Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012170.1 Corchorus olitorius cultivar O-4 contig12203, 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: 44877
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1419 original size:20 final size:21
Alignment explanation
Indices: 1377--1419 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1367 TCCTTTGTTG
1377 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
1398 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
1418 AT
1 AT
1420 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:4500 original size:11 final size:11
Alignment explanation
Indices: 4484--4518 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
4474 GGAATATTCA
4484 GGCTCGAACTC
1 GGCTCGAACTC
4495 GGCTCGAACTC
1 GGCTCGAACTC
4506 GGCTCGAAGCTC
1 GGCTCGAA-CTC
4518 G
1 G
4519 ACCAAGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (11 bp):
GGCTCGAACTC
Found at i:6566 original size:31 final size:31
Alignment explanation
Indices: 6531--6689 Score: 192
Period size: 31 Copynumber: 5.1 Consensus size: 31
6521 TGTCCGACGC
* * * * *
6531 GGCATGCCATGTGTACCAAAAGGCGACATGT
1 GGCACGCCACGTGTACCAAAAAGTGACACGT
* * *
6562 GGCATGCCACGTGTACCAAAAAGCGACATGT
1 GGCACGCCACGTGTACCAAAAAGTGACACGT
* * *
6593 AGCACGCCACATGAACCAAAAAGTGACACGT
1 GGCACGCCACGTGTACCAAAAAGTGACACGT
*
6624 GGCACGCCACATGTACCAAAAAGTGACACGT
1 GGCACGCCACGTGTACCAAAAAGTGACACGT
* *
6655 GTCACGCCATGTGTACCAAAAAGTGACACGT
1 GGCACGCCACGTGTACCAAAAAGTGACACGT
6686 GGCA
1 GGCA
6690 TGTGTCGTGC
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 114 1.00
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (31 bp):
GGCACGCCACGTGTACCAAAAAGTGACACGT
Found at i:7783 original size:24 final size:27
Alignment explanation
Indices: 7729--7791 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 27
7719 GAAGATGAAT
7729 CCAAACCAACCTCCACCAGATCAACCA
1 CCAAACCAACCTCCACCAGATCAACCA
* *
7756 CCAAACCAACCT-C-CTA-ATCAACCC
1 CCAAACCAACCTCCACCAGATCAACCA
7780 CCAAACCAACCT
1 CCAAACCAACCT
7792 GTAATCCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 19 0.56
25 2 0.06
26 1 0.03
27 12 0.35
ACGTcount: A:0.40, C:0.49, G:0.02, T:0.10
Consensus pattern (27 bp):
CCAAACCAACCTCCACCAGATCAACCA
Found at i:10418 original size:19 final size:18
Alignment explanation
Indices: 10394--10429 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10384 TGAAGATTTA
10394 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10413 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10430 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:17258 original size:19 final size:18
Alignment explanation
Indices: 17234--17269 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17224 TGAAGATTTA
17234 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
17253 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
17270 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:20809 original size:30 final size:30
Alignment explanation
Indices: 20752--20810 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
20742 GATGCTCGTG
20752 TTTGAAGATTCATTGAAGATAATTTGAAGA
1 TTTGAAGATTCATTGAAGATAATTTGAAGA
* *
20782 TTTGGAGA-TCATTGAAGAATTATTTGAAG
1 TTTGAAGATTCATTGAAG-ATAATTTGAAG
20811 GAGCAAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.37
Consensus pattern (30 bp):
TTTGAAGATTCATTGAAGATAATTTGAAGA
Found at i:27467 original size:32 final size:32
Alignment explanation
Indices: 27429--27519 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
27419 CATGGCCAGG
27429 CCACAGCCCGGCCATGGCCTAGCCATGTCGCA
1 CCACAGCCCGGCCATGGCCTAGCCATGTCGCA
* *
27461 CCACAGCCCGGCCATGGCATAGCCATGTCTCA
1 CCACAGCCCGGCCATGGCCTAGCCATGTCGCA
*
27493 CCACAGCTCGGCCATGGCCTAGCCATG
1 CCACAGCCCGGCCATGGCCTAGCCATG
27520 CTGCGCAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (32 bp):
CCACAGCCCGGCCATGGCCTAGCCATGTCGCA
Found at i:27547 original size:20 final size:22
Alignment explanation
Indices: 27508--27547 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27498 GCTCGGCCAT
*
27508 GGCCTAGCCATGCTGCGCAATA
1 GGCCAAGCCATGCTGCGCAATA
27530 GGCCAAGCCA-GC-GCGCAA
1 GGCCAAGCCATGCTGCGCAA
27548 CATGCACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.25, C:0.35, G:0.30, T:0.10
Consensus pattern (22 bp):
GGCCAAGCCATGCTGCGCAATA
Found at i:35477 original size:34 final size:34
Alignment explanation
Indices: 35432--35500 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
35422 TGGAGGAGAC
*
35432 CAAGTCCGATTAGTCCTTCTTGTTGTCACCTCCT
1 CAAGTCCGATTAGTCCTTCTTGCTGTCACCTCCT
*
35466 CAAGTCTGATTAGTCCTTCTTGCTGTCACCTCCT
1 CAAGTCCGATTAGTCCTTCTTGCTGTCACCTCCT
35500 C
1 C
35501 CTCGCGCCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.14, C:0.33, G:0.14, T:0.38
Consensus pattern (34 bp):
CAAGTCCGATTAGTCCTTCTTGCTGTCACCTCCT
Found at i:35623 original size:25 final size:25
Alignment explanation
Indices: 35595--35644 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
35585 TTTTAAACTC
35595 ATTATTTA-TTAGTTAAAATATATTA
1 ATTATTTATTTA-TTAAAATATATTA
*
35620 ATTATTTATTTATTAATATATATTA
1 ATTATTTATTTATTAAAATATATTA
35645 TATCTAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTATTTATTTATTAAAATATATTA
Found at i:37513 original size:32 final size:32
Alignment explanation
Indices: 37446--37530 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
37436 TTGGGTAACT
* * *
37446 TCGGGTTTGGGCT-TTTTCGGGCTCGGGTTAAG
1 TCGGGTTCGGG-TATTTTCAGGCTCGGATTAAG
**
37478 TCGGGTTCGGGTATTTTCAGGCTCGGATTCTG
1 TCGGGTTCGGGTATTTTCAGGCTCGGATTAAG
37510 TCGGGTTCGGGTATTTTCAGG
1 TCGGGTTCGGGTATTTTCAGG
37531 TTCGATCGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.02
32 46 0.98
ACGTcount: A:0.08, C:0.16, G:0.38, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCAGGCTCGGATTAAG
Found at i:37532 original size:16 final size:16
Alignment explanation
Indices: 37481--37534 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
37471 GGTTAAGTCG
37481 GGTTCGGGTATTTTCA
1 GGTTCGGGTATTTTCA
* *
37497 GGCTC-GG-ATTCTGTCG
1 GGTTCGGGTATT-T-TCA
37513 GGTTCGGGTATTTTCA
1 GGTTCGGGTATTTTCA
37529 GGTTCG
1 GGTTCG
37535 ATCGGCTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 18 0.60
17 3 0.10
18 3 0.10
ACGTcount: A:0.09, C:0.17, G:0.35, T:0.39
Consensus pattern (16 bp):
GGTTCGGGTATTTTCA
Found at i:37719 original size:15 final size:14
Alignment explanation
Indices: 37702--37753 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
37692 TTTATTGATA
37702 ATATATAATATAAT
1 ATATATAATATAAT
*
37716 A-ATATAATATAAC
1 ATATATAATATAAT
37729 ATTATTATCAATATAAT
1 A-TA-TAT-AATATAAT
37746 ATATATAA
1 ATATATAA
37754 AGATTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 12 0.38
14 3 0.09
15 4 0.12
16 5 0.16
17 8 0.25
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATAATATAAT
Found at i:37722 original size:13 final size:12
Alignment explanation
Indices: 37699--37752 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
37689 AAGTTTATTG
37699 ATAATATATAAT
1 ATAATATATAAT
37711 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
37724 ATAACAT-TATT
1 ATAATATATAAT
*
37735 ATCA-ATATAAT
1 ATAATATATAAT
37746 AT-ATATA
1 ATAATATA
37753 AAGATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.09
11 14 0.40
12 7 0.20
13 11 0.31
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:38039 original size:31 final size:31
Alignment explanation
Indices: 38004--38075 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
37994 TAAATTATTG
*
38004 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
38035 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
38066 CAAATTAAAA
1 CAAATTAAAA
38076 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:44034 original size:72 final size:72
Alignment explanation
Indices: 43917--44057 Score: 282
Period size: 72 Copynumber: 2.0 Consensus size: 72
43907 ATATGGTGAA
43917 ATTTCTATACTTATAATTTGGTATTTATTTTTGATAGATAGCATGTTAAACTCTGTTTTATTCCA
1 ATTTCTATACTTATAATTTGGTATTTATTTTTGATAGATAGCATGTTAAACTCTGTTTTATTCCA
43982 TGACGAG
66 TGACGAG
43989 ATTTCTATACTTATAATTTGGTATTTATTTTTGATAGATAGCATGTTAAACTCTGTTTTATTCCA
1 ATTTCTATACTTATAATTTGGTATTTATTTTTGATAGATAGCATGTTAAACTCTGTTTTATTCCA
44054 TGAC
66 TGAC
44058 CTTGATTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (72 bp):
ATTTCTATACTTATAATTTGGTATTTATTTTTGATAGATAGCATGTTAAACTCTGTTTTATTCCA
TGACGAG
Done.