Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022292.1 Corchorus olitorius cultivar O-4 contig22325, 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: 43738
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 10--48 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 TTACTTTAT
*
10 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49 GCATCCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15027 original size:10 final size:10
Alignment explanation
Indices: 15012--15043 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
15002 AAAGTTTTAG
15012 TTTTTCTTTT
1 TTTTTCTTTT
15022 TTTTTC--TT
1 TTTTTCTTTT
15030 TTTTTCTTTT
1 TTTTTCTTTT
15040 TTTT
1 TTTT
15044 ATTTCATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:17047 original size:25 final size:24
Alignment explanation
Indices: 17018--17074 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
17008 GTGGATTGTA
* *
17018 AAATAAATTGAATAGTTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
17043 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
17067 AAA-AAATT
1 AAATAAATT
17075 TCAAGGCTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:18283 original size:29 final size:31
Alignment explanation
Indices: 18250--18316 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
18240 ATGCAATTTG
* *
18250 GGATATTACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACATTACGAAAAGCAAGCAATTAA
* *
18279 TGATATAACATTACGAAAAGCGAGCAATTAA
1 GGATATAACATTACGAAAAGCAAGCAATTAA
18310 GGATATA
1 GGATATA
18317 GTCCGTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.35
30 4 0.13
31 16 0.52
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (31 bp):
GGATATAACATTACGAAAAGCAAGCAATTAA
Found at i:18470 original size:31 final size:31
Alignment explanation
Indices: 18435--18515 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
18425 CCCTAACTGA
* **
18435 TTATATTCTTAATTGCTTGAAATCGAAAACG
1 TTATATACTTAATTGCTTGAAATAAAAAACG
*
18466 TTATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATACTTAATTGCTTGAAATAAAAAACG
18497 TTATATACTTAATTGCTTG
1 TTATATACTTAATTGCTTG
18516 TTTTGTAACG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (31 bp):
TTATATACTTAATTGCTTGAAATAAAAAACG
Found at i:19656 original size:32 final size:31
Alignment explanation
Indices: 19554--19696 Score: 139
Period size: 31 Copynumber: 4.6 Consensus size: 31
19544 AGATGATAAG
* ***
19554 CAAGCAATTTAGGATATAACGTTTTCTG-CCG
1 CAAGCAATTAAGGATATAACGTTTTC-GATTT
* ***
19585 CAAGCAATTTAAGGATATAACG-TTAC-AAAA
1 CAAGCAA-TTAAGGATATAACGTTTTCGATTT
**
19615 CAAGCAATTAAGGATATAACGTTTTTTTATTT
1 CAAGCAATTAAGGATATAACG-TTTTCGATTT
*
19647 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
19678 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
19697 TCAGTTAGGG
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
29 14 0.15
30 7 0.08
31 38 0.41
32 34 0.37
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:19658 original size:61 final size:63
Alignment explanation
Indices: 19554--19696 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 63
19544 AGATGATAAG
* *
19554 CAAGCAATTTAGGATATAACGTTTTCTGCCGCAAGCAATTTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTTAAGGATATAACGTTTACGAAAA
* *** * * ***
19615 CAAGCAATTAAGGATATAACGTTTTTTTATTTCAAGCAA-TTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACG-TTTTCTACCGCAAGCAATTTAAGGATATAACGTTTACGAAAA
19678 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
19697 TCAGTTAGGG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
61 33 0.49
62 15 0.22
63 20 0.29
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (63 bp):
CAAGCAATTAAGGATATAACGTTTTCTACCGCAAGCAATTTAAGGATATAACGTTTACGAAAA
Found at i:19891 original size:29 final size:31
Alignment explanation
Indices: 19826--19892 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
19816 CTTAACGGAC
*
19826 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTACTCGCTTTTCGTAACGT
*
19857 TATATCCTTAATTACTTG-TTTT-GTAACGT
1 TATATCCTTAATTACTCGCTTTTCGTAACGT
19886 TATATCC
1 TATATCC
19893 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTACTCGCTTTTCGTAACGT
Found at i:27768 original size:31 final size:29
Alignment explanation
Indices: 27718--27779 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 29
27708 AAGATGTGTT
27718 AAGTTAATAAAAAATGGGGTAAATTGGAG
1 AAGTTAATAAAAAATGGGGTAAATTGGAG
27747 AAGTTAAT-AAAAATGGAGGGGTAAATTGGAG
1 AAGTTAATAAAAAAT---GGGGTAAATTGGAG
27778 AA
1 AA
27780 ATTAGATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 6 0.20
29 8 0.27
31 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (29 bp):
AAGTTAATAAAAAATGGGGTAAATTGGAG
Found at i:29029 original size:2 final size:2
Alignment explanation
Indices: 29022--29046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29012 TAACTTGTAA
29022 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 A
29047 AAGATATCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31501 original size:21 final size:21
Alignment explanation
Indices: 31477--31526 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
31467 TGTTAGGAGA
31477 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
31498 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
31519 TCATTGGA
1 TCATTGGA
31527 ATTGCCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:33148 original size:21 final size:21
Alignment explanation
Indices: 33122--33161 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33112 GTTGTCCGTC
*
33122 ACTCTCATAAGACTTAGGGTT
1 ACTCTCATAAGACTCAGGGTT
33143 ACTCTCATAAGACTCAGGG
1 ACTCTCATAAGACTCAGGG
33162 CACCAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
ACTCTCATAAGACTCAGGGTT
Found at i:34740 original size:25 final size:25
Alignment explanation
Indices: 34675--34743 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 25
34665 AAGATTACAC
*
34675 CTTGTAAAAACAAGGGTGATGTAAA
1 CTTGTAAAAACAAGGGTGATGCAAA
*
34700 ---GTAAATGACAAGGGTGAT-CACAA
1 CTTGTAAA-AACAAGGGTGATGCA-AA
34723 CTTGTAAAAACAAGGGTGATG
1 CTTGTAAAAACAAGGGTGATG
34744 AAAAGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
22 6 0.17
23 13 0.37
25 11 0.31
26 5 0.14
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (25 bp):
CTTGTAAAAACAAGGGTGATGCAAA
Found at i:35420 original size:37 final size:36
Alignment explanation
Indices: 35356--35426 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
35346 AATTTCGTCG
* * *
35356 GCACCACCCTAGCTTGGGGTGATCAAAATTTCCAACA
1 GCACCACCCTAACATGGGGTGACCAAAA-TTCCAACA
* *
35393 GCACCACCCTAACATGGTGTGGCCAAAATTCCAA
1 GCACCACCCTAACATGGGGTGACCAAAATTCCAA
35427 AACATGTCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 6 0.21
37 23 0.79
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (36 bp):
GCACCACCCTAACATGGGGTGACCAAAATTCCAACA
Found at i:36950 original size:21 final size:21
Alignment explanation
Indices: 36924--36965 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36914 GGGTTGTCTA
*
36924 TCACTCTCATAAGACTTAGGG
1 TCACTCTCATAAGACTCAGGG
36945 TCACTCTCATAAGACTCAGGG
1 TCACTCTCATAAGACTCAGGG
36966 CACCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
TCACTCTCATAAGACTCAGGG
Found at i:40496 original size:5 final size:5
Alignment explanation
Indices: 40488--40567 Score: 74
Period size: 5 Copynumber: 15.4 Consensus size: 5
40478 AAGTATATTA
* * *
40488 TATAT TATAT TATAT TATAAGT CATAC TGT-T T-TAT TAGTAT TATAT
1 TATAT TATAT TATAT TAT-A-T TATAT TATAT TATAT TA-TAT TATAT
40534 TATAT TATAT TATAT TATAT ATATAT ATATAT TA
1 TATAT TATAT TATAT TATAT -TATAT -TATAT TA
40568 GTGTTTATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
3 1 0.02
4 3 0.05
5 39 0.61
6 18 0.28
7 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:41019 original size:22 final size:22
Alignment explanation
Indices: 40973--41055 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
40963 AAATACTTGT
* * *
40973 TTATC-AAATTTAATAGTGAGA
1 TTATCAAAATTTTATAGTAAGG
40994 TTATCAAAATTTTATAAG-AAGG
1 TTATCAAAATTTTAT-AGTAAGG
* * *
41016 TTATCACATTTTTATAGTATGG
1 TTATCAAAATTTTATAGTAAGG
*
41038 TTATCAAAATTTCATAGT
1 TTATCAAAATTTTATAGT
41056 GTTCTTATCA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.14
22 41 0.82
23 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTAAGG
Found at i:41063 original size:22 final size:22
Alignment explanation
Indices: 41038--41161 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 22
41028 TATAGTATGG
*
41038 TTATCAAAATTTCATAGTGTTC
1 TTATCAAAATTTCATAGTGATC
* * * * **
41060 TTATCAATATTCCACAGGGAAG
1 TTATCAAAATTTCATAGTGATC
* *
41082 TTATCAAAATTTCTTAGT-TTAC
1 TTATCAAAATTTCATAGTGAT-C
** **
41104 TTATCAAAATTTCATAAAGAGA
1 TTATCAAAATTTCATAGTGATC
* **
41126 TTATCAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGATC
*
41148 TTATGAAAATTTCA
1 TTATCAAAATTTCA
41162 CATAAGAAAG
Statistics
Matches: 75, Mismatches: 25, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGATC
Found at i:41085 original size:44 final size:43
Alignment explanation
Indices: 41037--41142 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
41027 TTATAGTATG
* **
41037 GTTATCAAAATTTCATAGTGTT-CTTATCAATATTCCACAGGGAA
1 GTTATCAAAATTTCATAGT-TTACTTATCAAAATTCCACAAAG-A
* * *
41081 GTTATCAAAATTTCTTAGTTTACTTATCAAAATTTCATAAAGA
1 GTTATCAAAATTTCATAGTTTACTTATCAAAATTCCACAAAGA
41124 GATTATCAAAATTTCATAG
1 G-TTATCAAAATTTCATAG
41143 GGAGGTTATG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 4 0.08
44 49 0.92
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGTTTACTTATCAAAATTCCACAAAGA
Found at i:41201 original size:22 final size:22
Alignment explanation
Indices: 41105--41214 Score: 105
Period size: 22 Copynumber: 4.9 Consensus size: 22
41095 TTAGTTTACT
* *
41105 TATCAAAATTTCATAAAGAGAT
1 TATCAAAATTTCATAGAGAGAC
* **
41127 TATCAAAATTTCATAGGGAGGT
1 TATCAAAATTTCATAGAGAGAC
* *
41149 TATGAAAATTTCACATA-AGAAAGC
1 TATCAAAATTT--CATAGAGAGA-C
*
41173 TATCAAAATTTCATAGGGAGAC
1 TATCAAAATTTCATAGAGAGAC
*
41195 TACCAAAATTTCATAGAGAG
1 TATCAAAATTTCATAGAGAG
41215 GTTCTCGAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 52 0.73
23 5 0.07
24 14 0.20
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGAGAC
Done.