: 10834--10865 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
10824 AATTGTTATG
10834 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10866 GGCTTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14174 original size:30 final size:29
Alignment explanation
Indices: 14068--14174 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
14058 TAAACAACCA
** * *
14068 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
* *
14099 TTTTGTCCCCTGAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGACG
* *
14128 TTTTGCCCCCAGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
*
14158 TTTTGCCCCCTCAACTT
1 TTTTGCCCCCTGAACTT
14175 AACGGCTCCG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 26 0.41
30 19 0.30
31 18 0.29
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Done.