Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018475.1 Corchorus olitorius cultivar O-4 contig18508, 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: 27021
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2626 original size:20 final size:21
Alignment explanation
Indices: 2594--2634 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2584 AACTATTATA
2594 TATATGAATATAATAA-AATT
1 TATATGAATATAATAACAATT
2614 TATAT-AATAATAATAACAATT
1 TATATGAAT-ATAATAACAATT
2635 CAATGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TATATGAATATAATAACAATT
Found at i:2678 original size:2 final size:2
Alignment explanation
Indices: 2671--2699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2661 CTACTAATTA
2671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2700 ACTTAAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3417 original size:15 final size:15
Alignment explanation
Indices: 3397--3425 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3387 AAAACACCCT
3397 TATAAGTAATTAAAG
1 TATAAGTAATTAAAG
3412 TATAAGTAATTAAA
1 TATAAGTAATTAAA
3426 TACATGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
TATAAGTAATTAAAG
Found at i:13268 original size:8 final size:8
Alignment explanation
Indices: 13256--13302 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
13246 AAAAAAGAGA
13256 AAAAATATG
1 AAAAA-ATG
*
13265 AAAATATG
1 AAAAAATG
13273 AAAAAATG
1 AAAAAATG
*
13281 AAAGAATG
1 AAAAAATG
13289 AAAAAATG
1 AAAAAATG
13297 AAAAAA
1 AAAAAA
13303 GAAGAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 30 0.88
9 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (8 bp):
AAAAAATG
Found at i:13275 original size:18 final size:18
Alignment explanation
Indices: 13254--13295 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
13244 AAAAAAAAGA
13254 GAAAAAATATGAAA-ATAT
1 GAAAAAATATGAAAGA-AT
13272 G-AAAAA-ATGAAAGAAT
1 GAAAAAATATGAAAGAAT
13288 GAAAAAAT
1 GAAAAAAT
13296 GAAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 9 0.43
17 11 0.52
18 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAAAAATATGAAAGAAT
Found at i:13297 original size:24 final size:22
Alignment explanation
Indices: 13262--13315 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
13252 GAGAAAAAAT
*
13262 ATGAAAATATGAAAAAATGAAAGA
1 ATGAAAAAATGAAAAAA-G-AAGA
13286 ATGAAAAAATGAAAAAAGAAGA
1 ATGAAAAAATGAAAAAAGAAGA
13308 A-GAAAAAA
1 ATGAAAAAA
13316 AGCACTTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.24
22 5 0.17
23 1 0.03
24 16 0.55
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (22 bp):
ATGAAAAAATGAAAAAAGAAGA
Found at i:18451 original size:31 final size:32
Alignment explanation
Indices: 18410--18472 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
18400 ATTTTAGACC
* *
18410 TAATAACCAAATCTGCAC-CAAAACCGTTTAA
1 TAATAACCAAATCCGCACGCAAAACCATTTAA
*
18441 TAATATCCAAATCCGCACTGCAAAACCATTTA
1 TAATAACCAAATCCGCAC-GCAAAACCATTTA
18473 TTAAGCGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
33 11 0.41
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (32 bp):
TAATAACCAAATCCGCACGCAAAACCATTTAA
Found at i:20429 original size:2 final size:2
Alignment explanation
Indices: 20422--20451 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20412 TACCGAATAA
*
20422 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20452 TAGGTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21178 original size:19 final size:19
Alignment explanation
Indices: 21154--21195 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
21144 TTTTTAAAAA
21154 AAAAAAAGAAAAG-AAGAAG
1 AAAAAAA-AAAAGAAAGAAG
21173 AAAAAAAAAAAGAAAGAAG
1 AAAAAAAAAAAGAAAGAAG
21192 AAAA
1 AAAA
21196 GCGCCGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAGAAAGAAG
Found at i:21179 original size:22 final size:22
Alignment explanation
Indices: 21150--21193 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
21140 CAATTTTTTA
21150 AAAAAAAAAAAGAAAAGAAGAAG
1 AAAAAAAAAAAG-AAAGAAGAAG
21173 AAAAAAAAAAAGAAAGAAGAA
1 AAAAAAAAAAAGAAAGAAGAA
21194 AAGCGCCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAGAAGAAG
Found at i:22907 original size:11 final size:13
Alignment explanation
Indices: 22891--22922 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
22881 GTTGAGGAAC
22891 TGTTTTATT-AT-
1 TGTTTTATTAATA
22902 TGTTTTATTAATA
1 TGTTTTATTAATA
22915 TGTTTTAT
1 TGTTTTAT
22923 AAATGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (13 bp):
TGTTTTATTAATA
Done.