Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014512.1 Corchorus olitorius cultivar O-4 contig14545, 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: 29623
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4552 original size:14 final size:14
Alignment explanation
Indices: 4533--4561 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4523 TCAAATCCTA
4533 ATCGTGTCTTAATG
1 ATCGTGTCTTAATG
4547 ATCGTGTCTTAATG
1 ATCGTGTCTTAATG
4561 A
1 A
4562 ACTCGATCAT
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:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (14 bp):
ATCGTGTCTTAATG
Found at i:5401 original size:25 final size:25
Alignment explanation
Indices: 5367--5415 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5357 GATTGATTTG
*
5367 TAGAGACCAAGCGAGAGTGCTCAAA
1 TAGAGACCAAGCGAGAGTACTCAAA
5392 TAGAGACCAAGCGAGAGTACTCAA
1 TAGAGACCAAGCGAGAGTACTCAA
5416 GATTATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (25 bp):
TAGAGACCAAGCGAGAGTACTCAAA
Found at i:14638 original size:33 final size:33
Alignment explanation
Indices: 14564--14652 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 33
14554 AAATAATATT
* **
14564 TAAATTTTATTAGAAATATTTATTAATATGTAA
1 TAAATATTATTAGAAATATTTATTAATATACAA
14597 T-AA-A-TATTAG-AATATTTATTTAATATACAA
1 TAAATATTATTAGAAATATTTA-TTAATATACAA
14627 TAAATATTATTAGAAATATTTTATTA
1 TAAATATTATTAGAAATA-TTTATTA
14653 GAAATTAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
29 8 0.17
30 16 0.34
31 2 0.04
32 3 0.06
33 7 0.15
34 7 0.15
35 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (33 bp):
TAAATATTATTAGAAATATTTATTAATATACAA
Found at i:20790 original size:31 final size:31
Alignment explanation
Indices: 20755--20821 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
20745 TATCGAGTAG
20755 CTCGACGAGTATCGAATCAAGTATCATTGAA
1 CTCGACGAGTATCGAATCAAGTATCATTGAA
*
20786 CTCGACGAGTATCGAATCAAGTATCATTGAG
1 CTCGACGAGTATCGAATCAAGTATCATTGAA
20817 CTCGA
1 CTCGA
20822 GCTCGCTCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (31 bp):
CTCGACGAGTATCGAATCAAGTATCATTGAA
Found at i:23401 original size:32 final size:33
Alignment explanation
Indices: 23336--23406 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
23326 GTAATAAAAT
23336 TTTGATTAACCCATTGATAACTTTTCTTAATCC
1 TTTGATTAACCCATTGATAACTTTTCTTAATCC
* *
23369 TTTGATTAACCGATTGATAAC-TTTCTTGATCC
1 TTTGATTAACCCATTGATAACTTTTCTTAATCC
23401 TTTGAT
1 TTTGAT
23407 CTTGTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (33 bp):
TTTGATTAACCCATTGATAACTTTTCTTAATCC
Found at i:26400 original size:58 final size:58
Alignment explanation
Indices: 26336--26449 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
26326 AAGGTTGGAC
*
26336 AATTATGAAACTTTTCGTCTTAATTATTGTTTGCTTTGTCCAATGGCTGTGGGACATT
1 AATTATGAAACTTTTCGTCTTAATTATTGTTTGCTATGTCCAATGGCTGTGGGACATT
26394 AATTATGAAACTTTTCGTCTTAATTATTGTTTGCTATGTCCAATGGCTGTGGGACA
1 AATTATGAAACTTTTCGTCTTAATTATTGTTTGCTATGTCCAATGGCTGTGGGACA
26450 CCAATGCTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (58 bp):
AATTATGAAACTTTTCGTCTTAATTATTGTTTGCTATGTCCAATGGCTGTGGGACATT
Found at i:27313 original size:41 final size:41
Alignment explanation
Indices: 27240--27553 Score: 434
Period size: 41 Copynumber: 7.6 Consensus size: 41
27230 GTTTGATTTG
* * *
27240 ATTTAATTCAAGGG--TCGAATGACTTGGTCTTGAATTAACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGTTCTTGAATTGATA
* * * *
27280 ATCTAATTCAAGGGTCTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
* *
27321 ATAATTCGATTCAAGAGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
*
27365 ATTTAATTCAAGGGTCTCGATGACTTATTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
***
27406 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
27447 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
***
27488 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
27529 ATTTAATTCAAGGGTCTCGATGACT
1 ATTTAATTCAAGGGTCTCGATGACT
27554 CAATCTTGAA
Statistics
Matches: 247, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
40 13 0.05
41 195 0.79
42 4 0.02
43 1 0.00
44 34 0.14
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
Found at i:27676 original size:16 final size:16
Alignment explanation
Indices: 27657--27689 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27647 CATCTGAAAA
*
27657 TACTTCAGAGTTTTTC
1 TACTTCAGAGCTTTTC
27673 TACTTCAGAGCTTTTC
1 TACTTCAGAGCTTTTC
27689 T
1 T
27690 GCTTTCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (16 bp):
TACTTCAGAGCTTTTC
Done.