Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021790.1 Corchorus olitorius cultivar O-4 contig21823, 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: 18632
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9602 original size:45 final size:44
Alignment explanation
Indices: 9538--9633 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
9528 AACAACAATT
* *
9538 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTA-ACAGAAATGGAGGAGTAG
*
9583 AATATTAGCTTTATTTTGATGAATTACCAGAAATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTAACAGAAATGGAGGAGTAG
9627 AAT-TTAG
1 AATATTAG
9634 GTAATGCACT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
43 4 0.08
44 18 0.38
45 26 0.54
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (44 bp):
AATATTAGCTTTATTTTGATGAATTAACAGAAATGGAGGAGTAG
Found at i:10581 original size:28 final size:29
Alignment explanation
Indices: 10541--10596 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
10531 AAAGACTAGA
10541 TGGGATCTTTCCCTAAATT-AAAACTTTG
1 TGGGATCTTTCCCTAAATTGAAAACTTTG
10569 TGGGATCTTTCCCTAAATTGAAAACTTT
1 TGGGATCTTTCCCTAAATTGAAAACTTT
10597 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (29 bp):
TGGGATCTTTCCCTAAATTGAAAACTTTG
Found at i:10648 original size:29 final size:30
Alignment explanation
Indices: 10606--10733 Score: 120
Period size: 29 Copynumber: 4.1 Consensus size: 30
10596 TAAAAAAAAA
*
10606 AAAACCTTGATGGGATCTTTCCCTAAATTG
1 AAAACTTTGATGGGATCTTTCCCTAAATTG
10636 AAAACTTTG-TGGGATCTTTCCCTAAATTG
1 AAAACTTTGATGGGATCTTTCCCTAAATTG
10665 AAAACTTTAAAAAACTCGATGGGATCTTTCCCTAAATTG
1 AAAAC-TT-------T-GATGGGATCTTTCCCTAAATTG
* *
10704 AAAAC--TG-TGGGATCTTTCCTTGAATTG
1 AAAACTTTGATGGGATCTTTCCCTAAATTG
10731 AAA
1 AAA
10734 GCTTCTTAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 23
0.77 0.03 0.21
Matches are distributed among these distances:
27 21 0.25
28 1 0.01
29 26 0.31
30 10 0.12
37 1 0.01
38 1 0.01
39 25 0.29
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (30 bp):
AAAACTTTGATGGGATCTTTCCCTAAATTG
Found at i:10716 original size:27 final size:29
Alignment explanation
Indices: 10675--10733 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 29
10665 AAAACTTTAA
10675 AAAACTCGATGGGATCTTTCCCTAAATTG
1 AAAACTCGATGGGATCTTTCCCTAAATTG
* *
10704 AAAACT-G-TGGGATCTTTCCTTGAATTG
1 AAAACTCGATGGGATCTTTCCCTAAATTG
10731 AAA
1 AAA
10734 GCTTCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.75
28 1 0.04
29 6 0.21
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (29 bp):
AAAACTCGATGGGATCTTTCCCTAAATTG
Found at i:10743 original size:68 final size:68
Alignment explanation
Indices: 10500--10745 Score: 293
Period size: 68 Copynumber: 3.5 Consensus size: 68
10490 AAAACTTTAA
*
10500 TGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACTAGATGGGATCTTTCCCTAAATT-AAA
1 TGGGATCTTT-CCCTAAATTGAAAACTTTTAAAAA-ACTAGATGGGATCTTTCCCTAAATTGAAA
10563 ACTTTG
64 AC-TTG
* *
10569 TGGGATCTTTCCCTAAATTGAAAACTTTAAAAAAAAAAAAACCTTGATGGGATCTTTCCCTAAAT
1 TGGGATCTTTCCCTAAATTGAAAACTTT------TAAAAAA-CTAGATGGGATCTTTCCCTAAAT
10634 TGAAAACTTTG
59 TGAAAAC-TTG
*
10645 TGGGATCTTTCCCTAAATTGAAAAC-TTTAAAAAACTCGATGGGATCTTTCCCTAAATTGAAAAC
1 TGGGATCTTTCCCTAAATTGAAAACTTTTAAAAAACTAGATGGGATCTTTCCCTAAATTGAAAAC
10709 -TG
66 TTG
* * *
10711 TGGGATCTTTCCTTGAATTGAAAGCTTCTTAAAAA
1 TGGGATCTTTCCCTAAATTGAAAACTT-TTAAAAA
10746 CCTTTTTGAT
Statistics
Matches: 159, Mismatches: 7, Indels: 23
0.84 0.04 0.12
Matches are distributed among these distances:
66 24 0.15
67 1 0.01
68 40 0.25
69 29 0.18
74 1 0.01
75 30 0.19
76 34 0.21
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (68 bp):
TGGGATCTTTCCCTAAATTGAAAACTTTTAAAAAACTAGATGGGATCTTTCCCTAAATTGAAAAC
TTG
Found at i:14781 original size:42 final size:42
Alignment explanation
Indices: 14716--14796 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
14706 TAAGGCTTAG
14716 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
* * *
14758 GATTTGAGTTGAGTATTTTTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTC
14797 AAGACTTAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
Found at i:16426 original size:19 final size:19
Alignment explanation
Indices: 16402--16440 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16392 CCATGTTAAC
16402 TGCTGACATGTAATTTTTT
1 TGCTGACATGTAATTTTTT
**
16421 TGCTGATGTGTAATTTTTT
1 TGCTGACATGTAATTTTTT
16440 T
1 T
16441 CTATGGGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (19 bp):
TGCTGACATGTAATTTTTT
Found at i:17292 original size:16 final size:16
Alignment explanation
Indices: 17249--17299 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
17239 TTGATGAGAT
* * *
17249 ATCTCTGTAGAGACAT
1 ATCTCTTTAGAAACAC
17265 ATCTCTTT--AAACAC
1 ATCTCTTTAGAAACAC
17279 ATCTCTTTAGAAACAAC
1 ATCTCTTTAGAAAC-AC
17296 ATCT
1 ATCT
17300 ATCCACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.41
16 11 0.38
17 6 0.21
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (16 bp):
ATCTCTTTAGAAACAC
Done.