Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023273.1 Corchorus olitorius cultivar O-4 contig23306, 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: 27790
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4706 original size:31 final size:31
Alignment explanation
Indices: 4660--4721 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
4650 CCTCTATTAA
* * *
4660 CTCTTTCTTTCCCCAAATTCGCTAACCCTCT
1 CTCTCTCTTCCCCCAAATTCACTAACCCTCT
4691 CTCTCTCTTCCCCCAAATTCACTAACCCTCT
1 CTCTCTCTTCCCCCAAATTCACTAACCCTCT
4722 AAACCCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.18, C:0.45, G:0.02, T:0.35
Consensus pattern (31 bp):
CTCTCTCTTCCCCCAAATTCACTAACCCTCT
Found at i:7331 original size:15 final size:15
Alignment explanation
Indices: 7311--7341 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7301 CAATAGAAAA
7311 AAGCCAAATTGGATT
1 AAGCCAAATTGGATT
*
7326 AAGCCACATTGGATT
1 AAGCCAAATTGGATT
7341 A
1 A
7342 GACATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (15 bp):
AAGCCAAATTGGATT
Found at i:12365 original size:26 final size:25
Alignment explanation
Indices: 12336--12470 Score: 80
Period size: 26 Copynumber: 5.2 Consensus size: 25
12326 CTCTTTTTTT
12336 TTTTTAACTGATTTCATTTTCTACTC
1 TTTTT-ACTGATTTCATTTTCTACTC
* ** *
12362 TTTTTAACT-A-TTGATTACCCTTATTC
1 TTTTT-ACTGATTTCATT-TTC-TACTC
* * *
12388 TCTTTACTGATTACCATTTTTTACTC
1 TTTTTACTGATT-TCATTTTCTACTC
12414 TTTTTACT-ATTTATCATTTTCTTACTC
1 TTTTTACTGA-TT-TCATTTTC-TACTC
* *
12441 TTTTTACTGGTTTCCATTTTTTAC-C
1 TTTTTACTGATTT-CATTTTCTACTC
12466 TTTTT
1 TTTTT
12471 TACTTTAATT
Statistics
Matches: 84, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
24 5 0.06
25 12 0.14
26 42 0.50
27 22 0.26
28 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTTTACTGATTTCATTTTCTACTC
Found at i:12474 original size:26 final size:26
Alignment explanation
Indices: 12390--12470 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
12380 CCTTATTCTC
*
12390 TTTACTGATTACCATTTTTTACTCTT
1 TTTACTGATTTCCATTTTTTACTCTT
*
12416 TTTACT-ATTTATCATTTTCTTACTCTT
1 TTTACTGATTT-CCATTTT-TTACTCTT
*
12443 TTTACTGGTTTCCATTTTTTAC-CTT
1 TTTACTGATTTCCATTTTTTACTCTT
12468 TTT
1 TTT
12471 TACTTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 9 0.19
26 16 0.33
27 20 0.42
28 3 0.06
ACGTcount: A:0.16, C:0.19, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTACTGATTTCCATTTTTTACTCTT
Found at i:12506 original size:34 final size:34
Alignment explanation
Indices: 12458--12532 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
12448 TGGTTTCCAT
*
12458 TTTTTACCTTTTTTACTTTAATTACTGAATACCA
1 TTTTTACCTCTTTTACTTTAATTACTGAATACCA
*
12492 TTTTTACCTCTTTTACTTTAATTATTGAATACCA
1 TTTTTACCTCTTTTACTTTAATTACTGAATACCA
12526 TTTTTAC
1 TTTTTAC
12533 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTTTACCTCTTTTACTTTAATTACTGAATACCA
Found at i:12624 original size:8 final size:7
Alignment explanation
Indices: 12605--12815 Score: 91
Period size: 7 Copynumber: 29.7 Consensus size: 7
12595 ATTTTACTGA
12605 TTACTCT
1 TTACTCT
12612 TTACTCTT
1 TTACTC-T
**
12620 TTACTGA
1 TTACTCT
*
12627 TTACT-A
1 TTACTCT
12633 TTACTCT
1 TTACTCT
12640 TT-CT-T
1 TTACTCT
12645 GATTACTCT
1 --TTACTCT
12654 TTACTCT
1 TTACTCT
**
12661 TTACTGA
1 TTACTCT
*
12668 CTA-T-T
1 TTACTCT
12673 ATTACTCTT
1 -TTACTC-T
*
12682 TTACCCT
1 TTACTCT
12689 TTACTCT
1 TTACTCT
**
12696 TTACTGA
1 TTACTCT
*
12703 TTACT-A
1 TTACTCT
12709 TTACTCT
1 TTACTCT
*
12716 TT-CTCGA
1 TTACTC-T
12723 TTACTCT
1 TTACTCT
12730 TTACTCT
1 TTACTCT
12737 TTA--C-
1 TTACTCT
12741 TTACTACT
1 TTACT-CT
12749 ATTACTCTT
1 -TTACTC-T
**
12758 TTACTGA
1 TTACTCT
12765 TTACTCT
1 TTACTCT
12772 TTACTCTT
1 TTACTC-T
**
12780 TTACTAA
1 TTACTCT
*
12787 TTACCATTTT
1 TTA-C--TCT
12797 TTACTCT
1 TTACTCT
12804 TTACTCT
1 TTACTCT
12811 TTACT
1 TTACT
12816 GATTGCTATT
Statistics
Matches: 157, Mismatches: 24, Indels: 46
0.69 0.11 0.20
Matches are distributed among these distances:
4 3 0.02
5 2 0.01
6 20 0.13
7 90 0.57
8 29 0.18
9 9 0.06
10 4 0.03
ACGTcount: A:0.20, C:0.24, G:0.03, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:12637 original size:35 final size:35
Alignment explanation
Indices: 12601--12904 Score: 161
Period size: 42 Copynumber: 8.0 Consensus size: 35
12591 TACCATTTTA
12601 CTGATTACTCTTTACTCTTTTACTGATTACTATTACTCTTT
1 CTGATTACTCTTTACTC-TTTACTGATTACTATTA-----T
* *
12642 CTTGATTACTCTTTACTCTTTACTGACTATTATTACT
1 C-TGATTACTCTTTACTCTTTACTGATTACTATTA-T
* *
12679 CT-TTTACCCTTTACTCTTTACTGATTACTATTACTCTTT
1 CTGATTACTCTTTACTCTTTACTGATTACTATTA-----T
* *
12718 CTCGATTACTCTTTACTCTTTACTTACTACTATTACTCTTTT
1 CT-GATTACTCTTTACTCTTTACTGATTACTATTA------T
* *
12760 ACTGATTACTCTTTACTCTTTTACTAATTACCATT-T
1 -CTGATTACTCTTTACTC-TTTACTGATTACTATTAT
*
12796 -T--TTACTCTTTACTCTTTACTGATTGCTATTACTTTTTT
1 CTGATTACTCTTTACTCTTTACTGATTACTATTA------T
* *
12834 ACTGATTATTCTTTACTCTTTTACTGATTACTATTAC
1 -CTGATTACTCTTTACTC-TTTACTGATTACTATTAT
* **
12871 CAT-TTTACTGATTACTCTTTACTGATTACTATTA
1 C-TGATTACTCTTTACTCTTTACTGATTACTATTA
12905 ACATTTTACT
Statistics
Matches: 212, Mismatches: 28, Indels: 52
0.73 0.10 0.18
Matches are distributed among these distances:
31 13 0.06
32 13 0.06
34 1 0.00
35 44 0.21
36 13 0.06
37 3 0.01
38 1 0.00
39 3 0.01
40 1 0.00
41 43 0.20
42 46 0.22
43 31 0.15
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (35 bp):
CTGATTACTCTTTACTCTTTACTGATTACTATTAT
Found at i:12638 original size:21 final size:21
Alignment explanation
Indices: 12577--12685 Score: 109
Period size: 21 Copynumber: 5.2 Consensus size: 21
12567 TGAATTTTAA
*
12577 TTACTGATTACCATTAC-CATT
1 TTACTGATTACTATTACTC-TT
*
12598 TTACTGATTACTCTTTACTCTT
1 TTACTGATTACT-ATTACTCTT
12620 TTACTGATTACTATTACTC-T
1 TTACTGATTACTATTACTCTT
*
12640 TT-CTTGATTACTCTTTACTC-T
1 TTAC-TGATTACT-ATTACTCTT
* *
12661 TTACTGACTATTATTACTCTT
1 TTACTGATTACTATTACTCTT
12682 TTAC
1 TTAC
12686 CCTTTACTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.01
20 17 0.23
21 37 0.49
22 19 0.25
23 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (21 bp):
TTACTGATTACTATTACTCTT
Found at i:12705 original size:76 final size:76
Alignment explanation
Indices: 12605--12893 Score: 302
Period size: 76 Copynumber: 3.7 Consensus size: 76
12595 ATTTTACTGA
12605 TTACTCTTTACTCTTTTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCTTTACTGACT
1 TTACTCTTTACTC-TTTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCTTTACTGACT
*
12670 ATTATTACTCTT
65 ACTATTACTCTT
* * *
12682 TTACCCTTTACTCTTTACTGATTACTATTACTCTTTCTCGATTACTCTTTACTCTTTACTTACTA
1 TTACTCTTTACTCTTTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCTTTACTGACTA
12747 CTATTACTCTT
66 CTATTACTCTT
** ** * *
12758 TTACTGATTACTCTTTACTCTTTTACTAATTAC-CATT-TT--TTACTCTTTACTCTTTACTGAT
1 TTACTCTTTACTCTTTACT-GATTACT-ATTACTCTTTCTTGATTACTCTTTACTCTTTACTGAC
* *
12819 TGCTATTACTTTT
64 TACTATTACTCTT
12832 TTACTGATTATTCTTTACTCTTTTACTGATTACTATTAC-CATTT-TACTGATTACTCTTTACT
1 TTAC-------TCTTTACTC-TTTACTGATTACTATTACTC-TTTCT--TGATTACTCTTTACT
12894 GATTACTATT
Statistics
Matches: 177, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
74 35 0.20
76 77 0.44
77 20 0.11
78 5 0.03
80 6 0.03
81 15 0.08
82 6 0.03
83 1 0.01
85 12 0.07
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (76 bp):
TTACTCTTTACTCTTTACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCTTTACTGACTA
CTATTACTCTT
Found at i:12899 original size:21 final size:21
Alignment explanation
Indices: 12598--12921 Score: 123
Period size: 21 Copynumber: 15.2 Consensus size: 21
12588 CATTACCATT
**
12598 TTACTGATTACTCTTTACTCTT
1 TTACTGATTACTCTTTACT-GA
* *
12620 TTACTGATTACT-ATTACT-C
1 TTACTGATTACTCTTTACTGA
* **
12639 TTTCTTGATTACTCTTTACTCT
1 TTAC-TGATTACTCTTTACTGA
* **
12661 TTACTGACTA-T-TATTACTCTT
1 TTACTGATTACTCT-TTACT-GA
***
12682 TTACCCTTTACTCTTTACTGA
1 TTACTGATTACTCTTTACTGA
12703 TTACT-ATTACTCTTT-CTCGA
1 TTACTGATTACTCTTTACT-GA
** *
12723 TTACTCTTTACTCTTTACTTA
1 TTACTGATTACTCTTTACTGA
*
12744 CTACT-ATTACTCTTTTACTGA
1 TTACTGATTACTC-TTTACTGA
** *
12765 TTACTCTTTACTCTTTTACTAA
1 TTACTGATTACTC-TTTACTGA
** **
12787 TTACCATTTTTTACTCTTTACTCT
1 TTA-C--TGATTACTCTTTACTGA
* * **
12811 TTACTGATTGCT-ATTACTTTT
1 TTACTGATTACTCTTTAC-TGA
* **
12832 TTACTGATTATTCTTTACTCTT
1 TTACTGATTACTCTTTACT-GA
* *
12854 TTACTGATTACT-ATTACCAT-T
1 TTACTGATTACTCTTTA-C-TGA
12875 TTACTGATTACTCTTTACTGA
1 TTACTGATTACTCTTTACTGA
12896 TTACT-ATTAACAT-TTTACTGA
1 TTACTGATT-AC-TCTTTACTGA
12917 TTACT
1 TTACT
12922 TTTTACTTCT
Statistics
Matches: 239, Mismatches: 39, Indels: 49
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.03
20 44 0.18
21 106 0.44
22 62 0.26
23 4 0.02
24 9 0.04
25 8 0.03
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACTGATTACTCTTTACTGA
Found at i:12910 original size:35 final size:35
Alignment explanation
Indices: 12846--12928 Score: 139
Period size: 35 Copynumber: 2.3 Consensus size: 35
12836 TGATTATTCT
*
12846 TTACTCTTTTACTGATTACTATTACCATTTTACTGA
1 TTACTC-TTTACTGATTACTATTAACATTTTACTGA
12882 TTACTCTTTACTGATTACTATTAACATTTTACTGA
1 TTACTCTTTACTGATTACTATTAACATTTTACTGA
*
12917 TTACTTTTTACT
1 TTACTCTTTACT
12929 TCTTTGAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 39 0.87
36 6 0.13
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (35 bp):
TTACTCTTTACTGATTACTATTAACATTTTACTGA
Found at i:12912 original size:78 final size:81
Alignment explanation
Indices: 12577--12933 Score: 256
Period size: 78 Copynumber: 4.6 Consensus size: 81
12567 TGAATTTTAA
* * *
12577 TTACTGATTACCATTACCATTTTACTGATTACTCTTTAC-TCTTTTACTGATTACT-ATTA-C-T
1 TTACTGATTACTATTACTATTTTACTGATTACTTTTTACTTCTTTTACTGATTACTAATTACCAT
* *
12638 CTTT-CTTGATTACTCT
66 TTTTAC-TCATTACTCT
** * ** **
12654 TTACTCTTTAC--TGACTATTATTACTCTTTTACCCTTTAC-TC-TTTACTGATTACT-ATTACT
1 TTACTGATTACTATTACTATT-TTACT-GATTACTTTTTACTTCTTTTACTGATTACTAATTAC-
* *
12714 CTTTCTCGATTACTCTTTACTCT
63 CATT-T---TTACTCATTACTCT
* * * *
12737 TTACTTACTACTATTACTCTTTTACTGATTACTCTTTAC-TC---T--T--TTACTAATTACCAT
1 TTACTGATTACTATTACTATTTTACTGATTACTTTTTACTTCTTTTACTGATTACTAATTACCA-
*
12794 TTTTTACTCTTTACTCT
65 TTTTTACTCATTACTCT
* *
12811 TTACTGATTGCTATTACTTTTTTACTGATTA-TTCTTTAC-TCTTTTACTGATTACT-ATTACCA
1 TTACTGATTACTATTACTATTTTACTGATTACTT-TTTACTTCTTTTACTGATTACTAATTACCA
*
12873 -TTTTACTGATTACTCT
65 TTTTTACTCATTACTCT
12889 TTACTGATTACTATTAAC-ATTTTACTGATTACTTTTTACTTCTTT
1 TTACTGATTACTATT-ACTATTTTACTGATTACTTTTTACTTCTTT
12934 GAATTTTAAT
Statistics
Matches: 227, Mismatches: 28, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
73 1 0.00
74 48 0.21
75 6 0.03
76 22 0.10
77 29 0.13
78 53 0.23
79 12 0.05
80 8 0.04
81 6 0.03
83 30 0.13
84 6 0.03
85 6 0.03
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (81 bp):
TTACTGATTACTATTACTATTTTACTGATTACTTTTTACTTCTTTTACTGATTACTAATTACCAT
TTTTACTCATTACTCT
Found at i:13005 original size:14 final size:15
Alignment explanation
Indices: 12986--13015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12976 ACTCTTTTAT
12986 TCTTTAC-TAATTAC
1 TCTTTACTTAATTAC
13000 TCTTTACTTAATTAC
1 TCTTTACTTAATTAC
13015 T
1 T
13016 ACTTATCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTTACTTAATTAC
Found at i:13014 original size:22 final size:22
Alignment explanation
Indices: 12967--13016 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12957 CATTACCATT
* **
12967 TTACTGATTACTCTTTTATTCT
1 TTACTAATTACTCTTTTATTAA
12989 TTACTAATTACTC-TTTACTTAA
1 TTACTAATTACTCTTTTA-TTAA
13011 TTACTA
1 TTACTA
13017 CTTATCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.26, C:0.18, G:0.02, T:0.54
Consensus pattern (22 bp):
TTACTAATTACTCTTTTATTAA
Found at i:22166 original size:43 final size:43
Alignment explanation
Indices: 22105--22190 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
22095 CTAAAGCTGG
22105 GCCAAACCAACTTCTCATTATCGTGAGGCAAGAAAGTTGCAAA
1 GCCAAACCAACTTCTCATTATCGTGAGGCAAGAAAGTTGCAAA
22148 GCCAAACCAACTTCTCATTATCGTGAGGCAAGAAAGTTGCAAA
1 GCCAAACCAACTTCTCATTATCGTGAGGCAAGAAAGTTGCAAA
22191 CCTATCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (43 bp):
GCCAAACCAACTTCTCATTATCGTGAGGCAAGAAAGTTGCAAA
Found at i:27110 original size:31 final size:30
Alignment explanation
Indices: 27045--27110 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
27035 GGCGAAAATG
* * * *
27045 CAATTCAAGATATACCGTTATCATTTGTGT
1 CAATTCAAGATATAACGTTACCAATTCTGT
*
27075 CAATTCAGGATATAACGTTACCAAATTCTGT
1 CAATTCAAGATATAACGTTACC-AATTCTGT
27106 CAATT
1 CAATT
27111 TAGGCAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (30 bp):
CAATTCAAGATATAACGTTACCAATTCTGT
Done.