Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024767.1 Corchorus olitorius cultivar O-4 contig24800, 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: 47489
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:834 original size:19 final size:19
Alignment explanation
Indices: 810--848 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
800 GGTTGGGATA
810 CTCAAGTGGTGAAAATACG
1 CTCAAGTGGTGAAAATACG
*
829 CTCAAGTGGTGAACATACG
1 CTCAAGTGGTGAAAATACG
848 C
1 C
849 GGGCAAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (19 bp):
CTCAAGTGGTGAAAATACG
Found at i:885 original size:2 final size:2
Alignment explanation
Indices: 878--905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
868 TCTTAATCAA
878 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
906 GTATGTATGT
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:4180 original size:24 final size:23
Alignment explanation
Indices: 4144--4194 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
4134 TTTTTTAATT
**
4144 TTTTTAATTAATAATTAGTTATTA
1 TTTTTAAAAAATAATTA-TTATTA
*
4168 TTTTTAAAAAATAGTTATTATTA
1 TTTTTAAAAAATAATTATTATTA
4191 TTTT
1 TTTT
4195 ATATGATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTTTAAAAAATAATTATTATTA
Found at i:17799 original size:30 final size:30
Alignment explanation
Indices: 17764--17825 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
17754 CGTGTACGTC
17764 GACAAGTACAACCATAGTAGATAATGCAGA
1 GACAAGTACAACCATAGTAGATAATGCAGA
*
17794 GACAAGTACAAGCATAGTAGATAATGCAGA
1 GACAAGTACAACCATAGTAGATAATGCAGA
17824 GA
1 GA
17826 AGTCGCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.16
Consensus pattern (30 bp):
GACAAGTACAACCATAGTAGATAATGCAGA
Found at i:18261 original size:2 final size:2
Alignment explanation
Indices: 18254--18278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18244 TTAAAAAGAT
18254 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 T
18279 TGTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24022 original size:30 final size:29
Alignment explanation
Indices: 23935--24030 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
23925 GCTCAAAAAG
*
23935 GCCCTTGAACT-TACACAAAACGACCAAATAA
1 GCCCTTGAACTCTA-ATAAAA-G-CCAAATAA
* ***
23966 GCCCATGAACTCTAATTGCAGCCAAATAA
1 GCCCTTGAACTCTAATAAAAGCCAAATAA
*
23995 GCCCTTGAACTCTTATAAAAGGCCAAATAA
1 GCCCTTGAACTCTAATAAAA-GCCAAATAA
*
24025 ACCCTT
1 GCCCTT
24031 TTCTGATGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
29 23 0.44
30 15 0.29
31 12 0.23
32 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (29 bp):
GCCCTTGAACTCTAATAAAAGCCAAATAA
Found at i:24494 original size:30 final size:30
Alignment explanation
Indices: 24458--24537 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
24448 GCCATCAGAA
24458 AAGGGCTTATTTGGCCTTTTATAAGAGTTC
1 AAGGGCTTATTTGGCCTTTTATAAGAGTTC
*** *
24488 AAGGGCTTATTTGG-CTGCAATTAGAGTTC
1 AAGGGCTTATTTGGCCTTTTATAAGAGTTC
* *
24517 AGGGGTTTATTTGGCCGTTTT
1 AAGGGCTTATTTGGCC-TTTT
24538 GTGTAAGTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 23 0.59
30 15 0.38
31 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (30 bp):
AAGGGCTTATTTGGCCTTTTATAAGAGTTC
Found at i:25139 original size:21 final size:20
Alignment explanation
Indices: 25110--25158 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
25100 TGCTTTTCTT
* * *
25110 ATAAAAAAATTATATGATGTA
1 ATAACAAAATCATAT-ATATA
25131 ATAACAAAATCATATATATA
1 ATAACAAAATCATATATATA
25151 AT-ACAAAA
1 ATAACAAAA
25159 CTTGTTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 13 0.52
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAACAAAATCATATATATA
Found at i:25769 original size:12 final size:12
Alignment explanation
Indices: 25752--25776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25742 TTATCCTTCG
25752 GCAATAATATCA
1 GCAATAATATCA
25764 GCAATAATATCA
1 GCAATAATATCA
25776 G
1 G
25777 ATGCTTCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (12 bp):
GCAATAATATCA
Found at i:26354 original size:20 final size:19
Alignment explanation
Indices: 26315--26355 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
26305 TGGTGTTATT
*
26315 TCTGTGTTAATTTTTTTGA
1 TCTGTGTTAATTTATTTGA
26334 TCTGTGTTAATTTGATTTGA
1 TCTGTGTTAATTT-ATTTGA
26354 TC
1 TC
26356 AAATTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (19 bp):
TCTGTGTTAATTTATTTGA
Found at i:28334 original size:213 final size:214
Alignment explanation
Indices: 27987--28389 Score: 711
Period size: 213 Copynumber: 1.9 Consensus size: 214
27977 ATTTCGGTAC
*
27987 TTTTATGCTCAGTATTTTCGTTATTATTGTTGATTGTTGAGGGCATTTTGGGAATTTTAGGATAA
1 TTTTATGCTCAGTATTTTCGTTATTATTGTTGATTGTTGAGGGCATTTTGGGAACTTTAGGATAA
*
28052 AGTTACTATTTGGTGGATCCCACTCTCAATAAACAAATATCTTTTTGTTGGATTATTTATCAAAT
66 AGTTACTATTTGATGGATCCCACTCTCAATAAACAAATATCTTTTTGTTGGATTATTTATCAAAT
*
28117 GATCCTCATACTTTTATGTTTTATGCTATTTAATCCTTAATTCTGGG-TTGGACAATTGATGTGA
131 GATCCTCATACTTTTATGCTTTATGCTATTTAATCCTTAATTCTGGGTTTGGACAATTGATGTGA
28181 ACAAAATGTTAGGGGTATT
196 ACAAAATGTTAGGGGTATT
* * *
28200 TTTTATGCTCGGTATTTTCGTTATTATTGTTGATTGTTGATGGCGTTTTGGGAACTTTAGGATAA
1 TTTTATGCTCAGTATTTTCGTTATTATTGTTGATTGTTGAGGGCATTTTGGGAACTTTAGGATAA
* *
28265 AGTTATTATTTGATAGG-TCCCACTCTCAATAAACAAATATTTTTTTGTTGGATTATTTATCAAA
66 AGTTACTATTTGAT-GGATCCCACTCTCAATAAACAAATATCTTTTTGTTGGATTATTTATCAAA
28329 TGATCCTCATACTTTTATGCTTTATGCTATTTAATCCTTAATTCTGGGTTTGGACAATTGA
130 TGATCCTCATACTTTTATGCTTTATGCTATTTAATCCTTAATTCTGGGTTTGGACAATTGA
28390 ATGTTTCGGT
Statistics
Matches: 180, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
213 166 0.92
214 14 0.08
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.45
Consensus pattern (214 bp):
TTTTATGCTCAGTATTTTCGTTATTATTGTTGATTGTTGAGGGCATTTTGGGAACTTTAGGATAA
AGTTACTATTTGATGGATCCCACTCTCAATAAACAAATATCTTTTTGTTGGATTATTTATCAAAT
GATCCTCATACTTTTATGCTTTATGCTATTTAATCCTTAATTCTGGGTTTGGACAATTGATGTGA
ACAAAATGTTAGGGGTATT
Found at i:29013 original size:19 final size:19
Alignment explanation
Indices: 28989--29025 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28979 TCATCAACAC
28989 TAATCAAATGATAATGTAT
1 TAATCAAATGATAATGTAT
29008 TAATCAAATGATAATGTA
1 TAATCAAATGATAATGTA
29026 CCAATAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (19 bp):
TAATCAAATGATAATGTAT
Done.