Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018510.1 Corchorus olitorius cultivar O-4 contig18543, 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: 33667
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2221 original size:220 final size:220
Alignment explanation
Indices: 1828--2227 Score: 615
Period size: 220 Copynumber: 1.8 Consensus size: 220
1818 TTTTAGTTAT
1828 CAGGGAAATTACTAAAAGGCCAAATTGAGGATAAATGTGGTGCCACCTTTTGGCTTTTTTTGGTC
1 CAGGGAAATTACTAAAAGGCCAAATTGAGGATAAATGTGGTGCCACCTTTTGGCTTTTTTTGGTC
* *** *
1893 TTTTCTCATTTTTGGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCTCTTCCTTCTCCTGCTAC
66 TTTTCTCACTTTTCAAATCACTAAAAAGCCCCTCTATGAGTTTCCCCTCTTCCTTCTCCTGCTAC
***
1958 CCTTTTTGTAATTATTTATTTCACTTCCTTAATTGCTTTTAATTAATGTTCCCCCCCCCCTTTCT
131 CCTTTTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGTTCCCCCCCCCCTTTCT
2023 TTTTTCCTCTCACCAATTCAGTACC
196 TTTTTCCTCTCACCAATTCAGTACC
* * * ** *
2048 CAGGGTAATTGCTAAAAGGCCAAATTGAGGATTAATGTGGTGCCATTTTTTGGCTTTTTTTTTGT
1 CAGGGAAATTACTAAAAGGCCAAATTGAGGATAAATGTGGTGCCACCTTTTGGC-TTTTTTTGGT
*
2113 CTTTTCTCACTTTTCAAATCACT-AAAAGCCCCTCTATGAGTTTCCCC-CTTCCTTTTCCTGCTA
65 CTTTTCTCACTTTTCAAATCACTAAAAAGCCCCTCTATGAGTTTCCCCTCTTCCTTCTCCTGCTA
* *
2176 CCCTTTTTTGTAATTACCCATTTCCCTTCCTTAATTGTTTTTAATTAATGTT
130 CCC-TTTTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGTT
2228 TACGGCTTTT
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
219 18 0.11
220 116 0.72
221 27 0.17
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (220 bp):
CAGGGAAATTACTAAAAGGCCAAATTGAGGATAAATGTGGTGCCACCTTTTGGCTTTTTTTGGTC
TTTTCTCACTTTTCAAATCACTAAAAAGCCCCTCTATGAGTTTCCCCTCTTCCTTCTCCTGCTAC
CCTTTTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGTTCCCCCCCCCCTTTCT
TTTTTCCTCTCACCAATTCAGTACC
Found at i:3310 original size:7 final size:7
Alignment explanation
Indices: 3298--3324 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3288 TATTTTTTTA
3298 CAGTAGC
1 CAGTAGC
3305 CAGTAGC
1 CAGTAGC
3312 CAGTAGC
1 CAGTAGC
3319 CAGTAG
1 CAGTAG
3325 GTGCCACTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (7 bp):
CAGTAGC
Found at i:7285 original size:15 final size:15
Alignment explanation
Indices: 7267--7299 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
7257 AACAGAGGTG
7267 AGAGGAACA-AGAAGA
1 AGAGG-ACAGAGAAGA
7282 AGAGGACAGAGAAGA
1 AGAGGACAGAGAAGA
7297 AGA
1 AGA
7300 AGAAGATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.58, C:0.06, G:0.36, T:0.00
Consensus pattern (15 bp):
AGAGGACAGAGAAGA
Found at i:9534 original size:73 final size:75
Alignment explanation
Indices: 9421--9574 Score: 231
Period size: 75 Copynumber: 2.1 Consensus size: 75
9411 TTTTTATAAT
*
9421 TAAAATAGTAAAATGGTAAAATAAAATAATTATAAGGATATTAGATT-TAAATAAAAATAGAGTT
1 TAAAATAGTAAAATGGTAAAATAAAATAATTATAAAGATATTAGATTATAAATAAAAATAGAGTT
*
9485 TTTAGTTGAG
66 TTTACTTGAG
* * *
9495 TAAAATAGTAAAATGGT-GAATAAAATAGTTATAAAGATATTTGATTAGTAAATAAAAATAGAGT
1 TAAAATAGTAAAATGGTAAAATAAAATAATTATAAAGATATTAGATTA-TAAATAAAAATAGAGT
*
9559 TTTTACTTTAG
65 TTTTACTTGAG
9570 TAAAA
1 TAAAA
9575 CTATAAATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 25 0.35
74 17 0.24
75 30 0.42
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (75 bp):
TAAAATAGTAAAATGGTAAAATAAAATAATTATAAAGATATTAGATTATAAATAAAAATAGAGTT
TTTACTTGAG
Found at i:11978 original size:7 final size:7
Alignment explanation
Indices: 11966--11990 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11956 TTAAATAGGG
11966 TTTTCCT
1 TTTTCCT
11973 TTTTCCT
1 TTTTCCT
11980 TTTTCCT
1 TTTTCCT
11987 TTTT
1 TTTT
11991 TTAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCCT
Found at i:12013 original size:2 final size:2
Alignment explanation
Indices: 12003--12036 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11993 AAATATATGT
12003 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12037 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19011 original size:55 final size:55
Alignment explanation
Indices: 18848--19601 Score: 931
Period size: 55 Copynumber: 13.6 Consensus size: 55
18838 TATTATTACT
* * *
18848 TTTTACTTTTTAGTTTAATTACTCAGAACTAAACTAA-TTACTGC-TTAC-TCTTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGCTTTACTTC-TTC
* * * *
18902 TTTTACTCTTTAGCTTAATTA-CCAAAATTAAAGTAA-TTAATG-TTTAC-TCTTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGCTTTACTTC-TTC
* *
18955 TTTTACTCTTTTAGTTTAATTACCAAGAATTAAACT-AGTTACTG-TTTACTTCTTC
1 TTTTACTC-TTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGCTTTACTTCTTC
* * * *
19010 TTTTACTCATTAGTTTAATTACCCATAATTAAACTAA-TTACTG-TTTGCTCCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGCTTTACTTCTTC
* *
19064 TTTTACTATTTAGTTTAATTACCCGGAATTAAACTAACTTCTGCTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
19119 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TTACTG-TTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGCTTTACTTCTTC
* * * * *
19173 TCTTACTATTTAGTTTAATTGCCCCGAATTAAAACTAACTTCTGTTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATT-AAACTAACTTCTGCTTTACTTCTTC
* * * * *
19229 TTTTACTCTTTTTTTAGTTCAATTGCCCGGAATTAAACTAACTTCTGCTTTAATTCTTG
1 TTTTACTC----TTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
* * *
19288 TTTTACTCTTTTTTTTTAGTTCAATTGCCTAGAATTAAACTAACTTCTGCTTTACTTCTTC
1 TTTTACTC------TTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
** *
19349 TTTTACTCTTTTTTTTAGTTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
*
19404 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTTTGCTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
19459 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
* *
19514 TTTTACTCTTTAGTTTAATTACCCAGAAGTAAACTAATTTCTGCTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
*
19569 TTTTACTCTTTAGTTTAATTACCTAGAATTAAA
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAA
19602 TCTTTTACTC
Statistics
Matches: 627, Mismatches: 55, Indels: 35
0.87 0.08 0.05
Matches are distributed among these distances:
53 34 0.05
54 146 0.23
55 321 0.51
56 21 0.03
59 30 0.05
60 20 0.03
61 55 0.09
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (55 bp):
TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGCTTTACTTCTTC
Found at i:19550 original size:340 final size:338
Alignment explanation
Indices: 18963--19579 Score: 963
Period size: 340 Copynumber: 1.8 Consensus size: 338
18953 TCTTTTACTC
* *
18963 TTTTAGTTTAATTACCAAGAATTAAACTAGTTACTGTTTACTTCTTCTTTTACTCATTAGTTTAA
1 TTTTAGTTCAATTACCAAGAATTAAACTACTTACTGTTTACTTCTTCTTTTACTCATTAGTTTAA
* * *
19028 TTACCCATAATTAAACTAATTACTGTTTGCTCCTTCTTTTACTATTTAGTTTAATTACCCGGAAT
66 TTACCCAGAATTAAACTAATTACTGTTTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAAT
19093 TAAACTAACTTCTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATT
131 TAAACTAACTTCTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATT
* * * *
19158 ACTGTTTACTTCTTCTCTTACTATTTAGTTTAATTGCCCCGAATTAAAACTAACTTCTGTTTTAC
196 ACTGTTTACTTCTTCTCTTACTATTTAGTTTAATTACCCAGAAGTAAAACTAACTTCTGCTTTAC
19223 TTCTTCTTTTACTCTTTTTTTAGTTCAATTGCCCGGAATTAAACTAACTTCTGCTTTAATTCTTG
261 TTCTTCTTTTACTCTTTTTTTAGTTCAATTGCCCGGAATTAAACTAACTTCTGCTTTAATTCTTG
19288 TTTTACTCTTTTT
326 TTTTACTCTTTTT
* * * **
19301 TTTTAGTTCAATTGCCTAGAATTAAACTAACTT-CTGCTTTACTTCTTCTTTTACTCTTTTTTTT
1 TTTTAGTTCAATTACCAAGAATTAAACT-ACTTACTG-TTTACTTCTTCTTTTACTCATTAGTTT
* * *
19365 AGTTACCCAGAATTAAACTAACTT-CTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCA
64 AATTACCCAGAATTAAACTAA-TTACTG-TTTACTCCTTCTTTTACTATTTAGTTTAATTACCCA
*
19429 GAATTAAACTAACTTTTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACT
127 GAATTAAACTAACTTCTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACT
* * *
19494 AACTT-CTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAAGT-AAACTAATTTCTG
192 AA-TTACTG-TTTACTTCTTCTCTTACTATTTAGTTTAATTACCCAGAAGTAAAACTAACTTCTG
19557 CTTTACTTCTTCTTTTACTCTTT
255 CTTTACTTCTTCTTTTACTCTTT
19580 AGTTTAATTA
Statistics
Matches: 252, Mismatches: 21, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
338 28 0.11
339 49 0.19
340 137 0.54
341 38 0.15
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.49
Consensus pattern (338 bp):
TTTTAGTTCAATTACCAAGAATTAAACTACTTACTGTTTACTTCTTCTTTTACTCATTAGTTTAA
TTACCCAGAATTAAACTAATTACTGTTTACTCCTTCTTTTACTATTTAGTTTAATTACCCAGAAT
TAAACTAACTTCTGCTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATT
ACTGTTTACTTCTTCTCTTACTATTTAGTTTAATTACCCAGAAGTAAAACTAACTTCTGCTTTAC
TTCTTCTTTTACTCTTTTTTTAGTTCAATTGCCCGGAATTAAACTAACTTCTGCTTTAATTCTTG
TTTTACTCTTTTT
Found at i:19672 original size:22 final size:22
Alignment explanation
Indices: 19627--19696 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
19617 TTTAATTACT
* * **
19627 CTTCTAATTACTCTTTATTTTA
1 CTTCTGATTACTCTTTCTCCTA
19649 CTTCTGATTACTCTTTCTCCTA
1 CTTCTGATTACTCTTTCTCCTA
*
19671 CTTTTGATTACT-TTTCCTCC-A
1 CTTCTGATTACTCTTT-CTCCTA
19692 CTTCT
1 CTTCT
19697 TAGCTTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.20
22 33 0.80
ACGTcount: A:0.16, C:0.27, G:0.03, T:0.54
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTCCTA
Found at i:29059 original size:50 final size:50
Alignment explanation
Indices: 28991--29086 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
28981 GCGGGATTGG
* *
28991 CGCAGGATTTCGGCGTTATTTACCCTGGGATTGATCGAATAATTGGATGT
1 CGCAGGATTTCAGAGTTATTTACCCTGGGATTGATCGAATAATTGGATGT
* *
29041 CGCAGGATTTCAGAGTTATTTACCCTGGGTTTGATGGAATAATTGG
1 CGCAGGATTTCAGAGTTATTTACCCTGGGATTGATCGAATAATTGG
29087 CTTGTAATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (50 bp):
CGCAGGATTTCAGAGTTATTTACCCTGGGATTGATCGAATAATTGGATGT
Done.