Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022539.1 Corchorus olitorius cultivar O-4 contig22572, 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: 13718
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Found at i:412 original size:42 final size:42
Alignment explanation
Indices: 333--417 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
323 AGCAACAATT
**
333 AATATTAACTTTATTTTGATGAATTATTTAGAAATGGAGTAG
1 AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGTAG
**
375 AATATTAGA-TTTATTTTGATGAATTACCTAGTGATGGAGTAG
1 AATATTA-ACTTTATTTTGATGAATTACCTAGAAATGGAGTAG
417 A
1 A
418 GTTTTGATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (42 bp):
AATATTAACTTTATTTTGATGAATTACCTAGAAATGGAGTAG
Found at i:1106 original size:124 final size:126
Alignment explanation
Indices: 905--1160 Score: 399
Period size: 124 Copynumber: 2.0 Consensus size: 126
895 CTTTTACTTA
* * * * *
905 GAGTGAGAGCACCTTTAGGAGTGTTGCACCTTCTCTAGTTGCACCTCCAGGGAGTGCCTTTCTTT
1 GAGTGAGAGCACCGTTAGGAGTGCTGCACCTTCTCTAGTTGCACATCCAGGGAGTGCCCTTCATT
* *
970 GTTGATGTTTCTGGCCTATGTAGCCCATTAAAAAAGGAAAATATATATTTT-ACTTGGAGT
66 GTTGATGCTTCTGGCCTATGTAGCCCATTAAAAAAGAAAAATATATATTTTGACTTGGAGT
*
1030 -AGTGAGTGCACCGTTAGGAGTGCTGCACCTTCTCTAGTTGCACATCCAGGGAGTGCCCTTCATT
1 GAGTGAGAGCACCGTTAGGAGTGCTGCACCTTCTCTAGTTGCACATCCAGGGAGTGCCCTTCATT
* * *
1094 GTTGATGCTTCTGGCCTATGTAGCCTATTGAAAAAGAAAAATATATATTTTGATTTGGAGT
66 GTTGATGCTTCTGGCCTATGTAGCCCATTAAAAAAGAAAAATATATATTTTGACTTGGAGT
1155 GAGTGA
1 GAGTGA
1161 ACCCTTAGGG
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
124 105 0.89
125 8 0.07
126 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (126 bp):
GAGTGAGAGCACCGTTAGGAGTGCTGCACCTTCTCTAGTTGCACATCCAGGGAGTGCCCTTCATT
GTTGATGCTTCTGGCCTATGTAGCCCATTAAAAAAGAAAAATATATATTTTGACTTGGAGT
Found at i:1599 original size:39 final size:38
Alignment explanation
Indices: 1456--1601 Score: 107
Period size: 40 Copynumber: 3.7 Consensus size: 38
1446 CGTTCCTTGT
** *
1456 TGATGCTTTTGGCCTATGTAGCTCATTACTAATGCAACA
1 TGATGCTCATGGCCTATGTAGC-CATTACTTATGCAACA
* * * * *
1495 CGCATACTCATGGCCTTTGTCGCC-TTACATTTAAGCAACA
1 TG-ATGCTCATGGCCTATGTAGCCATTAC--TTATGCAACA
* *
1535 TGATTGCTCTTGGCCTAT-TCCGCCATTACTTATGCAACA
1 TGA-TGCTCATGGCCTATGT-AGCCATTACTTATGCAACA
* *
1574 TGTATGCTCCTGGCCTATGAAGCCATTA
1 TG-ATGCTCATGGCCTATGTAGCCATTA
1602 TTTTAAACAC
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
38 4 0.05
39 35 0.42
40 40 0.48
41 4 0.05
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (38 bp):
TGATGCTCATGGCCTATGTAGCCATTACTTATGCAACA
Found at i:1760 original size:133 final size:131
Alignment explanation
Indices: 1523--1871 Score: 484
Period size: 133 Copynumber: 2.6 Consensus size: 131
1513 GTCGCCTTAC
* * *
1523 ATTTAAGCAACATGATTGCTCTTGG-CCTATTCCGCCATTACTTATGCAACATGTATGCTCCTGG
1 ATTTAAGCAACATGATTGCTCTCGGCCCAAGT-CGCCATTACTTATGCAACATGTATGCTCCTGG
* ** *
1587 CCTATGAAGCCATTATTTTAAACACGCATAATTGTTATTGGCTTATGTTGCCTATTACTTTATTT
65 CCTATGTAGCCATTA-TTTAAACACGCATAATTGCAATTGGCTTACGTTGCCTATTACTTTATTT
1652 AAT
129 AAT
*
1655 ATTTAAGCAACATGATTGCTCTCGGCCCAAGTCGCCTATTACTTATGCAACATGTATGCTTCTGG
1 ATTTAAGCAACATGATTGCTCTCGGCCCAAGTCGCC-ATTACTTATGCAACATGTATGCTCCTGG
* * *
1720 CCGATGTTGACCATTATTTAAACATGCATAATTGCAATTGGCTTACGTTGCCTATTACTTTATTT
65 CCTATGTAG-CCATTATTTAAACACGCATAATTGCAATTGGCTTACGTTGCCTATTACTTTATTT
1785 AAT
129 AAT
* * * * *
1788 ATTTAAGCAACATGATTGCTTTCGACCCAAGTCGCCAAATATTTATGCAACATGTATGCTCCTGA
1 ATTTAAGCAACATGATTGCTCTCGGCCCAAGTCGCC-ATTACTTATGCAACATGTATGCTCCTGG
*
1853 CCTATGTCGCCCATTATTT
65 CCTATGTAG-CCATTATTT
1872 TTTTTTTATT
Statistics
Matches: 193, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
132 28 0.15
133 159 0.82
134 6 0.03
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (131 bp):
ATTTAAGCAACATGATTGCTCTCGGCCCAAGTCGCCATTACTTATGCAACATGTATGCTCCTGGC
CTATGTAGCCATTATTTAAACACGCATAATTGCAATTGGCTTACGTTGCCTATTACTTTATTTAA
T
Found at i:4587 original size:40 final size:40
Alignment explanation
Indices: 4543--4619 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
4533 CTTTATTTAA
4543 TGCTTAAGCAACATG-ATTGCTCTCGGCCTAAGTCGCCAAT
1 TGCTTAAGCAACATGTA-TGCTCTCGGCCTAAGTCGCCAAT
* * *
4583 TGCTTATGCAACATGTATGCTCTTGGCCTACGTCGCC
1 TGCTTAAGCAACATGTATGCTCTCGGCCTAAGTCGCC
4620 CATTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.30
Consensus pattern (40 bp):
TGCTTAAGCAACATGTATGCTCTCGGCCTAAGTCGCCAAT
Found at i:4635 original size:40 final size:40
Alignment explanation
Indices: 4545--4640 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
4535 TTATTTAATG
*
4545 CTTAAGCAACATGATTGCTCTCGGCCTAAGTCGCCAATTG
1 CTTAAGCAACATGATTGCTCTCGGCCTAAGTCGCCAATTA
* * * *
4585 CTTATGCAACATG-TATGCTCTTGGCCTACGTCGCCCATTA
1 CTTAAGCAACATGAT-TGCTCTCGGCCTAAGTCGCCAATTA
* * *
4625 TTTAAACAACACGATT
1 CTTAAGCAACATGATT
4641 ATTACATGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
39 1 0.02
40 43 0.96
41 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (40 bp):
CTTAAGCAACATGATTGCTCTCGGCCTAAGTCGCCAATTA
Found at i:4705 original size:82 final size:81
Alignment explanation
Indices: 4603--4824 Score: 270
Period size: 83 Copynumber: 2.7 Consensus size: 81
4593 ACATGTATGC
* * * *
4603 TCTTGGCCTACGTCGCCCATTATTTAAACAACACGATTATTACATGGCCTATGTCGCTCATTGCT
1 TCTTGGCCTATGTCGCCCATTATTTAAACAACATGATTATTACATGGCCTATGTCGCCCATTACT
4668 TATATATAGCAT-ACAAT
66 TATATA-A-CATGACAAT
* *
4685 TCTTGGCCTATGTCGCCCATTATTTAAACAACATGATTGTTAC-TGGCCTATGCCGCCCATTACT
1 TCTTGGCCTATGTCGCCCATTATTTAAACAACATGATTATTACATGGCCTATGTCGCCCATTACT
**
4749 TATATAACATGATTAT
66 TATATAACATGACAAT
* * * *
4765 TACATGGCTTATATGTAGCCCATTATTTAAACAACATGACTATTA-ATGGCCTATGTCGCC
1 T-CTTGGC--CTATGTCGCCCATTATTTAAACAACATGATTATTACATGGCCTATGTCGCC
4825 AATACAAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.02
80 5 0.04
81 29 0.24
82 40 0.33
83 44 0.36
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (81 bp):
TCTTGGCCTATGTCGCCCATTATTTAAACAACATGATTATTACATGGCCTATGTCGCCCATTACT
TATATAACATGACAAT
Found at i:4743 original size:40 final size:40
Alignment explanation
Indices: 4606--4824 Score: 199
Period size: 40 Copynumber: 5.3 Consensus size: 40
4596 TGTATGCTCT
* *
4606 TGGCCTACGTCGCCCATTATTTAAACAACACGATTATTAC
1 TGGCCTATGTCGCCCATTATTTAAACAACATGATTATTAC
* * * * * **
4646 ATGGCCTATGTCGCTCATTGCTTATATATAGCAT-ACAATT-C
1 -TGGCCTATGTCGCCCATT-ATT-TAAACAACATGATTATTAC
*
4687 TTGGCCTATGTCGCCCATTATTTAAACAACATGATTGTTAC
1 -TGGCCTATGTCGCCCATTATTTAAACAACATGATTATTAC
* * * *
4728 TGGCCTATGCCGCCCATTACTTATATAACATGATTATTAC
1 TGGCCTATGTCGCCCATTATTTAAACAACATGATTATTAC
* * * *
4768 ATGGCTTATATGTAGCCCATTATTTAAACAACATGACTATTAA
1 -TGGC--CTATGTCGCCCATTATTTAAACAACATGATTATTAC
4811 TGGCCTATGTCGCC
1 TGGCCTATGTCGCC
4825 AATACAAATT
Statistics
Matches: 138, Mismatches: 33, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
39 7 0.05
40 48 0.35
41 39 0.28
42 10 0.07
43 34 0.25
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (40 bp):
TGGCCTATGTCGCCCATTATTTAAACAACATGATTATTAC
Found at i:4894 original size:51 final size:51
Alignment explanation
Indices: 4811--4931 Score: 226
Period size: 51 Copynumber: 2.4 Consensus size: 51
4801 TGACTATTAA
4811 TGGCCTATGTCGCCAA-TACAAATTCAATATCTAAGCATTATGATTGCTCT
1 TGGCCTATGTCGCCAATTACAAATTCAATATCTAAGCATTATGATTGCTCT
4861 TGGCCTATGTCGCCAATTACAAATTCAATATCTAAGCATTATGATTGCTCT
1 TGGCCTATGTCGCCAATTACAAATTCAATATCTAAGCATTATGATTGCTCT
*
4912 TGGCCTATGTCGCCCATTAC
1 TGGCCTATGTCGCCAATTAC
4932 GTATATAACA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
50 16 0.23
51 53 0.77
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (51 bp):
TGGCCTATGTCGCCAATTACAAATTCAATATCTAAGCATTATGATTGCTCT
Done.