Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022095.1 Corchorus olitorius cultivar O-4 contig22128, 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: 34931
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2688 original size:9 final size:10
Alignment explanation
Indices: 2670--2699 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2660 ACAAAACCAG
2670 AACAAAAAAA
1 AACAAAAAAA
2680 AACAAAAAAA
1 AACAAAAAAA
2690 AACAAAAAAA
1 AACAAAAAAA
2700 CAGAGTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AACAAAAAAA
Found at i:4774 original size:18 final size:19
Alignment explanation
Indices: 4751--4796 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
4741 TTATCTTTTT
4751 ATTTCT-TTGTTTGTGTTA
1 ATTTCTATTGTTTGTGTTA
4769 ATTTCTCGTATTGTTTGTGTTA
1 A-TT-TC-TATTGTTTGTGTTA
4791 ATTTCT
1 ATTTCT
4797 CATTACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 4 0.17
21 3 0.12
22 13 0.54
ACGTcount: A:0.13, C:0.09, G:0.15, T:0.63
Consensus pattern (19 bp):
ATTTCTATTGTTTGTGTTA
Found at i:4881 original size:18 final size:18
Alignment explanation
Indices: 4858--4894 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4848 CATCTAAATG
*
4858 AGAATCCAACCCGAACTA
1 AGAATCCAACCCAAACTA
4876 AGAATCCAACCCAAACTA
1 AGAATCCAACCCAAACTA
4894 A
1 A
4895 AAAATTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.32, G:0.08, T:0.11
Consensus pattern (18 bp):
AGAATCCAACCCAAACTA
Found at i:4940 original size:16 final size:16
Alignment explanation
Indices: 4919--4953 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4909 TAGCCTACTT
* *
4919 AACAAACTATCAAATA
1 AACAAACAAACAAATA
4935 AACAAACAAACAAATA
1 AACAAACAAACAAATA
4951 AAC
1 AAC
4954 TAAATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (16 bp):
AACAAACAAACAAATA
Found at i:11155 original size:23 final size:22
Alignment explanation
Indices: 11121--11163 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
11111 TTCTGGGCGA
11121 ATTTTTTTTATTTTT-TATTTT
1 ATTTTTTTTATTTTTCTATTTT
11142 ATTTTTTTGATATTTTTCTATT
1 ATTTTTTT--TATTTTTCTATT
11164 AAATCGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
ATTTTTTTTATTTTTCTATTTT
Found at i:21505 original size:105 final size:106
Alignment explanation
Indices: 21309--21568 Score: 386
Period size: 105 Copynumber: 2.5 Consensus size: 106
21299 GGTTTAGCCT
* *
21309 TAATTTCACTAAGTTTAGCCCC--ATTAAAATTTTATTTTTATTTTAAAGGTAAATTTTAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
21372 AATAATTTATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA-TTATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
21414 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
* * *
21479 AATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATTATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
21519 TAA-TTCATTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
21569 TAGCAAAATT
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 30 0.21
104 13 0.09
105 57 0.40
107 43 0.30
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
AATAATTATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:22903 original size:122 final size:122
Alignment explanation
Indices: 22686--22927 Score: 441
Period size: 122 Copynumber: 2.0 Consensus size: 122
22676 TTTTATTAAT
*
22686 TATGGGGTCTATCGTAGCTCCCATTGATGTGAATGAGAAGATATTATTGTAAGCAAAGAGGATAA
1 TATGGGGTCTATCGTAGCTCCCATTGATGTGAATGAGAAGATACTATTGTAAGCAAAGAGGATAA
22751 TAGGAGTGAAAAAACTGAGAGTAAAGAAATCAAATAACAACAAAAAAAAAATATTAC
66 TAGGAGTGAAAAAACTGAGAGTAAAGAAATCAAATAACAACAAAAAAAAAATATTAC
22808 TATGGGGTCTATCGTAGCTCCCATTGATGTGAATGAGAAGCA-ACTATTGTAAGCAAAGAGGATA
1 TATGGGGTCTATCGTAGCTCCCATTGATGTGAATGAGAAG-ATACTATTGTAAGCAAAGAGGATA
* *
22872 ATAGGAGTGAAAAAACTGAGAGTAAAGAAATCGAATAACAACAAAAAAAAATTATT
65 ATAGGAGTGAAAAAACTGAGAGTAAAGAAATCAAATAACAACAAAAAAAAAATATT
22928 GCTTCCAACT
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
122 115 0.99
123 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (122 bp):
TATGGGGTCTATCGTAGCTCCCATTGATGTGAATGAGAAGATACTATTGTAAGCAAAGAGGATAA
TAGGAGTGAAAAAACTGAGAGTAAAGAAATCAAATAACAACAAAAAAAAAATATTAC
Found at i:27414 original size:15 final size:15
Alignment explanation
Indices: 27394--27443 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
27384 CTAGTTGGCC
*
27394 TGGTGGGCCAAGTAG
1 TGGTGGGCCAAGTGG
27409 TGGTGGGCCAAGTGG
1 TGGTGGGCCAAGTGG
**
27424 TGGTCTGCCAAGTGG
1 TGGTGGGCCAAGTGG
27439 TGGTG
1 TGGTG
27444 AGCCGAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.14, C:0.14, G:0.48, T:0.24
Consensus pattern (15 bp):
TGGTGGGCCAAGTGG
Found at i:30081 original size:21 final size:22
Alignment explanation
Indices: 30052--30097 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
30042 TATAGTTGGG
30052 AAATCTGATGGTAAAGGGTACC
1 AAATCTGATGGTAAAGGGTACC
**
30074 AAAT-TGATGGTTTAGGGTACC
1 AAATCTGATGGTAAAGGGTACC
30095 AAA
1 AAA
30098 ACATTGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (22 bp):
AAATCTGATGGTAAAGGGTACC
Found at i:30132 original size:34 final size:34
Alignment explanation
Indices: 30089--30165 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
30079 GATGGTTTAG
30089 GGTACCAAAACATTGATATATTTTG-TATATTCAA
1 GGTACCAAAACATTGATATATTTTGAT-TATTCAA
*
30123 GGTACCAAAACATTGATATATTTTGATTATTCAG
1 GGTACCAAAACATTGATATATTTTGATTATTCAA
30157 GGTACCAAA
1 GGTACCAAA
30166 TTCTGATTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 40 0.98
35 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (34 bp):
GGTACCAAAACATTGATATATTTTGATTATTCAA
Found at i:30866 original size:18 final size:18
Alignment explanation
Indices: 30843--30888 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
30833 AAATAAAAGG
30843 AAAAGAGAGAAAAACTGA
1 AAAAGAGAGAAAAACTGA
30861 AAAAGAGAG--AAACTGA
1 AAAAGAGAGAAAAACTGA
30877 AAAAGAAGAGAA
1 AAAAG-AGAGAA
30889 TTTTAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.48
17 4 0.16
18 9 0.36
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (18 bp):
AAAAGAGAGAAAAACTGA
Done.