Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015758.1 Corchorus olitorius cultivar O-4 contig15791, 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: 5046
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:27 original size:16 final size:16
Alignment explanation
Indices: 6--56 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1 TCATT
6 TATATATTAATAATAA
1 TATATATTAATAATAA
*
22 TATATATTATTAATAA
1 TATATATTAATAATAA
* *
38 AAT-TATAAAATAATAA
1 TATATAT-TAATAATAA
54 TAT
1 TAT
57 TCTATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:44 original size:19 final size:18
Alignment explanation
Indices: 6--123 Score: 60
Period size: 18 Copynumber: 6.8 Consensus size: 18
1 TCATT
6 TATATATTAATAATAATA
1 TATATATTAATAATAATA
24 TATATTATTAATAA-AAT-
1 TATA-TATTAATAATAATA
41 TATA-A--AATAATAATA
1 TATATATTAATAATAATA
* *
56 T-TCTATTATCTAAT-ATA
1 TATATATTA-ATAATAATA
* * *
73 TTTAAATTAA-AAT-TTA
1 TATATATTAATAATAATA
89 -AT-TATTATATAATATATA
1 TATATATTA-ATAATA-ATA
107 TATATAATTATATAATA
1 TATAT-ATTA-ATAATA
124 TTTTGTTCGT
Statistics
Matches: 76, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
13 5 0.07
14 8 0.11
15 5 0.07
16 8 0.11
17 9 0.12
18 18 0.24
19 11 0.14
20 1 0.01
21 11 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATATTAATAATAATA
Found at i:101 original size:11 final size:12
Alignment explanation
Indices: 87--120 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
77 AATTAAAATT
87 TAATTAT-TATA
1 TAATTATATATA
98 TAATATATATATA
1 TAAT-TATATATA
111 TAATTATATA
1 TAATTATATA
121 ATATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 9 0.43
13 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATATATA
Found at i:190 original size:18 final size:18
Alignment explanation
Indices: 163--197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
153 AATTATTACA
163 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
181 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
198 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:331 original size:35 final size:35
Alignment explanation
Indices: 291--361 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
281 GAACGAGCTT
* *
291 CGAACACTCTAAAT-TTTAAACGAGC-CGAGCTCGAA
1 CGAACAC-CAAAATATTTAAACGAACACGAGC-CGAA
326 CGAACACCAAAATATTTAAACGAACACGAGCCGAA
1 CGAACACCAAAATATTTAAACGAACACGAGCCGAA
361 C
1 C
362 TTGAACAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.16
35 22 0.69
36 5 0.16
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (35 bp):
CGAACACCAAAATATTTAAACGAACACGAGCCGAA
Found at i:890 original size:19 final size:19
Alignment explanation
Indices: 866--917 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
856 GAACTTTAAA
866 TTGCCACGTCAGCATAAGT
1 TTGCCACGTCAGCATAAGT
885 TTGCCACGTCAGCATAAGT
1 TTGCCACGTCAGCATAAGT
904 TTGCCACGTCAGCA
1 TTGCCACGTCAGCA
918 AATTTGGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (19 bp):
TTGCCACGTCAGCATAAGT
Found at i:2667 original size:17 final size:16
Alignment explanation
Indices: 2627--2677 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
2617 CATGTAATCT
*
2627 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
2643 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
2660 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
2677 T
1 T
2678 GAGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:3295 original size:42 final size:42
Alignment explanation
Indices: 3249--3350 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
3239 AAACGAGTTA
*
3249 GGGTAGGGTACGAGTAGTAGTTTTAGTACTCGCGACGGGTTC
1 GGGTAGGGTACGAGTAGTAGTTTTAGTACCCGCGACGGGTTC
3291 GGGTAGGGTACGAGTAGTAGTTTTAGTACCCGCGACGGGTTC
1 GGGTAGGGTACGAGTAGTAGTTTTAGTACCCGCGACGGGTTC
*
3333 GGGTAGGGTACGGGTAGT
1 GGGTAGGGTACGAGTAGT
3351 GACCTTAGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.19, C:0.14, G:0.41, T:0.26
Consensus pattern (42 bp):
GGGTAGGGTACGAGTAGTAGTTTTAGTACCCGCGACGGGTTC
Done.