Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018227.1 Corchorus olitorius cultivar O-4 contig18260, 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: 54989
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4017 original size:2 final size:2
Alignment explanation
Indices: 4010--4037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4000 TATTATCGCA
4010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4038 TAGTAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7941 original size:12 final size:12
Alignment explanation
Indices: 7924--7959 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
7914 TTGTAGCACG
7924 TTTCTTTTTTTT
1 TTTCTTTTTTTT
7936 TTTC--TTTTTT
1 TTTCTTTTTTTT
7946 TTTCTTTTTTTT
1 TTTCTTTTTTTT
7958 TT
1 TT
7960 GAGAATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:7945 original size:10 final size:10
Alignment explanation
Indices: 7930--7958 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
7920 CACGTTTCTT
7930 TTTTTTTTTC
1 TTTTTTTTTC
7940 TTTTTTTTTC
1 TTTTTTTTTC
7950 TTTTTTTTT
1 TTTTTTTTT
7959 TGAGAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:8390 original size:11 final size:11
Alignment explanation
Indices: 8376--8418 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
8366 ATTCATAACA
8376 AATTTATAATT
1 AATTTATAATT
8387 AATTTATAATT
1 AATTTATAATT
8398 -ATTTGATAATTT
1 AATTT-ATAA-TT
*
8410 ATTTTATAA
1 AATTTATAA
8419 AGGAAAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.14
11 15 0.54
12 6 0.21
13 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
AATTTATAATT
Found at i:8406 original size:22 final size:22
Alignment explanation
Indices: 8377--8418 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
8367 TTCATAACAA
8377 ATTTATAA-TTAATTTATAATT
1 ATTTATAATTTAATTTATAATT
*
8398 ATTTGATAATTTATTTTATAA
1 ATTT-ATAATTTAATTTATAA
8419 AGGAAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTATAATTTAATTTATAATT
Found at i:8734 original size:2 final size:2
Alignment explanation
Indices: 8723--8751 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8713 AGTTTAGACT
8723 TA TA TA -A 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
8752 GATGTATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11539 original size:20 final size:21
Alignment explanation
Indices: 11514--11564 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
11504 AACCATATTG
*
11514 AACTTTTTATTG-ACTTGTTA
1 AACTTTTTAGTGAACTTGTTA
*
11534 AACTTTTTAGTGAATTTGTTA
1 AACTTTTTAGTGAACTTGTTA
*
11555 AACATTTTAG
1 AACTTTTTAG
11565 AAATCTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (21 bp):
AACTTTTTAGTGAACTTGTTA
Found at i:14736 original size:6 final size:6
Alignment explanation
Indices: 14725--14753 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
14715 AGATCTGGCT
14725 GCTGCG GCTGCG GCTGCG GCTGCG GCTGC
1 GCTGCG GCTGCG GCTGCG GCTGCG GCTGC
14754 CGTTCCCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.48, T:0.17
Consensus pattern (6 bp):
GCTGCG
Found at i:22337 original size:20 final size:20
Alignment explanation
Indices: 22311--22352 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22301 GTAATTTTGT
22311 GAGAGAGAGGTAATGCTTGATA
1 GAGAGAGA-G-AATGCTTGATA
*
22333 GAGAGAGAGGATGCTTGATA
1 GAGAGAGAGAATGCTTGATA
22353 ACCGAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.38, T:0.21
Consensus pattern (20 bp):
GAGAGAGAGAATGCTTGATA
Found at i:28286 original size:31 final size:31
Alignment explanation
Indices: 28251--28311 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
28241 ATGTCTAGTT
* * * *
28251 AAATGCTTAATTTGGTCCTAAATTTTTAAAG
1 AAATGCTCAATTTGATACTAAACTTTTAAAG
28282 AAATGCTCAATTTGATACTAAACTTTTAAA
1 AAATGCTCAATTTGATACTAAACTTTTAAA
28312 CCTGTTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
AAATGCTCAATTTGATACTAAACTTTTAAAG
Found at i:28333 original size:29 final size:30
Alignment explanation
Indices: 28285--28352 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
28275 TTTAAAGAAA
* *
28285 TGCTCAATTTGATACTAAAC-TTTTAAACC
1 TGCTCAATTTGATACCAAACATTTCAAACC
*
28314 TGTTCAATTT-AGTACCAAACATTTCAAACC
1 TGCTCAATTTGA-TACCAAACATTTCAAACC
28344 TGCTCAATT
1 TGCTCAATT
28353 CAATCATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.48
30 16 0.48
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (30 bp):
TGCTCAATTTGATACCAAACATTTCAAACC
Found at i:30865 original size:21 final size:21
Alignment explanation
Indices: 30813--30866 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
30803 GGGAATGGAG
* *
30813 TATTTA-TTTATTTTGTTTCT
1 TATTTATTTTATTTTCTTGCT
*
30833 TAATTT-TATTATTTTCTTGCT
1 T-ATTTATTTTATTTTCTTGCT
30854 TATTTATTTTATT
1 TATTTATTTTATT
30867 GTTCCTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGCT
Found at i:33537 original size:12 final size:12
Alignment explanation
Indices: 33512--33558 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
33502 AATATCCACA
33512 GATATATCGAATG
1 GATATATCG-ATG
33525 GATATATCGATG
1 GATATATCGATG
*
33537 GATATATCGATT
1 GATATATCGATG
33549 GATATATCGA
1 GATATATCGA
33559 GGTATCGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (12 bp):
GATATATCGATG
Found at i:34431 original size:10 final size:10
Alignment explanation
Indices: 34419--34454 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
34409 AATTTAATAT
*
34419 GGATATTTAT
1 GGATATTTAC
34429 GGATATTTAC
1 GGATATTTAC
*
34439 AGATATTTAC
1 GGATATTTAC
34449 GGATAT
1 GGATAT
34455 ATCGAGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:41733 original size:2 final size:2
Alignment explanation
Indices: 41726--41752 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41716 TGTTGGTAAT
41726 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
41753 TATTTGTGAG
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.