Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021497.1 Corchorus olitorius cultivar O-4 contig21530, 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: 53188
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:1460 original size:11 final size:11
Alignment explanation
Indices: 1444--1468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1434 AGAAAATTGT
1444 TTGTTTTTGGA
1 TTGTTTTTGGA
1455 TTGTTTTTGGA
1 TTGTTTTTGGA
1466 TTG
1 TTG
1469 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:1536 original size:23 final size:24
Alignment explanation
Indices: 1488--1538 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1478 CAATTTTTTT
* *
1488 ATTTAAAAAAAAATTGATTTTCGA
1 ATTTAAAAAAAAATAGATTTTAGA
1512 ATTTAAAAAAAAA-AG-TTTTGAGA
1 ATTTAAAAAAAAATAGATTTT-AGA
1535 ATTT
1 ATTT
1539 TGAATTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 7 0.29
24 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (24 bp):
ATTTAAAAAAAAATAGATTTTAGA
Found at i:4678 original size:39 final size:39
Alignment explanation
Indices: 4624--4729 Score: 185
Period size: 39 Copynumber: 2.7 Consensus size: 39
4614 AAGATTCAAT
*
4624 CTTTCACTTAAAAAATCCAATCTTTATTTACAAATTGAA
1 CTTTCACTTAAAAAATTCAATCTTTATTTACAAATTGAA
*
4663 CTTTCACTTAAAAAATTCACTCTTTATTTACAAATTGAA
1 CTTTCACTTAAAAAATTCAATCTTTATTTACAAATTGAA
*
4702 CTTTCACTTAAAAAATTGAATCTTTATT
1 CTTTCACTTAAAAAATTCAATCTTTATT
4730 ATTGACAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (39 bp):
CTTTCACTTAAAAAATTCAATCTTTATTTACAAATTGAA
Found at i:4719 original size:20 final size:21
Alignment explanation
Indices: 4608--4726 Score: 106
Period size: 21 Copynumber: 6.0 Consensus size: 21
4598 TTTGCAAATT
* *
4608 ACTTAAAAGATTCAATCTTTC
1 ACTTAAAAAATTGAATCTTTC
**
4629 ACTTAAAAAATCCAATCTTT-
1 ACTTAAAAAATTGAATCTTTC
* *
4649 A-TTTACAAATTGAA-CTTTC
1 ACTTAAAAAATTGAATCTTTC
* *
4668 ACTTAAAAAATTCACTCTTT-
1 ACTTAAAAAATTGAATCTTTC
* *
4688 A-TTTACAAATTGAA-CTTTC
1 ACTTAAAAAATTGAATCTTTC
4707 ACTTAAAAAATTGAATCTTT
1 ACTTAAAAAATTGAATCTTT
4727 ATTATTGACA
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.11
19 20 0.26
20 22 0.29
21 26 0.34
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.39
Consensus pattern (21 bp):
ACTTAAAAAATTGAATCTTTC
Found at i:24261 original size:76 final size:76
Alignment explanation
Indices: 24069--24421 Score: 433
Period size: 76 Copynumber: 4.7 Consensus size: 76
24059 TGTGTGGACG
* * * * * *
24069 CTGTTTCACTAGTAGGCGAACGAGGGCGCCAGTGTAGGCACTCGGCCGTTGAGTGAGCGGCGTCT
1 CTGTCTCACTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCT
* *
24134 GCGTGGACG--
66 ACATGGACGCT
* * * * *
24143 CTGTCTCACTGATGGACGAAC-GGGGCTGCCAATGTAGGCACTCAGCCGTTAAGTGAGCGGCGTC
1 CTGTCTCACTGGTAGACGAACGGGGGC-GCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTC
24207 TACATGGACGCT
65 TACATGGACGCT
* *
24219 CTGTCTCATTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCAGCGTCT
1 CTGTCTCACTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCT
24284 ACATGGACGCT
66 ACATGGACGCT
* * *
24295 ATGTCTCACTGGTAGACGAACGAGGGCGCCAGTCTAGGCACTCAGCCATTGAGTGAGCGGCGTCT
1 CTGTCTCACTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCT
* *
24360 GCGTGGACGCT
66 ACATGGACGCT
* * * * * **
24371 CTGTCTCACTAGTGGGCGAACGGGGGCACCATTCTAGGTGCTCAGCCGTTG
1 CTGTCTCACTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTG
24422 TTTGAAATAT
Statistics
Matches: 240, Mismatches: 35, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
73 4 0.02
74 58 0.24
76 173 0.72
77 5 0.02
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (76 bp):
CTGTCTCACTGGTAGACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCT
ACATGGACGCT
Found at i:24370 original size:152 final size:150
Alignment explanation
Indices: 24039--24421 Score: 484
Period size: 152 Copynumber: 2.6 Consensus size: 150
24029 CAGGTGTTTG
* * * * *
24039 GCCATTGGGTGAGGGGCGTCTGTGTGGACG--CTGTTTCACTAGTAGGCGAACGAGGGCGCCAGT
1 GCCATTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTAGGCGAACGGGGGCGCCAGT
* * * * * *
24102 GTAGGCACTCGGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTGTCTCACTGATGGACGAACGGG
66 CTAGGCACTCAGCCGTTGAGTGAGCAGCGTCTACATGGACGCTGTCTCACTGATAGACGAACGGG
*
24167 GCTGCCAATGTAGGCACTCA
131 GCTGCCAATCTAGGCACTCA
* * * * * * *
24187 GCCGTTAAGTGAGCGGCGTCTACATGGACGCTCTGTCTCATTGGTAGACGAACGGGGGCGCCAGT
1 GCCATTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTAGGCGAACGGGGGCGCCAGT
*
24252 CTAGGCACTCAGCCGTTGAGTGAGCAGCGTCTACATGGACGCTATGTCTCACTGGTAGACGAACG
66 CTAGGCACTCAGCCGTTGAGTGAGCAGCGTCTACATGGACGC--TGTCTCACTGATAGACGAACG
*
24317 AGGGC-GCCAGTCTAGGCACTCA
129 -GGGCTGCCAATCTAGGCACTCA
* * *
24339 GCCATTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTGGGCGAACGGGGGCACCATT
1 GCCATTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTAGGCGAACGGGGGCGCCAGT
**
24404 CTAGGTGCTCAGCCGTTG
66 CTAGGCACTCAGCCGTTG
24422 TTTGAAATAT
Statistics
Matches: 197, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
148 23 0.12
150 65 0.33
152 105 0.53
153 4 0.02
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (150 bp):
GCCATTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTAGGCGAACGGGGGCGCCAGT
CTAGGCACTCAGCCGTTGAGTGAGCAGCGTCTACATGGACGCTGTCTCACTGATAGACGAACGGG
GCTGCCAATCTAGGCACTCA
Found at i:30338 original size:15 final size:15
Alignment explanation
Indices: 30309--30338 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30299 TTTGTCCTGA
30309 CAGGCTCCTGCCCCC
1 CAGGCTCCTGCCCCC
30324 CAGGCGTCCTGCCCC
1 CAGGC-TCCTGCCCC
30339 TGGATGGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.57, G:0.23, T:0.13
Consensus pattern (15 bp):
CAGGCTCCTGCCCCC
Found at i:41576 original size:2 final size:2
Alignment explanation
Indices: 41532--41566 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41522 TTTTCGGTGC
41532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41567 TGAGTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.