Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010935.1 Corchorus olitorius cultivar O-4 contig10967, 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: 18828
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:218 original size:18 final size:18
Alignment explanation
Indices: 183--219 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
173 TAATTAAAAT
*
183 TTAAAATTTCCAACTTAA
1 TTAAAATTTCCAAATTAA
*
201 TTAAAATTTCTAAATTAA
1 TTAAAATTTCCAAATTAA
219 T
1 T
220 ATAGAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATTTCCAAATTAA
Found at i:1666 original size:5 final size:5
Alignment explanation
Indices: 1656--1685 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1646 TAAAGAAGGA
1656 AAAAG AAAAG AAAA- AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1686 CCTCTACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1674 original size:14 final size:14
Alignment explanation
Indices: 1655--1683 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1645 ATAAAGAAGG
1655 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
1669 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
1683 A
1 A
1684 GACCTCTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:5575 original size:30 final size:32
Alignment explanation
Indices: 5541--5604 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
5531 CTTTTCCTTC
*
5541 TCTTCTCTTTCTGT-C-CTTTTATTTACTTTT
1 TCTTCTCTTTCGGTACACTTTTATTTACTTTT
* *
5571 TCTTCTTTTTCGGTACATCTTTTATTTATTTTT
1 TCTTCTCTTTCGGTACA-CTTTTATTTACTTTT
5604 T
1 T
5605 AAATCATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.43
31 1 0.04
33 15 0.54
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (32 bp):
TCTTCTCTTTCGGTACACTTTTATTTACTTTT
Found at i:7871 original size:42 final size:43
Alignment explanation
Indices: 7820--7913 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
7810 AGTGCATTAC
* *
7820 CTAA-ATTCTA-CTCAATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCAATCTCTAGATAATTCATCAAAATAAAA
* **
7861 CTCATATTCTACTCCTCCGTCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCAATCTCTAGATAATTCATCAAAATAAAA
7906 CTAATATT
1 CTAATATT
7914 AATTGTCGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.14
45 34 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCAATCTCTAGATAATTCATCAAAATAAAA
Found at i:10168 original size:22 final size:22
Alignment explanation
Indices: 10137--10189 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
10127 TTTACCCTTC
* *
10137 TTCTCTCTCCCCCCACTAACTCT
1 TTCTC-CTCCCCCCACCAACTAT
*
10160 TTCTCCTCCCCCCACCCACTAT
1 TTCTCCTCCCCCCACCAACTAT
10182 TTCTCCTC
1 TTCTCCTC
10190 ATAAATTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.11, C:0.55, G:0.00, T:0.34
Consensus pattern (22 bp):
TTCTCCTCCCCCCACCAACTAT
Found at i:11275 original size:2 final size:2
Alignment explanation
Indices: 11268--11298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11258 TACAAAAATA
11268 AT AT AT 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 AT AT AT A
11299 ATAGATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11491 original size:74 final size:74
Alignment explanation
Indices: 11365--11522 Score: 307
Period size: 74 Copynumber: 2.1 Consensus size: 74
11355 TGAAGTACAG
*
11365 ACTCTCTTCCTCTCTTACAACCATTATTATCTTTTCCACTCAAAAACTTAGATCTCTCCCACTCA
1 ACTCTCTTCCTCTCTTACAACCATTATTATCTTTTCCACTCAAAAACGTAGATCTCTCCCACTCA
11430 AAGGCTCAA
66 AAGGCTCAA
11439 ACTCTCTTCCTCTCTTACAACCATTATTATCTTTTCCACTCAAAAACGTAGATCTCTCCCACTCA
1 ACTCTCTTCCTCTCTTACAACCATTATTATCTTTTCCACTCAAAAACGTAGATCTCTCCCACTCA
11504 AAGGCTCAA
66 AAGGCTCAA
11513 ACTCTCTTCC
1 ACTCTCTTCC
11523 CCTTAGAGAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.34
Consensus pattern (74 bp):
ACTCTCTTCCTCTCTTACAACCATTATTATCTTTTCCACTCAAAAACGTAGATCTCTCCCACTCA
AAGGCTCAA
Found at i:12043 original size:48 final size:48
Alignment explanation
Indices: 11987--12083 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
11977 TTTTGGACGG
11987 GCCTTTGTCATAACATTTTATTTTTGGAATGGCTTGGACATAAATGAA
1 GCCTTTGTCATAACATTTTATTTTTGGAATGGCTTGGACATAAATGAA
12035 GCCTTTGTCATAACATTTTATTTTTGGAATGGCTTGGACATAAATGAA
1 GCCTTTGTCATAACATTTTATTTTTGGAATGGCTTGGACATAAATGAA
12083 G
1 G
12084 GCTCGTTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (48 bp):
GCCTTTGTCATAACATTTTATTTTTGGAATGGCTTGGACATAAATGAA
Found at i:12599 original size:13 final size:13
Alignment explanation
Indices: 12581--12605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12571 TAAACAATTT
12581 GAAACTATTCTTG
1 GAAACTATTCTTG
12594 GAAACTATTCTT
1 GAAACTATTCTT
12606 TGTTCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
GAAACTATTCTTG
Found at i:13061 original size:133 final size:130
Alignment explanation
Indices: 12826--13079 Score: 364
Period size: 133 Copynumber: 1.9 Consensus size: 130
12816 TACAACTTGC
** * *
12826 TGTTCAAGTTGATGGGTTCTTACATTGGCAAGTCATTGGTTCAAATCTTGATAGTGTTTTGACAT
1 TGTTCAAGTTGATGGGTTCTTACATTGGCAAGTCATTGGCCCAAATCCTGACAGTGTTTTGACAT
* ** * *
12891 TCGATTCAATTTGGGTGAAGAGAAATTTGGGGAGCTCATTAATATTTCGAAAAATCACCGGTTGT
66 TCGATTCAATTTGGGTGAAGAGAAATTCGAAGAGCTCATCAATATTCCGAAAAATCACCGGTTGT
*
12956 TGTTCAAGTTGATGGGTTCTTACATTGGCAAGTCATTGGCCCGAATCCTGACAGTCATGTTTTGA
1 TGTTCAAGTTGATGGGTTCTTACATTGGCAAGTCATTGGCCCAAATCCTGACAG---TGTTTTGA
* * *
13021 TATTCGATTCGATTTGGGTGAAGAGAAATTCGAAGAGCTCATCAATATTCCGAAGAATC
63 CATTCGATTCAATTTGGGTGAAGAGAAATTCGAAGAGCTCATCAATATTCCGAAAAATC
13080 CTGACGAGGA
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
130 49 0.45
133 59 0.55
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (130 bp):
TGTTCAAGTTGATGGGTTCTTACATTGGCAAGTCATTGGCCCAAATCCTGACAGTGTTTTGACAT
TCGATTCAATTTGGGTGAAGAGAAATTCGAAGAGCTCATCAATATTCCGAAAAATCACCGGTTGT
Found at i:13603 original size:13 final size:13
Alignment explanation
Indices: 13585--13610 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13575 TTTACTACTC
13585 CAATATGTAACTT
1 CAATATGTAACTT
13598 CAATATGTAACTT
1 CAATATGTAACTT
13611 GGGAAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
CAATATGTAACTT
Found at i:16951 original size:13 final size:12
Alignment explanation
Indices: 16913--16970 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 12
16903 GGTGAGTGAG
16913 GAAG-AAAGAAA
1 GAAGAAAAGAAA
16924 GAA-AAAAGAAA
1 GAAGAAAAGAAA
16935 -AAGAAAATGAAA
1 GAAGAAAA-GAAA
*
16947 GAAGAAGAGTAAA
1 GAAGAAAAG-AAA
16960 -AAGAAAA-AAA
1 GAAGAAAAGAAA
16970 G
1 G
16971 GTTTTATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
10 5 0.13
11 14 0.36
12 11 0.28
13 9 0.23
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.03
Consensus pattern (12 bp):
GAAGAAAAGAAA
Found at i:17382 original size:15 final size:15
Alignment explanation
Indices: 17362--17390 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17352 ATGGTCAATG
17362 AAGTGTTACAATACA
1 AAGTGTTACAATACA
17377 AAGTGTTACAATAC
1 AAGTGTTACAATAC
17391 GGGTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (15 bp):
AAGTGTTACAATACA
Done.