Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013684.1 Corchorus olitorius cultivar O-4 contig13717, 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: 6602
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:115 original size:50 final size:50
Alignment explanation
Indices: 51--640 Score: 1063
Period size: 50 Copynumber: 11.8 Consensus size: 50
41 AGGTTTAAAA
* *
51 TGACTAGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
101 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
151 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
201 TGACTCGTATGGAAACGTGTTTGGCTTGTGGAATAGCCTCTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
251 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
301 TGACTCGTATGGAAACGAGTTCGGCTTGTGGGAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
351 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
401 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
451 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
501 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* **
551 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAATTCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
601 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
641 AAGCATTCGG
Statistics
Matches: 519, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 519 1.00
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:832 original size:91 final size:91
Alignment explanation
Indices: 718--921 Score: 318
Period size: 91 Copynumber: 2.2 Consensus size: 91
708 AAGAAAATAC
* * *
718 CTTGGAAAATAACTCGGAATCTGATGTTGTAACCGAAAACTTCTTGATTGATGATGAAAAAGCAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACCGAAAACTTCTTGATTGATGATGAAAAAGCAC
*
783 CAATGTGCGGTCAACTTGAAAAACAA
66 CAATGTGCAGTCAACTTGAAAAACAA
* * *
809 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACCGAAAACTTCTTGATTGATGATGAAAAAGCAC
* * *
874 CAATTTGCAGTCAGCTTGACAAACAA
66 CAATGTGCAGTCAACTTGAAAAACAA
900 CTTGAAAAATAACTCTGAGTCT
1 CTTGAAAAATAACTCTGAGTCT
922 AACGTAATGA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 103 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (91 bp):
CTTGAAAAATAACTCTGAGTCTGATGTTGTAACCGAAAACTTCTTGATTGATGATGAAAAAGCAC
CAATGTGCAGTCAACTTGAAAAACAA
Found at i:1409 original size:50 final size:50
Alignment explanation
Indices: 1355--1450 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
1345 TCGAAAAGTG
* * *
1355 AATTTTGATCTTGGACTCACAAATGGAATGCAATCTTACTTTGAAAAGCA
1 AATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTGTGAAAAGCA
*
1405 AATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTACTGTGAAA
1 AATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTGTGAAA
1451 CTTCTTGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (50 bp):
AATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTACTGTGAAAAGCA
Found at i:2031 original size:13 final size:13
Alignment explanation
Indices: 2013--2039 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2003 ATCCATTCTC
2013 TTTTGATTTTGAT
1 TTTTGATTTTGAT
2026 TTTTGATTTTGAT
1 TTTTGATTTTGAT
2039 T
1 T
2040 GATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (13 bp):
TTTTGATTTTGAT
Found at i:2043 original size:17 final size:16
Alignment explanation
Indices: 2022--2081 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
2012 CTTTTGATTT
2022 TGATTTTTGATTTTGA
1 TGATTTTTGATTTTGA
*
2038 TTGATTTTT-TTTTATGA
1 -TGATTTTTGATTT-TGA
2055 TGATTTTTTGATTGATTGA
1 TGA-TTTTTGATT--TTGA
2074 TGATTTTT
1 TGATTTTT
2082 TTGAATTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 6 0.17
17 16 0.44
18 7 0.19
19 6 0.17
20 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.17, T:0.65
Consensus pattern (16 bp):
TGATTTTTGATTTTGA
Found at i:2083 original size:20 final size:19
Alignment explanation
Indices: 2025--2085 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
2015 TTGATTTTGA
2025 TTTTTGATT-TTGATTGATT
1 TTTTTGATTATTGA-TGATT
2044 TTTTT--TTA-TGATGA-T
1 TTTTTGATTATTGATGATT
2059 TTTTTGATTGATTGATGATT
1 TTTTTGATT-ATTGATGATT
2079 TTTTTGA
1 TTTTTGA
2086 ATTTCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.17
16 3 0.08
17 7 0.19
18 1 0.03
19 11 0.31
20 8 0.22
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (19 bp):
TTTTTGATTATTGATGATT
Found at i:2085 original size:16 final size:16
Alignment explanation
Indices: 2032--2085 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2022 TGATTTTTGA
2032 TTTTGATTGAT--TTT
1 TTTTGATTGATGATTT
*
2046 TTTTTA-TGATGATTTT
1 TTTTGATTGATGA-TTT
2062 TTGATTGATTGATGATTT
1 TT--TTGATTGATGATTT
2080 TTTTGA
1 TTTTGA
2086 ATTTCTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 5 0.16
16 9 0.28
18 8 0.25
19 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.65
Consensus pattern (16 bp):
TTTTGATTGATGATTT
Found at i:2481 original size:14 final size:14
Alignment explanation
Indices: 2462--2500 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2452 AAGTGCCTTT
*
2462 ATTTTCCTTTTTTC
1 ATTTTCATTTTTTC
2476 ATTTTCATTTTTTC
1 ATTTTCATTTTTTC
2490 AAATTTTCATT
1 --ATTTTCATT
2501 CATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTCATTTTTTC
Done.