Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024195.1 Corchorus olitorius cultivar O-4 contig24228, 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: 40280
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3959 original size:29 final size:29
Alignment explanation
Indices: 3907--3962 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
3897 AAGTTCGTGT
3907 TTGAAGACTTATTGAAGATAATTTAAAGA
1 TTGAAGACTTATTGAAGATAATTTAAAGA
*
3936 TTGAAGAC-TATTGAAGAATTATTTAAA
1 TTGAAGACTTATTGAAG-ATAATTTAAA
3963 AAGGCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (29 bp):
TTGAAGACTTATTGAAGATAATTTAAAGA
Found at i:12787 original size:81 final size:80
Alignment explanation
Indices: 12691--12882 Score: 221
Period size: 82 Copynumber: 2.4 Consensus size: 80
12681 GTAATTCAAG
* * * *
12691 GTGACAATTTATGGTGTCAACAGTAATTATAATTTA-C-TGGAGTA-ATACTTCTGGTGTCAA-A
1 GTGACAATTTCTGGTGTCAA-AGTAATT-TAATTTACCAAGGTG-ACA-ACTTCTAGTGTCAACA
* *
12752 GGTATTTTTAATTTACCAAA
62 -ATAATTTTAATTTACCAAA
12772 GTGACAATTTCTGGTGTCAAAAGTAACTTTAATTTACCAAGGTGACAACTTCTAGTGTCAACAAT
1 GTGACAATTTCTGGTGTC-AAAGTAA-TTTAATTTACCAAGGTGACAACTTCTAGTGTCAACAAT
12837 AATTTTAATTTACCAAA
64 AATTTTAATTTACCAAA
*
12854 GTGACAACTTCTGGTGTCAAAGGTAATTT
1 GTGACAATTTCTGGTGTCAAA-GTAATTT
12883 TCAATATTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
81 35 0.36
82 57 0.59
83 5 0.05
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (80 bp):
GTGACAATTTCTGGTGTCAAAGTAATTTAATTTACCAAGGTGACAACTTCTAGTGTCAACAATAA
TTTTAATTTACCAAA
Found at i:12790 original size:41 final size:41
Alignment explanation
Indices: 12737--12883 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
12727 CTGGAGTAAT
*
12737 ACTTCTGGTGTCAAAGGTATTTTTAATTTACCAAAGTGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
* * * *
12778 ATTTCTGGTGTCAAAAGTAACTTTAATTTACCAAGGTGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
* *
12819 ACTTCTAGTGTCAACA-ATAATTTTAATTTACCAAAGTGACA
1 ACTTCTGGTGTCAA-AGGTAATTTTAATTTACCAAAGTGACA
12860 ACTTCTGGTGTCAAAGGTAATTTT
1 ACTTCTGGTGTCAAAGGTAATTTT
12884 CAATATTATT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.01
41 90 0.98
42 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (41 bp):
ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
Found at i:12946 original size:15 final size:16
Alignment explanation
Indices: 12920--12949 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12910 AGATAACAAT
12920 ATAAACAACTTAAGAA
1 ATAAACAACTTAAGAA
12936 ATAAA-AACTTAAGA
1 ATAAACAACTTAAGA
12950 TTGGAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
ATAAACAACTTAAGAA
Found at i:17468 original size:16 final size:18
Alignment explanation
Indices: 17443--17482 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
17433 TAACTTGGAT
17443 TATA-TACTATAG-TACA
1 TATAGTACTATAGTTACA
17459 T-TAGTACTATAGTTACA
1 TATAGTACTATAGTTACA
17476 TATAGTA
1 TATAGTA
17483 ATTATAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 5 0.24
18 5 0.24
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
TATAGTACTATAGTTACA
Found at i:23372 original size:11 final size:11
Alignment explanation
Indices: 23348--23382 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
23338 TTGACAGCGC
23348 AACAAAAACAA
1 AACAAAAACAA
* *
23359 AACGAAAACGA
1 AACAAAAACAA
23370 AACAAAAACAA
1 AACAAAAACAA
23381 AA
1 AA
23383 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:26866 original size:35 final size:35
Alignment explanation
Indices: 26827--27081 Score: 291
Period size: 37 Copynumber: 7.1 Consensus size: 35
26817 TCATAAAGAA
26827 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
* * * *
26862 TCCCATTCAATTTTCAAAGTTTTTAAATTGGGAAAGT
1 TCCCA-CCAGTTTT-TAAGTTTTCAAATTGGGAAAGT
26899 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
* * *
26934 TCCCATTCAGTTTTCAAAGTTTTTAAATTGGGAAAGT
1 TCCCA-CCAGTTTT-TAAGTTTTCAAATTGGGAAAGT
*
26971 TCCCACCAGTTTTTTTCAAGTTTTCAAATTGTGAAAGT
1 TCCCACCAG--TTTTT-AAGTTTTCAAATTGGGAAAGT
* *
27009 TCTCATCCAGGTTTT-AGTTTTCAAATTGGGAAAGT
1 TCCCA-CCAGTTTTTAAGTTTTCAAATTGGGAAAGT
* * *
27044 TCCCATCAG-GTTT-AGTTTTCAATTTAGGGAAAGT
1 TCCCACCAGTTTTTAAGTTTTCAAATT-GGGAAAGT
27078 TCCC
1 TCCC
27082 GTCATTTTCA
Statistics
Matches: 189, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
33 14 0.07
34 15 0.08
35 53 0.28
36 22 0.12
37 54 0.29
38 27 0.14
39 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (35 bp):
TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
Found at i:26919 original size:72 final size:72
Alignment explanation
Indices: 26827--27081 Score: 358
Period size: 72 Copynumber: 3.5 Consensus size: 72
26817 TCATAAAGAA
*
26827 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAATTTTCAAAGTTTTTAAATTG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
26892 GGAAAGT
66 GGAAAGT
26899 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
26964 GGAAAGT
66 GGAAAGT
* * * *
26971 TCCCACCAGTTTTTTTCAAGTTTTCAAATTGTGAAAGTTCTCATCCAGGTTTT---AGTTTTCAA
1 TCCCACCAG--TTTTT-AAGTTTTCAAATTGGGAAAGTTCCCATTCA-GTTTTCAAAGTTTTTAA
27033 ATTGGGAAAGT
62 ATTGGGAAAGT
* * *
27044 TCCCATCAG-GTTT-AGTTTTCAATTTAGGGAAAGTTCCC
1 TCCCACCAGTTTTTAAGTTTTCAAATT-GGGAAAGTTCCC
27082 GTCATTTTCA
Statistics
Matches: 168, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
68 11 0.07
69 10 0.06
70 3 0.02
72 80 0.48
73 27 0.16
74 5 0.03
75 27 0.16
76 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (72 bp):
TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
GGAAAGT
Found at i:27033 original size:110 final size:106
Alignment explanation
Indices: 26827--27121 Score: 314
Period size: 110 Copynumber: 2.7 Consensus size: 106
26817 TCATAAAGAA
* * *
26827 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAATTTTCAAAGTTTTTAAATTG
1 TCCCATCAG-TTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAGTTTTCAAATTG
*
26892 GGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGT
65 GGAAAGTTCCCACCAGGTTTTAAGTTTTCAAATTGGGAAAGT
* *
26934 TCCCATTCAGTTTTCAAAGTTTTTAAATTGGGAAAGTTCCCA-CCAGTTTTTTTC-AAGTTTTCA
1 TCCCA-TCAGTTTT--AAGTTTTCAAATTGGGAAAGTTCCCATCCA---ATTTTCAAAGTTTTCA
* *
26997 AATTGTGAAAGTTCTCATCCAGGTTTT-AGTTTTCAAATTGGGAAAGT
60 AATTGGGAAAGTTCCCA-CCAGGTTTTAAGTTTTCAAATTGGGAAAGT
* * * *
27044 TCCCATCAGGTTT-AGTTTTCAATTTAGGGAAAGTTCCCGT-C-ATTTTCAGTTTTAGTTTTCAA
1 TCCCATCAGTTTTAAGTTTTCAAATT-GGGAAAGTTCCCATCCAATTTTCA----AAGTTTTCAA
*
27106 AGTGGGAAAGTTCCCA
61 ATTGGGAAAGTTCCCA
27122 TCAAAAGCAT
Statistics
Matches: 157, Mismatches: 17, Indels: 27
0.78 0.08 0.13
Matches are distributed among these distances:
103 5 0.03
106 10 0.06
107 22 0.14
108 27 0.17
109 32 0.20
110 48 0.31
111 13 0.08
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (106 bp):
TCCCATCAGTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAGTTTTCAAATTGG
GAAAGTTCCCACCAGGTTTTAAGTTTTCAAATTGGGAAAGT
Found at i:27096 original size:73 final size:70
Alignment explanation
Indices: 26827--27121 Score: 339
Period size: 72 Copynumber: 4.1 Consensus size: 70
26817 TCATAAAGAA
* *
26827 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCC-CATTCAATTTTCAAAGTTTTTAAATT
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCTCATTCAGTTTT---AGTTTTCAAATT
26891 GGGAAAGT
63 GGGAAAGT
*
26899 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCC-CATTCAGTTTTCAAAGTTTTTAAATT
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCTCATTCAGTTTT---AGTTTTCAAATT
26963 GGGAAAGT
63 GGGAAAGT
* *
26971 TCCCACCAGTTTTTTTCAAGTTTTCAAATTGTGAAAGTT-CTCATCCAGGTTTTAGTTTTCAAAT
1 TCCCACCAG--TTTTT-AAGTTTTCAAATTGGGAAAGTTCCTCATTCA-GTTTTAGTTTTCAAAT
27035 TGGGAAAGT
62 TGGGAAAGT
* * *
27044 TCCCATCAG-GTTT-AGTTTTCAATTTAGGGAAAGTTCCCGTCATTTTCAGTTTTAGTTTTCAAA
1 TCCCACCAGTTTTTAAGTTTTCAAATT-GGGAAAGTT-CC-TCA--TTCAGTTTTAGTTTTCAAA
*
27107 GTGGGAAAGT
61 TTGGGAAAGT
27117 TCCCA
1 TCCCA
27122 TCAAAAGCAT
Statistics
Matches: 202, Mismatches: 10, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
68 11 0.05
69 8 0.04
70 3 0.01
71 1 0.00
72 83 0.41
73 56 0.28
74 9 0.04
75 26 0.13
76 5 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (70 bp):
TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCTCATTCAGTTTTAGTTTTCAAATTGGG
AAAGT
Found at i:27120 original size:39 final size:34
Alignment explanation
Indices: 26828--27124 Score: 221
Period size: 35 Copynumber: 8.2 Consensus size: 34
26818 CATAAAGAAT
*
26828 CCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTT-
1 CCCATCAG-TTTT-AGTTTTCAAATTGGGAAAGTTC
* *
26863 CCCATTCAATTTTCAAAGTTTTTAAATTGGGAAAGTT-
1 CCCA-TCAGTTTT---AGTTTTCAAATTGGGAAAGTTC
*
26900 CCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTT-
1 CCCATCAG-TTTT-AGTTTTCAAATTGGGAAAGTTC
*
26935 CCCATTCAGTTTTCAAAGTTTTTAAATTGGGAAAGTT-
1 CCCA-TCAGTTTT---AGTTTTCAAATTGGGAAAGTTC
* *
26972 CCCACCAGTTTTTTTCAAGTTTTCAAATTGTGAAAGTT-
1 CCCATCAG---TTTT--AGTTTTCAAATTGGGAAAGTTC
*
27010 CTCATCCAGGTTTTAGTTTTCAAATTGGGAAAGTT-
1 CCCAT-CA-GTTTTAGTTTTCAAATTGGGAAAGTTC
* *
27045 CCCATCAGGTTTAGTTTTCAATTTAGGGAAAGTTC
1 CCCATCAGTTTTAGTTTTCAAATT-GGGAAAGTTC
*
27080 CCGTCATTTTCAGTTTTAGTTTTCAAAGTGGGAAAGTT-
1 CC--CA---TCAGTTTTAGTTTTCAAATTGGGAAAGTTC
27118 CCCATCA
1 CCCATCA
27125 AAAGCATTTT
Statistics
Matches: 222, Mismatches: 21, Indels: 40
0.78 0.07 0.14
Matches are distributed among these distances:
33 18 0.08
34 11 0.05
35 63 0.28
36 12 0.05
37 60 0.27
38 25 0.11
39 15 0.07
40 18 0.08
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (34 bp):
CCCATCAGTTTTAGTTTTCAAATTGGGAAAGTTC
Found at i:34120 original size:24 final size:24
Alignment explanation
Indices: 34087--34140 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
34077 AGTTGGTTTG
34087 AGTTCTGGTTATTCTGGTTCCAGGC
1 AGTT-TGGTTATTCTGGTTCCAGGC
34112 AGTTTGGTTATTCTGGTTCCAGGC
1 AGTTTGGTTATTCTGGTTCCAGGC
34136 AGTTT
1 AGTTT
34141 CAAATTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (24 bp):
AGTTTGGTTATTCTGGTTCCAGGC
Found at i:35686 original size:17 final size:17
Alignment explanation
Indices: 35666--35701 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35656 ACATCCCTAC
*
35666 ATCTATAACATCAATAT
1 ATCTATAACAACAATAT
*
35683 ATCTATAATAACAATAT
1 ATCTATAACAACAATAT
35700 AT
1 AT
35702 ATATCTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
ATCTATAACAACAATAT
Found at i:35701 original size:2 final size:2
Alignment explanation
Indices: 35696--35739 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
35686 TATAATAACA
* *
35696 AT AT AT AT AT CT AT A- ACT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
35738 AT
1 AT
35740 GGGTAATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.