Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018168.1 Corchorus olitorius cultivar O-4 contig18201, 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: 48130
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3853 original size:30 final size:30
Alignment explanation
Indices: 3809--3877 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
3799 CAATCGCTGC
*
3809 TCTAATA-ATCTTATCTGTACAGTATTTAA
1 TCTAATATGTCTTATCTGTACAGTATTTAA
3838 TCTAATATGTCTTATCTGTACAGTATTTAA
1 TCTAATATGTCTTATCTGTACAGTATTTAA
3868 TCTAATATGT
1 TCTAATATGT
3878 ACAGTGTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 7 0.18
30 31 0.82
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (30 bp):
TCTAATATGTCTTATCTGTACAGTATTTAA
Found at i:5328 original size:12 final size:13
Alignment explanation
Indices: 5311--5339 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5301 CATGGAGGGG
5311 ATATTATA-TTAT
1 ATATTATATTTAT
5323 ATATTATATTTAT
1 ATATTATATTTAT
5336 ATAT
1 ATAT
5340 GTGTGTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:6376 original size:11 final size:11
Alignment explanation
Indices: 6345--6370 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6335 ATTGAACAAC
6345 AGAAAAAAAAA
1 AGAAAAAAAAA
6356 AGAAAAAAAAA
1 AGAAAAAAAAA
6367 AGAA
1 AGAA
6371 GCAAAAGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:6791 original size:21 final size:21
Alignment explanation
Indices: 6765--6804 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6755 TTTAGCTAGG
6765 GGTCTTACAAGGTCAAGAAAA
1 GGTCTTACAAGGTCAAGAAAA
6786 GGTCTTACAAGGTCAAGAA
1 GGTCTTACAAGGTCAAGAA
6805 GAGGGTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCTTACAAGGTCAAGAAAA
Found at i:8233 original size:16 final size:16
Alignment explanation
Indices: 8212--8274 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
8202 ATTTTGTCAC
8212 TAAAATGCAAAATATA
1 TAAAATGCAAAATATA
*
8228 TAAAATGTAAAATATA
1 TAAAATGCAAAATATA
*
8244 TCTAAAAAATG-TAAA-ATA
1 --T--AAAATGCAAAATATA
8262 TAAAATGCAAAAT
1 TAAAATGCAAAAT
8275 CAGATGGCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 16 0.42
18 4 0.11
19 3 0.08
20 6 0.16
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAATGCAAAATATA
Found at i:22402 original size:21 final size:21
Alignment explanation
Indices: 22378--22417 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22368 AAGAGATTCG
*
22378 AAAGGAGACTACGGAGTTAGA
1 AAAGAAGACTACGGAGTTAGA
*
22399 AAAGAAGATTACGGAGTTA
1 AAAGAAGACTACGGAGTTA
22418 AAAGAACGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.17
Consensus pattern (21 bp):
AAAGAAGACTACGGAGTTAGA
Found at i:28362 original size:30 final size:30
Alignment explanation
Indices: 28328--28389 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
28318 ATTTTTATCT
* *
28328 TGACTTTCCTCTTAGATCCTCTAATTTTAA
1 TGACTTTCCTCTTAGACCCTCAAATTTTAA
* *
28358 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTAGACCCTCAAATTTTAA
28388 TG
1 TG
28390 GCTTGTTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTAGACCCTCAAATTTTAA
Found at i:28740 original size:28 final size:27
Alignment explanation
Indices: 28683--28740 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28673 GTTTTCTGAA
* *
28683 AAAAAAATGTAGAACATGCAGTCACCG
1 AAAAAAATGTAGAACATGCAATCAACG
*
28710 AAAAAAATGTAGAACATGCGAATCAATG
1 AAAAAAATGTAGAACATGC-AATCAACG
28738 AAA
1 AAA
28741 CAATTACTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAAAAATGTAGAACATGCAATCAACG
Found at i:31047 original size:15 final size:15
Alignment explanation
Indices: 31023--31052 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31013 CTTTCCTCAA
*
31023 GAAATGCTGACATGT
1 GAAATACTGACATGT
31038 GAAATACTGACATGT
1 GAAATACTGACATGT
31053 CATGCCGCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (15 bp):
GAAATACTGACATGT
Found at i:41807 original size:14 final size:14
Alignment explanation
Indices: 41788--41814 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41778 CTTTTCTGCG
41788 AAACCAGGAGCGGC
1 AAACCAGGAGCGGC
41802 AAACCAGGAGCGG
1 AAACCAGGAGCGG
41815 GAAGGCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (14 bp):
AAACCAGGAGCGGC
Found at i:42827 original size:4 final size:4
Alignment explanation
Indices: 42818--43045 Score: 447
Period size: 4 Copynumber: 57.0 Consensus size: 4
42808 TCTCCCTGAC
42818 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
42866 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
42914 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
42962 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
43010 GTAT GTAT GTAT GTAT GTGT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
43046 TTAACTAACA
Statistics
Matches: 222, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 222 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:46891 original size:16 final size:19
Alignment explanation
Indices: 46870--46905 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
46860 ATTTTATAAA
46870 TAAAAA-AA-TAT-ATTAT
1 TAAAAATAATTATCATTAT
46886 TAAAAATAATTATCATTAT
1 TAAAAATAATTATCATTAT
46905 T
1 T
46906 TCAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 3 0.18
19 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATAATTATCATTAT
Done.