Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013653.1 Corchorus olitorius cultivar O-4 contig13686, 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: 28690
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3417 original size:32 final size:32
Alignment explanation
Indices: 3282--3912 Score: 563
Period size: 32 Copynumber: 20.1 Consensus size: 32
3272 AAATTATCAT
* * *
3282 TTTTACTCTTTTCAACTTACTTACTGATTACCA
1 TTTTACTC-TTTGAATTTAATTACTGATTACCA
* * *
3315 -GTT--T-TTTGAATTGAATTACTGATTTCCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
** *
3343 TTTT-C-CTTATAGAACATAATTACTGATTATCA
1 TTTTACTCTT-T-GAATTTAATTACTGATTACCA
* * *
3375 --TTACTTTTTGAATTTACTTACTGATTTCCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
*
3405 TTTTACTCTTTGAATTTAATTACTGATTCCCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* *
3437 TTTTACTCTTCGAA---AATTATTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* * **
3466 --TTACTTTTTGAATTGAATTACTGATTTTCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* * *
3496 TTTTCCT-TATTGAATTTAATTATTGAGTACCA
1 TTTTACTCT-TTGAATTTAATTACTGATTACCA
* *
3528 TTTTACTCTTTGAATTTAATTACTGAATACTA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* * *
3560 TTTTACTTTTTGAACTTGAATTACTAATTACCA
1 TTTTACTCTTTGAA-TTTAATTACTGATTACCA
* * *
3593 -TTTACTTTTTGAATTGAATTACTGATTTCCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
**
3624 CCTTA----TTGAATTTAATTACTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
3652 TTTTACTCTTTGAATTTAATTACTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* *
3684 TTTTACTTTTTGAACTTGAATTACTGATTACCA
1 TTTTACTCTTTGAA-TTTAATTACTGATTACCA
* *
3717 TTTTACTCTCTGAA-TAAATTACTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* *
3748 TTTTACTCTTTGAATTGAATTACTGATTTCCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
*
3780 TTTTACTCTTAT-AATTTAATTACTAATTACCA
1 TTTTACTCTT-TGAATTTAATTACTGATTACCA
* *
3812 TTTTACTCATTGAATTTGATTACTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
* * *
3844 --TTACATTTTACTG-ATTTCCATTTTACTGATTATCA
1 TTTTAC-TCTT--TGAATTT--A-ATTACTGATTACCA
* *
3879 TTTTACTCTTTGAACTTGATTACTGATTACCA
1 TTTTACTCTTTGAATTTAATTACTGATTACCA
3911 TT
1 TT
3913 ACTTTTTACT
Statistics
Matches: 488, Mismatches: 75, Indels: 71
0.77 0.12 0.11
Matches are distributed among these distances:
27 10 0.02
28 43 0.09
29 15 0.03
30 37 0.08
31 52 0.11
32 260 0.53
33 47 0.10
34 2 0.00
35 15 0.03
36 3 0.01
37 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (32 bp):
TTTTACTCTTTGAATTTAATTACTGATTACCA
Found at i:3665 original size:156 final size:156
Alignment explanation
Indices: 3302--3912 Score: 584
Period size: 156 Copynumber: 3.9 Consensus size: 156
3292 TTCAACTTAC
** * * **
3302 TTACTGATTACCAGTTTTTTGAATTGAATTACTGATTTCCATTTT-C-CTTATAGAACATAATTA
1 TTACTGATTACCAACTTATTGAATTGAATTACTGATTACCATTTTACTCTT-T-GAATTTAATTA
* * * *
3365 CTGATTATCA--TTACTTTTTGAATTTACTTACTGATTTCCATTTTACTCTTTGAATTTAATTAC
64 CTGATTACCATTTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTAAATTAC
* *
3428 TGATTCCCATTTTACTCTTCGAA---AA
129 TGATTACCATTTTACTCTTTGAATTGAA
* * ** *
3453 TTATTGATTACCATTACTTTTTGAATTGAATTACTGATTTTCATTTTCCT-TATTGAATTTAATT
1 TTACTGATTACCA--ACTTATTGAATTGAATTACTGATTACCATTTTACTCT-TTGAATTTAATT
* * * * * * *
3517 ATTGAGTACCATTTTACTCTTTGAATTTAATTACTGAATACTATTTTACTTTTTGAACTTGAATT
63 ACTGATTACCATTTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAA-TTAAATT
* *
3582 ACTAATTACCA-TTTACTTTTTGAATTGAA
127 ACTGATTACCATTTTACTCTTTGAATTGAA
* * *
3611 TTACTGATTTCCACCTTATTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
1 TTACTGATTACCAACTTATTGAATTGAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
* *
3676 GATTACCATTTTACTTTTTGAACTTGAATTACTGATTACCATTTTACTCTCTGAA-TAAATTACT
66 GATTACCATTTTACTTTTTGAA-TTTAATTACTGATTACCATTTTACTCTTTGAATTAAATTACT
3740 GATTACCATTTTACTCTTTGAATTGAA
130 GATTACCATTTTACTCTTTGAATTGAA
* ** * * * * *
3767 TTACTGATTTCCATTTTACTCTTATAATTTAATTACTAATTACCATTTTACTCATTGAATTTGAT
1 TTACTGATTACCAACTTA---TT-GAATTGAATTACTGATTACCATTTTACTCTTTGAATTTAAT
* *
3832 TACTGATTACCA--TTACATTTTACTG-ATTTCCATTTTACTGATTATCATTTTACTCTTTGAAC
62 TACTGATTACCATTTTAC-TTTT--TGAATTT--A-ATTACTGATTACCATTTTACTCTTTGAA-
*
3894 TT-GATTACTGATTACCATT
120 TTAAATTACTGATTACCATT
3913 ACTTTTTACT
Statistics
Matches: 384, Mismatches: 50, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
151 12 0.03
153 45 0.12
154 3 0.01
155 65 0.17
156 111 0.29
157 28 0.07
158 17 0.04
159 8 0.02
160 50 0.13
161 3 0.01
162 25 0.07
163 16 0.04
164 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.49
Consensus pattern (156 bp):
TTACTGATTACCAACTTATTGAATTGAATTACTGATTACCATTTTACTCTTTGAATTTAATTACT
GATTACCATTTTACTTTTTGAATTTAATTACTGATTACCATTTTACTCTTTGAATTAAATTACTG
ATTACCATTTTACTCTTTGAATTGAA
Found at i:3867 original size:15 final size:15
Alignment explanation
Indices: 3843--3885 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
3833 ACTGATTACC
3843 ATTA-CATTTTACTG
1 ATTATCATTTTACTG
3857 ATT-TCCATTTTACTG
1 ATTAT-CATTTTACTG
3872 ATTATCATTTTACT
1 ATTATCATTTTACT
3886 CTTTGAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 22 0.85
16 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (15 bp):
ATTATCATTTTACTG
Found at i:7015 original size:16 final size:17
Alignment explanation
Indices: 6994--7025 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6984 GAAATTGCGT
6994 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
7010 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
7026 GCACTTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:28074 original size:19 final size:18
Alignment explanation
Indices: 28046--28083 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
28036 ATTCCCACCG
28046 AAAAAGAGAAAAAATGAAA
1 AAAAAGAGAAAAAA-GAAA
*
28065 AAAAATAGAAAAAAGAAA
1 AAAAAGAGAAAAAAGAAA
28083 A
1 A
28084 CAGAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAAAAAAGAAA
Found at i:28082 original size:26 final size:27
Alignment explanation
Indices: 28045--28101 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
28035 AATTCCCACC
*
28045 GAAAAAGAGAAAAAATGAAAAAA-AATA
1 GAAAAAGAGAAAAAA-GAAAAAAGAAGA
*
28072 GAAAAA-AGAAAACAGAAAAAAGAAGA
1 GAAAAAGAGAAAAAAGAAAAAAGAAGA
28098 GAAA
1 GAAA
28102 GGCACTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 7 0.26
26 14 0.52
27 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (27 bp):
GAAAAAGAGAAAAAAGAAAAAAGAAGA
Found at i:28088 original size:14 final size:14
Alignment explanation
Indices: 28062--28095 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28052 AGAAAAAATG
*
28062 AAAA-AAAATAGAA
1 AAAAGAAAACAGAA
28075 AAAAGAAAACAGAA
1 AAAAGAAAACAGAA
28089 AAAAGAA
1 AAAAGAA
28096 GAGAAAGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAGAAAACAGAA
Done.