Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020382.1 Corchorus olitorius cultivar O-4 contig20415, 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: 88516
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:8671 original size:41 final size:41
Alignment explanation
Indices: 8625--8707 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
8615 TCTTGGGTTC
8625 AACTCTCACGGAATGTAAGTTTGTTTGTAATTTCTTTGTTT
1 AACTCTCACGGAATGTAAGTTTGTTTGTAATTTCTTTGTTT
8666 AACTCTCACGGAATGTAAGTTTGTTTGTAATTTCTTTGTTT
1 AACTCTCACGGAATGTAAGTTTGTTTGTAATTTCTTTGTTT
8707 A
1 A
8708 TTTGGTAGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (41 bp):
AACTCTCACGGAATGTAAGTTTGTTTGTAATTTCTTTGTTT
Found at i:8895 original size:104 final size:100
Alignment explanation
Indices: 8704--9008 Score: 565
Period size: 100 Copynumber: 3.0 Consensus size: 100
8694 AATTTCTTTG
8704 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
1 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
8769 TATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
66 TATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
8804 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
1 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAG---
8869 TATTTATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
63 -ATTTATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
8908 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
1 TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
*
8973 TATTTGAATTGTAATGAGATTTCACTGGGTTTGTT
66 TATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
9008 T
1 T
9009 CATATAGCTA
Statistics
Matches: 200, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
100 100 0.50
104 100 0.50
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.50
Consensus pattern (100 bp):
TTTATTTGGTAGGTAGTTAGTTTATTTATGATATAGTTTCTAGTTTGGGTTGAATTCTAGAGATT
TATTTGAATCGTAATGAGATTTCACTGGGTTTGTT
Found at i:9038 original size:64 final size:64
Alignment explanation
Indices: 8967--9087 Score: 233
Period size: 64 Copynumber: 1.9 Consensus size: 64
8957 TTGAATTCTA
*
8967 GAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTTGTTTCATATAGCTAATCATGGGCATT
1 GAGATTTATTTGAATTGTAATGAGATTTCACTAGGTTTGTTTCATATAGCTAATCATGGGCATT
9031 GAGATTTATTTGAATTGTAATGAGATTTCACTAGGTTTGTTTCATATAGCTAATCAT
1 GAGATTTATTTGAATTGTAATGAGATTTCACTAGGTTTGTTTCATATAGCTAATCAT
9088 TTAGCGGTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (64 bp):
GAGATTTATTTGAATTGTAATGAGATTTCACTAGGTTTGTTTCATATAGCTAATCATGGGCATT
Found at i:36969 original size:2 final size:2
Alignment explanation
Indices: 36962--36987 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36952 CCTAAATAGA
36962 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
36988 TGTATCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41478 original size:21 final size:18
Alignment explanation
Indices: 41434--41481 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
41424 TTCTAAATAC
*
41434 TATATTAATTAAATTAAT
1 TATATTAATTAAACTAAT
41452 TA-ATTAATTAATTACTAATT
1 TATATTAATTAA--ACTAA-T
41472 TATATTAATT
1 TATATTAATT
41482 TCGATTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 4 0.16
20 3 0.12
21 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATTAATTAAACTAAT
Found at i:46355 original size:15 final size:15
Alignment explanation
Indices: 46335--46364 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46325 ACAATATAAC
46335 CTCTATAAAATAATA
1 CTCTATAAAATAATA
*
46350 CTCTATAAATTAATA
1 CTCTATAAAATAATA
46365 ATCACTGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
CTCTATAAAATAATA
Found at i:47422 original size:4 final size:4
Alignment explanation
Indices: 47415--47458 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
47405 TGTGTATATA
*
47415 TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47459 GGGTGGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:47519 original size:2 final size:2
Alignment explanation
Indices: 47514--47549 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47504 AAAGGGGACC
47514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47550 TCCGATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56861 original size:5 final size:5
Alignment explanation
Indices: 56847--56876 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
56837 TCAATATTCC
56847 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
56877 CTGTAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:63767 original size:2 final size:2
Alignment explanation
Indices: 63760--63822 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
63750 GTTTAATAAT
*
63760 TA TA TA TA T- TA T- TA TA TA TA TC TA -A TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
63797 TA TA TA -A TA TA TA TT TA -A T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63823 TACTAAACGG
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
1 8 0.16
2 41 0.84
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:63819 original size:21 final size:20
Alignment explanation
Indices: 63755--63822 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 20
63745 AGACCGTTTA
63755 ATAATTATATATATTATTATAT
1 ATAA-TATATAT-TTATTATAT
*
63777 AT-ATCTAATATTATTATATATAT
1 ATAATAT-ATA-T-TTAT-TATAT
63800 ATAATATATATTTAATTATAT
1 ATAATATATATTT-ATTATAT
63821 AT
1 AT
63823 TACTAAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.05
21 13 0.33
22 11 0.28
23 10 0.26
24 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATATATATTTATTATAT
Found at i:63821 original size:19 final size:19
Alignment explanation
Indices: 63760--63811 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
63750 GTTTAATAAT
63760 TATAT-ATATTATTATATA
1 TATATAATATTATTATATA
*
63778 TATCTAATATTATTATATA
1 TATATAATATTATTATATA
63797 TATATAATATATATT
1 TATATAATAT-TATT
63812 TAATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATAATATTATTATATA
Found at i:70185 original size:45 final size:46
Alignment explanation
Indices: 70125--70219 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
70115 GTAACTTTTA
* * *
70125 TTTTATTTCCCATTATCGATAATCCCTATTAGTAACT-CTAACC-AC
1 TTTTATATCCCATTATCAATAATCCCGATTAGTAA-TGCTAACCAAC
* *
70170 TTTTATATCCTATTATCAATAATCCCGATTATTAATGCTAACCAAC
1 TTTTATATCCCATTATCAATAATCCCGATTAGTAATGCTAACCAAC
70216 TTTT
1 TTTT
70220 TCAGTCATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 1 0.02
45 36 0.84
46 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (46 bp):
TTTTATATCCCATTATCAATAATCCCGATTAGTAATGCTAACCAAC
Found at i:73883 original size:15 final size:15
Alignment explanation
Indices: 73836--73883 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
73826 AGTTCATAGT
73836 TTATTTTCTTTCTAA
1 TTATTTTCTTTCTAA
73851 TT-TTTT-TTT-TAGA
1 TTATTTTCTTTCTA-A
*
73864 ATATTTTCTTTCTAA
1 TTATTTTCTTTCTAA
73879 TTATT
1 TTATT
73884 GGTATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 2 0.07
13 5 0.19
14 8 0.30
15 10 0.37
16 2 0.07
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTTCTTTCTAA
Found at i:74296 original size:15 final size:16
Alignment explanation
Indices: 74276--74313 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
74266 TTTTTTAATT
74276 AAAAAT-TATTTTTTA
1 AAAAATATATTTTTTA
* *
74291 AAAAATATGTTTTTTG
1 AAAAATATATTTTTTA
74307 AAAAATA
1 AAAAATA
74314 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
AAAAATATATTTTTTA
Found at i:86316 original size:24 final size:25
Alignment explanation
Indices: 86284--86335 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
86274 AGGCAATCTC
86284 AAACCATGATAT-ATCTTGGTCACT
1 AAACCATGATATAATCTTGGTCACT
86308 AAACCATGATATAATCTTGGTCACT
1 AAACCATGATATAATCTTGGTCACT
86333 AAA
1 AAA
86336 AAGATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (25 bp):
AAACCATGATATAATCTTGGTCACT
Done.