Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024364.1 Corchorus olitorius cultivar O-4 contig24397, 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: 29857
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1477 original size:13 final size:13
Alignment explanation
Indices: 1459--1484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1449 CTTGGCATGA
1459 GTGATGATTTTTG
1 GTGATGATTTTTG
1472 GTGATGATTTTTG
1 GTGATGATTTTTG
1485 TTGCTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:4938 original size:2 final size:2
Alignment explanation
Indices: 4929--4961 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4919 ATACACACTG
4929 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4962 AGGGTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5714 original size:19 final size:19
Alignment explanation
Indices: 5690--5728 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5680 ATATGGAAGG
*
5690 ATATTTTATAATTATTTTA
1 ATATTTTATAATTATCTTA
*
5709 ATATTTTATGATTATCTTA
1 ATATTTTATAATTATCTTA
5728 A
1 A
5729 AAGTGATATG
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:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATTTTATAATTATCTTA
Found at i:6435 original size:24 final size:25
Alignment explanation
Indices: 6406--6456 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6396 TTATGTGAAC
*
6406 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
6430 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
6455 AA
1 AA
6457 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:8728 original size:29 final size:31
Alignment explanation
Indices: 8664--8728 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
8654 AAATAGAGTT
8664 TTTTACCAAACCATTGTGACTTTTAAAAATAA
1 TTTT-CCAAACCATTGTGACTTTTAAAAATAA
*
8696 -TTTCCAAACCATTGT-ACTTTT-AAATTAA
1 TTTTCCAAACCATTGTGACTTTTAAAAATAA
8724 TTTTC
1 TTTTC
8729 ATTCCCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 12 0.39
31 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (31 bp):
TTTTCCAAACCATTGTGACTTTTAAAAATAA
Found at i:12172 original size:24 final size:23
Alignment explanation
Indices: 12140--12185 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
12130 GCTAACTTGT
*
12140 AAATGTTATCAAGGGTGCCAAAAA
1 AAATATTATCAAGGG-GCCAAAAA
**
12164 AAATATTATGTAGGGGCCAAAA
1 AAATATTATCAAGGGGCCAAAA
12186 GCATGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (23 bp):
AAATATTATCAAGGGGCCAAAAA
Found at i:16172 original size:24 final size:24
Alignment explanation
Indices: 16140--16188 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16130 TATCTGCTAG
*
16140 CATTATACTTCTATGAGTCTTCTT
1 CATTATACTTCCATGAGTCTTCTT
16164 CATTATACTTCCATGAGTCTTCTT
1 CATTATACTTCCATGAGTCTTCTT
16188 C
1 C
16189 CCTGCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
CATTATACTTCCATGAGTCTTCTT
Found at i:18934 original size:76 final size:76
Alignment explanation
Indices: 18676--18923 Score: 426
Period size: 76 Copynumber: 3.3 Consensus size: 76
18666 TGATGAAGTT
* *
18676 AACAGTACTAACGAACTTGATGAAAGGAAACTCAAGCATTCAACTTTAACTCCTAATACTGAATT
1 AACAGTAATAACGAACTTGATGAAAGGAACCTCAAGCATTCAACTTTAACTCCTAATACTGAATT
*
18741 AAAACAGATTC
66 AAAACAAATTC
*
18752 AACAGTAATTAA-GAACTTGATGAAAGGAACCTCAAGCATTCAACTTTAACTCCTAATACTGCAT
1 AACAGTAA-TAACGAACTTGATGAAAGGAACCTCAAGCATTCAACTTTAACTCCTAATACTGAAT
18816 TAAAACAAATTC
65 TAAAACAAATTC
* *
18828 AACAGTAATAAAGAACTTGATGAAAGGAACCTCAAGCATTCGACTTTAACTCCTAATACTGAATT
1 AACAGTAATAACGAACTTGATGAAAGGAACCTCAAGCATTCAACTTTAACTCCTAATACTGAATT
18893 AAAACAAATTC
66 AAAACAAATTC
18904 AACAGTAATAACGAACTTGA
1 AACAGTAATAACGAACTTGA
18924 CAAACGGAAC
Statistics
Matches: 163, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
75 3 0.02
76 157 0.96
77 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (76 bp):
AACAGTAATAACGAACTTGATGAAAGGAACCTCAAGCATTCAACTTTAACTCCTAATACTGAATT
AAAACAAATTC
Found at i:20347 original size:21 final size:21
Alignment explanation
Indices: 20321--20365 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20311 ATAATTATCC
*
20321 TTATTATAGATACATGAAAGT
1 TTATTATAGATACACGAAAGT
20342 TTATTATAGATACACGAAAGT
1 TTATTATAGATACACGAAAGT
20363 TTA
1 TTA
20366 CTAGATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (21 bp):
TTATTATAGATACACGAAAGT
Done.