Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019148.1 Corchorus olitorius cultivar O-4 contig19181, 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: 40574
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:470 original size:24 final size:25
Alignment explanation
Indices: 424--474 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
414 ATTGGAGTAT
*
424 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
449 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
473 TT
1 TT
475 GTTCACATAA
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:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:12064 original size:37 final size:38
Alignment explanation
Indices: 12000--12075 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
11990 ATGAAATAAT
*
12000 TTATATATTTATCAAAAAATTTAAAACCATTTATTATA
1 TTATATATTTATCAAAAAATTTAAAACCATTCATTATA
*
12038 TTATATATTTA-CGAAAAATTTAAAACCATTCATTATA
1 TTATATATTTATCAAAAAATTTAAAACCATTCATTATA
12075 T
1 T
12076 CATTTGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 25 0.69
38 11 0.31
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (38 bp):
TTATATATTTATCAAAAAATTTAAAACCATTCATTATA
Found at i:12970 original size:22 final size:22
Alignment explanation
Indices: 12942--13109 Score: 106
Period size: 22 Copynumber: 7.7 Consensus size: 22
12932 CTCCAACATA
*
12942 GAAATTTGGATAACCACACTGT
1 GAAATTTTGATAACCACACTGT
***
12964 GAAATTTTGATAACCACACAAA
1 GAAATTTTGATAACCACACTGT
** *
12986 GAAATTTTGATAACCTTAGTGT
1 GAAATTTTGATAACCACACTGT
* * * *
13008 GAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTGT
* * *
13030 GGAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTGT
* * ** *
13052 -AAA-GTTGATAGCTGCACTAT
1 GAAATTTTGATAACCACACTGT
** *
13072 GAAAATTTTGATAACCATGCTTT
1 G-AAATTTTGATAACCACACTGT
*
13095 GAAATTTCGATAACC
1 GAAATTTTGATAACC
13110 TCCCTATGAT
Statistics
Matches: 111, Mismatches: 32, Indels: 6
0.74 0.21 0.04
Matches are distributed among these distances:
20 12 0.11
21 2 0.02
22 86 0.77
23 11 0.10
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTGT
Found at i:13349 original size:22 final size:22
Alignment explanation
Indices: 13296--13468 Score: 95
Period size: 22 Copynumber: 7.9 Consensus size: 22
13286 AAATTTCCTC
**
13296 CCTATGAAATTTTGATAAC-CA
1 CCTATGAAATTTTGATAACTTT
*
13317 CACTATAAAATTTTGATAACTTT
1 C-CTATGAAATTTTGATAACTTT
* * * *
13340 CGTATGAAATTTTGTTAACCTC
1 CCTATGAAATTTTGATAACTTT
*
13362 CCTAAGAAATTTTGATAACCTTT
1 CCTATGAAATTTTGATAA-CTTT
* * * *
13385 -TTATGAAATCTTGGTAAC-CT
1 CCTATGAAATTTTGATAACTTT
* *
13405 -CTATGTGAAATTTTGA-AAATTA
1 CCTA--TGAAATTTTGATAACTTT
* *
13427 CACTATGAAGTTTTGATAACCTT
1 C-CTATGAAATTTTGATAACTTT
* * *
13450 CATACGAAATTTTGGTAAC
1 CCTATGAAATTTTGATAAC
13469 AACACTATTA
Statistics
Matches: 111, Mismatches: 32, Indels: 17
0.69 0.20 0.11
Matches are distributed among these distances:
20 3 0.03
21 4 0.04
22 94 0.85
23 7 0.06
24 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACTTT
Found at i:13404 original size:44 final size:44
Alignment explanation
Indices: 13298--13448 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 44
13288 ATTTCCTCCC
*
13298 TATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTTCG
1 TATGAAATTTTGATAACCTCACTATAAAATTTTGATAACTTTCG
* * *
13342 TATGAAATTTTGTTAACCTCCCTA-AGAAATTTTGATAACCTTT-T
1 TATGAAATTTTGATAACCTCACTATA-AAATTTTGATAA-CTTTCG
* * * * * * *
13386 TATGAAATCTTGGTAACCTCTA-TGTGAAATTTTGA-AAATTACAC
1 TATGAAATTTTGATAACCTC-ACTATAAAATTTTGATAACTTTC-G
*
13430 TATGAAGTTTTGATAACCT
1 TATGAAATTTTGATAACCT
13449 TCATACGAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 77 0.90
45 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCACTATAAAATTTTGATAACTTTCG
Found at i:13474 original size:44 final size:44
Alignment explanation
Indices: 13426--13509 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
13416 TTTGAAAATT
* *
13426 ACACTATGAAGTTTTGATAACCTTCATACGAAATTTTGGTAACA
1 ACACTATGAAATTTAGATAACCTTCATACGAAATTTTGGTAACA
* * * * *
13470 ACACTATTAAATTTAGATAGCCTTCCTATGTAATTTTGGT
1 ACACTATGAAATTTAGATAACCTTCATACGAAATTTTGGT
13510 TTTATTGTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (44 bp):
ACACTATGAAATTTAGATAACCTTCATACGAAATTTTGGTAACA
Found at i:20362 original size:6 final size:6
Alignment explanation
Indices: 20351--20385 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
20341 AAAATGATGG
20351 ATATCT ATATCT ATATCT ATATCT ATATACT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATAT-CT ATAT
20386 AAGTCTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATCT
Found at i:21553 original size:36 final size:36
Alignment explanation
Indices: 21506--21575 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
21496 GAGATTTTGG
* *
21506 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
21542 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
21576 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:25150 original size:204 final size:203
Alignment explanation
Indices: 24696--25088 Score: 585
Period size: 201 Copynumber: 1.9 Consensus size: 203
24686 AAATCGGATC
* * **
24696 TTAATATCTTTTATAATTTTGAAATTTTTTTTGACATTGATCTAATTTAATTTAATAAATCAACC
1 TTAATATCTTTTATAATTATGAAATATAGTTTGACATT-ATCTAATTTAATTTAATAAATCAACC
*
24761 ACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTA
65 ACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATAATGTGTTGTATCTTA
* * *
24826 TACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAATATTCACCTTTGATAAATTA
130 TACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAACATTCAACATTGATAAATTA
* *
24891 ATCGGATCT
195 ATAGCATCT
* * *
24900 TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACC
1 TTAATATCTTTTATAATTATGAAATATAGTTTGACATT-ATCTAATTTAATTTAATAAATCAACC
*
24965 ACTAATGTTCAACT-CTTTTTTTTGGTATAGTT-T-TATATATAATAATAATGTGTTGTATCTTA
65 ACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATAATGTGTTGTATCTTA
* * * *
25027 TTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTTAACATTGATAAA
130 TACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAACATTCAACATTGATAAA
25089 GTTATTAAGC
Statistics
Matches: 179, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
201 83 0.46
202 1 0.01
203 17 0.09
204 78 0.44
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (203 bp):
TTAATATCTTTTATAATTATGAAATATAGTTTGACATTATCTAATTTAATTTAATAAATCAACCA
CTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATAATGTGTTGTATCTTAT
ACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAACATTCAACATTGATAAATTAA
TAGCATCT
Found at i:36956 original size:27 final size:27
Alignment explanation
Indices: 36881--36963 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
36871 ATACCATTAA
*
36881 TAATAATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
36908 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
36938 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
36964 CTAAATTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:38990 original size:2 final size:2
Alignment explanation
Indices: 38985--39014 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38975 TTCCCCATTA
38985 AT 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 AT
39015 TACCCACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.