Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013163.1 Corchorus olitorius cultivar O-4 contig13196, 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: 29209
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8272 original size:21 final size:23
Alignment explanation
Indices: 8243--8287 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
8233 TCTTTGAATA
8243 ATTAATTTTAA-TTTT-ATTTTT
1 ATTAATTTTAATTTTTAATTTTT
*
8264 ATTATTTTTAATTTTTAATTTTT
1 ATTAATTTTAATTTTTAATTTTT
8287 A
1 A
8288 CACTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTAATTTTAATTTTTAATTTTT
Found at i:9058 original size:21 final size:20
Alignment explanation
Indices: 9028--9072 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
9018 AGCCGATAAG
9028 AAGGAAGCAAAGTTGTCGACTT
1 AAGGAAGC-AAG-TGTCGACTT
9050 AAGG-AGCAAGTGTCGACTT
1 AAGGAAGCAAGTGTCGACTT
9069 AAGG
1 AAGG
9073 TTGTCGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 3 0.13
21 3 0.13
22 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (20 bp):
AAGGAAGCAAGTGTCGACTT
Found at i:13282 original size:16 final size:16
Alignment explanation
Indices: 13257--13290 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13247 TCATTGAATC
*
13257 AACAACTTAATTATTT
1 AACAACTTAAGTATTT
*
13273 AACAATTTAAGTATTT
1 AACAACTTAAGTATTT
13289 AA
1 AA
13291 TACCTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
AACAACTTAAGTATTT
Found at i:18761 original size:49 final size:48
Alignment explanation
Indices: 18686--18825 Score: 153
Period size: 49 Copynumber: 2.9 Consensus size: 48
18676 AAAGCAATCT
* *
18686 TTTACATTTCC-TGCACTTTTTCTCAATTTTTACA-ACAAAATTGAATC
1 TTTACTTTTCCTTGCACTTTTTCTCAATTTTTA-AGACAAAATTGAATA
* *
18733 TTTATTTTTCCTTGCACCTTTTTCTCAATTTTTAAGATAAAATTGAATA
1 TTTACTTTTCCTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAATA
* * * *
18782 TTTACTTTTCATTTCTCTTTTTATCAATTTTT--GTACAAAATTGA
1 TTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAG-ACAAAATTGA
18826 TTGGCACGCT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
46 1 0.01
47 18 0.23
48 20 0.25
49 40 0.51
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (48 bp):
TTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAATA
Found at i:19682 original size:18 final size:15
Alignment explanation
Indices: 19642--19704 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
19632 AGGGTGAATT
19642 GTGCAAACAACAATG
1 GTGCAAACAACAATG
19657 GTGCAAACAACAATG
1 GTGCAAACAACAATG
*
19672 GTGCAAAAAACAATG
1 GTGCAAACAACAATG
*
19687 GTGCAAATAACAATG
1 GTGCAAACAACAATG
19702 GTG
1 GTG
19705 TGAACGATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (15 bp):
GTGCAAACAACAATG
Found at i:22010 original size:2 final size:2
Alignment explanation
Indices: 22003--22039 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21993 TGTATGAAAG
22003 TA TA TA TA TA 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 TA TA TA TA TA T
22040 GAGAGTGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27153 original size:37 final size:39
Alignment explanation
Indices: 27057--27361 Score: 319
Period size: 40 Copynumber: 7.9 Consensus size: 39
27047 TAAAATCTTG
*
27057 GATGGGATCTTTCCCCT-AATTGAAAGCTTGAAAAAGACTA
1 GATGGGATCTTT-CCCTAAATTGAAAACTTG-AAAAGACTA
* * *
27097 AATGGGATCTTTCCTTAAATTGAAAACTTG-AAA-ACTC
1 GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* * *
27134 GACGGGATCTTTCCCTAAATTTAAAAATTTTGAAGAAGACTA
1 GATGGGATCTTTCCCTAAA-TTGAAAA-CTTGAA-AAGACTA
27176 GATGGGATCTTTCCCTAAATT-AAAACTCTGAAAAAGAC-A
1 GATGGGATCTTTCCCTAAATTGAAAACT-TG-AAAAGACTA
*
27215 GGATGGGATCTTTCCCTAAATT-AAAACTT--AAATACTA
1 -GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* *
27252 GATGGGATCTTTCCCTAAATTGAAATCTTG--AATACTA
1 GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* *
27289 GATGGGATCTTTCCCTAATTTTGAAATCTTGAAAA-ACTA
1 GATGGGATCTTTCCCTAA-ATTGAAAACTTGAAAAGACTA
*
27328 GATGGGATCTTTCCCCAAATTG-AAACTTTGAAAA
1 GATGGGATCTTTCCCTAAATTGAAAAC-TTGAAAA
27362 ATACTTTGGT
Statistics
Matches: 231, Mismatches: 18, Indels: 34
0.82 0.06 0.12
Matches are distributed among these distances:
36 26 0.11
37 54 0.23
38 30 0.13
39 30 0.13
40 64 0.28
41 6 0.03
42 21 0.09
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (39 bp):
GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
Found at i:27268 original size:76 final size:75
Alignment explanation
Indices: 27056--27361 Score: 284
Period size: 76 Copynumber: 4.0 Consensus size: 75
27046 TTAAAATCTT
* * *
27056 GGATGGGATCTTTCCCCT-AATTGAAAGCTTGAAAAAGACTAAATGGGATCTTTCCTTAAATTGA
1 GGATGGGATCTTT-CCCTAAATTGAAAACTT--AAAAGACTAGATGGGATCTTTCCCTAAATT-A
*
27120 AAACT-TGAAAACT
62 AAACTCTGAAAACA
* * * *
27133 CGACGGGATCTTTCCCTAAATTTAAAAATTTTGAAGAAGACTAGATGGGATCTTTCCCTAAATTA
1 GGATGGGATCTTTCCCTAAA-TTGAAAA-CTT-AA-AAGACTAGATGGGATCTTTCCCTAAATTA
27198 AAACTCTGAAAAAGACA
62 AAACTCTG--AAA-ACA
* *
27215 GGATGGGATCTTTCCCTAAATT-AAAACTT-AAATACTAGATGGGATCTTTCCCTAAATTGAAA-
1 GGATGGGATCTTTCCCTAAATTGAAAACTTAAAAGACTAGATGGGATCTTTCCCTAAATTAAAAC
*
27277 TCTTGAATACTA
66 TC-TGAAAAC-A
* * * *
27289 -GATGGGATCTTTCCCTAATTTTGAAATCTTGAAAA-ACTAGATGGGATCTTTCCCCAAATTGAA
1 GGATGGGATCTTTCCCTAA-ATTGAAAACTT-AAAAGACTAGATGGGATCTTTCCCTAAATTAAA
*
27352 ACTTTGAAAA
64 ACTCTGAAAA
27362 ATACTTTGGT
Statistics
Matches: 194, Mismatches: 20, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
73 20 0.10
74 5 0.03
75 8 0.04
76 69 0.36
77 18 0.09
78 13 0.07
79 32 0.16
80 4 0.02
81 5 0.03
82 20 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (75 bp):
GGATGGGATCTTTCCCTAAATTGAAAACTTAAAAGACTAGATGGGATCTTTCCCTAAATTAAAAC
TCTGAAAACA
Found at i:27381 original size:24 final size:25
Alignment explanation
Indices: 27348--27394 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
27338 TTCCCCAAAT
27348 TGAAACTTTG-AAA-AATACTTTGG
1 TGAAACTTTGAAAAGAATACTTTGG
27371 TGAAATCTTTGAAAAGAATACTTT
1 TGAAA-CTTTGAAAAGAATACTTT
27395 AGTGGGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 3 0.14
26 8 0.38
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (25 bp):
TGAAACTTTGAAAAGAATACTTTGG
Done.